add xdmf wrapper generator for HDF5

Not recommended for large dataset due to potential memory leak currently plaguing Xdmf ilbrary.

processing/post/h5_addXdmfWapper.py

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+#!/usr/bin/env python2.7
+# -*- coding: UTF-8 no BOM -*-
+
+# ------------------------------------------------------------------- #
+# NOTE:                                                               #
+#   1. Current Xdmf rendering in Paraview has some memory issue where #
+#      large number of polyvertices will cause segmentation fault. By #
+#      default, paraview output a cell based xdmf description, which  #
+#      is working for small and medium mesh (<10,000) points. Hence a #
+#      rectangular mesh is used as the de facto Geometry description  #
+#      here.                                                          #
+#   2. Due to the unstable state Xdmf, it is safer to use port data   #
+#      to VTR rather than using xdmf as interpretive layer for data   #
+#      visualization.                                                 #
+# ------------------------------------------------------------------- #
+
+
+import damask
+import h5py
+import xml.etree.cElementTree as ET
+from xml.dom import minidom
+from damask.h5table import lables_to_path
+
+scriptName = os.path.splitext(os.path.basename(__file__))[0]
+scriptID   = ' '.join([scriptName,damask.version])
+
+
+# ----- HELPER FUNCTIONS -----#
+def addTopLvlCmt(xmlstr, topLevelCmt):
+    """add top level comment to string from ET"""
+    # a quick hack to add the top level comment to XML file
+    # --> somehow Elementtree does not provide this functionality
+    # --> by default
+    strList = xmlstr.split("\n")
+    strList[0] += "\n"+topLevelCmt
+    return "\n".join(strList)
+
+
+# --------------------------------------------------------------------
+#                                MAIN
+# --------------------------------------------------------------------
+
+msg = 'generate Xdmf wrapper for HDF5 file.'
+parser = OptionParser(option_class=damask.extendableOption,
+                      usage='%prog options [file[s]]',
+                      description = msg,
+                      version = scriptID)
+
+(options, filenames) = parser.parse_args()
+
+h5f = filenames[0]
+
+# ----- parse HDF5 file ----- #
+h5f_dataDim = {}
+h5f_dataPath = {}
+h5f_dataType = {}
+with h5py.File(h5f, 'a') as f:
+    labels = f.keys()
+    labels += f['/Constitutive'].keys()
+    labels += f['/Crystallite'].keys()
+    labels += ['Vx', 'Vy', "Vz"]
+    # remove group names as they do not contain real data
+    # TODO: use h5py/H5table API to detect dataset name to
+    #       avoid necessary name space pruning.
+    labels.remove('Constitutive')
+    labels.remove('Crystallite')
+    labels.remove('Geometry')
+    # loop through remaining labels
+    for label in labels:
+        dataType, h5Path = lables_to_path(label)
+        h5f_dataType[label] = dataType
+        h5f_dataDim[label] = " ".join(map(str,f[h5Path].shape))
+        h5f_dataPath[label] = h5Paths
+
+# ----- constructing xdmf elements ----- #
+root = ET.Element("Xdmf", version='3.3')
+root.set('xmlns:xi', "http://www.w3.org/2001/XInclude")
+root.append(ET.Comment('Generated Xdmf wapper for DAMASH H5 output'))
+
+# usually there should only be ONE domain
+domain = ET.SubElement(root, 'Domain',
+                       Name=h5f_base.split(".")[0])
+
+# use global topology through reference
+grid = ET.SubElement(domain, 'Grid', GridType="Uniform")
+# geometry section
+geometry = ET.SubElement(grid, 'Geometry', GeometryType="VXVYVZ")
+for vector in ["Vz", "Vy", "Vx"]:
+    dataitem = ET.SubElement(geometry, "DataItem",
+                             DataType="Float",
+                             Dimensions=h5f_dataDim[vector],
+                             Name=vector,
+                             Format="HDF")
+    dataitem.text = h5f_base.split("/")[-1] + ":{}".format(h5f_dataPath[vector])
+# topology section
+# TODO: support for other format based on given option
+meshDim = [h5f_dataDim["Vz"], h5f_dataDim["Vy"], h5f_dataDim["Vx"]]
+topology = ET.SubElement(grid, 'Topology',
+                         TopologyType="3DRectMesh",
+                         Dimensions=" ".join(map(str, meshDim)))
+
+# attributes section
+# Question: how to properly handle data mapping for multiphase situations
+labelsProcessed = ['Vx', 'Vy', 'Vz']
+# walk through each attributes
+for label in labels:
+    if label in labelsProcessed: continue
+    print "adding {}...".format(label)
+    attr = ET.SubElement(grid, 'Attribute',
+                         Name=label,
+                         Type="None",
+                         Center="Cell")
+    dataitem = ET.SubElement(attr, 'DataItem',
+                             Name=label,
+                             Format='HDF',
+                             Dimensions=h5f_dataDim[label])
+    dataitem.text = h5f_base + ":" + h5f_dataPath[label]
+    # update progress list
+    labelsProcessed.append(label)
+
+
+# pretty print the xdmf(xml) file content
+xmlstr = minidom.parseString(ET.tostring(root)).toprettyxml(indent="\t")
+xmlstr = addTopLvlCmt(xmlstr, '<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>')
+# write str to file through native python API
+with open(h5f.replace(".h5", ".xmf"), 'w') as f:
+    f.write(xmlstr)