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#ifndef ENVI_HEADER_H
#define ENVI_HEADER_H
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#include <string>
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#include <iostream>
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#include <fstream>
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#include <sstream>
#include <vector>
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#include <algorithm>
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#include <stdlib.h>
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#include <cmath>
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//information from an ENVI header file
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//A good resource can be found here: http://www.exelisvis.com/docs/enviheaderfiles.html
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namespace stim{
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struct envi_header
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{
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enum dataType {dummy0, int8, int16, int32, float32, float64, complex32, dummy7, dummy8, complex64, dummy10, dummy11, uint16, uint32, int64, uint64};
enum interleaveType {BIP, BIL, BSQ}; //bip = Z,X,Y; bil = X,Z,Y; bsq = X,Y,Z
enum endianType {endianLittle, endianBig};
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std::string name;
std::string description;
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size_t samples; //x-axis
size_t lines; //y-axis
size_t bands; //spectral axis
size_t header_offset; //header offset for binary file (in bytes)
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std::string file_type; //should be "ENVI Standard"
envi_header::dataType data_type; //data representation; common value is 4 (32-bit float)
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envi_header::interleaveType interleave;
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std::string sensor_type; //not really used
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envi_header::endianType byte_order; //little = least significant bit first (most systems)
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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
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void init(){
name = "";
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//specify default values for a new or empty ENVI file
samples = 0;
lines = 0;
bands = 0;
header_offset = 0;
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data_type = float32;
interleave = BSQ;
byte_order = endianLittle;
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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";
}
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envi_header(){
init();
}
envi_header(std::string name){
init();
load(name);
}
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//sets the wavelength vector given a starting value and uniform step size
void set_wavelengths(double start, double step){
size_t B = bands; //get the number of bands
wavelength.resize(B);
for(size_t b = 0; b < B; b++)
wavelength[b] = start + b * step;
}
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std::string trim(std::string line){
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if(line.length() == 0)
return line;
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//trims whitespace from the beginning and end of line
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size_t start_i, end_i;
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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--)
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if(line[end_i] != ' ' && line[end_i] != '\r')
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{
break;
}
return line.substr(start_i, end_i - start_i+1);
}
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std::string get_token(std::string line){
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//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;
}
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std::string get_data_str(std::string line){
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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
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std::vector<double> result;
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std::string entry;
size_t i;
do
{
i = sequence.find_first_of(',');
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entry = sequence.substr(0, i);
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sequence = sequence.substr(i+1);
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result.push_back(atof(entry.c_str()));
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//std::cout<<entry<<" ";
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}while(i != std::string::npos);
return result;
}
bool load(std::string filename)
{
//open the header file
std::ifstream file(filename.c_str());
if(!file)
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{
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std::cout<<"ERROR: unable to open header file: "<<filename<<std::endl;
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return false;
}
//the first line should just be "ENVI"
std::string line;
file>>line;
if(line != "ENVI")
{
std::cout<<"ENVI Header Error: The header doesn't appear to be an ENVI file. The first line should be 'ENVI'."<<std::endl;
exit(1);
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}
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//for each line in the file, get the token
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std::string token;
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//get a line
getline(file, line);
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while(file)
{
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//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")
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data_type = (dataType)atoi(get_data_str(line).c_str());
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else if(token == "interleave")
{
std::string interleave_str = get_data_str(line);
if(interleave_str == "bip")
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interleave = BIP;
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else if(interleave_str == "bil")
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interleave = BIL;
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else if(interleave_str == "bsq")
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interleave = BSQ;
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}
else if(token == "sensor type")
sensor_type = get_data_str(line);
else if(token == "byte order")
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byte_order = (endianType)atoi(get_data_str(line).c_str());
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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")
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wavelength_units = get_data_str(line);
//get the next line
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getline(file, line);
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}
//make sure the number of bands matches the number of wavelengths
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size_t wavelengths = wavelength.size();
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if(wavelengths && bands != wavelengths)
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{
std::cout<<"ENVI Header Error -- Number of wavelengths doesn't match the number of bands. Bands = "<<bands<<", Wavelengths = "<<wavelength.size()<<std::endl;
exit(1);
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}
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if(wavelength.size() == 0){ //if no list of wavelengths is given, create one based on band numbers
wavelength.resize(bands);
for(size_t b = 0; b < bands; b++)
wavelength[b] = (double)b;
}
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//close the file
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file.close();
//set the file name
name = filename;
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return true;
}
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 = ";
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if(interleave == BIP)
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outfile<<"bip";
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if(interleave == BIL)
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outfile<<"bil";
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if(interleave == BSQ)
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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;
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for(unsigned int i=0; i<band_names.size(); i++)
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{
outfile<<band_names[i];
if(i < band_names.size() - 1)
outfile<<", ";
}
outfile<<"}"<<std::endl;
}
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//if there is a list of wavelengths, output it
if(wavelength.size()){
outfile<<"wavelength = {"<<std::endl;
for(unsigned int i=0; i<wavelength.size()-1; i++)
outfile<<wavelength[i]<<", ";
outfile<<wavelength.back()<<"}"<<std::endl;
}
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outfile.close();
}
void save()
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{
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//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)
{
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case int8: //1 = 8-bit byte
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return 1;
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case int16: //16-bit signed integer
case uint16: //16-bit unsigned integer
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return 2;
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case int32: //32-bit signed long integer
case float32: //32-bit floating point
case uint32: //32-bit unsigned long integer
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return 4;
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case float64: //64-bit double-precision floating point
case complex32: //32-bit complex value
case int64: //64-bit signed long integer
case uint64: //64-bit unsigned long integer
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return 8;
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case complex64: //64-bit complex value
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return 16;
default:
return 0;
}
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}
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//return the number of bytes that SHOULD be in the data file
size_t data_bytes(){
return samples * lines * bands * valsize() + header_offset;
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}
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/// Convert an interleave type to a string
static std::string interleave_str(interleaveType t){
switch(t){
case stim::envi_header::BSQ:
return std::string("BSQ");
case stim::envi_header::BIL:
return std::string("BIL");
case stim::envi_header::BIP:
return std::string("BIP");
default:
std::cout<<"ERROR in stim::envi_header::typestr() - unrecognized type"<<std::endl;
exit(1);
}
}
/// Convert the current interleave type to a string
std::string interleave_str(){
return interleave_str(interleave);
}
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/// Convert a wavelength to a band index (or a pair of surrounding band indices)
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/// if the file doesn't specify wavelengths, w is assumed to be a band index
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std::vector<size_t> band_index(double w){
std::vector<size_t> idx; //create an empty array of indices
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if(wavelength.size() == 0){ //if a wavelength vector doesn't exist, assume the passed value is a band
if(w < 0 || w > bands-1) return idx; //if the band is outside the given band range, return an empty vector
size_t low, high; //allocate space for the floor and ceiling
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low = (size_t)std::floor(w); //calculate the floor
high = (size_t)std::ceil(w); //calculate the ceiling
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if(low == high) //if the floor and ceiling are the same
idx.push_back(low); //return a vector with one element (the given w matches a band exactly)
else{
idx.resize(2); //otherwise return the floor and ceiling
idx[0] = low;
idx[1] = high;
}
return idx;
}
else if(w < wavelength[0] || w > wavelength[bands-1]) return idx; //if the wavelength range is outside of the file, return an empty array
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for(size_t b = 0; b < bands; b++){ //for each band in the wavelength vector
if(wavelength[b] == w){ //if an exact match is found
idx.push_back(b); //add the band to the array and return it
return idx;
}
if(wavelength[b] >= w){ //if the current wavelength exceeds w
idx.resize(2);
idx[0] = b-1; //push both the previous and current band index
idx[1] = b;
return idx; //return the pair of indices
}
}
return idx;
}
/// Convert a wavelength range to a list of bands
std::vector<size_t> band_indices(double w0, double w1){
size_t idx0 = 0;
size_t idx1 = 0; //declare the interval indices for the band range
//get the indices for the first wavelength
std::vector<size_t> r;
if(w0 > wavelength[bands-1] || w1 < wavelength[0]){
std::cout<<"ERROR in envi_header::band_indices - wavelengths are completely out of range: ["<<w0<<", "<<w1<<"]"<<std::endl;
exit(1);
}
if(w0 < wavelength[0]) //if the lower wavelength is outside the file range
idx0 = 0; //just set it to zero
else{
r = band_index(w0);
if(r.size() == 1) //if there is an exact match, set the first interval index
idx0 = r[0];
else
idx0 = r[1]; //otherwise save the highest band index (this is the first band with wavelength > w0)
}
//get the indices for the second wavelength
if(w1 > wavelength[bands-1])
idx1 = bands-1;
else{
r = band_index(w1);
if(r.size() == 0)
idx1 = bands - 1;
else
idx1 = r[0]; //take the lowest band index (this is the last band < w1)
}
size_t n = idx1 - idx0 + 1; //calculate the number of bands in this interval
r.resize(n); //resize the band index array
for(size_t b = 0; b < n; b++){ //for each band in the interval
r[b] = idx0 + b; // insert the band in the array
}
return r; //return the index array
}
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}; //end EnviHeader
}
#endif
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