Merge branch 'master' of https://git.stim.ee.uh.edu/codebase/stimlib into pranathi_stimlib

pranathivemuri
2 parents 1ab6c061 f92397d2
Showing 3 changed files with 73 additions and 39 deletions Show diff stats
stim/envi/binary.h
stim/envi/envi.h
stim/parser/filename.h
@@ -66,6 +66,12 @@ protected:
 	}
+	/// Private helper function that resets the file pointer to the beginning of the data
+
+	void reset(){
+		file.seekg(header, std::ios_base::beg);
+	}
+
 	/// Private helper file that opens a specified binary file.
 	/// @param filename is the name of the binary file to stream
@@ -89,12 +95,14 @@ protected:
 			if(test_file_size())	//test the file size
 				return true;
 		}
-		
+
 		return false;
 	}
+
+
 public:
 	unsigned int get_thread_data(){
@@ -119,6 +127,8 @@ public:
 		if(!open_file(filename)) return false;	//open the binary file
+		//reset();
+
 		return test_file_size();
 	}
@@ -158,7 +168,7 @@ public:
 			exit(1);
 		}
-		file.seekg(R[1] * R[0] * page * sizeof(T), std::ios::beg);   //seek to the desired location on disk
+		file.seekg(R[1] * R[0] * page * sizeof(T) + header, std::ios::beg);   //seek to the desired location on disk
 		file.write((char *)p, R[0] * R[1] * sizeof(T));				 //write binary data
 		return true;
@@ -175,7 +185,7 @@ public:
 			return false;
 		}
-		file.seekg(R[1] * R[0] * page * sizeof(T), std::ios::beg);   //write into memory from the binary file
+		file.seekg(R[1] * R[0] * page * sizeof(T) + header, std::ios::beg);   //write into memory from the binary file
 		file.read((char *)p, R[0] * R[1] * sizeof(T));
 		return true;
@@ -220,7 +230,7 @@ public:
 		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
-		
+
 		return true;
 	}
@@ -15,7 +15,7 @@ namespace stim{
 	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{	
+class envi{
 	void* file;		//void pointer to the relevant file reader (bip, bsq, or bil - with appropriate data type)
@@ -23,6 +23,14 @@ public:
 	envi_header header;
+	/// Returns the size of the data type in bytes
+	unsigned int type_size(){
+		if(header.data_type == envi_header::float32) return 4;
+		if(header.data_type == envi_header::float64) return 8;
+
+		exit(1);
+	}
+
 	/// Returns the progress of the current processing operation as a percentage
 	void reset_progress(){
@@ -123,17 +131,14 @@ public:
 	}
-	/// Open an existing ENVI file given the file and header names.
+	/// Open an existing ENVI file given the filename and a header structure
 	/// @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
+	/// @param header is an ENVI header structure
+	bool open(std::string filename, stim::envi_header h){
 		allocate();
-		//load the header
-		header.load(headername);
+		header = h;
 		//load the file
 		if(header.interleave == envi_header::BSQ) {		//if the infile is bsq file
@@ -157,7 +162,7 @@ public:
 			else
 				return false;
 		}
-				
+
 		else if(header.interleave == envi_header::BIP) {		//if the infile is bip file
 			if(header.data_type == envi_header::float32) {
 				return ((bip<float>*)file)->open(filename, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
@@ -166,14 +171,30 @@ public:
 				return ((bip<double>*)file)->open(filename, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
 			}
 			else
-				return false;		
-		}
-		
-		else{
-		std::cout<<"ERROR: unidentified type file       "<<headername<<std::endl;
-		exit(1);
+				return false;
 		}
+		return true;
+
+	}
+
+	/// 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
+		//allocate();
+
+		stim::envi_header h;
+		h.load(headername);
+
+		//load the header
+		//header.load(headername);
+
+		return open(filename, h);
+
 	}
 	/// Normalize a hyperspectral ENVI file given a band number and threshold.
@@ -182,7 +203,7 @@ public:
 	/// @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
 			if(header.data_type ==envi_header::float32)
 				return ((bsq<float>*)file)->normalize(outfile, band, threshold);
@@ -245,7 +266,7 @@ public:
 			}
 		}
-		else if(header.interleave == envi_header::BIP){		//if the infile is bip file 
+		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
 			if(header.data_type ==envi_header::float32)
 				return ((bip<float>*)file)->baseline(outfile, w);
 			else if(header.data_type == envi_header::float64)
@@ -291,10 +312,10 @@ public:
 				else if(interleave == envi_header::BIP)
 					return ((bsq<double>*)file)->bip(outfile);
 			}
-			
+
 			else{
 				std::cout<<"ERROR: unidentified data type"<<std::endl;
-				exit(1);				
+				exit(1);
 			}
 		}
@@ -321,15 +342,15 @@ public:
 				else if(interleave == envi_header::BIP)
 					return ((bil<double>*)file)->bip(outfile);
 			}
-			
+
 			else{
 				std::cout<<"ERROR: unidentified data type"<<std::endl;
-				exit(1);				
+				exit(1);
 			}
 		}
 		else if(header.interleave == envi_header::BIP){
-		
+
 			if(header.data_type ==envi_header::float32){		//if the data type of infile is float
 				if(interleave == envi_header::BIP){
 					std::cout<<"ERROR:  is already BIP file"<<std::endl;
@@ -351,19 +372,19 @@ public:
 				else if(interleave == envi_header::BSQ)			//if the target file is bsq file
 					return ((bip<double>*)file)->bsq(outfile);
 			}
-			
+
 			else{
 				std::cout<<"ERROR: unidentified data type"<<std::endl;
-				exit(1);				
+				exit(1);
 			}
 		}
-		
+
 		else{
 			std::cout<<"ERROR: unidentified interleave type"<<std::endl;
 			exit(1);
 		}
 		return false;
-	
+
 	}
 	/// Builds a mask from a band image and threshold value
@@ -444,7 +465,7 @@ public:
 		return false;
 	}
-	/// sift-mask saves in an array only those spectra corresponding to nonzero values of the mask. 
+	/// sift-mask saves in an array only those spectra corresponding to nonzero values of the mask.
 	bool sift(std::string outfile, unsigned char* p)
 	{
@@ -459,7 +480,7 @@ public:
 		//if a BIL file is sifted, it's saved as a BIP
 		if(header.interleave == envi_header::BIL)
-			new_header.interleave = envi_header::BIP;		
+			new_header.interleave = envi_header::BIP;
 		//set the number of lines to 1 (this is a matrix with 1 line and N samples)
 		new_header.lines = 1;
@@ -500,7 +521,7 @@ public:
 			exit(1);
 		}
-		
+
 		return false;
 	}
@@ -525,12 +546,12 @@ public:
 		}
 		else if (header.interleave == envi_header::BIL){		//if the infile is bil file
-			
+
 				std::cout << "ERROR in stim::envi::unsift - BIL files aren't supported yet" << std::endl;
 		}
 		else if (header.interleave == envi_header::BIP){		//if the infile is bip file
-			
+
 			if (header.data_type == envi_header::float32)
 				return ((bip<float>*)file)->unsift(outfile, mask, samples, lines);
 			else if (header.data_type == envi_header::float64)
@@ -642,7 +663,7 @@ public:
 	/// @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 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){
@@ -922,7 +943,7 @@ public:
 		}
 		return false;
 	}
-	
+
 	/// Helper function that loads a mask into memory given a filename.
 	/// @param mask is a pointer to pre-allocated memory of size X*Y
@@ -3,6 +3,7 @@
 #include <stdio.h>  /* defines FILENAME_MAX */
 #ifdef _WIN32
+	#include <windows.h>
     #include <direct.h>
     #define GetCurrentDir _getcwd
 	#define STIM_FILENAME_DIV '\\'
@@ -17,6 +18,7 @@
 #include <vector>
 #include <stack>
 #include <algorithm>
+#include <iostream>
 #include "../parser/parser.h"
 namespace stim{
@@ -203,7 +205,6 @@ public:
 #ifdef _WIN32
-#include <windows.h>
 	//get a list of files matching the current template
 	std::vector<stim::filename> get_list(){
@@ -230,7 +231,7 @@ public:
 				file_list.push_back(current_file);
 			}
 			FindClose(hFind);
-
+
 		return file_list;
 	}
@@ -312,4 +313,6 @@ public:
 }	//end namespace stim
+
 #endif
+