removed old ENVI files

David Mayerich
1 parent f6aa45e7
Showing 7 changed files with 103 additions and 469 deletions Show diff stats
envi/EnviClose.h
envi/EnviFid.h
envi/EnviHeader.h
envi/EnviOpen.h
envi/EnviRead.h
envi/EnviWrite.h
envi/envi.h
-#ifndef ENVICLOSE_H
-#define ENVICLOSE_H
-
-
-#include <fstream>
-#include <stdio.h>
-#include "EnviHeader.h"
-#include "EnviFid.h"
-#include "EnviOpen.h"
-
-// this is to close all the opened files and to create a header file for the written files
-
-static void EnviClose(EnviFidClass &fid, int dimX=0)
-{
-
-    float* zeroPtr = (float*) malloc(sizeof(float) * fid.header.nF);
-    memset(zeroPtr, 0, sizeof(float) * fid.header.nF);
-
-	if(fid.mode=="r")
-	{
-		fclose(fid.file);
-	}
-
-	else
-	{
-        int totalPixels = fid.header.sX;
-        int dimY = totalPixels/dimX;
-
-        if(totalPixels % dimX > 0)
-        {
-            dimY++;
-
-            int padding = dimY*dimX-totalPixels;
-
-            for(int p=0; p < padding; p++)
-                fwrite(zeroPtr, sizeof(float), fid.header.nF, fid.file);
-        }
-
-        //write the calculated values to the header object
-        fid.header.sX = dimX;
-        fid.header.sY = dimY;
-
-
-        //write the header file to disk
-        //TODO
-
-
-        //close the binary file
-		fclose(fid.file);
-
-	}
-
-
-
-
-}
-#endif
-
-#ifndef ENVIFID_H
-#define ENVIFID_H
-
-#include <string>
-#include <iostream>
-#include <fstream>
-#include <ctime>
-#include <sstream>
-#include "EnviHeader.h"
-using namespace std;
-
-class EnviFidClass
-{
-public:
-    //binary file name
-    string fileName;
-
-    //header structure
-	EnviHeaderClass header;
-
-	//valid flag (is the current file valid)
-	int isValid;
-
-	//file mask (NULL if the whole file is to be read)
-	char* mask;
-
-	//current position (in pixels) in the file
-	int filePos;
-
-	//read/write mode ("r" or "w")
-	string mode;
-
-	//create a variable to store a pointer to the binary file
-	FILE * file;
-
-    //constructor, set default values
-	EnviFidClass()
-	{
-        isValid = 0;
-        filePos = 0;
-    }
-
-
-};
-
-
-#endif
-#ifndef ENVIHEADER_H
-#define ENVIHEADER_H
-#include <string>
-#include <iostream>
-#include <fstream>
-#include <ctime>
-#include <sstream>
-using namespace std;
-
-enum InterleaveType {bip, bil, bsq};
-class EnviHeaderClass	//"EnviheaderClass" will be used to store data into variables sX, sY, etc.
-{
-public:
-	unsigned int sX;				//samples = "sX"
-	unsigned int sY;				//lines = "sY"
-	unsigned int nF;				//bands = "nF"
-	unsigned int headersize;		//header offset = "headersize"
-	unsigned int datatype;		//data type = "datatype"
-	InterleaveType type;
-	string units;		//wavelength units = "units" (Usully in Wavenumber or Wavelength)
-	int LoadHeader(string filename)
-	{
-        ifstream inFile;
-        //Load the header file in the same directory, for future note, might want to modify code to either "cin" the file name of have a feature in the GUI which take into account different fileneames
-        inFile.open (filename.c_str());
-
-        //If or not there is a file
-        if (!inFile)
-        {
-            cout<<"Error"<<endl;
-            return 1;
-        }
-
-        string line;
-        getline(inFile,line);
-
-        //If the 1st line of text file does not read ENVI, spit out an error.
-        if (line.compare("ENVI"))
-        {
-            cout<<"Error, not an ENVI file"<<endl;
-            return 1;
-        }
-
-        while(inFile) //Loops through entire file
-        {
-                getline(inFile,line);
-                if(line.find("samples")==0)
-                {
-                    sX=getNumber(line);				//Calls getNumber function for "samples", stores in header.sX
-                }
-                if(line.find("lines")==0)
-                {
-                    sY=getNumber(line);				//Calls getNumber function for "lines", stores in header.sY
-                }
-                if(line.find("bands")==0)
-                {
-                    nF=getNumber(line);				//Calls getNumber function for "bands", stores in header.nF
-                }
-                if(line.find("header offset")==0)
-                {
-                    headersize=getNumber(line);		//Calls getNumber function for "header offset", stores in header.headersize
-                }
-                if(line.find("data type")==0)
-                {
-                    datatype=getNumber(line);		//Calls getNumber function for "data type", stores in header.datatype
-                }
-
-                line.find("interleave");
-                if(line.find("interleave")==0)
-                {
-                    string typeStr;
-                    typeStr=getString(line);
-                    if (typeStr.find("bip")==0)
-                        type=bip;
-                    else if(typeStr.find("bsq")==0)
-                        type=bsq;
-                    else if(typeStr.find("bil")==0)
-                        type=bil;
-                    else
-                    {
-                        //throw an error and exit
-                        cout<<"Type not recognized"<<endl;
-                        return 1;
-                    }
-
-                }
-                if(line.find("wavelength units")==0)
-                {
-                    //Calls getString function for "wavelength units", stores in header.units
-                    units=getString(line);
-                }
-            }
-        return 0;
-    }
-
-
-private:
-    //retrieves a numerical parameter from a line of text
-	int getNumber(string line)
-	{
-        int result=0;
-        int position;
-        position=line.find("="); //Finds the position of the equal sign
-
-        string numStr; //Creates a string for storing data called "numStr"
-        numStr=line.substr(position+2); //Moves from the position of "=" 2 spaces to the right...
-        istringstream convert(numStr);  //...and converts the string into numbers using "istringstream"
-
-        convert>>result; //converts result from previous line
-
-        return result;
-    }
-    //retrieves a string parameter from a line of text
-    string getString(string line)
-    {
-        int position;
-        position=line.find("="); //Finds the position of the equal sign
-
-        string word; //Creates a string for storing word data called "word"
-        word=line.substr(position+2); //Moves from the position of "=" 2 spaces to the right
-                                      //Note: We do not need to convert word using "istringstream"
-
-        return word;
-    }
-};
-#endif
-#ifndef ENVIOPEN_H
-#define ENVIOPEN_H
-#include <string>
-#include <iostream>
-#include <fstream>
-#include <ctime>
-#include <sstream>
-#include <stdio.h>
-#include "EnviHeader.h"
-#include "EnviFid.h"
-using namespace std;
-
-
-
-//return value is incorrect
-static EnviFidClass EnviOpen(string filename, char* mask = NULL, string mode = "r", int nBands = 0, int sX = 0)
-{
-	//create a file ID object
-	EnviFidClass fid;
-
-    //set the file read/write mode
-    fid.mode = mode;
-
-    //set the mask (if specified)
-	fid.mask = mask;
-
-	// load the header file only while reading
-	if(mode=="r")
-	{
-        //load the header file
-        int error = fid.header.LoadHeader(filename);
-
-        //if the LoadHeader function is not zero, the header is invalid
-        if (error != 0)
-        {
-            fid.isValid = 0;
-            return fid;
-        }
-
-	}
-
-	//default header to be used in case of writing a file
-	else
-	{
-
-		fid.header.datatype= 4;
-		fid.header.nF= nBands;
-		fid.header.sX=0;
-		fid.header.sY=1;
-		fid.header.headersize=0;
-	}
-    //load the binary file associated with this header
-        //get the binary file name
-
-	 //find the binary file name
-
-    //locate the position of the extension
-    int pos = filename.find(".hdr");
-    string binaryname = filename.substr(0, pos);
-        //load the binary file using fopen()
-        //store the resulting FILE pointer in the EnviFidClass variable
-	mode += "b";
-	fid.file = fopen (binaryname.c_str(), mode.c_str());
-	if(fid.file == NULL)
-	{
-		cout<<"Error opening binary file."<<endl;
-		fid.isValid = 0;
-		return fid;
-	}
-
-	//set the file name
-	fid.fileName = binaryname;
-
-    fid.isValid = 1;
-	return fid;
-}
-
-static EnviFidClass EnviOpen(EnviFidClass fid, char* mask = NULL, string mode = "r")
-{
-	string filename = fid.fileName;
-	filename += ".hdr";
-
-	return EnviOpen(filename, mask, mode);
-}
-
-#endif
-
-#ifndef ENVIREAD_H
-#define ENVIREAD_H
-
-#include <string>
-#include <iostream>
-#include <fstream>
-#include <ctime>
-#include <sstream>
-#include <stdio.h>
-#include "EnviHeader.h"
-#include "EnviFid.h"
-#include "EnviOpen.h"
-using namespace std;
-
-
-static int EnviRead(float* ptr, int nPixels, EnviFidClass &fid)
-{
-    //number of values to read from the file
-    int totalPixels = fid.header.sX * fid.header.sY;
-
-    //ERROR TEST: make sure that fid.file is a valid file pointer
-    if (fid.file == NULL)
-    {
-    cout<<"Binary file isn't open."<<endl;
-    return 0;
-    }
-
-    //---------MASK implementation
-
-
-    int i=0;
-    unsigned int sizeRead;
-    //iterate through every pixel in the image
-    //while we have not encountered the end of the file AND we have not read nPixels pixels
-    while(fid.filePos < totalPixels && i < nPixels)
-    {
-        //if there is no mask OR the current pixel is valid, read it
-        if(fid.mask == NULL || fid.mask[fid.filePos] == 1)
-        {
-            //read the pixel directly from disk
-            sizeRead = fread(&ptr[fid.header.nF * i], sizeof(float), fid.header.nF, fid.file);
-
-            //catch an error if one occurs
-            if (sizeRead != fid.header.nF)
-            {
-                cout<<"Error during read # "<<i<<endl;
-                return 0;
-            }
-            i++;
-        }
-
-
-        //otherwise, skip it
-        else
-            fseek(fid.file, sizeof(float) * fid.header.nF, SEEK_CUR);
-
-        //increment the file position (used to index into the mask)
-        fid.filePos++;
-
-    }
-
-    return i;
-}
-
-#endif
-#ifndef ENVIWRITE_H
-#define ENVIWRITE_H
-#include <fstream>
-#include <stdio.h>
-#include "EnviHeader.h"
-#include "EnviFid.h"
-#include "EnviOpen.h"
-
-// Take a memory pointer, and copy all of that data to disk.
-static int EnviWrite(float* ptr, int npixels, EnviFidClass &fid)
-{
-    if(fid.mode == "r") return 0;
-
-	//open a binary file for writing
-    if (fid.file == NULL)
-    {
-        cout<<"Binary file isn't open."<<endl;
-        return 1;
-    }
-
-    //allocate an array of zeros equal to the size of a single pixel
-    float* zeroPtr = (float*) malloc(sizeof(float) * fid.header.nF);
-    memset(zeroPtr, 0, sizeof(float) * fid.header.nF);
-
-
-    int j = 0;
-    //for each pixel send to the EnviRead function
-    for(int p = 0; p<npixels; p++)
-    {
-
-        //while the mask is zero
-        while(fid.mask[fid.filePos] == 0)
-        {
-            //increment filePos
-            fid.filePos++;
-            fid.header.sX++;
-            j++;
-
-            //write a sequence of zeros
-            size_t results= fwrite(zeroPtr, sizeof(float), fid.header.nF, fid.file);
-            //check for errors
-            if (results != fid.header.nF)
-            {
-                cout<<"Error during read # "<<j<<endl;
-                return 0;
-            }
-        }
-
-        //write a pixel
-        size_t results= fwrite(&ptr[fid.header.nF * p], sizeof(float), fid.header.nF, fid.file);
-        if (results != fid.header.nF)
-        {
-            cout<<"Error during read # "<<j<<endl;
-            return 0;
-        }
-
-        //increment filePos
-        fid.filePos++;
-        fid.header.sX++;
-        j++;
-    }
-
-    return j;
-
-}
-
-
-
-
-
-#endif
@@ -10,7 +10,11 @@
 namespace stim{
-//container class for an ENVI binary file reader
+/** This class implements reading of ENVI hyperspectral files. These files can be stored in multiple orientations
+	(including BSQ, BIP, and BIL) in order to optimize streaming speed depending on applications. Basic ENVI
+	files are stored on disk as a large binary file with a corresponding header. Code for reading and processing
+	ENVI header files is in the envi_header class.
+*/
 class envi{	
 	void* file;		//void pointer to the relevant file reader (bip, bsq, or bil - with appropriate data type)
@@ -19,6 +23,7 @@ public:
 	envi_header header;
+	/// Allocate memory for a new ENVI file based on the current interleave format (BIP, BIL, BSQ) and data type.
 	bool allocate(){
 		file = NULL;	//set file to a NULL pointer
@@ -46,6 +51,10 @@ public:
 	}
+	/// Open an existing ENVI file given the file and header names.
+
+	/// @param filename is the name of the ENVI binary file
+	/// @param headername is the name of the ENVI header file
 	bool open(std::string filename, std::string headername){
 		//allocate memory
@@ -95,7 +104,11 @@ public:
 	}
-	//perform normalization
+	/// Normalize a hyperspectral ENVI file given a band number and threshold.
+
+	/// @param outfile is the name of the normalized file to be output
+	/// @param band is the band label to be output
+	/// @param threshold is a threshold value specified such that normalization will only be done to values in the band > threshold (preventing division by small numbers)
 	bool normalize(std::string outfile, double band, double threshold = 0.0){
 		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
@@ -132,7 +145,10 @@ public:
 		return false;
 	}
-	//perform baseline correction
+	/// Performs piecewise linear baseline correction of a hyperspectral file/
+
+	/// @param outfile is the file name for the baseline corrected output
+	/// @param w is a list of band labels to serve as baseline points (zero values)
 	bool baseline(std::string outfile, std::vector<double> w){
 		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
@@ -174,7 +190,10 @@ public:
 		}
 	}
-	//perform conversion
+	/// Converts ENVI files between interleave types (BSQ, BIL, and BIP)
+
+	/// @param outfile is the file name for the converted output
+	/// @param interleave is the interleave format for the destination file
 	bool convert(std::string outfile, stim::envi_header::interleaveType interleave){
 		if(header.interleave == envi_header::BSQ){			//if the infile is bsq file
@@ -275,7 +294,11 @@ public:
 	}
-	//create a mask based on a band and threshold, save it to p (if p is not NULL)
+	/// Builds a mask from a band image and threshold value
+
+	/// @param mask_band is the label for the band that will be used to build the mask
+	/// @param threshold is a value selected such that all band values greater than threshold will have a mask value of 'true'
+	/// @param p is memory of size X*Y that will store the resulting mask
 	bool build_mask(double mask_band, double threshold, unsigned char* p = NULL)	{
 		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
@@ -308,7 +331,10 @@ public:
 		return false;
 	}
-	//apply mask
+	/// Applies a mask to the ENVI file.
+
+	/// @param outfile is the name of the resulting masked output file
+	/// @param p is memory of size X*Y containing the mask (0 = false, all other values are true)
 	bool apply_mask(std::string outfile, unsigned char* p)	
 	{
@@ -346,7 +372,15 @@ public:
 		return false;
 	}
-	//peak height to peak height ratio
+	/// Compute the ratio of two baseline-corrected peaks. The result is stored in a pre-allocated array.
+
+	/// @param lb1 is the label value for the left baseline point for the first peak (numerator)
+	/// @param rb1 is the label value for the right baseline point for the first peak (numerator)
+	/// @param pos1 is the label value for the first peak (numerator) position
+	/// @param lb2 is the label value for the left baseline point for the second peak (denominator)
+	/// @param rb2 is the label value for the right baseline point for the second peak (denominator)
+	/// @param pos2 is the label value for the second peak (denominator) position
+	/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
 	bool ph_to_ph(double lb1, double rb1, double pos1, double lb2, double rb2, double pos2, void * result){
 		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
 			if(header.data_type ==envi_header::float32)
@@ -382,7 +416,15 @@ public:
 		return false;
 	}
-	//peak area to peak height ratio
+	/// Compute the ratio between a peak area and peak height.
+
+	/// @param lb1 is the label value for the left baseline point for the first peak (numerator)
+	/// @param rb1 is the label value for the right baseline point for the first peak (numerator)
+	/// @param pos1 is the label value for the first peak (numerator) position
+	/// @param lb2 is the label value for the left baseline point for the second peak (denominator)
+	/// @param rb2 is the label value for the right baseline point for the second peak (denominator)
+	/// @param pos2 is the label value for the second peak (denominator) position
+	/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
 	bool pa_to_ph(double lb1, double rb1, double lab1, double rab1, double lb2, double rb2, double pos, void * result){
 		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
 			if(header.data_type ==envi_header::float32)
@@ -418,7 +460,17 @@ public:
 		return false;
 	}
-	//peak area to peak area ratio
+	/// Compute the ratio between two peak areas.
+
+	/// @param lb1 is the label value for the left baseline point for the first peak (numerator)
+	/// @param rb1 is the label value for the right baseline point for the first peak (numerator)
+	/// @param lab1 is the label value for the left bound (start of the integration) of the first peak (numerator)
+	/// @param rab1 is the label value for the right bound (end of the integration) of the first peak (numerator)
+	/// @param lb2 is the label value for the left baseline point for the second peak (denominator)
+	/// @param rb2 is the label value for the right baseline point for the second peak (denominator)
+	/// @param lab2 is the label value for the left bound (start of the integration) of the second peak (denominator)
+	/// @param rab2 is the label value for the right bound (end of the integration) of the second peak (denominator)	
+	/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
 	bool pa_to_pa(double lb1, double rb1, double lab1, double rab1,
 					double lb2, double rb2, double lab2, double rab2, void* result){
 		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
@@ -455,7 +507,13 @@ public:
 		return false;
 	}
-		//center of gravity
+	/// Compute the centroid of a baseline corrected peak.
+
+	/// @param lb is the label value for the left baseline point
+	/// @param rb is the label value for the right baseline point
+	/// @param lab is the label for the start of the peak
+	/// @param rab is the label for the end of the peak
+	/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
 	bool cpoint(double lb1, double rb1, double lab1, double rab1, void* result){
 		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
 			if(header.data_type ==envi_header::float32)
@@ -491,6 +549,7 @@ public:
 		return false;
 	}
+	/// Closes the ENVI file.
 	bool close(){
 		if(header.interleave == envi_header::BSQ){
 			if(header.data_type ==envi_header::float32)
@@ -526,7 +585,11 @@ public:
 		}
 		return false;
 	}
-	//get one pixel from binary file
+
+	/// Retrieve a single pixel and stores it in pre-allocated memory.
+
+	/// @param p is a pointer to pre-allocated memory at least sizeof(T) in size.
+	/// @param n is an integer index to the pixel using linear array indexing.
 	bool pixel(void * p, unsigned n){
 		if(header.interleave == envi_header::BSQ){
 			if(header.data_type ==envi_header::float32)
@@ -561,6 +624,7 @@ public:
 		return false;
 	}
+	/// Saves a header file describing the current ENVI file parameters.
 	bool save_header(std::string filename){
 		//save the header file here
@@ -569,6 +633,10 @@ public:
 		return true;
 	}
+	/// Retrieve a single band (by numerical label) and stores it in pre-allocated memory.
+
+	/// @param p is a pointer to an allocated region of memory at least X * Y * sizeof(T) in size.
+	/// @param wavelength is a floating point value (usually a wavelength in spectral data) used as a label for the band to be copied.
 	bool band(void* ptr, double wavelength){
 		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
@@ -604,6 +672,10 @@ public:
 		return false;
 	}
+	/// Retrieve a single band (based on index) and stores it in pre-allocated memory.
+
+	/// @param p is a pointer to an allocated region of memory at least X * Y * sizeof(T) in size.
+	/// @param page <= B is the integer number of the band to be copied.
 	bool band_index(void* ptr, unsigned int b){
 		if (header.interleave == envi_header::BSQ){		//if the infile is bsq file
 			if (header.data_type == envi_header::float32)
@@ -638,7 +710,10 @@ public:
 		return false;
 	}
-	//load mask from maskfile and save it into memory
+	/// Helper function that loads a mask into memory given a filename.
+
+	/// @param mask is a pointer to pre-allocated memory of size X*Y
+	/// @param maskname is the file name for the image that will serve as the mask
 	bool load_mask(unsigned char * mask, std::string maskname){
 		//open the mask file
 		stim::image<unsigned char> mask_image(maskname);
@@ -693,7 +768,10 @@ public:
 		return true;
 	}
-	//calculate band average
+	/// Calculate the mean value for all masked (or valid) pixels in a band and returns the average spectrum
+
+	/// @param p is a pointer to pre-allocated memory of size [B * sizeof(T)] that stores the mean spectrum
+	/// @param mask is a pointer to memory of size [X * Y] that stores the mask value at each pixel location
 	bool avg_band(void * p, unsigned char* mask){
 		if (header.interleave == envi_header::BSQ){
 			if (header.data_type == envi_header::float32)
@@ -728,7 +806,11 @@ public:
 		return false;
 	}
-	//calculate correlation coefficient matrix with mask
+	/// Calculate the covariance matrix for all masked pixels in the image.
+
+	/// @param co is a pointer to pre-allocated memory of size [B * B] that stores the resulting covariance matrix
+	/// @param avg is a pointer to memory of size B that stores the average spectrum
+	/// @param mask is a pointer to memory of size [X * Y] that stores the mask value at each pixel location
 	bool co_matrix(void* co, void* avg, unsigned char* mask){
 		if (header.interleave == envi_header::BSQ){
 			if (header.data_type == envi_header::float32)
@@ -764,7 +846,13 @@ public:
 	}
-	//crop specified area the of the original file
+	/// Crop a region of the image and save it to a new file.
+
+	/// @param outfile is the file name for the new cropped image
+	/// @param x0 is the lower-left x pixel coordinate to be included in the cropped image
+	/// @param y0 is the lower-left y pixel coordinate to be included in the cropped image
+	/// @param x1 is the upper-right x pixel coordinate to be included in the cropped image
+	/// @param y1 is the upper-right y pixel coordinate to be included in the cropped image
 	bool crop(std::string outfile,unsigned x0, unsigned y0, unsigned x1, unsigned y1){
 		if (header.interleave == envi_header::BSQ){