Heavy data based persistent field, example about mupif HOT 3 OPEN

mupif commented on May 29, 2024

Heavy data based persistent field, example

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Comments (3)

eudoxos commented on May 29, 2024

Putting here just as an example for now. Should be integrated somewhere later.

import mupif as mp
import numpy as np
import meshio
import meshzoo
points,cells=meshzoo.cube_tetra(np.linspace(0.0, 1.0, 11), np.linspace(0.0, 1.0, 11), np.linspace(0.0, 1.0, 11))
mm=meshio.Mesh(points,{'tetra':cells})
    
h5path='12-hm.h5'
xdmfPath='12-hm.xdmf'
    
with mp.HeavyUnstructuredMesh(h5path='12-hm.h5',mode='overwrite') as mesh:
    mesh.fromMeshioMesh(mm,progress=True,chunk=1000)
    fieldP=mesh.makeHeavyField(unit='Pa',fieldID=mp.DataID.FID_Pressure,fieldType=mp.FieldType.FT_cellBased,valueType=mp.ValueType.Scalar)
    fieldUVW=mesh.makeHeavyField(unit='m/s',fieldID=mp.DataID.FID_Velocity,fieldType=mp.FieldType.FT_cellBased,valueType=mp.ValueType.Vector)
    fieldP.value[:]=np.linspace(0,1,len(cells))
    mesh.writeXDMF(xdmfPath,fields=[fieldP,fieldUVW]) # this is actually not necessary
    print(fieldP.evaluate((.1,.1,.1)))

# load mesh and fields from HDF5, also opens the storage
mesh,fields=mp.HeavyUnstructuredMesh.load(h5path)
print(fields[0].evaluate((.1,.1,.1)))

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eudoxos commented on May 29, 2024

We are currently using our own convention of naming the HDF5 groups. This could be perhaps aligned with FEniCS conventions; pygimli.meshtoos.exportFenicsHdf5Mesh has a terse documentation on expected HDF5 group names; this should be compatible with Paraview and XDMF as it appears from this post

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eudoxos commented on May 29, 2024

The code above was integrated into unittests in

mupif/mupif/tests/test_heavydata.py

Lines 499 to 524 in ba850b6

 class HeavyMesh_TestCase(unittest.TestCase): 

 @classmethod 

 def setUpClass(cls): 

 cls.box=mp.demo.make_meshio_box_hexa(dim=(1,2,3),sz=.1) 

 cls.tmpdir=tempfile.TemporaryDirectory() 

 cls.tmp=cls.tmpdir.name 

 @classmethod 

 def tearDownClass(cls): 

 try: cls.tmpdir.cleanup() 

 except: pass # this would fail under Windows 

 def test_saveload(self): 

 cls=self.__class__ 

 h5path=f'{cls.tmp}/01-mesh.h5' 

 xdmfPath=f'{cls.tmp}/01-mesh.xdmf' 

 evalAt=(.1,.1,.1) 

 with mp.HeavyUnstructuredMesh(h5path=h5path,mode='overwrite') as mesh: 

 mesh.fromMeshioMesh(cls.box) 

 fieldP=mesh.makeHeavyField(unit='Pa',fieldID=mp.DataID.FID_Pressure,fieldType=mp.FieldType.FT_cellBased,valueType=mp.ValueType.Scalar) 

 fieldUVW=mesh.makeHeavyField(unit='m/s',fieldID=mp.DataID.FID_Velocity,fieldType=mp.FieldType.FT_cellBased,valueType=mp.ValueType.Vector) 

 fieldP.value[:]=np.linspace(0,1,mesh.getNumberOfCells()) 

 # mesh.writeXDMF(xdmfPath,fields=[fieldP,fieldUVW]) # this is actually not necessary 

 val0=fieldP.evaluate(evalAt) 

 # load mesh and fields from HDF5, also opens the storage 

 mesh,fields=mp.HeavyUnstructuredMesh.load(h5path) 

 val1=fields[0].evaluate((.1,.1,.1)) 

 self.assertEqual(val0,val1)

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Heavy data based persistent field, example about mupif HOT 3 OPEN

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	class HeavyMesh_TestCase(unittest.TestCase):
	@classmethod
	def setUpClass(cls):
	cls.box=mp.demo.make_meshio_box_hexa(dim=(1,2,3),sz=.1)
	cls.tmpdir=tempfile.TemporaryDirectory()
	cls.tmp=cls.tmpdir.name
	@classmethod
	def tearDownClass(cls):
	try: cls.tmpdir.cleanup()
	except: pass # this would fail under Windows
	def test_saveload(self):
	cls=self.__class__
	h5path=f'{cls.tmp}/01-mesh.h5'
	xdmfPath=f'{cls.tmp}/01-mesh.xdmf'
	evalAt=(.1,.1,.1)
	with mp.HeavyUnstructuredMesh(h5path=h5path,mode='overwrite') as mesh:
	mesh.fromMeshioMesh(cls.box)
	fieldP=mesh.makeHeavyField(unit='Pa',fieldID=mp.DataID.FID_Pressure,fieldType=mp.FieldType.FT_cellBased,valueType=mp.ValueType.Scalar)
	fieldUVW=mesh.makeHeavyField(unit='m/s',fieldID=mp.DataID.FID_Velocity,fieldType=mp.FieldType.FT_cellBased,valueType=mp.ValueType.Vector)
	fieldP.value[:]=np.linspace(0,1,mesh.getNumberOfCells())
	# mesh.writeXDMF(xdmfPath,fields=[fieldP,fieldUVW]) # this is actually not necessary
	val0=fieldP.evaluate(evalAt)
	# load mesh and fields from HDF5, also opens the storage
	mesh,fields=mp.HeavyUnstructuredMesh.load(h5path)
	val1=fields[0].evaluate((.1,.1,.1))
	self.assertEqual(val0,val1)