deprecated / bimsim

#ifndef RTS_ENVI_H
#define RTS_ENVI_H

#include <string>
#include <iostream>
#include <fstream>
#include <sstream>

/*	This is a class for reading and writing ENVI binary files. This class will be updated as needed.

What this class CAN currently do:
	*)  Write band images to a BSQ file.
	*)  Append band images to a BSQ file.

*/

//information from an ENVI header file
//A good resource can be found here: http://www.exelisvis.com/docs/enviheaderfiles.html
struct EnviHeader
{
	std::string name;

	std::string description;

	unsigned int samples;	//x-axis
	unsigned int lines;		//y-axis
	unsigned int bands;		//spectral axis
	unsigned int header_offset;		//header offset for binary file (in bytes)
	std::string file_type;			//should be "ENVI Standard"
	unsigned int data_type;			//data representation; common value is 4 (32-bit float)

	enum interleaveType {BIP, BIL, BSQ};	//bip = Z,X,Y; bil = X,Z,Y; bsq = X,Y,Z
	interleaveType interleave;

	std::string sensor_type;		//not really used

	enum endianType {endianLittle, endianBig};
	endianType byte_order;			//little = least significant bit first (most systems)

	double x_start, y_start;		//coordinates of the upper-left corner of the image
	std::string wavelength_units;	//stored wavelength units
	std::string z_plot_titles[2];

	double pixel_size[2];			//pixel size along X and Y

	std::vector<std::string> band_names;	//name for each band in the image
	std::vector<double> wavelength;		//wavelength for each band

	EnviHeader()
	{
        name = "";

		//specify default values for a new or empty ENVI file
		samples = 0;
		lines = 0;
		bands = 0;
		header_offset = 0;
		data_type = 4;
		interleave = BSQ;
		byte_order = endianLittle;
		x_start = y_start = 0;
		pixel_size[0] = pixel_size[1] = 1;

		//strings
		file_type = "ENVI Standard";
		sensor_type = "Unknown";
		wavelength_units = "Unknown";
		z_plot_titles[0] = z_plot_titles[1] = "Unknown";
	}

	std::string trim(std::string line)
	{
		//trims whitespace from the beginning and end of line
		int start_i, end_i;
		for(start_i=0; start_i < line.length(); start_i++)
			if(line[start_i] != 32)
			{
				break;
			}

		for(end_i = line.length()-1; end_i >= start_i; end_i--)
			if(line[end_i] != ' ')
			{
				break;
			}

		return line.substr(start_i, end_i - start_i+1);
	}


	std::string get_token(std::string line)
	{
		//returns a variable name; in this case we look for the '=' sign
		size_t i = line.find_first_of('=');

		std::string result;
		if(i != std::string::npos)
			result = trim(line.substr(0, i-1));

		return result;
	}

	std::string get_data_str(std::string line)
	{
		size_t i = line.find_first_of('=');

		std::string result;
		if(i != std::string::npos)
			result = trim(line.substr(i+1));
		else
		{
			std::cout<<"ENVI Header error - data not found for token: "<<get_token(line)<<std::endl;
			exit(1);
		}
		return result;
	}

	std::string get_brace_str(std::string token, std::string line, std::ifstream &file)
	{
		//this function assembles all of the characters between curly braces
		//this is how strings are defined within an ENVI file

		std::string result;

		//first, find the starting brace
		size_t i;
		do
		{
			i = line.find_first_of('{');
			if(i != std::string::npos)
				break;
		}while(file);

		//if i is still npos, we have reached the end of the file without a brace...something is wrong
		if(i == std::string::npos)
		{
			std::cout<<"ENVI Header error - string token declared without being defined: "<<token<<std::endl;
			exit(1);
		}
		line = line.substr(i+1);

		//copy character data into the result string until we find a closing brace
		while(file)
		{
			i = line.find_first_of('}');


			if(i != std::string::npos)
			{
				result += line.substr(0, i);
				break;
			}
			else
				result += line;

			getline(file, line);
		}

		if(i == std::string::npos)
		{
			std::cout<<"ENVI Header error - string token declared without a terminating '}': "<<token<<std::endl;
			exit(1);
		}

		return trim(result);
	}

	std::vector<std::string> get_string_seq(std::string token, std::string sequence)
	{
		//this function returns a sequence of comma-delimited strings
		std::vector<std::string> result;

		std::string entry;
		size_t i;
		do
		{
			i = sequence.find_first_of(',');
			entry = sequence.substr(0, i);
			sequence = sequence.substr(i+1);
			result.push_back(trim(entry));
		}while(i != std::string::npos);

		return result;
	}

	std::vector<double> get_double_seq(std::string token, std::string sequence)
	{
		//this function returns a sequence of comma-delimited strings
		std::vector<double> result;

		std::string entry;
		size_t i;
		do
		{
			i = sequence.find_first_of(',');
			entry = sequence.substr(0, i);
			sequence = sequence.substr(i+1);
			result.push_back(atof(entry.c_str()));
		}while(i != std::string::npos);

		return result;
	}

	void load(std::string filename)
	{
		name = filename;

		//open the header file
		std::ifstream file(name.c_str());

		if(!file)
		{
			std::cout<<"ENVI header file not found: "<<name<<std::endl;
			exit(1);
		}

		//the first line should just be "ENVI"
		std::string line;
		getline(file, line);
		if(line != "ENVI")
		{
			std::cout<<"The header doesn't appear to be an ENVI file. The first line should be 'ENVI'."<<std::endl;
			exit(1);
		}

		//for each line in the file, get the token
		std::string token;
		while(file)
		{

			//get a line
			getline(file, line);

			//get the token
			token = get_token(line);

			if(token == "description")
				description = get_brace_str(token, line, file);
			else if(token == "band names")
			{
				std::string string_sequence = get_brace_str(token, line, file);
				band_names = get_string_seq(token, string_sequence);
			}
			else if(token == "wavelength")
			{
				std::string string_sequence = get_brace_str(token, line, file);
				wavelength = get_double_seq(token, string_sequence);
			}
			else if(token == "pixel size")
			{
				std::string string_sequence = get_brace_str(token, line, file);
				std::vector<double> pxsize = get_double_seq(token, string_sequence);
				pixel_size[0] = pxsize[0];
				pixel_size[1] = pxsize[1];
			}
			else if(token == "z plot titles")
			{
				std::string string_sequence = get_brace_str(token, line, file);
				std::vector<std::string> titles = get_string_seq(token, string_sequence);
				z_plot_titles[0] = titles[0];
				z_plot_titles[1] = titles[1];
			}

			else if(token == "samples")
				samples = atoi(get_data_str(line).c_str());
			else if(token == "lines")
				lines = atoi(get_data_str(line).c_str());
			else if(token == "bands")
				bands = atoi(get_data_str(line).c_str());
			else if(token == "header offset")
				header_offset = atoi(get_data_str(line).c_str());
			else if(token == "file type")
				file_type = get_data_str(line);
			else if(token == "data type")
				data_type = atoi(get_data_str(line).c_str());
			else if(token == "interleave")
			{
				std::string interleave_str = get_data_str(line);
				if(interleave_str == "bip")
					interleave = BIP;
				else if(interleave_str == "bil")
					interleave = BIL;
				else if(interleave_str == "bsq")
					interleave = BSQ;
			}
			else if(token == "sensor type")
				sensor_type = get_data_str(line);
			else if(token == "byte order")
				byte_order = (endianType)atoi(get_data_str(line).c_str());
			else if(token == "x start")
				x_start = atof(get_data_str(line).c_str());
			else if(token == "y start")
				y_start = atof(get_data_str(line).c_str());
			else if(token == "wavelength units")
				wavelength_units = get_data_str(line);
		}

		//close the file
		file.close();
	}

	void save(std::string filename)
	{
		//open a file
		std::ofstream outfile(filename.c_str());

		//write the ENVI type identifier
		outfile<<"ENVI"<<std::endl;

		//output all of the data
		outfile<<"description = {"<<std::endl;
		outfile<<"  "<<description<<"}"<<std::endl;

		outfile<<"samples = "<<samples<<std::endl;
		outfile<<"lines = "<<lines<<std::endl;
		outfile<<"bands = "<<bands<<std::endl;
		outfile<<"header offset = "<<header_offset<<std::endl;
		outfile<<"file type = "<<file_type<<std::endl;
		outfile<<"data type = "<<data_type<<std::endl;
		outfile<<"interleave = ";
		if(interleave == BIP)
			outfile<<"bip";
		if(interleave == BIL)
			outfile<<"bil";
		if(interleave == BSQ)
			outfile<<"bsq";
			outfile<<std::endl;
		outfile<<"sensor type = "<<sensor_type<<std::endl;
		outfile<<"byte order = "<<byte_order<<std::endl;
		outfile<<"x start = "<<x_start<<std::endl;
		outfile<<"y start = "<<y_start<<std::endl;
		outfile<<"wavelength units = "<<wavelength_units<<std::endl;
		outfile<<"z plot titles = {";
			outfile<<z_plot_titles[0]<<", "<<z_plot_titles[1]<<"}"<<std::endl;
		outfile<<"pixel size = {"<<pixel_size[0]<<", "<<pixel_size[1]<<", units=Meters}"<<std::endl;
		if(band_names.size() > 0)
		{
			outfile<<"band names = {"<<std::endl;
			for(int i=0; i<band_names.size(); i++)
			{
				outfile<<band_names[i];
				if(i < band_names.size() - 1)
					outfile<<", ";
			}
			outfile<<"}"<<std::endl;
		}
		outfile<<"wavelength = {"<<std::endl;
			for(int i=0; i<wavelength.size()-1; i++)
				outfile<<wavelength[i]<<", ";
			outfile<<wavelength.back()<<"}"<<std::endl;

		outfile.close();
	}

	void save()
	{
        std::cout<<"ENVI Header Name: "<<name<<std::endl;
		save(name);
	}

	//returns the size of a single value (in bytes)
	unsigned int valsize()
	{
		switch(data_type)
		{
		case 1:			//1 = 8-bit byte
			return 1;
		case 2:			//16-bit signed integer
		case 12:		//16-bit unsigned integer
			return 2;
		case 3:			//32-bit signed long integer
		case 4:			//32-bit floating point
		case 13:		//32-bit unsigned long integer
			return 4;
		case 5:			//64-bit double-precision floating point
		case 6:			//32-bit complex value
		case 14:		//64-bit signed long integer
		case 15:		//64-bit unsigned long integer
			return 8;
		case 9:			//64-bit complex value
			return 16;
		default:
			return 0;
		}

	}
};		//end EnviHeader

class EnviFile
{
	EnviHeader header;
	FILE* data;
	std::string mode;

	//a locked file has alread had data written..certain things can't be changed
	//		accessor functions deal with these issues
	bool locked;

	void init()
	{
		locked = false;
		data = NULL;
	}

	void readonly()
	{
		if(mode == "r")
		{
			std::cout<<"ENVI Error: changes cannot be made to a read-only file."<<std::endl;
			exit(1);
		}
	}

	//this function determines if the current software is capable of the requested change
	bool caps(EnviHeader new_header)
	{
		readonly();		//if the file is read-only, throw an exception

		//we currently only support BSQ
		if(new_header.interleave == EnviHeader::BIP || new_header.interleave == EnviHeader::BIL)
		{
			std::cout<<"This software only supports BSQ.";
			return false;
		}

		//if the number of bands has changed
		if(header.bands != new_header.bands)
		{
			//the new header must be a BSQ file
			if(new_header.interleave != EnviHeader::BSQ)
			{
				std::cout<<"ENVI Error: can only add bands to a BSQ file."<<std::endl;
				return false;
			}
		}

		//disallow anything that can't be done when the file is locked
		if(locked)
		{
			if(header.lines != new_header.lines)
			{
				std::cout<<"ENVI Error: cannot change the number of lines in a locked BSQ file."<<std::endl;
				return false;
			}
			if(header.samples != new_header.samples)
			{
				std::cout<<"ENVI Error: cannot change the number of samples in a locked BSQ file."<<std::endl;
				return false;
			}
			if(header.data_type != new_header.data_type)
			{
				std::cout<<"ENVI Error: cannot change the data type of a locked file."<<std::endl;
				return false;
			}
			if(header.byte_order != new_header.byte_order)
			{
				std::cout<<"ENVI Error: cannot change the byte order of a locked file."<<std::endl;
				return false;
			}
		}

		return true;

	}

	EnviHeader load_header(std::string header_file)
	{
		EnviHeader new_header;
		new_header.load(header_file);
		return new_header;
	}

	void set_header(EnviHeader new_header)
	{
		if(caps(new_header))
			header = new_header;
		else
			exit(1);
	}

public:

	EnviFile()
	{
		init();
	}

	EnviFile(std::string filename, std::string file_mode = "r")
	{
		init();
		open(filename, filename + ".hdr", file_mode);
	}

	void open(std::string file_name, std::string header_name, std::string file_mode = "r")
	{
		mode = file_mode;

		header.name = header_name;

		//open the data file
		data = fopen(file_name.c_str(), mode.c_str());

		//lock the file if we are loading or appending
		if(mode == "r" || mode == "a" || mode == "r+" || mode == "a+")
		{
			locked = true;
			//load the ENVI header - failure will cause an exit
			set_header(load_header(header_name));
		}
		else
		{
			header.name = header_name;
		}


	}

	void setDescription(std::string desc)
	{
		readonly();		//if the file is read-only, throw an exception
		header.description = desc;
	}

	void setZPlotTitles(std::string spectrum, std::string value)
	{
		readonly();		//if the file is read-only, throw an exception
		header.z_plot_titles[0] = spectrum;
		header.z_plot_titles[1] = value;
	}

	void setPixelSize(double sx, double sy)
	{
		readonly();		//if the file is read-only, throw an exception
		header.pixel_size[0] = sx;
		header.pixel_size[1] = sy;
	}

	void setWavelengthUnits(std::string units)
	{
		readonly();		//if the file is read-only, throw an exception
		header.wavelength_units = units;
	}

	void setCoordinates(double x, double y)
	{
		readonly();		//if the file is read-only, throw an exception
		header.x_start = x;
		header.y_start = y;
	}

	//FUNCTIONS THAT MAY BE DISALLOWED IN A LOCKED FILE
	void setSamples(unsigned int samples)
	{
		EnviHeader newHeader = header;
		newHeader.samples = samples;
		set_header(newHeader);
	}

	void setLines(unsigned int lines)
	{
		EnviHeader newHeader = header;
		newHeader.lines = lines;
		set_header(newHeader);
	}

	void setBands(unsigned int bands)
	{
		EnviHeader newHeader = header;
		newHeader.bands = bands;
		set_header(newHeader);
	}

	//DATA MANIPULATION
	void addBand(void* band, unsigned int samples, unsigned int lines, double wavelength, std::string band_name ="")
	{
		//add a band to the file

		EnviHeader newHeader = header;
		newHeader.bands++;
		newHeader.samples = samples;
		newHeader.lines = lines;
		newHeader.wavelength.push_back(wavelength);
		if(band_name != "")
			newHeader.band_names.push_back(band_name);
		set_header(newHeader);

		//copy the data to the file
		fwrite(band, header.valsize(), samples * lines, data);

		//since data was written, the file must be locked
		locked = true;
	}

	//close file
	void close()
	{
        std::cout<<"ENVI File Mode: "<<mode<<std::endl;

		//close the data stream
		fclose(data);

		//close the header
		if(mode != "r")
			header.save();
	}

};		//end EnviFile


#endif