-// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.2 2003/05/12 14:32:43 frog Exp $
-#include "vtkGdcmReader.h"
-#include "vtkByteSwap.h"
+// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.8 2003/06/02 07:42:17 regrain Exp $
+//CLEANME#include <vtkByteSwap.h>
#include <stdio.h>
-#include "vtkObjectFactory.h"
-#include "vtkImageFlip.h"
+#include <vtkObjectFactory.h>
+#include <vtkImageData.h>
+#include <vtkPointData.h>
+#include "vtkGdcmReader.h"
#include "gdcm.h"
vtkGdcmReader::vtkGdcmReader()
// FIXME free memory
}
+//----------------------------------------------------------------------------
+// Adds a file name to the list of images to read.
+void vtkGdcmReader::AddFileName(const char* name)
+{
+ // We need to bypass the const pointer [since list<>.push_bash() only
+ // takes a char* (but not a const char*)] by making a local copy:
+ char * LocalName = new char[strlen(name) + 1];
+ strcpy(LocalName, name);
+ this->FileNameList.push_back(LocalName);
+ // Starting from two files we have a stack of images:
+ if(this->FileNameList.size() >= 2)
+ this->SetFileDimensionality(3);
+ this->Modified();
+}
+
+//----------------------------------------------------------------------------
+// Sets up a filename to be read.
+void vtkGdcmReader::SetFileName(const char *name) {
+ vtkImageReader2::SetFileName(name);
+ // Since we maintain a list of filenames (when building a volume)
+ // we additionaly need to maintain this list. First we clean-up the
+ // list and then positionate the incoming filename:
+ this->FileNameList.empty();
+ this->AddFileName(name);
+}
+
+//----------------------------------------------------------------------------
+// vtkGdcmReader can have the file names specified through two ways:
+// (1) by calling the vtkImageReader2::SetFileName(), SetFilePrefix() and
+// SetFilePattern()
+// (2) By successive calls to vtkGdcmReader::SetFileName()
+// When the first method was used by caller we need to update the local
+// filename list
+void vtkGdcmReader::BuilFileListFromPattern()
+{
+ if (! this->FileNameList.empty())
+ return;
+ if (!this->FileName && !this->FilePattern)
+ {
+ vtkErrorMacro("FileNames are not set. Either use AddFileName() or");
+ vtkErrorMacro("specify a FileName or FilePattern.");
+ return;
+ }
+ for (int idx = this->DataExtent[4]; idx <= this->DataExtent[5]; ++idx)
+ {
+ this->ComputeInternalFileName(idx);
+ vtkDebugMacro("Adding file " << this->InternalFileName);
+ this->AddFileName(this->InternalFileName);
+ }
+}
+
+//----------------------------------------------------------------------------
+// When more than one filename is specified (i.e. we expect loading
+// a stack or volume) we need to check the corresponding images are
+// coherent:
+// - they all share the same X dimensions
+// - they all share the same Y dimensions
+// - each file a Z dimension of 1
+// - they all share the same type ( 8 bit signed, or unsigned...)
+bool vtkGdcmReader::CheckFileCoherence()
+{
+ this->BuilFileListFromPattern();
+ if (this->FileNameList.empty())
+ {
+ vtkErrorMacro("FileNames are not set.");
+ return false;
+ }
+ if (this->FileNameList.size() == 1)
+ {
+ vtkDebugMacro("Single file specified.");
+ return true;
+ }
+
+ // Loop on the filenames:
+ // - check for their existence and gdcm "parasability"
+ // - get the coherence check done:
+ bool FoundReferenceFile = false;
+ int ReferenceNX;
+ int ReferenceNY;
+ int ReferenceNZ;
+ std::string ReferenceType;
+ for (std::list<std::string>::iterator FileName = FileNameList.begin();
+ FileName != FileNameList.end();
+ ++FileName)
+ {
+ // Check for file existence.
+ FILE *fp;
+ fp = fopen(FileName->c_str(),"rb");
+ if (!fp)
+ {
+ vtkErrorMacro("Unable to open file " << *FileName->c_str());
+ vtkErrorMacro("Removing this file from readed files " << *FileName->c_str());
+ FileNameList.remove(*FileName);
+ continue;
+ }
+ fclose(fp);
+
+ // Check for Gdcm parsability
+ gdcmHeader GdcmHeader(FileName->c_str());
+ if (!GdcmHeader.IsReadable())
+ {
+ vtkErrorMacro("Gdcm cannot parse file " << *FileName->c_str());
+ vtkErrorMacro("Removing this file from readed files " << *FileName->c_str());
+ FileNameList.remove(*FileName);
+ continue;
+ }
+
+ // Coherence stage:
+ int NX = GdcmHeader.GetXSize();
+ int NY = GdcmHeader.GetYSize();
+ int NZ = GdcmHeader.GetZSize();
+ std::string type = GdcmHeader.GetPixelType();
+ if (FoundReferenceFile)
+ {
+ if ( ( NX != ReferenceNX )
+ || ( NY != ReferenceNY )
+ || ( NZ != ReferenceNZ )
+ || ( type != ReferenceType ) )
+ {
+ vtkErrorMacro("This file is not coherent with previous ones"
+ << *FileName->c_str());
+ vtkErrorMacro("Removing this file from readed files " << *FileName->c_str());
+ FileNameList.remove(*FileName);
+ continue;
+ } else {
+ vtkDebugMacro("File is coherent with previous ones" << *FileName->c_str());
+ }
+ } else {
+ // This file shall be the reference:
+ FoundReferenceFile = true;
+ ReferenceNX = NX;
+ ReferenceNY = NY;
+ ReferenceNZ = NZ;
+ ReferenceType = type;
+ vtkDebugMacro("This file taken as coherence reference:" << *FileName->c_str());
+ }
+ } // End of loop on FileName
+
+ if (this->FileNameList.empty())
+ {
+ vtkDebugMacro("No gdcm parsable file.");
+ return false;
+ }
+ if (this->FileNameList.size() == 1)
+ {
+ vtkDebugMacro("Single parsable file left after coherence test.");
+ return true;
+ }
+ return true;
+}
+
+//----------------------------------------------------------------------------
// Configure the output e.g. WholeExtent, spacing, origin, scalar type...
void vtkGdcmReader::ExecuteInformation()
{
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)
+ if ( ! this->CheckFileCoherence() )
{
- 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;
+ vtkErrorMacro("File set is not coherent. Exiting...");
+ return;
}
+ std::string ReferenceFile = this->FileNameList.front();
+ gdcmHeader GdcmHeader(ReferenceFile.c_str());
int NX = GdcmHeader.GetXSize();
int NY = GdcmHeader.GetYSize();
(this->DataVOI[5] >= NZ))
{
vtkWarningMacro("The requested VOI is larger than the file's ("
- << this->InternalFileName << ") extent ");
+ << ReferenceFile.c_str() << ") extent ");
this->DataVOI[0] = 0;
this->DataVOI[1] = NX - 1;
this->DataVOI[2] = 0;
// 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();
+ // since the reading of the file is done by gdcm.
+ // But we do need to set up the data type for downstream filters:
+ std::string type = GdcmHeader.GetPixelType();
if ( type == "8U" )
{
vtkDebugMacro("8 bits unsigned image");
}
else
{
- vtkErrorMacro("Bad File Type " << this->InternalFileName
- << "Type " << type);
+ vtkErrorMacro("Bad File Type " << ReferenceFile.c_str()
+ << "Type " << type.c_str());
return;
}
vtkImageReader::ExecuteInformation();
}
+//----------------------------------------------------------------------------
+void vtkGdcmReader::LoadImageInMemory(std::string FileName,
+ unsigned char * Dest,
+ size_t size)
+{
+ vtkDebugMacro("Copying to memmory image" << FileName.c_str());
+ gdcmFile GdcmFile(FileName.c_str());
+
+ if (GdcmFile.GetZSize() != 1 )
+ vtkErrorMacro("Cannot handle images with multiple planes");
+
+ // First check the expected size of the image is the one found by gdcm.
+ if ( size != GdcmFile.GetImageDataSize() )
+ {
+ vtkErrorMacro("Inconsistency with GetImageDataSize for file"
+ << FileName.c_str());
+ vtkErrorMacro("Number of scalar components"
+ << this->NumberOfScalarComponents);
+ }
+
+ // 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
+ // 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 LineSize = NumColumns * GdcmFile.GetPixelSize();
+ unsigned char * Source = (unsigned char*)GdcmFile.GetImageData();
+ unsigned char * Destination = Dest + size - LineSize;
+ for (int i = 0; i < NumLines; i++)
+ {
+ memcpy((void*)Destination, (void*)Source, LineSize);
+ Source += LineSize;
+ Destination -= LineSize;
+ }
+}
+
+//----------------------------------------------------------------------------
// Update -> UpdateData -> Execute -> ExecuteData (see vtkSource.cxx for
// last step.
// This function (redefinition of vtkImageReader::ExecuteData, see
// same as the file extent/order.
void vtkGdcmReader::ExecuteData(vtkDataObject *output)
{
- if (!this->FileName)
+ if (this->FileNameList.empty())
{
- vtkErrorMacro("A valid FileName must be specified.");
+ vtkErrorMacro("A least a valid FileName must be specified.");
return;
}
vtkImageData *data = this->AllocateOutputData(output);
data->SetExtent(this->DataExtent);
- data->GetPointData()->GetScalars()->SetName("ImageFile");
+ data->GetPointData()->GetScalars()->SetName("DicomImage-Volume");
// First check the coherence between the DataExtent and the
- // size of the pixel data as annouced by gdcm (looks a bit paranoid).
- gdcmFile GdcmFile(this->InternalFileName);
+ // size of the pixel data as annouced by gdcm (looks a bit paranoid)
+ // for the reference file (i.e. the first one in the list):
+ std::string ReferenceFile = this->FileNameList.front();
+ gdcmFile GdcmFile(ReferenceFile.c_str());
int NumColumns = this->DataExtent[1] - this->DataExtent[0] + 1;
int NumLines = this->DataExtent[3] - this->DataExtent[2] + 1;
int NumPlanes = this->DataExtent[5] - this->DataExtent[4] + 1;
- int size = NumColumns * NumLines * NumPlanes * GdcmFile.GetPixelSize();
+ size_t size = NumColumns * NumLines * NumPlanes * GdcmFile.GetPixelSize();
if ( size != GdcmFile.GetImageDataSize() )
{
vtkDebugMacro("Inconsistency with GetImageDataSize");
vtkDebugMacro("Number of scalar components"
<< this->NumberOfScalarComponents);
}
+
+ // The memory size for a full stack of images of course depends
+ // on the number of images:
+ size_t stack_size = size * this->FileNameList.size();
// Allocate pixel data space itself.
- unsigned char *mem = new unsigned char [size];
+ unsigned char *mem = new unsigned char [stack_size];
- // If the data structure of vtk for image/volume representation
- // were straigthforwards the following would suffice:
- // GdcmFile.GetImageDataIntoVector((void*)mem, size);
- // But vtk chose 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 LineSize = NumColumns * GdcmFile.GetPixelSize();
- unsigned char * Source = (unsigned char*)GdcmFile.GetImageData();
- unsigned char * Destination = mem + size - LineSize;
- for (int i = 0; i < NumLines; i++)
+ unsigned char * Dest = mem;
+ for (std::list<std::string>::iterator FileName = FileNameList.begin();
+ FileName != FileNameList.end();
+ ++FileName)
{
- memcpy((void*)Destination, (void*)Source, LineSize);
- Source += LineSize;
- Destination -= LineSize;
+ this->LoadImageInMemory(*FileName, Dest, size);
+ Dest += size;
}
- data->GetPointData()->GetScalars()->SetVoidArray(mem, size, 0);
+
+ // The "size" of the vtkScalars data is expressed in number of points,
+ // and is not the memory size representing those points:
+ stack_size = stack_size / GdcmFile.GetPixelSize();
+ data->GetPointData()->GetScalars()->SetVoidArray(mem, stack_size, 0);
this->Modified();
}
+//----------------------------------------------------------------------------
void vtkGdcmReader::PrintSelf(ostream& os, vtkIndent indent)
{
vtkImageReader::PrintSelf(os,indent);
- //CLEANME os << indent << "TypeSize: " << this->TypeSize << "\n";
+ os << indent << "Filenames : " << endl;
+ vtkIndent nextIndent = indent.GetNextIndent();
+ for (std::list<std::string>::iterator FileName = FileNameList.begin();
+ FileName != FileNameList.end();
+ ++FileName)
+ {
+ os << nextIndent << *FileName->c_str() << endl ;
+ }
}
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff