DCMTK: json2dcm: Convert JSON document to DICOM file or data set

DCMTK Version 3.7.0 OFFIS DICOM Toolkit

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json2dcm: Convert JSON document to DICOM file or data set

# SYNOPSIS

    json2dcm [options] jsonfile-in dcmfile-out

# DESCRIPTION

The json2dcm utility converts the contents of a JSON (JavaScript Object Notation) document to a binary DICOM file or data set. The JSON document is expected to conform to the "DICOM JSON Model" as defined in DICOM Part 18 Section F. Such JSON files can be created, e.g., using the dcm2json tool.

# PARAMETERS

    jsonfile-in  JSON input filename to be converted ("-" for stdin)

    dcmfile-out  DICOM output filename ("-" for 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-meta-info
             read meta information if present (default)

      -f   --ignore-meta-info
             ignore file meta information

## 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

    bulkdata URI handling:

      +Bu  --parse-bulkdata-uri
             parse Bulkdata URIs (default)

      -Bu  --ignore-bulkdata-uri
             ignore Bulkdata URIs

      +Bd  --add-bulkdata-dir  [d]irectory: string
             add d to list of permitted bulk data sources

    handling of arrays with multiple data sets:

      -ar  --array-reject
             reject multiple data sets (default)

      +as  --array-select  [n]umber: integer
             select data set n from array

      +ar  --array-sequence
             store all data sets in private sequence

## 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 TS

      +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 document is invalid (default)

      +E   --ignore-errors
             attempt to write even if document is invalid

    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

    length encoding in sequences and items:

      +e   --length-explicit
             write with explicit lengths (default)

      -e   --length-undefined
             write with undefined lengths

    charset handling:

      +c   --charset-accept
             write with the given charset in JSON (default)

      -c   --charset-replace
             replace the given charset in JSON with UTF-8

    deflate compression level (only with --write-xfer-deflated):

      +cl  --compression-level  [l]evel: integer (default: 6)
             0=uncompressed, 1=fastest, 9=best compression

# NOTES

The basic structure of the JSON input expected 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
            ]
        }
    }

## Character Encoding

The JSON format only supports UTF-8 encoding. Thus the generated DICOM file will also contain UTF-8 encoding. If the JSON file does not contain a specific character set, or a specific character set other than "ISO_IR 192", a warning will be issued.

## Binary Data, Bulk Data, and Pixel Data

The DICOM JSON Model uses "InlineBinary" to store attribute values of binary value representations such as "OB", "OW", "OD", "OF", "OL", "OV" etc. in Base64 encoded form. This is supported in json2dcm for all binary attributes, including unencapsulated pixel data.

The DICOM JSON Model also permits attribute values to be stored separately from the JSON data set and to be referenced through a BulkDataURI. This is supported for file URIs that reference files in the local filesystem. json2dcm tool also supports the inofficial extension to the file URI scheme generated by DCM4CHE, where parameters named "offset" and "length" are appended to the file URI in order to refer to a specific part of a file. HTTP URIs as well as URIs that identify another part in a MIME multipart/related structure are not yet supported in json2dcm. If the command line option --ignore-bulkdata-uri is specified, then all bulk data URIs are ignored and attributes with bulk data will be written with empty value.

Finally, encapsulated (in particular, compressed) pixel data is not supported by json2dcm because the syntax of the DICOM JSON Model for this specific case is not defined in the DICOM standard yet.

## Arrays of Data Sets

The DICOM JSON Model uses a JSON array structure to return multiple data sets in DICOMweb services such as WADO-RS or QIDO-RS. JSON arrays containing a single DICOM data set are automatically recognized by json2dcm and treated like a data set without the surrounding array structure. JSON arrays containing multiple data sets are rejected by default. Alternatively, the --array-select option can be used to select one data set from the array to be converted. The --array-sequence option causes all data sets to be written as sequence items into a single private sequence with attribute tag (0009,1000). Such files, which are mostly intended for debugging purposes, can be recognized by the private creator element (0009,0010), which has the value "JSON2DCM_LIST_OF_DATASETS".

## Trailing Commas

Trailing commas are not permitted in JSON, but json2dcm will still accept such JSON data sets without warning or error message because they are handled gracefully by the underlying JSON parser. Users should, therefore, not assume that a JSON data set is valid just because json2dcm accepts it. This tool is not designed as a validator for JSON or the DICOM JSON Model.

# 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

## output file errors

    EXITCODE_CANNOT_WRITE_OUTPUT_FILE               40

## processing errors

    EXITCODE_INVALID_JSON_CONTENT                   65
    EXITCODE_BULKDATA_URI_NOT_SUPPORTED             66

# ENVIRONMENT

The json2dcm 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.

# SEE ALSO

dcm2json(1) dump2dcm(2)

# COPYRIGHT

Copyright (C) 2024-2025 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.

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