-// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.8 2003/06/02 07:42:17 regrain Exp $
-//CLEANME#include <vtkByteSwap.h>
+// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.25 2003/11/05 18:15:41 malaterre Exp $
+// //////////////////////////////////////////////////////////////
+// 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
+// 2b/ the core of ExecuteData then needs gdcmFile (which in turns
+// initialises gdcmHeader 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.
+// - 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...
+//
+// /////// 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 <stdio.h>
#include <vtkObjectFactory.h>
#include <vtkImageData.h>
#include <vtkPointData.h>
+#include <vtkLookupTable.h>
#include "vtkGdcmReader.h"
#include "gdcm.h"
+#include "gdcmHeaderHelper.h"
vtkGdcmReader::vtkGdcmReader()
{
// Constructor
+ this->LookupTable = vtkLookupTable::New();
}
//----------------------------------------------------------------------------
vtkGdcmReader::~vtkGdcmReader()
{
- // FIXME free memory
+ this->RemoveAllFileName();
+ this->InternalFileNameList.clear();
+ this->LookupTable->Delete();
+}
+
+//----------------------------------------------------------------------------
+// Remove all files from the list of images to read.
+void vtkGdcmReader::RemoveAllFileName(void)
+{
+ this->FileNameList.clear();
}
//----------------------------------------------------------------------------
// Adds a file name to the list of images to read.
void vtkGdcmReader::AddFileName(const char* name)
{
- // 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);
- // Starting from two files we have a stack of images:
- if(this->FileNameList.size() >= 2)
- this->SetFileDimensionality(3);
+ // 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);
this->Modified();
+ delete[] LocalName;
}
//----------------------------------------------------------------------------
// Sets up a filename to be read.
void vtkGdcmReader::SetFileName(const char *name) {
- vtkImageReader2::SetFileName(name);
- // Since we maintain a list of filenames (when building a volume)
- // we additionaly need to maintain this list. First we clean-up the
- // list and then positionate the incoming filename:
- this->FileNameList.empty();
- this->AddFileName(name);
+ vtkImageReader2::SetFileName(name);
+ // 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.
+ this->FileNameList.clear();
+ this->Modified();
+}
+
+//----------------------------------------------------------------------------
+// Adds a file name to the internal list of images to read.
+void vtkGdcmReader::RemoveAllInternalFileName(void)
+{
+ this->InternalFileNameList.clear();
+}
+
+//----------------------------------------------------------------------------
+// Adds a file name to the internal list of images to read.
+void vtkGdcmReader::AddInternalFileName(const char* name)
+{
+ char * LocalName = new char[strlen(name) + 1];
+ strcpy(LocalName, name);
+ this->InternalFileNameList.push_back(LocalName);
+ delete[] LocalName;
}
//----------------------------------------------------------------------------
// vtkGdcmReader can have the file names specified through two ways:
// (1) by calling the vtkImageReader2::SetFileName(), SetFilePrefix() and
// SetFilePattern()
-// (2) By successive calls to vtkGdcmReader::SetFileName()
+// (2) By successive calls to vtkGdcmReader::AddFileName()
// When the first method was used by caller we need to update the local
// filename list
-void vtkGdcmReader::BuilFileListFromPattern()
+void vtkGdcmReader::BuildFileListFromPattern()
{
- if (! this->FileNameList.empty())
- return;
+ 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");
+ return;
+ }
+
+ if (! this->FileNameList.empty() )
+ {
+ vtkDebugMacro("Using the AddFileName specified files");
+ this->InternalFileNameList=this->FileNameList;
+ return;
+ }
+
if (!this->FileName && !this->FilePattern)
{
vtkErrorMacro("FileNames are not set. Either use AddFileName() or");
vtkErrorMacro("specify a FileName or FilePattern.");
return;
}
- for (int idx = this->DataExtent[4]; idx <= this->DataExtent[5]; ++idx)
+
+ this->RemoveAllInternalFileName();
+ if( this->FileNameList.empty() )
{
- this->ComputeInternalFileName(idx);
+ //Multiframe case:
+ this->ComputeInternalFileName(this->DataExtent[4]);
vtkDebugMacro("Adding file " << this->InternalFileName);
- this->AddFileName(this->InternalFileName);
+ this->AddInternalFileName(this->InternalFileName);
}
+ else
+ {
+ //stack of 2D dicom case:
+ for (int idx = this->DataExtent[4]; idx <= this->DataExtent[5]; ++idx)
+ {
+ this->ComputeInternalFileName(idx);
+ 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 the corresponding images are
-// coherent:
-// - they all share the same X dimensions
-// - they all share the same Y dimensions
-// - each file a Z dimension of 1
-// - they all share the same type ( 8 bit signed, or unsigned...)
-bool vtkGdcmReader::CheckFileCoherence()
+// 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)
+int vtkGdcmReader::CheckFileCoherence()
{
- this->BuilFileListFromPattern();
- if (this->FileNameList.empty())
+ int ReturnedTotalNumberOfPlanes = 0; // The returned value.
+
+ this->BuildFileListFromPattern();
+ if (this->InternalFileNameList.empty())
{
vtkErrorMacro("FileNames are not set.");
- return false;
- }
- if (this->FileNameList.size() == 1)
- {
- vtkDebugMacro("Single file specified.");
- return true;
+ return 0;
}
+ bool FoundReferenceFile = false;
+ int ReferenceNZ = 0;
+
// Loop on the filenames:
- // - check for their existence and gdcm "parasability"
+ // - check for their existence and gdcm "parsability"
// - get the coherence check done:
- bool FoundReferenceFile = false;
- int ReferenceNX;
- int ReferenceNY;
- int ReferenceNZ;
- std::string ReferenceType;
- for (std::list<std::string>::iterator FileName = FileNameList.begin();
- FileName != FileNameList.end();
+ for (std::list<std::string>::iterator FileName = InternalFileNameList.begin();
+ FileName != InternalFileNameList.end();
++FileName)
{
- // Check for file existence.
+ // 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.
FILE *fp;
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());
- FileNameList.remove(*FileName);
+ vtkErrorMacro("Unable to open file " << FileName->c_str());
+ vtkErrorMacro("Removing this file from readed files "
+ << FileName->c_str());
+ *FileName = "GDCM_UNREADABLE";
continue;
}
fclose(fp);
- // Check for Gdcm parsability
- gdcmHeader GdcmHeader(FileName->c_str());
+ // Stage 1.2: check for Gdcm parsability
+ gdcmHeaderHelper GdcmHeader(FileName->c_str());
if (!GdcmHeader.IsReadable())
{
- vtkErrorMacro("Gdcm cannot parse file " << *FileName->c_str());
- vtkErrorMacro("Removing this file from readed files " << *FileName->c_str());
- FileNameList.remove(*FileName);
+ 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();
+ if ( (type != "8U") && (type != "8S")
+ && (type != "16U") && (type != "16S")
+ && (type != "32U") && (type != "32S") )
+ {
+ vtkErrorMacro("Bad File Type for file" << FileName->c_str());
+ vtkErrorMacro(" " << type.c_str());
+ vtkErrorMacro("Removing this file from readed files "
+ << FileName->c_str());
+ *FileName = "GDCM_UNREADABLE";
continue;
}
- // Coherence stage:
+ /////// Stage 2: check coherence of the set of files
int NX = GdcmHeader.GetXSize();
int NY = GdcmHeader.GetYSize();
int NZ = GdcmHeader.GetZSize();
- std::string type = GdcmHeader.GetPixelType();
if (FoundReferenceFile)
{
- if ( ( NX != ReferenceNX )
- || ( NY != ReferenceNY )
- || ( NZ != ReferenceNZ )
- || ( type != ReferenceType ) )
+
+ // 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());
- FileNameList.remove(*FileName);
- continue;
- } else {
- vtkDebugMacro("File is coherent with previous ones" << *FileName->c_str());
+ 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());
+ }
+
+ // 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());
+ }
+
+ // 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;
+
} else {
- // This file shall be the reference:
- FoundReferenceFile = true;
- ReferenceNX = NX;
- ReferenceNY = NY;
- ReferenceNZ = NZ;
- ReferenceType = type;
- vtkDebugMacro("This file taken as coherence reference:" << *FileName->c_str());
+ // 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->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();
+
+ //Set image origin
+ this->DataOrigin[0] = GdcmHeader.GetXOrigin();
+ this->DataOrigin[1] = GdcmHeader.GetYOrigin();
+ this->DataOrigin[2] = GdcmHeader.GetZOrigin();
+
}
} // End of loop on FileName
- if (this->FileNameList.empty())
+ ///////// 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)
{
- vtkDebugMacro("No gdcm parsable file.");
- return false;
+ if (*Filename != "GDCM_UNREADABLE")
+ NumberCoherentFiles++;
}
- if (this->FileNameList.size() == 1)
+ vtkDebugMacro("Number of coherent files: " << NumberCoherentFiles);
+
+ if (ReturnedTotalNumberOfPlanes == 0)
{
- vtkDebugMacro("Single parsable file left after coherence test.");
- return true;
+ vtkErrorMacro("No loadable file.");
}
- return true;
+
+ vtkDebugMacro("Total number of planes on the stack: "
+ << ReturnedTotalNumberOfPlanes);
+
+ return ReturnedTotalNumberOfPlanes;
}
//----------------------------------------------------------------------------
// Configure the output e.g. WholeExtent, spacing, origin, scalar type...
void vtkGdcmReader::ExecuteInformation()
{
- //FIXME free any old memory
+ 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 zaxis extent to the VOI z axis
+ // 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];
}
- if ( ! this->CheckFileCoherence() )
- {
- vtkErrorMacro("File set is not coherent. Exiting...");
- return;
- }
- std::string ReferenceFile = this->FileNameList.front();
- gdcmHeader GdcmHeader(ReferenceFile.c_str());
-
- int NX = GdcmHeader.GetXSize();
- int NY = GdcmHeader.GetYSize();
- int NZ = GdcmHeader.GetZSize();
- vtkDebugMacro("Image dimension as read from Gdcm:" <<
- NX << " " << NY << " " << NZ);
-
- if(NZ>1) this->SetFileDimensionality(3);
// When the user has set the VOI, check it's coherence with the file content.
if (this->DataVOI[0] || this->DataVOI[1] ||
this->DataVOI[4] || this->DataVOI[5])
{
if ((this->DataVOI[0] < 0) ||
- (this->DataVOI[1] >= NX) ||
+ (this->DataVOI[1] >= this->NumColumns) ||
(this->DataVOI[2] < 0) ||
- (this->DataVOI[3] >= NY) ||
+ (this->DataVOI[3] >= this->NumLines) ||
(this->DataVOI[4] < 0) ||
- (this->DataVOI[5] >= NZ))
+ (this->DataVOI[5] >= this->TotalNumberOfPlanes ))
{
- vtkWarningMacro("The requested VOI is larger than the file's ("
- << ReferenceFile.c_str() << ") extent ");
+ vtkWarningMacro("The requested VOI is larger than expected extent.");
this->DataVOI[0] = 0;
- this->DataVOI[1] = NX - 1;
+ this->DataVOI[1] = this->NumColumns - 1;
this->DataVOI[2] = 0;
- this->DataVOI[3] = NY - 1;
+ this->DataVOI[3] = this->NumLines - 1;
this->DataVOI[4] = 0;
- this->DataVOI[5] = NZ - 1;
+ this->DataVOI[5] = this->TotalNumberOfPlanes - 1;
}
}
// Positionate the Extent.
this->DataExtent[0] = 0;
- this->DataExtent[1] = NX - 1;
+ this->DataExtent[1] = this->NumColumns - 1;
this->DataExtent[2] = 0;
- this->DataExtent[3] = NY - 1;
- if(this->GetFileDimensionality()==3)
- {
- this->DataExtent[4] = 0;
- this->DataExtent[5] = NZ - 1;
- }
+ 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:
- std::string type = GdcmHeader.GetPixelType();
- if ( type == "8U" )
+ if ( ImageType == "8U" )
{
vtkDebugMacro("8 bits unsigned image");
this->SetDataScalarTypeToUnsignedChar();
}
- else if ( type == "8S" )
+ else if ( ImageType == "8S" )
{
vtkErrorMacro("Cannot handle 8 bit signed files");
return;
}
- else if ( type == "16U" )
+ else if ( ImageType == "16U" )
{
vtkDebugMacro("16 bits unsigned image");
this->SetDataScalarTypeToUnsignedShort();
}
- else if ( type == "16S" )
+ else if ( ImageType == "16S" )
{
vtkDebugMacro("16 bits signed image");
this->SetDataScalarTypeToShort();
//vtkErrorMacro("Cannot handle 16 bit signed files");
}
- else if ( type == "32U" )
+ else if ( ImageType == "32U" )
{
vtkDebugMacro("32 bits unsigned image");
vtkDebugMacro("WARNING: forced to signed int !");
this->SetDataScalarTypeToInt();
}
- else if ( type == "32S" )
+ else if ( ImageType == "32S" )
{
vtkDebugMacro("32 bits signed image");
this->SetDataScalarTypeToInt();
}
- else
- {
- vtkErrorMacro("Bad File Type " << ReferenceFile.c_str()
- << "Type " << type.c_str());
- return;
- }
+
+ //Set number of scalar components:
+ this->SetNumberOfScalarComponents(this->NumComponents);
vtkImageReader::ExecuteInformation();
}
//----------------------------------------------------------------------------
-void vtkGdcmReader::LoadImageInMemory(std::string FileName,
- unsigned char * Dest,
- size_t size)
+// Loads the contents of the image/volume contained by 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 memmory image" << FileName.c_str());
+ vtkDebugMacro("Copying to memory image" << FileName.c_str());
gdcmFile GdcmFile(FileName.c_str());
-
- if (GdcmFile.GetZSize() != 1 )
- vtkErrorMacro("Cannot handle images with multiple planes");
-
- // First check the expected size of the image is the one found by gdcm.
- if ( size != GdcmFile.GetImageDataSize() )
- {
- vtkErrorMacro("Inconsistency with GetImageDataSize for file"
- << FileName.c_str());
- vtkErrorMacro("Number of scalar components"
- << this->NumberOfScalarComponents);
- }
+ size_t size;
// If the data structure of vtk for image/volume representation
// were straigthforwards the following would suffice:
// GdcmFile.GetImageDataIntoVector((void*)Dest, size);
- // But vtk chose to invert the lines of an image, that is the last
+ // 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:
+ // to load the image line by line, starting from the end.
int NumColumns = GdcmFile.GetXSize();
int NumLines = GdcmFile.GetYSize();
- int LineSize = NumColumns * GdcmFile.GetPixelSize();
- unsigned char * Source = (unsigned char*)GdcmFile.GetImageData();
+ int NumPlanes = GdcmFile.GetZSize();
+ int LineSize = NumComponents * NumColumns * GdcmFile.GetPixelSize();
+
+ unsigned char * Source;
+ if( GdcmFile.HasLUT() )
+ {
+ size = GdcmFile.GetImageDataSizeRaw();
+ Source = (unsigned char*) GdcmFile.GetImageDataRaw();
+ unsigned char *Lut = (unsigned char*) GdcmFile.GetLUTRGBA();
+
+ 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,
+ 1);
+ }
+ this->LookupTable->SetRange(0,255);
+ vtkDataSetAttributes *a=this->GetOutput()->GetPointData();
+ a->GetScalars()->SetLookupTable(this->LookupTable);
+ 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;
- for (int i = 0; i < NumLines; i++)
+
+ for (int plane = 0; plane < NumPlanes; plane++)
{
- memcpy((void*)Destination, (void*)Source, LineSize);
- Source += LineSize;
- Destination -= LineSize;
+ for (int line = 0; line < NumLines; line++)
+ {
+ // Copy one line at proper destination:
+ memcpy((void*)Destination, (void*)Source, LineSize);
+ Source += LineSize;
+ Destination -= LineSize;
+ // Update progress related:
+ if (!(UpdateProgressCount%UpdateProgressTarget))
+ {
+ this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget));
+ }
+ UpdateProgressCount++;
+ }
}
+ //GetImageData allocate a (void*)malloc, remove it:
+ free(pSource);
+
+ return size;
}
//----------------------------------------------------------------------------
-// Update -> UpdateData -> Execute -> ExecuteData (see vtkSource.cxx for
-// last step.
+// 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
-// extent/axes are assumed to be the
-// same as the file extent/order.
+// extent/axes are assumed to be the same as the file extent/order.
void vtkGdcmReader::ExecuteData(vtkDataObject *output)
{
- if (this->FileNameList.empty())
+ 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");
- // First check the coherence between the DataExtent and the
- // size of the pixel data as annouced by gdcm (looks a bit paranoid)
- // for the reference file (i.e. the first one in the list):
- std::string ReferenceFile = this->FileNameList.front();
- gdcmFile GdcmFile(ReferenceFile.c_str());
- int NumColumns = this->DataExtent[1] - this->DataExtent[0] + 1;
- int NumLines = this->DataExtent[3] - this->DataExtent[2] + 1;
- int NumPlanes = this->DataExtent[5] - this->DataExtent[4] + 1;
- size_t size = NumColumns * NumLines * NumPlanes * GdcmFile.GetPixelSize();
- if ( size != GdcmFile.GetImageDataSize() )
+ // Test if output has valid extent
+ // Prevent memory errors
+ if((this->DataExtent[1]-this->DataExtent[0]>=0) &&
+ (this->DataExtent[3]-this->DataExtent[2]>=0) &&
+ (this->DataExtent[5]-this->DataExtent[4]>=0))
{
- vtkDebugMacro("Inconsistency with GetImageDataSize");
- vtkDebugMacro("Number of scalar components"
- << this->NumberOfScalarComponents);
- }
+ // 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;
+ // Allocate pixel data space itself.
+ unsigned char *mem = new unsigned char [stack_size];
- // The memory size for a full stack of images of course depends
- // on the number of images:
- size_t stack_size = size * this->FileNameList.size();
- // Allocate pixel data space itself.
- unsigned char *mem = new unsigned char [stack_size];
+ // Variables for the UpdateProgress. We shall use 50 steps to signify
+ // the advance of the process:
+ unsigned long UpdateProgressTarget = (unsigned long) ceil (this->NumLines
+ * this->TotalNumberOfPlanes
+ / 50.0);
+ // The actual advance measure:
+ unsigned long UpdateProgressCount = 0;
- unsigned char * Dest = mem;
- for (std::list<std::string>::iterator FileName = FileNameList.begin();
- FileName != FileNameList.end();
- ++FileName)
- {
- this->LoadImageInMemory(*FileName, Dest, size);
- Dest += size;
- }
+ // Feeling the allocated memory space with each image/volume:
+ unsigned char * Dest = mem;
+ 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
- // The "size" of the vtkScalars data is expressed in number of points,
- // and is not the memory size representing those points:
- stack_size = stack_size / GdcmFile.GetPixelSize();
- data->GetPointData()->GetScalars()->SetVoidArray(mem, stack_size, 0);
- this->Modified();
-
+ // The "size" of the vtkScalars data is expressed in number of points,
+ // and is not the memory size representing those points:
+ data->GetPointData()->GetScalars()->SetVoidArray(mem, StackNumPixels, 0);
+ //don't know why it's here, it's calling one more time ExecuteInformation:
+ //this->Modified();
+ }
}
//----------------------------------------------------------------------------
FileName != FileNameList.end();
++FileName)
{
- os << nextIndent << *FileName->c_str() << endl ;
+ os << nextIndent << FileName->c_str() << endl ;
}
}