GDCM: DecompressImageMultiframe.cs

GDCM 3.2.5

DecompressImageMultiframe.cs
/*=========================================================================
Program: GDCM (Grassroots DICOM). A DICOM library
Copyright (c) 2006-2011 Mathieu Malaterre
All rights reserved.
See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE. See the above copyright notice for more information.
=========================================================================*/
/*
$ gdcminfo ~/Desktop/angiogram-06.dcm
MediaStorage is 1.2.840.10008.5.1.4.1.1.12.1 [X-Ray Angiographic Image Storage]
TransferSyntax is 1.2.840.10008.1.2.4.50 [JPEG Baseline (Process 1): Default Transfer Syntax for Lossy JPEG 8 Bit Image Compression]
NumberOfDimensions: 3
Dimensions: (512,512,355)
Origin: (0,0,0)
Spacing: (1,1,40)
DirectionCosines: (1,0,0,0,1,0)
Rescale Intercept/Slope: (0,1)
SamplesPerPixel :1
BitsAllocated :8
BitsStored :8
HighBit :7
PixelRepresentation:0
ScalarType found :UINT8
PhotometricInterpretation: MONOCHROME2
PlanarConfiguration: 0
TransferSyntax: 1.2.840.10008.1.2.4.50
Orientation Label: AXIAL
*/
/*
* Description:
*
* Assume we have a file angiogram-06.dcm as described above.
* the following program will decompress directly from the extracted jpeg stream.
*
* First step extract the jpeg stream (but not the Basic Offset Table):
*
* $ gdcmraw -i angiogram-06.dcm -o /tmp/output/chris --split-frags --pattern %d.jpg
*
* Check that indeed there are 355 files, while there are 356 fragments in the original DICOM file, since
* gdcmraw always skip the first fragment (Basic Offset Table).
*
* Now from those individual jpeg stream, recreate a fake gdcm.DataElement...
*
* Usage:
*
* $ export LD_LIBRARY_PATH=$HOME/Projects/gdcm/debug-gcc/bin
* $ mono ./bin/DecompressImageMultiframe.exe /tmp/output
*/
using System;
using gdcm;
public class DecompressImageMultiframe
{
public static int Main(string[] args)
{
string directory = args[0];
gdcm.Directory dir = new gdcm.Directory();
uint nfiles = dir. Load(directory);
//System.Console.WriteLine(dir.toString());
gdcm.FilenamesType filenames = dir. GetFilenames();
Image image = new Image();
image. SetNumberOfDimensions( 3 ); // important for now
DataElement pixeldata = new DataElement( new gdcm.Tag(0x7fe0,0x0010) );
// Create a new SequenceOfFragments C++ object, store it as a SmartPointer :
SmartPtrFrag sq = SequenceOfFragments. New();
// Yeah, the files are not guaranteed to be in order, please adapt...
for(uint i = 0; i < nfiles; ++i)
{
System.Console.WriteLine( filenames[(int)i] );
string file = filenames[(int)i];
System.IO.FileStream infile =
new System.IO.FileStream(file, System.IO.FileMode.Open, System.IO.FileAccess.Read);
uint fsize = gdcm.PosixEmulation.FileSize(file);
byte[] jstream = new byte[fsize];
infile.Read(jstream, 0 , jstream.Length);
Fragment frag = new Fragment();
frag. SetByteValue( jstream, new gdcm.VL( (uint)jstream.Length) );
sq.AddFragment( frag );
}
// Pass by reference:
pixeldata. SetValue( sq.__ref__() );
// insert:
image. SetDataElement( pixeldata );
// JPEG use YBR to achieve better compression ratio by default (not RGB)
// FIXME hardcoded:
PhotometricInterpretation pi = new PhotometricInterpretation( PhotometricInterpretation. PIType.MONOCHROME2 );
image. SetPhotometricInterpretation( pi );
// FIXME hardcoded:
PixelFormat pixeltype = new PixelFormat(1,8,8,7);
image. SetPixelFormat( pixeltype );
// FIXME hardcoded:
image. SetTransferSyntax( new TransferSyntax( TransferSyntax. TSType.JPEGLosslessProcess14_1 ) );
image. SetDimension(0, 512);
image.SetDimension(1, 512);
image.SetDimension(2, 355);
// Decompress !
byte[] decompressedData = new byte[(int)image. GetBufferLength()];
image. GetBuffer(decompressedData);
// Write out the decompressed bytes
System.Console.WriteLine(image.toString());
using (System.IO.Stream stream =
System.IO.File.Open(@"/tmp/dd.raw",
System.IO.FileMode.Create))
{
System.IO.BinaryWriter writer = new System.IO.BinaryWriter(stream);
writer.Write(decompressedData);
}
return 0;
}
}
gdcm::Bitmap::SetNumberOfDimensions
void SetNumberOfDimensions(unsigned int dim)
gdcm::Bitmap::GetBufferLength
unsigned long GetBufferLength() const
gdcm::Bitmap::SetDataElement
void SetDataElement(DataElement const &de)
Definition gdcmBitmap.h:76
gdcm::Bitmap::SetDimension
void SetDimension(unsigned int idx, unsigned int dim)
gdcm::Bitmap::SetTransferSyntax
void SetTransferSyntax(TransferSyntax const &ts)
Transfer syntax.
Definition gdcmBitmap.h:69
gdcm::Bitmap::GetBuffer
bool GetBuffer(char *buffer) const
Access the raw data.
gdcm::Bitmap::SetPhotometricInterpretation
void SetPhotometricInterpretation(PhotometricInterpretation const &pi)
gdcm::Bitmap::SetPixelFormat
void SetPixelFormat(PixelFormat const &pf)
Definition gdcmBitmap.h:115
gdcm::DataElement
Class to represent a Data Element either Implicit or Explicit.
Definition gdcmDataElement.h:59
gdcm::DataElement::SetValue
void SetValue(Value const &vl)
Definition gdcmDataElement.h:100
gdcm::DataElement::SetByteValue
void SetByteValue(const char *array, VL length)
Definition gdcmDataElement.h:126
gdcm::Directory
Class for manipulation directories.
Definition gdcmDirectory.h:43
gdcm::Directory::Load
unsigned int Load(FilenameType const &name, bool recursive=false)
gdcm::Directory::GetFilenames
FilenamesType const & GetFilenames() const
Set/Get the file names within the directory.
Definition gdcmDirectory.h:58
gdcm::Fragment
Class to represent a Fragment.
Definition gdcmFragment.h:44
gdcm::Image
Image.
Definition gdcmImage.h:47
gdcm::PhotometricInterpretation
Class to represent an PhotometricInterpretation.
Definition gdcmPhotometricInterpretation.h:29
gdcm::PhotometricInterpretation::PIType
PIType
Definition gdcmPhotometricInterpretation.h:31
gdcm::PixelFormat
PixelFormat.
Definition gdcmPixelFormat.h:46
gdcm::SequenceOfFragments
Class to represent a Sequence Of Fragments.
Definition gdcmSequenceOfFragments.h:32
gdcm::SequenceOfFragments::New
static SmartPointer< SequenceOfFragments > New()
Definition gdcmSequenceOfFragments.h:289
gdcm::System
Class to do system operation.
Definition gdcmSystem.h:27
gdcm::Tag
Class to represent a DICOM Data Element (Attribute) Tag (Group, Element).
Definition gdcmTag.h:39
gdcm::TransferSyntax
Class to manipulate Transfer Syntax.
Definition gdcmTransferSyntax.h:40
gdcm::TransferSyntax::TSType
TSType
Definition gdcmTransferSyntax.h:61
gdcm::VL
Value Length.
Definition gdcmVL.h:30
gdcm
Definition gdcmASN1.h:21