-// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.9 2003/06/03 10:26:07 frog Exp $
-//CLEANME#include <vtkByteSwap.h>
-#include <stdio.h>
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: vtkGdcmReader.cxx,v $
+ Language: C++
+ Date: $Date: 2005/06/29 16:12:43 $
+ Version: $Revision: 1.72 $
+
+ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
+ l'Image). All rights reserved. See Doc/License.txt or
+ http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+
+//-----------------------------------------------------------------------------
+// //////////////////////////////////////////////////////////////
+// WARNING TODO CLEANME
+// 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...
+// --> to avoid loosing too much time :
+// If user is 150% sure *all* the files are coherent, that is to say :
+// they may be open, they are gdcm-readable, they have the same sizes,
+// they have the same 'pixel' type, they are single frame,
+// they have the same color convention ...
+// he may use SetCheckFileCoherenceLight() to request a 'light' coherence
+// checking
+// 2/ ExecuteData is then responsible for the next two loadings - 2 ?!?-:
+// 2a/ ExecuteData calls AllocateOutputData that in turn seems to
+// (indirectely call) ExecuteInformation which ends up in a second
+// header parsing
+// This is fixed by adding a test at the beginning of ExecuteInformation
+// on the modification of the object instance. If a modification have been
+// made (method Modified() ), the MTime value is increased. The fileTime
+// is compared to this new value to find a modification in the class
+// parameters
+// 2b/ the core of ExecuteData then needs gdcmFile (which in turns
+// initialises gdcmFile 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 vtkGdcmFile (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 vtkGdcmFile) the gdcmFile structure is loaded in memory.
+// The average size of a gdcm::File being of 100Ko,
+// - 100 Ko ? Better say 1 Mo; we are in 2005 ! -
+// if oneloads 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 "gdcmFileHelper.h"
+#include "gdcmFile.h"
+#include "gdcmDocument.h" // for NO_SEQ
+
+#include "vtkGdcmReader.h"
+#include "gdcmDebug.h"
+
+//#include <stdio.h>
#include <vtkObjectFactory.h>
#include <vtkImageData.h>
#include <vtkPointData.h>
-#include "vtkGdcmReader.h"
-#include "gdcm.h"
+#include <vtkLookupTable.h>
+vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.72 $");
+vtkStandardNewMacro(vtkGdcmReader);
+
+//-----------------------------------------------------------------------------
+// Constructor / Destructor
vtkGdcmReader::vtkGdcmReader()
{
- // Constructor
+ this->LookupTable = NULL;
+ this->AllowLookupTable = 0;
+ this->LightChecking = false;
+ this->LoadMode = 0; // Load everything (possible values : NO_SEQ, NO_SHADOW
+ // NO_SHADOWSEQ)
}
-//----------------------------------------------------------------------------
vtkGdcmReader::~vtkGdcmReader()
-{
- // FIXME free memory
+{
+ this->RemoveAllFileName();
+ this->InternalFileNameList.clear();
+ if(this->LookupTable)
+ this->LookupTable->Delete();
+}
+
+//-----------------------------------------------------------------------------
+// Print
+void vtkGdcmReader::PrintSelf(ostream &os, vtkIndent indent)
+{
+ this->Superclass::PrintSelf(os,indent);
+ os << indent << "Filenames : " << endl;
+ vtkIndent nextIndent = indent.GetNextIndent();
+ for (std::list<std::string>::iterator it = FileNameList.begin();
+ it != FileNameList.end();
+ ++it)
+ {
+ os << nextIndent << it->c_str() << endl ;
+ }
}
-//----------------------------------------------------------------------------
-// Adds a file name to the list of images to read.
+//-----------------------------------------------------------------------------
+// Public
+/*
+ * Remove all files from the list of images to read.
+ */
+void vtkGdcmReader::RemoveAllFileName(void)
+{
+ this->FileNameList.clear();
+ this->Modified();
+}
+
+/*
+ * 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];
+ 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);
- this->Modified();
+ delete[] LocalName;
+ this->Modified();
}
-//----------------------------------------------------------------------------
-// Sets up a filename to be read.
-void vtkGdcmReader::SetFileName(const char *name) {
+/*
+ * 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);
+ // 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();
}
-//----------------------------------------------------------------------------
-// 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()
-// When the first method was used by caller we need to update the local
-// filename list
-void vtkGdcmReader::BuilFileListFromPattern()
+/*
+ * Ask for a 'light' checking -actually : just initializing-
+ *if you are 150% sure *all* the files are coherent
+ */
+void vtkGdcmReader::SetCheckFileCoherenceLight()
{
- if (! this->FileNameList.empty())
+ LightChecking = true;
+}
+
+//-----------------------------------------------------------------------------
+// Protected
+/*
+ * Configure the output e.g. WholeExtent, spacing, origin, scalar type...
+ */
+void vtkGdcmReader::ExecuteInformation()
+{
+ if(this->MTime>this->fileTime)
+ {
+ if ( this->LightChecking )
+ this->TotalNumberOfPlanes = this->CheckFileCoherenceLight();
+ else
+ 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();
+ }
+ 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();
+}
+
+/*
+ * 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 data
+ * 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; //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;
+
+ // Filling the allocated memory space with each image/volume:
+ unsigned char *Dest = (unsigned char *)data->GetScalarPointer();
+ 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
+ */
+void vtkGdcmReader::BuildFileListFromPattern()
+{
+ this->RemoveAllInternalFileName();
+
+ if ((! this->FileNameList.empty()) && this->FileName )
+ {
+ vtkErrorMacro(<< "Both AddFileName and SetFileName schemes were used");
+ vtkErrorMacro(<< "No images loaded ! ");
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);
- vtkDebugMacro("Adding file " << this->InternalFileName);
- this->AddFileName(this->InternalFileName);
- }
+ }
+
+ 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->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
+ {
+ // 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 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()
+/*
+ * 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()
{
- this->BuilFileListFromPattern();
- if (this->FileNameList.empty())
- {
- vtkErrorMacro("FileNames are not set.");
- return false;
- }
- if (this->FileNameList.size() == 1)
- {
- vtkDebugMacro("Single file specified.");
- return true;
- }
+ 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"
+ // - 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();
- ++FileName)
- {
- // 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);
- continue;
- }
- fclose(fp);
-
- // 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());
- FileNameList.remove(*FileName);
- continue;
- }
-
- // We don't know how to handle multiple images in one file yet:
- int NZ = GdcmHeader.GetZSize();
- if (NZ > 1)
- {
- vtkErrorMacro("This file contains multiple planes (images)"
- << *FileName->c_str());
- vtkErrorMacro("Removing this file from readed files "
- << *FileName->c_str());
- FileNameList.remove(*FileName);
- continue;
- }
-
- // Coherence stage:
- int NX = GdcmHeader.GetXSize();
- int NY = GdcmHeader.GetYSize();
- std::string type = GdcmHeader.GetPixelType();
- if (FoundReferenceFile)
- {
- if ( ( NX != ReferenceNX )
- || ( NY != ReferenceNY )
- || ( NZ != ReferenceNZ )
- || ( type != ReferenceType ) )
+ 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:
+
+ // fixme : how can the filename be equal to "GDCM_UNREADABLE"
+ // right now ?!?
+
+ 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 read files: "
+ << filename->c_str());
+ *filename = "GDCM_UNREADABLE";
+ continue;
+ }
+ fclose(fp);
+
+ // Stage 1.2: check for Gdcm parsability
+
+ //gdcm::File GdcmFile( filename->c_str() );
+ // to save some parsing time.
+ gdcm::File GdcmFile;
+ GdcmFile.SetLoadMode( LoadMode );
+ GdcmFile.Load(filename->c_str() );
+ if (!GdcmFile.IsReadable())
+ {
+ vtkErrorMacro(<< "Gdcm cannot parse file " << filename->c_str());
+ vtkErrorMacro(<< "Removing this file from read files: "
+ << filename->c_str());
+ *filename = "GDCM_UNREADABLE";
+ continue;
+ }
+
+ // Stage 1.3: further gdcm compatibility on PixelType
+ std::string type = GdcmFile.GetPixelType();
+ if ( (type != "8U") && (type != "8S")
+ && (type != "16U") && (type != "16S")
+ && (type != "32U") && (type != "32S") )
+ {
+ vtkErrorMacro(<< "Bad File Type for file " << filename->c_str() << "\n"
+ << " File type found : " << type.c_str()
+ << " (might be 8U, 8S, 16U, 16S, 32U, 32S) \n"
+ << " Removing this file from readed files");
+ *filename = "GDCM_UNREADABLE";
+ continue;
+ }
+
+ // Stage 2: check coherence of the set of files
+ int NX = GdcmFile.GetXSize();
+ int NY = GdcmFile.GetYSize();
+ int NZ = GdcmFile.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());
- FileNameList.remove(*FileName);
+ 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;
- } else {
- vtkDebugMacro("File is coherent with previous ones"
- << *FileName->c_str());
}
- } else {
- // This file shall be the reference:
+
+ // 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 is 'multiframe', notify the caller.
+ if (NZ > 1)
+ {
+ vtkErrorMacro(<< "This file is a 'Multiframe' one: "
+ << 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;
- ReferenceNX = NX;
- ReferenceNY = NY;
- ReferenceNZ = NZ;
- ReferenceType = type;
- vtkDebugMacro("This file taken as coherence reference:"
- << *FileName->c_str());
- }
- } // End of loop on FileName
-
- if (this->FileNameList.empty())
- {
- vtkDebugMacro("No gdcm parsable file.");
- return false;
- }
- if (this->FileNameList.size() == 1)
- {
- vtkDebugMacro("Single parsable file left after coherence test.");
- return true;
- }
- return true;
-}
+ vtkDebugMacro(<< "This file taken as coherence reference:"
+ << filename->c_str());
+ vtkDebugMacro(<< "Image dimensions 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 = GdcmFile.GetPixelSize();
-//----------------------------------------------------------------------------
-// Configure the output e.g. WholeExtent, spacing, origin, scalar type...
-void vtkGdcmReader::ExecuteInformation()
-{
- //FIXME free any old memory
-
- // 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];
- }
- 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[2] || this->DataVOI[3] ||
- this->DataVOI[4] || this->DataVOI[5])
- {
- if ((this->DataVOI[0] < 0) ||
- (this->DataVOI[1] >= NX) ||
- (this->DataVOI[2] < 0) ||
- (this->DataVOI[3] >= NY) ||
- (this->DataVOI[4] < 0) ||
- (this->DataVOI[5] >= this->FileNameList.size()))
+ if( GdcmFile.HasLUT() && this->AllowLookupTable )
+ {
+ // I could raise an error is AllowLookupTable is on and HasLUT() off
+ this->NumComponents = GdcmFile.GetNumberOfScalarComponentsRaw();
+ }
+ else
+ {
+ this->NumComponents = GdcmFile.GetNumberOfScalarComponents(); //rgb or mono
+ }
+ //Set image spacing
+ this->DataSpacing[0] = GdcmFile.GetXSpacing();
+ this->DataSpacing[1] = GdcmFile.GetYSpacing();
+ this->DataSpacing[2] = GdcmFile.GetZSpacing();
+ }
+ } // End of loop on filename
+
+ ///////// The files we CANNOT load are flaged. On debugging purposes
+ // count the loadable number of files and display their number:
+ int NumberCoherentFiles = 0;
+ for (std::list<std::string>::iterator it = InternalFileNameList.begin();
+ it != InternalFileNameList.end();
+ ++it)
+ {
+ if (*it != "GDCM_UNREADABLE")
{
- vtkWarningMacro("The requested VOI is larger than the file's ("
- << ReferenceFile.c_str() << ") extent ");
- this->DataVOI[0] = 0;
- this->DataVOI[1] = NX - 1;
- this->DataVOI[2] = 0;
- this->DataVOI[3] = NY - 1;
- this->DataVOI[4] = 0;
- this->DataVOI[5] = this->FileNameList.size() - 1;
+ NumberCoherentFiles++;
}
- }
-
- // Positionate the Extent.
- this->DataExtent[0] = 0;
- this->DataExtent[1] = NX - 1;
- this->DataExtent[2] = 0;
- this->DataExtent[3] = NY - 1;
- if(this->FileNameList.size() > 1)
- {
- this->DataExtent[4] = 0;
- this->DataExtent[5] = this->FileNameList.size() - 1;
- }
+ }
+ vtkDebugMacro(<< "Number of coherent files: " << NumberCoherentFiles);
-
- // 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" )
- {
- vtkDebugMacro("8 bits unsigned image");
- this->SetDataScalarTypeToUnsignedChar();
- }
- else if ( type == "8S" )
- {
- vtkErrorMacro("Cannot handle 8 bit signed files");
- return;
- }
- else if ( type == "16U" )
- {
- vtkDebugMacro("16 bits unsigned image");
- this->SetDataScalarTypeToUnsignedShort();
- }
- else if ( type == "16S" )
- {
- vtkDebugMacro("16 bits signed image");
- this->SetDataScalarTypeToShort();
- //vtkErrorMacro("Cannot handle 16 bit signed files");
- }
- else if ( type == "32U" )
- {
- vtkDebugMacro("32 bits unsigned image");
- vtkDebugMacro("WARNING: forced to signed int !");
- this->SetDataScalarTypeToInt();
- }
- else if ( type == "32S" )
- {
- vtkDebugMacro("32 bits signed image");
- this->SetDataScalarTypeToInt();
- }
- else
- {
- vtkErrorMacro("Bad File Type " << ReferenceFile.c_str()
- << "Type " << type.c_str());
- return;
- }
-
- vtkImageReader::ExecuteInformation();
+ if (ReturnedTotalNumberOfPlanes == 0)
+ {
+ vtkErrorMacro(<< "No loadable file.");
+ }
+
+ vtkDebugMacro(<< "Total number of planes on the stack: "
+ << ReturnedTotalNumberOfPlanes);
+
+ return ReturnedTotalNumberOfPlanes;
}
-//----------------------------------------------------------------------------
-void vtkGdcmReader::LoadImageInMemory(std::string FileName,
- unsigned char * Dest,
- size_t size)
+//-----------------------------------------------------------------------------
+// Private
+/*
+ * Remove all file names to the internal list of images to read.
+ */
+void vtkGdcmReader::RemoveAllInternalFileName(void)
{
- 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);
- }
-
- // 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 LineSize = NumColumns * GdcmFile.GetPixelSize();
- unsigned char * Source = (unsigned char*)GdcmFile.GetImageData();
- unsigned char * Destination = Dest + size - LineSize;
- for (int i = 0; i < NumLines; i++)
- {
- memcpy((void*)Destination, (void*)Source, LineSize);
- Source += LineSize;
- Destination -= LineSize;
- }
+ this->InternalFileNameList.clear();
}
-//----------------------------------------------------------------------------
-// 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)
+/*
+ * Adds a file name to the internal list of images to read.
+ */
+void vtkGdcmReader::AddInternalFileName(const char *name)
{
- if (this->FileNameList.empty())
- {
- vtkErrorMacro("A least a valid FileName must be specified.");
- return;
- }
-
- 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 = 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();
- // Allocate pixel data space itself.
- unsigned char *mem = new unsigned char [stack_size];
-
- unsigned char * Dest = mem;
- for (std::list<std::string>::iterator FileName = FileNameList.begin();
- FileName != FileNameList.end();
- ++FileName)
- {
- this->LoadImageInMemory(*FileName, Dest, size);
- Dest += size;
- }
-
- // 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();
+ 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.
+ */
+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() << "]");
+ gdcm::File *f;
+ f = new gdcm::File();
+ f->SetLoadMode( LoadMode );
+ f->Load( fileName.c_str() );
+
+ gdcm::FileHelper fileH( f );
+ 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 = fileH.GetFile()->GetXSize();
+ int numLines = fileH.GetFile()->GetYSize();
+ int numPlanes = fileH.GetFile()->GetZSize();
+ int lineSize = NumComponents * numColumns * fileH.GetFile()->GetPixelSize();
+ int planeSize = lineSize * numLines;
+
+ unsigned char *src;
+
+ if( fileH.GetFile()->HasLUT() && AllowLookupTable )
+ {
+ size = fileH.GetImageDataSize();
+ src = (unsigned char*) fileH.GetImageDataRaw();
+ unsigned char *lut = (unsigned char*) fileH.GetLutRGBA();
+
+ if(!this->LookupTable)
+ {
+ this->LookupTable = vtkLookupTable::New();
+ }
+
+ this->LookupTable->SetNumberOfTableValues(256);
+ for (int tmp=0; tmp<256; tmp++)
+ {
+ this->LookupTable->SetTableValue(tmp,
+ (float)lut[4*tmp+0]/255.0,
+ (float)lut[4*tmp+1]/255.0,
+ (float)lut[4*tmp+2]/255.0,
+ 1);
+ }
+ this->LookupTable->SetRange(0,255);
+ vtkDataSetAttributes *a = this->GetOutput()->GetPointData();
+ a->GetScalars()->SetLookupTable(this->LookupTable);
+ free(lut);
+ }
+ else
+ {
+ size = fileH.GetImageDataSize();
+ src = (unsigned char*)fileH.GetImageData();
+ }
+
+ unsigned char *dst = dest + planeSize - lineSize;
+ for (int plane = 0; plane < numPlanes; plane++)
+ {
+ for (int line = 0; line < numLines; line++)
+ {
+ // Copy one line at proper destination:
+ memcpy((void*)dst, (void*)src, lineSize);
+ src += lineSize;
+ dst -= lineSize;
+ // Update progress related:
+ if (!(updateProgressCount%updateProgressTarget))
+ {
+ this->UpdateProgress(updateProgressCount/(50.0*updateProgressTarget));
+ }
+ updateProgressCount++;
+ }
+ dst += 2 * planeSize;
+ }
+ delete f;
+ return size;
}
-//----------------------------------------------------------------------------
-void vtkGdcmReader::PrintSelf(ostream& os, vtkIndent indent)
+// -------------------------------------------------------------------------
+
+// We assume the use *does* know all the files whose names
+// are in InternalFileNameList exist, may be open, are gdcm-readable
+// have the same sizes, have the same 'pixel' type, are single frame
+// have the same color convention, ..., anything else ?
+
+int vtkGdcmReader::CheckFileCoherenceLight()
{
- 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 ;
- }
+ std::list<std::string>::iterator filename = InternalFileNameList.begin();
+
+ gdcm::File GdcmFile;
+ GdcmFile.SetLoadMode( LoadMode );
+ GdcmFile.Load(filename->c_str() );
+ if (!GdcmFile.IsReadable())
+ {
+ vtkErrorMacro(<< "Gdcm cannot parse file " << filename->c_str());
+ vtkErrorMacro(<< "you should try vtkGdcmReader::CheckFileCoherence "
+ << "instead of try vtkGdcmReader::CheckFileCoherenceLight");
+ return 0;
+ }
+ int NX = GdcmFile.GetXSize();
+ int NY = GdcmFile.GetYSize();
+ // CheckFileCoherenceLight should be called *only* when user knows
+ // he deals with single frames files.
+ // Z size is then the number of files.
+ int NZ = InternalFileNameList.size();
+ std::string type = GdcmFile.GetPixelType();
+ vtkDebugMacro(<< "The first file is taken as reference: "
+ << filename->c_str());
+ vtkDebugMacro(<< "Image dimensions 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;
+ this->ImageType = type;
+ this->PixelSize = GdcmFile.GetPixelSize();
+
+ if( GdcmFile.HasLUT() && this->AllowLookupTable )
+ {
+ // I could raise an error is AllowLookupTable is on and HasLUT() off
+ this->NumComponents = GdcmFile.GetNumberOfScalarComponentsRaw();
+ }
+ else
+ {
+ this->NumComponents = GdcmFile.GetNumberOfScalarComponents(); //rgb or mono
+ }
+
+ //Set image spacing
+ this->DataSpacing[0] = GdcmFile.GetXSpacing();
+ this->DataSpacing[1] = GdcmFile.GetYSpacing();
+ this->DataSpacing[2] = GdcmFile.GetZSpacing();
+
+ return InternalFileNameList.size();
}
+//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff