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dump2dcm - Online in the Cloud

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This is the command dump2dcm 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


dump2dcm - Convert ASCII dump to DICOM file

SYNOPSIS


dump2dcm [options] dumpfile-in dcmfile-out

DESCRIPTION


The dump2dcm utility converts an ASCII dump file to a DICOM file. The dump file has the
same format as the output of dcmdump. Thus it is possible to capture the output of dcmdump
into a file, modify some attributes and create a new DICOM file.

PARAMETERS


dumpfile-in dump input filename

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

file contents byte ordering:

+rl --read-file-little
read OW data with little endian (default)

+rb --read-file-big
read OW data from file with big endian

other input options:

+l --line [m]ax-length: integer
maximum line length m (default: 4096)

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

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

+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 dump is damaged (default)

+E --ignore-errors
attempt to write even if dump is damaged

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


Dump File Description
The input file can be an output of dcmdump (default indented format only). One element
(tag, VR, value) must be written into one line separated by arbitrary spaces or tab
characters. A '#' begins a comment that ends at the line end. Empty lines are allowed.

The individual parts of a line have the following syntax:

Tag: (gggg,eeee)
with gggg and eeee are 4 character hexadecimal values
representing group and element tag. Spaces and tabs can be
anywhere in a tag specification.
VR: Value Representation must be written as 2 characters as in
Part 6 of the DICOM standard. No spaces or tabs are allowed
between the two characters. If the VR can be determined from
the tag, this part of a line is optional.
Value: There are several rules for writing values:
1. US, SS, SL, UL, FD, FL are written as decimal strings that
can be read by scanf().
2. AT is written as '(gggg,eeee)' with additional spaces
stripped off automatically and gggg and eeee being decimal
strings that can be read by scanf().
3. OB and OW values are written as byte or word hexadecimal
values separated by '\' character. Alternatively, OB or OW
values can be read from a separate file by writing the
filename prefixed by a '=' character (e.g. '=largepix.dat').
The contents of the file will be read as is. By default, 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.
In case of compressed pixel data, the line should start with
'(7fe0,0010) OB (PixelSequence' in order to distinguish from
uncompressed pixel data.
4. UI is written as '=Name' in data dictionary or as unique
identifier string (see 6.), e.g. '[1.2.840.....]'.
5. Strings without () <> [] spaces, tabs and # can be written
directly.
6. Other strings must be surrounded by '[' and ']'. No bracket
structure is passed. The value ends at the last ']' in the
line. Anything after the ']' is interpreted as comment.
7. '(' and '<' are interpreted special and may not be used when
writing an input file by hand as beginning characters of a
string. Multiple Value are separated by '\'. The lines
need not be sorted into ascending tag order. References in
DICOM Directories are not supported. Semantic errors are
not detected.

Example
(0008,0020) DA [19921012] # 8, 1 StudyDate
(0008,0016) UI =MRImageStorage # 26, 1 SOPClassUID
(0002,0012) UI [1.2.276.0.7230010.100.1.1]
(0020,0032) DS [0.0\0.0] # 8, 2 ImagePositionPatient
(0028,0009) AT (3004,000c) # 4, 1 FrameIncrementPointer
(0028,0010) US 256 # 4, 1 Rows
(0002,0001) OB 01\00

Limitations
Please note that dump2dcm 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 dump2dcm 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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