(Xdmf IO) better h5py optional support (f4b37abc) · Commits · DRTI / BasicTools

src/BasicTools/IO/XdmfReader.py

+81 −77

Original line number	Diff line number	Diff line
		@@ -13,10 +13,9 @@ import numpy as np
		import xml.sax

		from BasicTools.Helpers.TextFormatHelper import TFormat
		from BasicTools.IO.XdmfTools import FieldNotFound
		from BasicTools.NumpyDefs import PBasicFloatType

		import BasicTools.Containers.ElementNames as ElementNames
		from BasicTools.IO.XdmfTools import FieldNotFound, HasHdf5Support, XdmfNumber


		def ReadXdmf(fileName):
		@@ -102,7 +101,7 @@ class XdmfDomain(Xdmfbase):
		if isinstance(nameornumber,str):
		for g in self.grids:
		if g.Name == nameornumber : return g
		raise
		raise Exception(f" grid with name '{nameornumber}' not found")
		else:
		return self.grids[nameornumber]

		@@ -906,11 +905,16 @@ def CheckIntegrity():
		except Exception as e :
		pass

		res = XdmfReader(filename = TestDataPath + "Unstructured.xmf" )
		for filename in ["Unstructured.xmf", "UnstructuredBinary.xmf", "UnstructuredAscii.xmf" ]:

		if not HasHdf5Support() and filename == "Unstructured.xmf":
		continue

		res = XdmfReader(filename = TestDataPath + filename )
		res.lazy = False
		res.Read()

		res = XdmfReader(filename = TestDataPath + "Unstructured.xmf" )
		res = XdmfReader(filename = TestDataPath + filename )
		# read only the xml part
		res.Read()

		@@ -990,7 +994,7 @@ def CheckIntegrity():

		topo = res.xdmf.domains[0].GetGrid("Grid").topology.dataitems[0].GetData()
		#print(topo)
		if topo[2] != 1: raise
		if topo[0] != XdmfNumber[ElementNames.Hexaedron_8]: raise

		######################### Structured #########################
		res = XdmfReader(filename = TestDataPath + "Structured.xmf" )
		@@ -1016,7 +1020,7 @@ def CheckIntegrity():
		def Example1():
		import BasicTools.TestData as test
		# Create a Reader
		reader = XdmfReader(filename = test.GetTestDataPath() + "Unstructured.xmf")
		reader = XdmfReader(filename = test.GetTestDataPath() + "UnstructuredBinary.xmf")
		# Do the reading (only the xml part, to read all the data set lazy to False)
		#res.lazy = False
		reader.Read()

src/BasicTools/IO/XdmfTools.py

+7 −1

Original line number	Diff line number	Diff line
		@@ -63,10 +63,16 @@ class FieldNotFound(ValueError):
		def __str__(self):
		return repr(self.value) # pragma: no cover

		def HasHdf5Support():
		try:
		import h5py
		return True
		except:
		return False

		def CheckIntegrity():

		FieldNotFound('toto');
		FieldNotFound('toto')
		return 'OK'

		if __name__ == '__main__':

src/BasicTools/IO/XdmfWriter.py

+18 −4

Original line number	Diff line number	Diff line
		@@ -13,10 +13,10 @@ import os
		from BasicTools.Helpers.TextFormatHelper import TFormat

		import BasicTools.Containers.ElementNames as EN
		from BasicTools.IO.XdmfTools import XdmfName,XdmfNumber
		from BasicTools.IO.WriterBase import WriterBase as WriterBase
		from BasicTools.Helpers.MPIInterface import MPIInterface as MPI
		from BasicTools.NumpyDefs import PBasicIndexType
		from BasicTools.IO.XdmfTools import XdmfName,XdmfNumber, HasHdf5Support

		def ArrayToString(data):
		return " ".join(str(x) for x in data)
		@@ -237,7 +237,12 @@ class XdmfWriter(WriterBase):
		self.__chunkSize = 2**30
		self.automaticOpen = False

		try:
		import h5py
		self.__isHdf5 = True
		except:
		self.__isHdf5 = False

		self.__hdf5FileName = ""
		self.__hdf5FileNameOnly = None
		self.__hdf5FilePointer = None
		@@ -289,7 +294,13 @@ class XdmfWriter(WriterBase):
		if val :
		self.SetBinary(True)

		try:
		import h5py
		self.__isHdf5 = val
		except:
		self.__isHdf5 = False
		if val:
		print("h5py not available using binary file for output")

		def SetChunkSize(self,size):
		self.__chunkSize = size
		@@ -1518,7 +1529,10 @@ def CheckIntegrityDDM(GUI=False):
		writer.Write(mesh1D, CellFields = [np.arange(mesh1D.GetNumberOfElements())+0.1 ], CellFieldsNames=["IPId_0"])

		writer.Close()
		if HasHdf5Support():
		return "ok"
		else:
		return "ok, but no hdf5 support"


		if __name__ == '__main__':