-// vtkGdcmReader.cxx
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: vtkGdcmReader.cxx,v $
+ Language: C++
+ Date: $Date: 2005/06/29 16:12:43 $
+ Version: $Revision: 1.72 $
+
+ 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.
+
+=========================================================================*/
+
//-----------------------------------------------------------------------------
// //////////////////////////////////////////////////////////////
// WARNING TODO CLEANME
// 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
+// 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:
+// stack are "homogenous" (same size, same representation...).
+// This can only be achieved by parsing all the Dicom headers...
+// --> to avoid loosing too much time :
+// If user is 150% sure *all* the files are coherent, that is to say :
+// they may be open, they are gdcm-readable, they have the same sizes,
+// they have the same 'pixel' type, they are single frame,
+// they have the same color convention ...
+// he may use SetCheckFileCoherenceLight() to request a 'light' coherence
+// checking
+// 2/ ExecuteData is then responsible for the next two loadings - 2 ?!?-:
// 2a/ ExecuteData calls AllocateOutputData that in turn seems to
// (indirectely call) ExecuteInformation which ends up in a second
// header parsing
// 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
+// initialises gdcmFile 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
+// once and for all accross the life of vtkGdcmFile (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...
+// a vtkGdcmFile) the gdcmFile structure is loaded in memory.
+// The average size of a gdcm::File being of 100Ko,
+// - 100 Ko ? Better say 1 Mo; we are in 2005 ! -
+// if oneloads 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
// time...
// //////////////////////////////////////////////////////////////
+#include "gdcmFileHelper.h"
#include "gdcmFile.h"
-#include "gdcmHeader.h"
+#include "gdcmDocument.h" // for NO_SEQ
+
#include "vtkGdcmReader.h"
+#include "gdcmDebug.h"
//#include <stdio.h>
#include <vtkObjectFactory.h>
#include <vtkPointData.h>
#include <vtkLookupTable.h>
-vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.59 $");
+vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.72 $");
vtkStandardNewMacro(vtkGdcmReader);
//-----------------------------------------------------------------------------
{
this->LookupTable = NULL;
this->AllowLookupTable = 0;
+ this->LightChecking = false;
+ this->LoadMode = 0; // Load everything (possible values : NO_SEQ, NO_SHADOW
+ // NO_SHADOWSEQ)
}
vtkGdcmReader::~vtkGdcmReader()
//-----------------------------------------------------------------------------
// Print
-void vtkGdcmReader::PrintSelf(ostream& os, vtkIndent indent)
+void vtkGdcmReader::PrintSelf(ostream &os, vtkIndent indent)
{
this->Superclass::PrintSelf(os,indent);
os << indent << "Filenames : " << endl;
{
// 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];
+ char *LocalName = new char[strlen(name) + 1];
strcpy(LocalName, name);
this->FileNameList.push_back(LocalName);
delete[] LocalName;
this->Modified();
}
+/*
+ * Ask for a 'light' checking -actually : just initializing-
+ *if you are 150% sure *all* the files are coherent
+ */
+void vtkGdcmReader::SetCheckFileCoherenceLight()
+{
+ LightChecking = true;
+}
+
//-----------------------------------------------------------------------------
// Protected
/*
{
if(this->MTime>this->fileTime)
{
- this->TotalNumberOfPlanes = this->CheckFileCoherence();
+ if ( this->LightChecking )
+ this->TotalNumberOfPlanes = this->CheckFileCoherenceLight();
+ else
+ this->TotalNumberOfPlanes = this->CheckFileCoherence();
+
if ( this->TotalNumberOfPlanes == 0)
{
vtkErrorMacro(<< "File set is not coherent. Exiting...");
{
vtkDebugMacro(<< "16 bits signed image");
this->SetDataScalarTypeToShort();
- //vtkErrorMacro(<< "Cannot handle 16 bit signed files");
}
else if ( ImageType == "32U" )
{
* 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
+ * VTK/IO/vtkImageReader.cxx) reads a data from a file. The data
* extent/axes are assumed to be the same as the file extent/order.
*/
void vtkGdcmReader::ExecuteData(vtkDataObject *output)
}
// 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 actual advance measure:
unsigned long UpdateProgressCount = 0;
- // Feeling the allocated memory space with each image/volume:
+ // Filling the allocated memory space with each image/volume:
unsigned char *Dest = (unsigned char *)data->GetScalarPointer();
for (std::list<std::string>::iterator filename = InternalFileNameList.begin();
filename != InternalFileNameList.end();
ReturnedTotalNumberOfPlanes += 1;
/////// Stage 0: check for file name:
+
+ // fixme : how can the filename be equal to "GDCM_UNREADABLE"
+ // right now ?!?
+
if(*filename == std::string("GDCM_UNREADABLE"))
continue;
if (!fp)
{
vtkErrorMacro(<< "Unable to open file " << filename->c_str());
- vtkErrorMacro(<< "Removing this file from readed files "
+ vtkErrorMacro(<< "Removing this file from read files: "
<< filename->c_str());
*filename = "GDCM_UNREADABLE";
continue;
fclose(fp);
// Stage 1.2: check for Gdcm parsability
- gdcm::Header GdcmHeader(filename->c_str() );
- if (!GdcmHeader.IsReadable())
+
+ //gdcm::File GdcmFile( filename->c_str() );
+ // to save some parsing time.
+ gdcm::File GdcmFile;
+ GdcmFile.SetLoadMode( LoadMode );
+ GdcmFile.Load(filename->c_str() );
+ if (!GdcmFile.IsReadable())
{
vtkErrorMacro(<< "Gdcm cannot parse file " << filename->c_str());
- vtkErrorMacro(<< "Removing this file from readed files "
+ vtkErrorMacro(<< "Removing this file from read files: "
<< filename->c_str());
*filename = "GDCM_UNREADABLE";
continue;
}
// Stage 1.3: further gdcm compatibility on PixelType
- std::string type = GdcmHeader.GetPixelType();
+ std::string type = GdcmFile.GetPixelType();
if ( (type != "8U") && (type != "8S")
&& (type != "16U") && (type != "16S")
&& (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());
+ vtkErrorMacro(<< "Bad File Type for file " << filename->c_str() << "\n"
+ << " File type found : " << type.c_str()
+ << " (might be 8U, 8S, 16U, 16S, 32U, 32S) \n"
+ << " Removing this file from readed files");
*filename = "GDCM_UNREADABLE";
continue;
}
// Stage 2: check coherence of the set of files
- int NX = GdcmHeader.GetXSize();
- int NY = GdcmHeader.GetYSize();
- int NZ = GdcmHeader.GetZSize();
+ int NX = GdcmFile.GetXSize();
+ int NY = GdcmFile.GetYSize();
+ int NZ = GdcmFile.GetZSize();
if (FoundReferenceFile)
{
// Stage 2.1: mandatory coherence stage:
|| ( NY != this->NumLines )
|| ( type != this->ImageType ) )
{
- vtkErrorMacro(<< "This file is not coherent with previous ones"
+ vtkErrorMacro(<< "This file is not coherent with previous ones: "
<< filename->c_str());
- vtkErrorMacro(<< "Removing this file from readed files "
+ vtkErrorMacro(<< "Removing this file from readed files: "
<< filename->c_str());
*filename = "GDCM_UNREADABLE";
continue;
// Stage 2.2: optional coherence stage
if ( NZ != ReferenceNZ )
{
- vtkErrorMacro(<< "File is not coherent in Z with previous ones"
+ vtkErrorMacro(<< "File is not coherent in Z with previous ones: "
<< filename->c_str());
}
else
{
- vtkDebugMacro(<< "File is coherent with previous ones"
+ vtkDebugMacro(<< "File is coherent with previous ones: "
<< filename->c_str());
}
- // Stage 2.3: when the file contains a volume (as opposed to an image),
- // notify the caller.
+ // Stage 2.3: when the file is 'multiframe', notify the caller.
if (NZ > 1)
{
- vtkErrorMacro(<< "This file contains multiple planes (images)"
+ vtkErrorMacro(<< "This file is a 'Multiframe' one: "
<< filename->c_str());
}
}
else
{
- // We didn't have a workable reference file yet. Set this one
- // as the reference.
+ // We didn't have a workable reference file yet.
+ // Set this one as the reference.
FoundReferenceFile = true;
vtkDebugMacro(<< "This file taken as coherence reference:"
- << filename->c_str());
- vtkDebugMacro(<< "Image dimension of reference file as read from Gdcm:"
- << NX << " " << NY << " " << NZ);
+ << filename->c_str());
+ vtkDebugMacro(<< "Image dimensions of reference file as read from Gdcm:"
+ << NX << " " << NY << " " << NZ);
vtkDebugMacro(<< "Number of planes added to the stack: " << NZ);
// Set aside the size of the image
this->NumColumns = NX;
ReferenceNZ = NZ;
ReturnedTotalNumberOfPlanes += NZ - 1; // First plane already added
this->ImageType = type;
- this->PixelSize = GdcmHeader.GetPixelSize();
+ this->PixelSize = GdcmFile.GetPixelSize();
- if( GdcmHeader.HasLUT() && this->AllowLookupTable )
+ if( GdcmFile.HasLUT() && this->AllowLookupTable )
{
// I could raise an error is AllowLookupTable is on and HasLUT() off
- this->NumComponents = GdcmHeader.GetNumberOfScalarComponentsRaw();
+ this->NumComponents = GdcmFile.GetNumberOfScalarComponentsRaw();
}
else
{
- this->NumComponents = GdcmHeader.GetNumberOfScalarComponents(); //rgb or mono
- }
-
+ this->NumComponents = GdcmFile.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();
-
+ this->DataSpacing[0] = GdcmFile.GetXSpacing();
+ this->DataSpacing[1] = GdcmFile.GetYSpacing();
+ this->DataSpacing[2] = GdcmFile.GetZSpacing();
}
} // End of loop on filename
/*
* Adds a file name to the internal list of images to read.
*/
-void vtkGdcmReader::AddInternalFileName(const char* name)
+void vtkGdcmReader::AddInternalFileName(const char *name)
{
- char * LocalName = new char[strlen(name) + 1];
+ char *LocalName = new char[strlen(name) + 1];
strcpy(LocalName, name);
this->InternalFileNameList.push_back(LocalName);
delete[] LocalName;
*/
size_t vtkGdcmReader::LoadImageInMemory(
std::string fileName,
- unsigned char * dest,
+ unsigned char *dest,
const unsigned long updateProgressTarget,
- unsigned long & updateProgressCount)
+ unsigned long &updateProgressCount)
{
vtkDebugMacro(<< "Copying to memory image [" << fileName.c_str() << "]");
- gdcm::File file( fileName.c_str() );
+ gdcm::File *f;
+ f = new gdcm::File();
+ f->SetLoadMode( LoadMode );
+ f->Load( fileName.c_str() );
+
+ gdcm::FileHelper fileH( f );
size_t size;
// If the data structure of vtk for image/volume representation
// line comes first (for some axis related reasons?). Hence we need
// to load the image line by line, starting from the end.
- int numColumns = file.GetHeader()->GetXSize();
- int numLines = file.GetHeader()->GetYSize();
- int numPlanes = file.GetHeader()->GetZSize();
- int lineSize = NumComponents * numColumns * file.GetHeader()->GetPixelSize();
+ int numColumns = fileH.GetFile()->GetXSize();
+ int numLines = fileH.GetFile()->GetYSize();
+ int numPlanes = fileH.GetFile()->GetZSize();
+ int lineSize = NumComponents * numColumns * fileH.GetFile()->GetPixelSize();
+ int planeSize = lineSize * numLines;
- unsigned char * source;
+ unsigned char *src;
- if( file.GetHeader()->HasLUT() && AllowLookupTable )
+ if( fileH.GetFile()->HasLUT() && AllowLookupTable )
{
- size = file.GetImageDataSize();
- source = (unsigned char*) file.GetImageDataRaw();
- unsigned char *lut = (unsigned char*) file.GetLutRGBA();
+ size = fileH.GetImageDataSize();
+ src = (unsigned char*) fileH.GetImageDataRaw();
+ unsigned char *lut = (unsigned char*) fileH.GetLutRGBA();
if(!this->LookupTable)
{
}
else
{
- size = file.GetImageDataSize();
- source = (unsigned char*)file.GetImageData();
+ size = fileH.GetImageDataSize();
+ src = (unsigned char*)fileH.GetImageData();
}
-
- unsigned char * destination = dest + size - lineSize;
+ unsigned char *dst = dest + planeSize - lineSize;
for (int plane = 0; plane < numPlanes; plane++)
{
for (int line = 0; line < numLines; line++)
{
// Copy one line at proper destination:
- memcpy((void*)destination, (void*)source, lineSize);
- source += lineSize;
- destination -= lineSize;
+ memcpy((void*)dst, (void*)src, lineSize);
+ src += lineSize;
+ dst -= lineSize;
// Update progress related:
if (!(updateProgressCount%updateProgressTarget))
{
}
updateProgressCount++;
}
+ dst += 2 * planeSize;
}
-
-// DO NOT remove this commented out code .
-// Nobody knows what's expecting you ...
-// Just to 'see' what was actually read on disk :-(
-
-// FILE * f2;
-// f2 = fopen("SpuriousFile.RAW","wb");
-// fwrite(Dest,size,1,f2);
-// fclose(f2);
-
+ delete f;
return size;
}
+// -------------------------------------------------------------------------
+
+// We assume the use *does* know all the files whose names
+// are in InternalFileNameList exist, may be open, are gdcm-readable
+// have the same sizes, have the same 'pixel' type, are single frame
+// have the same color convention, ..., anything else ?
+
+int vtkGdcmReader::CheckFileCoherenceLight()
+{
+ std::list<std::string>::iterator filename = InternalFileNameList.begin();
+
+ gdcm::File GdcmFile;
+ GdcmFile.SetLoadMode( LoadMode );
+ GdcmFile.Load(filename->c_str() );
+ if (!GdcmFile.IsReadable())
+ {
+ vtkErrorMacro(<< "Gdcm cannot parse file " << filename->c_str());
+ vtkErrorMacro(<< "you should try vtkGdcmReader::CheckFileCoherence "
+ << "instead of try vtkGdcmReader::CheckFileCoherenceLight");
+ return 0;
+ }
+ int NX = GdcmFile.GetXSize();
+ int NY = GdcmFile.GetYSize();
+ // CheckFileCoherenceLight should be called *only* when user knows
+ // he deals with single frames files.
+ // Z size is then the number of files.
+ int NZ = InternalFileNameList.size();
+ std::string type = GdcmFile.GetPixelType();
+ vtkDebugMacro(<< "The first file is taken as reference: "
+ << filename->c_str());
+ vtkDebugMacro(<< "Image dimensions of reference file as read from Gdcm:"
+ << NX << " " << NY << " " << NZ);
+ vtkDebugMacro(<< "Number of planes added to the stack: " << NZ);
+ // Set aside the size of the image
+ this->NumColumns = NX;
+ this->NumLines = NY;
+ this->ImageType = type;
+ this->PixelSize = GdcmFile.GetPixelSize();
+
+ if( GdcmFile.HasLUT() && this->AllowLookupTable )
+ {
+ // I could raise an error is AllowLookupTable is on and HasLUT() off
+ this->NumComponents = GdcmFile.GetNumberOfScalarComponentsRaw();
+ }
+ else
+ {
+ this->NumComponents = GdcmFile.GetNumberOfScalarComponents(); //rgb or mono
+ }
+
+ //Set image spacing
+ this->DataSpacing[0] = GdcmFile.GetXSpacing();
+ this->DataSpacing[1] = GdcmFile.GetYSpacing();
+ this->DataSpacing[2] = GdcmFile.GetZSpacing();
+
+ return InternalFileNameList.size();
+}
//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff