Merge pull request #203 from slizzered/topic-readMeta_cc

ReadMeta function to get the CollectionType

Author: f-schmitt-zih

src/DCGroup.cpp

@@ -1,5 +1,6 @@
 /**
  * Copyright 2013 Felix Schmitt
+ *           2015 Carlchristian Eckert
  *
  * This file is part of libSplash. 
  * 
@@ -25,8 +26,11 @@
 #include <sstream>
 #include <cassert>
 #include <string.h>
+#include <typeinfo>
 
 #include "splash/core/DCGroup.hpp"
+#include "splash/basetypes/basetypes.hpp"
+#include <splash/basetypes/generateCollectionType.hpp>
 
 #define H5_TRUE 1
 #define H5_FALSE 0
@@ -196,8 +200,16 @@ namespace splash
             if (obj_info.type == H5O_TYPE_DATASET)
             {
                 if (param->entries)
+                {
                     param->entries[param->count].name = currentBaseName;
 
+                    hid_t dataset_id = H5Oopen_by_idx(base, ".", H5_INDEX_NAME, H5_ITER_INC, i, H5P_DEFAULT);
+                    hid_t datatype_id = H5Dget_type(dataset_id);
+                    param->entries[param->count].colType = generateCollectionType(datatype_id);
+                    H5Dclose(datatype_id);
+                    H5Oclose(dataset_id);
+                }
+
                 param->count++;
             }
         }

src/ParallelDataCollector.cpp

@@ -558,6 +558,20 @@ namespace splash
                 localSize, globalOffset, sizeRead, ndims, buf);
     }
 
+     CollectionType* ParallelDataCollector::readMeta(int32_t id,
+             const char* name,
+             const Dimensions dstBuffer,
+             const Dimensions dstOffset,
+             Dimensions& sizeRead) throw (DCException)
+     {
+         if (fileStatus != FST_READING && fileStatus != FST_WRITING)
+             throw DCException(getExceptionString("readMeta", "this access is not permitted"));
+
+         uint32_t ndims = 0;
+         return readDataSetMeta(handles.get(id), id, name, dstBuffer, dstOffset,
+                 Dimensions(0, 0, 0), sizeRead, ndims);
+     }
+
     void ParallelDataCollector::write(int32_t id, const CollectionType& type, uint32_t ndims,
             const Selection select, const char* name, const void* buf)
     throw (DCException)
@@ -957,6 +971,40 @@ namespace splash
         dataset.close();
     }
 
+    CollectionType* ParallelDataCollector::readDataSetMeta(H5Handle h5File,
+            int32_t id,
+            const char* name,
+            const Dimensions dstBuffer,
+            const Dimensions dstOffset,
+            const Dimensions srcOffset,
+            Dimensions &sizeRead,
+            uint32_t& srcDims)
+    throw (DCException)
+    {
+        log_msg(2, "readDataSetMeta");
+
+        std::string group_path, dset_name;
+        DCDataSet::getFullDataPath(name, SDC_GROUP_DATA, id, group_path, dset_name);
+
+        DCGroup group;
+        group.open(h5File, group_path);
+
+        DCDataSet dataset(dset_name.c_str());
+        dataset.open(group.getHandle());
+
+        size_t entrySize;
+        getEntriesForID(id, NULL, &entrySize);
+        std::vector<DataCollector::DCEntry> entries(entrySize);
+
+        getEntriesForID(id, &(*entries.begin()), NULL);
+
+        Dimensions src_size(dataset.getSize() - srcOffset);
+        dataset.read(dstBuffer, dstOffset, src_size, srcOffset, sizeRead, srcDims, NULL);
+        dataset.close();
+
+        return entries[0].colType;
+    }
+
     void ParallelDataCollector::writeDataSet(H5Handle group,
             const Dimensions globalSize,
             const Dimensions globalOffset,

src/SerialDataCollector.cpp

@@ -37,6 +37,7 @@
 #include "splash/core/DCHelper.hpp"
 #include "splash/core/SDCHelper.hpp"
 #include "splash/core/logging.hpp"
+#include "splash/basetypes/basetypes.hpp"
 
 namespace splash
 {
@@ -428,6 +429,21 @@ namespace splash
                 Dimensions(0, 0, 0), sizeRead, ndims, data);
     }
 
+    CollectionType* SerialDataCollector::readMeta(int32_t id,
+            const char* name,
+            const Dimensions dstBuffer,
+            const Dimensions dstOffset,
+            Dimensions &sizeRead)
+    throw (DCException)
+    {
+        if (fileStatus != FST_READING && fileStatus != FST_WRITING && fileStatus != FST_MERGING)
+            throw DCException(getExceptionString("readMeta", "this access is not permitted"));
+
+        uint32_t ndims = 0;
+        return readDataSetMeta(handles.get(id), id, name, dstBuffer, dstOffset,
+                Dimensions(0, 0, 0), sizeRead, ndims);
+    }
+
     void SerialDataCollector::write(int32_t id, const CollectionType& type, uint32_t ndims,
             const Selection select, const char* name, const void* data)
     throw (DCException)
@@ -960,6 +976,40 @@ namespace splash
         dataset.close();
     }
 
+    CollectionType* SerialDataCollector::readDataSetMeta(H5Handle h5File,
+            int32_t id,
+            const char* name,
+            const Dimensions dstBuffer,
+            const Dimensions dstOffset,
+            const Dimensions srcOffset,
+            Dimensions &sizeRead,
+            uint32_t& srcDims)
+    throw (DCException)
+    {
+        log_msg(2, "readDataSetMeta");
+
+        std::string group_path, dset_name;
+        DCDataSet::getFullDataPath(name, SDC_GROUP_DATA, id, group_path, dset_name);
+
+        DCGroup group;
+        group.open(h5File, group_path);
+
+        DCDataSet dataset(dset_name.c_str());
+        dataset.open(group.getHandle());
+
+        size_t entrySize;
+        getEntriesForID(id, NULL, &entrySize);
+        std::vector<DataCollector::DCEntry> entries(entrySize);
+
+        getEntriesForID(id, &(*entries.begin()), NULL);
+
+        Dimensions src_size(dataset.getSize() - srcOffset);
+        dataset.read(dstBuffer, dstOffset, src_size, srcOffset, sizeRead, srcDims, NULL);
+        dataset.close();
+
+        return entries[0].colType;
+    }
+
     void SerialDataCollector::readSizeInternal(H5Handle h5File,
             int32_t id,
             const char* name,

src/include/splash/CollectionType.hpp

@@ -1,5 +1,6 @@
 /**
  * Copyright 2013 Felix Schmitt
+ *           2015 Carlchristian Eckert
  *
  * This file is part of libSplash. 
  * 
@@ -25,6 +26,7 @@
 #define	COLLECTIONTYPE_H
 
 #include <hdf5.h>
+#include <string>
 
 #define H5DataType hid_t
 
@@ -55,6 +57,13 @@ namespace splash
          */
         virtual size_t getSize() const = 0;
 
+        /**
+         * Returns a human-readable representation of the datatype.
+         *
+         * @return the name of the datatype as a string
+         */
+        virtual std::string toString() const = 0;
+
         /**
          * Destructor
          */

src/include/splash/DataCollector.hpp

@@ -52,6 +52,7 @@
 #include "splash/CollectionType.hpp"
 #include "splash/Dimensions.hpp"
 #include "splash/Selection.hpp"
+#include "splash/core/DCDataSet.hpp"
 
 namespace splash
 {
@@ -113,6 +114,10 @@ namespace splash
              * Fully-qualified name of this dataset.
              */
             std::string name;
+            /**
+             * Pointer to an instance of the CollectionType of this dataset
+             */
+            CollectionType* colType;
         } DCEntry;
 
         /**
@@ -424,6 +429,25 @@ namespace splash
                 const Dimensions dstOffset,
                 Dimensions &sizeRead,
                 void* buf) = 0;
+
+        /**
+         * Reads meta data from HDF5 file.
+         *
+         * @param id ID of iteration.
+         * @param name Name of the dataset.
+         * @param dstBuffer Size of the dataset.
+         * @param dstOffset Offset in destination dataset.
+         * @param sizeRead Returns the size of the data in the file.
+         *
+         * @return The CollectionType of the dataset as a heap allocated
+         *         object. The object must be freed by the caller at the
+         *         end of the object's lifetime.
+         */
+        virtual CollectionType* readMeta(int32_t id,
+                const char* name,
+                const Dimensions dstBuffer,
+                const Dimensions dstOffset,
+                Dimensions &sizeRead) = 0;
     };
 
 }

src/include/splash/ParallelDataCollector.hpp

@@ -312,6 +312,12 @@ namespace splash
                 Dimensions &sizeRead,
                 void* buf) throw (DCException);
 
+        CollectionType* readMeta(int32_t id,
+                const char* name,
+                const Dimensions dstBuffer,
+                const Dimensions dstOffset,
+                Dimensions &sizeRead) throw (DCException);
+
         /**
          * Reads data from HDF5 file.
          * If data is to be read (instead of only its size in the file),
@@ -408,6 +414,20 @@ namespace splash
                 Dimensions /*count*/,
                 Dimensions /*offset*/,
                 Dimensions /*stride*/) throw (DCException);
+
+
+        /**
+         * Internal meta data reading method.
+         */
+        CollectionType* readDataSetMeta(H5Handle h5File,
+                int32_t id,
+                const char* name,
+                const Dimensions dstBuffer,
+                const Dimensions dstOffset,
+                const Dimensions srcOffset,
+                Dimensions &sizeRead,
+                uint32_t& srcDims)
+         throw (DCException);
     };
 
 }

src/include/splash/SerialDataCollector.hpp

@@ -175,6 +175,18 @@ namespace splash
                 uint32_t& srcDims,
                 void* dst) throw (DCException);
 
+        /**
+         * Internal meta data reading method.
+         */
+        CollectionType* readDataSetMeta(H5Handle h5File,
+                int32_t id,
+                const char* name,
+                const Dimensions dstBuffer,
+                const Dimensions dstOffset,
+                const Dimensions srcOffset,
+                Dimensions &sizeRead,
+                uint32_t& srcDims) throw (DCException);
+
         void readSizeInternal(H5Handle h5File,
                 int32_t id,
                 const char* name,
@@ -321,6 +333,12 @@ namespace splash
                 const Dimensions dstOffset,
                 Dimensions &sizeRead,
                 void* data) throw (DCException);
+
+        CollectionType* readMeta(int32_t id,
+                const char* name,
+                const Dimensions dstBuffer,
+                const Dimensions dstOffset,
+                Dimensions &sizeRead) throw (DCException);
     };
 
 } // namespace DataCollector

src/include/splash/basetypes/ColTypeBool.hpp

@@ -1,5 +1,6 @@
 /**
- * Copyright 2013, 2015 Felix Schmitt, René Widera, Axel Huebl
+ * Copyright 2013, 2015 Felix Schmitt, René Widera, Axel Huebl,
+ *                      Carlchristian Eckert
  *
  * This file is part of libSplash. 
  * 
@@ -26,6 +27,9 @@
 
 #include "splash/CollectionType.hpp"
 
+#include <string>
+#include <cstring>
+
 namespace splash
 {
 
@@ -55,6 +59,34 @@ class ColTypeBool : public CollectionType
     {
         return sizeof (bool);
     }
+
+    static CollectionType* genType(hid_t datatype_id)
+    {
+        bool found = false;
+        H5T_class_t h5_class = H5Tget_class(datatype_id);
+        if(h5_class == H5T_ENUM)
+        {
+            if(H5Tget_nmembers(datatype_id) == 2)
+            {
+                char* m0 = H5Tget_member_name(datatype_id,0);
+                char* m1 = H5Tget_member_name(datatype_id,1);
+                if(strcmp("true" , m0) == 0 && strcmp("false", m1) == 0)
+                    found = true;
+                free(m1);
+                free(m0);
+            }
+        }
+
+        if(found)
+            return new ColTypeBool;
+        else
+            return NULL;
+    }
+
+    std::string toString() const
+    {
+        return "Bool";
+    }
 };
 
 }