-// vtkGdcmReader.cxx
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: vtkGdcmReader.cxx,v $
+ Language: C++
+ Date: $Date: 2005/08/22 12:30:36 $
+ Version: $Revision: 1.76 $
+
+ 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 CLENAME
-// Actual limitations of this code:
+//
+//===> Many users expect from vtkGdcmReader it 'orders' the images
+// (that's the job of gdcm::SerieHelper ...)
+// When user *knows* the files with same Serie UID
+// have same sizes, same 'pixel' type, same color convention, ...
+// the right way to proceed is as follow :
+//
+// gdcm::SerieHelper *sh= new gdcm::SerieHelper();
+// // if user wants *not* to load some parts of the file headers
+// sh->SetLoadMode(loadMode);
+// // if user wants *not* to load some files
+// sh->AddRestriction(group, element, value, operator);
+// sh->AddRestriction( ...
+// sh->SetDirectory(directoryWithImages);
+//
+// // if user wants to sort reverse order
+// sh->SetSortOrderToReverse();
+// // here, we suppose only the first Coherent File List is of interest
+// gdcm::FileList *l = sh->GetFirstCoherentFileList();
+// // if user is doesn't trust too much the files with same Serie UID
+// if ( !sh->IsCoherent(l) )
+// return; // not same sizes, same 'pixel' type -> stop
+// sh->OrderFileList(l); // sort the list
+//
+// vtkGdcmReader *reader = vtkGdcmReader::New();
+// // if user wants to modify pixel order (Mirror, TopDown, 90°Rotate, ...)
+// // he has to supply the function that does the job
+// // (a *very* simple example is given in vtkgdcmSerieViewer.cxx)
+// reader->SetUserFunction (userSuppliedFunction);
+// // to pass a 'Coherent File List' as produced by gdcm::SerieHelper
+// reader->SetCoherentFileList(l);
+// reader->Update();
+
+// WARNING TODO CLEANME
+// Actual limitations of this code
+// when a Coherent File List from SerieHelper is not used (bad idea :-(
//
// /////// 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
+// 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
// 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
+// 2b/ the core of ExecuteData then needs gdcm::File (which in turns
+// initializes gdcm::File 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.
+// maintain a list of gdcm::Files (created by say ExecuteInformation) created
+// once and for all accross the life of vtkGdcmFile (it would only load
+// new gdcm::File if the user changes the list). ExecuteData would then use
+// those gdcm::File and hence avoid calling the constructor:
+// - advantage: the header of the files would only be parsed 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 gdcm::File structure is loaded in memory.
+// The average size of a gdcm::File being of 100Ko,
+// 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
// 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 "gdcmFileHelper.h"
#include "gdcmFile.h"
-#include "gdcmHeaderHelper.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: 1.76 $")
+vtkStandardNewMacro(vtkGdcmReader)
+
//-----------------------------------------------------------------------------
// Constructor / Destructor
vtkGdcmReader::vtkGdcmReader()
{
this->LookupTable = NULL;
this->AllowLookupTable = 0;
+ this->AllowLightChecking = 0;
+ this->LoadMode = 0; // Load everything (possible values : NO_SEQ, NO_SHADOW,
+ // NO_SHADOWSEQ)
+ this->CoherentFileList = 0;
+ this->UserFunction = 0;
}
vtkGdcmReader::~vtkGdcmReader()
//-----------------------------------------------------------------------------
// Print
-void vtkGdcmReader::PrintSelf(ostream& os, vtkIndent indent)
+void vtkGdcmReader::PrintSelf(ostream &os, vtkIndent indent)
{
- vtkImageReader::PrintSelf(os,indent);
+ this->Superclass::PrintSelf(os,indent);
os << indent << "Filenames : " << endl;
vtkIndent nextIndent = indent.GetNextIndent();
- for (std::list<std::string>::iterator FileName = FileNameList.begin();
- FileName != FileNameList.end();
- ++FileName)
+ for (std::list<std::string>::iterator it = FileNameList.begin();
+ it != FileNameList.end();
+ ++it)
{
- os << nextIndent << FileName->c_str() << endl ;
+ os << nextIndent << it->c_str() << 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;
// 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.
- vtkDebugMacro("Clearing all files given with AddFileName");
+ vtkDebugMacro(<< "Clearing all files given with AddFileName");
this->FileNameList.clear();
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->CoherentFileList != 0 )
+ this->TotalNumberOfPlanes = this->CheckFileCoherenceAlreadyDone();
+ else if ( this->AllowLightChecking )
+ this->TotalNumberOfPlanes = this->CheckFileCoherenceLight();
+ else
+ this->TotalNumberOfPlanes = this->CheckFileCoherence();
+
if ( this->TotalNumberOfPlanes == 0)
{
- vtkErrorMacro("File set is not coherent. Exiting...");
+ vtkErrorMacro(<< "File set is not coherent. Exiting...");
return;
}
(this->DataVOI[4] < 0) ||
(this->DataVOI[5] >= this->TotalNumberOfPlanes ))
{
- vtkWarningMacro("The requested VOI is larger than expected extent.");
+ vtkWarningMacro(<< "The requested VOI is larger than expected extent.");
this->DataVOI[0] = 0;
this->DataVOI[1] = this->NumColumns - 1;
this->DataVOI[2] = 0;
}
}
- // Positionate the Extent.
+ // Set the Extents.
this->DataExtent[0] = 0;
this->DataExtent[1] = this->NumColumns - 1;
this->DataExtent[2] = 0;
this->DataExtent[4] = 0;
this->DataExtent[5] = this->TotalNumberOfPlanes - 1;
- // We don't need to positionate the Endian related stuff (by using
+ // We don't need to set the Endian related stuff (by using
// this->SetDataByteOrderToBigEndian() or SetDataByteOrderToLittleEndian()
// since the reading of the file is done by gdcm.
// But we do need to set up the data type for downstream filters:
if ( ImageType == "8U" )
{
- vtkDebugMacro("8 bits unsigned image");
+ vtkDebugMacro(<< "8 bits unsigned image");
this->SetDataScalarTypeToUnsignedChar();
}
else if ( ImageType == "8S" )
{
- vtkErrorMacro("Cannot handle 8 bit signed files");
+ vtkErrorMacro(<< "Cannot handle 8 bit signed files");
return;
}
else if ( ImageType == "16U" )
{
- vtkDebugMacro("16 bits unsigned image");
+ vtkDebugMacro(<< "16 bits unsigned image");
this->SetDataScalarTypeToUnsignedShort();
}
else if ( ImageType == "16S" )
{
- vtkDebugMacro("16 bits signed image");
+ vtkDebugMacro(<< "16 bits signed image");
this->SetDataScalarTypeToShort();
- //vtkErrorMacro("Cannot handle 16 bit signed files");
}
else if ( ImageType == "32U" )
{
- vtkDebugMacro("32 bits unsigned image");
- vtkDebugMacro("WARNING: forced to signed int !");
+ vtkDebugMacro(<< "32 bits unsigned image");
+ vtkDebugMacro(<< "WARNING: forced to signed int !");
this->SetDataScalarTypeToInt();
}
else if ( ImageType == "32S" )
{
- vtkDebugMacro("32 bits signed image");
+ vtkDebugMacro(<< "32 bits signed image");
this->SetDataScalarTypeToInt();
}
else if ( ImageType == "FD" )
{
- vtkDebugMacro("64 bits Double image");
+ vtkDebugMacro(<< "64 bits Double image");
this->SetDataScalarTypeToDouble();
}
//Set number of scalar components:
this->Superclass::ExecuteInformation();
}
-
+
/*
* 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)
{
- if (this->InternalFileNameList.empty())
+ if ( CoherentFileList != 0 ) // When a list of names is passed
{
- vtkErrorMacro("A least a valid FileName must be specified.");
+ if (this->CoherentFileList->empty())
+ {
+ vtkErrorMacro(<< "Coherent File List must have at least a valid File*.");
+ return;
+ }
+ }
+ else 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 actual advance measure:
unsigned long UpdateProgressCount = 0;
- // Feeling the allocated memory space with each image/volume:
- unsigned char *Dest = (unsigned char *)data->GetPointData()->GetScalars()->GetVoidPointer(0);
- 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")
- {
- // 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)
+ // Filling the allocated memory space with each image/volume:
+
+ unsigned char *Dest = (unsigned char *)data->GetScalarPointer();
+
+ if ( CoherentFileList == 0 ) // When a list of names is passed
+ {
+ 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")
+ {
+ // Update progress related for good files is made in LoadImageInMemory
+ Dest += this->LoadImageInMemory(*filename, Dest,
+ UpdateProgressTarget,
+ UpdateProgressCount);
+ }
+ else
{
- if (!(UpdateProgressCount%UpdateProgressTarget))
+ // 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)
{
- this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget));
+ if (!(UpdateProgressCount%UpdateProgressTarget))
+ {
+ this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget));
+ }
}
- }
- } // Else, file not loadable
- } // Loop on files
+ } // Else, file not loadable
+ } // Loop on files
+
+ }
+ else // when a Coherent File List is passed
+ {
+ for (std::vector<gdcm::File* >::iterator it = CoherentFileList->begin();
+ it != CoherentFileList->end();
+ ++it)
+ {
+
+ //std::cout <<"----------------- " << (*it)->GetFileName() << std::endl;
+
+ Dest += this->LoadImageInMemory(*it, Dest,
+ UpdateProgressTarget,
+ UpdateProgressCount);
+ // Update progress related for bad files:
+ UpdateProgressCount += this->NumLines;
+ if (UpdateProgressTarget > 0)
+ {
+ if (!(UpdateProgressCount%UpdateProgressTarget))
+ {
+ this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget));
+ }
+ }
+ } // Loop on files
+
+ }
}
}
if ((! this->FileNameList.empty()) && this->FileName )
{
- vtkErrorMacro("Both AddFileName and SetFileName schemes were used");
- vtkErrorMacro("No images loaded ! ");
+ vtkErrorMacro(<< "Both AddFileName and SetFileName schemes were used");
+ vtkErrorMacro(<< "No images loaded ! ");
return;
}
if ((! this->FileNameList.empty()) && this->FilePrefix )
{
- vtkErrorMacro("Both AddFileName and SetFilePrefix schemes were used");
- vtkErrorMacro("No images loaded ! ");
+ vtkErrorMacro(<< "Both AddFileName and SetFilePrefix schemes were used");
+ vtkErrorMacro(<< "No images loaded ! ");
return;
}
if (this->FileName && this->FilePrefix)
{
- vtkErrorMacro("Both SetFileName and SetFilePrefix schemes were used");
- vtkErrorMacro("No images loaded ! ");
+ vtkErrorMacro(<< "Both SetFileName and SetFilePrefix schemes were used");
+ vtkErrorMacro(<< "No images loaded ! ");
return;
}
if (! this->FileNameList.empty() )
{
- vtkDebugMacro("Using the AddFileName specified files");
+ vtkDebugMacro(<< "Using the AddFileName specified files");
this->InternalFileNameList=this->FileNameList;
return;
}
if (!this->FileName && !this->FilePrefix)
{
- vtkErrorMacro("FileNames are not set. Either use AddFileName() or");
- vtkErrorMacro("specify a FileName or FilePrefix.");
+ vtkErrorMacro(<< "FileNames are not set. Either use AddFileName() or");
+ vtkErrorMacro(<< "specify a FileName or FilePrefix.");
return;
}
// Single file loading (as given with ::SetFileName()):
// Case of multi-frame file considered here
this->ComputeInternalFileName(this->DataExtent[4]);
- vtkDebugMacro("Adding file " << this->InternalFileName);
+ vtkDebugMacro(<< "Adding file " << this->InternalFileName);
this->AddInternalFileName(this->InternalFileName);
}
else
for (int idx = this->DataExtent[4]; idx <= this->DataExtent[5]; ++idx)
{
this->ComputeInternalFileName(idx);
- vtkDebugMacro("Adding file " << this->InternalFileName);
+ vtkDebugMacro(<< "Adding file " << this->InternalFileName);
this->AddInternalFileName(this->InternalFileName);
}
}
this->BuildFileListFromPattern();
if (this->InternalFileNameList.empty())
{
- vtkErrorMacro("FileNames are not set.");
+ vtkErrorMacro(<< "FileNames are not set.");
return 0;
}
// Loop on the filenames:
// - check for their existence and gdcm "parsability"
// - get the coherence check done:
- for (std::list<std::string>::iterator FileName = InternalFileNameList.begin();
- FileName != InternalFileNameList.end();
- ++FileName)
+ 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
ReturnedTotalNumberOfPlanes += 1;
/////// Stage 0: check for file name:
- if(*FileName==std::string("GDCM_UNREADABLE"))
+
+ // fixme : how can the filename be equal to "GDCM_UNREADABLE"
+ // right now ?!?
+
+ if(*filename == std::string("GDCM_UNREADABLE"))
continue;
/////// Stage 1: check for file readability:
// Stage 1.1: check for file existence.
FILE *fp;
- fp = fopen(FileName->c_str(),"rb");
+ 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());
- *FileName = "GDCM_UNREADABLE";
+ vtkErrorMacro(<< "Unable to open file " << filename->c_str());
+ vtkErrorMacro(<< "Removing this file from read files: "
+ << filename->c_str());
+ *filename = "GDCM_UNREADABLE";
continue;
}
fclose(fp);
// Stage 1.2: check for Gdcm parsability
- gdcmHeader GdcmHeader(FileName->c_str(), false, true);
- // true : for enableSequences
- if (!GdcmHeader.IsReadable())
+
+ // to save some parsing time.
+ gdcm::File GdcmFile;
+ GdcmFile.SetLoadMode( LoadMode );
+ GdcmFile.SetFileName(filename->c_str() );
+ GdcmFile.Load( );
+ if (!GdcmFile.IsReadable())
{
- vtkErrorMacro("Gdcm cannot parse file " << FileName->c_str());
- vtkErrorMacro("Removing this file from readed files "
- << FileName->c_str());
- *FileName = "GDCM_UNREADABLE";
+ vtkErrorMacro(<< "Gdcm cannot parse file " << filename->c_str());
+ 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") )
+ && (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());
- *FileName = "GDCM_UNREADABLE";
+ 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 read 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:
if ( ( NX != this->NumColumns )
- || ( NY != this->NumLines )
- || ( type != this->ImageType ) )
+ || ( NY != this->NumLines )
+ || ( type != this->ImageType ) )
{
- vtkErrorMacro("This file is not coherent with previous ones"
- << FileName->c_str());
- vtkErrorMacro("Removing this file from readed files "
- << FileName->c_str());
- *FileName = "GDCM_UNREADABLE";
+ vtkErrorMacro(<< "This file is not coherent with previous ones: "
+ << filename->c_str());
+ vtkErrorMacro(<< "Removing this file from read 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"
- << FileName->c_str());
+ vtkErrorMacro(<< "File is not coherent in Z with previous ones: "
+ << filename->c_str());
}
else
{
- vtkDebugMacro("File is coherent with previous ones"
- << FileName->c_str());
+ 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)"
- << FileName->c_str());
+ vtkErrorMacro(<< "This file is a 'Multiframe' one: "
+ << filename->c_str());
}
// Eventually, this file can be added on the stack. Update the
}
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);
- vtkDebugMacro("Number of planes added to the stack: " << NZ);
+ vtkDebugMacro(<< "This file taken as coherence 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;
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
+ } // End of loop on filename
///////// The files we CANNOT load are flaged. On debugging purposes
// count the loadable number of files and display their number:
int NumberCoherentFiles = 0;
- for (std::list<std::string>::iterator Filename = InternalFileNameList.begin();
- Filename != InternalFileNameList.end();
- ++Filename)
+ for (std::list<std::string>::iterator it = InternalFileNameList.begin();
+ it != InternalFileNameList.end();
+ ++it)
{
- if (*Filename != "GDCM_UNREADABLE")
- NumberCoherentFiles++;
+ if (*it != "GDCM_UNREADABLE")
+ {
+ NumberCoherentFiles++;
+ }
}
- vtkDebugMacro("Number of coherent files: " << NumberCoherentFiles);
+ vtkDebugMacro(<< "Number of coherent files: " << NumberCoherentFiles);
if (ReturnedTotalNumberOfPlanes == 0)
{
- vtkErrorMacro("No loadable file.");
+ vtkErrorMacro(<< "No loadable file.");
}
- vtkDebugMacro("Total number of planes on the stack: "
+ vtkDebugMacro(<< "Total number of planes on the stack: "
<< ReturnedTotalNumberOfPlanes);
return ReturnedTotalNumberOfPlanes;
/*
* 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;
}
/*
- * Loads the contents of the image/volume contained by Filename at
+ * Loads the contents of the image/volume contained by gdcm::File* f at
* the Dest memory address. Returns the size of the data loaded.
*/
size_t vtkGdcmReader::LoadImageInMemory(
- std::string FileName,
- unsigned char * Dest,
- const unsigned long UpdateProgressTarget,
- unsigned long & UpdateProgressCount)
+ gdcm::File *f,
+ unsigned char *dest,
+ const unsigned long updateProgressTarget,
+ unsigned long &updateProgressCount)
+{
+ // vtkDebugMacro(<< "Copying to memory image [" << f->GetFileName() << "]");
+
+ return DoTheLoadingJob (f,
+ dest,
+ updateProgressTarget,
+ updateProgressCount);
+}
+
+/*
+ * Loads the contents of the image/volume contained by char *fileName at
+ * the dest memory address. Returns the size of the data loaded.
+ */
+size_t vtkGdcmReader::LoadImageInMemory(
+ std::string fileName,
+ unsigned char *dest,
+ const unsigned long updateProgressTarget,
+ unsigned long &updateProgressCount)
+{
+ vtkDebugMacro(<< "Copying to memory image [" << fileName.c_str() << "]");
+
+ gdcm::File *f;
+ f = new gdcm::File();
+ f->SetLoadMode( LoadMode );
+ f->SetFileName( fileName.c_str() );
+ f->Load( );
+
+ return DoTheLoadingJob (f,
+ dest,
+ updateProgressTarget,
+ updateProgressCount);
+ delete f;
+}
+
+/*
+ * Service method for LoadImageInMemory
+*/
+size_t vtkGdcmReader::DoTheLoadingJob (gdcm::File *f,
+ unsigned char *dest,
+ const unsigned long updateProgressTarget,
+ unsigned long &updateProgressCount)
{
- vtkDebugMacro("Copying to memory image [" << FileName.c_str() << "]");
- gdcmFile GdcmFile(FileName.c_str(),false,true);
- // true : to enable SeQuences
+ gdcm::FileHelper *fileH = new gdcm::FileHelper( f );
+ fileH->SetUserFunction( UserFunction );
+
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 = GdcmFile.GetHeader()->GetXSize();
- int NumLines = GdcmFile.GetHeader()->GetYSize();
- int NumPlanes = GdcmFile.GetHeader()->GetZSize();
- int LineSize = NumComponents * NumColumns * GdcmFile.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( GdcmFile.GetHeader()->HasLUT() && this->AllowLookupTable )
+ if( fileH->GetFile()->HasLUT() && AllowLookupTable )
{
- size = GdcmFile.GetImageDataSizeRaw();
- Source = (unsigned char*) GdcmFile.GetImageDataRaw();
- unsigned char *Lut = GdcmFile.GetHeader()->GetLUTRGBA();
+ size = fileH->GetImageDataSize();
+ src = (unsigned char*) fileH->GetImageDataRaw();
+ unsigned char *lut = (unsigned char*) fileH->GetLutRGBA();
- if(!this->LookupTable)
+ 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,
+ (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();
+ vtkDataSetAttributes *a = this->GetOutput()->GetPointData();
a->GetScalars()->SetLookupTable(this->LookupTable);
- free(Lut);
+ free(lut);
}
else
{
- size = GdcmFile.GetImageDataSize();
- Source = (unsigned char*)GdcmFile.GetImageData();
+ size = fileH->GetImageDataSize();
+ src = (unsigned char*)fileH->GetImageData();
}
-
- unsigned char * pSource = Source; //pointer for later deletion
- unsigned char * Destination = Dest + size - LineSize;
- for (int plane = 0; plane < NumPlanes; plane++)
+ unsigned char *dst = dest + planeSize - lineSize;
+ for (int plane = 0; plane < numPlanes; plane++)
{
- for (int line = 0; line < NumLines; line++)
+ 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))
+ if (!(updateProgressCount%updateProgressTarget))
{
- this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget));
+ this->UpdateProgress(updateProgressCount/(50.0*updateProgressTarget));
}
- UpdateProgressCount++;
+ 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);
-
- //GetImageData allocate a (void*)malloc, remove it:
- free(pSource);
+ delete fileH;
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.SetFileName(filename->c_str() );
+ GdcmFile.Load( );
+
+ if (!GdcmFile.IsReadable())
+ {
+ vtkErrorMacro(<< "Gdcm cannot parse file " << filename->c_str());
+ vtkErrorMacro(<< "you should try vtkGdcmReader::CheckFileCoherence "
+ << "instead of 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();
+}
+
+// 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::CheckFileCoherenceAlreadyDone()
+{
+ if ( CoherentFileList->empty() )
+ {
+ vtkErrorMacro(<< "Coherent File List is empty ");
+ return 0;
+ }
+
+ gdcm::File *gdcmFile = (*CoherentFileList)[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.
+ // --> TODO : loop on the File* to get NZ of each one !
+ int NZ = CoherentFileList->size();
+ std::string type = gdcmFile->GetPixelType();
+ //vtkDebugMacro(<< "The first file is taken as reference: "
+ // << (*CoherentFileList)[0]->GetFileName() );
+ 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 NZ;
+}
//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff