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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@ -42,4 +42,6 @@ jobs:
python3-h5py python3-vtk7 python3-matplotlib python3-yaml -y python3-h5py python3-vtk7 python3-matplotlib python3-yaml -y
- name: Run unit tests - name: Run unit tests
run: | run: |
PYTHONPATH=${PWD}/python python -m pytest python export PYTHONPATH=${PWD}/python
export COLUMNS=256
python -m pytest python

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

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@ -1,5 +1,6 @@
import pytest import pytest
import numpy as np import numpy as np
import vtk
from damask import VTK from damask import VTK
from damask import Grid from damask import Grid
@ -410,6 +411,7 @@ class TestGrid:
@pytest.mark.parametrize('periodic',[True,False]) @pytest.mark.parametrize('periodic',[True,False])
@pytest.mark.parametrize('direction',['x','y','z',['x','y'],'zy','xz',['x','y','z']]) @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): def test_get_grain_boundaries(self,update,ref_path,periodic,direction):
grid = Grid.load(ref_path/'get_grain_boundaries_8g12x15x20.vti') grid = Grid.load(ref_path/'get_grain_boundaries_8g12x15x20.vti')
current = grid.get_grain_boundaries(periodic,direction) current = grid.get_grain_boundaries(periodic,direction)

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@ -18,6 +18,12 @@ from damask import tensor
from damask import mechanics from damask import mechanics
from damask import grid_filters 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 @pytest.fixture
def default(tmp_path,ref_path): def default(tmp_path,ref_path):
"""Small Result file in temp location for modification.""" """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('output',['F','*',['P'],['P','F']],ids=range(4))
@pytest.mark.parametrize('fname',['12grains6x7x8_tensionY.hdf5'],ids=range(1)) @pytest.mark.parametrize('fname',['12grains6x7x8_tensionY.hdf5'],ids=range(1))
@pytest.mark.parametrize('inc',[4,0],ids=range(2)) @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): 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) result = Result(ref_path/fname).view('increments',inc)
os.chdir(tmp_path) 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 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): def test_XDMF_shape(self,tmp_path,single_phase):
os.chdir(tmp_path) os.chdir(tmp_path)
@ -437,19 +444,14 @@ class TestResult:
dim_xdmf = reader_xdmf.GetOutput().GetDimensions() dim_xdmf = reader_xdmf.GetOutput().GetDimensions()
bounds_xdmf = reader_xdmf.GetOutput().GetBounds() 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' 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 = vtk.vtkXMLImageDataReader()
reader_vti.SetFileName(fname) reader_vti.SetFileName(fname)
reader_vti.Update() reader_vti.Update()
dim_vti = reader_vti.GetOutput().GetDimensions() dim_vti = reader_vti.GetOutput().GetDimensions()
bounds_vti = reader_vti.GetOutput().GetBounds() bounds_vti = reader_vti.GetOutput().GetBounds()
if dim_vti == dim_xdmf and bounds_vti == bounds_xdmf: assert dim_vti == dim_xdmf and bounds_vti == bounds_xdmf
return
time.sleep(.5)
assert False
def test_XDMF_invalid(self,default): def test_XDMF_invalid(self,default):
with pytest.raises(TypeError): with pytest.raises(TypeError):

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