DCMTK: dcm2json: Convert DICOM file and data set to JSON

DCMTK Version 3.7.0 OFFIS DICOM Toolkit

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dcm2json: Convert DICOM file and data set to JSON

# SYNOPSIS

    dcm2json [options] dcmfile-in [jsonfile-out]

# DESCRIPTION

The dcm2json utility converts the contents of a DICOM file (file format or raw data set) to JSON (JavaScript Object Notation). The output refers to the "DICOM JSON Model", which is found in DICOM Part 18 Section F.

If dcm2json reads a raw data set (DICOM data without a file format meta-header), it will attempt to guess the transfer syntax by examining the first few bytes of the file. It is not always possible to correctly guess the transfer syntax and it is better to convert a data set to a file format whenever possible (using the dcmconv utility). It is also possible to use the -f and -t[ieb] options to force dcm2json to read a data set with a particular transfer syntax.

# PARAMETERS

    dcmfile-in   DICOM input filename to be converted ("-" for stdin)

    jsonfile-out JSON output filename (default: stdout)

# 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-file
             read file format or data set (default)

      +fo  --read-file-only
             read file format only

      -f   --read-dataset
             read data set without file meta information

    input transfer syntax:

      -t=  --read-xfer-auto
             use TS recognition (default)

      -td  --read-xfer-detect
             ignore TS specified in the file meta header

      -te  --read-xfer-little
             read with explicit VR little endian TS

      -tb  --read-xfer-big
             read with explicit VR big endian TS

      -ti  --read-xfer-implicit
             read with implicit VR little endian TS

## processing options

    encoding of infinity and not-a-number:

      -es  --encode-strict
             report error for 'inf' and 'nan' (default)

      -ee  --encode-extended
             permit 'inf' and 'nan' in JSON numbers

    encoding of IS and DS (integer/decimal string) elements:

      -ia  --is-ds-auto
             encode as number if valid, as string otherwise (default)

      -in  --is-ds-num
             always encode as number, fail if invalid

      -is  --is-ds-string
             always encode as string

    bulk data URI options:

      -b   --bulk-disabled
             write everything as inline binary (default)

      +b   --bulk-enabled
             write large attributes as bulk data

      +bz  --bulk-size  [s]ize: integer (default: 1)
             use bulk data for attributes >= s kBytes

      +bp  --bulk-uri-prefix  [u]ri prefix: string
             use prefix u when generating bulk data URIs (default: file URI)

      +bd  --bulk-dir  [d]irectory: string
             write bulk data files to d (default: '.')

      +bs  --bulk-subdir
             create subdirectory for each SOP instance
             (default: no subdirectory)

## output options

    output format:

      +fc  --formatted-code
             enable whitespace formatting (default)

             # prints additional spaces and newlines for increased
             # readability

      -fc  --compact-code
             print only required characters

      +m   --write-meta
             write data set with meta information
             (warning: not conforming to the DICOM standard)

# JSON Format

The basic structure of the JSON output created from a DICOM file looks like the following (see DICOM Part 18 Section F for details):

    {
        "00080005": {
            "vr": "CS",
            "Value": [
                "ISO_IR 192"
            ]
        },
        "00080020": {
            "vr": "DT",
            "Value": [
                "20130409"
            ]
        },
        "00080030": {
            "vr": "TM",
            "Value": [
                "131600.0000"
            ]
        },
        "00080050": {
            "vr": "SH",
            "Value": [
                "11235813"
            ]
        },
        "00080056": {
            "vr": "CS",
            "Value": [
                "ONLINE"
            ]
        },
        "00080061": {
            "vr": "CS",
            "Value": [
                "CT",
                "PET"
            ]
        },
        "00080090": {
            "vr": "PN",
            "Value": [
              {
                "Alphabetic": "^Bob^^Dr."
              }
            ]
        },
        "00081190": {
            "vr": "UR",
            "Value": [
                "http://wado.nema.org/studies/
                1.2.392.200036.9116.2.2.2.1762893313.1029997326.945873"
            ]
        },
        "00090010": {
            "vr": "LO",
            "Value": [
                "Vendor A"
            ]
        },
        "00091002": {
            "vr": "UN",
            "InlineBinary": "z0x9c8v7"
        },
        "00100010": {
            "vr": "PN",
            "Value": [
              {
                "Alphabetic": "Wang^XiaoDong"
              }
            ]
        },
        "00100020": {
            "vr": "LO",
            "Value": [
                "12345"
            ]
        },
        "00100021": {
            "vr": "LO",
            "Value": [
                "Hospital A"
            ]
        },
        "00100030": {
            "vr": "DA",
            "Value": [
                "19670701"
            ]
        },
        "00100040": {
            "vr": "CS",
            "Value": [
                "M"
            ]
        },
        "00101002": {
            "vr": "SQ",
            "Value": [
                {
                    "00100020": {
                        "vr": "LO",
                        "Value": [
                            "54321"
                        ]
                    },
                    "00100021": {
                        "vr": "LO",
                        "Value": [
                            "Hospital B"
                        ]
                    }
                },
                {
                    "00100020": {
                        "vr": "LO",
                        "Value": [
                            "24680"
                        ]
                    },
                    "00100021": {
                        "vr": "LO",
                        "Value": [
                            "Hospital C"
                        ]
                    }
                }
            ]
        },
        "0020000D": {
            "vr": "UI",
            "Value": [
                "1.2.392.200036.9116.2.2.2.1762893313.1029997326.945873"
            ]
        },
        "00200010": {
            "vr": "SH",
            "Value": [
                "11235813"
            ]
        },
        "00201206": {
            "vr": "IS",
            "Value": [
                4
            ]
        },
        "00201208": {
            "vr": "IS",
            "Value": [
                942
            ]
        }
    }

## Bulk Data

By default, binary data, i.e. DICOM element values with Value Representations (VR) of OB, OD, OF, OL, OV, OW, and UN values are written as "InlineBinary" (base64 encoding) to the JSON output. Option --bulk-enabled causes binary data as well as DS, FD, FL, IS, SV and UV to be replaced by "BulkDataURI" values if the element value is larger than the cut-off threshold (default: 1 kByte). The cut-off threshold can be specified with the --bulk-size option. The element values themselves are written as files to the directory given by the --bulk-dir option (default: current directory). The filename is based on a SHA-256 checksum of the element value. By default, file URIs are generated that point to the bulk directory. For production use, a URI prefix for a WADO-RS service over which the element values can be retrieved should be specified using the --bulk-uri-prefix option. This can be implemented by configuring a web server that has read access to dcm2json's bulk directory. Finally, the option --bulk-subdir will cause a separate subdirectory to be created (and used in the bulk data URI) for each distinct SOP instance.

Note that the JSON syntax for the representation of encapsulated pixel data in "InlineBinary" form is unspecified in DICOM, as is the JSON representation of encapsulated multi-frame pixel data. These DICOM files cannot be converted to JSON using dcm2json.

The file name extension for the bulk data files generated can be used to determine the MIME type that should be returned by the WADO-RS server:

      Extension     MIME Type

      .bin          application/octet-stream
      .jpeg         image/jpeg
      .dicom-rle    image/dicom-rle
      .jls          image/jls
      .jp2          image/jp2
      .jpx          image/jpx
      .jphc         image/jphc
      .jxl          image/jxl
      .mpeg         video/mpeg
      .mp4          video/mp4
      .H265         video/H265

Finally, it should be noted that bulk data will be written "as is", i.e. dcm2json will not attempt to validate or modify the element value in any way. For example, dcm2json will not add a JFIF header in the case of JPEG baseline compressed images, which some JPEG viewers may expect.

# NOTES

## Numbers as Strings

The DICOM standard allows certain numeric DICOM value representations, DS, IS, SV and UV, to be converted either to a JSON number or a JSON string. dcm2json converts DS and IS values to JSON numbers if they are valid decimal strings or integer strings, and to strings if they contain any illegal character. dcm2json converts SV and UV values to numbers if they are not larger than 9007199254740991ll or smaller than -9007199254740991ll, and to strings otherwise. While the JSON specification permits larger numbers, these are the largest integers that JavaScript can handle. Therefore, many JSON parsers cannot process larger numbers.

## Character Encoding

As required by the DICOM JSON encoding, dcm2json always creates output in Unicode UTF-8 encoding and converts DICOM data sets accordingly. If this is not possible, for example because DCMTK has been compiled without character set conversion support, an error is returned.

# 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).

# EXIT CODES

The dcm2json utility uses the following exit codes when terminating. This enables the user to check for the reason why the application terminated.

## general

    EXITCODE_NO_ERROR                         0
    EXITCODE_COMMANDLINE_SYNTAX_ERROR         1

## input file errors

    EXITCODE_CANNOT_READ_INPUT_FILE          20
    EXITCODE_NO_INPUT_FILES                  21

## output file errors

    EXITCODE_CANNOT_WRITE_OUTPUT_FILE        40

## processing errors

    EXITCODE_CANNOT_CONVERT_TO_UNICODE       80
    EXITCODE_CANNOT_WRITE_VALID_JSON         81

# ENVIRONMENT

The dcm2json 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.

The dcm2json utility will attempt to load character set mapping tables. This happens when DCMTK was compiled with the oficonv library (which is the default) and the mapping tables are not built into the library (default when DCMTK uses shared libraries).

The mapping table files are expected in DCMTK's <datadir>. The DCMICONVPATH environment variable can be used to specify a different location. If a different location is specified, those mapping tables also replace any built-in tables.

# COPYRIGHT

Copyright (C) 2016-2025 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.

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