#3498 Connectivity Filter Threshold

diff --git a/bbtk_creaVtk_PKG/src/bbcreaVtkImageConnectivityFilter.cxx b/bbtk_creaVtk_PKG/src/bbcreaVtkImageConnectivityFilter.cxx
index 2f5c9e96745aa9fc6330f817bd3fa3b5d56ab20a..d9c051c9b297b9d94a06254097c35188d1355b7c 100644 (file)
--- a/bbtk_creaVtk_PKG/src/bbcreaVtkImageConnectivityFilter.cxx
+++ b/bbtk_creaVtk_PKG/src/bbcreaVtkImageConnectivityFilter.cxx
@@ -4,6 +4,10 @@
 #include "bbcreaVtkImageConnectivityFilter.h"
 #include "bbcreaVtkPackage.h"
 
+#include <vtkPolyData.h>
+#include <vtkPoints.h>
+#include <vtkPointData.h>
+
 namespace bbcreaVtk
 {
 
@@ -26,12 +30,12 @@ void ImageConnectivityFilter::Process()
 //      (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')
-
-
-       if (bbGetInputIn()!=NULL){
+    
+       if (bbGetInputIn()!=NULL)
+    {
                if (imgConnfilter) {imgConnfilter->Delete();}
                imgConnfilter=vtkImageConnectivityFilter::New();
-               imgConnfilter->SetInputData( bbGetInputIn() );
+        imgConnfilter->SetInputData( bbGetInputIn() );
                if (bbGetInputExtractionMode()==0)  // LargestRegion
                {
                        imgConnfilter->SetExtractionModeToLargestRegion();
@@ -41,21 +45,47 @@ void ImageConnectivityFilter::Process()
                {
                        printf("EED Warning!!!! ImageConnectivityFilter - AllRegions Not Implemented\n ");
                } // ExtractionMode
-               if (bbGetInputExtractionMode()==2)  // SeededRegions
+               if (bbGetInputExtractionMode()==2)  // SeedRegions
                {
-                       printf("EED Warning!!!! ImageConnectivityFilter  - SeededRegions Not Implemented\n ");
+            std::vector<double> lstX = bbGetInputLstX();
+            std::vector<double> lstY = bbGetInputLstY();
+            std::vector<double> lstZ = bbGetInputLstZ();
+            int size = lstX.size();
+            if ( (lstX.size()>0) && (lstX.size()==lstY.size()) && (lstX.size()==lstZ.size()) )
+            {
+                int i;
+                double p[3];
+                vtkPoints *points = vtkPoints::New();
+                for (i=0; i<size; i++)
+                {
+                    p[0] = lstX[i];
+                    p[1] = lstY[i];
+                    p[2] = lstZ[i];
+                    points->InsertNextPoint(p);
+                } // for i
+                vtkPolyData *seedData =  vtkPolyData::New();
+                seedData->SetPoints( points );
+//              vtkUnsignedCharArray  *seedScalars = vtkUnsignedCharArray::New();
+//              seedScalars->InsertNextValue(100);
+//              seedData->GetPointData()->SetScalars(seedScalars);
+                seedData->GetPointData()->SetScalars(nullptr);
+                
+                imgConnfilter->SetExtractionModeToSeededRegions();
+                imgConnfilter->SetSeedData( seedData );
+//              imgConnfilter->SetSizeRange(0, 99);
+            } // if lst
+
                } // ExtractionMode
 
                if (bbGetInputScalarRange().size()==2)  
                {
                        imgConnfilter->SetScalarRange( bbGetInputScalarRange()[0], bbGetInputScalarRange()[1] );
                } // Range
-               imgConnfilter->Update();
+               imgConnfilter->Update( );
                bbSetOutputOut( imgConnfilter->GetOutput() );
        } else {
                        printf("EED Warning!!!! ImageConnectivityFilter  - Input image not defined.\n ");
        }// In
-  
 }
 //===== 
 // 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)

diff --git a/bbtk_creaVtk_PKG/src/bbcreaVtkImageConnectivityFilter.h b/bbtk_creaVtk_PKG/src/bbcreaVtkImageConnectivityFilter.h
index bec7295ac8737e404e8a297bae3c10c245864fe2..2abf3993bfab83a4b039a0890ce02b755b35cb7c 100644 (file)
--- a/bbtk_creaVtk_PKG/src/bbcreaVtkImageConnectivityFilter.h
+++ b/bbtk_creaVtk_PKG/src/bbcreaVtkImageConnectivityFilter.h
@@ -25,6 +25,9 @@ class bbcreaVtk_EXPORT ImageConnectivityFilter
   BBTK_DECLARE_INPUT(In,vtkImageData*);
   BBTK_DECLARE_INPUT(ExtractionMode,int);
   BBTK_DECLARE_INPUT(ScalarRange,std::vector< double >);
+  BBTK_DECLARE_INPUT(LstX,std::vector< double >);
+  BBTK_DECLARE_INPUT(LstY,std::vector< double >);
+  BBTK_DECLARE_INPUT(LstZ,std::vector< double >);
 
   BBTK_DECLARE_OUTPUT(Out,vtkImageData*);
   BBTK_PROCESS(Process);
@@ -43,8 +46,11 @@ BBTK_BEGIN_DESCRIBE_BLACK_BOX(ImageConnectivityFilter,bbtk::AtomicBlackBox);
   BBTK_CATEGORY("empty");
 
   BBTK_INPUT(ImageConnectivityFilter,In,"Input image",vtkImageData*,"");
-  BBTK_INPUT(ImageConnectivityFilter,ExtractionMode,"(default 0) 0=LargestRegion  1=AllRegions   2=SeededRegions",int,"");
+  BBTK_INPUT(ImageConnectivityFilter,ExtractionMode,"(default 0) 0=LargestRegion,  1=AllRegions,   2=SeededRegions use LstX LstY LstZ,",int,"");
   BBTK_INPUT(ImageConnectivityFilter,ScalarRange,"threshold [Min Max]",std::vector< double >,"");
+  BBTK_INPUT(ImageConnectivityFilter,LstX,"list X",std::vector< double >,"");
+  BBTK_INPUT(ImageConnectivityFilter,LstY,"list Y",std::vector< double >,"");
+  BBTK_INPUT(ImageConnectivityFilter,LstZ,"list Z",std::vector< double >,"");
 
   BBTK_OUTPUT(ImageConnectivityFilter,Out,"Output image",vtkImageData*,"");
 

diff --git a/bbtk_creaVtk_PKG/src/bbcreaVtkImageThresholdConnectivity.cxx b/bbtk_creaVtk_PKG/src/bbcreaVtkImageThresholdConnectivity.cxx
index 71366434d86e5184c05c28be6b201ca48bbb589d..a7ddb49608e71098de98f90c15ea79e3b94cbb09 100644 (file)
--- a/bbtk_creaVtk_PKG/src/bbcreaVtkImageThresholdConnectivity.cxx
+++ b/bbtk_creaVtk_PKG/src/bbcreaVtkImageThresholdConnectivity.cxx
@@ -3,6 +3,9 @@
 //===== 
 #include "bbcreaVtkImageThresholdConnectivity.h"
 #include "bbcreaVtkPackage.h"
+#include "vtkImageThresholdConnectivity.h"
+#include "vtkPoints.h"
+
 namespace bbcreaVtk
 {
 
@@ -13,7 +16,6 @@ BBTK_BLACK_BOX_IMPLEMENTATION(ImageThresholdConnectivity,bbtk::AtomicBlackBox);
 //===== 
 void ImageThresholdConnectivity::Process()
 {
-
 // THE MAIN PROCESSING METHOD BODY
 //   Here we simply set the input 'In' value to the output 'Out'
 //   And print out the output value
@@ -26,49 +28,103 @@ void ImageThresholdConnectivity::Process()
 //    * TYPE is the C++ type of the input/output
 //      (the one provided in the attribute 'type' of the tag 'input')
 
-  
-       printf("EED ImageThresholdConnectivity::Process  Error this box is not implemented .... \n");
-       printf("EED ImageThresholdConnectivity::Process  Error this box is not implemented .... \n");
-       printf("EED ImageThresholdConnectivity::Process  Error this box is not implemented .... \n");
-       printf("EED ImageThresholdConnectivity::Process  Error this box is not implemented .... \n");
+    std::vector<int> lstX;
+    std::vector<int> lstY;
+    std::vector<int> lstZ;
+    std::vector<int> point = bbGetInputPoint();
+
+    if (bbGetInputPoint().size()==3)
+    {
+        lstX.push_back( point[0] );
+        lstY.push_back( point[1] );
+        lstZ.push_back( point[2] );
+    } else {
+        lstX = bbGetInputLstX();
+        lstY = bbGetInputLstY();
+        lstZ = bbGetInputLstZ();
+    }
+    
+    if ( (bbGetInputIn()!=NULL) && (lstX.size()>0) && (lstX.size()==lstY.size()) && (lstX.size()==lstZ.size()) )
+    {
+        vtkImageThresholdConnectivity *filter = vtkImageThresholdConnectivity::New();
+        double spc[3];
+        bbGetInputIn()->GetSpacing(spc);
+        int border  = bbGetInputBorder();
+        int minX    = 32000;
+        int minY    = 32000;
+        int minZ    = 32000;
+        int maxX    = -32000;
+        int maxY    = -32000;
+        int maxZ    = -32000;
+        int i,size  = lstX.size();
+        double p[3];
+        vtkPoints *points = vtkPoints::New();
+        for (i=0; i<size; i++)
+        {
+            p[0] = lstX[i]*spc[0];
+            p[1] = lstY[i]*spc[1];
+            p[2] = lstZ[i]*spc[2];
+            points->InsertNextPoint(p);
+            if ( lstX[i] < minX ) { minX = lstX[i]; }
+            if ( lstY[i] < minY ) { minY = lstY[i]; }
+            if ( lstZ[i] < minZ ) { minZ = lstZ[i]; }
+            if ( lstX[i] > maxX ) { maxX = lstX[i]; }
+            if ( lstY[i] > maxY ) { maxY = lstY[i]; }
+            if ( lstZ[i] > maxZ ) { maxZ = lstZ[i]; }
+        } // for i
+        filter->SetSeedPoints( points );
+        filter->SetInputData( bbGetInputIn() );
+        filter->ThresholdBetween(10, 100);
+    //    filter->SetNeighborhoodRadius (4, 4, 4 );
+        filter->SetInValue(255);
+        filter->SetOutValue(0);
+    //    filter->ReplaceInOn();
+    //    filter->ReplaceOutOn();
+        filter->SetSliceRangeX(minX-border,maxX+border);
+        filter->SetSliceRangeY(minY-border,maxY+border);
+        filter->SetSliceRangeZ(minZ-border,maxZ+border);
+        filter->Update();
+        bbSetOutputOut( filter->GetOutput() );
+    } // if lst
 }
 //===== 
 // 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 ImageThresholdConnectivity::bbUserSetDefaultValues()
 {
-
 //  SET HERE THE DEFAULT INPUT/OUTPUT VALUES OF YOUR BOX 
 //    Here we initialize the input 'In' to 0
-   bbSetInputIn(NULL);
-  
+    bbSetInputIn(NULL);
+    bbSetInputBorder(10);
+    std::vector<double> maskValue;
+    maskValue.push_back(0);
+    maskValue.push_back(255);
+    bbSetInputMaskValue(maskValue);
+
 }
+
 //===== 
 // 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 ImageThresholdConnectivity::bbUserInitializeProcessing()
 {
-
 //  THE INITIALIZATION METHOD BODY :
 //    Here does nothing 
 //    but this is where you should allocate the internal/output pointers 
-//    if any 
-
-  
+//    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 ImageThresholdConnectivity::bbUserFinalizeProcessing()
 {
-
 //  THE FINALIZATION METHOD BODY :
 //    Here does nothing 
 //    but this is where you should desallocate the internal/output pointers 
 //    if any
-  
-}
 }
-// EO namespace bbcreaVtk
+
+}// EO namespace bbcreaVtk
 
 

diff --git a/bbtk_creaVtk_PKG/src/bbcreaVtkImageThresholdConnectivity.h b/bbtk_creaVtk_PKG/src/bbcreaVtkImageThresholdConnectivity.h
index a629e1c407c1a11793830f4af4731e358ad5371c..ec9bcfad544381158d35f945741b89f6a68b17b3 100644 (file)
--- a/bbtk_creaVtk_PKG/src/bbcreaVtkImageThresholdConnectivity.h
+++ b/bbtk_creaVtk_PKG/src/bbcreaVtkImageThresholdConnectivity.h
@@ -23,6 +23,12 @@ class bbcreaVtk_EXPORT ImageThresholdConnectivity
 // 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,vtkImageData*);
+  BBTK_DECLARE_INPUT(Point,std::vector<int>);
+  BBTK_DECLARE_INPUT(LstX,std::vector<int>);
+  BBTK_DECLARE_INPUT(LstY,std::vector<int>);
+  BBTK_DECLARE_INPUT(LstZ,std::vector<int>);
+  BBTK_DECLARE_INPUT(MaskValue,std::vector<double>);
+  BBTK_DECLARE_INPUT(Border,int);
   BBTK_DECLARE_OUTPUT(Out,vtkImageData*);
   BBTK_PROCESS(Process);
   void Process();
@@ -38,6 +44,12 @@ BBTK_BEGIN_DESCRIBE_BLACK_BOX(ImageThresholdConnectivity,bbtk::AtomicBlackBox);
   BBTK_CATEGORY("empty");
 
   BBTK_INPUT(ImageThresholdConnectivity,In,"Input image",vtkImageData*,"");
+  BBTK_INPUT(ImageThresholdConnectivity,Point,"[x y z]  seed point",std::vector<int>,"");
+  BBTK_INPUT(ImageThresholdConnectivity,LstX,"LstX seeds in voxels",std::vector<int>,"");
+  BBTK_INPUT(ImageThresholdConnectivity,LstY,"LstY seeds in voxels",std::vector<int>,"");
+  BBTK_INPUT(ImageThresholdConnectivity,LstZ,"LstZ seeds in voxels",std::vector<int>,"");
+  BBTK_INPUT(ImageThresholdConnectivity,MaskValue,"( default [O 255] )    [Out In] values of the output mask",std::vector<double>,"");
+  BBTK_INPUT(ImageThresholdConnectivity,Border,"(default 10)Border of the min and max positions",int,"");
 
   BBTK_OUTPUT(ImageThresholdConnectivity,Out,"Output image",vtkImageData*,"");