From 0944dd461b920e97b6a5213e3b487f71f55c061a Mon Sep 17 00:00:00 2001
From: mutantturkey <mutantturke@gmail.com>
Date: Wed, 24 Oct 2012 09:46:36 -0400
Subject: fixed bug in background deriver when input files have a space. Using
 getline instead of the >> operator solves the problem

---
 fly-tools/background/main.cpp | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/fly-tools/background/main.cpp b/fly-tools/background/main.cpp
index b01305e..7504ab2 100644
--- a/fly-tools/background/main.cpp
+++ b/fly-tools/background/main.cpp
@@ -9,9 +9,13 @@
 #define array(i,j,k,l) (array[height*width*i + width*j + k + l])
 
 int nImages;
+
 unsigned long height = 0;
 unsigned long width = 0;
 
+using namespace std;
+using namespace cv;
+
 int findmax(long *p, int n) {
   int mx = 0, v = p[0];
   for (int i = 1; i < n; i++) {
@@ -23,8 +27,6 @@ int findmax(long *p, int n) {
   return mx;
 }
 
-using namespace std;
-using namespace cv;
 
 int main(int argc, char **argv ) {
 
@@ -59,9 +61,9 @@ int main(int argc, char **argv ) {
   IplImage *first_image = NULL;
   IplImage *output_image = NULL;
 
-  int i,j, k;
-  int height = 0;
-  int width = 0;
+  unsigned int i = 0;
+  unsigned int j = 0;
+  unsigned int k = 0;
 
   string filename;
 
@@ -75,11 +77,12 @@ int main(int argc, char **argv ) {
 
 
   // Read first line for our first image and rewind
-  input_file>>filename; 
+  getline(input_file, filename);
 
   first_image = cvLoadImage(filename.c_str(), CV_LOAD_IMAGE_UNCHANGED);
 
   if(!first_image) {
+
     cerr << "couldn't read first image" << endl;
     exit(1);
   } 
@@ -100,7 +103,7 @@ int main(int argc, char **argv ) {
 
   input_file.clear();
   input_file.seekg(0);
-  while(input_file>>filename) {
+  while (!getline(input_file, filename).eof()) {
     nImages++;
   }
 
@@ -116,7 +119,7 @@ int main(int argc, char **argv ) {
   input_file.clear();
   input_file.seekg(0);
 
-  while (input_file>>filename) {
+  while (!getline(input_file, filename).eof()) {
 
     IplImage *input_image = NULL;
     input_image = cvLoadImage(filename.c_str(), CV_LOAD_IMAGE_UNCHANGED);
-- 
cgit v1.2.1


From ade7d29b7158fb83517fd254265b866a6992efb4 Mon Sep 17 00:00:00 2001
From: mutantturkey <mutantturke@gmail.com>
Date: Wed, 24 Oct 2012 09:52:45 -0400
Subject: swap our output columns to fit our feature vector (mean first,
 std-dev second)

---
 fly-tools/std-deviation/StandardDeviation.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/fly-tools/std-deviation/StandardDeviation.cpp b/fly-tools/std-deviation/StandardDeviation.cpp
index 1d29d91..f2668ba 100644
--- a/fly-tools/std-deviation/StandardDeviation.cpp
+++ b/fly-tools/std-deviation/StandardDeviation.cpp
@@ -58,7 +58,7 @@ int main(int argc, char* argv[]) {
     exit(0);
   }
 
-  outputFile << left << setw(30) << "File Name" << left << setw(20) << "Standard deviation" << left << setw(20) << "Mean" << endl;
+  outputFile << left << setw(20) << "File Name" << left << setw(20) << "Mean" << left << setw(20) << "Standard Deviation" << endl;
 
   while( inputFileNames >> currentFileName ) {
 
@@ -103,7 +103,7 @@ int main(int argc, char* argv[]) {
     standardDev = sumSquaredResults/(N-1);
     standardDev = sqrt(standardDev);
 
-    outputFile<<left<<setw(30)<<currentFileName<<left<<setw(20)<<standardDev<<left<<setw(20)<<mean<<endl;
+    outputFile<<left<<setw(20)<<currentFileName<<left<<setw(20)<<mean<<left<<setw(20)<<standardDev<<endl;
 
     currentFile.close();
   }
-- 
cgit v1.2.1


From f715b377eb0b06092ec37d959b8dfc57dffbd7c7 Mon Sep 17 00:00:00 2001
From: mutantturkey <mutantturke@gmail.com>
Date: Wed, 24 Oct 2012 09:58:56 -0400
Subject: remove a misc test file, left over from Reza import

---
 fly-tools/misc/makeimage.cpp | 51 --------------------------------------------
 1 file changed, 51 deletions(-)
 delete mode 100644 fly-tools/misc/makeimage.cpp

diff --git a/fly-tools/misc/makeimage.cpp b/fly-tools/misc/makeimage.cpp
deleted file mode 100644
index 06e2897..0000000
--- a/fly-tools/misc/makeimage.cpp
+++ /dev/null
@@ -1,51 +0,0 @@
-#include <Magick++.h>
-#include <iostream>
-#include<fstream>
-#include<string>
-using namespace std;
-using namespace Magick;
-
-int main(int argc,char **argv)
-
-{
-	// Construct the image object. Seperating image construction from the
-	// the read operation ensures that a failure to read the image file
-	// doesn't render the image object useless.
-	
-	Image* img;
-	char buffer[100];
-	sprintf(buffer,"%ix%i",7,7);
-	
-	// residual image is initialized with black representing not visited.
-	//residual = new Image(buffer, "black");
-	
-	img = new Image(buffer, "white");
-	
-	for (int j=0; j<=3;j++) {
-		for (int i=0; i<=3-j; i++) {
-			img->pixelColor(i,j, "black");
-			img->pixelColor(6-i,j, "black");
-		}
-	}
-
-	int k;
-	for (int j=4; j<=6;j++) {
-		for (int i=0; i<=j-3; i++) {
-			img->pixelColor(i,j, "black");
-			img->pixelColor(6-i,j, "black");
-		}
-	}
-	
-	
-	//img->pixelColor(0,3, "red");
-
-	
-	string namei = "7x7.png";
-	img->write(namei.c_str());
-	
-	delete img;
-		    
-	return 0;
-    
-}
-
-- 
cgit v1.2.1


From fb645ae8efa9f9df252857d5a5cb0f6ce8f7074b Mon Sep 17 00:00:00 2001
From: mutantturkey <mutantturke@gmail.com>
Date: Wed, 24 Oct 2012 10:01:42 -0400
Subject: don't say we're adding work

---
 fly-tools/mask/main.c | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/fly-tools/mask/main.c b/fly-tools/mask/main.c
index 804f07f..6adf5e8 100644
--- a/fly-tools/mask/main.c
+++ b/fly-tools/mask/main.c
@@ -83,7 +83,7 @@ int main( int argc, char **argv){
   }
 
   thpool_t* threadpool;        
-  threadpool=thpool_init(4);
+  threadpool=thpool_init(2);
 
   char filename[256];	
   char *temp;
@@ -94,7 +94,6 @@ int main( int argc, char **argv){
       if (temp != NULL) *temp = '\0'; 
       char *filename_r = malloc(256);
       strncpy(filename_r, filename, sizeof(filename));
-      printf("add work: %s \n", filename);
 
       thpool_add_work(threadpool, (void*)convert_image, (void*)filename_r);
     }
-- 
cgit v1.2.1


From 36a6028d34e8481ac3078d1351eb4116082a152a Mon Sep 17 00:00:00 2001
From: mutantturkey <mutantturke@gmail.com>
Date: Wed, 24 Oct 2012 10:05:39 -0400
Subject: Frame Info spacing fixes

---
 fly-tools/FrameInfo.cpp | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/fly-tools/FrameInfo.cpp b/fly-tools/FrameInfo.cpp
index c97b651..c02e3f7 100644
--- a/fly-tools/FrameInfo.cpp
+++ b/fly-tools/FrameInfo.cpp
@@ -14,18 +14,22 @@ FrameInfo::FrameInfo(int frameNo, vector<FlyObject > fOVector, bool isSingleBlob
 	this->isSingleBlob = isSingleBlob;
 
 }
+
 FrameInfo::FrameInfo(const FrameInfo &f) {
 	this->frameNo = f.getFrameNo();
 	this->fOVector = f.getFOVector();
 	this->isSingleBlob = f.getIsSingleBlob();
 	
 }
+
 int FrameInfo::getFrameNo() const {
 	return frameNo;
 }
+
 bool FrameInfo::getIsSingleBlob() const {
 	return isSingleBlob;
 }
+
 vector<FlyObject > FrameInfo::getFOVector() const{
 	return fOVector;
 }
@@ -33,12 +37,15 @@ vector<FlyObject > FrameInfo::getFOVector() const{
 void FrameInfo::setFrameNo(int fn) {
 	this->frameNo = fn;
 }
+
 void FrameInfo::setIsSingleBlob(bool isSingleBlob)  {
 	this->isSingleBlob = isSingleBlob;
 }
+
 void FrameInfo::setFOVector(vector<FlyObject > fov)  {
 	this->fOVector = fov;
 }
+
 void FrameInfo ::swapTheFlyObject() {
 	if (fOVector.size() > 1) {
 		cout << "swapping\n";
@@ -47,13 +54,12 @@ void FrameInfo ::swapTheFlyObject() {
 		fOVector[1] = a;
 	}
 }
+
 void FrameInfo::output(ostream &out) {
 	out<<"FrameNo			: "<<frameNo<<endl;
 	out<<"IsSingleBlob		: "<<isSingleBlob<<endl;
-//	out<<"fOVector size "<<fOVector.size()<<endl;
-	for (int i=0; i<fOVector.size(); i++) {
+	for (unsigned int i=0; i<fOVector.size(); i++) {
 		FlyObject a = fOVector[i];
-//		out<<"FlyObject "<<i<<endl;
 		a.output(out);
 	}
 }
-- 
cgit v1.2.1


From e2cd8c01425c08e07d4ad6c6ed0a8535c46a9ae5 Mon Sep 17 00:00:00 2001
From: mutantturkey <mutantturke@gmail.com>
Date: Wed, 24 Oct 2012 10:06:35 -0400
Subject: remove unused, commented, functions

---
 fly-tools/FlyObject.h | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/fly-tools/FlyObject.h b/fly-tools/FlyObject.h
index 10dbd4f..e7c0b82 100644
--- a/fly-tools/FlyObject.h
+++ b/fly-tools/FlyObject.h
@@ -1,6 +1,5 @@
 /*
  *  FlyObject.h
- *  
  *
  *  Created by Md. Alimoor Reza on 6/26/10.
  *  Copyright 2010 Drexel University. All rights reserved.
@@ -14,7 +13,6 @@ using namespace std;
 
 class FlyObject {
 public:
-	//FlyObject(int area, pair<int, int> centroid, pair<double,double> majorAxisEV, pair<double,double> velocityV, vector<pair<int, int> > areaCoord);
 	FlyObject(int area, pair<int, int> centroid, pair<double,double> majorAxisEV, pair<double,double> velocityV,bool headIsInDirectionMAEV, pair<double, double> head, double speed);
 	FlyObject(const FlyObject &f);
 	int getArea() const;
@@ -24,7 +22,6 @@ public:
 	bool getHeadIsInDirectionMAEV() const;
 	pair<double,double> getHead() const;
 	double getSpeed() const;
-	//vector<pair<int, int> > getAreaCoord() const;
 	void setArea(int area);
 	void setCentroid(pair<int, int>);
 	void setMajorAxisEV(pair<double,double>);
@@ -33,13 +30,11 @@ public:
 	void setHeadIsInDirectionMAEV(bool);
 	void setHead(pair<double, double> head);
 	void setSpeed(double speed);
-	//void setAreaCoord(vector<pair<int , int> >);
 	void output(ostream &out);
 	
 
 private:
 	int area;
-	//vector<pair<int , int> > areaCoord;
 	pair<int, int> centroid; 
 	pair<double,double> majorAxisEV;
 	pair<double,double> velocityV;
-- 
cgit v1.2.1


From dd3b350d2eb06012f3d5ee08e2f4060536b57621 Mon Sep 17 00:00:00 2001
From: mutantturkey <mutantturke@gmail.com>
Date: Wed, 24 Oct 2012 10:07:44 -0400
Subject: update README to include preliminary information about k-means
 clustering

---
 README.markdown | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/README.markdown b/README.markdown
index fcb8026..9a95eba 100644
--- a/README.markdown
+++ b/README.markdown
@@ -150,5 +150,11 @@ pngs to make sure that the fly tracking was performed correctly.
 ### Into the Beyond ###
 
 Now that we've done the hard work of image processing the rest is up to you! The
-data is all there, now you need to do manually generate the feature vectors.
+data is all there, now you need to do manually generate the feature vectors, and
+you need to run our simple k-means clustering. 
+
+The K-Means clustering requires Java to run and our Least Squares Solution CCI
+calculator was written in Matlab and requires it to run.
+
+
 
-- 
cgit v1.2.1


From 765cbbb01e06a5e5cd913b04d467e80ec8cd5bc7 Mon Sep 17 00:00:00 2001
From: mutantturkey <mutantturke@gmail.com>
Date: Wed, 31 Oct 2012 17:27:38 -0400
Subject: Output CCI's into a seperate txt file from all the folds

---
 fly-tools/cci-calculator/LeastSquareSolution.m | 16 +++++-----------
 1 file changed, 5 insertions(+), 11 deletions(-)

diff --git a/fly-tools/cci-calculator/LeastSquareSolution.m b/fly-tools/cci-calculator/LeastSquareSolution.m
index 85d1326..1e4d822 100644
--- a/fly-tools/cci-calculator/LeastSquareSolution.m
+++ b/fly-tools/cci-calculator/LeastSquareSolution.m
@@ -17,6 +17,8 @@ function [x, e] = LeastSquareSolution(fileNameA, fileNameB, output)
    
    solution=[];
    
+   cci_output_file = strcat(output, '/CCIs_combined.txt');
+
    for i=0:(total_folds-1)
        
         % debug
@@ -84,26 +86,20 @@ function [x, e] = LeastSquareSolution(fileNameA, fileNameB, output)
         %saving the calculated cis
         CI = [CI; ci];         % store the ci values
        
-    
-        %fid_debug = fopen(debug_file,'w');
-        %fprintf(fid_debug, '%s\n','Train data');
-        %fprintf(fid_debug, '%8.6f\t%8.6f\t%8.6f\t%8.6f\t%8.6f\t%8.6f\t%8.6f\t%8.6f', A_);
-%         fprintf(fid_debug, '%s\n','Test data');
-%         fprintf(fid_debug, '%8.6f\t%8.6f\t%8.6f\t%8.6f\t%8.6f\t%8.6f\t%8.6f\t%8.6f', test_data);
         
         fid_debug = fopen(debug_file,'w');
-%         fprintf(fid_debug, '%s\n\n','Test data');
-        
         
         fprintf(fid_debug, '%s\n\n','new CI');
         fprintf(fid_debug, '%8.6f\n', ci);
         
+        %output our cci's A.K.A. "new CI" into a seperate file as well.
+        fprintf(cci_output_file, '%8.6f\n', ci);
+        
         fprintf(fid_debug, '%s\n\n','actual CI');
         actual_ci = b(test,:);
         fprintf(fid_debug, '%8.6f\n', actual_ci);
         fprintf(fid_debug, '%s\n\n','error');
         fprintf(fid_debug, '%8.6f\n', (ci-actual_ci));
-%         fprintf(fid_debug, '%s\n\n','Train data');
         
         
         fclose(fid_debug);
@@ -119,8 +115,6 @@ function [x, e] = LeastSquareSolution(fileNameA, fileNameB, output)
    fprintf(fid_ci, '%8.6f\n', CI);
    fclose(fid_ci);
    
-   %fid_solution_vectors = fopen('Solution_vectors.txt', 'w');
    dlmwrite('Solution_vectors.txt', solution, 'delimiter', '\t');
-   %fclose(fid_solution_vectors);
    
         
-- 
cgit v1.2.1


From 039ef3345967fe291b1487a9a588a37909531af0 Mon Sep 17 00:00:00 2001
From: mutantturkey <mutantturke@gmail.com>
Date: Wed, 31 Oct 2012 17:29:05 -0400
Subject: add a note to the README about the ordering

---
 fly-tools/cci-calculator/README.markdown | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/fly-tools/cci-calculator/README.markdown b/fly-tools/cci-calculator/README.markdown
index 065563c..1578fc2 100644
--- a/fly-tools/cci-calculator/README.markdown
+++ b/fly-tools/cci-calculator/README.markdown
@@ -28,3 +28,8 @@ If we have 21 specimen per fold, use number of folds + 2 for the head argument,
 and the number of folds for the tail. This will give you proper results!
 
     for i in Fold_*.txt; do head $i -n 23 |  tail -n 21 >> output.txt; echo $i; done;
+
+The output of the file is in the order of your input, so just copy your data
+back into whatever spreadsheet you are using and it be good. If you notice
+that the numbers don't match up, make sure your ordering correctly!
+
-- 
cgit v1.2.1


From 754edf136d1020462f65d60c963aeea4da5df1a6 Mon Sep 17 00:00:00 2001
From: mutantturkey <mutantturke@gmail.com>
Date: Wed, 31 Oct 2012 17:37:29 -0400
Subject: add basic explaination of how some of the tools work, and set line
 wrapping to 80 lines.

---
 fly-tools/README.markdown | 30 ++++++++++++++++++++++++++----
 1 file changed, 26 insertions(+), 4 deletions(-)

diff --git a/fly-tools/README.markdown b/fly-tools/README.markdown
index ac94d8c..60e2b98 100644
--- a/fly-tools/README.markdown
+++ b/fly-tools/README.markdown
@@ -1,6 +1,8 @@
 fly-tools
 =========
 
+These are the programs that do all the hard work!
+
 FlyTracking
 ------------
 
@@ -13,7 +15,8 @@ Usage:
 FilterFlyMask
 ------------
 
-FilterFlyMask runs some filtering operations on masks to ensure that the FlyTracking tool processes the information correctly.
+FilterFlyMask runs some filtering operations on masks to ensure that the 
+FlyTracking tool processes the information correctly.
 
 Usage:
 
@@ -22,8 +25,12 @@ Usage:
 filter-mask
 -----------
 
-filter-mask is an alternative fly filter that works much faster. It utilizes the OpenCV and CvBlob libraries.
+filter-mask is an alternative fly filter that works much faster. It utilizes 
+the OpenCV and CvBlob libraries.
 
+The filter works simply, it counts the number of blobs and grabs the largest
+two. Anything else is discarded and the two blobs are written to a new image.
+        
 Usage:
 
 	filter-mask -i <input-file> -o <output-file> -r <ratio>
@@ -31,7 +38,17 @@ Usage:
 mask-generator
 -------------
 
-This tool creates masks from cropped video frames, which the need to be filtered by the FilterFlyMask tool.
+This tool creates binary masks from cropped video frames, which the need to be 
+filtered by the FilterFlyMask tool.
+
+The program works by doing 3 specific image manipulations to the input images.
+
+1. subtract the background image from the input image
+2. auto-level the image. This operation sets the lightest pixel to white and 
+then normalizes the rest of the image accordingly. This step is important to 
+ensure that the mask output is relatively similar when ligt conditions are 
+changing during a sequence.
+3. Threshold the image, anything over 30% is marked as white, the rest is black
 
 Usage:
 
@@ -44,7 +61,12 @@ Todo:
 derive-background
 -----------------
 
-This tool will generate a common background image of a set of video frames (PNGs), based on the statistical mode of each pixel. 
+This tool will generate a common background image of a set of video frames
+(PNGs), based on the statistical mode of each pixel. 
+
+The program works by iterating through each image, through each pixel, adding 
+them to a histogram and then calculates each pixel's mode and spews out the 
+resulting image.
 
 Usage:
 
-- 
cgit v1.2.1


From 2ee9cae7ae0bb7a556910d0f8dcc6a14ba7ba7ee Mon Sep 17 00:00:00 2001
From: mutantturkey <mutantturke@gmail.com>
Date: Mon, 19 Nov 2012 10:01:18 -0500
Subject: use unsigned int

---
 fly-tools/FlyTrackingMain.cpp | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/fly-tools/FlyTrackingMain.cpp b/fly-tools/FlyTrackingMain.cpp
index c68fe3c..5dd94f7 100644
--- a/fly-tools/FlyTrackingMain.cpp
+++ b/fly-tools/FlyTrackingMain.cpp
@@ -111,8 +111,8 @@ ostream &operator<<(ostream &out, FrameInfo & fI) {
 }
 
 void bubbleSort(vector<FlyObject > & fov) {
-  for(int i=1; i<fov.size(); i++) {
-    for(int j=0; j<fov.size()-i; j++) {
+  for(unsigned int i=1; i<fov.size(); i++) {
+    for(unsigned int j=0; j<fov.size()-i; j++) {
       FlyObject a = fov[j];
       FlyObject b = fov[j+1];
 
@@ -1316,7 +1316,7 @@ void largestIncreasingPositiveDotProductSeq(vector<pair<double, double> > veloci
   int flag = false;
   int maxSeqSize = 0;
   int st = 0;
-  for (int j=0; j<velocityDirs.size()-1; j++) {
+  for (unsigned int j=0; j<velocityDirs.size()-1; j++) {
     pair<double,double> prevVel = velocityDirs[j];
     pair<double, double> currVel  = velocityDirs[j+1];
 
-- 
cgit v1.2.1


From 25ba5b17f86b76c1c99f6d09942362b13dcb18f8 Mon Sep 17 00:00:00 2001
From: mutantturkey <mutantturke@gmail.com>
Date: Mon, 19 Nov 2012 14:23:44 -0500
Subject: Clean ups left and right, Use proper exit codes, remove a useless
 header, alphabetize the function lists, concat declarations and more

---
 fly-tools/FlyTrackingMain.cpp | 258 ++++++++++++++++++------------------------
 1 file changed, 107 insertions(+), 151 deletions(-)

diff --git a/fly-tools/FlyTrackingMain.cpp b/fly-tools/FlyTrackingMain.cpp
index 5dd94f7..30dc3db 100644
--- a/fly-tools/FlyTrackingMain.cpp
+++ b/fly-tools/FlyTrackingMain.cpp
@@ -1,4 +1,3 @@
-#include <iostream>
 #include <iomanip>
 #include <string>
 #include <sstream>
@@ -21,14 +20,28 @@
 using namespace Magick;
 using namespace std;
 
+// One of these output streams will be used. If directed towards null, nothing happens, towards output, it will be printed
 ofstream nullLog;
 ostream* output;
 
+// Our output files for debugging and information
+ofstream foutLPS;
+ofstream foutSt;
+ofstream foutDebugCen;
+ofstream foutDebugSpeed;
+
+
 const double PI = atan(1.0)*4.0;
 const double FACTOR_EIGEN = 100;
 const int STUCKING_TO_A_SINGLE_BLOB = 1;
 const int SEPARATING_FROM_SINGLE_BLOB = 2;
 
+bool isInFemaleBlob;
+int maskImageHeight;
+int maskImageWidth;
+int diagLength;
+
+vector<pair<int,int> > bresenhamLine;
 Image* residual;
 
 vector<FlyObject > fOVector;
@@ -60,12 +73,12 @@ int sequenceSize=1;
 int startOfAOneObject = -1;
 int endOfAOneObject = -1;
 
-vector<string> fnVector;
-string inputFileName;
-
+// This decides if we want to output an overlay. You'll get the same results
+// either way but you won't be able to verify it. taken as an argument.
 bool writeFinalImages = false;
 
 // GLOBAL PATHS
+string inputFileName;
 string maskImagePath;
 string origImagePath;
 string finalOutputPath;
@@ -73,6 +86,7 @@ string outputFilePrefix;
 
 vector<pair<double, double> > velocityDirectionsF;
 vector<pair<double, double> > velocityDirectionsS;
+vector<string> fnVector;
 
 pair<double, double> avgVelocityF;
 pair<double, double> avgVelocityS;
@@ -83,6 +97,7 @@ pair<double, double> overAllVelocityS;
 vector<pair<double, double> > evDirectionF;
 vector<pair<double, double> > evDirectionS;
 
+// Information about frames that will be written out at the end of proessing.
 int totalMaleLookingAtFemale = 0;
 int totalFemaleLookingAtMale = 0;
 int totalSingleBlob = 0;
@@ -93,7 +108,6 @@ map<unsigned int, unsigned int> centroidDistanceMap;
 map<unsigned int, unsigned int> headDirAngleMap;
 map<unsigned int, unsigned int> speedMap;
 
-
 void initSequence(){
   startOfATrackSequence = -1;
   endOfATrackSequence = -1;
@@ -125,8 +139,7 @@ void bubbleSort(vector<FlyObject > & fov) {
   }
 }
 
-void writeHist(const char* filename, map<unsigned int, unsigned int> dataMap)
-{
+void writeHist(const char* filename, map<unsigned int, unsigned int> dataMap) {
   *output << "In the beginning of the write hist" << endl;
   *output << "dataMap size " << dataMap.size() << endl;
 
@@ -143,7 +156,6 @@ void writeHist(const char* filename, map<unsigned int, unsigned int> dataMap)
     back = dataMap.end();
   back--;
 
-
   unsigned int first = front->first, last = back->first;
   *output << "Min: " << first << " " << "Max: " << last << " " << "Count: " << last-first << endl;
   vector<unsigned int> hist(last+1, 0);
@@ -174,24 +186,22 @@ void writeHist(const char* filename, map<unsigned int, unsigned int> dataMap)
 
 }
 
-void findObj(Image* img, int x, int y, vector<pair<int,int> > & shape ,bool eightCon=true, bool colorLookingFor=true);
-void eightConnObj(Image* img, int x, int y, vector<pair<int, int> > & obj, bool color=true);
-void fourConnObj(Image* img, int x, int y, vector<pair<int, int> > & obj, bool color=true);
+double calculateDotProduct(pair<double, double> v, pair<double, double> eV);
+void calculateHeadVector(FlyObject fO, pair<double,double> &headDirection);
 vector<double> covariantDecomposition(vector<pair<int,int> > & points);
-pair<int,int> getCentroid(vector<pair<int,int> > & points);
-bool isInterface(Image* orig, unsigned int x, unsigned int y);
-void writeFrameImage(int fn, string imS);
+void determineHeadDirection(int fileCounter);
 void drawTheFlyObject(FrameInfo currentFI, string fileName, int isFirst, bool singleBlob=false,bool unprocessed = false);
 void drawTheSequence(int startIndex, int endIndex, int isFirst, bool singleBlob = false, bool unprocessed = false);
+void eightConnObj(Image* img, int x, int y, vector<pair<int, int> > & obj, bool color=true);
 double euclideanDist(FlyObject a, FlyObject b);
+void findObj(Image* img, int x, int y, vector<pair<int,int> > & shape ,bool eightCon=true, bool colorLookingFor=true);
+void fourConnObj(Image* img, int x, int y, vector<pair<int, int> > & obj, bool color=true);
+pair<int,int> getCentroid(vector<pair<int,int> > & points);
+bool isInterface(Image* orig, unsigned int x, unsigned int y);
 bool identifyFlyObjectFromFrameToFrame(FrameInfo prevFI, FrameInfo& currentFI, bool gotRidOfSingleBlob=false) ;
 int roundT(double v) {return int(v+0.5);}
-void determineHeadDirection(int fileCounter);
-
-
 void normalizeVector(pair<double,double> &a);
-double calculateDotProduct(pair<double, double> v, pair<double, double> eV);
-void calculateHeadVector(FlyObject fO, pair<double,double> &headDirection);
+void writeFrameImage(int fn, string imS);
 
 void normalizeVector(pair<double,double> &a) {
   double temp = a.first*a.first + a.second*a.second;
@@ -632,10 +642,7 @@ if (inWhite)
 }
 }*/
 
-bool isInFemaleBlob;
-int maskImageHeight;
-int maskImageWidth;
-vector<pair<int,int> > bresenhamLine;
+
 
 void putPixel(Image* maskImage, int x, int y) {
 
@@ -969,7 +976,7 @@ int draw_line_bm(Image* maskImage, int x0, int y0, int x1, int y1) {
 
     default:
       *output << "No octant which should be a bug\n";
-      exit(0);
+      exit(EXIT_FAILURE);
       break;
   }
 
@@ -977,14 +984,20 @@ int draw_line_bm(Image* maskImage, int x0, int y0, int x1, int y1) {
 }
 
 
-double euclideanDist(pair<int, int > newLocation, pair<int, int> initLocation) {
-
+inline double euclideanDist(pair<int, int > newLocation, pair<int, int> initLocation) {
   double temp = pow((newLocation.first - initLocation.first), 2.0) + pow((newLocation.second - initLocation.second), 2.0);
   temp = sqrt(temp);
   return temp;
+}
+
 
+inline double getSpeed(pair<double, double> vector) {
+  double value = vector.first*vector.first + vector.second*vector.second;
+  value = sqrt(value);
+  return value;
 }
 
+
 int sequenceCondition(FrameInfo prevFI,FrameInfo currentFI) {
   bool prevFIsSingleBlob = prevFI.getIsSingleBlob();
   bool currentFIsSingleBlob = currentFI.getIsSingleBlob();
@@ -1022,7 +1035,6 @@ void drawTheSequence(int startIndex, int endIndex, int isFirst, bool singleBlob,
 }
 
 
-
 void objectHeadDirection(FlyObject prevFO, FlyObject &currentFO) {
 
   // take the head direction from the previous frame
@@ -1200,11 +1212,9 @@ void velocityDirection(int st, int end, pair<double, double > &velDirectionF, pa
   pair<int, int> cFFCentroid = cFFirstFO.getCentroid();
   pair<int, int> cFSCentroid = cFSecondFO.getCentroid();
 
-
   pair<int, int> pFFCentroid = pFFirstFO.getCentroid();
   pair<int, int> pFSCentroid = pFSecondFO.getCentroid();
 
-
   int velXFirst = cFFCentroid.first - pFFCentroid.first;
   int velYFirst = cFFCentroid.second - pFFCentroid.second;
 
@@ -1220,23 +1230,13 @@ void velocityDirection(int st, int end, pair<double, double > &velDirectionF, pa
 
   velDirectionF = cFVV;
   velDirectionS = cSVV;
-
-
 }
 
 
-double getSpeed(pair<double, double> vector) {
-  double value = vector.first*vector.first + vector.second*vector.second;
-  value = sqrt(value);
-
-  return value;
-
 
-}
 
 void velocityDirections(int stIndex, int endIndex) {
 
-
   velocityDirectionsF.clear();
   velocityDirectionsS.clear();
   int i = 0;
@@ -1309,7 +1309,6 @@ void velocityDirections(int stIndex, int endIndex) {
 }
 
 
-ofstream foutLPS;
 void largestIncreasingPositiveDotProductSeq(vector<pair<double, double> > velocityDirs, int &startIndex, int &endIndex) {
 
   int positiveVelSeqSize = 0;
@@ -1347,8 +1346,6 @@ void largestIncreasingPositiveDotProductSeq(vector<pair<double, double> > veloci
       //*output << "end "<<endIndex<<endl;
     }
 
-
-
   }
 
   // if dot product is alternately 0 and nonzero then nothing will be updated. In that case take the first nonzero velocity index
@@ -1392,7 +1389,7 @@ void propagateDirections(int object, int s, int e, int origStart, int origEnd) {
     FrameInfo currentFI = fIVector[i];
     vector<FlyObject > cFOVector = currentFI.getFOVector();
     FlyObject cFFO = cFOVector[object-1];
-    pair<double , double> cFVV = cFFO.getVelocityV();
+    //pair<double , double> cFVV = cFFO.getVelocityV();
     //*output << "Velocity before normalization "<<cFVV.first<<","<<cFVV.second<<endl;
     //normalizeVector(cFVV);
     /**output << "Velocity after normalization "<<cFVV.first<<","<<cFVV.second<<endl;
@@ -1416,7 +1413,6 @@ void propagateDirections(int object, int s, int e, int origStart, int origEnd) {
       maxVelValIndex = i;
     }
 
-
   }
 
   *output << "Maximum speed is chosen for for frame "<<fnVector[maxVelValIndex]<<" : "<<maxVelValue<<endl;
@@ -1442,7 +1438,7 @@ void propagateDirections(int object, int s, int e, int origStart, int origEnd) {
     fIVector[t] = currentFI;
   }
   else {
-    pair<double, double> tempVelocity = cFSecondFO.getVelocityV();
+    //pair<double, double> tempVelocity = cFSecondFO.getVelocityV();
     //*output << "Velocity was "<<tempVelocity.first<<","<<tempVelocity.second<<endl;
     *output << "Setting the head direction according to the representative velocity in the longest positive sequence"<<endl;
 
@@ -1534,13 +1530,10 @@ void propagateDirections(int object, int s, int e, int origStart, int origEnd) {
       }
 
       currentFI.setFOVector(cFOVector);
-
       fIVector[i] = currentFI;
 
     }
 
-
-
   }
   // propagate upwards
   FrameInfo prevFI = fIVector[e];
@@ -1558,25 +1551,17 @@ void propagateDirections(int object, int s, int e, int origStart, int origEnd) {
       FlyObject cFSecondFO = cFOVector[1];
 
       if (object == 1) {
-        //*output << "First object extract"<<endl;
         objectHeadDirection(pFFirstFO, cFFirstFO, false);
-        //*output << "First object update"<<endl;
         cFOVector[0] = cFFirstFO;
-
         pFFirstFO = cFFirstFO;
 
       } else {
-        //*output << "Second object extract"<<endl;
         objectHeadDirection(pFSecondFO, cFSecondFO, false);
-        //*output << "Second object update"<<endl;
         cFOVector[1] = cFSecondFO;
-
         pFSecondFO = cFSecondFO;
-
       }
 
       currentFI.setFOVector(cFOVector);
-
       fIVector[i] = currentFI;
 
     }
@@ -1616,12 +1601,9 @@ void propagateDirections(int object, int s, int e, int origStart, int origEnd) {
       }
 
       currentFI.setFOVector(cFOVector);
-
       fIVector[i] = currentFI;
     }
-
   }
-
 }
 
 
@@ -1641,7 +1623,6 @@ void calculateHeadDirection(int st, int end, int maxDistIndex) {
   *output << "Size of evDirectionF "<<evDirectionF.size()<<endl;
   *output << "Size of evDirectionS "<<evDirectionS.size()<<endl;
 
-
   // debug
   *output << "------------ALL VELOCITY AND CORRESPONDING EV-------------\n";
   int a;
@@ -1659,14 +1640,14 @@ void calculateHeadDirection(int st, int end, int maxDistIndex) {
 
     *output << "Second object velocity = "<<w.first<<","<<w.second<<endl;
     *output << "Second object ev       = "<<wEV.first<<","<<wEV.second<<endl;
-
-
   }
+
   *output << "Last frame index wont have velocity a+st("<<(a+st)<<") = end("<<end<<") "<<fnVector[a+st]<<endl;
   *output << "------------END-------------\n";
 
   int s;
   int e;
+
   foutLPS<<"------------------------------------------------------------------"<<endl;
   largestIncreasingPositiveDotProductSeq(evDirectionF, s, e);
   *output << "Positive indexes are "<<fnVector[st+s]<<" to "<<fnVector[st+e]<<endl;
@@ -1686,6 +1667,8 @@ void calculateHeadDirection(int st, int end, int maxDistIndex) {
   propagateDirections(2, si, ei, st, end);
 
 }
+
+
 // min dist from prev frame's 0th index object
 void objectCorrespondence(FrameInfo &prevFI, FrameInfo &currentFI) {
 
@@ -1853,17 +1836,10 @@ void processASequence(int startOfATrackSequence, int endOfATrackSequence) {
     drawTheSequence(startOfATrackSequence, endOfATrackSequence, 0, false, false);
   }
 
-
 }
 
-int diagLength;
-ofstream foutSt;
-ofstream foutDebugCen;
-ofstream foutDebugSpeed;
 
-
-int main(int argc, char **argv)
-{
+int main(int argc, char **argv) {
 
   int c;	
   bool verbose = false;
@@ -1871,8 +1847,7 @@ int main(int argc, char **argv)
   opterr = 0;
 
   while ((c = getopt (argc, argv, "i:f:m:p:o:hxv")) != -1)
-    switch (c)
-    {
+    switch (c) {
       case 'i':
         inputFileName = optarg;
         break;
@@ -1890,7 +1865,7 @@ int main(int argc, char **argv)
         break;
       case 'h':
         cout << usage << endl;
-        exit(1);
+        exit(EXIT_FAILURE);
         break;
       case 'x':
         writeFinalImages = true;
@@ -1913,31 +1888,32 @@ int main(int argc, char **argv)
     cerr << "output path: " << finalOutputPath << endl;
     cerr << "mask path: " << maskImagePath << endl;
     cerr << "output prefix: " << outputFilePrefix << endl;
-    exit(1);
+    exit(EXIT_FAILURE);
   }	
+
   string fileName;	
   ifstream inputFile(inputFileName.c_str());
-  // save the input file name
 
   if (inputFile.fail() ) {
     cerr << "cannot open the input file that contains name of the input images\n";
-    exit(1);
+    exit(EXIT_FAILURE);
   }
 
   string statFileName = finalOutputPath + outputFilePrefix + "_statFile.txt";
-  //*output << "Statfilename is "<<statFileName<<endl;
   foutSt.open(statFileName.c_str());
+
   if (foutSt.fail()) {
     cerr<<"cannot open the statfile"<<endl;
-    exit(1);
+    exit(EXIT_FAILURE);
   }
 
   // debug file
   string foutDebugCenFN = finalOutputPath + outputFilePrefix + "_statFileDebug.txt";
   foutDebugCen.open(foutDebugCenFN.c_str());
+
   if (foutDebugCen.fail()) {
     cerr << "cannot open the statDebug file"<<endl;
-    exit(1);
+    exit(EXIT_FAILURE);
   }
 
   // debug file speed distribution
@@ -1945,7 +1921,7 @@ int main(int argc, char **argv)
   foutDebugSpeed.open(foutDebugSpeedFN.c_str());
   if (foutDebugSpeed.fail()) {
     cerr << "cannot open the speedDebug file"<<endl;
-    exit(1);
+    exit(EXIT_FAILURE);
   }
 
   // open the file for statistics
@@ -1954,9 +1930,8 @@ int main(int argc, char **argv)
   *output << "LongestPositive.txt file name is "<<lPSFileName<<endl;
   foutLPS.open(lPSFileName.c_str());
 
-  unsigned int objCount = 0;
-
-  int frameCounter = 0;
+  // unsigned int objCount = 0;
+  //int frameCounter = 0;
   int fileCounter=0;
 
   char buffer[100];
@@ -1966,11 +1941,12 @@ int main(int argc, char **argv)
   vector<FlyObject > tempFOV;
 
   // to find the new head direction
-  bool currentlyCalculatingHead = true;
+  //bool currentlyCalculatingHead = true;
 
   while (inputFile>>fileName) {
 
     int fi = fileName.find("_");
+    // Be aware that this limits us to sample size of 99,999 (55.55 minutes)
     // current sequence numbers spans from 0 - 18019, so 5 digits are needed
     int span = 5;
     string tempString = fileName.substr(fi+1,span);
@@ -1997,7 +1973,7 @@ int main(int argc, char **argv)
     // residual image is initialized with black representing not visited.
     residual = new Image(buffer, "black");
 
-    //*output<<"reading file "<<fileName<<endl;
+    *output<<"reading file "<<fileName<<endl;
 
     tempFOV.clear();
 
@@ -2011,10 +1987,8 @@ int main(int argc, char **argv)
 
         if ( s > 0 )
         {
-
           //		*output << "size of the object is: " << s <<endl;
           vector<double> eigenVal = covariantDecomposition(shape);
-
           {					
             //objCount++;
 
@@ -2028,14 +2002,11 @@ int main(int argc, char **argv)
                 pair<double, double> (eigenVal[4], eigenVal[5]),
                 0.0);
             tempFOV.push_back(tempFO);
-
           }
         }
-
       }
     }
 
-
     delete img;
     delete residual;
 
@@ -2045,10 +2016,8 @@ int main(int argc, char **argv)
     fOVector.clear();
 
     for (int ti=0; ti<tempFOV.size(); ti++){
-
       FlyObject a = tempFOV[ti];
       fOVector.push_back(a);
-
     }
 
     bool currentFrameIsSingleBlob = false;
@@ -2131,18 +2100,11 @@ int main(int argc, char **argv)
       //*output << "Done for "<<fnVector[fileCounter-1]<<endl;
     }
 
-    sequenceSize++;
-
     // increase the frame Counter
     fileCounter++;
 
-
-    //*output << "Going to the next step"<<endl;
-
-    //open this after debug
-    /**/
-
-
+    // increase the sequence size
+    sequenceSize++;
   }
 
   //*output << "No more files "<<startOfAOneObject<<" "<<endOfAOneObject<<endl;
@@ -2251,31 +2213,46 @@ int hitTheFly(Image* maskImage, int &intersectX, int &intersectY) {
 
 void findTheStartPoint(string fileName, int desiredSize, int otherSize, int cen_x, int cen_y,  bool eVDirection) {
 
-
   string segmImageFileName = maskImagePath + fileName;
 
+  int width = 0;
+  int height = 0;
+
+  int x0, y0, x1, y1;
+
+  x0 = cen_x;
+  y0 = cen_y;
+
+  double ev_x;
+  double ev_y;
+
+  char buffer[100];
+
+  bool found = false;	
+
+  vector<pair<int, int> > foundShape;
+  vector<pair<int,int> > shape;
+
+  Image *image, *mask;
+
   cout << "Segmented image "<<segmImageFileName<<"\n";
+
   if (desiredSize == otherSize) {
     foutDebugCen<<"File name "<<segmImageFileName<<endl;
     foutDebugCen<<"MaleSize == FemaleSize\n";
     foutDebugCen<<"DesiredCentroid.first, DesiredCentroid.second = ("<<cen_x<<","<<cen_y<<")"<<endl;
   }
 
-  Image* image = new Image(segmImageFileName.c_str());
-
+  image = new Image(segmImageFileName.c_str());
 
-  int width = image->columns();
-  int height = image->rows();
+  width = image->columns();
+  height = image->rows();
 
-  char buffer[100];
   sprintf(buffer,"%ix%i",width,height);
 
   // the residual image should be newed
   residual = new Image(buffer, "black");
 
-  bool found = false;	
-  vector<pair<int, int> > foundShape;
-  vector<pair<int,int> > shape;
   *output<<"Detecting the male object for finding the start point"<<endl;
   for (int x = 0; x<width and found == false; x++) {
     for (int y = 0; y<height and found == false; y++) {
@@ -2338,19 +2315,11 @@ void findTheStartPoint(string fileName, int desiredSize, int otherSize, int cen_
     *output<<"foundshape is assigned a value"<<endl;
   } else {
     *output<<"ERROR: foundshape is not assigned a value so the next step would draw a line over an empty image"<<endl;
-    exit(0);
+    exit(EXIT_FAILURE);
   }
 
   vector<double> eigenVal = covariantDecomposition(foundShape);
 
-  int x0, y0, x1, y1;
-
-  x0 = cen_x;
-  y0 = cen_y;
-
-  double ev_x;
-  double ev_y;
-
   if (eVDirection == true) {
     ev_x = static_cast<double> (x0) + static_cast<double> (diagLength)*eigenVal[4];
     ev_y = static_cast<double> (y0) + static_cast<double> (diagLength)*eigenVal[5];
@@ -2367,19 +2336,19 @@ void findTheStartPoint(string fileName, int desiredSize, int otherSize, int cen_
   *output<<"Endpoint: centroid (x0,y0)==("<<x0<<","<<y0<<")"<<endl;
   *output<<"Startpoint: OutsidePointInEVDirection (x1,y1)==("<<x1<<","<<y1<<")"<<endl;
 
-  Image* maskImage = new Image(buffer, "black");
+  mask = new Image(buffer, "black");
 
   for (int i=0; i<foundShape.size(); i++) {
     pair<int,int > point = foundShape[i];
-    maskImage->pixelColor(point.first, point.second,"white");
+    mask->pixelColor(point.first, point.second,"white");
   }
 
-  /*int hits= */ draw_line_bm(maskImage, x1, y1, x0, y0);
+  /*int hits= */ draw_line_bm(mask, x1, y1, x0, y0);
 
 
-  //maskImage->strokeColor("red");
-  //maskImage->draw(DrawableLine(x1, y1, x0, y0));
-  //maskImage->write("test.png");
+  //mask->strokeColor("red");
+  //mask->draw(DrawableLine(x1, y1, x0, y0));
+  //mask->write("test.png");
 
   *output<<"BresenhamLine size is "<<bresenhamLine.size()<<endl;
   /*	if (hits == 1) {
@@ -2389,7 +2358,7 @@ void findTheStartPoint(string fileName, int desiredSize, int otherSize, int cen_
   if (bresenhamLine.size() > 0) {
   pair<int, int> temp = bresenhamLine[bresenhamLine.size()-1];
   *output << "Finding the starting point: Hits source at "<<temp.first<<","<<temp.second<<endl;
-  ColorMono c = maskImage->pixelColor(temp.first, temp.second);
+  ColorMono c = mask->pixelColor(temp.first, temp.second);
   //maleSP_x = prev_x;
   //maleSP_y = prev_y;
 
@@ -2403,7 +2372,7 @@ void findTheStartPoint(string fileName, int desiredSize, int otherSize, int cen_
   } 
   else {
   isFoundStartPoint = false;
-  *output<<"The object is at the border in the mask image. BresenhamLine vector is empty. Size : "<<bresenhamLine.size()<<endl;
+  *output<<"The object is at the border in the ask image. BresenhamLine vector is empty. Size : "<<bresenhamLine.size()<<endl;
   }
 
   } else {
@@ -2416,13 +2385,13 @@ void findTheStartPoint(string fileName, int desiredSize, int otherSize, int cen_
   if (bresenhamLine.size() > 0) {
     pair<int, int> temp = bresenhamLine[bresenhamLine.size()-1];
     *output << "Finding the starting point: Hits source at "<<temp.first<<","<<temp.second<<endl;
-    ColorMono c = maskImage->pixelColor(temp.first, temp.second);
+    ColorMono c = mask->pixelColor(temp.first, temp.second);
     //maleSP_x = prev_x;
     //maleSP_y = prev_y;
 
     if (c.mono() == true) {
       *output << "start point from the source object should be black"<<endl;
-      exit(0);
+      exit(EXIT_FAILURE);
     }
     isFoundStartPoint = true;
     // reset it after its corresponding hitTheFly() function call
@@ -2433,10 +2402,9 @@ void findTheStartPoint(string fileName, int desiredSize, int otherSize, int cen_
     *output<<"The object is at the border in the mask image. BresenhamLine vector is empty. Size : "<<bresenhamLine.size()<<endl;
   }
 
-
   delete residual;
   delete image;
-  delete maskImage;
+  delete mask;
 }
 
 
@@ -2513,12 +2481,13 @@ void calculateStatistics(FrameInfo currentFI, string fileName, int isFirst, bool
 
     headDirAngleMap[a]++;
 
+    // TODO: what is going on with the constant comparison?
     foutSt<<"Dot product was "<<dp<<endl;
     foutSt<<"Angle between ("<<maleHeadDir.first<<","<<maleHeadDir.second<<") and ("<<femaleHeadDir.first<<","<<femaleHeadDir.second<<") : "<<a<<endl;
     if(a == -2147483648 || a == 2147483648) {
       *output<<"Angle between ("<<maleHeadDir.first<<","<<maleHeadDir.second<<") and ("<<femaleHeadDir.first<<","<<femaleHeadDir.second<<") : "<<a<<endl;
       *output<<"Incorrect angle calculation :"<<a<<endl;
-      exit(1);
+      exit(EXIT_FAILURE);
     }
     // 3. generate number of times male is looking at the female
     if (isHitting == true) {
@@ -2569,7 +2538,7 @@ void calculateStatistics(FrameInfo currentFI, string fileName, int isFirst, bool
 void drawTheFlyObject(FrameInfo currentFI, string fileName, int isFirst, bool singleBlob, bool unprocessed) {
 
   *output << "isFirst is "<<isFirst<<endl;
-  Image* img;
+  Image* img = NULL;
   string inputFileName;
   string outputFileName;
   if(writeFinalImages) {	
@@ -2590,7 +2559,7 @@ void drawTheFlyObject(FrameInfo currentFI, string fileName, int isFirst, bool si
   // the unprocessed flag is used to handle those sequence that are less than 15 frames long and flies are separated there.
   if (singleBlob == false and unprocessed == false) {
 
-    /////////// find the sizes for finding the start point
+    // find the sizes for finding the start point
     FlyObject fO = fOVector[isFirst];
     int maleSize = fO.getArea();
     fO = fOVector[1-isFirst];
@@ -2701,15 +2670,12 @@ void drawTheFlyObject(FrameInfo currentFI, string fileName, int isFirst, bool si
         }
 
         // draw the velocity vector
-
         img->strokeColor("blue");
         pair<double, double> velocityV = currentFO.getVelocityV();
         ev_x = static_cast<double>(centroid.first) + 30.0 * velocityV.first;
         ev_y = static_cast<double>(centroid.second) + 30.0 * velocityV.second;
         img->draw(DrawableLine( centroid.first, centroid.second, static_cast<int>(ev_x), static_cast<int>(ev_y) ));
 
-
-
         // draw the historical head vector
         img->strokeColor("white");
         pair<double, double> headV = currentFO.getHead();
@@ -2717,16 +2683,13 @@ void drawTheFlyObject(FrameInfo currentFI, string fileName, int isFirst, bool si
         ev_y = static_cast<double> (centroid.second) + 25.0*headV.second;
         img->draw( DrawableLine(centroid.first, centroid.second, static_cast<int> (ev_x), static_cast<int> (ev_y)) );
 
-
         //draw the object tracking circle
         if (n == isFirst and n==0) {
           *output << "Tracking the n = "<<n<<endl;
           img->strokeColor("yellow");
           img->draw(DrawableCircle(centroid.first, centroid.second, centroid.first+5, centroid.second));
           img->pixelColor(prev_x, prev_y, "red");
-
         } else if ( n == isFirst and n==1) {
-
           *output << "Tracking the "<<n<<endl;
           img->strokeColor("yellow");
           img->fillColor("none");
@@ -2734,7 +2697,6 @@ void drawTheFlyObject(FrameInfo currentFI, string fileName, int isFirst, bool si
           img->draw(DrawableCircle(centroid.first, centroid.second, centroid.first+5, centroid.second));
         }
 
-
       }
     }
   }
@@ -2743,11 +2705,9 @@ void drawTheFlyObject(FrameInfo currentFI, string fileName, int isFirst, bool si
     img->write(outputFileName.c_str());
     delete img;
   }
-
-  // when do not want to identify on the original comment below line and uncomment the above one
-
   delete maskImage;
 
+  // TODO: Wtf is going on here?
   if (isHitting == 1 || isHittingFemaleToMale == 0)
     calculateStatistics(currentFI, fileName, isFirst, singleBlob, true, false, unprocessed);
   else if (isHitting == 0 || isHittingFemaleToMale == 1)
@@ -2760,10 +2720,8 @@ void drawTheFlyObject(FrameInfo currentFI, string fileName, int isFirst, bool si
 }
 
 
-void findObj(Image* img, int x, int y, vector<pair<int,int> > & shape ,bool eightCon, bool colorLookingFor)
-{
+void findObj(Image* img, int x, int y, vector<pair<int,int> > & shape ,bool eightCon, bool colorLookingFor) {
   assert(residual != NULL);
-
   if (eightCon == true)
     eightConnObj(img, x, y, shape, colorLookingFor);
   else {
@@ -2772,8 +2730,7 @@ void findObj(Image* img, int x, int y, vector<pair<int,int> > & shape ,bool eigh
 }
 
 
-void fourConnObj(Image* img, int x, int y, vector<pair<int, int> > & obj, bool color)
-{
+void fourConnObj(Image* img, int x, int y, vector<pair<int, int> > & obj, bool color) {
   int width = img->columns(),height = img->rows();
 
   // boundary violation check
@@ -2813,8 +2770,7 @@ void fourConnObj(Image* img, int x, int y, vector<pair<int, int> > & obj, bool c
 
 }
 
-void eightConnObj(Image* img, int x, int y, vector<pair<int, int> > & obj, bool color)
-{
+void eightConnObj(Image* img, int x, int y, vector<pair<int, int> > & obj, bool color) {
   int width = img->columns(),height = img->rows();
 
   // boundary violation check
-- 
cgit v1.2.1


From 7d76e9aaee9dc40158117e7702b12fe6184e5d11 Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Sun, 30 Dec 2012 22:09:05 -0500
Subject: Update README.markdown

Fixed error in link
---
 README.markdown | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.markdown b/README.markdown
index 9a95eba..1e4791e 100644
--- a/README.markdown
+++ b/README.markdown
@@ -3,7 +3,7 @@ Automated Categorization of Drosophila Learning and Memory Behaviors using Video
 
 For more information about this project, goto:
 
-https://www.cs.drexel.edu/~david/Papers/Md_Reza_MS_Thesis.pdf_
+https://www.cs.drexel.edu/~david/Papers/Md_Reza_MS_Thesis.pdf
 
 This repository contains all of the source codes used for the Fly Tracking project.
 
-- 
cgit v1.2.1


From bda4a425da1073ca38b7ccf006d02f65b25a4755 Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Wed, 14 May 2014 15:23:05 -0400
Subject: add changes for histogramming

---
 fly-tools/FlyTrackingMain.cpp | 907 ++++++++++++++++++++++--------------------
 fly-tools/Makefile            |   4 +-
 2 files changed, 486 insertions(+), 425 deletions(-)

diff --git a/fly-tools/FlyTrackingMain.cpp b/fly-tools/FlyTrackingMain.cpp
index 30dc3db..d44d546 100644
--- a/fly-tools/FlyTrackingMain.cpp
+++ b/fly-tools/FlyTrackingMain.cpp
@@ -8,12 +8,13 @@
 #include <cassert>
 #include <cstdlib>
 
-#include <ImageMagick/Magick++.h>
+#include <Magick++.h>
 
 #include <gsl/gsl_matrix.h>
 #include <gsl/gsl_vector.h>
 #include <gsl/gsl_blas.h>
 #include <gsl/gsl_eigen.h>
+#include <unistd.h>
 
 #include "FrameInfo.h"
 
@@ -139,7 +140,48 @@ void bubbleSort(vector<FlyObject > & fov) {
   }
 }
 
-void writeHist(const char* filename, map<unsigned int, unsigned int> dataMap) {
+
+void getMeanStdDev(map<unsigned int, unsigned int> dataMap, double *mean, double *standardDev) {
+    // mean = 1/N*(sum(i*H_i)) for i = 0 to M-1
+    double sumOfValues = 0.0;
+    double i = 0.0;
+    double N = 0.0;
+    double M = 0.0;
+
+		vector<double> currentHistogramValues;
+
+		for(i = 0; i < dataMap.size(); i++) {
+			sumOfValues = sumOfValues + i*dataMap[i];
+			N += dataMap[i];
+
+			cout << "sum:" << sumOfValues << endl;
+			cout << "N:" << N << endl;
+			cout << "i:" << i << endl;
+		}
+
+    // mean
+    *mean = sumOfValues/N;
+		double lmean = 0;
+    lmean = sumOfValues/N;
+		cout << "mean:" << *mean << endl;
+		cout << "mean:" << lmean << " = " << sumOfValues << "/" << N << endl;
+
+    // sigma^2 = (sum( (i-mean)^2*H_i ) )/(N-1) for i = 0 to M-1
+    *standardDev = 0.0;
+    double sumSquaredResults = 0.0;
+    int j = 0;
+    for ( i = 0.0; i < dataMap.size(); i++) {
+      sumSquaredResults += pow((i-*mean), 2.0)*dataMap[j];
+			*output << "sumsqres:" << sumSquaredResults << endl;
+      j++;
+    }
+
+    // standard deviation
+    *standardDev = sumSquaredResults/(N-1);
+    *standardDev = sqrt(*standardDev);
+}
+
+double writeHist(const char* filename, map<unsigned int, unsigned int> dataMap) {
   *output << "In the beginning of the write hist" << endl;
   *output << "dataMap size " << dataMap.size() << endl;
 
@@ -148,7 +190,7 @@ void writeHist(const char* filename, map<unsigned int, unsigned int> dataMap) {
     ofstream fout(filename);
     fout <<"No entry in the histogram and size is " << dataMap.size() << endl;
     fout.close();
-    return;
+    return 0;
 
   }
 
@@ -183,7 +225,8 @@ void writeHist(const char* filename, map<unsigned int, unsigned int> dataMap) {
   catch (...) {
     cerr << "Bad memory loc for opening file" << endl;
   }
-
+	
+	return 0;
 }
 
 double calculateDotProduct(pair<double, double> v, pair<double, double> eV);
@@ -1839,465 +1882,130 @@ void processASequence(int startOfATrackSequence, int endOfATrackSequence) {
 }
 
 
-int main(int argc, char **argv) {
-
-  int c;	
-  bool verbose = false;
-  string usage = "Usage: FlyTracking -i <inputFile.txt> -o <originalImagePath> -f <finalOutputPath> -m <maskImagePath> -p <outputFilePrefix>";
-  opterr = 0;
 
-  while ((c = getopt (argc, argv, "i:f:m:p:o:hxv")) != -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(EXIT_FAILURE);
-        break;
-      case 'x':
-        writeFinalImages = true;
-        break;
-      case 'v':
-        verbose = true;
-        break;
-      default:
-        break;
-    }
+// is set each time the start is found
+// useful when one blob is detected on the border of the mask image
+bool isFoundStartPoint = false;
+int hitTheFly(Image* maskImage, int &intersectX, int &intersectY) {
 
-  (verbose) ? output = &cout : output = &nullLog; 
+  //Image* maskImage = new Image(fileName.c_str());
 
-  *output << "verbose logging out" << endl;
+  for (int i=bresenhamLine.size()-1; i>=0; i--) {
 
-  if( inputFileName.empty() || origImagePath.empty() || finalOutputPath.empty() || maskImagePath.empty() || outputFilePrefix.empty() ) {
-    cerr <<  usage << endl;
-    cerr << "input name: " << inputFileName << endl;
-    cerr << "original path: " << origImagePath << endl;
-    cerr << "output path: " << finalOutputPath << endl;
-    cerr << "mask path: " << maskImagePath << endl;
-    cerr << "output prefix: " << outputFilePrefix << endl;
-    exit(EXIT_FAILURE);
-  }	
+    pair<int,int> tempP = bresenhamLine[i];
 
-  string fileName;	
-  ifstream inputFile(inputFileName.c_str());
+    int x = tempP.first;
 
-  if (inputFile.fail() ) {
-    cerr << "cannot open the input file that contains name of the input images\n";
-    exit(EXIT_FAILURE);
-  }
+    int y = tempP.second;
 
-  string statFileName = finalOutputPath + outputFilePrefix + "_statFile.txt";
-  foutSt.open(statFileName.c_str());
+    ColorMono currPixelColor = ColorMono(maskImage->pixelColor(x,y));
 
-  if (foutSt.fail()) {
-    cerr<<"cannot open the statfile"<<endl;
-    exit(EXIT_FAILURE);
-  }
+    if (currPixelColor.mono() == true) {
+      *output << "Hit the target fly"<<" "<<x<<","<<y<<endl;
+      intersectX = x;
+      intersectY = y;
+      return 1;
+    } else if (currPixelColor.mono() == false and ( x == 0 || x == (maskImageWidth-1) || y == 0 || y == (maskImageHeight-1))) {
+      *output << "Is at the boundary"<<endl;
+      return 2;
+    }
+    else {
+      *output << "Going through" << x << "," << y << endl;
+    }
 
-  // debug file
-  string foutDebugCenFN = finalOutputPath + outputFilePrefix + "_statFileDebug.txt";
-  foutDebugCen.open(foutDebugCenFN.c_str());
 
-  if (foutDebugCen.fail()) {
-    cerr << "cannot open the statDebug file"<<endl;
-    exit(EXIT_FAILURE);
   }
+  return -1;
 
-  // debug file speed distribution
-  string foutDebugSpeedFN = finalOutputPath + outputFilePrefix + "_speedDebug.txt";
-  foutDebugSpeed.open(foutDebugSpeedFN.c_str());
-  if (foutDebugSpeed.fail()) {
-    cerr << "cannot open the speedDebug file"<<endl;
-    exit(EXIT_FAILURE);
-  }
+}
 
-  // open the file for statistics
-  string lPSFileName("LongestPositive.txt");
-  lPSFileName = finalOutputPath + outputFilePrefix + "_" + lPSFileName;
-  *output << "LongestPositive.txt file name is "<<lPSFileName<<endl;
-  foutLPS.open(lPSFileName.c_str());
+void findTheStartPoint(string fileName, int desiredSize, int otherSize, int cen_x, int cen_y,  bool eVDirection) {
 
-  // unsigned int objCount = 0;
-  //int frameCounter = 0;
-  int fileCounter=0;
+  string segmImageFileName = maskImagePath + fileName;
 
-  char buffer[100];
-  string imgSize;
-  //	FlyObject a,b;
-  vector<pair<int,int> > shape;
-  vector<FlyObject > tempFOV;
+  int width = 0;
+  int height = 0;
 
-  // to find the new head direction
-  //bool currentlyCalculatingHead = true;
+  int x0, y0, x1, y1;
 
-  while (inputFile>>fileName) {
+  x0 = cen_x;
+  y0 = cen_y;
 
-    int fi = fileName.find("_");
-    // Be aware that this limits us to sample size of 99,999 (55.55 minutes)
-    // current sequence numbers spans from 0 - 18019, so 5 digits are needed
-    int span = 5;
-    string tempString = fileName.substr(fi+1,span);
-    int frameCounter = atoi(tempString.c_str());
-    //*output << frameCounter<<endl;
+  double ev_x;
+  double ev_y;
 
-    string fileNameForSave = fileName;
+  char buffer[100];
 
-    // save the name in the vector
-    fnVector.push_back(fileName);
+  bool found = false;	
 
-    fileName = maskImagePath + fileName;
-    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) ) );
+  vector<pair<int, int> > foundShape;
+  vector<pair<int,int> > shape;
 
-    //*output << "Diagonal length is "<<diagLength<<endl;
-    //		Image* imgWithInfo;
-    //		imgWithInfo = new Image(fileName.c_str());
-    sprintf(buffer,"%ix%i",width,height);
-    string imsize(buffer);
-    imgSize = imsize;
-    // residual image is initialized with black representing not visited.
-    residual = new Image(buffer, "black");
+  Image *image, *mask;
 
-    *output<<"reading file "<<fileName<<endl;
+  cout << "Segmented image "<<segmImageFileName<<"\n";
 
-    tempFOV.clear();
+  if (desiredSize == otherSize) {
+    foutDebugCen<<"File name "<<segmImageFileName<<endl;
+    foutDebugCen<<"MaleSize == FemaleSize\n";
+    foutDebugCen<<"DesiredCentroid.first, DesiredCentroid.second = ("<<cen_x<<","<<cen_y<<")"<<endl;
+  }
 
-    for (int x = 0; x<width; x++) {
-      for (int y = 0; y<height; y++) {
+  image = new Image(segmImageFileName.c_str());
 
-        //*output<<"comes here"<<endl;
-        shape.clear();
-        findObj(img, x, y, shape, true, true);
-        unsigned int s = shape.size();
+  width = image->columns();
+  height = image->rows();
 
-        if ( s > 0 )
-        {
-          //		*output << "size of the object is: " << s <<endl;
-          vector<double> eigenVal = covariantDecomposition(shape);
-          {					
-            //objCount++;
+  sprintf(buffer,"%ix%i",width,height);
 
-            double velocity_x=0.0, velocity_y=0.0;
-            // save the object information
-            FlyObject tempFO(s, 
-                pair<int, int> (eigenVal[6], eigenVal[7]), 
-                pair<double, double> (eigenVal[4], eigenVal[5]), 
-                pair<double,double> (velocity_x, velocity_y),
-                false,
-                pair<double, double> (eigenVal[4], eigenVal[5]),
-                0.0);
-            tempFOV.push_back(tempFO);
-          }
-        }
-      }
-    }
+  // the residual image should be newed
+  residual = new Image(buffer, "black");
 
-    delete img;
-    delete residual;
+  *output<<"Detecting the male object for finding the start point"<<endl;
+  for (int x = 0; x<width and found == false; x++) {
+    for (int y = 0; y<height and found == false; y++) {
 
-    //		*output<<"Sorting the objects according to size"<<endl;
-    //		bubbleSort(tempFOV);
+      //*output<<"comes here"<<endl;
+      shape.clear();
+      findObj(image, x, y, shape, true, true);
+      unsigned int s = shape.size();
 
-    fOVector.clear();
+      if ( s > 0 )
+      {
 
-    for (int ti=0; ti<tempFOV.size(); ti++){
-      FlyObject a = tempFOV[ti];
-      fOVector.push_back(a);
-    }
+        *output << "size of the object is: " << s <<endl;
 
-    bool currentFrameIsSingleBlob = false;
-    // if there is only one object then state of the system is single blob
-    if (fOVector.size() == 1 and currentFrameIsSingleBlob == false) {
-      currentFrameIsSingleBlob = true;
+        if (desiredSize == otherSize) {
 
-      // if start as a single blob
-      if (fileCounter == 0) {
-        //	*output << "Start as a single blob"<<endl;
-        startOfAOneObject = fileCounter;
-      }
+          // debug:
+          *output << "Inside the maleSize == femaleSize where (cen_x, cen_y) = "<<cen_x<<","<<cen_y<<endl;
+          pair<int, int> tmpCentroid = getCentroid(shape);
+          foutDebugCen<<"tmpCentroid.first, tmpCentroid.second = ("<<tmpCentroid.first<<","<<tmpCentroid.second<<")"<<endl;
+          if (tmpCentroid.first == cen_x and tmpCentroid.second == cen_y) {
 
-    }
+            found = true;
+            *output << "Detected the desired object when the sizes are equal"<<endl;
+            foundShape = shape;
+            foutDebugCen<<"Found by desired object after recomputing the centroid"<<endl;
+          }
 
-    FrameInfo tempFI(frameCounter, fOVector, currentFrameIsSingleBlob);
-    fIVector.push_back(tempFI);
-    FrameInfo currentFI = fIVector[fileCounter];
+          // not correct logic when the centroid can be black pixel
+          /*for (int l=0; l<s and found == false; l++) {
 
-    // start processing the sequence if applicable
-    if (sequenceSize > 1) {
+            pair<int, int> point = shape[l];
+            *output << "point.first, point.second "<<point.first<<","<<point.second<<endl;
 
-      FrameInfo prevFI = fIVector[fileCounter-1];
+          // this should give most of the time when the centroid is not a black pixel
+          // a centroid can be black pixel when the shape of the fly is distorted inside
+          if (point.first == cen_x and point.second == cen_y) {
+          found = true;
+          *output << "Detected the male object when the sizes of male/female are equal"<<endl;
+          foundShape = shape;
+          }
+          }*/
 
-      int seqCond = sequenceCondition(prevFI, currentFI);
 
-      if (seqCond == STUCKING_TO_A_SINGLE_BLOB) {
-
-        endOfATrackSequence = fileCounter-1;
-
-        // save the index for printing the one object later on
-        startOfAOneObject = fileCounter;
-
-      } else if (seqCond == SEPARATING_FROM_SINGLE_BLOB) {
-
-        startOfATrackSequence = fileCounter;
-
-        // draw the single blob sequence
-        endOfAOneObject = fileCounter - 1;
-        *output << "Only one object StartIndex "<<startOfAOneObject<<" endIndex "<<endOfAOneObject<<" and seqSize "<<sequenceSize<<endl;
-        // use the two variables (startOfAOneObject, endOfAOneObject) pair to draw the single-blob objects.
-        // third parameter is used to indicate whether the current sequence is SINGLE_BLOB. So true is passed.
-        // fourth parameter is used to indicate whether the current sequence is processed(to separate it from the actual single blob state).
-        // since we are considering the sequence length >=  15 to be a single blob state, so pass false parameter.
-        drawTheSequence(startOfAOneObject, endOfAOneObject,0, true, false);
-        startOfAOneObject = -1;
-        endOfAOneObject = -1;
-        //startOfATrackSequence = 1;
-        sequenceSize = 1;
-      }
-
-
-      if(seqCond == STUCKING_TO_A_SINGLE_BLOB) {
-        *output << "StartIndex "<<startOfATrackSequence<<" endIndex "<<endOfATrackSequence<<" and seqSize "<<sequenceSize<<endl;	
-        // if a sequence size is greater than 15 then it is processed. endOfATrackSequence - startOfATrackSequence == 15 when the size of the sequence is 16.
-        // endOfATrackSequence - startOfATrackSequence > 15 when the size of the sequence is > 16.
-        if ((endOfATrackSequence - startOfATrackSequence) >=15 ) {
-          processASequence(startOfATrackSequence, endOfATrackSequence);
-          *output << "Done processing"<<endl;
-        } else {
-          // use the two variables (startOfATrackSequence, endOfATrackSequence) pair to draw the unprocessed frames.
-          // third parameter is used to indicate whether the current sequence is not actual SINGLE_BLOB. So false is passed.
-          // fourth parameter is used to indicate whether the current sequence is processed(to separate it from the actual single blob state).
-          // since we are considering the sequence length <  15 to be a single blob state, so pass false parameter.
-          *output << "Sequence is only "<<(endOfATrackSequence-startOfATrackSequence+1)<<" images long so assumed as a single blob"<<endl;
-          drawTheSequence(startOfATrackSequence, endOfATrackSequence, 0, false, true);
-
-          // increase the unprocessed frame counter
-          //totalUnprocessedFrame = totalUnprocessedFrame + (endOfATrackSequence - startOfATrackSequence + 1);
-          foutSt<<"-------------------------------"<<endl;
-          foutSt<<"Unprocessed size "<<(endOfATrackSequence-startOfATrackSequence+1)<<endl;
-          foutSt<<"Total unprocessed size "<<totalUnprocessedFrame<<endl;
-          foutSt<<"-------------------------------"<<endl;
-        }
-
-        initSequence();
-        //*output << "Start of a single blob "<<startOfAOneObject<<" and end of a single blob "<<endOfAOneObject<<endl;
-
-      }
-      //*output << "Done for "<<fnVector[fileCounter-1]<<endl;
-    }
-
-    // increase the frame Counter
-    fileCounter++;
-
-    // increase the sequence size
-    sequenceSize++;
-  }
-
-  //*output << "No more files "<<startOfAOneObject<<" "<<endOfAOneObject<<endl;
-  inputFile.close();
-
-  //open this after debug
-  /**/
-  if (startOfATrackSequence!=-1 && endOfATrackSequence == -1) {
-    if ((sequenceSize-1) > 15 ) {
-
-      *output << "Last sequence that does not stick to a single blob status startIndex "<<startOfATrackSequence<<" endIndex "<<(sequenceSize+startOfATrackSequence-2)<<endl;
-      processASequence(startOfATrackSequence, (sequenceSize+startOfATrackSequence-2));
-      *output << "Done processing"<<endl;
-
-    } else {
-      // this case was not handled earlier. It can happen that the flies are separated during the last sequences and less than 15 frames long.
-      *output << "Sequence is only "<<(sequenceSize-1)<<" images long so assumed as a single blob"<<endl;
-      drawTheSequence(startOfATrackSequence, (sequenceSize+startOfATrackSequence-2), 0, false, true);
-      foutSt<<"-------------------------------"<<endl;
-      foutSt<<"Unprocessed size "<<(sequenceSize-1)<<endl;
-      foutSt<<"Total unprocessed size "<<totalUnprocessedFrame<<endl;
-      foutSt<<"-------------------------------"<<endl;
-
-    }
-    initSequence();
-
-  } else if (startOfAOneObject != -1 && endOfAOneObject == -1) {
-    *output << "Last sequence that does not separate from one object state\n";
-    drawTheSequence(startOfAOneObject, (sequenceSize+startOfAOneObject - 2), 0, true, false);
-    endOfAOneObject = -1;
-    startOfAOneObject = -1;
-    sequenceSize = 1;
-  }
-
-
-  string cDDistFileName = finalOutputPath + outputFilePrefix + "_centroidDist.txt";
-  string hDAngleDistFileName = finalOutputPath + outputFilePrefix + "_headDist.txt";
-  string speedDistFileName = finalOutputPath + outputFilePrefix + "_speedDist.txt";
-
-  writeHist(cDDistFileName.c_str(), centroidDistanceMap);
-  writeHist(hDAngleDistFileName.c_str(), headDirAngleMap);
-  writeHist(speedDistFileName.c_str(), speedMap);
-
-  // new calculation of percentage look at should consider only those frames where the flies are separated
-  double percentageLookingAt = static_cast<double>(totalMaleLookingAtFemale+totalFemaleLookingAtMale)/static_cast<double>(totalSeparated);
-  percentageLookingAt *= 100.0;
-
-  double percentageSingleBlob = static_cast<double>(totalSingleBlob)/static_cast<double>(fileCounter);
-  percentageSingleBlob *= 100.0;
-
-  foutSt<<"Total number of single blob "<<totalSingleBlob<<endl;
-  foutSt<<"Total number of male looking at "<<totalMaleLookingAtFemale<<endl;
-  foutSt<<"Total number of female looking at "<<totalFemaleLookingAtMale<<endl;
-  foutSt<<"Total number of looking at "<<(totalMaleLookingAtFemale+totalFemaleLookingAtMale)<<endl;
-  foutSt<<"Total number of unprocessed frame "<<totalUnprocessedFrame<<endl;
-  foutSt<<"Total number of frame where flies are separated (from the counter totalSeparated) "<<totalSeparated<<endl;
-  foutSt<<"Total number of frame where flies are separated "<<(fileCounter-totalUnprocessedFrame-totalSingleBlob)<<endl;
-  foutSt<<"Total number of frame "<<fileCounter<<endl;
-  foutSt<<"Percentage of frame in looking at mode "<<percentageLookingAt<<endl;
-  foutSt<<"Percentage of frame single blob "<<percentageSingleBlob<<endl;
-
-  foutSt.close();
-  foutDebugCen.close();
-  foutLPS.close();
-  foutDebugSpeed.close();
-
-  return 0;
-}
-
-
-// is set each time the start is found
-// useful when one blob is detected on the border of the mask image
-bool isFoundStartPoint = false;
-int hitTheFly(Image* maskImage, int &intersectX, int &intersectY) {
-
-  //Image* maskImage = new Image(fileName.c_str());
-
-  for (int i=bresenhamLine.size()-1; i>=0; i--) {
-
-    pair<int,int> tempP = bresenhamLine[i];
-
-    int x = tempP.first;
-
-    int y = tempP.second;
-
-    ColorMono currPixelColor = ColorMono(maskImage->pixelColor(x,y));
-
-    if (currPixelColor.mono() == true) {
-      *output << "Hit the target fly"<<" "<<x<<","<<y<<endl;
-      intersectX = x;
-      intersectY = y;
-      return 1;
-    } else if (currPixelColor.mono() == false and ( x == 0 || x == (maskImageWidth-1) || y == 0 || y == (maskImageHeight-1))) {
-      *output << "Is at the boundary"<<endl;
-      return 2;
-    }
-    else {
-      *output << "Going through" << x << "," << y << endl;
-    }
-
-
-  }
-  return -1;
-
-}
-
-void findTheStartPoint(string fileName, int desiredSize, int otherSize, int cen_x, int cen_y,  bool eVDirection) {
-
-  string segmImageFileName = maskImagePath + fileName;
-
-  int width = 0;
-  int height = 0;
-
-  int x0, y0, x1, y1;
-
-  x0 = cen_x;
-  y0 = cen_y;
-
-  double ev_x;
-  double ev_y;
-
-  char buffer[100];
-
-  bool found = false;	
-
-  vector<pair<int, int> > foundShape;
-  vector<pair<int,int> > shape;
-
-  Image *image, *mask;
-
-  cout << "Segmented image "<<segmImageFileName<<"\n";
-
-  if (desiredSize == otherSize) {
-    foutDebugCen<<"File name "<<segmImageFileName<<endl;
-    foutDebugCen<<"MaleSize == FemaleSize\n";
-    foutDebugCen<<"DesiredCentroid.first, DesiredCentroid.second = ("<<cen_x<<","<<cen_y<<")"<<endl;
-  }
-
-  image = new Image(segmImageFileName.c_str());
-
-  width = image->columns();
-  height = image->rows();
-
-  sprintf(buffer,"%ix%i",width,height);
-
-  // the residual image should be newed
-  residual = new Image(buffer, "black");
-
-  *output<<"Detecting the male object for finding the start point"<<endl;
-  for (int x = 0; x<width and found == false; x++) {
-    for (int y = 0; y<height and found == false; y++) {
-
-      //*output<<"comes here"<<endl;
-      shape.clear();
-      findObj(image, x, y, shape, true, true);
-      unsigned int s = shape.size();
-
-      if ( s > 0 )
-      {
-
-        *output << "size of the object is: " << s <<endl;
-
-        if (desiredSize == otherSize) {
-
-          // debug:
-          *output << "Inside the maleSize == femaleSize where (cen_x, cen_y) = "<<cen_x<<","<<cen_y<<endl;
-          pair<int, int> tmpCentroid = getCentroid(shape);
-          foutDebugCen<<"tmpCentroid.first, tmpCentroid.second = ("<<tmpCentroid.first<<","<<tmpCentroid.second<<")"<<endl;
-          if (tmpCentroid.first == cen_x and tmpCentroid.second == cen_y) {
-
-            found = true;
-            *output << "Detected the desired object when the sizes are equal"<<endl;
-            foundShape = shape;
-            foutDebugCen<<"Found by desired object after recomputing the centroid"<<endl;
-          }
-
-          // not correct logic when the centroid can be black pixel
-          /*for (int l=0; l<s and found == false; l++) {
-
-            pair<int, int> point = shape[l];
-            *output << "point.first, point.second "<<point.first<<","<<point.second<<endl;
-
-          // this should give most of the time when the centroid is not a black pixel
-          // a centroid can be black pixel when the shape of the fly is distorted inside
-          if (point.first == cen_x and point.second == cen_y) {
-          found = true;
-          *output << "Detected the male object when the sizes of male/female are equal"<<endl;
-          foundShape = shape;
-          }
-          }*/
-
-
-        } else {
+        } else {
 
           *output<<"Elseblock: Inside the desiredSize is not equal the otherSize"<<endl;
           if (s == desiredSize) {
@@ -2939,3 +2647,356 @@ bool isInterface(Image* orig, unsigned int x, unsigned int y) {
   else
     return false;
 }
+
+int main(int argc, char **argv) {
+
+  int c;	
+  bool verbose = false;
+  string usage = "Usage: FlyTracking -i <inputFile.txt> -o <originalImagePath> -f <finalOutputPath> -m <maskImagePath> -p <outputFilePrefix>";
+  int opterr = 0;
+
+  while ((c = getopt (argc, argv, "i:f:m:p:o:hxv")) != -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(EXIT_FAILURE);
+        break;
+      case 'x':
+        writeFinalImages = true;
+        break;
+      case 'v':
+        verbose = true;
+        break;
+      default:
+        break;
+    }
+
+  (verbose) ? output = &cout : output = &nullLog; 
+
+  *output << "verbose logging out" << endl;
+
+  if( inputFileName.empty() || origImagePath.empty() || finalOutputPath.empty() || maskImagePath.empty() || outputFilePrefix.empty() ) {
+    cerr <<  usage << endl;
+    cerr << "input name: " << inputFileName << endl;
+    cerr << "original path: " << origImagePath << endl;
+    cerr << "output path: " << finalOutputPath << endl;
+    cerr << "mask path: " << maskImagePath << endl;
+    cerr << "output prefix: " << outputFilePrefix << endl;
+    exit(EXIT_FAILURE);
+  }	
+
+  string fileName;	
+  ifstream inputFile(inputFileName.c_str());
+
+  if (inputFile.fail() ) {
+    cerr << "cannot open the input file that contains name of the input images\n";
+    exit(EXIT_FAILURE);
+  }
+
+  string statFileName = finalOutputPath + outputFilePrefix + "_statFile.txt";
+  foutSt.open(statFileName.c_str());
+
+  if (foutSt.fail()) {
+    cerr<<"cannot open the statfile"<<endl;
+    exit(EXIT_FAILURE);
+  }
+
+  // debug file
+  string foutDebugCenFN = finalOutputPath + outputFilePrefix + "_statFileDebug.txt";
+  foutDebugCen.open(foutDebugCenFN.c_str());
+
+  if (foutDebugCen.fail()) {
+    cerr << "cannot open the statDebug file"<<endl;
+    exit(EXIT_FAILURE);
+  }
+
+  // debug file speed distribution
+  string foutDebugSpeedFN = finalOutputPath + outputFilePrefix + "_speedDebug.txt";
+  foutDebugSpeed.open(foutDebugSpeedFN.c_str());
+  if (foutDebugSpeed.fail()) {
+    cerr << "cannot open the speedDebug file"<<endl;
+    exit(EXIT_FAILURE);
+  }
+
+  // open the file for statistics
+  string lPSFileName("LongestPositive.txt");
+  lPSFileName = finalOutputPath + outputFilePrefix + "_" + lPSFileName;
+  *output << "LongestPositive.txt file name is "<<lPSFileName<<endl;
+  foutLPS.open(lPSFileName.c_str());
+
+  // unsigned int objCount = 0;
+  //int frameCounter = 0;
+  int fileCounter=0;
+
+  char buffer[100];
+  string imgSize;
+  //	FlyObject a,b;
+  vector<pair<int,int> > shape;
+  vector<FlyObject > tempFOV;
+
+  // to find the new head direction
+  //bool currentlyCalculatingHead = true;
+
+  while (inputFile>>fileName) {
+
+    int fi = fileName.find("_");
+    // Be aware that this limits us to sample size of 99,999 (55.55 minutes)
+    // current sequence numbers spans from 0 - 18019, so 5 digits are needed
+    int span = 5;
+    string tempString = fileName.substr(fi+1,span);
+    int frameCounter = atoi(tempString.c_str());
+    //*output << frameCounter<<endl;
+
+    string fileNameForSave = fileName;
+
+    // save the name in the vector
+    fnVector.push_back(fileName);
+
+    fileName = maskImagePath + fileName;
+    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) ) );
+
+    //*output << "Diagonal length is "<<diagLength<<endl;
+    //		Image* imgWithInfo;
+    //		imgWithInfo = new Image(fileName.c_str());
+    sprintf(buffer,"%ix%i",width,height);
+    string imsize(buffer);
+    imgSize = imsize;
+    // residual image is initialized with black representing not visited.
+    residual = new Image(buffer, "black");
+
+    *output<<"reading file "<<fileName<<endl;
+
+    tempFOV.clear();
+
+    for (int x = 0; x<width; x++) {
+      for (int y = 0; y<height; y++) {
+
+        //*output<<"comes here"<<endl;
+        shape.clear();
+        findObj(img, x, y, shape, true, true);
+        unsigned int s = shape.size();
+
+        if ( s > 0 )
+        {
+          //		*output << "size of the object is: " << s <<endl;
+          vector<double> eigenVal = covariantDecomposition(shape);
+          {					
+            //objCount++;
+
+            double velocity_x=0.0, velocity_y=0.0;
+            // save the object information
+            FlyObject tempFO(s, 
+                pair<int, int> (eigenVal[6], eigenVal[7]), 
+                pair<double, double> (eigenVal[4], eigenVal[5]), 
+                pair<double,double> (velocity_x, velocity_y),
+                false,
+                pair<double, double> (eigenVal[4], eigenVal[5]),
+                0.0);
+            tempFOV.push_back(tempFO);
+          }
+        }
+      }
+    }
+
+    delete img;
+    delete residual;
+
+    //		*output<<"Sorting the objects according to size"<<endl;
+    //		bubbleSort(tempFOV);
+
+    fOVector.clear();
+
+    for (int ti=0; ti<tempFOV.size(); ti++){
+      FlyObject a = tempFOV[ti];
+      fOVector.push_back(a);
+    }
+
+    bool currentFrameIsSingleBlob = false;
+    // if there is only one object then state of the system is single blob
+    if (fOVector.size() == 1 and currentFrameIsSingleBlob == false) {
+      currentFrameIsSingleBlob = true;
+
+      // if start as a single blob
+      if (fileCounter == 0) {
+        //	*output << "Start as a single blob"<<endl;
+        startOfAOneObject = fileCounter;
+      }
+
+    }
+
+    FrameInfo tempFI(frameCounter, fOVector, currentFrameIsSingleBlob);
+    fIVector.push_back(tempFI);
+    FrameInfo currentFI = fIVector[fileCounter];
+
+    // start processing the sequence if applicable
+    if (sequenceSize > 1) {
+
+      FrameInfo prevFI = fIVector[fileCounter-1];
+
+      int seqCond = sequenceCondition(prevFI, currentFI);
+
+      if (seqCond == STUCKING_TO_A_SINGLE_BLOB) {
+
+        endOfATrackSequence = fileCounter-1;
+
+        // save the index for printing the one object later on
+        startOfAOneObject = fileCounter;
+
+      } else if (seqCond == SEPARATING_FROM_SINGLE_BLOB) {
+
+        startOfATrackSequence = fileCounter;
+
+        // draw the single blob sequence
+        endOfAOneObject = fileCounter - 1;
+        *output << "Only one object StartIndex "<<startOfAOneObject<<" endIndex "<<endOfAOneObject<<" and seqSize "<<sequenceSize<<endl;
+        // use the two variables (startOfAOneObject, endOfAOneObject) pair to draw the single-blob objects.
+        // third parameter is used to indicate whether the current sequence is SINGLE_BLOB. So true is passed.
+        // fourth parameter is used to indicate whether the current sequence is processed(to separate it from the actual single blob state).
+        // since we are considering the sequence length >=  15 to be a single blob state, so pass false parameter.
+        drawTheSequence(startOfAOneObject, endOfAOneObject,0, true, false);
+        startOfAOneObject = -1;
+        endOfAOneObject = -1;
+        //startOfATrackSequence = 1;
+        sequenceSize = 1;
+      }
+
+
+      if(seqCond == STUCKING_TO_A_SINGLE_BLOB) {
+        *output << "StartIndex "<<startOfATrackSequence<<" endIndex "<<endOfATrackSequence<<" and seqSize "<<sequenceSize<<endl;	
+        // if a sequence size is greater than 15 then it is processed. endOfATrackSequence - startOfATrackSequence == 15 when the size of the sequence is 16.
+        // endOfATrackSequence - startOfATrackSequence > 15 when the size of the sequence is > 16.
+        if ((endOfATrackSequence - startOfATrackSequence) >=15 ) {
+          processASequence(startOfATrackSequence, endOfATrackSequence);
+          *output << "Done processing"<<endl;
+        } else {
+          // use the two variables (startOfATrackSequence, endOfATrackSequence) pair to draw the unprocessed frames.
+          // third parameter is used to indicate whether the current sequence is not actual SINGLE_BLOB. So false is passed.
+          // fourth parameter is used to indicate whether the current sequence is processed(to separate it from the actual single blob state).
+          // since we are considering the sequence length <  15 to be a single blob state, so pass false parameter.
+          *output << "Sequence is only "<<(endOfATrackSequence-startOfATrackSequence+1)<<" images long so assumed as a single blob"<<endl;
+          drawTheSequence(startOfATrackSequence, endOfATrackSequence, 0, false, true);
+
+          // increase the unprocessed frame counter
+          //totalUnprocessedFrame = totalUnprocessedFrame + (endOfATrackSequence - startOfATrackSequence + 1);
+          foutSt<<"-------------------------------"<<endl;
+          foutSt<<"Unprocessed size "<<(endOfATrackSequence-startOfATrackSequence+1)<<endl;
+          foutSt<<"Total unprocessed size "<<totalUnprocessedFrame<<endl;
+          foutSt<<"-------------------------------"<<endl;
+        }
+
+        initSequence();
+        //*output << "Start of a single blob "<<startOfAOneObject<<" and end of a single blob "<<endOfAOneObject<<endl;
+
+      }
+      //*output << "Done for "<<fnVector[fileCounter-1]<<endl;
+    }
+
+    // increase the frame Counter
+    fileCounter++;
+
+    // increase the sequence size
+    sequenceSize++;
+  }
+
+  //*output << "No more files "<<startOfAOneObject<<" "<<endOfAOneObject<<endl;
+  inputFile.close();
+
+  //open this after debug
+  /**/
+  if (startOfATrackSequence!=-1 && endOfATrackSequence == -1) {
+    if ((sequenceSize-1) > 15 ) {
+
+      *output << "Last sequence that does not stick to a single blob status startIndex "<<startOfATrackSequence<<" endIndex "<<(sequenceSize+startOfATrackSequence-2)<<endl;
+      processASequence(startOfATrackSequence, (sequenceSize+startOfATrackSequence-2));
+      *output << "Done processing"<<endl;
+
+    } else {
+      // this case was not handled earlier. It can happen that the flies are separated during the last sequences and less than 15 frames long.
+      *output << "Sequence is only "<<(sequenceSize-1)<<" images long so assumed as a single blob"<<endl;
+      drawTheSequence(startOfATrackSequence, (sequenceSize+startOfATrackSequence-2), 0, false, true);
+      foutSt<<"-------------------------------"<<endl;
+      foutSt<<"Unprocessed size "<<(sequenceSize-1)<<endl;
+      foutSt<<"Total unprocessed size "<<totalUnprocessedFrame<<endl;
+      foutSt<<"-------------------------------"<<endl;
+
+    }
+    initSequence();
+
+  } else if (startOfAOneObject != -1 && endOfAOneObject == -1) {
+    *output << "Last sequence that does not separate from one object state\n";
+    drawTheSequence(startOfAOneObject, (sequenceSize+startOfAOneObject - 2), 0, true, false);
+    endOfAOneObject = -1;
+    startOfAOneObject = -1;
+    sequenceSize = 1;
+  }
+
+
+  string cDDistFileName = finalOutputPath + outputFilePrefix + "_centroidDist.txt";
+  string hDAngleDistFileName = finalOutputPath + outputFilePrefix + "_headDist.txt";
+  string speedDistFileName = finalOutputPath + outputFilePrefix + "_speedDist.txt";
+
+	//TODO: rewrite to just generate the percentages
+	double centroidmean, centroidstd, headdirmean, headdirstd, speedmean, speedstd;
+	getMeanStdDev(centroidDistanceMap, &centroidmean, &centroidstd);
+	*output  << "centroid M :" <<  centroidmean << " S:" << centroidstd << endl;
+	getMeanStdDev(headDirAngleMap, &headdirmean, &headdirstd);
+	getMeanStdDev(speedMap, &speedmean, &speedstd);
+
+  double centroid = writeHist(cDDistFileName.c_str(), centroidDistanceMap);
+  double headDirAngle = writeHist(hDAngleDistFileName.c_str(), headDirAngleMap);
+  double speed  = writeHist(speedDistFileName.c_str(), speedMap);
+
+  // new calculation of percentage look at should consider only those frames where the flies are separated
+  double percentageLookingAt = static_cast<double>(totalMaleLookingAtFemale+totalFemaleLookingAtMale)/static_cast<double>(totalSeparated);
+  percentageLookingAt *= 100.0;
+
+  double percentageSingleBlob = static_cast<double>(totalSingleBlob)/static_cast<double>(fileCounter);
+  percentageSingleBlob *= 100.0;
+
+  foutSt<<"Total number of together "<<totalSingleBlob<<endl;
+  foutSt<<"Total number of male looking at "<<totalMaleLookingAtFemale<<endl;
+  foutSt<<"Total number of female looking at "<<totalFemaleLookingAtMale<<endl;
+  foutSt<<"Total number of looking at "<<(totalMaleLookingAtFemale+totalFemaleLookingAtMale)<<endl;
+  foutSt<<"Total number of unprocessed frame "<<totalUnprocessedFrame<<endl;
+  foutSt<<"Total number of frame where flies are separated (from the counter totalSeparated) "<<totalSeparated<<endl;
+  foutSt<<"Total number of frame where flies are separated "<<(fileCounter-totalUnprocessedFrame-totalSingleBlob)<<endl;
+  foutSt<<"Total number of frame "<<fileCounter<<endl;
+  foutSt<<"Percentage of frame in looking at mode "<<percentageLookingAt<<endl;
+  foutSt<<"Percentage of frame single blob "<<percentageSingleBlob<<endl;
+
+	foutSt<<"looking at\ttogether\tCentroid M\tCentroid Dev\tHeadDir M\tHeadDir Dev\tSpeed M\tSpeed Dev"<<endl;
+	foutSt<<percentageLookingAt << "\t";
+	foutSt<<percentageSingleBlob<< "\t";
+	foutSt<< centroidmean<<"\t";
+	foutSt<< centroidstd<<"\t";
+	foutSt<< headdirmean<<"\t";
+	foutSt<< headdirstd<<"\t";
+	foutSt<< speedmean <<"\t";
+	foutSt<< speedstd <<"\t" << endl;
+
+  foutSt.close();
+  foutDebugCen.close();
+  foutLPS.close();
+  foutDebugSpeed.close();
+
+  return 0;
+}
+
diff --git a/fly-tools/Makefile b/fly-tools/Makefile
index ab33ac1..b430235 100644
--- a/fly-tools/Makefile
+++ b/fly-tools/Makefile
@@ -1,7 +1,7 @@
 CPPC = g++
 CC = gcc
-CFLAGS= -O2 -Wall -s -Wextra -mtune=native
-CPPFLAGS= -O2 -Wall -s -Wextra -mtune=native
+CFLAGS= -O3 -Wall -s -Wextra -march=native
+CPPFLAGS= -O3 -Wall -s -Wextra -march=native
 MAGICKCPPFLAGS = $(shell pkg-config --cflags --libs ImageMagick++ gsl)
 MAGICKCFLAGS = $(shell pkg-config --cflags --libs MagickWand )
 CVBLOBCPPFLAGS = $(shell pkg-config --cflags --libs opencv cvblob )
-- 
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