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Diffstat (limited to 'fly-tools/FlyTrackingFilter.cpp')
| -rw-r--r-- | fly-tools/FlyTrackingFilter.cpp | 666 |
1 files changed, 0 insertions, 666 deletions
diff --git a/fly-tools/FlyTrackingFilter.cpp b/fly-tools/FlyTrackingFilter.cpp deleted file mode 100644 index 9020522..0000000 --- a/fly-tools/FlyTrackingFilter.cpp +++ /dev/null @@ -1,666 +0,0 @@ -#include <iostream> -#include <string> -#include <sstream> -#include <cmath> -#include <vector> -#include <list> -#include <fstream> -#include <cassert> -#include <cstdlib> - -#include <ImageMagick/Magick++.h> - -#include <gsl/gsl_matrix.h> -#include <gsl/gsl_vector.h> -#include <gsl/gsl_blas.h> -#include <gsl/gsl_eigen.h> - -#include "FrameInfo.h" - -using namespace Magick; -using namespace std; -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); -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); -int roundT(double v) {return int(v+0.5);} - - -const double PI = atan(1.0)*4.0; -const double FACTOR_EIGEN = 100; - -Image* residual; - -ostream &operator<<(ostream &out, FlyObject & fO) { - fO.output(out); - return out; -} - -ostream &operator<<(ostream &out, FrameInfo & fI) { - fI.output(out); - return out; -} - -vector<vector<pair<int, int> > > shapeVectors; -vector<pair<int,int> > shape; -vector<pair<int, int> > sizeNIndexVector; - -void bubbleSort() { - - for(int i=1; i<sizeNIndexVector.size(); i++) { - for(int j=0; j<sizeNIndexVector.size()-i; j++) { - pair<int, int> a = sizeNIndexVector[j]; - pair<int, int> b = sizeNIndexVector[j+1]; - - if (a.first < b.first) { - pair<int, int> c = sizeNIndexVector[j]; - sizeNIndexVector[j] = sizeNIndexVector[j+1]; - sizeNIndexVector[j+1] = c; - } - } - } - -} - -void fillResidualWithObj(vector<pair<int, int> > & obj, ColorRGB c) -{ - for (unsigned int i = 0; i<obj.size(); i++) - residual->pixelColor(obj[i].first, obj[i].second, c); -} - -void writeHist(const char* filename, map<unsigned int, unsigned int> & len) -{ - map<unsigned int,unsigned int>::iterator front = len.begin(), - back = len.end(); - back--; - - - unsigned int first = front->first, last = back->first; - /*if (cutoff != -1 && cutoff < int(last)) - last = cutoff; - */ - cout << "Min: " << first << endl - << "Max: " << last << endl - << "Count: " << last-first << endl; - //vector<unsigned int> hist(last-first, 0); - vector<unsigned int> hist(last+1, 0); - - cout << "hist size: " << hist.size() << endl; - try{ - for(unsigned int j = 0; j<first; j++) { - hist[j] = 0; - } - for (unsigned int j = first; j<=last; j++) - { - /*if ( roundT(j-first) >= int(hist.size()) ) - hist.resize(j-first,0); - hist[roundT(j-first)] = len[j]; - */ - - /*if ( roundT(j) >= int(hist.size()) ) - hist.resize(j,0); - hist[roundT(j)] = len[j]; - */ - hist[j] = len[j]; - } - } - catch (...) - { cerr << "Bad histogram bucketing" << endl; } - - /*if ( (cutoff >= 0) && (cutoff<int(hist.size())) ) - hist.resize(cutoff); - */ - len.clear(); - try - { - ofstream fout(filename); - for (unsigned int i = 0; i<hist.size(); i++) { - fout << hist[i] << endl; - } - fout << first << " " << last << " " << hist.size() << endl; - fout.close(); - } - catch (...) - { cerr << "Bad memory loc for opening file" << endl; } -} - -int main(int argc, char* argv[]) -{ - if (argc < 5) - { - cerr << "Usage: executablename <inputFile.txt> <ratio_largest_to_second_largest> <InputLocationOfMaskImage> <outputFolderName>" << endl; // input file contains name of the - // input image files - return -1; - } - - MagickCore::SetMagickResourceLimit(MagickCore::MemoryResource, 1536); - MagickCore::SetMagickResourceLimit(MagickCore::MapResource, 2048); - - string fileName; - ifstream inputFile(argv[1]); - if (inputFile.fail() ) { - cout << "cannot open the input file that contains name of the input images\n"; - exit(1); - } - - // get the output file name along with the location from argv[4] - string outputFileLocation(argv[4]); - string outputFileName = outputFileLocation + "final/outputFile.txt"; - ofstream outputFile(outputFileName.c_str()); - - // get the location of the input mask file - string inputMaskFileLocation(argv[3]); - - int frameCounter = 0; - // use 15, 20 or 10 - // 15 found to be working correct - double ratioSecondLargestToLargest = atof(argv[2]); - - cout << "Ratio is 1/"<<ratioSecondLargestToLargest<< " = "<<(1/ratioSecondLargestToLargest)<<endl; - - outputFile<<"Ratio given 1/"<<ratioSecondLargestToLargest<<" = "<<(1/ratioSecondLargestToLargest)<<endl; - - ratioSecondLargestToLargest = 1/ratioSecondLargestToLargest; - // to find the largest object avg size - - long totalSize = 0; - - char buffer[100]; - - while (inputFile>>fileName) { - - string savedFileName = fileName; - - // get the input mask file -// fileName = "input/"+fileName; - fileName = inputMaskFileLocation + fileName; - - Image* img = new Image(fileName.c_str()); - int width = img->columns(),height = img->rows(); - Image* imgForFilter; - sprintf(buffer,"%ix%i",width,height); - - // residual image is initialized with black representing not visited. - residual = new Image(buffer, "black"); - - imgForFilter = new Image(buffer, "white"); - cout << "Reading "<<savedFileName<<endl; - cout << "Filter wxh "<<width<<","<<height<<endl; - shape.clear(); - // find the black background from location (0,0) - findObj(img, 0, 0, shape, false, false); - int s = shape.size(); - if (s > 0) - cout << "black object size is "<<s; - for (int i=0; i<s; i++) { - imgForFilter->pixelColor(shape[i].first, shape[i].second, "black"); - } - - // store the intermediate file in temp folder under the output location -// string oFilteredFileName = "output/filtered/temp/"+outputFile; - string oFilteredFileName = outputFileLocation +"temp/"+savedFileName; - - cout << "Saving the filtered image "<< oFilteredFileName<<endl; - imgForFilter->write(oFilteredFileName.c_str()); - - delete residual; - /* - residual = new Image(buffer, "black"); - - shapeVectors.clear(); - sizeNIndexVector.clear(); - - // find the two largest object - int objectCounter = 0; - for (int x=0; x<width; x++) { - for (int y=0; y<height; y++) { - //find the white object now using eight connected neighbours - shape.clear(); - findObj(imgForFilter, x, y, shape, true, true); - int s = shape.size(); - if (s>0) { - shapeVectors.push_back(shape); - cout << "new object pushed back at position "<<x<<","<<y<<" of size "<<s<<endl; - pair<int, int> si(s, objectCounter); - sizeNIndexVector.push_back(si); - objectCounter++; - } - - } - } - - // sort the sizes and take the largest to find average largest - cout<<"shapeVectors size = "<<shapeVectors.size()<<endl; - - bubbleSort(); - - cout <<"Largest object size is "<<sizeNIndexVector[0].first<<endl; - - // add the largest size to sum - totalSize += static_cast<long>(sizeNIndexVector[0].first); - - cout << "Current total size is "<<totalSize<<" for object "<<(frameCounter+1)<<endl; - - cout << "-----------------------------------------------------------"<<endl; - */ - - frameCounter++; - - delete imgForFilter; - -// delete residual; - - delete img; - - - } - - inputFile.close(); - - /* - avgLargestSize = static_cast<long> (totalSize/frameCounter); - cout << "Average largest size is "<<avgLargestSize<<endl; - */ - - // previous loop calculates the average largest size - - inputFile.open(argv[1]); - - if (inputFile.fail() == true) { - cout << "Cannot open the input file again"<<endl; - exit(1); - } - - - while (inputFile>>fileName) { - - //string inputFileName = "output/filtered/temp/"+fileName; - string inputFileName = outputFileLocation + "temp/"+fileName; - - Image* img = new Image(inputFileName.c_str()); - int width = img->columns(); - int height = img->rows(); - - outputFile<<"File name is "<<inputFileName<<endl; - outputFile<<"----------------------------------------------\n"; - - sprintf(buffer,"%ix%i",width,height); - - // residual image is initialized with black representing not visited. - residual = new Image(buffer, "black"); - - cout << "Reading "<<inputFileName<<endl; - cout << "Filter wxh "<<width<<","<<height<<endl; - - shapeVectors.clear(); - sizeNIndexVector.clear(); - - // find the objects and sort according to size - int objectCounter = 0; - for (int x=0; x<width; x++) { - for (int y=0; y<height; y++) { - // find the white object using eight connected - shape.clear(); - findObj(img, x, y, shape, true, true); - int s = shape.size(); - - if (s > 0) { - - shapeVectors.push_back(shape); - cout << "New object found at position ("<<x<<","<<y<<") of size "<<s<<endl; - pair<int, int> si(s, objectCounter); - sizeNIndexVector.push_back(si); - objectCounter++; - - } - - } - } - - cout << "Total object found "<<sizeNIndexVector.size()<<endl; - - outputFile<<"Total objects found "<<sizeNIndexVector.size()<<endl; - - bubbleSort(); - - // take the largest object - double currentLargestSize = static_cast<double>(sizeNIndexVector[0].first); - - double secondLargest = 0; - double ratio = 0; - if (sizeNIndexVector.size() > 1) { - - secondLargest = static_cast<double>(sizeNIndexVector[1].first); - ratio = secondLargest/currentLargestSize; - cout << "Ratio is "<<secondLargest<<"/"<<currentLargestSize<<" = "<<ratio<<endl; - outputFile<<"secondLargest = "<<secondLargest<<"\ncurrentLargest = "<<currentLargestSize<<"\nRatio = "<<ratio<<endl; - - } - - // find the largest to second largest ratio if it is less than the defined ratio then - // the objects are single object - - int numberOfObjects = 0; - - if (sizeNIndexVector.size() == 1) { - cout << "Frame contains one object\n"; - outputFile << "Frame contains one object\n"; - numberOfObjects = 1; - } - else if (ratio <= ratioSecondLargestToLargest ) { - cout << "Single object calculated in the frame because current ratio = "<<ratio<<" is less than defined ratio = "<<ratioSecondLargestToLargest<<endl; - outputFile<< "Single object calculated in the frame because current ratio = "<<ratio<<" is less than defined ratio = "<<ratioSecondLargestToLargest<<endl; - numberOfObjects = 1; - } else { - cout << "Two objects in the frame\n"; - outputFile<<"Two objects in the frame\n"; - numberOfObjects = 2; - } - - cout << "Total object found "<<numberOfObjects<<endl; - outputFile << "Total object found "<<numberOfObjects<<endl; - - Image* imgFinal = new Image(buffer, "black"); - - for (int n=0; n<numberOfObjects; n++) { - - int totalPoints = sizeNIndexVector[n].first; - - for (int i=0; i<totalPoints; i++) { - - imgFinal->pixelColor(shapeVectors[ sizeNIndexVector[n].second ][i].first, shapeVectors[ sizeNIndexVector[n].second ][i].second, "white"); - } - - - } - - //string finalImageName = "output/filtered/final/"+fileName; - - string finalImageName = outputFileLocation + "final/"+fileName; - - imgFinal->write( finalImageName.c_str() ); - - - - - // writing the single in red - if (numberOfObjects == 1) { - - Image* singleObjectFinal = new Image(buffer, "black"); - - int totalPoints = sizeNIndexVector[0].first; - - cout << "Output the single object of size = "<<totalPoints<<endl; - - for (int i=0; i<totalPoints; i++) { - - singleObjectFinal->pixelColor(shapeVectors[ sizeNIndexVector[0].second ][i].first, shapeVectors[ sizeNIndexVector[0].second ][i].second, "red"); - } - - //string singleImageName = "output/filtered/single/"+fileName; - string singleImageName = outputFileLocation + "single/"+fileName; - - singleObjectFinal->write(singleImageName.c_str()); - - delete singleObjectFinal; - - } - - outputFile<<"----------------------------------------------------\n"; - - - delete img; - - delete residual; - - delete imgFinal; - - - } - - inputFile.close(); - outputFile.close(); - - return 0; -} - - -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 { - fourConnObj(img, x, y, shape, colorLookingFor); - } -} - -int barrier = 1000; -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 - if ( (x >= (width)) || (x < 0) || (y >= (height) ) || (y < 0) ) - return; - - // residualpixel.mono() == true implies it is visited. Otherwise not visited. - ColorMono residualpixel = ColorMono(residual->pixelColor(x,y)); - // originalpixel.mono() == true implies it is an object pixel. Otherwise it is blank region pixel. - ColorMono originalpixel = ColorMono(img->pixelColor(x,y)); - - // If the current pixel is already visited then return - if (residualpixel.mono() == true) - return; - - // Else if current pixel is not visited and it is black, which means it is not an object pixel; so return - else if (residualpixel.mono() == false && originalpixel.mono() != color) - return; - // If current pixel is not visited and its value is white, which means a new object is found. - else if (residualpixel.mono() == false && originalpixel.mono() == color) { - // Save the coordinates of the current pixel into the vector and make the pixel visited in the residual image - pair<int,int> p; - p.first = x; - p.second = y; - obj.push_back(p); - -// if (obj.size() > barrier) { -// cout<<obj.size()<<endl; -// barrier = barrier + 1000; -// } - // setting the residual image at pixel(x,y) to white. - residual->pixelColor(x,y, ColorMono(true)); - - // Recursively call all of it's eight neighbours. - fourConnObj(img, x+1, y, obj, color); - fourConnObj(img, x, y-1, obj, color); - - fourConnObj(img, x-1, y, obj, color); - fourConnObj(img, x, y+1, obj, 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 - if ( (x >= (width)) || (x < 0) || (y >= (height) ) || (y < 0) ) - return; - - // residualpixel.mono() == true implies it is visited. Otherwise not visited. - ColorMono residualpixel = ColorMono(residual->pixelColor(x,y)); - // originalpixel.mono() == true implies it is an object pixel. Otherwise it is blank region pixel. - ColorMono originalpixel = ColorMono(img->pixelColor(x,y)); - - // If the current pixel is already visited then return - if (residualpixel.mono() == true) - return; - - // Else if current pixel is not visited and it is black, which means it is not an object pixel; so return - else if (residualpixel.mono() == false && originalpixel.mono() != color) - return; - // If current pixel is not visited and its value is white, which means a new object is found. - else if (residualpixel.mono() == false && originalpixel.mono() == color) { - // Save the coordinates of the current pixel into the vector and make the pixel visited in the residual image - pair<int,int> p; - p.first = x; - p.second = y; - obj.push_back(p); - -// if (obj.size() > barrier) { -// //cout<<obj.size()<<endl; -// barrier = barrier + 1000; -// } - // setting the residual image at pixel(x,y) to white. - residual->pixelColor(x,y, ColorMono(true)); - - // Recursively call all of it's eight neighbours. - eightConnObj(img, x+1, y, obj, color); - eightConnObj(img, x+1, y-1, obj, color); - eightConnObj(img, x, y-1, obj, color); - eightConnObj(img, x-1, y-1, obj, color); - - eightConnObj(img, x-1, y, obj, color); - eightConnObj(img, x-1, y+1, obj, color); - eightConnObj(img, x, y+1, obj, color); - eightConnObj(img, x+1, y+1, obj, color); - - } - -} - -// Aspect Ratio -pair<int,int> getCentroid(vector<pair<int,int> > & points) -{ - pair<int,int> centroid; - centroid.first = 0; - centroid.second = 0; - - for (unsigned int i = 0; i<points.size(); i++) - { - centroid.first += points[i].first; - centroid.second += points[i].second; - } - - centroid.first = roundT(double(centroid.first)/points.size()); - centroid.second = roundT(double(centroid.second)/points.size()); - - return centroid; -} - - -vector<double> covariantDecomposition(vector<pair<int,int> > & points) -{ - unsigned int i,j,k; - pair<int,int> centroid = getCentroid(points); - vector<double> retval; - - gsl_matrix* matrice = gsl_matrix_alloc(2, 2); - - double sumX2 = 0, sumXY = 0, sumY2 = 0; - for (k = 0; k<points.size(); k++) - { - sumX2 += pow(double(points[k].first - centroid.first),2.0); - sumY2 += pow(double(points[k].second - centroid.second),2.0); - // should we take the absolute value of X*Y - sumXY += (points[k].first - centroid.first) * (points[k].second - centroid.second); - } - gsl_matrix_set(matrice, 0, 0, roundT(sumX2/points.size())); - gsl_matrix_set(matrice, 0, 1, roundT(sumXY/points.size())); - gsl_matrix_set(matrice, 1, 0, roundT(sumXY/points.size())); - gsl_matrix_set(matrice, 1, 1, roundT(sumY2/points.size())); - - // outputMatrix("Covariant", matrice); - - // This function allocates a workspace for computing eigenvalues of n-by-n - // real symmetric matrices. The size of the workspace is O(2n). - gsl_eigen_symmv_workspace* eigenSpace = gsl_eigen_symmv_alloc(2); - gsl_vector* eigenVal = gsl_vector_alloc(2); - gsl_matrix* eigenVec = gsl_matrix_alloc(2, 2); - // This function computes the eigenvalues and eigenvectors of the real - // symmetric matrix A. Additional workspace of the appropriate size must be - // provided in w. The diagonal and lower triangular part of A are destroyed - // during the computation, but the strict upper triangular part is not - // referenced. The eigenvalues are stored in the vector eval and are unordered. - // The corresponding eigenvectors are stored in the columns of the matrix evec. - // For example, the eigenvector in the first column corresponds to the first - // eigenvalue. The eigenvectors are guaranteed to be mutually orthogonal and - // normalised to unit magnitude. - gsl_eigen_symmv (matrice, eigenVal, eigenVec, eigenSpace); - gsl_eigen_symmv_free (eigenSpace); - - gsl_eigen_symmv_sort(eigenVal, eigenVec, GSL_EIGEN_SORT_VAL_ASC); - - for (i = 0; i<eigenVal->size; i++) - retval.push_back(gsl_vector_get(eigenVal, i)); - - for (j = 0; j<eigenVec->size2; j++) - for (i = 0; i<eigenVec->size1; i++) - retval.push_back(gsl_matrix_get(eigenVec, i, j)); - - retval.push_back(static_cast<double>(centroid.first)); - retval.push_back(static_cast<double> (centroid.second)); - -// for (i=0; i<2; i++) { -// gsl_vector_view evec_i = gsl_matrix_column (eigenVec, i); -// //printf ("eigenvalue = %g\n", eval_i); -// cout<<"eigenvector = \n"; -// gsl_vector_fprintf (stdout, &evec_i.vector, "%g"); -// } - - gsl_vector_free(eigenVal); - gsl_matrix_free(matrice); - gsl_matrix_free(eigenVec); - - return retval; -} - -// isInterface for binary image -bool isInterface(Image* orig, unsigned int x, unsigned int y) -{ - // Get the current pixel's color - ColorMono currentpixel = (ColorMono)orig->pixelColor(x,y); - // If the current pixel is black pixel then it is not boundary pixel - // error check - if (currentpixel.mono() == false) - return false; - - // If the current pixel is not black then it is white. So, now we need - // to check whether any four of its neighbor pixels (left, top, right, - // bottom ) is black. If any of this neighbor is black then current - // pixel is a neighbor pixel. Otherwise current pixel is not neighbor - // pixel. - - ColorMono leftneighborpixel = (ColorMono)orig->pixelColor(x-1,y); - ColorMono topneighborpixel = (ColorMono)orig->pixelColor(x,y-1); - ColorMono rightneighborpixel = (ColorMono)orig->pixelColor(x+1,y); - ColorMono bottomneighborpixel = (ColorMono)orig->pixelColor(x,y+1); - - // If leftneighborpixel is black and currentpixel is white then it is - // boundary pixel - if ( leftneighborpixel.mono() != currentpixel.mono()) - return true; - // If topneighborpixel is black and currentpixel is white then it is - // boundary pixel - else if (topneighborpixel.mono() != currentpixel.mono()) - return true; - // If rightneighborpixel is black and currentpixel is white then it - // is boundary pixel - else if (rightneighborpixel.mono() != currentpixel.mono()) - return true; - // If bottomneighborpixel is black and currentpixel is white then it - // is boundary pixel - else if (bottomneighborpixel.mono() != currentpixel.mono()) - return true; - // Else all of its neighbor pixels are white so it can not be a - // boundary pixel - else - return false; - -}
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