// vtkGdcmReader.cxx
//-----------------------------------------------------------------------------
// //////////////////////////////////////////////////////////////
-// WARNING TODO CLENAME
+// WARNING TODO CLEANME
// Actual limitations of this code:
//
// /////// Redundant and unnecessary header parsing
// 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.
#include <vtkPointData.h>
#include <vtkLookupTable.h>
+vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.53 $");
+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 ;
}
}
void vtkGdcmReader::RemoveAllFileName(void)
{
this->FileNameList.clear();
+ this->Modified();
}
/*
char * LocalName = new char[strlen(name) + 1];
strcpy(LocalName, name);
this->FileNameList.push_back(LocalName);
- this->Modified();
delete[] LocalName;
+ 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");
this->FileNameList.clear();
this->Modified();
}
*/
void vtkGdcmReader::ExecuteInformation()
{
- this->TotalNumberOfPlanes = this->CheckFileCoherence();
- if ( this->TotalNumberOfPlanes == 0)
+ if(this->MTime>this->fileTime)
{
- vtkErrorMacro("File set is not coherent. Exiting...");
- return;
- }
+ this->TotalNumberOfPlanes = this->CheckFileCoherence();
+ if ( this->TotalNumberOfPlanes == 0)
+ {
+ 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->DataExtent[4] = this->DataVOI[4];
- this->DataExtent[5] = this->DataVOI[5];
- }
-
- // When the user has set the VOI, check it's coherence with the file content.
- if (this->DataVOI[0] || this->DataVOI[1] ||
- this->DataVOI[2] || this->DataVOI[3] ||
- this->DataVOI[4] || this->DataVOI[5])
- {
- if ((this->DataVOI[0] < 0) ||
- (this->DataVOI[1] >= this->NumColumns) ||
- (this->DataVOI[2] < 0) ||
- (this->DataVOI[3] >= this->NumLines) ||
- (this->DataVOI[4] < 0) ||
- (this->DataVOI[5] >= this->TotalNumberOfPlanes ))
+ // 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]))
{
- vtkWarningMacro("The requested VOI is larger than expected extent.");
- this->DataVOI[0] = 0;
- this->DataVOI[1] = this->NumColumns - 1;
- this->DataVOI[2] = 0;
- this->DataVOI[3] = this->NumLines - 1;
- this->DataVOI[4] = 0;
- this->DataVOI[5] = this->TotalNumberOfPlanes - 1;
+ this->DataExtent[4] = this->DataVOI[4];
+ this->DataExtent[5] = this->DataVOI[5];
+ }
+
+ // When the user has set the VOI, check it's coherence with the file content.
+ if (this->DataVOI[0] || this->DataVOI[1] ||
+ this->DataVOI[2] || this->DataVOI[3] ||
+ this->DataVOI[4] || this->DataVOI[5])
+ {
+ if ((this->DataVOI[0] < 0) ||
+ (this->DataVOI[1] >= this->NumColumns) ||
+ (this->DataVOI[2] < 0) ||
+ (this->DataVOI[3] >= this->NumLines) ||
+ (this->DataVOI[4] < 0) ||
+ (this->DataVOI[5] >= this->TotalNumberOfPlanes ))
+ {
+ vtkWarningMacro("The requested VOI is larger than expected extent.");
+ this->DataVOI[0] = 0;
+ this->DataVOI[1] = this->NumColumns - 1;
+ this->DataVOI[2] = 0;
+ this->DataVOI[3] = this->NumLines - 1;
+ this->DataVOI[4] = 0;
+ this->DataVOI[5] = this->TotalNumberOfPlanes - 1;
+ }
}
- }
- // Positionate the Extent.
- this->DataExtent[0] = 0;
- this->DataExtent[1] = this->NumColumns - 1;
- this->DataExtent[2] = 0;
- this->DataExtent[3] = this->NumLines - 1;
- this->DataExtent[4] = 0;
- this->DataExtent[5] = this->TotalNumberOfPlanes - 1;
+ // Positionate the Extent.
+ this->DataExtent[0] = 0;
+ this->DataExtent[1] = this->NumColumns - 1;
+ this->DataExtent[2] = 0;
+ this->DataExtent[3] = this->NumLines - 1;
+ this->DataExtent[4] = 0;
+ this->DataExtent[5] = this->TotalNumberOfPlanes - 1;
- // We don't need to positionate 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");
- this->SetDataScalarTypeToUnsignedChar();
- }
- else if ( ImageType == "8S" )
- {
- vtkErrorMacro("Cannot handle 8 bit signed files");
- return;
- }
- else if ( ImageType == "16U" )
- {
- vtkDebugMacro("16 bits unsigned image");
- this->SetDataScalarTypeToUnsignedShort();
- }
- else if ( ImageType == "16S" )
- {
- 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 !");
- this->SetDataScalarTypeToInt();
- }
- else if ( ImageType == "32S" )
- {
- vtkDebugMacro("32 bits signed image");
- this->SetDataScalarTypeToInt();
- }
- else if ( ImageType == "FD" )
- {
- vtkDebugMacro("64 bits Double image");
- this->SetDataScalarTypeToDouble();
+ // We don't need to positionate 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");
+ this->SetDataScalarTypeToUnsignedChar();
+ }
+ else if ( ImageType == "8S" )
+ {
+ vtkErrorMacro("Cannot handle 8 bit signed files");
+ return;
+ }
+ else if ( ImageType == "16U" )
+ {
+ vtkDebugMacro("16 bits unsigned image");
+ this->SetDataScalarTypeToUnsignedShort();
+ }
+ else if ( ImageType == "16S" )
+ {
+ 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 !");
+ this->SetDataScalarTypeToInt();
+ }
+ else if ( ImageType == "32S" )
+ {
+ vtkDebugMacro("32 bits signed image");
+ this->SetDataScalarTypeToInt();
+ }
+ else if ( ImageType == "FD" )
+ {
+ vtkDebugMacro("64 bits Double image");
+ this->SetDataScalarTypeToDouble();
+ }
+ //Set number of scalar components:
+ this->SetNumberOfScalarComponents(this->NumComponents);
+
+ this->fileTime=this->MTime;
}
- //Set number of scalar components:
- this->SetNumberOfScalarComponents(this->NumComponents);
this->Superclass::ExecuteInformation();
}
{
// 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
// 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)
+ 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);
}
*/
void vtkGdcmReader::BuildFileListFromPattern()
{
+ this->RemoveAllInternalFileName();
+
if ((! this->FileNameList.empty()) && this->FileName )
{
- vtkErrorMacro("Both file patterns and AddFileName schemes were used");
- vtkErrorMacro("Only the files specified with AddFileName shall be used");
+ 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 ! ");
+ return;
+ }
+
+ if (this->FileName && this->FilePrefix)
+ {
+ vtkErrorMacro("Both SetFileName and SetFilePrefix schemes were used");
+ vtkErrorMacro("No images loaded ! ");
return;
}
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("specify a FileName or FilePrefix.");
return;
}
- this->RemoveAllInternalFileName();
- if( this->FileNameList.empty() )
+ if( this->FileName )
{
- //Multiframe case:
+ // Single file loading (as given with ::SetFileName()):
+ // Case of multi-frame file considered here
this->ComputeInternalFileName(this->DataExtent[4]);
vtkDebugMacro("Adding file " << this->InternalFileName);
this->AddInternalFileName(this->InternalFileName);
}
else
{
- //stack of 2D dicom case:
+ // Multi file loading (as given with ::SetFilePattern()):
for (int idx = this->DataExtent[4]; idx <= this->DataExtent[5]; ++idx)
{
this->ComputeInternalFileName(idx);
// 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("Unable to open file " << filename->c_str());
vtkErrorMacro("Removing this file from readed files "
- << FileName->c_str());
- *FileName = "GDCM_UNREADABLE";
+ << filename->c_str());
+ *filename = "GDCM_UNREADABLE";
continue;
}
fclose(fp);
-
+
// Stage 1.2: check for Gdcm parsability
- gdcmHeaderHelper GdcmHeader(FileName->c_str());
+ gdcm::Header GdcmHeader(filename->c_str() );
if (!GdcmHeader.IsReadable())
{
- vtkErrorMacro("Gdcm cannot parse file " << FileName->c_str());
+ vtkErrorMacro("Gdcm cannot parse file " << filename->c_str());
vtkErrorMacro("Removing this file from readed files "
- << FileName->c_str());
- *FileName = "GDCM_UNREADABLE";
+ << filename->c_str());
+ *filename = "GDCM_UNREADABLE";
continue;
}
// Stage 1.3: further gdcm compatibility on PixelType
std::string type = GdcmHeader.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("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";
+ << filename->c_str());
+ *filename = "GDCM_UNREADABLE";
continue;
}
{
// 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());
+ << filename->c_str());
vtkErrorMacro("Removing this file from readed files "
- << FileName->c_str());
- *FileName = "GDCM_UNREADABLE";
+ << filename->c_str());
+ *filename = "GDCM_UNREADABLE";
continue;
}
if ( NZ != ReferenceNZ )
{
vtkErrorMacro("File is not coherent in Z with previous ones"
- << FileName->c_str());
+ << filename->c_str());
}
else
{
vtkDebugMacro("File is coherent with previous ones"
- << FileName->c_str());
+ << filename->c_str());
}
// Stage 2.3: when the file contains a volume (as opposed to an image),
if (NZ > 1)
{
vtkErrorMacro("This file contains multiple planes (images)"
- << FileName->c_str());
+ << filename->c_str());
}
// Eventually, this file can be added on the stack. Update the
// as the reference.
FoundReferenceFile = true;
vtkDebugMacro("This file taken as coherence reference:"
- << FileName->c_str());
+ << 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);
this->ImageType = type;
this->PixelSize = GdcmHeader.GetPixelSize();
- if( GdcmHeader.HasLUT() )
+ if( GdcmHeader.HasLUT() && this->AllowLookupTable )
{
+ // I could raise an error is AllowLookupTable is on and HasLUT() off
this->NumComponents = GdcmHeader.GetNumberOfScalarComponentsRaw();
}
else
this->DataOrigin[2] = GdcmHeader.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);
* 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());
+ vtkDebugMacro("Copying to memory image [" << fileName.c_str() << "]");
+ gdcm::File file( fileName.c_str() );
size_t size;
// If the data structure of vtk for image/volume representation
- // were straigthforwards the following would suffice:
+ // were straigthforwards the following would be enough:
// GdcmFile.GetImageDataIntoVector((void*)Dest, size);
// But vtk chooses to invert the lines of an image, that is the last
// 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.GetHeader()->GetXSize();
+ int numLines = file.GetHeader()->GetYSize();
+ int numPlanes = file.GetHeader()->GetZSize();
+ int lineSize = NumComponents * numColumns * file.GetHeader()->GetPixelSize();
- unsigned char * Source;
- if( GdcmFile.GetHeader()->HasLUT() )
+ unsigned char * source;
+
+ if( file.GetHeader()->HasLUT() && AllowLookupTable )
{
- size = GdcmFile.GetImageDataSizeRaw();
- Source = (unsigned char*) GdcmFile.GetImageDataRaw();
- unsigned char *Lut = GdcmFile.GetHeader()->GetLUTRGBA();
+ size = file.GetImageDataSizeRaw();
+ source = (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();
- }
- unsigned char * pSource = Source; //pointer for later deletion
- unsigned char * Destination = Dest + size - LineSize;
+ size = file.GetImageDataSize();
+ source = (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++)
+ 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*)destination, (void*)source, lineSize);
+ source += lineSize;
+ destination -= lineSize;
// Update progress related:
- if (!(UpdateProgressCount%UpdateProgressTarget))
+ if (!(updateProgressCount%updateProgressTarget))
{
- this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget));
+ this->UpdateProgress(updateProgressCount/(50.0*updateProgressTarget));
}
- UpdateProgressCount++;
+ updateProgressCount++;
}
}
+
+// 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);
+ // CLEANME
+ // Now, the delete on values keep from GetImageData is useless (made in
+ // the PixelConvert class)
+ //delete[] pSource;
return size;
}
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff