-// vtkGdcmWriter.cxx
-//-----------------------------------------------------------------------------
-// //////////////////////////////////////////////////////////////
-// WARNING TODO CLEANME
-// 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
-// This is fixed by adding a test at the beginning of ExecuteInformation
-// on the modification of the object instance. If a modification have been
-// made (method Modified() ), the MTime value is increased. The fileTime
-// is compared to this new value to find a modification in the class
-// parameters
-// 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 "gdcmHeader.h"
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: vtkGdcmWriter.cxx,v $
+ Language: C++
+ Date: $Date: 2007/12/13 15:16:19 $
+ Version: $Revision: 1.36 $
+
+ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
+ l'Image). All rights reserved. See Doc/License.txt or
+ http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+
#include "gdcmFile.h"
+#include "gdcmFileHelper.h"
#include "gdcmDebug.h"
+#include "gdcmUtil.h"
#include "vtkGdcmWriter.h"
#include <vtkObjectFactory.h>
#include <vtkImageData.h>
#include <vtkPointData.h>
#include <vtkLookupTable.h>
+#if (VTK_MAJOR_VERSION >= 5)
+#include <vtkMedicalImageProperties.h>
+#endif
+#ifndef vtkFloatingPointType
+#define vtkFloatingPointType float
+#endif
-vtkCxxRevisionMacro(vtkGdcmWriter, "$Revision: 1.1 $");
-vtkStandardNewMacro(vtkGdcmWriter);
+vtkCxxRevisionMacro(vtkGdcmWriter, "$Revision: 1.36 $")
+vtkStandardNewMacro(vtkGdcmWriter)
+vtkCxxSetObjectMacro(vtkGdcmWriter,LookupTable,vtkLookupTable)
+#if (VTK_MAJOR_VERSION >= 5)
+vtkCxxSetObjectMacro(vtkGdcmWriter,MedicalImageProperties,vtkMedicalImageProperties)
+#endif
//-----------------------------------------------------------------------------
// Constructor / Destructor
vtkGdcmWriter::vtkGdcmWriter()
{
this->LookupTable = NULL;
+ this->MedicalImageProperties = NULL;
+ this->FileDimensionality = 3;
+ this->WriteType = VTK_GDCM_WRITE_TYPE_EXPLICIT_VR;
+ this->GdcmFile = 0;
+ this->ContentType = VTK_GDCM_WRITE_TYPE_USER_OWN_IMAGE;
}
vtkGdcmWriter::~vtkGdcmWriter()
{
+ this->SetMedicalImageProperties(NULL);
+ this->SetLookupTable(NULL);
}
//-----------------------------------------------------------------------------
// Print
-void vtkGdcmWriter::PrintSelf(ostream& os, vtkIndent indent)
+void vtkGdcmWriter::PrintSelf(ostream &os, vtkIndent indent)
{
- this->Superclass::PrintSelf(os,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";
+ }
+}
//-----------------------------------------------------------------------------
// Protected
-void SetImageInformation(gdcm::File *file,vtkImageData *image)
+/**
+ * Copy the image and reverse the Y axis
+ */
+// The output data must be deleted by the user of the method !!!
+size_t ReverseData(vtkImageData *image,unsigned char **data)
+{
+#if (VTK_MAJOR_VERSION >= 5)
+ vtkIdType inc[3];
+#else
+ int inc[3];
+#endif
+ 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;
+
+ if( size>0 )
+ {
+ *data = new unsigned char[size];
+
+ 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;
+ }
+ }
+ else
+ {
+ *data = NULL;
+ }
+
+ return size;
+}
+
+/**
+ * Set the medical informations in the file, based on the user passed
+ * vtkMedicalImageProperties
+ */
+#if (VTK_MAJOR_VERSION >= 5)
+void SetMedicalImageInformation(GDCM_NAME_SPACE::FileHelper *file, vtkMedicalImageProperties *medprop)
+{
+ // For now only do:
+ // PatientName, PatientID, PatientAge, PatientSex, PatientBirthDate, StudyID
+ std::ostringstream str;
+ if( medprop )
+ {
+ if (medprop->GetPatientName())
+ {
+ str.str("");
+ str << medprop->GetPatientName();
+ file->InsertEntryString(str.str(),0x0010,0x0010,"PN"); // PN 1 Patient's Name
+ }
+
+ if (medprop->GetPatientID())
+ {
+ str.str("");
+ str << medprop->GetPatientID();
+ file->InsertEntryString(str.str(),0x0010,0x0020,"LO"); // LO 1 Patient ID
+ }
+
+ if (medprop->GetPatientAge())
+ {
+ str.str("");
+ str << medprop->GetPatientAge();
+ file->InsertEntryString(str.str(),0x0010,0x1010,"AS"); // AS 1 Patient's Age
+ }
+
+ if (medprop->GetPatientSex())
+ {
+ str.str("");
+ str << medprop->GetPatientSex();
+ file->InsertEntryString(str.str(),0x0010,0x0040,"CS"); // CS 1 Patient's Sex
+ }
+
+ if (medprop->GetPatientBirthDate())
+ {
+ str.str("");
+ str << medprop->GetPatientBirthDate();
+ file->InsertEntryString(str.str(),0x0010,0x0030,"DA"); // DA 1 Patient's Birth Date
+ }
+
+ if (medprop->GetStudyID())
+ {
+ str.str("");
+ str << medprop->GetStudyID();
+ file->InsertEntryString(str.str(),0x0020,0x0010,"SH"); // SH 1 Study ID
+ }
+ }
+}
+#endif
+
+/**
+ * Set the data informations in the file
+ */
+void SetImageInformation(GDCM_NAME_SPACE::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->InsertEntryString(str.str(),0x0028,0x0011,"US"); // Columns
str.str("");
- str<<dim[1];
- file->ReplaceOrCreateByNumber(str.str(),0x0028,0x0010);
+ str << dim[1];
+ file->InsertEntryString(str.str(),0x0028,0x0010,"US"); // 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->InsertEntryString(str.str(),0x0028,0x0008,"IS"); // 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->InsertEntryString(str.str(),0x0028,0x0100,"US"); // Bits Allocated
+ file->InsertEntryString(str.str(),0x0028,0x0101,"US"); // Bits Stored
str.str("");
- str<<image->GetScalarSize()*8-1;
- file->ReplaceOrCreateByNumber(str.str(),0x0028,0x0102);
+ str << image->GetScalarSize()*8-1;
+ file->InsertEntryString(str.str(),0x0028,0x0102,"US"); // High Bit
+
+ // Pixel Repr
+ // FIXME : what do we do when the ScalarType is
+ // VTK_UNSIGNED_INT or VTK_UNSIGNED_LONG
+ str.str("");
+ if( image->GetScalarType() == VTK_UNSIGNED_CHAR ||
+ image->GetScalarType() == VTK_UNSIGNED_SHORT ||
+ image->GetScalarType() == VTK_UNSIGNED_INT ||
+ image->GetScalarType() == VTK_UNSIGNED_LONG )
+ {
+ str << "0"; // Unsigned
+ }
+ else
+ {
+ str << "1"; // Signed
+ }
+ file->InsertEntryString(str.str(),0x0028,0x0103,"US"); // Pixel Representation
// Samples per pixel
str.str("");
- str<<image->GetNumberOfScalarComponents();
- file->ReplaceOrCreateByNumber(str.str(),0x0028,0x0002);
- std::cout<<file->GetHeader()->GetEntryByNumber(0x0028,0x0002)<<"-"<<file->GetHeader()->GetNumberOfScalarComponents()<<"\n";
+ str << image->GetNumberOfScalarComponents();
+ file->InsertEntryString(str.str(),0x0028,0x0002,"US"); // Samples per Pixel
+
+ /// \todo : Spacing Between Slices is meaningfull ONLY for CT an MR modality
+ /// We should perform some checkings before forcing the Entry creation
// Spacing
- double *sp = image->GetSpacing();
+ vtkFloatingPointType *sp = image->GetSpacing();
str.str("");
- str<<sp[0]<<"\\"<<sp[1];
- file->ReplaceOrCreateByNumber(str.str(),0x0028,0x0030);
+ // We are about to enter floating point value.
+ // By default ostringstream are smart and don't do fixed point
+ // thus forcing to fixed point value
+ str.setf( std::ios::fixed );
+ str << sp[1] << "\\" << sp[0];
+ file->InsertEntryString(str.str(),0x0028,0x0030,"DS"); // Pixel Spacing
str.str("");
- str<<sp[2];
- file->ReplaceOrCreateByNumber(str.str(),0x0018,0x0088);
+ str << sp[2];
+ file->InsertEntryString(str.str(),0x0018,0x0088,"DS"); // Spacing Between Slices
// Origin
- double *org = image->GetOrigin();
+ vtkFloatingPointType *org = image->GetOrigin();
+
+ /// \todo : Image Position Patient is meaningfull ONLY for CT an MR modality
+ /// We should perform some checkings before forcing the Entry creation
str.str("");
- str<<org[0]<<"\\"<<org[1]<<"\\"<<org[2];
- file->ReplaceOrCreateByNumber(str.str(),0x0020,0x0032);
+ str << org[0] << "\\" << org[1] << "\\" << org[2];
+ file->InsertEntryString(str.str(),0x0020,0x0032,"DS"); // Image Position Patient
+ str.unsetf( std::ios::fixed ); //done with floating point values
// Window / Level
- double *rng=image->GetScalarRange();
+ vtkFloatingPointType *rng = image->GetScalarRange();
str.str("");
- str<<rng[1]-rng[0];
- file->ReplaceOrCreateByNumber(str.str(),0x0028,0x1051);
+ str << rng[1]-rng[0];
+ file->InsertEntryString(str.str(),0x0028,0x1051,"DS"); // 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->InsertEntryString(str.str(),0x0028,0x1050,"DS"); // Window Center
// Pixels
- size_t size = dim[0] * dim[1] * dim[2]
- * image->GetScalarSize()
- * image->GetNumberOfScalarComponents();
- file->SetImageData((unsigned char *)image->GetScalarPointer(),size);
+ unsigned char *data;
+ size_t size = ReverseData(image,&data);
+ file->SetUserData(data,size);
}
-void vtkGdcmWriter::RecursiveWrite(int dim, vtkImageData *region, ofstream *file)
+/**
+ * Write of the files
+ * The call to this method is recursive if there is some files to write
+ */
+void vtkGdcmWriter::RecursiveWrite(int axis, vtkImageData *image,
+ ofstream *file)
{
if(file)
{
- vtkErrorMacro(<< "File musn't be opened");
+ vtkErrorMacro( << "File must not be open");
+ return;
+ }
+
+ if( image->GetScalarType() == VTK_FLOAT ||
+ image->GetScalarType() == VTK_DOUBLE )
+ {
+ vtkErrorMacro(<< "Bad input type. Scalar type must not be of type "
+ << "VTK_FLOAT or VTK_DOUBLE (found:"
+ << image->GetScalarTypeAsString() << ")" );
return;
}
- if( region->GetScalarType() == VTK_FLOAT
- || region->GetScalarType() == VTK_DOUBLE )
+ RecursiveWrite(axis,image, image, file);
+ //WriteDcmFile(this->FileName,image);
+}
+
+void vtkGdcmWriter::RecursiveWrite(int axis, vtkImageData *cache,
+ vtkImageData *image, ofstream *file)
+{
+ int idx, min, max;
+
+ // if the file is already open then just write to it
+ if( file )
{
- vtkErrorMacro(<< "Bad input type. Scalar type musn't be of type "
- << "VTK_FLOAT or VTKDOUBLE (found:"
- << region->GetScalarTypeAsString());
+ vtkErrorMacro( << "File musn't be open");
return;
}
- gdcm::File *dcmFile = new gdcm::File();
+ // 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);
+ }
+// Remove this code in case user is using VTK 4.2...
+#if !(VTK_MAJOR_VERSION == 4 && VTK_MINOR_VERSION == 2)
+ if (this->FileNumber < this->MinimumFileNumber)
+ {
+ this->MinimumFileNumber = this->FileNumber;
+ }
+ else if (this->FileNumber > this->MaximumFileNumber)
+ {
+ this->MaximumFileNumber = this->FileNumber;
+ }
+#endif
+ }
+
+ // Write the file
+ WriteDcmFile(this->InternalFileName,image);
+ ++this->FileNumber;
+ return;
+ }
- ///////////////////////////////////////////////////////////////////////////
+ // if the current region is too high a dimension for the 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)
+{
+ GDCM_NAME_SPACE::FileHelper *dcmFile;
+ if ( GdcmFile != 0)
+ dcmFile = GDCM_NAME_SPACE::FileHelper::New(GdcmFile);
+ else
+ dcmFile = GDCM_NAME_SPACE::FileHelper::New();
+
+ // From here, the write of the file begins
+
+ // Set the medical informations:
+#if (VTK_MAJOR_VERSION >= 5)
+ SetMedicalImageInformation(dcmFile, this->MedicalImageProperties);
+#endif
+
// Set the image informations
- SetImageInformation(dcmFile,region);
+ SetImageInformation(dcmFile, image);
- ///////////////////////////////////////////////////////////////////////////
// Write the image
- if(!dcmFile->Write(this->FileName))
+ switch(this->WriteType)
{
- vtkErrorMacro(<< "File " << this->FileName << "couldn't be written by "
- << " the gdcm library");
- std::cerr<<"not written \n";
+ 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();
}
-
- delete dcmFile;
+
+ dcmFile->SetContentType((GDCM_NAME_SPACE::ImageContentType)ContentType);
+
+ if(!dcmFile->Write(fileName))
+ {
+ vtkErrorMacro( << "File " << this->FileName << "cannot be written by "
+ << " the gdcm library");
+ }
+ // Clean up
+ if( dcmFile->GetUserData() && dcmFile->GetUserDataSize()>0 )
+ {
+ delete[] dcmFile->GetUserData();
+ }
+ dcmFile->Delete();
}
//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff