GridSpacing: Per-Component UnitSI & UnitDimension

Update spatial gridSpacings (openPMD 1) to arbitrary-unit spacings
(openPMD 2).

openpmd_updater/Updater.py

@@ -7,8 +7,8 @@
 """
 import packaging.version
 from openpmd_updater.backends.HDF5 import HDF5
-from openpmd_updater.transforms.v2_0_0 import DataOrder, \
-    ExtensionString, Version, ParticleBoundary
+from openpmd_updater.transforms.v2_0_0 import \
+    DataOrder, GridUnit, ParticleBoundary, ExtensionString, Version
 
 
 class Updater(object):
@@ -30,7 +30,11 @@ def __init__(self, filename, verbose=False):
         self.updates = {
             "2.0.0" : [
                 DataOrder.DataOrder,  # must be before move of particleBoundary
+<<<<<<< HEAD
                 ParticleBoundary.ParticleBoundary,
+=======
+                GridUnit.GridUnit,
+>>>>>>> 899f494... GridSpacing: Per-Component UnitSI & UnitDimension
                 ExtensionString.ExtensionString,
                 Version.Version  # must be last
             ]

openpmd_updater/transforms/v2_0_0/GridUnit.py

@@ -0,0 +1,73 @@
+"""
+This file is part of the openPMD-updater.
+
+Copyright 2018 openPMD contributors
+Authors: Axel Huebl
+License: ISC
+"""
+
+from openpmd_updater.transforms.ITransform import ITransform
+import numpy as np
+
+
+class GridUnit(ITransform):
+    """
+    GridSpacing: Per-Component UnitSI & UnitDimension
+
+    In openPMD 1.*, mesh grid spacings were always spatial.
+    openPMD 2.0 introduces a notation to allow arbitrary axes on meshes.
+
+    openPMD standard: 1.*.* -> 2.0.0
+
+    Related openPMD-standard issues:
+        https://github.com/openPMD/openPMD-standard/pull/122
+        https://github.com/openPMD/openPMD-standard/pull/193
+    """
+
+    """Name and description of the transformation"""
+    name = "gridUnit", \
+           "allow non-spatial gridSpacing in meshes"
+
+    """Minimum openPMD standard version that is supported by this transformation"""
+    min_version = "1.0.0"
+
+    """openPMD standard version is fulfilled by this transformation"""
+    to_version = "2.0.0"
+
+    def __init__(self, backend):
+        """Open a file"""
+        self.fb = backend
+
+    def transform(self, in_place=True):
+        """Perform transformation"""
+        if not in_place:
+            raise NotImplementedError("Only in-place transformation implemented!")
+
+        self.fb.cd(None)
+        basePath = "/data/"  # fixed in openPMD v1
+        meshes_path = self.fb.get_attr("meshesPath").decode()
+
+        iterations = self.fb.list_groups("/data/")
+
+        for it in iterations:
+            abs_meshes_path = "/data/" + str(it) + "/" + meshes_path
+            #            vector/tensor                    and   scalar meshes
+            all_meshes = self.fb.list_groups(abs_meshes_path) + self.fb.list_data(abs_meshes_path)
+
+            self.fb.cd(abs_meshes_path)
+
+            for mesh in all_meshes:
+                old_grid_unit_SI = self.fb.get_attr("gridUnitSI", mesh)
+
+                grid_ndim = len(self.fb.get_attr("gridSpacing", mesh))
+
+                new_grid_unit_SI = np.ones((grid_ndim, ), dtype=np.float64) * \
+                    old_grid_unit_SI
+
+                self.fb.add_attr("gridUnitSI", new_grid_unit_SI, mesh)
+
+                # openPMD 1.* dimensions were spatial (L)
+                grid_unit_dimension = np.zeros((grid_ndim * 7, ), dtype=np.float64)
+                grid_unit_dimension[::7] = 1.0
+
+                self.fb.add_attr("gridUnitDimension", grid_unit_dimension, mesh)