-// vtkGdcmReader.cxx
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: vtkGdcmReader.cxx,v $
+ Language: C++
+ Date: $Date: 2005/01/21 11:40:56 $
+ Version: $Revision: 1.66 $
+
+ 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
+// WARNING TODO CLEANME
// Actual limitations of this code:
//
// /////// Redundant and unnecessary 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
+// a vtkGdcmFile) the gdcmFile structure is loaded in memory.
+// The average size of a gdcmFile being of 100Ko, is one
// loads 10 stacks of images with say 200 images each, you
// end-up with a loss of 200Mo...
//
// time...
// //////////////////////////////////////////////////////////////
+#include "gdcmFileHelper.h"
#include "gdcmFile.h"
-#include "gdcmHeaderHelper.h"
#include "vtkGdcmReader.h"
//#include <stdio.h>
#include <vtkPointData.h>
#include <vtkLookupTable.h>
+vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.66 $");
+vtkStandardNewMacro(vtkGdcmReader);
+
//-----------------------------------------------------------------------------
// Constructor / Destructor
vtkGdcmReader::vtkGdcmReader()
{
this->LookupTable = NULL;
+ this->AllowLookupTable = 0;
}
vtkGdcmReader::~vtkGdcmReader()
// Print
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 ;
}
}
// 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();
}
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;
// 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");
+ //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:
{
if (this->InternalFileNameList.empty())
{
- vtkErrorMacro("A least a valid FileName must be specified.");
+ vtkErrorMacro(<< "A least a valid FileName must be specified.");
return;
}
{
// The memory size for a full stack of images of course depends
// on the number of planes and the size of each image:
- size_t StackNumPixels = this->NumColumns * this->NumLines
- * this->TotalNumberOfPlanes * this->NumComponents;
- size_t stack_size = StackNumPixels * this->PixelSize;
+ //size_t StackNumPixels = this->NumColumns * this->NumLines
+ // * this->TotalNumberOfPlanes * this->NumComponents;
+ //size_t stack_size = StackNumPixels * this->PixelSize; //not used
// Allocate pixel data space itself.
// Variables for the UpdateProgress. We shall use 50 steps to signify
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)
+ unsigned char *Dest = (unsigned char *)data->GetScalarPointer();
+ 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")
+ if (*filename != "GDCM_UNREADABLE")
{
// Update progress related for good files is made in LoadImageInMemory
- Dest += this->LoadImageInMemory(*FileName, Dest,
+ Dest += this->LoadImageInMemory(*filename, Dest,
UpdateProgressTarget,
UpdateProgressCount);
}
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->FilePattern )
+ if ((! this->FileNameList.empty()) && this->FilePrefix )
{
- vtkErrorMacro("Both AddFileName and SetFilePattern schemes were used");
- vtkErrorMacro("No images loaded ! ");
+ vtkErrorMacro(<< "Both AddFileName and SetFilePrefix schemes were used");
+ vtkErrorMacro(<< "No images loaded ! ");
return;
}
- if (this->FileName && this->FilePattern)
+ if (this->FileName && this->FilePrefix)
{
- vtkErrorMacro("Both SetFileName and SetFilePattern 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->FilePattern)
+ if (!this->FileName && !this->FilePrefix)
{
- vtkErrorMacro("FileNames are not set. Either use AddFileName() or");
- vtkErrorMacro("specify a FileName or FilePattern.");
+ 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"))
+ 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 readed files "
+ << filename->c_str());
+ *filename = "GDCM_UNREADABLE";
continue;
}
fclose(fp);
// Stage 1.2: check for Gdcm parsability
- gdcmHeaderHelper GdcmHeader(FileName->c_str(), false, true);
- // true : for enableSequences
- if (!GdcmHeader.IsReadable())
+ gdcm::File GdcmFile(filename->c_str() );
+ 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 readed 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 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:
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 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());
+ 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.
if (NZ > 1)
{
- vtkErrorMacro("This file contains multiple planes (images)"
- << FileName->c_str());
+ vtkErrorMacro(<< "This file contains multiple planes (images)"
+ << filename->c_str());
}
// Eventually, this file can be added on the stack. Update the
// 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:"
+ 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(<< "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() )
+ if( GdcmFile.HasLUT() && this->AllowLookupTable )
{
- this->NumComponents = GdcmHeader.GetNumberOfScalarComponentsRaw();
+ // I could raise an error is AllowLookupTable is on and HasLUT() off
+ 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();
+ this->DataSpacing[0] = GdcmFile.GetXSpacing();
+ this->DataSpacing[1] = GdcmFile.GetYSpacing();
+ this->DataSpacing[2] = GdcmFile.GetZSpacing();
//Set image origin
- this->DataOrigin[0] = GdcmHeader.GetXOrigin();
- this->DataOrigin[1] = GdcmHeader.GetYOrigin();
- this->DataOrigin[2] = GdcmHeader.GetZOrigin();
+ //this->DataOrigin[0] = GdcmFile.GetXOrigin();
+ //this->DataOrigin[1] = GdcmFile.GetYOrigin();
+ //this->DataOrigin[2] = GdcmFile.GetZOrigin();
}
- } // 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;
* 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)
+ std::string fileName,
+ 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
+ vtkDebugMacro(<< "Copying to memory image [" << fileName.c_str() << "]");
+ gdcm::FileHelper file( fileName.c_str() );
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 = file.GetFile()->GetXSize();
+ int numLines = file.GetFile()->GetYSize();
+ int numPlanes = file.GetFile()->GetZSize();
+ int lineSize = NumComponents * numColumns * file.GetFile()->GetPixelSize();
+ int planeSize = lineSize * numLines;
- unsigned char * Source;
+ unsigned char *src;
- if( GdcmFile.GetHeader()->HasLUT() )
+ if( file.GetFile()->HasLUT() && AllowLookupTable )
{
- size = GdcmFile.GetImageDataSizeRaw();
- Source = (unsigned char*) GdcmFile.GetImageDataRaw();
- unsigned char *Lut = GdcmFile.GetHeader()->GetLUTRGBA();
+ size = file.GetImageDataSize();
+ src = (unsigned char*) file.GetImageDataRaw();
+ unsigned char *lut = (unsigned char*) file.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 = file.GetImageDataSize();
+ src = (unsigned char*)file.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);
return size;
}
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff