added sifting for BIL files, but it sifts as a BIP

David Mayerich
1 parent 90933f7f
Showing 2 changed files with 26 additions and 16 deletions Show diff stats
stim/envi/bil.h
stim/envi/envi.h
@@ -825,40 +825,46 @@ public:
 		return true;
 	}
-	///Saves to disk only those spectra corresponding to mask values != 0
+	/// Saves to disk only those spectra corresponding to mask values != 0
+	/// Unlike the BIP and BSQ versions of this function, this version saves a different format: the BIL file is saved as a BIP
 	bool sift(std::string outfile, unsigned char* p){
 		// Assume X() = X, Y() = Y, Z() = Z.
 		std::ofstream target(outfile.c_str(), std::ios::binary);
 		//for loading pages:
 		unsigned XZ = X() * Z();		//calculate the number of values in an XZ page on disk
+		unsigned int B = Z();			//calculate the number of bands
 		unsigned L = XZ * sizeof(T);	//calculate the size of the page (in bytes)
-		T * temp = (T*)malloc(L);		//allocate memory for a temporary page
-		//for saving spectra:
-		unsigned LZ = Z() * sizeof(T);			//calculate the size of the spectrum (in bytes)
-		T * tempZ = (T*)malloc(LZ);				//allocate memory for a temporary spectrum
-		spectrum(tempZ, X() - 1, Y() - 1);	//creates a dummy spectrum by taking the last spectrum in the image
+		//allocate temporary memory for a XZ slice
+		T* slice = (T*) malloc(L);
+
+		//allocate temporary memory for a spectrum
+		T* spec = (T*) malloc(B * sizeof(T));
-		for (unsigned i = 0; i < Y(); i++)			//Select a page by choosing Y coordinate, Y()
+		//for each slice along the y axis
+		for (unsigned int y = 0; y < Y(); y++)			//Select a page by choosing Y coordinate, Y()
 		{
-			read_plane_y(temp, i);							//retrieve an ZX page, store in "temp"
-			for (unsigned j = 0; j < X(); j++)		//Select a pixel by choosing X coordinate in the page, X()
+			read_plane_y(slice, y);							//retrieve an ZX page, store in "slice"
+
+			//for each sample along X			
+			for (unsigned x = 0; x < X(); x++)		//Select a pixel by choosing X coordinate in the page, X()
 			{
-				if (p[j * X() + i] != 0)					//if the mask != 0 at that XY pixel
+				//if the mask != 0 at that xy pixel
+				if (p[y * X() + x] != 0)					//if the mask != 0 at that XY pixel
 				{
-					for (unsigned k = 0; k < Z(); k++)		//Select a voxel by choosing Z coordinate at the pixel
+					//for each band at that pixel
+					for (unsigned int b = 0; b < B; b++)		//Select a voxel by choosing Z coordinate at the pixel
 					{
-						tempZ[k] = temp[k*X() + i];		//Pass the correct spectral value from XZ page into the spectrum to be saved.
+						spec[b] = slice[b*X() + x];		//Pass the correct spectral value from XZ page into the spectrum to be saved.
 					}
-					target.write(reinterpret_cast<const char*>(tempZ), LZ);		//write that spectrum to disk. Size is L2.
+					target.write((char*)spec, B * sizeof(T));		//write that spectrum to disk. Size is L2.
 				}
-				else
-					continue;
 			}
 		}
 		target.close();
-		free(temp);
+		free(slice);
+		free(spec);
 		return true;
 	}
@@ -385,6 +385,10 @@ public:
 		//create a new header
 		envi_header new_header = header;
+		//if a BIL file is sifted, it's saved as a BIP
+		if(header.interleave == envi_header::BIL)
+			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;
 		new_header.samples = nnz;