From 782a593bf28c3aabe7e8991bae8207744f3bb771 Mon Sep 17 00:00:00 2001 From: Philip Eisenlohr Date: Wed, 8 Mar 2023 18:03:22 +0000 Subject: [PATCH] separate import of vtk modules vtk is a collection of modules. Some are missing in some installations, so it is recommended to import only the functionality that is needed. --- python/damask/_colormap.py | 2 +- python/damask/_vtk.py | 170 +++++++++++++++++++++++------------- python/mypy.ini | 2 +- python/tests/test_Grid.py | 4 +- python/tests/test_Result.py | 21 +++-- python/tests/test_VTK.py | 8 +- 6 files changed, 127 insertions(+), 80 deletions(-) diff --git a/python/damask/_colormap.py b/python/damask/_colormap.py index 0d33a08ae..ccb8d3d70 100644 --- a/python/damask/_colormap.py +++ b/python/damask/_colormap.py @@ -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. diff --git a/python/damask/_vtk.py b/python/damask/_vtk.py index c6d88f0b4..f8a58d73b 100644 --- a/python/damask/_vtk.py +++ b/python/damask/_vtk.py @@ -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') diff --git a/python/mypy.ini b/python/mypy.ini index 5ef04daee..f64c9b8dd 100644 --- a/python/mypy.ini +++ b/python/mypy.ini @@ -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 diff --git a/python/tests/test_Grid.py b/python/tests/test_Grid.py index f81def323..f443bb94d 100644 --- a/python/tests/test_Grid.py +++ b/python/tests/test_Grid.py @@ -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) diff --git a/python/tests/test_Result.py b/python/tests/test_Result.py index 1e95c95de..d6ad27cc0 100644 --- a/python/tests/test_Result.py +++ b/python/tests/test_Result.py @@ -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() diff --git a/python/tests/test_VTK.py b/python/tests/test_VTK.py index 2efa148b2..fa1fa440d 100644 --- a/python/tests/test_VTK.py +++ b/python/tests/test_VTK.py @@ -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.,