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>

  
  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);
  		}

  		for(int i = 0; i < file_list.size(); i++)
  			std::cout << file_list[i].str() << std::endl;

  
  		//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] ]);

  		}
  	}
  

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

  
  		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;
  	}

  	///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());
  	}
  
  	///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