Merge pull request #390 from AngelFP/record_attributes

Add all record attributes to `FieldMetaInformation`

openpmd_viewer/openpmd_timeseries/data_reader/h5py_reader/field_reader.py

@@ -113,14 +113,16 @@ def read_field_cartesian( filename, iteration, field, coord, axis_labels,
  F = get_data( dset, list_i_cell, list_slicing_index )
  info = FieldMetaInformation( axes, shape, grid_spacing, global_offset,
  group.attrs['gridUnitSI'], dset.attrs['position'],
- time, iteration )
+ time, iteration, component_attrs=dict(dset.attrs),
+ field_attrs=dict(group.attrs) )
  else:
  F = get_data( dset )
  axes = { i: axis_labels[i] for i in range(len(axis_labels)) }
  info = FieldMetaInformation( axes, F.shape,
  group.attrs['gridSpacing'], group.attrs['gridGlobalOffset'],
  group.attrs['gridUnitSI'], dset.attrs['position'],
- time, iteration )
+ time, iteration, component_attrs=dict(dset.attrs),
+ field_attrs=dict(group.attrs) )
 
  # Close the file
  dfile.close()
@@ -217,7 +219,8 @@ def read_field_circ( filename, iteration, field, coord,
  info = FieldMetaInformation( coord_labels, N_pair,
  group.attrs['gridSpacing'], group.attrs['gridGlobalOffset'],
  group.attrs['gridUnitSI'], dset.attrs['position'], time,
- iteration, thetaMode=True )
+ iteration, thetaMode=True, component_attrs=dict(dset.attrs),
+ field_attrs=dict(group.attrs) )
 
  # Convert to a 3D Cartesian array if theta is None
  if theta is None:

openpmd_viewer/openpmd_timeseries/data_reader/io_reader/field_reader.py

@@ -78,6 +78,9 @@ def read_field_cartesian( series, iteration, field_name, component_name,
  grid_unit_SI = field.grid_unit_SI
  grid_position = component.position
  time = (it.time + field.time_offset) * it.time_unit_SI
+
+ field_attrs = {a: field.get_attribute(a) for a in field.attributes}
+ component_attrs = {a: component.get_attribute(a) for a in component.attributes} 
 
  # Slice selection
  # TODO put in general utilities
@@ -112,14 +115,16 @@ def read_field_cartesian( series, iteration, field_name, component_name,
  F = get_data( series, component, list_i_cell, list_slicing_index )
  info = FieldMetaInformation( axes, shape, grid_spacing, global_offset,
  grid_unit_SI, grid_position,
- time, iteration )
+ time, iteration, field_attrs=field_attrs,
+ component_attrs=component_attrs )
  else:
  F = get_data( series, component )
  axes = { i: axis_labels[i] for i in range(len(axis_labels)) }
  info = FieldMetaInformation( axes, F.shape,
  grid_spacing, global_offset,
  grid_unit_SI, grid_position,
- time, iteration )
+ time, iteration, field_attrs=field_attrs,
+ component_attrs=component_attrs )
 
  return F, info
 
@@ -189,6 +194,9 @@ def read_field_circ( series, iteration, field_name, component_name,
  component = next(field.items())[1]
  else:
  component = field[component_name]
+
+ field_attrs = {a: field.get_attribute(a) for a in field.attributes}
+ component_attrs = {a: component.get_attribute(a) for a in component.attributes} 
 
  # Extract the metainformation
  # FIXME here and in h5py reader, we need to invert the order on 'F' for
@@ -211,7 +219,9 @@ def read_field_circ( series, iteration, field_name, component_name,
  # Nm, Nr, Nz = component.shape
  info = FieldMetaInformation( coord_labels, N_pair,
  field.grid_spacing, field.grid_global_offset,
- field.grid_unit_SI, component.position, time, iteration, thetaMode=True )
+ field.grid_unit_SI, component.position, time, iteration,
+ thetaMode=True, field_attrs=field_attrs,
+ component_attrs=component_attrs )
 
  # Convert to a 3D Cartesian array if theta is None
  if theta is None:

openpmd_viewer/openpmd_timeseries/field_metainfo.py

@@ -39,7 +39,7 @@ class FieldMetaInformation(object):
  the values in `axes`. For instance, if `axes` is {0: 'x', 1: 'y'},
  then these variables will be called dx and dy.
 
-  - x, z: 1darrays of double
+ - x, z: 1darrays of double
  The position of all the gridpoints, along each axis
  Notice that the name of these variables change according to
  the values in `axes`. For instance, if `axes` is {0: 'x', 1: 'y'},
@@ -70,10 +70,17 @@ class FieldMetaInformation(object):
  get_particle method for a given iteration and vice versa.
  Either `t` or `iteration` should be given.
 
+ - field_attrs: dict
+ All the attributes of the field record in the openPMD file.
+
+ - component_attrs: dict
+ All the attributes of the field component record in the openPMD file.
+
  """
 
  def __init__(self, axes, shape, grid_spacing,
- global_offset, grid_unitSI, position, t, iteration, thetaMode=False):
+ global_offset, grid_unitSI, position, t, iteration,
+ thetaMode=False, field_attrs=None, component_attrs=None):
  """
  Create a FieldMetaInformation object
 
@@ -105,6 +112,8 @@ def __init__(self, axes, shape, grid_spacing,
  setattr(self, 'time', t)
  setattr(self, 'iteration', iteration)
 
+ self.field_attrs = field_attrs
+ self.component_attrs = component_attrs
  self._generate_imshow_extent()