-// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.16 2003/07/07 10:26:14 regrain Exp $
+// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.25 2003/11/05 18:15:41 malaterre 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 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 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...
+// 2/ ExecuteData is then responsible for the next two loadings:
+// 2a/ ExecuteData calls AllocateOutputData that in turn seems to
+// (indirectely call) ExecuteInformation which ends up in a second
+// header parsing
+// 2b/ the core of ExecuteData then needs gdcmFile (which in turns
+// 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 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 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...
+//
+// /////// Never unallocated memory:
+// 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 destructor nor when the
+// filename list is extended, ExecuteData is called a second (or third)
+// time...
+// //////////////////////////////////////////////////////////////
+
#include <stdio.h>
#include <vtkObjectFactory.h>
#include <vtkImageData.h>
#include <vtkPointData.h>
+#include <vtkLookupTable.h>
#include "vtkGdcmReader.h"
#include "gdcm.h"
+#include "gdcmHeaderHelper.h"
vtkGdcmReader::vtkGdcmReader()
{
// Constructor
+ this->LookupTable = vtkLookupTable::New();
}
//----------------------------------------------------------------------------
vtkGdcmReader::~vtkGdcmReader()
{
- // FIXME free memory
this->RemoveAllFileName();
this->InternalFileNameList.clear();
+ 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();
// Configure the output e.g. WholeExtent, spacing, origin, scalar type...
void vtkGdcmReader::ExecuteInformation()
{
- //FIXME free any old memory
this->TotalNumberOfPlanes = this->CheckFileCoherence();
if ( this->TotalNumberOfPlanes == 0)
{
}
// 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:
+ // 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();
+ int LineSize = NumComponents * NumColumns * GdcmFile.GetPixelSize();
+
+ unsigned char * Source;
+ if( GdcmFile.HasLUT() )
+ {
+ size = GdcmFile.GetImageDataSizeRaw();
+ Source = (unsigned char*) GdcmFile.GetImageDataRaw();
+ unsigned char *Lut = (unsigned char*) GdcmFile.GetLUTRGBA();
+
+ 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;
for (int plane = 0; plane < NumPlanes; plane++)
UpdateProgressCount++;
}
}
+ //GetImageData allocate a (void*)malloc, remove it:
+ free(pSource);
+
return size;
}
// (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.
+// extent/axes are assumed to be the same as the file extent/order.
void vtkGdcmReader::ExecuteData(vtkDataObject *output)
{
if (this->InternalFileNameList.empty())
return;
}
- // FIXME : the bad parse of header is made when allocating OuputData
+ // FIXME : extraneous parsing of header is made when allocating OuputData
vtkImageData *data = this->AllocateOutputData(output);
data->SetExtent(this->DataExtent);
data->GetPointData()->GetScalars()->SetName("DicomImage-Volume");
// 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