[med-svn] r16576 - in trunk/packages/vtk-dicom/trunk/debian: . patches source

Mathieu Malaterre malat at moszumanska.debian.org
Mon Apr 7 09:55:32 UTC 2014 

Author: malat
Date: 2014-04-07 09:55:31 +0000 (Mon, 07 Apr 2014)
New Revision: 16576

Added:
   trunk/packages/vtk-dicom/trunk/debian/source/options
Removed:
   trunk/packages/vtk-dicom/trunk/debian/dicomdump.1
   trunk/packages/vtk-dicom/trunk/debian/dicomtonifti.1
   trunk/packages/vtk-dicom/trunk/debian/niftidump.1
   trunk/packages/vtk-dicom/trunk/debian/niftitodicom.1
Modified:
   trunk/packages/vtk-dicom/trunk/debian/changelog
   trunk/packages/vtk-dicom/trunk/debian/patches/cmakefix.patch
   trunk/packages/vtk-dicom/trunk/debian/rules
Log:
next upload

Modified: trunk/packages/vtk-dicom/trunk/debian/changelog
===================================================================
--- trunk/packages/vtk-dicom/trunk/debian/changelog	2014-04-07 09:35:38 UTC (rev 16575)
+++ trunk/packages/vtk-dicom/trunk/debian/changelog	2014-04-07 09:55:31 UTC (rev 16576)
@@ -3,8 +3,10 @@
   * Add patch to allow backport to wheezy
   * Change to DebianMed uploaders
   * Properly set minimum vtk version
+  * Use xz compression
+  * Fix man pages generation
 
- -- Mathieu Malaterre <malat at debian.org>  Mon, 07 Apr 2014 11:35:26 +0200
+ -- Mathieu Malaterre <malat at debian.org>  Mon, 07 Apr 2014 11:55:21 +0200
 
 vtk-dicom (0.4.4-1) unstable; urgency=low
 

Deleted: trunk/packages/vtk-dicom/trunk/debian/dicomdump.1
===================================================================
--- trunk/packages/vtk-dicom/trunk/debian/dicomdump.1	2014-04-07 09:35:38 UTC (rev 16575)
+++ trunk/packages/vtk-dicom/trunk/debian/dicomdump.1	2014-04-07 09:55:31 UTC (rev 16576)
@@ -1,11 +0,0 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.44.1.
-.TH DICOMDUMP "1" "March 2014" "dicomdump 0.4.2" "User Commands"
-.SH NAME
-dicomdump \- manual page for dicomdump 0.4.2
-.SH DESCRIPTION
-ERROR: In \fI/home/mathieu/debian/debian\-med/trunk/packages/vtk\-dicom/trunk/vtk\-dicom\-0.4.2/vtkDICOMSorter.cxx\fP, line 507
-vtkDICOMSorter (0x200bd20): ERROR: In \fI/home/mathieu/debian/debian\-med/trunk/packages/vtk\-dicom/trunk/vtk\-dicom\-0.4.2/vtkDICOMParser.cxx\fP, line 1345
-vtkDICOMParser (0x200c200): ReadFile: Can't open file \fB\-\-help\fR
-.SH AUTHOR
-This  manual  page was written by Mathieu Malaterre <malat at debian.org> for
-the Debian GNU/Linux system, but may be used by others.

Deleted: trunk/packages/vtk-dicom/trunk/debian/dicomtonifti.1
===================================================================
--- trunk/packages/vtk-dicom/trunk/debian/dicomtonifti.1	2014-04-07 09:35:38 UTC (rev 16575)
+++ trunk/packages/vtk-dicom/trunk/debian/dicomtonifti.1	2014-04-07 09:55:31 UTC (rev 16576)
@@ -1,101 +0,0 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.44.1.
-.TH DICOMTONIFTI "1" "March 2014" "dicomtonifti 0.4.2" "User Commands"
-.SH NAME
-dicomtonifti \- manual page for dicomtonifti 0.4.2
-.SH DESCRIPTION
-dicomtonifti 0.4.2 (HEAD         , 20 Mar 2014, 20:37:31)
-usage: dicomtonifti \fB\-o\fR file.nii file1.dcm [file2.dcm ...]
-.IP
-dicomtonifti \fB\-o\fR directory \fB\-\-batch\fR file1.dcm [file2.dcm ...]
-.SS "options:"
-.TP
-\fB\-o\fR <output.nii[.gz]>
-The output file (or directory, if \fB\-\-batch\fR).
-.TP
-\fB\-z\fR \fB\-\-compress\fR
-Compress output files.
-.TP
-\fB\-r\fR \fB\-\-recurse\fR
-Recurse into subdirectories.
-.TP
-\fB\-b\fR \fB\-\-batch\fR
-Do multiple series at once.
-.TP
-\fB\-s\fR \fB\-\-silent\fR
-Do not echo output filenames.
-.TP
-\fB\-v\fR \fB\-\-verbose\fR
-Verbose error reporting.
-.TP
-\fB\-L\fR \fB\-\-follow\-symlinks\fR
-Follow symbolic links when recursing.
-.TP
-\fB\-\-fsl\fR
-Reformat the image for use in FSL.
-.TP
-\fB\-\-reformat\-to\-axial\fR
-Reformat the image into axial orientation.
-.TP
-\fB\-\-no\-slice\-reordering\fR
-Never reorder the slices.
-.TP
-\fB\-\-no\-row\-reordering\fR
-Never reorder the rows.
-.TP
-\fB\-\-no\-column\-reordering\fR
-Never reorder the columns.
-.TP
-\fB\-\-no\-reordering\fR
-Never reorder slices, rows, or columns.
-.TP
-\fB\-\-no\-qform\fR
-Don't include a qform in the NIFTI file.
-.TP
-\fB\-\-no\-sform\fR
-Don't include an sform in the NIFTI file.
-.TP
-\fB\-\-version\fR
-Print the version and exit.
-.TP
-\fB\-\-help\fR
-Documentation for dicomtonifti.
-.PP
-This program will convert a DICOM series into a NIfTI file.
-.PP
-It reads the DICOM Position and Orientation metadata, and uses this
-information to generate qform and sform entries for the NIfTI header,
-after doing a conversion from the DICOM coordinate system to the NIfTI
-coordinate system.
-.PP
-By default, it will also reorder the columns of the image so that
-columns with higher indices are further to the patient's right (or
-in the case of sagittal images, further anterior).  Likewise, rows
-will be rearranged so that rows with higher indices are superior (or
-anterior for axial images).  Finally, it will reorder the slices
-so that the column direction, row direction, and slice direction
-follow the right\-hand rule.
-.PP
-It is also possible to reformat the images into the axial orientation
-via the \fB\-\-reformat\-to\-axial\fR option  This option is mutually exclusive
-with the no\-reordering options.  The resulting orientation matrix will
-be the identity matrix.
-.PP
-If the output NIFTI files are to be used with the FMRIB FSL package,
-then use the \fB\-\-fsl\fR option to reformat the images to match the standard
-FSL orientation: axial images with the slices arranged from inferior to
-superior, column number increasing from right to left, and row number
-increasing from posterior to anterior.  This will also convert the data
-type from unsigned 16\-bit to signed 16\-bit if necessary.
-.PP
-If batch mode is enabled, then the filenames will automatically be
-generated from the series description in the DICOM meta data:
-"PatientName/StudyDescription\-ID/SeriesDescription_N.nii.gz".
-.PP
-Here is an example of batch mode that recurses into subdirectories
-and compresses the output files, putting the results in the current
-directory:
-.PP
-dicomtonifti \fB\-brz\fR \fB\-o\fR . \fI/path/to/dicom/files\fP
-.SH AUTHOR
-This  manual  page was written by Mathieu Malaterre <malat at debian.org> for
-the Debian GNU/Linux system, but may be used by others.

Deleted: trunk/packages/vtk-dicom/trunk/debian/niftidump.1
===================================================================
--- trunk/packages/vtk-dicom/trunk/debian/niftidump.1	2014-04-07 09:35:38 UTC (rev 16575)
+++ trunk/packages/vtk-dicom/trunk/debian/niftidump.1	2014-04-07 09:55:31 UTC (rev 16576)
@@ -1,32 +0,0 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.44.1.
-.TH NIFTIDUMP "1" "March 2014" "niftidump 0.4.2" "User Commands"
-.SH NAME
-niftidump \- manual page for niftidump 0.4.2
-.SH DESCRIPTION
-ERROR: In \fI/home/mathieu/debian/debian\-med/trunk/packages/vtk\-dicom/trunk/vtk\-dicom\-0.4.2/vtkNIFTIReader.cxx\fP, line 431
-vtkNIFTIReader (0x2777c90): Unable to locate header for file \fB\-\-help\fR
-.PP
-ERROR: In \fI/tmp/buildd/vtk6\-6.0.0/Common/ExecutionModel/vtkExecutive.cxx\fP, line 754
-vtkCompositeDataPipeline (0x2778540): Algorithm vtkNIFTIReader(0x2777c90) returned failure for request: vtkInformation (0x276b5c0)
-.IP
-Debug: Off
-Modified Time: 93
-Reference Count: 1
-Registered Events: (none)
-Request: REQUEST_INFORMATION
-ALGORITHM_AFTER_FORWARD: 1
-FORWARD_DIRECTION: 0
-.PP
-sizeof_hdr: 348
-vox_offset: 0
-dim_info: 0x0 (unknown)
-dim: 0 0 0 0 0 0 0 0
-pixdim: 0 0 0 0 0 0 0 0
-xyzt_units: 0x0 (unknown, unknown)
-datatype: 0 ()
-bitpix: 0
-descrip: ""
-aux_file: ""
-.SH AUTHOR
-This  manual  page was written by Mathieu Malaterre <malat at debian.org> for
-the Debian GNU/Linux system, but may be used by others.

Deleted: trunk/packages/vtk-dicom/trunk/debian/niftitodicom.1
===================================================================
--- trunk/packages/vtk-dicom/trunk/debian/niftitodicom.1	2014-04-07 09:35:38 UTC (rev 16575)
+++ trunk/packages/vtk-dicom/trunk/debian/niftitodicom.1	2014-04-07 09:55:31 UTC (rev 16576)
@@ -1,66 +0,0 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.44.1.
-.TH NIFTITODICOM "1" "March 2014" "niftitodicom 0.4.2" "User Commands"
-.SH NAME
-niftitodicom \- manual page for niftitodicom 0.4.2
-.SH DESCRIPTION
-niftitodicom 0.4.2 (HEAD         , 20 Mar 2014, 20:37:31)
-usage: niftitodicom \fB\-o\fR directory file.nii [file.dcm ...]
-options:
-.TP
-\fB\-o\fR directory
-The output directory.
-.TP
-\fB\-s\fR \fB\-\-silent\fR
-Do not print anything while executing.
-.TP
-\fB\-v\fR \fB\-\-verbose\fR
-Verbose error reporting.
-.TP
-\fB\-\-no\-reordering\fR
-Never reorder slices, rows, or columns.
-.TP
-\fB\-\-axial\fR
-Produce axial slices.
-.TP
-\fB\-\-coronal\fR
-Produce coronal slices.
-.TP
-\fB\-\-sagittal\fR
-Produce satittal slices.
-.TP
-\fB\-\-series\-description\fR
-Textual description of the series.
-.TP
-\fB\-\-series\-number\fR
-The series number ot use.
-.TP
-\fB\-\-modality\fR
-The modality: MR or CT or SC.
-.TP
-\fB\-\-uid\-prefix\fR
-A DICOM uid prefix (optional).
-.TP
-\fB\-\-help\fR
-Documentation for niftitodicom.
-.PP
-This program will convert a NIfTI file into a DICOM series.
-.PP
-It reads the NIfTI file header and does the best job that it can to
-generate a series of DICOM files.  To help it along, you can provide
-a DICOM file from the same series on the command line after the NIfTI
-file, or even better, list all of the DICOM files that were used as
-the source of the data in the NIfTI file.  Study\-related meta data will
-be copied from these DICOM files into the output DICOM files.
-.PP
-Unless the \fB\-\-no\-reordering\fR option is provided, it will ensure that
-the images are in the usual orientation (right is left, posterior is
-down) by reordering the columns or rows as compared to the NIFTI file.
-.PP
-If the NIFTI file is floating\-point, then the data might be rescaled
-when written to DICOM as 16\-bit integers.  If any data values are too
-large to fit into 16 bits, then all the data will be scaled down.  If
-the data values all have a magnitude smaller than 2.05, then all the
-data will be scaled up by a factor of 1000.
-.SH AUTHOR
-This  manual  page was written by Mathieu Malaterre <malat at debian.org> for
-the Debian GNU/Linux system, but may be used by others.

Modified: trunk/packages/vtk-dicom/trunk/debian/patches/cmakefix.patch
===================================================================
--- trunk/packages/vtk-dicom/trunk/debian/patches/cmakefix.patch	2014-04-07 09:35:38 UTC (rev 16575)
+++ trunk/packages/vtk-dicom/trunk/debian/patches/cmakefix.patch	2014-04-07 09:55:31 UTC (rev 16576)
@@ -1,13 +1,13 @@
 Index: vtk-dicom-0.4.4/CMakeLists.txt
 ===================================================================
---- vtk-dicom-0.4.4.orig/CMakeLists.txt	2014-04-03 18:17:15.000000000 +0200
-+++ vtk-dicom-0.4.4/CMakeLists.txt	2014-04-07 11:33:25.000000000 +0200
+--- vtk-dicom-0.4.4.orig/CMakeLists.txt	2014-04-07 11:39:37.000000000 +0200
++++ vtk-dicom-0.4.4/CMakeLists.txt	2014-04-07 11:39:53.000000000 +0200
 @@ -4,7 +4,7 @@
  cmake_minimum_required(VERSION 2.6.3)
  
  # Use LINK_INTERFACE_LIBRARIES instead of INTERFACE_LINK_LIBRARIES
 -if(CMAKE_VERSION VERSION_GREATER 2.6.11)
-+if(CMAKE_VERSION VERSION_GREATER 2.8.11)
++if(CMAKE_VERSION VERSION_GREATER 2.8.12)
    cmake_policy(SET CMP0022 OLD)
  endif()
  

Modified: trunk/packages/vtk-dicom/trunk/debian/rules
===================================================================
--- trunk/packages/vtk-dicom/trunk/debian/rules	2014-04-07 09:35:38 UTC (rev 16575)
+++ trunk/packages/vtk-dicom/trunk/debian/rules	2014-04-07 09:55:31 UTC (rev 16576)
@@ -38,14 +38,12 @@
 
 debian/%.1: debian/common.1.in
 	help2man --help-option=--help --include=$< --version-option=--version --version-string=$(VERSION) \
-    --output=$@ --no-info --no-discard-stderr `basename $@ .1`
+    --output=$@ --no-info --no-discard-stderr ./debian/tmp/usr/bin/`basename $@ .1`
 
 manpages: debian/dicomdump.1 debian/dicomtonifti.1 debian/niftidump.1 debian/niftitodicom.1
 	echo "manpages"
 
-build: manpages
-
-override_dh_installman:
+override_dh_installman: manpages
 	dh_installman -p$(pkg_bin) debian/*.1
 
 get-orig-source:

Added: trunk/packages/vtk-dicom/trunk/debian/source/options
===================================================================
--- trunk/packages/vtk-dicom/trunk/debian/source/options	                        (rev 0)
+++ trunk/packages/vtk-dicom/trunk/debian/source/options	2014-04-07 09:55:31 UTC (rev 16576)
@@ -0,0 +1,2 @@
+compression = xz
+compression-level = 9

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