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#ifndef STIM_IMAGE_H
#define STIM_IMAGE_H
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#ifdef USING_OPENCV
#include <opencv2/core/core.hpp>
#include <opencv2/highgui/highgui.hpp>
#endif
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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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T* img; //pointer to the image data (interleaved RGB for color)
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size_t R[3];
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inline size_t X() const { return R[1]; }
inline size_t Y() const { return R[2]; }
inline 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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inline size_t idx(size_t x, size_t y, size_t c = 0) const {
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return y * R[0] * R[1] + x * R[0] + c;
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}
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#ifdef USING_OPENCV
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int cv_type(){
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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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#endif
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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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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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///Resize an image
void resize(size_t x, size_t y, size_t c = 1) {
allocate(x, y, c);
}
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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) {
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std::ifstream infile(filename.c_str(), std::ios::in | std::ios::binary); //open an output file
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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);
}
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size_t nc; //allocate space for the number of channels
char format[2]; //allocate space to hold the image format tag
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infile.read(format, 2); //read the image format tag
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infile.seekg(1, std::ios::cur); //skip the newline character
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if (format[0] != 'P') {
std::cout << "Error in image::load_netpbm() - file format tag is invalid: " << format[0] << format[1] << std::endl;
exit(1);
}
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if (format[1] == '5') nc = 1; //get the number of channels from the format flag
else if (format[1] == '6') nc = 3;
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else {
std::cout << "Error in image::load_netpbm() - file format tag is invalid: " << format[0] << format[1] << std::endl;
exit(1);
}
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unsigned char c; //stores a character
while (infile.peek() == '#') { //if the next character indicates the start of a comment
while (true) {
c = infile.get();
if (c == 0x0A) break;
}
}
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std::string sw; //create a string to store the width of the image
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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);
}
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while (true) { //skip the maximum value
c = infile.get();
if (c == 0x0A) break;
}
size_t h = atoi(sh.c_str()); //convert the string into an integer
allocate(w, h, nc); //allocate space for the image
infile.read((char*)img, size()); //copy the binary data from the file to the image
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infile.close();
}
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#ifdef USING_OPENCV
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;
}
}
}
}
#endif
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/// Load an image from a file
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void load(std::string filename){
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#ifdef USING_OPENCV
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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());
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#else
load_netpbm(filename);
#endif
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}
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//save a Netpbm file
void save_netpbm(std::string filename) {
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std::ofstream outfile(filename.c_str(), std::ios::out | std::ios::binary); //open an output file
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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);
}
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size_t w = width();
size_t h = height();
outfile << w << " " << h << (char)0x0A; //save the width and height
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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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#ifdef USING_OPENCV
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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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#else
save_netpbm(filename);
#endif
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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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Pavel Govyadinov
completed merge f...
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318
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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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904614c3
David Mayerich
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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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/// Return an image representing a specified channel
/// @param c is the channel to be returned
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86dfa80b
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added 2D gaussian...
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348
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image<T> channel(size_t c) const {
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dbeb83f2
David Mayerich
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image<T> r(X(), Y(), 1); //create a new image
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for(size_t x = 0; x < X(); x++){
for(size_t y = 0; y < Y(); y++){
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fixed a segmentat...
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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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David Mayerich
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}
/// Returns an std::vector containing each channel as a separate image
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683f216a
David Mayerich
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std::vector< image<T> > split() const {
std::vector< image<T> > r; //create an image array
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dbeb83f2
David Mayerich
added separable c...
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r.resize(C()); //create images for each channel
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41acaf5d
David Mayerich
added a CUDA Gaus...
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for (size_t c = 0; c < C(); c++) { //for each channel
r[c] = channel(c); //copy the channel image to the array
}
return r;
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41acaf5d
David Mayerich
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}
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86dfa80b
David Mayerich
added 2D gaussian...
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/// Merge a series of single-channel images into a multi-channel image
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683f216a
David Mayerich
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void merge(std::vector< image<T> >& list) {
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size_t x = list[0].width(); //calculate the size of the image
size_t y = list[0].height();
allocate(x, y, list.size()); //re-allocate the image
for (size_t c = 0; c < list.size(); c++) //for each channel
set_channel(list[c].channel(0).data(), c); //insert the channel into the output image
}
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David Mayerich
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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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David Mayerich
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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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c8c976a9
David Mayerich
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size_t N = size();
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388
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for(size_t n = 0; n < N; n++)
img[n] = v;
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fixed hsiproc bug...
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return *this;
}
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f186dbda
Tianshu Cheng
header file for b...
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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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c8c976a9
David Mayerich
replaced CImg wit...
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401
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void set_channel(T* buffer, size_t c){
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6d30a707
Tianshu Cheng
add cuda/array_ad...
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402
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c8c976a9
David Mayerich
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size_t x, y;
for(y = 0; y < Y(); y++){
for(x = 0; x < X(); x++){
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2e5e3a26
David Mayerich
added 2D convolut...
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406
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img[idx(x, y, c)] = buffer[y * X() + x];
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c8c976a9
David Mayerich
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}
}
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6d30a707
Tianshu Cheng
add cuda/array_ad...
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}
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86dfa80b
David Mayerich
added 2D gaussian...
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size_t channels() const{
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c8c976a9
David Mayerich
replaced CImg wit...
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412
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return C();
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8b7be670
David Mayerich
implemented savin...
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}
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86dfa80b
David Mayerich
added 2D gaussian...
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415
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size_t width() const{
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c8c976a9
David Mayerich
replaced CImg wit...
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416
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return X();
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8b7be670
David Mayerich
implemented savin...
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417
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}
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86dfa80b
David Mayerich
added 2D gaussian...
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419
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size_t height() const{
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c8c976a9
David Mayerich
replaced CImg wit...
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420
|
return Y();
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3d0b6243
David Mayerich
fixed hsiproc bug...
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421
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}
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6d30a707
Tianshu Cheng
add cuda/array_ad...
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423
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T* data(){
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c8c976a9
David Mayerich
replaced CImg wit...
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424
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return img;
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6d30a707
Tianshu Cheng
add cuda/array_ad...
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425
426
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}
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7b3948ab
David Mayerich
added support for...
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427
|
//returns the size (number of values) of the image
|
c8c976a9
David Mayerich
replaced CImg wit...
|
428
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size_t size(){ return C() * X() * Y(); }
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d32a1854
David Mayerich
added framework f...
|
429
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faef7718
David Mayerich
updates to stim::...
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430
|
/// Returns the number of nonzero values
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9d3ba0b1
David Mayerich
added stim::hsi a...
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431
|
size_t nnz(){
|
faef7718
David Mayerich
updates to stim::...
|
432
|
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c8c976a9
David Mayerich
replaced CImg wit...
|
433
|
size_t N = X() * Y() * C();
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faef7718
David Mayerich
updates to stim::...
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434
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c8c976a9
David Mayerich
replaced CImg wit...
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435
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size_t nz = 0;
for(size_t n = 0; n < N; n++)
if(img[n] != 0) nz++;
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faef7718
David Mayerich
updates to stim::...
|
438
|
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c8c976a9
David Mayerich
replaced CImg wit...
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439
|
return nz; //return the number of nonzero pixels
|
faef7718
David Mayerich
updates to stim::...
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440
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}
//this function returns indices of pixels that have nonzero values
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9d3ba0b1
David Mayerich
added stim::hsi a...
|
444
|
std::vector<size_t> sparse_idx(){
|
faef7718
David Mayerich
updates to stim::...
|
445
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c8c976a9
David Mayerich
replaced CImg wit...
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446
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std::vector<size_t> s; //allocate an array
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faef7718
David Mayerich
updates to stim::...
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447
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s.resize(nnz()); //allocate space in the array
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c8c976a9
David Mayerich
replaced CImg wit...
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size_t N = size();
//size_t C = channels();
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faef7718
David Mayerich
updates to stim::...
|
451
|
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c8c976a9
David Mayerich
replaced CImg wit...
|
452
|
//T* ptr = img.data(); //get a pointer to the image data
|
faef7718
David Mayerich
updates to stim::...
|
453
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
454
|
size_t i = 0;
|
c8c976a9
David Mayerich
replaced CImg wit...
|
455
456
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458
|
for(size_t n = 0; n < N; n++){
if(img[n] != 0){
s[i] = n;
i++;
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faef7718
David Mayerich
updates to stim::...
|
459
460
461
462
463
|
}
}
return s; //return the index list
}
|
6d30a707
Tianshu Cheng
add cuda/array_ad...
|
464
|
|
1a224b6a
David Mayerich
fixed linux compa...
|
465
|
|
6d30a707
Tianshu Cheng
add cuda/array_ad...
|
466
|
/// Returns the maximum pixel value in the image
|
96f9b10f
Laila Saadatifard
change the header...
|
467
|
T maxv(){
|
c8c976a9
David Mayerich
replaced CImg wit...
|
468
469
|
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...
|
470
|
|
c8c976a9
David Mayerich
replaced CImg wit...
|
471
|
for (size_t n=0; n<N; n++){ //for every value
|
6d30a707
Tianshu Cheng
add cuda/array_ad...
|
472
|
|
c8c976a9
David Mayerich
replaced CImg wit...
|
473
474
|
if (img[n] > max_val){ //if the value is higher than the current max
max_val = img[n];
|
1a224b6a
David Mayerich
fixed linux compa...
|
475
|
}
|
6d30a707
Tianshu Cheng
add cuda/array_ad...
|
476
477
|
}
|
1a224b6a
David Mayerich
fixed linux compa...
|
478
|
return max_val;
|
6d30a707
Tianshu Cheng
add cuda/array_ad...
|
479
|
}
|
d32a1854
David Mayerich
added framework f...
|
480
|
|
c8c976a9
David Mayerich
replaced CImg wit...
|
481
|
/// Returns the maximum pixel value in the image
|
96f9b10f
Laila Saadatifard
change the header...
|
482
|
T minv(){
|
c8c976a9
David Mayerich
replaced CImg wit...
|
483
484
|
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...
|
485
|
|
c8c976a9
David Mayerich
replaced CImg wit...
|
486
487
488
|
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...
|
489
|
}
|
6d30a707
Tianshu Cheng
add cuda/array_ad...
|
490
491
|
}
|
1a224b6a
David Mayerich
fixed linux compa...
|
492
|
return min_val;
|
6d30a707
Tianshu Cheng
add cuda/array_ad...
|
493
494
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
495
496
497
498
499
500
|
/// 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...
|
501
|
|
a2bf1d08
David Mayerich
general bug fixes...
|
502
503
|
return r; //return the inverted image
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
504
|
|
6d30a707
Tianshu Cheng
add cuda/array_ad...
|
505
|
image<T> srgb2lab(){
|
c8c976a9
David Mayerich
replaced CImg wit...
|
506
507
|
std::cout<<"ERROR stim::image::srgb2lab - function has been broken, re-implement."<<std::endl;
exit(1);
|
6d30a707
Tianshu Cheng
add cuda/array_ad...
|
508
509
510
|
}
image<T> convolve2(image<T> mask){
|
1a224b6a
David Mayerich
fixed linux compa...
|
511
|
|
c8c976a9
David Mayerich
replaced CImg wit...
|
512
513
|
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...
|
514
|
}
|
d32a1854
David Mayerich
added framework f...
|
515
516
|
|
f186dbda
Tianshu Cheng
header file for b...
|
517
|
image<T> rotate(float angle, float cx, float cy){
|
c8c976a9
David Mayerich
replaced CImg wit...
|
518
519
|
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...
|
520
|
}
|
945ee13c
Laila Saadatifard
the get_list func...
|
521
|
|
945ee13c
Laila Saadatifard
the get_list func...
|
522
523
|
// leila's code for non_interleaving data in 3D
//create an data set from an interleaved buffer
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
524
|
void set_interleaved3(T* buffer, size_t width, size_t height, size_t depth, size_t channels = 3){
|
c8c976a9
David Mayerich
replaced CImg wit...
|
525
526
|
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...
|
527
|
}
|
1a224b6a
David Mayerich
fixed linux compa...
|
528
|
|
dbeb83f2
David Mayerich
added separable c...
|
529
|
/// Casting operator, casts every value in an image to a different data type V
|
2e5e3a26
David Mayerich
added 2D convolut...
|
530
531
|
template<typename V>
operator image<V>() {
|
dbeb83f2
David Mayerich
added separable c...
|
532
533
534
|
image<V> r(X(), Y(), C()); //create a new image
std::copy(img, img + size(), r.data()); //copy and cast the data
return r; //return the new image
|
2e5e3a26
David Mayerich
added 2D convolut...
|
535
536
|
}
|
d32a1854
David Mayerich
added framework f...
|
537
538
|
};
|
7b3948ab
David Mayerich
added support for...
|
539
540
|
}; //end namespace stim
|
d32a1854
David Mayerich
added framework f...
|
541
542
|
#endif
|