-// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.5 2003/05/28 19:36:21 frog Exp $
-//CLEANME#include <vtkByteSwap.h>
+// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.15 2003/07/07 09:10:33 regrain Exp $
#include <stdio.h>
#include <vtkObjectFactory.h>
#include <vtkImageData.h>
vtkGdcmReader::~vtkGdcmReader()
{
// FIXME free memory
+ this->RemoveAllFileName();
+ this->InternalFileNameList.clear();
}
+//----------------------------------------------------------------------------
+// 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);
+ 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,
+ // (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::AddFileName()
+// When the first method was used by caller we need to update the local
+// filename list
+void vtkGdcmReader::BuildFileListFromPattern()
+{
+ 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;
+ }
+
+ this->RemoveAllInternalFileName();
+ 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 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()
+{
+ int ReturnedTotalNumberOfPlanes = 0; // The returned value.
+
+ this->BuildFileListFromPattern();
+ if (this->InternalFileNameList.empty())
+ {
+ vtkErrorMacro("FileNames are not set.");
+ return 0;
+ }
+
+ bool FoundReferenceFile = false;
+ int ReferenceNZ = 0;
+
+ // Loop on the filenames:
+ // - check for their existence and gdcm "parasability"
+ // - 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 place 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());
+ *FileName = "GDCM_UNREADABLE";
+ continue;
+ }
+ fclose(fp);
+
+ // Stage 1.2: check for Gdcm parsability
+ gdcmHeader 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());
+ *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("Removing this file from readed files "
+ << FileName->c_str());
+ *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();
+ if (FoundReferenceFile)
+ {
+
+ // 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());
+ }
+
+ // 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 {
+ // 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();
+ }
+ } // End of loop on FileName
+
+ ///////// The files we CANNOT load are flaged. On debugging purposes
+ // count the loadable number of files and display thir number:
+ int NumberCoherentFiles = 0;
+ for (std::list<std::string>::iterator Filename = InternalFileNameList.begin();
+ Filename != InternalFileNameList.end();
+ ++Filename)
+ {
+ if (*Filename != "GDCM_UNREADABLE")
+ NumberCoherentFiles++;
+ }
+ vtkDebugMacro("Number of coherent files: " << NumberCoherentFiles);
+
+ if (ReturnedTotalNumberOfPlanes == 0)
+ {
+ vtkErrorMacro("No loadable file.");
+ }
+
+ 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
+ //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
this->DataExtent[5] = this->DataVOI[5];
}
- this->ComputeInternalFileName(this->DataExtent[4]);
-
- // Check for file existence.
- FILE *fp;
- fp = fopen(this->InternalFileName,"rb");
- if (!fp)
- {
- vtkErrorMacro("Unable to open file " << this->InternalFileName);
- return;
- }
- fclose(fp);
-
- // Check for Gdcm parsability
- gdcmHeader GdcmHeader(this->InternalFileName);
- if (!GdcmHeader.IsReadable())
- {
- vtkErrorMacro("Gdcm cannot parse file " << this->InternalFileName);
- return;
- }
-
- 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[2] || this->DataVOI[3] ||
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 ("
- << this->InternalFileName << ") 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[3] = this->NumLines - 1;
+ if(this->InternalFileNameList.size() > 1)
{
- this->DataExtent[4] = 0;
- this->DataExtent[5] = NZ - 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 need to set up the data type for downstream filters:
- std::string type = GdcmHeader.GetPixelType();
- if ( type == "8U" )
+ // 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 ( 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 " << this->InternalFileName
- << "Type " << type.c_str());
- return;
- }
vtkImageReader::ExecuteInformation();
}
-// Update -> UpdateData -> Execute -> ExecuteData (see vtkSource.cxx for
-// last step.
+//----------------------------------------------------------------------------
+// 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());
+ gdcmFile GdcmFile(FileName.c_str());
+ size_t size = GdcmFile.GetImageDataSize();
+
+ // 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
+ // 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.GetXSize();
+ int NumLines = GdcmFile.GetYSize();
+ int NumPlanes = GdcmFile.GetZSize();
+ int LineSize = NumColumns * GdcmFile.GetPixelSize();
+ unsigned char * Source = (unsigned char*)GdcmFile.GetImageData();
+ unsigned char * Destination = Dest + size - LineSize;
+
+ for (int plane = 0; plane < NumPlanes; plane++)
+ {
+ 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++;
+ }
+ }
+ return size;
+}
+
+//----------------------------------------------------------------------------
+// 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.
void vtkGdcmReader::ExecuteData(vtkDataObject *output)
{
- if (!this->FileName)
+ if (this->InternalFileNameList.empty())
{
- vtkErrorMacro("A valid FileName must be specified.");
+ vtkErrorMacro("A least a valid FileName must be specified.");
return;
}
+ // FIXME : the bad parse of header is made when allocating OuputData
vtkImageData *data = this->AllocateOutputData(output);
data->SetExtent(this->DataExtent);
- data->GetPointData()->GetScalars()->SetName("ImageFile");
-
- // First check the coherence between the DataExtent and the
- // size of the pixel data as annouced by gdcm (looks a bit paranoid).
- gdcmFile GdcmFile(this->InternalFileName);
- 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() )
- {
- vtkDebugMacro("Inconsistency with GetImageDataSize");
- vtkDebugMacro("Number of scalar components"
- << this->NumberOfScalarComponents);
- }
- // Allocate pixel data space itself.
- unsigned char *mem = new unsigned char [size];
+ data->GetPointData()->GetScalars()->SetName("DicomImage-Volume");
- // If the data structure of vtk for image/volume representation
- // were straigthforwards the following would suffice:
- // GdcmFile.GetImageDataIntoVector((void*)mem, size);
- // But vtk chose 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 LineSize = NumColumns * GdcmFile.GetPixelSize();
- unsigned char * Source = (unsigned char*)GdcmFile.GetImageData();
- unsigned char * Destination = mem + size - LineSize;
- for (int i = 0; i < NumLines; i++)
+ // 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))
{
- memcpy((void*)Destination, (void*)Source, LineSize);
- Source += LineSize;
- Destination -= LineSize;
- }
- // The "size" of the vtkScalars data is expressed in number of points,
- // and is not the memory size representing those points:
- size = size / GdcmFile.GetPixelSize();
- data->GetPointData()->GetScalars()->SetVoidArray(mem, size, 0);
- this->Modified();
+ // 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;
+ size_t stack_size = StackNumPixels * this->PixelSize;
+ // 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;
+
+ // 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:
+ data->GetPointData()->GetScalars()->SetVoidArray(mem, StackNumPixels, 0);
+ this->Modified();
+ }
}
+//----------------------------------------------------------------------------
void vtkGdcmReader::PrintSelf(ostream& os, vtkIndent indent)
{
vtkImageReader::PrintSelf(os,indent);
- //CLEANME os << indent << "TypeSize: " << this->TypeSize << "\n";
+ os << indent << "Filenames : " << endl;
+ vtkIndent nextIndent = indent.GetNextIndent();
+ for (std::list<std::string>::iterator FileName = FileNameList.begin();
+ FileName != FileNameList.end();
+ ++FileName)
+ {
+ os << nextIndent << FileName->c_str() << endl ;
+ }
}
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff