dcm2xml - Online in the Cloud

PROGRAM:

NAME

dcm2xml - Convert DICOM file and data set to XML

SYNOPSIS

dcm2xml [options] dcmfile-in [xmlfile-out]

DESCRIPTION

The dcm2xml utility converts the contents of a DICOM file (file format or raw data set) to
XML (Extensible Markup Language). There are two output formats. The first one is specific
to DCMTK with its DTD (Document Type Definition) described in the file dcm2xml.dtd. The
second one refers to the 'Native DICOM Model' which is specified for the DICOM Application
Hosting service found in DICOM part 19.

If dcm2xml 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 dcm2xml to read a data set with a
particular transfer syntax.

PARAMETERS

dcmfile-in DICOM input filename to be converted

xmlfile-out XML 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

long tag values:

+M --load-all
load very long tag values (e.g. pixel data)

-M --load-short
do not load very long values (default)

+R --max-read-length [k]bytes: integer (4..4194302, default: 4)
set threshold for long values to k kbytes

processing options
specific character set:

+Cr --charset-require
require declaration of extended charset (default)

+Ca --charset-assume [c]harset: string
assume charset c if no extended charset declared

+Cc --charset-check-all
check all data elements with string values
(default: only PN, LO, LT, SH, ST and UT)

# this option is only used for the mapping to an appropriate
# XML character encoding, but not for the conversion to UTF-8

+U8 --convert-to-utf8
convert all element values that are affected
by Specific Character Set (0008,0005) to UTF-8

# requires support from the libiconv toolkit

output options
general XML format:

-dtk --dcmtk-format
output in DCMTK-specific format (default)

-nat --native-format
output in Native DICOM Model format (part 19)

+Xn --use-xml-namespace
add XML namespace declaration to root element

DCMTK-specific format (not with --native-format):

+Xd --add-dtd-reference
add reference to document type definition (DTD)

+Xe --embed-dtd-content
embed document type definition into XML document

+Xf --use-dtd-file [f]ilename: string
use specified DTD file (only with +Xe)
(default: /usr/local/share/dcmtk/dcm2xml.dtd)

+Wn --write-element-name
write name of the DICOM data elements (default)

-Wn --no-element-name
do not write name of the DICOM data elements

+Wb --write-binary-data
write binary data of OB and OW elements
(default: off, be careful with --load-all)

encoding of binary data:

+Eh --encode-hex
encode binary data as hex numbers
(default for DCMTK-specific format)

+Eu --encode-uuid
encode binary data as a UUID reference
(default for Native DICOM Model)

+Eb --encode-base64
encode binary data as Base64 (RFC 2045, MIME)

DCMTK Format

The basic structure of the DCMTK-specific XML output created from a DICOM file looks like
the following:

<?xml version="1.0" encoding="ISO-8859-1"?>
<!DOCTYPE file-format SYSTEM "dcm2xml.dtd">
<file-format xmlns="http://dicom.offis.de/dcmtk">
<meta-header xfer="1.2.840.10008.1.2.1" name="Little Endian Explicit">
<element tag="0002,0000" vr="UL" vm="1" len="4"
name="MetaElementGroupLength">
166
</element>
...
<element tag="0002,0013" vr="SH" vm="1" len="16"
name="ImplementationVersionName">
OFFIS_DCMTK_353
</element>
</meta-header>
<data-set xfer="1.2.840.10008.1.2" name="Little Endian Implicit">
<element tag="0008,0005" vr="CS" vm="1" len="10"
name="SpecificCharacterSet">
ISO_IR 100
</element>
...
<sequence tag="0028,3010" vr="SQ" card="2" name="VOILUTSequence">
<item card="3">
<element tag="0028,3002" vr="xs" vm="3" len="6"
name="LUTDescriptor">
256\0\8
</element>
...
</item>
...
</sequence>
...
<element tag="7fe0,0010" vr="OW" vm="1" len="262144"
name="PixelData" loaded="no" binary="hidden">
</element>
</data-set>
</file-format>

The 'file-format' and 'meta-header' tags are absent for DICOM data sets.

XML Encoding
Attributes with very large value fields (e.g. pixel data) are not loaded by default. They
can be identified by the additional attribute 'loaded' with a value of 'no' (see example
above). The command line option --load-all forces to load all value fields including the
very long ones.

Furthermore, binary information of OB and OW attributes are not written to the XML output
file by default. These elements can be identified by the additional attribute 'binary'
with a value of 'hidden' (default is 'no'). The command line option --write-binary-data
causes also binary value fields to be printed (attribute value is 'yes' or 'base64'). But,
be careful when using this option together with --load-all because of the large amounts of
pixel data that might be printed to the output. Please note that in this context element
values with a VR of OD or OF are not regarded as 'binary information'.

Multiple values (i.e. where the DICOM value multiplicity is greater than 1) are separated
by a backslash '\' (except for Base64 encoded data). The 'len' attribute indicates the
number of bytes for the particular value field as stored in the DICOM data set, i.e. it
might deviate from the XML encoded value length e.g. because of non-significant padding
that has been removed. If this attribute is missing in 'sequence' or 'item' start tags,
the corresponding DICOM element has been stored with undefined length.

Native DICOM Model Format

The description of the Native DICOM Model format can be found in the DICOM standard, part
19 ('Application Hosting').

Bulk Data
Binary data, i.e. DICOM element values with Value Representations (VR) of OB or OW, as
well as OD, OF and UN values are by default not written to the XML output because of their
size. Instead, for each element, a new Universally Unique Identifier (UUID) is being
generated and written as an attribute of a <BulkData> XML element. So far, there is no
possibility to write an additional file to hold the binary data for each of the binary
data chunks. This is not required by the standard, however, it might be useful for
implementing an Application Hosting interface; thus this feature may be available in
future versions of dcm2xml.

In addition, Supplement 163 (Store Over the Web by Representational State Transfer
Services) introduces a new <InlineBinary> XML element that allows for encoding binary data
as Base64. Currently, the command line option --encode-base64 enables this encoding for
the following VRs: OB, OD, OF, OW, and UN.

Known Issues
In addition to what is written in the above section on 'Bulk Data', there are further
known issues with the current implementation of the Native DICOM Model format. For
example, large element values with a VR other than OB, OD, OF, OW or UN are currently
never written as bulk data, although it might be useful, e.g. for very long text elements
(especially UT) or very long numeric fields (of various VRs).

NOTES

Character Encoding
The XML encoding is determined automatically from the DICOM attribute (0008,0005)
'Specific Character Set' using the following mapping:

ASCII (ISO_IR 6) => "UTF-8"
UTF-8 "ISO_IR 192" => "UTF-8"
ISO Latin 1 "ISO_IR 100" => "ISO-8859-1"
ISO Latin 2 "ISO_IR 101" => "ISO-8859-2"
ISO Latin 3 "ISO_IR 109" => "ISO-8859-3"
ISO Latin 4 "ISO_IR 110" => "ISO-8859-4"
ISO Latin 5 "ISO_IR 148" => "ISO-8859-9"
Cyrillic "ISO_IR 144" => "ISO-8859-5"
Arabic "ISO_IR 127" => "ISO-8859-6"
Greek "ISO_IR 126" => "ISO-8859-7"
Hebrew "ISO_IR 138" => "ISO-8859-8"

If this DICOM attribute is missing in the input file, although needed, option --charset-
assume can be used to specify an appropriate character set manually (using one of the
DICOM defined terms).

Multiple character sets using code extension techniques are not supported. If needed,
option --convert-to-utf8 can be used to convert the DICOM file or data set to UTF-8
encoding prior to the conversion to XML format. This is also useful for DICOMDIR files
where each directory record can have a different character set.

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 dcm2xml 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.

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