added unsifting for BSQ files (BIP and BIL still not supported)

David Mayerich
1 parent 40a669b8
Showing 4 changed files with 118 additions and 12 deletions Show diff stats
stim/envi/bil.h
stim/envi/bip.h
stim/envi/bsq.h
stim/envi/envi.h
@@ -826,7 +826,7 @@ public:
 	}
  
 	///Saves to disk only those spectra corresponding to mask values != 0
-	bool sift_mask(std::string outfile, unsigned char* p){
+	bool sift(std::string outfile, unsigned char* p){
 		// Assume X() = X, Y() = Y, Z() = Z.
 		std::ofstream target(outfile.c_str(), std::ios::binary);
  
@@ -836,8 +836,8 @@ public:
 	}
  
  
-	///Saves to disk only those spectra corresponding to mask values != 0
-	bool sift_mask(std::string outfile, unsigned char* p){
+	/// Saves to disk only those spectra corresponding to mask values != 0
+	bool sift(std::string outfile, unsigned char* p){
 		// Assume X() = X, Y() = Y, Z() = Z.
 		std::ofstream target(outfile.c_str(), std::ios::binary);
  
@@ -759,8 +759,8 @@ public:
 		return true;
 	}
  
-	///Saves to disk only those spectra corresponding to mask values != 0
-	bool sift_mask(std::string outfile, unsigned char* p){
+	/// Saves to disk only those spectra corresponding to mask values != 0
+	bool sift(std::string outfile, unsigned char* p){
 		std::ofstream target(outfile.c_str(), std::ios::binary);
 		// open a band (XY plane)
 		unsigned XY = X() * Y(); //Number of XY pixels
@@ -788,6 +788,57 @@ public:
 		return true;
 	}
  
+	/// Generates a spectral image from a matrix of spectral values in lexicographic order and a mask
+	bool unsift(std::string outfile, unsigned char* p, unsigned int samples, unsigned int lines){
+
+		//create a binary output stream
+		std::ofstream target(outfile.c_str(), std::ios::binary);
+
+		//make sure that there's only one line
+		if(Y() != 1){
+			std::cout<<"ERROR in stim::bsq::sift() - number of lines does not equal 1"<<std::endl;
+			return false;
+		}
+
+		std::cout<<"started sifting"<<std::endl;
+
+		//get the number of pixels and bands in the input image
+		unsigned int P = X(); 					//Number of pixels
+		unsigned int B = Z();					//number of bands
+		unsigned int XY = samples * lines;		//total number of pixels in an unsifted image
+
+		// allocate memory for a sifted band
+		T * sifted = (T*)malloc(P * sizeof(T)); //allocate memory for a band
+
+		//allocate memory for an unsifted band image
+		T* unsifted = (T*) malloc(XY * sizeof(T));
+
+		//for each band
+		for(unsigned int b = 0; b < B; b++){
+
+			//set the unsifted index value to zero
+			unsigned int i = 0;
+
+			//retrieve the sifted band (masked pixels only)
+			band_index(sifted, b);
+
+			//for each pixel in the final image (treat it as a 1D image)
+			for(unsigned int xi = 0; xi < XY; xi++){
+				if( p[xi] == 0 )
+					unsifted[xi] = 0;
+				else{
+					unsifted[xi] = sifted[i];
+					i++;
+				}
+			}
+
+			//write the band image to disk
+			target.write(reinterpret_cast<const char*>(unsifted), sizeof(T) * XY);
+		}
+
+		return true;
+	}
+
  
 	/// Calculate the mean band value (average along B) at each pixel location.
  
@@ -373,32 +373,48 @@ public:
 	}
  
 	/// sift-mask saves in an array only those spectra corresponding to nonzero values of the mask. 
-	bool sift_mask(std::string outfile, unsigned char* p)
+	bool sift(std::string outfile, unsigned char* p)
 	{
  
+		//calculate the number of non-zero values in the mask
+		unsigned int nnz = 0;
+		unsigned int npixels = header.lines * header.samples;
+		for(unsigned int i = 0; i < npixels; i++)
+			if( p[i] > 0 ) nnz++;
+
+		//create a new header
+		envi_header new_header = header;
+
+		//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;
+		new_header.save(outfile + ".hdr");
+
+		std::cout<<"Saved: "<<outfile+".hdr"<<std::endl;
+
 		if (header.interleave == envi_header::BSQ){		//if the infile is bsq file
 			if (header.data_type == envi_header::float32)
-				return ((bsq<float>*)file)->sift_mask(outfile, p);
+				return ((bsq<float>*)file)->sift(outfile, p);
 			else if (header.data_type == envi_header::float64)
-				return ((bsq<double>*)file)->sift_mask(outfile, p);
+				return ((bsq<double>*)file)->sift(outfile, p);
 			else
 				std::cout << "ERROR: unidentified data type" << std::endl;
 		}
  
 		else if (header.interleave == envi_header::BIL){		//if the infile is bil file
 			if (header.data_type == envi_header::float32)
-				return ((bil<float>*)file)->sift_mask(outfile, p);
+				return ((bil<float>*)file)->sift(outfile, p);
 			else if (header.data_type == envi_header::float64)
-				return ((bil<double>*)file)->sift_mask(outfile, p);
+				return ((bil<double>*)file)->sift(outfile, p);
 			else
 				std::cout << "ERROR: unidentified data type" << 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)->sift_mask(outfile, p);
+				return ((bip<float>*)file)->sift(outfile, p);
 			else if (header.data_type == envi_header::float64)
-				return ((bip<double>*)file)->sift_mask(outfile, p);
+				return ((bip<double>*)file)->sift(outfile, p);
 			else
 				std::cout << "ERROR: unidentified data type" << std::endl;
 		}
@@ -407,9 +423,48 @@ public:
 			std::cout << "ERROR: unidentified file type" << std::endl;
 			exit(1);
 		}
+
+		
 		return false;
 	}
  
+	bool unsift(std::string outfile, unsigned char* mask, unsigned int samples, unsigned int lines){
+
+		//create a new header
+		envi_header new_header = header;
+
+		//set the number of lines and samples in the output file (that's all that changes)
+		new_header.lines = lines;
+		new_header.samples = samples;
+		new_header.save(outfile + ".hdr");
+
+
+		if (header.interleave == envi_header::BSQ){		//if the infile is bsq file
+			if (header.data_type == envi_header::float32)
+				return ((bsq<float>*)file)->unsift(outfile, mask, samples, lines);
+			else if (header.data_type == envi_header::float64)
+				return ((bsq<double>*)file)->unsift(outfile, mask, samples, lines);
+			else
+				std::cout << "ERROR: unidentified data type" << std::endl;
+		}
+
+		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
+			
+				std::cout << "ERROR in stim::envi::unsift - BIP files aren't supported yet" << std::endl;
+		}
+
+		else{
+			std::cout << "ERROR: unidentified file type" << std::endl;
+			exit(1);
+		}
+
+	}
+
 	/// Compute the ratio of two baseline-corrected peaks. The result is stored in a pre-allocated array.
  
 	/// @param lb1 is the label value for the left baseline point for the first peak (numerator)