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#ifndef STIM_IMAGE_H
#define STIM_IMAGE_H
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#include <opencv2/core/core.hpp>
#include <opencv2/highgui/highgui.hpp>
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#include <vector>
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#include <iostream>
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#include <limits>
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#include <typeinfo>
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#include <fstream>
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namespace stim{
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/// This static class provides the STIM interface for loading, saving, and storing 2D images.
/// Data is stored in an interleaved (BIP) format (default for saving and loading is RGB).
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//currently this interface uses CImg
// T = data type (usually unsigned char)
template <class T>
class image{
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//cimg_library::CImg<T> img;
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T* img; //pointer to the image data (interleaved RGB for color)
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size_t R[3];
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size_t X() const { return R[1]; }
size_t Y() const { return R[2]; }
size_t C() const { return R[0]; }
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void init(){ //initializes all variables, assumes no memory is allocated
memset(R, 0, sizeof(size_t) * 3); //set the resolution and number of channels to zero
img = NULL;
}
void unalloc(){ //frees any resources associated with the image
if(img) free(img); //if memory has been allocated, free it
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}
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void clear(){ //clears all image data
unalloc(); //unallocate previous memory
init(); //re-initialize the variables
}
void allocate(){
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unalloc();
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img = (T*) malloc( sizeof(T) * R[0] * R[1] * R[2] ); //allocate memory
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}
void allocate(size_t x, size_t y, size_t c){ //allocate memory based on the resolution
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R[0] = c; R[1] = x; R[2] = y; //set the resolution
allocate(); //allocate memory
}
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size_t bytes(){ return size() * sizeof(T); }
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size_t idx(size_t x, size_t y, size_t c = 0){
return y * C() * X() + x * C() + c;
}
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int cv_type(){
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// The following is C++ 11 code, but causes problems on some compilers (ex. nvcc). Below is my best approximation to a solution
//if(std::is_same<T, unsigned char>::value) return CV_MAKETYPE(CV_8U, (int)C());
//if(std::is_same<T, char>::value) return CV_MAKETYPE(CV_8S, (int)C());
//if(std::is_same<T, unsigned short>::value) return CV_MAKETYPE(CV_16U, (int)C());
//if(std::is_same<T, short>::value) return CV_MAKETYPE(CV_16S, (int)C());
//if(std::is_same<T, int>::value) return CV_MAKETYPE(CV_32S, (int)C());
//if(std::is_same<T, float>::value) return CV_MAKETYPE(CV_32F, (int)C());
//if(std::is_same<T, double>::value) return CV_MAKETYPE(CV_64F, (int)C());
if(typeid(T) == typeid(unsigned char)) return CV_MAKETYPE(CV_8U, (int)C());
if(typeid(T) == typeid(char)) return CV_MAKETYPE(CV_8S, (int)C());
if(typeid(T) == typeid(unsigned short)) return CV_MAKETYPE(CV_16U, (int)C());
if(typeid(T) == typeid(short)) return CV_MAKETYPE(CV_16S, (int)C());
if(typeid(T) == typeid(int)) return CV_MAKETYPE(CV_32S, (int)C());
if(typeid(T) == typeid(float)) return CV_MAKETYPE(CV_32F, (int)C());
if(typeid(T) == typeid(double)) return CV_MAKETYPE(CV_64F, (int)C());
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std::cout<<"ERROR in stim::image::cv_type - no valid data type found"<<std::endl;
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exit(1);
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}
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/// Returns the value for "white" based on the dynamic range (assumes white is 1.0 for floating point images)
T white(){
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// The following is C++ 11 code, but causes problems on some compilers (ex. nvcc). Below is my best approximation to a solution
//if(std::is_same<T, unsigned char>::value) return UCHAR_MAX;
//if(std::is_same<T, unsigned short>::value) return SHRT_MAX;
//if(std::is_same<T, unsigned>::value) return UINT_MAX;
//if(std::is_same<T, unsigned long>::value) return ULONG_MAX;
//if(std::is_same<T, unsigned long long>::value) return ULLONG_MAX;
//if(std::is_same<T, float>::value) return 1.0f;
//if(std::is_same<T, double>::value) return 1.0;
if(typeid(T) == typeid(unsigned char)) return UCHAR_MAX;
if(typeid(T) == typeid(unsigned short)) return SHRT_MAX;
if(typeid(T) == typeid(unsigned)) return UINT_MAX;
if(typeid(T) == typeid(unsigned long)) return ULONG_MAX;
if(typeid(T) == typeid(unsigned long long)) return ULLONG_MAX;
if(typeid(T) == typeid(float)) return 1.0f;
if(typeid(T) == typeid(double)) return 1.0;
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std::cout<<"ERROR in stim::image::white - no white value known for this data type"<<std::endl;
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exit(1);
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}
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public:
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/// Default constructor - creates an empty image object
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image(){ init(); } //initialize all variables to zero, don't allocate any memory
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/// Constructor with a filename - loads the specified file
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image(std::string filename){ //constructor initialize the image with an image file
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init();
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load(filename);
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}
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/// Create a new image from scratch given a number of samples and channels
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image(size_t x, size_t y = 1, size_t c = 1){
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init();
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allocate(x, y, c);
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}
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/// Create a new image with the data given in 'data'
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image(T* data, size_t x, size_t y, size_t c = 1){
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init();
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allocate(x, y, c);
memcpy(img, data, bytes());
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}
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/// Copy constructor - duplicates an image object
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image(const stim::image<T>& I){
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init();
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allocate(I.X(), I.Y(), I.C());
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memcpy(img, I.img, bytes());
}
/// Destructor - clear memory
~image(){
free(img);
}
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stim::image<T>& operator=(const stim::image<T>& I){
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init();
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if(&I == this) //handle self-assignment
return *this;
allocate(I.X(), I.Y(), I.C());
memcpy(img, I.img, bytes());
return *this;
}
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//save a Netpbm file
void load_netpbm(std::string filename) {
std::ifstream infile(filename, std::ios::in | std::ios::binary); //open an output file
if (!infile) {
std::cout << "Error opening input file in image::load_netpbm()" << std::endl;
exit(1);
}
if (sizeof(T) != 1) {
std::cout << "Error in image::load_netpbm() - data type must be 8-bit integer." << std::endl;
exit(1);
}
size_t c; //allocate space for the number of channels
unsigned char format[2]; //allocate space to hold the image format tag
infile.read(format, 2); //read the image format tag
infile.seekg(1); //skip the newline character
if (format[0] != 'P') {
std::cout << "Error in image::load_netpbm() - file format tag is invalid: " << format[0] << format[1] << std::endl;
exit(1);
}
if (format[1] == '5') c = 1; //get the number of channels from the format flag
else if (format[1] == '6') c = 3;
else {
std::cout << "Error in image::load_netpbm() - file format tag is invalid: " << format[0] << format[1] << std::endl;
exit(1);
}
std::string sw; //create a string to store the width of the image
unsigned char c;
while(true){
c = infile.get(); //get a single character
if (c == ' ') break; //exit if we've encountered a space
sw.push_back(c); //push the character on to the string
}
size_t w = atoi(sw.c_str()); //convert the string into an integer
std::string sh;
while (true) {
c = infile.get();
if (c == 0x0A) break;
sh.push_back(c);
}
size_t h = atoi(ah.c_str()); //convert the string into an integer
allocate(w, h, c); //allocate space for the image
infile.read(img, size()); //copy the binary data from the file to the image
infile.close();
}
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/// Load an image from a file
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void load(std::string filename){
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cv::Mat cvImage = cv::imread(filename, CV_LOAD_IMAGE_UNCHANGED); //use OpenCV to open the image file
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if(!cvImage.data){
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std::cout<<"ERROR stim::image::load() - unable to find image "<<filename<<std::endl;
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exit(1);
}
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int cols = cvImage.cols;
int rows = cvImage.rows;
int channels = cvImage.channels();
allocate(cols, rows, channels); //allocate space for the image
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unsigned char* cv_ptr = (unsigned char*)cvImage.data;
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if(C() == 1) //if this is a single-color image, just copy the data
memcpy(img, cv_ptr, bytes());
if(C() == 3) //if this is a 3-color image, OpenCV uses BGR interleaving
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from_opencv(cv_ptr, X(), Y());
}
void from_opencv(unsigned char* buffer, size_t width, size_t height){
allocate(width, height, 3);
T value;
size_t i;
for(size_t c = 0; c < C(); c++){ //copy directly
for(size_t y = 0; y < Y(); y++){
for(size_t x = 0; x < X(); x++){
i = y * X() * C() + x * C() + (2-c);
value = buffer[i];
img[idx(x, y, c)] = value;
}
}
}
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}
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//save a Netpbm file
void save_netpbm(std::string filename) {
std::ofstream outfile(filename, std::ios::out | std::ios::binary); //open an output file
if(!outfile) {
std::cout << "Error generating output file in image::save_netpbm()" << std::endl;
exit(1);
}
if (sizeof(T) != 1) {
std::cout << "Error in image::save_netpbm() - data type must be 8-bit integer." << std::endl;
exit(1);
}
std::string format;
if (channels() == 1) outfile << "P5" << (char)0x0A; //output P5 if the file is grayscale
else if (channels() == 3) outfile << "P6" << (char)0x0A; //output P6 if the file is color
else {
std::cout << "Error in image::save_netpbm() - data must be grayscale or RGB." << std::endl;
exit(1);
}
outfile << width() << " " << height() << (char)0x0A; //save the width and height
outfile << "255" << (char)0x0A; //output the maximum value
outfile.write((const char*)img, size()); //write the binary data
outfile.close();
}
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//save a file
void save(std::string filename){
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//OpenCV uses an interleaved format, so convert first and then output
T* buffer = (T*) malloc(bytes());
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if(C() == 1)
memcpy(buffer, img, bytes());
else if(C() == 3)
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get_interleaved_bgr(buffer);
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cv::Mat cvImage((int)Y(), (int)X(), cv_type(), buffer);
cv::imwrite(filename, cvImage);
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free(buffer);
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}
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void set_interleaved(T* buffer, size_t width, size_t height, size_t channels){
allocate(width, height, channels);
memcpy(img, buffer, bytes());
}
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//create an image from an interleaved buffer
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void set_interleaved_rgb(T* buffer, size_t width, size_t height){
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set_interleaved(buffer, width, height, 3);
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}
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void set_interleaved_bgr(T* buffer, size_t width, size_t height){
allocate(width, height, 3);
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T value;
size_t i;
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for(size_t c = 0; c < C(); c++){ //copy directly
for(size_t y = 0; y < Y(); y++){
for(size_t x = 0; x < X(); x++){
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i = y * X() * C() + x * C() + (2-c);
value = buffer[i];
img[idx(x, y, c)] = value;
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}
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}
}
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}
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void set_interleaved(T* buffer, size_t width, size_t height){
set_interleaved_rgb(buffer, width, height);
}
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void get_interleaved_bgr(T* data){
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//for each channel
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for(size_t y = 0; y < Y(); y++){
for(size_t x = 0; x < X(); x++){
for(size_t c = 0; c < C(); c++){
data[y * X() * C() + x * C() + (2-c)] = img[idx(x, y, c)];
}
}
}
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}
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void get_interleaved_rgb(T* data){
memcpy(data, img, bytes());
}
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//copies data in the given channel order as a non-interleaved image
void get_noninterleaved(T* data){
//for each channel
for(size_t y = 0; y < Y(); y++){
for(size_t x = 0; x < X(); x++){
for(size_t c = 0; c < C(); c++){
data[c * Y() * X() + y * X() + x] = img[idx(x, y, c)];
}
}
}
}
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image<T> channel(size_t c){
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//create a new image
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image<T> r(X(), Y(), 1);
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for(size_t x = 0; x < X(); x++){
for(size_t y = 0; y < Y(); y++){
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r.img[r.idx(x, y, 0)] = img[idx(x, y, c)];
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}
}
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return r;
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}
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T& operator()(size_t x, size_t y, size_t c = 0){
return img[idx(x, y, c)];
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359
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}
/// Set all elements in the image to a given scalar value
/// @param v is the value used to set all values in the image
image<T> operator=(T v){
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size_t N = size();
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361
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for(size_t n = 0; n < N; n++)
img[n] = v;
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return *this;
}
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/// Copy the given data to the specified channel
/// @param c is the channel number that the data will be copied to
/// @param buffer is a pointer to the image to be copied to channel c
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void set_channel(T* buffer, size_t c){
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size_t x, y;
for(y = 0; y < Y(); y++){
for(x = 0; x < X(); x++){
img[idx(x, y, c)] = buffer[c];
}
}
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}
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size_t channels(){
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return C();
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}
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size_t width(){
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return X();
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}
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|
size_t height(){
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return Y();
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}
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396
|
T* data(){
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return img;
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}
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7b3948ab
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400
|
//returns the size (number of values) of the image
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|
401
|
size_t size(){ return C() * X() * Y(); }
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|
402
|
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faef7718
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|
403
|
/// Returns the number of nonzero values
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9d3ba0b1
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|
404
|
size_t nnz(){
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faef7718
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|
405
|
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|
406
|
size_t N = X() * Y() * C();
|
faef7718
David Mayerich
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|
407
|
|
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|
408
409
410
|
size_t nz = 0;
for(size_t n = 0; n < N; n++)
if(img[n] != 0) nz++;
|
faef7718
David Mayerich
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|
411
|
|
c8c976a9
David Mayerich
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|
412
|
return nz; //return the number of nonzero pixels
|
faef7718
David Mayerich
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|
413
414
415
416
|
}
//this function returns indices of pixels that have nonzero values
|
9d3ba0b1
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added stim::hsi a...
|
417
|
std::vector<size_t> sparse_idx(){
|
faef7718
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|
418
|
|
c8c976a9
David Mayerich
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|
419
|
std::vector<size_t> s; //allocate an array
|
faef7718
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|
420
421
|
s.resize(nnz()); //allocate space in the array
|
c8c976a9
David Mayerich
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|
422
423
|
size_t N = size();
//size_t C = channels();
|
faef7718
David Mayerich
updates to stim::...
|
424
|
|
c8c976a9
David Mayerich
replaced CImg wit...
|
425
|
//T* ptr = img.data(); //get a pointer to the image data
|
faef7718
David Mayerich
updates to stim::...
|
426
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
427
|
size_t i = 0;
|
c8c976a9
David Mayerich
replaced CImg wit...
|
428
429
430
431
|
for(size_t n = 0; n < N; n++){
if(img[n] != 0){
s[i] = n;
i++;
|
faef7718
David Mayerich
updates to stim::...
|
432
433
434
435
436
|
}
}
return s; //return the index list
}
|
6d30a707
Tianshu Cheng
add cuda/array_ad...
|
437
|
|
1a224b6a
David Mayerich
fixed linux compa...
|
438
|
|
6d30a707
Tianshu Cheng
add cuda/array_ad...
|
439
|
/// Returns the maximum pixel value in the image
|
96f9b10f
Laila Saadatifard
change the header...
|
440
|
T maxv(){
|
c8c976a9
David Mayerich
replaced CImg wit...
|
441
442
|
T max_val = img[0]; //initialize the maximum value to the first one
size_t N = size(); //get the number of pixels
|
6d30a707
Tianshu Cheng
add cuda/array_ad...
|
443
|
|
c8c976a9
David Mayerich
replaced CImg wit...
|
444
|
for (size_t n=0; n<N; n++){ //for every value
|
6d30a707
Tianshu Cheng
add cuda/array_ad...
|
445
|
|
c8c976a9
David Mayerich
replaced CImg wit...
|
446
447
|
if (img[n] > max_val){ //if the value is higher than the current max
max_val = img[n];
|
1a224b6a
David Mayerich
fixed linux compa...
|
448
|
}
|
6d30a707
Tianshu Cheng
add cuda/array_ad...
|
449
450
|
}
|
1a224b6a
David Mayerich
fixed linux compa...
|
451
|
return max_val;
|
6d30a707
Tianshu Cheng
add cuda/array_ad...
|
452
|
}
|
d32a1854
David Mayerich
added framework f...
|
453
|
|
c8c976a9
David Mayerich
replaced CImg wit...
|
454
|
/// Returns the maximum pixel value in the image
|
96f9b10f
Laila Saadatifard
change the header...
|
455
|
T minv(){
|
c8c976a9
David Mayerich
replaced CImg wit...
|
456
457
|
T min_val = img[0]; //initialize the maximum value to the first one
size_t N = size(); //get the number of pixels
|
6d30a707
Tianshu Cheng
add cuda/array_ad...
|
458
|
|
c8c976a9
David Mayerich
replaced CImg wit...
|
459
460
461
|
for (size_t n=0; n<N; n++){ //for every value
if (img[n] < min_val){ //if the value is higher than the current max
min_val = img[n];
|
1a224b6a
David Mayerich
fixed linux compa...
|
462
|
}
|
6d30a707
Tianshu Cheng
add cuda/array_ad...
|
463
464
|
}
|
1a224b6a
David Mayerich
fixed linux compa...
|
465
|
return min_val;
|
6d30a707
Tianshu Cheng
add cuda/array_ad...
|
466
467
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
468
469
470
471
472
473
|
/// Invert an image by calculating I1 = alpha - I0, where alpha is the maximum image value
image<T> invert(T white_val){
size_t N = size(); //calculate the total number of values in the image
image<T> r(X(), Y(), C()); //allocate space for the resulting image
for(size_t n = 0; n < N; n++)
r.img[n] = white_val - img[n]; //perform the inversion
|
1a224b6a
David Mayerich
fixed linux compa...
|
474
|
|
a2bf1d08
David Mayerich
general bug fixes...
|
475
476
|
return r; //return the inverted image
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
477
|
|
6d30a707
Tianshu Cheng
add cuda/array_ad...
|
478
|
image<T> srgb2lab(){
|
c8c976a9
David Mayerich
replaced CImg wit...
|
479
480
|
std::cout<<"ERROR stim::image::srgb2lab - function has been broken, re-implement."<<std::endl;
exit(1);
|
6d30a707
Tianshu Cheng
add cuda/array_ad...
|
481
482
483
|
}
image<T> convolve2(image<T> mask){
|
1a224b6a
David Mayerich
fixed linux compa...
|
484
|
|
c8c976a9
David Mayerich
replaced CImg wit...
|
485
486
|
std::cout<<"ERROR stim::image::convolve2 - function has been broken, and shouldn't really be in here."<<std::endl;
exit(1);
|
6d30a707
Tianshu Cheng
add cuda/array_ad...
|
487
|
}
|
d32a1854
David Mayerich
added framework f...
|
488
489
|
|
f186dbda
Tianshu Cheng
header file for b...
|
490
|
image<T> rotate(float angle, float cx, float cy){
|
c8c976a9
David Mayerich
replaced CImg wit...
|
491
492
|
std::cout<<"ERROR stim::image::rotate - function has been broken, and shouldn't really be in here."<<std::endl;
exit(1);
|
f186dbda
Tianshu Cheng
header file for b...
|
493
|
}
|
945ee13c
Laila Saadatifard
the get_list func...
|
494
|
|
945ee13c
Laila Saadatifard
the get_list func...
|
495
496
|
// leila's code for non_interleaving data in 3D
//create an data set from an interleaved buffer
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
497
|
void set_interleaved3(T* buffer, size_t width, size_t height, size_t depth, size_t channels = 3){
|
c8c976a9
David Mayerich
replaced CImg wit...
|
498
499
|
std::cout<<"ERROR stim::image::set_interleaved3 - stim::image no longer supports 3D images."<<std::endl;
exit(1);
|
945ee13c
Laila Saadatifard
the get_list func...
|
500
|
}
|
1a224b6a
David Mayerich
fixed linux compa...
|
501
|
|
d32a1854
David Mayerich
added framework f...
|
502
503
|
};
|
7b3948ab
David Mayerich
added support for...
|
504
505
|
}; //end namespace stim
|
d32a1854
David Mayerich
added framework f...
|
506
507
|
#endif
|