-// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.9 2003/06/03 10:26:07 frog Exp $
+// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.10 2003/06/11 13:36:54 frog Exp $
//CLEANME#include <vtkByteSwap.h>
#include <stdio.h>
#include <vtkObjectFactory.h>
// 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();
}
//----------------------------------------------------------------------------
// 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.empty();
+ this->Modified();
}
//----------------------------------------------------------------------------
// 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");
+ 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->ComputeInternalFileName(idx);
//----------------------------------------------------------------------------
// 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();
+ int ReturnedTotalNumberOfPlanes = 0; // The returned value.
+
+ this->BuildFileListFromPattern();
if (this->FileNameList.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"
// - 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();
++FileName)
{
- // Check for file existence.
+ /////// 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("Unable to open file " << FileName->c_str());
vtkErrorMacro("Removing this file from readed files "
- << *FileName->c_str());
- FileNameList.remove(*FileName);
+ << FileName->c_str());
+ *FileName = "GDCM_UNREADABLE";
continue;
}
fclose(fp);
- // Check for Gdcm parsability
+ // Stage 1.2: check for Gdcm parsability
gdcmHeader 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());
- FileNameList.remove(*FileName);
+ << FileName->c_str());
+ *FileName = "GDCM_UNREADABLE";
continue;
}
- // We don't know how to handle multiple images in one file yet:
- int NZ = GdcmHeader.GetZSize();
- if (NZ > 1)
+ // 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("This file contains multiple planes (images)"
- << *FileName->c_str());
- vtkErrorMacro("Removing this file from readed files "
- << *FileName->c_str());
- FileNameList.remove(*FileName);
+ vtkErrorMacro("Bad File Type for file" << FileName->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();
- std::string type = GdcmHeader.GetPixelType();
+ int NZ = GdcmHeader.GetZSize();
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());
+ *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 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 contains multiple planes (images)"
+ << FileName->c_str());
+ vtkErrorMacro("Removing this file from readed files "
+ << 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;
+ 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;
+ this->ImageType = type;
+ this->PixelSize = GdcmHeader.GetPixelSize();
}
} // 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 thir number:
+ int NumberCoherentFiles = 0;
+ for (std::list<std::string>::iterator FileName = FileNameList.begin();
+ FileName != FileNameList.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;
}
//----------------------------------------------------------------------------
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
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);
// 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] >= this->FileNameList.size()))
+ (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] = this->FileNameList.size() - 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;
+ this->DataExtent[3] = this->NumLines - 1;
if(this->FileNameList.size() > 1)
{
this->DataExtent[4] = 0;
- this->DataExtent[5] = this->FileNameList.size() - 1;
+ 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;
- }
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());
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 = GdcmFile.GetImageDataSize();
// If the data structure of vtk for image/volume representation
// were straigthforwards the following would suffice:
// 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 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++;
+ }
}
+ return size;
}
//----------------------------------------------------------------------------
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 = 1; // This has been checked in CheckFileCoherence
- size_t size = NumColumns * NumLines * NumPlanes * GdcmFile.GetPixelSize();
- if ( size != GdcmFile.GetImageDataSize() )
- {
- 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 images:
- size_t stack_size = size * this->FileNameList.size();
+ // 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) 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 = FileNameList.begin();
FileName != FileNameList.end();
++FileName)
- {
- this->LoadImageInMemory(*FileName, Dest, size);
- Dest += size;
- }
+ {
+ // 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")
+ {
+ 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:
+ UpdateProgressCount += this->NumLines;
+ 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);
+ data->GetPointData()->GetScalars()->SetVoidArray(mem, StackNumPixels, 0);
this->Modified();
}
FileName != FileNameList.end();
++FileName)
{
- os << nextIndent << *FileName->c_str() << endl ;
+ os << nextIndent << FileName->c_str() << endl ;
}
}
projects / gdcm.git / commitdiff