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xml2dcm - Online in the Cloud

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This is the command xml2dcm that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


xml2dcm - Convert XML document to DICOM file or data set

SYNOPSIS


xml2dcm [options] xmlfile-in dcmfile-out

DESCRIPTION


The xml2dcm utility converts the contents of an XML (Extensible Markup Language) document
to DICOM file or data set. The XML document is expected to validate against the DTD
(Document Type Definition) which is described in file dcm2xml.dtd. An appropriate XML file
can be created using the dcm2xml tool (option +Wb recommended to include binary data).

PARAMETERS


xmlfile-in XML input filename to be converted (stdin: "-")

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

processing options
validation:

+Vd --validate-document
validate XML document against DTD

+Vn --check-namespace
check XML namespace in document root

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 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

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


The basic structure of the XML input expected 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 may be absent for DICOM data sets.

Character Encoding
The DICOM character encoding is determined automatically from the element with tag
'0008,0005' (Specific Character Set) - if present. The following character sets are
currently supported (requires libxml to include iconv support, see --version output):

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)

Multiple character sets are not supported (only the first value of the 'Specific Character
Set' is used for the character encoding in case of value multiplicity).

See dcm2xml documentation for more details on the XML structure.

Binary Data
Binary data can be encoded either as a sequence of hex numbers separated by a backslash
'\' or in Base64 format (binary='base64'). In addition, binary data can also be read from
file (binary='file'). In this case, the filename has to be specified as the element value,
e.g.

<element tag="7fe0,0010" vr="OW" ... binary="file">subdir/pixeldata.raw</element>

Please note that the contents of the file will be read as is. 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.

Compression
If libxml is compiled with zlib support, the input file (xmlfile-in) can also be
compressed with ZIP, which usually results in much smaller files. See output of option
--version in order to check whether zlib support is available.

Limitations
Different versions of libxml might have different limits for the maximum length of an XML
element value. Therefore, it should be avoided to use very long element values (e.g. for
pixel data).

Please note that xml2dcm 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 xml2dcm 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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