implemented spectral cropping in BIL and BIP files

David Mayerich
1 parent 177c7863
Showing 2 changed files with 72 additions and 25 deletions Show diff stats
stim/envi/bil.h
stim/envi/bip.h
@@ -1012,27 +1012,48 @@ public:
 								   unsigned long long b0,
 								   unsigned long long b1){
-		//calculate the new number of samples and lines
-		unsigned long long sam = x1 - x0;		//samples
-		unsigned long long lin = y1 - y0;		//lines
-		unsigned long long L = sam * Z() * sizeof(T);
-		//get specified band and save
-		T* temp = (T*)malloc(L);
+		//calculate the new image parameters
+		unsigned long long samples = x1 - x0;
+		unsigned long long lines = y1 - y0;
+		unsigned long long bands = b1 - b0;
+
+		//calculate the size of a line
+		unsigned long long L = samples * sizeof(T);
+
+
+		//allocate space for a line
+		T* temp = (T*)malloc(bands * L);
+
+		//create an output stream to store the cropped file
 		std::ofstream out(outfile.c_str(), std::ios::binary);
-		unsigned long long jumpb = (X() - sam) * sizeof(T);		//jump pointer to the next band
-		//get start
-		file.seekg((y0 * X() * Z() + x0) * sizeof(T), std::ios::beg);
-		for (unsigned i = 0; i < lin; i++)
+
+		//calculate the distance between bands
+		unsigned long long jumpb = (X() - samples) * sizeof(T);
+
+		//distance needed to jump from the previous line of the last band to the next line of the first band
+		unsigned long long longjump = ((Z() - b1) * X() + b0 * X()) * sizeof(T);
+
+		//set the start position for the cropped region
+		file.seekg((y0 * X() * Z() + b0 * X() + x0) * sizeof(T), std::ios::beg);
+
+		for (unsigned x = 0; x < lines; x++)
 		{
-			for (unsigned j = 0; j < Z(); j++)
+			for (unsigned z = b0; z < b1; z++)
 			{
-				file.read((char *)(temp + j * sam), sizeof(T) * sam);
+				file.read((char *)(temp + z * samples), sizeof(T) * samples);
 				file.seekg(jumpb, std::ios::cur);    //go to the next band	
-				thread_data = (double)(i * Z() + j) / (lin * Z()) * 100;
+				thread_data = (double)(x * Z() + z) / (lines * Z()) * 100;
 			}
-			out.write(reinterpret_cast<const char*>(temp), L);   //write slice data into target file	
+
+			//write slice data into target file
+			out.write(reinterpret_cast<const char*>(temp), bands * L);
+
+			//seek to the beginning of the next X-Z slice
+			file.seekg(longjump, std::ios::cur);
 		}
+
+		//free the temporary frame
 		free(temp);
 		thread_data = 100;
@@ -1068,24 +1068,50 @@ public:
 								   unsigned long long b0,
 								   unsigned long long b1){
-		//calculate the new number of samples and lines
-		unsigned long long sam = x1 - x0;		//samples
-		unsigned long long lin = y1 - y0;		//lines
-		unsigned long long L = Z() * sizeof(T);
-		//get specified band and save
+		//calculate the new number of samples, lines, and bands
+		unsigned long long samples = x1 - x0;
+		unsigned long long lines = y1 - y0;
+		unsigned long long bands = b1 - b0;
+
+		//calculate the length of one cropped spectrum
+		unsigned long long L = bands * sizeof(T);
+
+		//unsigned long long L = Z() * sizeof(T);
+
+		//allocate space for the spectrum
 		T* temp = (T*)malloc(L);
+
+		//open an output file for binary writing
 		std::ofstream out(outfile.c_str(), std::ios::binary);
-		//get start
-		unsigned long long sp = y0 * X() + x0;		//start pixel
-		for (unsigned i = 0; i < lin; i++)
+
+		//seek to the first pixel in the cropped image
+		file.seekg( (y0 * X() * Z() + x0 * Z() + b0) * sizeof(T), std::ios::beg);
+
+		//distance between sample spectra in the same line
+		unsigned long long jump_sample = ( (Z() - b1) + b0 ) * sizeof(T);
+
+		//distance between sample spectra in adjacent lines
+		unsigned long long jump_line = (X() - x1) * Z() * sizeof(T);
+
+
+		//unsigned long long sp = y0 * X() + x0;		//start pixel
+
+		//for each pixel in the image
+		for (unsigned y = 0; y < lines; y++)
 		{
-			for (unsigned j = 0; j < sam; j++)
+			for (unsigned x = 0; x < samples; x++)
 			{
-				pixel(temp, sp + j + i * X());
+				//read the cropped spectral region
+				file.read( (char*) temp, L );
+				//pixel(temp, sp + x + y * X());
 				out.write(reinterpret_cast<const char*>(temp), L);   //write slice data into target file	
-				thread_data = (double)(i * sam + j) / (lin * sam) * 100;
+				file.seekg(jump_sample, std::ios::cur);
+
+				thread_data = (double)(y * samples + x) / (lines * samples) * 100;
 			}
+
+			file.seekg(jump_line, std::ios::cur);
 		}
 		free(temp);