Merge pull request #301 from ax3l/fix-h5pyGroupBased

h5py: Support groupBased

openpmd_viewer/openpmd_timeseries/data_reader/data_reader.py

@@ -118,7 +118,7 @@ def read_openPMD_params(self, iteration, extract_parameters=True):
         if backend == 'h5py':
             filename = self.iteration_to_file[iteration]
             return h5py_reader.read_openPMD_params(
-                    filename, extract_parameters)
+                    filename, iteration, extract_parameters)
 
         elif backend == 'openpmd-api':
             return io_reader.read_openPMD_params(
@@ -169,7 +169,7 @@ def read_field_cartesian( self, iteration, field, coord, axis_labels,
         if backend == 'h5py':
             filename = self.iteration_to_file[iteration]
             return h5py_reader.read_field_cartesian(
-                filename, field, coord, axis_labels,
+                filename, iteration, field, coord, axis_labels,
                 slice_relative_position, slice_across )
         elif backend == 'openpmd-api':
             return io_reader.read_field_cartesian(
@@ -227,7 +227,7 @@ def read_field_circ( self, iteration, field, coord, slice_relative_position,
         if backend == 'h5py':
             filename = self.iteration_to_file[iteration]
             return h5py_reader.read_field_circ(
-                filename, field, coord, slice_relative_position,
+                filename, iteration, field, coord, slice_relative_position,
                 slice_across, m, theta )
         elif backend == 'openpmd-api':
             return io_reader.read_field_circ(
@@ -256,7 +256,7 @@ def read_species_data( self, iteration, species, record_comp, extensions):
         if backend == 'h5py':
             filename = self.iteration_to_file[iteration]
             return h5py_reader.read_species_data(
-                    filename, species, record_comp, extensions )
+                    filename, iteration, species, record_comp, extensions )
         elif backend == 'openpmd-api':
             return io_reader.read_species_data(
                     self.series, iteration, species, record_comp, extensions )
@@ -292,7 +292,7 @@ def get_grid_parameters(self, iteration, avail_fields, metadata ):
         if backend == 'h5py':
             filename = self.iteration_to_file[iteration]
             return h5py_reader.get_grid_parameters(
-                filename, avail_fields, metadata )
+                filename, iteration, avail_fields, metadata )
         elif backend == 'openpmd-api':
             return io_reader.get_grid_parameters(
                 self.series, iteration, avail_fields, metadata )

openpmd_viewer/openpmd_timeseries/data_reader/h5py_reader/field_reader.py

@@ -10,12 +10,12 @@
 
 import h5py
 import numpy as np
-from .utilities import get_shape, get_data, get_bpath, join_infile_path
+from .utilities import get_shape, get_data, join_infile_path
 from openpmd_viewer.openpmd_timeseries.field_metainfo import FieldMetaInformation
 from openpmd_viewer.openpmd_timeseries.utilities import construct_3d_from_circ
 
 
-def read_field_cartesian( filename, field, coord, axis_labels,
+def read_field_cartesian( filename, iteration, field, coord, axis_labels,
                           slice_relative_position, slice_across ):
     """
     Extract a given field from an HDF5 file in the openPMD format,
@@ -26,6 +26,9 @@ def read_field_cartesian( filename, field, coord, axis_labels,
     filename : string
        The absolute path to the HDF5 file
 
+    iteration : int
+        The iteration at which to obtain the data
+
     field : string, optional
        Which field to extract
 
@@ -64,7 +67,7 @@ def read_field_cartesian( filename, field, coord, axis_labels,
         field_path = field
     else:
         field_path = join_infile_path( field, coord )
-    group, dset = find_dataset( dfile, field_path )
+    group, dset = find_dataset( dfile, iteration, field_path )
 
     # Dimensions of the grid
     shape = list( get_shape( dset ) )
@@ -115,8 +118,8 @@ def read_field_cartesian( filename, field, coord, axis_labels,
     return( F, info )
 
 
-def read_field_circ( filename, field, coord, slice_relative_position,
-                    slice_across, m=0, theta=0. ):
+def read_field_circ( filename, iteration, field, coord,
+                     slice_relative_position, slice_across, m=0, theta=0. ):
     """
     Extract a given field from an HDF5 file in the openPMD format,
     when the geometry is thetaMode
@@ -126,6 +129,9 @@ def read_field_circ( filename, field, coord, slice_relative_position,
     filename : string
        The absolute path to the HDF5 file
 
+    iteration : int
+        The iteration at which to obtain the data
+
     field : string, optional
        Which field to extract
 
@@ -168,7 +174,7 @@ def read_field_circ( filename, field, coord, slice_relative_position,
         field_path = field
     else:
         field_path = join_infile_path( field, coord )
-    group, dset = find_dataset( dfile, field_path )
+    group, dset = find_dataset( dfile, iteration, field_path )
 
     # Extract the metainformation
     Nm, Nr, Nz = get_shape( dset )
@@ -260,7 +266,7 @@ def read_field_circ( filename, field, coord, slice_relative_position,
     return( F_total, info )
 
 
-def find_dataset( dfile, field_path ):
+def find_dataset( dfile, iteration, field_path ):
     """
     Extract the dataset that corresponds to field_path,
     and the corresponding group
@@ -285,7 +291,7 @@ def find_dataset( dfile, field_path ):
     - an h5py.Dataset object
     """
     # Find the meshes path
-    base_path = get_bpath( dfile )
+    base_path = '/data/{0}'.format( iteration )
     relative_meshes_path = dfile.attrs["meshesPath"].decode()
 
     # Get the proper dataset
@@ -301,7 +307,7 @@ def find_dataset( dfile, field_path ):
     return( group, dset )
 
 
-def get_grid_parameters( filename, avail_fields, metadata ):
+def get_grid_parameters( filename, iteration, avail_fields, metadata ):
     """
     Return the parameters of the spatial grid (grid size and grid range)
     in two dictionaries
@@ -311,6 +317,9 @@ def get_grid_parameters( filename, avail_fields, metadata ):
     filename : string
        The absolute path to the HDF5 file
 
+    iteration : int
+        The iteration at which to obtain the data
+
     avail_fields: list
        A list of the available fields
        e.g. ['B', 'E', 'rho']
@@ -342,7 +351,7 @@ def get_grid_parameters( filename, avail_fields, metadata ):
     field_name = avail_fields[ index_best_field ]
 
     # Get the corresponding field data
-    group, dset = find_dataset( dfile, field_name )
+    group, dset = find_dataset( dfile, iteration, field_name )
     if metadata[field_name]['type'] == 'vector':
         # For field vector, extract the first coordinate, to get the dataset
         first_coord = next(iter(group.keys()))

openpmd_viewer/openpmd_timeseries/data_reader/h5py_reader/params_reader.py

@@ -10,10 +10,10 @@
 
 import h5py
 import numpy as np
-from .utilities import is_scalar_record, get_shape, get_bpath, join_infile_path
+from .utilities import is_scalar_record, get_shape, join_infile_path
 
 
-def read_openPMD_params(filename, extract_parameters=True):
+def read_openPMD_params(filename, iteration, extract_parameters=True):
     """
     Extract the time and some openPMD parameters from a file
 
@@ -22,6 +22,9 @@ def read_openPMD_params(filename, extract_parameters=True):
     filename: string
         The path to the file from which parameters should be extracted
 
+    iteration : int
+        The iteration at which to obtain the data
+
     extract_parameters: bool, optional
         Whether to extract all parameters or only the time
         (Function execution is faster when extract_parameters is False)
@@ -42,7 +45,7 @@ def read_openPMD_params(filename, extract_parameters=True):
             "%s)" % (filename, version))
 
     # Find the base path object, and extract the time
-    bpath = f[get_bpath(f)]
+    bpath = f['/data/{0}'.format( iteration )]
     t = bpath.attrs["time"] * bpath.attrs["timeUnitSI"]
 
     # If the user did not request more parameters, close file and exit

openpmd_viewer/openpmd_timeseries/data_reader/h5py_reader/particle_reader.py

@@ -12,10 +12,10 @@
 import h5py
 import numpy as np
 from scipy import constants
-from .utilities import get_data, get_bpath, join_infile_path
+from .utilities import get_data, join_infile_path
 
 
-def read_species_data(filename, species, record_comp, extensions):
+def read_species_data(filename, iteration, species, record_comp, extensions):
     """
     Extract a given species' record_comp
 
@@ -24,6 +24,9 @@ def read_species_data(filename, species, record_comp, extensions):
     filename : string
        The absolute path to the HDF5 file
 
+    iteration : int
+        The iteration at which to obtain the data
+
     species: string
         The name of the species to extract (in the openPMD file)
 
@@ -50,7 +53,7 @@ def read_species_data(filename, species, record_comp, extensions):
         opmd_record_comp = record_comp
 
     # Open the HDF5 file
-    base_path = get_bpath(dfile)
+    base_path = '/data/{0}'.format( iteration )
     particles_path = dfile.attrs['particlesPath'].decode()
 
     # Extract the right dataset

openpmd_viewer/openpmd_timeseries/data_reader/h5py_reader/utilities.py

@@ -54,22 +54,6 @@ def list_files(path_to_dir):
     return iterations, iteration_to_file
 
 
-def get_bpath(f):
-    """
-    Return a string that corresponds to the base path of the data.
-
-    NB: For openPMD 1.0.0, the basePath is always of the form
-    '/data/%T' where %T is replaced by the actual iteration which
-    is present in the file.
-
-    Parameters:
-    -----------
-    f: am h5py.File object
-    """
-    iteration = list(f['/data'].keys())[0]
-    return('/data/%s' % iteration)
-
-
 def is_scalar_record(record):
     """
     Determine whether a record is a scalar record or a vector record