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DAMASK_EICMD
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fixes for old VTK and/or old numpy

This commit is contained in:
Martin Diehl 2021-09-02 08:04:09 +02:00
parent 06d62b42cb
commit 2b9d416734
5 changed files with 27 additions and 18 deletions
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4
.github/workflows/.github-actions-demo.yml vendored
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@ -42,4 +42,6 @@ jobs:
python3-h5py python3-vtk7 python3-matplotlib python3-yaml -y
- name: Run unit tests
run: |
PYTHONPATH=${PWD}/python python -m pytest python
export PYTHONPATH=${PWD}/python
export COLUMNS=256
python -m pytest python

4
python/damask/_vtk.py
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@ -121,7 +121,7 @@ class VTK:
"""
vtk_nodes = vtk.vtkPoints()
vtk_nodes.SetData(np_to_vtk(nodes))
vtk_nodes.SetData(np_to_vtk(np.ascontiguousarray(nodes)))
cells = vtk.vtkCellArray()
cells.SetNumberOfCells(connectivity.shape[0])
T = np.concatenate((np.ones((connectivity.shape[0],1),dtype=np.int64)*connectivity.shape[1],
@ -157,7 +157,7 @@ class VTK:
"""
N = points.shape[0]
vtk_points = vtk.vtkPoints()
vtk_points.SetData(np_to_vtk(points))
vtk_points.SetData(np_to_vtk(np.ascontiguousarray(points)))
vtk_cells = vtk.vtkCellArray()
vtk_cells.SetNumberOfCells(N)

2
python/tests/test_Grid.py
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@ -1,5 +1,6 @@
import pytest
import numpy as np
import vtk
from damask import VTK
from damask import Grid
@ -410,6 +411,7 @@ class TestGrid:
@pytest.mark.parametrize('periodic',[True,False])
@pytest.mark.parametrize('direction',['x','y','z',['x','y'],'zy','xz',['x','y','z']])
@pytest.mark.xfail(int(vtk.vtkVersion.GetVTKVersion().split('.')[0])<8, reason='missing METADATA')
def test_get_grain_boundaries(self,update,ref_path,periodic,direction):
grid = Grid.load(ref_path/'get_grain_boundaries_8g12x15x20.vti')
current = grid.get_grain_boundaries(periodic,direction)

28
python/tests/test_Result.py
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@ -18,6 +18,12 @@ from damask import tensor
from damask import mechanics
from damask import grid_filters
def vtk_hasXdmfReader():
if hasattr(vtk,'vtkXdmfReader'):
r = vtk.vtkXdmfReader()
if hasattr(r,'getOutput'): return True
return False
@pytest.fixture
def default(tmp_path,ref_path):
"""Small Result file in temp location for modification."""
@ -374,6 +380,7 @@ class TestResult:
@pytest.mark.parametrize('output',['F','*',['P'],['P','F']],ids=range(4))
@pytest.mark.parametrize('fname',['12grains6x7x8_tensionY.hdf5'],ids=range(1))
@pytest.mark.parametrize('inc',[4,0],ids=range(2))
@pytest.mark.xfail(int(vtk.vtkVersion.GetVTKVersion().split('.')[0])<9, reason='missing "Direction" attribute')
def test_vtk(self,request,tmp_path,ref_path,update,patch_execution_stamp,patch_datetime_now,output,fname,inc):
result = Result(ref_path/fname).view('increments',inc)
os.chdir(tmp_path)
@ -425,7 +432,7 @@ class TestResult:
assert sorted(open(tmp_path/fname).read()) == sorted(open(ref_path/fname).read()) # XML is not ordered
@pytest.mark.skipif(not hasattr(vtk,'vtkXdmfReader'),reason='https://discourse.vtk.org/t/2450')
@pytest.mark.skipif(not vtk_hasXdmfReader(),reason='https://discourse.vtk.org/t/2450')
def test_XDMF_shape(self,tmp_path,single_phase):
os.chdir(tmp_path)
@ -437,19 +444,14 @@ class TestResult:
dim_xdmf = reader_xdmf.GetOutput().GetDimensions()
bounds_xdmf = reader_xdmf.GetOutput().GetBounds()
single_phase.view('increments',0).export_VTK()
single_phase.view('increments',0).export_VTK(parallel=False)
fname = os.path.splitext(os.path.basename(single_phase.fname))[0]+'_inc00.vti'
for i in range(10): # waiting for parallel IO
reader_vti = vtk.vtkXMLImageDataReader()
reader_vti.SetFileName(fname)
reader_vti.Update()
dim_vti = reader_vti.GetOutput().GetDimensions()
bounds_vti = reader_vti.GetOutput().GetBounds()
if dim_vti == dim_xdmf and bounds_vti == bounds_xdmf:
return
time.sleep(.5)
assert False
reader_vti = vtk.vtkXMLImageDataReader()
reader_vti.SetFileName(fname)
reader_vti.Update()
dim_vti = reader_vti.GetOutput().GetDimensions()
bounds_vti = reader_vti.GetOutput().GetBounds()
assert dim_vti == dim_xdmf and bounds_vti == bounds_xdmf
def test_XDMF_invalid(self,default):
with pytest.raises(TypeError):

7
python/tests/test_VTK.py
View File

@ -5,6 +5,7 @@ import time
import pytest
import numpy as np
import numpy.ma as ma
import vtk
from damask import VTK
from damask import grid_filters
@ -162,6 +163,7 @@ class TestVTK:
new = VTK.load(tmp_path/'with_comments.vtr')
assert new.get_comments() == ['this is a comment']
@pytest.mark.xfail(int(vtk.vtkVersion.GetVTKVersion().split('.')[0])<8, reason='missing METADATA')
def test_compare_reference_polyData(self,update,ref_path,tmp_path):
points=np.dstack((np.linspace(0.,1.,10),np.linspace(0.,2.,10),np.linspace(-1.,1.,10))).squeeze()
polyData = VTK.from_poly_data(points)
@ -173,14 +175,15 @@ class TestVTK:
assert polyData.__repr__() == reference.__repr__() and \
np.allclose(polyData.get('coordinates'),points)
@pytest.mark.xfail(int(vtk.vtkVersion.GetVTKVersion().split('.')[0])<8, reason='missing METADATA')
def test_compare_reference_rectilinearGrid(self,update,ref_path,tmp_path):
cells = np.array([5,6,7],int)
size = np.array([.6,1.,.5])
rectilinearGrid = VTK.from_rectilinear_grid(cells,size)
c = grid_filters.coordinates0_point(cells,size).reshape(-1,3,order='F')
n = grid_filters.coordinates0_node(cells,size).reshape(-1,3,order='F')
rectilinearGrid.add(c,'cell')
rectilinearGrid.add(n,'node')
rectilinearGrid.add(np.ascontiguousarray(c),'cell')
rectilinearGrid.add(np.ascontiguousarray(n),'node')
if update:
rectilinearGrid.save(ref_path/'rectilinearGrid')
else: