[med-svn] r8095 - trunk/packages/openslide/trunk/debian

Thu Oct 6 12:17:46 UTC 2011

Author: malat-guest
Date: 2011-10-06 12:17:46 +0000 (Thu, 06 Oct 2011)
New Revision: 8095

Modified:
   trunk/packages/openslide/trunk/debian/openslide-show-properties.1
Log:
adding MIRAX and other

Modified: trunk/packages/openslide/trunk/debian/openslide-show-properties.1
===================================================================

--- trunk/packages/openslide/trunk/debian/openslide-show-properties.1	2011-10-06 11:55:25 UTC (rev 8094)
+++ trunk/packages/openslide/trunk/debian/openslide-show-properties.1	2011-10-06 12:17:46 UTC (rev 8095)
@@ -14,9 +14,12 @@
 .IP openslide.comment
 A free-form text comment, the same as returned from openslide_get_comment.
 .IP openslide.quickhash-1
-A non-cryptographic hash of a subset of the slide data. It can be used to uniquely identify a particular virtual slide, but cannot be used to detect file corruption or modification.
+A non-cryptographic hash of a subset of the slide data. It can be used to
+uniquely identify a particular virtual slide, but cannot be used to detect file
+corruption or modification.
 .IP openslide.background-color
-The background color of the slide, given as an RGB hex triplet. This property is not always present.
+The background color of the slide, given as an RGB hex triplet. This property
+is not always present.
 .PP
 .SS "Properties from the JPEG backend"
 
@@ -57,7 +60,8 @@
 .SH Trestle format
 
 .IP Format 0.4i
-single-file pyramidal tiled TIFF, with non-standard metadata and overlaps; additional files can contain more metadata and detailed overlap info
+single-file pyramidal tiled TIFF, with non-standard metadata and overlaps;
+additional files can contain more metadata and detailed overlap info
 .IP "File extensions"
 \&.tif
 .IP "OpenSlide vendor backend"
@@ -68,7 +72,8 @@
 .SS Detection
 
 .nr step 1 1
-Trestle slides are stored in single-file TIFF format. OpenSlide will detect a file as Trestle if:
+Trestle slides are stored in single-file TIFF format. OpenSlide will detect a
+file as Trestle if:
 .IP \n[step] 3
 The file is TIFF.
 .IP \n+[step]
@@ -128,7 +133,8 @@
 
 .SS Known Properties
 
-All data encoded in the ImageDescription TIFF field is represented as properties prefixed with \*(lqtrestle.\*(rq.
+All data encoded in the ImageDescription TIFF field is represented as
+properties prefixed with \*(lqtrestle.\*(rq.
 
 .SH Hamamatsu format
 
@@ -354,7 +360,8 @@
 
 .SS Known Properties
 
-All key-value data stored in the VMS/VMU file are encoded as properties prefixed with \*(lqhamamatsu.\*(rq.
+All key-value data stored in the VMS/VMU file are encoded as properties
+prefixed with \*(lqhamamatsu.\*(rq.
 
 .SS Preliminary NDPI Notes
 
@@ -434,7 +441,8 @@
 .SS Detection
 
 .nr step 1 1
-Aperio slides are stored in single-file TIFF format. OpenSlide will detect a file as Aperio if:
+Aperio slides are stored in single-file TIFF format. OpenSlide will detect a
+file as Aperio if:
 .IP \n[step] 3
 The file is TIFF.
 .IP \n+[step]
@@ -469,8 +477,11 @@
 
 .SS TIFF Image Directory Organization
 
-http://www.aperio.com/documents/api/Aperio_Digital_Slides_and_Third-party_data_interchange.pdf page 14:
+From
 
+http://www.aperio.com/documents/api/Aperio_Digital_Slides_and_Third-party_data_interchange.pdf
+
+page 14:
   The first image in an SVS file is always the baseline image (full resolution).
   This image is always tiled, usually with a tile size of 240x240 pixels. The
   second image is always a thumbnail, typically with dimensions of about 1024x768
@@ -505,8 +516,160 @@
 .PP
 .SS Known Properties
 
-All key-value data encoded in the ImageDescription TIFF field is represented as properties prefixed with \*(lqaperio.\*(rq.
+All key-value data encoded in the ImageDescription TIFF field is represented as
+properties prefixed with \*(lqaperio.\*(rq.
 
+.SH MIRAX format
+.PP
+.IP Format
+multi-file JPEG with very complicated proprietary metadata and indexes
+.IP "File extensions"
+\&.mrxs
+.IP "OpenSlide vendor backend"
+mirax
+.IP "OpenSlide ops backend"
+jpeg
+
+.SS Detection
+
+.B Note: MIRAX is incredibly complicated. These detection steps are probably not complete.
+
+.nr step 1 1
+OpenSlide will detect a file as MIRAX if:
+.IP \n[step] 3
+The file ends with .mrxs.
+.IP \n+[step]
+A directory exists in the same location as the file, with the same name as the
+file minus the extension.
+.IP \n+[step]
+A file named Slidedat.ini exists in the directory.
+.IP \n+[step]
+The slidedat file is readable as a Windows INI-style file.
+.IP \n+[step]
+The slidedat file has a [GENERAL] section with the following keys:
+SLIDE_VERSION, SLIDE_ID, IMAGENUMBER_X, IMAGENUMBER_Y,
+CameraImageDivisionsPerSide.
+.IP \n+[step]
+The slidedat file has a [HIERARCHICAL] section with the following keys:
+HIER_COUNT, NONHIER_COUNT, INDEXFILE.
+.IP \n+[step]
+A key exists in the [HIERARCHICAL] section with the value of Slide zoom level.
+The key matches this printf-style template: HIER_%d_NAME. The %d is bound to
+the variable zoom_level. Currently, zoom_level must be 0.
+.IP \n+[step]
+The [HIERARCHICAL] section has a key with the name HIER_%d_COUNT where %d is
+the value of zoom_level in the previous step. The value must be an integer,
+interpreted as zoom_count.
+.IP \n+[step]
+Setting x to zoom_level and y from 0 to zoom_count, the [HIERARCHICAL] section
+has a key with the name HIER_x_VAL_y_SECTION. Let section_names[] be an array
+of length zoom_count, holding the values for each key.
+.IP \n+[step]
+The [DATAFILE] section must exist, with the following keys: FILE_COUNT.
+.IP \n+[step]
+There are FILE_COUNT keys in the [DATAFILE] section with the following names:
+FILE_%d, where %d goes from 0 to FILE_COUNT-1.
+.IP \n+[step]
+For each value in section_names, a group must exist with that name. Each group
+must contain the keys: OVERLAP_X, OVERLAP_Y, IMAGE_FILL_COLOR_BGR,
+DIGITIZER_WIDTH, DIGITIZER_HEIGHT. The overlap values must be parseable as
+doubles, the rest as integers. The key IMAGE_FORMAT must exist, with the value
+JPEG.
+.IP \n+[step]
+Each section_names section must have the key IMAGE_CONCAT_FACTOR. The value of
+the first section's IMAGE_CONCAT_FACTOR must be 0, the rest 1.
+.IP \n+[step]
+The [HIERARCHICAL] section has a key with the name NONHIER_%d_NAME (%d is an
+integer) and with the value VIMSLIDE_POSITION_BUFFER. Bind %d to the variable
+position_nonhier_offset.
+.IP \n+[step]
+The [HIERARCHICAL] section has a key with the name NONHIER_%d_NAME (%d is an
+integer) and with the value Scan data layer. Bind %d to the variable
+scan_nonhier_offset.
+.IP \n+[step]
+The [HIERARCHICAL] section has a key with the name NONHIER_%d_VAL_%d where the
+first %d is the value of scan_nonhier_offset. The key has a value of
+ScanDataLayer_SlideThumbnail.
+.IP \n+[step]
+The [HIERARCHICAL] section has a key with the name NONHIER_%d_VAL_%d where the
+first %d is the value of scan_nonhier_offset. The key has a value of
+ScanDataLayer_SlideBarcode.
+.IP \n+[step]
+The [HIERARCHICAL] section has a key with the name NONHIER_%d_VAL_%d where the
+first %d is the value of scan_nonhier_offset. The key has a value of
+ScanDataLayer_SlidePreview.
+.IP \n+[step]
+The value of the INDEXFILE key above is the name of a readable file.
+.IP \n+[step]
+The index file is of a valid format, and all data referred to by it is valid
+(see below).
+
+.SS Overview
+
+Because JPEG does not allow for large files, multiple JPEG files are needed to
+encode large images.
+
+Unfortunately, (unlike TIFF) JPEG provides very poor support for random-access
+decoding of parts of a file. To avoid having many individual files, MIRAX packs
+JPEG files into a small number of data files. The index file provides offsets
+into the data files for each required piece of data.
+
+.SS Index File
+
+The index file is a crazy beast.
+
+It starts with ASCII strings matching the SLIDE_VERSION and SLIDE_ID values
+from the slidedat file. Then, all hell breaks loose. The rest of the file
+consists of 32-bit little-endian integers (unaligned) with seemingly no
+structure.
+
+More info coming, for now see misc/print-mirax.py.
+
+.SS Data Files
+
+.SS Slide Position File
+
+.SS Associated Images
+
+.SS Known Properties
+
+.SH Generic tiled TIFF format
+.PP
+.IP Format
+single-file pyramidal tiled TIFF
+.IP "File extensions"
+\&.tif
+.IP "OpenSlide vendor backend"
+generic-tiff
+.IP "OpenSlide ops backend"
+tiff
+.PP
+
+.SS Detection
+
+.nr step 1 1
+OpenSlide will detect a file as generic TIFF if:
+.IP \n[step] 3
+No other detections succeed.
+.IP \n+[step]
+The file is TIFF.
+.IP \n+[step]
+The initial image is tiled.
+
+.SS TIFF Image Directory Organization
+
+The first image in the TIFF file is the full-resolution image. Any other tiled
+images in the file with the \*(lqreduced resolution\*(rq bit set are assumed to
+be reduced-resolution versions of the original.
+
+.SS Associated Images
+
+None.
+
+.SS Known Properties
+
+Many TIFF tags are encoded as properties starting with \*(lqtiff.\*(rq.
+
 .SH "SEE ALSO"
 
 .IR openslide-write-png(1),


