1 /*=========================================================================
4 Module: $RCSfile: vtkGdcmReader.cxx,v $
6 Date: $Date: 2011/03/29 07:36:02 $
7 Version: $Revision: 1.99 $
9 Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
10 l'Image). All rights reserved. See Doc/License.txt or
11 http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
13 This software is distributed WITHOUT ANY WARRANTY; without even
14 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 PURPOSE. See the above copyright notices for more information.
17 =========================================================================*/
19 //-----------------------------------------------------------------------------
20 // //////////////////////////////////////////////////////////////
22 //===> Many users expect from vtkGdcmReader it 'orders' the images
23 // (that's the job of GDCM_NAME_SPACE::SerieHelper ...)
24 // When user *knows* the files with same Serie UID
25 // have same sizes, same 'pixel' type, same color convention, ...
26 // the right way to proceed is as follow :
28 // GDCM_NAME_SPACE::SerieHelper *sh= new GDCM_NAME_SPACE::SerieHelper();
29 // // if user wants *not* to load some parts of the file headers
30 // sh->SetLoadMode(loadMode);
32 // // if user wants *not* to load some files
33 // sh->AddRestriction(group, element, value, operator);
34 // sh->AddRestriction( ...
35 // sh->SetDirectory(directoryWithImages);
37 // // if user wants to sort reverse order
38 // sh->SetSortOrderToReverse();
40 // // here, we suppose only the first 'Serie' is of interest
41 // // it's up to the user to decide !
42 // GDCM_NAME_SPACE::FileList *l = sh->GetFirstSingleSerieUIDFileSet();
44 // // if user is doesn't trust too much the files with same Serie UID
45 // if ( !sh->IsCoherent(l) )
46 // return; // not same sizes, same 'pixel' type -> stop
48 // // WARNING : all that follows works only with 'bona fide' Series
49 // // (In some Series; there are more than one 'orientation'
50 // // Don't expected to build a 'volume' with that!
52 // // -> use sh->SplitOnOrientation(l)
53 // // - or sh->SplitOnPosition(l), or SplitOnTagValue(l, gr, el) -
54 // // depending on what you want to do
55 // // and iterate on the various 'X Coherent File Sets'
57 // // if user *knows* he has to drop the 'duplicates' images
59 // sh->SetDropDuplicatePositions(true);
61 // // Sorting the list is mandatory
62 // // a side effect is to compute ZSpacing for the file set
63 // sh->OrderFileList(l); // sort the list
65 // vtkGdcmReader *reader = vtkGdcmReader::New();
67 // // if user wants to modify pixel order (Mirror, TopDown, 90°Rotate, ...)
68 // // he has to supply the function that does the job
69 // // (a *very* simple example is given in vtkgdcmSerieViewer.cxx)
70 // reader->SetUserFunction (userSuppliedFunction);
72 // // to pass a 'Coherent File List' as produced by GDCM_NAME_SPACE::SerieHelper
73 // reader->SetCoherentFileList(l);
76 // WARNING TODO CLEANME
77 // Actual limitations of this code
78 // when a Coherent File List from SerieHelper is not used (bad idea :-(
80 // //////////////////////////////////////////////////////////////
82 #include "gdcmFileHelper.h"
84 #include "gdcmSerieHelper.h" // for ImagePositionPatientOrdering()
86 #include "vtkGdcmReader.h"
87 #include "gdcmDebug.h"
88 #include "gdcmCommon.h"
90 #include <vtkObjectFactory.h>
91 #include <vtkImageData.h>
92 #include <vtkPointData.h>
93 #include <vtkLookupTable.h>
95 vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.99 $")
96 vtkStandardNewMacro(vtkGdcmReader)
98 //-----------------------------------------------------------------------------
99 // Constructor / Destructor
100 vtkGdcmReader::vtkGdcmReader()
102 this->LookupTable = NULL;
103 this->AllowLookupTable = false;
104 //this->AllowLightChecking = false;
105 this->LoadMode = GDCM_NAME_SPACE::LD_ALL; // Load everything (possible values :
109 this->CoherentFileList = 0;
110 this->UserFunction = 0;
113 // this->Execution=false; // For VTK5.0
115 this->KeepOverlays = false;
116 this->FlipY = true; // to keep old behaviour
119 vtkGdcmReader::~vtkGdcmReader()
121 this->RemoveAllFileName();
122 this->InternalFileNameList.clear();
123 if(this->LookupTable)
124 this->LookupTable->Delete();
127 //-----------------------------------------------------------------------------
129 void vtkGdcmReader::PrintSelf(ostream &os, vtkIndent indent)
131 this->Superclass::PrintSelf(os,indent);
132 os << indent << "Filenames : " << endl;
133 vtkIndent nextIndent = indent.GetNextIndent();
134 for (std::list<std::string>::iterator it = FileNameList.begin();
135 it != FileNameList.end();
138 os << nextIndent << it->c_str() << endl ;
142 //-----------------------------------------------------------------------------
145 * Remove all files from the list of images to read.
147 void vtkGdcmReader::RemoveAllFileName(void)
149 this->FileNameList.clear();
154 * Adds a file name to the list of images to read.
156 void vtkGdcmReader::AddFileName(const char* name)
158 // We need to bypass the const pointer [since list<>.push_bash() only
159 // takes a char* (but not a const char*)] by making a local copy:
160 this->FileNameList.push_back(name);
165 * Sets up a filename to be read.
167 void vtkGdcmReader::SetFileName(const char *name)
169 vtkImageReader2::SetFileName(name);
170 // Since we maintain a list of filenames, when building a volume,
171 // (see vtkGdcmReader::AddFileName), we additionaly need to purge
172 // this list when we manually positionate the filename.
173 vtkDebugMacro(<< "Clearing all files given with AddFileName");
174 this->FileNameList.clear();
178 //-----------------------------------------------------------------------------
181 * Configure the output e.g. WholeExtent, spacing, origin, scalar type...
183 void vtkGdcmReader::ExecuteInformation()
185 // if(this->Execution) // For VTK5.0
188 // this->Execution=true; // end For VTK5.0
189 this->RemoveAllInternalFile();
190 if(this->MTime>this->fileTime)
192 this->TotalNumberOfPlanes = 0;
194 if ( this->CoherentFileList != 0 )
196 this->UpdateFileInformation();
200 this->BuildFileListFromPattern();
201 this->LoadFileInformation();
204 if ( this->TotalNumberOfPlanes == 0)
206 vtkErrorMacro(<< "File set is not coherent. Exiting...");
210 // if the user has not set the extent, but has set the VOI
211 // set the z axis extent to the VOI z axis
212 if (this->DataExtent[4]==0 && this->DataExtent[5] == 0 &&
213 (this->DataVOI[4] || this->DataVOI[5]))
215 this->DataExtent[4] = this->DataVOI[4];
216 this->DataExtent[5] = this->DataVOI[5];
219 // When the user has set the VOI, check it's coherence with the file content.
220 if (this->DataVOI[0] || this->DataVOI[1] ||
221 this->DataVOI[2] || this->DataVOI[3] ||
222 this->DataVOI[4] || this->DataVOI[5])
224 if ((this->DataVOI[0] < 0) ||
225 (this->DataVOI[1] >= this->NumColumns) ||
226 (this->DataVOI[2] < 0) ||
227 (this->DataVOI[3] >= this->NumLines) ||
228 (this->DataVOI[4] < 0) ||
229 (this->DataVOI[5] >= this->TotalNumberOfPlanes ))
231 vtkWarningMacro(<< "The requested VOI is larger than expected extent.");
232 this->DataVOI[0] = 0;
233 this->DataVOI[1] = this->NumColumns - 1;
234 this->DataVOI[2] = 0;
235 this->DataVOI[3] = this->NumLines - 1;
236 this->DataVOI[4] = 0;
237 this->DataVOI[5] = this->TotalNumberOfPlanes - 1;
242 this->DataExtent[0] = 0;
243 this->DataExtent[1] = this->NumColumns - 1;
244 this->DataExtent[2] = 0;
245 this->DataExtent[3] = this->NumLines - 1;
246 this->DataExtent[4] = 0;
247 this->DataExtent[5] = this->TotalNumberOfPlanes - 1;
249 // We don't need to set the Endian related stuff (by using
250 // this->SetDataByteOrderToBigEndian() or SetDataByteOrderToLittleEndian()
251 // since the reading of the file is done by gdcm.
252 // But we do need to set up the data type for downstream filters:
253 if ( ImageType == "8U" )
255 vtkDebugMacro(<< "8 bits unsigned image");
256 this->SetDataScalarTypeToUnsignedChar();
258 else if ( ImageType == "8S" )
260 vtkErrorMacro(<< "Cannot handle 8 bit signed files");
263 else if ( ImageType == "16U" )
265 vtkDebugMacro(<< "16 bits unsigned image");
266 this->SetDataScalarTypeToUnsignedShort();
268 else if ( ImageType == "16S" )
270 vtkDebugMacro(<< "16 bits signed image");
271 this->SetDataScalarTypeToShort();
273 else if ( ImageType == "32U" )
275 vtkDebugMacro(<< "32 bits unsigned image");
276 vtkDebugMacro(<< "WARNING: forced to signed int !");
277 this->SetDataScalarTypeToInt();
279 else if ( ImageType == "32S" )
281 vtkDebugMacro(<< "32 bits signed image");
282 this->SetDataScalarTypeToInt();
284 else if ( ImageType == "FD" ) // This is not genuine DICOM, but so usefull
286 vtkDebugMacro(<< "64 bits Double image");
287 this->SetDataScalarTypeToDouble();
289 //Set number of scalar components:
290 this->SetNumberOfScalarComponents(this->NumComponents);
292 this->fileTime=this->MTime;
295 this->Superclass::ExecuteInformation();
297 //this->GetOutput()->SetUpdateExtentToWholeExtent();// For VTK5.0
298 //this->BuildData(this->GetOutput());
300 //this->Execution=false;
301 //this->RemoveAllInternalFile(); // End For VTK5.0
305 * Update => ouput->Update => UpdateData => Execute => ExecuteData
306 * (see vtkSource.cxx for last step).
307 * This function (redefinition of vtkImageReader::ExecuteData, see
308 * VTK/IO/vtkImageReader.cxx) reads a data from a file. The data
309 * extent/axes are assumed to be the same as the file extent/order.
311 void vtkGdcmReader::ExecuteData(vtkDataObject *output)
313 vtkImageData *data=vtkImageData::SafeDownCast(output);
314 data->SetExtent(this->DataExtent);
316 /* if ( CoherentFileList != 0 ) // When a list of names is passed
318 if (this->CoherentFileList->empty())
320 vtkErrorMacro(<< "Coherent File List must have at least a valid File*.");
324 else if (this->InternalFileNameList.empty())
326 vtkErrorMacro(<< "A least a valid FileName must be specified.");
331 // data->AllocateScalars(); // For VTK5.0
332 // if (this->UpdateExtentIsEmpty(output))
336 //} // end For VTK5.0
338 data->AllocateScalars(); // For VTK5.0
340 #if (VTK_MAJOR_VERSION >= 5) || ( VTK_MAJOR_VERSION == 4 && VTK_MINOR_VERSION > 2 )
341 //#if (VTK_MAJOR_VERSION >= 5)
342 if (this->UpdateExtentIsEmpty(output))
348 data->GetPointData()->GetScalars()->SetName("DicomImage-Volume");
350 // Test if output has valid extent
351 // Prevent memory errors
352 if((this->DataExtent[1]-this->DataExtent[0]>=0) &&
353 (this->DataExtent[3]-this->DataExtent[2]>=0) &&
354 (this->DataExtent[5]-this->DataExtent[4]>=0))
356 // The memory size for a full stack of images of course depends
357 // on the number of planes and the size of each image:
358 //size_t StackNumPixels = this->NumColumns * this->NumLines
359 // * this->TotalNumberOfPlanes * this->NumComponents;
360 //size_t stack_size = StackNumPixels * this->PixelSize; //not used
361 // Allocate pixel data space itself.
363 // Variables for the UpdateProgress. We shall use 50 steps to signify
364 // the advance of the process:
365 unsigned long UpdateProgressTarget = (unsigned long) ceil (this->NumLines
366 * this->TotalNumberOfPlanes
368 // The actual advance measure:
369 unsigned long UpdateProgressCount = 0;
371 // Filling the allocated memory space with each image/volume:
373 size_t size = this->NumColumns * this->NumLines * this->NumPlanes
374 * data->GetScalarSize() * this->NumComponents;
375 unsigned char *Dest = (unsigned char *)data->GetScalarPointer();
376 for (std::vector<GDCM_NAME_SPACE::File* >::iterator it = InternalFileList.begin();
377 it != InternalFileList.end();
380 this->LoadImageInMemory(*it, Dest,
381 UpdateProgressTarget,
382 UpdateProgressCount);
386 this->RemoveAllInternalFile(); // For VTK5.0
390 * vtkGdcmReader can have the file names specified through two ways:
391 * (1) by calling the vtkImageReader2::SetFileName(), SetFilePrefix() and
393 * (2) By successive calls to vtkGdcmReader::AddFileName()
394 * When the first method was used by caller we need to update the local
397 void vtkGdcmReader::BuildFileListFromPattern()
399 this->RemoveAllInternalFileName();
401 // Test miscellanous cases
402 if ((! this->FileNameList.empty()) && this->FileName )
404 vtkErrorMacro(<< "Both AddFileName and SetFileName schemes were used");
405 vtkErrorMacro(<< "No images loaded ! ");
409 if ((! this->FileNameList.empty()) && this->FilePrefix )
411 vtkErrorMacro(<< "Both AddFileName and SetFilePrefix schemes were used");
412 vtkErrorMacro(<< "No images loaded ! ");
416 if (this->FileName && this->FilePrefix)
418 vtkErrorMacro(<< "Both SetFileName and SetFilePrefix schemes were used");
419 vtkErrorMacro(<< "No images loaded ! ");
423 // Create the InternalFileNameList
424 if (! this->FileNameList.empty() )
426 vtkDebugMacro(<< "Using the AddFileName specified files");
427 this->InternalFileNameList=this->FileNameList;
431 if (!this->FileName && !this->FilePrefix)
433 vtkErrorMacro(<< "FileNames are not set. Either use AddFileName() or");
434 vtkErrorMacro(<< "specify a FileName or FilePrefix.");
440 // Single file loading (as given with ::SetFileName()):
441 // Case of multi-frame file considered here
442 this->ComputeInternalFileName(this->DataExtent[4]);
443 vtkDebugMacro(<< "Adding file " << this->InternalFileName);
444 this->AddInternalFileName(this->InternalFileName);
448 // Multi file loading (as given with ::SetFilePattern()):
449 for (int idx = this->DataExtent[4]; idx <= this->DataExtent[5]; ++idx)
451 this->ComputeInternalFileName(idx);
452 vtkDebugMacro(<< "Adding file " << this->InternalFileName);
453 this->AddInternalFileName(this->InternalFileName);
459 * Load all the files and set it in the InternalFileList
460 * For each file, the readability and the coherence of image caracteristics
461 * are tested. If an image doesn't agree the required specifications, it
462 * isn't considered and no data will be set for the planes corresponding
465 * The source of this work is the list of file name generated by the
466 * BuildFileListFromPattern method
468 void vtkGdcmReader::LoadFileInformation()
470 GDCM_NAME_SPACE::File *file;
471 bool foundReference=false;
475 for (std::list<std::string>::iterator filename = InternalFileNameList.begin();
476 filename != InternalFileNameList.end();
479 // check for file readability
481 fp = fopen(filename->c_str(),"rb");
484 vtkErrorMacro(<< "Unable to open file " << filename->c_str());
485 vtkErrorMacro(<< "Removing this file from read files: "
486 << filename->c_str());
488 InternalFileList.push_back(file);
494 file=GDCM_NAME_SPACE::File::New();
495 file->SetLoadMode( LoadMode );
496 file->SetFileName(filename->c_str() );
499 // Test the Dicom file readability
500 if(!file->IsReadable())
502 vtkErrorMacro(<< "Gdcm cannot parse file " << filename->c_str());
503 vtkErrorMacro(<< "Removing this file from read files: "
504 << filename->c_str());
507 InternalFileList.push_back(file);
511 // Test the Pixel Type recognition
512 type = file->GetPixelType();
513 if ( (type != "8U") && (type != "8S")
514 && (type != "16U") && (type != "16S")
515 && (type != "32U") && (type != "32S")
516 && (type != "FD") ) // Sure this one is NOT kosher
518 vtkErrorMacro(<< "Bad File Type for file " << filename->c_str() << "\n"
519 << " File type found : " << type.c_str()
520 << " (might be 8U, 8S, 16U, 16S, 32U, 32S, FD) \n"
521 << " Removing this file from read files");
524 InternalFileList.push_back(file);
528 // Test the image informations
531 foundReference = true;
532 GetFileInformation(file);
534 vtkDebugMacro(<< "This file taken as coherence reference:"
535 << filename->c_str());
536 vtkDebugMacro(<< "Image dimensions of reference file as read from Gdcm:"
537 << this->NumColumns << " " << this->NumLines << " "
540 else if(!TestFileInformation(file))
546 InternalFileList.push_back(file);
551 * Update the file informations.
552 * This works exactly like LoadFileInformation, but the source of work
553 * is the list of coherent files
555 void vtkGdcmReader::UpdateFileInformation()
557 this->InternalFileList=*(this->CoherentFileList);
560 for(gdcmFileList::iterator it=InternalFileList.begin();
561 it!=InternalFileList.end();
566 GetFileInformation(*it);
573 * Get the informations from a file.
574 * These informations are required to specify the output image
577 void vtkGdcmReader::GetFileInformation(GDCM_NAME_SPACE::File *file)
579 // Get the image caracteristics
580 this->NumColumns = file->GetXSize();
581 this->NumLines = file->GetYSize();
582 this->NumPlanes = file->GetZSize();
584 if (CoherentFileList == 0)
585 this->TotalNumberOfPlanes = this->NumPlanes*InternalFileNameList.size();
587 this->TotalNumberOfPlanes = this->NumPlanes*CoherentFileList->size();
589 this->ImageType = file->GetPixelType();
590 this->PixelSize = file->GetPixelSize();
592 this->DataSpacing[0] = file->GetXSpacing();
593 this->DataSpacing[1] = file->GetYSpacing();
595 // Most of the file headers have NO z spacing
596 // It must be calculated from the whole GDCM_NAME_SPACE::Serie (if any)
597 // using Jolinda Smith's algoritm.
598 // see GDCM_NAME_SPACE::SerieHelper::ImagePositionPatientOrdering()
599 if (CoherentFileList == 0)
600 this->DataSpacing[2] = file->GetZSpacing();
603 // Just because OrderFileList() is a member of GDCM_NAME_SPACE::SerieHelper
604 // we need to instanciate sh.
605 GDCM_NAME_SPACE::SerieHelper *sh = GDCM_NAME_SPACE::SerieHelper::New();
606 sh->OrderFileList(CoherentFileList); // calls ImagePositionPatientOrdering()
607 this->DataSpacing[2] = sh->GetZSpacing();
611 // Get the image data caracteristics
612 if( file->HasLUT() && this->AllowLookupTable )
614 // I could raise an error is AllowLookupTable is on and HasLUT() off
615 this->NumComponents = file->GetNumberOfScalarComponentsRaw();
619 this->NumComponents = file->GetNumberOfScalarComponents(); //rgb or mono
624 * When more than one filename is specified (i.e. we expect loading
625 * a stack or volume) we need to check that the corresponding images/volumes
626 * to be loaded are coherent i.e. to make sure:
627 * - they all share the same X dimensions
628 * - they all share the same Y dimensions
629 * - they all share the same ImageType ( 8 bit signed, or unsigned...)
631 * Eventually, we emit a warning when all the files do NOT share the
632 * Z dimension, since we can still build a stack but the
633 * files are not coherent in Z, which is probably a source a trouble...
634 * When files are not readable (either the file cannot be opened or
635 * because gdcm cannot parse it), they are flagged as "GDCM_UNREADABLE".
636 * This method returns the total number of planar images to be loaded
637 * (i.e. an image represents one plane, but a volume represents many planes)
640 * Test the coherent informations of the file with the reference informations
641 * used as image caracteristics. The tested informations are :
642 * - they all share the same X dimensions
643 * - they all share the same Y dimensions
644 * - they all share the same Z dimensions
645 * - they all share the same number of components
646 * - they all share the same ImageType ( 8 bit signed, or unsigned...)
648 * \return True if the file match, False otherwise
650 bool vtkGdcmReader::TestFileInformation(GDCM_NAME_SPACE::File *file)
652 int numColumns = file->GetXSize();
653 int numLines = file->GetYSize();
654 int numPlanes = file->GetZSize();
656 unsigned int pixelSize = file->GetPixelSize();
658 if( file->HasLUT() && this->AllowLookupTable )
659 numComponents = file->GetNumberOfScalarComponentsRaw();
661 numComponents = file->GetNumberOfScalarComponents(); //rgb or mono
663 if( numColumns != this->NumColumns )
665 vtkErrorMacro(<< "File X value doesn't match with the previous ones: "
666 << file->GetFileName().c_str()
667 << ". Found " << numColumns << ", must be "
668 << this->NumColumns);
671 if( numLines != this->NumLines )
673 vtkErrorMacro(<< "File Y value doesn't match with the previous ones: "
674 << file->GetFileName().c_str()
675 << ". Found " << numLines << ", must be "
679 if( numPlanes != this->NumPlanes )
681 vtkErrorMacro(<< "File Z value doesn't match with the previous ones: "
682 << file->GetFileName().c_str()
683 << ". Found " << numPlanes << ", must be "
687 if( numComponents != this->NumComponents )
689 vtkErrorMacro(<< "File Components count doesn't match with the previous ones: "
690 << file->GetFileName().c_str()
691 << ". Found " << numComponents << ", must be "
692 << this->NumComponents);
695 if( pixelSize != this->PixelSize )
697 vtkErrorMacro(<< "File pixel size doesn't match with the previous ones: "
698 << file->GetFileName().c_str()
699 << ". Found " << pixelSize << ", must be "
707 //-----------------------------------------------------------------------------
710 * Remove all file names to the internal list of images to read.
712 void vtkGdcmReader::RemoveAllInternalFileName(void)
714 this->InternalFileNameList.clear();
718 * Adds a file name to the internal list of images to read.
720 void vtkGdcmReader::AddInternalFileName(const char *name)
722 char *LocalName = new char[strlen(name) + 1];
723 strcpy(LocalName, name);
724 this->InternalFileNameList.push_back(LocalName);
729 * Remove all file names to the internal list of images to read.
731 void vtkGdcmReader::RemoveAllInternalFile(void)
735 for(gdcmFileList::iterator it=InternalFileList.begin();
736 it!=InternalFileList.end();
742 this->InternalFileList.clear();
745 void vtkGdcmReader::IncrementProgress(const unsigned long updateProgressTarget,
746 unsigned long &updateProgressCount)
748 // Update progress related for bad files:
749 updateProgressCount += this->NumLines;
750 if (updateProgressTarget > 0)
752 if (!(updateProgressCount%updateProgressTarget))
754 this->UpdateProgress(
755 updateProgressCount/(50.0*updateProgressTarget));
761 * Loads the contents of the image/volume contained by char *fileName at
762 * the dest memory address. Returns the size of the data loaded.
764 /*void vtkGdcmReader::LoadImageInMemory(
765 std::string fileName,
767 const unsigned long updateProgressTarget,
768 unsigned long &updateProgressCount)
770 vtkDebugMacro(<< "Copying to memory image [" << fileName.c_str() << "]");
772 GDCM_NAME_SPACE::File *f;
773 f = new GDCM_NAME_SPACE::File();
774 f->SetLoadMode( LoadMode );
775 f->SetFileName( fileName.c_str() );
778 LoadImageInMemory(f,dest,
779 updateProgressTarget,
780 updateProgressCount);
785 * Loads the contents of the image/volume contained by GDCM_NAME_SPACE::File* f at
786 * the Dest memory address. Returns the size of the data loaded.
787 * \ param f File to consider. NULL if the file must be skiped
788 * \remarks Assume that if (f != NULL) then its caracteristics match
789 * with the previous ones
791 void vtkGdcmReader::LoadImageInMemory(
792 GDCM_NAME_SPACE::File *f,
794 const unsigned long updateProgressTarget,
795 unsigned long &updateProgressCount)
800 GDCM_NAME_SPACE::FileHelper *fileH = GDCM_NAME_SPACE::FileHelper::New( f );
801 fileH->SetUserFunction( UserFunction );
803 fileH->SetKeepOverlays ( this->KeepOverlays);
805 int numColumns = f->GetXSize();
806 int numLines = f->GetYSize();
807 int numPlanes = f->GetZSize();
810 if( f->HasLUT() && this->AllowLookupTable )
811 numComponents = f->GetNumberOfScalarComponentsRaw();
813 numComponents = f->GetNumberOfScalarComponents(); //rgb or mono
814 vtkDebugMacro(<< "numComponents:" << numComponents);
815 vtkDebugMacro(<< "Copying to memory image [" << f->GetFileName().c_str() << "]");
818 // If the data structure of vtk for image/volume representation
819 // were straigthforwards the following would be enough:
820 // GdcmFile.GetImageDataIntoVector((void*)Dest, size);
821 // But vtk chooses to invert the lines of an image, that is the last
822 // line comes first (for some axis related reasons?). Hence we need
823 // to load the image line by line, starting from the end.
825 int lineSize = NumComponents * numColumns * f->GetPixelSize();
826 int planeSize = lineSize * numLines;
830 if( fileH->GetFile()->HasLUT() && AllowLookupTable )
832 // to avoid bcc 5.5 w
833 /*size = */ fileH->GetImageDataSize();
834 src = (unsigned char*) fileH->GetImageDataRaw();
835 unsigned char *lut = (unsigned char*) fileH->GetLutRGBA();
837 if(!this->LookupTable)
839 this->LookupTable = vtkLookupTable::New();
842 this->LookupTable->SetNumberOfTableValues(256);
843 for (int tmp=0; tmp<256; tmp++)
845 this->LookupTable->SetTableValue(tmp,
846 (float)lut[4*tmp+0]/255.0,
847 (float)lut[4*tmp+1]/255.0,
848 (float)lut[4*tmp+2]/255.0,
851 this->LookupTable->SetRange(0,255);
852 vtkDataSetAttributes *a = this->GetOutput()->GetPointData();
853 a->GetScalars()->SetLookupTable(this->LookupTable);
858 //size = fileH->GetImageDataSize();
859 // useless - just an accessor; 'size' unused
860 //if (this->GetFlipY())
861 src = (unsigned char*)fileH->GetImageData();
863 // very strange, but it doesn't work (I have to memcpy the pixels ?!?)
864 // dest = (unsigned char*)fileH->GetImageData();
867 if (this->GetFlipY()) {
868 unsigned char *dst = dest + planeSize - lineSize;
869 for (int plane = 0; plane < numPlanes; plane++)
871 for (int line = 0; line < numLines; line++)
873 // Copy one line at proper destination:
874 memcpy((void*)dst, (void*)src, lineSize);
877 // Update progress related:
878 if (!(updateProgressCount%updateProgressTarget))
880 this->UpdateProgress(
881 updateProgressCount/(50.0*updateProgressTarget));
883 updateProgressCount++;
885 dst += 2 * planeSize;
888 else // we don't flip (upside down) the image
890 memcpy((void*)dest, (void*)src, numPlanes * numLines * lineSize);
895 //-----------------------------------------------------------------------------