Merge pull request #346 from ax3l/support-group-based-singlefile

Support groupBased Encoding (Single File Reads)

openpmd_viewer/openpmd_timeseries/data_reader/data_reader.py

@@ -88,23 +88,33 @@ def list_iterations(self, path_to_dir):
         elif self.backend == 'openpmd-api':
             # guess file ending from first file in directory
             first_file_name = None
-            for file_name in os.listdir( path_to_dir ):
-                if file_name.split(os.extsep)[-1] in io.file_extensions:
-                    first_file_name = file_name
+
+            is_single_file = os.path.isfile(path_to_dir)
+            if is_single_file:
+                first_file_name = path_to_dir
+            else:
+                for file_name in os.listdir( path_to_dir ):
+                    if file_name.split(os.extsep)[-1] in io.file_extensions:
+                        first_file_name = file_name
             if first_file_name is None:
                 raise RuntimeError(
                     "Found no valid files in directory {0}.\n"
                     "Please check that this is the path to the openPMD files."
                     "(valid files must have one of the following extensions: {1})"
                     .format(path_to_dir, io.file_extensions))
 
-            # match last occurance of integers and replace with %T wildcards
-            # examples: data00000100.h5 diag4_00000500.h5 io12.0.bp
-            #           te42st.1234.yolo.json scan7_run14_data123.h5
-            file_path = re.sub(r'(\d+)(\.(?!\d).+$)', r'%T\2', first_file_name)
+            if is_single_file:
+                file_path = path_to_dir
+                series_name = file_path
+            else:
+                # match last occurance of integers and replace with %T wildcards
+                # examples: data00000100.h5 diag4_00000500.h5 io12.0.bp
+                #           te42st.1234.yolo.json scan7_run14_data123.h5
+                file_path = re.sub(r'(\d+)(\.(?!\d).+$)', r'%T\2', first_file_name)
+                series_name = os.path.join( path_to_dir, file_path)
 
             self.series = io.Series(
-                os.path.join( path_to_dir, file_path),
+                series_name,
                 io.Access.read_only )
             iterations = np.array( self.series.iterations )
 

openpmd_viewer/openpmd_timeseries/data_reader/h5py_reader/utilities.py

@@ -29,17 +29,26 @@ def list_files(path_to_dir):
     - an array of integers which correspond to the iteration of each file
     - a dictionary that matches iterations to the corresponding filename
     """
-    # Find all the files in the provided directory
-    all_files = os.listdir(path_to_dir)
+    # group based encoding?
+    is_single_file = os.path.isfile(path_to_dir)
+
+    if is_single_file:
+        all_files = [path_to_dir]
+    else:
+        # Find all the files in the provided directory
+        all_files = os.listdir(path_to_dir)
 
     # Select the hdf5 files, and fill dictionary of correspondence
     # between iterations and files
     iteration_to_file = {}
     for filename in all_files:
         # Use only the name that end with .h5 or .hdf5
         if filename.endswith('.h5') or filename.endswith('.hdf5'):
-            full_name = os.path.join(
-                os.path.abspath(path_to_dir), filename)
+            if is_single_file:
+                full_name = filename
+            else:
+                full_name = os.path.join(
+                    os.path.abspath(path_to_dir), filename)
             # extract all iterations from hdf5 file
             f = h5py.File(full_name, 'r')
             iterations = list(f['/data'].keys())