1 #include <creaImageIOGimmickView.h>
2 #include <creaImageIOSystem.h>
3 #include "boost/filesystem.hpp"
6 #include <gdcmGlobal.h>
7 #include <gdcmSerieHelper.h>
8 #include <vtkGdcmReader.h>
11 #if defined(USE_GDCM2)
12 #include <vtkGDCMImageReader.h>
13 #include "gdcmSystem.h"
14 #include "gdcmCryptographicMessageSyntax.h"
15 #include "gdcmUIDGenerator.h"
16 #include "gdcmAnonymizer.h"
17 #include "gdcmGlobal.h"
21 namespace fs = boost::filesystem;
25 ///Class used to represent the actual state of the image selected and to perform comparisons on its values
29 ImageExtent(const std::string& x, const std::string& y, const std::string& z, const std::string& t)
31 sscanf(x.c_str(),"%d",&mExtent[0]);
32 sscanf(y.c_str(),"%d",&mExtent[1]);
33 sscanf(z.c_str(),"%d",&mExtent[2]);
34 sscanf(t.c_str(),"%d",&mExtent[3]);
35 if(x==""){mExtent[0]=1;}
36 if(y==""){mExtent[1]=1;}
37 if(z==""){mExtent[2]=1;}
38 if(t==""){mExtent[3]=1;}
40 if (mExtent[3]>1) mDim=4;
41 else if (mExtent[2]>1) mDim=3;
42 else if (mExtent[1]>1) mDim=2;
43 else if (mExtent[0]>1) mDim=1;
49 void Clear() { mExtent[0] = mExtent[1] = mExtent[2] = mExtent[3] = 1; }
51 ///Returns true if the two extents are compatible
52 bool IsCompatible( const ImageExtent& );
54 ///Adds the extent passed as a parameter to the current extent
55 void Add ( const ImageExtent& );
57 ///Returns the ieth position of the extent
58 int Get(int i) { return mExtent[i]; }
60 ///Returns the dimension of the current image
61 void SetDimension(int dim) { mDim=dim; }
63 ///Returns the dimension of the current image
64 int GetDimension() { return mDim; }
71 //======================================================================
73 //======================================================================
75 GimmickView::GimmickView(boost::shared_ptr<Gimmick> gimmick, int threads)
79 GimmickDebugMessage(1,"GimmickView::GimmickView"
81 // Anciently started the threads ...
82 // Threads now automatically start at first image request
86 //======================================================================
88 //======================================================================
90 GimmickView::~GimmickView()
92 GimmickDebugMessage(1,"GimmickView::~GimmickView"
95 //======================================================================
97 //======================================================================
98 /// Initializes the view :
99 /// Creates the TreeViews for all the TreeHandler of the Controller
101 void GimmickView::Initialize()
103 mReaderStarted=false;
105 //======================================================================
107 //======================================================================
109 void GimmickView::Finalize()
113 //======================================================================
115 //======================================================================
116 /// Create the tree views
117 void GimmickView::CreateTreeViews()
119 GimmickMessage(2,"Creating the tree views"<<std::endl);
120 Gimmick::TreeHandlerMapType::const_iterator i;
121 for (i = mGimmick->GetTreeHandlerMap().begin();
122 i!= mGimmick->GetTreeHandlerMap().end();
125 this->CreateTreeView(i->second);
129 /// Create a tree view with a given name
130 void GimmickView::CreateSingleTreeView(std::string &i_name)
132 this->CreateTreeView(mGimmick->GetTreeHandlerMap()[i_name]);
137 //======================================================================
139 //======================================================================
140 /// Updates the TreeView of given name from level l to bottom
141 /// (calls the virtual method TreeView::Update())
142 void GimmickView::UpdateTreeViewLevel(const std::string& t, int l)
144 TreeViewMapType::iterator i;
145 i = GetTreeViewMap().find(t);
146 if ( i == GetTreeViewMap().end() )
148 GimmickError("INTERNAL ERROR : GimmickView::UpdateTreeView : '"
149 <<t<<"' is not in TreeViewMap");
151 i->second->UpdateLevel(l);
154 //======================================================================
155 /// Clears the status and begins a new selection process
156 void GimmickView::ResetExtent()
160 mImageExtent.reset();
165 //======================================================================
167 //======================================================================
168 bool ImageExtent::IsCompatible(const ImageExtent& ie)
170 bool compatible=true;
171 ImageExtent * extent= (ImageExtent*)&ie;
172 if((*extent).Get(0)!=Get(0)
173 || (*extent).Get(1)!=Get(1))
180 //======================================================================
182 //======================================================================
183 void ImageExtent::Add(const ImageExtent& ie)
185 ImageExtent * extent= (ImageExtent*)&ie;
186 mExtent[2]+=(*extent).Get(2);
193 //======================================================================
194 /// No selected image
195 bool GimmickView::NoValidateSelected ()
197 GimmickDebugMessage(2,"Validating selected"<<std::endl);
198 std::string mMessage;
199 mMessage="Cannot have 0 images selected!";
201 modifyValidationSignal(valid);
202 SetMessage(mMessage);
206 //======================================================================
207 ///Validates the dimension compliance of the images with the maximum and
208 ///minimum given, and between their sizes
209 bool GimmickView::ValidateSelected (tree::Node* sel, int min_dim, int max_dim)
211 GimmickDebugMessage(2,"Validating selected"<<std::endl);
212 std::string mMessage;
216 mMessage="Cannot have 0 images selected!";
221 std::string extentx = (*sel).GetAttribute("D0028_0010");
222 std::string extenty = (*sel).GetAttribute("D0028_0011");
223 std::string extentz = (*sel).GetAttribute("D0028_0012");
224 std::string extentt = (*sel).GetAttribute("D0028_0010");
225 if( extentx == "" && extenty == "" && extentz == "")
227 // we try to create a vtkImageData just to get dim informations
228 // Long method need to improve it!
229 std::string name = (*sel).GetAttribute("FullFileName");
234 mReader.GetImage(name)->GetDimensions(dim);
235 sprintf(c,"%d", dim[0]);
237 sprintf(c,"%d", dim[1]);
239 sprintf(c,"%d", dim[2]);
244 boost::shared_ptr<ImageExtent> ie=boost::shared_ptr<ImageExtent>(new ImageExtent(extentx, extenty, extentz,extentt));
248 if((mImageExtent->Get(min_dim-1)<2)||(mImageExtent->Get(max_dim)>1))
254 std::stringstream out;
255 out << mImageExtent->GetDimension() << "D image " << mImageExtent->Get(0) << "x"<< mImageExtent->Get(1) << "x"<< mImageExtent->Get(2) <<" selected";
256 mMessage = out.str();
257 mImageExtent->SetDimension(2);
263 if(mImageExtent->IsCompatible(*ie))
265 if(mImageExtent->GetDimension()==max_dim && mImageExtent->Get(max_dim)>2)
267 std::stringstream out;
268 out<<"Cannot add this image to selection : would result in a "<<mImageExtent->GetDimension()+1<<"D image!";
274 std::stringstream out;
275 out<<"Selecting "<<mImageExtent->GetDimension()<<"D images is not allowed !";
279 else if(min_dim==3 && (ie->Get(2)+mImageExtent->Get(2))<2)
281 std::stringstream out;
282 out << "Cannot build the selection as it would result in a ";
283 out << mImageExtent->GetDimension();
284 out << "D image, and the minimum is ";
292 mImageExtent->Add(*ie);
293 std::stringstream out;
294 out << mImageExtent->GetDimension() << "D image " << mImageExtent->Get(0) << "x"<< mImageExtent->Get(1) << "x"<< mImageExtent->Get(2) <<" selected";
295 mMessage = out.str();
300 mMessage="The selected images are not compatible.";
306 modifyValidationSignal(valid);
307 SetMessage(mMessage);
311 //======================================================================
312 void GimmickView::modifyValidationSignal(bool ivalid)
315 mValidationSignal(ivalid);
318 //======================================================================
319 ///Reads Images (Non Threaded)
320 void GimmickView::ReadImagesNotThreaded(std::vector<vtkImageData*>& s, std::vector<std::string> im, int dimension)
325 #define GIMMICK_NO_IMAGE_SELECTION 0
326 #define GIMMICK_2D_IMAGE_SELECTION 2
327 #define GIMMICK_3D_IMAGE_SELECTION 3
328 #define GIMMICK_4D_IMAGE_SELECTION 4
335 // Create the output data
338 vtkImageData * out=vtkImageData::New();
339 out->ShallowCopy(mReader.GetImage(im.front()));
342 else if (im.size()>1) // Test inutile ? JPR
344 vtkImageData* first = mReader.GetImage( im.front());
348 std::vector<std::string>::iterator it;
349 for (it=im.begin(); it!=im.end(); ++it)
351 vtkImageData* out = vtkImageData::New();
352 out->ShallowCopy(mReader.GetImage(*it));
359 vtkImageData* out = vtkImageData::New();
360 // out->CopyStructure(first);
361 out->SetScalarType(first->GetScalarType());
362 out->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents());
364 //first->GetExtent(ext); // JPR
365 first->GetWholeExtent(ext); // renvoie egalement 0,0 en Z // JPR
369 ext[5] = im.size()-1;
373 ext[5] = ext[5] * im.size()-1; // to deal with multiframes - JPR
377 // LG : TODO : Z Spacing ?
380 first->GetDimensions(dim);
382 out->SetDimensions(dim[0], dim[1], im.size() );
383 out->AllocateScalars();
386 unsigned long imsize = dim[0] * dim[1];
387 imsize = imsize * dim[2] ; // deal with multiframes // JPR
391 // differents formats char , short, etc...
392 // differents components 1..3 ex. jpg ->RGB 3
393 imsize = imsize * first->GetScalarSize() * first->GetNumberOfScalarComponents();
396 // Order the file name vector
399 first->GetSpacing(spc);
401 // OrderTheFileNameVector is not here anymore.
402 // Try orderFilesWithZSpacing from OutputModel FCY
403 // spc[2]=OrderTheFileNameVector(im);
406 out->SetSpacing(spc);
409 std::vector<std::string>::iterator it;
411 for (it=im.begin(); it!=im.end(); ++it)
413 vtkImageData* cur = mReader.GetImage( (*it) );
414 memcpy(out->GetScalarPointer(0,0,slice), cur->GetScalarPointer(0,0,0), imsize);
424 //======================================================================
428 //////////////////////////////////////////////////////////
429 // Test if the image is a multiple or single frame.
430 // For the moment only with the creation of vtkImageDta.
431 // TO DO with image size and dim!!!
432 //////////////////////////////////////////////////////////
433 bool GimmickView::isSingle(const std::string i_file)
436 vtkImageData* first = mReader.GetImage( i_file);
438 first->GetDimensions(dim);
449 //////////////////////////////////////////////////////////
450 // get Attributes values for a file
451 //////////////////////////////////////////////////////////
453 void GimmickView::getAttributes(const std::string i_file, std::map<std::string, std::string> &o_infos, OutputAttr i_attr)
455 if(i_attr.inside.size() >0)
457 mGimmick->GetAttributes(i_file,o_infos,i_attr);
459 if(i_attr.outside.size()>0)
461 mReader.getAttributes(i_file,o_infos, i_attr.outside);
465 //////////////////////////////////////////////////////////
466 // create an output structure with n entries = n output
467 //////////////////////////////////////////////////////////
468 void GimmickView::readImages1(std::vector<OutStrGimmick>& o_output, std::vector<std::string> im,
471 std::vector<std::string>::iterator it;
472 for (it=im.begin(); it!=im.end(); ++it)
475 out.img = vtkImageData::New();
476 out.img->ShallowCopy(mReader.GetImage(*it));
478 getAttributes((*it),out.infos,i_attr);
479 o_output.push_back(out);
481 // If we want only one output information structure, we set it outside the loop
484 getAttributes(im.front(), o_output.front().infos,i_attr);
489 //////////////////////////////////////////////////////////
490 // create an output structure with n entries = 1 output
491 //////////////////////////////////////////////////////////
492 void GimmickView::readImages3(std::vector<OutStrGimmick>& o_output, std::vector<std::string> im,
493 OutputAttr i_attr, double i_zspc)
496 vtkImageData* first = mReader.GetImage( im.front());
497 out.img = vtkImageData::New();
498 out.img->SetScalarType(first->GetScalarType());
499 out.img->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents());
501 first->GetWholeExtent(ext); // send also 0,0 in Z
504 ext[5] = im.size()-1;
508 ext[5] = ext[5] * im.size()-1; // to deal with multiframes
510 out.img->SetExtent(ext);
512 first->GetDimensions(dim);
513 out.img->SetDimensions(dim[0], dim[1], im.size() );
514 out.img->AllocateScalars();
516 unsigned long imsize = dim[0] * dim[1];
517 imsize = imsize * dim[2] ; // deal with multiframes here
518 // differents formats char , short, etc...
519 // differents components 1..3 ex. jpg ->RGB 3
520 imsize = imsize * first->GetScalarSize() * first->GetNumberOfScalarComponents();
521 // Order the file name vector already did with the OutputModel!!!
522 //!!!!out.img->SetSpacing(i_zspc);
524 std::vector<std::string>::iterator it;
525 for (it=im.begin(); it!=im.end(); ++it)
527 vtkImageData* cur = mReader.GetImage( (*it) );
528 memcpy(out.img->GetScalarPointer(0,0,slice), cur->GetScalarPointer(0,0,0), imsize);
531 getAttributes(im.front(),out.infos, i_attr);
532 o_output.push_back(out);
536 // TO DO NO VERY SURE : NEED TO BE TESTED
537 //////////////////////////////////////////////////////////
538 // create an output structure with n entries (T size) = T output (n size)
539 //////////////////////////////////////////////////////////
540 void GimmickView::readImages2(std::vector<OutStrGimmick>& o_output, std::vector<std::string> im,
541 OutputAttr i_attr, double i_zspc)
543 vtkImageData* first = mReader.GetImage( im.front());
545 first->GetDimensions(dim);
546 // differents formats char , short, etc...
547 // differents components 1..3 ex. jpg ->RGB 3
548 unsigned long imsize = dim[0] * dim[1];
549 imsize = imsize * first->GetScalarSize() * first->GetNumberOfScalarComponents();
551 // Order the file name vector already did with the OutputModel!!!
552 std::vector<std::string>::iterator it;
553 std::vector<OutStrGimmick>::iterator it_out = o_output.begin();
555 for (it=im.begin(); it!=im.end(); ++it, it_out += dim[2])
557 vtkImageData* cur = mReader.GetImage( (*it) );
558 for (int slice= 0 ; slice <dim[2]; slice++)
561 out.img = vtkImageData::New();
562 out.img->SetScalarType(first->GetScalarType());
564 out.img->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents());
566 first->GetWholeExtent(ext); // send also 0,0 in Z
568 out.img->SetExtent(ext);
570 out.img->SetDimensions(dim[0], dim[1], 1 );
571 out.img->AllocateScalars();
573 memcpy(out.img->GetScalarPointer(0,0,0), cur->GetScalarPointer(0,0,slice), imsize);
574 o_output.push_back(out);
577 getAttributes((*it),(*it_out).infos,i_attr);
581 getAttributes(im.front(), o_output.front().infos,i_attr);
586 //////////////////////////////////////////////////////////
587 // create an output structure with n entries (T size) = T + n output
588 //////////////////////////////////////////////////////////
589 void GimmickView::readImages4(std::vector<OutStrGimmick>& o_output, std::vector<std::string> im,
592 std::vector<std::string>::iterator it;
593 std::vector<OutStrGimmick>::iterator it_out = o_output.begin();
594 vtkImageData* first = mReader.GetImage( im.front());
596 first->GetDimensions(dim);
598 for (int slice= 0 ; slice <dim[2]; slice++)
601 out.img = vtkImageData::New();
602 out.img->SetScalarType(first->GetScalarType());
603 out.img->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents());
606 first->GetWholeExtent(ext); // send also 0,0 in Z
608 out.img->SetExtent(ext);
610 out.img->SetDimensions(dim[0], dim[1], im.size() );
611 out.img->AllocateScalars();
613 unsigned long imsize = dim[0] * dim[1];
614 imsize = imsize * first->GetScalarSize() * first->GetNumberOfScalarComponents();
617 for (it=im.begin(); it!=im.end(); ++it, index ++)
619 vtkImageData* cur = mReader.GetImage( (*it) );
620 memcpy(out.img->GetScalarPointer(0,0,index), cur->GetScalarPointer(0,0,slice), imsize);
621 o_output.push_back(out);
624 if(!i_attr.mult) // No sense to take informations in all images
626 getAttributes(im.front(), o_output.front().infos,i_attr);
632 //////////////////////////////////////////////////////////////////////////////////////////////////////////////
633 // Global function to read Images and create wished output (informations, multiple, type and size of output...)
634 // In function of type (file, vector) and size, the correct readImages function is selected
635 //////////////////////////////////////////////////////////////////////////////////////////////////////////////
636 void GimmickView::readImages(std::vector<OutStrGimmick>& o_output, std::vector<std::string> im,
637 OutputAttr i_attr, int i_dim, double i_zspc)
639 int size = im.size();
647 // Only one image : give it
648 // But take in count multiframe possibility
649 if ( isSingle(im.front()) || i_dim != 1)
651 readImages1(o_output,im, i_attr);
655 readImages2(o_output,im, i_attr,i_zspc);
661 // multiple or single frame
662 if ( isSingle(im.front()) )
664 //we deal with 2D images
668 readImages3(o_output,im, i_attr,i_zspc);
672 readImages1(o_output,im, i_attr);
677 // we deal with multiple frames n x (2D x T)
678 // Differents outputs are avaialable
681 // put all in one output
682 readImages3(o_output,im, i_attr,i_zspc);
687 // put in a vector of n x T (2D)
688 readImages2(o_output,im, i_attr,i_zspc);
692 // put in a vector of n (2D x T)
693 // No transformations.
694 readImages1(o_output,im, i_attr);
698 // put in a vector of T (2D x n)
699 readImages4(o_output,im, i_attr);
708 void GimmickView::ReadImagesNotThreadedInVector(std::vector<vtkImageData*>& s, std::vector<std::string> im, int dimension)
710 // Create the output data
713 // Only one image : give it
714 vtkImageData* out = vtkImageData::New();
715 GimmickDebugMessage(3, "State Check: Full Filename: "
718 out->ShallowCopy(mReader.GetImage(im.front()));
721 else if (im.size()>1) // Test inutile ? JPR
723 vtkImageData* first = mReader.GetImage( im.front());
727 std::vector<std::string>::iterator it;
728 for (it=im.begin(); it!=im.end(); ++it)
730 vtkImageData* out = vtkImageData::New();
731 out->ShallowCopy(mReader.GetImage(*it));
738 // n *2D + T in a vector :
740 std::vector<std::string>::iterator it;
741 for (it=im.begin(); it!=im.end(); ++it)
743 vtkImageData* out = mReader.GetImage( (*it));
749 //======================================================================
751 //======================================================================
752 ///Requests the reading of an image
753 void GimmickView::RequestReading(tree::Node* n,
754 int prio, int selection_index, boost::shared_ptr<ImagePointerHolder> p)
761 ImageEventType t(n,selection_index);
763 mImageEventMap[n->GetAttribute("FullFileName")] = t;
764 mReader.Request(this,n->GetAttribute("FullFileName"),prio);
766 //======================================================================
768 //======================================================================
770 OnMultiThreadImageReaderEvent(const std::string& filename,
771 MultiThreadImageReaderUser::EventType e,
774 GimmickDebugMessage(7,
775 "MultiThreadImageReader event : "<<e<<std::endl);
778 if (filename.size()==0)
780 //What to do in this case?
782 GimmickDebugMessage(5,
783 "Pushing unknown image in queue"
785 mImageEventQueue.push_back(ImageEventType(image));*/
788 ImageEventTypeMap::iterator i;
789 //JCP 22-06-2009, test mImageEventMap.size() > 0
790 if(mImageEventMap.size()>0){
791 i = mImageEventMap.find(filename);
792 if (i!=mImageEventMap.end())
794 GimmickDebugMessage(5,
795 "Putting image of file '"<<filename<<"' on pointer"
797 ImageEventType ie(i->second);
799 ie.pointerHolder->Set(ie.image);
800 //mImageEventMap.erase(i);
806 std::string mess="ERROR: MultiThreadImageReader: Cannot read image in file ";
809 GimmickMessage(1,mess);
810 ImageEventTypeMap::iterator i;
811 i = mImageEventMap.find(filename);
812 if (i!=mImageEventMap.end())
814 ImageEventType ie(i->second);
816 ie.pointerHolder->Set(GetDefaultImage());
817 //mImageEventMap.erase(i);
821 else if (e==ImageUnloaded)
823 std::string mess="Unloaded image in file ";
826 GimmickMessage(1,mess);
827 ImageEventTypeMap::iterator i;
828 i = mImageEventMap.find(filename);
829 if (i!=mImageEventMap.end())
831 ImageEventType ie(i->second);
833 ie.pointerHolder->Set(GetDefaultImage());
834 //mImageEventMap.erase(i);
839 //====================================================================
841 //====================================================================
842 void GimmickView::ConnectValidationObserver(ValidationCallbackType callback)
844 mValidationSignal.connect(callback);
849 ////////////////////////////////////////////////////////////////////////
850 //void GimmickView::Anonymize(std::vector<std::string> i_filenames, int type)
853 // gdcm::FileMetaInformation::SetSourceApplicationEntityTitle( "gdcmanon" );
854 // gdcm::Global& g = gdcm::Global::GetInstance();
855 // //if( !resourcespath )
857 // // const char *xmlpathenv = getenv("GDCM_RESOURCES_PATH");
858 // // if( xmlpathenv )
860 // // // Make sure to look for XML dict in user explicitly specified dir first:
861 // // xmlpath = xmlpathenv;
862 // // resourcespath = 1;
865 // // if( resourcespath )
867 // // // xmlpath is set either by the cmd line option or the env var
868 // // if( !g.Prepend( xmlpath.c_str() ) )
870 // // std::cerr << "Specified Resources Path is not valid: " << xmlpath << std::endl;
874 // // All set, then load the XML files:
875 // if( !g.LoadResourcesFiles() )
879 // const gdcm::Defs &defs = g.GetDefs(); (void)defs;
882 // // only read the env var if no explicit cmd line option
883 // // maybe there is an env var defined... let's check
884 // const char *rootuid_env = getenv("GDCM_ROOT_UID");
888 // root = rootuid_env;
893 // // root is set either by the cmd line option or the env var
894 // if( !gdcm::UIDGenerator::IsValid( root.c_str() ) )
896 // std::cerr << "specified Root UID is not valid: " << root << std::endl;
899 // gdcm::UIDGenerator::SetRoot( root.c_str() );
904 // // Get private key/certificate
905 // gdcm::CryptographicMessageSyntax cms;
908 // if( !GetRSAKeys(cms, rsa_path.c_str(), cert_path.c_str() ) )
912 // cms.SetCipherType( ciphertype );
915 // // Setup gdcm::Anonymizer
916 // gdcm::Anonymizer anon;
918 // anon.SetCryptographicMessageSyntax( &cms );
922 // for(unsigned int i = 0; i < nfiles; ++i)
924 // const char *in = filenames[i].c_str();
925 // const char *out = outfilenames[i].c_str();
926 // if( !AnonymizeOneFileDumb(anon, in, out, empty_tags, remove_tags, replace_tags_value) )
928 // //std::cerr << "Could not anonymize: " << in << std::endl;
935 // // for(unsigned int i = 0; i < nfiles; ++i)
937 // // const char *in = filenames[i].c_str();
938 // // const char *out = outfilenames[i].c_str();
939 // // if( !AnonymizeOneFile(anon, in, out) )
941 // // //std::cerr << "Could not anonymize: " << in << std::endl;
949 } // EO namespace creaImageIO