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changeset 17709:5415a9cd61d4

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Implement faster partial loading of HDF5 files. * libinterp/corefcn/load-save.cc(do_load): Call read_hdf5_data with extra arguments for variables to load. * libinterp/corefcn/ls-hdf5.h: Re-define read_Hdf5_data function prototype. * libinterp/corefcn/ls-hdf5.cc: Check for any variable names to load, instead of whole file.
author Rik <rik@octave.org>
date Sun, 20 Oct 2013 20:30:11 -0700
parents f10b7a578e2c
children 3dec0a57ab55
files libinterp/corefcn/load-save.cc libinterp/corefcn/ls-hdf5.cc libinterp/corefcn/ls-hdf5.h
diffstat 3 files changed, 37 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/libinterp/corefcn/load-save.cc	Tue Jul 02 14:17:33 2013 +0100
+++ b/libinterp/corefcn/load-save.cc	Sun Oct 20 20:30:11 2013 -0700
@@ -380,7 +380,8 @@
 
 #ifdef HAVE_HDF5
         case LS_HDF5:
-          name = read_hdf5_data (stream, orig_fname, global, tc, doc);
+          name = read_hdf5_data (stream, orig_fname, global, tc, doc,
+                                 argv, argv_idx, argc);
           break;
 #endif /* HAVE_HDF5 */
 
--- a/libinterp/corefcn/ls-hdf5.cc	Tue Jul 02 14:17:33 2013 +0100
+++ b/libinterp/corefcn/ls-hdf5.cc	Sun Oct 20 20:30:11 2013 -0700
@@ -580,7 +580,8 @@
 // and error.
 std::string
 read_hdf5_data (std::istream& is, const std::string& /* filename */,
-                bool& global, octave_value& tc, std::string& doc)
+                bool& global, octave_value& tc, std::string& doc, 
+                const string_vector& argv, int argv_idx, int argc)
 {
   std::string retval;
 
@@ -599,6 +600,37 @@
 #endif
   H5Gget_num_objs (group_id, &num_obj);
   H5Gclose (group_id);
+
+  // For large datasets and out-of-core functionality,
+  // check if only parts of the data is requested
+  bool load_named_vars = argv_idx < argc;
+  while (load_named_vars && hs.current_item < static_cast<int> (num_obj))
+    {
+      std::vector<char> var_name;
+      bool found = false;
+      size_t len = 0;
+
+      len = H5Gget_objname_by_idx (hs.file_id, hs.current_item, 0, 0);
+      var_name.resize (len+1);
+      H5Gget_objname_by_idx( hs.file_id, hs.current_item, &var_name[0], len+1);
+
+      for (int i = argv_idx; i < argc; i++)
+        {
+          glob_match pattern (argv[i]);
+          if (pattern.match (std::string (&var_name[0])))
+            {
+              found = true;
+              break;
+            }
+        }
+
+      if (found)
+        break;
+
+      hs.current_item++;
+    }
+
+
   if (hs.current_item < static_cast<int> (num_obj))
     H5Giterate_retval = H5Giterate (hs.file_id, "/", &hs.current_item,
                                     hdf5_read_next_data, &d);
--- a/libinterp/corefcn/ls-hdf5.h	Tue Jul 02 14:17:33 2013 +0100
+++ b/libinterp/corefcn/ls-hdf5.h	Sun Oct 20 20:30:11 2013 -0700
@@ -180,7 +180,8 @@
 
 extern OCTINTERP_API std::string
 read_hdf5_data (std::istream& is,  const std::string& filename, bool& global,
-                octave_value& tc, std::string& doc);
+                octave_value& tc, std::string& doc,								
+                const string_vector& argv, int argv_idx, int argc);
 
 extern OCTINTERP_API bool
 save_hdf5_data (std::ostream& os, const octave_value& tc,