Invalid stream when trying to read from buffer

[martinrame]

Hi, I need to read some tags from an image my program receives via network, as the files are really big (XA), I would like to load a buffer containing just the first 128kb for example, and look for the info I need.

I did some tests by writing my buffer to a file, and using "dcmdump +E -M file.dcm" and it was parsed as I expected.

I'm trying to read the dataset in a similar way as dcmdump does, but I'm getting "Invalid stream", here's the code:

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DcmInputBufferStream dataBuf;
dataBuf.setBuffer(buffer, buflen);
dataBuf.setEos();

DcmFileFormat fileFormat;
fileFormat.transferInit();
OFCondition cond = fileFormat.read(dataBuf, EXS_Unknown, EGL_noChange, buflen);
fileFormat.transferEnd();
cond.text(); // <--- Invalid stream

What I'm doing wrong?.

[J. Riesmeier]

So, you receive the DICOM dataset directly to file?

Would the "maxReadLength" parameter of DcmFileFormat::loadFile() help? By default, this method only loads element values that have a maximum length of 4 Kbytes (see "DCM_MaxReadLength").

[martinrame]

So, you receive the DICOM dataset directly to file?

Would the "maxReadLength" parameter of DcmFileFormat::loadFile() help? By default, this method only loads element values that have a maximum length of 4 Kbytes (see "DCM_MaxReadLength").

Thanks for your answer Jörg. No, I cannot use loadFile, because I don't have a file, but a buffer containing just part of a dicom file.

I've tried using this:

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OFCondition cond = fileFormat.read(dataBuf, EXS_Unknown, EGL_noChange, 4096);

But I get the same error.

In another post you mentioned that my buffer (DcmInputBufferStream in this case) doesn't allow aleatory access (can't use seek or similar). Is this the case?, any workaround?.

[J. Riesmeier]

If you have no DICOM file why do you use DcmFileFormat at all (instead of DcmDataset)?

[martinrame]

If you have no DICOM file why do you use DcmFileFormat at all (instead of DcmDataset)?

Good question.

I modified my code to use a DcmDataset instead of DcmFileFormat:

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  DcmInputBufferStream dataBuf;
  dataBuf.setBuffer(buffer, buflen);
  dataBuf.setEos();

  DcmDataset dset;
  OFCondition cond = dset.read(dataBuf, EXS_Unknown, EGL_noChange, 2048);
  cond.text();  

But I'm getting the same "Invalid stream" message. Any hint?.

[martinrame]

I did some more tests using DcmItem and DcmMetaInfo, instead of DcmDataset. None of them stopped with an "Invalid stream" error, but they (of course) don't get the information I need.

Here are the results:

DcmMetaInfo:

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# Dicom-Meta-Information-Header
# Used TransferSyntax: Little Endian Explicit
(0002,0000) UL 188                                      #   4, 1 FileMetaInformationGroupLength
(0002,0001) OB 00\01                                    #   2, 1 FileMetaInformationVersion
(0002,0002) UI =SecondaryCaptureImageStorage            #  26, 1 MediaStorageSOPClassUID
(0002,0003) UI [G08008453.20140607124845.1]             #  26, 1 MediaStorageSOPInstanceUID
(0002,0010) UI =JPEGLossless:Non-hierarchical-1stOrderPrediction #  22, 1 TransferSyntaxUID
(0002,0012) UI [1.2.276.0.7230010.3.0.3.6.0]            #  28, 1 ImplementationClassUID
(0002,0013) SH [OFFIS_DCMTK_360]                        #  16, 1 ImplementationVersionName
(0002,0016) AE [PACSLINK]                               #   8, 1 SourceApplicationEntityTitle

DcmItem:

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(fffe,e000) na (Item with explicit length #=0)          #   0, 1 Item
(fffe,e00d) na (ItemDelimitationItem for re-encoding)   #   0, 0 ItemDelimitationItem

[J. Riesmeier]

The information in the meta-header indicate that your buffer actually contains the byte stream of a DICOM file...

Where is the buffer content coming from?

[martinrame]

The information in the meta-header indicate that your buffer actually contains the byte stream of a DICOM file...

Where is the buffer content coming from?

I have a client app that requests an image stored on a http server that serve requests using a CGI app. When part of the data comes to the client, I need to start parsing the header of it, before loading the whole file (because this can take too long for large files like Angio images XA).

[J. Riesmeier]

OK, I understand. If it's really a DICOM file (with meta-header) then DcmFileFormat is the correct class.

Btw, I tried dcmdump with a DICOM XA file cut off after 128K (using "dd") and it works when I use option --ignore-errors (+E) or -ignore-parse-errors (+Ep). So, the input buffer stream approach should work in the same manner (though I haven't tried it). The error message for the dcmdump example (without the ignore error options) was:

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E: dcmdump: I/O suspension or premature end of stream: reading file: test.dcm

[martinrame]

Can you load that 128k file into a (void *) buffer, then try to open with DcmFileFormat?, then Print it's header (at least the part that can be read)?. That's exactly what I'm trying to do.

[J. Riesmeier]

I tested it, and it works in the same manner.

I don't know whether it makes any difference, but I used the current development version of the DCMTK.

[martinrame]

Jörg, here's a small program to show what I'm trying to do:

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#include <dcmtk/config/osconfig.h>
#define INCLUDE_CSTDLIB
#define INCLUDE_CSTDIO
#define INCLUDE_CSTRING
#include "dcmtk/ofstd/ofstdinc.h"
#include "dcmtk/dcmdata/dcistrmb.h"
#include "dcmtk/dcmdata/dcdict.h"
#include <dcmtk/dcmdata/dcfilefo.h>

using namespace std;

int main(int argc, char *argv[])
{
  FILE *f;
  int const MAX_FILE_SIZE = 8192;
  void *  buffer[MAX_FILE_SIZE];
  int buflen;

  if(argc == 1) {
    cerr << "Please provide a file." << endl;
    return 0;
  };

  f = fopen(argv[1], "rb");
  if (f)
  {
      buflen = fread(buffer, MAX_FILE_SIZE, 1, f);
      DcmInputBufferStream dataBuf;
      dataBuf.setBuffer(buffer, buflen);
      dataBuf.setEos();

      DcmFileFormat fileFormat;
      fileFormat.transferInit();
      OFCondition cond = fileFormat.read(dataBuf, EXS_Unknown, EGL_noChange, buflen);
      fileFormat.transferEnd();

      cout << "Result: " << cond.text() << endl;
      cout << "Dump: " << endl;
      fileFormat.print(cout);
  }
  else
  {
      cout << "Error opening file " << argv[1] << endl;
  }
}

I truncated an XA file to 128k using this command:

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truncate -s KB 128 file.dcm

This is the output of ./dumpbuffer file.dcm:

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Result: End of stream
Dump: 

# Dicom-File-Format

# Dicom-Meta-Information-Header
# Used TransferSyntax: Little Endian Explicit

# Dicom-Data-Set
# Used TransferSyntax: Unknown Transfer Syntax

Do you know why there's no dicom tag shown?.

P.s.: Compiled against 3.6.0.

[J. Riesmeier]

I haven't compiled your code, but guess that the error is in this line:

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buflen = fread(buffer, MAX_FILE_SIZE, 1, f);

You read 1 element of data, which has a size of 8192 bytes. So, fread() returns 1 (for the number of read elements)...

[martinrame]

I just want to read 8192 bytes, Is my code correct?.

[J. Riesmeier]

As far as I can see, NO. Reading the man page of fread() you'll notice that you have to swap the second and third parameter.