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stim/envi/binary.h 10.8 KB
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  //make sure that this header file is only loaded once
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  #ifndef RTS_BINARY_H
  #define RTS_BINARY_H
  
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  #include "../envi/envi_header.h"
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  #include "../math/vector.h"
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  #include <fstream>
  #include <sys/stat.h>
  
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  namespace stim{
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  /** This class manages the streaming of large multidimensional binary files.
   *  Generally these are hyperspectral files with 2 spatial and 1 spectral dimension. However, this class supports
   *  other dimensions via the template parameter D.
   *
   *  @param T is the data type used to store data to disk (generally float or double)
   *  @param D is the dimension of the data (default 3)
   */
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  template< typename T, unsigned int D = 3 >
  class binary{
  
  protected:
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  	std::fstream file;		//file stream used for reading and writing
  	std::string name;		//file name
  
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  	unsigned long long int R[D];		//resolution
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  	unsigned int header;	//header size (in bytes)
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  	unsigned char* mask;	//pointer to a character array: 0 = background, 1 = foreground (or valid data)
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  	unsigned int thread_data;		//unsigned integer used to pass data to threads during processing
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  	/// Private initialization function used to set default parameters in the data structure.
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  	void init(){
  		memset(R, 0, sizeof(unsigned int) * D);		//initialize the resolution to zero
  		header = 0;									//initialize the header size to zero
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  		mask = NULL;
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  		thread_data = 0;
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  	}
  
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  	/// Private helper function that returns the size of the file on disk using system functions.
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  	long long int get_file_size(){
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  #ifdef _WIN32
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  		struct _stat64 results;
  		if(_stat64(name.c_str(), &results) == 0)
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  			return results.st_size;
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  #else
  		struct stat results;
  		if(stat(name.c_str(), &results) == 0)
  			return results.st_size;
  #endif
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  		else return 0;
  	}
  
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  	/// Private helper function that tests to make sure that the calculated data size specified by the structure is the same as the data size on disk.
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  	bool test_file_size(){
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  		long long int npts = 1;				//initialize the number of data points to 1
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  		for(unsigned int i = 0; i<D; i++)	//iterate over each dimension
  			npts *= R[i];					//compute the total number of data points in the file
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  		long long int datasize = npts * sizeof(T);//multiply the sum by the size of the template parameter
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  		if(datasize + header == get_file_size()) return true;	//if the byte size matches the file size, we're golden
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  		else return false;					//otherwise return an error
  
  	}
  
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  	/// Private helper function that resets the file pointer to the beginning of the data
  
  	void reset(){
  		file.seekg(header, std::ios_base::beg);
  	}
  
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  	/// Private helper file that opens a specified binary file.
  
  	/// @param filename is the name of the binary file to stream
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  	bool open_file(std::string filename){
  		//open the file as binary for reading and writing
  		file.open(filename.c_str(), std::ios::in | std::ios::out | std::ios::binary);
  
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  		//if the file isn't open, the user may only have read access
  		if(!file.is_open()){
  			std::cout<<"class BINARY - failed to open file, trying for read only"<<std::endl;
  			file.open(filename.c_str(), std::ios::in | std::ios::binary);
  			if(!file.is_open()){
  				std::cout<<"               still unable to load the file"<<std::endl;
  				return false;
  			}
  		}
  
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  		//if the file is successful
  		if(file){
  			name = filename;		//set the name
  			if(test_file_size())	//test the file size
  				return true;
  		}
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  		return false;
  	}
  
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  public:
  
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  	unsigned int get_thread_data(){
  		return thread_data;
  	}
  
  	void reset_thread_data(){
  		thread_data = 0;
  	}
  
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  	/// Open a binary file for streaming.
  
  	/// @param filename is the name of the binary file
  	/// @param r is a STIM vector specifying the size of the binary file along each dimension
  	/// @param h is the length (in bytes) of any header file (default zero)
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  	bool open(std::string filename, vec<unsigned int> r, unsigned int h = 0){
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  		for(unsigned int i = 0; i < D; i++)		//set the dimensions of the binary file object
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  			R[i] = r[i];
  
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  		header = h;				//save the header size
  
  		if(!open_file(filename)) return false;	//open the binary file
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  		//reset();
  
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  		return test_file_size();
  	}
  
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  	/// Creates a new binary file for streaming
  
  	/// @param filename is the name of the binary file to be created
  	/// @param r is a STIM vector specifying the size of the file along each dimension
  	/// @offset specifies how many bytes to offset the file (used to leave room for a header)
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  	bool create(std::string filename, vec<unsigned int> r, unsigned int offset = 0){
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  		std::ofstream target(filename.c_str(), std::ios::binary);
  
  		//initialize binary file
  		T p = 0;
  		for(unsigned int i =0; i < r[0] * r[1] * r[2]; i++){
  			target.write((char*)(&p), sizeof(T));
  		}
  
  		for(unsigned int i = 0; i < D; i++)		//set the dimensions of the binary file object
  			R[i] = r[i];
  
  		header = offset;				//save the header size
  
  		if(!open_file(filename)) return false;	//open the binary file
  
  		return test_file_size();
  	}
  
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  	/// Writes a single page of data to disk. A page consists of a sequence of data of size R[0] * R[1] * ... * R[D-1].
  
  	/// @param p is a pointer to the data to be written
  	/// @param page is the page number (index of the highest-numbered dimension)
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  	bool write_page( T * p, unsigned int page){
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  		if(p == NULL){
  			std::cout<<"ERROR: unable to write into file, empty pointer"<<std::endl;
  			exit(1);
  		}
  
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  		file.seekg(R[1] * R[0] * page * sizeof(T) + header, std::ios::beg);   //seek to the desired location on disk
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  		file.write((char *)p, R[0] * R[1] * sizeof(T));				 //write binary data
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  		return true;
  	}
  
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  	/// Reads a page from disk. A page consists of a sequence of data of size R[0] * R[1] * ... * R[D-1].
  
  	/// @param p is a pointer to pre-allocated memory equal to the page size
  	/// @param page is the index of the page
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  	bool read_page( T * p, unsigned int page){
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  		if (page >= R[2]){										//make sure the bank number is right
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  			std::cout<<"ERROR: page out of range"<<std::endl;
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  			return false;
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  		}
  
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  		file.seekg(R[1] * R[0] * page * sizeof(T) + header, std::ios::beg);   //write into memory from the binary file
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  		file.read((char *)p, R[0] * R[1] * sizeof(T));
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  		return true;
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  	}
  
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  	///Reads a line Z (slowest dimension) for a given XY value
  
  	/// @param p is a pointer to pre-allocated memory equal to the line size R[2]
  	/// @param x is the x coordinate
  	/// @param y is the y coordinate
  	bool read_line_01( T * p, unsigned int x, unsigned int y){
  		unsigned int i;
  
  		if ( x >= R[0] || y >= R[1]){							//make sure the sample and line number is right
  			std::cout<<"ERROR: sample or line out of range"<<std::endl;
  			return false;
  		}
  
  		file.seekg((x + y * R[0]) * sizeof(T), std::ios::beg);           //point to the certain sample and line
  		for (i = 0; i < R[2]; i++)
  		{
  			file.read((char *)(p + i), sizeof(T));
  			file.seekg((R[1] * R[0] - 1) * sizeof(T), std::ios::cur);    //go to the next band
  		}
  
  		return true;
  	}
  
  	///Reads a line X (fastest dimension) for a given YZ value
  
  	/// @param p is a pointer to pre-allocated memory equal to the line size R[2]
  	/// @param x is the y coordinate
  	/// @param y is the z coordinate
  	bool read_line_12(T * p, unsigned int y, unsigned int z){
  		//test to make sure the specified value is within range
  		if( y >= R[1] || z >= R[2] ){
  			std::cout<<"ERROR: sample or line out of range"<<std::endl;
  			return false;
  		}
  
  		file.seekg((z * R[0] * R[1] + y * R[0]) * sizeof(T), std::ios::beg);	//seek to the start of the line
  		file.read((char *)p, sizeof(T) * R[0]);									//read the line
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  		return true;
  	}
  
  	///Reads a line Y (second fastest dimension) for a given XZ value
  
  	/// @param p is a pointer to pre-allocated memory equal to the line size R[2]
  	/// @param x is the y coordinate
  	/// @param z is the z coordinate
  	bool read_line_02(T * p, unsigned int x, unsigned int z){
  		//test to make sure the specified value is within range
  		if( x >= R[0] || z >= R[2] ){
  			std::cout<<"ERROR: sample or line out of range"<<std::endl;
  			return false;
  		}
  
  		file.seekg((z * R[0] * R[1] + x) * sizeof(T), std::ios::beg);           //seek to the start of the line
  		for (unsigned int i = 0; i < R[1]; i++){									//for each pixel in the line
  			file.read((char *)(p + i), sizeof(T));					//read the pixel
  			file.seekg((R[0] - 1) * sizeof(T), std::ios::cur);		//seek to the next pixel in the line
  		}
  
  		return true;
  	}
  
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  	/// Reads a plane given a coordinate along the 0-axis (YZ plane)
  
  	/// @param p is a pointer to pre-allocated memory of size R[1] * R[2] * sizeof(T)
  	/// @param n is the 0-axis coordinate used to retrieve the plane
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  	bool read_plane_0(T* p, unsigned int n){
  
  		if (n >= R[0]){										//make sure the number is within the possible range
  			std::cout<<"ERROR read_plane_0: page out of range"<<std::endl;
  			return false;
  		}
  		unsigned int jump = (R[0] - 1) * sizeof(T);		//number of bytes to skip between samples
  
  		//seek to the start of the plane
  		file.seekg(n * sizeof(T), std::ios::beg);
  
  		unsigned int N = R[1] * R[2];
  		for(unsigned int i = 0; i<N; i++){
  			file.read((char*)(p+i), sizeof(T));
  			file.seekg(jump, std::ios::cur);
  		}
  
  		return true;
  
  
  	}
  
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  	/// Reads a plane given a coordinate along the 1-axis (XZ plane)
  
  	/// @param p is a pointer to pre-allocated memory of size R[0] * R[2] * sizeof(T)
  	/// @param n is the 1-axis coordinate used to retrieve the plane
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  	bool read_plane_1(T* p, unsigned int n){
  
  		unsigned int L = R[0] * sizeof(T);		//caculate the number of bytes in a sample line
  		unsigned int jump = R[0] * (R[1] - 1) * sizeof(T);
  
  		if (n >= R[1]){										//make sure the bank number is right
  			std::cout<<"ERROR read_plane_1: page out of range"<<std::endl;
  			return false;
  		}
  
  		file.seekg(R[0] * n * sizeof(T), std::ios::beg);
  		for (unsigned i = 0; i < R[2]; i++){
  
  			file.read((char *)(p + i * R[0]), L);
  			file.seekg( jump, std::ios::cur);
  			std::cout<<i<<"    ";
  		}
  
  		return true;
  	}
  
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  	/// Reads a plane given a coordinate along the 2-axis (XY plane)
  
  	/// @param p is a pointer to pre-allocated memory of size R[0] * R[1] * sizeof(T)
  	/// @param n is the 2-axis coordinate used to retrieve the plane
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  	bool read_plane_2(T* p, unsigned int n){
  		return read_page(p, n);
  	}
  
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  	/// Reads a single pixel, treating the entire data set as a linear array
  
  	/// @param p is a pointer to pre-allocated memory of size sizeof(T)
  	/// @param i is the index to the pixel using linear indexing
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  	bool read_pixel(T* p, unsigned int i){
  		if(i >= R[0] * R[1] * R[2]){
  			std::cout<<"ERROR read_pixel: n is out of range"<<std::endl;
  			return false;
  		}
  
  		file.seekg(i * sizeof(T), std::ios::cur);
  		file.read((char*)p, sizeof(T));
  
  	}
  
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  	/// Reads a single pixel, given an x, y, z coordinate
  
  	/// @param p is a pointer to pre-allocated memory of size sizeof(T)
  	/// @param x is the x (0) axis coordinate
  	/// @param y is the y (1) axis coordinate
  	/// @param z is the z (2) axis coordinate
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  	bool read_pixel(T* p, unsigned int x, unsigned int y, unsigned int z){
  
  		if(x < 0 || x >= R[0] || y < 0 || y >= R[1] || z < 0 || z > R[2]){
  			std::cout<<"ERROR read_pixel: (x,y,z) is out of range"<<std::endl;
  			return false;
  		}
  
  		unsigned int i = z * R[0] * R[1] + y * R[0] + z;
  		return read_pixel(p, i);
  	}
  
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  };
  
  }
  
  #endif