Minor debugging

slsDetectorCalibration/dataStructures/HDF5File.cpp

@@ -35,6 +35,17 @@ void conditionalIncrement(std::vector<hsize_t>& vec, hsize_t max_value) {
     }
 }
 
+void printDatatypeSize(hid_t dataset) {
+
+	hid_t datatype = H5Dget_type(dataset);
+	H5T_class_t class_id = H5Tget_class(datatype);
+	size_t type_size = H5Tget_size(datatype);
+
+	std::cout << " dataset type class: " << class_id 
+          	  << ", size: " << type_size << " bytes\n";
+
+}
+
 /* 
  * Class member functions
  */
@@ -55,9 +66,15 @@ HDF5File::~HDF5File () {
 }
 */
 
-void HDF5File::SetImageDataPath (std::string const& name) { data_datasetname = name; }
+void HDF5File::SetImageDataPath (std::string const& name) { 
+	std::cout << "Image dataset path set to " << name << std::endl;
+	data_datasetname = name; 
+}
 
-void HDF5File::SetFrameIndexPath (std::string const& name) { index_datasetname = name; }
+void HDF5File::SetFrameIndexPath (std::string const& name) { 
+	std::cout << "Frame index dataset path set to " << name << std::endl;
+	index_datasetname = name; 
+}
 
 void HDF5File::InitializeDimensions () {
 
@@ -173,11 +190,15 @@ bool HDF5File::OpenFrameIndexDataset() {
 	H5Sclose (fi_dataspace);
 
 	// allocate frame index memory
-	frame_index_list.resize(file_dims[0]);
+	frame_index_list.resize(fi_dims[0]); //file_dims
+
+	// print datatype size of dataset
+	std::cout << "Frame index";
+	printDatatypeSize(fi_dataset);
 
 	//read frame index values
 	//Is u32 correct? I would think not. But I get a segmentation fault if I use u64.
-	if (H5Dread (fi_dataset, H5T_STD_U32LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, frame_index_list.data()) < 0) {
+	if (H5Dread (fi_dataset, H5T_STD_U64LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, frame_index_list.data()) < 0) {
 		cprintf (RED,"Could not read frame index dataset %s\n", index_datasetname.c_str());
 		std::cerr << "Error: Could not read frame index dataset\n";
 		H5Dclose (fi_dataset);
@@ -208,6 +229,10 @@ int HDF5File::OpenResources (char const*const fname, bool validate) {
 	}
 	cprintf(BLUE, "Opened Dataset: %s\n", data_datasetname.c_str());
 
+	// print datatype size of dataset
+	std::cout << "Image";
+	printDatatypeSize(dataset);
+
 	// Create Dataspace
 	dataspace = H5Dget_space (dataset);
 	if (dataspace < 0){
@@ -289,20 +314,6 @@ int HDF5File::ReadImage (uint16_t* image, std::vector<hsize_t>& offset ) {
 	// Initialize frame_offset
 	if (frame_offset.empty())
 		frame_offset.resize(rank,0);
-	
-	// Validate frame_offset index
-    if (frame_offset[0] >= frame_index_list.size()) {
-        std::cerr << "Error: frame_offset[0] out of bounds.\n";
-        return -99;
-    }
-
-	// Check if images exist at the current frame offset
-	if (frame_index_list[frame_offset[0]] == 0) {
-		cprintf (RED,"No images at this frame offset %llu\n", frame_offset[0]);
-		std::cerr << "Error: Framenumber 0 at this frame offset\n";
-		CloseResources ();
-		return -99;
-	}
 
 	// Check if we reached the end of file
 	// Compares that the offsets of frame and storage cell (Z and S) have reached the end of file
@@ -318,6 +329,20 @@ int HDF5File::ReadImage (uint16_t* image, std::vector<hsize_t>& offset ) {
 	}
 	*/
 
+	// Validate frame_offset index
+    if (frame_offset[0] >= frame_index_list.size()) {
+        std::cerr << "Error: frame_offset[0] = " << frame_offset[0] << " of bounds.\n";
+        return -99;
+    }
+
+	// Check if images exist at the current frame offset
+	if (frame_index_list[frame_offset[0]] == 0) {
+		cprintf (RED,"No images at this frame offset %llu\n", frame_offset[0]);
+		std::cerr << "Error: Framenumber 0 at this frame offset\n";
+		CloseResources ();
+		return -99;
+	}
+
 	// Optional: Ensure dataset and dataspace are valid
     if (dataset < 0) {
         std::cerr << "Error: Invalid dataset ID.\n";

slsDetectorCalibration/dataStructures/HDF5File.h

@@ -20,13 +20,13 @@
 
 //#define MAX_STR_LENGTH	1000
 
-#define RANK	4                       // Dimension of the image dataset, only for validation
+#define RANK	3                       // Dimension of the image dataset, only for validation
 #define DEFAULT_Z_DIMS	10000			// only for validation
 #define DEFAULT_Y_DIMS	1024			// only for validation
 #define DEFAULT_X_DIMS	512				// only for validation
 //#define DEFAULT_S_DIMS	1       	// Storage cells
 
-#define DEFAULT_CHUNK_Z_DIMS	100		// only for validation
+#define DEFAULT_CHUNK_Z_DIMS	1		// only for validation
 #define DEFAULT_CHUNK_Y_DIMS	1024	// only for validation
 #define DEFAULT_CHUNK_X_DIMS	512		// only for validation
 //#define DEFAULT_CHUNK_S_DIMS	1

slsDetectorCalibration/dataStructures/jungfrauLGADStrixelsDataQuadH5.h

@@ -377,7 +377,8 @@ class jungfrauLGADStrixelsDataQuadH5 : public slsDetectorData<uint16_t> {
     char* readNextFrame( HDF5File& hfile, int& framenumber, std::vector<hsize_t>& h5offset, char* data ) {
 
       if (framenumber >= 0) {
-        std::cout << "*";
+        if (h5offset[0] % 10 == 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)

slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess_filetxtH5.cpp

@@ -237,7 +237,7 @@ int main(int argc, char *argv[]) {
     mt->popFree(buff);
 
     int ifr = 0; //frame counter of while loop
-    int framenumber = -1; //framenumber as read from file (detector)
+    int framenumber = 0; //framenumber as read from file (detector)
     std::vector<hsize_t> h5offset(1,0); //frame counter internal to HDF5File::ReadImage (provided for sanity check/debugging)
 
     if (pedfilename.length()>1) {
@@ -257,12 +257,12 @@ int main(int argc, char *argv[]) {
 	      //HDF5File pedefile;
 	      auto pedefile = std::make_unique<HDF5File>();
         pedefile->SetFrameIndexPath(frameindexpath);
-        pedefile->SetFrameIndexPath(datasetpath);
+        pedefile->SetImageDataPath(datasetpath);
 	      //      //open file
 	      if ( pedefile->OpenResources(fname.c_str(),validate_rank) ) {
 	        std::cout << "bbbb " << std::ctime(&end_time) << std::endl;
 	    
-	        framenumber = -1;
+	        framenumber = 0;
 
 	        while ( decoder->readNextFrame(*pedefile, framenumber, h5offset, buff) ) {
 
@@ -282,7 +282,7 @@ int main(int argc, char *argv[]) {
 	      
 	          if (ifr >= 1000)
 	            break;
-	          framenumber = -1;
+	          //framenumber = 0;
 	        }
 	    
 	        pedefile->CloseResources();
@@ -371,7 +371,7 @@ int main(int argc, char *argv[]) {
 	      }
 	
 	//     //while read frame
-	      framenumber = -1;
+	      framenumber = 0;
 	      h5offset[0] = 0;
 	      ifr = 0;
 	      //std::cout << "Here! " << framenumber << " ";
@@ -403,7 +403,7 @@ int main(int argc, char *argv[]) {
 	          }
 	        }
 
-	        framenumber = -1;
+	        //framenumber = 0;
 	      }
 
 	      //std::cout << "aa --" << std::endl;