table of contents
| dcm2json(1) | OFFIS DCMTK | dcm2json(1) |
NAME¶
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
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¶
Binary data, i.e. DICOM element values with Value Representations (VR) of OB or OW, as well as OD, OF, OL, OV and UN values are always written as 'InlineBinary' (base64 encoding) to the JSON output. A future version of this tool might optionally use a 'BulkDataURI' instead, i.e. the WADO-RS URL of a bulk data item that contains the element value. This would be particularly useful for large amounts of data, such as pixel data.
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 datasets accordingly. If this is not possible, for example because DCMTK has been compiled without either iconv or ICU library, 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) 2016-2023 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.
| Tue Dec 19 2023 | Version 3.6.8 |