+2003-05-5 Eric Boix <Eric.Boix@creatis.insa-lyon.fr> with JPR
+ * vtk subdir added. Contains vtkGdcmReader.[cxx|h] a vtk class
+ inherinting from vtkImageReader and testvtkGdcmReader.cxx a small
+ demo of the usage of this class.
+ Compilation of this vtk part is only done when using the --enable-vtk
+ at configure (or autogen.sh) stage.
+
2003-04-16 Eric Boix <Eric.Boix@creatis.insa-lyon.fr> with JPR
* More memmory link related corrections and documentation fixes.
Notes on valgrind:
* -# <TT>./autogen.sh --prefix=/where/ever/you/want</TT>
* to configure the script to force installation in a specified
* place.
- * -# <TT>./autogen.sh --configure-python</TT> to generate the
+ * -# <TT>./autogen.sh --enable-python</TT> to generate the
* python wrappers.
* .
* - <TT>make</TT> (or <TT>make 'CFLAGS=-g</TT>...)
* - <TT>make instal</TT>
- * - As usual, you can optionnaly:
+ * - As usual, you can optionnally:
* -# <TT>make clean</TT>
* -# <TT>make 'CFLAGS='</TT> if you are in hurry and want to omit
* "-g -O2" default flags
./autogen.sh
./configure (optional if just after autogen.sh)
make
-make install
+make instal
You can use the --prefix option of the configure script to force installation
in some place (default is /usr/local/DCMlib):
## Process this file with automake to produce Makefile.in
-SUBDIRS = src gdcmPython Test Dicts Doc
+SUBDIRS = src gdcmPython Test Dicts Doc vtk
EXTRA_DIST = \
dnl Checks for Python
AC_ARG_ENABLE(python,
- [ --enable-python Enable Python language support (default=no).],,
+ [ --enable-python Enable Python language support (default=no).],,
[enable_python="no"])
dnl AC_MSG_RESULT($enable_python)
build_python=no
fi
AM_CONDITIONAL(BUILD_PYTHON, test x$build_python = xyes)
+dnl Checks for vtk
+AC_ARG_ENABLE(vtk,
+ [ --enable-vtk Enable vtk extensions support (default=no).],,
+ [enable_vtk="no"])
+AM_CONDITIONAL(BUILD_VTK, test x$enable_vtk = xyes)
+
dnl produce Makefile.in files
AC_OUTPUT([
Makefile
gdcmPython/Makefile
Test/Makefile
Dicts/Makefile
+vtk/Makefile
Doc/Makefile])
-////////////////////////////////////////////////////////////////////////////
-// A single DICOM dictionary i.e. a container for a collection of dictionary
-// entries. There should be a single public dictionary (THE dictionary of
-// the actual DICOM v3) but as many shadow dictionaries as imagers
-// combined with all software versions...
+// gdcmDict.h
#ifndef GDCMDICT_H
#define GDCMDICT_H
typedef map<TagKey, gdcmDictEntry*> TagKeyHT;
typedef map<TagName, gdcmDictEntry*> TagNameHT;
-/// Build a memory representation of a dicom dictionary by parsing
-/// an ascii file
+/*
+ * \defgroup gdcmDict
+ * \brief gdcmDict acts a memory representation of a dicom dictionary i.e.
+ * it is a container for a collection of dictionary entries. The
+ * dictionary is loaded from in an ascii file.
+ * There should be a single public dictionary (THE dictionary of
+ * the actual DICOM v3) but as many shadow dictionaries as imagers
+ * combined with all software versions...
+ * \see gdcmDictSet
+ */
class GDCM_EXPORT gdcmDict {
string name;
string filename;
-// gdcmHeader.cxx
+// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.61 2003/05/05 14:13:59 frog Exp $
#include <stdio.h>
#include <cerrno>
-// gdcmHeader.h
+// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.h,v 1.21 2003/05/05 14:13:59 frog Exp $
#ifndef GDCMHEADER_H
#define GDCMHEADER_H
--- /dev/null
+.deps
+.libs
+Makefile.in
+Makefile
+vtkgdcmdemo
--- /dev/null
+## Process this file with automake to produce Makefile.in
+LIBS_VTK=-L/usr/lib/vtk \
+ -lvtkCommon -lvtkIO -lvtkFiltering -lvtkRendering -lvtkGraphics \
+ -lvtkImaging -lvtkpng -lvtkzlib -lvtkjpeg -lvtkexpat -lvtktiff \
+ -lvtkftgl -lvtkfreetype
+INCLUDE_VTK=-I/usr/include/vtk
+
+LIBS_X11= -L/usr/X11R6/lib -lX11 -lXt -lSM -lICE -lXext -lGL
+## $(x_ldflags)
+## $(x_libs)
+
+INCLUDES = \
+ -I. \
+ -I$(top_srcdir)/src \
+ $(INCLUDE_VTK)
+
+LDADD = \
+ $(top_builddir)/src/libgdcm.la \
+ $(LIBS_VTK) \
+ $(LIBS_X11)
+
+if BUILD_VTK
+noinst_PROGRAMS = vtkgdcmdemo
+vtkgdcmdemo_SOURCES = testvtkGdcmReader.cxx vtkGdcmReader.cxx
+
+else
+all:
+endif
+
+
--- /dev/null
+// $Header: /cvs/public/gdcm/vtk/Attic/testvtkGdcmReader.cxx,v 1.1 2003/05/05 14:13:59 frog Exp $
+
+#include "vtkRenderer.h"
+#include "vtkRenderWindow.h"
+#include "vtkRenderWindowInteractor.h"
+#include "vtkPolyDataMapper.h"
+#include "vtkActor.h"
+#include "vtkImageMapper.h"
+#include "vtkImageViewer.h"
+#include "vtkMatrix4x4.h"
+#include "vtkLookupTable.h"
+#include "vtkMatrixToLinearTransform.h"
+#include "vtkTexture.h"
+#include "vtkPlaneSource.h"
+#include "vtkTextureMapToPlane.h"
+#include "vtkDataSetMapper.h"
+#include "vtkActor.h"
+#include "vtkImageCast.h"
+#include "vtkPNGWriter.h"
+#include "vtkTexture.h"
+
+#include "vtkGdcmReader.h"
+
+
+int main( int argc, char *argv[] )
+{
+ char a;
+ 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("../Data/CT-MONO2-8-abdo.dcm");
+ // 16 12 11 U : OK but saturated
+ // reader->SetFileName("../Data/CT-MONO2-12-lomb-an2.acr2");
+ // 16 12 11 U OK
+ //OKreader->SetFileName("../Data/MR-MONO2-12-an2.acr2");
+ // 16 10 9 U OK
+ //reader->SetFileName("../Data/CR-MONO1-10-chest.dcm");
+ //reader->Update();
+ // 16 16 15 S: OK saturation ?
+ // reader->SetFileName("../Data/CT-MONO2-16-ort.dcm");
+ // 16 16 15 S:
+ reader->SetFileName("../Data/CT-MONO2-16-ankle.dcm");
+ reader->UpdateWholeExtent();
+ vtkImageData *ima = reader->GetOutput();
+ taille=ima->GetDimensions();
+ x = taille[0]; y = taille[1];
+ cout << "Taille de l'image en X=" << x << " et en Y=" << y << endl;
+
+ vtkLookupTable *VTKtable = vtkLookupTable::New();
+ VTKtable->SetNumberOfColors(1000);
+ VTKtable->SetTableRange(0,1000);
+ VTKtable->SetSaturationRange(0,0);
+ VTKtable->SetHueRange(0,1);
+ VTKtable->SetValueRange(0,1);
+ VTKtable->SetAlphaRange(1,1);
+ VTKtable->Build();
+ // Texture
+ vtkTexture * VTKtexture = vtkTexture::New();
+ VTKtexture->SetInput(ima);
+ VTKtexture->InterpolateOn();
+ VTKtexture->SetLookupTable(VTKtable);
+ // 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
+ vtkPolyDataMapper *VTKplaneMapper = vtkPolyDataMapper::New();
+ VTKplaneMapper->SetInput(VTKplane->GetOutput());
+ // Actor
+ vtkActor* VTKplaneActor = vtkActor::New();
+ VTKplaneActor->SetTexture(VTKtexture);
+ VTKplaneActor->SetMapper(VTKplaneMapper);
+ VTKplaneActor->PickableOn();
+ //
+ vtkRenderer *ren = vtkRenderer::New();
+ vtkRenderWindow *renwin = vtkRenderWindow::New();
+ renwin->AddRenderer(ren);
+ vtkRenderWindowInteractor *iren = vtkRenderWindowInteractor::New();
+ iren->SetRenderWindow(renwin);
+ ren->AddActor(VTKplaneActor);
+ ren->SetBackground(0,0,0.5);
+ renwin->Render();
+ iren->Start();
+
+ return(0);
+}
+
--- /dev/null
+// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.1 2003/05/05 14:13:59 frog Exp $
+#include "vtkGdcmReader.h"
+#include "vtkByteSwap.h"
+#include <stdio.h>
+#include "vtkObjectFactory.h"
+#include "vtkImageFlip.h"
+#include "gdcm.h"
+
+vtkGdcmReader::vtkGdcmReader()
+{
+ // Constructor
+}
+
+//----------------------------------------------------------------------------
+vtkGdcmReader::~vtkGdcmReader()
+{
+ // FIXME free memory
+}
+
+// Configure the output e.g. WholeExtent, spacing, origin, scalar type...
+void vtkGdcmReader::ExecuteInformation()
+{
+ //FIXME free any old memory
+
+ // if the user has not set the extent, but has set the VOI
+ // set the zaxis extent to the VOI z axis
+ if (this->DataExtent[4]==0 && this->DataExtent[5] == 0 &&
+ (this->DataVOI[4] || this->DataVOI[5]))
+ {
+ this->DataExtent[4] = this->DataVOI[4];
+ this->DataExtent[5] = this->DataVOI[5];
+ }
+
+ this->ComputeInternalFileName(this->DataExtent[4]);
+
+ // Check for file existence.
+ FILE *fp;
+ fp = fopen(this->InternalFileName,"rb");
+ if (!fp)
+ {
+ vtkErrorMacro("Unable to open file " << this->InternalFileName);
+ return;
+ }
+ fclose(fp);
+
+ // Check for Gdcm parsability
+ gdcmHeader GdcmHeader(this->InternalFileName);
+ if (!GdcmHeader.IsReadable())
+ {
+ vtkErrorMacro("Gdcm cannot parse file " << this->InternalFileName);
+ return;
+ }
+
+ int NX = GdcmHeader.GetXSize();
+ int NY = GdcmHeader.GetYSize();
+ int NZ = GdcmHeader.GetZSize();
+ vtkDebugMacro("Image dimension as read from Gdcm:" <<
+ NX << " " << NY << " " << NZ);
+
+ if(NZ>1) this->SetFileDimensionality(3);
+
+ // When the user has set the VOI, check it's coherence with the file content.
+ if (this->DataVOI[0] || this->DataVOI[1] ||
+ this->DataVOI[2] || this->DataVOI[3] ||
+ this->DataVOI[4] || this->DataVOI[5])
+ {
+ if ((this->DataVOI[0] < 0) ||
+ (this->DataVOI[1] >= NX) ||
+ (this->DataVOI[2] < 0) ||
+ (this->DataVOI[3] >= NY) ||
+ (this->DataVOI[4] < 0) ||
+ (this->DataVOI[5] >= NZ))
+ {
+ vtkWarningMacro("The requested VOI is larger than the file's ("
+ << this->InternalFileName << ") extent ");
+ this->DataVOI[0] = 0;
+ this->DataVOI[1] = NX - 1;
+ this->DataVOI[2] = 0;
+ this->DataVOI[3] = NY - 1;
+ this->DataVOI[4] = 0;
+ this->DataVOI[5] = NZ - 1;
+ }
+ }
+
+ // Positionate the Extent.
+ this->DataExtent[0] = 0;
+ this->DataExtent[1] = NX - 1;
+ this->DataExtent[2] = 0;
+ this->DataExtent[3] = NY - 1;
+ if(this->GetFileDimensionality()==3)
+ {
+ this->DataExtent[4] = 0;
+ this->DataExtent[5] = NZ - 1;
+ }
+
+ // We don't need to positionate the Endian related stuff (by using
+ // this->SetDataByteOrderToBigEndian() or SetDataByteOrderToLittleEndian()
+ // since the // reading of the file is done by gdcm
+
+ // But we need to set up the data type for downstream filters:
+ string type = GdcmHeader.GetPixelType();
+ if ( type == "8U" )
+ {
+ vtkDebugMacro("8 bits unsigned image");
+ this->SetDataScalarTypeToUnsignedChar();
+ }
+ else if ( type == "8S" )
+ {
+ vtkErrorMacro("Cannot handle 8 bit signed files");
+ return;
+ }
+ else if ( type == "16U" )
+ {
+ vtkDebugMacro("16 bits unsigned image");
+ this->SetDataScalarTypeToUnsignedShort();
+ }
+ else if ( type == "16S" )
+ {
+ vtkDebugMacro("16 bits signed image");
+ this->SetDataScalarTypeToShort();
+ //vtkErrorMacro("Cannot handle 16 bit signed files");
+ }
+ else if ( type == "32U" )
+ {
+ vtkDebugMacro("32 bits unsigned image");
+ vtkDebugMacro("WARNING: forced to signed int !");
+ this->SetDataScalarTypeToInt();
+ }
+ else if ( type == "32S" )
+ {
+ vtkDebugMacro("32 bits signed image");
+ this->SetDataScalarTypeToInt();
+ }
+ else
+ {
+ vtkErrorMacro("Bad File Type " << this->InternalFileName
+ << "Type " << type);
+ return;
+ }
+
+ vtkImageReader::ExecuteInformation();
+}
+
+// Update -> UpdateData -> Execute -> ExecuteData (see vtkSource.cxx for
+// last step.
+// This function (redefinition of vtkImageReader::ExecuteData, see
+// VTK/IO/vtkImageReader.cxx) reads a data from a file. The datas
+// extent/axes are assumed to be the
+// same as the file extent/order.
+void vtkGdcmReader::ExecuteData(vtkDataObject *output)
+{
+ if (!this->FileName)
+ {
+ vtkErrorMacro("A valid FileName must be specified.");
+ return;
+ }
+
+ vtkImageData *data = this->AllocateOutputData(output);
+ data->SetExtent(this->DataExtent);
+ data->GetPointData()->GetScalars()->SetName("ImageFile");
+
+ int size =
+ (this->DataExtent[1] - this->DataExtent[0]+1) *
+ (this->DataExtent[3] - this->DataExtent[2]+1) *
+ (this->DataExtent[5] - this->DataExtent[4]+1) *
+ 2;
+ gdcmFile GdcmFile(this->InternalFileName);
+ size = GdcmFile.GetImageDataSize();
+ unsigned char *mem = new unsigned char [size];
+ if ( size != GdcmFile.GetImageDataSize() )
+ {
+ vtkDebugMacro("Inconsistency with GetImageDataSize");
+ vtkDebugMacro("Number of scalar components"
+ << this->NumberOfScalarComponents);
+ }
+ GdcmFile.GetImageDataIntoVector((void*)mem, size);
+ data->GetPointData()->GetScalars()->SetVoidArray(mem, size, 0);
+ //vtkImageFlip * Flip = vtkImageFlip::New();
+ //Flip->SetInput(data);
+ //Flip->Update();
+ //data = Flip->GetOutput();
+ //Flip->SetInput(NULL);
+ this->Modified();
+
+}
+
+void vtkGdcmReader::PrintSelf(ostream& os, vtkIndent indent)
+{
+ vtkImageReader::PrintSelf(os,indent);
+ //CLEANME os << indent << "TypeSize: " << this->TypeSize << "\n";
+}
--- /dev/null
+// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.h,v 1.1 2003/05/05 14:13:59 frog Exp $
+
+#ifndef __vtkGdcmReader_h
+#define __vtkGdcmReader_h
+
+#include "vtkImageReader.h"
+
+class VTK_EXPORT vtkGdcmReader : public vtkImageReader
+{
+public:
+ static vtkGdcmReader *New() {return new vtkGdcmReader;};
+ vtkTypeMacro(vtkGdcmReader, vtkImageReader);
+ void PrintSelf(ostream& os, vtkIndent indent);
+protected:
+ vtkGdcmReader();
+ ~vtkGdcmReader();
+ void ExecuteData(vtkDataObject *output);
+ virtual void ExecuteInformation();
+};
+#endif
+
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