Merge pull request #5 from openPMD/particleBoundary

Move Particle Boundaries

openpmd_updater/Updater.py

@@ -7,7 +7,8 @@
 """
 import packaging.version
 from openpmd_updater.backends.HDF5 import HDF5
-from openpmd_updater.transforms.v2_0_0 import DataOrder, ExtensionString, Version
+from openpmd_updater.transforms.v2_0_0 import DataOrder, \
+    ExtensionString, Version, ParticleBoundary
 
 
 class Updater(object):
@@ -29,6 +30,7 @@ def __init__(self, filename, verbose=False):
         self.updates = {
             "2.0.0" : [
                 DataOrder.DataOrder,  # must be before move of particleBoundary
+                ParticleBoundary.ParticleBoundary,
                 ExtensionString.ExtensionString,
                 Version.Version  # must be last
             ]

openpmd_updater/transforms/v2_0_0/ParticleBoundary.py

@@ -0,0 +1,63 @@
+"""
+This file is part of the openPMD-updater.
+
+Copyright 2018 openPMD contributors
+Authors: Axel Huebl, Remi Lehe
+License: ISC
+"""
+
+from openpmd_updater.transforms.ITransform import ITransform
+import numpy as np
+
+
+class ParticleBoundary(ITransform):
+    """
+    Moves the `particleBoundary` attribute from the mesh records
+    to the species records
+
+    openPMD standard: 1.*.* -> 2.0.0
+
+    Related openPMD-standard issues:
+        https://github.com/openPMD/openPMD-standard/issues/105
+    """
+
+    """Name and description of the transformation"""
+    name = "particleBoundary", \
+           "move the particleBoundary attribute from the mesh records to the species records"
+
+    """Minimum openPMD standard version that is supported by this transformation"""
+    min_version = "1.0.0"
+
+    """openPMD standard version is fulfulled 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()
+        particles_path = self.fb.get_attr("particlesPath").decode()
+        iterations = self.fb.list_groups("/data/")
+
+        for it in iterations:
+            # Get the old particle_boundary attribute, from the mesh level
+            abs_meshes_path = "/data/" + str(it) + "/" + meshes_path
+            particle_boundary = self.fb.get_attr("particleBoundary", abs_meshes_path)
+
+            # Go through the list of species, and set this attribute
+            # at the species level
+            abs_particle_path = "/data/" + str(it) + "/" + particles_path
+            all_species = self.fb.list_groups(abs_particle_path)
+            self.fb.cd(abs_particle_path)
+            for species in all_species:
+                self.fb.add_attr("particleBoundary", particle_boundary, species)
+
+            # Delete the old particle_boundary attribute
+            self.fb.del_attr("particleBoundary", abs_meshes_path)