[med-svn] [Git][med-team/connectome-workbench][master] 1456 commits: improve tfce help info
Andreas Tille (@tille)
gitlab at salsa.debian.org
Fri Apr 10 23:02:49 BST 2026
Andreas Tille pushed to branch master at Debian Med / connectome-workbench
Commits:
5d8ed26b by Tim Coalson at 2021-02-24T16:05:11-06:00
improve tfce help info
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6066fa9c by Tim Coalson at 2021-02-24T16:07:10-06:00
improve comment
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ef7c87b3 by Tim Coalson at 2021-02-24T16:07:57-06:00
improve single-map case of getting cifti column, converting to memory
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e4322b97 by Tim Coalson at 2021-02-24T16:08:42-06:00
reduce fallthrough warnings
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c9689282 by Tim Coalson at 2021-02-24T16:09:12-06:00
explain percentile option
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1ff15cc1 by Tim Coalson at 2021-02-24T16:10:35-06:00
rework OperationParameters to lazy load, change cifti average to operation to improve performance
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f31a4edc by Tim Coalson at 2021-02-24T16:42:19-06:00
fix errors
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72308b67 by Tim Coalson at 2021-02-25T16:26:58-06:00
parallelize cifti merge xml parsing like cifti average
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94b6180f by Tim Coalson at 2021-03-01T19:14:02-06:00
extrapolate option for volume dilation
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7cd52c20 by Tim Coalson at 2021-03-03T21:28:58-06:00
let omp env variables override parallel XML parsing loops
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2a66b847 by John Harwell at 2021-03-04T13:56:04-06:00
WB-907 Free Hand Lines: Many updates including: separate annotation types for polygon and polyline; changed drawing to allow clicks, dragging, or both; insertion and removal of points in polygons and polylines; fixed pasting of lines and added pasting of polygons and polylines.
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542844fe by John Harwell at 2021-03-04T14:23:19-06:00
WB-907 Free Hand Lines: Fix / improve tooltips on button for inserting annotation polygons and polylines.
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986460d6 by John Harwell at 2021-03-05T10:07:17-06:00
Updated annotation help files.
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dc203bd8 by John Harwell at 2021-03-05T10:39:32-06:00
Fixed compilation warnings from last update.
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854272f1 by Tim Coalson at 2021-03-15T02:06:36-05:00
fix singularity tests in volume gradient
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d8f385d7 by John Harwell at 2021-03-15T16:43:04-05:00
Enable alpha (transparency) when viewing images.
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5517e849 by John Harwell at 2021-03-16T11:40:06-05:00
Fixed a crash pasting annotation into window space not in a browser tab. Fixed pasting of annotation into spacer tab.
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f6e0ed6a by John Harwell at 2021-03-16T11:55:42-05:00
Correct text in toolbar annotation coordinate widget to show "sp" when the selected annotation is in "spacer" space.
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78e98e4c by John Harwell at 2021-03-17T11:48:14-05:00
Qt6 Compatibility: Update cmake_minimum to 3.0. Add Project(Workbench) to top-level CMakeLists.txt file. These changes eliminate warnings when using cmake 3.19.x.
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9712c4d6 by John Harwell at 2021-03-17T11:48:14-05:00
Replace deprecated code in Qwt Module.
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2bbe8390 by John Harwell at 2021-03-17T11:48:14-05:00
Replace deprecated Qt code in GuiQt Module.
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214710c1 by John Harwell at 2021-03-17T11:48:14-05:00
Replace deprecated Qt code in Cifti Module.
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0d7c157d by John Harwell at 2021-03-17T11:48:14-05:00
Replace deprecated Qt code in Common Module.
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6c2c55b9 by John Harwell at 2021-03-17T11:48:14-05:00
Replace deprecated Qt code in Files Module.
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41a5a149 by John Harwell at 2021-03-17T11:48:14-05:00
Replace deprecated Qt code in Quazip Module.
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b6db2bcc by John Harwell at 2021-03-17T11:48:14-05:00
Replace deprecated Qt code in Operations Module.
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6d077570 by John Harwell at 2021-03-17T11:48:14-05:00
Replace deprecated Qt code in Brain Module.
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a78c19a6 by John Harwell at 2021-03-17T11:48:14-05:00
Replace deprecated Qt code in FilesBase Module.
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2d273390 by John Harwell at 2021-03-17T11:48:14-05:00
Removed usage of WORKBENCH_REPLACE_QT_DEPRECATED in Qwt Module.
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ea2bfeca by John Harwell at 2021-03-17T11:48:14-05:00
Removed usage of WORKBENCH_REPLACE_QT_DEPRECATED in Quazip Module.
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a5322d9e by John Harwell at 2021-03-17T11:48:14-05:00
Removed usage of WORKBENCH_REPLACE_QT_DEPRECATED from src/CMakeLists.txt
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8e7e6ef3 by John Harwell at 2021-03-17T11:48:14-05:00
Removed usage of QT_VERSION when testing against 5.0 from CaretHttpManager. Verified downloading from ConnectomeDB and uploading to BALSA still function.
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0ce4d6b6 by John Harwell at 2021-03-17T11:48:14-05:00
Removed usage of QT_VERSION when testing against Qt 5.0.
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8ccf57e6 by John Harwell at 2021-03-17T11:48:14-05:00
Removed QT4_FOUND code from all CMakeLists.txt files.
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e3487e50 by John Harwell at 2021-03-17T11:48:14-05:00
Qt6: Source code updated so that it compiles on my Mac with Qt 6.0.2, on my Mac with Qt 5.15.2, and on linux build with Qt 5.7.
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09baa9eb by John Harwell at 2021-03-17T11:48:14-05:00
Qt6 changed the names of signals so that the names are no longer overloaded.
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551c9518 by John Harwell at 2021-03-17T11:48:14-05:00
Fixed usage of QtConcurrent::run() in Qt6 (changed order of parameters); Updated desktop.cxx to use QScreen as replacement for QDesktopWidget.
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55e982f6 by John Harwell at 2021-03-17T11:48:15-05:00
Removed unused Scene File SAX reader and related class used for testing. A stream reader was added for the scene file long ago.
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44e47ca7 by John Harwell at 2021-03-17T11:48:15-05:00
Removed unused Scene SAX reader that was used by recently deleted Scene File SAX reader.
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66518efb by John Harwell at 2021-03-17T11:48:15-05:00
Conditionally compile unexpectedHandler() when a C++17 compiler is used as std::set_unexpected() is removed in C++17.
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adc96704 by John Harwell at 2021-03-17T11:48:15-05:00
Removed usage of deprecated QRegExp and replaced with QRegularExpression
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17551226 by John Harwell at 2021-03-17T16:07:17-05:00
Fixed crash. Had attempted to replace QApplication::desktopWidget() with QApplication::activeWindow() but it resulted in a crash. So, replaced with QApplication::topLevelWidgets().at(0) that returns a paint device.
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b583e5d0 by John Harwell at 2021-03-18T09:18:40-05:00
Fixed compilation error with Qt5 by adding a header file include.
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94f40013 by John Harwell at 2021-03-18T11:38:36-05:00
Header file added in last commit for Qt5 not available in Qt6. So, add conditional compilation for the header file.
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371862e5 by John Harwell at 2021-03-18T14:52:37-05:00
Fixed uploading to BALSA with Qt6. In Qt 6, redirection is automatically handled but is now disabled. CaretHttpManager manually handles redirect requests as early versions of Qt did not. Allowing automatic redirects breaks the login to BALSA.
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b26c21a0 by Tim Coalson at 2021-03-22T13:43:52-05:00
fix chunking math to not divide by 0
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29960d88 by Tim Coalson at 2021-03-22T16:38:01-05:00
avoid edge case of -cifti-convert on a billion rows resulting in too-large files
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1dd62a5f by Tim Coalson at 2021-03-22T16:42:04-05:00
some optimization of cifti XML parsing for qt5, attempted optimization for qt6
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69b9c4cc by Tim Coalson at 2021-03-22T16:49:00-05:00
fix build for older QT5
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be4d5b27 by John Harwell at 2021-03-24T17:00:58-05:00
Updated mac_plist/MacOSXBundleInfo.plist.in to include wb_spec and wb_scene so that if files with those extensions are double-clicked in Finder, wb_view will open the file. Also, added extensions for a few data files.
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f318c445 by John Harwell at 2021-03-25T11:24:26-05:00
Add some code to detect image formats that support "clipRect" that Qt defines as the ability to read part of an image defined by a rectangle. Since this requires creating actual image files (in the temp directory), this code is disabled at this time.
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4ac13a84 by John Harwell at 2021-03-25T11:24:26-05:00
Added function 'nearestPointOnLine3D'. Given a point, find the nearest point on a line defined by two points.
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51073d32 by John Harwell at 2021-03-25T11:24:26-05:00
WB-907 Draw free hand lines: Redesign for inserting a coordinate into an existing polygon/polyline. Right-Click the mouse over a line segment in the object, and select Insert Coordinate from the pop-up menu. Symbols highlighting the selected polyline/polygon are now all the same size.
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c1c8f18e by John Harwell at 2021-03-25T11:24:26-05:00
WB-907 Free hand lines: Updated help information for new functionality for inserting coordinates into polylines/polygons.
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ff508699 by John Harwell at 2021-03-25T11:24:26-05:00
WB-907 Free hand lines: Updated insertion of coordinate into polyline/polygon so that it works for annotations in surface space.
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b8549654 by John Harwell at 2021-03-25T11:24:26-05:00
WB-937 If editing tile tabs configuration, warn if aspect locked and show tab outlines: If window and/or tab aspects are locked, display a short message informing the user with a link to a more detailed explanation.
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4f39eac9 by John Harwell at 2021-03-25T11:24:26-05:00
Fixed compilation warning caused by an unused line of code.
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ee72e8fb by John Harwell at 2021-03-25T11:24:26-05:00
WB-907 Free hand lines: When (1) There is only one annotation selected; (2) It is a polyline/polygon; (3) And the mouse is over one of its line segments: Change the cursor to a "plus" symbol and if the user clicks the mouse, insert a new coordinate into the polyline/polygon.
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83461d47 by John Harwell at 2021-03-25T11:24:26-05:00
WB-907 Free Hand Lines: Improved selection or polyline/polygon annotations. Corrected polyline/polygon coordinate symbols so that they are about the same diameter as the line segments.
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8ba7b2c0 by John Harwell at 2021-03-25T11:24:26-05:00
WB-907 Free Hand Lines: Update help documentation for inserting coordinates into an annotation polyline/polygon.
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feb30fc1 by John Harwell at 2021-03-25T12:22:02-05:00
On About Workbench "More" dialog, list Qt image formats that support the "clipRect" (region of interest) reading. From the QImageIOHandler documentation: The clip rect, or ROI (Region Of Interest). A handler that supports this option is expected to only read the provided QRect area from the original image in read(), before any other transformation is applied.
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b66ecb55 by John Harwell at 2021-03-25T16:43:29-05:00
Fixed polyline/polygon annotation coordinate dragging. Was incorrectly inserting a new coordinate when user clicked the mouse to drag the coordinate to a new location.
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f16bfe26 by John Harwell at 2021-03-30T11:23:15-05:00
On About Workbench "More" dialog, list image file formats that support QImage's key/value metadata for reading and writing.
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3a68e820 by John Harwell at 2021-03-30T16:46:14-05:00
Image File Metadata: For those image files that support metadata: (1) Show metadata in file information output; (2) Fixed editing of file metadata through Spec File Management Dialog (click "sprocket" and choose Edit File Metadata); (3) Add a "supportsFileMetaData()" method to CaretDataFile and override it in ImageFile (only some image file formats support metadata, on my Mac they are JPG and PNG).
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d8a5f74a by John Harwell at 2021-03-31T09:47:31-05:00
Washington-University / workbench: ffmpeg has "/" hard coded in path #48: Replaced several instances of a forward slash with QDir::separator(). I thought Qt would handle forward/backward slashes in paths but it does not do so for QProcess. This bug fix still needs to be tested on Windows.
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7cc54459 by John Harwell at 2021-04-01T15:48:12-05:00
WB-938 If editing tile tabs configuration, warnings if aspect locked and show tab outlines: Added selection of the Tile Tabs Mode (Automatic, Grid, Manual) to Tile Layout Toolbar. It also includes setting Custom Grid rows/columns and a button to set the Manual Layout.
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0e44d7b9 by John Harwell at 2021-04-02T12:17:28-05:00
WB-938 If editing tile tabs configuration, warnings if aspect locked and show tab outlines: When in tile tab editing mode, draw outlines around tabs for Automatic and Custom Grid modes.
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61fcd8df by John Harwell at 2021-04-02T12:24:12-05:00
WB-938 If editing tile tabs configuration, warnings if aspect locked and show tab outlines: When Tile Layout mode is selected in the toolbar, do not set the Tile Tabs Configuration to Manual since Tile Layout mode now supports editing of all tile tab configuration types (Automatic Grid, Custom Grid, and Manual).
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e7be4d05 by John Harwell at 2021-04-02T12:33:13-05:00
WB-938 If editing tile tabs configuration, warnings if aspect locked and show tab outlines: When in Tile Layout mode, only show context (right-click menu) when the Tile Tabs Configuration is Manual.
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e9cc83d0 by John Harwell at 2021-04-02T13:50:30-05:00
WB-938 If editing tile tabs configuration, warnings if aspect locked and show tab outlines: Renamed some classes that now apply to all tile tabs modes and not just manual mode.
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650ed8d6 by John Harwell at 2021-04-02T16:57:56-05:00
WB-938 If editing tile tabs configuration, warnings if aspect locked and show tab outlines:: TileTabsLayoutConfigurationTypeWidget is now used the Tile Tabs Configurations Dialog in addition to the Tile Layout Toolbar.
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b720ffa3 by John Harwell at 2021-04-05T12:40:45-05:00
WB-938 If editing tile tabs configuration, warnings if aspect locked and show tab outlines: In Tile Layout Toolbar's Layout Type section, change "Set..." button to "Adv..." and to its menu, add item to display the Tile Tabs Configuration dialog for more advanced editing.
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15c7006d by John Harwell at 2021-04-05T16:25:08-05:00
In tab layout toolbar, names of some sections were at the top and others at the bottom of the toolbar. For consistency names of sections are now at the bottom of the toolbar.
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0ceaf1c3 by John Harwell at 2021-04-06T11:50:17-05:00
WB-938 If editing tile tabs configuration, warnings if aspect locked and show tab outlines: Update help documentation with tile layout toolbar changes.
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f8ba3b5c by John Harwell at 2021-04-07T12:21:08-05:00
Fixed compilation warning.
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f8a40932 by John Harwell at 2021-04-09T16:54:11-05:00
WB-932 "SEVERE" message produced by wb_command -show-scene: Starting on OperationShowSceneTwo that improves and fixes bugs in OperationShowScene.
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8164aefa by John Harwell at 2021-04-23T17:01:48-05:00
WB-932 "SEVERE" message produced by wb_command -show-scene: For "-show-scene-two": added option to print settings from the scene that define the image captured; moved mesa rendering to its own subclass of a new base class for offscreen renderers; tried creating an offscreen rendering instance using newer Qt classes such as QOffscreenSurface but could not get it to work.
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f3ea2734 by John Harwell at 2021-04-26T20:57:58-05:00
WB-932: Continuing development of new show scene command.
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c96d7d72 by John Harwell at 2021-04-26T21:10:09-05:00
WB-932: Add include file 'memory' to fix compilation error on operating systems other than macOS.
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79872344 by John Harwell at 2021-04-26T21:14:49-05:00
WB-932: Fix compilation on Windows due to Mesa3D not available.
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00ed66a0 by John Harwell at 2021-04-28T09:39:38-05:00
WB-932 Show scene: continuing development of new show scene command
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e22ea8db by John Harwell at 2021-04-28T16:35:44-05:00
Fixed bug with image size when adding a new scene on scene dialog.
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3c50663f by Tim Coalson at 2021-04-29T15:19:33-05:00
put filename in cifti XML errors
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9694771a by Tim Coalson at 2021-04-29T22:00:02-05:00
initial version of -surface-sphere-triangular-patches
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e93a89cb by John Harwell at 2021-04-30T14:20:13-05:00
WB-932 Show scene: Continuing development of new show scene command that seems to be functioning correctly.
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34c46c36 by John Harwell at 2021-04-30T15:45:40-05:00
WB-932 Show scene: Correct conversion to different systems of 'pixel per unit' in image capture settings and dialog.
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2443ea4c by John Harwell at 2021-04-30T16:04:48-05:00
WB-932 Show scene: Include spatial information for file information with image file.
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0cc0d988 by John Harwell at 2021-04-30T16:43:28-05:00
WB-932 Show scene: Created new class (without any implementation yet) for command line show scene that will use an OpenGL Window to generate the image. While it will require a display to work, it will allow MS Window users to generate images. Also could be used if there is a problem with the Mesa offscreen show scene.
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1a7408c3 by John Harwell at 2021-05-04T10:06:20-05:00
Temporary fix for images with width and/or height greater than the maximum allowable texture dimension. When this occurs, resample the image to fit single texture. Longer term solution may be to use multiple textures for an image file.
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afc461f9 by John Harwell at 2021-05-04T12:53:40-05:00
When "wb_command -fileinformation" is run with no parameters, include all supported file types and extensions in help text.
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3c2899a0 by John Harwell at 2021-05-04T13:17:02-05:00
In "wb_command -file-information: Include all library paths reported by Qt. Need to know where plugins are being loaded from on a non-build system linux.
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ef0b3f98 by John Harwell at 2021-05-07T09:42:04-05:00
WB-932 Show scene: Fixed problems with margin color being incorrect. Improved help including adding examples.
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50a16c53 by John Harwell at 2021-05-07T10:13:46-05:00
WB-941 Qt Plugins for Image Reading/Writing of TIFF and other formats: Add library paths and supported file extensions to the "More" option of the About Wb_view dialog. Removed printout of library paths and supported file extensions from the file information command when run with no parameters.
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c6d59bab by John Harwell at 2021-05-07T11:47:44-05:00
WB-941 Qt Plugins for Image Reading/Writing of TIFF and other formats: Added code to test setting plugins path on MacOS. Must be tested by running the distribution's wb_view on my Mac.
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c72ae40c by John Harwell at 2021-05-07T14:06:36-05:00
WB-941 Qt Plugins for Image Reading/Writing of TIFF and other formats: (1) Recently found that there is a qt.conf in the Mac app's resource directory that is supposed to set the plugins path so will try it. (2) The data file types were getting the supported file extensions as a result of SessionManager creation. But, SessionManager is created prior to QApplication and QApplication probably initializes the plugs path.
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6cdce7f1 by John Harwell at 2021-05-07T15:35:22-05:00
WB-941 Qt Plugins for Image Reading/Writing of TIFF and other formats: Trying a new strategy by setting QT_PLUGIN_PATH environment variable at startup of wb_view.
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3a73f518 by John Harwell at 2021-05-07T16:08:48-05:00
WB-941 Qt Plugins for Image Reading/Writing of TIFF and other formats: Setting QT_PLUGIN_PATH environment variable at beginning of "main()" for wb_view fixes image plugin loading on MacOS when wb_view is launched from the Finder.
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38035655 by John Harwell at 2021-05-11T09:22:27-05:00
WB-942 Image panning/zooming improvements: Starting development; zoom about mouse starting to work.
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37d5d432 by John Harwell at 2021-05-12T14:54:13-05:00
WB-942 Image panning/zooming improvements: Zooming about mouse for media (images) is working. Needs updates for when tile tabs is enabled and for zooming when the mouse is not over an image (needs an image XY to know what to zoom about).
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65cd9129 by John Harwell at 2021-05-12T15:14:39-05:00
WB-942 Image panning/zooming improvements: Added zooming for images when mouse is not over the image.
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84511759 by John Harwell at 2021-05-12T15:39:32-05:00
WB-941 Qt Plugins for Image Reading/Writing of TIFF and other formats: Fixed image zooming about mouse when tile tabs is enabled.
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934ea0dd by John Harwell at 2021-05-12T16:37:22-05:00
Move function for scaling about mouse out of ViewingTransformations and into ViewingTransformationsMedia since it is specialized for image scaling.
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bcf46b38 by John Harwell at 2021-05-12T17:14:20-05:00
WB-942 Image panning/zooming improvements: Adding GraphicsRegionSelectionBox that will be used for selecting a region in the graphics area for image bounds selection.
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3459e2d8 by John Harwell at 2021-05-14T09:16:14-05:00
WB-942 Image panning/zooming improvements: Adding coordinate system to image file. It will be used for resizing image view by selection of part of image with a box.
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a32d455b by John Harwell at 2021-05-16T19:31:44-05:00
WB-942 Image panning/zooming improvements: Use VolumeSpace for pixel/spatial coordinate system in image. Adding selection of region with mouse in GUI.
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55499d67 by John Harwell at 2021-05-17T09:23:40-05:00
WB-942 Image panning/zooming improvements: Finished implementation of setting the view of an image to a region selected from the image. To select the region, the user drags the mouse, creating a box with one corner at where the mouse was pressed and a second corner where the mouse is released.
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90c03e28 by John Harwell at 2021-05-17T14:01:54-05:00
WB-943 Developer Options: Remove developer options from Develop Menu and add to new "Develop" tab in Preferences. Add tooltips to the developer flags in Preferences dialog.
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cd71b5d4 by John Harwell at 2021-05-17T15:57:33-05:00
WB-942 Image panning/zooming improvements: Improve zooming of images so that it is more "reflective?". For example, moving the mouse 100 pixels up doubles the image size and 100 pixels down halves the image size.
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e54274ee by John Harwell at 2021-05-18T11:18:08-05:00
WB-942 Image panning/zooming improvements: Improve mouse wheel scrolling with images; disable trackpad gestures for images and fix it at a later time.
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e115abcb by John Harwell at 2021-05-18T16:36:48-05:00
WB-943 Developer Options: Moved items off of Develop menu and into new Develop tab in the Preferences dialog. Add tooltips to all items in Develop tab. Add texture mapping options (minify and magnify) for images displayed in media views.
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7a15494c by John Harwell at 2021-05-19T15:17:03-05:00
WB-943 Developer Options: Added "Show Frames Per Second" to OpenGL tab of the Preferences dialog. When "Show Frames Per Second" is enabled, the frame rate is displayed in the bottom right corner of the window.
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40c66ea8 by John Harwell at 2021-05-19T15:31:29-05:00
WB-941 Qt Plugins for Image Reading/Writing of TIFF and other formats: Plugin path will fail for a development version of wb_view that has not been run with 'macdeployqt'. So in the error message, indicate that a development build will cause the error.
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8fa8065e by John Harwell at 2021-05-19T15:44:08-05:00
WB-943 Developer Options: Add a note to the Develop tab in Preferences. This note indicates that these developer options are not saved in the user's preferences and any non-default values will need to be set each time wb_view is started.
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955bcd2e by John Harwell at 2021-05-24T15:36:44-05:00
The frame-rate timer has been revised. Previously, it was only measuring the time during OpenGL drawing (time spent in 'BrainOpenGLWidget::paintEvent') by starting and stopping the timer at the beginning and end of the function. This timing excluded that spent swapping the frame buffer, performing user-interaction, user-interface updates, etc. As a result, the frame rates were inaccurately too fast.
Now, the timing for the frame rate is updated once at the end of the graphics loop in 'BrainOpenGLWidget:paintGL'. The 'frame-rate' is calculated from the entire time between each pair of successive calls that update the timer. As a result, this interval of time includes buffer swapping, user-interface updates, user-interaction, etc and reflects the all of the time required to make one frame update. One defect is that if the user does nothing for a while, the time between frames will include "that nothing". To prevent this from distorting the frames-per-second, frames exceeding five seconds are excluded from any timing.
The frames-per-second displayed in the window is an average of the time required to produce the last 10 frames.
Note that unlike a video game that may update its graphics at a regular interval, wb_view updates its graphics 'as needed'.
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f37a4a5c by John Harwell at 2021-05-24T16:04:03-05:00
Fixed compiler warning that identified a problem.
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5ff1bae9 by John Harwell at 2021-05-25T14:28:04-05:00
WB-943 Developer Options: There are now two numbers displayed in the window. The top number with suffix “pnt” measures the average time required to perform painting (the OpenGL function calls). The bottom number with suffix “fps” remains unchanged and is the average of the total time between graphics drawings including all user interactions, computations, graphics drawing, etc. When these numbers are roughly the same, it indicates that all of the time is spent performing graphics operations (eg: oblique volume drawing) and when different indicates activity by non-graphics operations.
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c1e8ce0e by John Harwell at 2021-05-25T14:53:28-05:00
WB-942 Image panning/zooming improvements: Correct jumping of image when user followed panning by zooming about a point with the trackpad or mouse wheel (zooms about a point on screen properly).
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4659bf42 by John Harwell at 2021-05-26T08:38:09-05:00
WB-943 Developer Options: Changed a lambda function used by graphics timing display so that it should compile on Windows.
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40b15fb5 by John Harwell at 2021-05-27T11:31:52-05:00
WB-943 Developer Options: For graphics timing, only show the "frames-per-second" for the most recent graphics drawing (NOT an average).
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7299218f by John Harwell at 2021-05-27T11:45:54-05:00
WB-942 Image panning/zooming improvements: Reduce width of lines for box that selects a pan/zoom region.
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30ad217f by Tim Coalson at 2021-05-27T16:53:26-05:00
add sinc function to -*-math
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2ec9f386 by John Harwell at 2021-06-01T09:24:33-05:00
WB-942 Image panning/zooming improvements: Add a default scaling for images so that an image fills the screen in its default (reset) view.
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2d425e0e by John Harwell at 2021-06-01T14:19:28-05:00
WB-942 Image panning/zooming improvements: Updates to default scaling so that old scenes load correctly. When an old scene is loaded, the default scaling is disabled for a displayed image. If, after loading the scene, the user clicks the "Reset" button in Toolbar:Orientation, default scaling is enabled for the image and the default scaling is set so that the image best-fits the window.
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45d80eb2 by John Harwell at 2021-06-03T16:01:41-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Adding CZI library modified to compile on all operating systems. There are many compilation warnings.
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7c6b9366 by John Harwell at 2021-06-04T09:53:21-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Updated 'wb_command -file-information' so that it will print information for a CZI file. It does this my calling 'czi_main' (a program in the CZI library converted to a function).
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71c7e9f3 by Tim Coalson at 2021-06-04T16:50:13-05:00
update -*-stats help for multimap ROIs, missing include
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8f7a8db7 by John Harwell at 2021-06-08T09:13:12-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Now have a preliminary ability read a CZI file and display it in wb_view. The file is read using the 'single channel scaling tile accessor' that reads the CZI file and scales the image to fit into a maximum dimension of 4096.
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bb424568 by John Harwell at 2021-06-08T12:14:04-05:00
Moved definition from CZIlib/CMakeLists.txt to src/CMakeLists.txt to fix linking problem on windows OS.
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5b179fcf by John Harwell at 2021-06-09T13:55:42-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: CZI image files contain coordinates associated with the image. Support for using these coordinates has been added but is off by default. It is enabled on Preferences -> Develop -> Use Coordinates from CZI Image File. When enabled, it only affects newly read image files.
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8d8730cf by John Harwell at 2021-06-09T14:25:11-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: The scaling tile accessor for reading CZI files accepts a background color. This background color is used to fill pixels for which there is no image data. The media background color from the user's preferences is now used to fill these pixels.
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c80baabc by John Harwell at 2021-06-11T14:43:19-05:00
Add a progress dialog for the simple display of a message while some processing is performed.
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880982eb by John Harwell at 2021-06-11T14:48:40-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Added a section to the toolbar titled "Resolution" that is displayed when an image is viewed. It contains a toggle button with the text "High Res". If the user toggles this button to its on status and then performs a rectangular selection of a CZI image using the mouse, the enclosed region is loaded as a new higher resolution image and is displayed (the original image remains available for selection in the overlay controls). After loading the new high-res image, the "High Res" button toggles to off.
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0fedfc0c by John Harwell at 2021-06-11T15:37:21-05:00
Fix compilation error on Linux operating systems.
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d4aa4923 by John Harwell at 2021-06-14T15:53:26-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Fixes for very large image files; increase maximum dimensions of an ROI image read from a CZI file.
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c51522e5 by John Harwell at 2021-06-15T10:25:10-05:00
Do not allow saving of an image file if the filename's extension does not match a supported image file type that allows writing.
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7f1f8964 by John Harwell at 2021-06-15T15:04:46-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Added 'Redo' and 'Undo' functionality for selection of image region (drag with mouse to create box).
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b5b62046 by Tim Coalson at 2021-06-15T18:30:51-05:00
fix -border option of -border-to-vertices
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5ee60c55 by Tim Coalson at 2021-06-23T17:15:31-05:00
make -volume-capture-plane output opaque
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be84ce09 by John Harwell at 2021-06-25T17:01:20-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Adding a new file, CziImageFile, for CZI files. ImageFile was previously used but CZI has requirements that are not compatible with standard image files.
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30ed7b1c by John Harwell at 2021-06-25T17:01:20-05:00
Added metadata content to file information output.
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c3750081 by John Harwell at 2021-06-25T17:01:20-05:00
Added classes for transforming between rectangular spaces for use with images (image pixels; coordinates; ROIs, origin at top/bottom).
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c8abcd2f by John Harwell at 2021-06-25T17:01:20-05:00
Adding new CziImageFile for reading and display of CZI images. CZI image support will be removed from ImageFile later. CZI has too many unique behaviors that make it a bad fit for ImageFile.
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0d551465 by John Harwell at 2021-06-25T17:01:20-05:00
Removed CZI support from ImageFile now that CziImageFile has been created.
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059e1be1 by John Harwell at 2021-06-28T08:21:46-05:00
Fixing compilation error on some operating systems by adding an include directive.
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160f6af0 by John Harwell at 2021-06-28T08:43:57-05:00
Removed "using namespace libCZI" from CziImageFile.h to fix compilation errors on Windows. Symbols, such as IStream, are in both libCZI and in C:\Program Files (x86)\Windows Kits\8.1\include\\um\objidlbase.h on Windows.
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ead5cbe3 by John Harwell at 2021-06-28T08:55:30-05:00
Fixed compilation error on Windows. Using ERROR in an enumerated type does not compile. Changed it too ERRORED.
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35a619f1 by John Harwell at 2021-06-28T16:15:49-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Continuing development of new file format and supporting classes.
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f77b4e95 by Tim Coalson at 2021-06-29T20:59:37-05:00
detailed matching errors for -cifti-merge
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bbef770e by Tim Coalson at 2021-06-30T21:23:16-05:00
fix empty provenance
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d6b12ce7 by John Harwell at 2021-07-01T16:33:31-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Continuing revisions for new CZI Image File.
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5a833ff2 by John Harwell at 2021-07-01T16:33:31-05:00
Added scene support for 64-bit integer data.
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21f29a99 by John Harwell at 2021-07-01T16:33:31-05:00
Added scene support for 64-bit integer data part 2. Forgot to add these files that should have been in the previous commit.
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1ce0f922 by John Harwell at 2021-07-01T16:33:31-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Cleanup of ImageFile and CziFile.
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e6fe86cf by John Harwell at 2021-07-01T16:33:31-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Cleanup of ImageFile.
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28cd25c6 by John Harwell at 2021-07-01T16:33:31-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Finished cleanup of ImageFile and CziFile.
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c8e20a18 by John Harwell at 2021-07-01T16:33:31-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: CziFiles were not included in "all data files" that caused scene error and clear the modified status after reading from CZI file.
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438e7978 by John Harwell at 2021-07-01T16:33:31-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Added yoking for media (images and CZI images).
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8ed326ee by John Harwell at 2021-07-02T12:39:45-05:00
Fixed memory leak caused by failure to destroy graphics box used for image region selection.
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c089a160 by John Harwell at 2021-07-02T12:42:42-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Hide "High Res" tool button as it will be replaced soon with better functionality.
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70157802 by John Harwell at 2021-07-02T13:40:30-05:00
Added missing include file for compiling on Linux.
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4a406797 by Tim Coalson at 2021-07-12T22:53:55-05:00
typo
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bdf41cde by John Harwell at 2021-07-13T19:32:09-05:00
Added option to Develop section of Preferences that can disable cropping of "scene preview images". Disabling the cropping may be useful if debugging a panning zooming issue with a scene.
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b747cfee by John Harwell at 2021-07-13T19:32:09-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Fixed zooming of media files (images, CZI) through the Custom View dialog (zooms about the center of the image).
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960e2120 by John Harwell at 2021-07-13T19:32:09-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Improve loading of scenes with images that were created prior to default scaling. Some scenes load correctly and others are pretty close for pan/scale of image.
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b31201a8 by John Harwell at 2021-07-13T19:32:09-05:00
Added a "Reset View" button to the Custom Orientation dialog. Without this button, the user must click Reset button in the Window's Toolbar.
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3303b00f by John Harwell at 2021-07-13T19:32:09-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Added data tooltips for CZI images and normal images.
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fe9d9213 by John Harwell at 2021-07-13T19:32:09-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Added data tooltips for CZI images and normal images. Add enable/disable for media tooltips.
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224baf8f by John Harwell at 2021-07-13T19:32:09-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Starting to add manual loading of higher resolution images.
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197ca280 by John Harwell at 2021-07-13T19:32:09-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Added controls for manually changing the resolution of CZI images.
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ea7e7285 by John Harwell at 2021-07-13T19:32:09-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Attempting to load the high-resolution pyramid image results in an infinite loop in the CZI library. For now, reduce the number of available pyramid resolutions by one to prevent selection of the highest resolution image and the accompanying infinite loop.
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1de6921e by John Harwell at 2021-07-13T19:32:09-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Found a way to load the highest resolution pyramid layer without getting into an infinite loop. The highest resolution pyramid layer has its minification factor set to zero unlike all other pyramid layers that have a minification factor of two. So, using two for the highest resolution pyramid layer's minification factor prevents the infinite loop.
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51c9452d by John Harwell at 2021-07-13T19:32:09-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Starting to add support for automatic resolution selection for CZI Images.
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953f76e3 by John Harwell at 2021-07-13T19:32:09-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: First version of automatic image resolution selection for CZI Images has been added and is functioning.
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dd6a601e by John Harwell at 2021-07-14T12:08:48-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Fixed pyramid layer for a cloned tab.
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9087c346 by John Harwell at 2021-07-14T14:03:12-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Some code cleanup.
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ece7bcb6 by John Harwell at 2021-07-14T16:29:03-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Fixing zoom on Custom View dialog when used with CZI images.
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af4cb57f by John Harwell at 2021-07-20T16:46:13-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Some redesign of CZI image drawing to simplify it a bit and to fix several bugs with zooming from Custom View dialog.
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018ca99d by John Harwell at 2021-07-21T11:52:26-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Improvements for panning of CZI images using mouse or custom view dialog.
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455ed02a by John Harwell at 2021-07-21T12:08:05-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Remove loading of a user selectable ROI from CZI files. It is no longer used as it was used for testing prior to addition of the Auto Resolution mode that loads CZI image data as the user zooms in/out.
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7c16677c by John Harwell at 2021-07-21T14:28:14-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Default view logic is no longer used and has been removed from Images and CZI Images.
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61da5d2a by John Harwell at 2021-07-21T15:25:48-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Fixed "Reset" View in Toolbar and on Custom View Dialog for CZI Images so that it works correctly when the pyramid layer is not the lowest resolution.
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c845bf1a by John Harwell at 2021-07-22T09:24:42-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Fixed problems with scenes and CZI Images.
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7f7cc57b by John Harwell at 2021-07-23T16:42:42-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Add new "Media Space" for annotations on Media (Images, CZI Images).
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f406835a by John Harwell at 2021-07-26T10:37:12-05:00
Fix compilation error with newer version of clang.
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c18b19fd by John Harwell at 2021-07-26T10:43:37-05:00
CiftiBrainModelsMap did not compile with Qt 6.1.2 due to an error with QString::tokenize (line 900). Logic has been added so that if Qt 6.1.2 or later is detected, QStringView::split is used to split up the string.
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ed8e654e by John Harwell at 2021-07-26T15:48:53-05:00
Fixed crash found when testing scenes after last updates.
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c6bd63a4 by John Harwell at 2021-07-27T11:43:38-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Correct media (image) yoking when the images are different sizes.
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8a0b8f86 by John Harwell at 2021-07-27T13:08:14-05:00
Fix a couple of compilation warnings and logged warnings.
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4bd4392a by John Harwell at 2021-07-28T16:05:29-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Added a new Auto Mode for CZI image viewing the loads image data as the user pans and zooms. The previous Auto Mode that only loaded image data when the user zoomed is still available as "Auto Old". CZI image viewing also now defaults to the new Auto Mode.
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2a7ab41c by John Harwell at 2021-07-29T09:26:04-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: When loading higher-resolution CZI images, load a rectangular image (instead of a square image) when the viewport shape is more rectangular than square.
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e575c809 by John Harwell at 2021-07-29T10:34:41-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: In Auto mode when testing if new image data needs to be loaded, expand the region of the viewport by a small amount. As the user pans the current image, this results in new image data being loaded just before the edge of the image moves into the viewport. If we do not do this, as the user pans, the edge of the image moves into the viewport and a small amount of the background becomes visible (until new image data is loaded).
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2e7bdc26 by John Harwell at 2021-07-29T12:10:08-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: When loading CZI image data, avoid loading new data if the logical region has not changed. This is a rare situation and will only occur if the maximum image is size is smaller than the viewport (current image maximum is 2048 when viewport is similar to a square and 4096 when the viewport is similar to a rectangle). It was tested by making the maximum size 512. A future change will add a preference for the maximum image size in the event a user has a gigantic monitor (8K ?).
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554d1b69 by John Harwell at 2021-07-29T15:49:15-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Add a preference for adjusting the dimension (width/height) used when loading CZI higher-resolution images. Limit the width/height to the maximum supported by OpenGL for textures.
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d7ed4061 by John Harwell at 2021-07-30T15:17:45-05:00
WB-944 CZI I(Zeiss Microscope) image file formats: Finally found source of an uncaught exception (std::out_of_range) in the CZI library. Now catch it and log a message.
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c6c66e20 by John Harwell at 2021-08-02T11:23:39-05:00
Resolve WB-946 Failure to read file with relative path if after spec file: If wb_view was started with a command similar to this "wb_test -spec-load-all relative_directory/test_relative.spec p54_M150_LHRH_215_KA215_PV.czi", wb_view failed to read the data file listed after the spec file. The reason was that after reading the spec file, an internal "current directory" was set to the directory containing the spec file. If a file with a relative path was encountered, wb_view then prefixed the relative path of the file with the "current directory" which in this instance is different than the path of the data file. This has been corrected so that if a file with a relative path is encountered and exists, its absolute path is used and it fixes the problem with the above command. As a last resort, if a file with a relative path is encountered and it cannot be located and if the "current directory" is valid, wb_view will try to find the file using the "current directory".
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60f7d323 by John Harwell at 2021-08-02T12:40:51-05:00
WB-944 CZI (Zeiss Microscope) image file formats: If there is more than one image displayed in a tab, align the images at the top left since that is the location of the origin in image files.
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6f263dc3 by John Harwell at 2021-08-02T16:09:00-05:00
Log at the FINE level when and how a filename is converted to absolute path in Brain::convertFilePathNameToAbsolutePathName().
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4dc6dee3 by John Harwell at 2021-08-02T16:27:42-05:00
Add some logging at the fine level in the show scene command to view the scene file name after conversion to an absolute path.
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bfc44118 by John Harwell at 2021-08-02T16:52:54-05:00
Log a little more in show scene command to see Qt's reported current directory.
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15ae93f4 by Tim Coalson at 2021-08-05T16:10:01-05:00
try to fix cifti overwriting issue on smb/cifs
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a4220c1a by John Harwell at 2021-08-09T11:33:08-05:00
WB-947 Edit Scene Name/Description Without Needing to "Replace" Scene: Added "Edit..." button to Scene Dialog. When clicked, it allows the user to edit the name and/or description of the selected scene without having to recreate the scene.
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25147399 by John Harwell at 2021-08-09T12:43:54-05:00
WB-947 Edit Scene Name/Description Without Needing to "Replace" Scene: Add BALSA Scene ID to editable scene items.
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ea2e4537 by John Harwell at 2021-08-12T14:56:34-05:00
Remove some logging statements from show scene command that were used to debug the symbolic links in file path problem.
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ca64ff3b by John Harwell at 2021-08-12T14:56:34-05:00
Added constructor to Matrix4x4 that accepts vector<vector<float>>.
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e0854857 by John Harwell at 2021-08-12T14:56:34-05:00
WB-944 CZI (Zeiss Microscope) image file formats: Initial implementation of using hist2mri.nii.gz to convert a CZI Pixel Index into a Stereotaxic Coordinate.
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511af525 by John Harwell at 2021-08-12T14:56:34-05:00
Added image pixel mode to Brainordinate Identification Dialog. Changed layout of dialog so that controls are only displayed for the selected identification type (dialog was getting too tall will all controls for all ID types).
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e3638cf5 by John Harwell at 2021-08-12T14:56:34-05:00
Added methods to get/set the column of a matrix.
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03d1f7cd by John Harwell at 2021-08-12T14:56:34-05:00
WB-944 CZI (Zeiss Microscope) image file formats: Revised brainordinate identification dialog to support pixel identification. Incorporate NIFTI files for conversion between pixel and stereotaxic coordinates.
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45b6db62 by John Harwell at 2021-08-13T10:02:25-05:00
std::round() failed to compile on mac build system so trying std::roundf().
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5ebc6536 by John Harwell at 2021-08-13T10:05:52-05:00
std::roundf() did not work on mac build system so trying ::round().
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4b708e8e by John Harwell at 2021-08-13T10:10:24-05:00
::round() failed so remembered MathFunctions::round() so trying it.
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5b070183 by John Harwell at 2021-08-13T10:11:52-05:00
::round() failed so remembered MathFunctions::round() so trying it.
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c0e8a9f8 by Tim Coalson at 2021-08-13T15:33:37-05:00
fix typo in duplicate argument checking
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2605e8a9 by Tim Coalson at 2021-08-17T16:11:36-05:00
add missing <limits>, cleanup
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8ec99036 by Yaroslav Halchenko at 2021-08-17T18:55:31-04:00
Include upstream patch https://github.com/Washington-University/workbench/commit/2605e8a98d23d229d54a9e6847ad64f678217ea7.patch to resolve FTBFS with gcc-11 (Closes: #984024)
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cef5928b by Tim Coalson at 2021-08-17T17:59:11-05:00
restore deleted libCZI license, update copyright info
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4d5ccc6b by John Harwell at 2021-09-02T11:45:49-05:00
Resolve WB-932 SEVERE message produced by wb_command -show-scene: A kludge has been added that disables the message when the show scene command is run. The show scene command will be replaced with an improved version sometime in the future.
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dae94fdc by John Harwell at 2021-09-13T12:45:34-05:00
Renamed IdentifiedItem to IdentifiedItemBase as first step of identification revision.
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fdc81b65 by John Harwell at 2021-09-13T12:45:34-05:00
Clean up scene saving for identified items.
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58ac3d84 by John Harwell at 2021-09-13T12:45:34-05:00
Bug fix from last commit that failed to restore some scene identification items.
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da4efb47 by John Harwell at 2021-09-13T12:45:34-05:00
WB-944 CZI (Zeiss Microscope) image file formats: Continuing revision of identification system to support images and showing an identification symbol on another model type (ie: surface symbol on volume slice).
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5539df36 by John Harwell at 2021-09-13T12:45:34-05:00
WB-944 CZI (Zeiss Microscope) image file formats: Continuing revision of identification system. Replaced media/surface/voxel ID symbol with a universal symbol.
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c0c8d7a7 by John Harwell at 2021-09-13T12:45:34-05:00
WB-944 CZI (Zeiss Microscope) image file formats: Continuing revision of identification system. Replaced media/surface/voxel ID symbol with a universal symbol.
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82744465 by John Harwell at 2021-09-13T12:45:34-05:00
WB-944 CZI (Zeiss Microscope) image file formats: Continuing revision of identification system. Added logic to display an identification symbol from surface or volume with XYZ coordinate on a CZI image. This is not testable until a surface/volume is available that matches available CZI images.
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c8ada29e by John Harwell at 2021-09-13T12:45:34-05:00
WB-944 CZI (Zeiss Microscope) image file formats: Continuing revision of identification system. Fixed display of surface identification symbols on volume slices and added tooltip to identification symbols.
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93fc8412 by John Harwell at 2021-09-13T12:45:34-05:00
CZI Library: Fix compilation warnings for unused local variables and function parameters.
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a88c41cb by John Harwell at 2021-09-13T12:45:34-05:00
Fixed pixel index when getting RGBA value from CZI file.
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4b933c41 by John Harwell at 2021-09-13T12:45:34-05:00
Fixed size of symbols caused by error in GUI (size spin box was not blocked when updating and caused emission of values changed signal); Fixed identification symbol tooltip to omit the XYZ coordinate when unavailable (image with not spatial data).
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4d399d2c by John Harwell at 2021-09-13T12:45:34-05:00
Add "doneCurrent()" to end of BrainOpenGLWidget's destructor to reset the current OpenGL context (makeCurrent is called at beginning).
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a663c2f0 by John Harwell at 2021-09-13T12:45:34-05:00
WB-944 CZI (Zeiss Microscope) image file formats: Continuing revision of identification system. Displaying ID symbols from surface on media and vice versa is working but probably needs more testing.
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4599bee8 by John Harwell at 2021-09-13T12:45:34-05:00
WB-944 CZI (Zeiss Microscope) image file formats: Fixed display of image or volume identification symbols on surfaces by examining X-coordinate to determine if it should be displayed on left or right hemisphere. Improved tooltip for "show on other models" in Identification widget.
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231e9992 by John Harwell at 2021-09-13T12:45:34-05:00
in the CZI CMakeLists.txt file, disable some compilation warnings to reduce the excessive warning messages.
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8f3d2ada by John Harwell at 2021-09-14T09:59:25-05:00
WB-944 CZI (Zeiss Microscope) image file formats: Fixed problem with ambiguous constructors for PixelIndex. Added item to developer menu that performs Pixel to XYZ and back to Pixel for testing CZI transforms.
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7d7c7d86 by John Harwell at 2021-09-14T09:59:53-05:00
Added method to get rows/columns in StringTableModel.
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717e0f5a by John Harwell at 2021-09-14T10:00:20-05:00
Add option for file selection combo box in WuQDataEntryDialog.
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0d15b7c8 by John Harwell at 2021-09-14T15:15:50-05:00
Add image support to data entry dialog and add method to get a fixed Qt Font from Qt Utilities.
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8f8d5fe3 by John Harwell at 2021-09-14T15:19:07-05:00
WB-944 CZI (Zeiss Microscope) image file formats: Item for testing CZI transforms in the Develop Menu has been updated to show the output in a dialog. In the dialog is text output containing the results of the pixels used in the test. There is also an image that shows the error measurements where white is more error and black is less error.
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7ab5e5a0 by John Harwell at 2021-09-15T09:22:19-05:00
Add a parallel Qt loop just for testing but now disabled.
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700d1b6d by John Harwell at 2021-09-15T10:09:53-05:00
Fix compilation errors on some build systems. In CZI module, placed disabling of some compilation warnings (to suppress the many warnings) in an 'if compiler version'.
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3f135f58 by John Harwell at 2021-09-15T12:58:36-05:00
In show scene command, log, at the FINE level, information about OpenGL.
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307b745f by John Harwell at 2021-09-15T12:58:36-05:00
WB-932 SEVERE message produced by wb_command -show-scene: Suppress the message about inability to delete texture.
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89490cdf by John Harwell at 2021-09-15T15:03:07-05:00
WB-944 CZI (Zeiss Microscope) image file formats: When drawing non-surface ID symbols on a surface, attach them to the nearest vertex in the surface. If symbol is "too far" from surface, it is not drawn on surface.
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87d856a7 by Tim Coalson at 2021-09-21T22:13:51-05:00
add warning for affines that have a malformed fourth row
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fc15596d by John Harwell at 2021-09-22T11:58:46-05:00
Remove two unused variables reported by compiler warnings.
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7f0aeb60 by John Harwell at 2021-09-22T11:58:46-05:00
WB-950 Allow copying and pasting of multiple annotations: Annotations that are in the same space (must be tab or window) now support cut/copy/paste. If all of the copied annotations are in the same user group, the pasted annotations will be placed into a new user group.
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97453450 by John Harwell at 2021-09-22T16:00:36-05:00
For chart axes, do not use any padding when axis is off. Also no numerics padding when labels are off.
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5f56c108 by John Harwell at 2021-09-23T14:22:52-05:00
Line Chart Mean/Dev Request: Line charts (ability to do actual mean + factor and actual std * factor) so that data can be rescaled in a way that preserves relative scaling of different lines, rather than completely replacing the mean and standard deviation. While a factor can be added to mean, it may have no effect because we subtract the mean and later add it back in. We only compute deviation when "New Deviation" is enabled so it must be enabled for "Multiply Deviation" to have an effect.
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ca6bc22c by John Harwell at 2021-09-23T16:17:11-05:00
For chart line normalization, replace "Add to Data Mean" with a "Data Offset". Data Offset is applied after all other computations and is used to simply offset the data in a vertical direction.
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35ec9178 by John Harwell at 2021-09-24T10:40:33-05:00
Fixed chart axes so that ticks can be displayed even if the numeric values are off.
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0343ff2a by John Harwell at 2021-09-24T10:46:24-05:00
Remove some commented out code.
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96bb5966 by John Harwell at 2021-09-24T11:23:03-05:00
Chart line layer normalization: Changed the way "Multiply Deviation" is applied. It will now multiply the deviation (previously New Deviation also had to be on). "Multiply Deviation" takes precedence over "New Deviation". These two parameters are actually doing the same thing. A "Multiply Deviation" of 2 is the equivalent of setting "New Deviation" to double the actual data deviation.
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2c189073 by John Harwell at 2021-09-24T17:45:12-05:00
Fixed using arrow keys to move multiple selected annotations.
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4a96ba7f by John Harwell at 2021-09-27T11:28:30-05:00
Fixed failure of moving multiple selected annotation using arrow keys. Fixed moving of media space annotations with arrow keys and with mouse.
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c71636a0 by John Harwell at 2021-09-27T16:16:54-05:00
WB-949 Graphics occupy only bottom corner of window on Mac with newer versions of Qt: On High DPI Displays, the OpenGL viewport is actually double the actual size of the widget. When resizeGL(width, height) is called the width and height must be multiplied by devicePixelRatio to get the true OpenGL drawing size. High DPI must be enabled by setting a preference on the OpenGL tab of the Preferences dialog. High-DPI is needed only on Macs when the version of Qt is something after 5.7.
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13bd3588 by John Harwell at 2021-09-28T16:28:28-05:00
WB-949 Graphics occupy only bottom corner of window on Mac with newer versions of Qt: Instead of a boolean for enabling and disabling high DPI display logic, replace it with an enum with Off, On, and Auto. When Auto is used, wb_view determines the high DPI status using the operating system and Qt version. Add a new tab to the Preferences dialog for "Displays". This contains the Off, On, Auto High DPI selection. It also contains text explaining High DPI, how the Auto selection works, and information about all displays.
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3aa650ec by John Harwell at 2021-09-30T09:04:36-05:00
Correct compilation warnings.
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3c8735fa by John Harwell at 2021-10-01T16:15:19-05:00
Fix warning for a multiline comment in CZI.
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84766a1f by John Harwell at 2021-10-01T16:16:04-05:00
Fixed crash after reading a CZI file that was created from a JPEG. The file contained less metadata than other CZI files we have.
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313654b0 by John Harwell at 2021-10-06T11:35:29-05:00
Disable all warnings in the CZI module using '-w'. There are many warnings in it and after upgrading Xcode on my Mac there are now hundreds more. Note: This only suppresses warnings in CZI and does not affect other modules.
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c74fa589 by John Harwell at 2021-10-06T13:12:51-05:00
Replaced #ifdef statement that tested for Qt 6 with tests for the specific version when the new function was added. This reduces compilation warnings.
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bb8ca19d by John Harwell at 2021-10-06T13:46:11-05:00
Use CHECK_CXX_COMPILER_FLAG to test support for compiler option Wno-deprecated-copy. This prevents many warnings in Qt that occur on MacOS with the latest Xcode.
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a964fb41 by John Harwell at 2021-10-06T13:58:40-05:00
Removed the Q_OBJECT macro from ChartTwoAxisPropertiesEditorDialog.h. There are no signal/slots in this class and the presence of the Q_OBJECT macro caused a linking error with Qt 6.2.
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76e6d523 by John Harwell at 2021-10-06T15:26:48-05:00
Correct compilation warnings.
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5abaeb30 by John Harwell at 2021-10-07T14:42:16-05:00
For oblique volume slice drawing, add two options to the Develop tab on the Preferences Dialog. (1) Oblique Interpolation Type allows the user to change the voxel interpolation type in order to prioritize faster drawing time or better quality volume slice drawing. (2) Oblique Voxel Scaling allows the user to change the size of "pseudo voxels" used when drawing voxel slices. Larger voxels reduce quality of the slice images but reduce the drawing time. If zoomed in enough that the voxels in the slice drawing look "blocky", lowering the Oblique Voxel scaling improves the quality of the slice images. Changing the voxel interpolation type from Cubic to Trilinear does not seem to alter the image quality much but the reduction in drawing time is not much either. Increasing the voxel size provides noticeable reductions in drawing time but also reduces the quality of the image slice drawing. A useful strategy may be to use a larger voxel size when panning/zooming/rotating oblique slices and then a normal voxel size (1) for analyzing or capturing images.
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e08c7dd2 by John Harwell at 2021-10-07T14:48:47-05:00
Fixed compiler warning by removing the file ChartTwoAxisPropertiesEditorDialog from the "moc" portion of the GuiQt/CMakeLists.txt file. This file contains no Q_OBJECT macro and thus should not be processed by the "moc" processing tool.
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0b7e399c by John Harwell at 2021-10-08T12:37:07-05:00
For identification object displayed from other sources (eg: surface symbol on media), add a preference on ID page of preferences dialog that allows the user to adjust the stereotaxic distance that permits display of the id symbol.
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19155573 by John Harwell at 2021-10-08T12:45:15-05:00
Fixed data tooltip display for High DPI displays.
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d004cdba by John Harwell at 2021-10-15T12:38:30-05:00
WB-952 Scene dialog and scene file path: Added a "Move" button that is used to move the scene file to a new location. The old scene file is renamed with a ".bak" extension in case something goes wrong.
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1301546e by John Harwell at 2021-10-18T13:34:10-05:00
Fixed bug in FileInformation::assembleFileComponents. If the input path was "/", the output filename began with "//". This has been corrected so that the output filename begins with a single "/".
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436a61a2 by John Harwell at 2021-10-18T13:42:35-05:00
WB-952 Scene Dialog and Path: When the “New” button is clicked on the Scene Dialog to create a new scene file, pop-up a dialog that contains the new file path and name. If the “base path” is valid, it is the path of the new file. In the event the base path is invalid or is the root directory (data files may be on separate disks), the path will be one of: (1) path name of a selected scene file (if valid); (2) path name of current spec file (if valid); (3) the current directory.
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8150036b by John Harwell at 2021-10-20T09:34:47-05:00
WB-952 Scene dialog and scene path: Add tooltips to the Scene Dialog's Save, Save As, Move, and New buttons. The tooltips suggest placing the scene file in the "base path" or a subdirectory of the base path.
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e1390003 by John Harwell at 2021-10-25T10:04:51-05:00
Cleanup of graphics: GraphicsPrimitiveV3fT3f was incorrectly named as it accepted only 2, not 3, texture coordinates. It has been renamed to GraphicsPrimitiveV3fT2f. A new GraphicsPrimitiveV3fT3f was then created that can be used with 3D texture coordinates for volume files.
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e767b779 by John Harwell at 2021-10-25T10:04:51-05:00
Fixed/Improved graphics primitives for textures to support both 2D and 3D textures. Revised experimental textured volume drawing so that it is no longer a kludge. Now, it supports volume drawing including updates to the map coloring. Added a "volume texture manager" that manages the textures for VolumeFile and will be used for drawing CIFTI volumes in the future. Textured volume drawing must be enabled on the Preferences dialog. Textured volume drawing does not offer cubic interpolation so that may be a drawback but a cubic algorithm could be written using an OpenGL shader. Lastly, the advantage of textured volume drawing is that it offers very high frame rates for both orthogonal and oblique drawing (80+ fps).
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fb188688 by John Harwell at 2021-10-25T10:04:51-05:00
Textured volume drawing: Add support for CIFTI volume data. Added separate smoothing controls for anatomy and functional data drawn using textures.
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d358fe61 by John Harwell at 2021-10-25T10:04:51-05:00
Improve graphics performance: Added drawing of surfaces using vertex buffers instead of vertex arrays. Must be enabled in Develop tab of Preferences Dialog.
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038575f0 by John Harwell at 2021-10-25T10:04:51-05:00
Changed text of a couple developer flags to indicate that they affect oblique volume views.
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254b23d7 by John Harwell at 2021-10-25T10:04:51-05:00
Removed print statement from scene restoration of dialog settings.
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bf859178 by John Harwell at 2021-10-25T10:04:51-05:00
Added option "-enable-perf" to wb_view. This option enables the developer flags for drawing surfaces as buffers and volume slices using textures.
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c9932b5b by John Harwell at 2021-10-25T10:04:51-05:00
For wb_command -show-scene: the call to OSMesaMakeCurrent may fail if the output image size is too large so inform user of this.
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286e9398 by John Harwell at 2021-10-25T11:15:09-05:00
Fix compilation errors on Linux and Windows systems.
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dd2e9886 by Tim Coalson at 2021-10-28T23:05:13-05:00
fix for bug in PR #57
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3cd2e21e by John Harwell at 2021-11-23T10:47:01-06:00
WB-952 Scene dialog and scene path: Discovered bug. If data files were loaded but no scene file was loaded, launching the scene dialog displayed the scene dialog and then popped up a file selection dialog. This file selection dialog popped up because there was no scene file and the scene dialog was trying to create a default scene file. This scene file dialog popped up due to recent changes made for this issue to induce the user to create a new scene file in the base directory. Call to create a default scene file (SceneDialog::createDefaultSceneFile()) had been removed. The user will need to press the New button to create a scene file prior to creating scenes.
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253c562f by John Harwell at 2021-11-24T12:17:53-06:00
WB-952 Scene dialog and scene path: Fix another bug. If a new scene file was created, the scene file does not exist (has not been written yet), and a scene is added, the "Save" button was not getting enabled.
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512c76f8 by John Harwell at 2021-12-13T10:45:57-06:00
Encountered a stack overflow runtime error in FTGL font drawing on a computer (nvidia graphics system) that has a maximum stack depth of 4 for the OpenGL projection matrix. On my Mac the maximum projection stack depth is 10. The OpenGL 4.x spec states that 2 is the minimum stack depth. Added push/pop for the projection matrix to Graphics Utilities (uses its own stack) and it is used in FTGL font drawing and in Annotation drawing. This seems to keep the projection matrix stack depth at 2. Note that I was not able to duplicate the error on a computer so this fix may not fix the problem.
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2aebabd6 by Tim Coalson at 2021-12-13T21:16:39-06:00
qt 5.9 doesn't have QVector(begin, end), attempt other solutions
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05922fff by Tim Coalson at 2021-12-13T23:05:20-06:00
fix memory leak in point locator
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2915890b by Tim Coalson at 2021-12-14T17:38:58-06:00
use deprecated rects instead of fromStdVector for qt 5.9, etc
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6e5a91e5 by Tim Coalson at 2021-12-30T17:01:43-06:00
add compatibility flag system, deprecate old -show-scene
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2302e3e5 by Tim Coalson at 2022-01-13T16:37:26-06:00
add option for non-spherical resampling surfaces to basic surface based resampling commands
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8502476d by John Harwell at 2022-01-25T12:05:45-06:00
MPR: Started on a volume MPR (Multi-Planar Reconstruction) viewer. It is available in the combo box in Slice Indices/Coords in the toolbar.
Fixed conflict in GraphicsUtilitiesOpenGL.h and cxx
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9cb675da by John Harwell at 2022-01-25T12:07:20-06:00
WB-944 CZI (Zeiss Microscope) image file formats: Revised drawing to drawing in "logical coordinates" instead of pixel coordinates. CZI logical coordinates contain x, y, width, height. The x, y are at the top left corner of the image and are typically non-zero.
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1f072385 by John Harwell at 2022-01-25T12:07:20-06:00
WB-944 CZI (Zeiss Microscope) image file formats: Revised to draw images in "logical coordinates". Updated to support reading and display of individual "czi scenes" which are actually separate, discontiguous images in a CZI file. Replaced most "Pixel" functions with "Logical Pixel" functions.
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690d28bd by John Harwell at 2022-01-25T12:07:20-06:00
WB-944 CZI (Zeiss Microscope) image file formats: Starting on implementation of a new multi-resolution image loader that supports different images in each tab/layer.
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be9f91b4 by John Harwell at 2022-01-25T12:07:20-06:00
WB-944 CZI (Zeiss Microscope) image file formats: Implemented new loader for CZI image data.
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cb0098a1 by John Harwell at 2022-01-25T12:07:20-06:00
WB-944 CZI (Zeiss Microscope) image file formats: Continuing implementation of new Image Loader.
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bc8a9aac by John Harwell at 2022-01-25T12:07:20-06:00
WB-944 CZI (Zeiss Microscope) image file formats: Fixed bug with image being improperly destroyed. Clean out "default image" that is no longer needed.
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b9185e4c by John Harwell at 2022-01-25T12:07:20-06:00
WB-944 CZI (Zeiss Microscope) image file formats: Add menu item for exporting CZI to image file on Save/Manage Files more (sprocket icon) column. Was able to write a 53481 x 37932 image to several different files formats. When testing, was able to write to JP2, JPG, PNG, PPM, and TIFF. JPG and TIFF displayed in MacOS Preview App; the others did not.
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efb5447d by John Harwell at 2022-01-25T12:07:20-06:00
WB-944 CZI (Zeiss Microscope) image file formats: Improve loading of older czi/image scenes. Use the scaling and approximately center the image.
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e4b45e9f by John Harwell at 2022-01-25T12:07:20-06:00
WB-944 CZI (Zeiss Microscope) image file formats: Revise CZI selection to make RGB value optional. Get RGB value by reading from file rather than the QImage in CziImage. QImage will be removed in a later update.
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d01e0a7c by John Harwell at 2022-01-25T12:07:20-06:00
WB-944 CZI (Zeiss Microscope) image file formats: No longer copy CZI bitmap data into a QImage (code remains if needed in the future). Instead, use the CZI bitmap data directly when creating the graphics primitive for drawing a CZI image. Update the graphics primitives that use textures to support a 'row stride' (sometimes image rows are padded to preserve a byte alignment) and to support images with the origin in the top left corner.
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878330d6 by John Harwell at 2022-01-25T12:07:20-06:00
Fixed problems with sizes of identification symbols on surfaces and images. For surfaces, no symbol was displayed if size was changed to percentage. On images, if zoomed in symbol became way too large.
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2fcf7684 by John Harwell at 2022-01-25T14:51:56-06:00
Fixed compilation warnings.
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d6514cb9 by John Harwell at 2022-01-26T09:43:33-06:00
Fixed compilation warnings from other compilers.
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8c240bc4 by John Harwell at 2022-01-26T11:28:02-06:00
Fixed compilation error on Mac ARM build.
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2545fb86 by John Harwell at 2022-01-27T08:25:39-06:00
WB-944 CZI (Zeiss Microscope) image file formats: Add option "-czi-develop" to "wb_command -file-information". It is used to print information about the segments (content) of the CZI file and is for use by developers.
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a47dde70 by John Harwell at 2022-01-27T08:26:35-06:00
WB-944 CZI (Zeiss Microscope) image file formats: Removed "CZI" section of toolbar as it it currently empty. Fixed layout issues for vertical media overlay toolbox (Add "All" label to all checkbox; add a label for "Yoke").
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83163728 by John Harwell at 2022-01-27T08:37:54-06:00
Trying to fix compilation errors with Qt5 (I'm on Qt6).
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92105a12 by John Harwell at 2022-01-27T09:08:14-06:00
Adding a QtGlobal include to try and fix compilation errors with usage of QDataStream.
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9919f002 by John Harwell at 2022-02-01T13:38:09-06:00
Add the README.md from CZI library into our source's copy of the CZI library
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809e3fff by John Harwell at 2022-02-01T13:44:10-06:00
Renamed CziFileReader to CziFileTestReader. This class is only used in the file information command and may be removed. A CZI File Spec was found (http://www.physics.hmc.edu/~gerbode/wppriv/wp-content/uploads/2012/06/DS_ZISRAW-FileFormat_Rel_ZEN2011.pdf) and this code was written to read directly from the CZI file, without CZIlib to better understand the organization and content of the CZI file. While we might be able to use this document to write a CZI file, indications online are that ZEISS prohibits writing of CZI files (The file format design specification [1] is confidential and the licence agreement does not permit to write data into CZI files. https://github.com/AllenCellModeling/czifile).
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13468aa2 by John Harwell at 2022-02-01T13:48:20-06:00
WB-944 CZI (Zeiss Microscope) image file formats: Improved export of an image file from a loaded CZI image file. Export is on the 'sprocket' icon in Save/Manage Files Dialog. A dialog now pops up allowing selection of the export image file name, an option to include an alpha channel, and an option to limit the width/height of the output image file.
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8b1137e9 by John Harwell at 2022-02-02T14:09:04-06:00
Qt 6.x has a memory limit of 128 megabytes when reading an image file. Histology images may be much larger than this. If one tries to read a large image, this message is logged: "QImageIOHandler: Rejecting image as it exceeds the current allocation limit of 128 megabytes". Qt 6.0 adds the static method QImageReader::setAllocationLimit(0) and calling it with zero removes the memory limit. The downside is that if one tries to read a corrupt image, it may cause allocation of a large amount of memory causing the application to hang or crash. Qt 5 appears to have the same limit with no way to override it.
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5adc9a6f by John Harwell at 2022-02-04T15:26:28-06:00
Improvements and bug fixes for prototype Multi-Planar Reconstruction Volume Viewer.
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546a5a68 by John Harwell at 2022-02-07T13:42:47-06:00
For OpenGL error reporting, include the current and maximum depths of the Attribute Stack.
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efa9632b by John Harwell at 2022-02-07T13:44:19-06:00
Improvements for prototype Mult-Planar Reconstruction Volume Viewer: Added volume surface outline, annotations, and identification symbols. Fixed OpenGL attribute stack overflow error.
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e3193df6 by John Harwell at 2022-02-07T13:57:57-06:00
Removed test code for reading a CZI file.
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4f0657fc by John Harwell at 2022-02-08T09:19:53-06:00
Fixed compilation errors with Qt versions less than 6.
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830bbb5b by Tim Coalson at 2022-02-14T16:06:55-06:00
fix uninitialized value in cifti average in exclude mode with all inputs non-numeric
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47440811 by Tim Coalson at 2022-02-14T20:23:40-06:00
improve error messages for improperly written ASCII gifti file, simplify SurfaceFile error logic to immediate throw
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f53ea70a by Tim Coalson at 2022-02-17T17:55:32-06:00
allow -file-information to return more informative errors
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b985f5dc by Tim Coalson at 2022-02-22T17:48:23-06:00
help text improvements
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b2aa276a by John Harwell at 2022-02-24T08:51:23-06:00
MPR Volume drawing: Change cursor to "4-arrows" when mouse dragging will change slices of other planes; change cursor to rotation symbol when mouse dragging will perform rotation.
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05d72d20 by John Harwell at 2022-02-24T08:51:23-06:00
MPR Volume drawing: Changed slice scrolling to move along the vector that is orthogonal to the current plane of the slice being viewed. Previously, it moved along the vector of coronal, parasagittal, or axial slice.
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937cfca6 by John Harwell at 2022-02-24T08:51:23-06:00
MPR Volume Drawing: Changed slice scrolling so that move the mouse from the bottom of the screen towards the top increases the slice coordinate in all axes (moving down decreases).
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82e91648 by John Harwell at 2022-02-24T08:51:23-06:00
MPR Volume Drawing: Fixed "flipping" of slices during rotation. When setting the "view transformation", the "up vector" was improperly set and became parallel to the "look at vector" causing the flip. Setting of the up vector has been corrected.
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4b5e9ce3 by John Harwell at 2022-02-24T08:51:23-06:00
MPR Volume Drawing: Cleanup of code including replacing std::array<float, 3> with Vector3D.
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58cea0fd by John Harwell at 2022-02-24T08:51:23-06:00
Scene Show Files and Folders Dialog: Fixed bug with missing "NOT FOUND" list file list, show NOT FOUND in red. Add scene file information in a third tab as it shows a file breakdown by scene.
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33034367 by John Harwell at 2022-02-24T08:51:23-06:00
In AString.h, changed all of the fromNumbers() methods to use a default value of ", " for the separator parameter. Added a fromNumbers method that accepts a Vector3D.
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0e81aa8b by John Harwell at 2022-02-24T08:51:23-06:00
Added OpenMP support on MacOS. The src/CMakeLists.txt file contain logic that used environment variables for finding OpenMP as an alternative to CMake's Find OpenMP logic. These environment variables were unused in our builds and did not function correctly when tried. They have been replaced with cached variables beginning with WORKBENCH_OPENMP for the include directory, compiler flags, and library. These new variables are used on MacOS to support OpenMP in Workbench. While it would be nice to use CMake's FindOpenMP to find OpenMP on MacOS, I could not get it to work. Some notes I found online indicated it only worked when OpenMP was installed with the "Brew" tools.
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0ab643cf by John Harwell at 2022-02-24T08:51:23-06:00
Added an item to developer menu for verifying OpenMP functionality. If compiled without OpenMP, it just pops up a message stating so. If compiled with OpenMP it list the maximum number of threads and runs a small for-loop that should produce "out of sequential order" results if OpenMP is working.
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63c08732 by John Harwell at 2022-03-01T09:46:50-06:00
For 'wb_command -zip-scene-file': If the user does not provide a base path, print the base directory that was automatically created by the command.
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863c668a by John Harwell at 2022-03-01T10:41:46-06:00
Add 'wb_command -scene-file-update'. Palette settings for a data file are saved in a scene. If the number of maps in the data file changes after a scene has been created, the number of palette settings in the scene does not match the number of maps in the file. This command will update the palette settings in the scene to match the number of maps in the file by copying the palettes settings from the first map to all maps.
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32dd1b1d by John Harwell at 2022-03-01T15:12:52-06:00
Update to 'wb_command -scene-file-update'. Parameter '-copy-one-palette' is now a repeatable parameter so that palettes can be repaired for multiple files.
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8ab9f17a by John Harwell at 2022-03-02T14:07:42-06:00
Update to 'wb_command -scene-file-update'. Command has been redesigned to find files with palette problems (number of maps in file does not match the number of palette settings for the file in the scene). Options have also been added to print files for which palettes are updated (-verbose) and to ignore errors when a file cannot be found for fixing its palettes or the palette cannot be fixed (-Werror).
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0a7c1704 by John Harwell at 2022-03-02T14:49:52-06:00
When 'wb_command -zip-scene-file' find that the scene file is outside the base directory, add the base path and the scene path to the error message. This might be caused by symbolic links but need to see these paths to verify.
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68e228ec by John Harwell at 2022-03-02T17:37:06-06:00
For wb_command -scene-file-update, reenable the -copy-map-one-palette option.
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2ac8ec7f by John Harwell at 2022-03-03T14:01:35-06:00
Add option -write-scene to -zip-scene-file command that allows writing of the scene file and it may be needed to change fix paths of files from determination of base path.
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267e4582 by John Harwell at 2022-03-03T15:01:04-06:00
Previous change with allowing writing of scene file has fixed problem. Added setting of custom path into scene file and ignore writing of scene when zipping file in the GUI since the Zip Scene File Dialog updates the scene file prior to calling this operation.
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911aea73 by John Harwell at 2022-03-04T09:44:51-06:00
When file information command is run on a scene file, list the base path type, custom base path, extract directory, BALSA Study Title, and BALSA Study ID.
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953b0dee by John Harwell at 2022-03-08T14:18:47-06:00
Updated wb_command -scene-file-update with options to add files to a scene or to remove files from a scene. The user may specify the name of a file or a text file containing a list of files.
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ad3110e0 by John Harwell at 2022-03-08T14:29:02-06:00
Fix Qt5/Qt6 compilation problem. Qt6 uses Qt::SkipEmptyParts and Qt5 uses QString::SkipEmptyParts.
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79893f14 by John Harwell at 2022-03-08T15:17:03-06:00
Improve help text for wb_command -scene-file-update.
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6ecb6b25 by Tim Coalson at 2022-03-10T16:22:50-06:00
move -cifti-palette off of CiftiXMLOld, work properly for file palettes
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ea4f8604 by John Harwell at 2022-03-14T09:33:47-05:00
Enable automatic fixing of palette color mapping that is save in a scene. The number of palette color mappings for a file must be different than the number of maps, the file must support per-map color mapping, and apply to all maps must be enabled in the scene. This functionality can be disabled by setting "enablePaletteFixingFlag" to false in CaretMappableDataFile.cxx.
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10bfda9a by John Harwell at 2022-03-14T09:33:47-05:00
Fixed formatting of DataFileException error message.
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94ab2d21 by John Harwell at 2022-03-14T09:33:47-05:00
Fixes and updates to wb_command -scene-file-update. For removal of a file by name, fixed removal of a file that does not exist. Add new option "-remove-missing-files" that removes files that are in spec file but do not exist. Allow user to specify parameters in any order but process commands in proper order (remove files before adding; update palettes after adding). Allow command to complete even if there are errors in any of the operations and print error messages but allow command to abort if new option "-error" is specified.
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3f5e6b45 by John Harwell at 2022-03-14T09:38:36-05:00
Remove unused parameter.
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c513d68f by John Harwell at 2022-03-14T10:51:04-05:00
When wb_command -file-information is run on a scene file, add "NOT FOUND" after the names any files that are not found.
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4a80c79c by John Harwell at 2022-03-14T11:09:20-05:00
For scene file update command, if there are errors loading the scene and the user has specified the remove missing files option, add a message explaining that errors loading the scene (missing files) can be ignored since the scene errors are for the missing files that will be removed by the command.
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3549b300 by John Harwell at 2022-03-14T11:24:23-05:00
Improve the scene loading error message for the scene file update command.
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17f8c880 by John Harwell at 2022-03-15T15:19:18-05:00
When a scene is created, include the Workbench Version, Date and Time, Commit Date, and Commit Version in the SceneInfo section of the Scene XML.
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b5ca5cdc by John Harwell at 2022-03-15T16:00:51-05:00
Remove unused classes for writing scene file that were replaced by the Stream Writer.
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512308ec by John Harwell at 2022-03-17T08:53:20-05:00
Fixed scrolling of slices with mouse in Orthogonal View.
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26396217 by John Harwell at 2022-03-17T15:23:19-05:00
Move GiftiMetaData, GiftiException, GiftiMetaDataXmlElements, and GiftiXmlElements from FilesBase to XML so that they can be used for SceneInfo's metadata.
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69fc8a35 by John Harwell at 2022-03-17T15:27:22-05:00
When a scene is created by the user, add this metadata to the scene: the Commit, Commit Date, Current Date/Time, Workbench Version, and OS Version. This same metadata is also added/updated in the scene file when it is written. Metadata is added to scenes as scenes in the same file may be created by different versions of Workbench.
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2dc8fba9 by John Harwell at 2022-03-18T12:45:57-05:00
Display a scenes metadata: (1) In output of wb_command -file-information when run on a scene file; (2) In Scenes tab of Files and Folders dialog displayed when Show Files and Folders button is clicked on Scene dialog; (3) In Scene Preview dialog.
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089a44bd by John Harwell at 2022-03-18T14:50:42-05:00
Modified commands -show-scene and -scene-image-capture. If Workbench is built without Mesa3D, the commands will start but exit with an error message indicating that the commands will not run due to the lack of Mesa3D when the software was compiled. Previously, a command not found message was printed.
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105e6b81 by John Harwell at 2022-03-22T15:16:12-05:00
Image Capture Methods: Removed "Render Pixmap". It is only available in the obsolete QOpenGLWidget, available in Qt 5 but not Qt 6. Default capture method changed to "Offscreen Renderer".
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f9d35729 by Tim Coalson at 2022-03-23T17:41:22-05:00
fix segfault in SceneInfo copy constructor
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f6e960f6 by John Harwell at 2022-03-24T09:47:03-05:00
When writing SceneInfo, write the MetaData before any other elements. One of the SceneInfo children is 'Name' and 'Name' contains the name of the scene. MetaData also contains a child 'Name'. When BALSA scans SceneInfo looking for the name of the scene, the last 'Name' element becomes the name of the scene. By writing MetaData first, BALSA gets the name of the scene from SceneInfo:Name and not MetaData:Name.
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44f55b47 by John Harwell at 2022-03-25T14:23:39-05:00
WB-955 Replace surf/vol millimeters/percentage combo box with radio buttons: Radiobuttons have replaced the combo box. The millimeter/percentage size spin boxes are enabled only when the corresponding size type is selected.
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eb4d7bfe by John Harwell at 2022-03-25T14:49:00-05:00
Fix signals incompatible between Qt5 and Qt6.
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b812b13f by John Harwell at 2022-03-28T08:55:34-05:00
Suppress diagnostic message "Populating font family aliases..." that occurs on MacOS in Qt6.
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5b742b7c by John Harwell at 2022-03-28T11:33:36-05:00
WB-955 Replace surf/vol millimeters/percentage combo box with radio buttons: Added separate symbol sizes for media since media is always percentage.
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f03d84fd by John Harwell at 2022-03-30T08:58:21-05:00
WB-956 Dialog listing modified files is too tall: Replaced usage of a Qt dialog with a new, custom dialog that contains a scrollable region (if needed) for listing modified files.
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643f985c by John Harwell at 2022-03-30T14:02:07-05:00
Updated images for message dialog.
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5bec23dd by John Harwell at 2022-04-01T14:09:57-05:00
Add a new message box dialog that places the text in a scroll area when the text is long. The Qt message box is too tall when the text is long.
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0ca22002 by John Harwell at 2022-04-01T14:52:05-05:00
Fixed memory leaks when surface type files (surface, metric, label, rgba) are rejected when their number of vertices does not match the number of vertices in the corresponding structure (ie read both 32K and 164K surface for right hemisphere).
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ecfe9070 by John Harwell at 2022-04-04T13:28:52-05:00
MPR Volume Viewing: Fixed panning in (1) AP was backwards in parasagittal view; (2) LR was backwards in Axial and Coronal when in a radiological view.
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44adf330 by John Harwell at 2022-04-05T12:21:59-05:00
MPR Volume Viewing: Changed panning with mouse so that the anatomical location under the mouse when the mouse is pressed follows the mouse while panning. Works well with zooming. Does not work well when there is rotation.
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6b38dcdf by John Harwell at 2022-04-06T08:13:13-05:00
MPR Volume Viewing: continuing MPR panning with rotation.
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196f8757 by John Harwell at 2022-04-06T15:58:28-05:00
MPR Volume Viewing: Redesign of translation when applied to MPR volume view. When translating with mouse, the anatomical location under the mouse now follows the mouse and works with any existing translation, rotation, or zooming.
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36c810ff by John Harwell at 2022-04-06T16:39:14-05:00
MPR Volume Viewing: Cleanup of some code.
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14cf4483 by John Harwell at 2022-04-07T11:36:07-05:00
Fixed compilation warnings reported by mac universal build with Qt 6.
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28781d53 by John Harwell at 2022-04-11T09:51:29-05:00
Improve tooltip for identification symbols so now "ID from <type>" where <type> is media/surface/volume. This helps differentiate from a pixel/vertex/voxel tooltip.
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b83c1350 by John Harwell at 2022-04-12T11:31:02-05:00
Revised Identification "Show Symbols On <type>" checkboxes. Previously, they controlled the display of ID symbols based upon the type of model on which the identification was CREATED. Now, the checkboxes control the display of symbols on the type of model. Thus, unchecking "Surface" inhibits the display of identification symbols on all surfaces (regardless of where the symbol was created). Text of checkboxes also changed to "Show ID Symbols on Surface", etc. Removed "Show ID Symbols on Other Type" checkbox as it is no longer needed.
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9a6df688 by John Harwell at 2022-04-12T16:04:26-05:00
MPR Volume Viewing: All view MPR slices working for neurological mode.
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b27b49b8 by John Harwell at 2022-04-12T16:04:26-05:00
MPR Volume Viewing: Fixed rotation in axial plane so that counter-clockwise rotation always increases the rotation angle.
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1cef9ae6 by John Harwell at 2022-04-12T16:04:26-05:00
MPR Volume Viewing: Correct drawing rotation of crosshairs and rotation with mouse for Axial and Coronal views when radiological mode is selected.
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80af9320 by John Harwell at 2022-04-13T16:38:08-05:00
MPR Volume Viewing: Several fixes and improvements for drawing of rotated slices in ALL view.
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e4aaa0a5 by John Harwell at 2022-04-13T16:47:13-05:00
MPR Volume Viewing: Removed code for an experimental method for drawing all view slices and its related developer flag.
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db2f7a94 by John Harwell at 2022-04-14T10:40:51-05:00
Cleanup of Preferences Dialog: Consolidate image items to new Image tab.
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6d78a833 by John Harwell at 2022-04-14T11:27:08-05:00
Removed experimental texture volume drawing some of which is incorporated in new MPR volume drawing.
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5cd15695 by John Harwell at 2022-04-14T13:35:37-05:00
Removed preference for cropping of scene preview images. The option is now on the scene create dialog. This option is rarely used in development, when debugging a scene and wanting to preserve empty spaces (such as when a model is zoomed/panned).
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c537600f by John Harwell at 2022-04-14T14:43:47-05:00
Preferences Cleanup: Improve naming and organization of items listed on Develop tab of Preferences Dialog.
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19ae43ab by John Harwell at 2022-04-20T11:17:32-05:00
Media Frame Control updates:• If there is only one frame (CZI scene) in the file, the All Checkbox, Index Spin Box, and Frame Name combo box are disabled. If there is more than one frame (CZI scene) in the file, the All Checkbox is enabled. The Index Spin Box and Frame Name combo boxes are enabled only when the All Checkbox is UNCHECKED. Tooltips for these controls have also been updated
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fd7a06e6 by Tim Coalson at 2022-05-02T18:23:35-05:00
protect against nan/inf in nifti scl_* fields
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b22c38ca by Tim Coalson at 2022-05-02T20:39:59-05:00
copy/paste typo in error message
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9819ae23 by John Harwell at 2022-05-04T12:32:37-05:00
If a duplicate file is loaded (same file loaded a second time), the file's name is modified with an underscore followed by a number and this sets the file's modified status. If the file does not support writing, clear the modified status since the file cannot be written.
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5e02dc2a by John Harwell at 2022-05-04T12:32:37-05:00
Fixed bug that resulted in two exit dialogs. If the user clicks the close button in the window's titlebar, this issues a close event. In the handling of the close event, the exit dialog is displayed. If the user selects Exit from the File Menu, it displays the exit dialog and if the user confirms exiting, the window's close event gets called by Qt and it was displaying the exit dialog a second time. Now, the close event will not display the exit dialog if the user selected exit from the file menu.
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128acadd by John Harwell at 2022-05-04T12:32:37-05:00
Media Overlays: Removed "All" checkbox. "All Frames" is now the first item in the frame name combo box and used to select all frames. Cleaned up code including updating to modern signal/slots in GUI for media overlay.
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a3b0a35e by John Harwell at 2022-05-04T12:32:37-05:00
CZI / Media: Added yoking of media frames including yoking with brainordinate overlays. Does not yoke to "All Frames" at this yet.
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d90bdf43 by John Harwell at 2022-05-04T12:32:37-05:00
CZI and Media: Added yoking support for "All Frames".
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08325bd1 by John Harwell at 2022-05-06T12:41:12-05:00
Staring on Maximum Intensity Projection for Volumes. Is working for orthogonal views.
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21374cca by John Harwell at 2022-05-06T17:02:50-05:00
Maximum Intensity Projection Volume Mode: Fixed display of volume when there is rotation.
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291cee8b by John Harwell at 2022-05-09T13:38:53-05:00
Correct getting of Cull Face in OpenGL info.
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e806ba31 by John Harwell at 2022-05-11T15:18:09-05:00
Add polygon modes to OpenGL Information.
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cc8f8480 by John Harwell at 2022-05-11T15:55:40-05:00
Fixed blending for MIP and MinIP modes by drawing a black (MIP) or white (MinIP) slice just prior to drawing any slices. The black or white slice is needed since these intensity modes use blending with MAX or MIN and drawing of all slices along the viewing vector.
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1d0ea7a3 by John Harwell at 2022-05-12T16:25:36-05:00
Volume Intensity Drawing: Cleanup and improvements.
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efae8fdd by John Harwell at 2022-05-13T17:10:36-05:00
Volume Intensity Modes: Show ID symbols from other sources (surfaces or volume slices).
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a167d6f5 by John Harwell at 2022-05-16T11:54:40-05:00
Volume Intensity: Add MIP / MinIP for CIFTI volume data in slice and all views.
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c0025cad by John Harwell at 2022-05-17T08:54:54-05:00
Removed some old code that forward referenced a class that no longer exists.
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3865bd15 by John Harwell at 2022-05-17T15:48:04-05:00
Clipping Planes Improvement: (1) If user toggles the clipping plane button in the toolbar to enable clipping and none of the X/Y/Z clipping planes are enabled, enable the three clipping planes; (2) On clipping planes pop-up widget, if user enables one of the X/Y/Z clipping planes but the global clipping planes display status is disabled, enable the global clipping planes display status; (3) Add a new "Pan Mode" with a selection that allows using the Volume Slice Coordinates from Toolbar as the panning for the clipping planes (changing the slice indices/coordinate moves the clipping planes.) Default for "Pan Mode" is the pre-existing pan x/y/z values on the clipping widget.
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71e88d41 by John Harwell at 2022-05-19T10:00:33-05:00
For Volume MPR: An identification operation is used to determine if an MPR crosshair is under the mouse. Add filtering so that only identification of crosshairs is performed instead of identifying everything.
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bef3a8a7 by John Harwell at 2022-05-19T11:34:48-05:00
Volume Intensity Modes: Added identification of voxels in volume maximum/minimum projections. This is performed by finding the voxel with the greatest/least intensity along a vector that intersects the volume with the vector starting at the location of the mouse click.
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d8297c35 by John Harwell at 2022-05-20T16:10:41-05:00
Added new cached CMAKE variable named WORKBENCH_APPLE_WB_COMMAND_BUNDLE_FLAG that is only used in Apple builds. When this variable is true, wb_command is built as a MacOS Bundle (wb_command.app). When false, wb_command is built as a normal UNIX executable. The default value for this variable is TRUE.
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2c91d8f7 by John Harwell at 2022-05-23T09:05:35-05:00
In movie recorder, update finding path of ffmpeg for newer wb_view app structure on MacOS.
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58eb62fc by John Harwell at 2022-05-24T13:40:13-05:00
Volume Modes: Updated controls in Toolbar:Slice Indices/Coords. Combo box selects slice viewing mode (Orthogonal, Oblique, MPR, MIP, MinIP. Button to right of combo box selects sub-modes: Masking for Oblique, and Neurological/Radiological for MPR, MIP, and MinIP.
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3e06d84d by John Harwell at 2022-05-24T15:30:26-05:00
Volume Modes: Fixed yoking of orientation mode (neurological / radiological) for MPR, MIP, and MinIP volume slice modes.
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fca18e63 by John Harwell at 2022-05-24T15:31:51-05:00
Volume MPR, MIP, and MinIP modes: When radiological orientation is selected, change the color to red for the "R" in the tool button to make it obvious.
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c22556ae by John Harwell at 2022-05-27T16:45:59-05:00
Volume MPR: Revising controls in toolbar.
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3c7dde62 by John Harwell at 2022-05-31T14:17:33-05:00
Volume MPR: Implemented slice thickness used in MIP, MinIP modes. Slice thickness limits the number of slices to a thickness that is centered on the selected slice coordinates.
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07e724f8 by John Harwell at 2022-06-01T09:21:41-05:00
Volume MPR: Initial implementation of Average Intensity Projection.
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6c8108c3 by John Harwell at 2022-06-01T12:37:18-05:00
Volume Intensity: The button used to select MPR options pop-up widget and Oblique options widget in Toolbar -> Slice Indices Coords has been updated. The arrow to pop-up the options widget remains. Now, clicking the non-arrow portion of the button cycles through each of the MPR modes or Oblique Masking modes and displays the current mode instead of the text "Opts".
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001534c5 by John Harwell at 2022-06-01T12:45:15-05:00
Volume Intensity: Fixed compilations warnings by removed unused method parameters.
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6491e5d6 by John Harwell at 2022-06-01T17:00:10-05:00
Fixed MathFunctions::nearestPointOnLine3D(). Its output of "pointOnLineOut" was incorrect. This output was not used until today with volume intensity processing.
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0e2ade20 by John Harwell at 2022-06-01T17:01:01-05:00
Volume Intensity: Add "thickness" usage in ALL view with new checkbox on the Volume Intensity Widget. Using a thickness helps with the Average Intensity Mode.
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66e10e39 by John Harwell at 2022-06-06T16:46:21-05:00
Volume Intensity: Set parameters for slice thickness spin box range, decimals.
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a4c5fc92 by John Harwell at 2022-06-07T08:54:52-05:00
Fixed compilation errors and qt version incompatibilities on other systems.
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c1a1f78a by John Harwell at 2022-06-07T14:35:42-05:00
Fixed problems with incorrect percentage symbol size on volume slices. When percentage was used for volume data, the percentage was based upon the longest volume dimension. If the "brain" filled the volume file, this worked okay. However, if the brain was much smaller than the volume (lots of empty voxels around brain data), the symbol was too large. Now, the "non-zero voxel extent" is found in the volume and it is used for the percentage symbol size.
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42bb36a0 by John Harwell at 2022-06-08T15:06:01-05:00
WB-959 ID Improvements: In Identification -> Filter tab, added a "Vertex/Voxel Geometry checkbox. When checked, the default, information about the surface vertex (index, XYZ) and / or voxel (IJK, XYZ) is displayed when an identification operation is performed. When off, this information is not displayed.
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d70b65c6 by John Harwell at 2022-06-10T09:50:47-05:00
WB-960 ID improvements: Change Identification -> Files tab. A checkbox that force a file's inclusion in identification information was removed. It was replaced with a combo box that allows the user to always include the file, include the file only if the file is in an overlay, or to never show the file information.
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4504af45 by John Harwell at 2022-06-10T10:12:04-05:00
WB-960 ID improvements: Fixed bug that caused Identification -> Files to be empty. Content (list of identifiable files) was empty until an identification operation was performed. It is now updated when a user-interface update is received.
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fc8f5c28 by John Harwell at 2022-06-14T15:14:22-05:00
WB-960 ID improvements: Revised Filtering of Files displayed during identification. User now has option to display a file: (1) "Always" - always displays identification data for file; (2) "Never" - never displays identification data for file; or (3) "Overlay" - only displays identification data for a file if the file is in an enabled overlay. Also, some revisions to media (CZI, image) identification text generation.
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1f058b35 by John Harwell at 2022-06-15T10:40:16-05:00
WB-960 ID improvements: Fixes for media identification. For CZI files, only successfully identify if the mouse is clicked over valid image data in one of scenes (frames) that is displayed.
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16384bd4 by John Harwell at 2022-06-15T14:43:57-05:00
WB-957 Volume Intensity Modes: Updates to user interface. Replace combination toggle button and menu arrow with a a "down arrow" button that pops up the MPR options (or Oblique options if in Oblique mode). Note that disable toggle button cycled through the intensity modes and was an improper usage of a tool button.
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3e08da1d by John Harwell at 2022-06-16T09:43:53-05:00
WB-960 ID improvements: Improved tooltips on radio buttons in Identification -> Filter to clarify their functionality.
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6c817e66 by John Harwell at 2022-06-16T09:54:20-05:00
Add an "UnLock" button to prevent improper editing of BALSA Scene ID: Unlock button with warning dialog has been added to Edit Scene Dialog (and Add/insert/Replace Scene dialog).
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8447ec75 by John Harwell at 2022-06-16T10:11:15-05:00
Added missing header file needed on Linux and Windows.
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22fa1cfc by John Harwell at 2022-06-17T10:16:20-05:00
WB-960 ID improvements: Fixed failure to include Volume files in Identification -> Files tab.
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1e6d5c5c by John Harwell at 2022-06-17T12:32:16-05:00
WB-957 Volume Intensity Modes - Fixed All View (3D) of intensity volume to draw the correct map (not first) for multi-brick volume files.
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d3bcec2d by John Harwell at 2022-06-17T15:27:32-05:00
WB-960 Dialogs improperly displaying when a scene is loaded. A user experienced display of Surface and/or Volume Properties dialog when restoring scenes on a specific version of Linux. These dialogs do not need to be saved to scenes so scene support for the dialogs has been removed.
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8f6a0c1a by John Harwell at 2022-07-11T16:42:36-05:00
Fixed volume dynamic connectivity for single voxel. It failed to update the scalar coloring after loading data and has been corrected.
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b5963bd5 by John Harwell at 2022-08-05T11:43:58-05:00
Moved SceneClassInfoWidget into its own file and removed it from SceneDialog.h/cxx.
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d301b652 by John Harwell at 2022-08-05T11:43:58-05:00
In OpenGL information, include supported texture compression formats. Fix comments on glTexImage*() calls in graphics primitive.
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06908fcc by John Harwell at 2022-08-05T11:43:58-05:00
Added reading of CZI meta file including creation of transforms involving pixel, plane, and millimeters.
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5fd9e90d by John Harwell at 2022-08-05T11:43:59-05:00
Cleanup of image file code including replacing std::array<float, 3> with Vector3D.
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1abbcb80 by John Harwell at 2022-08-05T11:43:59-05:00
Continuing CZI Meta File development.
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de91ceb2 by John Harwell at 2022-08-05T11:43:59-05:00
Added drawing of PNG images containing transforms using new image coordinate drawing.
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5b022e97 by John Harwell at 2022-08-05T11:43:59-05:00
Starting on some redesign of textures used in graphics primitives.
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8f8d11c9 by John Harwell at 2022-08-05T11:43:59-05:00
Continuing on some redesign of textures used in graphics primitives.
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31d9a148 by John Harwell at 2022-08-05T11:43:59-05:00
Removed some unused methods from ImageFile
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6cb43b1b by John Harwell at 2022-08-05T11:43:59-05:00
Finished redesign of texture revisions that pass CZI image data and QImage data directly to OpenGL texture processing 'BGRA' color mode. Previously, the images were copied to intermediate store with conversion to RGB. These changes improve both CPU and memory performance.
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4f0f3fe5 by John Harwell at 2022-08-05T11:43:59-05:00
Revise display of, and add a few, texture compression formats.
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dc08dbe3 by John Harwell at 2022-08-05T11:43:59-05:00
Enabled texture compression for ImageFiles since the images can be large.
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af1dbd52 by John Harwell at 2022-08-05T11:43:59-05:00
Added a preference for image file texture compression and only if uncompressed size is greater than 512MB. Also fixed reloading of image file so that the texture image is recreated.
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6a17cf15 by John Harwell at 2022-08-05T11:43:59-05:00
Fixed normal CZI loading for updates to texture images that now have origin at top and updates in preparation for "plane coordinate" CZI viewing/loading.
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8504d055 by John Harwell at 2022-08-05T11:43:59-05:00
CZI Plane Coordinates: Loading of CZI images in plane coordinates seems to be working.
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8d9a4564 by John Harwell at 2022-08-05T11:43:59-05:00
CZI images in plane coordinates: fixed panning with mouse so that part of image under mouse remains under mouse as mouse is dragged.
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8d22310a by John Harwell at 2022-08-05T11:43:59-05:00
For graphics primitive textures: (1) Log a message if mip mapping is off but the filter is set to a mip mapping filter; (2) If mip mapping is off and a mip mapping filter is used, use a non mip mapping filter. Note that if a mip mapping texture filter is used but mip mapping is off, white triangles are produced.
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d94187b1 by John Harwell at 2022-08-05T11:43:59-05:00
CZI: (1) Added "tinting" that adjusts coloring of a CZI image using information from the CZI file. Tinting makes the images match the coloring displayed in the ZEN software. Until now, the image, without tinting, were too dark in Workbench when compared to Zen. Unfortunately, there is a bug in the CZI library's tinting code. It works the first time but running it additional times adds artifacts, sort of ghost images to the output. So, tinting has been disabled until it can be fixed. (2) Updated export of CZI to image files to allow RGB or RGBA and to optionally include pixel to plane and plane to millimeter matrices in the image file's metadata. (3) Reduced duplicate code in ImageFile for creating graphics primitives.
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af4e87b9 by John Harwell at 2022-08-05T11:43:59-05:00
Image Textures: If the image data does not have an alpha channel, use an OpenGL internal texture format of GL_RGB. It saves some, but not much memory when compared to GL_RGBA.
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dfaa20ef by John Harwell at 2022-08-05T11:43:59-05:00
For Image Files that are only RGB (no Alpha channel) use QImage::Format_RGB888 (3 bytes per pixel) in place of QImage::Format_RGB32 (4 bytes per pixel with an alpha that is always 0xff). Saves 25% in memory usage
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ae684406 by John Harwell at 2022-08-05T11:43:59-05:00
Update GraphicsPrimitive so that it can draw a subset of its coordinates. Changed ImageFile so that it uses the same GraphicsPrimitive for both Pixel and Plane (if available) coordinates. This allows them to use the same OpenGL texture. Previously, two primitives were used, each with their own texture. Using one copy of the texture cuts memory usage in half.
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529558d4 by John Harwell at 2022-08-05T11:43:59-05:00
When switching the image view between Pixel and Plane, reset the view. Otherwise, due to the differences in pixel/plane coordinates the image data may not be seen until the Reset button is clicked.
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243b31aa by John Harwell at 2022-08-05T11:43:59-05:00
Cleanup of ImageFile from using one primitive for both pixel and plane coordinates.
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5b7edbb2 by John Harwell at 2022-08-05T11:43:59-05:00
Save CZI "display settings" after reading file so that they do not have to be reread each time image data is loaded.
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e5cc2fef by John Harwell at 2022-08-05T11:43:59-05:00
Default OpenGL texture compression on in preferences.
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9e95d40b by John Harwell at 2022-08-05T12:35:14-05:00
Fixed compilation problems on other operating systems and computers.
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0809baf3 by John Harwell at 2022-08-05T12:51:14-05:00
Part 2: Fixed compilation problems on other operating systems and computers.
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05e619e0 by John Harwell at 2022-08-08T08:31:40-05:00
When copying palette settings to other maps/files, also copy the histogram settings.
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f7f08e98 by John Harwell at 2022-08-08T09:11:19-05:00
CZI: Fixed crash that occurred when an identification operation was performed on a volume and CZI images in plane coordinates were displayed.
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5e7dfdfb by John Harwell at 2022-08-08T15:05:23-05:00
Add method to DataFileContentInformation to display a Vector3D object.
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63aec427 by John Harwell at 2022-08-08T15:06:47-05:00
Display bounds of images in millimeters in data file information. Add swapping of X and Y values when multiplying by matrices that convert between plane and millimeter coordinates.
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ee73a01f by John Harwell at 2022-08-09T12:38:52-05:00
Seem to have fixed problem with image millimeter coordinates. When applying the plane to millimeters transform, swap the X and Y components before multiplying by plane-to-millimeters matrix but DO NOT swap X and Y components after the matrix multiplication. Display of identification symbols between the image and volume has been improved.
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566c9e37 by John Harwell at 2022-08-09T12:45:19-05:00
Fixed scene problem for IdentifiedItemUniversal. m_pixelPlaneCoordinate was being saved two times.
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de770835 by John Harwell at 2022-08-09T15:10:06-05:00
CZI: Improvements to identification between image and volume (plane coordinates was mistakenly used in place of stereotaxic for image id). Cleaned up code in a couple of files.
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a4dd2784 by John Harwell at 2022-08-11T08:19:59-05:00
Fixed zooming for images displayed in plane coordinates.
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3c86426c by John Harwell at 2022-08-12T09:19:09-05:00
CZI Update for new metaczi file that contains matrices now in "right then down" convention. No longer need to swap X and Y.
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e53765e1 by John Harwell at 2022-08-12T09:19:59-05:00
Fixed selection of an image region by dragging the mouse to create a box for images displayed in plane coordinates.
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6980bab6 by John Harwell at 2022-08-29T15:08:08-06:00
Adding support for new Histology Slices File.
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230321d2 by John Harwell at 2022-09-08T09:58:01-05:00
Histology: Continuing developer of histology functionality.
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c6c5f37e by John Harwell at 2022-09-12T15:40:24-05:00
Histology: Continuing developer of histology functionality.
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240193b9 by John Harwell at 2022-09-14T09:51:27-05:00
Histology: Continuing development, annotations now working.
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c201e073 by John Harwell at 2022-09-14T11:12:00-05:00
Histology: Correct percentage sizing of histology identification symbols and add controls for sizes of histology identification symbols.
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6da3ac76 by John Harwell at 2022-09-15T16:49:42-05:00
Histology: Fixes and improvements for placing annotations and identification symbols on histology slices.
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98a643b0 by John Harwell at 2022-09-16T09:55:22-05:00
Histology: Some cleanup of the HistologyCoordinate class.
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e8ef7518 by John Harwell at 2022-09-16T12:39:43-05:00
Histology: When saving histology file name in some objects, make its path relative to scene file (for scenes) or annotation file (for saving as annotation file).
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3b6c472c by John Harwell at 2022-09-16T15:58:19-05:00
Histology: Fix crashes that occurred when CZI file were not found for reading. After reading a HistologySlicesFile, list any missing child files (chi).
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807c3122 by John Harwell at 2022-09-19T15:39:09-05:00
Histology: Add logic to get name of data files (CZI image, distance, non-linear) files used by a Histology (CZI metadata file). These names are then used in the ZIP scene command so that scenes are correctly zipped.
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4ffbedcf by John Harwell at 2022-09-19T16:34:06-05:00
Histology: Updated zip spec file command so that it includes images/distance/non-linear files from the CZI meta file.
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6a5544eb by John Harwell at 2022-09-20T08:32:43-05:00
Fixed message about unrestored scene objects. There are a couple of items in scenes that are saved but may not be needed when restoring scenes (eg. filenames saved for use by operation zip scene).
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2d2ed658 by John Harwell at 2022-09-20T10:38:27-05:00
Removed CziMetaFile (replaced by HistologySlicesFile). Renamed CziMetaFileXmlStream* files and classes to HistologySlicesFileXmlStream*.
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445c9dde by John Harwell at 2022-09-21T13:40:09-05:00
Histology: Started on loading and use of NIFTI files for non-linear transformation between millimeter and plane coordinates. This partial implementation is disabled so that an update can be put out in advance of a BICANN meeting.
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fb026c9f by John Harwell at 2022-09-21T14:05:44-05:00
Fix compilation error for Qt5.
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8de2a08a by John Harwell at 2022-09-21T14:23:56-05:00
More fixes for windows compilation.
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dfd2bf43 by John Harwell at 2022-09-23T08:00:12-05:00
Histology: Starting on non-linear offsets
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bed28573 by John Harwell at 2022-09-26T08:27:08-05:00
Fixed crash after restoring scene caused by recent update.
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dd6d812f by John Harwell at 2022-09-28T15:41:21-05:00
Histology: Non-linear offset for plane to millimeters seems to be working correctly. Added some id information for assistance with verification of millimeters to plane. Add more info to file information for histology slices file.
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77906380 by John Harwell at 2022-10-10T09:55:04-05:00
Histology: Numerous updates with revised transforms between various media coordinate systems.
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c8d46ad6 by John Harwell at 2022-10-10T10:14:41-05:00
Fixed point and click yoking between volumes and surfaces.
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9e26c1ef by John Harwell at 2022-10-10T12:30:58-05:00
Add attribute maximum stack depth to OpenGL information.
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8d04f6d6 by John Harwell at 2022-10-10T12:37:27-05:00
Histology: A few small updates.
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4b4b42c7 by John Harwell at 2022-10-10T14:03:26-05:00
Fix compilation issues on other platforms.
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a862c4ce by Tim Coalson at 2022-10-11T21:31:34-05:00
use existing custom base path in -zip-scene-file, make warning more visible and accurate
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712c95f0 by Tim Coalson at 2022-10-11T21:31:59-05:00
fix pngs being effectively uncompressed
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e452ef6a by Tim Coalson at 2022-10-11T21:34:17-05:00
don't copy metadata from cifti template
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0628ae57 by Tim Coalson at 2022-10-11T21:35:53-05:00
fix unclosed parenthetical in -cifti-help
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b46ea2c4 by John Harwell at 2022-10-17T10:46:38-05:00
Histology: Some improvements with drawing histology using millimeter coordinates.
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fccdf2ef by John Harwell at 2022-10-17T10:46:38-05:00
Added option on Identify Brainordinate dialog to add an identification symbol at a stereotaxic location.
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bd146bb2 by John Harwell at 2022-10-17T10:46:38-05:00
Disable some debug printouts
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87e07b0d by John Harwell at 2022-10-18T16:08:33-05:00
Histology: When user increments/decrements by one slice using the spin box in the toolbar, get coordinate at center of screen, project to new slice, and move projected coordinate to center. This keeps the slices "aligned" as they are changed.
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100fc136 by John Harwell at 2022-10-19T09:44:36-05:00
Histology: Enable drawing of stereotaxic annotations on histology slices. Fixed drawing of histology space annotations so that they appear only on slice on which they were drawn.
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5e9623ae by John Harwell at 2022-10-19T09:50:04-05:00
Use slice spacing (that was added to histology file in last commit) when drawing identification symbols.
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184a1dee by John Harwell at 2022-10-19T11:23:54-05:00
Histology: Allow slice "re-centering" regardless of the change in the slice index. Previously, re-centering was applied only when moving to an adjacent slice.
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f6db5a68 by John Harwell at 2022-10-21T12:22:22-05:00
Histology: Started on using distance files but putting on hold at this time.
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1c722c65 by John Harwell at 2022-10-21T13:04:48-05:00
Histology: Move volume surface outline of BrainOpenGLVolumeSliceDrawing and into its own class BrainOpenGLVolumeSurfaceOutlineDrawing. This is in preparation for drawing surface outlines on histology slices.
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f15ab70a by John Harwell at 2022-10-24T10:17:56-05:00
Histology: Added surface outline to histology slices. Added a checkbox labeled "Non-Linear" in the Toolbar->Histology that allows one to toggle non-linear correction on/off.
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cabaecb3 by John Harwell at 2022-10-24T12:23:23-05:00
Histology: Added yoking of tabs containing histology slices.
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b9b3fc55 by John Harwell at 2022-10-24T14:16:33-05:00
Fixed compilation warnings reported by a Linux system.
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dd0751da by John Harwell at 2022-10-24T16:38:49-05:00
Histology: Fixes for yoking of tabs containing histology to other tabs containing histology.
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18f53d58 by John Harwell at 2022-10-25T10:28:43-05:00
Histology: Fixed yoking for the plane/stereotaxic selection.
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e6e0dd5b by John Harwell at 2022-10-25T11:50:25-05:00
Histology: For histology file's file information, include stereotaxic coordinates without non-linear correction for corners of images.
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dfa9844f by John Harwell at 2022-10-25T12:21:12-05:00
Fixed compilation error; qsizetype not in older versions Qt.
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d0f042ae by John Harwell at 2022-10-25T14:44:56-05:00
Histology: Fixed crash in yoking when histology data was not loaded.
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41b1db10 by John Harwell at 2022-10-25T14:58:02-05:00
Histology: When reporting name of media file during histology identification, include the path after the filename since many files have the same name but different paths.
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628917ec by Tim Coalson at 2022-10-26T19:30:16-05:00
fix the inverses the right way, remove "add a 1" hack from XML reader and undo "swap dim" in previous equivalent code
the extra inverse transform is now redundant
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d72b5065 by Tim Coalson at 2022-10-26T19:51:07-05:00
Use constructor form to avoid narrowing float complaints
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5b9b694d by John Harwell at 2022-10-27T14:32:52-05:00
Foci: Add new class, BrainOpenGLFociDrawing to use for all foci drawing. Use the new class for all volume (orthogonal, oblique, MPR) foci drawing and remove foci drawing from some of those volume drawing classes.
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c52006d8 by John Harwell at 2022-10-27T14:32:52-05:00
Foci: Foci now created and drawn on histology slices. Cannot delete foci from histology yet.
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8b54b01b by John Harwell at 2022-10-27T15:00:12-05:00
Fixed compilation errors and warnings.
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d8046d8d by John Harwell at 2022-10-27T16:39:53-05:00
A recent change changed ortho near far from (-1, 1) to (-100, 100) fixed drawing of foci as spheres on histology slices (spheres were clipped). However, this has been found to cause the window to model transform to be incorrect. This causes problems with identification of histology including the plane coord Z to be 100. So, changing near far back to (-1, 1).
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5a9c61b6 by John Harwell at 2022-10-28T13:01:34-05:00
Foci: Revised identification of foci on volume, added foci identification on histology, and starting to consolidate foci identification.
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642d1c43 by John Harwell at 2022-10-31T11:04:59-05:00
Histology: Some improvements to prevent crashing when files are missing that are loaded through a czi meta histology slices file.
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088b93a4 by John Harwell at 2022-10-31T11:57:05-05:00
Histology: When reading a histology slices file (czi meta), test each of the czi image files to see if they can be opened. This allows missing image file or file with incorrect permissions to be caught and avoid creation of invalid histology slices and an invalid histology slices file. While permissions can be tested, the permissions test may report incorrect results if an NFS disk is mounted with 'defer_permissions'. QFileInfo documentation also reports problems with permissions on NTFS file systems. Only the image files are tested, not the non-linear and distance NIFTI files. Doing this prevents putting wb_view in an unstable state and reports the errors to the user in an error dialog.
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f707cd66 by John Harwell at 2022-10-31T13:13:06-05:00
Removed usage of EventAlertUser in HistologySliceImage since it is no longer need as errors are caught elsewhere when histology slices file is read.
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69718ed5 by John Harwell at 2022-11-07T14:23:50-06:00
Fix for MPR crashing. A pointer had been created that pointed to data local to a function for storage of image data. A shared_ptr is now used to allocate the image rgba data for 3D textures (volumes).
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42ce80a5 by John Harwell at 2022-11-08T16:01:03-06:00
Fixed problems with scale bars not appearing. Each tab contains an instance of a scale bar and each scale bar kept the index of the tab to which the scale bar belonged. If tabs were deleted and a scene was created and saved, the tab index in the scale bar was not correctly set when the scene was restored. This prevented scale bars from being drawn in some situations.
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bea0ab05 by John Harwell at 2022-11-09T09:54:45-06:00
In BrainOpenGLWidget, there should always be a corresponding call to 'doneCurrent()' for each call to 'makeCurrent()'. There were some places where this was not occurring, particularly if the deprecated QGLWidget was used.
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5a8acef1 by Tim Coalson at 2022-11-15T18:40:11-06:00
add MIT exceptions for FSL/MSM to octtree-related code
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b681efa8 by John Harwell at 2022-11-16T12:06:31-06:00
Histology: When user changes control in Toolbar -> Histology (slice index, slice number, plane X/Y, or Stereotaxic X/Y/Z) update any volume slices in yoked tabs to match the histology coordinate.
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9f3bb971 by John Harwell at 2022-11-16T12:06:31-06:00
Histology: When converting a window coordinate to a plane coordinate, always use a depth value of 0.5 for the window-Z. If a histology image pixel is clicked, it does have a depth of 0.5. But, if the user clicks where there are no image pixels, the reported depth value is 1.0 and this will result in a non-zero plane-Z when the window coord is converted to a plane coord. If this is allowed to occur, the selected histology slice may change and we don't want that to happen.
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99072c7a by John Harwell at 2022-11-16T12:06:31-06:00
Histology: Removed unneeded code and cleaned up code for setting the view of histology using the selection box dragged with mouse.
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a0d4e150 by John Harwell at 2022-11-16T12:06:31-06:00
Histology: When user selects a region in a histology slice, select the same region in any yoked volume slices (orthogonal only at this time).
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f5255168 by John Harwell at 2022-11-16T12:06:31-06:00
Histology: When user selects a region in a histology slice, select the same region in any yoked volume slices (added for oblique and MPR).
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5f8e90b7 by John Harwell at 2022-11-16T12:06:31-06:00
Histology: When transforming a volume view to match a histology region selection, make sure the volume tab is yoked to the same group.
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aabc768e by John Harwell at 2022-11-16T12:06:31-06:00
Added a preference for displaying a cross at center of histology and volume views.
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f3d424b6 by John Harwell at 2022-11-16T12:06:31-06:00
Histology: When a histology region is selected for pan/zoom, wb_view tries to find another yoked tab with a volume displayed in it. If none found, use dimensions of current tab to set the yoked volume pan/zoom.
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9414cf12 by John Harwell at 2022-11-16T12:06:31-06:00
Histology: When a histology region is selected for pan/zoom, any volume tabs with same yoking group are also panned/zoomed. Make sure tab with histology's yoking group is NOT off.
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b9b19779 by John Harwell at 2022-11-16T12:06:31-06:00
Added tooltips for histology slices.
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cbdd9a7c by John Harwell at 2022-11-16T12:06:31-06:00
Identification: Computer histology slice spacing with average distance between slices (distance between all divided by number of slices minus 1). Use slice spacing for determining if an identification symbol is close enough to drawn on a slice. Add distance to previously identified item in ID text window.
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e29ce58e by John Harwell at 2022-11-16T12:06:31-06:00
Identification: Add distance to previous identification to tooltip for histology, surface, volume.
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d63fa0c6 by John Harwell at 2022-11-16T12:06:31-06:00
Log at Fine level when a texture image is loaded by a graphics primitive; reduce minimum texture size to 256 for CZI image; include texture settings when graphics primitive text information is created; in scene capture image command, log at the fine level the OpenGL information.
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4e1ccf22 by John Harwell at 2022-11-16T12:06:31-06:00
In wb_command -scene-capture-image, log at the 'fine' level, information about OpenGL (shows capabilities of Mesa3D library). When loading CZI image, switched back to storing image data in a CziBitMap instead of QImage. Using QImage was crashing in wb_command when Mesa3D attempted to create mipmaps and the image dimensions was set to 2048. Qt documentation states the pixel data in a QImage should be accessed by calling a function to get the start of each row. A pointer to just the first row was passed to OpenGL. Qt also keeps each row on particular boundaries. If QImage is used, the image data will need to be copied out of QImage. In addition, may want to read CZI data into images that have width/height equal to powers of two so OpenGL/Mesa3D do not need to resize images, possibly with downsizing.
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a9ae634d by Tim Coalson at 2022-11-23T21:19:14-06:00
add warnings based on how workbench recomputes qform
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04b46d60 by John Harwell at 2022-11-28T15:12:53-06:00
Move Undo/Redo buttons from Toolbar->Image to Toolbar->Tab so that buttons are available in all modes.
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910cb80c by John Harwell at 2022-11-28T15:12:53-06:00
Enable selection of Redo and Undo from wb_view's Edit menu when viewing histology.
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f1cec69a by John Harwell at 2022-11-28T15:12:53-06:00
Show Toolbar->Orientation section of toolbar when in Volume Mode. Use its "Reset" button to reset the volume view. Remove "Reset" button from Toolbar->Slice Plane (makes all modes consistent for reseting the view). Move Redo and Undo buttons from Toolbar-Tab to Toolbar->Orientation.
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e80725d4 by John Harwell at 2022-11-28T15:12:53-06:00
Remove "Custom" button from Toolbar->Slice Plane since "Custom" button is in Toolbar-Orientation that is now shown in Volume mode.
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af5f15e3 by John Harwell at 2022-11-28T15:12:53-06:00
Improve Custom button in Toolbar->Orientation: Button is clicked to display the Custom View dialog, the "menu arrow" is clicked to select and apply any available custom views. Add icons to redo and undo buttons in Toolbar->Orientation.
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d15769e5 by John Harwell at 2022-11-28T15:26:44-06:00
When Reset button is clicked, only reset MPR rotations if a volume is displayed.
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c96f964e by John Harwell at 2022-11-28T16:00:23-06:00
In Volume Create dialog used in voxel editing, default the voxel information (dimensions, spacing, origin) to that of the underlay volume. Volume Type now defaults to "Select Type" that forces user to choose Functional or Label. Improve some labels on the dialog.
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01a6730f by Tim Coalson at 2022-12-09T20:18:02-06:00
fix not setting pixdim on volume files
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cf4eab76 by John Harwell at 2022-12-20T11:19:39-06:00
Removed stereotaxic drawing of histology slices. It was incomplete and was not being used. Histology slices are drawn using plane coordinates.
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332db32e by John Harwell at 2022-12-20T11:19:39-06:00
Updated VoxelEditing.html help file.
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5f8f49bd by John Harwell at 2022-12-20T11:19:39-06:00
Updated VoxelEditing.html help file (again).
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8fb5d7ce by John Harwell at 2022-12-20T11:19:39-06:00
Enable voxel editing in MPR volume viewing mode.
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1e410583 by John Harwell at 2022-12-20T11:19:39-06:00
In Toolbar -> Orientation, add a "region selection" button. At this time, it is valid only for histology and media. It defaults to on but user can turn it off to prevent selection of a region when the mouse is dragged.
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16b6e11d by John Harwell at 2022-12-20T11:19:39-06:00
Reorganization of select region logic so that it can support bounds selection on a volume slice.
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0d40722f by John Harwell at 2022-12-20T11:19:39-06:00
Add new class ViewingTransformationToFitRegion. User can now drag the mouse to form a box when viewing orthogonal slices. The volume slices is then panned/zoomed so that the region in the box fills the viewport.
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d5a03a94 by John Harwell at 2022-12-20T11:19:39-06:00
Moved MouseEvent from GuiQt to Brain as mouse information is needed by 'fit volume region to viewport' when volume slice view is 'ALL' so that it can determine which slice plane is being manipulated. Also fixed 'fit volume to viewport region' to account for any current zooming so new view (zoom) is set correctly.
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caa68c3b by John Harwell at 2022-12-20T11:19:39-06:00
Fitting a region selected on a volume slice in MPR into the viewport now functioning.
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aaeb2f71 by John Harwell at 2022-12-20T11:19:39-06:00
Change cursor to a cross (plus sign) when mouse mode is enabled for selecting a region.
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cc11ecdf by John Harwell at 2022-12-20T11:19:39-06:00
Move region selection for media/histology from ViewingTransformationsMedia to ViewingTransformationToFitRegion.
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c27a73d7 by John Harwell at 2022-12-20T11:19:39-06:00
Region Selection: When a histology region is selected, select the same region in any tabs containing volume slices. Works for MPR and Orthogonal.
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9bab0475 by John Harwell at 2022-12-20T11:19:39-06:00
Eliminated "Primitive invalid, all points may be coincident" warning message in debug mode that occurred when the region selection box is initialized and has no geometric area.
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926bd8a2 by John Harwell at 2022-12-20T11:19:39-06:00
Region Selection: When a histology region is selected, select the same region in any tabs containing volume slices. Fixed for when a montage slice view is enabled to that the viewport is for one slice in the montage, not the viewport containing all of the slices.
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e87f6723 by John Harwell at 2022-12-20T11:19:39-06:00
Fixed selection of annotations in MPR volume viewing.
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e0fae321 by John Harwell at 2022-12-20T11:19:39-06:00
Fixed update of cursor. (1) Cursor selection was from the selected tab and has been corrected to select the cursor from the tab containing the mouse; (2) Update the cursor as the mouse moves, not just after a paint event.
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b32cc15f by John Harwell at 2022-12-20T11:19:39-06:00
Fixed display of annotation in stereotaxic space displayed on a histology slice. Disabled depth testing for this situation since the distance of the annotation from the slice is also computed and the annotation is only drawn if within a 'half-slice" distance of the histology slice. Also fixes when annotation is "just behind" the slice.
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74b6affd by John Harwell at 2022-12-20T11:19:39-06:00
Do not allow slice scrolling with mouse when viewing orthogonal slices while in Annotation editing mode.
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8a63923b by John Harwell at 2022-12-20T11:19:39-06:00
Fixed problems with spin boxes on Custom View dialog. Prevent updates to spin boxes as user is entering new values.
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a3730ced by John Harwell at 2022-12-20T11:19:39-06:00
Fixed problems with spin boxes on Custom View dialog. Prevent updates to spin boxes as user is entering new values.
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f8c8ae10 by John Harwell at 2022-12-20T11:19:39-06:00
Increase voxel editing brush maximum size from 99 to 9999.
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72cc6c1a by John Harwell at 2022-12-20T11:19:39-06:00
Fixed rotation of volume slices in MPR mode volume slice views. Slices were rotating opposite direction of crosshairs.
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909b7c56 by John Harwell at 2022-12-20T11:19:39-06:00
Added CaretPreferencesDataValueList that stores a list (array) for something in preferences.
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5c3aab32 by John Harwell at 2022-12-20T11:19:39-06:00
Added a "recent scenes menu" that is displayed on the File Menu and the Scene button in the toolbar. It allows selection and immediate loading of the five most recently loaded scene files. In addition, if wb_view is started with the new option "-scene-recent" the most recently loaded scene is loaded into wb_view.
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bf726523 by John Harwell at 2022-12-20T11:19:39-06:00
When a "default tab" is created for histology, default the tab's yoking to off.
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adaaac4b by John Harwell at 2022-12-20T11:19:39-06:00
Removed assertions for validity of transforms in MediaFileTransforms. If a CZI file loaded directly (not through a CZI meta file), the transforms are invalid which is valid in this case.
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596c8d63 by John Harwell at 2022-12-20T11:46:39-06:00
When histology region selection changes a volume tab view, make sure the volume tab is set to the same yoking group as the histology slice tab.
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e4cea231 by John Harwell at 2022-12-20T12:10:06-06:00
Added Variant include.
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8cc4fcd5 by John Harwell at 2022-12-20T14:40:08-06:00
Fixed compilation warnings and errors when building on other operating systems. Some are due to Qt 5 and 6 differences.
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afccb276 by John Harwell at 2022-12-21T10:53:13-06:00
Display a progress dialog when loading a recent scene.
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f6dda650 by John Harwell at 2022-12-27T09:10:32-06:00
Updated slice scrolling with mouse so that one slice is scrolled for every 4 (8 on high DPI screens) pixels the mouse moves vertically. This allows the user to move by a single slice by moving the mouse slowly or many slices by moving the mouse quickly. Also added a "System" button to the About Workbench dialog. Clicking the system button shows information about the user's computer and in particular the monitor resolutions and 'high dpi' status.
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13959b95 by John Harwell at 2022-12-27T09:57:21-06:00
Fixed restoration of scale bar. In function for restoring a browser tab, the scale bar was initialized after restoration of the scale bar. This has been corrected to initialize the scale bar before restoring the scale bar from the scene.
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6596db1f by John Harwell at 2022-12-27T16:27:12-06:00
Fixed display of an image that is displayed using the Features Toolbox -> Image tab.
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9271f364 by John Harwell at 2022-12-27T16:30:23-06:00
Added an "Overlap" checkbox that will be used for testing CZI overlap at a later time.
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070fd5fd by John Harwell at 2022-12-27T17:53:36-06:00
Fix and temporarily patch compilation errors on other operating systems.
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d316c14e by John Harwell at 2022-12-28T08:28:16-06:00
Fix issues compiling on other systems (compiler and Qt differences).
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1dd2f91d by John Harwell at 2022-12-28T11:46:14-06:00
Added new surface drawing type "Cut Edges" (on surface properties dialog) that only draws edges that are attached to one triangle. It can be used to draw only the outline of a flat surface.
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64d5ccad by John Harwell at 2023-01-03T15:57:51-06:00
For wb_command -scene-capture-image, log the OpenGL information at the CONFIG level (was FINE) and test the OpenGL version for compatibility with Workbench (will print message if too old but will try to continue). Change minimum recommended from from OpenGL 1.5 to 2.1.
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b3d70077 by John Harwell at 2023-01-03T17:10:19-06:00
When getting OpenGL version, detect between failure (null pointer) or empty string.
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5bb2ae88 by John Harwell at 2023-01-04T08:52:39-06:00
For wb_command -scene-capture-image, throw exception if OpenGL version is less than 2.1 which will terminate the command.
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b0bfd468 by John Harwell at 2023-01-04T15:02:14-06:00
If the OpenGL version test fails while running wb_command, indicate that this may occur if Virtual GL is enabled and that Virtual GL if running, must be disabled so that the Mesa3D OpenGL libraries are used.
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d6c940d4 by John Harwell at 2023-01-05T09:28:42-06:00
Fixed Zip Scene File bug that occurred when the scene file contained the base path type=CUSTOM but the custom base path was empty. In the Zip Scene File dialog, the Custom Path combo box had a value, that was the default value. Fix was to transfer the custom path in the combo box to the scene file.
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8409be8a by John Harwell at 2023-01-09T09:30:13-06:00
The Exit Workbench dialog contains a suggestion to create scenes but does not explain how to do so. Added some instructions on how to create scenes. However, a standard Qt dialog is used for the 'show details' and the text region is small and cannot be increased in size.
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fd0dc093 by John Harwell at 2023-01-13T14:15:26-06:00
Added reading of the CZI distance file. When ID performed print to terminal the distance value from all distance files associated with the current slice.
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b9d96296 by John Harwell at 2023-01-13T14:15:26-06:00
Meta CZI: Use distance files to create masks for czi images. These masks are then placed into the OpenGL stencil buffer to fix overlapping of CZI images.
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bf6d97f3 by John Harwell at 2023-01-13T14:15:26-06:00
Meta CZI: Compute CZI overlap stencil masks after reading czi meta file. Use "Overlap" checkbox in Toolbar:Histology to enable/disable overlap correction.
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88a562ed by John Harwell at 2023-01-17T15:17:00-06:00
Remove unused variable.
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772ee7ae by John Harwell at 2023-01-17T15:17:40-06:00
Prevent crash if distance file is not available when getting text for depth information.
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ab536424 by John Harwell at 2023-01-18T13:40:45-06:00
When converting a Vector3D to a string, use 'f' for format of floating point numbers (avoids long scientific notation for values near zero).
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9f1d9ece by John Harwell at 2023-01-18T13:42:42-06:00
MPR montage slice drawing: For slices in the montage, move along the 'slice vector' using coordinates instead of using slice indices along an axis. Draw crosshairs at correct location in the slice.
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67b6699e by John Harwell at 2023-01-18T14:13:26-06:00
For MPR slice montage, add "mm" to slice offset characters.
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2cbff07f by John Harwell at 2023-01-19T08:48:57-06:00
Added missing requests for OpenGL stencil buffer.
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727a1f1f by John Harwell at 2023-01-20T14:07:18-06:00
Fixes and additions for enabling/disabling the display of volume parcels using the Features Toolbox. Tested with both CIFTI and Volume Label Files.
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9c7bafd7 by John Harwell at 2023-01-20T14:52:17-06:00
Fix compilation warnings encountered on non MacOS operating systems.
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5ae1b6f0 by John Harwell at 2023-01-20T16:03:17-06:00
Fixed additional compilation warnings
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1d94924c by John Harwell at 2023-01-25T13:53:54-06:00
Fix MPR montage mode. Slices in montage were in wrong order (Top left slice should be at 'highest' coordinate along axis; Bottom right slice should be at 'lowest' coordinate along axis).
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ad4d4047 by John Harwell at 2023-01-25T13:55:25-06:00
Do not log an error when an image file's 'plane coordinates' are invalid as this is normal for most image files.
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6b27da97 by John Harwell at 2023-01-25T14:39:47-06:00
Fixed compilation warnings / unused code reported by compilation warnings.
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4f40ee1d by John Harwell at 2023-01-26T10:45:37-06:00
In Toolbar: Montage, add a menu to the "XYZ" button for coordinate display. Menu allows choice of offset or XYZ on montage slices.
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20254eb4 by John Harwell at 2023-01-26T11:17:03-06:00
Fix compilation warnings. Change "Xyz" to "XYZ" for montage coordinate menu in toolbar.
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e8a89c92 by John Harwell at 2023-01-27T11:20:44-06:00
Preferences Dialog: (1) When setting foreground and background colors, warn if user tries to set the foreground and background colors to the same color; (2) Show scene colors along with user colors; (3) Add checkbox that indicates when scene colors are active so that user can uncheck it and switch to user colors. Note: When a scene is created, the color preferences and added to the scene so that the scene is displayed correctly. Workbench switches to user colors if the user changes a users color, loads a spec files, closes all files and a few other ways.
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3f4a888e by John Harwell at 2023-01-27T14:50:02-06:00
Noticed that zooming in on a CZI image on a Mac high-resolution display that the image was noticeably smaller than the amount of screen available. I had recently reduced the size of image for CZI loading (Preferences Dialog -> Image) to reduce load times. However, the image size was too small for the screen resolution and problem was fixed setting the preferred size to a larger image. So, if the CZI image loading size is changed on the Preferences Dialog, warn the user that if the size is too small, the user will notice that image data loaded does not fill the available screen region.
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03052061 by John Harwell at 2023-01-27T15:53:07-06:00
Toolbar->Montage: Add control of font height on montage slices with a spin box on the XYZ menu.
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96dd13aa by Tim Coalson at 2023-01-31T11:29:04-06:00
warn and reset type when changing volume palette of label volume
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1aec910b by John Harwell at 2023-02-02T15:36:06-06:00
Fixed bug with Volume MPR montage drawing. The object to window transform was not set when the montage contained an even number of slices. This was due to recent update that redesigned montage slice drawing to draw along viewed axis instead of orthogonal axis.
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483fd7af by John Harwell at 2023-02-03T12:48:20-06:00
Add "View" button to Custom View dialog so that user can view the underlying matrices.
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620ac6c8 by John Harwell at 2023-02-07T12:22:12-06:00
When uploading to BALSA, send the scene file's Study ID and all Scene IDs to BALSA so that BALSA can check if any of the Scene IDs need replacement. If any Scene IDs do need to be replaced, BALSA returns new Scene IDs that wb_view updates in the scenes.
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c6bb9b0d by John Harwell at 2023-02-07T12:22:12-06:00
Adding one usage of new WuQHyperlinkToolTip.
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0f332d43 by John Harwell at 2023-02-07T12:22:12-06:00
Added WuQHyperlinkToolTip. A tooltip is text that pops up when the mouse is moved over a widget. Tooltips do not support hyperlinks. There is also QWhatsThis that displays help information when the user clicks on a widget while the application is in a "What's This" mode that must be explicitly activated by the user (must select item in GUI to enter What's This mode and is exited when user clicks mouse). WuQToolTip inserts an event filter into a widget and intercepts tooltip events. When a tooltip event is received that contains a hyperlink, WuQToolTip displays the tooltip using the QWhatsThis:show() method. In addition, WuQToolTip also intercepts a QWhatThisLlinkClickedEvent that occurs when a hyperlink is clicked in a WhatsThis widget. In this instance, WuQToolTIp issues a signal indicating a hyperlink has been clicked that can be connected to and processed by a Object subclass.
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87faef56 by John Harwell at 2023-02-07T12:22:12-06:00
When uploading to BALSA and if any scenes have their IDs changed, list the scene names in the 'upload successful' dialog.
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a070f608 by John Harwell at 2023-02-07T12:22:12-06:00
Updates for improving volume file create dialog.
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0ca8d1f4 by John Harwell at 2023-02-07T12:22:12-06:00
Made improvements to Create Volume dialog (used in Edit Voxels mode) including a resample option that allows the user to enter the new spacing with automatic updates to dimensions and origin.
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8d876a87 by John Harwell at 2023-02-07T12:22:12-06:00
Use WuQHyperlinkToolTip to add tooltips with links to help information for toolbar's voxel editing controls.
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94f4c036 by John Harwell at 2023-02-07T16:50:49-06:00
Add the left rotation matrix in the Custom View dialog's View Transformation. But, do not know if it is correct.
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c5527d26 by John Harwell at 2023-02-08T10:41:07-06:00
Add a close link to hyperlink tooltip.
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55a7475f by John Harwell at 2023-02-08T14:57:04-06:00
A few improvements to Recent Scene Menu. When menu is on scene tool button in toolbar, enable tooltips indicating file that contains scene name.
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f4383225 by John Harwell at 2023-02-10T10:18:04-06:00
Added text alignment for volume montage slice coordinates display.
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e98bd3a8 by John Harwell at 2023-02-10T11:42:35-06:00
For volume montage coordinates menu (displayed by clicking arrow on XYX button), replace menu selections of Offset or XYZ with a combo box.
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29267b93 by John Harwell at 2023-02-10T14:18:49-06:00
Disable hyperlink tooltips until a GUI option for enabling them is added.
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f8273987 by John Harwell at 2023-02-10T14:21:21-06:00
Enhance tooltip on montage XYZ coordinates tool button.
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6971d744 by John Harwell at 2023-02-10T15:03:50-06:00
Add <cmath> include to fix compilation errors.
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374a0d98 by Tim Coalson at 2023-02-16T22:37:03-06:00
add filename to warnings about pixdim rounding, etc
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f1d0e948 by John Harwell at 2023-02-21T11:53:29-06:00
For volume MPR mode, show rotation crosshairs on a single slice view (just one of axial, coronal, or parasagittal) and allow rotation. In single slice view, user will not notice anything changing when rotating crosshairs unless there is another MPR view in another visible tab.
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91e8c1a0 by Tim Coalson at 2023-02-22T23:05:11-06:00
fix bad logic in volume rois from extrema
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1b846c69 by Tim Coalson at 2023-02-27T18:33:24-06:00
increase accuracy of stdev and related in outlier exclusion and reductions
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9c65b15c by Tim Coalson at 2023-02-28T22:10:50-06:00
don't warn about recomputed pixdims from oblique volumes
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ed408b8d by John Harwell at 2023-03-02T14:17:25-06:00
Correct help text for wb_command -scene-capture-image. The examples in the help text were using the old command switch (-show-scene-two) and it has been replaced with a call to getCommandSwitch().
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faaa98c3 by John Harwell at 2023-03-20T15:31:53-05:00
When the coordinate (0, 0, 0) does not map to a valid voxel in the underlay volume, set the selected voxel coordinate to the middle of the volume when BrowserTabContent is initialized or when user clicks ORIGIN button in the toolbar.
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b14f484d by John Harwell at 2023-03-21T14:21:25-05:00
In Toolbar->Slice Indices / Coords, corrected problems with slice indices and coordinate selections and updates when the selected volume had an orientation where parasagittal was not in first dimension and/or coronal was not in second dimension and/or axial was not in the third dimension. A new method, getDimensionsPCA, was added to VolumeMappableInterface that gets the correct maximum dimensions for the parasagittal, coronal, and axial axes correctly for any plumb volume orientations.
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a031771f by John Harwell at 2023-03-22T08:57:41-05:00
Fixed orthogonal drawing of volume slices for an SLA oriented volume file with non-uniform voxel spacing. Added getVoxelSpacingPCA() to VolumeMappableInterface that gets the spacing for parasagittal (X), coronal (Y), and Axial (Z) axes for any plumb orientation.
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45919ac2 by John Harwell at 2023-03-22T11:14:10-05:00
Added new SubvolumeAttribures::VolumeType::RGB_WORKBENCH. This new volume type receives red, green, blue coloring using the first three maps in the volume file. There is a kludge at the end of VolumeFile::readFile() that sets the volume's type to RGB_WORKBENCH if the file has a specific name for testing the coloring. This kludge should be removed once there is a way to set the volume type correctly for files.
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1461f0ef by John Harwell at 2023-03-22T12:04:02-05:00
Fixed problem with no overlays enabled if one loaded only an RGB_WORKBENCH volume file. Now, when initializing overlays, if no overlays are enabled for a tab and the bottom most layer contains a valid file and map index, enable the overlay. Without this fix, nothing is drawn and it looks like an error as if the file did not load.
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1401f060 by John Harwell at 2023-03-22T15:43:27-05:00
Fixed drawing of RGB_WORKBENCH volume files in oblique viewing mode.
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ca8c89f3 by John Harwell at 2023-03-22T16:31:59-05:00
Fixed MPR volume identification problem caused by an incorrect index into an array.
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63f7cadd by Tim Coalson at 2023-03-23T22:07:32-05:00
fix segfault, likely from volume rendering of cifti
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1999da91 by John Harwell at 2023-03-29T13:56:22-05:00
Fixed texture coordinate computation for MPR volume drawing. Texture coordinates were off by 1/2 voxel. the problem is that the OpenGL texture coordinates (0, 1) are at the CORNER of the first and last voxel and the code is mapping the texture coordinates (0, 1) to the CENTER of the first and last voxel.
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aa96f1ee by John Harwell at 2023-03-30T09:13:20-05:00
Fixed cropping with margin for Image Capture Dialog.
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3d47f1a9 by John Harwell at 2023-03-30T12:02:48-05:00
Volume Editing: (1) Fixed assertion failure when editing a non-plumb volume; (2) When "Lock" button is unchecked, warn user if volume is not 'plumb'; (3) Fixed crash if editing voxel is not at a valid voxel index.
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1beb44b8 by John Harwell at 2023-03-30T15:58:39-05:00
Enabled 3D mip-mapping for anatomical volumes.
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9108695a by John Harwell at 2023-03-31T09:45:24-05:00
MPR Volume: Fixed problem with an outline box that appear around the volume slice by blending color and alpha components separately.
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495479f5 by John Harwell at 2023-03-31T13:35:14-05:00
Disable mip maps for 3D volume textures until I (John H) can test the code on Linux and Windows. This was enabled about 2 commits ago. Note: Changes in files GraphicsEngineDataOpenGL.cxx and VolumeGraphicsPrimitiveManager.cxx.
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778cda1c by John Harwell at 2023-03-31T16:41:07-05:00
Layer opacity blending for MPR has been fixed.
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a3a6d3cf by John Harwell at 2023-04-03T11:01:18-05:00
Starting on MPR "three" a revised version of volume MPR drawing. For each axis view, rotation now appears to be about the screen vector. Improvements also made so that rotation is about the selected slice coordinates and the rotation is estimated using an angle formed by the screen coordinate of the selected slices, the current mouse screen coordinate, and the previous mouse screen coordinate.
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80e66ac3 by John Harwell at 2023-04-03T11:01:18-05:00
Disable developer flag for new MPR with rotation corrections that is in work
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7ffed212 by John Harwell at 2023-04-07T10:21:33-05:00
Workbench was crashing when trying to read data from new CZI images. When Workbench reads image data, it requests the image data in Bgr24 (8-bit RGB) format. These new CZI images are in Gray16 format. The CZI library does not support conversion of image data from Gray16 to Bgr24 and throws a std::logic error that Workbench did not catch. Workbench now catches the std::logic error that prevents a crash and logs it to the terminal. Either the images need to be converted to Gray8 or Workbench needs to be updated to detect the color format and do the necessary conversions.
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4d3cfbe0 by John Harwell at 2023-04-12T09:26:29-05:00
Added another overloaded method to add name and value that accepts 'const char*' for value. This fixes problems with 'const char*' implicitly cast to a bool.
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f84b3252 by John Harwell at 2023-04-12T09:27:38-05:00
Add information from media file to data file content information.
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92e1153e by John Harwell at 2023-04-12T09:40:36-05:00
CZI multi-channel file support. A multi-channel file with datatype of Gray16 was not loading correctly. There was an image displayed but it was very dim. Apparently, when the datatype is 'Gray', tinting must be used to color the data. (1) Enable tinting for blending channels from a multi-channel file; (2) Add logic for loading a single channel and tinting it; (3) Using the scaling tile accessor when getting RGB of one pixel (single channel accessor fails if datatype is Gray16 as it will not convert it to RGB).
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e80aeffb by John Harwell at 2023-04-12T15:03:22-05:00
Updates for detecting channels in CZI files but not yet allowing selection of the channels.
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6c15cc94 by John Harwell at 2023-04-13T16:54:26-05:00
Fixed crash when a CIFIT file with volume data was loaded. A cast from VolumeMappableInterface to VolumeFile was not tested for success in a recent change to get the volume type for RGB volume files.
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dc0f744b by John Harwell at 2023-04-26T08:31:39-05:00
New compilers on macOS Ventura produced over a thousand "Implicit conversion loses integer precision" compiler warnings in our code, Qwt, Qt, etc. So, suppressed the warnings when the clang version is greater than 14.0.2.
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5baeefd8 by John Harwell at 2023-04-26T08:31:39-05:00
Allow selection of individual channels in CZI files that contain multiple channels. Controls are in the Media Layers menu displayed by clicking the Wrench icon in the layer toolbox.
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b18884db by John Harwell at 2023-04-26T08:31:39-05:00
Consolidated controls for CZI channels selection. Checkbox for 'All' channels is now first option in spin box for channel number.
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3f32d3f6 by John Harwell at 2023-04-26T08:31:39-05:00
Fixed compilation warnings on unused variables produced by newer macOS compiler.
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7df74161 by John Harwell at 2023-04-26T09:30:29-05:00
If only one channel in a CZI file, disable channel section in the media overlay settings menu.
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3b420bc8 by John Harwell at 2023-04-26T09:49:12-05:00
Fixed bug with using arrow keys to increment/decrement the CZI channel number in layer menu control.
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c35d9250 by John Harwell at 2023-05-01T11:20:43-05:00
Fixed bug with volume surface outlines not always restoring correctly when coloring is set to a tab. If the index of the tab referenced by the volume surface outline was greater than the tab index containing the volume surface outline, restoration from scene failed due to the referenced tab not having been restored yet. Now, volume surface outlines for all tabs are restored after all of the tabs have been restored.
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2c06bea2 by John Harwell at 2023-05-01T11:27:00-05:00
During bug fix for volume surface outline, noticed that clipping planes were not correctly saved to scene and is now fixed.
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e67773ab by John Harwell at 2023-05-24T09:23:06-05:00
Indices into RGBA colors overflowed int32_t and were changed to int64_t for a volume with dimensions 1098, 979, 1011 (multiply by 4 for RGBA).
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94d0c2e2 by John Harwell at 2023-05-24T15:31:16-05:00
Code that computes non-zero voxel extent in a volume can be very slow for a very large (1000 x 1000 x 1000) volume. Using OpenMP improved performance but it still may take a couple of minutes on an M1 Mac. So, until the code can be further optimized, just use the full voxel extent for semi large (#voxels > 400 * 400 * 400). This non-zero voxel extent is only used for sizing of identification symbols.
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857ebf1f by John Harwell at 2023-05-24T15:38:06-05:00
When wb_view is started, test for NULL when creating the first new window. If NULL, print error message indicating computer may not have a display. Trying to prevent crash in this condition.
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77911c8f by John Harwell at 2023-05-26T09:16:00-05:00
Change some indices to 64-bit intergers to prevent crashes with large volume files
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f2b73ec6 by John Harwell at 2023-05-28T15:29:02-05:00
Removed a std::cout << std::endl from GroupAndNameHierarcyItem.
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4a35f378 by John Harwell at 2023-06-14T10:00:43-05:00
Added a new palette named "Special-RGB-Volume". When this palette is selected for a volume file and the volume file contains at least three maps, the first three maps interpreted as Red, Green, Blue coloring.
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c4d64b39 by John Harwell at 2023-06-14T10:01:30-05:00
When quitting and there are modified files without a name, put "unnamed <data-file-type" instead of an empty name in the warning dialog.
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45ea7ad6 by Tim Coalson at 2023-06-19T21:09:39-05:00
whitelist MEAN and SUM from length=1 reduction warning
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d8d8e7d2 by Tim Coalson at 2023-06-19T21:45:52-05:00
consolidate length=1 whitelist in a function, add some other operators that seem reasonable
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d3dffb99 by John Harwell at 2023-07-11T15:35:37-05:00
Added method to compute the signed angle between two vectors to Vector3D.
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c31793cc by John Harwell at 2023-07-11T15:35:37-05:00
Continuing development of revised MPR volume slice drawing.
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8c773bdc by John Harwell at 2023-07-11T15:35:37-05:00
If switch to volume MPR viewing, do not set to all planes (axial, coronal, parasagittal) if montage slice viewing is enabled.
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2a548522 by John Harwell at 2023-07-11T15:35:37-05:00
Fixed wrong primitive for volume MPR drawing (was returning the triangle fan primitive when triangle strip was requested)
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6a1e09be by John Harwell at 2023-07-11T15:35:37-05:00
Updating MPR: Fixed display of identification symbols, volume surface outline, and intensity modes.
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3ab67551 by John Harwell at 2023-07-11T15:35:37-05:00
Updating MPR: continuing development.
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f1ae0bf2 by John Harwell at 2023-07-11T15:35:37-05:00
Updating MPR: Correct position of slices with rotation and voxel coordinates in work.
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a6e4db6d by John Harwell at 2023-07-11T15:35:37-05:00
Reduce warnings about coincident points in OpenGL polyline drawing since it can be caused by zooming way in so outlines are very tiny spatially.
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53ed5044 by John Harwell at 2023-07-11T15:35:37-05:00
Add an inverse transform method that returns a vector to EventOpenGLObjectToWindowTransform.
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a0b4cd65 by John Harwell at 2023-07-11T15:35:37-05:00
Add methods to GraphicsViewport that return each of the viewport corners in a Vector3D.
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b6cc9f71 by John Harwell at 2023-07-11T15:35:37-05:00
Add a projectPointToPlane method that returns a Vector3D to Plane.
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07652e25 by John Harwell at 2023-07-11T15:35:37-05:00
Add rayIntersection method to Plane that returns a Vector3D containing the intersection point.
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e5a37f77 by John Harwell at 2023-07-11T15:35:37-05:00
Add method that intersects a ray with a volume to VolumePlaneIntersection.
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0c6eb4c3 by John Harwell at 2023-07-11T15:35:37-05:00
Continuing MPR volume viewing development including 2D intensity slice drawing.
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dd1311e1 by John Harwell at 2023-07-11T15:35:37-05:00
Volume MPR: Fixes for 2D intensity max/min modes. Disable intensity modes for ALL view since the slices may overlap and the intensity modes 'accumulate' in the framebuffer (may be fixable by drawing each slice into an offscreen buffer).
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7b29e8f5 by John Harwell at 2023-07-11T15:35:37-05:00
Volume MPR fixed rotation of mpr axes.
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78a8e546 by John Harwell at 2023-07-11T15:35:37-05:00
MPR Volume viewing: Fixed problems with intensity modes when there were just a few slices.
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fc0b829d by John Harwell at 2023-07-11T15:35:37-05:00
BrainOpenGLFixedPipeline::getPixelDepthAndRGBA() Fixed test for inside viewport.
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ac8df009 by John Harwell at 2023-07-11T15:35:37-05:00
Volume MPR: Fixes to keep slices in place when a voxel is selected.
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62e94541 by John Harwell at 2023-07-11T15:35:37-05:00
When getting depth from BrainOpenGLFixedPipeline::getPixelDepthAndRGBA, warn if depth testing is disabled as it results in an invalid depth value.
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eaf9c84a by John Harwell at 2023-07-11T15:35:37-05:00
Volume MPR: New mode that fixes the view but transforms the volume.
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bf266118 by John Harwell at 2023-07-11T15:35:37-05:00
Had a file opened in editor that caused Brain/.VolumeSliceSettings.h.swp to be added to git now removing it
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22199760 by John Harwell at 2023-07-11T15:35:37-05:00
MPR Volume Viewing: Add an "inverse" rotation for each axis. When rotating in an axis, the "inverse" rotation allows the current axis to remain static (not rotate) while the other axes rotate.
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09a9c835 by John Harwell at 2023-07-11T15:35:37-05:00
Volume MPR: Cleanup of MPR code.
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59eec9ce by John Harwell at 2023-07-11T15:35:37-05:00
Volume MPR: Fixed volume surface outline on MPR slices.
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bb49676d by John Harwell at 2023-07-11T15:35:37-05:00
Volume MPR: Fixed problems with volume surface outline.
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f5453c48 by John Harwell at 2023-07-11T15:35:37-05:00
Graphics Polylines: Do not attempt to draw polylines that become degenerate (all same coordinates).
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89a1b2d4 by John Harwell at 2023-07-11T15:35:37-05:00
Volume MPR: Fixes for rotation; volume surface outline on 2D volume slices.
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842e50da by John Harwell at 2023-07-11T15:35:37-05:00
Volume MPR: Fixes for slices in ALL view and drawing volume surface outline on ALL view slices
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4068d496 by John Harwell at 2023-07-11T15:35:37-05:00
Fixed crash when graphics primitive was drawing spheres using a float color. The float color was converted to bytes incorrectly.
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d7a7267f by John Harwell at 2023-07-11T15:35:37-05:00
Add new class, VolumeVerticesEdgesFaces, to simplify access to vertices, edges, and faces in a volume file.
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287ab1dc by John Harwell at 2023-07-11T15:35:37-05:00
Volume MPR: Add a box that shows rotated vs non-rotated volume in ALL slices (parasagittal, coronal, axial) view. It also shows location of the selected slice coordinates.
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279b3cc8 by John Harwell at 2023-07-11T15:35:37-05:00
Volume MPR: Use newer class VolumeVerticesEdgesFaces in VolumePlaneIntersection; Add antialiasing to some line drawing.
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811ca2c1 by John Harwell at 2023-07-11T15:35:37-05:00
Volume MPR: Fixed strange white border at edge of texture by enabling blending.
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c6c9ddbe by John Harwell at 2023-07-11T15:35:37-05:00
Volume MPR: Removed developer flag for new MPR and added another MPR selection in the toolbar so that old MPR still works and new MPR is available.
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37ad82cc by John Harwell at 2023-07-11T15:35:37-05:00
Volume MPR: Some attempts to load scenes created with old MPR implementation into the new MPR implementation.
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e7215248 by John Harwell at 2023-07-11T15:35:37-05:00
Volume MPR: Fixes for rotation axes.
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62066725 by John Harwell at 2023-07-11T15:35:37-05:00
Volume MPR: Located in the slice views are labels that identify the axes (anterior, left, inferior, etc). These labels are identical to those displayed in an orthogonal view. However, once there is rotation in MPR, the labels may no longer be valid. Now, the labels are dynamic and are only displayed when the slice's axes align with one or the orthogonal axes. For example, with no rotation the axial slice's labels are L, R, P, A. If one rotates 90 degrees in the parasagittal view, the axial slice's labels become L, R, I, S.
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234cef0b by John Harwell at 2023-07-11T15:35:37-05:00
Volume MPR: Add option to allow "in-plane" rotation to the toolbar's MPR options widget. This allows the user to rotate the slice that is being rotated.
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c9540f42 by John Harwell at 2023-07-11T15:35:37-05:00
Volume MPR: Switch MPR rotation to a quaternion instead of a matrix.
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062b5121 by John Harwell at 2023-07-11T15:35:37-05:00
Volume MPR: Use premultiply for the axes "inverse rotation" quaternions.
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fe595e68 by John Harwell at 2023-07-11T15:35:37-05:00
Volume MPR: Fixed rotation crosshairs.
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8397be2b by John Harwell at 2023-07-11T15:35:37-05:00
Volume MPR: Fixed orientation labels when in Radiological Orientation.
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481a3aeb by John Harwell at 2023-07-11T15:35:37-05:00
Volume MPR: Fixed MPR Average and opacity blending for normal MPR viewing.
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e0aff64d by John Harwell at 2023-07-11T15:35:37-05:00
Volume MPR: Cleanup of code for intensity drawing modes.
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633b1f41 by John Harwell at 2023-07-11T15:35:37-05:00
Volume MPR: Fixed/implemented Volume Properties opacity that is used for ALL view slices. Added polygon offset to ALL view layers to prevent flashing of overlay/underlay (fixes depth buffer issues).
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a861bb64 by John Harwell at 2023-07-11T15:35:37-05:00
Volume MPR: Fixed identification problem caused by wrong alpha value from previous fix for texture artifact white lines around edges.
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0044711a by John Harwell at 2023-07-11T16:30:55-05:00
For yoking, do not copy the volume slice montage On/Off setting.
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2dd1cfd6 by John Harwell at 2023-07-12T08:46:41-05:00
Volume MPR: Fix compilation errors and warnings from other build systems.
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85f47679 by John Harwell at 2023-07-12T09:42:28-05:00
Volume MPR: Fix compilation warning about unused parameters from other build systems.
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af2bb1a3 by John Harwell at 2023-07-13T14:44:37-05:00
Volume MPR: Adding a new cursor type for rotation that rotates only the axis containing the cursor.
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14343720 by John Harwell at 2023-07-14T11:26:37-05:00
Volume MPR: Added "view rotation" functionality. Axes now have three sections. Starting at selected coordinate, thinnest section changes slice coordinates; second thicker section rotates only the slice containing the cursor (no changes to other slices); thickest section rotates the slice planes.
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4b5398e4 by John Harwell at 2023-07-19T15:40:51-05:00
Add method to Plane to get normal vector in a Vector3D instance.
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74d1c6b7 by John Harwell at 2023-07-19T15:47:20-05:00
Volume MPR: Using inverse rotation for each axis was found to work incorrectly causing planes to become non-orthogonal. For example, suppose in a default view, the user rotates in the axial plane (around the vector 0, 0, 1). The inverse rotation for the axial slice corrects for rotation around 0, 0, 1. Now suppose the user rotates around in the coronal slice. The normal vector in the axial view is NOT 0, 0, 1 anymore due rotation in the coronal view. However, the inverse rotation for the axial view corrects for rotation about the normal vector 0, 0, 1 so the correction for the axial slice is now incorrect. The solution is to use a separate rotation quaternion for each slice axis. Each of the quaternions is always rotated when the user rotates a slice but the slice being rotated is also receives an inverse rotation.
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4a9e8524 by John Harwell at 2023-07-19T16:47:51-05:00
Removed unused code that performed MPR rotation using matrices (now uses quaternions).
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c55de9eb by John Harwell at 2023-07-20T12:09:10-05:00
Add method to verify if three planes (normal vectors) are orthogonal.
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ba2956be by John Harwell at 2023-07-20T13:00:30-05:00
Volume MPR: Add developer flag that allows switching between "inverse transforms" and "separate transforms". Note that the "inverse transforms" fail to keep the volume slices orthogonal.
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7e692bc5 by John Harwell at 2023-07-21T16:00:39-05:00
Volume MPR: New implementation of crosshairs in stereotaxic coordinates. However, rotations are incorrect so that still needs to be fixed.
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a02016ed by John Harwell at 2023-07-23T13:47:51-05:00
Volume MPR: Correct normal vectors of "virtual slices" so that crosshairs represent the 'other' slice planes.
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10556370 by John Harwell at 2023-07-24T09:26:53-05:00
Volume MPR: Corrections for rotations and crosshairs so that they move in same direction.
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f2d50dd0 by John Harwell at 2023-07-24T10:27:15-05:00
Volume MPR: Corrections for montage slice offset vector.
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1c322ee4 by John Harwell at 2023-07-24T12:20:12-05:00
Volume MPR: Fixed drawing of mouse dragged selection box.
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f850dd7c by John Harwell at 2023-07-24T15:00:09-05:00
Volume MPR: Attempt to apply rotations from scenes created with old MPR to the new MPR.
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e6e42a68 by John Harwell at 2023-07-24T16:53:33-05:00
Edit Samples: Added support, but no functionality for the new "Edit Samples" mode. Button in Toolbar -> Mode is disabled and hidden (code in BrainBrowserWindowToolBar::createModeWidget()).
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cd008c68 by John Harwell at 2023-07-25T08:17:03-05:00
Edit Samples: Added support, but no functionality for the new "Edit Samples" mode. Button in Toolbar -> Mode is disabled and hidden (code in BrainBrowserWindowToolBar::createModeWidget()).
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63cc124f by John Harwell at 2023-07-25T11:00:47-05:00
Volume MPR: Fixes for ALL view in MPR mode.
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797b0a43 by John Harwell at 2023-07-25T11:16:55-05:00
Fix compilation warning with unused parameters.
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9a80feec by John Harwell at 2023-07-26T10:49:19-05:00
Volume MPR: Put some gaps in the crosshairs so that there are three distinct sections (select slices, rotate only slice, rotate transform).
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131e84f7 by John Harwell at 2023-07-28T10:16:53-05:00
SceneFile::writeFile() was not converting the input scene file name to an absolute file path. When a scene file is written, the paths to the data files are converted to paths relative to the the path of the scene file. This conversion to relative paths fails when the path to the scene file is not absolute. This bug was noticed when a user ran 'wb_command -scene-file-relocate' with a relative path for the output scene file name.
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748016de by John Harwell at 2023-08-03T12:52:54-05:00
Samples: Continuing work on toolbar for Edit Samples mode.
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ba63a417 by John Harwell at 2023-08-03T12:52:54-05:00
Samples: Added new samples file.
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21b1eca8 by John Harwell at 2023-08-03T12:52:54-05:00
Samples: Implemented drawing and dragging of polyhedron annotations.
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4b1fb535 by John Harwell at 2023-08-03T12:52:54-05:00
Fixed identification problems so that identified coordinate is used (not moved to voxel center); Fixed volume crosshair gap in MPR viewing; Various improvements for annotation polyhedron drawing.
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bd189e37 by John Harwell at 2023-08-03T16:12:43-05:00
Fixed crash when there was a failure to create a new polyhedron annotation.
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08ccc7b4 by John Harwell at 2023-08-04T09:59:11-05:00
Add plane of slice to identification so that it can be used for annotation drawing.
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d85d7e88 by John Harwell at 2023-08-07T09:47:26-05:00
Polyhedron Annotations: Save 'plane' of volume slice on which the polyhedron was drawn.
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40bc163e by John Harwell at 2023-08-07T12:21:18-05:00
Polyhedron annotation: Allow selection of polyhedron when drawn 'between" the near and far slices. When selected the size handles on in between slices are drawn as unfilled circles indicating that they cannot be edited (editable size handles are filled circles on near and far slices".
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bf062f43 by John Harwell at 2023-08-07T13:34:03-05:00
Polyhedron Annotation: Add depth from when user creates polyhedron to annotation file.
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85ecc20d by John Harwell at 2023-08-07T17:00:22-05:00
Added insertion and deletion of coordinates into/from polyhedron annotations.
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d0535213 by John Harwell at 2023-08-08T14:02:14-05:00
Volume MPR: Fixed rotation in slice montage view.
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c9739381 by John Harwell at 2023-08-08T14:28:14-05:00
Volume MPR: Fixed crosshairs so that they are sized in pixels (and do not scale with volume slice zooming).
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21675e7b by John Harwell at 2023-08-09T13:20:43-05:00
Adding finish and cancel buttons for annotation drawing but not yet complete.
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90194927 by John Harwell at 2023-08-09T15:59:43-05:00
Reduced size of circles displayed at polyhedron (and poly line, polygon) when the annotation is selected.
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4e52f3c9 by John Harwell at 2023-08-09T16:44:05-05:00
When identification is performed on a volume slice, set the selected slices to the center of the voxel. In the identification window, the actual XYZ selected (not necessarily at the voxel center) is displayed in one row and the IJK and voxel center XYZ in another row.
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28affc6f by John Harwell at 2023-08-09T17:09:18-05:00
Fixed typename of annotation for redo/undo of a coordinate insertion or deletion (was displaying polyline for a polygon).
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3e3acfcb by John Harwell at 2023-08-09T17:28:14-05:00
Annotation Toolbar: Implemented function for Cancel button (cancels drawing of a poly type annotation).
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f87a3aa3 by John Harwell at 2023-08-11T12:19:14-05:00
Fixed recent bug that snuck in and failed to create box, line, or oval annotations when mouse was dragged to draw the annotation.
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5dd3c3c1 by John Harwell at 2023-08-16T12:34:43-05:00
Event for inserting new annotations was going to all open windows and not just the window in which the new annotation was requested.
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49eea939 by John Harwell at 2023-08-16T12:34:43-05:00
Polyhedron: Partial implementation of drawing polyhedron on slices not on original drawing plane.
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eb45f08c by John Harwell at 2023-08-16T12:34:44-05:00
Annotation MetaData: Added reading and writing of metadata to individual annotations.
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5382d470 by John Harwell at 2023-08-16T12:34:44-05:00
Removed print statements.
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728b21c2 by John Harwell at 2023-08-16T12:34:44-05:00
On Open Data File dialog, change default file filter to scene file (was spec file)
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d915de1d by John Harwell at 2023-08-16T12:34:44-05:00
Added Edit Metadata to right-click menu in Annotations Mode.
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2ed74afc by John Harwell at 2023-08-16T12:49:55-05:00
Annotations: Fixed drawing of some annotations (box, oval, line, text) when created from start to finish by mouse dragging. When drawing an annotation, allow editing of the line thickness, foreground color, and background color as the thickness may be too great for some poly-type annotations.
Fixed conflict.
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64eca715 by John Harwell at 2023-08-16T12:50:16-05:00
Include metadata in an annotation's modified status.
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73bf146a by John Harwell at 2023-08-16T12:50:16-05:00
Added metadata editor to annotation create dialog for polyhedron metadata.
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0cdb5b43 by John Harwell at 2023-08-16T12:50:16-05:00
Disable slice dragging in MPR montage as it uses the coordinate of the slice in the montage. It needs to use the middle slice but this is difficult as an ID operation is used to get the coordinate.
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dbbd22b1 by John Harwell at 2023-08-16T12:50:16-05:00
Volume MPR: Fixed identification failure that prevented dragging the crosshairs over an identification symbol. Also renamed performIdentification() to performIdentificationAll() and added performIdentificationSome() to BrainOpenGLWidget.
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21ca1a42 by John Harwell at 2023-08-16T12:50:16-05:00
Create new custom metadata editor for annotation create dialog. The custom metadata editor shows only specific metadata items in a particular order.
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3eb4fc38 by John Harwell at 2023-08-16T12:50:16-05:00
Implemented Annotation toolbar's "Finish" button. The button is enabled when a poly-type annotation has a least 3 points. When enabled, the background of the button is green to make its availability obvious to the user. Alternatively, the user can shift-click the mouse to finish the poly-type annotation but this functionality is not obvious.
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b119af10 by John Harwell at 2023-08-16T12:50:16-05:00
Improve size (not too large) of the sizing handles (circles) on poly-type annotation points.
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e47d9348 by John Harwell at 2023-08-17T11:40:13-05:00
Volume MPR: Fixed rotation (rotation did not work for the vertical axes).
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ec775822 by John Harwell at 2023-08-17T12:22:53-05:00
Polyhedron annotation: Fixed line width for "other axis" views.
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fed35167 by John Harwell at 2023-08-17T13:43:43-05:00
Allows stretching the widget of annotation created dialog and metadata editor dialog.
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e805f8de by John Harwell at 2023-08-17T14:03:03-05:00
Annotation Toolbar: Rearrange width, height, and rotation controls to reduce horizontal space used by these controls.
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306a90a1 by John Harwell at 2023-08-18T12:16:28-05:00
Added "X" button to remove the last coordinate from a poly-type annotation that is being drawn.
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4f3aa407 by John Harwell at 2023-08-18T13:05:08-05:00
Add a "Drawing" label to the section of annotation toolbar containing finish and cancel buttons.
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055a0352 by John Harwell at 2023-08-18T14:28:33-05:00
Disable insertion of a coordinate into a poly-type annotation since this can accidentally happen while trying to drag a coordinate with mouse. To insert a coordinate, right-click the annotation and select Insert Coordinate from the pop-up menu.
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8796ee5a by John Harwell at 2023-08-21T12:04:06-05:00
Polyhedron: On create dialog, number of slices is total number of slices; previously was additional number of slices. Metadata is now validated but user can use new "Require metadata" checkbox to finish the polyhedron without entering metadata.
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06d45795 by John Harwell at 2023-08-21T15:42:52-05:00
Poly-type annotations: Fixed problem with line width incorrect (was using window height for thickness percentage) during the time a poly-type annotation was being drawn.
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9d785b3f by John Harwell at 2023-08-22T12:22:25-05:00
Add cmath include for linux compiler error.
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a4b0d9f6 by John Harwell at 2023-08-22T12:47:28-05:00
Add cmath include for linux compiler error with QGLwidget::update/updateGL.
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e8e9a471 by John Harwell at 2023-08-22T13:09:31-05:00
Add cmath include for linux compiler error with QGLwidget::update/updateGL trying again.
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24ea4751 by Tim Coalson at 2023-08-22T16:52:02-05:00
attempt to fix windows building
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5da40c25 by John Harwell at 2023-08-31T14:22:14-06:00
Removed kludge that checked for the filename photo_recon_SLA.nii.gz when reading a volume file and changed the volume type to RGB_WORKBENCH. New way is to use the Special-RGB-Volume palette.
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e03815c4 by John Harwell at 2023-08-31T16:00:46-06:00
Changes for volume palette SPECIAL-RGB-VOLUME: (1) Removed test for this special volume type from VolumeFileVoxelColorizor; (2) Changed VolumeFile::getType() to test for SPECIAL-RGB-VOLUME palette and if found, return type RGB_WORKBENCH; (3) Changed MPR drawing to use discrete coloring when the volume type is RGB_WORKBENCH. With these changes, 'enclosing' voxel is used if drawing in MPR with SPECIAL-RGB-VOLUME.
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d06f78f0 by John Harwell at 2023-09-21T09:02:07-05:00
Change order of volume modes so that MPR is before Oblique. If the user loads an oblique volume, it will now display in MPR mode instead of Oblique.
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c13905b8 by Tim Coalson at 2023-09-21T19:45:40-05:00
Fix crash from VolumeFile::getType accessing a palette without checking if the file is label-type
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abcdacb4 by Tim Coalson at 2023-10-16T18:56:32-05:00
fix longstanding typo in -volume-erode
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a9f8f00b by Tim Coalson at 2023-10-16T19:54:00-05:00
replace buggy QFile::remove with cstdio
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3bfbc5ca by John Harwell at 2023-10-23T12:14:48-05:00
Polyhedron annotations: Draw size handles on a polyhedron while the polyhedron is being drawn. But, the size handles are too big since the annotation uses window coordinates space while it is being drawn (converts to actual space when finished). All annotations will need to be drawn in the selected space instead of drawing in window space and converting to selected space when annotation is finished.
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e00bac06 by John Harwell at 2023-10-23T12:14:48-05:00
>From EventAnnotationCreateNewType, removed the CONTINUOUS mode that was not being used. At one time there were two modes continuous (user had to drag mouse to create poly type annotation) and discrete (user could only click mouse to create poly type annotations). The DISCRETE mode had been modified to support both clicks and dragging. DISCRETE mode has been renamed to CLICK_AND_OR_DRAG to better reflect its functionality.
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2cabd8f8 by John Harwell at 2023-10-23T12:14:48-05:00
Some cleanup of UserModeAnnotations mode enum so that names better reflect their function due to functionality changes made over time.
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566b01de by John Harwell at 2023-10-23T12:14:48-05:00
>From UserInputAnnotations, removed unused mode and code for setting the coordinates of an annotation with a dialog (AnnotationChangeCoordinateDialog).
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c362a3e5 by John Harwell at 2023-10-23T12:14:48-05:00
Removed AnnotationCoordinateSelectionWidget and AnnotationChangeCoordinateDialog as they are not used anymore.
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e05aba32 by John Harwell at 2023-10-23T12:14:48-05:00
Fixed leak of a GiftiMetaData instance in AnnotationCreateDialog when an polyhedron was created.
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b183979e by John Harwell at 2023-10-23T12:14:48-05:00
A little more cleanup of UserInputModeAnnotations.
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a0628e1d by John Harwell at 2023-10-23T12:14:48-05:00
Adding new modes to UserInputModeAnnotations to draw polyhedrons in stereotaxic space.
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61f72a76 by John Harwell at 2023-10-23T12:14:48-05:00
Revising how size of viewports used for annotations is obtained into a "drawing viewport manager". Also adding drawing of polyhedron annotations in stereotaxic coordinates.
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c825abdf by John Harwell at 2023-10-23T12:14:48-05:00
Annotation - Updates for editing the line color, background color, and line thickness of the annotation being drawn by the user.
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6c6d7a9d by John Harwell at 2023-10-23T12:14:48-05:00
Updates so that the annotation widgets can support annotations or samples.
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23be946e by John Harwell at 2023-10-23T12:14:48-05:00
Adding Edit Samples Mode.
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aacaa61c by John Harwell at 2023-10-23T12:14:48-05:00
Samples Editing: Extensive changes for new "Edit Samples" mode that is an subset, with additions, of Annotations Mode.
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bba01c49 by John Harwell at 2023-10-23T12:14:48-05:00
Annotations and Samples: Cleanup of clipboard. Pasting is now to the file selected in the toolbar. Previously, it was to the file of the annotation that was copied. However, the user user could close that file between the time of copying and pasting.
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ebd5b88d by John Harwell at 2023-10-23T12:14:48-05:00
Fixes for Annotation Depth Widget. It is used to change the depth (extent) of the two faces in a polyhedron annotation. Depth is in millimeters but also show a slice count derived from the underlay volume spacing.
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e60e1b96 by John Harwell at 2023-10-23T12:14:48-05:00
Fix adjustment of polyhedron depth while drawing a new polyhedron
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ba3d38ff by John Harwell at 2023-10-23T12:14:48-05:00
Improve layout and functionality of Samples Toolbar Insert new sample widget.
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fd8f115b by John Harwell at 2023-10-23T12:14:48-05:00
Improve layout and functionality of Samples Toolbar Insert new sample widget (part 2). Forgot to add new files.
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1efb7523 by John Harwell at 2023-10-23T12:14:48-05:00
Insert New Sample Widget: Added a Save button that simplifies saving of the Samples File since samples must be saved to a file and not the scene (like annotations are typically saved).
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cf2e62ce by John Harwell at 2023-10-23T12:14:48-05:00
Add DisplayPropertiesSamples so that the display of samples can be turned on/off through Features Toolbox.
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2b11a3a2 by John Harwell at 2023-10-23T12:14:48-05:00
When entering Edit Samples mode or creating a new sample, turn on the display of samples.
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7b2ec740 by John Harwell at 2023-10-23T12:14:48-05:00
Fix some Edit Samples control's tooltips.
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e246dc86 by John Harwell at 2023-10-23T12:14:48-05:00
Improve some tooltip on the Edit Samples Insert widget.
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9d408d46 by John Harwell at 2023-10-23T12:14:48-05:00
Allow cancellation of new sample before the first point has been added.
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a4cb3f56 by John Harwell at 2023-10-23T12:14:48-05:00
Fixed selection of Samples in Editing Samples mode.
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457baee1 by John Harwell at 2023-10-23T12:14:48-05:00
Display a pencil cursor when drawing samples or annotation poly types.
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aa143f37 by John Harwell at 2023-10-23T12:14:48-05:00
When drawing polyhedron size handles, draw the background color slightly larger than the foreground color to make the symbols more obvious.
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82624fd0 by John Harwell at 2023-10-23T12:14:48-05:00
Show "two-tone" size handles on poly lines and polygons. These handles have the background color around the foreground color so that they are easier to see.
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43a18cf9 by John Harwell at 2023-10-23T12:14:48-05:00
Started on improvements for line widths in annotation drawing but will have to work on it at a later time.
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50d34bfb by John Harwell at 2023-10-23T12:14:48-05:00
Disable Annotation (and Edit Samples) Redo/Undo buttons while a new annotation (or sample) is being drawn.
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67b77b1a by John Harwell at 2023-10-23T12:14:48-05:00
For EventAnnotationGetBeingDrawnInWindow, add the user input mode (annotations or samples) to ensure event goes only to widgets with the same input mode.
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15240270 by John Harwell at 2023-10-23T12:14:48-05:00
Implementing a new system for tracking all drawing viewports and their contents to for use with annotations and samples.
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a666f35a by John Harwell at 2023-10-23T12:14:48-05:00
Samples: Redesign of samples drawing. User draws on all slices in montage or chooses slice to exclude from drawing.
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f793f517 by John Harwell at 2023-10-23T12:14:48-05:00
Manage drawing viewports with shared_ptr's to fix invalid pointer bug.
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ff1e3214 by John Harwell at 2023-10-23T12:14:49-05:00
Copy AnnotationCreateDialogTwo to AnnotationSamplesCreateDialog since this dialog will be specialized for samples creation. Enable/disable items in the Sample Insert New widget based upon mode selected and whether or not an annotation is being drawn.
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eea5b457 by John Harwell at 2023-10-23T12:14:49-05:00
Fixed drawing of scale bar for MPR volume viewing modes.
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64f11bb5 by John Harwell at 2023-10-23T12:14:49-05:00
Ding Ontology Terms: Created CommaSeparatedValuesFile that is extended by DingOntologyTermsFile for reading the Ding Ontology Terms File. The file is in the Resources. Created a dialog for displaying the ontology has both a sort list and a hierarchy that the user uses to select a term.
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52e6d69d by John Harwell at 2023-10-23T12:14:49-05:00
Samples: Cleanup of annotation samples create dialog. Improvements in custom metadata editor including support for selecting from pre-defined values for some elements.
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7a1a0643 by John Harwell at 2023-10-23T12:14:49-05:00
Improvements in annotation samples metadata editing. Use a combo box with list of values for some elements (instead of a button that pops up a dialog with the list); Add support for a date editor for date elements.
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fe85d66d by John Harwell at 2023-10-23T12:14:49-05:00
Ding Ontology Dialog: Add "Expand to Level" option and save the expansion level and selected item for next time dialog is displayed.
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0abd15c3 by John Harwell at 2023-10-23T12:14:49-05:00
Ding Ontology Terms Dialog: Fix for Tree View Collapse All button.
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4178fec1 by John Harwell at 2023-10-23T12:14:49-05:00
Remove Polyhedron button from Annotations since polyhedrons are only used in the newer Samples Mode.
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c9b8ef95 by John Harwell at 2023-10-23T12:14:49-05:00
Use 'shorthand id' metadata value for the name of a polyhedron annotation. The annotation's name is displayed in the Features Toolbox.
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f5c35843 by John Harwell at 2023-10-23T12:14:49-05:00
Show name of a polyhedron (sample) annotation at the center of polyhedron. Names can be turned on/off on Samples page in Features Toolbox.
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14ddf9fc by John Harwell at 2023-10-23T12:14:49-05:00
Annotation Samples Create Dialog: Save metadata entries for next time dialog is displayed in the current session. Default the dissection date to the current date.
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6a43a4d1 by John Harwell at 2023-10-23T12:14:49-05:00
Added MetaDataCustomEditorDialog that is used when editing metadata from a Sample Polyhedron.
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1c2126d8 by John Harwell at 2023-10-23T12:14:49-05:00
Fixed selection (deselection) of sample polyhedrons on Samples tab of Features Toolbox.
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e824d8e0 by John Harwell at 2023-10-23T12:14:49-05:00
Samples Metadata Updates: Optional vs Required, Structure replaced with Hemisphere, Default some sample metadata to off.
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5569af9e by John Harwell at 2023-10-23T12:14:49-05:00
Add font attributes (font name, size, color, bold, italic, underline) to the name displayed for an AnnotationPolyhedron.
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8c013d33 by John Harwell at 2023-10-23T12:14:49-05:00
Improve layout of samples toolbar widget to reduce its vertical height. Small size improvements in annotation toolbar widget.
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236ec4c3 by Tim Coalson at 2023-10-26T18:07:04-05:00
new -volume-components-to-frames command, to deal with complex/rgb types
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4779ed89 by Tim Coalson at 2023-10-27T15:10:22-05:00
add absolute mm-convention reading to -convert-warpfield
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824653bf by John Harwell at 2023-10-31T09:28:40-05:00
Fixed compilation warning.
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ecf21c23 by John Harwell at 2023-11-01T16:35:39-05:00
Add locking of the selected Edit Samples polyhedron. There must be only one polyhedron selected for it to be locked. Once locked, it can be unlocked by clicking the 'Lock' button, cutting or deleting the polyhedron, selecting Edit Menu Select All or Deselect All, loading a new spec file or scene.
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e30818cf by John Harwell at 2023-11-01T16:47:34-05:00
Fixed scene restoration error of SamplesDrawingSettings that caused improper 'X's over some tabs in a tab montage in Edit Samples Mode.
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7c0f13b2 by John Harwell at 2023-11-02T13:25:11-05:00
Edit Samples: Fix for dragging polyhedron vertex when the polyhedron is 'Locked'. Some selection information was not reset when user released the mouse button and it caused incorrect vertex movement next time mouse was dragged, even if away from the polyhedron.
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b5c7887f by John Harwell at 2023-11-02T13:44:35-05:00
Edit Samples 'Lock' button: Turn off lock user exits Edit Samples mode; Improve the Lock button's tooltip.
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76aa085f by Tim Coalson at 2023-11-17T22:33:05-06:00
fix wb_command default for cifti to write output on-disk
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a878e270 by Tim Coalson at 2023-11-20T22:42:27-06:00
improve IO error checking, sanitize CiftiXML mutable state on set/IO
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4446e3a0 by John Harwell at 2023-11-22T09:10:29-06:00
Fixed memory leak if user canceled creation of an annotation on the New Sample dialog.
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6e30587c by John Harwell at 2023-11-22T09:10:29-06:00
Edit Samples: Updates for new Sample metadata items that are selected from labels in label type files including logic to split label into the metadata ID and metadata Description.
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a1ef5df2 by John Harwell at 2023-11-22T09:10:29-06:00
Fixed problem with incorrect modified status for a sample's metadata.
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cdfb24bf by John Harwell at 2023-11-22T09:10:29-06:00
Edit Samples: This mode extends the Annotation editing mode but there are a number of items on the right-click menu that do not apply to samples editing. So, remove those items in Edit Samples mode.
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7d60d5ae by John Harwell at 2023-11-22T09:10:29-06:00
Add new "Modify" section to the Edit Samples toolbar. Move "Lock" from "Edit" to the "Modify" section. In the "Modify" section is a "More" button, that when clicked displays a menu with addition operations. "Reset Slice Range" has been added to this menu and it resets the extent (depth) of the polyhedron to the displayed volume montage slices that are not excluded.
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58a1274e by John Harwell at 2023-11-22T09:10:29-06:00
Add second plane to sample so that there are two planes representing the first and last volume slices used to create the sample. Implement the "Info" option in the "More" button's menu to show information about a polyhedron (planes, coordinates, and metadata).
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fc89b347 by John Harwell at 2023-11-22T09:10:29-06:00
Cleaned out code from when a polyhedron (sample) was drawn in annotation mode.
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96800f57 by John Harwell at 2023-11-22T09:10:29-06:00
Fix a few compilation warnings.
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950ca328 by John Harwell at 2023-11-22T09:10:29-06:00
Matrix4x4: Add rotationTo() that computes a rotation matrix for rotating a vector to match another vector. Uses OpenGL math quaternion for generating the matrix.
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bdcf647c by John Harwell at 2023-11-22T09:10:29-06:00
MathFunctions: Added method polygonArea() that calculates the area of a polygon (polygon may be concave) using the "Shoelace Formula".
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3c2a7c8d by John Harwell at 2023-11-22T09:10:29-06:00
Samples: Added display of polyhedron area in the polyhedron Info text.
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b1f46abc by John Harwell at 2023-11-22T09:10:29-06:00
Fixed bug with polygon, polyline, and polyhedron: Coordinates were being saved in the scene data for these annotation types but this is not needed as the coordinates are saved to the AnnotationFile (which may be on disk or embedded in the scene file). This bug was only noticed if one manually edited annotation coordinates in a disk file. When the scene restored, it loaded the coordinates a second time and overwrote the coordinates from the disk file.
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26f61f85 by John Harwell at 2023-11-22T09:10:29-06:00
Edit Samples: Remove "Reset Slice Range" from the Modify sections "More" tool button menu. The reason is that the tab containing the polyhedron is needed but we don't know which tab (if in tile tabs) contains the polyhedron since the polyhedron can be in multiple tabs. "Reset Slice Range" is now on the right-click menu since the location of the mouse click must be over the polyhedron and thus identifies the tab containing the polyhedron. Also added Info, Lock, and Unlock selections to the right-click menu.
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ed330d5c by John Harwell at 2023-11-22T09:10:29-06:00
Polyhedron volume calculation: Improvements including testing that points are coplanar on the two ends and in information, list areas of the two ends and distance between the two ends.
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1b4c412f by John Harwell at 2023-11-22T09:10:29-06:00
Add "Reset Polyhedron Range" back to the menu on the "More" tool button in Edit Samples Toolbar. If user selects option and Tile Tabs is enabled, warn user to verify that the selected browser tab contains the sample.
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c6f1b801 by John Harwell at 2023-11-22T09:10:29-06:00
Improvements / corrections to polyhedron volume calculation.
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45aaecac by John Harwell at 2023-11-22T09:10:29-06:00
Add a static "fromString() method to Vector3D. This method reads the vector's components from a comma separated string.
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66ac4b53 by John Harwell at 2023-11-22T09:10:29-06:00
Edit Samples Mode: Enabled dragging of a polyhedron (sample) name while the polyhedron is selected. When the polyhedron is selected, the name is enclosed in a box. When the cursor is moved over the name, the cursor becomes a "four arrows" symbol and the user can then drag the name to a new location.
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87f7e5a5 by John Harwell at 2023-11-22T09:10:29-06:00
Enable use of system proxies by calling QNetworkProxyFactory::setUseSystemConfiguration() but only in wb_view. List any proxies on the About Workbench More Info dialog. This should allow proxies on user's computers to function when uploading to BALSA. However, I have no way to test this.
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d56226b8 by John Harwell at 2023-11-22T09:10:29-06:00
Fix for Edit Samples Mode -> Reset Slice Range: The redo/undo command processing failed to copy the planes and the coordinates of the names on the end slices. This fixes a bug where the name was missing on an end slice after using Reset Slice Range.
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6ebd1be6 by John Harwell at 2023-11-22T09:10:29-06:00
Removed an overloaded rayIntersection method from Plane whose parameters could be used incorrectly. Switched usage to the other rayIntersection method.
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63cf39d5 by John Harwell at 2023-11-22T09:10:29-06:00
Palette Mapping Fix: In Full Mode, data most negative, zero, and most positive, are mapped to -1, 0, and 1 in the palette. The data coloring code was mapping the least negative and least positive values to palette zero which was incorrect when the least negative and/or least positive data values were not zero. This has been corrected so that data zero is mapped to palette zero. This problem was noticed when the data coloring did not match the color bar.
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257dea17 by John Harwell at 2023-11-22T10:56:05-06:00
Fix compilation error on Linux systems.
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e0f72671 by John Harwell at 2023-11-22T11:51:36-06:00
Fix Qt 5 compilation error on Linux systems.
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8828019a by John Harwell at 2023-11-22T20:51:07-06:00
Fix crashes when there is an attempt to display an enormously large matrix in matrix chart view. There is nothing in the GUI that says the matrix is too large but a message is logged at the severe level in the terminal window.
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a0a87b9b by John Harwell at 2023-11-27T10:11:13-06:00
Ding Ontology Dialog: Fixed problem with QCompleter selection for Abbreviation when there were multiple matches (CaH, CaHdl, CaHr, CaHvm). Code was only using completer result if there was exactly one match and now uses the first match of one or more matches. Enabled completer selection in the Descriptive line edit by matching to any items that contain the text entered by the user.
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8431a6f3 by John Harwell at 2023-11-27T10:17:17-06:00
Add "Edit Metadata" item to menu display when "More" button in "Modify" section of Edit Samples toolbar.
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af7fb83b by John Harwell at 2023-11-27T11:47:55-06:00
When a matrix file is too large to be displayed (a dimension exceeds OpenGL's 2D texture limit), display a warning to the user indicating that the file was read successfully but will not be displayed as a matrix.
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05b3da17 by John Harwell at 2023-11-28T12:42:29-06:00
Correct title on metadata editor to be "Edit Sample Metadata" when a polyhedron's metadata is edited. For all other types, use title "Edit Annotation Metadata".
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094e2d07 by John Harwell at 2023-11-28T12:56:57-06:00
DingOntologyTermsDialog: Fix selection of abbreviated name when the QCompleter returns multiple items.
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12e32052 by John Harwell at 2023-11-28T14:44:39-06:00
Add label "Samples" to the section of the toolbar containing the widgets for editing samples. To prevent the toolbar from becoming "too tall", other items in toolbar were rearranged into horizontal layouts.
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67cec7dd by John Harwell at 2023-11-28T15:15:35-06:00
Use up empty space in Edit Samples toolbar by allowing the filename combo box to stretch and fill the empty space.
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a6787b48 by John Harwell at 2023-11-28T16:12:25-06:00
Fixed crash in Label Selection Dialog/Widget when the user presses cancel and no label file is selected.
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359aba61 by John Harwell at 2023-11-29T09:21:22-06:00
For Edit Samples Mode: When creating a new sample, default the metadata values to the FIRST OF:
* - The most recently drawn sample since wb_view was started
* - The last sample in the selected sample file in the Edit Samples Toolbar
* - The last sample in the most recently loaded sample file (this will likely
* never happen since there will always be a file in the Edit Samples Toolbar).
* - Empty
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5dfc98d0 by John Harwell at 2023-11-29T09:27:47-06:00
Add tooltips to abbreviation and description line edit indicating that entering text will show matching entries.
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d4e17950 by Tim Coalson at 2023-12-11T17:07:32-06:00
make -covariance work in roi modes
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42ea9f53 by John Harwell at 2023-12-12T08:38:52-06:00
Fix Conflict.Dynamic Connectivity: Modified CIFTI Dense Dynamic to use ConnectivityCorrelation for its computations (Metric and Volume dynamic already use ConnectivityCorrelation). Add ConnectivityCorrelationSettings for new dynamic connectivity options to the dynamic connectivity files; update the Connectivity tab with an options button for these settings; settings are not used yet.
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00400e8a by John Harwell at 2023-12-12T08:38:52-06:00
ConnectivityCorrelation Menu: Disable correlation options when the mode is covariance.
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dd2deba1 by John Harwell at 2023-12-12T08:38:52-06:00
Added CIFT Parcel Dynamic file that computes correlation from a CIFTI Parcel Series File.
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68f226ce by John Harwell at 2023-12-12T08:38:52-06:00
Parcel Dynamic Connectivity: Fixes for loading of dynamic data and correct color mapping.
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9f035c60 by John Harwell at 2023-12-12T08:38:52-06:00
Removed calls to a debugging function.
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5a3d5689 by John Harwell at 2023-12-12T08:38:52-06:00
Fixes for the recent updates to dynamic connectivity.
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5d76b43f by John Harwell at 2023-12-12T08:38:52-06:00
Add new ConnectivityCorrelationTwo that will replaced ConnectivityCorrelation. This new version is much simpler than the previous version. Updated CiftiConnectivityMatrixDenseDynamicFile to use this new connectivity code and fixed region of interest connectivity bugs.
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5ea37d4d by John Harwell at 2023-12-12T08:38:52-06:00
Updates for parcel dynamic to use new correlation code.
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df668881 by John Harwell at 2023-12-12T08:38:52-06:00
Correlation: Updates to VolumeDynamicConnectivityFile() to use new ConnectivityCorrelationTwo. Fixed bug in existing functionality that was using indexToSpace() instead of enclosingVoxel() that caused loading data using a neighboring voxel instead of the correct voxel (reported by enclosingVoxel()).
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f434229f by John Harwell at 2023-12-12T08:38:52-06:00
Metric Dynamic Connectivity: Updates to use new correlation code and bug fixes for averaging in ROI.
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24a01a9f by John Harwell at 2023-12-12T08:38:52-06:00
Removed old correlation code used by dynamic connectivity files.
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8e6702b9 by John Harwell at 2023-12-12T08:38:52-06:00
Improve consistency of number of digits right of decimal in formatted text identification.
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a5b23afd by John Harwell at 2023-12-12T08:38:52-06:00
Make some optimizations to ConnectivityCorrelationTwo.
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471dd13b by John Harwell at 2023-12-12T08:38:52-06:00
Fixed compilation error caused by a new data file type (parcel dynamic) after pulling update.
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81da6d3a by John Harwell at 2023-12-12T10:34:31-06:00
Fixed crash if a scene was loaded, containing a dynamic connectivity ROI, and nothing else had been previously loaded.
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6645c99e by John Harwell at 2023-12-12T10:59:08-06:00
Fixed compilation error on Linux and Windows caused by an overloaded Qt method used with signals in Qt 5.
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56fd40e5 by John Harwell at 2023-12-12T11:38:27-06:00
Enabled histogram chart view for Scalar Data Series File.
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3c464d8d by John Harwell at 2023-12-12T12:03:29-06:00
When matrix is too large to draw, only log message to terminal one time instead of on every attempt to draw the matrix.
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481f0cbf by John Harwell at 2023-12-12T14:30:01-06:00
Correction for digits right of decimal in formatted information display.
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06517526 by John Harwell at 2023-12-14T12:25:34-06:00
Add support for drawing chart matrices with one but not both dimensions larger than OpenGL's maximum dimension.
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6d0309bd by John Harwell at 2023-12-15T11:45:46-06:00
Improve tooltips for annotation poly line and polygon tool buttons; Edit Samples Insert Sample tool button.
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03fbd1b1 by John Harwell at 2023-12-18T10:31:01-06:00
Add logic for selection of the annotation that is being drawn. This will be used when logic for editing a new polyhedron samples that is in the process of being drawn.
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8d645529 by John Harwell at 2023-12-18T10:36:50-06:00
Added "BICAN_Donor_id" to Sample Polyhedron metadata.
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6f944c5f by John Harwell at 2023-12-18T12:40:09-06:00
Removed developer flag DEVELOPER_FLAG_MPR_AXIS_SEPARATE_ROTATION_MATRICES and its usage.
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69e7dadf by John Harwell at 2023-12-18T12:54:06-06:00
Removed obsolete code that allowed (but was not used) to allow in-plane rotation for MPR three (slice rotated instead of crosshairs).
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2c9182e1 by John Harwell at 2023-12-19T15:41:02-06:00
Custom View Dialog: When reading from and writing the rotation values for MPR into the dialog, flip the sign so that the angles in the dialog are the same as the Oblique view angles. Add a new row for MPR (Old) since it uses different angles than the new MPR. Also, for MPR old, when reading from and writing rotation values into the dialog flip the sign so that the rotation values are the same as oblique (between MPR old and Oblique the slice will appear rotated differently but the crosshairs intersect the same parts of the brain).
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4e332931 by John Harwell at 2023-12-20T12:26:07-06:00
Hide selection of "MPR (Old)" for volume slice viewing UNLESS a scene is loaded that uses "MPR (Old)" mode.
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820698af by John Harwell at 2023-12-21T15:19:50-06:00
Add a "Move" button to Samples -> Drawing section of the toolbar. This button is enabled while the user is drawing a new sample polyhedron. When clicked, the mouse switches to "move" mode so that the user can drag coordinates in the sample polyhedron before finishing the sample polyhedron. When done with moving coordinates, the button is clicked again to resume adding coordinates to the sample polyhedron being drawn and finish the sample polyhedron.
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7af6e70c by John Harwell at 2023-12-22T10:52:23-06:00
Fixed inconsistency in Annotation and Edit Samples Toolbars with the title of the individual sections. Title of a section is grayed out if all of the controls in the section are grayed out.
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9d389e82 by John Harwell at 2023-12-22T16:45:34-06:00
Fixed memory leak that occurred if the user canceled drawing of a sample polyhedron.
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53cfa21e by John Harwell at 2023-12-27T11:11:54-06:00
Fixed new sample polyhedron "disappearing" while the Finish Dialog is displayed (annotation reappeared after dialog was closed).
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53afd9f7 by John Harwell at 2023-12-27T12:33:46-06:00
The MPR three overall quaternion was not updated when rotating using the mouse
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4c6d8b59 by John Harwell at 2023-12-28T09:33:40-06:00
Fixed problems with MPR rotation sometimes going a little crazy on Custom View dialog. Also changed all of the rotation spin boxes to turn keyboard tracking off. If the user enters a rotation value using the keyboard, the user must press the return key to apply the new value with keyboard tracking off. When keyboard tracking was on, the rotation value was applied as the user entered or removed a character and often caused large changes in the display of the surface or volume.
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47e49d87 by John Harwell at 2023-12-28T15:02:38-06:00
Add more information to VolumeMprVirtualSliceView::toString().
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50e2f33c by John Harwell at 2024-01-03T11:11:12-06:00
Add developer flag DEVELOPER_FLAG_MPR_THREE_SLICES_CHANGED_JUMP_FIX for testing fix to MPR three slice 'jumping' problem.
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0c796365 by John Harwell at 2024-01-03T11:12:00-06:00
Fixed problem with MPR three slices 'jumping' if the selected slices were changed and the slice rotation(s) were non-zero. Fix is on developer flag: DEVELOPER_FLAG_MPR_THREE_SLICES_CHANGED_JUMP_FIX.
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6d48770d by John Harwell at 2024-01-04T11:30:39-06:00
Some improvements for voxel editing in MPR and Oblique slice viewing.
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2ce0e2e7 by John Harwell at 2024-01-05T11:45:16-06:00
If a Qt message (warning, error, info) is not sent to the CaretLogger, display the message in the terminal window but only if the source is compiled in debug mode.
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1626e073 by John Harwell at 2024-01-05T12:18:28-06:00
Rename AnnotationFinishCancelWidget to AnnotationPolyTypeDrawEditWidget to better reflect its functionality.
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00f2080e by John Harwell at 2024-01-08T09:44:38-06:00
Small reductions in height of annotations / samples toolbar.
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66861ccd by John Harwell at 2024-01-09T15:44:18-06:00
Revise drawing/editing/finishing a sample polyhedron. There are now three exclusive buttons for editing, del (delete coordinates), ins (insert coordinates), and move (move coordinates). Editing is only allows on the first and last slices in the polyhedron's extent. Tooltips on draw and edit buttons have been improved. To make the last coordinates move visible its 'sizing handle' is larger (user may mix drawing and editing so knowing which is last coordinate may be helpful if resuming drawing after editing). Each edit mode has its own cursor shape when the operation is allowed: delete (an 'X'), insert (a 'plus'), and move (two arrows).
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3c6d7772 by John Harwell at 2024-01-09T16:35:18-06:00
When editing a sample polyhedron before is has been finished: If the user moves a coordinate it only moves on the slice on which moving takes place. The other 'paired' coordinate on the other end of the polyhedron no longer moves.
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23fba3b9 by John Harwell at 2024-01-10T11:21:32-06:00
Polyhedron sample drawing: If "Cancel" button in toolbar or "Cancel" button on Finish dialog is clicked, warn user that polyhedron that has been drawn will be discarded.
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ace36fbd by John Harwell at 2024-01-11T09:16:33-06:00
Bug Fix: If user was in Edit Samples Mode, started to draw a new sample polyhedron, switched from View Mode and back to Edit Samples Mode, user was unable to resume drawing/editing the sample polyhedron.
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9d4dcffe by John Harwell at 2024-01-11T09:50:26-06:00
If user is drawing an annotation that is being placed in a disk file or drawing a sample and the target annotation/sample file gets deleted, cancel drawing of the annotation/sample (note that target file is selected before drawing). It is highly unlikely that somebody would delete a file while in the middle of drawing an annotation or sample, but this change prevents a possible crash.
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40c8c35c by John Harwell at 2024-01-11T12:06:46-06:00
Change orientation of Redo/Undo and Lock/More buttons to vertical to save horizontal space.
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3404e611 by John Harwell at 2024-01-11T13:58:06-06:00
For sample polyhedron add a second move mode ("Move2"). This mode alllows the user to move the coordinate under the mouse and simultaneously moves the paired coordinate at the other end of the polyhedron.
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fc91171e by John Harwell at 2024-01-11T15:17:03-06:00
Fixed "Finish" button in Annotation toolbar overlapping widget on its left.
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b4667a55 by John Harwell at 2024-01-17T12:12:43-06:00
Annotations and Edit Samples: For samples, now have two buttons for moving coordinates in a sample polyhedron. 'Move' moves only the coordinate under the mouse. 'Move2' moves both the coordinate under the mouse and the 'paired' coordinate at the other end of the polyhedron. Buttons for removing, inserting, and moving were rearranged for Edit Samples mode and also added to Annotations mode for editing poly lines and polygons.
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7309fb4b by John Harwell at 2024-01-17T13:56:22-06:00
Remove items for inserting a coordinate and remove a coordinate for poly-type shapes from the Annotations/Edit Samples pop-up (right-click) menu. These functions are now selectable in the toolbar.
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7960e0ff by John Harwell at 2024-01-18T10:59:30-06:00
Fixed selection of annotations and samples. If the Edit Mode was Insert or Remove and the annotation/samples was not selected and the user then clicked the annotation/sample to select it, a coordinate might have gotten inserted or removed by the selection click. Also fixed cursor so that the insert cursor was not displayed over a non-selected annotation/sample.
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bea222f8 by John Harwell at 2024-01-19T10:06:26-06:00
Fixed voxel on/off editing for MPR and Oblique volume slice viewing. It just sets voxels on/off as if in an orthogonal view.
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88a8c639 by John Harwell at 2024-01-19T10:34:21-06:00
Enable some other voxel editing modes for MPR and Oblique Viewing.
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6b06492d by John Harwell at 2024-01-19T11:42:11-06:00
Do not try to project new foci if there are no anatomical surfaces loaded.
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f3c774da by John Harwell at 2024-01-22T14:57:33-06:00
For volume surface outline, include UNKNOWN for the 'GeometricType' (in addition to the 3D surface types), when searching for surfaces to display a outlines.
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d9358d1f by Tim Coalson at 2024-01-22T23:09:07-06:00
support map names in -cifti-math -select
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cdffe023 by John Harwell at 2024-02-01T10:09:42-06:00
Samples Finish Dialog: If user clicks the dialog's Cancel button, do not delete the sample that the user has drawn. Instead, keep the sample so that the user can resume drawing/editing the new sample. The user can use the toolbar's Cancel button if the user no longer wants the sample.
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ed118a1c by John Harwell at 2024-02-01T10:09:42-06:00
Fixed size handles on samples and poly-type annotations so that they scale with zooming (applies only to those drawn in stereotaxic space).
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1324e693 by John Harwell at 2024-02-01T10:09:42-06:00
A number of refinements to Annotations and Edit Samples Mode: Enable editing (insert / move / remove) while drawing; Changes to names of buttons; Undo/Redo support also.
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daaf116a by John Harwell at 2024-02-01T10:09:42-06:00
Fixed incorrect assertion on border color array when drawing border.
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1a189f95 by John Harwell at 2024-02-01T10:09:42-06:00
Split up events for repainting windows into one set for "repainting now" and a second set for "repainting soon". "Repainting now" essentially blocks until the window is repainted. "Repainting soon" allows the window system to decide when to paint the window and is used when an immediate repaint is not needed and allows for multiple paint requests issued in a short amount of time to only cause one paint event (the most common usage).
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5366e840 by John Harwell at 2024-02-01T10:09:42-06:00
When editing voxels, request an immediate repaint of graphics and not wait for windowing system to do the repaint.
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34116d4e by John Harwell at 2024-02-01T10:09:42-06:00
Fixed text for insert redo (was using incorrect text 'remove').
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7e2f3dfb by John Harwell at 2024-02-01T10:09:42-06:00
Rearrange a few buttons in the poly-type draw edit toolbar widget.
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b8d8bf00 by John Harwell at 2024-02-01T10:09:42-06:00
Starting on adding a redo/undo functionality to drawing of a new sample polyhedron.
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f9224f47 by John Harwell at 2024-02-01T10:09:42-06:00
Add Redo/Undo support for when a sample polyhedron is being drawn, prior to Finishing.
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7e2cd15c by John Harwell at 2024-02-01T10:09:42-06:00
Fixed memory leak in moving sample polyhedron coordinate.
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f1392210 by John Harwell at 2024-02-01T10:09:42-06:00
Fixed compilation warnings about unused variables.
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ccc99b3d by John Harwell at 2024-02-01T10:09:42-06:00
Enable Redo and Undo for editing operations while drawing a new sample polyhedron.
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18c1898a by John Harwell at 2024-02-01T10:09:42-06:00
Improve text in Edit Menu for Redo and Undo of Sample Polyhedron
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c6dfafd9 by John Harwell at 2024-02-01T10:09:42-06:00
Improve Voxel Editing Performance for turning voxels On and Off in a Label Volume: Previously, when a voxel was edited, coloring was reassigned for every voxel in the volume. Now, the coloring is assigned only for the voxels that change.
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4ad9b84d by John Harwell at 2024-02-01T10:09:42-06:00
Rearranged buttons for poly-type annotation and sample into a "Draw New" section and an "Edit" section.
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7176b9fc by John Harwell at 2024-02-01T10:09:42-06:00
Add methods to VoxelIJK to return each of the I, J, and K components.
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7b6adfa6 by John Harwell at 2024-02-01T10:09:42-06:00
Improvements in voxel editing performance for LABEL volumes and turning voxels of/off: (1) Do not recolor the entire volume, update the colors for only the voxels that have been edited; (2) Do not reload the entire 3D OpenGL texture, use glTexSubImage3D() to load only the rgba colors that have changed. A developer flag is available to turn off these changes to compare before and after performance (there is a print statement that times the voxel editing operation). The print statement will be removed after changes are tested on other platforms.
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b67c3605 by John Harwell at 2024-02-01T10:09:42-06:00
Removed developer flag for MPR slice rotation fix.
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39d995b9 by John Harwell at 2024-02-01T10:09:42-06:00
Revert "Removed developer flag for MPR slice rotation fix."
Need develper flag back to test MPR problem.
This reverts commit cbbe5e4be1f6dc79ad9a9c8d25ebce816a3b7dd2.
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5d5b5e9f by John Harwell at 2024-02-01T10:49:33-06:00
Change print statement that print time to perform a voxel edit operation into a logger statement at the INFO level.
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d9daae5f by John Harwell at 2024-02-01T14:18:19-06:00
Remove testing version of Ding Ontology Dialog from the Develop menu.
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537d208c by John Harwell at 2024-02-06T12:29:12-06:00
Update label selection dialog to get name of label file, map name, and map index.
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07db938b by John Harwell at 2024-02-06T15:24:20-06:00
In CONFIG text when wb_view is started, include info about all screens, not just the primary screen.
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751bdc6d by John Harwell at 2024-02-06T16:03:31-06:00
Partial implementation of Sample's Metadata revisions.
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9f94a24c by John Harwell at 2024-02-08T10:03:54-06:00
Add event to get the pixel size for a window or a qt widget (window containing qt widget).
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a463e62a by John Harwell at 2024-02-08T10:08:06-06:00
Fixed bugs and problems with poly-type annotation line width and size handle diameters including size handles being too large. Use the screen's pixel size to calculate a minimum size for the size handle. The diameter of the size handle for a poly-type annotation is now the same as the width of the line. However, the size handle will not get smaller than a minimum size so that the user can still grab the size handle and drag it with the mouse. Also fixed bug getting the drawing viewport when aspect was locked and the window's bottom left corner was not the OpenGL widget's bottom left corner.
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397ff152 by John Harwell at 2024-02-12T15:50:59-06:00
Added AnnotationMetaData, that extends GiftiMetaData, and added some virtual methods to GiftiMetaData that are used by AnnotationMetaData. These methods are used for replacing obsolete metadata names with new names, getting data type for metadata elements, and editing the metadata in the custom metadata editor.
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b78cf639 by John Harwell at 2024-02-13T17:06:07-06:00
Update metadata system to support composite elements. When requested from the metadata, a composite element is composed from other metadata elements. Composite elements are not stored in the metadata to avoid inconsistencies. This new composite metadata element system is used by AnnotationMetaData.
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cf149f4a by John Harwell at 2024-02-14T09:13:02-06:00
Move Samples metadata names out of GiftiMetaDataXmlElements and into new AnnotationMetaDataNames.
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8f894d19 by John Harwell at 2024-02-14T12:08:18-06:00
Allow an empty name for a sample polyhedron (instead of displaying "Polyhedron #"); Add some tooltips for Sample Polyhedron metadata; Default the Entry Date to today's date.
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b6280e3e by John Harwell at 2024-02-14T12:14:27-06:00
Change label in polytype draw edit section from "Edit" to "Edit Coordinates" since the buttons under the label are for editing coordinates a poly-type annotation.
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6310f10c by John Harwell at 2024-02-14T12:15:05-06:00
When finishing an annotation and copying metadata from the most recently drawn annotation, to not copy any composite metadata items.
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b455f5fc by John Harwell at 2024-02-14T16:28:49-06:00
Samples: First implementation of generating a unique Sample Number for an Allen Slab Number.
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482d83d9 by John Harwell at 2024-02-15T09:59:11-06:00
Fix compilation errors and warnings reported on Linux systems.
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feb67c40 by John Harwell at 2024-02-15T10:21:38-06:00
Fix compilation errors.
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3232cc98 by John Harwell at 2024-02-15T10:43:18-06:00
Fix compilation errors due to Qt version differences on Linux/WIndows vs macOS.
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7d3e3a5c by John Harwell at 2024-02-15T10:53:38-06:00
More Fix compilation errors due to Qt version differences on Linux/WIndows vs macOS.
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c5c9a6fb by John Harwell at 2024-02-21T14:48:37-06:00
Remove Alt_Shorthand_ID from sample polyhedron metadata elements.
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3ed09742 by Tim Coalson at 2024-02-27T23:02:28-06:00
rework -cifti-merge for 3D and direction choice, add legacy option support
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532f0798 by John Harwell at 2024-02-29T09:46:56-06:00
Removed assertion for an RGB_WORKBENCH volume type with a palette mapped volume since RGB_WORKBENCH is a special type used for a functional volume whose 3 maps are mapped to RGB colors.
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57570059 by John Harwell at 2024-02-29T09:46:56-06:00
Previous commit that removed assertion should have set volume color assignment using discrete coloring. Note this and previous commit apply to the obsolete MPR 2; not the current MPR.
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92c086dc by Tim Coalson at 2024-03-01T21:29:45-06:00
fix copy-paste error
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e1cb0dae by John Harwell at 2024-03-04T09:37:03-06:00
Do not allow main window toolbar to float (be in its own window).
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79a060d5 by John Harwell at 2024-03-04T09:37:03-06:00
Fixed crash if metric file read had a different number of vertices than the surface file with the same structure.
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c17464d3 by John Harwell at 2024-03-04T09:37:03-06:00
When in full screen mode, do not disable options to show toolbar, overlay toolbox, and features toolbox.
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7ed9b3ba by John Harwell at 2024-03-04T09:37:03-06:00
Revised processing of full screen mode so that it works properly when user clicks the buttons in the window's title bar. Add View Maximize to View Menu. On macOS clicking the green button in window title bar goes to Full Screen Mode. Holding down the Option Key and clicking the green button in the window toolbar goes to Maximize Mode.
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eddf43d0 by John Harwell at 2024-03-04T09:37:03-06:00
Revert "Revised processing of full screen mode so that it works properly when user clicks the buttons in the window's title bar. Add View Maximize to View Menu. On macOS clicking the green button in window title bar goes to Full Screen Mode. Holding down the Option Key and clicking the green button in the window toolbar goes to Maximize Mode."
This reverts commit ce47b83d23e90337da93ddd08efeacd460fbbefa.
Some of the changes are causing a problem and need to start over with them.
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f0f18e85 by John Harwell at 2024-03-04T09:37:03-06:00
Fixed View Full Screen mode so that it functions if the user clicks the 'green' button in macOS toolbar. Also, add "Show Maximized" to View Menu to enter/exit maximize mode. On macOS holding down the option key when clicking the green button enters "Maximized Window". Fixes/updates to Escape key for exiting Full Screen or Maximized mode. The different between Full Screen and Maximized is that Full Screen removes the Overlay and Features Toolboxes. Maximized does not.
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066e1719 by John Harwell at 2024-03-04T09:37:03-06:00
Add a small amount of Objective-C code that removes items that Apple adds to menus: Edit Menu - Start Dictation; Edit Menu - Emoji & Symbols; View Menu - Enter Full Screen. This code is from https://opencor.ws or https://github.com/opencor/opencor. Specifically the files macos.h and macos.mm.
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a5228cba by John Harwell at 2024-03-04T09:37:03-06:00
On Overlay and Map Settings Dialog, increase digits right of decimal from 3 to 6 for low and high thresholds. Do not use a fixed width for threshold spin so that they can expand in width if needed.
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3f06b836 by John Harwell at 2024-03-04T09:37:03-06:00
Fixed problems typing into horizontal and vertical range spin boxes in chart toolbar. Problem was that when a spin box value was changed, the commands issued where also updating the spin box and this caused the problem.
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dcb76c0c by John Harwell at 2024-03-04T09:37:03-06:00
In window's toolbar, add an "Undo" button on the right side of the Lock Aspect button. If the user unlocks the aspect ratio, clicking this new button re-locks the aspect ratios to what they were at the time the Lock Aspect button was clicked. If the tabs have changed, a warning message is displayed allowing the user to continue or cancel.
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2a75b317 by John Harwell at 2024-03-04T09:37:03-06:00
Add code to allow a timeout for HTTP Post requests. However, code is commented out until it can be tested when ConnectomeDB is back up.
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70b4d98f by John Harwell at 2024-03-04T13:44:04-06:00
Finished implementation of http timeout. It is used only by CIFTI file and defaults to 30 seconds. Testing was done by setting the timeout very short when reading a row from ConnectomeDB. An uncaught exception was fixed when data was loaded as a result of displaying a scene.
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c385920b by John Harwell at 2024-03-04T14:04:34-06:00
Fix compilation warning on new class. Fixed compilation error on Linux and Windows as they have older versions of Qt that do not support the network request timeout.
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cbc1131c by John Harwell at 2024-03-06T11:45:55-06:00
Removed a couple of unused variables.
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3aa65640 by John Harwell at 2024-03-08T16:30:43-06:00
On the Tile Tabs Configuration Dialog, add an "Undo" button next to the "Set" button for the Manual Configuration mode. Anytime the Manual configuration is replaced, clicking the "Undo" button will restore the previous Manual Configuration.
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ebdd28da by John Harwell at 2024-03-11T08:36:56-05:00
Fixed tooltip on Tile Tabs Configuration dialog's 'Revert' button.
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a27a04c5 by John Harwell at 2024-03-11T09:07:10-05:00
Custom View Dialog: Fixed problem with changing one MPR angle caused all MPR angles to change.
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90b3d2d9 by John Harwell at 2024-03-11T15:21:09-05:00
For Map Settings Dialog Threshold controls, in unlimited mode, min/max are now int32_t min/max. Previously were double range of data in file. Note that QSlider operates in integers.
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b9b4c1c5 by John Harwell at 2024-03-11T15:59:09-05:00
For Map Settings Threshold controls, limit step value to one. Otherwise it may be so large it is unusable.
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7b73d89b by John Harwell at 2024-03-12T09:32:41-05:00
Adapt the HistologySlicesFile (which reads a *.metaczi file) to read Tim's new *.meta-image file.
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613f98e3 by John Harwell at 2024-03-13T09:36:09-05:00
Fixed histology slices file. Old slices were not removed when the file was reloaded and a couple of other slice dependent items were not reset.
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64e5c372 by John Harwell at 2024-03-14T13:40:02-05:00
When files are added, read, reloaded, or deleted: Clear the volume surface outline cache since the file may affect the surface outlines (this does not include loading a spec file and its data files).
- - - - -
1038bd76 by John Harwell at 2024-03-15T12:26:08-05:00
Update HistologySlicesFile so that it reads new meta-image format that replaces Slice Number with SliceName. In toolbar, replace slice number spin box with a slice name combo box.
- - - - -
c0ed6553 by John Harwell at 2024-03-18T14:31:48-05:00
Initial implementation of volume surface outline that allows for a "surface thickness".
- - - - -
983d6d1e by John Harwell at 2024-03-18T15:25:04-05:00
For drawing volume surface outlines on histology slices, use the spacing from the file when computing steps size when outline depth is used.
- - - - -
d8256649 by John Harwell at 2024-03-19T11:55:37-05:00
When Volume Surface Outline Depth is greater than zero, use OpenMP for computation of the volume surface outlines (iterating through them).
- - - - -
928389f1 by John Harwell at 2024-03-19T12:14:36-05:00
Include OMP number of threads and maximum number of threads (when compiled with OpenMP) in ApplicationInformation.
- - - - -
19f9fcfb by John Harwell at 2024-03-19T14:04:55-05:00
Do not draw volume surface outlines when performing identification.
- - - - -
cb40cdfb by John Harwell at 2024-03-20T09:43:32-05:00
Display number of OMP threads and maximum number of threads on About Workbench Dialog's "More" dialog rather than in ApplicationInformation.
- - - - -
a2c2ce3b by John Harwell at 2024-03-20T09:50:37-05:00
Cleanup of BrainOpenGLVolumeSurfaceOutlineDrawing including it is no longer all static methods.
- - - - -
003b051a by John Harwell at 2024-03-20T11:54:18-05:00
Fixed compilation errors and warnings from Linux and Windows.
- - - - -
1192254e by John Harwell at 2024-03-20T13:25:11-05:00
Fixed width (was too wide) of Depth Spin Box in Volume Surface Outline tab of Overlay Toolbox.
- - - - -
83f52b52 by Tim Coalson at 2024-03-20T17:45:12-05:00
fix map name and label table copying in -cifti-merge
- - - - -
2259797c by John Harwell at 2024-03-21T14:09:46-05:00
Add caching to Volume Surface Outlines when drawn on MPR slices. Limit to 100 volume surface outlines in the cache. Add a right-click menu to outline depth that allows user to override the Workbench calculated separation between consecutive outlines when the depth is greater than zero. Overriding the depth can eliminate gaps between multiple surface outlines but may require additional computation time.
- - - - -
eaedb735 by John Harwell at 2024-03-21T14:51:40-05:00
For volume surface outline separation dialog spin box, use the "special value text" set to "default" instead of zero for Workbench to calculate the separation. Update (redraw) the volume surface outlines when the value in the spin box is changed.
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42e3e99a by John Harwell at 2024-03-26T13:19:16-05:00
For CZI, change logging level of invalid NIFTI index for non-linear volume from Warning to Fine since this is not an error.
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822cf1bc by John Harwell at 2024-03-26T14:11:56-05:00
When getting the coordinate for histology slices there is a test to see if the underlay file has changed. If the histology coordinate was copied from another tab (yoked), the filename associated with the coordinate may not be valid. If this is the case it causes the coordinate to reset to "the center" and yoking does not work for this tab. So, this test for a change in filename has been disabled to prevent the coordinate from being reset.
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9a18b1ef by John Harwell at 2024-03-26T15:06:32-05:00
Added a preference for showing identification symbols on histology slices.
- - - - -
a05799f2 by John Harwell at 2024-03-26T15:21:23-05:00
Change logging of an invalid histology coordinate from severe to fine as it can occur before histology fully initializes.
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03a35184 by John Harwell at 2024-03-26T17:09:40-05:00
Fixed crash if trying to drawn an invalid image index and display "No Images" in this case.
- - - - -
406d96c9 by John Harwell at 2024-03-29T13:23:19-05:00
Add a new surface outline drawing mode that draws a surface but clips the surface above and below the volume slice. User can draw surface outlines with three modes: A lines (previous implementation), as a clipped surface, or as both lines and surface.
- - - - -
d013b958 by John Harwell at 2024-04-09T14:52:45-05:00
Removed incorrect 'break' statement in VolumeFile::parseExtensions at the end of the loop that iterated through the extensions. The break caused exiting of the loop after the processing first extension. This prevented reading of the CaretExtension if it was not the first extension.
- - - - -
0061ca99 by John Harwell at 2024-04-10T09:35:41-05:00
Fixed gaps appearing in volume surface outlines when the preferences Volume Surface Outline Separation value was less than 0.5.
- - - - -
5c19ab55 by John Harwell at 2024-04-10T09:35:41-05:00
For volume surface outline depth: When the value is zero, display "Default" in the spin box. When the value is "Default", volume surface outline "Lines" are drawn with a depth of zero (same as before depth control was added) and volume surface outline "Surface" is drawn with a depth of 0.5mm. This fixes a problem with drawing the outline as a Surface using clipping planes as a depth of zero place the clipping planes at the same location resulting in no surface being drawn.
- - - - -
383e8467 by John Harwell at 2024-04-10T09:35:41-05:00
Renamed BackgroundAndForegroundColorsModeEnum CaretPreferenceSceneDataValueModeEnum so that it can be used with other preferences that get saved to a scene but can be overridden by a user after loading the scene.
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f0925edf by John Harwell at 2024-04-10T16:44:59-05:00
Updates and bug fixes to save the Preference's Volume Surface Outline Separation value to scenes. On Preference's Dialog, when separation value from the scene is being used, indicate it by a checked checkbox. User can revert to the Preference's value by unchecking the checkbox.
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2e663bdf by John Harwell at 2024-04-23T15:19:21-05:00
Attempting to fix running of ffmpeg on Windows. Added ".exe" to ffmpeg.
- - - - -
66264dcb by John Harwell at 2024-05-01T13:45:54-05:00
In OperationZipSpecFile, log a message at the Fine level for any files that are outside the base path to help with debugging. Using logging at the fine level should prevent message from being seen by users since this logger level is unlikely to be used.
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4f8013dd by John Harwell at 2024-05-01T14:48:12-05:00
In OperationZipSpecFile, log information about the spec file name and related path at the FINE level.
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ea02da92 by John Harwell at 2024-05-01T15:19:29-05:00
Log one more item in OperationZipSpecFile.
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9e6dfdbb by John Harwell at 2024-05-06T13:43:37-05:00
Fixed yoking of Samples Display Settings in Features Toolbox.
- - - - -
bf8b6bcd by John Harwell at 2024-05-06T13:43:37-05:00
Enable Samples Tab in Features Toolbox when selected tab is viewing a volume model.
- - - - -
f92e98e4 by John Harwell at 2024-05-06T13:43:37-05:00
Added drawing of polyhedron samples on Histology Images (meta-image) file slices.
- - - - -
b1eceefc by John Harwell at 2024-05-06T13:43:37-05:00
Allow selection of a sample polyhedron on the "in-between" slices.
- - - - -
7fae76eb by John Harwell at 2024-05-06T13:43:37-05:00
Display sample polyhedrons on histology slices.
- - - - -
5649af90 by John Harwell at 2024-05-06T13:43:37-05:00
Suppress Qt warning message about incorrect PNG profile "iCCP: known incorrect sRGB profile".
- - - - -
758a3dc6 by John Harwell at 2024-05-06T13:43:37-05:00
Enabled selection of a sample polyhedron on a histology slice (meta-image) file.
- - - - -
c482f9ac by John Harwell at 2024-05-06T13:43:37-05:00
Fixed bug that turned on the display of annotations when a new sample polyhedron was inserted.
- - - - -
99c84b9c by John Harwell at 2024-05-06T13:43:37-05:00
Add a method to test equality of an AnnotationCoordinate's XYZ with an XYZ in a Vector3D.
- - - - -
a3131a21 by John Harwell at 2024-05-06T13:43:37-05:00
Add a polygon tessellation named GraphicsPolygonTessellator. It tessellates polygons into triangles and can handle polygons that are self-intersecting.
- - - - -
c1fe8b4d by John Harwell at 2024-05-06T13:43:37-05:00
Use new polygon tessellatior for drawing annotation polyhedrons on volume slices that are not parallel to the planes of the polygons at the ends of the polyhedron.
- - - - -
564eaa72 by John Harwell at 2024-05-06T13:43:37-05:00
Add static method to covert a SubvolumeAttributes volume type enum to a string name.
- - - - -
987d181f by John Harwell at 2024-05-06T13:43:37-05:00
Add method to VolumeMappableInterface, VolumeFile, CiftiMappableDataFile to get the rgba color for a voxel without needing the DisplayGroup and tab number.
- - - - -
1cef0c17 by John Harwell at 2024-05-06T13:43:38-05:00
Partial implementation of displaying volume label files on histology images.
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057cb469 by John Harwell at 2024-05-06T13:43:38-05:00
Mapping volume to histology image now working for Cifti Label File.
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e9994eae by John Harwell at 2024-05-06T13:43:38-05:00
Performance improvements for mapping volumes to images and allow any type of volume file, not just label volumes.
- - - - -
6209824c by John Harwell at 2024-05-06T13:43:38-05:00
Display volume labels over histology images: Improve efficiency of mapping CIFTI label files by caching voxel RGBA coloring values (faster than requesting RGBA for same voxel many times from Cifti). Note that many image pixel may map to the same Voxel.
- - - - -
49531081 by John Harwell at 2024-05-06T13:43:38-05:00
Do not need to update coloring in a CIFTI label file in response to an invalidate coloring event.
- - - - -
4be71f04 by John Harwell at 2024-05-06T13:43:38-05:00
Remove "Non-Linear" and "Overlap" checkboxes on Toolbar Histology Widget to Developer options on Preferences Dialog.
- - - - -
4a204994 by John Harwell at 2024-05-06T13:43:38-05:00
Improve performance of mapping volume voxel to image by move PixelIndex outside of loop. Construction/Deconstruction of it many times becomes slow.
- - - - -
0ec25452 by John Harwell at 2024-05-06T13:43:38-05:00
Further performance improvement in volume to image mapping by eliminating a PixelIndex constructor in a loop.
- - - - -
43e31bcb by John Harwell at 2024-05-06T13:43:38-05:00
Add method to set a full row of pixels to ImageFile.
- - - - -
04164f9b by John Harwell at 2024-05-06T13:43:38-05:00
More optimizations for mapping a volume to an image.
- - - - -
7e8ec8f4 by John Harwell at 2024-05-06T13:43:38-05:00
Update volume to image mapping to support CZI files. Add ability to change resolution of image used when mapping volume to image (smaller is faster).
- - - - -
73a95ae9 by John Harwell at 2024-05-06T13:43:38-05:00
Rename developer flags for histology items. Add a new developer flag that allows any volume file or any volume mappable CIFTI file as a layer for display over histology slices.
- - - - -
46bb8a73 by John Harwell at 2024-05-06T13:43:38-05:00
Removed developer flag for allowing all volume types as histology layers and since that is now the desired behavior.
- - - - -
9d9d96c1 by John Harwell at 2024-05-06T13:43:38-05:00
Fixed adjustment of zooming on custom view dialog for histology slices.
- - - - -
38adc4b3 by John Harwell at 2024-05-06T13:43:38-05:00
Disable unfinished code for limiting dimension of output image for mapping volume data to histology.
- - - - -
0290ffc7 by John Harwell at 2024-05-06T14:42:29-05:00
Change order of libraries in Desktop and CommandLine CMakeLists.txt to try to fix linking of Annotations to Graphics (move Graphics to after Annotations in list of libraries).
- - - - -
e2608539 by John Harwell at 2024-05-06T16:04:47-05:00
Windows is failing to compile with an enumerated type value named AnnotationRedoUndoCommandModeEnum::COLOR_BACKGROUND so changing it to COLOR_OF_BACKGROUND to see if it fixes the problem.
- - - - -
f3ac07a8 by John Harwell at 2024-05-06T16:15:14-05:00
Variable named 'near' failed to compile on Windows. Renamed it to 'nearValue'.
- - - - -
1e32635b by John Harwell at 2024-05-06T16:36:55-05:00
Windows: rename 'near' and 'far' to 'nearValue' and 'farValue' in GraphicsOrthographicProjection.
- - - - -
03df9208 by Tim Coalson at 2024-05-08T18:33:41-05:00
update brainordinates/timepoints private variables to cifti return type, which should also fix "total elements" multiplication for large files
- - - - -
48d3b9d0 by John Harwell at 2024-05-09T10:21:35-05:00
Add method go get basis vectors from Matrix4x4.
- - - - -
3f7ddd47 by John Harwell at 2024-05-09T10:21:35-05:00
Add a "Yoke Orientation to MPR" checkbox to histology toolbar. When this is on, the image's orientation is copied to the MPR orientation in the tab's yoking group.
- - - - -
e2ba357f by John Harwell at 2024-05-09T11:41:41-05:00
Fixed compilation warnings.
- - - - -
8cb1ac57 by John Harwell at 2024-05-13T11:19:30-05:00
Corrected drawing order of volume surface outlines so that they are drawn bottom layer to top layer. Previously all layers with lines were drawn first and then all layers with surface clipping. This prevent a line in a higher layer from appearing over a surface clipping in a lower layer.
- - - - -
2abd3cde by John Harwell at 2024-05-13T15:12:00-05:00
Fixed panning of Volume MPR - did not work if the MPR tab was yoked.
- - - - -
59e03a9e by John Harwell at 2024-05-13T15:28:54-05:00
Fixed compilation error on windows and linux.
- - - - -
0396f4ba by John Harwell at 2024-05-13T16:49:49-05:00
When surface file computes a normal vector for a vertex, the normal vectors from all triangles used by the vertex are accumulated in the vertex's normal data and then the normal's data is divided by the number of triangles used by the vertex. When this normal vector computation was called more than once for a surface (such as when a surface is reloaded in wb_view), the normal data was NOT being set to zeros at the beginning of the computations causing the normal vectors to be incorrect.
- - - - -
f5f12c44 by John Harwell at 2024-05-14T10:26:42-05:00
Add button to histology toolbar to show/hide the crosshairs on histology slices. This property is yoked and saved to scenes.
- - - - -
49bd46c1 by John Harwell at 2024-05-15T09:44:00-05:00
Volume Surface Outline - Add opacity.
- - - - -
a9ab9e89 by John Harwell at 2024-05-15T14:13:03-05:00
Fixed display of identification symbols in MPR mode. It was using the orthogonal plane equation and not the actual plane equation that results from rotation for drawing the identification symbols.
- - - - -
d9283fdb by John Harwell at 2024-05-15T15:56:42-05:00
Correct panning of a parasagittal view in the horizontal direction (panning of brain Y was backward from brain Y panning of axial).
- - - - -
04f5ed94 by John Harwell at 2024-05-16T11:34:32-05:00
Tried OpenGL lines for volume surface outline drawing with opacity but it results in gaps and looks worse than poly lines. Disabled selection of it this mode. Perhaps it can be improved at a later time.
- - - - -
19a01c9a by John Harwell at 2024-05-21T14:24:02-05:00
Display volumes on histology slices: Add intensity modes: Average, Minimum, Maximum.
- - - - -
48a6648b by John Harwell at 2024-05-22T09:54:05-05:00
Remove unused function from histology slice drawing.
- - - - -
b54d6743 by John Harwell at 2024-05-22T09:55:07-05:00
Improve performance of volume to image mapping for average intensity.
- - - - -
2fe31439 by John Harwell at 2024-05-22T14:54:45-05:00
When mapping a volume to an image with stereotaxic coordinates, the image is often at a much higher resolution (pixels per millimeter) than the volume. So, calculate the approximate number of pixels that map to one voxel and map the volume to a lower resolution image (approximately three pixels to a voxel). This speeds up the mapping substantially and the quality of the lower-resolution output image looks the same as the full-resolution output image.
- - - - -
fe5ba55c by John Harwell at 2024-05-28T16:13:07-05:00
Add display of histology slice angles to histology toolbar.
- - - - -
5b3688b0 by John Harwell at 2024-05-29T12:19:03-05:00
When identification updates volume slices, use the stereotaxic coordinate to update the volume slices; NOT the center of the voxel containing the stereotaxic coordinate.
- - - - -
19c3e557 by John Harwell at 2024-05-29T14:53:55-05:00
In Toolbar->Volume Montage, move the precision spin box into the "Coordinates Format" menu that is displayed by pushing the arrow on the right side of the XYZ button. Doing so creates space for the a new control for slice direction (polarity) that will be added.
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2ac803c2 by John Harwell at 2024-05-30T15:26:49-05:00
Added GUI functionality for controlling volume montage slice order that will be added next.
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bd4b6d22 by John Harwell at 2024-05-31T13:06:47-05:00
Implemented volume montage slice ordering. Use can choose to have coordinate increasing, decreasing, or "Workbench" mode that preserves older mixed ordering (oblique and ortho are increasing for parasagittal and decreasing for axial and coronal).
- - - - -
d3625ab5 by John Harwell at 2024-05-31T17:06:34-05:00
Fixed macro setup in volume montage toolbar for new slice direction combo box.
- - - - -
66169ea3 by John Harwell at 2024-06-03T15:29:38-05:00
Fixed error with macro support for slide direction control in volume montage toolbar widget.
- - - - -
61cac175 by John Harwell at 2024-06-04T10:54:06-05:00
Revised metadata validation to allow more sophisticated validation of edited metadata including warnings. Previously, the only validation test was to verify an entry was not empty. When user creates a sample, added warning for Allen Slab Number if it is out of range for the selected hemisphere. Added an advanced tab to the Edit Samples dialog that allows the user to set the range of Allen Slab Number for a left or right hemisphere. At this time, this range is not saved when the user exits Workbench.
- - - - -
5956bb1f by John Harwell at 2024-06-05T14:19:51-05:00
Fixed identification display of "All Maps" for files that were selected for identification when the file is in an overlay.
- - - - -
d8380574 by John Harwell at 2024-06-05T14:20:08-05:00
Fixed compilation warnings reported by Linux.
- - - - -
f3076aa0 by John Harwell at 2024-06-06T09:31:17-05:00
Fixed slow reading of a large CIFTI Dense Label File. Initialization of the label hierarchy was sending out color invalidation requests for each label as its status was turned on. These invalidation requests are now blocked during initialization. Reading time on a Mac dropped from 180 seconds to 12 seconds.
- - - - -
dba8bd44 by John Harwell at 2024-06-06T11:32:32-05:00
For Histology: Show slice indices as 1 to N when the indices are viewed by the user (toolbar, identification, file information). In the code, the slice indices remain 0..N-1. Previously created scenes function correctly but the slice indices displayed to the user is now one more.
- - - - -
8806f9fb by John Harwell at 2024-06-06T15:47:44-05:00
Rearrange widgets in Histology section of toolbar so that the length of the Slice Name can be increased.
- - - - -
5b3b27ac by John Harwell at 2024-06-06T15:56:13-05:00
In Toolbar Histology section, remove the Z-coordinate for plane coordinates. Plane coordinates are two-dimensional so this control is not needed.
- - - - -
b38d205f by John Harwell at 2024-06-13T09:33:21-05:00
Attempt to make MPR neurological/radiological orientation selection more obivious to user. Added some text to panel that contains orientation selection and a checkbox for enabling the axis labels. If user changes orientation the axis labels are turned on.
- - - - -
e72f6423 by John Harwell at 2024-06-13T11:39:35-05:00
Removed some unused code from old color index identification from oblique slice drawing.
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34c32167 by John Harwell at 2024-06-14T10:43:27-05:00
For Volume Oblique identification, use stereotaxic coordinate of mouse instead of center of the voxel.
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706322f1 by John Harwell at 2024-06-14T14:05:50-05:00
Change two copyright years from 2015 to 2024 in Desktop/CMakeLists.txt. These dates are used with the macOS bundle.
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9dba65e4 by Tim Coalson at 2024-06-14T14:48:48-05:00
set version
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a4824b22 by Tim Coalson at 2024-06-14T15:38:26-05:00
update some copyright dates
- - - - -
30ff9101 by Yaroslav Halchenko at 2024-06-18T14:01:42-04:00
Merge tag 'v2.0.0' into releases
v2.0.0
* tag 'v2.0.0': (1112 commits)
update some copyright dates
set version
Change two copyright years from 2015 to 2024 in Desktop/CMakeLists.txt. These dates are used with the macOS bundle.
For Volume Oblique identification, use stereotaxic coordinate of mouse instead of center of the voxel.
Removed some unused code from old color index identification from oblique slice drawing.
Attempt to make MPR neurological/radiological orientation selection more obivious to user. Added some text to panel that contains orientation selection and a checkbox for enabling the axis labels. If user changes orientation the axis labels are turned on.
In Toolbar Histology section, remove the Z-coordinate for plane coordinates. Plane coordinates are two-dimensional so this control is not needed.
Rearrange widgets in Histology section of toolbar so that the length of the Slice Name can be increased.
For Histology: Show slice indices as 1 to N when the indices are viewed by the user (toolbar, identification, file information). In the code, the slice indices remain 0..N-1. Previously created scenes function correctly but the slice indices displayed to the user is now one more.
Fixed slow reading of a large CIFTI Dense Label File. Initialization of the label hierarchy was sending out color invalidation requests for each label as its status was turned on. These invalidation requests are now blocked during initialization. Reading time on a Mac dropped from 180 seconds to 12 seconds.
Fixed compilation warnings reported by Linux.
Fixed identification display of "All Maps" for files that were selected for identification when the file is in an overlay.
Revised metadata validation to allow more sophisticated validation of edited metadata including warnings. Previously, the only validation test was to verify an entry was not empty. When user creates a sample, added warning for Allen Slab Number if it is out of range for the selected hemisphere. Added an advanced tab to the Edit Samples dialog that allows the user to set the range of Allen Slab Number for a left or right hemisphere. At this time, this range is not saved when the user exits Workbench.
Fixed error with macro support for slide direction control in volume montage toolbar widget.
Fixed macro setup in volume montage toolbar for new slice direction combo box.
Implemented volume montage slice ordering. Use can choose to have coordinate increasing, decreasing, or "Workbench" mode that preserves older mixed ordering (oblique and ortho are increasing for parasagittal and decreasing for axial and coronal).
Added GUI functionality for controlling volume montage slice order that will be added next.
In Toolbar->Volume Montage, move the precision spin box into the "Coordinates Format" menu that is displayed by pushing the arrow on the right side of the XYZ button. Doing so creates space for the a new control for slice direction (polarity) that will be added.
When identification updates volume slices, use the stereotaxic coordinate to update the volume slices; NOT the center of the voxel containing the stereotaxic coordinate.
Add display of histology slice angles to histology toolbar.
...
- - - - -
5c843c4d by Yaroslav Halchenko at 2024-06-18T14:01:54-04:00
Merge branch 'releases' into debian
* releases: (1112 commits)
update some copyright dates
set version
Change two copyright years from 2015 to 2024 in Desktop/CMakeLists.txt. These dates are used with the macOS bundle.
For Volume Oblique identification, use stereotaxic coordinate of mouse instead of center of the voxel.
Removed some unused code from old color index identification from oblique slice drawing.
Attempt to make MPR neurological/radiological orientation selection more obivious to user. Added some text to panel that contains orientation selection and a checkbox for enabling the axis labels. If user changes orientation the axis labels are turned on.
In Toolbar Histology section, remove the Z-coordinate for plane coordinates. Plane coordinates are two-dimensional so this control is not needed.
Rearrange widgets in Histology section of toolbar so that the length of the Slice Name can be increased.
For Histology: Show slice indices as 1 to N when the indices are viewed by the user (toolbar, identification, file information). In the code, the slice indices remain 0..N-1. Previously created scenes function correctly but the slice indices displayed to the user is now one more.
Fixed slow reading of a large CIFTI Dense Label File. Initialization of the label hierarchy was sending out color invalidation requests for each label as its status was turned on. These invalidation requests are now blocked during initialization. Reading time on a Mac dropped from 180 seconds to 12 seconds.
Fixed compilation warnings reported by Linux.
Fixed identification display of "All Maps" for files that were selected for identification when the file is in an overlay.
Revised metadata validation to allow more sophisticated validation of edited metadata including warnings. Previously, the only validation test was to verify an entry was not empty. When user creates a sample, added warning for Allen Slab Number if it is out of range for the selected hemisphere. Added an advanced tab to the Edit Samples dialog that allows the user to set the range of Allen Slab Number for a left or right hemisphere. At this time, this range is not saved when the user exits Workbench.
Fixed error with macro support for slide direction control in volume montage toolbar widget.
Fixed macro setup in volume montage toolbar for new slice direction combo box.
Implemented volume montage slice ordering. Use can choose to have coordinate increasing, decreasing, or "Workbench" mode that preserves older mixed ordering (oblique and ortho are increasing for parasagittal and decreasing for axial and coronal).
Added GUI functionality for controlling volume montage slice order that will be added next.
In Toolbar->Volume Montage, move the precision spin box into the "Coordinates Format" menu that is displayed by pushing the arrow on the right side of the XYZ button. Doing so creates space for the a new control for slice direction (polarity) that will be added.
When identification updates volume slices, use the stereotaxic coordinate to update the volume slices; NOT the center of the voxel containing the stereotaxic coordinate.
Add display of histology slice angles to histology toolbar.
...
- - - - -
7a778e50 by Yaroslav Halchenko at 2024-06-18T14:03:48-04:00
Changelog and drop patch
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68b668a7 by Yaroslav Halchenko at 2024-06-18T14:11:39-04:00
debian/watch - URL adjusted to work (stopped, didn't dig why prior one did not work)
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7ba3345d by Tim Coalson at 2024-06-18T15:31:13-05:00
fix missing include in CZIlib
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09dae89d by Yaroslav Halchenko at 2024-06-21T13:31:18+09:00
One more patch
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e25b9f72 by John Harwell at 2024-07-01T09:14:35-05:00
Fixed uploading to BALSA by testing equality of response headers elements as case insensitive.
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647872ef by Tim Coalson at 2024-07-17T19:02:48-05:00
minor fix for -metadata-string-replace cifti handling, and .surf.gii support
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0c4c663b by Tim Coalson at 2024-07-23T21:00:50-05:00
add -background option to -volume-resample
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6690b11f by Tim Coalson at 2024-07-29T17:34:20-05:00
typo in help info
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252a1236 by Tim Coalson at 2024-08-02T21:15:29-05:00
fix valgrind-caught uninitialized member
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42283d24 by John Harwell at 2024-08-05T11:02:45-05:00
Fixed crash when drawing a new text annotation by dragging the mouse that creates a box. Do not allow selection of the temporary box annotation as it is out of scope when selection is processed.
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fd06f2d6 by Tim Coalson at 2024-08-16T20:00:58-05:00
implement hierarchy json import for just volume files
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b94abcc6 by Tim Coalson at 2024-08-16T20:43:33-05:00
fix qt6 xml.name() == incompatibility with bare "" literals
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267aadfc by John Harwell at 2024-08-19T14:47:33-05:00
Update volume RGB coloring so that it detects if the range of data is [0,1] (new) or [0,255] (original) when the "Special-RGB-Volume" palette is used.
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99a78a55 by John Harwell at 2024-08-19T14:47:33-05:00
Fixed oblique volume drawing for volume files drawn using the Special-RGB-Volume palette. First, these volumes (drawn using three maps as RGB components) were not getting detected. Second, coloring logic did not work for volumes with data ranging [0,1] so coloring logic was updated to use that in NodeAndVoxelColoring that is also used by orthogonal and MPR volume viewing.
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758bc481 by John Harwell at 2024-08-19T14:47:33-05:00
Changed RGB threshold used in orthogonal drawing of volumes using the Special-RGB-Volume palette. It was excluding too many voxels leaving strange, squiggly black lines in volumes.
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ae5facc0 by John Harwell at 2024-08-19T17:11:46-05:00
This change applies only to Orthogonal Volume Slice View of Axial, Coronal, or Parasagittal View (not ALL) with Montage OFF. If identification is performed on the orthogonal slice in the selected tab, the coordinate in the toolbar will update to the center of the voxel that was selected. So if the in-plane coordinate in the toolbar is not at the center of the voxel it will change. Prior to this change, the in-plane coordinate would not change. It appears that this update reverses the commit eab50af from 07 July 2016 that was part of WB-631. Today's update was requested by TC.
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07908caf by Tim Coalson at 2024-08-27T17:37:08-05:00
new sparse output limited geodesic distance command
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74e3032d by Tim Coalson at 2024-08-28T17:06:10-05:00
add corrected areas to new sparse text geodesic command, remove unused helper from AllToAll and update help text
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8dea768f by John Harwell at 2024-09-05T09:13:56-05:00
Removed some unused methods and members for 'selection' from GiftiLabel and GiftiLabelTable. At one time, there was one label selection that applied to all tabs and these items were not removed when the separate selection for tab and display group were added with the GroupAndNameHierarchyItem.
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e001be68 by John Harwell at 2024-09-05T09:13:56-05:00
Partial implementation of GUI for Hierarchical Label Selection in Features ToolBox.
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0eee911a by John Harwell at 2024-09-05T09:13:56-05:00
Continuing label hierarchy development. Hierarchy is working, scenes are working.
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c80ca8f2 by John Harwell at 2024-09-05T09:13:56-05:00
Label Hierarchy: Fixed MPR drawing for when same map in in multiple tabs with different label selections. Previously, one graphics primitive was created for a map in all tabs. Now for label volumes only, each tab has its own primitive for each map.
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b47ddf5b by John Harwell at 2024-09-05T09:13:56-05:00
Fixed pre-existing label selection for oblique drawing and implemented hierarchy label selection for oblique drawing.
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a28fb5c4 by John Harwell at 2024-09-05T09:13:56-05:00
Fixed a couple of compilation warnings.
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66b5d156 by John Harwell at 2024-09-05T09:13:56-05:00
Label Hierarchy: Implemented restoration of expanded/collapsed status of label hierarchy in features toolbox. Include file and map name for childless labels in hierarchy that do not have a corresponding label in the label table.
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f3c65d9c by John Harwell at 2024-09-05T09:13:56-05:00
Label Hierarchy: Log at the warning level labels that do not appear in the hierarchy and labels that are in the hierarchy but the item in the hierarchy has children.
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3f2b414d by John Harwell at 2024-09-05T09:13:56-05:00
Label Hierarchy: Remove unused element from LabelSelectionItem class.
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b3612480 by John Harwell at 2024-09-05T09:13:56-05:00
Label Hierarchy: Allow items in the hierarchy that have children and have a corresponding label in the label table to turn labels on and off.
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1157c614 by John Harwell at 2024-09-05T09:13:56-05:00
Label Hierarchy: Add labels from label table that are not in hierarchy to their own group in the hierarchy. Fixed crash for file that does not support hierarchy.
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4c757a07 by John Harwell at 2024-09-05T09:13:56-05:00
Label Hierarchy: Removed empty top level item in label hierarchy in features toolbox. If model in label hierarchy viewer is changed and all top level items are collapsed, expand all.
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abb19f78 by John Harwell at 2024-09-05T09:13:56-05:00
Label Hierarchy: Removed empty top level item in label hierarchy in features toolbox. If model in label hierarchy viewer is changed and all top level items are collapsed, expand all.
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b23a2bff by John Harwell at 2024-09-05T09:13:56-05:00
Label Hierarchy: Fixed crash when saving a scene when there is no valid model in the GUI's label tree view.
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4252acff by John Harwell at 2024-09-05T09:13:56-05:00
Label Hierarchy: Add button to turn all labels on or off to Label Hierarchy in Features Toolbox.
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9df4010a by John Harwell at 2024-09-05T10:10:38-05:00
Fix compilation problems on other systems.
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c2401f71 by John Harwell at 2024-09-05T10:37:21-05:00
Trying to fix compilation problem on Linux.
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8fabdcd3 by John Harwell at 2024-09-05T13:21:38-05:00
Fix compilation warnings produced by newer compiler.
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a021350c by John Harwell at 2024-09-09T13:59:04-05:00
Implement volume modulation. A new tab named "Modulate" has been adde to the Overlay and Map Settings dialog. On the tab the user selects the file and map for modulation. The files available selection are limited to those with the same volume dimensions. The modulate volume should range [0,1] and any values outside this range are clampled. The RGB values of the displayed volume are multiplied by the corresponding dimension index value from the modulation volume.
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7dc7b2a3 by John Harwell at 2024-09-09T15:19:46-05:00
Label Hierarchy: Include the hierarchy containing the labels in file information. Also, in LabelSelectionItem constructor, only create a pixmap containing the color for the label if in a GUI application (wb_view). Creating a pixmap in a non-gui application (wb_command) caused a crash.
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30c3d4c5 by John Harwell at 2024-09-09T17:00:42-05:00
Label Hierarchy: Fixed label coloring for labels in the hierarchy that contained child elements (voxels were not set).
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05e23be4 by John Harwell at 2024-09-11T12:03:22-05:00
Label Hierarchy: Add context menu for right clicking label names in features toolbox label hierarchy but not yet implemented.
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60363154 by John Harwell at 2024-09-11T14:34:12-05:00
LabelHierarchy: When a checked status is changed in the hierarchy GUI, synchronize the selections with the List view of the labels.
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6bce8026 by John Harwell at 2024-09-11T15:55:15-05:00
Label Hierarchy: For items in the hierarchy that map to a label AND have child labels, allow their checked status to be independent of the children's checked status. Why: The user may want the parent label on but all children off or the parent label off and all children on.
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762fe7f0 by John Harwell at 2024-09-13T17:39:47-05:00
Added operator less than to Vector3D for sorting
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9340e6ca by John Harwell at 2024-09-13T17:50:03-05:00
Add CaretMappableDataFileClusterFinder for finding clusters in data files. Currently it finds label clusters in a volume file. At this time, the clusters are printed to file information for a volume label file.
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b0d6e659 by John Harwell at 2024-09-17T14:52:18-05:00
Label Hierarchy: (1) Allow user to right click label names in the Label Hierarchy (in Features Toolbox). When right clicked, a menu is displayed that lists all the center-of-gravity for disjoint clusters that exist for the label. If an item is selected from the menu, the volume crosshairs move to the center-of-gravity for the label. (2) Disabled labels in the label hierarchy if either: (a) The name from the hierarchy does not correspond to a label in the label table; or (b) the cluster finder found that the label name is not used by any voxels.
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c501c5ed by John Harwell at 2024-09-17T16:00:34-05:00
Label Hierarchy: Fix recreation of label hierarchy if a volume file is reloaded. Add info that volume file will need to be reloaded if there is voxel editing and a new label is added.
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ea1a4495 by John Harwell at 2024-09-18T10:54:10-05:00
Fixed bug in neighbor finder that incorrectly marked voxels as searched
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0cc042e8 by John Harwell at 2024-09-18T11:02:29-05:00
Label Hiearchy: For Labels that have children, compute center-of-gravity from childen, and in Label Hierarchy in Features toolbox, right-click menu now has item to move crosshairs to this center of gravity.
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fafa0d65 by John Harwell at 2024-09-18T11:46:06-05:00
Label Hierarchy: Improvements for menu item that goes to center of gravity of children.
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da1f8e46 by John Harwell at 2024-09-18T14:38:05-05:00
Label Hierarchy: Add a Find capability that allows users to enter text and find matching name(s) in the label hierarchy. Matching item in hierarchy is scrolled to.
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240168c4 by John Harwell at 2024-09-18T16:03:21-05:00
Label Hierarchy: Add the ID from the ontology file as 'Ontology ID' to the LabelSelectionItem. Show this ID in the tooltip.
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b804fb57 by John Harwell at 2024-09-19T08:57:58-05:00
Label Hieararchy: Correct problem with scroll area for Label Widget.
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b2985e4a by John Harwell at 2024-09-19T09:16:44-05:00
Label Hierarchy: Add tooltips to buttons (expand, collapse, etc).
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1aca1efa by John Harwell at 2024-09-19T09:37:24-05:00
Correct problem with size of orginal label list widget caused by changes to container it shares with the label hierarchy widget.
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359eb252 by John Harwell at 2024-09-19T11:02:24-05:00
Fixed compilation errors on Linux.
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e2c82862 by John Harwell at 2024-09-19T11:40:09-05:00
Fixed compilation warnings from Linux.
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5278899b by John Harwell at 2024-09-19T15:07:24-05:00
Add support for Hippocampus in surface view.
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58ebcba5 by Tim Coalson at 2024-09-19T18:04:19-05:00
add normalization mode to -cifti-palette
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341ef564 by Tim Coalson at 2024-09-19T19:04:30-05:00
normalization mode for metric and volume palette commands
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7c543cad by John Harwell at 2024-09-25T09:41:27-05:00
For Surface Display, include selections for all structures but always list at the top (if available) R/L cortex, cerebellum, and R/L hippocampus.
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659e2f1c by John Harwell at 2024-09-25T09:41:27-05:00
Hippocampus Montage: initial implementation of a surface montage for hippocampi.
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4226684e by John Harwell at 2024-09-25T09:41:27-05:00
Label Hierarchy: Continuing revision of label clustering but still more work needed.
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7d892b90 by John Harwell at 2024-09-25T09:41:27-05:00
Enable copying the currently loaded row from a PCONN file into a new PSCALAR file.
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2c43a332 by John Harwell at 2024-09-25T09:41:27-05:00
Label Hierarchy: Fixed restoration of scenes for label list view for scenes created before label hiearchy was added.
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4fcad86c by John Harwell at 2024-09-26T13:42:07-05:00
Label Hierarchy: Revised creation of center of gravity clusters for Label Selections in the Features Toolbox and summation of center-of-gravity into parent labels.
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8c893aa8 by John Harwell at 2024-09-26T14:06:38-05:00
A small revision in LabelSelectionItem.
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814121d1 by Tim Coalson at 2024-09-26T19:27:09-05:00
copy palette from input in -cifti-create-dense-*
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cec52f4b by John Harwell at 2024-09-27T14:51:03-05:00
Label Hierarchy: Add an Info button to display to info about the selected label or go to the label's center(s) of gravity.
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8cfcbba2 by John Harwell at 2024-09-27T14:51:03-05:00
Label Hierarchy: If label volume file is reloaded, clear the clusters.
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1a279e23 by Yaroslav Halchenko at 2024-09-27T17:57:23-04:00
Set -DWORKBENCH_USE_QT5_QOPENGL_WIDGET:BOOL=ON to avoid rendered window blinking (see https://github.com/Washington-University/workbench/issues/77)
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8b157b1f by John Harwell at 2024-10-01T13:31:53-05:00
Fixed scale bar problems: (1) When a scale bar was restored from a scene, the scale bar's tab index may not have matched that tab containing the scale bar resulting in the scale bar not being drawn. (2) Scale bars were not implemented for Histology Display and now they are.
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f03f3962 by John Harwell at 2024-10-01T15:40:01-05:00
The scale bar thickness was not saved to scenes and this has been corrected.
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b4b9cf17 by Tim Coalson at 2024-10-11T00:37:08-05:00
add support for ordered extra info values in hierarchy (qjson is sorting them, though)
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4fa72f1e by John Harwell at 2024-10-14T10:16:42-05:00
Add additional information about set-cookie response to BALSA error message "Login was successful but BALSA failed to provide a Session ID".
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344ede9a by Chris Markiewicz at 2024-10-15T16:59:21-05:00
Fix unsafe narrowing
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601d9953 by Chris Markiewicz at 2024-10-15T17:03:40-05:00
Import cstdint into libCZI.h
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150de12f by Tim Coalson at 2024-10-15T17:38:41-05:00
temporarily reset master to bugfix branch for build infra reasons
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8b171504 by Tim Coalson at 2024-10-15T18:14:34-05:00
Revert "temporarily reset master to bugfix branch for build infra reasons"
This reverts commit 150de12f4f4b94b39bec6d9133ad2e7019d2d3ef.
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4a37b314 by Tim Coalson at 2024-10-15T18:16:26-05:00
update version
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802344b9 by John Harwell at 2024-10-16T16:01:15-05:00
Fixed foci drawn on all histology slabs (line for testing drawing was mistakenly left in code long ago).
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aeeecdb6 by John Harwell at 2024-10-16T16:16:52-05:00
Fixed foci being drawn behind volume surface outline on MPR volulme slices (Fix is draw foci after volume surface outline).
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4f99e752 by John Harwell at 2024-10-16T17:13:57-05:00
For a flat surface foci drawing with "Paste onto Surface" enabled for foci, raise the foci above the surface (Z=1).
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6c972a3d by Yaroslav Halchenko at 2024-10-17T11:39:23-04:00
Merge tag 'v2.0.1' into releases
v2.0.1
* tag 'v2.0.1': (73 commits)
temporarily reset master to bugfix branch for build infra reasons
Import cstdint into libCZI.h
Fix unsafe narrowing
Add additional information about set-cookie response to BALSA error message "Login was successful but BALSA failed to provide a Session ID".
add support for ordered extra info values in hierarchy (qjson is sorting them, though)
The scale bar thickness was not saved to scenes and this has been corrected.
Fixed scale bar problems: (1) When a scale bar was restored from a scene, the scale bar's tab index may not have matched that tab containing the scale bar resulting in the scale bar not being drawn. (2) Scale bars were not implemented for Histology Display and now they are.
Label Hierarchy: If label volume file is reloaded, clear the clusters.
Label Hierarchy: Add an Info button to display to info about the selected label or go to the label's center(s) of gravity.
copy palette from input in -cifti-create-dense-*
A small revision in LabelSelectionItem.
Label Hierarchy: Revised creation of center of gravity clusters for Label Selections in the Features Toolbox and summation of center-of-gravity into parent labels.
Label Hierarchy: Fixed restoration of scenes for label list view for scenes created before label hiearchy was added.
Enable copying the currently loaded row from a PCONN file into a new PSCALAR file.
Label Hierarchy: Continuing revision of label clustering but still more work needed.
Hippocampus Montage: initial implementation of a surface montage for hippocampi.
For Surface Display, include selections for all structures but always list at the top (if available) R/L cortex, cerebellum, and R/L hippocampus.
normalization mode for metric and volume palette commands
add normalization mode to -cifti-palette
Add support for Hippocampus in surface view.
...
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e925bbf2 by Yaroslav Halchenko at 2024-10-17T11:40:04-04:00
Merge branch 'releases' into debian
* releases: (73 commits)
temporarily reset master to bugfix branch for build infra reasons
Import cstdint into libCZI.h
Fix unsafe narrowing
Add additional information about set-cookie response to BALSA error message "Login was successful but BALSA failed to provide a Session ID".
add support for ordered extra info values in hierarchy (qjson is sorting them, though)
The scale bar thickness was not saved to scenes and this has been corrected.
Fixed scale bar problems: (1) When a scale bar was restored from a scene, the scale bar's tab index may not have matched that tab containing the scale bar resulting in the scale bar not being drawn. (2) Scale bars were not implemented for Histology Display and now they are.
Label Hierarchy: If label volume file is reloaded, clear the clusters.
Label Hierarchy: Add an Info button to display to info about the selected label or go to the label's center(s) of gravity.
copy palette from input in -cifti-create-dense-*
A small revision in LabelSelectionItem.
Label Hierarchy: Revised creation of center of gravity clusters for Label Selections in the Features Toolbox and summation of center-of-gravity into parent labels.
Label Hierarchy: Fixed restoration of scenes for label list view for scenes created before label hiearchy was added.
Enable copying the currently loaded row from a PCONN file into a new PSCALAR file.
Label Hierarchy: Continuing revision of label clustering but still more work needed.
Hippocampus Montage: initial implementation of a surface montage for hippocampi.
For Surface Display, include selections for all structures but always list at the top (if available) R/L cortex, cerebellum, and R/L hippocampus.
normalization mode for metric and volume palette commands
add normalization mode to -cifti-palette
Add support for Hippocampus in surface view.
...
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5beaecda by Yaroslav Halchenko at 2024-10-17T11:58:46-04:00
changelog
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74c0d289 by John Harwell at 2024-10-17T13:51:43-05:00
Fixed drawing of foci as spheres on histology slices. Problem was that near and far planes of orthographic projection were to small and clipped the spheres.
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2d1560e9 by John Harwell at 2024-10-17T15:20:37-05:00
Add a new focus shape DISKS that draws foci as disks (flat, filled, circles with lighting off).
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c85db93b by Tim Coalson at 2024-10-18T17:34:48-05:00
reword readme given that qt6 is supported
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98be91d4 by Tim Coalson at 2024-10-28T17:40:42-05:00
fix use-after-free from vector reallocations, disable cluster finding in -file-information due to potential large memory use
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ae3bd5c5 by John Harwell at 2024-10-29T10:44:55-05:00
Fixed crash if focus projected with barycentric projection with a weight equal to zero (XYZ is at a vertex).
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77c31b64 by John Harwell at 2024-10-29T10:44:55-05:00
Implemented move foci mode. Currently, the user can drag a focus to a new location on surfaces, histology slices, and volume slices. Fixed issue in SurfaceProjector for Node projection that may have moved a focus to the wrong node but in the same triangle.
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0d5319ae by John Harwell at 2024-10-29T10:44:55-05:00
Disable lighting for symbols drawn as disks (filled circles).
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716e7c79 by John Harwell at 2024-10-29T10:44:55-05:00
Improve move foci mode for surface foci so that foci no longer only move to a vertex. Now, triangle identification is used that allows move a focus to anywhere in a triangle, not just a vertex of the triangle.
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50027670 by John Harwell at 2024-10-29T10:44:55-05:00
Improve foci creation on surface. Previously, when the mouse was clicked on a surface, the focus was created at the nearest surface vertex. Now, the focus is created where the mouse is clicked by deriving the XYZ location in the triangle in which the mouse is clicked.
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7024fce1 by John Harwell at 2024-10-29T10:44:55-05:00
When a focus is created on a cortical hemisphere and there is NOT an antomical surface loaded for the hemiphere, warn the user that the focus may be created at an incorrect stereotaxic coordinate. Dialog has a "Do not show again" checkbox.
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81290a5d by John Harwell at 2024-10-29T10:44:55-05:00
In Foci Mode, enable right-click menu so that user can select tab containing mouse while in tile tabs. Don't show Foci sub-menu in Foci Mode (it is intended for use in View mode).
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517b490f by John Harwell at 2024-10-29T10:44:55-05:00
For Upload to BALSA's progress dialog: Display all steps in the upload process followed by the time when the step started.
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ed563862 by John Harwell at 2024-10-29T10:44:55-05:00
Volume Modulation: When the value from the modulate volume is zero, and zeros are turned off for the palette, set the alpha to zero (transparent).
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40249efd by John Harwell at 2024-10-29T10:44:55-05:00
When uploading to BALSA, some of the operations (uploading the zip file, processing the upload) may take an amount of time longer that the BALSA login timeout. So, issue login a request before uploading the zip file and before requesting that BALSA process the uploaded data. This may fix a problem a user with a very large data set had where it appeared that the user's BALSA login timed out.
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33ba2504 by John Harwell at 2024-10-30T09:39:46-05:00
Reduce memory usage by cluster finder: Removed CaretObject as parent class of Cluster.
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4487b972 by John Harwell at 2024-10-30T11:09:45-05:00
If there is no CaretHierarichy available, do not create the hierarchical label selection model. This prevents calling the label cluster finder which can be a little slow for unusally large label volume files.
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7447b068 by Tim Coalson at 2024-10-31T16:53:39-05:00
improve -cifti-convert help text, add warning to detect probably-wrong conversions
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ea80d069 by John Harwell at 2024-11-11T12:06:30-06:00
Log at the info level, the time to create a new scene.
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f79e224d by John Harwell at 2024-11-11T13:31:48-06:00
In CaretMappableDataFile, when saving to a scene, improve performance of saving the threshold selections.
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f5d998e0 by John Harwell at 2024-11-11T13:35:13-06:00
Fixed text wrapping in dialog displayed when uploading to BALSA database is finished.
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e83fa54a by John Harwell at 2024-11-20T11:15:18-06:00
For chart axes, add a mode that allows displaying map names instead of numeric subdivisions along an axis.
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2fa521e0 by John Harwell at 2024-11-21T08:42:54-06:00
Fixed crash for Right Click Menu -> Show Charts for Vertices Inside Border. When comparing a line chart to see if it is already in displayed chart, it failed to verify the number of points were equal before comparing all points equal.
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30b03314 by Tim Coalson at 2024-12-02T21:05:17-06:00
remove "add abbreviation" option from volume hierarchy, some error checking
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d1962ad3 by Tim Coalson at 2024-12-02T21:05:49-06:00
improved comment
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3a967ca6 by Tim Coalson at 2024-12-02T21:16:10-06:00
make error message more precise
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a9d6b8a8 by Tim Coalson at 2024-12-02T21:35:42-06:00
fix bug while populating extraInfo
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6edbaddb by Tim Coalson at 2024-12-03T18:50:25-06:00
fix hierarchy XML reading, support non-array children/root in json
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fa05ba7f by Tim Coalson at 2024-12-03T19:09:24-06:00
note that hierarchy id member is defunct
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6dea6f2d by Tim Coalson at 2024-12-03T19:11:10-06:00
missing paren
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0683a7ed by John Harwell at 2024-12-04T10:03:11-06:00
Annotation Text Substitution: (1) allows placing text substitutions into "groups" to allows simultaneous usage of more than one annotation text substitution file; (2) Support older scenes.
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01a1d999 by John Harwell at 2024-12-04T10:03:11-06:00
Display a fixed number (10) of annotation substitutions in the features toolbox.
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9ccbcc66 by John Harwell at 2024-12-05T11:13:06-06:00
Update Volume Label Hierarchy GUI for updates to the hiearachy that include the ability to select different fields to display in the Features Toolbox's label hierarchy.
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b89e1ce8 by John Harwell at 2024-12-05T15:20:02-06:00
Fixed warning caused by improper setup of macros on Annotation text substitution GUI
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d5d97da7 by John Harwell at 2024-12-06T10:35:33-06:00
Improve performance of label coloring. Instead of coloring each brainordinate by looking up its label and getting the color, put label colors into a map indexed by label index, and then apply label colors to brainordinates. Reduces lookup of labels a significant amount. Also use OpenMP in part of coloring. Reduces time by about 80%.
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1cd35308 by John Harwell at 2024-12-06T11:37:33-06:00
Fix glitches in label hierarchy so that fields displayed in Features Toolbox are correct after loading a scene; Fixed expansion status when all items are collapsed when loading a scene.
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3362f675 by John Harwell at 2024-12-06T11:43:54-06:00
Fix compilation warnings.
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cf4b91dd by John Harwell at 2024-12-06T11:53:28-06:00
Fixed crash when yoked annotation text substitution files have a different number of rows and the selected row is out of range in one of the yoked files.
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f35f4524 by John Harwell at 2024-12-06T12:19:49-06:00
Fix compilation error on systems using Qt 5.
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549c40de by John Harwell at 2024-12-06T12:41:27-06:00
Fix another Qt5 issue.
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6752e05b by John Harwell at 2024-12-09T14:52:45-06:00
Correct Info button in Features Toolbox Label Hierarchy by including alternative names in info output.
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4782097b by John Harwell at 2024-12-09T14:54:31-06:00
Listen for an annotation toolbar update event in AnnotationTextSubstitutionLayerSet so that text substitution identifiers get updated after a text annotation is added or has text edited.
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5e4191bf by John Harwell at 2024-12-09T14:55:22-06:00
Starting on revised metadata system for samples (polyhedron annotations).
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1ffa4a3b by John Harwell at 2024-12-09T15:19:12-06:00
Added new StructureEnum's: HIPPOCAMPUS_DENTATE_LEFT and HIPPOCAMPUS_DENTATE_RIGHT.
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9a6776dd by John Harwell at 2024-12-09T15:28:56-06:00
Update surface and montage models to recognize HIPPOCAMPUS_DENTATE_LEFT and HIPPOCAMPUS_DENTATE_RIGHT.
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03a7bb5f by Tim Coalson at 2024-12-16T15:25:31-06:00
reorder hippocampus dentate
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a60a8f6b by John Harwell at 2024-12-17T10:05:00-06:00
Add controls and settings for image capture background alpha. The GUI controls are disabled as this functionality still needs to be implemented.
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b8bf6e1f by John Harwell at 2024-12-17T10:05:00-06:00
Add FunctionResult, a small class modeled after Tensorstore's Result template. This class can be returned from a function and contains a status and an error message. FunctionResultValue extends FunctionResult and is a template that allows adding any class in addition to the status and the error message. There are also typedefs for some commonly used data types.
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62878d69 by John Harwell at 2024-12-17T10:05:00-06:00
Initial implementation of support for reading OME-ZARR files using the Tensorstore library. Support for OME-ZARR is off by default but can be enabled by configurating the source with WORKBENCH_USE_TENSORSTORE set to true when running CMake. When WORKBENCH_USE_TENSORSTORE is true, the Tensorstore library and all dependent libraries are pulled into the build directory in a sub-directory named "_deps". Since an OME-ZARR file is actually a directory, an "Open OME-ZARR Directory" menu item has been added to the File Menu. To do: (1) Be able to select an OME-ZARR directory in the Open Data File dialog; (2) be able to read from a ZIP file; (3) read as a volume file; and (4) move the Tensorstore out of Workbench (updated files may get pulled while building and if there are errors in the new files they cause the Workbench build to fail. Having Tensorstore in the build slows down the builds and the code editor).
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826e528c by John Harwell at 2024-12-17T10:05:00-06:00
Replace usage of TensorStore with Z5 for reading OME-ZARR files. Z5 is MUCH smaller than and seems to be easier to use.
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80e88966 by John Harwell at 2024-12-17T10:05:00-06:00
Continuing adding support for OME-ZARR files including converting an OME-ZARR file to an RGBA volume file and viewing as volume slices.
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6394d45c by John Harwell at 2024-12-17T10:05:00-06:00
For OME-ZARR file show dimensions of selected pyramid level in Media Overlays settings toolbutton pop-up menu.
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bbc19ddb by John Harwell at 2024-12-17T10:05:00-06:00
The Z5 library accepts a "number of threads" when reading zarr data and uses the c++ <thread> class. Use std::thread::hardware_concurrency() for the number of threads (maximum number of threads supported by computer).
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93a238b7 by John Harwell at 2024-12-17T10:05:00-06:00
Change way a VolumeFile containing all slices from an OmeZarrImageFile is handled and accessed.
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a1d627dc by John Harwell at 2024-12-17T10:05:00-06:00
Correction in Brain::getReloadableDataFiles(), do not include a parcel dynamic file.
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df32853f by John Harwell at 2024-12-17T10:05:00-06:00
Clean up a few OME ZARR items.
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a24b636a by John Harwell at 2024-12-17T10:05:00-06:00
Fix for crash during identification of a smaller (height/width) pyramid level OME-ZARR image.
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6ba3d1a4 by John Harwell at 2024-12-17T10:05:00-06:00
Added RGB/RGBA volumes to formatted identification text.
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98cd8428 by John Harwell at 2024-12-17T10:05:00-06:00
When exporting an OME-ZARR image file to a volume file, use the pyrmide level with the best resolution that OpenGL can draw as a volume file.
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b429013a by John Harwell at 2024-12-17T10:05:00-06:00
Correct RGBA values from OmeZarr image identification.
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fa1e0af4 by John Harwell at 2024-12-17T10:05:00-06:00
Fixed crash in Feature Toolbox's Annotation Substitutions GUI. QSpinBox has only one method to set its value and when the value changes it issues a signal. This signal needs to be blocked when setting the value in the GUI and the failure to do so caused the crash. Almost all other Qt GUI widgets have mutiple methods for setting the value including one or more that do not issue a signal when the value changes. Also fixed two bugs: (1) the Annotation Substitution components now synchronize if multiple windows are open; (2) On the Annotations Substitution GUI, push all widgets to the top when there is extra available vertical space.
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a6781f41 by John Harwell at 2024-12-17T10:05:00-06:00
In label hierarchy GUI, if the field (name) selected for display is empty, use the label name.
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46c47d4a by Tim Coalson at 2024-12-17T23:08:26-06:00
fix -cifti-convert -from-text warnings about converting exact zeros
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25f2de47 by Tim Coalson at 2024-12-17T23:10:51-06:00
add arbitrary surface support to -cifti-smoothing
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4e28b6db by John Harwell at 2024-12-19T14:13:30-06:00
Fixed two bug with Annotation Text Substitution and Yoking: (1) Overlay indices in the GUI are 1..N and text substitution file row indices are now 1..N (were 0..N-1). This fixes yoking overlay to text substitution; (2) Surface colors are now updated when text substitution is yoked (fixes surface colors failing to update when yoking causes overlay index to change).
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b67c9e97 by John Harwell at 2024-12-19T15:10:55-06:00
Another fix for ensuring text substituions update with yoking.
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1cdb2a36 by Tim Coalson at 2024-12-19T20:30:43-06:00
make valgrind happy with gifti base64 gzip decoding, possibly fix debug builds reporting already-destroyed objects
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6c4e7ba3 by Tim Coalson at 2024-12-19T23:33:54-06:00
reorder StructureEnum::Enum to match getAll, add repeatable generic surface options to a few initial cifti commands
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15c49160 by John Harwell at 2024-12-20T13:12:16-06:00
Correct name for hippocampus's montage overlay set.
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8d050891 by John Harwell at 2024-12-20T13:12:16-06:00
Continuing significant revision to Edit Samples Dialog and unerlying functionality.
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095b066a by John Harwell at 2024-12-20T13:12:16-06:00
Cleanup and improvements of metadata for annotations.
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26004c66 by John Harwell at 2024-12-20T13:12:16-06:00
Added "Metadata" button to Samples Toolbar. When clicked, it displays a menu listing all samples in memory by name and number. If a sample is selected its metadata is loaded in the samples metadata editor. Also fixed usage of require metadata checkbox for editing metadata.
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7d416928 by John Harwell at 2024-12-20T13:12:16-06:00
For Edit Metadata through Samples Toolbar, show "no-num" or "no-name" when the sample number or names is invalid.
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40bb6285 by John Harwell at 2024-12-20T14:20:10-06:00
Fix Qt5 and Qt6 incompatibilities.
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5dc3b1a1 by Tim Coalson at 2024-12-20T22:19:32-06:00
sync order of ALL_WHITE_MATTER, add generic surface to -cifti-create-label, help text improvements
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f3218085 by Tim Coalson at 2024-12-23T20:14:23-06:00
mark left/right surfaces as "cortical" in help info
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e73a86af by John Harwell at 2025-01-03T12:29:20-06:00
Fix initialization of hippocampus surface montage.
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6597147a by John Harwell at 2025-01-03T12:29:20-06:00
Added surface montage for flat hippocamus.
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df114670 by John Harwell at 2025-01-03T12:29:20-06:00
On Overlay and Map Settings' Palette Tab, controls to set thresholding (high, low, etc) were not enabled when the the Threshold Type was set to File.
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b4d99517 by John Harwell at 2025-01-03T12:29:20-06:00
Added new SecondarySurfaceTypeEnum's INNER and OUTER. Update initialization of Volume Surface Outlines to select INNER and OUTER hippocampus surfaces with LIME ane BLUE coloring.
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3c4b0db7 by John Harwell at 2025-01-03T12:29:20-06:00
Added hippocampus and dentate hippocampus to ALL view.
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eb5ddbe1 by John Harwell at 2025-01-03T12:29:20-06:00
Add "H" and "D" to surface montage checkboxes for hippocampus and dentate hippocampus surface selection rows.
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f3b3c8b5 by John Harwell at 2025-01-03T12:29:20-06:00
Fixed memory leaks in hippocampus surface selectors in ALL view toolbar.
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d6883005 by John Harwell at 2025-01-03T12:29:20-06:00
Fixed crash in Label Hierarchy. When a cluters that spanned right and left was split into left and right, it was not properly merged with any existing, disjoint right and left clusters.
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e1b65e35 by Tim Coalson at 2025-01-06T21:26:34-06:00
add -match-surface-area option to -surface-distortion
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d5749553 by John Harwell at 2025-01-08T11:23:54-06:00
Revise CaretObject instance's call stack, used to track down memory leaks, that is enabled when compiled in debug mode. The call stack was a fixed size, 1024, and has been changed to a vector size 512 that is resized and shrinked to fit the call stack's size. This results in memory usage dropping from 19.x GB to 3.x GB.
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125c2156 by John Harwell at 2025-01-08T11:23:54-06:00
(1) Default both hippocampus and dentate surfaces on in anatomical and flat map montages; (2) Change "Fit To" mode for hippocampus and dentate flat maps so that they are the same width in the viewer; (3) Fix incorrectly listing dentate left surfaces in controls for selecting dentate right surfaces; (4) Enable hippocampus layers in overlays for ALL view; (5) In Toolbar for Hippocampus Flat Montage, add checkboxes for hippo left/right and dentate left/right in popup for selecting the surfaces.
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31c8bdcd by John Harwell at 2025-01-08T11:23:54-06:00
Volume Surface Outlines: Default colors for Hippocampus/Dentate Inner and Outer surfaces were swapped and have been corrected; When default volume surfaces outlines are initialized after loading a spec file, ensure that the number of displayed outlines supports all of the anatomical surfaces.
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5542b34d by John Harwell at 2025-01-08T11:23:54-06:00
Revise initialization of overlays after loading a spec file. This is needed to support dentate/hippocampus viewing and for ALL view which may contain many structures.
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6c271258 by John Harwell at 2025-01-08T11:23:54-06:00
Removed old code for initializing overlays.
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addc6efa by John Harwell at 2025-01-08T13:48:38-06:00
Correct spelling of "Collapse" in the label selector in Features Toolbox.
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2b8cccf2 by John Harwell at 2025-01-08T14:14:31-06:00
Correct missing tooltips on hippocampus whole brain surface selection checkboxes that cause a WARNING level message by Macro System.
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aca50231 by John Harwell at 2025-01-09T13:57:37-06:00
In Surface Montage Flat Hippocampus View and when both Hippocampus and Dentate surfaces are displayed: When drawing the Dentate surface, use the Hippocampus surface for setting the orthographic projection so that the Dentate and Hippocampus surfaces are the same width when drawn.
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1d8364c0 by Tim Coalson at 2025-01-10T22:56:05-06:00
add hierarchy support to -metric- and -cifti-label-import
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dba9e383 by Tim Coalson at 2025-01-11T00:24:43-06:00
fix bugs in cifti label import hierarchy (passed through XMLOld), add hierarchy reading support to file IO
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aaf57bf7 by Tim Coalson at 2025-01-11T00:40:48-06:00
propagate hierarchy through -volume-label-to-surface-mapping
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3714cd40 by John Harwell at 2025-01-14T11:37:09-06:00
In hippocampus flat maps surface montage, shift dentate flat maps in second row up so they are closer to the hippocampus flat maps.
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fb9184da by John Harwell at 2025-01-14T11:37:09-06:00
In sample metadata, correct spelling of Slab polyhedron (was "Slap").
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2e9e9d65 by John Harwell at 2025-01-14T11:37:09-06:00
Features Toolbox Label Hierarchy: When a label is right-clicked, include the "Info..." option in the pop-up menu.
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0df785b1 by John Harwell at 2025-01-14T11:37:09-06:00
Add "Move" and "Resize" buttons to sample's editing toolbar. These modes allow the user to move the end of a polyhedron or to shrink/expand the end of the polyhedron.
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9e8a2aa1 by Tim Coalson at 2025-01-14T20:39:01-06:00
add generic surface option to -cifti-gradient
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bbde2d71 by John Harwell at 2025-01-17T09:43:46-06:00
Do not load dynamic connectivity data (from dynamic version of data-series, metric, and volume files) if the file is NOT enabled as a layer. When the enabled status transitions from enabled to disabled, clear any loaded data.
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1a1b05b1 by John Harwell at 2025-01-17T09:43:46-06:00
In Overlay Toolbox's Connectivity Tab, the Layer checkboxes are disabled for normal connectivity files (dense, parcel, etc) since they are normal layer files. Even though the these checkboxes are disabled, set them as checked to indicate data will be loaded for these files.
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0fe60952 by John Harwell at 2025-01-17T09:43:46-06:00
Samples Metadata: Add fields for "Border ID" and "Focus ID". When creating a new sample copy border and foci metadata (except names) from the most recently created sample in the current session.
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9d146fa2 by John Harwell at 2025-01-17T09:43:46-06:00
Fix Thresholding on Palette Mapping Dialog: (1) Added support for Parcel mapped files to thresholding (was only allowing brainordinate mapped files); (2) Fixed use of thresholding during color that was incorrectly using the thresholded file for threshold settings and has been correct to use the file that is being colored.
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c40d03b1 by John Harwell at 2025-01-17T09:43:46-06:00
For volume surface outlines, draw using a line strip instead of a line loop. A line loop connects the first and last vertices whereas a line strip does not. We do not want a loop because is caues open volume surface outline, such as with a hippocampus, to be closed lines.
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ff716532 by John Harwell at 2025-01-17T09:43:46-06:00
On Map Settings Dialog, fixed blue background in Histogram Plot that shows region(s) not being drawn due to threshold settings.
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97ae0b6a by John Harwell at 2025-01-17T15:22:10-06:00
In Features Toolbox, enable Samples tab anytime samles are loaded. Not just when a Volume tab is selected with samples loaded.
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a541d2b2 by John Harwell at 2025-01-21T11:28:14-06:00
Added thresholding support to parcel files viewed as matrices.
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876e1a85 by John Harwell at 2025-01-22T09:53:37-06:00
Default High DPI MODE to AUTO (was off). This is needed for Mac Retinta Displays. If not set correctly, the graphics are drawn in only the bottom left corner of the graphics region.
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9eed4d1f by John Harwell at 2025-01-22T15:12:52-06:00
On Overlay and Map Settings Dialog's Palette tab: In the histogram with thresholding enabled, a blue background shows ranges of data not displayed due to thresholding. Only display this blue background when the Thresholding Source is Self; do NOT display when the source is File.
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64003906 by John Harwell at 2025-01-23T10:03:51-06:00
Starting on adding additional controls in Features Toolbox. All On, Off, Collapse, and Expand are functioning. Find controls have been added but are non-functional and disabled.
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4319646b by John Harwell at 2025-01-23T11:17:35-06:00
Fixed performance issue when using Overlay and Map Settings Dialog. For thresholding, only other files that have a compatible mapping can be used. This test for compatibility was performed each time the dialog was updated. With Parcel type files, the compatibility test requires verifying that the other file maps to the same parcels. When there are many files (50) this testing takes a very long time. Now, for each mappable file, the compatibly mapped status for files is cached so that the test with another file is perfomed only one time. This assumes that a file's mapping does not change after the file has been loaded.
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c59d83ce by John Harwell at 2025-01-23T11:41:37-06:00
Fix compilation errors on Linux and Windows.
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4e0776f1 by John Harwell at 2025-01-24T15:40:26-06:00
Disable use of OpenMP when saving a scene. A recent change was made to speed up finding compatible files (files that have the same brainordinate or parcel mapping) for thresholding. This was done by caching the results of finding compatible files in a map which is not thread safe and resulted in a crash. Removing use of OpenMP prevents this crash and there is not a noticable change in performance. While an attempt was made to prevent concurrent access to the map, it resulted in deadlock. This issue may be revisited when there is more time as this fix is critically needed.
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c2b73e89 by John Harwell at 2025-02-05T09:12:51-06:00
Implement Find controls in Features Toolbox.
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6e0a73bd by John Harwell at 2025-02-05T09:12:51-06:00
Add All On, Off, Expand, Collapse, Find, Next, and Find Text Box controls to Annotation and Sample controls in Features Toolbox.
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18fbb78d by John Harwell at 2025-02-05T09:12:51-06:00
Change metadata in Annotation from a unique pointer to a shared pointer. This will allow a desired sample polyhedron to share its metadata with the correspoinding actual sample polyhedron
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d6f41625 by John Harwell at 2025-02-05T09:12:51-06:00
Added AnnotationPolyhedronTypeEnum that identifies a Polyhedron (Sample) as either DESIRED or ACTUAL. Update Samples File (Annotation File) to support the polyhedron type. Modify current drawing to set new samples as DESIRED.
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3bce8a8c by John Harwell at 2025-02-05T09:12:51-06:00
Fixed recent update for On and Off buttons in Features Toolbox for Annotations and Samples. The button should only affect selected items, not all items.
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b0c31b8f by John Harwell at 2025-02-05T09:12:51-06:00
Samples: Revised Samples Toolbar to allow insertion of Desired and Actual Samples.
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3c5e6a3f by John Harwell at 2025-02-05T09:12:51-06:00
Remove Actual / Desired Location from Samples Metadata since the Actual and Desired Samples are two separate polyhedrons.
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4997e401 by John Harwell at 2025-02-05T09:12:51-06:00
Add Actual and Desired Groups to Samples Files. For previously created Samples Files (before actual and desired), add all samples to the desired group when reading the file.
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b458ea87 by John Harwell at 2025-02-05T09:12:51-06:00
Share metadata between corresonding Desired and Actual Samples.
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af667d8b by John Harwell at 2025-02-05T09:12:51-06:00
Revised sharing of metadata by desired and actual samples. Store a unique identifier in the two samples and when the metadata is requested for the actual sample, use a message to get the metadata from the desired sample. Also, do not allow creating more than one actual sample that is linked to a desired sample.
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9b57d065 by John Harwell at 2025-02-05T09:12:51-06:00
Consolidate code for deleting annotations from Edit Menu, Toolbar trash can button, right-click menu, and Delete key.
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d11767d9 by John Harwell at 2025-02-05T09:12:51-06:00
Add a static method to WuQMessgeBoxTwo to create a mask from one or more of the Standard Buttons
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8b09f4bc by John Harwell at 2025-02-05T09:12:51-06:00
Updated deletion of Sample Polyhedrons now that there are two types, Desired and Actual, and a pair Desired and Actual Sample Polyhedrons may be linked to each other. If the user attempts to delete an Actual Sample and the linked Desired Sample is not selected, warn user and allow user to delete both or just the Actual Sample. If the user attempts to delete a Desired Sample and there is a linked Actual Sample, warn user that the linked Actual Sample will also be deleted. This logic also supports warnings for both conditions.
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791afe1e by John Harwell at 2025-02-05T09:12:52-06:00
When drawing sample polyhedrons, draw actual samples after desired samples so that the actual samples are on top of the desired samples. For Sample Information, show sample type (actual or desired).
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a3e7ce83 by John Harwell at 2025-02-05T09:12:52-06:00
When reading a samples file, do not set the linked identifier if it is empty as it will overwrite the existing linked identifer that is initialized when an older sample (before linked identifiers were addded) is read.
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18b48104 by John Harwell at 2025-02-05T09:12:52-06:00
When creating an Actual Sample by copying a Desired Sample, select the newly created Actual Sample for editing.
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c281d8f0 by John Harwell at 2025-02-05T09:48:26-06:00
Fix compiler errors on Linux an Window caused by different versions of Qt than on macOS.
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74c6fa14 by John Harwell at 2025-02-05T10:40:02-06:00
QTreeWidget::indexFromItem() is public in Qt6 and protected in Qt5. Add a method getIndexFromItem() to WuQTreeWidget that calls indexFromItem() to get around this public/protected problem.
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e1d69aa8 by John Harwell at 2025-02-05T10:41:36-06:00
Use WuQTreeWidget (derived from QTreeWidget) that fixes a problem with QTreeWidget::indexFromItem() being public in Qt6 and protected in Qt5.
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c8315cf2 by John Harwell at 2025-02-05T11:03:13-06:00
Fix another QTreeWidget::indexFromItem Qt5/Qt6 issue.
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04eda916 by John Harwell at 2025-02-05T14:55:01-06:00
Fix layout problem in Features Toolbox Samples Page. If all items collapsed, a very short widget was displayed in the middle vertically.
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e148b174 by John Harwell at 2025-02-06T11:26:36-06:00
Improve Title of Sample Metadata Dialog when creating new samples with unique title for new desired sample, adding actual sample to desired sample, and an unlinked actual sample. When editing metadata, indicate actual or desired in title.
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6ea46f9e by John Harwell at 2025-02-06T15:13:58-06:00
On Samples Metadata Dialog's Border/Foci tab, there are now two borders and two foci. Adding additional border/foci on this page can be changed by alterning the number of border/foci within AnnotationsSampleMetaData.h.
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73be0421 by John Harwell at 2025-02-07T10:29:55-06:00
Append an A (for actual) or D (for Desired) to name of Sample Polyhedron.
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edd1f14f by John Harwell at 2025-02-07T11:07:57-06:00
Correction for appending A or D to fix a warning caused by invalid character position while drawing new polyhedron.
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45de4eca by John Harwell at 2025-02-07T11:13:24-06:00
Fix width of separator lines on Borders/Foci tab of Samples Metadata dialog.
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e17329c3 by John Harwell at 2025-02-07T12:19:40-06:00
For Annotations and Edit Samples mode, add a "Select this Tab" to the top of the right-click menu so that one can make the tab containing the mouse the selected tab. This item is enabled only when tile tabs is enabled.
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1f8c32fa by John Harwell at 2025-02-07T16:18:05-06:00
Corrections for initializing dates for both actual and desired polyhedrons.
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4c281af4 by John Harwell at 2025-02-10T10:56:20-06:00
If user attempts to draw a new sample, display an error message if the selected tab is not a volume montage.
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234dd05e by John Harwell at 2025-02-10T11:29:51-06:00
Remove unused code from SamplesDrawingSettings.
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51333264 by John Harwell at 2025-02-10T16:35:12-06:00
Move SamplesDrawingSettings from BrowserTabContent (an instance for each tab) to BrowserWindowContent (one instance for each window). This fixes problems when the user draws a new sample in a tab that is different than the selected tab.
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2d750612 by John Harwell at 2025-02-10T16:59:33-06:00
Append ".D" for desired or ".A" for Actual to the Local Sample ID.
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23e9242f by John Harwell at 2025-02-11T08:59:23-06:00
Allow any tab selected when starting a new sample polyhedron.
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2583e192 by John Harwell at 2025-02-11T11:14:52-06:00
If a scene file is loaded via File Menu -> Open Data File, select the scene file in the scene dialog.
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c9ca9e34 by John Harwell at 2025-02-11T17:16:17-06:00
Added additional dialog for critical, warning, and information that show a message with only an Ok button.
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09da33d3 by John Harwell at 2025-02-11T17:17:50-06:00
Started adding a context sensitive (right-click) menu for the Samples Selection tab in the Features Toolbox. Currently, it supports displaying information or editing metadata for a single sample that is right-clicked.
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78b8c189 by John Harwell at 2025-02-12T11:23:54-06:00
In Toolbar's Edit Samples Insert New section's Metadata button's menu, show names of samples as <number>.[A|D].
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2f8c91da by John Harwell at 2025-02-12T16:38:49-06:00
Include annotations in annotation file information (note that samples file extends annotation file).
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e6af2a46 by John Harwell at 2025-02-12T17:03:19-06:00
Added File Information for the selected samples file to the Annotation Insert New widget in the toolbar.
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f94f2e78 by John Harwell at 2025-02-13T10:41:34-06:00
Improve formatting of polyhedron and samples file information by using HTML. Add file information to the "Metadata" button in the Samples Toolbar.
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4e4bb3bf by John Harwell at 2025-02-13T11:18:53-06:00
Fixed compilation error on Windows.
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e9886c58 by Tim Coalson at 2025-02-25T16:36:17-06:00
add dilate options to ribbon mapping
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301253cc by Tim Coalson at 2025-02-25T16:37:56-06:00
obey output datatype in a couple commands that write manually
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7b606619 by John Harwell at 2025-02-27T11:08:07-06:00
Added new dialog for editing border and foci files. It is available on the Data Menu.
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935fea2e by John Harwell at 2025-02-27T11:46:50-06:00
added tooltips to dialog for editing border and foci files.
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18db0537 by John Harwell at 2025-02-27T11:58:09-06:00
Add header include to fix compilation errors on Linux and Windows.
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5dc9977b by Tim Coalson at 2025-02-28T15:55:01-06:00
fix -file-information -only-number-of-maps to not read data values from dtseries
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a37cc173 by John Harwell at 2025-03-05T15:36:32-06:00
For polyhedron names: Text for 'name' is <sample name>.<sample number>.<A for actual or D for Desired> (eg Slab.3.D). Add checkboxes to control display of Name, Number and Actual/Desired in polyhedron name displayed in the graphics region to Samples page of Features Toolbox. Name displayed in information always displayes all components.
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3d8eb036 by John Harwell at 2025-03-05T15:36:32-06:00
For border and foci editing: Fixed class colors becoming invalid; make default sorting by class and then name; display two files in editor, side by side; warn if an item is copied and color in destination file color table is different.
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284623a0 by John Harwell at 2025-03-05T15:36:32-06:00
Fixed crash when identification filtering encountered an non-mappable file, specifically a CIFTI fiber orientation file (it should be ignored)
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bb3bd11a by John Harwell at 2025-03-05T15:36:32-06:00
Fixes for editing border and foci files. Started on editing of Annotations and Samples but disabled until further testing can be done.
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ddee9ec4 by John Harwell at 2025-03-05T15:36:32-06:00
Fix saving and restoring of scenes where there are files with the same filename but in different paths for border, foci, and volume file in Features Toolbox (enabling individual borders, foci, or volume labels). A path relative to the scene file is now used. Problem was noticed with logged message during scene restoration "WARNING: Scene class named "m_brains" contains more than one child named "density.nii.gz"".
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2beefacc by John Harwell at 2025-03-05T15:36:32-06:00
Fixed assertion failure in identification processing when a fiber orientation file is loaded.
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d796043f by John Harwell at 2025-03-05T16:25:59-06:00
Fix windows compilation error.
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60698d78 by John Harwell at 2025-03-05T17:13:08-06:00
Fixed crash when loads a CIFTI file row but still no data displayed.
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36be7527 by Chris Markiewicz at 2025-03-07T17:17:16-06:00
fix(build): Detect GL libraries for GuiQt (#89)
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e77f71ff by Tim Coalson at 2025-03-07T21:30:45-06:00
make -cifti-math convert output scalar maps in place of label maps, sanity checks
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4231412e by John Harwell at 2025-03-11T11:02:53-05:00
Fixes for editing of annotations, borders, and foci. Enable Annotation and Sample editing.
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36f70726 by John Harwell at 2025-03-11T11:02:53-05:00
Added background color for text annotations to the Font Widget in Annotations and Samples Editing. Previously, the fill color was used for text background. However, a text only background color is needed for Sample Names and the fill color applies to the entire annotation but we only want the background to apply to the text characters (and not the entire polygon). For text annotations, the text background color is used. For older scenes, the fill color for text annotations is now restored to the text background color.
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6acb9cb3 by John Harwell at 2025-03-11T11:02:53-05:00
In annotation toolbar, add "Edit" button for editing the text of a text annotation in a text editor dialog. Added ability to enter unicode characters in the text editor dialog with buttons for superscript 2 or 3 and a pop-up to enter other unicode characters by entering the hexadecimal code. Note: not all unicode characters are supported by FTGL.
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dfea1c7e by John Harwell at 2025-03-11T11:20:59-05:00
Fix compilation errors on Linux and Windows.
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0db044e1 by John Harwell at 2025-03-13T16:28:41-05:00
Added ability to color samples using the samples associated focis' name or class.
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19d1aa34 by John Harwell at 2025-03-13T17:00:13-05:00
Add insertion of unicode character for "less than or equal to", "greater than or equal to", and "not equal to" to the annontation text editor.
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4f7b5b67 by John Harwell at 2025-03-14T11:05:07-05:00
Add focus ID to foci.
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45c0ddae by John Harwell at 2025-03-17T15:17:23-05:00
Add focus id to identification
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96f9156e by John Harwell at 2025-03-17T15:43:09-05:00
Revise creation of DataFileEditorModel used for edting Annotations, Borders, Foci, and Samples. Use DataFileEditorModel for selection of foci and borders assigned to Sample metadata.
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21255a2a by John Harwell at 2025-03-18T10:38:17-05:00
For Sample Metadata, the Sample Name is now a required element.
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834eee6e by John Harwell at 2025-03-18T10:55:24-05:00
For sample metadata, when the first focus is selected and the focus has a non-empty Focus ID, copy the Focus ID to the Sample Number.
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3d16a273 by John Harwell at 2025-03-18T11:27:06-05:00
In Sample Metadata, Local sample ID is populated as: <Allen local name>.<Allen tissue type>.<Allen slab number>.<Hmba parcel Ding abbreviation>.<P or R>.Sample number. If a component is empty, it is substituted with ???.
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c854d705 by John Harwell at 2025-03-19T09:33:57-05:00
Samples types "Desired" and "Actual" were renamed to "Prospective" and "Retrospective". All code and comments were updated too.
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105cc655 by John Harwell at 2025-03-19T09:44:38-05:00
If no sample had been selected and a new sample was drawn, the text foreground and background colors were the same resulting in a white box. So, default the text background color to 'NONE'.
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a42b1cf3 by John Harwell at 2025-03-19T10:46:36-05:00
Fixed sorting of Annotations, Borders, and Foci in the editing and selection dialogs that use a DataFileEditorModel.
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107bf8bf by John Harwell at 2025-03-19T13:24:22-05:00
For dialog used to choose a border or focus for sample metadata, default the dialog to a reasonable size and preset the selected border/focus with one currently in the metadata.
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e7925a6a by John Harwell at 2025-03-19T15:51:27-05:00
Fixed some compilation warnings.
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f19dc8f5 by John Harwell at 2025-03-20T10:25:41-05:00
QTreeWidget::itemFromIndex() is protected in Qt5 but public in Qt6. So, added getItemFromIndex() to WuQTreeWidget to fix this problem.
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0a380882 by John Harwell at 2025-03-20T10:26:53-05:00
Fixed having a file in vi during last commit which added a .swp file
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07473379 by John Harwell at 2025-03-20T10:38:13-05:00
Created an enumerated value 'GROUP_NAME' which did not compile on windows to trying 'GROUP_NAMED'.
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7399cbcc by John Harwell at 2025-03-20T17:24:45-05:00
Fix background color for new text annotation (background color was same as foreground color if creating a new annotation without first selecting a text annotation). Now background color defaults to NONE instead of WHITE.
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70552d51 by Tim Coalson at 2025-03-24T20:58:55-05:00
new -spec-file-modify command, deprecates -add-to-spec-file
update years
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5db7b6ad by John Harwell at 2025-03-26T09:22:27-05:00
Added support for right-click menu to borders and foci in Features Toolbox but not used yet.
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c8a3a9ee by John Harwell at 2025-03-26T09:22:27-05:00
Move the text editor with a toolbar for entering unicode characters from the AnnotationTextEditorDialog into its own widget class named WuQTextEditWithToolBarWidget. Use it in dialog for creating an annotation and for editing a text annotation.
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8b26ca39 by John Harwell at 2025-03-26T09:22:27-05:00
Added WorkbenchInstallationAssistant that starts with the path of wb_view in a Workbench distribution and finds the "bin" directory that can be added to the user's PATH to allow running wb_view/wb_command from a terminal. Seems to work on macOS but still needs to be tested on Linux and Windows.
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414cb60d by John Harwell at 2025-03-26T15:08:59-05:00
A little more work on WorkbenchInstallationAssistant including display of commands to update PATH for user.
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6ef853b0 by John Harwell at 2025-03-27T10:24:29-05:00
Added missing enums to enum vector is cxx file for AnnotationSizingHandleTypeEnum.
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f92a76e9 by John Harwell at 2025-03-27T10:25:56-05:00
Fixed cursor flashing between double arrow (to move one coordinate) and cross (mouse over annotation).
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7e07a269 by John Harwell at 2025-03-27T10:26:35-05:00
Increase distance can be from a polyhedron coordinate and still drag the coordinate to a new location.
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8283f40c by John Harwell at 2025-03-27T12:00:48-05:00
Fix compilation errors on Linux and Windows due to Qt version differences.
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e98eb44e by John Harwell at 2025-03-28T19:26:38-05:00
Partial implementation of flipping histlogy slices. Should be tab specific but is yoked.
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2ca017c2 by Tim Coalson at 2025-04-08T22:04:53-05:00
add hierarchy option to -*-label-export-table commands
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3530c73a by Tim Coalson at 2025-04-16T22:55:54-05:00
add warning for substantially mismatched pixdim between sform and qform
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9999e876 by John Harwell at 2025-04-18T09:51:32-05:00
Fixed drawing of sample names on histology slices. Names might be 'slightly under' the histology slice and when drawing with depth testing, the name is not drawn. Now name is drawn without depth testing.
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07cd8ba8 by John Harwell at 2025-04-18T09:51:32-05:00
Fixed crash in GraphicsPolygonTessellator. Need to ignore vertex data from tessellator when its weight is zero.
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a371b8da by John Harwell at 2025-04-18T09:51:32-05:00
Added a second method for calculating the volume of a polyhedron using the Curl Theorem: https://mathworld.wolfram.com/PolyhedronVolume.html
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075bf48d by John Harwell at 2025-04-18T09:51:32-05:00
Added a method to get an average of Vector3D elements to Vector3D.
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3b30e1a9 by John Harwell at 2025-04-18T09:51:32-05:00
Add methods to compute a polygon area and to tessellate a polygon to GraphicsUtilitiesOpenGL.
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ac2aec92 by John Harwell at 2025-04-18T09:51:32-05:00
Improve method that calculates the volume of a polyhedron by breaking it into small 'slices'.
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42c18b22 by John Harwell at 2025-04-18T09:51:32-05:00
Add computation of polyhedron volume using divergence theorem. Add conversion of polyhedrons to surfaces (metadata menu in Edit Samples toolbar) for debugging purposes.
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5a3fd0fc by John Harwell at 2025-04-18T09:51:32-05:00
FIxed crash that occurred if: tried to load a scene when starting wb_view and the scene did not contain window 1. Caused by progress dialog being a child of window 1 and the progress dialog closing too early due to the progress dialog being a child of window 1.
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8a086a7f by John Harwell at 2025-04-18T09:51:32-05:00
Fix for incorrectly oriented triangles in curl and divergence theorem calculations of polyhedron volume.
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3b7056e0 by John Harwell at 2025-04-18T09:51:32-05:00
Fixed crash when trying to project foci to a cerebellum (only allow projection to left/right).
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16db725d by John Harwell at 2025-04-18T09:51:32-05:00
Warn if polygon tessellator outputs a triangle with a normal vector pointing in the opposite direction of the input normal vector.
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65f6f454 by John Harwell at 2025-04-18T09:51:32-05:00
Rearrange some data in output of information for a sample polyhedron.
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0e354517 by John Harwell at 2025-04-18T09:51:32-05:00
For conversion of sample polyhedrons to surface: Fixes for name of file and modified status.
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a188a571 by John Harwell at 2025-04-18T09:51:32-05:00
Fixed panning for Histology View when "Flip" is on.
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b0124e2f by John Harwell at 2025-04-18T09:51:32-05:00
Dispable depth testing for annotations drawing in histology space. Note that the slice is included in the histology space information.
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2dbcc62f by John Harwell at 2025-04-18T10:24:06-05:00
Fix compilation errors on windows and linux.
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78f26dcd by John Harwell at 2025-04-21T10:17:57-05:00
Change conversion of samples to surfaces to a static method in AnnotationManager.
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b5dbd0d9 by John Harwell at 2025-04-25T16:13:13-05:00
Initial implementation of CIFTI fiber trajectory MAP file.
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1c07947f by John Harwell at 2025-04-25T16:34:07-05:00
Add additional file extensions for (macOS Finder shows a 'brain' icon for the file) to MacOSXBundleInfo.plist.in
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5c1ebeae by John Harwell at 2025-04-29T13:25:23-05:00
Disable code that attempts to keep histology slices aligned. It was causing big jumps when a slice was changed and it uses the custom view panning overriding values entered by the user.
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ff2d5107 by John Harwell at 2025-04-29T15:52:57-05:00
Added a developer flag to test disabling depth testing when drawing surfaces in ALL view to improve surface transparency. Flag is changed on Preferences Dialog's Develop page.
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135e0d95 by John Harwell at 2025-04-30T11:11:56-05:00
Backface culling in Surface Properties is now saved to scenes.
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926b7d7f by John Harwell at 2025-04-30T14:04:47-05:00
Added a developer flag that enables drawing fiber trajectories with a cleared depth buffer at the end of ALL view drawing (as suggested by Tim).
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84008805 by John Harwell at 2025-04-30T14:35:14-05:00
When getting displayed data files, include the fiber orientation file associated with fiber trajectory map file.
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75e68a05 by John Harwell at 2025-05-01T10:30:04-05:00
Add "Draw Fiber Trajectories in Front" checkbox to Features Toolbox Fibers tab. When checked, fiber trajectories are drawn last in All view so that they appear to be in front of everything else.
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3346dea0 by John Harwell at 2025-05-01T12:44:50-05:00
Fix for drawing fiber trajectories in front.
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62657a88 by John Harwell at 2025-05-01T15:33:05-05:00
Enable display of fiber trajectories in Surface and Surface Montage views.
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8c4eb0ba by John Harwell at 2025-05-02T15:51:57-05:00
Add option in Toolbar:Histology to display dynamic axis labels (label is displayed if slice orientation is close to being in an orthogonal plane) to Histology View.
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385b9641 by John Harwell at 2025-05-05T13:20:16-05:00
Added support for label hierarchy to CIFTI Label file.
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048bad3e by John Harwell at 2025-05-06T09:32:45-05:00
Partial implementation of label hierarchy for CIFTI label file. Labels hierarchy displays on Surface and in Features Toolbox. Still need to implement the clustering.
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8864a02b by John Harwell at 2025-05-07T10:39:30-05:00
Bug fix and increase tolerance to 30 degrees for displaying axis labels on Histology Slices.
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08bdc0ff by John Harwell at 2025-05-09T12:09:16-05:00
Added label hierarchy support to CIFT and GIFTI label files.
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0b11f54f by John Harwell at 2025-05-09T17:01:14-05:00
Added File Menu -> Open File Quickly that allows user to enter the path to a file and open the file. While a path to a file can be entered in the Open File dialog, the file browsing dialog can be very slow if accessing directories containing many files on a remotely mounted disk.
- - - - -
47d7531d by John Harwell at 2025-05-12T16:32:51-05:00
Added an experimental features to wb_view that 'combines' the features and overlay vertical toolboxes (Vertical Overlay Toolbox also contains tabs from Features Toolbox; Features Toolbox also contains tabs from Overlay Vertical Toolbox). Due to the number of tabs, scrolling of tabs is enabled. While Qt supports hiding of tabs, that can be used to hide disabled tabs, use of it causes a crash when the parent window is drawn. To use this option, start wb_view from the command line with the option '-toolbox'. This option may be useful when both the features and overlay toolboxes are needed but take up too much space such as on a smaller monitor / laptop.
- - - - -
13e0aac1 by John Harwell at 2025-05-13T11:10:12-05:00
Add a method to Matrix4x4 to get the basis vectors as normalized (length = 1) vectors.
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1f6c2519 by John Harwell at 2025-05-13T11:12:02-05:00
Changed code that determines the histology axis labels to use the basis vectors from the histology slice's plane to millimeters matrix instead of vectors calculated from the slice corners.
- - - - -
ec158c12 by John Harwell at 2025-05-13T11:12:57-05:00
Fixed crash that occurred when yoking histology slice views with files that contained a different number of slices and the selected slice was outside the range of slices in one of the files.
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727f6004 by John Harwell at 2025-05-13T15:48:06-05:00
Save path entered in Open File Quickly dialog for next time dialog is displayed.
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fe69987d by John Harwell at 2025-05-13T16:00:24-05:00
Move Open File Quickly to immediately below Open File in the File Menu.
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7df25f17 by John Harwell at 2025-05-14T10:06:33-05:00
Fix compilation error and warning on Linux and Windows.
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889dd26f by Christopher J. Markiewicz at 2025-05-15T11:03:50-04:00
chore: Bump minimum cmake
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074c817b by John Harwell at 2025-05-15T11:20:29-05:00
Updated CMAKE_MINIMUM_REQUIRED to '3.5...4.0'. cmake-4.0.2 will produce a fatal error is version is less than 3.5. If just '3.5' cmake-4.0.2 runs but produces warnings. cmake 4.0.2 produces no warnings if '3.5...4.0'.
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35ae996b by johnvelab at 2025-05-15T12:01:17-05:00
Merge branch 'master' into minimum-cmake
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5b4b44d9 by johnvelab at 2025-05-15T12:02:39-05:00
Merge pull request #91 from effigies/minimum-cmake
chore: Bump minimum cmake
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105f6e6b by John Harwell at 2025-05-22T17:03:29-05:00
Change CiftiFiberTrajectoryFile so that it is "Surface Mappable" that allows drawing of its trajectories in surface view.
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d64a6b4d by Tim Coalson at 2025-05-22T23:11:40-05:00
set version
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9a46a53b by Tim Coalson at 2025-05-22T23:14:12-05:00
update copyright year
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99bf66b2 by John Harwell at 2025-05-29T13:57:32-05:00
Remove print statment left over from debugging.
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f6509cb6 by Yaroslav Halchenko at 2025-07-30T08:46:05-04:00
Merge tag 'v2.1.0' into releases
v2.1.0
* tag 'v2.1.0': (255 commits)
Remove print statment left over from debugging.
update copyright year
set version
Change CiftiFiberTrajectoryFile so that it is "Surface Mappable" that allows drawing of its trajectories in surface view.
Updated CMAKE_MINIMUM_REQUIRED to '3.5...4.0'. cmake-4.0.2 will produce a fatal error is version is less than 3.5. If just '3.5' cmake-4.0.2 runs but produces warnings. cmake 4.0.2 produces no warnings if '3.5...4.0'.
chore: Bump minimum cmake
Fix compilation error and warning on Linux and Windows.
Move Open File Quickly to immediately below Open File in the File Menu.
Save path entered in Open File Quickly dialog for next time dialog is displayed.
Fixed crash that occurred when yoking histology slice views with files that contained a different number of slices and the selected slice was outside the range of slices in one of the files.
Changed code that determines the histology axis labels to use the basis vectors from the histology slice's plane to millimeters matrix instead of vectors calculated from the slice corners.
Add a method to Matrix4x4 to get the basis vectors as normalized (length = 1) vectors.
Added an experimental features to wb_view that 'combines' the features and overlay vertical toolboxes (Vertical Overlay Toolbox also contains tabs from Features Toolbox; Features Toolbox also contains tabs from Overlay Vertical Toolbox). Due to the number of tabs, scrolling of tabs is enabled. While Qt supports hiding of tabs, that can be used to hide disabled tabs, use of it causes a crash when the parent window is drawn. To use this option, start wb_view from the command line with the option '-toolbox'. This option may be useful when both the features and overlay toolboxes are needed but take up too much space such as on a smaller monitor / laptop.
Added File Menu -> Open File Quickly that allows user to enter the path to a file and open the file. While a path to a file can be entered in the Open File dialog, the file browsing dialog can be very slow if accessing directories containing many files on a remotely mounted disk.
Added label hierarchy support to CIFT and GIFTI label files.
Bug fix and increase tolerance to 30 degrees for displaying axis labels on Histology Slices.
Partial implementation of label hierarchy for CIFTI label file. Labels hierarchy displays on Surface and in Features Toolbox. Still need to implement the clustering.
Added support for label hierarchy to CIFTI Label file.
Add option in Toolbar:Histology to display dynamic axis labels (label is displayed if slice orientation is close to being in an orthogonal plane) to Histology View.
Enable display of fiber trajectories in Surface and Surface Montage views.
...
- - - - -
ca8ed929 by Yaroslav Halchenko at 2025-07-30T08:46:39-04:00
Merge branch 'releases' into debian
* releases: (255 commits)
Remove print statment left over from debugging.
update copyright year
set version
Change CiftiFiberTrajectoryFile so that it is "Surface Mappable" that allows drawing of its trajectories in surface view.
Updated CMAKE_MINIMUM_REQUIRED to '3.5...4.0'. cmake-4.0.2 will produce a fatal error is version is less than 3.5. If just '3.5' cmake-4.0.2 runs but produces warnings. cmake 4.0.2 produces no warnings if '3.5...4.0'.
chore: Bump minimum cmake
Fix compilation error and warning on Linux and Windows.
Move Open File Quickly to immediately below Open File in the File Menu.
Save path entered in Open File Quickly dialog for next time dialog is displayed.
Fixed crash that occurred when yoking histology slice views with files that contained a different number of slices and the selected slice was outside the range of slices in one of the files.
Changed code that determines the histology axis labels to use the basis vectors from the histology slice's plane to millimeters matrix instead of vectors calculated from the slice corners.
Add a method to Matrix4x4 to get the basis vectors as normalized (length = 1) vectors.
Added an experimental features to wb_view that 'combines' the features and overlay vertical toolboxes (Vertical Overlay Toolbox also contains tabs from Features Toolbox; Features Toolbox also contains tabs from Overlay Vertical Toolbox). Due to the number of tabs, scrolling of tabs is enabled. While Qt supports hiding of tabs, that can be used to hide disabled tabs, use of it causes a crash when the parent window is drawn. To use this option, start wb_view from the command line with the option '-toolbox'. This option may be useful when both the features and overlay toolboxes are needed but take up too much space such as on a smaller monitor / laptop.
Added File Menu -> Open File Quickly that allows user to enter the path to a file and open the file. While a path to a file can be entered in the Open File dialog, the file browsing dialog can be very slow if accessing directories containing many files on a remotely mounted disk.
Added label hierarchy support to CIFT and GIFTI label files.
Bug fix and increase tolerance to 30 degrees for displaying axis labels on Histology Slices.
Partial implementation of label hierarchy for CIFTI label file. Labels hierarchy displays on Surface and in Features Toolbox. Still need to implement the clustering.
Added support for label hierarchy to CIFTI Label file.
Add option in Toolbar:Histology to display dynamic axis labels (label is displayed if slice orientation is close to being in an orthogonal plane) to Histology View.
Enable display of fiber trajectories in Surface and Surface Montage views.
...
- - - - -
169740e4 by Yaroslav Halchenko at 2025-07-30T08:50:24-04:00
Changelog, drop patch, adjust name of section in gbp
- - - - -
cb7ec599 by Yaroslav Halchenko at 2025-07-31T21:15:53-04:00
added debian/patches/0001-attempted-*.patch to address FTBFS for Qt5
- - - - -
1999 changed files:
- README
- debian/changelog
- debian/gbp.conf
- + debian/patches/0001-attempted-general-fix-for-qEnvironment-include.patch
- debian/patches/series
- debian/rules
- debian/watch
- mac_plist/MacOSXBundleInfo.plist.in
- src/Algorithms/AlgorithmBorderToVertices.cxx
- − src/Algorithms/AlgorithmCiftiAverage.cxx
- src/Algorithms/AlgorithmCiftiCorrelation.cxx
- src/Algorithms/AlgorithmCiftiCreateDenseScalar.cxx
- src/Algorithms/AlgorithmCiftiCreateDenseScalar.h
- src/Algorithms/AlgorithmCiftiCreateDenseTimeseries.cxx
- src/Algorithms/AlgorithmCiftiCreateDenseTimeseries.h
- src/Algorithms/AlgorithmCiftiCreateLabel.cxx
- src/Algorithms/AlgorithmCiftiCreateLabel.h
- src/Algorithms/AlgorithmCiftiGradient.cxx
- src/Algorithms/AlgorithmCiftiGradient.h
- src/Algorithms/AlgorithmCiftiParcellate.cxx
- src/Algorithms/AlgorithmCiftiReduce.cxx
- src/Algorithms/AlgorithmCiftiReplaceStructure.cxx
- src/Algorithms/AlgorithmCiftiSeparate.cxx
- src/Algorithms/AlgorithmCiftiSmoothing.cxx
- src/Algorithms/AlgorithmCiftiSmoothing.h
- src/Algorithms/AlgorithmLabelResample.cxx
- src/Algorithms/AlgorithmLabelResample.h
- src/Algorithms/AlgorithmMetricReduce.cxx
- src/Algorithms/AlgorithmMetricRegression.cxx
- src/Algorithms/AlgorithmMetricResample.cxx
- src/Algorithms/AlgorithmMetricResample.h
- src/Algorithms/AlgorithmMetricTFCE.cxx
- src/Algorithms/AlgorithmNodesInsideBorder.cxx
- src/Algorithms/AlgorithmSurfaceDistortion.cxx
- src/Algorithms/AlgorithmSurfaceDistortion.h
- src/Algorithms/AlgorithmSurfaceResample.cxx
- src/Algorithms/AlgorithmSurfaceResample.h
- src/Algorithms/AlgorithmTemplate.cxx.txt
- src/Algorithms/AlgorithmTemplate.h.txt
- src/Algorithms/AlgorithmVolumeDilate.cxx
- src/Algorithms/AlgorithmVolumeDilate.h
- src/Algorithms/AlgorithmVolumeErode.cxx
- src/Algorithms/AlgorithmVolumeGradient.cxx
- src/Algorithms/AlgorithmVolumeLabelToSurfaceMapping.cxx
- src/Algorithms/AlgorithmVolumeLabelToSurfaceMapping.h
- src/Algorithms/AlgorithmVolumeROIsFromExtrema.cxx
- src/Algorithms/AlgorithmVolumeReduce.cxx
- src/Algorithms/AlgorithmVolumeResample.cxx
- src/Algorithms/AlgorithmVolumeResample.h
- src/Algorithms/AlgorithmVolumeTFCE.cxx
- src/Algorithms/AlgorithmVolumeToSurfaceMapping.cxx
- src/Algorithms/AlgorithmVolumeToSurfaceMapping.h
- src/Algorithms/AlgorithmVolumeWarpfieldAffineRegression.cxx
- src/Algorithms/CMakeLists.txt
- src/Annotations/Annotation.cxx
- src/Annotations/Annotation.h
- + src/Annotations/AnnotationAndFile.cxx
- + src/Annotations/AnnotationAndFile.h
- src/Annotations/AnnotationColorBar.cxx
- src/Annotations/AnnotationColorBar.h
- src/Annotations/AnnotationCoordinate.cxx
- src/Annotations/AnnotationCoordinate.h
- src/Annotations/AnnotationCoordinateSpaceEnum.cxx
- src/Annotations/AnnotationCoordinateSpaceEnum.h
- src/Annotations/AnnotationEditingSelectionInformation.cxx
- + src/Annotations/AnnotationFontAttributes.cxx
- + src/Annotations/AnnotationFontAttributes.h
- src/Annotations/AnnotationFontAttributesInterface.h
- src/Annotations/AnnotationGroup.cxx
- src/Annotations/AnnotationGroup.h
- src/Annotations/AnnotationGroupKey.cxx
- src/Annotations/AnnotationGroupKey.h
- src/Annotations/AnnotationGroupTypeEnum.cxx
- src/Annotations/AnnotationGroupTypeEnum.h
- src/Annotations/AnnotationImage.cxx
- src/Annotations/AnnotationImage.h
- src/Annotations/AnnotationMultiCoordinateShape.cxx
- src/Annotations/AnnotationMultiCoordinateShape.h
- + src/Annotations/AnnotationMultiPairedCoordinateShape.cxx
- + src/Annotations/AnnotationMultiPairedCoordinateShape.h
- src/Annotations/AnnotationOneCoordinateShape.cxx
- src/Annotations/AnnotationOneCoordinateShape.h
- src/Annotations/AnnotationPolyLine.cxx
- src/Annotations/AnnotationPolyLine.h
- + src/Annotations/AnnotationPolygon.cxx
- + src/Annotations/AnnotationPolygon.h
- + src/Annotations/AnnotationPolyhedron.cxx
- + src/Annotations/AnnotationPolyhedron.h
- + src/Annotations/AnnotationPolyhedronTypeEnum.cxx
- + src/Annotations/AnnotationPolyhedronTypeEnum.h
- src/Annotations/AnnotationRedoUndoCommand.cxx
- src/Annotations/AnnotationRedoUndoCommand.h
- src/Annotations/AnnotationRedoUndoCommandModeEnum.cxx
- src/Annotations/AnnotationRedoUndoCommandModeEnum.h
- + src/Annotations/AnnotationSampleMetaData.cxx
- + src/Annotations/AnnotationSampleMetaData.h
- src/Annotations/AnnotationScaleBar.cxx
- src/Annotations/AnnotationScaleBar.h
- src/Annotations/AnnotationSizingHandleTypeEnum.cxx
- src/Annotations/AnnotationSizingHandleTypeEnum.h
- src/Annotations/AnnotationSpatialModification.cxx
- src/Annotations/AnnotationSpatialModification.h
- src/Annotations/AnnotationStackingOrderOperation.cxx
- src/Annotations/AnnotationText.cxx
- src/Annotations/AnnotationText.h
- src/Annotations/AnnotationTextFontNameEnum.cxx
- + src/Annotations/AnnotationTextSubstitution.cxx
- + src/Annotations/AnnotationTextSubstitution.h
- src/Annotations/AnnotationTwoCoordinateShape.cxx
- src/Annotations/AnnotationTwoCoordinateShape.h
- src/Annotations/AnnotationTypeEnum.cxx
- src/Annotations/AnnotationTypeEnum.h
- src/Annotations/CMakeLists.txt
- + src/Annotations/EventAnnotationPolyhedronGetByLinkedIdentifier.cxx
- + src/Annotations/EventAnnotationPolyhedronGetByLinkedIdentifier.h
- + src/Annotations/EventAnnotationPolyhedronNameComponentSettings.cxx
- + src/Annotations/EventAnnotationPolyhedronNameComponentSettings.h
- src/Annotations/EventAnnotationTextSubstitutionGet.cxx
- src/Annotations/EventAnnotationTextSubstitutionGet.h
- + src/Annotations/EventAnnotationTextSubstitutionGetAllGroupIDs.cxx
- + src/Annotations/EventAnnotationTextSubstitutionGetAllGroupIDs.h
- + src/Annotations/HistologySpaceKey.cxx
- + src/Annotations/HistologySpaceKey.h
- src/Brain/AnnotationArrangerExecutor.cxx
- + src/Brain/AnnotationClipboard.cxx
- + src/Brain/AnnotationClipboard.h
- src/Brain/AnnotationManager.cxx
- src/Brain/AnnotationManager.h
- + src/Brain/AnnotationTextSubstitutionLayer.cxx
- + src/Brain/AnnotationTextSubstitutionLayer.h
- + src/Brain/AnnotationTextSubstitutionLayerSet.cxx
- + src/Brain/AnnotationTextSubstitutionLayerSet.h
- src/Brain/Brain.cxx
- src/Brain/Brain.h
- src/Brain/BrainOpenGL.cxx
- src/Brain/BrainOpenGL.h
- src/Brain/BrainOpenGLAnnotationDrawingFixedPipeline.cxx
- src/Brain/BrainOpenGLAnnotationDrawingFixedPipeline.h
- src/Brain/BrainOpenGLChartDrawingFixedPipeline.cxx
- src/Brain/BrainOpenGLChartTwoDrawingFixedPipeline.cxx
- src/Brain/BrainOpenGLChartTwoDrawingFixedPipeline.h
- src/Brain/BrainOpenGLFixedPipeline.cxx
- src/Brain/BrainOpenGLFixedPipeline.h
- + src/Brain/BrainOpenGLFociDrawing.cxx
- + src/Brain/BrainOpenGLFociDrawing.h
- + src/Brain/BrainOpenGLHistologySliceDrawing.cxx
- + src/Brain/BrainOpenGLHistologySliceDrawing.h
- + src/Brain/BrainOpenGLIdentificationDrawing.cxx
- + src/Brain/BrainOpenGLIdentificationDrawing.h
- + src/Brain/BrainOpenGLMediaCoordinateDrawing.cxx
- + src/Brain/BrainOpenGLMediaCoordinateDrawing.h
- src/Brain/BrainOpenGLMediaDrawing.cxx
- src/Brain/BrainOpenGLMediaDrawing.h
- src/Brain/BrainOpenGLViewportContent.cxx
- src/Brain/BrainOpenGLViewportContent.h
- + src/Brain/BrainOpenGLVolumeMprThreeDrawing.cxx
- + src/Brain/BrainOpenGLVolumeMprThreeDrawing.h
- + src/Brain/BrainOpenGLVolumeMprTwoDrawing.cxx
- + src/Brain/BrainOpenGLVolumeMprTwoDrawing.h
- src/Brain/BrainOpenGLVolumeObliqueSliceDrawing.cxx
- src/Brain/BrainOpenGLVolumeObliqueSliceDrawing.h
- src/Brain/BrainOpenGLVolumeSliceDrawing.cxx
- src/Brain/BrainOpenGLVolumeSliceDrawing.h
- + src/Brain/BrainOpenGLVolumeSurfaceClippedOutlineDrawing.cxx
- + src/Brain/BrainOpenGLVolumeSurfaceClippedOutlineDrawing.h
- + src/Brain/BrainOpenGLVolumeSurfaceOutlineDrawing.cxx
- + src/Brain/BrainOpenGLVolumeSurfaceOutlineDrawing.h
- − src/Brain/BrainOpenGLVolumeTextureSliceDrawing.cxx
- − src/Brain/BrainOpenGLVolumeTextureSliceDrawing.h
- src/Brain/BrainStructure.cxx
- src/Brain/BrainStructure.h
- src/Brain/BrowserTabContent.cxx
- src/Brain/BrowserTabContent.h
- src/Brain/BrowserWindowContent.cxx
- src/Brain/BrowserWindowContent.h
- src/Brain/CMakeLists.txt
- src/Brain/ChartTwoOverlay.cxx
- src/Brain/ChartTwoOverlay.h
- src/Brain/ClippingPlaneGroup.cxx
- src/Brain/ClippingPlaneGroup.h
- + src/Brain/ClippingPlanePanningModeEnum.cxx
- + src/Brain/ClippingPlanePanningModeEnum.h
- src/Brain/DataToolTipsManager.cxx
- src/Brain/DataToolTipsManager.h
- src/Brain/DisplayPropertiesAnnotation.cxx
- src/Brain/DisplayPropertiesAnnotation.h
- src/Brain/DisplayPropertiesAnnotationTextSubstitution.cxx
- + src/Brain/DisplayPropertiesCziImages.cxx
- + src/Brain/DisplayPropertiesCziImages.h
- src/Brain/DisplayPropertiesFiberOrientation.cxx
- src/Brain/DisplayPropertiesFiberOrientation.h
- src/Brain/DisplayPropertiesFoci.cxx
- src/Brain/DisplayPropertiesLabels.cxx
- src/Brain/DisplayPropertiesLabels.h
- + src/Brain/DisplayPropertiesSamples.cxx
- + src/Brain/DisplayPropertiesSamples.h
- src/Brain/DisplayPropertiesSurface.cxx
- + src/Brain/DrawingViewportContent.cxx
- + src/Brain/DrawingViewportContent.h
- + src/Brain/DrawingViewportContentManager.cxx
- + src/Brain/DrawingViewportContentManager.h
- + src/Brain/DrawingViewportContentSurface.cxx
- + src/Brain/DrawingViewportContentSurface.h
- + src/Brain/DrawingViewportContentTypeEnum.cxx
- + src/Brain/DrawingViewportContentTypeEnum.h
- + src/Brain/DrawingViewportContentVolumeSlice.cxx
- + src/Brain/DrawingViewportContentVolumeSlice.h
- + src/Brain/EventAnnotationGetBeingDrawnInWindow.cxx
- + src/Brain/EventAnnotationGetBeingDrawnInWindow.h
- + src/Brain/EventBrowserTabGetAtWindowXY.cxx
- + src/Brain/EventBrowserTabGetAtWindowXY.h
- + src/Brain/EventBrowserTabIndexGetWindowIndex.cxx
- + src/Brain/EventBrowserTabIndexGetWindowIndex.h
- + src/Brain/EventBrowserTabValidate.cxx
- + src/Brain/EventBrowserTabValidate.h
- src/Brain/EventCaretMappableDataFilesAndMapsInDisplayedOverlays.cxx
- src/Brain/EventCaretMappableDataFilesAndMapsInDisplayedOverlays.h
- + src/Brain/EventDrawingViewportContentAdd.cxx
- + src/Brain/EventDrawingViewportContentAdd.h
- + src/Brain/EventDrawingViewportContentClear.cxx
- + src/Brain/EventDrawingViewportContentClear.h
- + src/Brain/EventDrawingViewportContentGet.cxx
- + src/Brain/EventDrawingViewportContentGet.h
- src/Brain/EventIdentificationHighlightLocation.cxx
- src/Brain/EventIdentificationHighlightLocation.h
- + src/Brain/EventImageCapture.cxx
- src/GuiQt/EventImageCapture.h → src/Brain/EventImageCapture.h
- src/Brain/EventNodeIdentificationColorsGetFromCharts.h
- src/Brain/FiberOrientationSamplesLoader.cxx
- src/Brain/FociDrawingTypeEnum.cxx
- src/Brain/FociDrawingTypeEnum.h
- src/Brain/FtglFontTextRenderer.cxx
- + src/Brain/HistologyOverlay.cxx
- + src/Brain/HistologyOverlay.h
- + src/Brain/HistologyOverlaySet.cxx
- + src/Brain/HistologyOverlaySet.h
- + src/Brain/HistologyOverlaySetArray.cxx
- + src/Brain/HistologyOverlaySetArray.h
- + src/Brain/HistologySliceSettings.cxx
- + src/Brain/HistologySliceSettings.h
- src/Brain/IdentificationFilter.cxx
- src/Brain/IdentificationFilter.h
- src/Brain/IdentificationFilterTabSelectionEnum.cxx
- src/Brain/IdentificationFormattedTextGenerator.cxx
- src/Brain/IdentificationFormattedTextGenerator.h
- src/Brain/IdentificationManager.cxx
- src/Brain/IdentificationManager.h
- src/Brain/IdentificationSimpleTextGenerator.cxx
- src/Brain/IdentificationSimpleTextGenerator.h
- src/Brain/IdentificationWithColor.cxx
- src/Brain/IdentificationWithColor.h
- src/Brain/IdentifiedItem.cxx → src/Brain/IdentifiedItemBase.cxx
- src/Brain/IdentifiedItem.h → src/Brain/IdentifiedItemBase.h
- src/Brain/IdentifiedItemNode.cxx
- src/Brain/IdentifiedItemNode.h
- + src/Brain/IdentifiedItemUniversal.cxx
- + src/Brain/IdentifiedItemUniversal.h
- + src/Brain/IdentifiedItemUniversalTypeEnum.cxx
- + src/Brain/IdentifiedItemUniversalTypeEnum.h
- src/Brain/IdentifiedItemVoxel.cxx
- src/Brain/IdentifiedItemVoxel.h
- src/Brain/MediaOverlay.cxx
- src/Brain/MediaOverlay.h
- src/Brain/MediaOverlaySet.cxx
- src/Brain/MediaOverlaySet.h
- src/Brain/Model.cxx
- src/Brain/Model.h
- src/Brain/ModelChart.cxx
- + src/Brain/ModelHistology.cxx
- + src/Brain/ModelHistology.h
- src/Brain/ModelMedia.cxx
- src/Brain/ModelMedia.h
- src/Brain/ModelSurfaceMontage.cxx
- src/Brain/ModelSurfaceMontage.h
- src/Brain/ModelSurfaceSelector.cxx
- src/Brain/ModelTypeEnum.cxx
- src/Brain/ModelTypeEnum.h
- src/Brain/ModelWholeBrain.cxx
- src/Brain/ModelWholeBrain.h
- src/GuiQt/MouseEvent.cxx → src/Brain/MouseEvent.cxx
- src/GuiQt/MouseEvent.h → src/Brain/MouseEvent.h
- + src/Brain/MouseLeftDragModeEnum.cxx
- + src/Brain/MouseLeftDragModeEnum.h
- src/Brain/MovieRecorder.cxx
- src/Brain/MovieRecorder.h
- + src/Brain/OffScreenSceneRendererBase.cxx
- + src/Brain/OffScreenSceneRendererBase.h
- + src/Brain/OffScreenSceneRendererOSMesa.cxx
- + src/Brain/OffScreenSceneRendererOSMesa.h
- + src/Brain/OffScreenSceneRendererOpenGLWindow.cxx
- + src/Brain/OffScreenSceneRendererOpenGLWindow.h
- src/Brain/Overlay.cxx
- src/Brain/Overlay.h
- src/Brain/OverlaySet.cxx
- src/Brain/OverlaySet.h
- + src/Brain/OverlaySetInitializer.cxx
- + src/Brain/OverlaySetInitializer.h
- src/Brain/ProjectionViewTypeEnum.h
- + src/Brain/SamplesDrawingModeEnum.cxx
- + src/Brain/SamplesDrawingModeEnum.h
- + src/Brain/SamplesDrawingSettings.cxx
- + src/Brain/SamplesDrawingSettings.h
- + src/Brain/SamplesMetaDataManager.cxx
- + src/Brain/SamplesMetaDataManager.h
- src/Brain/SelectionItem.cxx
- src/Brain/SelectionItem.h
- src/Brain/SelectionItemAnnotation.cxx
- src/Brain/SelectionItemAnnotation.h
- src/Brain/SelectionItemChartTwoLineLayerVerticalNearest.cxx
- src/Brain/SelectionItemDataTypeEnum.cxx
- src/Brain/SelectionItemDataTypeEnum.h
- src/Brain/SelectionItemFocusVolume.cxx → src/Brain/SelectionItemFocus.cxx
- src/Brain/SelectionItemFocusVolume.h → src/Brain/SelectionItemFocus.h
- src/Brain/SelectionItemFocusSurface.cxx
- src/Brain/SelectionItemImage.cxx → src/Brain/SelectionItemHistologyCoordinate.cxx
- + src/Brain/SelectionItemHistologyCoordinate.h
- + src/Brain/SelectionItemMediaLogicalCoordinate.cxx
- + src/Brain/SelectionItemMediaLogicalCoordinate.h
- + src/Brain/SelectionItemMediaPlaneCoordinate.cxx
- + src/Brain/SelectionItemMediaPlaneCoordinate.h
- src/Brain/SelectionItemSurfaceTriangle.cxx
- src/Brain/SelectionItemSurfaceTriangle.h
- + src/Brain/SelectionItemUniversalIdentificationSymbol.cxx
- + src/Brain/SelectionItemUniversalIdentificationSymbol.h
- + src/Brain/SelectionItemVolumeMprCrosshair.cxx
- + src/Brain/SelectionItemVolumeMprCrosshair.h
- src/Brain/SelectionItemVoxel.cxx
- src/Brain/SelectionItemVoxel.h
- src/Brain/SelectionManager.cxx
- src/Brain/SelectionManager.h
- src/Brain/SessionManager.cxx
- src/Brain/SessionManager.h
- src/Brain/SurfaceDrawingTypeEnum.cxx
- src/Brain/SurfaceDrawingTypeEnum.h
- src/Brain/SurfaceMontageConfigurationCerebellar.cxx
- src/Brain/SurfaceMontageConfigurationCerebral.cxx
- src/Brain/SurfaceMontageConfigurationFlatMaps.cxx
- + src/Brain/SurfaceMontageConfigurationHippocampus.cxx
- + src/Brain/SurfaceMontageConfigurationHippocampus.h
- + src/Brain/SurfaceMontageConfigurationHippocampusFlatMaps.cxx
- + src/Brain/SurfaceMontageConfigurationHippocampusFlatMaps.h
- src/Brain/SurfaceMontageConfigurationTypeEnum.cxx
- src/Brain/SurfaceMontageConfigurationTypeEnum.h
- src/Brain/SurfaceMontageViewport.cxx
- src/Brain/SurfaceMontageViewport.h
- src/Brain/SurfaceNodeColoring.cxx
- src/Brain/UserInputModeEnum.cxx
- src/Brain/UserInputModeEnum.h
- + src/Brain/ViewingTransformationToFitRegion.cxx
- + src/Brain/ViewingTransformationToFitRegion.h
- src/Brain/ViewingTransformations.cxx
- src/Brain/ViewingTransformations.h
- src/Brain/ViewingTransformationsMedia.cxx
- src/Brain/ViewingTransformationsMedia.h
- + src/Brain/ViewingTransformationsUndoCommand.cxx
- + src/Brain/ViewingTransformationsUndoCommand.h
- src/Brain/ViewingTransformationsVolume.cxx
- src/Brain/ViewingTransformationsVolume.h
- + src/Brain/VolumeMontageCoordinateTextAlignmentEnum.cxx
- + src/Brain/VolumeMontageCoordinateTextAlignmentEnum.h
- + src/Brain/VolumeMontageSliceOrderModeEnum.cxx
- + src/Brain/VolumeMontageSliceOrderModeEnum.h
- + src/Brain/VolumeMprOrientationModeEnum.cxx
- + src/Brain/VolumeMprOrientationModeEnum.h
- + src/Brain/VolumeMprSettings.cxx
- + src/Brain/VolumeMprSettings.h
- + src/Brain/VolumeMprViewModeEnum.cxx
- + src/Brain/VolumeMprViewModeEnum.h
- + src/Brain/VolumeMprViewportSlice.cxx
- src/Files/SceneFileXmlStreamFormatTester.h → src/Brain/VolumeMprViewportSlice.h
- + src/Brain/VolumeMprVirtualSliceView.cxx
- + src/Brain/VolumeMprVirtualSliceView.h
- src/Brain/VolumeSliceInterpolationEdgeEffectsMaskingEnum.cxx
- src/Brain/VolumeSliceInterpolationEdgeEffectsMaskingEnum.h
- src/Brain/VolumeSliceSettings.cxx
- src/Brain/VolumeSliceSettings.h
- src/Brain/VolumeSurfaceOutlineColorOrTabModel.cxx
- src/Brain/VolumeSurfaceOutlineColorOrTabModel.h
- + src/Brain/VolumeSurfaceOutlineDrawingModeEnum.cxx
- + src/Brain/VolumeSurfaceOutlineDrawingModeEnum.h
- src/Brain/VolumeSurfaceOutlineModel.cxx
- src/Brain/VolumeSurfaceOutlineModel.h
- src/Brain/VolumeSurfaceOutlineModelCacheKey.cxx
- src/Brain/VolumeSurfaceOutlineModelCacheKey.h
- src/Brain/VolumeSurfaceOutlineSetModel.cxx
- src/Brain/VolumeSurfaceOutlineSetModel.h
- src/Brain/WholeBrainSurfaceSettings.cxx
- src/Brain/WholeBrainSurfaceSettings.h
- + src/Brain/WindowTabAspectRatios.cxx
- + src/Brain/WindowTabAspectRatios.h
- src/CMakeLists.txt
- + src/CZIlib/CMakeLists.txt
- + src/CZIlib/CZI/BitmapOperations.cpp
- + src/CZIlib/CZI/BitmapOperations.h
- + src/CZIlib/CZI/BitmapOperations.hpp
- + src/CZIlib/CZI/CMakeLists.txt
- + src/CZIlib/CZI/CZIReader.cpp
- + src/CZIlib/CZI/CZIReader.h
- + src/CZIlib/CZI/CreateBitmap.cpp
- + src/CZIlib/CZI/CziAttachment.cpp
- + src/CZIlib/CZI/CziAttachment.h
- + src/CZIlib/CZI/CziAttachmentsDirectory.cpp
- + src/CZIlib/CZI/CziAttachmentsDirectory.h
- + src/CZIlib/CZI/CziDataStructs.h
- + src/CZIlib/CZI/CziDimensionInfo.cpp
- + src/CZIlib/CZI/CziDimensionInfo.h
- + src/CZIlib/CZI/CziDisplaySettings.cpp
- + src/CZIlib/CZI/CziDisplaySettings.h
- + src/CZIlib/CZI/CziMetadata.cpp
- + src/CZIlib/CZI/CziMetadata.h
- + src/CZIlib/CZI/CziMetadataDocumentInfo.cpp
- + src/CZIlib/CZI/CziMetadataDocumentInfo.h
- + src/CZIlib/CZI/CziMetadataSegment.cpp
- + src/CZIlib/CZI/CziMetadataSegment.h
- + src/CZIlib/CZI/CziParse.cpp
- + src/CZIlib/CZI/CziParse.h
- + src/CZIlib/CZI/CziStructs.h
- + src/CZIlib/CZI/CziSubBlock.cpp
- + src/CZIlib/CZI/CziSubBlock.h
- + src/CZIlib/CZI/CziSubBlockDirectory.cpp
- + src/CZIlib/CZI/CziSubBlockDirectory.h
- + src/CZIlib/CZI/CziUtils.cpp
- + src/CZIlib/CZI/CziUtils.h
- + src/CZIlib/CZI/DimCoordinate.cpp
- + src/CZIlib/CZI/ImportExport.h
- + src/CZIlib/CZI/IndexSet.cpp
- + src/CZIlib/CZI/IndexSet.h
- + src/CZIlib/CZI/MD5Sum.cpp
- + src/CZIlib/CZI/MD5Sum.h
- + src/CZIlib/CZI/MultiChannelCompositor.cpp
- + src/CZIlib/CZI/MultiChannelCompositor.h
- + src/CZIlib/CZI/SingleChannelAccessorBase.cpp
- + src/CZIlib/CZI/SingleChannelAccessorBase.h
- + src/CZIlib/CZI/SingleChannelPyramidLevelTileAccessor.cpp
- + src/CZIlib/CZI/SingleChannelPyramidLevelTileAccessor.h
- + src/CZIlib/CZI/SingleChannelScalingTileAccessor.cpp
- + src/CZIlib/CZI/SingleChannelScalingTileAccessor.h
- + src/CZIlib/CZI/SingleChannelTileAccessor.cpp
- + src/CZIlib/CZI/SingleChannelTileAccessor.h
- + src/CZIlib/CZI/SingleChannelTileCompositor.cpp
- + src/CZIlib/CZI/SingleChannelTileCompositor.h
- + src/CZIlib/CZI/Site.h
- + src/CZIlib/CZI/StreamImpl.cpp
- + src/CZIlib/CZI/StreamImpl.h
- + src/CZIlib/CZI/bitmapData.h
- + src/CZIlib/CZI/decoder.cpp
- + src/CZIlib/CZI/decoder.h
- + src/CZIlib/CZI/decoder_wic.cpp
- + src/CZIlib/CZI/decoder_wic.h
- + src/CZIlib/CZI/dllmain.cpp
- + src/CZIlib/CZI/eigen/Array
- + src/CZIlib/CZI/eigen/Cholesky
- + src/CZIlib/CZI/eigen/CholmodSupport
- + src/CZIlib/CZI/eigen/Core
- + src/CZIlib/CZI/eigen/Dense
- + src/CZIlib/CZI/eigen/Eigen
- + src/CZIlib/CZI/eigen/Eigen2Support
- + src/CZIlib/CZI/eigen/Eigenvalues
- + src/CZIlib/CZI/eigen/Geometry
- + src/CZIlib/CZI/eigen/Householder
- + src/CZIlib/CZI/eigen/IterativeLinearSolvers
- + src/CZIlib/CZI/eigen/Jacobi
- + src/CZIlib/CZI/eigen/LU
- + src/CZIlib/CZI/eigen/LeastSquares
- + src/CZIlib/CZI/eigen/MetisSupport
- + src/CZIlib/CZI/eigen/OrderingMethods
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- + src/CZIlib/CZI/splines.cpp
- + src/CZIlib/CZI/splines.h
- + src/CZIlib/CZI/stdAllocator.cpp
- + src/CZIlib/CZI/stdAllocator.h
- + src/CZIlib/CZI/stdafx.cpp
- + src/CZIlib/CZI/stdafx.h
- + src/CZIlib/CZI/targetver.h
- + src/CZIlib/CZI/utilities.cpp
- + src/CZIlib/CZI/utilities.h
- + src/CZIlib/CZICmd/CMakeLists.txt
- + src/CZIlib/CZICmd/CZIcmd.cpp
- + src/CZIlib/CZICmd/CZIcmd.h
- + src/CZIlib/CZICmd/DisplaySettingsHelper.h
- + src/CZIlib/CZICmd/SaveBitmap.cpp
- + src/CZIlib/CZICmd/SaveBitmap.h
- + src/CZIlib/CZICmd/cmdlineoptions.cpp
- + src/CZIlib/CZICmd/cmdlineoptions.h
- + src/CZIlib/CZICmd/consoleio.cpp
- + src/CZIlib/CZICmd/consoleio.h
- + src/CZIlib/CZICmd/execute.cpp
- + src/CZIlib/CZICmd/execute.h
- + src/CZIlib/CZICmd/getOpt.cpp
- + src/CZIlib/CZICmd/getOpt.h
- + src/CZIlib/CZICmd/inc_libCZI.h
- + src/CZIlib/CZICmd/inc_rapidjson.h
- + src/CZIlib/CZICmd/platform_defines.h
- + src/CZIlib/CZICmd/rapidjson/allocators.h
- + src/CZIlib/CZICmd/rapidjson/document.h
- + src/CZIlib/CZICmd/rapidjson/encodedstream.h
- + src/CZIlib/CZICmd/rapidjson/encodings.h
- + src/CZIlib/CZICmd/rapidjson/error/en.h
- + src/CZIlib/CZICmd/rapidjson/error/error.h
- + src/CZIlib/CZICmd/rapidjson/filereadstream.h
- + src/CZIlib/CZICmd/rapidjson/filewritestream.h
- + src/CZIlib/CZICmd/rapidjson/internal/biginteger.h
- + src/CZIlib/CZICmd/rapidjson/internal/diyfp.h
- + src/CZIlib/CZICmd/rapidjson/internal/dtoa.h
- + src/CZIlib/CZICmd/rapidjson/internal/ieee754.h
- + src/CZIlib/CZICmd/rapidjson/internal/itoa.h
- + src/CZIlib/CZICmd/rapidjson/internal/meta.h
- + src/CZIlib/CZICmd/rapidjson/internal/pow10.h
- + src/CZIlib/CZICmd/rapidjson/internal/stack.h
- + src/CZIlib/CZICmd/rapidjson/internal/strfunc.h
- + src/CZIlib/CZICmd/rapidjson/internal/strtod.h
- + src/CZIlib/CZICmd/rapidjson/internal/swap.h
- + src/CZIlib/CZICmd/rapidjson/memorybuffer.h
- + src/CZIlib/CZICmd/rapidjson/memorystream.h
- + src/CZIlib/CZICmd/rapidjson/msinttypes/inttypes.h
- + src/CZIlib/CZICmd/rapidjson/msinttypes/stdint.h
- + src/CZIlib/CZICmd/rapidjson/pointer.h
- + src/CZIlib/CZICmd/rapidjson/prettywriter.h
- + src/CZIlib/CZICmd/rapidjson/rapidjson.h
- + src/CZIlib/CZICmd/rapidjson/reader.h
- + src/CZIlib/CZICmd/rapidjson/stringbuffer.h
- + src/CZIlib/CZICmd/rapidjson/writer.h
- + src/CZIlib/CZICmd/stdafx.cpp
- + src/CZIlib/CZICmd/stdafx.h
- + src/CZIlib/CZICmd/streamimpl.cpp
- + src/CZIlib/CZICmd/streamimpl.h
- + src/CZIlib/CZICmd/targetver.h
- + src/CZIlib/CZICmd/utils.cpp
- + src/CZIlib/CZICmd/utils.h
- + src/CZIlib/CZIJxrDecode/CMakeLists.txt
- + src/CZIlib/CZIJxrDecode/Jxr/JXRGlue.c
- + src/CZIlib/CZIJxrDecode/Jxr/JXRGlue.h
- + src/CZIlib/CZIJxrDecode/Jxr/JXRGlueJxr.c
- + src/CZIlib/CZIJxrDecode/Jxr/JXRGluePFC.c
- + src/CZIlib/CZIJxrDecode/Jxr/JXRMeta.c
- + src/CZIlib/CZIJxrDecode/Jxr/JXRMeta.h
- + src/CZIlib/CZIJxrDecode/Jxr/JXRTest.c
- + src/CZIlib/CZIJxrDecode/Jxr/JXRTest.h
- + src/CZIlib/CZIJxrDecode/Jxr/JXRTestBmp.c
- + src/CZIlib/CZIJxrDecode/Jxr/JXRTestHdr.c
- + src/CZIlib/CZIJxrDecode/Jxr/JXRTestPnm.c
- + src/CZIlib/CZIJxrDecode/Jxr/JXRTestTif.c
- + src/CZIlib/CZIJxrDecode/Jxr/JXRTestWrapper.c
- + src/CZIlib/CZIJxrDecode/Jxr/JXRTestWrapper.h
- + src/CZIlib/CZIJxrDecode/Jxr/JXRTestYUV.c
- + src/CZIlib/CZIJxrDecode/Jxr/JXRTranscode.c
- + src/CZIlib/CZIJxrDecode/Jxr/_x86/_x86.h
- + src/CZIlib/CZIJxrDecode/Jxr/adapthuff.c
- + src/CZIlib/CZIJxrDecode/Jxr/ansi.h
- + src/CZIlib/CZIJxrDecode/Jxr/common.h
- + src/CZIlib/CZIJxrDecode/Jxr/decode.c
- + src/CZIlib/CZIJxrDecode/Jxr/decode.h
- + src/CZIlib/CZIJxrDecode/Jxr/encode.c
- + src/CZIlib/CZIJxrDecode/Jxr/encode.h
- + src/CZIlib/CZIJxrDecode/Jxr/image.c
- + src/CZIlib/CZIJxrDecode/Jxr/jxr_defines.h
- + src/CZIlib/CZIJxrDecode/Jxr/perfTimer.h
- + src/CZIlib/CZIJxrDecode/Jxr/perfTimerANSI.c
- + src/CZIlib/CZIJxrDecode/Jxr/postprocess.c
- + src/CZIlib/CZIJxrDecode/Jxr/priv_guiddef.h
- + src/CZIlib/CZIJxrDecode/Jxr/segdec.c
- + src/CZIlib/CZIJxrDecode/Jxr/segenc.c
- + src/CZIlib/CZIJxrDecode/Jxr/strFwdTransform.c
- + src/CZIlib/CZIJxrDecode/Jxr/strInvTransform.c
- + src/CZIlib/CZIJxrDecode/Jxr/strPredQuant.c
- + src/CZIlib/CZIJxrDecode/Jxr/strPredQuantDec.c
- + src/CZIlib/CZIJxrDecode/Jxr/strPredQuantEnc.c
- + src/CZIlib/CZIJxrDecode/Jxr/strTransform.c
- + src/CZIlib/CZIJxrDecode/Jxr/strTransform.h
- + src/CZIlib/CZIJxrDecode/Jxr/strcodec.c
- + src/CZIlib/CZIJxrDecode/Jxr/strcodec.h
- + src/CZIlib/CZIJxrDecode/Jxr/strdec.c
- + src/CZIlib/CZIJxrDecode/Jxr/strdec_x86.c
- + src/CZIlib/CZIJxrDecode/Jxr/strenc.c
- + src/CZIlib/CZIJxrDecode/Jxr/strenc_x86.c
- + src/CZIlib/CZIJxrDecode/Jxr/windowsmediaphoto.h
- + src/CZIlib/CZIJxrDecode/Jxr/wmsal.h
- + src/CZIlib/CZIJxrDecode/Jxr/wmspecstring.h
- + src/CZIlib/CZIJxrDecode/Jxr/wmspecstrings_adt.h
- + src/CZIlib/CZIJxrDecode/Jxr/wmspecstrings_strict.h
- + src/CZIlib/CZIJxrDecode/Jxr/wmspecstrings_undef.h
- + src/CZIlib/CZIJxrDecode/JxrDecode.cpp
- + src/CZIlib/CZIJxrDecode/JxrDecode.h
- + src/CZIlib/CZIJxrDecode/stdafx.cpp
- + src/CZIlib/CZIJxrDecode/stdafx.h
- + src/CZIlib/CZIJxrDecode/targetver.h
- + src/CZIlib/LICENSE
- + src/CZIlib/README.md
- − src/Charting/2
- src/Charting/CMakeLists.txt
- src/Charting/ChartDataCartesian.cxx
- src/Charting/ChartTwoCartesianCustomSubdivisions.cxx
- src/Charting/ChartTwoCartesianOrientedAxes.cxx
- src/Charting/ChartTwoCartesianOrientedAxes.h
- src/Charting/ChartTwoCartesianSubdivisionsModeEnum.cxx
- src/Charting/ChartTwoCartesianSubdivisionsModeEnum.h
- src/Charting/EventChartTwoCartesianOrientedAxesYoking.cxx
- src/Charting/MapFileDataSelector.cxx
- src/Cifti/CMakeLists.txt
- src/Cifti/CiftiBrainModelsMap.cxx
- src/Cifti/CiftiFile.cxx
- src/Cifti/CiftiLabelsMap.cxx
- src/Cifti/CiftiParcelsMap.cxx
- src/Cifti/CiftiScalarsMap.cxx
- src/Cifti/CiftiSeriesMap.cxx
- src/Cifti/CiftiXML.cxx
- src/Cifti/CiftiXMLReader.cxx
- src/Cifti/CiftiXMLWriter.cxx
- src/CommandLine/CMakeLists.txt
- src/Commands/CMakeLists.txt
- src/Commands/CommandClassCreate.cxx
- src/Commands/CommandClassCreateEnum.cxx
- src/Commands/CommandClassCreateEnum.h
- src/Commands/CommandOperation.cxx
- src/Commands/CommandOperation.h
- src/Commands/CommandOperationManager.cxx
- src/Commands/CommandParser.cxx
- src/Commands/CommandParser.h
- src/Common/AString.cxx
- src/Common/AString.h
- src/Common/ApplicationInformation.cxx.in
- src/Common/ApplicationInformation.h
- src/Common/BackgroundAndForegroundColors.cxx
- src/Common/BackgroundAndForegroundColors.h
- src/Common/BoundingBox.cxx
- src/Common/BoundingBox.h
- src/Common/CMakeLists.txt
- src/Common/CaretBinaryFile.cxx
- src/Common/CaretColorEnum.cxx
- src/Common/CaretColorEnum.h
- + src/Common/CaretHierarchy.cxx
- + src/Common/CaretHierarchy.h
- src/Common/CaretHttpManager.cxx
- src/Common/CaretHttpManager.h
- src/Common/CaretMathExpression.cxx
- src/Common/CaretMutex.h
- src/Common/CaretObject.cxx
- src/Common/CaretObject.h
- src/Common/CaretPointLocator.h
- src/Common/CaretPointer.h
- src/Common/CaretPreferenceDataValue.cxx
- src/Common/CaretPreferenceDataValue.h
- + src/Common/CaretPreferenceDataValueList.cxx
- + src/Common/CaretPreferenceDataValueList.h
- src/Common/BackgroundAndForegroundColorsModeEnum.cxx → src/Common/CaretPreferenceValueSceneOverrideModeEnum.cxx
- src/Common/BackgroundAndForegroundColorsModeEnum.h → src/Common/CaretPreferenceValueSceneOverrideModeEnum.h
- src/Common/CaretPreferences.cxx
- src/Common/CaretPreferences.h
- + src/Common/Cluster.cxx
- + src/Common/Cluster.h
- + src/Common/ClusterContainer.cxx
- + src/Common/ClusterContainer.h
- − src/Common/ConnectivityCorrelation.cxx
- − src/Common/ConnectivityCorrelation.h
- src/Common/DataFile.cxx
- src/Common/DataFile.h
- src/Common/DataFileContentInformation.cxx
- src/Common/DataFileContentInformation.h
- src/Common/DataFileException.cxx
- src/Common/DataFileTypeEnum.cxx
- src/Common/DataFileTypeEnum.h
- src/Common/DeveloperFlagsEnum.cxx
- src/Common/DeveloperFlagsEnum.h
- + src/Common/DisplayHighDpiModeEnum.cxx
- + src/Common/DisplayHighDpiModeEnum.h
- src/Common/ElapsedTimer.cxx
- src/Common/ElapsedTimer.h
- + src/Common/EventBrowserWindowPixelSizeInfoEvent.cxx
- + src/Common/EventBrowserWindowPixelSizeInfoEvent.h
- src/Common/EventManager.cxx
- + src/Common/EventResetView.cxx
- + src/Common/EventResetView.h
- src/Common/EventTypeEnum.cxx
- src/Common/EventTypeEnum.h
- src/Common/FileInformation.cxx
- + src/Common/FunctionResult.h
- + src/Common/HemisphereEnum.cxx
- + src/Common/HemisphereEnum.h
- src/Common/HtmlTableBuilder.cxx
- src/Common/HtmlTableBuilder.h
- src/Common/ImageCaptureMethodEnum.cxx
- src/Common/ImageCaptureMethodEnum.h
- + src/Common/InfoItem.cxx
- + src/Common/InfoItem.h
- + src/Common/LinearEquationTransform.cxx
- + src/Common/LinearEquationTransform.h
- src/Common/MathFunctionEnum.cxx
- src/Common/MathFunctionEnum.h
- src/Common/MathFunctions.cxx
- src/Common/MathFunctions.h
- src/Common/Matrix4x4Interface.h
- src/Common/ModelTransform.cxx
- src/Common/ModelTransform.h
- src/Common/MultiDimIterator.h
- src/Common/NumericTextFormatting.cxx
- src/Common/OctTree.h
- src/Common/Plane.cxx
- src/Common/Plane.h
- + src/Common/QtPluginsPathSetup.cxx
- + src/Common/QtPluginsPathSetup.h
- src/Common/RecentFileItemsFilter.cxx
- src/Common/RecentFileItemsFilter.h
- + src/Common/RecentSceneInfoContainer.cxx
- + src/Common/RecentSceneInfoContainer.h
- src/Common/ReductionOperation.cxx
- src/Common/ReductionOperation.h
- src/Common/StringTableModel.cxx
- src/Common/StringTableModel.h
- src/Common/StructureEnum.cxx
- src/Common/StructureEnum.h
- src/Common/SystemUtilities.cxx
- src/Common/SystemUtilities.h
- src/Common/TileTabsLayoutBaseConfiguration.cxx
- src/Common/TileTabsLayoutBaseConfiguration.h
- src/Common/TileTabsLayoutConfigurationTypeEnum.cxx
- src/Common/TileTabsLayoutConfigurationTypeEnum.h
- src/Common/TileTabsLayoutGridConfiguration.cxx
- src/Common/TileTabsLayoutGridConfiguration.h
- src/Common/TileTabsLayoutManualConfiguration.cxx
- src/Common/TileTabsLayoutManualConfiguration.h
- + src/Common/UnitsConversion.cxx
- + src/Common/UnitsConversion.h
- src/Common/Vector3D.cxx
- src/Common/Vector3D.h
- + src/Common/VolumeMontageCoordinateDisplayTypeEnum.cxx
- + src/Common/VolumeMontageCoordinateDisplayTypeEnum.h
- + src/Common/VoxelColorUpdate.cxx
- + src/Common/VoxelColorUpdate.h
- src/Common/VoxelIJK.h
- + src/Common/WorkbenchInstallationAssistant.cxx
- + src/Common/WorkbenchInstallationAssistant.h
- src/Common/WorkbenchQtMessageHandler.cxx
- src/Common/WuQMacroGroupXmlStreamReader.cxx
- src/Common/WuQMacroGroupXmlStreamWriter.cxx
- src/Desktop/CMakeLists.txt
- src/Desktop/desktop.cxx
- src/Files/AffineFile.cxx
- src/Files/AffineSeriesFile.cxx
- src/Files/AnnotationFile.cxx
- src/Files/AnnotationFile.h
- src/Files/AnnotationFileXmlFormatBase.cxx
- src/Files/AnnotationFileXmlFormatBase.h
- src/Files/AnnotationFileXmlReader.cxx
- src/Files/AnnotationFileXmlReader.h
- src/Files/AnnotationFileXmlWriter.cxx
- src/Files/AnnotationFileXmlWriter.h
- src/Files/AnnotationTextSubstitutionFile.cxx
- src/Files/AnnotationTextSubstitutionFile.h
- src/Files/Border.cxx
- src/Files/BorderFile.cxx
- src/Files/BorderFile.h
- src/Files/CMakeLists.txt
- src/Files/CaretDataFile.cxx
- src/Files/CaretDataFile.h
- src/Files/CaretDataFileHelper.cxx
- src/Files/CaretDataFileSelectionModel.cxx
- src/Files/CaretDataFileSelectionModel.h
- src/Files/CaretMappableDataFile.cxx
- src/Files/CaretMappableDataFile.h
- src/Files/CaretMappableDataFileAndMapSelectionModel.cxx
- src/Files/CaretMappableDataFileAndMapSelectionModel.h
- + src/Files/CaretMappableDataFileClusterFinder.cxx
- + src/Files/CaretMappableDataFileClusterFinder.h
- + src/Files/CaretMappableDataFileLabelSelectionDelegate.cxx
- + src/Files/CaretMappableDataFileLabelSelectionDelegate.h
- src/Files/CaretVolumeExtension.cxx
- src/Files/CaretVolumeExtension.h
- src/Files/ChartableTwoFileBaseChart.cxx
- src/Files/ChartableTwoFileBaseChart.h
- src/Files/ChartableTwoFileDelegate.cxx
- src/Files/ChartableTwoFileMatrixChart.cxx
- src/Files/CiftiConnectivityMatrixDenseDynamicFile.cxx
- src/Files/CiftiConnectivityMatrixDenseDynamicFile.h
- + src/Files/CiftiConnectivityMatrixParcelDynamicFile.cxx
- + src/Files/CiftiConnectivityMatrixParcelDynamicFile.h
- src/Files/CiftiFiberTrajectoryFile.cxx
- src/Files/CiftiFiberTrajectoryFile.h
- + src/Files/CiftiFiberTrajectoryMapFile.cxx
- + src/Files/CiftiFiberTrajectoryMapFile.h
- src/Files/CiftiMappableConnectivityMatrixDataFile.cxx
- src/Files/CiftiMappableConnectivityMatrixDataFile.h
- src/Files/CiftiMappableDataFile.cxx
- src/Files/CiftiMappableDataFile.h
- src/Files/CiftiParcelReorderingModel.cxx
- src/Files/CiftiParcelScalarFile.cxx
- src/Files/CiftiParcelScalarFile.h
- src/Files/CiftiParcelSeriesFile.cxx
- src/Files/CiftiParcelSeriesFile.h
- src/Files/CiftiScalarDataSeriesFile.cxx
- src/Files/CiftiScalarDataSeriesFile.h
- + src/Files/CommaSeparatedValuesFile.cxx
- + src/Files/CommaSeparatedValuesFile.h
- + src/Files/ConnectivityCorrelationModeEnum.cxx
- + src/Files/ConnectivityCorrelationModeEnum.h
- + src/Files/ConnectivityCorrelationSettings.cxx
- + src/Files/ConnectivityCorrelationSettings.h
- + src/Files/ConnectivityCorrelationTwo.cxx
- + src/Files/ConnectivityCorrelationTwo.h
- + src/Files/CziDistanceFile.cxx
- + src/Files/CziDistanceFile.h
- + src/Files/CziImage.cxx
- + src/Files/CziImage.h
- + src/Files/CziImageFile.cxx
- + src/Files/CziImageFile.h
- + src/Files/CziImageLoaderBase.cxx
- + src/Files/CziImageLoaderBase.h
- + src/Files/CziImageLoaderMultiResolution.cxx
- + src/Files/CziImageLoaderMultiResolution.h
- + src/Files/CziImageResolutionChangeModeEnum.cxx
- + src/Files/CziImageResolutionChangeModeEnum.h
- + src/Files/CziNonLinearTransform.cxx
- + src/Files/CziNonLinearTransform.h
- + src/Files/CziPixelCoordSpaceEnum.cxx
- + src/Files/CziPixelCoordSpaceEnum.h
- + src/Files/CziUtilities.cxx
- + src/Files/CziUtilities.h
- + src/Files/DataFileColorModulateSelector.cxx
- + src/Files/DataFileColorModulateSelector.h
- src/Brain/SelectionItemSurfaceNodeIdentificationSymbol.cxx → src/Files/DataFileEditorColumnContent.cxx
- + src/Files/DataFileEditorColumnContent.h
- + src/Files/DataFileEditorItem.cxx
- + src/Files/DataFileEditorItem.h
- + src/Files/DataFileEditorItemTypeEnum.cxx
- + src/Files/DataFileEditorItemTypeEnum.h
- + src/Files/DataFileEditorModel.cxx
- + src/Files/DataFileEditorModel.h
- + src/Files/DingOntologyTermsFile.cxx
- + src/Files/DingOntologyTermsFile.h
- src/Files/EventCaretDataFilesGet.cxx
- src/Files/EventCaretDataFilesGet.h
- + src/Files/EventFocusFileGetColor.cxx
- + src/Files/EventFocusFileGetColor.h
- + src/Files/EventHistologySlicesFilesGet.cxx
- + src/Files/EventHistologySlicesFilesGet.h
- src/Files/EventMapYokingSelectMap.cxx
- src/Files/EventMapYokingSelectMap.h
- src/Files/EventMapYokingValidation.cxx
- src/Files/EventMapYokingValidation.h
- + src/Files/EventSurfaceFileGet.cxx
- + src/Files/EventSurfaceFileGet.h
- + src/Files/EventVolumeColoringInvalidate.cxx
- + src/Files/EventVolumeColoringInvalidate.h
- src/Files/FileIdentificationAttributes.cxx
- src/Files/FileIdentificationAttributes.h
- + src/Files/FileIdentificationDisplayModeEnum.cxx
- + src/Files/FileIdentificationDisplayModeEnum.h
- src/Files/FilePathNamePrefixCompactor.cxx
- src/Files/FociFile.cxx
- src/Files/FociFile.h
- src/Files/Focus.cxx
- src/Files/Focus.h
- src/Files/GiftiTypeFile.cxx
- src/Files/GiftiTypeFile.h
- src/Files/GroupAndNameHierarchyGroup.cxx
- src/Files/GroupAndNameHierarchyGroup.h
- src/Files/GroupAndNameHierarchyItem.cxx
- src/Files/GroupAndNameHierarchyItem.h
- src/Files/GroupAndNameHierarchyModel.cxx
- src/Files/GroupAndNameHierarchyModel.h
- src/Files/GroupAndNameHierarchyName.cxx
- src/Files/GroupAndNameHierarchyName.h
- + src/Files/GroupAndNameHierarchyUserInterface.h
- + src/Files/HistologyCoordinate.cxx
- + src/Files/HistologyCoordinate.h
- + src/Files/HistologySlice.cxx
- + src/Files/HistologySlice.h
- + src/Files/HistologySliceImage.cxx
- + src/Files/HistologySliceImage.h
- + src/Files/HistologySlicesFile.cxx
- + src/Files/HistologySlicesFile.h
- + src/Files/HistologySlicesFileXmlStreamBase.cxx
- + src/Files/HistologySlicesFileXmlStreamBase.h
- + src/Files/HistologySlicesFileXmlStreamReader.cxx
- + src/Files/HistologySlicesFileXmlStreamReader.h
- src/Files/ImageCaptureSettings.cxx → src/Files/ImageCaptureDialogSettings.cxx
- src/Files/ImageCaptureSettings.h → src/Files/ImageCaptureDialogSettings.h
- src/Files/ImageCaptureDimensionsModeEnum.cxx
- src/Files/ImageFile.cxx
- src/Files/ImageFile.h
- src/Files/ImageResolutionUnitsEnum.cxx
- src/Files/ImageResolutionUnitsEnum.h
- src/Files/ImageSpatialUnitsEnum.cxx
- src/Files/ImageSpatialUnitsEnum.h
- src/Files/LabelFile.cxx
- src/Files/LabelFile.h
- + src/Files/LabelSelectionItem.cxx
- + src/Files/LabelSelectionItem.h
- + src/Files/LabelSelectionItemModel.cxx
- + src/Files/LabelSelectionItemModel.h
- src/Files/MapYokingGroupEnum.cxx
- src/Files/MapYokingGroupEnum.h
- + src/Files/MediaDisplayCoordinateModeEnum.cxx
- + src/Files/MediaDisplayCoordinateModeEnum.h
- src/Files/MediaFile.cxx
- src/Files/MediaFile.h
- + src/Files/MediaFileChannelInfo.cxx
- + src/Files/MediaFileChannelInfo.h
- + src/Files/MediaFileTransforms.cxx
- + src/Files/MediaFileTransforms.h
- src/Files/MetricDynamicConnectivityFile.cxx
- src/Files/MetricDynamicConnectivityFile.h
- src/Files/NodeAndVoxelColoring.cxx
- src/Files/NodeAndVoxelColoring.h
- + src/Files/OmeZarrImageFile.cxx
- + src/Files/OmeZarrImageFile.h
- src/Files/PaletteFile.cxx
- + src/Files/PixelCoordinate.cxx
- + src/Files/PixelCoordinate.h
- + src/Files/PixelIndex.cxx
- + src/Files/PixelIndex.h
- + src/Files/PixelLogicalIndex.cxx
- + src/Files/PixelLogicalIndex.h
- + src/Files/RectangleTransform.cxx
- + src/Files/RectangleTransform.h
- + src/Files/SamplesColorModeEnum.cxx
- + src/Files/SamplesColorModeEnum.h
- + src/Files/SamplesFile.cxx
- + src/Files/SamplesFile.h
- src/Files/SceneDataFileInfo.cxx
- src/Files/SceneFile.cxx
- src/Files/SceneFile.h
- − src/Files/SceneFileSaxReader.cxx
- − src/Files/SceneFileSaxReader.h
- − src/Files/SceneFileXmlStreamFormatTester.cxx
- src/Files/SceneFileXmlStreamReader.cxx
- src/Files/SignedDistanceHelper.cxx
- src/Files/SignedDistanceHelper.h
- src/Files/SpecFile.cxx
- src/Files/SpecFile.h
- src/Files/SpecFileDataFile.cxx
- src/Files/SpecFileDataFile.h
- src/Files/StudyMetaDataLink.cxx
- src/Files/StudyMetaDataLinkSet.cxx
- src/Files/SurfaceFile.cxx
- src/Files/SurfaceFile.h
- src/Files/SurfacePlaneIntersectionToContour.cxx
- src/Files/SurfacePlaneIntersectionToContour.h
- src/Files/SurfaceProjectedItem.cxx
- src/Files/SurfaceProjectedItem.h
- src/Files/SurfaceProjectionBarycentric.cxx
- src/Files/SurfaceProjectionBarycentric.h
- src/Files/SurfaceProjector.cxx
- src/Files/SurfaceResamplingHelper.cxx
- src/Files/SurfaceResamplingHelper.h
- src/Files/SurfaceTypeEnum.cxx
- src/Files/SurfaceTypeEnum.h
- src/Files/TextFile.cxx
- src/Files/TextFile.h
- src/Files/TopologyHelper.cxx
- src/Files/VolumeDynamicConnectivityFile.cxx
- src/Files/VolumeDynamicConnectivityFile.h
- src/Files/VolumeEditingModeEnum.cxx
- src/Files/VolumeFile.cxx
- src/Files/VolumeFile.h
- src/Files/VolumeFileEditorDelegate.cxx
- src/Files/VolumeFileEditorDelegate.h
- src/Files/VolumeFileVoxelColorizer.cxx
- src/Files/VolumeFileVoxelColorizer.h
- + src/Files/VolumeGraphicsPrimitiveManager.cxx
- + src/Files/VolumeGraphicsPrimitiveManager.h
- + src/Files/VolumePlaneIntersection.cxx
- + src/Files/VolumePlaneIntersection.h
- src/Files/VolumeSliceProjectionTypeEnum.cxx
- src/Files/VolumeSliceProjectionTypeEnum.h
- + src/Files/VolumeToImageMapping.cxx
- + src/Files/VolumeToImageMapping.h
- + src/Files/VolumeVerticesEdgesFaces.cxx
- + src/Files/VolumeVerticesEdgesFaces.h
- + src/Files/VoxelInterpolationTypeEnum.cxx
- + src/Files/VoxelInterpolationTypeEnum.h
- src/Files/WarpfieldFile.cxx
- src/Files/WarpfieldFile.h
- src/Files/XmlStreamReaderHelper.cxx
- src/Files/XmlStreamReaderHelper.h
- src/FilesBase/CMakeLists.txt
- src/FilesBase/GiftiLabel.cxx
- src/FilesBase/GiftiLabel.h
- src/FilesBase/GiftiLabelTable.cxx
- src/FilesBase/GiftiLabelTable.h
- + src/FilesBase/LabelViewModeEnum.cxx
- + src/FilesBase/LabelViewModeEnum.h
- + src/FilesBase/TabDrawingInfo.cxx
- + src/FilesBase/TabDrawingInfo.h
- src/FilesBase/VolumeBase.cxx
- src/FilesBase/VolumeBase.h
- src/FilesBase/VolumeMappableInterface.cxx
- src/FilesBase/VolumeMappableInterface.h
- src/FilesBase/VolumeSliceViewPlaneEnum.cxx
- src/FilesBase/VolumeSliceViewPlaneEnum.h
- src/FilesBase/VolumeSpace.cxx
- + src/FilesBase/VolumeTextureCoordinateMapper.cxx
- src/Brain/SelectionItemVoxelIdentificationSymbol.h → src/FilesBase/VolumeTextureCoordinateMapper.h
- + src/FilesBase/VolumeToImageMappingModeEnum.cxx
- + src/FilesBase/VolumeToImageMappingModeEnum.h
- src/FtglFont/CMakeLists.txt
- src/Gifti/CMakeLists.txt
- src/Gifti/GiftiDataArray.cxx
- src/Gifti/GiftiFile.cxx
- src/Gifti/GiftiFileWriter.cxx
- src/Gifti/GiftiMetaDataSaxReader.cxx
- src/Graphics/CMakeLists.txt
- src/Graphics/EventGraphicsOpenGLDeleteTextureName.cxx
- src/Graphics/EventGraphicsOpenGLDeleteTextureName.h
- src/Graphics/EventOpenGLObjectToWindowTransform.cxx
- src/Graphics/EventOpenGLObjectToWindowTransform.h
- src/Graphics/GraphicsEngineDataOpenGL.cxx
- src/Graphics/GraphicsEngineDataOpenGL.h
- + src/Graphics/GraphicsFramesPerSecond.cxx
- + src/Graphics/GraphicsFramesPerSecond.h
- + src/Graphics/GraphicsLineMeanDeviationSettings.cxx
- + src/Graphics/GraphicsLineMeanDeviationSettings.h
- + src/Graphics/GraphicsObjectToWindowTransform.cxx
- + src/Graphics/GraphicsObjectToWindowTransform.h
- src/Graphics/GraphicsOpenGLError.cxx
- src/Graphics/GraphicsOpenGLError.h
- src/Graphics/GraphicsOpenGLPolylineTriangles.cxx
- + src/Graphics/GraphicsOrthographicProjection.cxx
- + src/Graphics/GraphicsOrthographicProjection.h
- + src/Graphics/GraphicsPolygonTessellator.cxx
- + src/Graphics/GraphicsPolygonTessellator.h
- src/Graphics/GraphicsPrimitive.cxx
- src/Graphics/GraphicsPrimitive.h
- src/Graphics/GraphicsPrimitiveSelectionHelper.cxx
- src/Graphics/GraphicsPrimitiveV3f.cxx
- src/Graphics/GraphicsPrimitiveV3fC4f.cxx
- src/Graphics/GraphicsPrimitiveV3fC4ub.cxx
- src/Graphics/GraphicsPrimitiveV3fN3f.cxx
- + src/Graphics/GraphicsPrimitiveV3fN3fC4f.cxx
- + src/Graphics/GraphicsPrimitiveV3fN3fC4f.h
- src/Graphics/GraphicsPrimitiveV3fN3fC4ub.cxx
- + src/Graphics/GraphicsPrimitiveV3fT2f.cxx
- + src/Graphics/GraphicsPrimitiveV3fT2f.h
- src/Graphics/GraphicsPrimitiveV3fT3f.cxx
- src/Graphics/GraphicsPrimitiveV3fT3f.h
- + src/Graphics/GraphicsRegionSelectionBox.cxx
- + src/Graphics/GraphicsRegionSelectionBox.h
- src/Graphics/GraphicsShape.cxx
- src/Graphics/GraphicsShape.h
- + src/Graphics/GraphicsTextureMagnificationFilterEnum.cxx
- + src/Graphics/GraphicsTextureMagnificationFilterEnum.h
- + src/Graphics/GraphicsTextureMinificationFilterEnum.cxx
- + src/Graphics/GraphicsTextureMinificationFilterEnum.h
- + src/Graphics/GraphicsTextureRectangle.cxx
- + src/Graphics/GraphicsTextureRectangle.h
- + src/Graphics/GraphicsTextureSettings.cxx
- + src/Graphics/GraphicsTextureSettings.h
- src/Graphics/GraphicsUtilitiesOpenGL.cxx
- src/Graphics/GraphicsUtilitiesOpenGL.h
- + src/Graphics/GraphicsViewport.cxx
- + src/Graphics/GraphicsViewport.h
- src/GuiQt/AboutWorkbenchDialog.cxx
- src/GuiQt/AboutWorkbenchDialog.h
- src/GuiQt/AnnotationBackgroundTypeWidget.cxx
- src/GuiQt/AnnotationBoundsWidget.cxx
- − src/GuiQt/AnnotationChangeCoordinateDialog.cxx
- src/GuiQt/AnnotationColorWidget.cxx
- src/GuiQt/AnnotationColorWidget.h
- src/GuiQt/AnnotationCoordinateCenterXYWidget.cxx
- src/GuiQt/AnnotationCoordinateInformation.cxx
- src/GuiQt/AnnotationCoordinateInformation.h
- − src/GuiQt/AnnotationCoordinateSelectionWidget.cxx
- src/GuiQt/AnnotationCoordinateSpaceWidget.cxx
- src/GuiQt/AnnotationCoordinatesWidget.cxx
- src/GuiQt/AnnotationCreateDialog.cxx
- src/GuiQt/AnnotationCreateDialog.h
- src/GuiQt/AnnotationDeleteWidget.cxx
- src/GuiQt/AnnotationDeleteWidget.h
- src/GuiQt/AnnotationFontWidget.cxx
- src/GuiQt/AnnotationFontWidget.h
- src/GuiQt/AnnotationInsertNewWidget.cxx
- src/GuiQt/AnnotationInsertNewWidget.h
- src/GuiQt/AnnotationLineArrowTipsWidget.cxx
- src/GuiQt/AnnotationLineArrowTipsWidget.h
- src/GuiQt/AnnotationMenuArrange.cxx
- src/GuiQt/AnnotationMenuArrange.h
- src/GuiQt/AnnotationMenuFileSelection.cxx
- src/GuiQt/AnnotationMenuFileSelection.h
- src/GuiQt/AnnotationNameWidget.cxx
- src/GuiQt/AnnotationPasteDialog.cxx
- src/GuiQt/AnnotationPasteDialog.h
- + src/GuiQt/AnnotationPastingInformation.cxx
- + src/GuiQt/AnnotationPastingInformation.h
- + src/GuiQt/AnnotationPolyTypeDrawEditWidget.cxx
- src/GuiQt/AnnotationCoordinateSelectionWidget.h → src/GuiQt/AnnotationPolyTypeDrawEditWidget.h
- src/GuiQt/AnnotationRedoUndoWidget.cxx
- src/GuiQt/AnnotationRedoUndoWidget.h
- src/GuiQt/AnnotationRotationWidget.cxx
- + src/GuiQt/AnnotationSamplesInsertNewWidget.cxx
- + src/GuiQt/AnnotationSamplesInsertNewWidget.h
- + src/GuiQt/AnnotationSamplesMetaDataDialog.cxx
- + src/GuiQt/AnnotationSamplesMetaDataDialog.h
- + src/GuiQt/AnnotationSamplesModifyWidget.cxx
- src/GuiQt/AnnotationChangeCoordinateDialog.h → src/GuiQt/AnnotationSamplesModifyWidget.h
- src/GuiQt/AnnotationSelectionViewController.cxx
- src/GuiQt/AnnotationSelectionViewController.h
- src/GuiQt/AnnotationTextAlignmentWidget.cxx
- src/GuiQt/AnnotationTextAlignmentWidget.h
- src/GuiQt/AnnotationTextEditorDialog.cxx
- src/GuiQt/AnnotationTextEditorDialog.h
- src/GuiQt/AnnotationTextEditorWidget.cxx
- src/GuiQt/AnnotationTextEditorWidget.h
- src/GuiQt/AnnotationTextOrientationWidget.cxx
- src/GuiQt/AnnotationTextOrientationWidget.h
- + src/GuiQt/AnnotationTextSubstitutionLayerSetViewController.cxx
- + src/GuiQt/AnnotationTextSubstitutionLayerSetViewController.h
- + src/GuiQt/AnnotationTextSubstitutionLayerViewController.cxx
- + src/GuiQt/AnnotationTextSubstitutionLayerViewController.h
- − src/GuiQt/AnnotationTextSubstitutionViewController.cxx
- src/GuiQt/AnnotationWidthHeightWidget.cxx
- src/GuiQt/BalsaDatabaseManager.cxx
- src/GuiQt/BalsaDatabaseManager.h
- src/GuiQt/BalsaDatabaseUploadSceneFileDialog.cxx
- src/GuiQt/BorderFileSplitDialog.cxx
- src/GuiQt/BorderOptimizeDialog.cxx
- src/GuiQt/BorderSelectionViewController.cxx
- src/GuiQt/BrainBrowserWindow.cxx
- src/GuiQt/BrainBrowserWindow.h
- src/GuiQt/BrainBrowserWindowEditMenuItemEnum.cxx
- src/GuiQt/BrainBrowserWindowOrientedToolBox.cxx
- src/GuiQt/BrainBrowserWindowOrientedToolBox.h
- src/GuiQt/BrainBrowserWindowToolBar.cxx
- src/GuiQt/BrainBrowserWindowToolBar.h
- src/GuiQt/BrainBrowserWindowToolBarAllSurface.cxx
- src/GuiQt/BrainBrowserWindowToolBarAllSurface.h
- src/GuiQt/BrainBrowserWindowToolBarChartAttributes.cxx
- src/GuiQt/BrainBrowserWindowToolBarChartTwoAttributes.cxx
- src/GuiQt/BrainBrowserWindowToolBarChartTwoOrientedAxes.cxx
- src/GuiQt/BrainBrowserWindowToolBarChartTwoType.cxx
- src/GuiQt/BrainBrowserWindowToolBarChartType.cxx
- src/GuiQt/BrainBrowserWindowToolBarComponent.cxx
- src/GuiQt/BrainBrowserWindowToolBarComponent.h
- + src/GuiQt/BrainBrowserWindowToolBarHistology.cxx
- + src/GuiQt/BrainBrowserWindowToolBarHistology.h
- + src/GuiQt/BrainBrowserWindowToolBarImage.cxx
- + src/GuiQt/BrainBrowserWindowToolBarImage.h
- src/GuiQt/BrainBrowserWindowToolBarOrientation.cxx
- src/GuiQt/BrainBrowserWindowToolBarOrientation.h
- src/GuiQt/BrainBrowserWindowToolBarSlicePlane.cxx
- src/GuiQt/BrainBrowserWindowToolBarSlicePlane.h
- src/GuiQt/BrainBrowserWindowToolBarSliceSelection.cxx
- src/GuiQt/BrainBrowserWindowToolBarSliceSelection.h
- src/GuiQt/BrainBrowserWindowToolBarSurfaceMontage.cxx
- src/GuiQt/BrainBrowserWindowToolBarSurfaceMontage.h
- src/GuiQt/BrainBrowserWindowToolBarTab.cxx
- src/GuiQt/BrainBrowserWindowToolBarTab.h
- src/GuiQt/BrainBrowserWindowToolBarTabPopUpMenu.cxx
- src/GuiQt/BrainBrowserWindowToolBarView.cxx
- src/GuiQt/BrainBrowserWindowToolBarView.h
- + src/GuiQt/BrainBrowserWindowToolBarVolumeMPR.cxx
- src/Brain/SelectionItemSurfaceNodeIdentificationSymbol.h → src/GuiQt/BrainBrowserWindowToolBarVolumeMPR.h
- src/GuiQt/BrainBrowserWindowToolBarVolumeMontage.cxx
- src/GuiQt/BrainBrowserWindowToolBarVolumeMontage.h
- src/GuiQt/BrainOpenGLWidget.cxx
- src/GuiQt/BrainOpenGLWidget.h
- src/GuiQt/CMakeLists.txt
- src/GuiQt/CaretDataFileSelectionComboBox.cxx
- src/GuiQt/CaretDataFileSelectionComboBox.h
- src/GuiQt/CaretFileDialog.cxx
- src/GuiQt/CaretFileDialog.h
- src/GuiQt/CaretFileDialogExtendable.h
- src/GuiQt/CaretFileRemoteDialog.cxx
- src/GuiQt/CaretMappableDataFileAndMapSelectorObject.cxx
- src/GuiQt/CaretMappableDataFileAndMapSelectorObject.h
- src/GuiQt/ChartHistoryViewController.cxx
- src/GuiQt/ChartLinesSelectionViewController.cxx
- src/GuiQt/ChartMatrixParcelSelectionViewController.cxx
- src/GuiQt/ChartMatrixSeriesSelectionViewController.cxx
- src/GuiQt/ChartTwoAxisPropertiesEditorDialog.h
- src/GuiQt/ChartTwoAxisPropertiesEditorWidget.cxx
- src/GuiQt/ChartTwoAxisPropertiesEditorWidget.h
- src/GuiQt/ChartTwoCartesianCustomSubdivisionsEditorWidget.cxx
- src/GuiQt/ChartTwoLineLayerNormalizationWidget.cxx
- src/GuiQt/ChartTwoLineLayerNormalizationWidget.h
- src/GuiQt/ChartTwoOverlaySetViewController.cxx
- src/GuiQt/ChartTwoOverlayViewController.cxx
- src/GuiQt/ChartTwoTitleEditorWidget.cxx
- + src/GuiQt/ChooseBorderFocusFromFileDialog.cxx
- + src/GuiQt/ChooseBorderFocusFromFileDialog.h
- src/GuiQt/CiftiConnectivityMatrixViewController.cxx
- src/GuiQt/CiftiConnectivityMatrixViewController.h
- src/GuiQt/CiftiParcelSelectionComboBox.cxx
- src/GuiQt/ClippingPlanesWidget.cxx
- src/GuiQt/ClippingPlanesWidget.h
- + src/GuiQt/ConnectivityCorrelationSettingsMenu.cxx
- + src/GuiQt/ConnectivityCorrelationSettingsMenu.h
- + src/GuiQt/ContextSensitiveMenuItemsEnum.cxx
- + src/GuiQt/ContextSensitiveMenuItemsEnum.h
- src/GuiQt/CopyPaletteColorMappingToFilesDialog.cxx
- src/GuiQt/CursorEnum.cxx
- src/GuiQt/CursorEnum.h
- src/GuiQt/CursorManager.cxx
- src/GuiQt/CursorManager.h
- src/GuiQt/CustomViewDialog.cxx
- src/GuiQt/CustomViewDialog.h
- + src/GuiQt/CziImageExportDialog.cxx
- + src/GuiQt/CziImageExportDialog.h
- + src/GuiQt/DataFileEditorDialog.cxx
- + src/GuiQt/DataFileEditorDialog.h
- + src/GuiQt/DingOntologyTermsDialog.cxx
- + src/GuiQt/DingOntologyTermsDialog.h
- src/GuiQt/DisplayGroupAndTabItemViewController.cxx
- src/GuiQt/DisplayGroupAndTabItemViewController.h
- src/GuiQt/EventAnnotationCreateNewType.cxx
- src/GuiQt/EventAnnotationCreateNewType.h
- + src/GuiQt/EventAnnotationDrawingFinishCancel.cxx
- + src/GuiQt/EventAnnotationDrawingFinishCancel.h
- src/GuiQt/EventAnnotationGetDrawnInWindow.cxx
- src/GuiQt/EventAnnotationGetDrawnInWindow.h
- + src/GuiQt/EventAnnotationGetSelectedInsertNewFile.cxx
- + src/GuiQt/EventAnnotationGetSelectedInsertNewFile.h
- + src/GuiQt/EventGraphicsPaintNowAllWindows.cxx
- + src/GuiQt/EventGraphicsPaintNowAllWindows.h
- + src/GuiQt/EventGraphicsPaintNowOneWindow.cxx
- + src/GuiQt/EventGraphicsPaintNowOneWindow.h
- src/GuiQt/EventGraphicsUpdateAllWindows.cxx → src/GuiQt/EventGraphicsPaintSoonAllWindows.cxx
- src/GuiQt/EventGraphicsUpdateAllWindows.h → src/GuiQt/EventGraphicsPaintSoonAllWindows.h
- src/GuiQt/EventGraphicsUpdateOneWindow.cxx → src/GuiQt/EventGraphicsPaintSoonOneWindow.cxx
- src/GuiQt/EventGraphicsUpdateOneWindow.h → src/GuiQt/EventGraphicsPaintSoonOneWindow.h
- − src/GuiQt/EventImageCapture.cxx
- src/GuiQt/EventUpdateInformationWindows.cxx
- src/GuiQt/EventUserInterfaceUpdate.cxx
- + src/GuiQt/ExitProgramModifiedFilesDialog.cxx
- + src/GuiQt/ExitProgramModifiedFilesDialog.h
- src/GuiQt/FiberOrientationSelectionViewController.cxx
- src/GuiQt/FiberOrientationSelectionViewController.h
- src/GuiQt/FiberSamplesOpenGLWidget.cxx
- src/GuiQt/FociProjectionDialog.cxx
- src/GuiQt/FociPropertiesEditorDialog.cxx
- src/GuiQt/FociPropertiesEditorDialog.h
- src/GuiQt/FociSelectionViewController.cxx
- src/GuiQt/GapsAndMarginsDialog.cxx
- src/GuiQt/GiftiLabelTableEditor.cxx
- src/GuiQt/GroupAndNameHierarchyViewController.cxx
- src/GuiQt/GroupAndNameHierarchyViewController.h
- src/GuiQt/GuiManager.cxx
- src/GuiQt/GuiManager.h
- src/GuiQt/HelpViewerDialog.cxx
- src/GuiQt/HelpViewerDialog.h
- + src/GuiQt/HistologyOverlaySetViewController.cxx
- + src/GuiQt/HistologyOverlaySetViewController.h
- + src/GuiQt/HistologyOverlaySettingsMenu.cxx
- + src/GuiQt/HistologyOverlaySettingsMenu.h
- + src/GuiQt/HistologyOverlayViewController.cxx
- + src/GuiQt/HistologyOverlayViewController.h
- src/GuiQt/IdentificationDisplayWidget.cxx
- src/GuiQt/IdentificationDisplayWidget.h
- − src/GuiQt/IdentificationFileFilteringRow.cxx
- src/GuiQt/IdentificationFileFilteringTableWidget.cxx
- src/GuiQt/IdentificationFileFilteringTableWidget.h
- src/GuiQt/IdentifyBrainordinateDialog.cxx
- src/GuiQt/IdentifyBrainordinateDialog.h
- src/GuiQt/ImageCaptureDialog.cxx
- src/GuiQt/ImageCaptureDialog.h
- src/GuiQt/ImageFileConvertToVolumeFileDialog.cxx
- src/GuiQt/ImageSelectionViewController.cxx
- src/GuiQt/InformationDisplayDialog.cxx
- src/GuiQt/InformationDisplayPropertiesDialog.cxx
- src/GuiQt/InformationDisplayPropertiesDialog.h
- + src/GuiQt/LabelSelectionDialog.cxx
- + src/GuiQt/LabelSelectionDialog.h
- src/GuiQt/LabelSelectionViewController.cxx
- src/GuiQt/LabelSelectionViewController.h
- + src/GuiQt/LabelSelectionViewHierarchyController.cxx
- + src/GuiQt/LabelSelectionViewHierarchyController.h
- + src/GuiQt/LabelSelectionViewWidget.cxx
- + src/GuiQt/LabelSelectionViewWidget.h
- + src/GuiQt/LabelSelectionWidget.cxx
- + src/GuiQt/LabelSelectionWidget.h
- src/GuiQt/MacDockMenu.cxx
- src/GuiQt/MapSettingsChartTwoLineHistoryWidget.cxx
- src/GuiQt/MapSettingsColorBarPaletteOptionsWidget.cxx
- src/GuiQt/MapSettingsColorBarWidget.cxx
- src/GuiQt/MapSettingsFiberTrajectoryWidget.cxx
- src/GuiQt/MapSettingsFiberTrajectoryWidget.h
- src/GuiQt/MapSettingsLabelsWidget.cxx
- src/GuiQt/MapSettingsLayerWidget.cxx
- src/GuiQt/MapSettingsLayerWidget.h
- + src/GuiQt/MapSettingsModulateWidget.cxx
- + src/GuiQt/MapSettingsModulateWidget.h
- src/GuiQt/MapSettingsPaletteColorMappingWidget.cxx
- src/GuiQt/MapSettingsParcelsWidget.cxx
- src/GuiQt/MapYokingGroupComboBox.cxx
- src/GuiQt/MapYokingGroupComboBox.h
- src/GuiQt/MediaOverlaySetViewController.cxx
- + src/GuiQt/MediaOverlaySettingsMenu.cxx
- src/GuiQt/IdentificationFileFilteringRow.h → src/GuiQt/MediaOverlaySettingsMenu.h
- src/GuiQt/MediaOverlayViewController.cxx
- src/GuiQt/MediaOverlayViewController.h
- src/GuiQt/MetaDataEditorDialog.cxx
- src/GuiQt/MetaDataEditorDialog.h
- src/GuiQt/MetaDataEditorWidget.cxx
- − src/GuiQt/MovieDialog.cxx
- − src/GuiQt/MovieDialog.h
- − src/GuiQt/MovieDialog.ui
- src/GuiQt/MovieRecordingDialog.cxx
- + src/GuiQt/OpenFileQuicklyDialog.cxx
- + src/GuiQt/OpenFileQuicklyDialog.h
- src/GuiQt/OverlaySetViewController.cxx
- src/GuiQt/OverlaySettingsEditorDialog.cxx
- src/GuiQt/OverlaySettingsEditorDialog.h
- src/GuiQt/OverlayViewController.cxx
- src/GuiQt/PalettePixmapPainter.cxx
- + src/GuiQt/PreferencesDevelopOptionsWidget.cxx
- + src/GuiQt/PreferencesDevelopOptionsWidget.h
- src/GuiQt/PreferencesDialog.cxx
- src/GuiQt/PreferencesDialog.h
- + src/GuiQt/PreferencesDisplayWidget.cxx
- + src/GuiQt/PreferencesDisplayWidget.h
- + src/GuiQt/PreferencesImageWidget.cxx
- + src/GuiQt/PreferencesImageWidget.h
- src/GuiQt/ProgressReportingDialog.cxx
- src/GuiQt/ProgressReportingDialog.h
- src/GuiQt/ProgressReportingWithSlots.cxx
- src/GuiQt/RecentFilesDialog.cxx
- + src/GuiQt/RecentSceneMenu.cxx
- + src/GuiQt/RecentSceneMenu.h
- src/GuiQt/RegionOfInterestCreateFromBorderDialog.cxx
- + src/GuiQt/SamplesSelectionViewController.cxx
- src/GuiQt/AnnotationTextSubstitutionViewController.h → src/GuiQt/SamplesSelectionViewController.h
- src/GuiQt/ScaleBarWidget.cxx
- src/GuiQt/SceneBasePathWidget.cxx
- + src/GuiQt/SceneClassInfoWidget.cxx
- + src/GuiQt/SceneClassInfoWidget.h
- src/GuiQt/SceneCreateReplaceDialog.cxx
- src/GuiQt/SceneCreateReplaceDialog.h
- src/GuiQt/SceneDataFileTreeItem.cxx
- src/GuiQt/SceneDataFileTreeItemModel.cxx
- src/GuiQt/SceneDialog.cxx
- src/GuiQt/SceneDialog.h
- src/GuiQt/SceneFileInformationDialog.cxx
- src/GuiQt/SceneFileInformationDialog.h
- src/GuiQt/ScenePreviewDialog.cxx
- + src/GuiQt/SceneSelectionWidget.cxx
- + src/GuiQt/SceneSelectionWidget.h
- src/GuiQt/SceneWindowGeometry.cxx
- src/GuiQt/SpecFileManagementDialog.cxx
- src/GuiQt/SurfacePropertiesEditorDialog.cxx
- src/GuiQt/TileTabsConfigurationDialog.cxx
- src/GuiQt/TileTabsConfigurationDialog.h
- + src/GuiQt/TileTabsLayoutConfigurationTypeWidget.cxx
- + src/GuiQt/TileTabsLayoutConfigurationTypeWidget.h
- + src/GuiQt/UnicodeCharacterEntryDialog.cxx
- + src/GuiQt/UnicodeCharacterEntryDialog.h
- src/GuiQt/UserInputModeAbstract.cxx
- src/GuiQt/UserInputModeAbstract.h
- src/GuiQt/UserInputModeAnnotations.cxx
- src/GuiQt/UserInputModeAnnotations.h
- src/GuiQt/UserInputModeAnnotationsContextMenu.cxx
- src/GuiQt/UserInputModeAnnotationsContextMenu.h
- src/GuiQt/UserInputModeAnnotationsWidget.cxx
- src/GuiQt/UserInputModeAnnotationsWidget.h
- src/GuiQt/UserInputModeBorders.cxx
- src/GuiQt/UserInputModeBorders.h
- src/GuiQt/UserInputModeBordersWidget.cxx
- src/GuiQt/UserInputModeFoci.cxx
- src/GuiQt/UserInputModeFoci.h
- src/GuiQt/UserInputModeFociWidget.cxx
- src/GuiQt/UserInputModeFociWidget.h
- src/GuiQt/UserInputModeImage.cxx
- src/GuiQt/UserInputModeImage.h
- src/GuiQt/UserInputModeImageWidget.cxx
- + src/GuiQt/UserInputModeSamplesEdit.cxx
- src/GuiQt/UserInputModeTileTabsManualLayout.h → src/GuiQt/UserInputModeSamplesEdit.h
- src/GuiQt/UserInputModeTileTabsManualLayout.cxx → src/GuiQt/UserInputModeTileTabsLayout.cxx
- + src/GuiQt/UserInputModeTileTabsLayout.h
- src/GuiQt/UserInputModeTileTabsManualLayoutContextMenu.cxx → src/GuiQt/UserInputModeTileTabsLayoutContextMenu.cxx
- src/GuiQt/UserInputModeTileTabsManualLayoutContextMenu.h → src/GuiQt/UserInputModeTileTabsLayoutContextMenu.h
- src/GuiQt/UserInputModeView.cxx
- src/GuiQt/UserInputModeView.h
- src/GuiQt/UserInputModeViewContextMenu.cxx
- src/GuiQt/UserInputModeViewContextMenu.h
- src/GuiQt/UserInputModeVolumeEdit.cxx
- src/GuiQt/UserInputModeVolumeEdit.h
- src/GuiQt/UserInputModeVolumeEditWidget.cxx
- src/GuiQt/VolumeFileCreateDialog.cxx
- src/GuiQt/VolumeFileCreateDialog.h
- + src/GuiQt/VolumeFileResampleDialog.cxx
- + src/GuiQt/VolumeFileResampleDialog.h
- + src/GuiQt/VolumeMprSettingsWidget.cxx
- + src/GuiQt/VolumeMprSettingsWidget.h
- + src/GuiQt/VolumeObliqueOptionsWidget.cxx
- + src/GuiQt/VolumeObliqueOptionsWidget.h
- src/GuiQt/VolumePropertiesEditorDialog.cxx
- src/GuiQt/VolumeSurfaceOutlineSetViewController.cxx
- src/GuiQt/VolumeSurfaceOutlineViewController.cxx
- src/GuiQt/VolumeSurfaceOutlineViewController.h
- src/GuiQt/WbMacroCustomOperationAnimateOverlayCrossFade.cxx
- src/GuiQt/WbMacroCustomOperationAnimateVolumeSliceSequence.cxx
- src/GuiQt/WbMacroCustomOperationBase.cxx
- src/GuiQt/WbMacroCustomOperationIncrementRotation.cxx
- src/GuiQt/WbMacroCustomOperationIncrementVolumeSlice.cxx
- src/GuiQt/WbMacroHelper.cxx
- + src/GuiQt/WorkbenchInstallationAssistantDialog.cxx
- + src/GuiQt/WorkbenchInstallationAssistantDialog.h
- src/GuiQt/WuQColorEditorWidget.cxx
- src/GuiQt/WuQColorEditorWidget.h
- src/GuiQt/WuQDataEntryDialog.cxx
- src/GuiQt/WuQDataEntryDialog.h
- src/GuiQt/WuQDialog.cxx
- src/GuiQt/WuQDialog.h
- src/GuiQt/WuQDialogModal.h
- src/GuiQt/WuQDialogNonModal.h
- src/GuiQt/WuQDoubleSpinBox.cxx
- src/GuiQt/WuQGridLayoutGroup.h
- + src/GuiQt/WuQHyperlinkToolTip.cxx
- + src/GuiQt/WuQHyperlinkToolTip.h
- src/GuiQt/WuQImageLabel.cxx
- src/GuiQt/WuQMacroDialog.cxx
- src/GuiQt/WuQMacroExecutor.cxx
- src/GuiQt/WuQMacroManager.cxx
- src/GuiQt/WuQMacroWidgetAction.cxx
- src/GuiQt/WuQMessageBox.cxx
- src/GuiQt/WuQMessageBox.h
- + src/GuiQt/WuQMessageBoxTwo.cxx
- + src/GuiQt/WuQMessageBoxTwo.h
- src/GuiQt/WuQSpecialIncrementDoubleSpinBox.cxx
- src/GuiQt/WuQTabWidget.cxx
- + src/GuiQt/WuQTextEditWithToolBarWidget.cxx
- + src/GuiQt/WuQTextEditWithToolBarWidget.h
- src/GuiQt/WuQTextEditorDialog.cxx
- src/GuiQt/WuQTextEditorDialog.h
- src/GuiQt/WuQTreeWidget.cxx
- src/GuiQt/WuQTreeWidget.h
- src/GuiQt/WuQtUtilities.cxx
- src/GuiQt/WuQtUtilities.h
- + src/GuiQt/macos.h
- + src/GuiQt/macos.mm
- src/Nifti/CMakeLists.txt
- src/Nifti/Matrix4x4.cxx
- src/Nifti/Matrix4x4.h
- src/Nifti/NiftiHeader.cxx
- src/Nifti/NiftiHeader.h
- src/OSMesaDummy/CMakeLists.txt
- src/OSMesaDummy/OSMesaDummy.c
- + src/OmeZarr/CMakeLists.txt
- + src/OmeZarr/OmeAttrsV0p4JsonFile.cxx
- + src/OmeZarr/OmeAttrsV0p4JsonFile.h
- src/Brain/SelectionItemVoxelIdentificationSymbol.cxx → src/OmeZarr/OmeAxis.cxx
- src/Brain/SelectionItemImage.h → src/OmeZarr/OmeAxis.h
- + src/OmeZarr/OmeAxisTypeEnum.cxx
- + src/OmeZarr/OmeAxisTypeEnum.h
- + src/OmeZarr/OmeCoordinateTransformationTypeEnum.cxx
- + src/OmeZarr/OmeCoordinateTransformationTypeEnum.h
- + src/OmeZarr/OmeCoordinateTransformations.cxx
- + src/OmeZarr/OmeCoordinateTransformations.h
- + src/OmeZarr/OmeDataSet.cxx
- + src/OmeZarr/OmeDataSet.h
- + src/OmeZarr/OmeDimensionIndices.cxx
- + src/OmeZarr/OmeDimensionIndices.h
- + src/OmeZarr/OmeDimensionSizes.cxx
- + src/OmeZarr/OmeDimensionSizes.h
- + src/OmeZarr/OmeFileReader.cxx
- + src/OmeZarr/OmeFileReader.h
- + src/OmeZarr/OmeImage.cxx
- + src/OmeZarr/OmeImage.h
- + src/OmeZarr/OmeSpaceUnitEnum.cxx
- + src/OmeZarr/OmeSpaceUnitEnum.h
- + src/OmeZarr/OmeTimeUnitEnum.cxx
- + src/OmeZarr/OmeTimeUnitEnum.h
- + src/OmeZarr/OmeVersionEnum.cxx
- + src/OmeZarr/OmeVersionEnum.h
- + src/OmeZarr/ZarrCompressorTypeEnum.cxx
- + src/OmeZarr/ZarrCompressorTypeEnum.h
- + src/OmeZarr/ZarrDataTypeByteOrderEnum.cxx
- + src/OmeZarr/ZarrDataTypeByteOrderEnum.h
- + src/OmeZarr/ZarrDataTypeEnum.cxx
- + src/OmeZarr/ZarrDataTypeEnum.h
- + src/OmeZarr/ZarrDimensionSeparatorEnum.cxx
- + src/OmeZarr/ZarrDimensionSeparatorEnum.h
- + src/OmeZarr/ZarrDriverTypeEnum.cxx
- + src/OmeZarr/ZarrDriverTypeEnum.h
- + src/OmeZarr/ZarrHelper.cxx
- + src/OmeZarr/ZarrHelper.h
- + src/OmeZarr/ZarrImageReader.cxx
- + src/OmeZarr/ZarrImageReader.h
- + src/OmeZarr/ZarrJsonFileBase.cxx
- + src/OmeZarr/ZarrJsonFileBase.h
- + src/OmeZarr/ZarrRowColumnMajorOrderTypeEnum.cxx
- + src/OmeZarr/ZarrRowColumnMajorOrderTypeEnum.h
- + src/OmeZarr/ZarrV2ArrayJsonFile.cxx
- + src/OmeZarr/ZarrV2ArrayJsonFile.h
- + src/OmeZarr/ZarrV2GroupJsonFile.cxx
- + src/OmeZarr/ZarrV2GroupJsonFile.h
- src/Operations/CMakeLists.txt
- src/Operations/OperationAddToSpecFile.cxx
- + src/Operations/OperationCiftiAverage.cxx
- src/Algorithms/AlgorithmCiftiAverage.h → src/Operations/OperationCiftiAverage.h
- src/Operations/OperationCiftiConvert.cxx
- src/Operations/OperationCiftiCreateDenseFromTemplate.cxx
- src/Operations/OperationCiftiCreateScalarSeries.cxx
- src/Operations/OperationCiftiLabelExportTable.cxx
- src/Operations/OperationCiftiLabelImport.cxx
- src/Operations/OperationCiftiMath.cxx
- src/Operations/OperationCiftiMerge.cxx
- src/Operations/OperationCiftiMerge.h
- src/Operations/OperationCiftiPalette.cxx
- src/Operations/OperationCiftiStats.cxx
- src/Operations/OperationCiftiWeightedStats.cxx
- src/Operations/OperationConvertWarpfield.cxx
- src/Operations/OperationFileInformation.cxx
- src/Operations/OperationLabelExportTable.cxx
- src/Operations/OperationMetadataStringReplace.cxx
- src/Operations/OperationMetricLabelImport.cxx
- src/Operations/OperationMetricPalette.cxx
- src/Operations/OperationMetricStats.cxx
- src/Operations/OperationMetricWeightedStats.cxx
- + src/Operations/OperationSceneFileUpdate.cxx
- + src/Operations/OperationSceneFileUpdate.h
- src/Operations/OperationShowScene.cxx
- src/Operations/OperationShowScene.h
- + src/Operations/OperationShowSceneTwo.cxx
- + src/Operations/OperationShowSceneTwo.h
- + src/Operations/OperationSpecFileModify.cxx
- + src/Operations/OperationSpecFileModify.h
- src/Operations/OperationSurfaceGeodesicDistanceAllToAll.cxx
- + src/Operations/OperationSurfaceGeodesicDistanceSparseText.cxx
- + src/Operations/OperationSurfaceGeodesicDistanceSparseText.h
- + src/Operations/OperationSurfaceSphereTriangularPatches.cxx
- + src/Operations/OperationSurfaceSphereTriangularPatches.h
- src/Operations/OperationTemplate.cxx.txt
- src/Operations/OperationTemplate.h.txt
- src/Operations/OperationVolumeCapturePlane.cxx
- + src/Operations/OperationVolumeComponentsToFrames.cxx
- + src/Operations/OperationVolumeComponentsToFrames.h
- src/Operations/OperationVolumeLabelExportTable.cxx
- src/Operations/OperationVolumeLabelImport.cxx
- src/Operations/OperationVolumePalette.cxx
- src/Operations/OperationVolumeReorient.cxx
- src/Operations/OperationVolumeSetSpace.cxx
- src/Operations/OperationVolumeStats.cxx
- src/Operations/OperationVolumeWeightedStats.cxx
- src/Operations/OperationZipSceneFile.cxx
- src/Operations/OperationZipSceneFile.h
- src/Operations/OperationZipSpecFile.cxx
- src/Operations/OperationZipSpecFile.h
- src/OperationsBase/AbstractOperation.cxx
- src/OperationsBase/AbstractOperation.h
- src/OperationsBase/CMakeLists.txt
- src/Common/CaretCommandGlobalOptions.cxx → src/OperationsBase/CaretCommandGlobalOptions.cxx
- src/Common/CaretCommandGlobalOptions.h → src/OperationsBase/CaretCommandGlobalOptions.h
- src/OperationsBase/OperationParameters.cxx
- src/OperationsBase/OperationParameters.h
- src/OperationsBase/OperationParametersEnum.cxx
- src/OperationsBase/OperationParametersEnum.h
- src/Palette/CMakeLists.txt
- src/Palette/Palette.h
- src/Palette/PaletteColorMapping.cxx
- src/Quazip/CMakeLists.txt
- src/Quazip/quagzipfile.cpp
- src/Quazip/quaziodevice.cpp
- src/Quazip/quazipdir.cpp
- src/Quazip/quazipfileinfo.cpp
- src/Qwt/CMakeLists.txt
- src/Qwt/qwt_clipper.cpp
- src/Qwt/qwt_date.cpp
- src/Qwt/qwt_date_scale_draw.cpp
- src/Qwt/qwt_date_scale_engine.cpp
- src/Qwt/qwt_dyngrid_layout.cpp
- src/Qwt/qwt_event_pattern.cpp
- src/Qwt/qwt_graphic.cpp
- src/Qwt/qwt_legend.cpp
- src/Qwt/qwt_legend_label.cpp
- src/Qwt/qwt_magnifier.cpp
- src/Qwt/qwt_painter.cpp
- src/Qwt/qwt_painter_command.h
- src/Qwt/qwt_picker.cpp
- src/Qwt/qwt_plot.cpp
- src/Qwt/qwt_plot_barchart.cpp
- src/Qwt/qwt_plot_barchart.h
- src/Qwt/qwt_plot_canvas.cpp
- src/Qwt/qwt_plot_curve.h
- src/Qwt/qwt_plot_dict.cpp
- src/Qwt/qwt_plot_histogram.h
- src/Qwt/qwt_plot_intervalcurve.h
- src/Qwt/qwt_plot_item.cpp
- src/Qwt/qwt_plot_layout.cpp
- src/Qwt/qwt_plot_layout.h
- src/Qwt/qwt_plot_marker.h
- src/Qwt/qwt_plot_multi_barchart.cpp
- src/Qwt/qwt_plot_multi_barchart.h
- src/Qwt/qwt_plot_picker.cpp
- src/Qwt/qwt_plot_rasteritem.cpp
- src/Qwt/qwt_plot_rasteritem.h
- src/Qwt/qwt_plot_renderer.cpp
- src/Qwt/qwt_plot_rescaler.cpp
- src/Qwt/qwt_plot_seriesitem.h
- src/Qwt/qwt_plot_shapeitem.h
- src/Qwt/qwt_plot_spectrocurve.h
- src/Qwt/qwt_plot_spectrogram.cpp
- src/Qwt/qwt_plot_spectrogram.h
- src/Qwt/qwt_plot_tradingcurve.h
- src/Qwt/qwt_plot_xml.cpp
- src/Qwt/qwt_scale_widget.cpp
- src/Qwt/qwt_text.cpp
- src/Qwt/qwt_text.h
- src/Qwt/qwt_text_engine.cpp
- src/Qwt/qwt_text_label.cpp
- src/Qwt/qwt_widget_overlay.cpp
- src/QxtCore/CMakeLists.txt
- + src/Resources/Data/DingOntology/DingOntologyTerms.csv
- + src/Resources/Data/data_resources.qrc
- + src/Resources/Gui/MessageDialog/BrainCriticalImage.png
- + src/Resources/Gui/MessageDialog/BrainInformationImage.png
- + src/Resources/Gui/MessageDialog/BrainQuestionImage.png
- + src/Resources/Gui/MessageDialog/BrainWarningImage.png
- + src/Resources/Gui/ToolBar/redo.png
- + src/Resources/Gui/ToolBar/select-region.png
- + src/Resources/Gui/ToolBar/undo.png
- src/Resources/Gui/gui_resources.qrc
- − src/Resources/Help/HelpFiles/Annotations/Annotations_1.4.2.fld/image021.png
- src/Resources/Help/HelpFiles/Annotations/Annotations_1.4.2.fld/image001.png → src/Resources/Help/HelpFiles/Annotations/Annotations_Guide.fld/image001.png
- src/Resources/Help/HelpFiles/Annotations/Annotations_1.4.2.fld/image002.png → src/Resources/Help/HelpFiles/Annotations/Annotations_Guide.fld/image002.png
- src/Resources/Help/HelpFiles/Annotations/Annotations_1.4.2.fld/image003.png → src/Resources/Help/HelpFiles/Annotations/Annotations_Guide.fld/image003.png
- src/Resources/Help/HelpFiles/Annotations/Annotations_1.4.2.fld/image004.png → src/Resources/Help/HelpFiles/Annotations/Annotations_Guide.fld/image004.png
- src/Resources/Help/HelpFiles/Annotations/Annotations_1.4.2.fld/image005.png → src/Resources/Help/HelpFiles/Annotations/Annotations_Guide.fld/image005.png
- src/Resources/Help/HelpFiles/Annotations/Annotations_1.4.2.fld/image006.png → src/Resources/Help/HelpFiles/Annotations/Annotations_Guide.fld/image006.png
- src/Resources/Help/HelpFiles/Annotations/Annotations_1.4.2.fld/image007.png → src/Resources/Help/HelpFiles/Annotations/Annotations_Guide.fld/image007.png
- src/Resources/Help/HelpFiles/Annotations/Annotations_1.4.2.fld/image008.png → src/Resources/Help/HelpFiles/Annotations/Annotations_Guide.fld/image008.png
- src/Resources/Help/HelpFiles/Annotations/Annotations_1.4.2.fld/image009.png → src/Resources/Help/HelpFiles/Annotations/Annotations_Guide.fld/image009.png
- src/Resources/Help/HelpFiles/Annotations/Annotations_1.4.2.fld/image010.png → src/Resources/Help/HelpFiles/Annotations/Annotations_Guide.fld/image010.png
- src/Resources/Help/HelpFiles/Annotations/Annotations_1.4.2.fld/image011.png → src/Resources/Help/HelpFiles/Annotations/Annotations_Guide.fld/image011.png
- src/Resources/Help/HelpFiles/Annotations/Annotations_1.4.2.fld/image012.png → src/Resources/Help/HelpFiles/Annotations/Annotations_Guide.fld/image012.png
- src/Resources/Help/HelpFiles/Annotations/Annotations_1.4.2.fld/image013.png → src/Resources/Help/HelpFiles/Annotations/Annotations_Guide.fld/image013.png
- src/Resources/Help/HelpFiles/Annotations/Annotations_1.4.2.fld/image014.png → src/Resources/Help/HelpFiles/Annotations/Annotations_Guide.fld/image014.png
- src/Resources/Help/HelpFiles/Annotations/Annotations_1.4.2.fld/image015.png → src/Resources/Help/HelpFiles/Annotations/Annotations_Guide.fld/image015.png
- src/Resources/Help/HelpFiles/Annotations/Annotations_1.4.2.fld/image016.png → src/Resources/Help/HelpFiles/Annotations/Annotations_Guide.fld/image016.png
- src/Resources/Help/HelpFiles/Annotations/Annotations_1.4.2.fld/image017.png → src/Resources/Help/HelpFiles/Annotations/Annotations_Guide.fld/image017.png
- src/Resources/Help/HelpFiles/Annotations/Annotations_1.4.2.fld/image018.png → src/Resources/Help/HelpFiles/Annotations/Annotations_Guide.fld/image018.png
- src/Resources/Help/HelpFiles/Annotations/Annotations_1.4.2.fld/image019.png → src/Resources/Help/HelpFiles/Annotations/Annotations_Guide.fld/image019.png
- src/Resources/Help/HelpFiles/Annotations/Annotations_1.4.2.fld/image020.png → src/Resources/Help/HelpFiles/Annotations/Annotations_Guide.fld/image020.png
- + src/Resources/Help/HelpFiles/Annotations/Annotations_Guide.fld/image021.png
- src/Resources/Help/HelpFiles/Annotations/Annotations_1.4.2.fld/image022.png → src/Resources/Help/HelpFiles/Annotations/Annotations_Guide.fld/image022.png
- src/Resources/Help/HelpFiles/Annotations/Annotations_1.4.2.fld/image023.png → src/Resources/Help/HelpFiles/Annotations/Annotations_Guide.fld/image023.png
- src/Resources/Help/HelpFiles/Annotations/Annotations_1.4.2.fld/image024.png → src/Resources/Help/HelpFiles/Annotations/Annotations_Guide.fld/image024.png
- src/Resources/Help/HelpFiles/Annotations/Annotations_1.4.2.fld/image025.png → src/Resources/Help/HelpFiles/Annotations/Annotations_Guide.fld/image025.png
- src/Resources/Help/HelpFiles/Annotations/Annotations_1.4.2.fld/image026.png → src/Resources/Help/HelpFiles/Annotations/Annotations_Guide.fld/image026.png
- src/Resources/Help/HelpFiles/Annotations/Annotations_1.4.2.fld/image027.png → src/Resources/Help/HelpFiles/Annotations/Annotations_Guide.fld/image027.png
- src/Resources/Help/HelpFiles/Annotations/Annotations_Guide.html
- src/Resources/Help/HelpFiles/Menus/View_Menu/Tile_Tabs_Configuration/Tile_Tabs_Configuration.html
- src/Resources/Help/HelpFiles/Menus/View_Menu/Tile_Tabs_Configuration/Tile_Tabs_Configuration_Manual.png
- src/Resources/Help/HelpFiles/Menus/View_Menu/Tile_Tabs_Configuration/Window_Tile_Editing_Toolbar.png
- src/Resources/Help/HelpFiles/Toolbar/Mode/Voxel Editing/VoxelEditing.html
- − src/Resources/Help/OLD_help_resources.qrc
- src/Resources/Help/help_resources.qrc
- src/Scenes/CMakeLists.txt
- src/Scenes/Scene.cxx
- src/Scenes/Scene.h
- src/Scenes/SceneAttributes.cxx
- src/Scenes/SceneAttributes.h
- src/Scenes/SceneBoolean.cxx
- src/Scenes/SceneBoolean.h
- src/Scenes/SceneBooleanArray.cxx
- src/Scenes/SceneBooleanArray.h
- src/Scenes/SceneClass.cxx
- src/Scenes/SceneClass.h
- src/Scenes/SceneClassArray.cxx
- src/Scenes/SceneClassArray.h
- src/Scenes/SceneClassAssistant.cxx
- src/Scenes/SceneClassAssistant.h
- src/Scenes/SceneFloat.cxx
- src/Scenes/SceneFloat.h
- src/Scenes/SceneFloatArray.cxx
- src/Scenes/SceneFloatArray.h
- src/Scenes/SceneInfo.cxx
- src/Scenes/SceneInfo.h
- − src/Scenes/SceneInfoSaxReader.cxx
- − src/Scenes/SceneInfoSaxReader.h
- src/Scenes/SceneInfoXmlStreamBase.h
- src/Scenes/SceneInfoXmlStreamReader.cxx
- src/Scenes/SceneInfoXmlStreamWriter.cxx
- src/Scenes/SceneInteger.cxx
- src/Scenes/SceneInteger.h
- src/Scenes/SceneIntegerArray.cxx
- src/Scenes/SceneIntegerArray.h
- + src/Scenes/SceneLongInteger.cxx
- src/Scenes/SceneWriterXml.h → src/Scenes/SceneLongInteger.h
- + src/Scenes/SceneLongIntegerArray.cxx
- + src/Scenes/SceneLongIntegerArray.h
- src/Scenes/SceneObjectDataTypeEnum.h
- src/Scenes/SceneObjectMapIntegerKey.cxx
- src/Scenes/SceneObjectMapIntegerKey.h
- src/Scenes/ScenePrimitive.h
- src/Scenes/ScenePrimitiveArray.cxx
- src/Scenes/ScenePrimitiveArray.h
- − src/Scenes/SceneSaxReader.cxx
- − src/Scenes/SceneSaxReader.h
- src/Scenes/SceneString.cxx
- src/Scenes/SceneString.h
- src/Scenes/SceneStringArray.cxx
- src/Scenes/SceneStringArray.h
- src/Scenes/SceneUnsignedByte.cxx
- src/Scenes/SceneUnsignedByte.h
- src/Scenes/SceneUnsignedByteArray.cxx
- src/Scenes/SceneUnsignedByteArray.h
- − src/Scenes/SceneWriterXml.cxx
- − src/Scenes/SceneXmlElements.h
- src/Scenes/SceneXmlStreamReader.cxx
- src/Scenes/SceneXmlStreamWriter.cxx
- src/Tests/CMakeLists.txt
- src/Xml/CMakeLists.txt
- src/FilesBase/GiftiException.cxx → src/Xml/GiftiException.cxx
- src/FilesBase/GiftiException.h → src/Xml/GiftiException.h
- src/FilesBase/GiftiMetaData.cxx → src/Xml/GiftiMetaData.cxx
- src/FilesBase/GiftiMetaData.h → src/Xml/GiftiMetaData.h
- + src/Xml/GiftiMetaDataElementDataTypeEnum.cxx
- + src/Xml/GiftiMetaDataElementDataTypeEnum.h
- + src/Xml/GiftiMetaDataValidatorInterface.h
- src/FilesBase/GiftiMetaDataXmlElements.h → src/Xml/GiftiMetaDataXmlElements.h
- src/FilesBase/GiftiXmlElements.cxx → src/Xml/GiftiXmlElements.cxx
- src/FilesBase/GiftiXmlElements.h → src/Xml/GiftiXmlElements.h
- src/Xml/XmlUnexpectedElementSaxParser.cxx
- src/debian/copyright
- src/kloewe/cpuinfo/CMakeLists.txt
- src/kloewe/dot/CMakeLists.txt
The diff was not included because it is too large.
View it on GitLab: https://salsa.debian.org/med-team/connectome-workbench/-/compare/8db09ff43bc09772b35d9ba5f82370694410fd69...cb7ec599f218f686cc500d6feb7572a3cfe60bd5
--
View it on GitLab: https://salsa.debian.org/med-team/connectome-workbench/-/compare/8db09ff43bc09772b35d9ba5f82370694410fd69...cb7ec599f218f686cc500d6feb7572a3cfe60bd5
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