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