0d840342
 David Mayerich
public release co...
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#include <iostream>
#include <fstream>
#include <thread>
#include <random>
#include <vector>
//#include <algorithm>
#define NOMINMAX
//stim libraries
#include <stim/envi/envi.h>
#include <stim/image/image.h>
#include <stim/parser/arguments.h>
#include <stim/ui/progressbar.h>
#include <stim/parser/filename.h>
//#include <stim/visualization/colormap.h>
#include <stim/parser/table.h>
std::vector< stim::image<unsigned char> > C; //2D array used to access each mask C[m][p], where m = mask# and p = pixel#
//loads spectral features into a feature matrix based on a set of class images (or masks)
float* load_features(size_t nC, size_t tP, size_t B, stim::envi E, std::vector< unsigned int > nP){
float progress = 0; //initialize the progress bar variable
unsigned long long bytes_fmat = sizeof(float) * tP * B; //calculate the number of bytes in the feature matrix
std::cout<<"totalnumber of samples "<<tP<<std::endl;
std::cout<<"Allocating space for the feature matrix: "<<tP<<" x "<<B<<" = "<<(float)bytes_fmat/(float)1048576<<"MB"<<std::endl;
float* F = (float*) malloc(bytes_fmat); //allocate space for the sifted matrix
std::cout<<"Loading Training Data ("<<nC<<" classes)"<<std::endl;
//load all of the training spectra into an array
unsigned long long F_idx = 0; //initialize the matrix index to 0
//unsigned long long R_idx = 0;
for(unsigned c = 0; c < nC; c++){ //for each class image
std::cout<<"\tSifting class "<<c+1<<" = "<<nP[c]<<" pixels..."<<std::endl;
// std::thread t1 = std::thread(progress_thread_envi, &E); //start the progress bar thread
E.sift((void*)&F[F_idx], C[c].data(), true); //sift that class into the matrix at the proper location
F_idx += nP[c] * B;
progress = (float)(c+1) / (float)nC * 100;
// t1.join();
}
return F;
}
/// Load responses for a Random Forest Classifier
unsigned int* ga_load_responses(size_t tP, size_t nC, std::vector< unsigned int > nP){
unsigned int* T = (unsigned int*)malloc(tP*sizeof(unsigned int)); //generate an OpenCV vector of responses
size_t R_idx = 0; //index into the response array
for(size_t c = 0; c < nC; c++){ //for each class image
for(unsigned long long l = 0; l < nP[c]; l++){ //assign a response for all pixels of class c loaded in the training matrix
T[R_idx + l] = (unsigned int)c+1;
}
R_idx += nP[c]; //increment the response vector index
}
return T;
}
//loads the necessary data for training a random forest classifier
std::vector< unsigned int > ga_load_class_images(int argc, stim::arglist args, size_t* nC, size_t* tP){
if(args["classes"].nargs() < 2){ //if fewer than two classes are specified, there's a problem
std::cout<<"ERROR: training requires at least two class masks"<<std::endl;
exit(1);
}
std::vector< unsigned int > nP;
size_t num_images = args["classes"].nargs(); //count the number of class images
//size_t num_images = args["rf"].nargs(); //count the number of class images
//std::vector<std::string> filenames(num_images); //initialize an array of file names to store the names of the images
std::string filename; //allocate space to store the filename for an image
for(size_t c = 0; c < num_images; c++){ //for each image
filename = args["classes"].as_string(c);; //get the class image file name
stim::image<unsigned char> image(filename); //load the image
//push_training_image(image.channel(0), nC, tP, nP); //push channel zero (all class images are assumed to be single channel)
C.push_back(image.channel(0));
unsigned int npixels = (unsigned int)image.channel(0).nnz();
nP.push_back(npixels); //push the number of pixels onto the pixel array
*tP += npixels; //add to the running total of pixels
*nC = *nC + 1;
}
return nP;
}
void display_PixelfeatureNclass(float* F, unsigned int* T, size_t B, size_t Idx){
//display code for debug, displaying Idx th pixel from feature matrix F with all features B
std::cout<<"class of pixel["<<Idx<<"]" <<"is: "<<T[Idx]<<std::endl;
std::cout<<"feature["<<Idx<<"] is: "<<std::endl;
for (size_t i = 0; i< B; i++)
std::cout<<" "<<F[Idx * B + i];
}
void display_args(int argc, stim::arglist args){
std::cout<<"number of arguments "<<argc<<std::endl;
std::cout<<"arg 0 "<<args.arg(0)<<std::endl;
std::cout<<"arg 1 "<<args.arg(1)<<std::endl;
}
void display_dataSize(size_t X, size_t Y, size_t B){
std::cout<<"number of samples "<<X*Y<<std::endl;
std::cout<<"number of bands "<<B<<std::endl;
}
void display_phe(float* phe, unsigned int* P, size_t p,size_t f, size_t i, size_t j){
//display code for debug, displaying jth pixel from new feature matrix which is created for gnome i
std::cout<<"phe["<<i<<"]["<<j<<"]"<<std::endl;
for(unsigned int n = 0; n < f; n++){
std::cout<<P[i * f + n]; //spectral feature indices from gnome i of current population
std::cout<<" "<<phe[i* (p * f) +j * f + n]<<std::endl; //display 100th pixel value corresponding to feature indices in the gnome
}
}
void display_gnome(unsigned int* P,size_t f,size_t gIdx){
//display code for debug, displaying gnome gIdx of current population, gnome is subset of feature indices
for (size_t i = 0; i< f; i++)
std::cout<<" "<<P[gIdx * f + i];
}
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