almost compiles, error: undefined reference to vtable for jungfrauLGADStrixelsDataQuadH5

slsDetectorCalibration/dataStructures/HDF5File.cpp

@@ -231,8 +231,17 @@ void HDF5File::CloseResources () {
 	//if (memspace >= 0)      H5Sclose(memspace); // VH: I am getting memory leaks after recompilation
 }
 
-
+/*
-int HDF5File::ReadImage (uint16_t** image, int& iFrame) {
+ * Function takes uint16_t* argument to make explicit that the caller has to handle memory allocation and deallocation.
+ * This is legacy caused by the structure with which the slsDetectorCalibration cluster finder is written.
+ * Best practice for modern C++ would be to rewrite using smart pointers.
+ */
+int HDF5File::ReadImage (uint16_t* image, int& iFrame) {
+  /*
+   * Originially, this function took uint16_t** but this may lead to memory management issues since image gets redirected
+   * to point to current_image, which is owned by HDF5File.
+   * (Usually, this would be good practice and classic C-style.)
+   */
 
 	// no images in this frame
 	if (frame_index_list[frame_offset[Z]] == 0) {
@@ -252,7 +261,7 @@ int HDF5File::ReadImage (uint16_t** image, int& iFrame) {
 	hid_t memspace = H5Screate_simple (RANK, frame_size, NULL);
 
 	// create hyperslab
-	// If I understand correctly, this puts dataspace such that we read the correct frame
+	// This aligns dataspace such that we read the correct frame
 	if (H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, frame_offset, NULL, frame_size, NULL) < 0 ) {
 		cprintf (RED,"Could not create hyperslab for frame count %llu\n", frame_offset[Z]);
 		CloseResources ();
@@ -260,12 +269,12 @@ int HDF5File::ReadImage (uint16_t** image, int& iFrame) {
 	}
 
 	// read dataset into current_image
-	if (H5Dread(dataset, H5T_STD_U16LE, memspace, dataspace, H5P_DEFAULT, current_image) < 0 ) {
+	if (H5Dread(dataset, H5T_STD_U16LE, memspace, dataspace, H5P_DEFAULT, image /*was 'current_image'*/) < 0 ) {
 		cprintf (RED,"Could not read dataset for frame count %llu\n", frame_offset[Z]);
 		CloseResources ();
 		return -99;
 	}
-	*image = current_image;
+	//*image = current_image; //if uint16_t** is passed, HDF5File owns the resource image points to, which is potentially dangerous
 
 	// return frame number and then increment frame count number
 	unsigned int retval = frame_index_list[frame_offset[Z]];

slsDetectorCalibration/dataStructures/HDF5File.h

@@ -71,7 +71,7 @@ public:
 	 * Read an image into current_image
 	 * @returns frame number read,
 	 */
-	int ReadImage (uint16_t** image, int& iFrame);
+	int ReadImage (uint16_t* image, int& iFrame);
 
 	/**
 	 * Print current image in memory

slsDetectorCalibration/dataStructures/jungfrauLGADStrixelsDataQuadH5.h

@@ -248,6 +248,11 @@ class jungfrauLGADStrixelsDataQuadH5 : public slsDetectorData<uint16_t> {
       remap( xmin, xmax, ymin, ymax );
     }
 
+    //The following functions are pure virtual in the base class. But I don't want them to be accessible here!
+    char* readNextFrame( std::ifstream &filebin );
+    int getFrameNumber(char *buff); //Provided via public method readNextFrame
+    int getPacketNumber(char *buff); //Not provided
+
   public:
 
     using header = sls::defs::sls_receiver_header;
@@ -317,75 +322,62 @@ class jungfrauLGADStrixelsDataQuadH5 : public slsDetectorData<uint16_t> {
         return val;
     };   
     
-    /**
 
-    Returns the frame number for the given dataset. Purely virtual func.
+    char* readNextFrame( HDF5File& hfile ) {
-    \param buff pointer to the dataset
-    \returns frame number
-
-    */
-    /*
-    int getFrameNumber(char *buff) {
-#ifdef ALDO                                      // VH
-        return ((jf_header *)buff)->bunchNumber; // VH
-#endif                                           // VH
-        return ((header *)buff)->detHeader.frameNumber;
-    };
-    */
-
-    /**
-
-       Returns the packet number for the given dataset. purely virtual func
-       \param buff pointer to the dataset
-       \returns packet number number
-
-    */
-    /*
-    int getPacketNumber(char *buff) {
-#ifdef ALDO // VH
-        // uint32_t fakePacketNumber = 1000;
-        // return fakePacketNumber; //VH //TODO: Keep in mind in case of bugs!
-        // //This is definitely bad!
-        return 1000;
-#endif // VH
-        return ((header *)buff)->detHeader.packetNumber;
-    };
-    */
-
-    char* readNextFrame(const HDF5File& hfile) {
         int fn = 0, iframe = 0;
         return readNextFrame(hfile, fn, iframe);
     };
 
-    char* readNextFrame(const HDF5File& hfile, int& fn) {
+    char* readNextFrame( HDF5File& hfile, int& fn ) {
         int iframe = 0;
         return readNextFrame(hfile, fn, iframe);
     };
 
-    char *readNextFrame(const HDF5File& hfile, int& fn, int& iframe) {
+    char* readNextFrame( HDF5File& hfile, int& fn, int& iframe ) {
-        char *data = new char[dataSize];
-        char *d = readNextFrame(hfile, fn, iframe, data);
-        if (d == NULL) {
-            delete[] data;
-            data = NULL;
-        }
-        return data;
-    };
 
-    //framenumber: Framenumber as written in the file (defined by the time of detector power on)
+      // Ensure dataSize is a valid size for allocation
-    //iframe: Counter how often ReadImage has been called, ReadImage return value
+      if (dataSize <= 0) {
-    char* readNextFrame(const HDF5File& hfile, int& framenumber, int& iframe, char* data) {
+        // Handle error case appropriately, e.g., log an error message
-
+        return nullptr;
-      if (iframe>=0) {
-	std::cout << "*";
-	iframe = hfile.ReadImage( data, framenumber )
-	  return data;
       }
-      std::cout << "#";
 
-      return NULL;
+      char* data = new char[dataSize];
+      char* readResult = readNextFrame(hfile, fn, iframe, data);
+      
+      // Check if reading failed
+      if (readResult == nullptr) {
+        delete[] data;  // Free allocated memory
+        data = nullptr;  // Set to nullptr to avoid dangling pointer
+      }
+      
+      return data; //returning data is equivalent to returning reinterpret_cast<char*>(data_ptr) as they both point to the same memory
+      
     };
 
+
+    /*
+     * This is the most recent function. This is used in the cluster finder!
+     * The overloads are legacy!
+     * Note that caller has to allocate and deallocate memory for data!
+     */
+    char* readNextFrame( HDF5File& hfile, int& framenumber, int& iframe, char* data ) {
+
+      if (iframe >= 0) {
+        std::cout << "*";
+
+	//Storing the reinterpret_cast in the variable data_ptr ensures that I can pass it to a function that expects at uint16_t*
+	uint16_t* data_ptr = reinterpret_cast<uint16_t*>(data); //now data_ptr points where data points (thus modifies the same memory)
+
+        iframe = hfile.ReadImage( data_ptr, framenumber );
+        return data; // return reinterpret_cast<char*>(data_ptr); // Equivalent
+      }
+
+      std::cout << "#";
+      return nullptr;
+    };
+
+ 
+
     /*    Loops over a memory slot until a complete frame is found (i.e. all */
     /*    packets 0 to nPackets, same frame number). purely virtual func \param
      */

slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess_filetxtH5.cpp

@@ -113,7 +113,7 @@ int main(int argc, char *argv[]) {
     double *gainmap = NULL;
     // float *gm;
 
-    int ff, np;
+    //int ff, np;
     // cout << " data size is " << dsize;
 
     const std::string txtfilename(argv[1]);
@@ -375,7 +375,9 @@ int main(int argc, char *argv[]) {
 
     //  cout << "mt " << endl;
 
-    int ifr = 0;
+    int ifr = 0; //frame counter of while loop
+    int framenumber = -1; //framenumber as read from file (detector)
+    int iframe = 0; //frame counter internal to HDF5File::ReadImage (provided for sanity check/debugging)
 
     if (pedfilename.length()>1) {
 
@@ -391,13 +393,16 @@ int main(int argc, char *argv[]) {
 
 	  mt->setFrameMode(ePedestal);
 
-	  std::ifstream pedefile(fname, ios::in | ios::binary);
+	  //std::ifstream pedefile(fname, ios::in | ios::binary);
+	  HDF5File pedefile;
 	  //      //open file
-	  if (pedefile.is_open()) {
+	  if ( pedefile.OpenResources(fname.c_str(),1) ) {
 	    std::cout << "bbbb " << std::ctime(&end_time) << std::endl;
 	    
-	    ff = -1;
+	    framenumber = -1;
-	    while (decoder->readNextFrame(pedefile, ff, np, buff)) {
+
+	    while ( decoder->readNextFrame(pedefile, framenumber, iframe, buff) ) {
+
 	      // if (np == 40) {
 	      if ((ifr + 1) % 100 == 0) {
 		std::cout
@@ -407,17 +412,18 @@ int main(int argc, char *argv[]) {
 	      mt->pushData(buff);
 	      mt->nextThread();
 	      mt->popFree(buff);
-	      ifr++;
+	      ++ifr;
 	      if (ifr % 100 == 0) {
-		std::cout << " ****" << ifr << " " << ff << " " << np
+		std::cout << " ****" << ifr << " " << framenumber << " " << iframe
 			  << std::endl;
 	      } // else
 	      //std::cout << ifr << " " << ff << " " << np << std::endl;
 	      if (ifr >= 1000)
 		break;
-	      ff = -1;
+	      framenumber = -1;
 	    }
-	    pedefile.close();
+	    //pedefile.close();
+	    pedefile.CloseResources();
 	    while (mt->isBusy()) {
 	      ;
 	    }
@@ -471,10 +477,11 @@ int main(int argc, char *argv[]) {
       std::time(&end_time);
       std::cout << std::ctime(&end_time) << std::endl;
 
-      std::ifstream filebin(filenames[ifile], ios::in | ios::binary);
+      //std::ifstream filebin(filenames[ifile], ios::in | ios::binary);
+      HDF5File fileh5;
       //      //open file
       ioutfile = 0;
-      if (filebin.is_open()) {
+      if ( fileh5.OpenResources(filenames[ifile].c_str(), 1) ) {
 	if (thr <= 0 && cf != 0) { // cluster finder
 	  if (of == NULL) {
 	    of = fopen(cfname.c_str(), "w");
@@ -490,9 +497,12 @@ int main(int argc, char *argv[]) {
 	  }
 	}
 	//     //while read frame
-	ff = -1;
+	framenumber = -1;
+	iframe = 0;
 	ifr = 0;
-	while (decoder->readNextFrame(filebin, ff, np, buff)) {
+
+	while ( decoder->readNextFrame(fileh5, framenumber, iframe, buff) ) {
+
 	  //  if (np == 40) {
 	  //         //push
 	  
@@ -507,7 +517,7 @@ int main(int argc, char *argv[]) {
 	  
 	  ifr++;
 	  if (ifr % 100 == 0)
-	    std::cout << " " << ifr << " " << ff << std::endl;
+	    std::cout << " " << ifr << " " << framenumber << std::endl;
 	  if (nframes > 0) {
 	    if (ifr % nframes == 0) {
 	      imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", ioutfile );
@@ -518,10 +528,11 @@ int main(int argc, char *argv[]) {
 	  }
 	  // } else
 	  //std::cout << ifr << " " << ff << " " << np << std::endl;
-	  ff = -1;
+	  framenumber = -1;
 	}
 	std::cout << "aa --" << std::endl;
-	filebin.close();
+	//filebin.close();
+	fileh5.CloseResources();
 	std::cout << "bb --" << std::endl;
 	while (mt->isBusy()) {
 	  ;