Updated man pages for DCMTK release 3.6.4.

doxygen/manpages/man1/cda2dcm.1

@@ -1,7 +1,8 @@
-.TH "cda2dcm" 1 "Wed Aug 15 2018" "Version 3.6.3+" "OFFIS DCMTK" \" -*- nroff -*-
+.TH "cda2dcm" 1 "Thu Nov 29 2018" "Version 3.6.4" "OFFIS DCMTK" \" -*- nroff -*-
 .nh
 .SH NAME
-cda2dcm \- Encapsulate CDA file into DICOM format\&.
+cda2dcm \- Encapsulate CDA file into DICOM file format
+
 .SH "SYNOPSIS"
 .PP
 .PP
@@ -61,7 +62,7 @@ document title:
          document title
 
   +cn  --concept-name  [CSD] [CV] [CM]: string (default: empty)
-         document title as concept name code sequence with coding
+         coded representation of document title defined by coding
          scheme designator CSD, code value CV and code meaning CM
 
 patient data:
@@ -97,78 +98,75 @@ instance number:
   +ii  --instance-inc
          increment instance number (only with +se)
 
-  +is  --instance-set  [i]nstance number: integer
+  +is  --instance-set [i]nstance number: integer
          use instance number i
 
 burned-in annotation:
 
   +an  --annotation-yes
-         CDA file (or an encapsulated document within)
-         contains patient identifying data (default)
+         document contains patient identifying data (default)
 
   -an  --annotation-no
-         CDA file (or an encapsulated document)
-         does not contain patient identifying data
+         document does not contain patient identifying data
 
 override CDA file data:
 
   -ov  --no-override
          CDA patient and document data must match study,
-         series or manually entered information.
-         Otherwise, an error occurs (default).
+         series or manually entered information (default)
 
   +ov  --override
-         CDA's data will be overwritten by study, series
-         or manually entered information
+         data obtained from the CDA file will be overwritten
+         by study, series, or manually entered information
 .fi
 .PP
 .SS "processing options"
 .PP
 .nf
 other processing options:
 
-  -k    --key  [k]ey: gggg,eeee="str", path or dictionary name="str"
-          add further attribute
+  -k   --key  [k]ey: gggg,eeee="str", path or dictionary name="str"
+         add further attribute
 .fi
 .PP
 .SS "output options"
 .PP
 .nf
 output file format:
 
-  +F    --write-file
-          write file format (default)
+  +F   --write-file
+         write file format (default)
 
-  -F    --write-dataset
-          write data set without file meta information
+  -F   --write-dataset
+         write data set without file meta information
 
 group length encoding:
 
-  +g=   --group-length-recalc
-          recalculate group lengths if present (default)
+  +g=  --group-length-recalc
+         recalculate group lengths if present (default)
 
-  +g    --group-length-create
-          always write with group length elements
+  +g   --group-length-create
+         always write with group length elements
 
-  -g    --group-length-remove
-          always write without group length elements
+  -g   --group-length-remove
+         always write without group length elements
 
 length encoding in sequences and items:
 
-  +e    --length-explicit
-          write with explicit lengths (default)
+  +e   --length-explicit
+         write with explicit lengths (default)
 
-  -e    --length-undefined
-          write with undefined lengths
+  -e   --length-undefined
+         write with undefined lengths
 
 data set trailing padding (not with --write-dataset):
 
-  -p    --padding-off
-          no padding (implicit if --write-dataset)
+  -p   --padding-off
+         no padding (implicit if --write-dataset)
 
-  +p    --padding-create  [f]ile-pad [i]tem-pad: integer
-          align file on multiple of f bytes
-          and items on multiple of i bytes
+  +p   --padding-create  [f]ile-pad [i]tem-pad: integer
+         align file on multiple of f bytes
+         and items on multiple of i bytes
 .fi
 .PP
 .SH "LOGGING"
@@ -189,23 +187,23 @@ The \fBcda2dcm\fP utility uses the following exit codes when terminating\&. This
 .SS "general"
 .PP
 .nf
-EXITCODE_NO_ERROR                         0
-EXITCODE_COMMANDLINE_SYNTAX_ERROR         1
-EXITCODE_MEMORY_EXHAUSTED                 4
+EXITCODE_NO_ERROR                 0
+EXITCODE_COMMANDLINE_SYNTAX_ERROR 1
+EXITCODE_MEMORY_EXHAUSTED         4
 .fi
 .PP
 .SS "input file errors"
 .PP
 .nf
-EXITCODE_CANNOT_READ_INPUT_FILE          20
-EXITCODE_NO_INPUT_FILES                  21
-EXITCODE_INVALID_INPUT_FILE              22
+EXITCODE_CANNOT_READ_INPUT_FILE   20
+EXITCODE_NO_INPUT_FILES           21
+EXITCODE_INVALID_INPUT_FILE       22
 .fi
 .PP
 .SS "output file errors"
 .PP
 .nf
-EXITCODE_CANNOT_WRITE_OUTPUT_FILE        40
+EXITCODE_CANNOT_WRITE_OUTPUT_FILE 40
 .fi
 .PP
 .SH "ENVIRONMENT"

doxygen/manpages/man1/dcm2json.1

@@ -1,4 +1,4 @@
-.TH "dcm2json" 1 "Mon Feb 5 2018" "Version 3.6.3" "OFFIS DCMTK" \" -*- nroff -*-
+.TH "dcm2json" 1 "Thu Nov 29 2018" "Version 3.6.4" "OFFIS DCMTK" \" -*- nroff -*-
 .nh
 .SH NAME
 dcm2json \- Convert DICOM file and data set to JSON

doxygen/manpages/man1/dcm2pdf.1

@@ -1,4 +1,4 @@
-.TH "dcm2pdf" 1 "Mon Feb 5 2018" "Version 3.6.3" "OFFIS DCMTK" \" -*- nroff -*-
+.TH "dcm2pdf" 1 "Thu Nov 29 2018" "Version 3.6.4" "OFFIS DCMTK" \" -*- nroff -*-
 .nh
 .SH NAME
 dcm2pdf \- Extract PDF file from DICOM encapsulated PDF

doxygen/manpages/man1/dcm2pnm.1

@@ -1,4 +1,4 @@
-.TH "dcm2pnm" 1 "Mon Feb 5 2018" "Version 3.6.3" "OFFIS DCMTK" \" -*- nroff -*-
+.TH "dcm2pnm" 1 "Thu Nov 29 2018" "Version 3.6.4" "OFFIS DCMTK" \" -*- nroff -*-
 .nh
 .SH NAME
 dcm2pnm \- Convert DICOM images to PGM/PPM, PNG, TIFF or BMP

doxygen/manpages/man1/dcm2xml.1

@@ -1,4 +1,4 @@
-.TH "dcm2xml" 1 "Mon Feb 5 2018" "Version 3.6.3" "OFFIS DCMTK" \" -*- nroff -*-
+.TH "dcm2xml" 1 "Thu Nov 29 2018" "Version 3.6.4" "OFFIS DCMTK" \" -*- nroff -*-
 .nh
 .SH NAME
 dcm2xml \- Convert DICOM file and data set to XML

doxygen/manpages/man1/dcmcjpeg.1

@@ -1,4 +1,4 @@
-.TH "dcmcjpeg" 1 "Mon Feb 5 2018" "Version 3.6.3" "OFFIS DCMTK" \" -*- nroff -*-
+.TH "dcmcjpeg" 1 "Thu Nov 29 2018" "Version 3.6.4" "OFFIS DCMTK" \" -*- nroff -*-
 .nh
 .SH NAME
 dcmcjpeg \- Encode DICOM file to JPEG transfer syntax
@@ -280,44 +280,76 @@ decompression color space conversion
 
   # Never convert color space during decompression.
 
-standard YCbCr component subsampling (not with +tl):
+decompr. workaround options for incorrect encodings (if input is compressed):
 
-  +s4   --sample-444
-          4:4:4 sampling with YBR_FULL (default)
+  +w6   --workaround-pred6
+          enable workaround for JPEG lossless images
+          with overflow in predictor 6
 
-  # This option disables color component subsampling for compression in
-  # the YCbCr color space. The DICOM photometric interpretation is
-  # encoded as YBR_FULL.
+  # DICOM images with 16 bits/pixel have been observed "in the wild"
+  # that are compressed with lossless JPEG and need special handling
+  # because the encoder produced an 16-bit integer overflow in predictor
+  # 6, which needs to be compensated (reproduced) during decompression.
+  # This flag enables a correct decompression of such faulty images, but
+  # at the same time will cause an incorrect decompression of correctly
+  # compressed images. Use with care.
+
+  +wi   --workaround-incpl
+          enable workaround for incomplete JPEG data
+
+  # This option causes dcmjpeg to ignore incomplete JPEG data
+  # at the end of a compressed fragment and to start decompressing
+  # the next frame from the next fragment (if any). This permits
+  # images with incomplete JPEG data to be decoded.
+
+  +wc   --workaround-cornell
+          enable workaround for 16-bit JPEG lossless
+          Cornell images with Huffman table overflow
+
+  # One of the first open-source implementations of lossless JPEG
+  # compression, the "Cornell" library, has a well-known bug that leads
+  # to invalid values in the Huffmann table when images with 16 bit/sample
+  # are compressed. This flag enables a workaround that permits such
+  # images to be decoded correctly.
+
+YCbCr component subsampling (lossy JPEG only):
 
   +s2   --sample-422
-          4:2:2 subsampling with YBR_FULL_422
+          4:2:2 subsampling with YBR_FULL_422 (default)
 
   # This option enables a 4:2:2 color component subsampling for
   # compression in the YCbCr color space. The DICOM photometric
-  # interpretation is encoded as YBR_FULL.
+  # interpretation is encoded as YBR_FULL_422.
 
 non-standard YCbCr component subsampling (not with +tl):
 
+  +s4   --nonstd-444
+          4:4:4 sampling with YBR_FULL
+
+  # This option disables color component subsampling for compression in
+  # the YCbCr color space. The DICOM photometric interpretation is
+  # encoded as YBR_FULL, which violates DICOM rules for lossy JPEG.
+
   +n2   --nonstd-422-full
           4:2:2 subsampling with YBR_FULL
 
   # This option enables a 4:2:2 color component subsampling for
   # compression in the YCbCr color space. The DICOM photometric
-  # interpretation is encoded as YBR_FULL which violates DICOM rules.
+  # interpretation is encoded as YBR_FULL, which violates DICOM rules.
 
   +n1   --nonstd-411-full
           4:1:1 subsampling with YBR_FULL
 
   # This option enables a 4:1:1 color component subsampling for
   # compression in the YCbCr color space. The DICOM photometric
-  # interpretation is encoded as YBR_FULL which violates DICOM rules.
+  # interpretation is encoded as YBR_FULL, which violates DICOM rules.
 
   +np   --nonstd-411
           4:1:1 subsampling with YBR_FULL_422
 
   # This option enables a 4:1:1 color component subsampling for
   # compression in the YCbCr color space. The DICOM photometric
-  # interpretation is encoded as YBR_FULL_422 which violates DICOM rules.
+  # interpretation is encoded as YBR_FULL_422, which violates DICOM rules.
 .fi
 .PP
 .SS "encapsulated pixel data encoding options:"
@@ -529,7 +561,7 @@ data set trailing padding:
 .PP
 .SH "NOTES"
 .PP
-The \fBdcmcjpeg\fP utility compresses DICOM images of all SOP classes\&. Special handling has been implemented for CT images (where the modality transformation is required to create Hounsfield units) and the XA/RF/Biplane SOP classes (where the modality transformation has 'inversed' semantics)\&. However, \fBdcmcjpeg\fP does not attempt to ensure that the compressed image still complies with all restrictions of the object's IOD\&.
+The \fBdcmcjpeg\fP utility compresses DICOM images of all SOP classes\&. It processes all Pixel Data (7fe0,0010) elements in the dataset, i\&.e\&. compression is also performed on an icon image\&. Special handling has been implemented for CT images (where the modality transformation is required to create Hounsfield units) and the XA/RF/Biplane SOP classes (where the modality transformation has 'inversed' semantics)\&. However, \fBdcmcjpeg\fP does not attempt to ensure that the compressed image still complies with all restrictions of the object's IOD\&.
 .PP
 A few examples:
 .PP
@@ -615,4 +647,4 @@ The default behavior should be preferred and the \fIDCMDICTPATH\fP environment v
 \fBdcmdjpeg\fP(1)
 .SH "COPYRIGHT"
 .PP
-Copyright (C) 2001-2016 by OFFIS e\&.V\&., Escherweg 2, 26121 Oldenburg, Germany\&.
+Copyright (C) 2001-2018 by OFFIS e\&.V\&., Escherweg 2, 26121 Oldenburg, Germany\&.

doxygen/manpages/man1/dcmcjpls.1

@@ -1,4 +1,4 @@
-.TH "dcmcjpls" 1 "Mon Feb 5 2018" "Version 3.6.3" "OFFIS DCMTK" \" -*- nroff -*-
+.TH "dcmcjpls" 1 "Thu Nov 29 2018" "Version 3.6.4" "OFFIS DCMTK" \" -*- nroff -*-
 .nh
 .SH NAME
 dcmcjpls \- Encode DICOM file to JPEG-LS transfer syntax
@@ -282,7 +282,7 @@ data set trailing padding:
 .PP
 .SH "NOTES"
 .PP
-The \fBdcmcjpls\fP utility compresses DICOM images of all SOP classes\&. However, \fBdcmcjpls\fP does not attempt to ensure that the compressed image still complies with all restrictions of the object's IOD\&.
+The \fBdcmcjpls\fP utility compresses DICOM images of all SOP classes\&. It processes all Pixel Data (7fe0,0010) elements in the dataset, i\&.e\&. compression is also performed on an icon image\&. However, \fBdcmcjpls\fP does not attempt to ensure that the compressed image still complies with all restrictions of the object's IOD\&.
 .PP
 The user is responsible for making sure that the compressed images he creates are compliant with the DICOM standard\&. If in question, the \fBdcmcjpls\fP utility allows one to convert an image to secondary capture - this SOP class does not pose restrictions as the ones mentioned above\&.
 .SH "TRANSFER SYNTAXES"
@@ -330,4 +330,4 @@ The default behavior should be preferred and the \fIDCMDICTPATH\fP environment v
 \fBdcmdjpls\fP(1)
 .SH "COPYRIGHT"
 .PP
-Copyright (C) 2009-2016 by OFFIS e\&.V\&., Escherweg 2, 26121 Oldenburg, Germany\&.
+Copyright (C) 2009-2018 by OFFIS e\&.V\&., Escherweg 2, 26121 Oldenburg, Germany\&.

doxygen/manpages/man1/dcmconv.1

@@ -1,4 +1,4 @@
-.TH "dcmconv" 1 "Mon Feb 5 2018" "Version 3.6.3" "OFFIS DCMTK" \" -*- nroff -*-
+.TH "dcmconv" 1 "Thu Nov 29 2018" "Version 3.6.4" "OFFIS DCMTK" \" -*- nroff -*-
 .nh
 .SH NAME
 dcmconv \- Convert DICOM file encoding

doxygen/manpages/man1/dcmcrle.1

@@ -1,4 +1,4 @@
-.TH "dcmcrle" 1 "Mon Feb 5 2018" "Version 3.6.3" "OFFIS DCMTK" \" -*- nroff -*-
+.TH "dcmcrle" 1 "Thu Nov 29 2018" "Version 3.6.4" "OFFIS DCMTK" \" -*- nroff -*-
 .nh
 .SH NAME
 dcmcrle \- Encode DICOM file to RLE transfer syntax
@@ -165,7 +165,9 @@ data set trailing padding:
 .PP
 .SH "NOTES"
 .PP
-Please note that the DICOM standard does not allow for storing the pixel data with multiple fragments per frame (when RLE compression is used)\&. So limiting the fragment size with option \fI--fragment-size\fP (or \fI+fs\fP) may result in a non-standard conformant DICOM image\&.
+The \fBdcmcrle\fP utility compresses DICOM images of all SOP classes\&. It processes all Pixel Data (7fe0,0010) elements in the dataset, i\&.e\&. compression is also performed on an icon image\&.
+.PP
+Please note that the DICOM standard does not allow for storing the pixel data with multiple fragments per frame (when RLE compression is used)\&. So limiting the fragment size with option \fI--fragment-size\fP (or \fI+fs\fP) may result in a non-standard compliant DICOM image\&.
 .SH "TRANSFER SYNTAXES"
 .PP
 \fBdcmcrle\fP supports the following transfer syntaxes for input (\fIdcmfile-in\fP):
@@ -210,4 +212,4 @@ The default behavior should be preferred and the \fIDCMDICTPATH\fP environment v
 \fBdcmdrle\fP(1)
 .SH "COPYRIGHT"
 .PP
-Copyright (C) 2002-2014 by OFFIS e\&.V\&., Escherweg 2, 26121 Oldenburg, Germany\&.
+Copyright (C) 2002-2018 by OFFIS e\&.V\&., Escherweg 2, 26121 Oldenburg, Germany\&.

doxygen/manpages/man1/dcmdjpeg.1

@@ -1,4 +1,4 @@
-.TH "dcmdjpeg" 1 "Mon Feb 5 2018" "Version 3.6.3" "OFFIS DCMTK" \" -*- nroff -*-
+.TH "dcmdjpeg" 1 "Thu Nov 29 2018" "Version 3.6.4" "OFFIS DCMTK" \" -*- nroff -*-
 .nh
 .SH NAME
 dcmdjpeg \- Decode JPEG-compressed DICOM file
@@ -171,7 +171,17 @@ workaround options for incorrect JPEG encodings:
   # This option causes dcmjpeg to ignore incomplete JPEG data
   # at the end of a compressed fragment and to start decompressing
   # the next frame from the next fragment (if any). This permits
-  # images with incomplete JPEG data to be decoded..fi
+  # images with incomplete JPEG data to be decoded.
+
+  +wc   --workaround-cornell
+          enable workaround for 16-bit JPEG lossless
+          Cornell images with Huffman table overflow
+
+  # One of the first open-source implementations of lossless JPEG
+  # compression, the "Cornell" library, has a well-known bug that leads
+  # to invalid values in the Huffmann table when images with 16 bit/sample
+  # are compressed. This flag enables a workaround that permits such
+  # images to be decoded correctly..fi
 .PP
 .SS "output options"
 .PP
@@ -287,4 +297,4 @@ The default behavior should be preferred and the \fIDCMDICTPATH\fP environment v
 \fBdcmcjpeg\fP(1)
 .SH "COPYRIGHT"
 .PP
-Copyright (C) 2001-2016 by OFFIS e\&.V\&., Escherweg 2, 26121 Oldenburg, Germany\&.
+Copyright (C) 2001-2018 by OFFIS e\&.V\&., Escherweg 2, 26121 Oldenburg, Germany\&.

doxygen/manpages/man1/dcmdjpls.1

@@ -1,4 +1,4 @@
-.TH "dcmdjpls" 1 "Mon Feb 5 2018" "Version 3.6.3" "OFFIS DCMTK" \" -*- nroff -*-
+.TH "dcmdjpls" 1 "Thu Nov 29 2018" "Version 3.6.4" "OFFIS DCMTK" \" -*- nroff -*-
 .nh
 .SH NAME
 dcmdjpls \- Decode JPEG-LS compressed DICOM file

doxygen/manpages/man1/dcmdrle.1

@@ -1,4 +1,4 @@
-.TH "dcmdrle" 1 "Mon Feb 5 2018" "Version 3.6.3" "OFFIS DCMTK" \" -*- nroff -*-
+.TH "dcmdrle" 1 "Thu Nov 29 2018" "Version 3.6.4" "OFFIS DCMTK" \" -*- nroff -*-
 .nh
 .SH NAME
 dcmdrle \- Decode RLE-compressed DICOM file

doxygen/manpages/man1/dcmdspfn.1

@@ -1,4 +1,4 @@
-.TH "dcmdspfn" 1 "Mon Feb 5 2018" "Version 3.6.3" "OFFIS DCMTK" \" -*- nroff -*-
+.TH "dcmdspfn" 1 "Thu Nov 29 2018" "Version 3.6.4" "OFFIS DCMTK" \" -*- nroff -*-
 .nh
 .SH NAME
 dcmdspfn \- Export standard display curves to a text file

doxygen/manpages/man1/dcmdump.1

@@ -1,4 +1,4 @@
-.TH "dcmdump" 1 "Mon Feb 5 2018" "Version 3.6.3" "OFFIS DCMTK" \" -*- nroff -*-
+.TH "dcmdump" 1 "Thu Nov 29 2018" "Version 3.6.4" "OFFIS DCMTK" \" -*- nroff -*-
 .nh
 .SH NAME
 dcmdump \- Dump DICOM file and data set