-// vtkGdcmReader.cxx
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: vtkGdcmReader.cxx,v $
+ Language: C++
+ Date: $Date: 2009/04/18 14:42:51 $
+ Version: $Revision: 1.95 $
+
+ 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:
//
-// /////// 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.
+//===> Many users expect from vtkGdcmReader it 'orders' the images
+// (that's the job of GDCM_NAME_SPACE::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 :
//
-// 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...
+// GDCM_NAME_SPACE::SerieHelper *sh= new GDCM_NAME_SPACE::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 'Serie' is of interest
+// // it's up to the user to decide !
+// GDCM_NAME_SPACE::FileList *l = sh->GetFirstSingleSerieUIDFileSet();
+//
+// // 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
+//
+// // WARNING : all that follows works only with 'bona fide' Series
+// // (In some Series; there are more than one 'orientation'
+// // Don't expected to build a 'volume' with that!
+// //
+// // -> use sh->SplitOnOrientation(l)
+// // - or sh->SplitOnPosition(l), or SplitOnTagValue(l, gr, el) -
+// // depending on what you want to do
+// // and iterate on the various 'X Coherent File Sets'
+//
+// // if user *knows* he has to drop the 'duplicates' images
+// // (same Position)
+// sh->SetDropDuplicatePositions(true);
+//
+// // Sorting the list is mandatory
+// // a side effect is to compute ZSpacing for the file set
+// 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_NAME_SPACE::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 :-(
//
-// /////// 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 "gdcmFileHelper.h"
#include "gdcmFile.h"
-#include "gdcmHeaderHelper.h"
+#include "gdcmSerieHelper.h" // for ImagePositionPatientOrdering()
+
#include "vtkGdcmReader.h"
+#include "gdcmDebug.h"
+#include "gdcmCommon.h"
-//#include <stdio.h>
#include <vtkObjectFactory.h>
#include <vtkImageData.h>
#include <vtkPointData.h>
#include <vtkLookupTable.h>
-vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.46 $");
-vtkStandardNewMacro(vtkGdcmReader);
+vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.95 $")
+vtkStandardNewMacro(vtkGdcmReader)
//-----------------------------------------------------------------------------
// Constructor / Destructor
vtkGdcmReader::vtkGdcmReader()
{
this->LookupTable = NULL;
- this->AllowLookupTable = 0;
+ this->AllowLookupTable = false;
+ //this->AllowLightChecking = false;
+ this->LoadMode = GDCM_NAME_SPACE::LD_ALL; // Load everything (possible values :
+ // - LD_NOSEQ,
+ // - LD_NOSHADOW,
+ // - LD_NOSHADOWSEQ)
+ this->CoherentFileList = 0;
+ this->UserFunction = 0;
+
+ this->OwnFile=true;
+ // this->Execution=false; // For VTK5.0
+
+ this->KeepOverlays = false;
+
+ this->FlipY = true; // to keep old behaviour
}
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];
- strcpy(LocalName, name);
- this->FileNameList.push_back(LocalName);
- delete[] LocalName;
+ this->FileNameList.push_back(name);
this->Modified();
}
// 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();
}
*/
void vtkGdcmReader::ExecuteInformation()
{
+// if(this->Execution) // For VTK5.0
+// return;
+//
+// this->Execution=true; // end For VTK5.0
+ this->RemoveAllInternalFile();
if(this->MTime>this->fileTime)
{
- this->TotalNumberOfPlanes = this->CheckFileCoherence();
+ this->TotalNumberOfPlanes = 0;
+
+ if ( this->CoherentFileList != 0 )
+ {
+ this->UpdateFileInformation();
+ }
+ else
+ {
+ this->BuildFileListFromPattern();
+ this->LoadFileInformation();
+ }
+
if ( this->TotalNumberOfPlanes == 0)
{
- vtkErrorMacro("File set is not coherent. Exiting...");
+ vtkErrorMacro(<< "File set is not coherent. Exiting...");
return;
}
-
+
// if the user has not set the extent, but has set the VOI
// set the z axis extent to the VOI z axis
if (this->DataExtent[4]==0 && this->DataExtent[5] == 0 &&
- (this->DataVOI[4] || this->DataVOI[5]))
+ (this->DataVOI[4] || this->DataVOI[5]))
{
this->DataExtent[4] = this->DataVOI[4];
this->DataExtent[5] = this->DataVOI[5];
(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->fileTime=this->MTime;
}
- this->Superclass::ExecuteInformation();
-}
+ this->Superclass::ExecuteInformation();
+ //this->GetOutput()->SetUpdateExtentToWholeExtent();// For VTK5.0
+ //this->BuildData(this->GetOutput());
+
+ //this->Execution=false;
+ //this->RemoveAllInternalFile(); // End For VTK5.0
+}
+
/*
* 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())
+ vtkImageData *data=vtkImageData::SafeDownCast(output);
+ data->SetExtent(this->DataExtent);
+
+/* if ( CoherentFileList != 0 ) // When a list of names is passed
+ {
+ 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;
+ }
+*/
+
+ // data->AllocateScalars(); // For VTK5.0
+ // if (this->UpdateExtentIsEmpty(output))
+ // {
+ // return;
+ // }
+//} // end For VTK5.0
+
+ data->AllocateScalars(); // For VTK5.0
+
+#if (VTK_MAJOR_VERSION >= 5) || ( VTK_MAJOR_VERSION == 4 && VTK_MINOR_VERSION > 2 )
+//#if (VTK_MAJOR_VERSION >= 5)
+ if (this->UpdateExtentIsEmpty(output))
{
- vtkErrorMacro("A least a valid FileName must be specified.");
return;
}
+#endif
- // 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");
// Test if output has valid extent
// 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)
- {
- if (!(UpdateProgressCount%UpdateProgressTarget))
- {
- this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget));
- }
- }
- } // Else, file not loadable
- } // Loop on files
+ // Filling the allocated memory space with each image/volume:
+
+ size_t size = this->NumColumns * this->NumLines * this->NumPlanes
+ * data->GetScalarSize() * this->NumComponents;
+ unsigned char *Dest = (unsigned char *)data->GetScalarPointer();
+ for (std::vector<GDCM_NAME_SPACE::File* >::iterator it = InternalFileList.begin();
+ it != InternalFileList.end();
+ ++it)
+ {
+ this->LoadImageInMemory(*it, Dest,
+ UpdateProgressTarget,
+ UpdateProgressCount);
+ Dest += size;
+ }
}
+ this->RemoveAllInternalFile(); // For VTK5.0
}
/*
{
this->RemoveAllInternalFileName();
+ // Test miscellanous cases
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;
}
+ // Create the InternalFileNameList
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);
}
}
}
-/*
- * When more than one filename is specified (i.e. we expect loading
- * a stack or volume) we need to check that the corresponding images/volumes
- * to be loaded are coherent i.e. to make sure:
- * - they all share the same X dimensions
- * - they all share the same Y dimensions
- * - they all share the same ImageType ( 8 bit signed, or unsigned...)
+/**
+ * Load all the files and set it in the InternalFileList
+ * For each file, the readability and the coherence of image caracteristics
+ * are tested. If an image doesn't agree the required specifications, it
+ * isn't considered and no data will be set for the planes corresponding
+ * to this image
*
- * Eventually, we emit a warning when all the files do NOT share the
- * Z dimension, since we can still build a stack but the
- * files are not coherent in Z, which is probably a source a trouble...
- * When files are not readable (either the file cannot be opened or
- * because gdcm cannot parse it), they are flagged as "GDCM_UNREADABLE".
- * This method returns the total number of planar images to be loaded
- * (i.e. an image represents one plane, but a volume represents many planes)
+ * The source of this work is the list of file name generated by the
+ * BuildFileListFromPattern method
*/
-int vtkGdcmReader::CheckFileCoherence()
+void vtkGdcmReader::LoadFileInformation()
{
- int ReturnedTotalNumberOfPlanes = 0; // The returned value.
-
- this->BuildFileListFromPattern();
- if (this->InternalFileNameList.empty())
+ GDCM_NAME_SPACE::File *file;
+ bool foundReference=false;
+ std::string type;
+
+ this->OwnFile=true;
+ for (std::list<std::string>::iterator filename = InternalFileNameList.begin();
+ filename != InternalFileNameList.end();
+ ++filename)
{
- vtkErrorMacro("FileNames are not set.");
- return 0;
- }
-
- bool FoundReferenceFile = false;
- int ReferenceNZ = 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)
- {
- // 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
- // ExecuteData method
- // - If file has more than 1 plane, other planes will be added later to
- // to the ReturnedTotalNumberOfPlanes variable counter
- ReturnedTotalNumberOfPlanes += 1;
-
- /////// Stage 0: check for file name:
- if(*FileName==std::string("GDCM_UNREADABLE"))
- continue;
-
- /////// Stage 1: check for file readability:
- // Stage 1.1: check for file existence.
+ // check for file readability
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());
+ file = NULL;
+ InternalFileList.push_back(file);
continue;
}
fclose(fp);
- // Stage 1.2: check for Gdcm parsability
- gdcmHeader GdcmHeader(FileName->c_str(), false, true);
- // true : for enableSequences
- if (!GdcmHeader.IsReadable())
+ // Read the file
+ file=GDCM_NAME_SPACE::File::New();
+ file->SetLoadMode( LoadMode );
+ file->SetFileName(filename->c_str() );
+ file->Load();
+
+ // Test the Dicom file readability
+ if(!file->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());
+ file->Delete();
+ file=NULL;
+ InternalFileList.push_back(file);
continue;
}
- // Stage 1.3: further gdcm compatibility on PixelType
- std::string type = GdcmHeader.GetPixelType();
+ // Test the Pixel Type recognition
+ type = file->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");
+ file->Delete();
+ file=NULL;
+ InternalFileList.push_back(file);
continue;
}
- // Stage 2: check coherence of the set of files
- int NX = GdcmHeader.GetXSize();
- int NY = GdcmHeader.GetYSize();
- int NZ = GdcmHeader.GetZSize();
- if (FoundReferenceFile)
+ // Test the image informations
+ if(!foundReference)
{
- // Stage 2.1: mandatory coherence stage:
- if ( ( NX != this->NumColumns )
- || ( 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";
- continue;
- }
-
- // Stage 2.2: optional coherence stage
- if ( NZ != ReferenceNZ )
- {
- vtkErrorMacro("File is not coherent in Z with previous ones"
- << FileName->c_str());
- }
- else
- {
- vtkDebugMacro("File is coherent with previous ones"
- << FileName->c_str());
- }
+ foundReference = true;
+ GetFileInformation(file);
+
+ vtkDebugMacro(<< "This file taken as coherence reference:"
+ << filename->c_str());
+ vtkDebugMacro(<< "Image dimensions of reference file as read from Gdcm:"
+ << this->NumColumns << " " << this->NumLines << " "
+ << this->NumPlanes);
+ }
+ else if(!TestFileInformation(file))
+ {
+ file->Delete();
+ file=NULL;
+ }
- // Stage 2.3: when the file contains a volume (as opposed to an image),
- // notify the caller.
- if (NZ > 1)
- {
- vtkErrorMacro("This file contains multiple planes (images)"
- << FileName->c_str());
- }
+ InternalFileList.push_back(file);
+ }
+}
- // Eventually, this file can be added on the stack. Update the
- // full size of the stack
- vtkDebugMacro("Number of planes added to the stack: " << NZ);
- ReturnedTotalNumberOfPlanes += NZ - 1; // First plane already added
- continue;
+/**
+ * Update the file informations.
+ * This works exactly like LoadFileInformation, but the source of work
+ * is the list of coherent files
+ */
+void vtkGdcmReader::UpdateFileInformation()
+{
+ this->InternalFileList=*(this->CoherentFileList);
+ this->OwnFile=false;
- }
- else
+ for(gdcmFileList::iterator it=InternalFileList.begin();
+ it!=InternalFileList.end();
+ ++it)
+ {
+ if( *it != NULL)
{
- // 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);
- // 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();
-
- if( GdcmHeader.HasLUT() && this->AllowLookupTable )
- {
- // I could raise an error is AllowLookupTable is on and HasLUT() off
- this->NumComponents = GdcmHeader.GetNumberOfScalarComponentsRaw();
- }
- else
- {
- this->NumComponents = GdcmHeader.GetNumberOfScalarComponents(); //rgb or mono
- }
-
- //Set image spacing
- this->DataSpacing[0] = GdcmHeader.GetXSpacing();
- this->DataSpacing[1] = GdcmHeader.GetYSpacing();
- this->DataSpacing[2] = GdcmHeader.GetZSpacing();
+ GetFileInformation(*it);
+ break;
+ }
+ }
+}
- //Set image origin
- this->DataOrigin[0] = GdcmHeader.GetXOrigin();
- this->DataOrigin[1] = GdcmHeader.GetYOrigin();
- this->DataOrigin[2] = GdcmHeader.GetZOrigin();
+/**
+ * Get the informations from a file.
+ * These informations are required to specify the output image
+ * caracteristics
+ */
+void vtkGdcmReader::GetFileInformation(GDCM_NAME_SPACE::File *file)
+{
+ // Get the image caracteristics
+ this->NumColumns = file->GetXSize();
+ this->NumLines = file->GetYSize();
+ this->NumPlanes = file->GetZSize();
- }
- } // 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)
+ if (CoherentFileList == 0)
+ this->TotalNumberOfPlanes = this->NumPlanes*InternalFileNameList.size();
+ else
+ this->TotalNumberOfPlanes = this->NumPlanes*CoherentFileList->size();
+
+ this->ImageType = file->GetPixelType();
+ this->PixelSize = file->GetPixelSize();
+
+ this->DataSpacing[0] = file->GetXSpacing();
+ this->DataSpacing[1] = file->GetYSpacing();
+
+ // Most of the file headers have NO z spacing
+ // It must be calculated from the whole GDCM_NAME_SPACE::Serie (if any)
+ // using Jolinda Smith's algoritm.
+ // see GDCM_NAME_SPACE::SerieHelper::ImagePositionPatientOrdering()
+ if (CoherentFileList == 0)
+ this->DataSpacing[2] = file->GetZSpacing();
+ else
+ {
+ // Just because OrderFileList() is a member of GDCM_NAME_SPACE::SerieHelper
+ // we need to instanciate sh.
+ GDCM_NAME_SPACE::SerieHelper *sh = GDCM_NAME_SPACE::SerieHelper::New();
+ sh->OrderFileList(CoherentFileList); // calls ImagePositionPatientOrdering()
+ this->DataSpacing[2] = sh->GetZSpacing();
+ sh->Delete();
+ }
+
+ // Get the image data caracteristics
+ if( file->HasLUT() && this->AllowLookupTable )
{
- if (*Filename != "GDCM_UNREADABLE")
- NumberCoherentFiles++;
+ // I could raise an error is AllowLookupTable is on and HasLUT() off
+ this->NumComponents = file->GetNumberOfScalarComponentsRaw();
}
- vtkDebugMacro("Number of coherent files: " << NumberCoherentFiles);
+ else
+ {
+ this->NumComponents = file->GetNumberOfScalarComponents(); //rgb or mono
+ }
+}
+
+/*
+ * When more than one filename is specified (i.e. we expect loading
+ * a stack or volume) we need to check that the corresponding images/volumes
+ * to be loaded are coherent i.e. to make sure:
+ * - they all share the same X dimensions
+ * - they all share the same Y dimensions
+ * - they all share the same ImageType ( 8 bit signed, or unsigned...)
+ *
+ * Eventually, we emit a warning when all the files do NOT share the
+ * Z dimension, since we can still build a stack but the
+ * files are not coherent in Z, which is probably a source a trouble...
+ * When files are not readable (either the file cannot be opened or
+ * because gdcm cannot parse it), they are flagged as "GDCM_UNREADABLE".
+ * This method returns the total number of planar images to be loaded
+ * (i.e. an image represents one plane, but a volume represents many planes)
+ */
+/**
+ * Test the coherent informations of the file with the reference informations
+ * used as image caracteristics. The tested informations are :
+ * - they all share the same X dimensions
+ * - they all share the same Y dimensions
+ * - they all share the same Z dimensions
+ * - they all share the same number of components
+ * - they all share the same ImageType ( 8 bit signed, or unsigned...)
+ *
+ * \return True if the file match, False otherwise
+ */
+bool vtkGdcmReader::TestFileInformation(GDCM_NAME_SPACE::File *file)
+{
+ int numColumns = file->GetXSize();
+ int numLines = file->GetYSize();
+ int numPlanes = file->GetZSize();
+ int numComponents;
+ unsigned int pixelSize = file->GetPixelSize();
+
+ if( file->HasLUT() && this->AllowLookupTable )
+ numComponents = file->GetNumberOfScalarComponentsRaw();
+ else
+ numComponents = file->GetNumberOfScalarComponents(); //rgb or mono
- if (ReturnedTotalNumberOfPlanes == 0)
+ if( numColumns != this->NumColumns )
+ {
+ vtkErrorMacro(<< "File X value doesn't match with the previous ones: "
+ << file->GetFileName().c_str()
+ << ". Found " << numColumns << ", must be "
+ << this->NumColumns);
+ return false;
+ }
+ if( numLines != this->NumLines )
+ {
+ vtkErrorMacro(<< "File Y value doesn't match with the previous ones: "
+ << file->GetFileName().c_str()
+ << ". Found " << numLines << ", must be "
+ << this->NumLines);
+ return false;
+ }
+ if( numPlanes != this->NumPlanes )
+ {
+ vtkErrorMacro(<< "File Z value doesn't match with the previous ones: "
+ << file->GetFileName().c_str()
+ << ". Found " << numPlanes << ", must be "
+ << this->NumPlanes);
+ return false;
+ }
+ if( numComponents != this->NumComponents )
{
- vtkErrorMacro("No loadable file.");
+ vtkErrorMacro(<< "File Components count doesn't match with the previous ones: "
+ << file->GetFileName().c_str()
+ << ". Found " << numComponents << ", must be "
+ << this->NumComponents);
+ return false;
+ }
+ if( pixelSize != this->PixelSize )
+ {
+ vtkErrorMacro(<< "File pixel size doesn't match with the previous ones: "
+ << file->GetFileName().c_str()
+ << ". Found " << pixelSize << ", must be "
+ << this->PixelSize);
+ return false;
}
- vtkDebugMacro("Total number of planes on the stack: "
- << ReturnedTotalNumberOfPlanes);
-
- return ReturnedTotalNumberOfPlanes;
+ return true;
}
//-----------------------------------------------------------------------------
/*
* 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
+ * Remove all file names to the internal list of images to read.
+ */
+void vtkGdcmReader::RemoveAllInternalFile(void)
+{
+ if(this->OwnFile)
+ {
+ for(gdcmFileList::iterator it=InternalFileList.begin();
+ it!=InternalFileList.end();
+ ++it)
+ {
+ (*it)->Delete();
+ }
+ }
+ this->InternalFileList.clear();
+}
+
+void vtkGdcmReader::IncrementProgress(const unsigned long updateProgressTarget,
+ unsigned long &updateProgressCount)
+{
+ // Update progress related for bad files:
+ updateProgressCount += this->NumLines;
+ if (updateProgressTarget > 0)
+ {
+ if (!(updateProgressCount%updateProgressTarget))
+ {
+ this->UpdateProgress(
+ updateProgressCount/(50.0*updateProgressTarget));
+ }
+ }
+}
+
+/*
+ * Loads the contents of the image/volume contained by char *fileName at
+ * the dest memory address. Returns the size of the data loaded.
+ */
+/*void vtkGdcmReader::LoadImageInMemory(
+ std::string fileName,
+ unsigned char *dest,
+ const unsigned long updateProgressTarget,
+ unsigned long &updateProgressCount)
+{
+ vtkDebugMacro(<< "Copying to memory image [" << fileName.c_str() << "]");
+
+ GDCM_NAME_SPACE::File *f;
+ f = new GDCM_NAME_SPACE::File();
+ f->SetLoadMode( LoadMode );
+ f->SetFileName( fileName.c_str() );
+ f->Load( );
+
+ LoadImageInMemory(f,dest,
+ updateProgressTarget,
+ updateProgressCount);
+ delete f;
+}*/
+
+/*
+ * Loads the contents of the image/volume contained by GDCM_NAME_SPACE::File* f at
* the Dest memory address. Returns the size of the data loaded.
+ * \ param f File to consider. NULL if the file must be skiped
+ * \remarks Assume that if (f != NULL) then its caracteristics match
+ * with the previous ones
*/
-size_t vtkGdcmReader::LoadImageInMemory(
- std::string FileName,
- unsigned char * Dest,
- const unsigned long UpdateProgressTarget,
- unsigned long & UpdateProgressCount)
+void vtkGdcmReader::LoadImageInMemory(
+ GDCM_NAME_SPACE::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
- size_t size;
+ if(!f)
+ return;
+
+ GDCM_NAME_SPACE::FileHelper *fileH = GDCM_NAME_SPACE::FileHelper::New( f );
+ fileH->SetUserFunction( UserFunction );
+
+ fileH->SetKeepOverlays ( this->KeepOverlays);
+
+ int numColumns = f->GetXSize();
+ int numLines = f->GetYSize();
+ int numPlanes = f->GetZSize();
+ int numComponents;
+
+ if( f->HasLUT() && this->AllowLookupTable )
+ numComponents = f->GetNumberOfScalarComponentsRaw();
+ else
+ numComponents = f->GetNumberOfScalarComponents(); //rgb or mono
+ vtkDebugMacro(<< "numComponents:" << numComponents);
+ vtkDebugMacro(<< "Copying to memory image [" << f->GetFileName().c_str() << "]");
+ //size_t size;
// If the data structure of vtk for image/volume representation
// were straigthforwards the following would be enough:
// 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 lineSize = NumComponents * numColumns * f->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();
+ // to avoid bcc 5.5 w
+ /*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);
+ delete[] lut;
}
else
{
- size = GdcmFile.GetImageDataSize();
- Source = (unsigned char*)GdcmFile.GetImageData();
+ //size = fileH->GetImageDataSize();
+ // useless - just an accessor; 'size' unused
+ //if (this->GetFlipY())
+ src = (unsigned char*)fileH->GetImageData();
+ //else
+ // dest = (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++)
+
+if (this->GetFlipY()) {
+ 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:
- delete[] pSource;
- return size;
+}
+else
+{
+ memcpy((void*)dest, (void*)src, numPlanes * numLines * lineSize);
+}
+ fileH->Delete();
}
//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff