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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
View File

@ -276,7 +276,7 @@ class Colormap(mpl.colors.ListedColormap):
def shade(self,
field: np.ndarray,
bounds: Optional[FloatSequence] = None,
gap: Optional[float] = None) -> Image:
gap: Optional[float] = None) -> Image.Image:
"""
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
import numpy as np
import vtk
from vtk.util.numpy_support import numpy_to_vtk as np_to_vtk
from vtk.util.numpy_support import numpy_to_vtkIdTypeArray as np_to_vtkIdTypeArray
from vtk.util.numpy_support import vtk_to_numpy as vtk_to_np
from vtkmodules.vtkCommonCore import (
vtkPoints,
vtkStringArray,
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 . import util
@ -23,16 +67,16 @@ class VTK:
"""
def __init__(self,
vtk_data: vtk.vtkDataSet):
vtk_data: vtkDataSet):
"""
New spatial visualization.
Parameters
----------
vtk_data : subclass of vtk.vtkDataSet
vtk_data : subclass of vtkDataSet
Description of geometry and topology, optionally with attached data.
Valid types are vtk.vtkImageData, vtk.vtkUnstructuredGrid,
vtk.vtkPolyData, and vtk.vtkRectilinearGrid.
Valid types are vtkImageData, vtkUnstructuredGrid,
vtkPolyData, and vtkRectilinearGrid.
"""
self.vtk_data = vtk_data
@ -76,14 +120,14 @@ class VTK:
def copy(self):
if isinstance(self.vtk_data,vtk.vtkImageData):
dup = vtk.vtkImageData()
elif isinstance(self.vtk_data,vtk.vtkUnstructuredGrid):
dup = vtk.vtkUnstructuredGrid()
elif isinstance(self.vtk_data,vtk.vtkPolyData):
dup = vtk.vtkPolyData()
elif isinstance(self.vtk_data,vtk.vtkRectilinearGrid):
dup = vtk.vtkRectilinearGrid()
if isinstance(self.vtk_data,vtkImageData):
dup = vtkImageData()
elif isinstance(self.vtk_data,vtkUnstructuredGrid):
dup = vtkUnstructuredGrid()
elif isinstance(self.vtk_data,vtkPolyData):
dup = vtkPolyData()
elif isinstance(self.vtk_data,vtkRectilinearGrid):
dup = vtkRectilinearGrid()
else:
raise TypeError
@ -114,7 +158,7 @@ class VTK:
Comments.
"""
s = vtk.vtkStringArray()
s = vtkStringArray()
s.SetName('comments')
for c in comments:
s.InsertNextValue(c)
@ -154,7 +198,7 @@ class VTK:
size: FloatSequence,
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.
@ -173,7 +217,7 @@ class VTK:
VTK-based geometry without nodal or cell data.
"""
vtk_data = vtk.vtkImageData()
vtk_data = vtkImageData()
vtk_data.SetDimensions(*(np.array(cells)+1))
vtk_data.SetOrigin(*(np.array(origin)))
vtk_data.SetSpacing(*(np.array(size)/np.array(cells)))
@ -186,7 +230,7 @@ class VTK:
connectivity: np.ndarray,
cell_type: str) -> 'VTK':
"""
Create VTK of type vtk.vtkUnstructuredGrid.
Create VTK of type vtkUnstructuredGrid.
This is the common type for mesh solver results.
@ -198,7 +242,7 @@ class VTK:
Cell connectivity (0-based), first dimension determines #Cells,
second dimension determines #Nodes/Cell.
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
-------
@ -206,18 +250,18 @@ class VTK:
VTK-based geometry without nodal or cell data.
"""
vtk_nodes = vtk.vtkPoints()
vtk_nodes.SetData(np_to_vtk(np.ascontiguousarray(nodes)))
cells = vtk.vtkCellArray()
vtk_nodes = vtkPoints()
vtk_nodes.SetData(numpy_to_vtk(np.ascontiguousarray(nodes)))
cells = vtkCellArray()
cells.SetNumberOfCells(connectivity.shape[0])
T = np.concatenate((np.ones((connectivity.shape[0],1),dtype=np.int64)*connectivity.shape[1],
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)
cell_types = {'TRIANGLE':vtk.VTK_TRIANGLE, 'QUAD':vtk.VTK_QUAD,
'TETRA' :vtk.VTK_TETRA, 'HEXAHEDRON':vtk.VTK_HEXAHEDRON}
cell_types = {'TRIANGLE':VTK_TRIANGLE, 'QUAD':VTK_QUAD,
'TETRA' :VTK_TETRA, 'HEXAHEDRON':VTK_HEXAHEDRON}
vtk_data.SetCells(cell_types[cell_type.split("_",1)[-1].upper()],cells)
return VTK(vtk_data)
@ -226,7 +270,7 @@ class VTK:
@staticmethod
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.
@ -242,15 +286,15 @@ class VTK:
"""
N = points.shape[0]
vtk_points = vtk.vtkPoints()
vtk_points.SetData(np_to_vtk(np.ascontiguousarray(points)))
vtk_points = vtkPoints()
vtk_points.SetData(numpy_to_vtk(np.ascontiguousarray(points)))
vtk_cells = vtk.vtkCellArray()
vtk_cells = vtkCellArray()
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))
vtk_data = vtk.vtkPolyData()
vtk_data = vtkPolyData()
vtk_data.SetPoints(vtk_points)
vtk_data.SetVerts(vtk_cells)
@ -260,7 +304,7 @@ class VTK:
@staticmethod
def from_rectilinear_grid(grid: FloatSequence) -> 'VTK':
"""
Create VTK of type vtk.vtkRectilinearGrid.
Create VTK of type vtkRectilinearGrid.
Parameters
----------
@ -273,9 +317,9 @@ class VTK:
VTK-based geometry without nodal or cell data.
"""
vtk_data = vtk.vtkRectilinearGrid()
vtk_data = vtkRectilinearGrid()
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'])]
vtk_data.SetXCoordinates(coord[0])
vtk_data.SetYCoordinates(coord[1])
@ -296,7 +340,7 @@ class VTK:
Filename to read.
Valid extensions are .vti, .vtu, .vtp, .vtr, and .vtk.
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
-------
@ -307,7 +351,7 @@ class VTK:
if not Path(fname).expanduser().is_file(): # vtk has a strange error handling
raise FileNotFoundError(f'file "{fname}" not found')
if (ext := Path(fname).suffix) == '.vtk' or dataset_type is not None:
reader = vtk.vtkGenericDataObjectReader()
reader = vtkGenericDataObjectReader()
reader.SetFileName(str(Path(fname).expanduser()))
if dataset_type is None:
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')
else:
if ext == '.vti':
reader = vtk.vtkXMLImageDataReader()
reader = vtkXMLImageDataReader()
elif ext == '.vtu':
reader = vtk.vtkXMLUnstructuredGridReader()
reader = vtkXMLUnstructuredGridReader()
elif ext == '.vtp':
reader = vtk.vtkXMLPolyDataReader()
reader = vtkXMLPolyDataReader()
elif ext == '.vtr':
reader = vtk.vtkXMLRectilinearGridReader()
reader = vtkXMLRectilinearGridReader()
else:
raise TypeError(f'unknown file extension "{ext}"')
@ -352,7 +396,7 @@ class VTK:
def as_ASCII(self) -> str:
"""ASCII representation of the VTK data."""
writer = vtk.vtkDataSetWriter()
writer = vtkDataSetWriter()
writer.SetHeader(f'# {util.execution_stamp("VTK")}')
writer.WriteToOutputStringOn()
writer.SetInputData(self.vtk_data)
@ -377,14 +421,14 @@ class VTK:
Compress with zlib algorithm. Defaults to True.
"""
if isinstance(self.vtk_data,vtk.vtkImageData):
writer = vtk.vtkXMLImageDataWriter()
elif isinstance(self.vtk_data,vtk.vtkUnstructuredGrid):
writer = vtk.vtkXMLUnstructuredGridWriter()
elif isinstance(self.vtk_data,vtk.vtkPolyData):
writer = vtk.vtkXMLPolyDataWriter()
elif isinstance(self.vtk_data,vtk.vtkRectilinearGrid):
writer = vtk.vtkXMLRectilinearGridWriter()
if isinstance(self.vtk_data,vtkImageData):
writer = vtkXMLImageDataWriter()
elif isinstance(self.vtk_data,vtkUnstructuredGrid):
writer = vtkXMLUnstructuredGridWriter()
elif isinstance(self.vtk_data,vtkPolyData):
writer = vtkXMLPolyDataWriter()
elif isinstance(self.vtk_data,vtkRectilinearGrid):
writer = vtkXMLRectilinearGridWriter()
default_ext = '.'+writer.GetDefaultFileExtension()
ext = Path(fname).suffix
@ -456,11 +500,11 @@ class VTK:
.astype(np.single if data.dtype in [np.double,np.longdouble] else data.dtype)
if data.dtype.type is np.str_:
d = vtk.vtkStringArray()
d = vtkStringArray()
for s in np.squeeze(data_):
d.InsertNextValue(s)
else:
d = np_to_vtk(data_,deep=True)
d = numpy_to_vtk(data_,deep=True)
d.SetName(label)
@ -518,7 +562,7 @@ class VTK:
for a in range(cell_data.GetNumberOfArrays()):
if cell_data.GetArrayName(a) == label:
try:
return vtk_to_np(cell_data.GetArray(a))
return vtk_to_numpy(cell_data.GetArray(a))
except AttributeError:
vtk_array = cell_data.GetAbstractArray(a) # string array
@ -526,7 +570,7 @@ class VTK:
for a in range(point_data.GetNumberOfArrays()):
if point_data.GetArrayName(a) == label:
try:
return vtk_to_np(point_data.GetArray(a))
return vtk_to_numpy(point_data.GetArray(a))
except AttributeError:
vtk_array = point_data.GetAbstractArray(a) # string array
@ -572,7 +616,7 @@ class VTK:
width = 1024
height = 768
lut = vtk.vtkLookupTable()
lut = vtkLookupTable()
colormap_ = Colormap.from_predefined(colormap) if isinstance(colormap,str) else \
colormap
lut.SetNumberOfTableValues(len(colormap_.colors))
@ -581,33 +625,33 @@ class VTK:
lut.Build()
self.vtk_data.GetCellData().SetActiveScalars(label)
mapper = vtk.vtkDataSetMapper()
mapper = vtkDataSetMapper()
mapper.SetInputData(self.vtk_data)
mapper.SetLookupTable(lut)
mapper.SetScalarRange(self.vtk_data.GetScalarRange())
actor = vtk.vtkActor()
actor = vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetColor(230/255,150/255,68/255)
ren = vtk.vtkRenderer()
ren = vtkRenderer()
ren.AddActor(actor)
if label is None:
ren.SetBackground(67/255,128/255,208/255)
else:
colormap_vtk = vtk.vtkScalarBarActor()
colormap_vtk = vtkScalarBarActor()
colormap_vtk.SetLookupTable(lut)
colormap_vtk.SetTitle(label)
colormap_vtk.SetMaximumWidthInPixels(width//100)
ren.AddActor2D(colormap_vtk)
ren.SetBackground(0.3,0.3,0.3)
window = vtk.vtkRenderWindow()
window = vtkRenderWindow()
window.AddRenderer(ren)
window.SetSize(width,height)
window.SetWindowName(util.execution_stamp('VTK','show'))
iren = vtk.vtkRenderWindowInteractor()
iren = vtkRenderWindowInteractor()
iren.SetRenderWindow(window)
if os.name == 'posix' and 'DISPLAY' not in os.environ:
print('Found no rendering device')

2
python/mypy.ini
View File

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

4
python/tests/test_Grid.py
View File

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

21
python/tests/test_Result.py
View File

@ -10,7 +10,12 @@ import random
from datetime import datetime
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 numpy as np
@ -389,7 +394,7 @@ class TestResult:
'4grains2x4x3_compressionY.hdf5',
'6grains6x7x8_single_phase_tensionY.hdf5'],ids=range(3))
@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):
result = Result(ref_path/fname).view(increments=inc)
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)
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')),
reason='https://discourse.vtk.org/t/2450')
@pytest.mark.skipif(not hasattr(vtkXdmfReader,'GetOutput'),reason='https://discourse.vtk.org/t/2450')
def test_XDMF_shape(self,tmp_path,single_phase):
single_phase.export_XDMF(target_dir=single_phase.fname.parent)
fname = single_phase.fname.with_suffix('.xdmf')
reader_xdmf = vtk.vtkXdmfReader()
reader_xdmf = vtkXdmfReader()
reader_xdmf.SetFileName(fname)
reader_xdmf.Update()
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)
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.Update()
dim_vti = reader_vti.GetOutput().GetDimensions()
@ -474,11 +478,10 @@ class TestResult:
single_phase.export_XDMF(target_dir=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')),
reason='https://discourse.vtk.org/t/2450')
@pytest.mark.skipif(not hasattr(vtkXdmfReader,'GetOutput'),reason='https://discourse.vtk.org/t/2450')
def test_XDMF_relabs_path(self,single_phase,tmp_path):
def dims(xdmf):
reader_xdmf = vtk.vtkXdmfReader()
reader_xdmf = vtkXdmfReader()
reader_xdmf.SetFileName(xdmf)
reader_xdmf.Update()
return reader_xdmf.GetOutput().GetDimensions()

8
python/tests/test_VTK.py
View File

@ -7,7 +7,7 @@ import sys
import pytest
import numpy as np
import numpy.ma as ma
import vtk
from vtkmodules.vtkCommonCore import vtkVersion
from damask import VTK
from damask import Table
@ -32,7 +32,7 @@ class TestVTK:
print('patched damask.util.execution_stamp')
@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):
monkeypatch.delenv('DISPLAY',raising=False)
default.show(colormap=cmap)
@ -222,7 +222,7 @@ class TestVTK:
new = VTK.load(tmp_path/'with_comments.vti')
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):
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)
@ -233,7 +233,7 @@ class TestVTK:
assert polyData.as_ASCII() == reference.as_ASCII() and \
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):
grid = [np.arange(4)**2.,
np.arange(5)**2.,