image_stack.h
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#ifndef STIM_IMAGE_STACK_H
#define STIM_IMAGE_STACK_H
#include "../parser/wildcards.h"
#include "../parser/filename.h"
#include "../grids/grid.h"
#include "../image/image.h"
namespace stim{
/**This class is used to load 3D grid data from stacks of images
The class uses a 4D grid object, where the first dimension is a color value.
**/
template<typename T>
class image_stack : public virtual stim::grid<T, 4>{
enum image_type {stimAuto, stimMono, stimRGB, stimRGBA};
protected:
using stim::grid<T, 4>::S;
using stim::grid<T, 4>::R;
using stim::grid<T, 4>::ptr;
using stim::grid<T, 4>::samples;
using stim::grid<T, 4>::read;
public:
///Load an image stack based on a file mask. Images are loaded in alphanumeric order.
/// @param file_mask is the mask describing images to be loaded
void load_images(std::string file_mask){
stim::filename file_path(file_mask);
//if the file path is relative, update it with the current working directory
if(file_path.is_relative()){
stim::filename wd = stim::filename::cwd();
file_path = wd.get_relative(file_mask);
}
//get the list of files
std::vector<stim::filename> file_list = file_path.get_list();
//if there are no matching files, exit
if(file_list.size() == 0){
std::cout<<"STIM ERROR (image_stack): No matching files for loading a stack."<<std::endl;
exit(1);
}
//load the first image and set all of the image_stack properties
std::cout<<"File to Load: "<<file_list[0].str()<<std::endl;
stim::image<T> I(file_list[0].str());
//set the image resolution and number of channels
R.push(I.channels());
R.push(I.width());
R.push(I.height());
R.push(file_list.size());
//allocate storage space
ptr = (T*)malloc(sizeof(T) * samples());
//load and copy each image into the grid
for(unsigned int i = 0; i<R[3]; i++){
std::cout<<"File to Load: "<<file_list[i].str()<<std::endl;
//load the image
stim::image<T> I(file_list[i].str());
//retrieve the interlaced data from the image - store it in the grid
I.get_interleaved_rgb(&ptr[ i * R[0] * R[1] * R[2] ]);
}
}
///Saves a single page to an image file
/// @param file_name is the name of the image file to be created
/// @param i is the page to be saved
void save_image(std::string file_name, unsigned int i){
//create an image
stim::image<T> I;
//retrieve the interlaced data from the image - store it in the grid
I.set_interleaved(&ptr[ i * R[0] * R[1] * R[2] ], R[1], R[2], R[0]);
I.save(file_name);
}
///Sets the dimensions of the image in each direction
///Voxel-size.
/// @param x size in the x direction
/// @param y size in the y direction
/// @param z size in the z direction
void
set_dim(float x, float y, float z)
{
S[0] = 1;
S[1] = x;
S[2] = y;
S[3] = z;
}
///Saves the entire stack to a set of images
/// @param file_mask is the mask describing how the file names will be saved (ex. image????.bmp)
void save_images(std::string file_mask){
stim::filename file_path(file_mask);
//if the file path is relative, update it with the current working directory
if(file_path.is_relative()){
stim::filename wd = stim::filename::cwd();
file_path = wd.get_relative(file_mask);
}
//create a list of file names
std::vector<std::string> file_list = stim::wildcards::increment(file_path.str(), 0, R[3]-1, 1);
for(int i=0; i<R[3]; i++)
save_image(file_list[i], i);
}
/// Returns the pixel at the specified point
T get(unsigned int x, unsigned int y, unsigned int z, unsigned int c = 0){
return ptr[z * R[0] * R[1] * R[2] + y * R[0] * R[1] + x * R[0] + c];
}
void read(std::string file, unsigned int X, unsigned int Y, unsigned int Z, unsigned int C = 1, unsigned int header = 0){
read(file, stim::vec<unsigned long>(C, X, Y, Z), header);
}
T* data(){
return ptr;
}
};
}
#endif