Program: gdcm
Module: $RCSfile: vtkgdcmSerieViewer.cxx,v $
Language: C++
- Date: $Date: 2005/07/17 04:36:14 $
- Version: $Revision: 1.1 $
+ Date: $Date: 2007/06/21 14:47:16 $
+ Version: $Revision: 1.18 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
-// This example illustrates how the vtkGdcmReader vtk class can be
-// used in order to:
-// * produce a simple (vtk based) Dicom image STACK VIEWER.
-// * dump the stack considered as a volume in a vtkStructuredPoints
-// vtk file: the vtk gdcm wrappers can be seen as a simple way to convert
-// a stack of Dicom images into a native vtk volume.
-//
+// This example illustrates how the vtkGdcmReader vtk class can
+// use the result of GDCM_NAME_SPACE::SerieHelper constructor and check
+// the various Setters :
+// SerieHelper::SetOrderToReverse,
+// SerieHelper::SetUserLessThanFunction
+// SerieHelper::SetLoadMode
+// vtkGdcmReader::SetUserFunction
+// vtkGdcmReader::SetCoherentFileList
// Usage:
-// * the filenames of the Dicom images constituting the stack should be
-// given as command line arguments,
+// * the Directory name that contains the Dicom images constituting the stack
+// should be given as command line argument (keyword : dirname=),
// * you can navigate through the stack by hitting any character key,
// * the produced vtk file is named "foo.vtk" (in the invocation directory).
//
#include "gdcmDocument.h" // for NO_SHADOWSEQ
#include "gdcmSerieHelper.h"
#include "gdcmDebug.h"
+#include "gdcmDataEntry.h"
+
+#include "gdcmArgMgr.h" // for Argument Manager functions
+#include <string.h> // for strcmp
#ifndef vtkFloatingPointType
#define vtkFloatingPointType float
#endif
+void userSuppliedMirrorFunction (uint8_t *im, GDCM_NAME_SPACE::File *f);
+void userSuppliedTopDownFunction(uint8_t *im, GDCM_NAME_SPACE::File *f);
+bool userSuppliedLessThanFunction(GDCM_NAME_SPACE::File *f1, GDCM_NAME_SPACE::File *f2);
+bool userSuppliedLessThanFunction2(GDCM_NAME_SPACE::File *f1, GDCM_NAME_SPACE::File *f2);
+
+int orderNb;
+uint16_t *elemsToOrderOn;
+
//----------------------------------------------------------------------------
// Callback for the interaction
class vtkgdcmObserver : public vtkCommand
{
return "vtkgdcmObserver";
}
+
static vtkgdcmObserver *New()
{
return new vtkgdcmObserver;
}
+
vtkgdcmObserver()
{
this->ImageViewer = NULL;
}
+
virtual void Execute(vtkObject *, unsigned long event, void* )
{
if ( this->ImageViewer )
vtkImageViewer *ImageViewer;
};
-
int main(int argc, char *argv[])
{
- if( argc < 2 )
+ START_USAGE(usage)
+ " \n vtkgdcmSerieViewer : \n",
+ " Display a 'Serie' (same Serie UID) within a Directory ",
+ " You can navigate through the stack by hitting any character key. ",
+ " usage: vtkgdcmSerieViewer dirname=sourcedirectory ",
+ " [noshadowseq][noshadow][noseq] ",
+ " [reverse] [{[mirror]|[topdown]|[rotate]}] ",
+ " [order=] [check][debug] ",
+ " sourcedirectory : name of the directory holding the images ",
+ " if it holds more than one serie, ",
+ " only the first one id displayed. ",
+ " noshadowseq: user doesn't want to load Private Sequences ",
+ " noshadow : user doesn't want to load Private groups (odd number) ",
+ " noseq : user doesn't want to load Sequences ",
+ " reverse : user wants to sort the images reverse order ",
+ " mirror : user wants to 'mirror' the images | just some simple ",
+ " topdown : user wants to 'topdown' the images| examples of user ",
+ " rotate : NOT YET MADE (useless?) | supplied functions ",
+ " check : user wants to force more coherence checking ",
+ " order= : group1-elem1,group2-elem2,... (in hexa, no space) ",
+ " if we want to use them as a sort criterium ",
+ " Right now : ValEntries only -just an example- ",
+ " or ",
+ " order= : order=name if we want to sort on file name (why not ?) ",
+ " debug : user wants to run the program in 'debug mode' ",
+ FINISH_USAGE
+
+
+ // Initialize Arguments Manager
+ GDCM_NAME_SPACE::ArgMgr *am= new GDCM_NAME_SPACE::ArgMgr(argc, argv);
+
+ if (argc == 1 || am->ArgMgrDefined("usage") )
+ {
+ am->ArgMgrUsage(usage); // Display 'usage'
+ delete am;
return 0;
+ }
+
+ char *dirName = am->ArgMgrWantString("dirname",usage);
+
+ int loadMode = GDCM_NAME_SPACE::LD_ALL;
+ if ( am->ArgMgrDefined("noshadowseq") )
+ loadMode |= GDCM_NAME_SPACE::LD_NOSHADOWSEQ;
+ else
+ {
+ if ( am->ArgMgrDefined("noshadow") )
+ loadMode |= GDCM_NAME_SPACE::LD_NOSHADOW;
+ if ( am->ArgMgrDefined("noseq") )
+ loadMode |= GDCM_NAME_SPACE::LD_NOSEQ;
+ }
+
+ int reverse = am->ArgMgrDefined("reverse");
- if( argc > 2 )
- gdcm::Debug::DebugOn();
+ int mirror = am->ArgMgrDefined("mirror");
+ int topdown = am->ArgMgrDefined("topdown");
+ int rotate = am->ArgMgrDefined("rotate");
+
+ if ( mirror && topdown )
+ {
+ std::cout << "mirror *OR* topDown !"
+ << std::endl;
+ delete am;
+ return 0;
+ }
+ if ( rotate )
+ {
+ std::cout << "'rotate' undealt with -> ignored !"
+ << std::endl;
+ }
+ int check = am->ArgMgrDefined("check");
- vtkGdcmReader *reader = vtkGdcmReader::New();
- reader->AllowLookupTableOff();
+ // This is so ugly, a cstring is NOT a char * (god damit!)
+ bool bname = ( strcmp(am->ArgMgrGetString("order", "not found"),"name")==0 );
+ if (bname)
+ elemsToOrderOn = am->ArgMgrGetXInt16Enum("order", &orderNb);
+
+ if (am->ArgMgrDefined("debug"))
+ GDCM_NAME_SPACE::Debug::DebugOn();
+
+ /* if unused Param we give up */
+ if ( am->ArgMgrPrintUnusedLabels() )
+ {
+ am->ArgMgrUsage(usage);
+ delete am;
+ return 0;
+ }
- // ------------ to check Coherent File List as a parameter
+ delete am; // we don't need Argument Manager any longer
- gdcm::SerieHelper *sh = new gdcm::SerieHelper();
- sh->SetLoadMode(NO_SHADOWSEQ);
- sh->SetDirectory( argv[1], true);
+ // ----------------------- End Arguments Manager ----------------------
+
+ GDCM_NAME_SPACE::SerieHelper *sh = GDCM_NAME_SPACE::SerieHelper::New();
+ sh->SetLoadMode(loadMode);
+ if (reverse)
+ sh->SetSortOrderToReverse();
+ sh->SetDirectory( dirName, true);
// Just to see
int nbFiles;
- // For all the Coherent Files lists of the gdcm::Serie
- gdcm::FileList *l = sh->GetFirstCoherentFileList();
+ // For all the 'Single Serie UID' FileSets of the GDCM_NAME_SPACE::Serie
+ GDCM_NAME_SPACE::FileList *l = sh->GetFirstSingleSerieUIDFileSet();
if (l == 0 )
{
- std::cout << "Oops! No CoherentFileList found ?!?" << std::endl;
+ std::cout << "Oops! No 'Single Serie UID' FileSet found ?!?" << std::endl;
return 0;
}
+
+ if (bname)
+ sh->SetUserLessThanFunction(userSuppliedLessThanFunction2);
+ else if (orderNb != 0)
+ sh->SetUserLessThanFunction(userSuppliedLessThanFunction);
+
while (l)
{
nbFiles = l->size() ;
- if ( l->size() > 0 ) // Why not ? Just an example, for testing
+ if ( l->size() > 1 )
{
std::cout << "Sort list : " << nbFiles << " long" << std::endl;
sh->OrderFileList(l); // sort the list
}
else
{
- std::cout << "Oops! Empty CoherentFileList found ?!?" << std::endl;
+ std::cout << "Oops! Empty 'Single Serie UID' FileSet found ?!?"
+ << std::endl;
}
- l = sh->GetNextCoherentFileList();
+ l = sh->GetNextSingleSerieUIDFileSet();
}
- reader->SetCoherentFileList(l);
+ if (check)
+ {
+ if ( !sh->IsCoherent(l) ) // just be sure (?)
+ {
+ std::cout << "Files are not coherent. Stop everything " << std::endl;
+ sh->Delete();
+ return 0;
+ }
+ }
-/*
- if( argc == 2 )
- reader->SetFileName( argv[1] );
- else
- for(int i=1; i< argc; i++)
- reader->AddFileName( argv[i] );
-*/
+ vtkGdcmReader *reader = vtkGdcmReader::New();
+ reader->AllowLookupTableOff();
+
+ if (mirror)
+ reader->SetUserFunction (userSuppliedMirrorFunction);
+ else if (topdown)
+ reader->SetUserFunction (userSuppliedTopDownFunction);
-// TODO : allow user to choose Load Mode
+ // Only the first FileList is dealt with (just an example)
+ // (The files will not be parsed twice by the reader)
- // reader->SetLoadMode(NO_SHADOWSEQ);
+ //---------------------------------------------------------
+ reader->SetCoherentFileList(l);
+ //---------------------------------------------------------
+
+ // because we passed a Coherent File List from a SerieHelper,
+ // setting LoadMode is useless in this case
+ // reader->SetLoadMode(NO_SHADOWSEQ);
reader->Update();
//print debug info:
return 0;
}
+
+
+// --------------------------------------------------------
+// This is just a *very* simple example of user supplied function
+// to mirror (why not ?) the image
+// It's *not* part of gdcm.
+// --------------------------------------------------------
+
+#define UF(ty) \
+ 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; \
+ } \
+ }
+
+void userSuppliedMirrorFunction(uint8_t *im, GDCM_NAME_SPACE::File *f)
+{
+ if (f->GetZSize() != 1)
+ {
+ std::cout << "mirror : Multiframe images not yet dealt with" << std::endl;
+ return;
+ }
+
+ if (f->GetSamplesPerPixel() != 1 || f->GetBitsAllocated() == 24)
+ {
+ std::cout << "mirror : RGB / YBR not yet dealt with" << std::endl;
+ return;
+ }
+ int nx = f->GetXSize();
+ int ny = f->GetYSize();
+
+ std::string pixelType = f->GetPixelType();
+ if ( pixelType == "8U" || pixelType == "8S" )
+ {
+ UF(uint8_t)
+ return;
+ }
+ if ( pixelType == "16U" || pixelType == "16S")
+ {
+ UF(uint16_t)
+ return;
+ }
+ std::cout << "mirror : Pixel Size (!=8, !=16) not yet dealt with"
+ << std::endl;
+ return;
+}
+
+
+// --------------------------------------------------------
+// This is just a *very* simple example of user supplied function
+// to topdown (why not ?) the image
+// It's *not* part of gdcm.
+// --------------------------------------------------------
+
+#define UF2(ty) \
+ 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; \
+ } \
+ }
+
+void userSuppliedTopDownFunction(uint8_t *im, GDCM_NAME_SPACE::File *f)
+{
+ if (f->GetZSize() != 1)
+ {
+ std::cout << "mirror : Multiframe images not yet dealt with" << std::endl;
+ return;
+ }
+
+ if (f->GetSamplesPerPixel() != 1 || f->GetBitsAllocated() == 24)
+ {
+ std::cout << "mirror : RGB / YBR not yet dealt with" << std::endl;
+ return;
+ }
+ int nx = f->GetXSize();
+ int ny = f->GetYSize();
+
+ std::string pixelType = f->GetPixelType();
+ if ( pixelType == "8U" || pixelType == "8S" )
+ {
+ UF2(uint8_t)
+ return;
+ }
+ if ( pixelType == "16U" || pixelType == "16S")
+ {
+ UF2(uint16_t)
+ return;
+ }
+ std::cout << "topdown : Pixel Size (!=8, !=16) not yet dealt with"
+ << std::endl;
+ return;
+}
+
+// --------------------------------------------------------
+// This is just a *very* simple example of user supplied 'LessThan' function
+// It's *not* part of gdcm.
+//
+// Note : orderNb and elemsToOrderOn are here global variables.
+// Within a 'normal' function they would't be any orderNb and elemsToOrderOn var
+// User *knows* on what field(s) he wants to compare;
+// He just writes a decent function.
+// Here, we want to get info from the command line Argument Manager.
+//
+// Warning : it's up to 'vtkgdcmSerieViewer' user to find a suitable data set !
+// --------------------------------------------------------
+
+
+bool userSuppliedLessThanFunction(GDCM_NAME_SPACE::File *f1, GDCM_NAME_SPACE::File *f2)
+{
+ // for *this* user supplied function, I supposed only ValEntries are checked.
+//
+ std::string s1, s2;
+ GDCM_NAME_SPACE::DataEntry *e1,*e2;
+ for (int ri=0; ri<orderNb; ri++)
+ {
+ std::cout << std::hex << elemsToOrderOn[2*ri] << "|"
+ << elemsToOrderOn[2*ri+1]
+ << std::endl;
+
+ e1= f1->GetDataEntry( elemsToOrderOn[2*ri],
+ elemsToOrderOn[2*ri+1]);
+
+ e2= f2->GetDataEntry( elemsToOrderOn[2*ri],
+ elemsToOrderOn[2*ri+1]);
+ if(!e2 || !e2)
+ {
+ std::cout << std::hex << elemsToOrderOn[2*ri] << "|"
+ << elemsToOrderOn[2*ri+1]
+ << " not found" << std::endl;
+ continue;
+ }
+ s1 = e1->GetString();
+ s2 = e2->GetString();
+ std::cout << "[" << s1 << "] vs [" << s2 << "]" << std::endl;
+ if ( s1 < s2 )
+ return true;
+ else if (s1 == s2 )
+ continue;
+ else
+ return false;
+ }
+ return false; // all fields equal
+}
+
+// --------------------------------------------------------
+// This is just an other *very* simple example of user supplied 'LessThan'
+// function
+// It's *not* part of gdcm.
+//
+// Warning : it's up to 'vtkgdcmSerieViewer' user to find a suitable data set !
+// --------------------------------------------------------
+
+bool userSuppliedLessThanFunction2(GDCM_NAME_SPACE::File *f1, GDCM_NAME_SPACE::File *f2)
+{
+ std::cout << "[" << f1->GetFileName() << "] vs ["
+ << f2->GetFileName() << "]" << std::endl;
+ return f1->GetFileName() < f2->GetFileName();
+}
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff