From 7d43100a324109f10f92d2a4127868f320f39ead Mon Sep 17 00:00:00 2001
From: dmayerich <dmayerich@gmail.com>
Date: Tue, 10 Sep 2013 10:21:59 -0500
Subject: [PATCH] allow appending to binary files

---
 defaults.h     |   3 ++-
 fileout.cu     |   8 +++-----
 fileout.h      |   4 +++-
 main.cpp       |   4 ++--
 options.h      |   6 +++++-
 rtsEnvi.h      | 610 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
 scalarslice.cu |   6 +-----
 7 files changed, 16 insertions(+), 625 deletions(-)
 delete mode 100644 rtsEnvi.h

diff --git a/defaults.h b/defaults.h
index d2bc201..dc5182f 100644
--- a/defaults.h
+++ b/defaults.h
@@ -32,6 +32,7 @@
 //default flags
 #define DEFAULT_PLANEWAVE		false
 #define DEFAULT_VECTORSIM		false
+#define DEFAULT_APPEND          false
 //#define DEFAULT_OUTPUT_POINT	fileoutStruct::imageObjective
 
 
@@ -72,7 +73,7 @@
 #define DEFAULT_PADDING			1
 #define DEFAULT_SUPERSAMPLE		1
 
-#define DEFAULT_INTENSITY_FILE	    "out_di.bmp"
+#define DEFAULT_INTENSITY_FILE	    "testappend"
 #define DEFAULT_TRANSMITTANCE_FILE	""
 #define DEFAULT_ABSORBANCE_FILE	    ""
 #define DEFAULT_NEAR_FILE		    "out_n.bmp"
diff --git a/fileout.cu b/fileout.cu
index 9dc7bcd..076ea1a 100644
--- a/fileout.cu
+++ b/fileout.cu
@@ -113,9 +113,7 @@ void fileoutStruct::saveDetector(microscopeStruct* scope)
         scalarslice I = scope->getIntensity();
 
         if(is_binary(intFile))
-            I.toEnvi(intFile, scope->nf.lambda);
-        else
-            I.toImage(intFile);
+            I.toEnvi(intFile, scope->nf.lambda, append);
     }
     //absorbance
     if(absFile != "")
@@ -123,7 +121,7 @@ void fileoutStruct::saveDetector(microscopeStruct* scope)
         scalarslice I = scope->getAbsorbance();
 
         if(is_binary(absFile))
-            I.toEnvi(absFile, scope->nf.lambda);
+            I.toEnvi(absFile, scope->nf.lambda, append);
         else
             I.toImage(absFile);
     }
@@ -133,7 +131,7 @@ void fileoutStruct::saveDetector(microscopeStruct* scope)
         scalarslice I = scope->getTransmittance();
 
         if(is_binary(transFile))
-            I.toEnvi(transFile, scope->nf.lambda);
+            I.toEnvi(transFile, scope->nf.lambda, append);
         else
             I.toImage(transFile);
     }
diff --git a/fileout.h b/fileout.h
index e3f8887..d312e8c 100644
--- a/fileout.h
+++ b/fileout.h
@@ -18,7 +18,9 @@ struct fileoutStruct{
 	std::string farFile;		//far field filename
 	std::string intFile;		//detector intensity filename
 	std::string absFile;        //detector absorbance filename
-	std::string transFile;      //detector transmission filename
+	std::string transFile;      //detector transmission filename
+
+	bool append;                //append simulation results to existing binary files
 
 	//output type
 	enum field_type {fieldMag, fieldIntensity, fieldAbsorbance, fieldPolar, fieldImag, fieldReal, fieldAngularSpectrum};
diff --git a/main.cpp b/main.cpp
index dfdba62..f5e80ca 100644
--- a/main.cpp
+++ b/main.cpp
@@ -19,7 +19,7 @@ microscopeStruct* SCOPE;
 #include "rts/rtsMatrix.h"
 #include "rts/rtsQuaternion.h"
 
-#include "rtsEnvi.h"
+#include "envi/rtsEnvi.h"
 
 #include "warnings.h"
 
@@ -60,6 +60,6 @@ int main(int argc, char *argv[])
 	SCOPE->destroy();
 
 
-    
+
 
 }
diff --git a/options.h b/options.h
index dd0878e..8d76646 100644
--- a/options.h
+++ b/options.h
@@ -135,7 +135,7 @@ static void loadMaterials(po::variables_map vm)
 			exit(1);
 		}
 
-		
+
 		for(int i=0; i<matVec.size(); i+=2)
 		{
 			rts::material<ptype> newM(vm["lambda"].as<ptype>(), matVec[i], matVec[i+1]);
@@ -252,6 +252,10 @@ static void loadMicroscopeParams(po::variables_map vm)
 
 static void loadOutputParams(po::variables_map vm)
 {
+    //append simulation results to previous binary files
+    gFileOut.append = DEFAULT_APPEND;
+    if(vm.count("append"))
+        gFileOut.append = true;
 
 	//image parameters
 	//component of the field to be saved
diff --git a/rtsEnvi.h b/rtsEnvi.h
deleted file mode 100644
index 250526c..0000000
--- a/rtsEnvi.h
+++ /dev/null
@@ -1,610 +0,0 @@
-#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
diff --git a/scalarslice.cu b/scalarslice.cu
index 00cf806..d46976c 100644
--- a/scalarslice.cu
+++ b/scalarslice.cu
@@ -2,7 +2,7 @@
 
 #include "rts/cuda_handle_error.h"
 #include "cublas_v2.h"
-#include "rtsEnvi.h"
+#include "envi/rtsEnvi.h"
 
 scalarslice::scalarslice(int x, int y)
 {
@@ -54,7 +54,6 @@ void scalarslice::toImage(std::string filename, bool positive, rts::colormap::co
     //retrieve the maximum value
     ptype maxVal;
     HANDLE_ERROR(cudaMemcpy(&maxVal, S + result, sizeof(ptype), cudaMemcpyDeviceToHost));
-    std::cout<<"Maximum value: "<<maxVal<<std::endl;
 
     //destroy the CUBLAS handle
     cublasDestroy(handle);
@@ -80,11 +79,8 @@ void scalarslice::toEnvi(std::string filename, ptype wavelength, bool append)
     ptype* cpuData = (ptype*) malloc( memsize );
     HANDLE_ERROR(cudaMemcpy( cpuData, S, memsize, cudaMemcpyDeviceToHost));
 
-    std::cout<<"Adding band."<<std::endl;
-    std::cout<<"First value: "<<cpuData[0]<<std::endl;
     //add a band to the ENVI file
     outfile.addBand(cpuData, R[0], R[1], wavelength);
-    std::cout<<"Added band."<<std::endl;
 
     outfile.close();
 
--
libgit2 0.21.4