Commit f51866f335cbc3c06695c3392fdc67a438cec67e

Authored by David Mayerich
0 parents

initial commit

CMakeLists.txt 0 โ†’ 100644
  1 +++ a/CMakeLists.txt
  1 +#Specify the version being used aswell as the language
  2 +cmake_minimum_required(VERSION 2.8.11)
  3 +
  4 +#Name your project here
  5 +project(pointmets)
  6 +
  7 +#set the module directory
  8 +set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}")
  9 +
  10 +#find the STIM library
  11 +find_package(STIM REQUIRED)
  12 +
  13 +#find the approximate nearest neighbor library
  14 +find_package(ANN REQUIRED)
  15 +
  16 +#find the pthreads package
  17 +find_package(Threads)
  18 +
  19 +include_directories(
  20 + ${STIM_INCLUDE_DIRS}
  21 + ${ANN_INCLUDE_DIR}
  22 + )
  23 +
  24 +#Assign source files to the appropriate variables
  25 +file(GLOB SRC_CPP "*.cpp")
  26 +file(GLOB SRC_H "*.h")
  27 +
  28 +#create an executable file
  29 +add_executable(pointmets
  30 + ${SRC_H}
  31 + ${SRC_CPP}
  32 + )
  33 +
  34 +#set the link libraries
  35 +target_link_libraries(pointmets
  36 + ${CMAKE_THREAD_LIBS_INIT}
  37 + ${ANN_LIBRARY}
  38 + )
  39 +
  40 +#copy an OBJ test case
  41 +configure_file(data/blue_gt.txt blue_gt.txt COPYONLY)
  42 +configure_file(data/blue_t.txt blue_t.txt COPYONLY)
  43 +configure_file(data/blue_gt.bmp blue_gt.bmp COPYONLY)
0 44 \ No newline at end of file
... ...
FindANN.cmake 0 โ†’ 100644
  1 +++ a/FindANN.cmake
  1 +# - Try to find ANN
  2 +# Once done this will define
  3 +#
  4 +# ANN_FOUND - system has ANN
  5 +# ANN_INCLUDE_DIR - the ANN include directory
  6 +# ANN_LIBRARY - Link these to use ANN
  7 +#
  8 +
  9 +IF (ANN_INCLUDE_DIRS)
  10 + # Already in cache, be silent
  11 + SET(ANN_FIND_QUIETLY TRUE)
  12 +ENDIF (ANN_INCLUDE_DIRS)
  13 +
  14 +FIND_PATH( ANN_INCLUDE_DIR ANN/ANN.h
  15 + PATHS "/usr/include" "C:/libs/ANN/include")
  16 +
  17 +if( WIN32 )
  18 +
  19 + set(ANN_LIBRARY $ENV{ANN_PATH}\\ANN.lib)
  20 + set(ANN_INCLUDE_DIR $ENV{ANN_PATH})
  21 +
  22 +
  23 + # Store the library dir. May be used for linking to dll!
  24 + # GET_FILENAME_COMPONENT( ANN_LIBRARY_DIR ${ANN_LIBRARY} PATH )
  25 +
  26 + find_package_handle_standard_args(ANN DEFAULT_MSG ANN_INCLUDE_DIR)
  27 +
  28 +else (WIN32)
  29 +
  30 + FIND_LIBRARY( ANN_LIBRARY
  31 + NAMES ann ANN
  32 + PATHS /lib /usr/lib /usr/lib64 /usr/local/lib )
  33 +
  34 +endif( WIN32)
  35 +
  36 +
  37 +IF (ANN_INCLUDE_DIR AND ANN_LIBRARY)
  38 + SET(ANN_FOUND TRUE)
  39 +ELSE (ANN_INCLUDE_DIR AND ANN_LIBRARY)
  40 + SET( ANN_FOUND FALSE )
  41 +ENDIF (ANN_INCLUDE_DIR AND ANN_LIBRARY)
  42 +
... ...
FindSTIM.cmake 0 โ†’ 100644
  1 +++ a/FindSTIM.cmake
  1 +include(FindPackageHandleStandardArgs)
  2 +
  3 +set(STIM_INCLUDE_DIR $ENV{STIMLIB_PATH})
  4 +
  5 +find_package_handle_standard_args(STIM DEFAULT_MSG STIM_INCLUDE_DIR)
  6 +
  7 +if(STIM_FOUND)
  8 + set(STIM_INCLUDE_DIRS ${STIM_INCLUDE_DIR})
  9 +endif()
0 10 \ No newline at end of file
... ...
data/blue_gt.bmp 0 โ†’ 100644
No preview for this file type
data/blue_gt.txt 0 โ†’ 100644
  1 +++ a/data/blue_gt.txt
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0 211 \ No newline at end of file
... ...
data/blue_t.txt 0 โ†’ 100644
  1 +++ a/data/blue_t.txt
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... ...
main.cpp 0 โ†’ 100644
  1 +++ a/main.cpp
  1 +#include <iostream>
  2 +#include <fstream>
  3 +#include <vector>
  4 +#include <string>
  5 +#include <fstream>
  6 +#include <stim/math/vector.h>
  7 +#include <stim/parser/arguments.h>
  8 +#include <stim/parser/filename.h>
  9 +#include <stim/image/image.h>
  10 +#include <ANN/ANN.h>
  11 +
  12 +//load a set of points from an ASCII file
  13 +std::vector< stim::vec<float> > points_from_list(std::string filename){
  14 +
  15 + std::vector< stim::vec<float> > result; //create an array to store the result
  16 +
  17 + std::string str;
  18 +
  19 + //load the ground truth
  20 + std::ifstream gfile(filename.c_str());
  21 + while(std::getline(gfile, str)){
  22 + stim::vec<float> v(str);
  23 + result.push_back(v);
  24 + }
  25 +
  26 + return result; //return the list of points
  27 +}
  28 +
  29 +//load a set of points from an image (nonzero values are point positions)
  30 +std::vector< stim::vec<float> > points_from_image(std::string filename){
  31 +
  32 + stim::image<unsigned char> I; //create an image object
  33 +
  34 + I.load(filename); //load the image file
  35 +
  36 + std::vector<unsigned long> idx = I.sparse_idx(); //get the 1D indices for each nonzero pixel
  37 +
  38 + std::vector< stim::vec<float> > result; //generate an array to store the 2D pixel positions
  39 + result.resize(idx.size()); //allocate the space to save time
  40 +
  41 + unsigned long w = I.width(); //get the image width (used to resolve the 2D pixel position from the 1D index)
  42 +
  43 + unsigned long x, y;
  44 + for(unsigned long i = 0; i < idx.size(); i++){
  45 + y = idx[i] / w;
  46 + x = idx[i] - y * w;
  47 +
  48 + result[i] = stim::vec<float>(x, y);
  49 + }
  50 +
  51 +
  52 + return result; //return the array of points
  53 +
  54 +}
  55 +
  56 +/// This function calculates the number of hits (
  57 +void calc_hitlist(std::vector< unsigned int >& hits,
  58 + std::vector< float >& dists,
  59 + std::vector< stim::vec<float> > data,
  60 + std::vector< stim::vec<float> > query){
  61 +
  62 + int n_data = data.size();
  63 + int n_query = query.size();
  64 +
  65 + //allocate space in the hit lists
  66 + hits.resize(n_query);
  67 + dists.resize(n_query);
  68 +
  69 + //calculate the spatial dimension
  70 + unsigned int dim = 1;
  71 + for(unsigned int i = 0; i < data.size(); i++)
  72 + if(data[i].size() > dim) dim = data[i].size();
  73 +
  74 + //number of data points
  75 + ANNpointArray dataPts = annAllocPts(n_data, dim); //array of data points
  76 + ANNpoint queryPt = annAllocPt(dim); //query point
  77 + ANNidxArray nnIdx = new ANNidx[1]; //indices of nearest neighbors
  78 + ANNdistArray sq_dist = new ANNdist[1]; //array of squared distances to nearest neighbors
  79 +
  80 + //load the ground truth points into the ANN point array
  81 + for(unsigned int i = 0; i < data.size(); i++){
  82 + for(unsigned int d = 0; d < dim; d++){
  83 + dataPts[i][d] = data[i][d];
  84 + }
  85 + }
  86 +
  87 + //create a KD-tree
  88 + ANNkd_tree* kdTree; //KD tree search structure
  89 + kdTree = new ANNkd_tree(dataPts, n_data, dim); //create the KD tree search structure
  90 +
  91 +
  92 + //submit each query point to the KD tree to find the nearest neighbor
  93 + for(unsigned int q = 0; q < n_query; q++){
  94 +
  95 + for(unsigned int d = 0; d < dim; d++){
  96 + queryPt[d] = query[q][d];
  97 + }
  98 +
  99 + //query the KD-tree
  100 + kdTree->annkSearch(queryPt, 1, nnIdx, sq_dist);
  101 +
  102 + //put the result in the hit array
  103 + hits[q] = nnIdx[0];
  104 + dists[q] = sqrt(sq_dist[0]);
  105 + }
  106 +}
  107 +
  108 +int main(int argc, char** argv){
  109 +
  110 + //output advertisement
  111 + std::cout<<std::endl<<std::endl;
  112 + std::cout<<"========================================================================="<<std::endl;
  113 + std::cout<<"Thank you for using the PointMets validation tool!"<<std::endl;
  114 + std::cout<<"Scalable Tissue Imaging and Modeling (STIM) Lab, University of Houston"<<std::endl;
  115 + std::cout<<"Developers: David Mayerich"<<std::endl;
  116 + std::cout<<"Source: https://github.com/stimlab/hsiproc.git"<<std::endl;
  117 + std::cout<<"========================================================================="<<std::endl<<std::endl;
  118 +
  119 +
  120 + stim::arglist args;
  121 +
  122 +#ifdef _WIN32
  123 + args.set_ansi(false);
  124 +#endif
  125 +
  126 + //add arguments
  127 + args.add("help", "prints this help");
  128 + args.add("r", "maximum possible distance to consider a point 'detected'", "10", "[positive value]");
  129 +
  130 + //parse the command line arguments
  131 + args.parse(argc, argv);
  132 +
  133 + //display the help text if requested
  134 + if(args["help"].is_set()){
  135 + std::cout<<std::endl<<"usage: pointmets ground_truth test_case --option [A B C ...]"<<std::endl;
  136 + std::cout<<std::endl<<std::endl
  137 + << "examples: pointmets blue_gt.txt blue_t.txt"<<std::endl;
  138 + std::cout << " pointmets blue_gt.bmp blue_t.bmp" << std::endl;
  139 + std::cout<<std::endl<<std::endl;
  140 + std::cout<<args.str()<<std::endl;
  141 + exit(1);
  142 + }
  143 +
  144 + //if the input and output files aren't specified, throw an error and exit
  145 + if(args.nargs() < 2){
  146 + std::cout<<"ERROR: Two files must be specified for comparison, enter pointmets --help for options."<<std::endl<<std::endl;
  147 + exit(1);
  148 + }
  149 +
  150 + //get the ground truth and test file
  151 + stim::filename gfilename(args.arg(0));
  152 + stim::filename tfilename(args.arg(1));
  153 +
  154 + //set the radius
  155 + float r = args["r"].as_float();
  156 +
  157 + std::vector< stim::vec<float> > G;
  158 + std::vector< stim::vec<float> > T;
  159 +
  160 +
  161 + //if an ASCII list of points is specified
  162 + if(gfilename.get_extension() == "bmp")
  163 + G = points_from_image(gfilename.str());
  164 + else
  165 + G = points_from_list(gfilename.str());
  166 +
  167 + if(tfilename.get_extension() == "bmp")
  168 + T = points_from_image(gfilename.str());
  169 + else
  170 + T = points_from_list(tfilename.str());
  171 +
  172 + //calculate the hit list and distances for the test array
  173 + std::vector< unsigned int > T_hits;
  174 + std::vector< float > T_dists;
  175 + calc_hitlist(T_hits, T_dists, G, T);
  176 +
  177 + //calculate the hit list and distances for the ground truth array
  178 + std::vector< unsigned int > G_hits;
  179 + std::vector< float > G_dists;
  180 + calc_hitlist(G_hits, G_dists, T, G);
  181 +
  182 + //count up metrics for each test point
  183 + std::vector< unsigned int > TP;
  184 + std::vector< unsigned int > FP;
  185 + unsigned int g, t;
  186 + for(t = 0; t < T.size(); t++){
  187 +
  188 + //a true positive has a matching hit in both hit lists, with a distance less than the radius
  189 + g = T_hits[t];
  190 + if(G_hits[g] == t && T_dists[t] <= r) TP.push_back(t);
  191 + else FP.push_back(t);
  192 + }
  193 +
  194 + std::vector< unsigned int > FN;
  195 + for(g = 0; g < G.size(); g++){
  196 + t = G_hits[g];
  197 + if(T_hits[t] != g || G_dists[g] > r) FN.push_back(g);
  198 + }
  199 +
  200 + std::cout<<"N: "<<G.size()<<std::endl;
  201 + std::cout<<"TP: "<<TP.size()<<" ( "<<(double)TP.size() / (double)G.size() * 100<<"% detected)"<<std::endl;
  202 + std::cout<<"FN: "<<FN.size()<<" ( "<<(double)FN.size() / (double)G.size() * 100<<"% undetected)"<<std::endl;
  203 + std::cout<<"FP: "<<FP.size()<<" ( "<<(double)FP.size() / (double)T.size() * 100<<"% incorrectly detected)"<<std::endl;
  204 +
  205 +
  206 +
  207 +}
... ...