-// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.11 2003/06/12 16:58:31 malaterre Exp $
-//CLEANME#include <vtkByteSwap.h>
-#include <stdio.h>
+// $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 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 "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;
}
//----------------------------------------------------------------------------
vtkGdcmReader::~vtkGdcmReader()
{
- // FIXME free memory
+ this->RemoveAllFileName();
+ this->InternalFileNameList.clear();
+ if(this->LookupTable) this->LookupTable->Delete();
+}
+
+//----------------------------------------------------------------------------
+// Remove all files from the list of images to read.
+void vtkGdcmReader::RemoveAllFileName(void)
+{
this->FileNameList.clear();
}
vtkImageReader2::SetFileName(name);
// Since we maintain a list of filenames, when building a volume,
// (see vtkGdcmReader::AddFileName), we additionaly need to purge
- // this list when we manually positionate the filename:
+ // this list when we manually positionate the filename.
this->FileNameList.clear();
this->Modified();
}
+//----------------------------------------------------------------------------
+// Adds a file name to the internal list of images to read.
+void vtkGdcmReader::RemoveAllInternalFileName(void)
+{
+ this->InternalFileNameList.clear();
+}
+
+//----------------------------------------------------------------------------
+// Adds a file name to the internal list of images to read.
+void vtkGdcmReader::AddInternalFileName(const char* name)
+{
+ char * LocalName = new char[strlen(name) + 1];
+ strcpy(LocalName, name);
+ this->InternalFileNameList.push_back(LocalName);
+ delete[] LocalName;
+}
+
//----------------------------------------------------------------------------
// vtkGdcmReader can have the file names specified through two ways:
// (1) by calling the vtkImageReader2::SetFileName(), SetFilePrefix() and
if (! this->FileNameList.empty() )
{
vtkDebugMacro("Using the AddFileName specified files");
+ this->InternalFileNameList=this->FileNameList;
return;
}
return;
}
- for (int idx = this->DataExtent[4]; idx <= this->DataExtent[5]; ++idx)
+ this->RemoveAllInternalFileName();
+ if( this->FileNameList.empty() )
{
- this->ComputeInternalFileName(idx);
+ //Multiframe case:
+ this->ComputeInternalFileName(this->DataExtent[4]);
vtkDebugMacro("Adding file " << this->InternalFileName);
- this->AddFileName(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);
+ }
+ }
}
//----------------------------------------------------------------------------
int ReturnedTotalNumberOfPlanes = 0; // The returned value.
this->BuildFileListFromPattern();
- if (this->FileNameList.empty())
+ if (this->InternalFileNameList.empty())
{
vtkErrorMacro("FileNames are not set.");
return 0;
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 = FileNameList.begin();
- FileName != FileNameList.end();
+ 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 plane in the
+ // ExecuteData method
+ // - If file has more than 1 plane, other planes will be added later to
+ // to the ReturnedTotalNumberOfPlanes variable counter
+ ReturnedTotalNumberOfPlanes += 1;
+
+ /////// Stage 0: check for file name:
+ if(*FileName==std::string("GDCM_UNREADABLE"))
+ continue;
+
/////// Stage 1: check for file readability:
// Stage 1.1: check for file existence.
FILE *fp;
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";
{
vtkErrorMacro("This file contains multiple planes (images)"
<< FileName->c_str());
- vtkErrorMacro("Removing this file from readed files "
- << FileName->c_str());
}
// Eventually, this file can be added on the stack. Update the
// full size of the stack
vtkDebugMacro("Number of planes added to the stack: " << NZ);
- ReturnedTotalNumberOfPlanes += NZ;
+ ReturnedTotalNumberOfPlanes += NZ - 1; // First plane already added
continue;
} else {
this->NumColumns = NX;
this->NumLines = NY;
ReferenceNZ = NZ;
- ReturnedTotalNumberOfPlanes += NZ;
+ 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 = FileNameList.begin();
- FileName != FileNameList.end();
- ++FileName)
+ for (std::list<std::string>::iterator Filename = InternalFileNameList.begin();
+ Filename != InternalFileNameList.end();
+ ++Filename)
{
- if (*FileName != "GDCM_UNREADABLE")
+ if (*Filename != "GDCM_UNREADABLE")
NumberCoherentFiles++;
}
vtkDebugMacro("Number of coherent files: " << NumberCoherentFiles);
vtkDebugMacro("Total number of planes on the stack: "
<< ReturnedTotalNumberOfPlanes);
- return ReturnedTotalNumberOfPlanes;
+
+ return ReturnedTotalNumberOfPlanes;
}
//----------------------------------------------------------------------------
// 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->FileNameList.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;
for (int plane = 0; plane < NumPlanes; plane++)
UpdateProgressCount++;
}
}
+ //GetImageData allocate a (void*)malloc, remove it:
+ free(pSource);
+
return size;
}
//----------------------------------------------------------------------------
-// Update -> UpdateData -> Execute -> ExecuteData (see vtkSource.cxx for
-// last step.
+// Update => ouput->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.
+// extent/axes are assumed to be the same as the file extent/order.
void vtkGdcmReader::ExecuteData(vtkDataObject *output)
{
- if (this->FileNameList.empty())
+ if (this->InternalFileNameList.empty())
{
vtkErrorMacro("A least a valid FileName must be specified.");
return;
}
+ // 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;
- size_t stack_size = StackNumPixels * this->PixelSize;
- // Allocate pixel data space itself.
- unsigned char *mem = new unsigned char [stack_size];
-
- // Variables for the UpdateProgress. We shall use 50 steps to signify
- // the advance of the process:
- unsigned long UpdateProgressTarget = (unsigned long) this->NumLines
- * this->TotalNumberOfPlanes
- / 50.0;
- // The actual advance measure:
- unsigned long UpdateProgressCount = 0;
-
- // Feeling the allocated memory space with each image/volume:
- unsigned char * Dest = mem;
- for (std::list<std::string>::iterator FileName = FileNameList.begin();
- FileName != FileNameList.end();
- ++FileName)
- {
- // Images that were tagged as unreadable in CheckFileCoherence()
- // are substituted with a black image to let the caller visually
- // notice something wrong is going on:
- if (*FileName != "GDCM_UNREADABLE")
- {
- Dest += this->LoadImageInMemory(*FileName, Dest,
- UpdateProgressTarget,
- UpdateProgressCount);
- } else {
- // We insert a black image in the stack for the user to be aware that
- // this image/volume couldn't be loaded. We simply skip one image
- // size:
- Dest += this->NumColumns * this->NumLines * this->PixelSize;
- // Update progress related:
- UpdateProgressCount += this->NumLines;
- if (!(UpdateProgressCount%UpdateProgressTarget))
+ // Test if output has valid extent
+ // Prevent memory errors
+ if((this->DataExtent[1]-this->DataExtent[0]>=0) &&
+ (this->DataExtent[3]-this->DataExtent[2]>=0) &&
+ (this->DataExtent[5]-this->DataExtent[4]>=0))
+ {
+ // 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->NumComponents;
+ size_t stack_size = StackNumPixels * this->PixelSize;
+ // Allocate pixel data space itself.
+ unsigned char *mem = new unsigned char [stack_size];
+
+ // Variables for the UpdateProgress. We shall use 50 steps to signify
+ // the advance of the process:
+ unsigned long UpdateProgressTarget = (unsigned long) ceil (this->NumLines
+ * this->TotalNumberOfPlanes
+ / 50.0);
+ // The actual advance measure:
+ unsigned long UpdateProgressCount = 0;
+
+ // Feeling the allocated memory space with each image/volume:
+ unsigned char * Dest = mem;
+ for (std::list<std::string>::iterator FileName = InternalFileNameList.begin();
+ FileName != InternalFileNameList.end();
+ ++FileName)
+ {
+ // Images that were tagged as unreadable in CheckFileCoherence()
+ // are substituted with a black image to let the caller visually
+ // notice something wrong is going on:
+ if (*FileName != "GDCM_UNREADABLE")
{
- this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget));
- }
- } // Else, file not loadable
- } // Loop on files
-
- // 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();
+ // Update progress related for good files is made in LoadImageInMemory
+ Dest += this->LoadImageInMemory(*FileName, Dest,
+ UpdateProgressTarget,
+ UpdateProgressCount);
+ } else {
+ // We insert a black image in the stack for the user to be aware that
+ // this image/volume couldn't be loaded. We simply skip one image
+ // size:
+ Dest += this->NumColumns * this->NumLines * this->PixelSize;
+
+ // Update progress related for bad files:
+ UpdateProgressCount += this->NumLines;
+ if (UpdateProgressTarget > 0)
+ {
+ if (!(UpdateProgressCount%UpdateProgressTarget))
+ {
+ this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget));
+ }
+ }
+ } // Else, file not loadable
+ } // Loop on files
+
+ // 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);
+ //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