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DataLinuxWindoze » gdcmNew » gdcm » vtk

vtkgdcmSerieViewer.cxx File Reference

#include <vtkRenderWindowInteractor.h>
#include <vtkImageViewer.h>
#include <vtkStructuredPoints.h>
#include <vtkStructuredPointsWriter.h>
#include <vtkCommand.h>
#include <vtkRenderer.h>
#include <vtkImageMapToColors.h>
#include <vtkLookupTable.h>
#include "vtkGdcmReader.h"
#include "gdcmDocument.h"
#include "gdcmSerieHelper.h"
#include "gdcmDebug.h"
#include "gdcmDataEntry.h"
#include "gdcmArgMgr.h"
#include <string.h>

Include dependency graph for vtkgdcmSerieViewer.cxx:

Go to the source code of this file.

Classes

class  vtkgdcmObserver

Defines

#define vtkFloatingPointType   float
#define UF(ty)
#define UF2(ty)

Functions

void userSuppliedMirrorFunction (uint8_t *im, gdcm::File *f)
void userSuppliedTopDownFunction (uint8_t *im, gdcm::File *f)
bool userSuppliedLessThanFunction (gdcm::File *f1, gdcm::File *f2)
bool userSuppliedLessThanFunction2 (gdcm::File *f1, gdcm::File *f2)
int main (int argc, char *argv[])

Variables

int orderNb
uint16_t * elemsToOrderOn

Define Documentation

#define UF (  ty   ) 
 

Value:

int i, j;                            \
   ty *imj;                             \
   ty tamp;                             \
   for (j=0;j<ny;j++)                   \
   {                                    \
      imj = (ty *)im +j*nx;             \
      for (i=0;i<nx/2;i++)              \
      {                                 \
        tamp       =imj[i];             \
        imj[i]     =imj[nx-1-i];        \
        imj[nx-1-i]=tamp;               \
      }                                 \
   }                                    \
   if (nx%2 != 0)                       \
   {                                    \
      i = nx / 2;                       \
      for (j=0;j<ny;j++)                \
      {                                 \
        imj = (ty *)im  +j*nx;          \
        tamp       =imj[i];             \
        imj[i]     =imj[nx/2+1];        \
        imj[nx/2+1]=tamp;               \
      }                                 \
   }

Definition at line 325 of file vtkgdcmSerieViewer.cxx.

Referenced by userSuppliedMirrorFunction().

#define UF2 (  ty   ) 
 

Value:

int i, j;                            \
   ty *imj, *imJ;                       \
   ty tamp;                             \
   for (j=0;j<ny/2;j++)                 \
   {                                    \
      imj = (ty *)im +j*nx;             \
      imJ = (ty *)im +(ny-1-j)*nx;      \
      for (i=0;i<nx;i++)                \
      {                                 \
        tamp       =imj[i];             \
        imj[i]     =imJ[i];             \
        imJ[i]     =tamp;               \
      }                                 \
   }

Definition at line 390 of file vtkgdcmSerieViewer.cxx.

Referenced by userSuppliedTopDownFunction().

#define vtkFloatingPointType   float
 

Definition at line 51 of file vtkgdcmSerieViewer.cxx.

Referenced by main(), and SetImageInformation().

Function Documentation

int main (  int  argc,
char *  argv[]
) 
 

Definition at line 99 of file vtkgdcmSerieViewer.cxx.

References gdcm::Debug::DebugOn(), gdcm::RefCounter::Delete(), elemsToOrderOn, FINISH_USAGE, gdcm::SerieHelper::GetFirstSingleSerieUIDFileSet(), gdcm::SerieHelper::GetNextSingleSerieUIDFileSet(), vtkgdcmObserver::ImageViewer, gdcm::SerieHelper::IsCoherent(), gdcm::LD_ALL, gdcm::LD_NOSEQ, gdcm::LD_NOSHADOW, gdcm::LD_NOSHADOWSEQ, vtkgdcmObserver::New(), vtkGdcmReader::New(), gdcm::SerieHelper::New(), gdcm::SerieHelper::OrderFileList(), orderNb, vtkGdcmReader::SetCoherentFileList(), gdcm::SerieHelper::SetDirectory(), gdcm::SerieHelper::SetLoadMode(), gdcm::SerieHelper::SetSortOrderToReverse(), vtkGdcmReader::SetUserFunction(), gdcm::SerieHelper::SetUserLessThanFunction(), START_USAGE, userSuppliedLessThanFunction(), userSuppliedLessThanFunction2(), userSuppliedMirrorFunction(), userSuppliedTopDownFunction(), and vtkFloatingPointType.

00100 {
00101    START_USAGE(usage)
00102    " \n vtkgdcmSerieViewer : \n",
00103    " Display a 'Serie' (same Serie UID) within a Directory                    ",
00104    " You can navigate through the stack by hitting any character key.         ",
00105    " usage: vtkgdcmSerieViewer dirname=sourcedirectory                        ",
00106    "                           [noshadowseq][noshadow][noseq]                 ",
00107    "                           [reverse] [{[mirror]|[topdown]|[rotate]}]      ",
00108    "                           [order=] [check][debug]                        ",
00109    "      sourcedirectory : name of the directory holding the images          ",
00110    "                        if it holds more than one serie,                  ",
00111    "                        only the first one id displayed.                  ",
00112    "      noshadowseq: user doesn't want to load Private Sequences            ",
00113    "      noshadow   : user doesn't want to load Private groups (odd number)  ",
00114    "      noseq      : user doesn't want to load Sequences                    ",
00115    "      reverse    : user wants to sort the images reverse order            ",
00116    "      mirror     : user wants to 'mirror' the images | just some simple   ",
00117    "      topdown    : user wants to 'topdown' the images| examples of user   ",
00118    "      rotate     : NOT YET MADE (useless?)           | supplied functions ",
00119    "      check      : user wants to force more coherence checking            ",
00120    "      order=     : group1-elem1,group2-elem2,... (in hexa, no space)      ",
00121    "                   if we want to use them as a sort criterium             ",
00122    "                   Right now : ValEntries only -just an example-          ",
00123    "        or                                                                ",
00124    "      order=     : order=name if we want to sort on file name (why not ?) ",
00125    "      debug      : user wants to run the program in 'debug mode'          ",
00126    FINISH_USAGE
00127 
00128 
00129    // Initialize Arguments Manager   
00130    gdcm::ArgMgr *am= new gdcm::ArgMgr(argc, argv);
00131   
00132    if (argc == 1 || am->ArgMgrDefined("usage") )
00133    {
00134       am->ArgMgrUsage(usage); // Display 'usage'
00135       delete am;
00136       return 0;
00137    }
00138 
00139    char *dirName = am->ArgMgrWantString("dirname",usage);
00140 
00141    int loadMode = gdcm::LD_ALL;
00142    if ( am->ArgMgrDefined("noshadowseq") )
00143       loadMode |= gdcm::LD_NOSHADOWSEQ;
00144    else 
00145    {
00146       if ( am->ArgMgrDefined("noshadow") )
00147          loadMode |= gdcm::LD_NOSHADOW;
00148       if ( am->ArgMgrDefined("noseq") )
00149          loadMode |= gdcm::LD_NOSEQ;
00150    }
00151 
00152    int reverse = am->ArgMgrDefined("reverse");
00153 
00154    int mirror  = am->ArgMgrDefined("mirror");
00155    int topdown = am->ArgMgrDefined("topdown");
00156    int rotate  = am->ArgMgrDefined("rotate");
00157 
00158    if ( mirror && topdown )
00159    {
00160       std::cout << "mirror *OR* topDown !"
00161                 << std::endl;
00162       delete am;
00163       return 0;
00164    }
00165    if ( rotate )
00166    {
00167       std::cout << "'rotate' undealt with -> ignored !"
00168                 << std::endl;
00169    }
00170 
00171    int check   = am->ArgMgrDefined("check");
00172   
00173    // This is so ugly, a cstring is NOT a char * (god damit!)
00174    bool bname = ( strcmp(am->ArgMgrGetString("order", (char*)"not found"),"name")==0 );
00175    if (bname)
00176       elemsToOrderOn = am->ArgMgrGetXInt16Enum("order", &orderNb);
00177 
00178    if (am->ArgMgrDefined("debug"))
00179       gdcm::Debug::DebugOn();
00180 
00181    /* if unused Param we give up */
00182    if ( am->ArgMgrPrintUnusedLabels() )
00183    {
00184       am->ArgMgrUsage(usage);
00185       delete am;
00186       return 0;
00187    } 
00188 
00189    delete am;  // we don't need Argument Manager any longer
00190 
00191    // ----------------------- End Arguments Manager ----------------------
00192   
00193    gdcm::SerieHelper *sh = gdcm::SerieHelper::New();
00194    sh->SetLoadMode(loadMode);
00195    if (reverse)
00196       sh->SetSortOrderToReverse();
00197    sh->SetDirectory( dirName, true);
00198     
00199    // Just to see
00200 
00201    int nbFiles;
00202    // For all the 'Single Serie UID' FileSets of the gdcm::Serie
00203    gdcm::FileList *l = sh->GetFirstSingleSerieUIDFileSet();
00204    if (l == 0 )
00205    {
00206       std::cout << "Oops! No 'Single Serie UID' FileSet found ?!?" << std::endl;
00207       return 0;
00208    }
00209 
00210    if (bname)
00211      sh->SetUserLessThanFunction(userSuppliedLessThanFunction2);
00212    else if (orderNb != 0)
00213       sh->SetUserLessThanFunction(userSuppliedLessThanFunction);
00214 
00215    while (l)
00216    { 
00217       nbFiles = l->size() ;
00218       if ( l->size() > 1 )
00219       {
00220          std::cout << "Sort list : " << nbFiles << " long" << std::endl;
00221          sh->OrderFileList(l);  // sort the list
00222          break;  // The first one is OK. user will have to check
00223       }
00224       else
00225       {
00226          std::cout << "Oops! Empty 'Single Serie UID' FileSet found ?!?"
00227                    << std::endl;
00228       }
00229       l = sh->GetNextSingleSerieUIDFileSet();
00230    }
00231 
00232    if (check)
00233    {
00234       if ( !sh->IsCoherent(l) ) // just be sure (?)
00235       {
00236          std::cout << "Files are not coherent. Stop everything " << std::endl;
00237          sh->Delete();
00238          return 0;
00239       }
00240    }
00241 
00242    vtkGdcmReader *reader = vtkGdcmReader::New();
00243    reader->AllowLookupTableOff();
00244 
00245    if (mirror)
00246       reader->SetUserFunction (userSuppliedMirrorFunction);
00247    else if (topdown)
00248       reader->SetUserFunction (userSuppliedTopDownFunction);
00249 
00250    // Only the first FileList is dealt with (just an example)
00251    // (The files will not be parsed twice by the reader)
00252 
00253    //---------------------------------------------------------
00254    reader->SetCoherentFileList(l);
00255    //---------------------------------------------------------
00256 
00257    // because we passed a Coherent File List from a SerieHelper,
00258    // setting LoadMode is useless in this case
00259    //  reader->SetLoadMode(NO_SHADOWSEQ);  
00260    reader->Update();
00261 
00262    //print debug info:
00263    reader->GetOutput()->Print( cout );
00264 
00265    vtkRenderWindowInteractor *iren = vtkRenderWindowInteractor::New();
00266 
00267    vtkImageViewer *viewer = vtkImageViewer::New();
00268 
00269    if( reader->GetLookupTable() )
00270    {
00271       //convert to color:
00272       vtkImageMapToColors *map = vtkImageMapToColors::New ();
00273       map->SetInput (reader->GetOutput());
00274       map->SetLookupTable (reader->GetLookupTable());
00275       map->SetOutputFormatToRGB();
00276       viewer->SetInput ( map->GetOutput() );
00277       map->Delete();
00278    }
00279    else
00280    {
00281       vtkFloatingPointType *range = reader->GetOutput()->GetScalarRange();
00282       viewer->SetColorLevel (0.5 * (range[1] + range[0]));
00283       viewer->SetColorWindow (range[1] - range[0]);
00284 
00285       viewer->SetInput ( reader->GetOutput() );
00286    }
00287    viewer->SetupInteractor (iren);
00288   
00289    //vtkFloatingPointType *range = reader->GetOutput()->GetScalarRange();
00290    //viewer->SetColorWindow (range[1] - range[0]);
00291    //viewer->SetColorLevel (0.5 * (range[1] + range[0]));
00292 
00293    // Here is where we setup the observer, 
00294    vtkgdcmObserver *obs = vtkgdcmObserver::New();
00295    obs->ImageViewer = viewer;
00296    iren->AddObserver(vtkCommand::CharEvent,obs);
00297    obs->Delete();
00298 
00299    //viewer->Render();
00300    iren->Initialize();
00301    iren->Start();
00302 
00303    //if you wish you can export dicom to a vtk file  
00304    vtkStructuredPointsWriter *writer = vtkStructuredPointsWriter::New();
00305    writer->SetInput( reader->GetOutput());
00306    writer->SetFileName( "foo.vtk" );
00307    writer->SetFileTypeToBinary();
00308    //writer->Write();
00309 
00310    reader->Delete();
00311    iren->Delete();
00312    viewer->Delete();
00313    writer->Delete();
00314 
00315    return 0;
00316 }

bool userSuppliedLessThanFunction (  gdcm::File *  f1,
gdcm::File *  f2
) 
 

Definition at line 452 of file vtkgdcmSerieViewer.cxx.

References elemsToOrderOn, gdcm::DocEntrySet::GetDataEntry(), gdcm::DataEntry::GetString(), and orderNb.

Referenced by main().

00453 {
00454    // for *this* user supplied function, I supposed only ValEntries are checked.
00455 // 
00456    std::string s1, s2;
00457    gdcm::DataEntry *e1,*e2;
00458    for (int ri=0; ri<orderNb; ri++)
00459    {
00460       std::cout << std::hex << elemsToOrderOn[2*ri] << "|" 
00461                             << elemsToOrderOn[2*ri+1]
00462                             << std::endl;
00463  
00464       e1= f1->GetDataEntry( elemsToOrderOn[2*ri],
00465                  elemsToOrderOn[2*ri+1]);
00466 
00467       e2= f2->GetDataEntry( elemsToOrderOn[2*ri],
00468                                  elemsToOrderOn[2*ri+1]);
00469       if(!e2 || !e2)
00470       {
00471          std::cout << std::hex << elemsToOrderOn[2*ri] << "|"
00472                               << elemsToOrderOn[2*ri+1]
00473                               << " not found" << std::endl;
00474          continue;
00475       }
00476       s1 = e1->GetString();      
00477       s2 = e2->GetString();
00478       std::cout << "[" << s1 << "] vs [" << s2 << "]" << std::endl;
00479       if ( s1 < s2 ) 
00480          return true;
00481       else if (s1 == s2 )
00482          continue;
00483       else 
00484          return false;
00485    }
00486    return false; // all fields equal
00487 }

bool userSuppliedLessThanFunction2 (  gdcm::File *  f1,
gdcm::File *  f2
) 
 

Definition at line 497 of file vtkgdcmSerieViewer.cxx.

References gdcm::Document::GetFileName().

Referenced by main().

00498 {
00499    std::cout << "[" << f1->GetFileName() << "] vs [" 
00500                     << f2->GetFileName() << "]" << std::endl;
00501    return f1->GetFileName() < f2->GetFileName();
00502 }

void userSuppliedMirrorFunction (  uint8_t *  im,
gdcm::File *  f
) 
 

Definition at line 351 of file vtkgdcmSerieViewer.cxx.

References gdcm::File::GetBitsAllocated(), gdcm::File::GetPixelType(), gdcm::File::GetSamplesPerPixel(), gdcm::File::GetXSize(), gdcm::File::GetYSize(), gdcm::File::GetZSize(), and UF.

Referenced by main().

00352 {
00353    if (f->GetZSize() != 1)
00354    {
00355       std::cout << "mirror : Multiframe images not yet dealt with" << std::endl;
00356       return;
00357    }
00358 
00359    if (f->GetSamplesPerPixel() != 1 || f->GetBitsAllocated() == 24)
00360    {
00361       std::cout << "mirror : RGB / YBR not yet dealt with" << std::endl;
00362       return;
00363    }
00364    int nx = f->GetXSize();
00365    int ny = f->GetYSize();
00366 
00367    std::string pixelType = f->GetPixelType();
00368    if ( pixelType ==  "8U" || pixelType == "8S" )
00369    {
00370       UF(uint8_t)
00371       return;
00372    }
00373    if ( pixelType == "16U" || pixelType == "16S")
00374    {
00375       UF(uint16_t)
00376       return;
00377    }
00378    std::cout << "mirror : Pixel Size (!=8, !=16) not yet dealt with" 
00379              << std::endl;
00380    return;
00381 }

void userSuppliedTopDownFunction (  uint8_t *  im,
gdcm::File *  f
) 
 

Definition at line 406 of file vtkgdcmSerieViewer.cxx.

References gdcm::File::GetBitsAllocated(), gdcm::File::GetPixelType(), gdcm::File::GetSamplesPerPixel(), gdcm::File::GetXSize(), gdcm::File::GetYSize(), gdcm::File::GetZSize(), and UF2.

Referenced by main().

00407 {
00408    if (f->GetZSize() != 1)
00409    {
00410       std::cout << "mirror : Multiframe images not yet dealt with" << std::endl;
00411       return;
00412    }
00413 
00414    if (f->GetSamplesPerPixel() != 1 || f->GetBitsAllocated() == 24)
00415    {
00416       std::cout << "mirror : RGB / YBR not yet dealt with" << std::endl;
00417       return;
00418    }
00419    int nx = f->GetXSize();
00420    int ny = f->GetYSize();
00421 
00422    std::string pixelType = f->GetPixelType();
00423    if ( pixelType ==  "8U" || pixelType == "8S" )
00424    {
00425       UF2(uint8_t)
00426       return;
00427    }
00428    if ( pixelType == "16U" || pixelType == "16S")
00429    {
00430       UF2(uint16_t)
00431       return;
00432    }
00433    std::cout << "topdown : Pixel Size (!=8, !=16) not yet dealt with" 
00434              << std::endl;
00435    return;
00436 }

Variable Documentation

uint16_t* elemsToOrderOn
 

Definition at line 60 of file vtkgdcmSerieViewer.cxx.

Referenced by main(), and userSuppliedLessThanFunction().

int orderNb
 

Definition at line 59 of file vtkgdcmSerieViewer.cxx.

Referenced by main(), and userSuppliedLessThanFunction().

Generated on Fri Jan 20 10:14:59 2006 for gdcm by  doxygen 1.4.4