Grassroots DICOM (GDCM) is a cross-platform library written in C++ for DICOM medical files. It's automatically wrapped to Python/C#/Java & PHP (using swig). It supports RAW, JPEG (lossy/lossless), J2K, JPEG-LS, RLE and deflated. Parts 3, 6 & 7 of the DICOM standard are included as XML files. GDCM can be used to build a JPIP or WADO server. Questions about just using the bundled applications are off-topic for Stack Overflow, unless programming specific.
Questions tagged [gdcm]
100 questions
6
votes
0 answers
Get single frames byte array from multiframe dicom image using vtk gdcm
I am reading multiframe dicom as follows and get total pixel data of image in byte array.
gdcm.ImageReader _reader = new gdcm.ImageReader();
_reader.SetFileName("FileName");
_reader.Read();
byte[] byteArray= new…
Namrata
- 173
- 8
5
votes
3 answers
PyDICOM can't read pixel data and needs GDCM or Pillow
I'm using pydicom and my code is pretty straightforward:
image = np.stack([s.pixel_array for s in scans])
But this gives a runtime error:
RuntimeError: The following handlers are available to decode the pixel data however they are missing required…
Shamoon
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5
votes
2 answers
Display DICOM monochrome2 having bits stored less than bits allocated
I want to display DICOM file having photometric interpretation MONOCHROME2.
some of the specifications of image are-
Rows: 1024
Columns: 1024
No of Frames: 622
Bits Allocated: 16
Bits Stored: 10
High Bit: 9
Pixel…
Namrata
- 173
- 8
5
votes
1 answer
DICOM C_MOVE with gdcm's "CompositeNetworkFunctions"
I am trying to get DICOMS from a server using gdcm's CompositeNetworkFunctions.
My test server is set up using "Orthanc".
When I run the Move request, I get:
terminate called after throwing an instance of 'gdcm::Exception'
what(): …
Germanunkol
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4
votes
1 answer
Emscripten library make from CMake cannot link
I am using Grassroot Dicom viewer version 2.8.9 to compile into Emscripten library bc on Windows 10 64-bit platform.
I followed the instruction from this website
emconfigure cmake .
emmake make VERBOSE=1
After that I got library file ending with…
MooMoo
- 1,086
- 12
- 22
4
votes
1 answer
Reading pixel values of an image
I am trying to read the pixel values of an image contained in a DICOM file in my simple c++ application using the Grassroots DICOM (GDCM) library. When reading the file metadata I get the following information about the picture:
Bits allocated:…
MrCravon
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- 4
4
votes
1 answer
warning: disabled expansion of recursive macro
I am currently building the GDCM project using MacOSX default compiler: clang. This compiler trigger a warning in its own header (see ref):
In file included from…
malat
- 12,152
- 13
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4
votes
2 answers
How do I read a DICOM tag within another tag with ITK?
I'm using ITK to read a DICOM file, calling
dicomIO->GetValueFromTag(...)
to read a tag value. This works fine for tags like "300a|011e" (gantry angle). The problem comes trying to read tag "0018|0060" which is embedded inside "3002|0030".
If I use…
imekon
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4
votes
4 answers
Access Violation Exception only appearing when running C# app without debugger attached
I have an application that works fine in Visual Studios 2008, and I am trying to get it into VS 2010 in order to use .NET 4, and I have a really weird problem. When I run the code from either Release mode or Debug mode with the debugger attached…
Jon
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4
votes
0 answers
gdcm libs link order
I am trying to link my Qt app to gdcm library.
When I build it, I get several errors like this: undefined reference to 'gdcm::System::FileExists(char const*)'.
I think the problem comes from the link order specified in my .pro file:
LIBS +=…
Andrea Caloni
- 91
- 1
- 5
3
votes
1 answer
"TypeError: a bytes-like object is required, not 'str'" reading compressed DICOM volume into numpy array
I am using Python 3.7.3 on Anaconda Spyder on CentOS 7.
I have a 3D DICOM volume that is in a single file:/usr/share/aliza/datasets/DICOM/00_MR/Tra_FLAIR.dcm
print(image.file_meta.TransferSyntaxUID)
returns
1.2.840.10008.1.2.4.70
import pydicom…
OtagoHarbour
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- 81
3
votes
1 answer
How to read multi frame DICOM files using GDCM?
I'm trying to read multi frame DICOM files using gdcm library.
But i can only read single frame dicom files data with this code :
gdcm::ImageReader reader;
reader.SetFileName(path);
if(!reader.Read()) return false;
const gdcm::Pixmap &image =…
masoud khanlo
- 189
- 1
- 14
3
votes
1 answer
Convert a dicom tag to its string name in gdcm in C++
Given a gdcm tag, e.g. gdcm::Tag(0x0010,0x0010) how can it be convert to the corresponding tag name string, in this case "PatientsName" in C++?
Dov Grobgeld
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3
votes
2 answers
Writing 16-bit image to DICOM file format using GDCM
I have successfully written an 8-bit image as a DICOM file using GDCM library. Now I am trying to write 16-bit image as a DICOM file. Here is my code. Could anyone point out what I am missing or what should be done.
static public void…
Haris Iltifat
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3
votes
2 answers
Using GDCM via CMake
I downloaded source of GDCM 2.4.1 and used CMake 2.8.12.1 and Visual Studio 2010 to build the libraries. I want to use GDCM in my C++ project.
Unfortunately, it seems that after building the GDCM solution with VS, there are only the lib-files in the…
MichaelXanadu
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