diff options
| -rw-r--r-- | fly-tools/FlyTrackingMain.cpp | 739 | ||||
| -rw-r--r-- | fly-tools/Makefile | 4 |
2 files changed, 402 insertions, 341 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); @@ -1839,341 +1882,6 @@ 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; - } - - (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"; - - 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 @@ -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, ¢roidmean, ¢roidstd); + *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 ) |