Merge pull request #56 from AngelFP/update_openpmd_viewer

Update attributes in `FieldMetaInformation`

visualpic/data_reading/openpmd_data_reader.py

@@ -12,6 +12,10 @@
 from openpmd_viewer.openpmd_timeseries.data_reader.h5py_reader import (
     field_reader as fr)
 from openpmd_viewer.openpmd_timeseries import FieldMetaInformation
+from openpmd_viewer import __version__
+viewer_version = __version__.split('.')
+viewer_version = [int(v) for v in viewer_version]
+new_metainformation = (viewer_version[0] > 1) or (viewer_version[1] >= 8)
 
 
 class OpenPMDDataReader(DataReader):
@@ -66,7 +70,8 @@ def read_field_metadata(self, iteration, field_name, component_name):
         # Axis metadata.
         md['axis'] = {}
         info = self.get_field_meta_info(
-            iteration, field_name, component_name, axis_labels, field_geometry)
+            iteration, field_name, component_name, axis_labels, field_geometry,
+            t)
         for axis in axis_labels:
             md['axis'][axis] = {}
             md['axis'][axis]['units'] = 'm'
@@ -78,27 +83,27 @@ def read_field_metadata(self, iteration, field_name, component_name):
         return md
 
     def get_field_meta_info(self, iteration, field, comp, axis_labels,
-                            geometry):
+                            geometry, t):
         """ Get the `FieldMetaInformation` of the field. """
         if self.backend == 'h5py':
             filename = self.iteration_to_file[iteration]
             if geometry in ['thetaMode']:
                 return read_circ_field_metadata_h5py(
-                    filename, iteration, field, comp)
+                    filename, iteration, field, comp, t)
             elif geometry in ["1dcartesian", "2dcartesian", "3dcartesian"]:
                 return read_cartesian_field_metadata_h5py(
-                    filename, iteration, field, comp, axis_labels)
+                    filename, iteration, field, comp, axis_labels, t)
         elif self.backend == 'openpmd-api':
             if geometry in ['thetaMode']:
                 return read_circ_field_metadata_io(
-                    self.series, iteration, field, comp)
+                    self.series, iteration, field, comp, t)
             elif geometry in ["1dcartesian", "2dcartesian", "3dcartesian"]:
                 return read_cartesian_field_metadata_io(
-                    self.series, iteration, field, comp, axis_labels)
+                    self.series, iteration, field, comp, axis_labels, t)
 
 
 def read_cartesian_field_metadata_h5py(filename, iteration, field_name,
-                                       component_name, axis_labels):
+                                       component_name, axis_labels, t):
     """
     Get `FieldMetaInformation` of cartesian field using `h5py` backend.
 
@@ -127,15 +132,22 @@ def read_cartesian_field_metadata_h5py(filename, iteration, field_name,
     # Extract the metainformation
     shape = list(fr.get_shape(dset))
     axes = {i: axis_labels[i] for i in range(len(axis_labels))}
-    info = FieldMetaInformation(
-        axes, shape, group.attrs['gridSpacing'],
-        group.attrs['gridGlobalOffset'], group.attrs['gridUnitSI'],
-        dset.attrs['position'])
+
+    if new_metainformation:
+        info = FieldMetaInformation(
+            axes, shape, group.attrs['gridSpacing'],
+            group.attrs['gridGlobalOffset'], group.attrs['gridUnitSI'],
+            dset.attrs['position'], t, iteration)
+    else:
+        info = FieldMetaInformation(
+            axes, shape, group.attrs['gridSpacing'],
+            group.attrs['gridGlobalOffset'], group.attrs['gridUnitSI'],
+            dset.attrs['position'])
     return info
 
 
 def read_cartesian_field_metadata_io(series, iteration, field_name,
-                                     component_name, axis_labels):
+                                     component_name, axis_labels, t):
     """
     Get `FieldMetaInformation` of cartesian field using `io` backend.
 
@@ -164,15 +176,22 @@ def read_cartesian_field_metadata_io(series, iteration, field_name,
     # Extract the metainformation
     shape = component.shape
     axes = {i: axis_labels[i] for i in range(len(axis_labels))}
-    info = FieldMetaInformation(
-        axes, shape,
-        field.grid_spacing, field.grid_global_offset,
-        field.grid_unit_SI, component.position)
+    if new_metainformation:
+        info = FieldMetaInformation(
+            axes, shape,
+            field.grid_spacing, field.grid_global_offset,
+            field.grid_unit_SI, component.position,
+            t, iteration)
+    else:
+        info = FieldMetaInformation(
+            axes, shape,
+            field.grid_spacing, field.grid_global_offset,
+            field.grid_unit_SI, component.position)
     return info
 
 
 def read_circ_field_metadata_h5py(filename, iteration, field_name,
-                                  component_name):
+                                  component_name, t):
     """
     Get `FieldMetaInformation` of thetaMode field using `h5py` backend.
 
@@ -198,15 +217,23 @@ def read_circ_field_metadata_h5py(filename, iteration, field_name,
 
     # Extract the metainformation
     Nm, Nr, Nz = fr.get_shape(dset)
-    info = FieldMetaInformation(
-        {0: 'r', 1: 'z'}, (Nr, Nz),
-        group.attrs['gridSpacing'], group.attrs['gridGlobalOffset'],
-        group.attrs['gridUnitSI'], dset.attrs['position'], thetaMode=True)
+    if new_metainformation:
+        info = FieldMetaInformation(
+            {0: 'r', 1: 'z'}, (Nr, Nz),
+            group.attrs['gridSpacing'], group.attrs['gridGlobalOffset'],
+            group.attrs['gridUnitSI'], dset.attrs['position'], t, iteration,
+            thetaMode=True)
+    else:
+        info = FieldMetaInformation(
+            {0: 'r', 1: 'z'}, (Nr, Nz),
+            group.attrs['gridSpacing'], group.attrs['gridGlobalOffset'],
+            group.attrs['gridUnitSI'], dset.attrs['position'], thetaMode=True)
 
     return info
 
 
-def read_circ_field_metadata_io(series, iteration, field_name, component_name):
+def read_circ_field_metadata_io(series, iteration, field_name, component_name,
+                                t):
     """
     Get `FieldMetaInformation` of thetaMode field using `io` backend.
 
@@ -232,11 +259,19 @@ def read_circ_field_metadata_io(series, iteration, field_name, component_name):
 
     # Extract the metainformation
     Nm, Nr, Nz = component.shape
-    info = FieldMetaInformation(
-        {0: 'r', 1: 'z'}, (Nr, Nz),
-        field.grid_spacing, field.grid_global_offset,
-        field.grid_unit_SI, component.position, thetaMode=True)
-    return info
+    if new_metainformation:
+        info = FieldMetaInformation(
+            {0: 'r', 1: 'z'}, (Nr, Nz),
+            field.grid_spacing, field.grid_global_offset,
+            field.grid_unit_SI, component.position, t, iteration,
+            thetaMode=True)
+        return info
+    else:
+        info = FieldMetaInformation(
+            {0: 'r', 1: 'z'}, (Nr, Nz),
+            field.grid_spacing, field.grid_global_offset,
+            field.grid_unit_SI, component.position, thetaMode=True)
+        return info
 
 
 def determine_field_units(field_name):