vtkGdcmReader.cxx

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00001 /*=========================================================================
00002                                                                                 
00003   Program:   gdcm
00004   Module:    $RCSfile: vtkGdcmReader.cxx,v $
00005   Language:  C++
00006   Date:      $Date: 2007/06/21 14:47:16 $
00007   Version:   $Revision: 1.91 $
00008                                                                                 
00009   Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
00010   l'Image). All rights reserved. See Doc/License.txt or
00011   http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
00012                                                                                 
00013      This software is distributed WITHOUT ANY WARRANTY; without even
00014      the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
00015      PURPOSE.  See the above copyright notices for more information.
00016                                                                                 
00017 =========================================================================*/
00018                                                                                 
00019 //-----------------------------------------------------------------------------
00020 // //////////////////////////////////////////////////////////////
00021 //
00022 //===>  Many users expect from vtkGdcmReader it 'orders' the images
00023 //     (that's the job of GDCM_NAME_SPACE::SerieHelper ...)
00024 //     When user *knows* the files with same Serie UID 
00025 //        have same sizes, same 'pixel' type, same color convention, ...
00026 //     the right way to proceed is as follow :
00027 //
00028 //      GDCM_NAME_SPACE::SerieHelper *sh= new GDCM_NAME_SPACE::SerieHelper();
00029 //      // if user wants *not* to load some parts of the file headers
00030 //      sh->SetLoadMode(loadMode);
00031 //
00032 //      // if user wants *not* to load some files 
00033 //      sh->AddRestriction(group, element, value, operator);
00034 //      sh->AddRestriction( ...
00035 //      sh->SetDirectory(directoryWithImages);
00036 //
00037 //      // if user wants to sort reverse order
00038 //      sh->SetSortOrderToReverse(); 
00039 //
00040 //      // here, we suppose only the first 'Serie' is of interest
00041 //      // it's up to the user to decide !
00042 //      GDCM_NAME_SPACE::FileList *l = sh->GetFirstSingleSerieUIDFileSet();
00043 //
00044 //      // if user is doesn't trust too much the files with same Serie UID 
00045 //      if ( !sh->IsCoherent(l) )
00046 //         return; // not same sizes, same 'pixel' type -> stop
00047 //
00048 //      // WARNING : all  that follows works only with 'bona fide' Series
00049 //      // (In some Series; there are more than one 'orientation'
00050 //      // Don't expected to build a 'volume' with that!
00051 //      //
00052 //      // -> use sh->SplitOnOrientation(l)
00053 //      //  - or sh->SplitOnPosition(l), or SplitOnTagValue(l, gr, el) -
00054 //      // depending on what you want to do
00055 //      // and iterate on the various 'X Coherent File Sets'
00056 //
00057 //      // if user *knows* he has to drop the 'duplicates' images
00058 //      // (same Position)
00059 //      sh->SetDropDuplicatePositions(true);
00060 //
00061 //      // Sorting the list is mandatory
00062 //      // a side effect is to compute ZSpacing for the fle set
00063 //      sh->OrderFileList(l);        // sort the list
00064 //
00065 //      vtkGdcmReader *reader = vtkGdcmReader::New();
00066 //
00067 //      // if user wants to modify pixel order (Mirror, TopDown, 90°Rotate, ...)
00068 //      // he has to supply the function that does the job 
00069 //      // (a *very* simple example is given in vtkgdcmSerieViewer.cxx)
00070 //      reader->SetUserFunction (userSuppliedFunction);
00071 //
00072 //      // to pass a 'Coherent File List' as produced by GDCM_NAME_SPACE::SerieHelper
00073 //      reader->SetCoherentFileList(l); 
00074 //      reader->Update();
00075 //
00076 // WARNING TODO CLEANME 
00077 // Actual limitations of this code 
00078 //  when a Coherent File List from SerieHelper is not used (bad idea :-(
00079 //
00080 // //////////////////////////////////////////////////////////////
00081 
00082 #include "gdcmFileHelper.h"
00083 #include "gdcmFile.h"
00084 #include "gdcmSerieHelper.h" // for ImagePositionPatientOrdering()
00085 
00086 #include "vtkGdcmReader.h"
00087 #include "gdcmDebug.h"
00088 #include "gdcmCommon.h"
00089 
00090 #include <vtkObjectFactory.h>
00091 #include <vtkImageData.h>
00092 #include <vtkPointData.h>
00093 #include <vtkLookupTable.h>
00094 
00095 vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.91 $")
00096 vtkStandardNewMacro(vtkGdcmReader)
00097 
00098 //-----------------------------------------------------------------------------
00099 // Constructor / Destructor
00100 vtkGdcmReader::vtkGdcmReader()
00101 {
00102    this->LookupTable = NULL;
00103    this->AllowLookupTable = false;
00104    //this->AllowLightChecking = false;
00105    this->LoadMode = GDCM_NAME_SPACE::LD_ALL; // Load everything (possible values : 
00106                                   //  - LD_NOSEQ, 
00107                                   //  - LD_NOSHADOW,
00108                                   //  - LD_NOSHADOWSEQ)
00109    this->CoherentFileList = 0;
00110    this->UserFunction     = 0;
00111 
00112    this->OwnFile=true;
00113    // this->Execution=false; // For VTK5.0
00114 }
00115 
00116 vtkGdcmReader::~vtkGdcmReader()
00117 {
00118    this->RemoveAllFileName();
00119    this->InternalFileNameList.clear();
00120    if(this->LookupTable) 
00121       this->LookupTable->Delete();
00122 }
00123 
00124 //-----------------------------------------------------------------------------
00125 // Print
00126 void vtkGdcmReader::PrintSelf(ostream &os, vtkIndent indent)
00127 {
00128    this->Superclass::PrintSelf(os,indent);
00129    os << indent << "Filenames  : " << endl;
00130    vtkIndent nextIndent = indent.GetNextIndent();
00131    for (std::list<std::string>::iterator it = FileNameList.begin();
00132         it != FileNameList.end();
00133         ++it)
00134    {
00135       os << nextIndent << it->c_str() << endl ;
00136    }
00137 }
00138 
00139 //-----------------------------------------------------------------------------
00140 // Public
00141 /*
00142  * Remove all files from the list of images to read.
00143  */
00144 void vtkGdcmReader::RemoveAllFileName(void)
00145 {
00146    this->FileNameList.clear();
00147    this->Modified();
00148 }
00149 
00150 /*
00151  * Adds a file name to the list of images to read.
00152  */
00153 void vtkGdcmReader::AddFileName(const char* name)
00154 {
00155    // We need to bypass the const pointer [since list<>.push_bash() only
00156    // takes a char* (but not a const char*)] by making a local copy:
00157    this->FileNameList.push_back(name);
00158    this->Modified();
00159 }
00160 
00161 /*
00162  * Sets up a filename to be read.
00163  */
00164 void vtkGdcmReader::SetFileName(const char *name) 
00165 {
00166    vtkImageReader2::SetFileName(name);
00167    // Since we maintain a list of filenames, when building a volume,
00168    // (see vtkGdcmReader::AddFileName), we additionaly need to purge
00169    // this list when we manually positionate the filename.
00170    vtkDebugMacro(<< "Clearing all files given with AddFileName");
00171    this->FileNameList.clear();
00172    this->Modified();
00173 }
00174 
00175 //-----------------------------------------------------------------------------
00176 // Protected
00177 /*
00178  * Configure the output e.g. WholeExtent, spacing, origin, scalar type...
00179  */
00180 void vtkGdcmReader::ExecuteInformation()
00181 {
00182 //   if(this->Execution)  // For VTK5.0
00183 //      return;
00184 //
00185 //   this->Execution=true; // end For VTK5.0
00186    this->RemoveAllInternalFile();
00187    if(this->MTime>this->fileTime)
00188    {
00189       this->TotalNumberOfPlanes = 0;
00190 
00191       if ( this->CoherentFileList != 0 )
00192       {
00193          this->UpdateFileInformation();
00194       }
00195       else
00196       {
00197          this->BuildFileListFromPattern();
00198          this->LoadFileInformation();
00199       }
00200 
00201       if ( this->TotalNumberOfPlanes == 0)
00202       {
00203          vtkErrorMacro(<< "File set is not coherent. Exiting...");
00204          return;
00205       }
00206 
00207       // if the user has not set the extent, but has set the VOI
00208       // set the z axis extent to the VOI z axis
00209       if (this->DataExtent[4]==0 && this->DataExtent[5] == 0 &&
00210          (this->DataVOI[4] || this->DataVOI[5]))
00211       {
00212          this->DataExtent[4] = this->DataVOI[4];
00213          this->DataExtent[5] = this->DataVOI[5];
00214       }
00215 
00216       // When the user has set the VOI, check it's coherence with the file content.
00217       if (this->DataVOI[0] || this->DataVOI[1] || 
00218       this->DataVOI[2] || this->DataVOI[3] ||
00219       this->DataVOI[4] || this->DataVOI[5])
00220       { 
00221          if ((this->DataVOI[0] < 0) ||
00222              (this->DataVOI[1] >= this->NumColumns) ||
00223              (this->DataVOI[2] < 0) ||
00224              (this->DataVOI[3] >= this->NumLines) ||
00225              (this->DataVOI[4] < 0) ||
00226              (this->DataVOI[5] >= this->TotalNumberOfPlanes ))
00227          {
00228             vtkWarningMacro(<< "The requested VOI is larger than expected extent.");
00229             this->DataVOI[0] = 0;
00230             this->DataVOI[1] = this->NumColumns - 1;
00231             this->DataVOI[2] = 0;
00232             this->DataVOI[3] = this->NumLines - 1;
00233             this->DataVOI[4] = 0;
00234             this->DataVOI[5] = this->TotalNumberOfPlanes - 1;
00235          }
00236       }
00237 
00238       // Set the Extents.
00239       this->DataExtent[0] = 0;
00240       this->DataExtent[1] = this->NumColumns - 1;
00241       this->DataExtent[2] = 0;
00242       this->DataExtent[3] = this->NumLines - 1;
00243       this->DataExtent[4] = 0;
00244       this->DataExtent[5] = this->TotalNumberOfPlanes - 1;
00245   
00246       // We don't need to set the Endian related stuff (by using
00247       // this->SetDataByteOrderToBigEndian() or SetDataByteOrderToLittleEndian()
00248       // since the reading of the file is done by gdcm.
00249       // But we do need to set up the data type for downstream filters:
00250       if      ( ImageType == "8U" )
00251       {
00252          vtkDebugMacro(<< "8 bits unsigned image");
00253          this->SetDataScalarTypeToUnsignedChar(); 
00254       }
00255       else if ( ImageType == "8S" )
00256       {
00257          vtkErrorMacro(<< "Cannot handle 8 bit signed files");
00258          return;
00259       }
00260       else if ( ImageType == "16U" )
00261       {
00262          vtkDebugMacro(<< "16 bits unsigned image");
00263          this->SetDataScalarTypeToUnsignedShort();
00264       }
00265       else if ( ImageType == "16S" )
00266       {
00267          vtkDebugMacro(<< "16 bits signed image");
00268          this->SetDataScalarTypeToShort();
00269       }
00270       else if ( ImageType == "32U" )
00271       {
00272          vtkDebugMacro(<< "32 bits unsigned image");
00273          vtkDebugMacro(<< "WARNING: forced to signed int !");
00274          this->SetDataScalarTypeToInt();
00275       }
00276       else if ( ImageType == "32S" )
00277       {
00278          vtkDebugMacro(<< "32 bits signed image");
00279          this->SetDataScalarTypeToInt();
00280       }
00281       else if ( ImageType == "FD" )
00282       {
00283          vtkDebugMacro(<< "64 bits Double image");
00284          this->SetDataScalarTypeToDouble();
00285       }
00286       //Set number of scalar components:
00287       this->SetNumberOfScalarComponents(this->NumComponents);
00288 
00289       this->fileTime=this->MTime;
00290    }
00291 
00292    this->Superclass::ExecuteInformation();  
00293 
00294    //this->GetOutput()->SetUpdateExtentToWholeExtent();// For VTK5.0
00295    //this->BuildData(this->GetOutput());
00296 
00297    //this->Execution=false;
00298    //this->RemoveAllInternalFile();                   // End For VTK5.0
00299 }
00300  
00301 /*
00302  * Update => ouput->Update => UpdateData => Execute => ExecuteData 
00303  * (see vtkSource.cxx for last step).
00304  * This function (redefinition of vtkImageReader::ExecuteData, see 
00305  * VTK/IO/vtkImageReader.cxx) reads a data from a file. The data
00306  * extent/axes are assumed to be the same as the file extent/order.
00307  */
00308 void vtkGdcmReader::ExecuteData(vtkDataObject *output)
00309 {
00310    vtkImageData *data=vtkImageData::SafeDownCast(output);
00311    data->SetExtent(this->DataExtent);
00312 
00313 /*   if ( CoherentFileList != 0 )   // When a list of names is passed
00314    {
00315       if (this->CoherentFileList->empty())
00316       {
00317          vtkErrorMacro(<< "Coherent File List must have at least a valid File*.");
00318          return;
00319       }
00320    }
00321    else if (this->InternalFileNameList.empty())
00322    {
00323       vtkErrorMacro(<< "A least a valid FileName must be specified.");
00324       return;
00325    }
00326 */
00327   
00328   // data->AllocateScalars();  // For VTK5.0
00329   // if (this->UpdateExtentIsEmpty(output))
00330   // {
00331   //    return;
00332   // }
00333 //}                           // end For VTK5.0
00334 
00335    data->AllocateScalars();  // For VTK5.0
00336    if (this->UpdateExtentIsEmpty(output))
00337    {
00338       return;
00339    }
00340    
00341 //void vtkGdcmReader::BuildData(vtkDataObject *output)  // For VTK5.0
00342 //{
00343 //   vtkImageData *data = this->AllocateOutputData(output);  // end For VTK5.0
00344 
00345    data->GetPointData()->GetScalars()->SetName("DicomImage-Volume");
00346 
00347    // Test if output has valid extent
00348    // Prevent memory errors
00349    if((this->DataExtent[1]-this->DataExtent[0]>=0) &&
00350       (this->DataExtent[3]-this->DataExtent[2]>=0) &&
00351       (this->DataExtent[5]-this->DataExtent[4]>=0))
00352    {
00353       // The memory size for a full stack of images of course depends
00354       // on the number of planes and the size of each image:
00355       //size_t StackNumPixels = this->NumColumns * this->NumLines
00356       //                      * this->TotalNumberOfPlanes * this->NumComponents;
00357       //size_t stack_size = StackNumPixels * this->PixelSize; //not used
00358       // Allocate pixel data space itself.
00359 
00360       // Variables for the UpdateProgress. We shall use 50 steps to signify
00361       // the advance of the process:
00362       unsigned long UpdateProgressTarget = (unsigned long) ceil (this->NumLines
00363                                          * this->TotalNumberOfPlanes
00364                                          / 50.0);
00365       // The actual advance measure:
00366       unsigned long UpdateProgressCount = 0;
00367 
00368       // Filling the allocated memory space with each image/volume:
00369 
00370       size_t size = this->NumColumns * this->NumLines * this->NumPlanes
00371                   * data->GetScalarSize() * this->NumComponents;
00372       unsigned char *Dest = (unsigned char *)data->GetScalarPointer();
00373       for (std::vector<GDCM_NAME_SPACE::File* >::iterator it =  InternalFileList.begin();
00374                                                it != InternalFileList.end();
00375                                              ++it)
00376       {
00377          this->LoadImageInMemory(*it, Dest,
00378                                  UpdateProgressTarget,
00379                                  UpdateProgressCount); 
00380          Dest += size;
00381       }
00382    }
00383    this->RemoveAllInternalFile(); // For VTK5.0
00384 }
00385 
00386 /*
00387  * vtkGdcmReader can have the file names specified through two ways:
00388  * (1) by calling the vtkImageReader2::SetFileName(), SetFilePrefix() and
00389  *     SetFilePattern()
00390  * (2) By successive calls to vtkGdcmReader::AddFileName()
00391  * When the first method was used by caller we need to update the local
00392  * filename list
00393  */
00394 void vtkGdcmReader::BuildFileListFromPattern()
00395 {
00396    this->RemoveAllInternalFileName();
00397 
00398    // Test miscellanous cases
00399    if ((! this->FileNameList.empty()) && this->FileName )
00400    {
00401       vtkErrorMacro(<< "Both AddFileName and SetFileName schemes were used");
00402       vtkErrorMacro(<< "No images loaded ! ");
00403       return;
00404    }
00405 
00406    if ((! this->FileNameList.empty()) && this->FilePrefix )
00407    {
00408       vtkErrorMacro(<< "Both AddFileName and SetFilePrefix schemes were used");
00409       vtkErrorMacro(<< "No images loaded ! ");
00410       return;
00411    }
00412 
00413    if (this->FileName && this->FilePrefix)
00414    {
00415       vtkErrorMacro(<< "Both SetFileName and SetFilePrefix schemes were used");
00416       vtkErrorMacro(<< "No images loaded ! ");
00417       return;
00418    }
00419 
00420    // Create the InternalFileNameList
00421    if (! this->FileNameList.empty()  )
00422    {
00423       vtkDebugMacro(<< "Using the AddFileName specified files");
00424       this->InternalFileNameList=this->FileNameList;
00425       return;
00426    }
00427 
00428    if (!this->FileName && !this->FilePrefix)
00429    {
00430       vtkErrorMacro(<< "FileNames are not set. Either use AddFileName() or");
00431       vtkErrorMacro(<< "specify a FileName or FilePrefix.");
00432       return;
00433    }
00434 
00435    if( this->FileName )
00436    {
00437       // Single file loading (as given with ::SetFileName()):
00438       // Case of multi-frame file considered here
00439       this->ComputeInternalFileName(this->DataExtent[4]);
00440       vtkDebugMacro(<< "Adding file " << this->InternalFileName);
00441       this->AddInternalFileName(this->InternalFileName);
00442    }
00443    else
00444    {
00445       // Multi file loading (as given with ::SetFilePattern()):
00446       for (int idx = this->DataExtent[4]; idx <= this->DataExtent[5]; ++idx)
00447       {
00448          this->ComputeInternalFileName(idx);
00449          vtkDebugMacro(<< "Adding file " << this->InternalFileName);
00450          this->AddInternalFileName(this->InternalFileName);
00451       }
00452    }
00453 }
00454 
00465 void vtkGdcmReader::LoadFileInformation()
00466 {
00467    GDCM_NAME_SPACE::File *file;
00468    bool foundReference=false;
00469    std::string type;
00470 
00471    this->OwnFile=true;
00472    for (std::list<std::string>::iterator filename = InternalFileNameList.begin();
00473         filename != InternalFileNameList.end();
00474         ++filename)
00475    {
00476       // check for file readability
00477       FILE *fp;
00478       fp = fopen(filename->c_str(),"rb");
00479       if (!fp)
00480       {
00481          vtkErrorMacro(<< "Unable to open file " << filename->c_str());
00482          vtkErrorMacro(<< "Removing this file from read files: "
00483                        << filename->c_str());
00484          file = NULL;
00485          InternalFileList.push_back(file);
00486          continue;
00487       }
00488       fclose(fp);
00489 
00490       // Read the file
00491       file=GDCM_NAME_SPACE::File::New();
00492       file->SetLoadMode( LoadMode );
00493       file->SetFileName(filename->c_str() );
00494       file->Load();
00495 
00496       // Test the Dicom file readability
00497       if(!file->IsReadable())
00498       {
00499          vtkErrorMacro(<< "Gdcm cannot parse file " << filename->c_str());
00500          vtkErrorMacro(<< "Removing this file from read files: "
00501                         << filename->c_str());
00502          file->Delete();
00503          file=NULL;
00504          InternalFileList.push_back(file);
00505          continue;
00506       }
00507 
00508       // Test the Pixel Type recognition
00509       type = file->GetPixelType();
00510       if (   (type !=  "8U") && (type !=  "8S")
00511           && (type != "16U") && (type != "16S")
00512           && (type != "32U") && (type != "32S") )
00513       {
00514          vtkErrorMacro(<< "Bad File Type for file " << filename->c_str() << "\n"
00515                        << "   File type found : " << type.c_str() 
00516                        << " (might be 8U, 8S, 16U, 16S, 32U, 32S) \n"
00517                        << "   Removing this file from read files");
00518          file->Delete();
00519          file=NULL;
00520          InternalFileList.push_back(file);
00521          continue;
00522       }
00523 
00524       // Test the image informations
00525       if(!foundReference)
00526       {
00527          foundReference = true;
00528          GetFileInformation(file);
00529 
00530          vtkDebugMacro(<< "This file taken as coherence reference:"
00531                         << filename->c_str());
00532          vtkDebugMacro(<< "Image dimensions of reference file as read from Gdcm:" 
00533                         << this->NumColumns << " " << this->NumLines << " " 
00534                         << this->NumPlanes);
00535       }
00536       else if(!TestFileInformation(file))
00537       {
00538          file->Delete();
00539          file=NULL;
00540       }
00541 
00542       InternalFileList.push_back(file);
00543    }
00544 }
00545 
00551 void vtkGdcmReader::UpdateFileInformation()
00552 {
00553    this->InternalFileList=*(this->CoherentFileList);
00554    this->OwnFile=false;
00555 
00556    for(gdcmFileList::iterator it=InternalFileList.begin();
00557                               it!=InternalFileList.end();
00558                               ++it)
00559    {
00560       if( *it != NULL)
00561       {
00562          GetFileInformation(*it);
00563          break;
00564       }
00565    }
00566 }
00567 
00573 void vtkGdcmReader::GetFileInformation(GDCM_NAME_SPACE::File *file)
00574 {
00575    // Get the image caracteristics
00576    this->NumColumns = file->GetXSize();
00577    this->NumLines   = file->GetYSize();
00578    this->NumPlanes  = file->GetZSize();
00579 
00580    if (CoherentFileList == 0)
00581       this->TotalNumberOfPlanes = this->NumPlanes*InternalFileNameList.size();
00582    else
00583       this->TotalNumberOfPlanes = this->NumPlanes*CoherentFileList->size();
00584 
00585    this->ImageType = file->GetPixelType();
00586    this->PixelSize = file->GetPixelSize();
00587 
00588    this->DataSpacing[0] = file->GetXSpacing();
00589    this->DataSpacing[1] = file->GetYSpacing();
00590    
00591    //  Most of the file headers have NO z spacing
00592    //  It must be calculated from the whole GDCM_NAME_SPACE::Serie (if any)
00593    //  using Jolinda Smith's algoritm.
00594    //  see GDCM_NAME_SPACE::SerieHelper::ImagePositionPatientOrdering()
00595    if (CoherentFileList == 0)   
00596       this->DataSpacing[2] = file->GetZSpacing();
00597    else
00598    {
00599        // Just because OrderFileList() is a member of GDCM_NAME_SPACE::SerieHelper
00600        // we need to instanciate sh.
00601       GDCM_NAME_SPACE::SerieHelper *sh = GDCM_NAME_SPACE::SerieHelper::New();
00602       sh->OrderFileList(CoherentFileList); // calls ImagePositionPatientOrdering()
00603       this->DataSpacing[2] = sh->GetZSpacing();
00604       sh->Delete();         
00605    } 
00606 
00607    // Get the image data caracteristics
00608    if( file->HasLUT() && this->AllowLookupTable )
00609    {
00610       // I could raise an error is AllowLookupTable is on and HasLUT() off
00611       this->NumComponents = file->GetNumberOfScalarComponentsRaw();
00612    }
00613    else
00614    {
00615       this->NumComponents = file->GetNumberOfScalarComponents(); //rgb or mono
00616    }
00617 }
00618 
00619 /*
00620  * When more than one filename is specified (i.e. we expect loading
00621  * a stack or volume) we need to check that the corresponding images/volumes
00622  * to be loaded are coherent i.e. to make sure:
00623  *     - they all share the same X dimensions
00624  *     - they all share the same Y dimensions
00625  *     - they all share the same ImageType ( 8 bit signed, or unsigned...)
00626  *
00627  * Eventually, we emit a warning when all the files do NOT share the
00628  * Z dimension, since we can still build a stack but the
00629  * files are not coherent in Z, which is probably a source a trouble...
00630  *   When files are not readable (either the file cannot be opened or
00631  * because gdcm cannot parse it), they are flagged as "GDCM_UNREADABLE".  
00632  *   This method returns the total number of planar images to be loaded
00633  * (i.e. an image represents one plane, but a volume represents many planes)
00634  */
00646 bool vtkGdcmReader::TestFileInformation(GDCM_NAME_SPACE::File *file)
00647 {
00648    int numColumns = file->GetXSize();
00649    int numLines   = file->GetYSize();
00650    int numPlanes  = file->GetZSize();
00651    int numComponents;
00652    unsigned int pixelSize  = file->GetPixelSize();
00653 
00654    if( file->HasLUT() && this->AllowLookupTable )
00655       numComponents = file->GetNumberOfScalarComponentsRaw();
00656    else
00657       numComponents = file->GetNumberOfScalarComponents(); //rgb or mono
00658 
00659    if( numColumns != this->NumColumns )
00660    {
00661       vtkErrorMacro(<< "File X value doesn't match with the previous ones: "
00662                     << file->GetFileName().c_str()
00663                     << ". Found " << numColumns << ", must be "
00664                     << this->NumColumns);
00665       return false;
00666    }
00667    if( numLines != this->NumLines )
00668    {
00669       vtkErrorMacro(<< "File Y value doesn't match with the previous ones: "
00670                     << file->GetFileName().c_str()
00671                     << ". Found " << numLines << ", must be "
00672                     << this->NumLines);
00673       return false;
00674    }
00675    if( numPlanes != this->NumPlanes )
00676    {
00677       vtkErrorMacro(<< "File Z value doesn't match with the previous ones: "
00678                     << file->GetFileName().c_str()
00679                     << ". Found " << numPlanes << ", must be "
00680                     << this->NumPlanes);
00681       return false;
00682    }
00683    if( numComponents != this->NumComponents )
00684    {
00685       vtkErrorMacro(<< "File Components count doesn't match with the previous ones: "
00686                     << file->GetFileName().c_str()
00687                     << ". Found " << numComponents << ", must be "
00688                     << this->NumComponents);
00689       return false;
00690    }
00691    if( pixelSize != this->PixelSize )
00692    {
00693       vtkErrorMacro(<< "File pixel size doesn't match with the previous ones: "
00694                     << file->GetFileName().c_str()
00695                     << ". Found " << pixelSize << ", must be "
00696                     << this->PixelSize);
00697       return false;
00698    }
00699 
00700    return true;
00701 }
00702 
00703 //-----------------------------------------------------------------------------
00704 // Private
00705 /*
00706  * Remove all file names to the internal list of images to read.
00707  */
00708 void vtkGdcmReader::RemoveAllInternalFileName(void)
00709 {
00710    this->InternalFileNameList.clear();
00711 }
00712 
00713 /*
00714  * Adds a file name to the internal list of images to read.
00715  */
00716 void vtkGdcmReader::AddInternalFileName(const char *name)
00717 {
00718    char *LocalName = new char[strlen(name) + 1];
00719    strcpy(LocalName, name);
00720    this->InternalFileNameList.push_back(LocalName);
00721    delete[] LocalName;
00722 }
00723 
00724 /*
00725  * Remove all file names to the internal list of images to read.
00726  */
00727 void vtkGdcmReader::RemoveAllInternalFile(void)
00728 {
00729    if(this->OwnFile)
00730    {
00731       for(gdcmFileList::iterator it=InternalFileList.begin();
00732                                  it!=InternalFileList.end();
00733                                  ++it)
00734       {
00735          (*it)->Delete();
00736       }
00737    }
00738    this->InternalFileList.clear();
00739 }
00740 
00741 void vtkGdcmReader::IncrementProgress(const unsigned long updateProgressTarget,
00742                                       unsigned long &updateProgressCount)
00743 {
00744    // Update progress related for bad files:
00745    updateProgressCount += this->NumLines;
00746    if (updateProgressTarget > 0)
00747    {
00748       if (!(updateProgressCount%updateProgressTarget))
00749       {
00750          this->UpdateProgress(
00751              updateProgressCount/(50.0*updateProgressTarget));
00752       }
00753    }
00754 }
00755 
00756 /*
00757  * Loads the contents of the image/volume contained by char *fileName at
00758  * the dest memory address. Returns the size of the data loaded.
00759  */
00760 /*void vtkGdcmReader::LoadImageInMemory(
00761              std::string fileName, 
00762              unsigned char *dest,
00763              const unsigned long updateProgressTarget,
00764              unsigned long &updateProgressCount)
00765 {
00766    vtkDebugMacro(<< "Copying to memory image [" << fileName.c_str() << "]");
00767 
00768    GDCM_NAME_SPACE::File *f;
00769    f = new GDCM_NAME_SPACE::File();
00770    f->SetLoadMode( LoadMode );
00771    f->SetFileName( fileName.c_str() );
00772    f->Load( );
00773 
00774    LoadImageInMemory(f,dest,
00775                      updateProgressTarget,
00776                      updateProgressCount);
00777    delete f;
00778 }*/
00779 
00780 /*
00781  * Loads the contents of the image/volume contained by GDCM_NAME_SPACE::File* f at
00782  * the Dest memory address. Returns the size of the data loaded.
00783  * \ param f File to consider. NULL if the file must be skiped
00784  * \remarks Assume that if (f != NULL) then its caracteristics match
00785  * with the previous ones
00786  */
00787 void vtkGdcmReader::LoadImageInMemory(
00788              GDCM_NAME_SPACE::File *f, 
00789              unsigned char *dest,
00790              const unsigned long updateProgressTarget,
00791              unsigned long &updateProgressCount)
00792 {
00793    if(!f)
00794       return;
00795 
00796    GDCM_NAME_SPACE::FileHelper *fileH = GDCM_NAME_SPACE::FileHelper::New( f );
00797    fileH->SetUserFunction( UserFunction );
00798 
00799    int numColumns = f->GetXSize();
00800    int numLines   = f->GetYSize();
00801    int numPlanes  = f->GetZSize();
00802    int numComponents;
00803 
00804    if( f->HasLUT() && this->AllowLookupTable )
00805       numComponents = f->GetNumberOfScalarComponentsRaw();
00806    else
00807       numComponents = f->GetNumberOfScalarComponents(); //rgb or mono
00808    vtkDebugMacro(<< "numComponents:" << numComponents);
00809    vtkDebugMacro(<< "Copying to memory image [" << f->GetFileName().c_str() << "]");
00810    //size_t size;
00811 
00812    // If the data structure of vtk for image/volume representation
00813    // were straigthforwards the following would be enough:
00814    //    GdcmFile.GetImageDataIntoVector((void*)Dest, size);
00815    // But vtk chooses to invert the lines of an image, that is the last
00816    // line comes first (for some axis related reasons?). Hence we need
00817    // to load the image line by line, starting from the end.
00818 
00819    int lineSize   = NumComponents * numColumns * f->GetPixelSize();
00820    int planeSize  = lineSize * numLines;
00821 
00822    unsigned char *src;
00823    
00824    if( fileH->GetFile()->HasLUT() && AllowLookupTable )
00825    {
00826       // to avoid bcc 5.5 w
00827       /*size               = */ fileH->GetImageDataSize(); 
00828       src                = (unsigned char*) fileH->GetImageDataRaw();
00829       unsigned char *lut = (unsigned char*) fileH->GetLutRGBA();
00830 
00831       if(!this->LookupTable)
00832       {
00833          this->LookupTable = vtkLookupTable::New();
00834       }
00835 
00836       this->LookupTable->SetNumberOfTableValues(256);
00837       for (int tmp=0; tmp<256; tmp++)
00838       {
00839          this->LookupTable->SetTableValue(tmp,
00840          (float)lut[4*tmp+0]/255.0,
00841          (float)lut[4*tmp+1]/255.0,
00842          (float)lut[4*tmp+2]/255.0,
00843          1);
00844       }
00845       this->LookupTable->SetRange(0,255);
00846       vtkDataSetAttributes *a = this->GetOutput()->GetPointData();
00847       a->GetScalars()->SetLookupTable(this->LookupTable);
00848       free(lut);
00849    }
00850    else
00851    {
00852       //size = fileH->GetImageDataSize(); 
00853       // useless - just an accessor;  'size' unused
00854       src  = (unsigned char*)fileH->GetImageData();  
00855    } 
00856 
00857    unsigned char *dst = dest + planeSize - lineSize;
00858    for (int plane = 0; plane < numPlanes; plane++)
00859    {
00860       for (int line = 0; line < numLines; line++)
00861       {
00862          // Copy one line at proper destination:
00863          memcpy((void*)dst, (void*)src, lineSize);
00864          src += lineSize;
00865          dst -= lineSize;
00866          // Update progress related:
00867          if (!(updateProgressCount%updateProgressTarget))
00868          {
00869             this->UpdateProgress(
00870                updateProgressCount/(50.0*updateProgressTarget));
00871          }
00872          updateProgressCount++;
00873       }
00874       dst += 2 * planeSize;
00875    }
00876 
00877    fileH->Delete();
00878 }
00879 
00880 //-----------------------------------------------------------------------------

Generated on Fri Aug 24 12:59:32 2007 for gdcm by  doxygen 1.4.6