added a larger buffer to BSQ->BIL conversion

David Mayerich
1 parent 3c714475
Showing 2 changed files with 52 additions and 5 deletions Show diff stats
stim/envi/binary.h
stim/envi/bsq.h
@@ -30,6 +30,8 @@ protected:
  
 	double progress;		//stores the progress on the current operation (accessible using a thread)
  
+	static const size_t bufferSize = 1000000000;
+
  
 	/// Private initialization function used to set default parameters in the data structure.
 	void init(){
@@ -377,18 +377,63 @@ public:
 	}
  
 	/// Convert the current BSQ file to a BIL file with the specified file name.
+	bool bil(std::string outname, bool PROGRESS = false){
+		size_t XY = X() * Y();												//number of elements in a band
+		size_t XYbytes = XY * sizeof(T);									//number of bytes in a band
+		size_t batchB = binary<T>::bufferSize / (XYbytes);					//calculate the number of slices that can fit in memory
+		size_t batchXB = X() * batchB;										//number of elements in a batch
  
+		T* ptrBatch = (T*) malloc(batchB * XYbytes);						//allocate a large buffer storing the read data
+		T* ptrSlice = (T*) malloc(sizeof(T) * batchB * X());					//allocate space for storing an output buffer
+
+		size_t jump = (Z() - batchB) * X() * sizeof(T);			//jump between writes in the output file
+
+		std::ofstream target(outname.c_str(), std::ios::binary);
+		std::string headername = outname + ".hdr";
+
+		size_t batches = ceil((double)(Z()) / (double)batchB);				//calculate the number of batches
+		T* ptrDst;
+		T* ptrSrc;
+		for(size_t c = 0; c < batches; c++){
+			target.seekp(c * batchB * sizeof(T) * X(), std::ios::beg);	//seek to the start of the current batch in the output file
+			file.read((char*)ptrBatch, sizeof(T) * X() * Y() * batchB);		//read a batch
+			if(c == (batches - 1)){
+				batchB = Z() - (batches - 1) * batchB;					//if this is the last batch, calculate the remaining # of bands
+				jump = (Z() - batchB) * X() * sizeof(T);
+			}
+			for(size_t y = 0; y < Y(); y++){								//for each line, store an XB slice in ptrDest
+				ptrDst = ptrSlice;										//initialize ptrDst to the start of the XB output slice
+				ptrSrc = ptrBatch + (y * X());
+				for(size_t b = 0; b < batchB; b++){						//for each band in the current line
+					memcpy(ptrDst, ptrSrc, X() * sizeof(T));			//copy the band line from the source to the destination
+					ptrDst += X();
+					ptrSrc += X() * Y();
+				}
+				target.write((char*)ptrSlice, sizeof(T) * X() * batchB);	//write the XB slice to disk
+				target.seekp(jump, std::ios::cur);						//seek to the beginning of the next XB slice in the batch
+			}
+			if(PROGRESS) progress = (double)(c+1)/(double)(batches) * 100;
+		}
+
+		//if(PROGRESS) progress = 100;
+
+		free(ptrBatch);
+		free(ptrSlice);
+		target.close();
+
+		return true;
+	}
 	/// @param outname is the name of the output BIL file to be saved to disk.
-	bool bil(std::string outname, bool PROGRESS = false)
-	{
+	/*bool bil(std::string outname, bool PROGRESS = false){
+
 		//simplify image resolution
 		unsigned long long jump = (Y() - 1) * X() * sizeof(T);
  
 		std::ofstream target(outname.c_str(), std::ios::binary);
 		std::string headername = outname + ".hdr";
  
-		unsigned long long L = X();
-		T* line = (T*)malloc(sizeof(T) * L);
+		unsigned long long L = X();											//calculate the number of pixels in a line
+		T* line = (T*)malloc(sizeof(T) * L);								//allocate space for a line
  
 		for ( unsigned long long y = 0; y < Y(); y++)									//for each y position
 		{
@@ -406,7 +451,7 @@ public:
 		target.close();
  
 		return true;
-	}
+	}*/
  
 	/// Return a baseline corrected band given two adjacent baseline points and their bands. The result is stored in a pre-allocated array.