added handling of missing model files

CCSeg/CCsegtool.cxx

@@ -54,12 +54,13 @@ int main(int argc, char *argv[])
 		/* Preview */
 		if(debug)
 			std::cout<<"INITIALIZE"<<std::endl;
-		initialize(Image_filename, Mask_filename, CCAtlasDirectory, OuputFolder, nameofproject,
-			interpolationlinear, vesselRemoveOn, segLabel, averageNum, permute_x_y, reflectXOn, 
-			reflectYOn, openOn, doubleOn, sliceDir, MidPlaneSliceNumber, Number_Pts,
-			FSXForm, PSDistance, Unconstrained, WMintensity, MPSDisplacement, Number_iteration,
-			Lambdamax, Coefofoptim, debug, false, ViewImage, parameters, &lastX, &lastY, &lastScale,
-			&lastRot,scalefactor, othercompo,addangle);
+		if (!initialize(Image_filename, Mask_filename, CCAtlasDirectory, OuputFolder, nameofproject,
+				interpolationlinear, vesselRemoveOn, segLabel, averageNum, permute_x_y, reflectXOn,
+				reflectYOn, openOn, doubleOn, sliceDir, MidPlaneSliceNumber, Number_Pts,
+				FSXForm, PSDistance, Unconstrained, WMintensity, MPSDisplacement, Number_iteration,
+				Lambdamax, Coefofoptim, debug, false, ViewImage, parameters, &lastX, &lastY, &lastScale,
+				&lastRot,scalefactor, othercompo,addangle))
+		  return 0;
 
 		/* Run */
 		if(debug)

CCSeg/CCsegtool_initialization.cxx

@@ -36,8 +36,8 @@ CCsegtool_initialization::CCsegtool_initialization(bool interpolationlinear, flo
  * Compute the initialization, transform the input image (3D to 2D) and
  * several other operation ( opening, rotation ....)
  ***************************************************************************/
-int CCsegtool_initialization::compute_initialization(std::string inputFileName,std::string segFile, bool vesselRemoveOn,
-		 bool segLabel, int averageNum, bool permute_x_y, bool reflectXOn, bool reflectYOn, bool openOn, 
+int CCsegtool_initialization::compute_initialization(std::string inputFileName,std::string segFileName, bool vesselRemoveOn,
+		 int segLabel, int averageNum, bool permute_x_y, bool reflectXOn, bool reflectYOn, bool openOn,
 		 bool doubleOn, int sliceDir, std::string outfileBase, std::string nameofproject, 
 		 std::string MidPlaneSliceNumber, bool othercompo, int angle, bool debug)
 {
@@ -49,7 +49,7 @@ int CCsegtool_initialization::compute_initialization(std::string inputFileName,s
 	m_angle = angle;
 
 	// load
-	loadinginputimage(inputFileName, segFile);
+	loadinginputimage(inputFileName, segFileName);
 
 	//Vessel removal
 	if(vesselRemoveOn)
@@ -166,7 +166,7 @@ int CCsegtool_initialization::compute_initialization(std::string inputFileName,s
 /***************************************************************************
  * Load the input and Mask image
  ***************************************************************************/
-void CCsegtool_initialization::loadinginputimage(std::string inputFileName, std::string segFile)
+void CCsegtool_initialization::loadinginputimage(std::string inputFileName, std::string segFileName)
 {
 	try 
 	{
@@ -221,7 +221,7 @@ void CCsegtool_initialization::loadinginputimage(std::string inputFileName, std:
 	{
 		// load segmentation
 		BinaryVolumeReaderType::Pointer binaryImageReader = BinaryVolumeReaderType::New();
-		binaryImageReader->SetFileName(segFile.c_str()) ;
+		binaryImageReader->SetFileName(segFileName.c_str()) ;
 		binaryImageReader->Update();
 		m_loadMask=binaryImageReader->GetOutput();
 	}
@@ -235,7 +235,7 @@ void CCsegtool_initialization::loadinginputimage(std::string inputFileName, std:
 /***************************************************************************
  * Do a vesselremoval
  ***************************************************************************/
-void CCsegtool_initialization::vesselremoval(bool segLabel)
+void CCsegtool_initialization::vesselremoval(int segLabel)
 {
 	try 
 	{
@@ -253,13 +253,10 @@ void CCsegtool_initialization::vesselremoval(bool segLabel)
 	try 
 	{
 		//Vessel removal
-		int seglabel=1;
-		if(segLabel)
-			seglabel=0;
 		VesselRemover::Pointer VesselFilter = VesselRemover::New();
 		VesselFilter->SetImage(m_loadImage);
 		VesselFilter->SetEMSseg(m_castfilter->GetOutput());
-		VesselFilter->SetWMlabel(seglabel);
+		VesselFilter->SetWMlabel(segLabel);
 		VesselFilter->RemoveVessels();
 		m_preProcImage = VesselFilter->GetResultImage();
 	}
@@ -506,17 +503,14 @@ void CCsegtool_initialization::reflectY()
 /***************************************************************************
  * Extract the Label
  ***************************************************************************/
-void CCsegtool_initialization::extractLabel(bool segLabel)
+void CCsegtool_initialization::extractLabel(int segLabel)
 {
 	try 
 	{
-		int seglabel=1;
-		if(segLabel)
-			seglabel=0;
 		m_threshFilter = BinaryThresholdFilterType::New();
 		m_threshFilter->SetInput(m_mask);
-		m_threshFilter->SetUpperThreshold(seglabel);
-		m_threshFilter->SetLowerThreshold(seglabel);
+		m_threshFilter->SetUpperThreshold(segLabel);
+		m_threshFilter->SetLowerThreshold(segLabel);
 		m_threshFilter->SetOutsideValue(BG_VALUE);
 		m_threshFilter->SetInsideValue(LABEL_VALUE);
 		m_threshFilter->Update();

CCSeg/CCsegtool_initialization.h

@@ -127,9 +127,9 @@ class CCsegtool_initialization
 		static const int LABEL_VALUE = 1;
 		static const int NUM_COMPONENTS = 5;
 
-		int compute_initialization(std::string inputFileName, std::string segFile, bool vesselRemoveOn, 
-					    bool segLabel, int averageNum, bool permute_x_y, bool reflectXOn, 
-					    bool reflectYOn, bool openOn, bool doubleOn, int sliceDir, 
+		int compute_initialization(std::string inputFileName, std::string segFileName, bool vesselRemoveOn,
+					    int segLabel, int averageNum, bool permute_x_y, bool reflectXOn,
+					    bool reflectYOn, bool openOn, bool doubleOn, int sliceDir,
 					    std::string outfilebase, std::string nameofproject,
 					    std::string MidPlaneSliceNumber, bool othercompo, int angle, bool debug=false);
 		void SetLambdaMax(int lambdaMax){m_LambdaMax=lambdaMax;}
@@ -151,20 +151,19 @@ class CCsegtool_initialization
 		ImagePointer Get3DImage();
 
 	protected:
-		void loadinginputimage(std::string inputFileName, std::string segFile);
-		void vesselremoval(bool segLabel);
+		void loadinginputimage(std::string inputFileName, std::string segFileName);
+		void vesselremoval(int segLabel);
 		void extract_Midsagittal_planes(int sliceDir, std::string MidPlaneSliceNumber);
 		void averaging(int averageNum, int sliceDir, std::string MidPlaneSliceNumber);
 		void dopermute_x_y();
 		void reflectX();
 		void reflectY();
-		void extractLabel(bool segLabel);
+		void extractLabel(int segLabel);
 		void closingop();
 		void dodoubleOn();
 		void writeInput(std::string outfilebase, std::string nameofproject);
 		void writeoutput(std::string outfilebase, std::string nameofproject);
 
-
 	private:
 		/** Use in compute_parameters **/
 		typedef   itk::Image<short,ImageEDimension>     CCLOutputImageType;

CCSeg/CCsegtool_parameters.cxx

@@ -40,17 +40,17 @@ CCsegtool_parameters::CCsegtool_parameters (ExtractImageConstPointer Image,	//fi
 	//load the Image
 	SetImage(Image);
 
-	//Each files have a number
+	//Each file has a number
 	//SSMean
-	readf4(Way,1);
+	if (!readf4(Way,1)) throw std::runtime_error("Could not read model file");
 	//Eigenvectors
-	readf4(Way,2);
+	if (!readf4(Way,2)) throw std::runtime_error("Could not read model file");
 	//Bounds
-	readf(Way,3);
+	if (!readf(Way,3)) throw std::runtime_error("Could not read model file");
 	//PMMean
-	readf(Way,4);
+	if (!readf(Way,4)) throw std::runtime_error("Could not read model file");
 	//PMSigmaInv
-	readf(Way,5);
+	if (!readf(Way,5)) throw std::runtime_error("Could not read model file");
 
 	if(debug)
 	{
@@ -95,9 +95,9 @@ CCsegtool_parameters::CCsegtool_parameters (ExtractImageConstPointer Image,	//fi
 
 
 /********************************************************************************* 
- * Fill a vector with the CC atlas directory
+ * Fill a vector with model data from the CC atlas directory
  ********************************************************************************/
-void CCsegtool_parameters::readf(std::string way, int nbfile)
+bool CCsegtool_parameters::readf(std::string way, int nbfile)
 {
 	int i[3];
 	float j;
@@ -115,6 +115,9 @@ void CCsegtool_parameters::readf(std::string way, int nbfile)
 		case 5:
 			filename=way + "/Profile_sigmainv.asc";
 			break;
+	        default:
+			cerr << "Error (readf): Wrong file number" << endl;
+			return false;
 	}
 
 	std::ifstream file(filename.c_str() , ios::in);  // open in reading
@@ -164,16 +167,20 @@ void CCsegtool_parameters::readf(std::string way, int nbfile)
 		}
 
 		file.close();
+		return true;
+	}
+	else {
+	  cerr << "Error: The opening of the file failed" << endl;
+	  return false;
 	}
-	else cerr << "Error: The opening of the file failed" << endl;
 }
 
 
 /********************************************************************************* 
  * Fill a vector with the data of a file where there are 4 value on a line
  * like in CC atlas directory
  ********************************************************************************/
-void CCsegtool_parameters::readf4(std::string way, int nbfile)
+bool CCsegtool_parameters::readf4(std::string way, int nbfile)
 {
 	char c;
 	int i[2];
@@ -188,6 +195,9 @@ void CCsegtool_parameters::readf4(std::string way, int nbfile)
 		case 2:
 			filename = way + "/Shape_eigvecs.asc";
 			break;
+	        default:
+	                cerr << "Error (readf4): Wrong file number" << endl;
+			return false;
 	}
 
 	std::ifstream file(filename.c_str() , ios::in);  // open in reading
@@ -228,9 +238,13 @@ void CCsegtool_parameters::readf4(std::string way, int nbfile)
 		}
 
 		file.close();
+		return true;
 	}
 
-	else cerr << "Error: The opening of the file failed" << endl;
+	else {
+	  cerr << "Error: The opening of the file failed" << endl;
+	  return false;
+	}
 }
 
 

CCSeg/CCsegtool_parameters.h

@@ -48,10 +48,10 @@ class CCsegtool_parameters
 				     int numSlice, int X, int Y,float Rotation, float Scale, bool FSXForm, 
 				     double PSDistance, int WMIntensity,int MPSDisplacement, int OSteps, 
 				     SizeType ImageSize, bool Debug=false);
-		//to accede to the private attributs
-		//Methods for Parameter Specifications
-		void readf(std::string way, int nbfile);
-		void readf4(std::string way, int nbfile);
+		//to access the private attributes
+		//Methods for parameter specifications
+		bool readf(std::string way, int nbfile);
+		bool readf4(std::string way, int nbfile);
 		void getsizeof(int *i, int nbfile);
 		void writeoutput(std::string path_output, std::string _nameofproject);
 		void setparam(double X, double Y, double Scale, double Rot);

CCSeg/Globalfunc.cxx

@@ -131,13 +131,18 @@ int initialize( std::string Image_filename, std::string Seg_filename, std::strin
 	int numslice = initialization->GetImageSSize();
 	if(MidPlaneSliceNumber.compare("default")==0)
 		numslice = (numslice-1)/2;
-
-	CCsegtool_parameters* parameters = new CCsegtool_parameters(initialization->GetOutputImage(), CCAtlasDirectory,
-					      initialization->Get3DImage(), permute_x_y, reflectXOn, reflectYOn, doubleOn,
-					      sliceDir, numslice ,initialization->GetCenterX(),initialization->GetCenterY(),
-					      initialization->GetRotation(),initialization->GetScale(), FSXForm, PSDistance,
-					      WMvalue1,10,50,initialization->Get3DImageSize(), debug);
-
+	CCsegtool_parameters* parameters;
+	try {
+	  parameters = new CCsegtool_parameters(initialization->GetOutputImage(), CCAtlasDirectory,
+					        initialization->Get3DImage(), permute_x_y, reflectXOn, reflectYOn, doubleOn,
+					        sliceDir, numslice ,initialization->GetCenterX(),initialization->GetCenterY(),
+					        initialization->GetRotation(),initialization->GetScale(), FSXForm, PSDistance,
+					        WMvalue1,10,50,initialization->Get3DImageSize(), debug);
+	}
+	catch (std::exception &ex) {
+	  std::cerr << ex.what() << std::endl;
+	  return 0;
+	}
 	// Save the value from the initialization in parameters
 	parameters->SetGlobalvalue(initialization->GetWMvalue(), initialization->GetvoxelsizeX(),
 				    initialization->GetvoxelsizeY());