fixed BIP cropping bug

David Mayerich
1 parent dd5aab2f
Showing 2 changed files with 22 additions and 17 deletions Show diff stats
stim/envi/bip.h
stim/envi/envi.h
@@ -1479,9 +1479,9 @@ public:
 								   bool PROGRESS = false){
 		//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;
+		unsigned long long samples = x1 - x0 + 1;
+		unsigned long long lines = y1 - y0 + 1;
+		unsigned long long bands = b1 - b0 + 1;
 		//calculate the length of one cropped spectrum
 		unsigned long long L = bands * sizeof(T);
@@ -1489,32 +1489,36 @@ public:
 		//unsigned long long L = Z() * sizeof(T);
 		//allocate space for the spectrum
-		T* temp = (T*)malloc(L);
+		char* temp = (char*)malloc(L);
 		//open an output file for binary writing
 		std::ofstream out(outfile.c_str(), std::ios::binary);
 		//seek to the first pixel in the cropped image
-		file.seekg( (y0 * X() * Z() + x0 * Z() + b0) * sizeof(T), std::ios::beg);
+		size_t startx = x0 * Z();
+		size_t starty = y0 * X() * Z();
+		size_t startb = b0;
+		file.seekg( (starty + startx + startb) * sizeof(T), std::ios::beg);
 		//distance between sample spectra in the same line
-		unsigned long long jump_sample = ( (Z() - b1) + b0 ) * sizeof(T);
+		size_t dist_between_samples = Z() - bands;
+		size_t jump_sample = dist_between_samples * sizeof(T);
 		//distance between sample spectra in adjacent lines
-		unsigned long long jump_line = ( X() - x1 + x0 ) * Z() * sizeof(T);
+		//unsigned long long jump_line = ( X() - x1 + x0 ) * Z() * sizeof(T);
+		size_t dist_between_lines = X() - samples;
+		size_t jump_line = dist_between_lines * 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 x = 0; x < samples; x++)
-			{
+		for (unsigned y = 0; y < lines; y++) {
+			for (unsigned x = 0; x < samples; x++) {
 				//read the cropped spectral region
-				file.read( (char*) temp, L );
+				file.read(temp, L );
 				//pixel(temp, sp + x + y * X());
-				out.write(reinterpret_cast<const char*>(temp), L);   //write slice data into target file
+				out.write(temp, L);   //write slice data into target file
 				file.seekg(jump_sample, std::ios::cur);
@@ -1524,6 +1528,7 @@ public:
 			file.seekg(jump_line, std::ios::cur);
 		}
 		free(temp);
+		out.close();
 		return true;
 	}
@@ -1545,11 +1545,11 @@ public:
 		//save the header for the cropped file
 		stim::envi_header new_header = header;
-		new_header.samples = x1 - x0;
-		new_header.lines = y1 - y0;
-		new_header.bands = b1 - b0;
+		new_header.samples = x1 - x0 + 1;
+		new_header.lines = y1 - y0 + 1;
+		new_header.bands = b1 - b0 + 1;
 		std::vector<double>::const_iterator first = new_header.wavelength.begin() + b0;
-		std::vector<double>::const_iterator last = new_header.wavelength.begin() + b1;
+		std::vector<double>::const_iterator last = new_header.wavelength.begin() + b1 + 1;
 		new_header.wavelength = std::vector<double>(first, last);
 		new_header.save(outfile + ".hdr");