+2004-10-01 Eric Boix <Eric.Boix@creatis.insa-lyon.fr>
+ * Added documentation of vtkgdcmReader on Website:
+ - testvtkGdcmReader.cxx renamed to vtkGdcmDemo.cxx (to be compatible
+ with it's binary name).
+ - vtk/vtkGdcmDemo.cxx and vtkgdcmViewer.cxx: added comments for
+ the Website to be more complete.
+ - Doc/doxygen.config.in: vtk/vtkGdcmReader.cxx now appears on
+ doxygenated documentation.
+ - Doc/DoxyVtkGdcmReaderExamples.txt added
+ (see http://www.creatis.insa-lyon.fr/Public/Gdcm/html.developper/
+ DoxyVtkGdmReaderExamples.html )
+ * src/win32, vtk/win32 manually maintained .dsp and .dsw removed.
+ * CLEANUP_ROUND (3) for gdcmPixelConvert
+ - src/gdcmFile.cxx, gdcmFile.h splitting GetImageDataIntoVectorRaw
+
2004-09-29 Eric Boix <Eric.Boix@creatis.insa-lyon.fr>
* CLEANUP_ROUND (2) for gdcmPixelConvert
- src/gdcmFile.cxx, gdcmFile.h splitting GetImageDataIntoVectorRaw
# http://www.cmake.org/pipermail/cmake/2003-April/003673.html
# Too bad CMake doesn't support multiline ""
SET(GDCM_DOCUMENTATION_INPUT_COMMON
- "${GDCM_SOURCE_DIR}/src ${GDCM_SOURCE_DIR}/Doc/DoxyPython.txt"
+ "${GDCM_SOURCE_DIR}/src ${GDCM_SOURCE_DIR}/Doc/DoxyPython.txt ${GDCM_SOURCE_DIR}/Doc/DoxyVtkGdmReaderExamples.txt"
)
SET(GDCM_DOCUMENTATION_EXCLUDE_COMMON
"${GDCM_SOURCE_DIR}/src/gdcmJpeg.cxx"
)
+
+ IF(GDCM_VTK)
+ SET(GDCM_DOCUMENTATION_INPUT_COMMON
+ "${GDCM_DOCUMENTATION_INPUT_COMMON} ${GDCM_SOURCE_DIR}/vtk")
+ ENDIF(GDCM_VTK)
#Should rewrote this thing with FOREACH:
#-----------------------------------------------------------------------------
--- /dev/null
+/**
+ * \page DoxyVtkGdmReaderExamples VtkGdmReader examples
+ * Below you will find, by order of complexity, two examples that
+ * illustate how the vtkGdcmReader vtk class can be used.
+ * Basically, vtkGdcmReader behaves like any other derived class of
+ * vtkImageReader...
+ * \include vtkGdcmDemo.cxx
+ * \include vtkgdcmViewer.cxx
+ */
<UL>
<LI>the integration of (optional) overlays on image.
</LI>
+ <LI>a more complete supports of the
+ <A HREF="ConformanceSummary.html">various Jpeg encodings</A>
+ </LI>
+</UL>
+Gdcm also still needs
+<UL>
+<LI> an enhanced and simpler API to access the various forms of pixel data
+ (e.g. RGB, GrayLevel, RawData...),
+</LI>
+<LI> a decent user's guide (currently, only a partial doxygenation is
+ available),
+</LI>
+<LI> the python wrappers to be fixed,
+</LI>
+<LI> a simple wxWdiget Dicom file editor.
+</LI>
+</UL>
</UL>
<HR size="1"><ADDRESS style="align: right;"></ADDRESS>
<LI> this class is wrapped for vtkPython (by using native VTK wrappers).
</UL>
+For a quick, but probably sufficient, introduction to the
+usage of <TT>vtkGdcmReader</TT> please refer to the
+<A HREF="html.developper/DoxyVtkGdmReaderExamples.html">
+simple examples</A>.
+
+The documentation of vtkGdcmReader is available in both forms
+<UL>
+<LI>
+ <A HREF="html.user/classvtkGdcmReader.html">for users</A>,
+</LI>
+<LI>
+ <A HREF="html.developper/classvtkGdcmReader.html">for developpers</A>.
+</LI>
+</UL>
+
<HR size="1"><ADDRESS style="align: right;"></ADDRESS>
</BODY>
# directories that contain example code fragments that are included (see
# the \include command).
-EXAMPLE_PATH = @GDCM_SOURCE_DIR@/gdcmPython/demo
+EXAMPLE_PATH = @GDCM_SOURCE_DIR@/gdcmPython/demo @GDCM_SOURCE_DIR@/vtk
# If the value of the EXAMPLE_PATH tag contains directories, you can use the
# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
# and *.h) to filter out the source-files in the directories. If left
# blank all files are included.
-EXAMPLE_PATTERNS =
+EXAMPLE_PATTERNS = *.py *.cxx
# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
# searched for input files to be used with the \include or \dontinclude
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
+Description: vtk/vtkGdcmReader doesn't positionate the normal to the image
+Date: 2004 Oct 1
+Attributed:
+Details: vtkGdcmReader::CheckFileCoherence() sets the DataOrigin[i]
+ but doesn't set the plane (image seen in 3D) normal (is it
+ possible any how). This plane normal could be extracted from
+ the "orientation" info of the gdcmHeader ( refer to
+ grep "Orientation" Dicts/dicomV3.dic).
+ Problem exhibiting this defect: cine loop on a pile of images
+ whose Origin is correct, but whose normal is not set will
+ plainly suck !
+Comments:
+ * vtkGdcmReader inherits from vtkImageReader which aggregates
+ a vtkTranform. vtkGdcmReader could store (when the user requires
+ it, see below) the origin/normal taken from the Dicom Header
+ within this vtkTransform (looks like a natural place to store
+ this spacial information).
+ * Both settings of the origin and/OR the normal of the plane (image)
+ should be an option defined with a flag (On/Off) in the
+ vtkGdcmReader...
+-----------------------------------------------------------------------------
Description: Fix the Python wrappers
Date: 2004 Sep 24
Attributed: no
Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2004/09/30 12:51:55 $
- Version: $Revision: 1.133 $
+ Date: $Date: 2004/10/01 12:40:57 $
+ Version: $Revision: 1.134 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
return false;
}
- // ---------------------- Compacted File (12 Bits Per Pixel)
- // unpack 12 Bits pixels into 16 Bits pixels
- // 2 pixels 12bit = [0xABCDEF]
- // 2 pixels 16bit = [0x0ABD] + [0x0FCE]
-
if ( Header->GetBitsAllocated() == 12 )
{
- int nbPixels = Header->GetXSize() * Header->GetYSize();
- uint8_t b0, b1, b2;
-
- uint16_t* pdestination = (uint16_t*)destination;
- for(int p = 0; p < nbPixels; p += 2 )
- {
- fread(&b0,1,1,fp);
- fread(&b1,1,1,fp);
- fread(&b2,1,1,fp);
-
- //Two steps is necessary to please VC++
- *pdestination++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f);
- // A B D
- *pdestination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4);
- // F C E
-
- // Troubles expected on Big-Endian processors ?
- }
-
+ ConvertDecompress12BitsTo16Bits( (uint8_t*)destination,
+ Header->GetXSize(),
+ Header->GetYSize(),
+ fp);
Header->CloseFile();
return true;
}
}
// --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000
- int nb;
- std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100);
- if ( str_nb == GDCM_UNFOUND )
- {
- nb = 16;
- }
- else
+ int numberBitsAllocated = Header->GetBitsAllocated();
+ if ( ( numberBitsAllocated == 0 ) || ( numberBitsAllocated == 12 ) )
{
- nb = atoi( str_nb.c_str() );
- if ( nb == 12 )
- {
- nb = 16; // ?? 12 should be ACR-NEMA only
- }
+ numberBitsAllocated = 16;
}
- int nBytes= nb/8;
+ int nBytes= numberBitsAllocated/8;
int taille = Header->GetXSize() * Header->GetYSize()
* Header->GetSamplesPerPixel();
long fragmentBegining; // for ftell, fseek
Header->CloseFile();
return res;
}
+
+/**
+ * \brief Read from file a 12 bits per pixel image and uncompress it
+ * into a 16 bits per pixel image.
+ */
+void gdcmFile::ConvertDecompress12BitsTo16Bits(
+ uint8_t* pixelZone,
+ int sizeX,
+ int sizeY,
+ FILE* filePtr)
+ throw ( gdcmFormatError )
+{
+ int nbPixels = sizeX * sizeY;
+ uint16_t* destination = (uint16_t*)pixelZone;
+
+ for( int p = 0; p < nbPixels; p += 2 )
+ {
+ uint8_t b0, b1, b2;
+ size_t ItemRead;
+
+ ItemRead = fread( &b0, 1, 1, filePtr);
+ if ( ItemRead != 1 )
+ {
+ throw gdcmFormatError( "gdcmFile::ConvertDecompress12BitsTo16Bits()",
+ "Unfound first block" );
+ }
+
+ ItemRead = fread( &b1, 1, 1, filePtr);
+ if ( ItemRead != 1 )
+ {
+ throw gdcmFormatError( "gdcmFile::ConvertDecompress12BitsTo16Bits()",
+ "Unfound second block" );
+ }
+
+ ItemRead = fread( &b2, 1, 1, filePtr);
+ if ( ItemRead != 1 )
+ {
+ throw gdcmFormatError( "gdcmFile::ConvertDecompress12BitsTo16Bits()",
+ "Unfound second block" );
+ }
+
+ // Two steps are necessary to please VC++
+ //
+ // 2 pixels 12bit = [0xABCDEF]
+ // 2 pixels 16bit = [0x0ABD] + [0x0FCE]
+ // A B D
+ *destination++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f);
+ // F C E
+ *destination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4);
+
+ /// \todo JPR Troubles expected on Big-Endian processors ?
+ }
+}
//-----------------------------------------------------------------------------
Program: gdcm
Module: $RCSfile: gdcmFile.h,v $
Language: C++
- Date: $Date: 2004/09/30 12:51:55 $
- Version: $Revision: 1.54 $
+ Date: $Date: 2004/10/01 12:40:57 $
+ Version: $Revision: 1.55 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
void ConvertRGBPlanesToRGBPixels( uint8_t* source, uint8_t* destination );
void ConvertYcBcRPlanesToRGBPixels( uint8_t* source, uint8_t* destination );
- void ConvertReArrangeBits( uint8_t* pixelZone,
- size_t imageDataSize,
- int numberBitsStored,
- int numberBitsAllocated,
- int highBitPosition ) throw ( gdcmFormatError );
- void ConvertReorderEndianity( uint8_t* pixelZone,
- size_t imageDataSize,
- int numberBitsStored,
- int numberBitsAllocated,
- bool signedPixel );
-
+ void ConvertReArrangeBits(
+ uint8_t* pixelZone,
+ size_t imageDataSize,
+ int numberBitsStored,
+ int numberBitsAllocated,
+ int highBitPosition ) throw ( gdcmFormatError );
+ void ConvertReorderEndianity(
+ uint8_t* pixelZone,
+ size_t imageDataSize,
+ int numberBitsStored,
+ int numberBitsAllocated,
+ bool signedPixel );
+ void ConvertDecompress12BitsTo16Bits(
+ uint8_t* pixelZone,
+ int sizeX,
+ int sizeY,
+ FILE* filePtr) throw ( gdcmFormatError);
/// Accessor to \ref ImageDataSize
size_t GetImageDataSize(){ return ImageDataSize; };
+++ /dev/null
-*Debug*
-*Release*
-*.plg
\ No newline at end of file
+++ /dev/null
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SET(vtkgdcmdemo_SOURCES\r
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-# vtkGdcmReader.cxx\r
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vtkgdcmViewer.cxx\r
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TARGET_LINK_LIBRARIES(vtkgdcmViewer \r
-// $Header: /cvs/public/gdcm/vtk/Attic/testvtkGdcmReader.cxx,v 1.9 2004/03/30 09:00:40 regrain Exp $
+// $Header: /cvs/public/gdcm/vtk/vtkGdcmDemo.cxx,v 1.1 2004/10/01 12:40:58 frog Exp $
+
+//----------------------------------------------------------------------------
+// A simple straightfoward example of vtkGdcmReader vtk class usage.
+//
+// The vtkGdcmReader vtk class behaves like any other derived class of
+// vtkImageReader. It's usage within a vtk pipeline hence follows the
+// classical vtk pattern.
+// This example is a really simple Dicom image viewer demo.
+// It builds the minimal vtk rendering pipeline in order to display
+// (with the native vtk classes) a single Dicom image parsed with gdcm.
+//
+// Usage: the filename of the Dicom image to display should be given as
+// command line arguments,
+//----------------------------------------------------------------------------
#include <vtkRenderer.h>
#include <vtkRenderWindow.h>
int main( int argc, char *argv[] )
{
- int *taille;
- int x,y;
-
- // Lecture de l'image
vtkGdcmReader *reader = vtkGdcmReader::New();
-// reader->DebugOn();
- // Alloc Used High
- // 8 8 7 U : OK
- // reader->SetFileName("../gdcmData/CT-MONO2-8-abdo.dcm");
- // 16 12 11 U : OK but saturated
- // reader->SetFileName("../gdcmData/CT-MONO2-12-lomb-an2.acr2");
- // 16 12 11 U OK
- //OKreader->SetFileName("../gdcmData/MR-MONO2-12-an2.acr2");
- // 16 10 9 U OK
- //reader->SetFileName("../gdcmData/CR-MONO1-10-chest.dcm");
- //reader->Update();
- // 16 16 15 S: OK saturation ?
- // reader->SetFileName("../gdcmData/CT-MONO2-16-ort.dcm");
- // 16 16 15 S:
-
- if (argc > 1)
- reader->SetFileName( argv[1] );
- else
- reader->SetFileName("../gdcmData/CT-MONO2-16-ankle.dcm");
+
+ if (argc < 2)
+ {
+ std::cerr << "Usage: " << argv[0] << " image.dcm\n";
+ return 0;
+ }
+
+ reader->SetFileName( argv[1] );
reader->UpdateWholeExtent();
-// reader->Update();
- vtkImageData *ima = reader->GetOutput();
- taille=ima->GetDimensions();
- x = taille[0]; y = taille[1];
+ vtkImageData* ima = reader->GetOutput();
+
+ ///////// Display image size on terminal:
+ int* Size = ima->GetDimensions();
cout << "Dimensions of the picture as read with gdcm: "
- << x << " x " << y << endl;
+ << Size[0] << " x " << Size[1] << endl;
- vtkLookupTable *VTKtable = vtkLookupTable::New();
+ ///////// A simple display pipeline:
+ //
+ vtkLookupTable* VTKtable = vtkLookupTable::New();
VTKtable->SetNumberOfColors(1000);
VTKtable->SetTableRange(0,1000);
VTKtable->SetSaturationRange(0,0);
VTKtable->SetValueRange(0,1);
VTKtable->SetAlphaRange(1,1);
VTKtable->Build();
- // Texture
- vtkTexture * VTKtexture = vtkTexture::New();
+
+ //// Texture
+ vtkTexture* VTKtexture = vtkTexture::New();
VTKtexture->SetInput(ima);
VTKtexture->InterpolateOn();
VTKtexture->SetLookupTable(VTKtable);
- // PlaneSource
- vtkPlaneSource *VTKplane = vtkPlaneSource::New();
+
+ //// PlaneSource
+ vtkPlaneSource* VTKplane = vtkPlaneSource::New();
VTKplane->SetOrigin( -0.5, -0.5, 0.0);
VTKplane->SetPoint1( 0.5, -0.5, 0.0);
VTKplane->SetPoint2( -0.5, 0.5, 0.0);
- // PolyDataMapper
+
+ //// PolyDataMapper
vtkPolyDataMapper *VTKplaneMapper = vtkPolyDataMapper::New();
VTKplaneMapper->SetInput(VTKplane->GetOutput());
- // Actor
+
+ //// Actor
vtkActor* VTKplaneActor = vtkActor::New();
VTKplaneActor->SetTexture(VTKtexture);
VTKplaneActor->SetMapper(VTKplaneMapper);
VTKplaneActor->PickableOn();
- //
+
+ //// Final rendering with simple interactor:
vtkRenderer *ren = vtkRenderer::New();
vtkRenderWindow *renwin = vtkRenderWindow::New();
renwin->AddRenderer(ren);
renwin->Render();
iren->Start();
+ //// Clean up:
reader->Delete();
VTKtable->Delete();
VTKtexture->Delete();
return(0);
}
-
+// This example illustrates how the vtkGdcmReader vtk class can be
+// used in order to:
+// * produce a simple (vtk based) Dicom image STACK VIEWER.
+// * dump the stack considered as a volume in a vtkStructuredPoints
+// vtk file: the vtk gdcm wrappers can be seen as a simple way to convert
+// a stack of Dicom images into a native vtk volume.
+//
+// Usage:
+// * the filenames of the Dicom images constituting the stack should be
+// given as command line arguments,
+// * you can navigate through the stack by hitting any character key,
+// * the produced vtk file is named "foo.vtk" (in the invocation directory).
+//
+//----------------------------------------------------------------------------
#include <iostream>
#include <vtkRenderWindowInteractor.h>
+++ /dev/null
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git://git.creatis.insa-lyon.fr / gdcm.git / commitdiff