Program: gdcm
Module: $RCSfile: vtkGdcmWriter.cxx,v $
Language: C++
- Date: $Date: 2004/12/09 10:59:59 $
- Version: $Revision: 1.4 $
+ Date: $Date: 2005/01/28 10:07:35 $
+ Version: $Revision: 1.16 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
=========================================================================*/
-#include "gdcmHeader.h"
#include "gdcmFile.h"
+#include "gdcmFileHelper.h"
#include "gdcmDebug.h"
+#include "gdcmUtil.h"
#include "vtkGdcmWriter.h"
#include <vtkObjectFactory.h>
#include <vtkPointData.h>
#include <vtkLookupTable.h>
-vtkCxxRevisionMacro(vtkGdcmWriter, "$Revision: 1.4 $");
+vtkCxxRevisionMacro(vtkGdcmWriter, "$Revision: 1.16 $");
vtkStandardNewMacro(vtkGdcmWriter);
//-----------------------------------------------------------------------------
vtkGdcmWriter::vtkGdcmWriter()
{
this->LookupTable = NULL;
+ this->FileDimensionality = 3;
+ this->WriteType = VTK_GDCM_WRITE_TYPE_EXPLICIT_VR;
+
+ UIDPrefix = "";
+ StudyInstanceUID = "";
+ SeriesInstanceUID = "";
+ FrameOfReferenceInstanceUID = "";
}
vtkGdcmWriter::~vtkGdcmWriter()
void vtkGdcmWriter::PrintSelf(ostream& os, vtkIndent indent)
{
this->Superclass::PrintSelf(os,indent);
+
+ os << indent << "Write type : " << this->GetWriteTypeAsString();
}
//-----------------------------------------------------------------------------
// Public
+const char *vtkGdcmWriter::GetWriteTypeAsString()
+{
+ switch(WriteType)
+ {
+ case VTK_GDCM_WRITE_TYPE_EXPLICIT_VR :
+ return "Explicit VR";
+ case VTK_GDCM_WRITE_TYPE_IMPLICIT_VR :
+ return "Implicit VR";
+ case VTK_GDCM_WRITE_TYPE_ACR :
+ return "ACR";
+ case VTK_GDCM_WRITE_TYPE_ACR_LIBIDO :
+ return "ACR Libido";
+ default :
+ return "Unknow type";
+ }
+}
+
+void vtkGdcmWriter::SetUIDPrefix(const char *prefix)
+{
+ UIDPrefix = prefix;
+}
+
+const char *vtkGdcmWriter::GetUIDPrefix()
+{
+ return UIDPrefix.c_str();
+}
+
+void vtkGdcmWriter::NewStudyInstanceUID()
+{
+ StudyInstanceUID = "";
+}
+
+void vtkGdcmWriter::NewSeriesInstanceUID()
+{
+ SeriesInstanceUID = "";
+}
+
+void vtkGdcmWriter::NewFrameOfReferenceInstanceUID()
+{
+ FrameOfReferenceInstanceUID = "";
+}
//-----------------------------------------------------------------------------
// Protected
* Copy the image and reverse the Y axis
*/
// The output datas must be deleted by the user of the method !!!
-size_t ReverseData(vtkImageData *img,unsigned char **data)
+size_t ReverseData(vtkImageData *image,unsigned char **data)
{
- int *dim = img->GetDimensions();
- size_t lineSize = dim[0] * img->GetScalarSize()
- * img->GetNumberOfScalarComponents();
+ int inc[3];
+ int *extent = image->GetUpdateExtent();
+ int dim[3] = {extent[1]-extent[0]+1,
+ extent[3]-extent[2]+1,
+ extent[5]-extent[4]+1};
+
+ size_t lineSize = dim[0] * image->GetScalarSize()
+ * image->GetNumberOfScalarComponents();
size_t planeSize = dim[1] * lineSize;
size_t size = dim[2] * planeSize;
- *data = new unsigned char[size];
-
- unsigned char *src = (unsigned char *)img->GetScalarPointer();
- unsigned char *dst = *data + planeSize - lineSize;
- for (int plane = 0; plane < dim[2]; plane++)
+ if( size>0 )
{
- for (int line = 0; line < dim[1]; line++)
- {
- // Copy one line at proper destination:
- memcpy((void*)dst, (void*)src, lineSize);
+ *data = new unsigned char[size];
- src += lineSize;
- dst -= lineSize;
+ image->GetIncrements(inc);
+ unsigned char *src = (unsigned char *)image->GetScalarPointerForExtent(extent);
+ unsigned char *dst = *data + planeSize - lineSize;
+ for (int plane = extent[4]; plane <= extent[5]; plane++)
+ {
+ for (int line = extent[2]; line <= extent[3]; line++)
+ {
+ // Copy one line at proper destination:
+ memcpy((void*)dst, (void*)src, lineSize);
+
+ src += inc[1] * image->GetScalarSize();
+ dst -= lineSize;
+ }
+ dst += 2 * planeSize;
}
- dst += 2 * planeSize;
+ }
+ else
+ {
+ *data = NULL;
}
return size;
/**
* Set the datas informations in the file
*/
-void SetImageInformation(gdcm::File *file,vtkImageData *image)
+void SetImageInformation(gdcm::FileHelper *file,vtkImageData *image)
{
std::ostringstream str;
// Image size
- int *dim = image->GetDimensions();
+ int *extent = image->GetUpdateExtent();
+ int dim[3] = {extent[1]-extent[0]+1,
+ extent[3]-extent[2]+1,
+ extent[5]-extent[4]+1};
str.str("");
- str<<dim[0];
- file->ReplaceOrCreateByNumber(str.str(),0x0028,0x0011);
+ str << dim[0];
+ file->InsertValEntry(str.str(),0x0028,0x0011); // Columns
str.str("");
- str<<dim[1];
- file->ReplaceOrCreateByNumber(str.str(),0x0028,0x0010);
+ str << dim[1];
+ file->InsertValEntry(str.str(),0x0028,0x0010); // Rows
if(dim[2]>1)
{
str.str("");
- str<<dim[2];
- file->ReplaceOrCreateByNumber(str.str(),0x0028,0x0012);
+ str << dim[2];
+ //file->Insert(str.str(),0x0028,0x0012); // Planes
+ file->InsertValEntry(str.str(),0x0028,0x0008); // Number of Frames
}
// Pixel type
str.str("");
- str<<image->GetScalarSize()*8;
- file->ReplaceOrCreateByNumber(str.str(),0x0028,0x0100);
- file->ReplaceOrCreateByNumber(str.str(),0x0028,0x0101);
+ str << image->GetScalarSize()*8;
+ file->InsertValEntry(str.str(),0x0028,0x0100); // Bits Allocated
+ file->InsertValEntry(str.str(),0x0028,0x0101); // Bits Stored
str.str("");
- str<<image->GetScalarSize()*8-1;
- file->ReplaceOrCreateByNumber(str.str(),0x0028,0x0102);
+ str << image->GetScalarSize()*8-1;
+ file->InsertValEntry(str.str(),0x0028,0x0102); // High Bit
// Pixel Repr
// FIXME : what do we do when the ScalarType is
image->GetScalarType() == VTK_UNSIGNED_INT ||
image->GetScalarType() == VTK_UNSIGNED_LONG )
{
- str<<"0"; // Unsigned
+ str << "0"; // Unsigned
}
else
{
- str<<"1"; // Signed
+ str << "1"; // Signed
}
- file->ReplaceOrCreateByNumber(str.str(),0x0028,0x0103);
+ file->InsertValEntry(str.str(),0x0028,0x0103); // Pixel Representation
// Samples per pixel
str.str("");
- str<<image->GetNumberOfScalarComponents();
- file->ReplaceOrCreateByNumber(str.str(),0x0028,0x0002);
+ str << image->GetNumberOfScalarComponents();
+ file->InsertValEntry(str.str(),0x0028,0x0002); // Samples per Pixel
// Spacing
double *sp = image->GetSpacing();
str.str("");
- str<<sp[0]<<"\\"<<sp[1];
- file->ReplaceOrCreateByNumber(str.str(),0x0028,0x0030);
+ str << sp[0] << "\\" << sp[1];
+ file->InsertValEntry(str.str(),0x0028,0x0030); // Pixel Spacing
str.str("");
- str<<sp[2];
- file->ReplaceOrCreateByNumber(str.str(),0x0018,0x0088);
+ str << sp[2];
+ file->InsertValEntry(str.str(),0x0018,0x0088); // Spacing Between Slices
// Origin
double *org = image->GetOrigin();
str.str("");
- str<<org[0]<<"\\"<<org[1]<<"\\"<<org[2];
- file->ReplaceOrCreateByNumber(str.str(),0x0020,0x0032);
+ str << org[0] << "\\" << org[1] << "\\" << org[2];
+ file->InsertValEntry(str.str(),0x0020,0x0032); // Image Position Patient
// Window / Level
double *rng=image->GetScalarRange();
str.str("");
- str<<rng[1]-rng[0];
- file->ReplaceOrCreateByNumber(str.str(),0x0028,0x1051);
+ str << rng[1]-rng[0];
+ file->InsertValEntry(str.str(),0x0028,0x1051); // Window Width
str.str("");
- str<<(rng[1]+rng[0])/2.0;
- file->ReplaceOrCreateByNumber(str.str(),0x0028,0x1050);
+ str << (rng[1]+rng[0])/2.0;
+ file->InsertValEntry(str.str(),0x0028,0x1050); // Window Center
// Pixels
unsigned char *data;
size_t size = ReverseData(image,&data);
- file->SetImageData(data,size);
+ file->SetUserData(data,size);
}
/**
*/
void vtkGdcmWriter::RecursiveWrite(int axis, vtkImageData *image, ofstream *file)
{
- (void)axis; // To avoid warning
if(file)
{
- vtkErrorMacro(<< "File musn't be opened");
+ vtkErrorMacro( << "File musn't be opened");
return;
}
return;
}
- WriteDcmFile(this->FileName,image);
+ RecursiveWrite(axis,image,image,file);
+ //WriteDcmFile(this->FileName,image);
}
-void vtkGdcmWriter::RecursiveWrite(int axis, vtkImageData *image,
- vtkImageData *cache, ofstream *file)
+void vtkGdcmWriter::RecursiveWrite(int axis, vtkImageData *cache,
+ vtkImageData *image, ofstream *file)
{
- (void)axis; // To avoid warning
- (void)image; // To avoid warning
- (void)cache; // To avoid warning
- (void)file; // To avoid warning
+ int idx, min, max;
+
+ // if the file is already open then just write to it
+ if( file )
+ {
+ vtkErrorMacro( << "File musn't be opened");
+ return;
+ }
+
+ // if we need to open another slice, do it
+ if( (axis + 1) == this->FileDimensionality )
+ {
+ // determine the name
+ if (this->FileName)
+ {
+ sprintf(this->InternalFileName,"%s",this->FileName);
+ }
+ else
+ {
+ if (this->FilePrefix)
+ {
+ sprintf(this->InternalFileName, this->FilePattern,
+ this->FilePrefix, this->FileNumber);
+ }
+ else
+ {
+ sprintf(this->InternalFileName, this->FilePattern,this->FileNumber);
+ }
+ if (this->FileNumber < this->MinimumFileNumber)
+ {
+ this->MinimumFileNumber = this->FileNumber;
+ }
+ else if (this->FileNumber > this->MaximumFileNumber)
+ {
+ this->MaximumFileNumber = this->FileNumber;
+ }
+ }
+
+ // Write the file
+ WriteDcmFile(this->InternalFileName,image);
+ ++this->FileNumber;
+ return;
+ }
+
+ // if the current region is too high a dimension forthe file
+ // the we will split the current axis
+ cache->GetAxisUpdateExtent(axis, min, max);
+
+ // if it is the y axis then flip by default
+ if (axis == 1 && !this->FileLowerLeft)
+ {
+ for(idx = max; idx >= min; idx--)
+ {
+ cache->SetAxisUpdateExtent(axis, idx, idx);
+ this->RecursiveWrite(axis - 1, cache, image, file);
+ }
+ }
+ else
+ {
+ for(idx = min; idx <= max; idx++)
+ {
+ cache->SetAxisUpdateExtent(axis, idx, idx);
+ this->RecursiveWrite(axis - 1, cache, image, file);
+ }
+ }
+
+ // restore original extent
+ cache->SetAxisUpdateExtent(axis, min, max);
}
void vtkGdcmWriter::WriteDcmFile(char *fileName,vtkImageData *image)
{
// From here, the write of the file begins
- gdcm::File *dcmFile = new gdcm::File();
+ gdcm::FileHelper *dcmFile = new gdcm::FileHelper();
+
+ // Set the image UID
+ if( StudyInstanceUID.empty() )
+ StudyInstanceUID = gdcm::Util::CreateUniqueUID( UIDPrefix );
+ if( SeriesInstanceUID.empty() )
+ SeriesInstanceUID = gdcm::Util::CreateUniqueUID( UIDPrefix );
+ if( FrameOfReferenceInstanceUID.empty() )
+ FrameOfReferenceInstanceUID = gdcm::Util::CreateUniqueUID( UIDPrefix );
+ std::string uid = gdcm::Util::CreateUniqueUID( UIDPrefix );
+
+ dcmFile->InsertValEntry(uid,0x0008,0x0018); //[SOP Instance UID]
+ dcmFile->InsertValEntry(uid,0x0002,0x0003); //[Media Stored SOP Instance UID]
+ dcmFile->InsertValEntry(StudyInstanceUID,0x0020,0x000d); //[Study Instance UID]
+ dcmFile->InsertValEntry(SeriesInstanceUID,0x0020,0x000e); //[Series Instance UID]
+ dcmFile->InsertValEntry(FrameOfReferenceInstanceUID,0x0020, 0x0052); //[Frame of Reference UID]
// Set the image informations
SetImageInformation(dcmFile,image);
// Write the image
+ switch(this->WriteType)
+ {
+ case VTK_GDCM_WRITE_TYPE_EXPLICIT_VR :
+ dcmFile->SetWriteTypeToDcmExplVR();
+ break;
+ case VTK_GDCM_WRITE_TYPE_IMPLICIT_VR :
+ dcmFile->SetWriteTypeToDcmImplVR();
+ break;
+ case VTK_GDCM_WRITE_TYPE_ACR :
+ dcmFile->SetWriteTypeToAcr();
+ break;
+ case VTK_GDCM_WRITE_TYPE_ACR_LIBIDO :
+ dcmFile->SetWriteTypeToAcrLibido();
+ break;
+ default :
+ dcmFile->SetWriteTypeToDcmExplVR();
+ }
+
if(!dcmFile->Write(fileName))
{
- vtkErrorMacro(<< "File " << this->FileName << "couldn't be written by "
- << " the gdcm library");
- std::cerr<<"not written \n";
+ vtkErrorMacro( << "File " << this->FileName << "couldn't be written by "
+ << " the gdcm library");
}
+ // Clean up
+ if( dcmFile->GetUserData() && dcmFile->GetUserDataSize()>0 )
+ {
+ delete[] dcmFile->GetUserData();
+ }
delete dcmFile;
}