Merge branch 'master' of ssh://github.com/mutantturkey/FlyTracking

2 files changed, 63 insertions, 50 deletions

diff --git a/fly-tools/FlyTrackingMain.cpp b/fly-tools/FlyTrackingMain.cpp
index 4114a08..2e963a8 100644
--- a/fly-tools/FlyTrackingMain.cpp
+++ b/fly-tools/FlyTrackingMain.cpp
@@ -1976,7 +1976,7 @@ void processASequence(int startOfATrackSequence, int endOfATrackSequence) {
 		vector<FlyObject > fOVector = currentFI.getFOVector();
 		FlyObject cFFirstFO = fOVector[0];
 		FlyObject cFSecondFO = fOVector[1];
-		
+	 	
 		sequenceFirstAverage += cFFirstFO.getArea();
 		sequenceSecondAverage += cFSecondFO.getArea();
 		
@@ -2021,22 +2021,55 @@ ofstream foutSt;
 ofstream foutDebugCen;
 ofstream foutDebugSpeed;
 
-int main(int argc, char* argv[])
+int main(int argc, char **argv)
 {
-	if (argc < 5)
-	{
-		cerr << "Usage: executablename <inputFile.txt> <originalImagePath> <finalOutputPath> <maskImagePath> <outputFilePrefix>" << endl; // input file contains name of the
-		// input image files
-		return -1;
-	}
-	
-	MagickCore::SetMagickResourceLimit(MagickCore::MemoryResource, 1536);
-	MagickCore::SetMagickResourceLimit(MagickCore::MapResource, 4092);
-	
-	string ifns(argv[1]);
-	inputFileName = ifns;
-//	cout << "input file name is "<<inputFileName<<endl;
-	
+    int c;	
+		int writeFinalImages;
+	  string usage = "Usage: FlyTracking -i <inputFile.txt> -o <originalImagePath> -f <finalOutputPath> -m <maskImagePath> -O <outputFilePrefix>";
+		string origImagePath;
+		string finalOutputPath;
+		string outputFilePrefix;
+		string maskImagePath;
+		string inputFileName;
+    opterr = 0;
+
+    while ((c = getopt (argc, argv, "i:f:m:p:o:hx")) != -1)
+        switch (c)
+        {
+        case 'i':
+            inputFileName = optarg;
+            break;
+        case 'o':
+            origImagePath = optarg;
+            break;
+        case 'f':
+            finalOutputPath = optarg;
+            break;
+        case 'm':
+            maskImagePath = optarg;
+            break;
+        case 'p':
+            outputFilePrefix = optarg;
+            break;
+        case 'h':
+						cout << usage << endl;
+        		exit(1);
+						break;
+				case 'x':
+						writeFinalImages;
+						break;
+        default:
+						break;
+        }
+
+	//MagickCore::SetMagickResourceLimit(MagickCore::MemoryResource, 1536);
+	//MagickCore::SetMagickResourceLimit(MagickCore::MapResource, 4092);
+	
+	i	
+	if( inputFileName.empty() || origImagePath.empty() || finalOutputPath.empty() || maskImagePath.empty() || outputFilePrefix.empty() ) {
+	cerr << usage << endl;
+	exit(1);
+	}	
 	string fileName;	
 	ifstream inputFile(inputFileName.c_str());
 	// save the input file name
@@ -2045,25 +2078,8 @@ int main(int argc, char* argv[])
 		cout << "cannot open the input file that contains name of the input images\n";
 		exit(1);
 	}
-	
-  //cout<<"come here ------------------------- 1"<<endl;
-	// set the global paths
-	string tempOIP(argv[2]);
-	origImagePath = tempOIP;
-
-	//cout<<"come here ------------------------- 2"<<endl;
-
-	string tempFOP(argv[3]);
-	finalOutputPath = tempFOP;
 
-	//cout<<"come here ------------------------- 3"<<endl;
-
-	string tempOFP(argv[5]);
-	outputFilePrefix = tempOFP;
-
-	//cout<<"come here ------------------------- 4"<<endl;
-
-	string statFileName = tempFOP + outputFilePrefix + "_statFile.txt";
+	string statFileName = finalOutputPath + outputFilePrefix + "_statFile.txt";
 	//cout << "Statfilename is "<<statFileName<<endl;
 	foutSt.open(statFileName.c_str());
 	if (foutSt.fail()) {
@@ -2072,7 +2088,7 @@ int main(int argc, char* argv[])
 	}
 	
 	// debug file
-	string foutDebugCenFN = tempFOP + outputFilePrefix + "_statFileDebug.txt";
+	string foutDebugCenFN = finalOutputPath + outputFilePrefix + "_statFileDebug.txt";
 	foutDebugCen.open(foutDebugCenFN.c_str());
 	if (foutDebugCen.fail()) {
 		cout << "cannot open the statDebug file"<<endl;
@@ -2081,15 +2097,14 @@ int main(int argc, char* argv[])
 	
 	
 	// debug file speed distribution
-	string foutDebugSpeedFN = tempFOP + outputFilePrefix + "_speedDebug.txt";
+	string foutDebugSpeedFN = finalOutputPath + outputFilePrefix + "_speedDebug.txt";
 	foutDebugSpeed.open(foutDebugSpeedFN.c_str());
 	if (foutDebugSpeed.fail()) {
 		cout << "cannot open the speedDebug file"<<endl;
 		exit(1);
 	}
 	
-	string tempMIP(argv[4]);
-	maskImagePath = tempMIP;
+
 	
 	// open the file for statistics
 	string lPSFileName("LongestPositive.txt");
@@ -2114,10 +2129,10 @@ int main(int argc, char* argv[])
 	bool currentlyCalculatingHead = true;
 	
 	
-	
+
 	while (inputFile>>fileName) {
 		
-//	Image* img = new Image(argv[1]);// = new Image(argv[1]);
+  	//	Image* img = new Image(argv[1]);// = new Image(argv[1]);
 
 		int fi = fileName.find("_");
 		// current sequence numbers spans from 0 - 18019, so 5 digits are needed
@@ -2136,7 +2151,7 @@ int main(int argc, char* argv[])
 		cout << "Reading file "<<fileName<<endl;
 		Image* img = new Image(fileName.c_str());
 		int width = img->columns(),height = img->rows();
-		diagLength= static_cast<int> ( sqrt( (height*height) + (width*width) ) );
+		 diagLength= static_cast<int> ( sqrt( (height*height) + (width*width) ) );
 		//cout << "Diagonal length is "<<diagLength<<endl;
 //		Image* imgWithInfo;
 //		imgWithInfo = new Image(fileName.c_str());
@@ -2184,13 +2199,12 @@ int main(int argc, char* argv[])
 			}
 		}
 		
-		
+
 		delete img;
-		
 		delete residual;
 		
-//		cout<<"Sorting the objects according to size"<<endl;
-//		bubbleSort(tempFOV);
+   //		cout<<"Sorting the objects according to size"<<endl;
+   //		bubbleSort(tempFOV);
 		
 		fOVector.clear();
 		
@@ -2793,8 +2807,8 @@ void drawTheFlyObject(FrameInfo currentFI, string fileName, int isFirst, bool si
 		bool eVDirection = currentFO.getHeadIsInDirectionMAEV();
 				
 		// debug:
-		cout<<"Calling the findTheStartPoint() function"<<endl;
-		cout<<"Female size "<<femaleSize<<" maleSize "<<maleSize<<" MaleCentroid = "<<centroid.first<<", "<<centroid.second<<endl;
+		//cout<<"Calling the findTheStartPoint() function"<<endl;
+		//cout<<"Female size "<<femaleSize<<" maleSize "<<maleSize<<" MaleCentroid = "<<centroid.first<<", "<<centroid.second<<endl;
 
 		// initialize the flag with false for the next found of findTheStartPoint()
 		isFoundStartPoint = false;
@@ -2837,7 +2851,7 @@ void drawTheFlyObject(FrameInfo currentFI, string fileName, int isFirst, bool si
 		
 			bool eVDirection = currentFO.getHeadIsInDirectionMAEV();
 		
-			double ev_x, ev_y;
+			//double ev_x, ev_y;
 			
 			// draw the female when tracked by the male fly
 			if (isHitting == 1) {
diff --git a/process-video-beta b/process-video-beta
index e37980e..97aeffa 100755
--- a/process-video-beta
+++ b/process-video-beta
@@ -202,7 +202,7 @@ while read crop; do
 	cd $output_dir
 
 	#parallel -i FlyTrackingIterativeFilter {} 15 $output_dir/Masks/$setname/Masks/ $output_dir/Filtered/$setname/ -- $( ls $output_dir/Masks/$setname/Masks/ )
-  ls $output_dir/Masks/$setname/Masks/ | parallel -v -j +0 -S $server_list /site/kuiper/jcm357/FlyTrackingIterativeFilter {} 15 $output_dir/Masks/$setname/Masks/ $output_dir/Filtered/$setname/
+  ls $output_dir/Masks/$setname/Masks/ | parallel -v -j +0 -S $server_list /site/kuiper/jcm357/FilterFlyMask {} 15 $output_dir/Masks/$setname/Masks/ $output_dir/Filtered/$setname/
 	i=$(( $i + 1 ))	
 done < $crop_file
 
@@ -227,4 +227,3 @@ done < $crop_file
 wait
 fi
 
-echo "Finished"