-// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.21 2003/10/24 15:38:56 malaterre Exp $
+// vtkGdcmReader.cxx
+//-----------------------------------------------------------------------------
// //////////////////////////////////////////////////////////////
// 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 corrersponding image gets loaded in the
+// 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 purpous
+// 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...
// 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
-// initialiszes gdcmHeader in the constructor) in order to access
+// 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 consctutor:
+// 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 sctructue is loaded in memory.
+// 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...
// 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 desctutor nor when the
+// 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 "gdcmFile.h"
+#include "gdcmHeaderHelper.h"
+#include "vtkGdcmReader.h"
+
+//#include <stdio.h>
#include <vtkObjectFactory.h>
#include <vtkImageData.h>
#include <vtkPointData.h>
-#include "vtkGdcmReader.h"
-#include "gdcm.h"
-#include "gdcmHeaderHelper.h"
+#include <vtkLookupTable.h>
+vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.46 $");
+vtkStandardNewMacro(vtkGdcmReader);
+
+//-----------------------------------------------------------------------------
+// Constructor / Destructor
vtkGdcmReader::vtkGdcmReader()
{
- // Constructor
+ this->LookupTable = NULL;
+ this->AllowLookupTable = 0;
}
-//----------------------------------------------------------------------------
vtkGdcmReader::~vtkGdcmReader()
-{
- this->RemoveAllFileName();
- this->InternalFileNameList.clear();
+{
+ this->RemoveAllFileName();
+ this->InternalFileNameList.clear();
+ if(this->LookupTable)
+ this->LookupTable->Delete();
}
-//----------------------------------------------------------------------------
-// Remove all files from the list of images to read.
+//-----------------------------------------------------------------------------
+// Print
+void vtkGdcmReader::PrintSelf(ostream& os, vtkIndent indent)
+{
+ vtkImageReader::PrintSelf(os,indent);
+ 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 ;
+ }
+}
+
+//-----------------------------------------------------------------------------
+// Public
+/*
+ * Remove all files from the list of images to read.
+ */
void vtkGdcmReader::RemoveAllFileName(void)
{
- this->FileNameList.clear();
+ this->FileNameList.clear();
+ this->Modified();
}
-//----------------------------------------------------------------------------
-// Adds a file name to the list of images to read.
+/*
+ * 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;
+ // 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);
+ delete[] 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,
- // (see vtkGdcmReader::AddFileName), we additionaly need to purge
- // this list when we manually positionate the filename.
- this->FileNameList.clear();
- 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,
+ // (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();
}
-//----------------------------------------------------------------------------
-// Adds a file name to the internal list of images to read.
-void vtkGdcmReader::RemoveAllInternalFileName(void)
+//-----------------------------------------------------------------------------
+// Protected
+/*
+ * Configure the output e.g. WholeExtent, spacing, origin, scalar type...
+ */
+void vtkGdcmReader::ExecuteInformation()
{
- this->InternalFileNameList.clear();
+ if(this->MTime>this->fileTime)
+ {
+ 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 ))
+ {
+ 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;
+
+ // 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;
+ }
+
+ this->Superclass::ExecuteInformation();
}
-//----------------------------------------------------------------------------
-// Adds a file name to the internal list of images to read.
-void vtkGdcmReader::AddInternalFileName(const char* name)
+/*
+ * 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)
{
- char * LocalName = new char[strlen(name) + 1];
- strcpy(LocalName, name);
- this->InternalFileNameList.push_back(LocalName);
- delete[] LocalName;
+ 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");
+
+ // 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))
+ {
+ // 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; //not used
+ // Allocate pixel data space itself.
+
+ // 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 = (unsigned char *)data->GetPointData()->GetScalars()->GetVoidPointer(0);
+ 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
+ }
}
-//----------------------------------------------------------------------------
-// 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
+/*
+ * 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()
{
+ 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");
- return;
- }
+ {
+ 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;
+ }
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();
- if( this->FileNameList.empty() )
- {
- //Multiframe case:
- this->ComputeInternalFileName(this->DataExtent[4]);
- vtkDebugMacro("Adding file " << this->InternalFileName);
- this->AddInternalFileName(this->InternalFileName);
- }
+ {
+ vtkDebugMacro("Using the AddFileName specified files");
+ this->InternalFileNameList=this->FileNameList;
+ return;
+ }
+
+ if (!this->FileName && !this->FilePrefix)
+ {
+ vtkErrorMacro("FileNames are not set. Either use AddFileName() or");
+ vtkErrorMacro("specify a FileName or FilePrefix.");
+ return;
+ }
+
+ if( this->FileName )
+ {
+ // 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:
- for (int idx = this->DataExtent[4]; idx <= this->DataExtent[5]; ++idx)
- {
- this->ComputeInternalFileName(idx);
- vtkDebugMacro("Adding file " << this->InternalFileName);
- this->AddInternalFileName(this->InternalFileName);
- }
- }
+ {
+ // Multi file loading (as given with ::SetFilePattern()):
+ 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)
+/*
+ * 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.
+ int ReturnedTotalNumberOfPlanes = 0; // The returned value.
this->BuildFileListFromPattern();
if (this->InternalFileNameList.empty())
- {
- vtkErrorMacro("FileNames are not set.");
- return 0;
- }
+ {
+ vtkErrorMacro("FileNames are not set.");
+ 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:
- 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
- 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());
- *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 "
+ 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
+ // 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;
- }
-
- /////// 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());
+ *FileName = "GDCM_UNREADABLE";
+ continue;
+ }
+ fclose(fp);
+
+ // Stage 1.2: check for Gdcm parsability
+ gdcmHeader GdcmHeader(FileName->c_str(), false, true);
+ // true : for enableSequences
+ if (!GdcmHeader.IsReadable())
+ {
+ vtkErrorMacro("Gdcm cannot parse file " << FileName->c_str());
vtkErrorMacro("Removing this file from readed files "
- << FileName->c_str());
+ << 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;
+ }
+
+ // 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 )
+ // 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
+ 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)
+ // 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
- // 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();
- 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();
+ // 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();
+
+ if( GdcmHeader.HasLUT() && this->AllowLookupTable )
+ {
+ // I could raise an error is AllowLookupTable is on and HasLUT() off
+ this->NumComponents = GdcmHeader.GetNumberOfScalarComponentsRaw();
+ }
+ else
+ {
+ this->NumComponents = GdcmHeader.GetNumberOfScalarComponents(); //rgb or mono
+ }
- }
- } // End of loop on FileName
+ //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
///////// The files we CANNOT load are flaged. On debugging purposes
- // count the loadable number of files and display thir number:
+ // 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 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.");
- }
+ {
+ vtkErrorMacro("No loadable file.");
+ }
vtkDebugMacro("Total number of planes on the stack: "
- << ReturnedTotalNumberOfPlanes);
+ << ReturnedTotalNumberOfPlanes);
- return ReturnedTotalNumberOfPlanes;
+ return ReturnedTotalNumberOfPlanes;
}
-//----------------------------------------------------------------------------
-// Configure the output e.g. WholeExtent, spacing, origin, scalar type...
-void vtkGdcmReader::ExecuteInformation()
+//-----------------------------------------------------------------------------
+// Private
+/*
+ * Remove all file names to the internal list of images to read.
+ */
+void vtkGdcmReader::RemoveAllInternalFileName(void)
{
- 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
- 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 ))
- {
- 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;
-
- // 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();
- }
-
- //Set number of scalar components:
- this->SetNumberOfScalarComponents(this->NumComponents);
-
- vtkImageReader::ExecuteInformation();
+ 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;
}
-//----------------------------------------------------------------------------
-// Loads the contents of the image/volume contained by Filename at
-// the Dest memory address. Returns the size of the data loaded.
+/*
+ * 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 memory 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 = NumComponents * NumColumns * GdcmFile.GetPixelSize();
- unsigned char * Source = (unsigned char*)GdcmFile.GetImageData();
- unsigned char * pSource = Source; //pointer for later deletion
- 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++;
- }
- }
- //GetImageData allocate a (void*)malloc, remove it:
- free(pSource);
+ vtkDebugMacro("Copying to memory image [" << FileName.c_str() << "]");
+ gdcmFile GdcmFile(FileName.c_str(),false,true);
+ // true : to enable SeQuences
+ size_t size;
+
+ // If the data structure of vtk for image/volume representation
+ // 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();
+
+ unsigned char * Source;
+
+ if( GdcmFile.GetHeader()->HasLUT() && this->AllowLookupTable )
+ {
+ size = GdcmFile.GetImageDataSizeRaw();
+ Source = (unsigned char*) GdcmFile.GetImageDataRaw();
+ unsigned char *Lut = GdcmFile.GetHeader()->GetLUTRGBA();
- return size;
-}
+ if(!this->LookupTable)
+ this->LookupTable = vtkLookupTable::New();
-//----------------------------------------------------------------------------
-// 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->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");
-
- // 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))
- {
- // 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];
-
- // 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
+ 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;
- // 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();
- }
+ 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++;
+ }
+ }
+
+// 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:
+ delete[] pSource;
+ return size;
}
-//----------------------------------------------------------------------------
-void vtkGdcmReader::PrintSelf(ostream& os, vtkIndent indent)
-{
- vtkImageReader::PrintSelf(os,indent);
- 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