man dump2dcm (1): Convert ASCII dump to DICOM file

SYNOPSIS

dump2dcm [options] dumpfile-in dcmfile-out

DESCRIPTION

The dump2dcm utility converts an ASCII dump file to a DICOM file. The dump file has the same format as the output of dcmdump. Thus it is possible to capture the output of dcmdump into a file, modify some attributes and create a new DICOM file.

PARAMETERS

dumpfile-in  dump input filename
dcmfile-out  DICOM output filename

OPTIONS

general options

  -h   --help
         print this help text and exit
       --version
         print version information and exit
       --arguments
         print expanded command line arguments
  -q   --quiet
         quiet mode, print no warnings and errors
  -v   --verbose
         verbose mode, print processing details
  -d   --debug
         debug mode, print debug information
  -ll  --log-level  [l]evel: string constant
         (fatal, error, warn, info, debug, trace)
         use level l for the logger
  -lc  --log-config  [f]ilename: string
         use config file f for the logger

input options

input file format:
  +f   --read-meta-info
         read meta information if present (default)
  -f   --ignore-meta-info
         ignore file meta information
file contents byte ordering:
  +rl  --read-file-little
         read OW data with little endian (default)
  +rb  --read-file-big
         read OW data from file with big endian
other input options:
  +l   --line  [m]ax-length: integer
         maximum line length m (default: 4096)

processing options

unique identifiers:
  +Ug  --generate-new-uids
         generate new Study/Series/SOP Instance UID
  -Uo  --dont-overwrite-uids
         do not overwrite existing UIDs (default)
  +Uo  --overwrite-uids
         overwrite existing UIDs

output options

output file format:
  +F   --write-file
         write file format (default)
  -F   --write-dataset
         write data set without file meta information
  +Fu  --update-meta-info
         update particular file meta information
output transfer syntax:
  +t=  --write-xfer-same
         write with same TS as input (default)
  +te  --write-xfer-little
         write with explicit VR little endian
  +tb  --write-xfer-big
         write with explicit VR big endian TS
  +ti  --write-xfer-implicit
         write with implicit VR little endian TS
  +td  --write-xfer-deflated
         write with deflated explicit VR little endian TS
error handling:
  -E   --stop-on-error
         do not write if dump is damaged (default)
  +E   --ignore-errors
         attempt to write even if dump is damaged
post-1993 value representations:
  +u   --enable-new-vr
         enable support for new VRs (UN/UT) (default)
  -u   --disable-new-vr
         disable support for new VRs, convert to OB
group length encoding:
  +g=  --group-length-recalc
         recalculate group lengths if present (default)
  +g   --group-length-create
         always write with 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-undefined
         write with undefined lengths
data set trailing padding (not with --write-dataset):
  -p=  --padding-retain
         do not change padding (default if not --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
deflate compression level (only with --write-xfer-deflated):
  +cl  --compression-level  [l]evel: integer (default: 6)
         0=uncompressed, 1=fastest, 9=best compression

NOTES

Dump File Description

The input file can be an output of dcmdump (default indented format only). One element (tag, VR, value) must be written into one line separated by arbitrary spaces or tab characters. A '#' begins a comment that ends at the line end. Empty lines are allowed.

The individual parts of a line have the following syntax:

Tag:   (gggg,eeee)
       with gggg and eeee are 4 character hexadecimal values
       representing group and element tag.  Spaces and tabs can be
       anywhere in a tag specification.
VR:    Value Representation must be written as 2 characters as in
       Part 6 of the DICOM standard.  No spaces or tabs are allowed
       between the two characters.  If the VR can be determined from
       the tag, this part of a line is optional.
Value: There are several rules for writing values:
       1. US, SS, SL, UL, FD, FL, OD, OF and OL are written as decimal
          strings that can be read by scanf().
       2. AT is written as '(gggg,eeee)' with additional spaces
          stripped off automatically and gggg and eeee being decimal
          strings that can be read by scanf().
       3. OB and OW values are written as byte or word hexadecimal
          values separated by '\' character.  Alternatively, OB or OW
          values can be read from a separate file by writing the
          filename prefixed by a '=' character (e.g. '=largepix.dat').
          The contents of the file will be read as is.  By default, OW
          data is expected to be little endian ordered and will be
          swapped if necessary.  No checks will be made to ensure that
          the amount of data is reasonable in terms of other attributes
          such as Rows or Columns.
          In case of compressed pixel data, the line should start with
          '(7fe0,0010) OB (PixelSequence' in order to distinguish from
          uncompressed pixel data.
       4. UI is written as '=Name' in data dictionary or as unique
          identifier string (see 6.), e.g. '[1.2.840.....]'.
       5. Strings without () <> [] spaces, tabs and # can be written
          directly.
       6. Other strings must be surrounded by '[' and ']'.  No bracket
          structure is passed.  The value ends at the last ']' in the
          line.  Anything after the ']' is interpreted as comment.
       7. '(' and '<' are interpreted special and may not be used when
          writing an input file by hand as beginning characters of a
          string.  Multiple Value are separated by '\'.  The lines
          need not be sorted into ascending tag order.  References in
          DICOM Directories are not supported.  Semantic errors are
          not detected.

Example

 (0008,0020) DA [19921012]            #  8, 1 StudyDate
 (0008,0016) UI =MRImageStorage       # 26, 1 SOPClassUID
 (0002,0012) UI [1.2.276.0.7230010.100.1.1]
 (0020,0032) DS [0.0\0.0]             #  8, 2 ImagePositionPatient
 (0028,0009) AT (3004,000c)           #  4, 1 FrameIncrementPointer
 (0028,0010) US 256                   #  4, 1 Rows
 (0002,0001) OB 01\00

Limitations

Please note that dump2dcm currently does not fully support DICOMDIR files. Specifically, the value of the various offset data elements is not updated automatically by this tool.

LOGGING

The level of logging output of the various command line tools and underlying libraries can be specified by the user. By default, only errors and warnings are written to the standard error stream. Using option --verbose also informational messages like processing details are reported. Option --debug can be used to get more details on the internal activity, e.g. for debugging purposes. Other logging levels can be selected using option --log-level. In --quiet mode only fatal errors are reported. In such very severe error events, the application will usually terminate. For more details on the different logging levels, see documentation of module 'oflog'.

In case the logging output should be written to file (optionally with logfile rotation), to syslog (Unix) or the event log (Windows) option --log-config can be used. This configuration file also allows for directing only certain messages to a particular output stream and for filtering certain messages based on the module or application where they are generated. An example configuration file is provided in <etcdir>/logger.cfg.

COMMAND LINE

All command line tools use the following notation for parameters: square brackets enclose optional values (0-1), three trailing dots indicate that multiple values are allowed (1-n), a combination of both means 0 to n values.

Command line options are distinguished from parameters by a leading '+' or '-' sign, respectively. Usually, order and position of command line options are arbitrary (i.e. they can appear anywhere). However, if options are mutually exclusive the rightmost appearance is used. This behavior conforms to the standard evaluation rules of common Unix shells.

In addition, one or more command files can be specified using an '@' sign as a prefix to the filename (e.g. @command.txt). Such a command argument is replaced by the content of the corresponding text file (multiple whitespaces are treated as a single separator unless they appear between two quotation marks) prior to any further evaluation. Please note that a command file cannot contain another command file. This simple but effective approach allows one to summarize common combinations of options/parameters and avoids longish and confusing command lines (an example is provided in file <datadir>/dumppat.txt).

ENVIRONMENT

The dump2dcm utility will attempt to load DICOM data dictionaries specified in the DCMDICTPATH environment variable. By default, i.e. if the DCMDICTPATH environment variable is not set, the file <datadir>/dicom.dic will be loaded unless the dictionary is built into the application (default for Windows).

The default behavior should be preferred and the DCMDICTPATH environment variable only used when alternative data dictionaries are required. The DCMDICTPATH environment variable has the same format as the Unix shell PATH variable in that a colon (':') separates entries. On Windows systems, a semicolon (';') is used as a separator. The data dictionary code will attempt to load each file specified in the DCMDICTPATH environment variable. It is an error if no data dictionary can be loaded.