| Re: Problem reading DICOM files with IDL [message #35866] |
Wed, 30 July 2003 06:38 |
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Wonko[3]
Messages: 9
Registered: February 2003
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Junior Member |
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nuno@ibili.uc.pt (Nuno Ferreira) writes:
> Are you aware of a DICOM viewer that reads compressed DICOM files and
> creates uncompressed files compatible with IDL? Do you have other ideas?
> Thanks in advance...
The Dicom Toolkit (DCMTK) from Offis (http://dicom.offis.de/) can do
this. These are many command line utilities, available for Win32,
Linux and Solaris in binary format, and as well as source code. What
you need is the dcmdjpeg utility.
wonko@weird wonko $ dcmdjpeg --help
$dcmtk: dcmdjpeg v3.5.2 2002-12-23 $
dcmdjpeg: Decode JPEG-compressed DICOM file
usage: dcmdjpeg [options] dcmfile-in dcmfile-out
parameters:
dcmfile-in DICOM input filename to be converted
dcmfile-out DICOM output filename
general options:
-h --help print this help text and exit
--version print version information and exit
-v --verbose verbose mode, print processing details
-d --debug debug mode, print debug information
processing options:
color space conversion options:
+cp --conv-photometric convert if YCbCr photom. interpr. (default)
+cl --conv-lossy convert YCbCr to RGB if lossy JPEG
+ca --conv-always always convert YCbCr to RGB
+cn --conv-never never convert color space
planar configuration options:
+pa --planar-auto automatically determine planar configuration
from SOP class and color space (default)
+px --color-by-pixel always store color-by-pixel
+pl --color-by-plane always store color-by-plane
SOP Instance UID options:
+ud --uid-default keep same SOP Instance UID (default)
+ua --uid-always always assign new UID
output options:
output file format:
+F --write-file write file format (default)
-F --write-dataset write data set without file meta information
output transfer syntax:
+te --write-xfer-little write with explicit VR little endian (default)
+tb --write-xfer-big write with explicit VR big endian TS
+ti --write-xfer-implicit write with implicit 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
Alex
--
Alex Schuster Wonko@wonkology.org PGP Key available
alex@pet.mpin-koeln.mpg.de
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| Re: Problem reading DICOM files with IDL [message #35933 is a reply to message #35866] |
Tue, 29 July 2003 07:52  |
Nuno Ferreira
Messages: 16
Registered: July 2003
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Junior Member |
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David Fanning wrote:
> It would be more helpful to see the error messages
> caused by reading the uncompressed files, since even
> you admit IDL isn't going to read the compressed files.
>
> Sigh...
I was hoping that IDL versions more recent than 5.4 would be able to read
DICOM compressed files. In that case, the error message could be useful.
Anyway, here is the error message I get with the uncompressed files created
with the Osiris DICOM viewer:
IDL> img=read_dicom(file)
% Compiled module: READ_DICOM.
% Loaded DLM: DICOM.
READ_DICOM: The file D:\TEMP\xa0001.dcm is not in a supported DICOM format.
Not very helpful, I know...
Just to check, I also tried the commands to read the header info that David
mentioned in another message, which of course didn't work since IDL cannot
read the file...
IDL> thisObject = Obj_New('IDLffDicom', file)
IDL> thisObject -> DumpElements
IDL> modality = thisObject -> GetValue('0008'xL, '0060'xL)
IDL> Print, "Modality: ", *modality
% Pointer type required in this context: MODALITY.
% Execution halted at: $MAIN$
Are you aware of a DICOM viewer that reads compressed DICOM files and creates
uncompressed files compatible with IDL? Do you have other ideas?
Thanks in advance...
Nuno
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| Re: Problem reading DICOM files with IDL [message #35948 is a reply to message #35933] |
Mon, 28 July 2003 09:15 |
Rick Towler
Messages: 821
Registered: August 1998
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Senior Member |
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"Nuno Chichorro Ferreira" wrote in message ...
> I apologize if this has already been answered before. I have been unable
> to read DICOM files with IDL 5.3/5.4, can someone help me?
>
> % IDLFFDICOM::READ: This file uses the following compression type for
> its image(s): JPEG Lossless, Non-Hierarchical, First Order Prediction
> (Process 14)
This format "JPEG Lossless, Non-Hierarchical, First Order Prediction" isn't
supported by IDLffDICOM. For a full list of supported/unsupported types
check the docs, specifically the section on "IDL DICOM v3.0 Conformance
Summary"
-Rick
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| Re: Problem reading DICOM files with IDL [message #35951 is a reply to message #35948] |
Mon, 28 July 2003 08:02 |
David Fanning
Messages: 11724
Registered: August 2001
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Senior Member |
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Nuno Chichorro Ferreira writes:
> I apologize if this has already been answered before. I have been unable
> to read DICOM files with IDL 5.3/5.4, can someone help me?
>
> The files I want to read are in DICOM compressed format (JPEG), but IDL
> only reads the size of the image, not the data. I know that IDL does not
> support compressed files (at least the 5.3/5.4 versions), but the same
> happens with the uncompressed files I have created by reading them with
> a DICOM viewer - Osiris - and saving them without compression.
>
> Can anyone find an easy solution for the problem?
> Many thanks,
>
> Nuno
>
> P.S. - The following is the error message I get when reading the
> compressed DICOM files:
>
> IDL> img=read_dicom(file)
> % Compiled module: READ_DICOM.
> % Loaded DLM: DICOM.
> % IDLFFDICOM::READ: This file uses the following compression type for
> its image(s): JPEG Lossless, Non-Hierarchical, First Order Prediction
> (Process 14)
>
> % IDLFFDICOM::READ: ** Unable to handle compressed data!!! **
>
> % IDLFFDICOM::READ: This image has an undefined length and may not be
> read properly.
It would be more helpful to see the error messages
caused by reading the uncompressed files, since even
you admit IDL isn't going to read the compressed files.
Sigh...
Cheers,
David
--
David W. Fanning, Ph.D.
Fanning Software Consulting, Inc.
Phone: 970-221-0438, E-mail: david@dfanning.com
Coyote's Guide to IDL Programming: http://www.dfanning.com/
Toll-Free IDL Book Orders: 1-888-461-0155
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