From: Claire Mouton <claire.mouton@creatis.insa-lyon.fr>
Date: Thu, 13 Mar 2014 15:24:57 +0000 (+0100)
Subject: Merge branch 'master' of ssh://git.creatis.insa-lyon.fr/creaImageIO
X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=68975087396fa3f3e1adb04073cd30dc79b535a3;hp=7e7a6a1fa4b88ed6a998f50aabfa5e66b190cb87;p=creaImageIO.git

Merge branch 'master' of ssh://git.creatis.insa-lyon.fr/creaImageIO
---

diff --git a/bbtk/src/bbcreaImageIOGetDicomAttributesFromMaps.cxx b/bbtk/src/bbcreaImageIOGetDicomAttributesFromMaps.cxx
new file mode 100644
index 0000000..bd45183
--- /dev/null
+++ b/bbtk/src/bbcreaImageIOGetDicomAttributesFromMaps.cxx
@@ -0,0 +1,84 @@
+//===== 
+// Before editing this file, make sure it's a file of your own (i.e.: it wasn't generated from xml description; if so : your modifications will be lost)
+//===== 
+#include "bbcreaImageIOGetDicomAttributesFromMaps.h"
+#include "bbcreaImageIOPackage.h"
+namespace bbcreaImageIO
+{
+
+BBTK_ADD_BLACK_BOX_TO_PACKAGE(creaImageIO,GetDicomAttributesFromMaps)
+BBTK_BLACK_BOX_IMPLEMENTATION(GetDicomAttributesFromMaps,bbtk::AtomicBlackBox);
+//===== 
+// Before editing this file, make sure it's a file of your own (i.e.: it wasn't generated from xml description; if so : your modifications will be lost)
+//===== 
+void GetDicomAttributesFromMaps::Process()
+{
+
+// THE MAIN PROCESSING METHOD BODY
+//   Here we simply set the input 'In' value to the output 'Out'
+//   And print out the output value
+// INPUT/OUTPUT ACCESSORS ARE OF THE FORM :
+//    void bbSet{Input|Output}NAME(const TYPE&)
+//    const TYPE& bbGet{Input|Output}NAME() const 
+//    Where :
+//    * NAME is the name of the input/output
+//      (the one provided in the attribute 'name' of the tag 'input')
+//    * TYPE is the C++ type of the input/output
+//      (the one provided in the attribute 'type' of the tag 'input')
+
+    std::vector< std::string > lstResult;
+    std::map <std::string,std::string> tmpMap;
+    int i,size=bbGetInputIn().size();
+    std::string strElement;
+
+    for (i=0;i<size;i++)
+    { 
+	tmpMap 		= bbGetInputIn()[i];
+        printf("EED GetDicomAttributesFromMaps::Process %d", tmpMap.size() );
+
+	strElement 	= tmpMap.find( bbGetInputKeyDicom() )->second;
+	lstResult.push_back( strElement );
+    } // for i
+    bbSetOutputOut( lstResult );
+  
+}
+//===== 
+// Before editing this file, make sure it's a file of your own (i.e.: it wasn't generated from xml description; if so : your modifications will be lost)
+//===== 
+void GetDicomAttributesFromMaps::bbUserSetDefaultValues()
+{
+
+//  SET HERE THE DEFAULT INPUT/OUTPUT VALUES OF YOUR BOX 
+//    Here we initialize the input 'In' to 0
+//   bbSetInputIn(0);
+  
+}
+//===== 
+// Before editing this file, make sure it's a file of your own (i.e.: it wasn't generated from xml description; if so : your modifications will be lost)
+//===== 
+void GetDicomAttributesFromMaps::bbUserInitializeProcessing()
+{
+
+//  THE INITIALIZATION METHOD BODY :
+//    Here does nothing 
+//    but this is where you should allocate the internal/output pointers 
+//    if any 
+
+  
+}
+//===== 
+// Before editing this file, make sure it's a file of your own (i.e.: it wasn't generated from xml description; if so : your modifications will be lost)
+//===== 
+void GetDicomAttributesFromMaps::bbUserFinalizeProcessing()
+{
+
+//  THE FINALIZATION METHOD BODY :
+//    Here does nothing 
+//    but this is where you should desallocate the internal/output pointers 
+//    if any
+  
+}
+}
+// EO namespace bbcreaImageIO
+
+
diff --git a/bbtk/src/bbcreaImageIOGetDicomAttributesFromMaps.h b/bbtk/src/bbcreaImageIOGetDicomAttributesFromMaps.h
new file mode 100644
index 0000000..3b98bfd
--- /dev/null
+++ b/bbtk/src/bbcreaImageIOGetDicomAttributesFromMaps.h
@@ -0,0 +1,49 @@
+//===== 
+// Before editing this file, make sure it's a file of your own (i.e.: it wasn't generated from xml description; if so : your modifications will be lost)
+//===== 
+#ifndef __bbcreaImageIOGetDicomAttributesFromMaps_h_INCLUDED__
+#define __bbcreaImageIOGetDicomAttributesFromMaps_h_INCLUDED__
+#include "bbcreaImageIO_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+#include "iostream"
+
+namespace bbcreaImageIO
+{
+
+typedef std::map <std::string, std::string> mapString;
+
+class bbcreaImageIO_EXPORT GetDicomAttributesFromMaps
+ : 
+   public bbtk::AtomicBlackBox
+{
+  BBTK_BLACK_BOX_INTERFACE(GetDicomAttributesFromMaps,bbtk::AtomicBlackBox);
+//===== 
+// Before editing this file, make sure it's a file of your own (i.e.: it wasn't generated from xml description; if so : your modifications will be lost)
+//===== 
+  BBTK_DECLARE_INPUT(In,std::vector< mapString > );
+  BBTK_DECLARE_INPUT(KeyDicom, std::string);
+  BBTK_DECLARE_OUTPUT(Out,std::vector <std::string>);
+  BBTK_PROCESS(Process);
+  void Process();
+//===== 
+// Before editing this file, make sure it's a file of your own (i.e.: it wasn't generated from xml description; if so : your modifications will be lost)
+//===== 
+};
+
+BBTK_BEGIN_DESCRIBE_BLACK_BOX(GetDicomAttributesFromMaps,bbtk::AtomicBlackBox);
+BBTK_NAME("GetDicomAttributesFromMaps");
+BBTK_AUTHOR("Info-Dev, Eduardo DAVIL");
+BBTK_DESCRIPTION("eduardo.davila[at]creatis.insa-lyon.fr -");
+BBTK_CATEGORY("empty");
+  BBTK_INPUT(GetDicomAttributesFromMaps,In,"Vector of maps with DICOM attributes",std::vector< mapString >,"");
+  BBTK_INPUT(GetDicomAttributesFromMaps,KeyDicom,"Key DICOM",std::string ,"");
+  BBTK_OUTPUT(GetDicomAttributesFromMaps,Out,"Vector of the attribute asked.",std::vector <std::string>,"");
+BBTK_END_DESCRIBE_BLACK_BOX(GetDicomAttributesFromMaps);
+//===== 
+// Before editing this file, make sure it's a file of your own (i.e.: it wasn't generated from xml description; if so : your modifications will be lost)
+//===== 
+}
+// EO namespace bbcreaImageIO
+
+#endif // __bbcreaImageIOGetDicomAttributesFromMaps_h_INCLUDED__
+
diff --git a/bbtk/src/bbcreaImageIOImagesChooserDialogBox.xml b/bbtk/src/bbcreaImageIOImagesChooserDialogBox.xml
index 9c07473..454f883 100644
--- a/bbtk/src/bbcreaImageIOImagesChooserDialogBox.xml
+++ b/bbtk/src/bbcreaImageIOImagesChooserDialogBox.xml
@@ -45,27 +45,49 @@
     INPUTS/OUTPUTS DECLARATION -->
 
   <input name="Title" type="std::string" description="Title of the dialog"/>
+
+
+
   <typedef>
     <PRE>
-      typedef std::vector<vtkImageData*> OutputImagesType;</PRE>
+      typedef std::vector<std::string> VectorStringType;</PRE>
   </typedef>
+  <input name="DicomTags" type="VectorStringType" description="Dicom Tags (vector of Dicom tags ex: D0028_0030  D0020_0037)"/>
 
+  <typedef>
+    <PRE>
+      typedef std::vector<vtkImageData*> OutputImagesType;</PRE>
+  </typedef>
   <output name="Out" type="vtkImageData*" description="The selected image"/>
   <output name="OutImages" type="OutputImagesType" description="Vector of selected images"/>
+
+  <typedef>
+    <PRE>
+      typedef std::map<std::string, std::string> MapInfoDicom;</PRE>
+  </typedef>
+
+  <typedef>
+    <PRE>
+      typedef std::vector< MapInfoDicom > VectorMapInfoDicom;</PRE>
+  </typedef>
+
+  <output name="DicomInfo" type="VectorMapInfoDicom" description="vector of maps of Dicom tags"/>
   
   <!--========================================================================
     PROCESS section -->
 
   <process>
     <PRE>
+     
         creaImageIO::WxSimpleDlg dlg(0,crea::std2wx(bbGetInputTitle()),"localdatabase_Descriptor.dscp","Local Database"); 
+                dlg.SetAttrDicomTags( bbGetInputDicomTags() );
 		dlg.ShowModal(); 
+                bbSetOutputDicomInfo( dlg.getDicomInfoImagesSelected() );
 		if (dlg.getImagesSelected().size()!=0){ 
 		  if(dlg.getImagesSelected().size() ==1)
 		  {
 			bbSetOutputOut( dlg.getImagesSelected()[0] );  
 		  } else {
-printf("EED  creaImageIOWxSimpleDlg 1 \n");
 			  // FCY: it will be a big problem if we have several kind of data in the same folder.
 			  // creation of a huge vtkImageData!!!!
 			  vtkImageData* first = dlg.getImagesSelected()[0];
@@ -101,11 +123,9 @@ printf("EED  creaImageIOWxSimpleDlg 1 \n");
 			  	// differents formats char , short, etc...
 			  	// differents components 1..3  ex. jpg ->RGB 3
 			  	imsize = imsize * first->GetScalarSize() * first->GetNumberOfScalarComponents();
-printf("EED  creaImageIOWxSimpleDlg 2 \n");
   		        	int slice,sizeImageVector=dlg.getImagesSelected().size();
                         	for (slice=0 ; slice<sizeImageVector ; slice++)
 			 	{
-printf("EED  creaImageIOWxSimpleDlg 3 slice %d     sizeImageVector %d\n",slice,sizeImageVector);
 					vtkImageData *img = dlg.getImagesSelected()[slice];
 					memcpy(out->GetScalarPointer(0,0,slice), img->GetScalarPointer(0,0,0), imsize);
 				//img->Delete();
@@ -124,7 +144,6 @@ printf("EED  creaImageIOWxSimpleDlg 3 slice %d     sizeImageVector %d\n",slice,s
 // 			//	(*it)->Delete();
 //			//  }
 
-printf("EED  creaImageIOWxSimpleDlg 4 \n");
 			 	bbSetOutputOut(out);
 			} else {
 			 bbSetOutputOut(first);
diff --git a/src/creaImageIOVtkImageReader.cpp b/src/creaImageIOVtkImageReader.cpp
index 60ef13a..6cb4def 100644
--- a/src/creaImageIOVtkImageReader.cpp
+++ b/src/creaImageIOVtkImageReader.cpp
@@ -43,7 +43,7 @@ namespace creaImageIO{
   {
 	  
 	//EED 21 mars 2012  FLIP probleme  ..PLOP..
-	mReader->FileLowerLeftOn();
+	mReader->FileLowerLeftOff();
 	  
     if (name.size() == 0) 
       {
@@ -98,13 +98,56 @@ namespace creaImageIO{
     vtkImageData* im = 0;
     try
       {
-	
-	mReader->SetFileName(filename.c_str());
+	printf("EED VtkImageReader::ReadImage  Name:%s\n", GetName().c_str() );
+	mReader->SetFileName( filename.c_str() );
 	mReader->Update();
 	im = vtkImageData::New();
-        mReader->FileLowerLeftOff();
+
 	im->ShallowCopy(mReader->GetOutput());
-printf("EED VtkImageReader::ReadImage GetFileLowerLeft %d\n" , mReader->GetFileLowerLeft() );
+
+
+printf("EED ......\n"); 
+printf("EED ......\n");
+printf("EED VtkImageReader::ReadImage line 108   Missing FlipImage for JPEG, PNG, etc\n");
+printf("EED ......\n"); 
+printf("EED ......\n"); 
+/*
+        im=FlipImageY(im);          
+
+	if ( (GetName()=="JPEG") || (GetName()=="PNG") )
+	{
+
+		im->Update();
+		int inputdims[3];
+		im->GetDimensions (inputdims);
+
+                int nbScalComp	= im->GetNumberOfScalarComponents();
+		int scalarSize	= im->GetScalarSize();
+		int lineSize	= inputdims[0]*scalarSize*nbScalComp;	   
+		int planeSize	= inputdims[1]*lineSize;
+                int volumeSize  = inputdims[2]*planeSize;
+		char *pixelsIn	= (char *)im->GetScalarPointer();
+		char *pixelsOut = (char *)mImageOut->GetScalarPointer();
+	
+		char *lineIn;
+		char *lineOut;
+		char *debPlanIn;
+		char *debPlanOut;
+		int i,j,k;
+
+            	for(k=0; k<inputdims[2]; k++)  // iterate  planes
+			{  
+				debPlanIn	= pixelsIn+k*planeSize;
+				debPlanOut	= pixelsOut+k*planeSize;
+				for(j=0; j<inputdims[1]; j++)  // iterates  rows
+				{ 
+					lineIn = debPlanIn+j*lineSize;
+					lineOut = debPlanOut+(inputdims[1]-1-j)*lineSize;
+					memcpy(lineOut,  lineIn, lineSize);
+				}	// for j
+			} // for k
+	} // FLIP : JPEG PNG
+*/
       }
     catch (...)
       {
diff --git a/src/creaImageIOWxSimpleDlg.cpp b/src/creaImageIOWxSimpleDlg.cpp
index db55ad1..a537b32 100644
--- a/src/creaImageIOWxSimpleDlg.cpp
+++ b/src/creaImageIOWxSimpleDlg.cpp
@@ -143,27 +143,28 @@ namespace creaImageIO
 		 dlg.ShowModal();
 		 if (dlg.GetReturnCode() == wxID_OK)
 	     {
-			std::vector<creaImageIO::OutStrGimmick> out;
-			std::vector<std::string> attr;
 				dlg.stopReading();
-				dlg.getSelected(out, attr,true,"");
+
+				std::vector<creaImageIO::OutStrGimmick> outStrGimmick;
+				dlg.getSelected(outStrGimmick, m_attrDicomTags,true,"");
+
 			m_results.clear();
-			int size=(int)out.size();
+			int size=(int)outStrGimmick.size();
 			int ii;
-			if(!bInfo)
-			{
+//			if(!bInfo)
+//			{
 				for (ii=0;ii<size;ii++)
 				{
-					m_results.push_back(out[ii].img);
+					m_results.push_back(outStrGimmick[ii].img);
+					m_resultsDicomAtr.push_back( outStrGimmick[ii].infos );
 				}
-			}
-			else
-			{
-				for (ii=0;ii<size;ii++)
-				{
-					m_resultsInfo.push_back(out[ii]);
-				}
-			}
+//			} else {
+//				for (ii=0;ii<size;ii++)
+//				{
+//					m_resultsInfo.push_back(outStrGimmick[ii]);
+//				}
+//			}
+
 			dlg.OnExit();
 		 }
 		 SetReturnCode( dlg.GetReturnCode() );
@@ -183,6 +184,17 @@ namespace creaImageIO
 		  return m_results;
 	  }
 
+	std::vector< std::map<std::string, std::string> >  WxSimpleDlg::getDicomInfoImagesSelected()
+	{
+		return m_resultsDicomAtr;
+	}
+
+	void WxSimpleDlg::SetAttrDicomTags( std::vector<std::string> attr )
+	{
+		m_attrDicomTags=attr;
+	}
 	  
+
+
 }
 
diff --git a/src/creaImageIOWxSimpleDlg.h b/src/creaImageIOWxSimpleDlg.h
index 7fd3335..5e3f5f0 100644
--- a/src/creaImageIOWxSimpleDlg.h
+++ b/src/creaImageIOWxSimpleDlg.h
@@ -58,9 +58,12 @@ namespace creaImageIO
 
 		   /// return a vtkImageData vector of selected images, if available
 		   std::vector<vtkImageData*> getImagesSelected();
-		
 		   wxString getInfoImage();
 
+		   std::vector< std::map<std::string,std::string> >  getDicomInfoImagesSelected();
+		   void SetAttrDicomTags( std::vector<std::string> attr );
+
+
 		   void setInfo(bool i_val){bInfo = i_val;}
 		   
 		   // OutStrGimmick:
@@ -69,19 +72,20 @@ namespace creaImageIO
 		   std::vector<creaImageIO::OutStrGimmick> getMapInfos(){return m_resultsInfo;}
 
 	private:
-		bool 					bInfo;
-		std::string 				namedescp; 
-		std::string 				namedb;
-		wxString 				infoimage;
+		bool 							bInfo;
+		std::string 						namedescp; 
+		std::string 						namedb;
+		wxString 						infoimage;
 
 		/// interface to read data
-		SimpleView 				m_view;
+		SimpleView 						m_view;
 
 		/// vtkImageData vector
-		std::vector<vtkImageData*> 		m_results;
+		std::vector<vtkImageData*> 				m_results;
+		std::vector< std::map<std::string,std::string> > 	m_resultsDicomAtr;
+		std::vector<std::string> 				m_attrDicomTags;    // DXXXX_YYYY DAAAA_BBBB ...
 
 		std::vector<creaImageIO::OutStrGimmick> m_resultsInfo;
 		
-
 	};
 }