HSIproc bug fixes and speed enhancements

David Mayerich
1 parent 63fc1df8
Showing 4 changed files with 25 additions and 52 deletions Show diff stats
stim/envi/bil.h
stim/envi/bip.h
stim/envi/bsq.h
stim/envi/envi.h
@@ -419,7 +419,7 @@ public:
 	/// @param outname is the name of the output BIP file to be saved to disk.
 	bool bip(std::string outname, bool PROGRESS = false)
 	{
-		unsigned int S = X() * Z() * sizeof(T);		//calculate the number of bytes in a ZX slice
+		unsigned long long S = X() * Z() * sizeof(T);		//calculate the number of bytes in a ZX slice
  
 		std::ofstream target(outname.c_str(), std::ios::binary);
 		std::string headername = outname + ".hdr";
@@ -844,7 +844,7 @@ public:
  
 	/// 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){
+	bool sift(std::string outfile, unsigned char* p, bool PROGRESS = false){
 		// Assume X() = X, Y() = Y, Z() = Z.
 		std::ofstream target(outfile.c_str(), std::ios::binary);
  
@@ -878,14 +878,13 @@ public:
 					target.write((char*)spec, B * sizeof(T));		//write that spectrum to disk. Size is L2.
 				}
  
-				progress = (double) (y * X() + x) / (Y() * X()) * 100;
+				if(PROGRESS) progress = (double) ((y+1) * X() + x+1) / (Y() * X()) * 100;
 			}
 		}
 		target.close();
 		free(slice);
 		free(spec);
  
-		progress = 100;
 		return true;
 	}
  
@@ -836,7 +836,7 @@ public:
  
  
 	/// Saves to disk only those spectra corresponding to mask values != 0
-	bool sift(std::string outfile, unsigned char* mask){
+	bool sift(std::string outfile, unsigned char* mask, bool PROGRESS = false){
  
 		//reset the file pointer to the beginning of the file
 		file.seekg(0, std::ios::beg);		
@@ -875,7 +875,7 @@ public:
 				//write this pixel out
 				target.write((char *)spectrum, B * sizeof(T));
  
-				progress = (double) x / XY * 100;
+				if(PROGRESS) progress = (double) (x+1) / XY * 100;
 			}
  
 		}
@@ -884,8 +884,6 @@ public:
 		target.close();
 		free(spectrum);
  
-		progress = 100;
-
 		return true;
 	}
  
@@ -324,59 +324,35 @@ public:
 		return true;
 	}
  
-	/// Convert the current BSQ file to a BIP file with the specified file name.
-
-	/// @param outname is the name of the output BIP file to be saved to disk.
-	/*bool bip(std::string outname)
-	{
-		std::string temp = outname + "_temp";
-		std::string headtemp = temp + ".hdr";
-		//first creat a temporary bil file and convert bsq file to bil file
-		bil(temp);
-
-		stim::bil<T> n;
-		if(n.open(temp, X(), Y(), Z(), offset, w)==false){        //open infile
-			std::cout<<"ERROR: unable to open input file"<<std::endl;
-			exit(1);
-		}
-		//then convert bil file to bip file
-		progress = 0;
-		n.bip(outname);
-		n.close();
-		remove(temp.c_str());
-		remove(headtemp.c_str());
-		return true;
-	}*/
-
 	/// Convert the current BSQ file to a BIL file with the specified file name.
  
 	/// @param outname is the name of the output BIL file to be saved to disk.
 	bool bil(std::string outname, bool PROGRESS = false)
 	{
 		//simplify image resolution
-		unsigned int L = X() * Z() * sizeof(T);		//calculate the number of bytes of a ZX slice
+		//unsigned int L = X() * Z() * sizeof(T);		//calculate the number of bytes of a ZX slice
 		unsigned int jump = (Y() - 1) * X() * sizeof(T);
  
 		std::ofstream target(outname.c_str(), std::ios::binary);
 		std::string headername = outname + ".hdr";
  
-		unsigned int xz_bytes = X() * Z() * sizeof(T);
-		T * xz_slice;						//pointer to the current spectrum
-		xz_slice = (T*)malloc(xz_bytes);
+		unsigned int L = X();
+		T* line = (T*)malloc(sizeof(T) * L);
  
 		for ( unsigned y = 0; y < Y(); y++)									//for each y position
 		{
 			file.seekg(y * X() * sizeof(T), std::ios::beg);					//seek to the beginning of the xz slice
 			for ( unsigned z = 0; z < Z(); z++ )							//for each band
 			{
-				file.read((char *)(xz_slice + z * X()), sizeof(T) * X());	//read a line
+				file.read((char *)line, sizeof(T) * X());					//read a line
+				target.write((char*)line, sizeof(T) * X());					//write the line to the output file
 				file.seekg(jump, std::ios::cur);							//seek to the next band
-				if(PROGRESS) progress = (double)(y * Z() + z + 1) / (Z() * Y()) * 100;	//update the progress counter
+				if(PROGRESS) progress = (double)((y+1) * Z() + z + 1) / (Z() * Y()) * 100;	//update the progress counter
 			}
-			target.write(reinterpret_cast<const char*>(xz_slice), xz_bytes);   //write the generated XZ slice to the target file
+			//std::cout<<progress<<": "<<y<<std::endl;
 		}
  
-		free(xz_slice);
+		free(line);
 		target.close();
  
 		return true;
@@ -842,16 +818,17 @@ public:
 	/// Saves to disk only those spectra corresponding to mask values != 0
 	/// @param outfile is the name of the sifted ENVI file to be written to disk
 	/// @param unsigned char* p is the mask file used for sifting
-	bool sift(std::string outfile, unsigned char* p){
+	bool sift(std::string outfile, unsigned char* p, bool PROGRESS = false){
 		std::ofstream target(outfile.c_str(), std::ios::binary);
 		// open a band (XY plane)
 		unsigned long XY = X() * Y(); //Number of XY pixels
 		unsigned long L = XY * sizeof(T); //size of XY pixels
+		unsigned long long B = Z();
  
 		T * temp = (T*)malloc(L); //allocate memory for a band
 		T * temp_vox = (T*)malloc(sizeof(T)); //allocate memory for one voxel
  
-		for (unsigned long i = 0; i < Z(); i++)			//for each spectral bin
+		for (unsigned long i = 0; i < B; i++)			//for each spectral bin
 		{
 			band_index(temp, i);					//get the specified band (XY sheet by index)
 			for (unsigned long j = 0; j < XY; j++)		// for each pixel
@@ -864,8 +841,9 @@ public:
 					continue;
 				}
  
-				progress = (double)(i * XY + j) / (XY * Z()) * 100;
+				
 			}
+			if(PROGRESS) progress = (double)(i+1)/ B * 100;
 		}
 		target.close();
 		free(temp);
@@ -573,7 +573,7 @@ public:
 	/// Saves in an array only those spectra corresponding to nonzero values of the mask.
 	/// @param outfile is the name of the sifted output file
 	/// @param p is the mask
-	bool sift(std::string outfile, unsigned char* p)
+	bool sift(std::string outfile, unsigned char* p, bool PROGRESS = false)
 	{
  
 		//calculate the number of non-zero values in the mask
@@ -594,31 +594,29 @@ public:
 		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(outfile, p);
+				return ((bsq<float>*)file)->sift(outfile, p, PROGRESS);
 			else if (header.data_type == envi_header::float64)
-				return ((bsq<double>*)file)->sift(outfile, p);
+				return ((bsq<double>*)file)->sift(outfile, p, PROGRESS);
 			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(outfile, p);
+				return ((bil<float>*)file)->sift(outfile, p, PROGRESS);
 			else if (header.data_type == envi_header::float64)
-				return ((bil<double>*)file)->sift(outfile, p);
+				return ((bil<double>*)file)->sift(outfile, p, PROGRESS);
 			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(outfile, p);
+				return ((bip<float>*)file)->sift(outfile, p, PROGRESS);
 			else if (header.data_type == envi_header::float64)
-				return ((bip<double>*)file)->sift(outfile, p);
+				return ((bip<double>*)file)->sift(outfile, p, PROGRESS);
 			else
 				std::cout << "ERROR: unidentified data type" << std::endl;
 		}