[dcm4che] Handling very big data

[samue...@irm.kr]

I have been trying to create or read very big DICOM files containing MPEG4 video (about 2GB) with dcm4che library.

I have two problems in handling big DICOM files.

First, creating the big DICOM Video file was ok, but my question is if it is possible to load image/video data without loading them into memory. Loading big image data into memory and saving them to file require quite long time. I tried to use Java MappedByteBuffer, but I had to allocated additional byte[] to feed the data to DICOM dataset. My code looks as  

MappedByteBuffer pixelDataBuffer = null;

byte[] pixelData = null;

try {

File mp4File = new File(input);

RandomAccessFile randomAccessFile = new RandomAccessFile(mp4File, "r");

FileChannel fileChannel = randomAccessFile.getChannel();

pixelDataBuffer = fileChannel.map(FileChannel.MapMode.READ_ONLY, 0, fileChannel.size());

pixelData = new byte[pixelDataBuffer.capacity()];

pixelDataBuffer.get(pixelData, 0, pixelDataBuffer.capacity());

fileChannel.close();

randomAccessFile.close();

} catch (FileNotFoundException e1) {

e1.printStackTrace();

} catch (IOException e) {

e.printStackTrace();

} 

Attributes dataset = new Attributes();

(abbreviated...)

Fragments fragments = new Fragments(VR.OB, false, 0);

fragments.add(null);

fragments.add(pixelData);

dataset.setValue(Tag.PixelData, VR.OB, fragments);

File dcmFile = new File(output);

try {

DicomOutputStream dos = new DicomOutputStream(dcmFile);

dos.writeDataset(fmi, dataset);

dos.close();

} catch (IOException e) {

e.printStackTrace();

}

The above code works, and I got a big DICOM video file. But the second problem is that dcm4che could not handle this big DICOM file.

When I tried to dcmdump the file, I got the following error message.

846: (7FE0,0010) OB #-1 PixelData

858: (FFFE,E000) #0 [] Item

Exception in thread "main" java.lang.NegativeArraySizeException

at java.util.Arrays.copyOf(Arrays.java:3236)

at org.dcm4che3.io.DicomInputStream.readValue(DicomInputStream.java:733)

at org.dcm4che3.tool.dcmdump.DcmDump.appendFragment(DcmDump.java:204)

at org.dcm4che3.tool.dcmdump.DcmDump.readValue(DcmDump.java:165)

at org.dcm4che3.io.DicomInputStream.readFragments(DicomInputStream.java:705)

at org.dcm4che3.io.DicomInputStream.readValue(DicomInputStream.java:538)

at org.dcm4che3.tool.dcmdump.DcmDump.readValue(DcmDump.java:111)

at org.dcm4che3.io.DicomInputStream.readAttributes(DicomInputStream.java:516)

at org.dcm4che3.io.DicomInputStream.readDataset(DicomInputStream.java:444)

at org.dcm4che3.tool.dcmdump.DcmDump.parse(DcmDump.java:87)

at org.dcm4che3.tool.dcmdump.DcmDump.main(DcmDump.java:245)

When I tried to dump with other tool such as DCMTK's dcmdump, it works well.

(0028,0103) US 0                                        #   2, 1 PixelRepresentation

(7fe0,0010) OB (PixelSequence #=2)                      # u/l, 1 PixelData

  (fffe,e000) pi (no value available)                     #   0, 1 Item

  (fffe,e000) pi 00\00\00\20\66\74\79\70\69\73\6f\6d\00\00\02\00\69\73\6f\6d\69\73... # 1939383416, 1 Item

(fffe,e0dd) na (SequenceDelimitationItem)               #   0, 0 SequenceDelimitationItem

Is there anybody who has tried to handle big image/video with dcm4che, and have any solution?

Thanks,

Samuel

[m.faro...@gmail.com]

reviving an old thread.

I am also seeing same problems with storing dicom files with segment larger than 2GB.

Is this a known issue?

Are there any plans on fixing this?

Or any suggestion what will be required to fix this issue?

Thanks

[Vibha Maini]

Is there any fix for this issue?