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Merge branch '277-python-vtkmodules-import' into 'development' 

Resolve "python vtk: import"

Closes #277

See merge request damask/DAMASK!742
This commit is contained in:
Martin Diehl 2023-03-08 18:03:23 +00:00
parent c879fb933c 782a593bf2
commit c7f8647cfd
6 changed files with 127 additions and 80 deletions
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2
python/damask/_colormap.py
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@ -276,7 +276,7 @@ class Colormap(mpl.colors.ListedColormap):
def shade(self, def shade(self,
field: np.ndarray, field: np.ndarray,
bounds: Optional[FloatSequence] = None, bounds: Optional[FloatSequence] = None,
gap: Optional[float] = None) -> Image: gap: Optional[float] = None) -> Image.Image:
""" """
Generate PIL image of 2D field using colormap. Generate PIL image of 2D field using colormap.

170
python/damask/_vtk.py
View File

@ -4,10 +4,54 @@ from pathlib import Path
from typing import Optional, Union, Literal, List, Sequence from typing import Optional, Union, Literal, List, Sequence
import numpy as np import numpy as np
import vtk from vtkmodules.vtkCommonCore import (
from vtk.util.numpy_support import numpy_to_vtk as np_to_vtk vtkPoints,
from vtk.util.numpy_support import numpy_to_vtkIdTypeArray as np_to_vtkIdTypeArray vtkStringArray,
from vtk.util.numpy_support import vtk_to_numpy as vtk_to_np vtkLookupTable,
)
from vtkmodules.vtkCommonDataModel import (
vtkDataSet,
vtkCellArray,
vtkImageData,
vtkRectilinearGrid,
vtkUnstructuredGrid,
vtkPolyData,
)
from vtkmodules.vtkIOLegacy import (
vtkGenericDataObjectReader,
vtkDataSetWriter,
)
from vtkmodules.vtkIOXML import (
vtkXMLImageDataReader,
vtkXMLImageDataWriter,
vtkXMLRectilinearGridReader,
vtkXMLRectilinearGridWriter,
vtkXMLUnstructuredGridReader,
vtkXMLUnstructuredGridWriter,
vtkXMLPolyDataReader,
vtkXMLPolyDataWriter,
)
from vtkmodules.vtkRenderingCore import (
vtkDataSetMapper,
vtkActor,
vtkRenderer,
vtkRenderWindow,
vtkRenderWindowInteractor,
)
from vtkmodules.vtkRenderingAnnotation import (
vtkScalarBarActor,
)
from vtkmodules.util.vtkConstants import (
VTK_TRIANGLE,
VTK_QUAD,
VTK_TETRA,
VTK_HEXAHEDRON,
)
from vtkmodules.util.numpy_support import (
numpy_to_vtk,
numpy_to_vtkIdTypeArray,
vtk_to_numpy,
)
from ._typehints import FloatSequence, IntSequence from ._typehints import FloatSequence, IntSequence
from . import util from . import util
@ -23,16 +67,16 @@ class VTK:
""" """
def __init__(self, def __init__(self,
vtk_data: vtk.vtkDataSet): vtk_data: vtkDataSet):
""" """
New spatial visualization. New spatial visualization.
Parameters Parameters
---------- ----------
vtk_data : subclass of vtk.vtkDataSet vtk_data : subclass of vtkDataSet
Description of geometry and topology, optionally with attached data. Description of geometry and topology, optionally with attached data.
Valid types are vtk.vtkImageData, vtk.vtkUnstructuredGrid, Valid types are vtkImageData, vtkUnstructuredGrid,
vtk.vtkPolyData, and vtk.vtkRectilinearGrid. vtkPolyData, and vtkRectilinearGrid.
""" """
self.vtk_data = vtk_data self.vtk_data = vtk_data
@ -76,14 +120,14 @@ class VTK:
def copy(self): def copy(self):
if isinstance(self.vtk_data,vtk.vtkImageData): if isinstance(self.vtk_data,vtkImageData):
dup = vtk.vtkImageData() dup = vtkImageData()
elif isinstance(self.vtk_data,vtk.vtkUnstructuredGrid): elif isinstance(self.vtk_data,vtkUnstructuredGrid):
dup = vtk.vtkUnstructuredGrid() dup = vtkUnstructuredGrid()
elif isinstance(self.vtk_data,vtk.vtkPolyData): elif isinstance(self.vtk_data,vtkPolyData):
dup = vtk.vtkPolyData() dup = vtkPolyData()
elif isinstance(self.vtk_data,vtk.vtkRectilinearGrid): elif isinstance(self.vtk_data,vtkRectilinearGrid):
dup = vtk.vtkRectilinearGrid() dup = vtkRectilinearGrid()
else: else:
raise TypeError raise TypeError
@ -114,7 +158,7 @@ class VTK:
Comments. Comments.
""" """
s = vtk.vtkStringArray() s = vtkStringArray()
s.SetName('comments') s.SetName('comments')
for c in comments: for c in comments:
s.InsertNextValue(c) s.InsertNextValue(c)
@ -154,7 +198,7 @@ class VTK:
size: FloatSequence, size: FloatSequence,
origin: FloatSequence = np.zeros(3)) -> 'VTK': origin: FloatSequence = np.zeros(3)) -> 'VTK':
""" """
Create VTK of type vtk.vtkImageData. Create VTK of type vtkImageData.
This is the common type for grid solver results. This is the common type for grid solver results.
@ -173,7 +217,7 @@ class VTK:
VTK-based geometry without nodal or cell data. VTK-based geometry without nodal or cell data.
""" """
vtk_data = vtk.vtkImageData() vtk_data = vtkImageData()
vtk_data.SetDimensions(*(np.array(cells)+1)) vtk_data.SetDimensions(*(np.array(cells)+1))
vtk_data.SetOrigin(*(np.array(origin))) vtk_data.SetOrigin(*(np.array(origin)))
vtk_data.SetSpacing(*(np.array(size)/np.array(cells))) vtk_data.SetSpacing(*(np.array(size)/np.array(cells)))
@ -186,7 +230,7 @@ class VTK:
connectivity: np.ndarray, connectivity: np.ndarray,
cell_type: str) -> 'VTK': cell_type: str) -> 'VTK':
""" """
Create VTK of type vtk.vtkUnstructuredGrid. Create VTK of type vtkUnstructuredGrid.
This is the common type for mesh solver results. This is the common type for mesh solver results.
@ -198,7 +242,7 @@ class VTK:
Cell connectivity (0-based), first dimension determines #Cells, Cell connectivity (0-based), first dimension determines #Cells,
second dimension determines #Nodes/Cell. second dimension determines #Nodes/Cell.
cell_type : str cell_type : str
Name of the vtk.vtkCell subclass. Tested for TRIANGLE, QUAD, TETRA, and HEXAHEDRON. Name of the vtkCell subclass. Tested for TRIANGLE, QUAD, TETRA, and HEXAHEDRON.
Returns Returns
------- -------
@ -206,18 +250,18 @@ class VTK:
VTK-based geometry without nodal or cell data. VTK-based geometry without nodal or cell data.
""" """
vtk_nodes = vtk.vtkPoints() vtk_nodes = vtkPoints()
vtk_nodes.SetData(np_to_vtk(np.ascontiguousarray(nodes))) vtk_nodes.SetData(numpy_to_vtk(np.ascontiguousarray(nodes)))
cells = vtk.vtkCellArray() cells = 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],
connectivity),axis=1).ravel() connectivity),axis=1).ravel()
cells.SetCells(connectivity.shape[0],np_to_vtkIdTypeArray(T,deep=True)) cells.SetCells(connectivity.shape[0],numpy_to_vtkIdTypeArray(T,deep=True))
vtk_data = vtk.vtkUnstructuredGrid() vtk_data = vtkUnstructuredGrid()
vtk_data.SetPoints(vtk_nodes) vtk_data.SetPoints(vtk_nodes)
cell_types = {'TRIANGLE':vtk.VTK_TRIANGLE, 'QUAD':vtk.VTK_QUAD, cell_types = {'TRIANGLE':VTK_TRIANGLE, 'QUAD':VTK_QUAD,
'TETRA' :vtk.VTK_TETRA, 'HEXAHEDRON':vtk.VTK_HEXAHEDRON} 'TETRA' :VTK_TETRA, 'HEXAHEDRON':VTK_HEXAHEDRON}
vtk_data.SetCells(cell_types[cell_type.split("_",1)[-1].upper()],cells) vtk_data.SetCells(cell_types[cell_type.split("_",1)[-1].upper()],cells)
return VTK(vtk_data) return VTK(vtk_data)
@ -226,7 +270,7 @@ class VTK:
@staticmethod @staticmethod
def from_poly_data(points: np.ndarray) -> 'VTK': def from_poly_data(points: np.ndarray) -> 'VTK':
""" """
Create VTK of type vtk.polyData. Create VTK of type polyData.
This is the common type for point-wise data. This is the common type for point-wise data.
@ -242,15 +286,15 @@ class VTK:
""" """
N = points.shape[0] N = points.shape[0]
vtk_points = vtk.vtkPoints() vtk_points = vtkPoints()
vtk_points.SetData(np_to_vtk(np.ascontiguousarray(points))) vtk_points.SetData(numpy_to_vtk(np.ascontiguousarray(points)))
vtk_cells = vtk.vtkCellArray() vtk_cells = vtkCellArray()
vtk_cells.SetNumberOfCells(N) vtk_cells.SetNumberOfCells(N)
vtk_cells.SetCells(N,np_to_vtkIdTypeArray(np.stack((np.ones (N,dtype=np.int64), vtk_cells.SetCells(N,numpy_to_vtkIdTypeArray(np.stack((np.ones (N,dtype=np.int64),
np.arange(N,dtype=np.int64)),axis=1).ravel(),deep=True)) np.arange(N,dtype=np.int64)),axis=1).ravel(),deep=True))
vtk_data = vtk.vtkPolyData() vtk_data = vtkPolyData()
vtk_data.SetPoints(vtk_points) vtk_data.SetPoints(vtk_points)
vtk_data.SetVerts(vtk_cells) vtk_data.SetVerts(vtk_cells)
@ -260,7 +304,7 @@ class VTK:
@staticmethod @staticmethod
def from_rectilinear_grid(grid: FloatSequence) -> 'VTK': def from_rectilinear_grid(grid: FloatSequence) -> 'VTK':
""" """
Create VTK of type vtk.vtkRectilinearGrid. Create VTK of type vtkRectilinearGrid.
Parameters Parameters
---------- ----------
@ -273,9 +317,9 @@ class VTK:
VTK-based geometry without nodal or cell data. VTK-based geometry without nodal or cell data.
""" """
vtk_data = vtk.vtkRectilinearGrid() vtk_data = vtkRectilinearGrid()
vtk_data.SetDimensions(*map(len,grid)) vtk_data.SetDimensions(*map(len,grid))
coord = [np_to_vtk(np.array(grid[i]),deep=True) for i in [0,1,2]] coord = [numpy_to_vtk(np.array(grid[i]),deep=True) for i in [0,1,2]]
[coord[i].SetName(n) for i,n in enumerate(['x','y','z'])] [coord[i].SetName(n) for i,n in enumerate(['x','y','z'])]
vtk_data.SetXCoordinates(coord[0]) vtk_data.SetXCoordinates(coord[0])
vtk_data.SetYCoordinates(coord[1]) vtk_data.SetYCoordinates(coord[1])
@ -296,7 +340,7 @@ class VTK:
Filename to read. Filename to read.
Valid extensions are .vti, .vtu, .vtp, .vtr, and .vtk. Valid extensions are .vti, .vtu, .vtp, .vtr, and .vtk.
dataset_type : {'ImageData', 'UnstructuredGrid', 'PolyData', 'RectilinearGrid'}, optional dataset_type : {'ImageData', 'UnstructuredGrid', 'PolyData', 'RectilinearGrid'}, optional
Name of the vtk.vtkDataSet subclass when opening a .vtk file. Name of the vtkDataSet subclass when opening a .vtk file.
Returns Returns
------- -------
@ -307,7 +351,7 @@ class VTK:
if not Path(fname).expanduser().is_file(): # vtk has a strange error handling if not Path(fname).expanduser().is_file(): # vtk has a strange error handling
raise FileNotFoundError(f'file "{fname}" not found') raise FileNotFoundError(f'file "{fname}" not found')
if (ext := Path(fname).suffix) == '.vtk' or dataset_type is not None: if (ext := Path(fname).suffix) == '.vtk' or dataset_type is not None:
reader = vtk.vtkGenericDataObjectReader() reader = vtkGenericDataObjectReader()
reader.SetFileName(str(Path(fname).expanduser())) reader.SetFileName(str(Path(fname).expanduser()))
if dataset_type is None: if dataset_type is None:
raise TypeError('dataset type for *.vtk file not given') raise TypeError('dataset type for *.vtk file not given')
@ -327,13 +371,13 @@ class VTK:
raise TypeError(f'unknown dataset type "{dataset_type}" for vtk file') raise TypeError(f'unknown dataset type "{dataset_type}" for vtk file')
else: else:
if ext == '.vti': if ext == '.vti':
reader = vtk.vtkXMLImageDataReader() reader = vtkXMLImageDataReader()
elif ext == '.vtu': elif ext == '.vtu':
reader = vtk.vtkXMLUnstructuredGridReader() reader = vtkXMLUnstructuredGridReader()
elif ext == '.vtp': elif ext == '.vtp':
reader = vtk.vtkXMLPolyDataReader() reader = vtkXMLPolyDataReader()
elif ext == '.vtr': elif ext == '.vtr':
reader = vtk.vtkXMLRectilinearGridReader() reader = vtkXMLRectilinearGridReader()
else: else:
raise TypeError(f'unknown file extension "{ext}"') raise TypeError(f'unknown file extension "{ext}"')
@ -352,7 +396,7 @@ class VTK:
def as_ASCII(self) -> str: def as_ASCII(self) -> str:
"""ASCII representation of the VTK data.""" """ASCII representation of the VTK data."""
writer = vtk.vtkDataSetWriter() writer = vtkDataSetWriter()
writer.SetHeader(f'# {util.execution_stamp("VTK")}') writer.SetHeader(f'# {util.execution_stamp("VTK")}')
writer.WriteToOutputStringOn() writer.WriteToOutputStringOn()
writer.SetInputData(self.vtk_data) writer.SetInputData(self.vtk_data)
@ -377,14 +421,14 @@ class VTK:
Compress with zlib algorithm. Defaults to True. Compress with zlib algorithm. Defaults to True.
""" """
if isinstance(self.vtk_data,vtk.vtkImageData): if isinstance(self.vtk_data,vtkImageData):
writer = vtk.vtkXMLImageDataWriter() writer = vtkXMLImageDataWriter()
elif isinstance(self.vtk_data,vtk.vtkUnstructuredGrid): elif isinstance(self.vtk_data,vtkUnstructuredGrid):
writer = vtk.vtkXMLUnstructuredGridWriter() writer = vtkXMLUnstructuredGridWriter()
elif isinstance(self.vtk_data,vtk.vtkPolyData): elif isinstance(self.vtk_data,vtkPolyData):
writer = vtk.vtkXMLPolyDataWriter() writer = vtkXMLPolyDataWriter()
elif isinstance(self.vtk_data,vtk.vtkRectilinearGrid): elif isinstance(self.vtk_data,vtkRectilinearGrid):
writer = vtk.vtkXMLRectilinearGridWriter() writer = vtkXMLRectilinearGridWriter()
default_ext = '.'+writer.GetDefaultFileExtension() default_ext = '.'+writer.GetDefaultFileExtension()
ext = Path(fname).suffix ext = Path(fname).suffix
@ -456,11 +500,11 @@ class VTK:
.astype(np.single if data.dtype in [np.double,np.longdouble] else data.dtype) .astype(np.single if data.dtype in [np.double,np.longdouble] else data.dtype)
if data.dtype.type is np.str_: if data.dtype.type is np.str_:
d = vtk.vtkStringArray() d = vtkStringArray()
for s in np.squeeze(data_): for s in np.squeeze(data_):
d.InsertNextValue(s) d.InsertNextValue(s)
else: else:
d = np_to_vtk(data_,deep=True) d = numpy_to_vtk(data_,deep=True)
d.SetName(label) d.SetName(label)
@ -518,7 +562,7 @@ class VTK:
for a in range(cell_data.GetNumberOfArrays()): for a in range(cell_data.GetNumberOfArrays()):
if cell_data.GetArrayName(a) == label: if cell_data.GetArrayName(a) == label:
try: try:
return vtk_to_np(cell_data.GetArray(a)) return vtk_to_numpy(cell_data.GetArray(a))
except AttributeError: except AttributeError:
vtk_array = cell_data.GetAbstractArray(a) # string array vtk_array = cell_data.GetAbstractArray(a) # string array
@ -526,7 +570,7 @@ class VTK:
for a in range(point_data.GetNumberOfArrays()): for a in range(point_data.GetNumberOfArrays()):
if point_data.GetArrayName(a) == label: if point_data.GetArrayName(a) == label:
try: try:
return vtk_to_np(point_data.GetArray(a)) return vtk_to_numpy(point_data.GetArray(a))
except AttributeError: except AttributeError:
vtk_array = point_data.GetAbstractArray(a) # string array vtk_array = point_data.GetAbstractArray(a) # string array
@ -572,7 +616,7 @@ class VTK:
width = 1024 width = 1024
height = 768 height = 768
lut = vtk.vtkLookupTable() lut = vtkLookupTable()
colormap_ = Colormap.from_predefined(colormap) if isinstance(colormap,str) else \ colormap_ = Colormap.from_predefined(colormap) if isinstance(colormap,str) else \
colormap colormap
lut.SetNumberOfTableValues(len(colormap_.colors)) lut.SetNumberOfTableValues(len(colormap_.colors))
@ -581,33 +625,33 @@ class VTK:
lut.Build() lut.Build()
self.vtk_data.GetCellData().SetActiveScalars(label) self.vtk_data.GetCellData().SetActiveScalars(label)
mapper = vtk.vtkDataSetMapper() mapper = vtkDataSetMapper()
mapper.SetInputData(self.vtk_data) mapper.SetInputData(self.vtk_data)
mapper.SetLookupTable(lut) mapper.SetLookupTable(lut)
mapper.SetScalarRange(self.vtk_data.GetScalarRange()) mapper.SetScalarRange(self.vtk_data.GetScalarRange())
actor = vtk.vtkActor() actor = vtkActor()
actor.SetMapper(mapper) actor.SetMapper(mapper)
actor.GetProperty().SetColor(230/255,150/255,68/255) actor.GetProperty().SetColor(230/255,150/255,68/255)
ren = vtk.vtkRenderer() ren = vtkRenderer()
ren.AddActor(actor) ren.AddActor(actor)
if label is None: if label is None:
ren.SetBackground(67/255,128/255,208/255) ren.SetBackground(67/255,128/255,208/255)
else: else:
colormap_vtk = vtk.vtkScalarBarActor() colormap_vtk = vtkScalarBarActor()
colormap_vtk.SetLookupTable(lut) colormap_vtk.SetLookupTable(lut)
colormap_vtk.SetTitle(label) colormap_vtk.SetTitle(label)
colormap_vtk.SetMaximumWidthInPixels(width//100) colormap_vtk.SetMaximumWidthInPixels(width//100)
ren.AddActor2D(colormap_vtk) ren.AddActor2D(colormap_vtk)
ren.SetBackground(0.3,0.3,0.3) ren.SetBackground(0.3,0.3,0.3)
window = vtk.vtkRenderWindow() window = vtkRenderWindow()
window.AddRenderer(ren) window.AddRenderer(ren)
window.SetSize(width,height) window.SetSize(width,height)
window.SetWindowName(util.execution_stamp('VTK','show')) window.SetWindowName(util.execution_stamp('VTK','show'))
iren = vtk.vtkRenderWindowInteractor() iren = vtkRenderWindowInteractor()
iren.SetRenderWindow(window) iren.SetRenderWindow(window)
if os.name == 'posix' and 'DISPLAY' not in os.environ: if os.name == 'posix' and 'DISPLAY' not in os.environ:
print('Found no rendering device') print('Found no rendering device')

2
python/mypy.ini
View File

@ -4,7 +4,7 @@ warn_redundant_casts = True
ignore_missing_imports = True ignore_missing_imports = True
[mypy-h5py.*] [mypy-h5py.*]
ignore_missing_imports = True ignore_missing_imports = True
[mypy-vtk.*] [mypy-vtkmodules.*]
ignore_missing_imports = True ignore_missing_imports = True
[mypy-PIL.*] [mypy-PIL.*]
ignore_missing_imports = True ignore_missing_imports = True

4
python/tests/test_Grid.py
View File

@ -2,7 +2,7 @@ import sys
import pytest import pytest
import numpy as np import numpy as np
import vtk from vtkmodules.vtkCommonCore import vtkVersion
from damask import VTK from damask import VTK
from damask import Grid from damask import Grid
@ -470,7 +470,7 @@ 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') @pytest.mark.xfail(vtkVersion.GetVTKMajorVersion()<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)

21
python/tests/test_Result.py
View File

@ -10,7 +10,12 @@ import random
from datetime import datetime from datetime import datetime
import pytest import pytest
import vtk from vtkmodules.vtkIOXML import vtkXMLImageDataReader
from vtkmodules.vtkCommonCore import vtkVersion
try:
from vtkmodules.vtkIOXdmf2 import vtkXdmfReader
except ImportError:
vtkXdmfReader=None # noqa type: ignore
import h5py import h5py
import numpy as np import numpy as np
@ -389,7 +394,7 @@ class TestResult:
'4grains2x4x3_compressionY.hdf5', '4grains2x4x3_compressionY.hdf5',
'6grains6x7x8_single_phase_tensionY.hdf5'],ids=range(3)) '6grains6x7x8_single_phase_tensionY.hdf5'],ids=range(3))
@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') @pytest.mark.xfail(vtkVersion.GetVTKMajorVersion()<9, reason='missing "Direction" attribute')
def test_export_vtk(self,request,tmp_path,ref_path,update,patch_execution_stamp,patch_datetime_now,output,fname,inc): def test_export_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)
result.export_VTK(output,target_dir=tmp_path,parallel=False) result.export_VTK(output,target_dir=tmp_path,parallel=False)
@ -442,12 +447,11 @@ class TestResult:
shutil.copy(xdmf_path,ref_path/xdmf_path.name) shutil.copy(xdmf_path,ref_path/xdmf_path.name)
assert sorted(open(xdmf_path).read()) == sorted(open(ref_path/xdmf_path.name).read()) assert sorted(open(xdmf_path).read()) == sorted(open(ref_path/xdmf_path.name).read())
@pytest.mark.skipif(not (hasattr(vtk,'vtkXdmfReader') and hasattr(vtk.vtkXdmfReader(),'GetOutput')), @pytest.mark.skipif(not hasattr(vtkXdmfReader,'GetOutput'),reason='https://discourse.vtk.org/t/2450')
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):
single_phase.export_XDMF(target_dir=single_phase.fname.parent) single_phase.export_XDMF(target_dir=single_phase.fname.parent)
fname = single_phase.fname.with_suffix('.xdmf') fname = single_phase.fname.with_suffix('.xdmf')
reader_xdmf = vtk.vtkXdmfReader() reader_xdmf = vtkXdmfReader()
reader_xdmf.SetFileName(fname) reader_xdmf.SetFileName(fname)
reader_xdmf.Update() reader_xdmf.Update()
dim_xdmf = reader_xdmf.GetOutput().GetDimensions() dim_xdmf = reader_xdmf.GetOutput().GetDimensions()
@ -455,7 +459,7 @@ class TestResult:
single_phase.view(increments=0).export_VTK(target_dir=single_phase.fname.parent,parallel=False) single_phase.view(increments=0).export_VTK(target_dir=single_phase.fname.parent,parallel=False)
fname = single_phase.fname.with_name(single_phase.fname.stem+'_inc00.vti') fname = single_phase.fname.with_name(single_phase.fname.stem+'_inc00.vti')
reader_vti = vtk.vtkXMLImageDataReader() reader_vti = 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()
@ -474,11 +478,10 @@ class TestResult:
single_phase.export_XDMF(target_dir=export_dir) single_phase.export_XDMF(target_dir=export_dir)
assert single_phase.fname.with_suffix('.xdmf').name in os.listdir(export_dir) assert single_phase.fname.with_suffix('.xdmf').name in os.listdir(export_dir)
@pytest.mark.skipif(not (hasattr(vtk,'vtkXdmfReader') and hasattr(vtk.vtkXdmfReader(),'GetOutput')), @pytest.mark.skipif(not hasattr(vtkXdmfReader,'GetOutput'),reason='https://discourse.vtk.org/t/2450')
reason='https://discourse.vtk.org/t/2450')
def test_XDMF_relabs_path(self,single_phase,tmp_path): def test_XDMF_relabs_path(self,single_phase,tmp_path):
def dims(xdmf): def dims(xdmf):
reader_xdmf = vtk.vtkXdmfReader() reader_xdmf = vtkXdmfReader()
reader_xdmf.SetFileName(xdmf) reader_xdmf.SetFileName(xdmf)
reader_xdmf.Update() reader_xdmf.Update()
return reader_xdmf.GetOutput().GetDimensions() return reader_xdmf.GetOutput().GetDimensions()

8
python/tests/test_VTK.py
View File

@ -7,7 +7,7 @@ import sys
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 vtkmodules.vtkCommonCore import vtkVersion
from damask import VTK from damask import VTK
from damask import Table from damask import Table
@ -32,7 +32,7 @@ class TestVTK:
print('patched damask.util.execution_stamp') print('patched damask.util.execution_stamp')
@pytest.mark.parametrize('cmap',[Colormap.from_predefined('cividis'),'strain']) @pytest.mark.parametrize('cmap',[Colormap.from_predefined('cividis'),'strain'])
@pytest.mark.skipif(sys.platform == 'win32', reason='DISPLAY has no effect on windows') @pytest.mark.skipif(sys.platform == 'win32', reason='DISPLAY has no effect on Windows OS')
def test_show(sef,default,cmap,monkeypatch): def test_show(sef,default,cmap,monkeypatch):
monkeypatch.delenv('DISPLAY',raising=False) monkeypatch.delenv('DISPLAY',raising=False)
default.show(colormap=cmap) default.show(colormap=cmap)
@ -222,7 +222,7 @@ class TestVTK:
new = VTK.load(tmp_path/'with_comments.vti') new = VTK.load(tmp_path/'with_comments.vti')
assert new.comments == ['this is a comment'] assert new.comments == ['this is a comment']
@pytest.mark.xfail(int(vtk.vtkVersion.GetVTKVersion().split('.')[0])<8, reason='missing METADATA') @pytest.mark.xfail(vtkVersion.GetVTKMajorVersion()<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).set('coordinates',points) polyData = VTK.from_poly_data(points).set('coordinates',points)
@ -233,7 +233,7 @@ class TestVTK:
assert polyData.as_ASCII() == reference.as_ASCII() and \ assert polyData.as_ASCII() == reference.as_ASCII() 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') @pytest.mark.xfail(vtkVersion.GetVTKMajorVersion()<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):
grid = [np.arange(4)**2., grid = [np.arange(4)**2.,
np.arange(5)**2., np.arange(5)**2.,