Merge pull request #4 from ic97usop/elisabeth/messaging/hdf-reading

Elisabeth/messaging/hdf reading

messaging/hdf_reader/Readme.md

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+1. Download and install CMake:  
+	▪	https://cmake.org/download/  	
+	▪	https://cmake.org/install

+2. Build HDF5 library with CMake:  
+	▪	https://www.hdfgroup.org/HDF5/release/cmakebuild.html#build
+
+3. Build and run example:    
+
+	$ cd src  
+	$ cmake CMakeLists.txt  
+	$ make  
+	$ ./HDFFileReaderExample

messaging/hdf_reader/src/CMakeLists.txt

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+cmake_minimum_required (VERSION 3.1.0)
+project (HDF5FileReaderExample)
+
+find_package (HDF5 NAMES hdf5 COMPONENTS CXX static)
+#find_package (HDF5) 
+#include_directories(${HDF5_INCLUDE_DIR})
+
+set (LINK_LIBS ${LINK_LIBS} ${HDF5_C_STATIC_LIBRARY})
+
+set (example HDFFileReaderExample)
+
+add_executable (${example} ${PROJECT_SOURCE_DIR}/${example}.cpp)
+
+target_link_libraries (${example} ${LINK_LIBS})

messaging/hdf_reader/src/HDFFileReaderExample.cpp

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+//
+// HDFFileReaderExample.cpp
+// Projectname: amos-ss16-proj5
+//
+// Created by Elisabeth Hoppe on 24.04.16.
+// Copyright (c) 2016 de.fau.cs.osr.amos2016.gruppe5
+//
+// This file is part of the AMOS Project 2016 @ FAU
+// (Friedrich-Alexander University Erlangen-Nürnberg)
+//
+// This program is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Affero General Public License as
+// published by the Free Software Foundation, either version 3 of the
+// License, or (at your option) any later version.
+//
+// This program is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU Affero General Public License for more details.
+//
+// You should have received a copy of the GNU Affero General Public
+// License along with this program. If not, see
+// <http://www.gnu.org/licenses/>.
+//
+
+#ifdef OLD_HEADER_FILENAME
+#include <iostream.h>
+#else
+#include <iostream>
+#endif
+#include <string>
+#include <vector>
+
+#ifndef H5_NO_NAMESPACE
+#ifndef H5_NO_STD
+    using std::cout;
+    using std::endl;
+#endif  // H5_NO_STD
+#endif
+
+#include "H5Cpp.h"
+
+#ifndef H5_NO_NAMESPACE
+    using namespace H5;
+#endif
+
+const H5std_string FILE_NAME( "measurement_2016-04-08-13-27-15-507.hdf5" );
+const H5std_string DATASET_NAME( "MFCImageRight" );
+
+
+int main(void)
+{
+
+   // Try block to detect exceptions raised by any of the calls inside it
+   try
+   {
+
+      // Turn off the auto-printing when failure occurs so that we can
+      // handle the errors appropriately
+      Exception::dontPrint();
+
+      // create the file and open it with read-only access.
+      H5File * file = new H5File( FILE_NAME, H5F_ACC_RDONLY );
+      DataSet dataSet = file->openDataSet(DATASET_NAME);
+
+	   // get the class of the datatype that is used by the dataset.
+       H5T_class_t typeClass = dataSet.getTypeClass();
+
+
+       // get the data space of the dataset for obtaining information about dimension, sizes, etc.
+       DataSpace dataSpace = dataSet.getSpace();
+
+       // get info about dataspace
+       int dimNumber = dataSpace.getSimpleExtentNdims();
+       hssize_t elemsNumber = dataSpace.getSimpleExtentNpoints();
+       bool isSimple = dataSpace.isSimple();
+
+       // get dimension size of each dimension
+       hsize_t dimsOut[2];
+       int nDims = dataSpace.getSimpleExtentDims(dimsOut, NULL);
+
+       if(dimsOut[1] != 2)
+       {
+    	   //TODO exception handling
+       }
+
+       if(typeClass == H5T_INTEGER)
+       {
+    	   IntType intType = dataSet.getIntType();
+
+    	   // get order of the int type
+    	   H5std_string order_string;
+    	   H5T_order_t order = intType.getOrder(order_string);
+
+    	   // get size of int type
+    	   size_t size = intType.getSize();
+
+       }
+
+       // read raw data (timestamp + imageid)
+       // go to dataset with the imageid
+       // read the dataset behind image id
+       // = protobuf file
+
+       // create buffer for reading the data
+       int64_t buffer[dimsOut[0]][dimsOut[1]];
+
+       // initialize
+       for(int i = 0; i<dimsOut[0]; i++)
+       {
+    	   for(int j = 0; j<dimsOut[1]; j++)
+    	   {
+    		   buffer[i][j] = 0;
+    	   }
+       }
+
+
+       // read buffer -> without input for memory data space the whole data space will be read
+
+       dataSet.read(buffer, PredType::NATIVE_INT64);
+
+       // read the image ids from the buffer
+
+       // vector which holds all the image ids
+       std::vector<int> vecImages;
+       for(int i = 0; i<dimsOut[0]; i++)
+       {
+    	   vecImages.push_back(buffer[i][1]);
+       }
+
+       // open dataset for every image id; read it
+       for(int i = 0; i < vecImages.size(); i++)
+       {
+    	   int currentId = vecImages.at(i);
+    	   std::string sId = std::to_string(currentId);
+    	   DataSet currentImage = file->openDataSet(sId);
+
+    	  // get the class of the datatype that is used by the dataset.
+		  H5T_class_t typeClass = dataSet.getTypeClass();
+
+		  // get the data space of the dataset for obtaining information about dimension, sizes, etc.
+		  DataSpace dataSpace = dataSet.getSpace();
+
+		  // get info about dataspace
+		  int dimNumber = dataSpace.getSimpleExtentNdims();
+		  hssize_t elemsNumber = dataSpace.getSimpleExtentNpoints();
+		  bool isSimple = dataSpace.isSimple();
+
+		  // get dimension size of each dimension
+		  hsize_t dimsOut[1];
+		  int nDims = dataSpace.getSimpleExtentDims(dimsOut, NULL);
+
+		  if(typeClass != H5T_INTEGER)
+		  {
+			   // TODO exception handling
+		  }
+
+
+		  // create buffer for reading the image data
+		  int64_t imageBuffer[dimsOut[0]];
+
+		  // initialize
+		  for(int i = 0; i<dimsOut[0]; i++)
+		  {
+			  imageBuffer[i] = 0;
+		  }
+
+
+		  // read buffer -> without input for memory data space the whole data space will be read
+
+		  dataSet.read(imageBuffer, PredType::NATIVE_INT64);
+
+		  // TODO give this data to protobuf deserializer
+
+       }
+
+       //close file
+       file->close();
+
+   }  // end of try block
+
+   // catch failure caused by the H5File operations
+   catch( FileIException error )
+   {
+      error.printError();
+      return -1;
+   }
+
+   // catch failure caused by the DataSet operations
+   catch( DataSetIException error )
+   {
+      error.printError();
+      return -1;
+   }
+
+   // catch failure caused by the DataSpace operations
+   catch( DataSpaceIException error )
+   {
+      error.printError();
+      return -1;
+   }
+
+   // catch failure caused by the DataSpace operations
+   catch( DataTypeIException error )
+   {
+      error.printError();
+      return -1;
+   }
+
+   return 0;
+}