codebase / stimlib

  #ifndef STIM_IMAGE_STACK_H
  #define STIM_IMAGE_STACK_H
  

  #include <stim/parser/wildcards.h>
  #include <stim/parser/filename.h>
  #include <stim/grids/grid.h>
  #include <stim/image/image.h>

  #include <stim/math/vec3.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, typename F = float>
  class image_stack : public virtual stim::grid<T, 4, F>{

  
  	enum image_type {stimAuto, stimMono, stimRGB, stimRGBA};
  
  protected:

  	//using stim::grid<T, 4>::S;

  	using stim::grid<T, 4, F>::R;
  	using stim::grid<T, 4, F>::ptr;

  	using stim::grid<T, 4, F>::S;

  public:

  	//default constructor

  	image_stack() : grid<T, 4, F>() {

  	}

  	/// Overloads grid::samples() to return the number of samples associated with a given spatial dimension
  	///		this is necessary because R[0] stores the color
  	size_t samples(size_t d){
  		return grid<T, 4, F>::samples(d + 1);
  	}
  
  	size_t samples(){
  		return R[1] * R[2] * R[3];						//return the number of spatial samples
  	}
  

  	// get the number of pixels in each dimension
  	size_t nc() {
  		return R[0];
  	}
  	size_t nx() {
  		return R[1];
  	}
  	size_t ny() {
  		return R[2];
  	}
  	size_t nz() {
  		return R[3];
  	}
  

  	/// Returns the number of color channels
  	size_t channels(){
  		return R[0];
  	}
  
  	/// Overloads grid::size() to return the size of the grid associated with a given spatial dimension
  	F size(size_t d){
  		return grid<T, 4, F>::size(d + 1);
  	}
  
  	/// Sets the spacing between samples in the image stack
  	void spacing(F sx, F sy, F sz){
  		grid<T, 4, F>::S[1] = sx;			//set the sample spacing for the appropriate spatial dimension
  		grid<T, 4, F>::S[2] = sy;
  		grid<T, 4, F>::S[3] = sz;
  	}
  
  	F spacing(size_t d){
  		return grid<T, 4, F>::spacing(d + 1);
  	}
  
  	/// Overloads the spacing parameter to set the size of the grid associated with a given spatial dimension
  	//void spacing(F sx, F sy = 1.0f, F sz = 1.0f){
  	//	grid<T, 4, F>::spacing((F)1.0, sx, sy, sz);
  	//}
  

  	/// Load all of the images specified by a list of strings
  	/// @param string_list is a list of file names specifying images
  	void load_images(std::vector<std::string> string_list){

  
  		//if there are no matching files, exit

  		if(string_list.size() == 0){

  			std::cout<<"STIM ERROR (image_stack): No matching files for loading a stack."<<std::endl;
  			exit(1);
  		}

  		stim::image<T> I(string_list[0]);		//load the first image and set all of the image_stack proparties

  		R[0] = I.channels();				//set the number of color channels
  		R[1] = I.width();				//set the stack height and width based on the image size

  		R[2] = I.height();

  		R[3] = string_list.size();			//set the stack z-resolution based on the number of images

  		ptr = (T*)malloc(grid<T, 4, F>::bytes());	//allocate storage space

  
  		//load and copy each image into the grid

  		for(unsigned int i = 0; i<R[3]; i++){				//for each image in the list			
  			stim::image<T> I(string_list[i]);			//load the image			

  			I.get_interleaved_rgb(&ptr[ i * R[0] * R[1] * R[2] ]);	//retrieve the interlaced data from the image - store it in the grid			

  		}
  	}
  

  	/// Load a stack of images based on a file mask. Images are loaded in alphanumeric order
  	/// @param file_mask is the mask describing the images to be loaded
  	void load_images(std::string file_mask){
  		stim::filename file_path(file_mask);				//get the path for the images
  		std::vector<stim::filename> file_list = file_path.get_list();	//get the list of files
  		std::vector<std::string> string_list(file_list.size());		//allocate space for an array of strings
  		for(size_t f = 0; f < file_list.size(); f++){			//for each file name in the list
  			string_list[f] = file_list[f].str();			//convert the file name to a string
  		}
  		load_images(string_list);					//load all of the images in the list
  	}
  

  	///Inserts image I into slot i.
  	/// @param stim::image<T> I; image to insert.
  	/// @int I, where to place the image.

  	void insert_image(stim::image<T> I, int i){

  		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){		
  		stim::image<T> I;											//create an image		

  		I.set_interleaved(&ptr[ i * R[0] * R[1] * R[2] ], R[1], R[2], R[0]);	//retrieve the interlaced data from the image - store it in the grid
  //		I.set_interleaved_rgb(&ptr[ i * R[0] * R[1] * R[2] ], R[1], R[2], R[0]);	//retrieve the interlaced data from the image - store it in the grid

  		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)
  	{

  		grid<T, 4, F>::S[0] = 1;
  		grid<T, 4, F>::S[1] = x;
  		grid<T, 4, F>::S[2] = y;
  		grid<T, 4, F>::S[3] = z;

  	}

  	///set dimensions of the grid.
  	/// @param channels, number of channels in each image.
  	/// @param width,  number of pixels in width each image.
  	/// @param height, number of pixels in height.
  	/// @param depth,  number of pixels in depth.
  	void init(int channels, int width, int height, int depth)
  	{

  		//R.resize(4);

  		R[0] = channels;
  		R[1] = width;
  		R[2] = height;
  		R[3] = depth;
  
  		ptr = (T*)malloc(sizeof(T) * samples());

  		memset(ptr, 0, sizeof(T) * samples());

  	}
  
  	///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);

  		//stim::filename abs_file_path = file_pat

  		//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];
  	}
  

  	/// Returns the world-space position at an index point (i, j, k)
  	vec3<F> p(size_t i, size_t j, size_t k){
  		vec3<F> result;

  		result[0] = (F)i * S[1];
  		result[1] = (F)j * S[2];
  		result[2] = (F)k * S[3];

  		return result;
  	}
  

  	// set the pixel at the specified point
  	void set(size_t i, size_t j, size_t k, T value, size_t c = 0){
  		ptr[k * R[0] * R[1] * R[2] + j * R[0] * R[1] + i * R[0] + c] = value;
  	}
  	void set(T* Ptr, size_t k) {
  		
  		for (unsigned i = 0; i < R[0] * R[1] * R[2]; i++)
  			ptr[i + k * R[0] * R[1] * R[2]] = Ptr[i];
  	}

  	void copy(T* Ptr) {
  		ptr = Ptr;
  	}
  

  	/* This was causing compiler errors. I don't think this function call exists anywhere:
  

  	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