-// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.18 2003/08/29 09:47:13 malaterre Exp $
+// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.29 2003/12/22 12:46:19 regrain Exp $
// //////////////////////////////////////////////////////////////
// WARNING TODO CLENAME
// Actual limitations of this code:
//
// /////// Redundant and unnecessary header parsing
// In it's current state this code actually parses three times the Dicom
-// header of a file before the corrersponding image gets loaded in the
+// header of a file before the corresponding image gets loaded in the
// ad-hoc vtkData !
// Here is the process:
// 1/ First loading happens in ExecuteInformation which in order to
-// positionate the vtk extents calls CheckFileCoherence. The purpous
+// positionate the vtk extents calls CheckFileCoherence. The purpose
// of CheckFileCoherence is to make sure all the images in the future
// stack are "homogenous" (same size, same representation...). This
// can only be achieved by parsing all the Dicom headers...
// (indirectely call) ExecuteInformation which ends up in a second
// header parsing
// 2b/ the core of ExecuteData then needs gdcmFile (which in turns
-// initialiszes gdcmHeader in the constructor) in order to access
+// initialises gdcmHeader in the constructor) in order to access
// the data-image.
//
// Possible solution:
// maintain a list of gdcmFiles (created by say ExecuteInformation) created
// once and for all accross the life of vtkGdcmHeader (it would only load
// new gdcmFile if the user changes the list). ExecuteData would then use
-// those gdcmFile and hence avoid calling the consctutor:
+// those gdcmFile and hence avoid calling the construtor:
// - advantage: the header of the files would only be parser once.
// - drawback: once execute information is called (i.e. on creation of
-// a vtkGdcmHeader) the gdcmFile sctructue is loaded in memory.
+// a vtkGdcmHeader) the gdcmFile structure is loaded in memory.
// The average size of a gdcmHeader being of 100Ko, is one
// loads 10 stacks of images with say 200 images each, you
// end-up with a loss of 200Mo...
// ExecuteData allocates space for the pixel data [which will get pointed
// by the vtkPointData() through the call
// data->GetPointData()->GetScalars()->SetVoidArray(mem, StackNumPixels, 0);]
-// This data is never "freed" neither in the desctutor nor when the
+// This data is never "freed" neither in the destructor nor when the
// filename list is extended, ExecuteData is called a second (or third)
// time...
// //////////////////////////////////////////////////////////////
-#include <stdio.h>
+#include "gdcmFile.h"
+#include "gdcmHeaderHelper.h"
+#include "vtkGdcmReader.h"
+
+//#include <stdio.h>
#include <vtkObjectFactory.h>
#include <vtkImageData.h>
#include <vtkPointData.h>
-#include "vtkGdcmReader.h"
-#include "gdcm.h"
+#include <vtkLookupTable.h>
+
vtkGdcmReader::vtkGdcmReader()
{
// Constructor
+ this->LookupTable = NULL;
}
//----------------------------------------------------------------------------
{
this->RemoveAllFileName();
this->InternalFileNameList.clear();
+ if(this->LookupTable) this->LookupTable->Delete();
}
//----------------------------------------------------------------------------
}
this->RemoveAllInternalFileName();
- for (int idx = this->DataExtent[4]; idx <= this->DataExtent[5]; ++idx)
+ if( this->FileNameList.empty() )
{
- this->ComputeInternalFileName(idx);
+ //Multiframe case:
+ this->ComputeInternalFileName(this->DataExtent[4]);
vtkDebugMacro("Adding file " << this->InternalFileName);
this->AddInternalFileName(this->InternalFileName);
}
+ else
+ {
+ //stack of 2D dicom case:
+ for (int idx = this->DataExtent[4]; idx <= this->DataExtent[5]; ++idx)
+ {
+ this->ComputeInternalFileName(idx);
+ vtkDebugMacro("Adding file " << this->InternalFileName);
+ this->AddInternalFileName(this->InternalFileName);
+ }
+ }
}
//----------------------------------------------------------------------------
// (i.e. an image represents one plane, but a volume represents many planes)
int vtkGdcmReader::CheckFileCoherence()
{
- int ReturnedTotalNumberOfPlanes = 0; // The returned value.
+ int ReturnedTotalNumberOfPlanes = 0; // The returned value.
this->BuildFileListFromPattern();
if (this->InternalFileNameList.empty())
int ReferenceNZ = 0;
// Loop on the filenames:
- // - check for their existence and gdcm "parasability"
+ // - check for their existence and gdcm "parsability"
// - get the coherence check done:
for (std::list<std::string>::iterator FileName = InternalFileNameList.begin();
FileName != InternalFileNameList.end();
++FileName)
{
// The file is always added in the number of planes
- // - If file doesn't exist, it will be replaced by a black place in the
+ // - If file doesn't exist, it will be replaced by a black plane in the
// ExecuteData method
// - If file has more than 1 plane, other planes will be added later to
// to the ReturnedTotalNumberOfPlanes variable counter
fclose(fp);
// Stage 1.2: check for Gdcm parsability
- gdcmHeader GdcmHeader(FileName->c_str());
+ gdcmHeaderHelper GdcmHeader(FileName->c_str());
if (!GdcmHeader.IsReadable())
{
vtkErrorMacro("Gdcm cannot parse file " << FileName->c_str());
&& (type != "32U") && (type != "32S") )
{
vtkErrorMacro("Bad File Type for file" << FileName->c_str());
+ vtkErrorMacro(" " << type.c_str());
vtkErrorMacro("Removing this file from readed files "
<< FileName->c_str());
*FileName = "GDCM_UNREADABLE";
ReturnedTotalNumberOfPlanes += NZ - 1; // First plane already added
this->ImageType = type;
this->PixelSize = GdcmHeader.GetPixelSize();
+
+ if( GdcmHeader.HasLUT() )
+ {
+ this->NumComponents = GdcmHeader.GetNumberOfScalarComponentsRaw();
+ }
+ else
+ {
+ this->NumComponents = GdcmHeader.GetNumberOfScalarComponents(); //rgb or mono
+ }
+
+ //Set image spacing
+ this->DataSpacing[0] = GdcmHeader.GetXSpacing();
+ this->DataSpacing[1] = GdcmHeader.GetYSpacing();
+ this->DataSpacing[2] = GdcmHeader.GetZSpacing();
+
+ //Set image origin
+ this->DataOrigin[0] = GdcmHeader.GetXOrigin();
+ this->DataOrigin[1] = GdcmHeader.GetYOrigin();
+ this->DataOrigin[2] = GdcmHeader.GetZOrigin();
+
}
} // End of loop on FileName
///////// The files we CANNOT load are flaged. On debugging purposes
- // count the loadable number of files and display thir number:
+ // count the loadable number of files and display their number:
int NumberCoherentFiles = 0;
for (std::list<std::string>::iterator Filename = InternalFileNameList.begin();
Filename != InternalFileNameList.end();
}
// if the user has not set the extent, but has set the VOI
- // set the zaxis extent to the VOI z axis
+ // set the z axis extent to the VOI z axis
if (this->DataExtent[4]==0 && this->DataExtent[5] == 0 &&
(this->DataVOI[4] || this->DataVOI[5]))
{
this->DataExtent[1] = this->NumColumns - 1;
this->DataExtent[2] = 0;
this->DataExtent[3] = this->NumLines - 1;
- if(this->InternalFileNameList.size() > 1)
- {
- this->DataExtent[4] = 0;
- this->DataExtent[5] = this->TotalNumberOfPlanes - 1;
- }
+ this->DataExtent[4] = 0;
+ this->DataExtent[5] = this->TotalNumberOfPlanes - 1;
// We don't need to positionate the Endian related stuff (by using
// this->SetDataByteOrderToBigEndian() or SetDataByteOrderToLittleEndian()
this->SetDataScalarTypeToInt();
}
+ //Set number of scalar components:
+ this->SetNumberOfScalarComponents(this->NumComponents);
+
vtkImageReader::ExecuteInformation();
}
const unsigned long UpdateProgressTarget,
unsigned long & UpdateProgressCount)
{
- vtkDebugMacro("Copying to memmory image" << FileName.c_str());
+ vtkDebugMacro("Copying to memory image" << FileName.c_str());
gdcmFile GdcmFile(FileName.c_str());
- size_t size = GdcmFile.GetImageDataSize();
+ size_t size;
// If the data structure of vtk for image/volume representation
// were straigthforwards the following would suffice:
// GdcmFile.GetImageDataIntoVector((void*)Dest, size);
- // But vtk chose to invert the lines of an image, that is the last
+ // But vtk chooses to invert the lines of an image, that is the last
// line comes first (for some axis related reasons?). Hence we need
- // to load the image line by line, starting from the end:
- int NumColumns = GdcmFile.GetXSize();
- int NumLines = GdcmFile.GetYSize();
- int NumPlanes = GdcmFile.GetZSize();
- int LineSize = NumColumns * GdcmFile.GetPixelSize();
- unsigned char * Source = (unsigned char*)GdcmFile.GetImageData();
+ // to load the image line by line, starting from the end.
+ int NumColumns = GdcmFile.GetHeader()->GetXSize();
+ int NumLines = GdcmFile.GetHeader()->GetYSize();
+ int NumPlanes = GdcmFile.GetHeader()->GetZSize();
+ int LineSize = NumComponents * NumColumns * GdcmFile.GetHeader()->GetPixelSize();
+
+ unsigned char * Source;
+ if( GdcmFile.GetHeader()->HasLUT() )
+ {
+ size = GdcmFile.GetImageDataSizeRaw();
+ Source = (unsigned char*) GdcmFile.GetImageDataRaw();
+ unsigned char *Lut = GdcmFile.GetHeader()->GetLUTRGBA();
+
+ if(!this->LookupTable) this->LookupTable = vtkLookupTable::New();
+ this->LookupTable->SetNumberOfTableValues(256);
+ for (int tmp=0; tmp<256; tmp++)
+ {
+ this->LookupTable->SetTableValue(tmp,
+ (float)Lut[4*tmp+0]/255.0,
+ (float)Lut[4*tmp+1]/255.0,
+ (float)Lut[4*tmp+2]/255.0,
+ 1);
+ }
+ this->LookupTable->SetRange(0,255);
+ vtkDataSetAttributes *a=this->GetOutput()->GetPointData();
+ a->GetScalars()->SetLookupTable(this->LookupTable);
+ free(Lut);
+ }
+ else
+ {
+ size = GdcmFile.GetImageDataSize();
+ Source = (unsigned char*)GdcmFile.GetImageData();
+ }
unsigned char * pSource = Source; //pointer for later deletion
unsigned char * Destination = Dest + size - LineSize;
// The memory size for a full stack of images of course depends
// on the number of planes and the size of each image:
size_t StackNumPixels = this->NumColumns * this->NumLines
- * this->TotalNumberOfPlanes;
+ * this->TotalNumberOfPlanes * this->NumComponents;
size_t stack_size = StackNumPixels * this->PixelSize;
// Allocate pixel data space itself.
unsigned char *mem = new unsigned char [stack_size];
// The "size" of the vtkScalars data is expressed in number of points,
// and is not the memory size representing those points:
data->GetPointData()->GetScalars()->SetVoidArray(mem, StackNumPixels, 0);
- this->Modified();
+ //don't know why it's here, it's calling one more time ExecuteInformation:
+ //this->Modified();
}
}
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff