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Merge branch 'development' into misc-improvements

This commit is contained in:
Martin Diehl 2020-06-28 19:23:17 +02:00
parent 1f9b5280cb c33c5a18a8
commit 37f7362cbe
18 changed files with 166 additions and 352 deletions
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15
.gitlab-ci.yml
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@ -192,21 +192,6 @@ Post_addGradient:
- master
- release
Post_ParaviewRelated:
stage: postprocessing
script: ParaviewRelated/test.py
except:
- master
- release
Post_OrientationConversion:
stage: postprocessing
script:
- OrientationConversion/test.py
except:
- master
- release
Post_OrientationAverageMisorientation:
stage: postprocessing
script:

2
PRIVATE

@ -1 +1 @@
Subproject commit a6109acd264c683fd335b1d1f69934fc4a4078e3
Subproject commit 073913bf152b3c48f358dfbea5145807c0f7690d

2
VERSION
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@ -1 +1 @@
v2.0.3-2706-g8ce5da55
v2.0.3-2717-g52aacf37

0
processing/post/addAPS34IDEstrainCoords.py → processing/legacy/addAPS34IDEstrainCoords.py
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0
processing/post/addCumulative.py → processing/legacy/addCumulative.py
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0
processing/post/addEhkl.py → processing/legacy/addEhkl.py
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0
processing/post/imageData.py → processing/legacy/imageData.py
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0
processing/post/imageDataDeformed.py → processing/legacy/imageDataDeformed.py
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0
processing/post/imageDataRGB.py → processing/legacy/imageDataRGB.py
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143
processing/post/binXY.py
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@ -1,143 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
Produces a binned grid of two columns from an ASCIItable, i.e. a two-dimensional probability density map.
""", version = scriptID)
parser.add_option('-d','--data',
dest = 'data',
type = 'string', nargs = 2, metavar = 'string string',
help = 'column labels containing x and y ')
parser.add_option('-w','--weight',
dest = 'weight',
type = 'string', metavar = 'string',
help = 'column label containing weight of (x,y) point')
parser.add_option('-b','--bins',
dest = 'bins',
type = 'int', nargs = 2, metavar = 'int int',
help = 'number of bins in x and y direction [%default]')
parser.add_option('-t','--type',
dest = 'type',
type = 'string', nargs = 3, metavar = 'string string string',
help = 'type (linear/log) of x, y, and z axis [%default]')
parser.add_option('-x','--xrange',
dest = 'xrange',
type = 'float', nargs = 2, metavar = 'float float',
help = 'min max limits in x direction (optional)')
parser.add_option('-y','--yrange',
dest = 'yrange',
type = 'float', nargs = 2, metavar = 'float float',
help = 'min max limits in y direction (optional)')
parser.add_option('-z','--zrange',
dest = 'zrange',
type = 'float', nargs = 2, metavar = 'float float',
help = 'min max limits in z direction (optional)')
parser.add_option('-i','--invert',
dest = 'invert',
action = 'store_true',
help = 'invert probability density')
parser.add_option('-r','--rownormalize',
dest = 'normRow',
action = 'store_true',
help = 'normalize probability density in each row')
parser.add_option('-c','--colnormalize',
dest = 'normCol',
action = 'store_true',
help = 'normalize probability density in each column')
parser.set_defaults(bins = (10,10),
type = ('linear','linear','linear'),
xrange = (0.0,0.0),
yrange = (0.0,0.0),
zrange = (0.0,0.0),
)
(options,filenames) = parser.parse_args()
if filenames == []: filenames = [None]
minmax = np.array([options.xrange,options.yrange,options.zrange])
result = np.empty((options.bins[0],options.bins[1],3),'f')
if options.data is None: parser.error('no data columns specified.')
for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
data = np.hstack((table.get(options.data[0]),table.get(options.data[1])))
for c in (0,1): # check data minmax for x and y (i = 0 and 1)
if (minmax[c] == 0.0).all(): minmax[c] = [data[:,c].min(),data[:,c].max()]
if options.type[c].lower() == 'log': # if log scale
data[:,c] = np.log(data[:,c]) # change x,y coordinates to log
minmax[c] = np.log(minmax[c]) # change minmax to log, too
delta = minmax[:,1]-minmax[:,0]
(grid,xedges,yedges) = np.histogram2d(data[:,0],data[:,1],
bins=options.bins,
range=minmax[:2],
weights=table.get(options.weight) if options.weight else None)
if options.normCol:
for x in range(options.bins[0]):
sum = np.sum(grid[x,:])
if sum > 0.0:
grid[x,:] /= sum
if options.normRow:
for y in range(options.bins[1]):
sum = np.sum(grid[:,y])
if sum > 0.0:
grid[:,y] /= sum
if (minmax[2] == 0.0).all(): minmax[2] = [grid.min(),grid.max()] # auto scale from data
if minmax[2,0] == minmax[2,1]:
minmax[2,0] -= 1.
minmax[2,1] += 1.
if (minmax[2] == 0.0).all(): # no data in grid?
damask.util.croak('no data found on grid...')
minmax[2,:] = np.array([0.0,1.0]) # making up arbitrary z minmax
if options.type[2].lower() == 'log':
grid = np.log(grid)
minmax[2] = np.log(minmax[2])
delta[2] = minmax[2,1]-minmax[2,0]
for x in range(options.bins[0]):
for y in range(options.bins[1]):
result[x,y,:] = [minmax[0,0]+delta[0]/options.bins[0]*(x+0.5),
minmax[1,0]+delta[1]/options.bins[1]*(y+0.5),
np.clip((grid[x,y]-minmax[2,0])/delta[2],0.0,1.0)]
for c in (0,1):
if options.type[c].lower() == 'log': result[:,:,c] = np.exp(result[:,:,c])
if options.invert: result[:,:,2] = 1.0 - result[:,:,2]
comments = scriptID + '\t' + ' '.join(sys.argv[1:])
shapes = {'bin_%s'%options.data[0]:(1,),'bin_%s'%options.data[1]:(1,),'z':(1,)}
table = damask.Table(result.reshape(options.bins[0]*options.bins[1],3),shapes,[comments])
if name:
outname = os.path.join(os.path.dirname(name),'binned-{}-{}_'.format(*options.data) +
('weighted-{}_'.format(options.weight) if options.weight else '') +
os.path.basename(name))
table.to_ASCII(outname)
else:
table.to_ASCII(sys.stdout)

65
processing/post/vtk_addData.py
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@ -1,65 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption,
usage='%prog options [ASCIItable(s)]',
description = 'Add scalars/vectors, tensors, and/or a RGB tuples from ASCIItable '
+ 'to existing VTK file (.vtr/.vtu/.vtp).',
version = scriptID)
parser.add_option( '--vtk',
dest = 'vtk',
type = 'string', metavar = 'string',
help = 'VTK file name')
parser.add_option('-d', '--data',
dest = 'data',
action = 'extend', metavar = '<string LIST>',
help = 'scalar/vector value(s) label(s)')
parser.add_option('-t', '--tensor',
dest = 'tensor',
action = 'extend', metavar = '<string LIST>',
help = 'tensor (3x3) value label(s)')
parser.add_option('-c', '--color',
dest = 'color',
action = 'extend', metavar = '<string LIST>',
help = 'RGB color tuple label')
parser.set_defaults(data = [],
tensor = [],
color = [],
)
(options, filenames) = parser.parse_args()
if filenames == []: filenames = [None]
if not options.vtk:
parser.error('No VTK file specified.')
for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
vtk = damask.VTK.from_file(options.vtk)
for data in options.data+options.tensor:
vtk.add(table.get(data),data)
for color in options.color:
vtk.add((table.get(color)*255).astype(np.uint8),color)
vtk.write(options.vtk)

45
processing/post/vtk_pointCloud.py
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@ -1,45 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
Produce a VTK point cloud dataset based on coordinates given in an ASCIItable.
""", version = scriptID)
parser.add_option('-p',
'--pos', '--position',
dest = 'pos',
type = 'string', metavar = 'string',
help = 'label of coordinates [%default]')
parser.set_defaults(pos = 'pos',
)
(options, filenames) = parser.parse_args()
if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
v = damask.VTK.from_polyData(table.get(options.pos))
if name:
v.write(os.path.splitext(name)[0])
else:
sys.stdout.write(v.__repr__())

58
processing/post/vtk_rectilinearGrid.py
View File

@ -1,58 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
Create regular voxel grid from points in an ASCIItable.
""", version = scriptID)
parser.add_option('-m',
'--mode',
dest = 'mode',
metavar='string',
type = 'choice', choices = ['cell','point'],
help = 'cell-centered or point-centered coordinates')
parser.add_option('-p',
'--pos', '--position',
dest = 'pos',
type = 'string', metavar = 'string',
help = 'label of coordinates [%default]')
parser.set_defaults(mode = 'cell',
pos = 'pos',
)
(options, filenames) = parser.parse_args()
if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
if options.mode == 'cell':
grid, size, origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
elif options.mode == 'point':
grid, size, origin = damask.grid_filters.node_coord0_gridSizeOrigin(table.get(options.pos))
v = damask.VTK.from_rectilinearGrid(grid,size,origin)
if name:
v.write('{}_{}({})'.format(os.path.splitext(name)[0],options.pos,options.mode))
else:
sys.stdout.write(v.__repr__())

16
python/damask/_vtk.py
View File

@ -52,9 +52,11 @@ class VTK:
"""
geom = vtk.vtkRectilinearGrid()
geom.SetDimensions(*(grid+1))
geom.SetXCoordinates(np_to_vtk(np.linspace(origin[0],origin[0]+size[0],grid[0]+1),deep=True))
geom.SetYCoordinates(np_to_vtk(np.linspace(origin[1],origin[1]+size[1],grid[1]+1),deep=True))
geom.SetZCoordinates(np_to_vtk(np.linspace(origin[2],origin[2]+size[2],grid[2]+1),deep=True))
coord = [np_to_vtk(np.linspace(origin[i],origin[i]+size[i],grid[i]+1),deep=True) for i in [0,1,2]]
[coord[i].SetName(n) for i,n in enumerate(['x','y','z'])]
geom.SetXCoordinates(coord[0])
geom.SetYCoordinates(coord[1])
geom.SetZCoordinates(coord[2])
return VTK(geom)
@ -120,7 +122,7 @@ class VTK:
Parameters
----------
fname : str
fname : str or pathlib.Path
Filename for reading. Valid extensions are .vtr, .vtu, .vtp, and .vtk.
dataset_type : str, optional
Name of the vtk.vtkDataSet subclass when opening an .vtk file. Valid types are vtkRectilinearGrid,
@ -130,7 +132,7 @@ class VTK:
ext = Path(fname).suffix
if ext == '.vtk' or dataset_type:
reader = vtk.vtkGenericDataObjectReader()
reader.SetFileName(fname)
reader.SetFileName(str(fname))
reader.Update()
if dataset_type is None:
raise TypeError('Dataset type for *.vtk file not given.')
@ -152,7 +154,7 @@ class VTK:
else:
raise TypeError(f'Unknown file extension {ext}')
reader.SetFileName(fname)
reader.SetFileName(str(fname))
reader.Update()
geom = reader.GetOutput()
@ -168,7 +170,7 @@ class VTK:
Parameters
----------
fname : str
fname : str or pathlib.Path
Filename for writing.
parallel : boolean, optional
Write data in parallel background process. Defaults to True.

4
python/tests/conftest.py
View File

@ -1,4 +1,4 @@
import os
from pathlib import Path
import pytest
@ -15,4 +15,4 @@ def update(request):
@pytest.fixture
def reference_dir_base():
"""Directory containing reference results."""
return os.path.join(os.path.dirname(__file__),'reference')
return Path(__file__).parent/'reference'

67
python/tests/reference/VTK/polyData.vtp Normal file
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@ -0,0 +1,67 @@
<?xml version="1.0"?>
<VTKFile type="PolyData" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<PolyData>
<Piece NumberOfPoints="10" NumberOfVerts="0" NumberOfLines="0" NumberOfStrips="0" NumberOfPolys="0">
<PointData>
<DataArray type="Float64" Name="coordinates" NumberOfComponents="3" format="binary" RangeMin="0.7453559924999299" RangeMax="2.449489742783178">
AQAAAACAAADwAAAAagAAAA==eF5jYMAGPuyXOV4IRHvsIfQZe8u+xxZ9j1/sh/Eh9B37IjDj4f5QMLhqD6Gf2odB+Pth6iD0G3sFiLn7ofqg+j/CxOH6IfRX+xCouRYQ+6H0D/sCqH6YuRD6D1wd1B9QmsEBxgcAJsNfhw==
<InformationKey name="L2_NORM_RANGE" location="vtkDataArray" length="2">
<Value index="0">
0.7453559925
</Value>
<Value index="1">
2.4494897428
</Value>
</InformationKey>
</DataArray>
</PointData>
<CellData>
</CellData>
<Points>
<DataArray type="Float64" Name="Points" NumberOfComponents="3" format="binary" RangeMin="0.7453559924999299" RangeMax="2.449489742783178">
AQAAAACAAADwAAAAagAAAA==eF5jYMAGPuyXOV4IRHvsIfQZe8u+xxZ9j1/sh/Eh9B37IjDj4f5QMLhqD6Gf2odB+Pth6iD0G3sFiLn7ofqg+j/CxOH6IfRX+xCouRYQ+6H0D/sCqH6YuRD6D1wd1B9QmsEBxgcAJsNfhw==
<InformationKey name="L2_NORM_RANGE" location="vtkDataArray" length="2">
<Value index="0">
0.7453559925
</Value>
<Value index="1">
2.4494897428
</Value>
</InformationKey>
</DataArray>
</Points>
<Verts>
<DataArray type="Int64" Name="connectivity" format="binary" RangeMin="1e+299" RangeMax="-1e+299">
AAAAAACAAAAAAAAA
</DataArray>
<DataArray type="Int64" Name="offsets" format="binary" RangeMin="1e+299" RangeMax="-1e+299">
AAAAAACAAAAAAAAA
</DataArray>
</Verts>
<Lines>
<DataArray type="Int64" Name="connectivity" format="binary" RangeMin="1e+299" RangeMax="-1e+299">
AAAAAACAAAAAAAAA
</DataArray>
<DataArray type="Int64" Name="offsets" format="binary" RangeMin="1e+299" RangeMax="-1e+299">
AAAAAACAAAAAAAAA
</DataArray>
</Lines>
<Strips>
<DataArray type="Int64" Name="connectivity" format="binary" RangeMin="1e+299" RangeMax="-1e+299">
AAAAAACAAAAAAAAA
</DataArray>
<DataArray type="Int64" Name="offsets" format="binary" RangeMin="1e+299" RangeMax="-1e+299">
AAAAAACAAAAAAAAA
</DataArray>
</Strips>
<Polys>
<DataArray type="Int64" Name="connectivity" format="binary" RangeMin="1e+299" RangeMax="-1e+299">
AAAAAACAAAAAAAAA
</DataArray>
<DataArray type="Int64" Name="offsets" format="binary" RangeMin="1e+299" RangeMax="-1e+299">
AAAAAACAAAAAAAAA
</DataArray>
</Polys>
</Piece>
</PolyData>
</VTKFile>

44
python/tests/reference/VTK/rectilinearGrid.vtr Normal file
View File

@ -0,0 +1,44 @@
<?xml version="1.0"?>
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<RectilinearGrid WholeExtent="0 5 0 6 0 7">
<Piece Extent="0 5 0 6 0 7">
<PointData>
<DataArray type="Float64" Name="node" NumberOfComponents="3" format="binary" RangeMin="0" RangeMax="1.268857754044952">
AQAAAACAAACAHwAAywMAAA==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
<InformationKey name="L2_NORM_RANGE" location="vtkDataArray" length="2">
<Value index="0">
0
</Value>
<Value index="1">
1.268857754
</Value>
</InformationKey>
</DataArray>
</PointData>
<CellData>
<DataArray type="Float64" Name="cell" NumberOfComponents="3" format="binary" RangeMin="0.10871961482881586" RangeMax="1.160792402743735">
AQAAAACAAACwEwAAZQIAAA==eF511r2KFEEYRmHjjY2N9Ao0lQ79yQy8jBVjc29gL0Ezhc1maDBfU0FB3NVgNyqQuged1leZ56sqBpo5HRx4+wS13nn989l6vjzfzm45u/vk9+/NcvL17cuHJx8Lf3D/cD4XfvPq9vmj68vCH19vLwpf/3pvbedT8crjlccrj1ce77vtXBavPF55vPJ45fG+3/hN8crjlccrj1d+vHOb7NyKV368cyte+XrUVZ901YtXftxVL175Ss/f96dX+9MPpedwew6353B7DrdnvXJ71iu3Z73pTa/cnvXK7VlvetMrt2e9cnse79wmO7fildvzeOdWvOlt3FUvXrk9j7vqE+9uWQ/46qL0HG7P4fYcbs/h9qxXbs965fasN73plduzXrk9601veuX2rFduz+Od22TnVrxyex7v3Io3vY276sUrt+dxV33i3f37/vYcbs/h9hxuz+H2rFduz3rl9pynPYfbs165PeuV27NeuT3rlduz3j//22TnVrxyew6353B7DrdnvXJ71iu353uHa8jZl9JzuD2H23O4PYfbs165PeuV27Pe9KZXbs965fasN73plduzXrk9j3duk51b8crtebxzK970Nu6qF6/cnsdd9Yl3tzzdLtbfSs/h9hxuz+H2HG7PeuX2rFduz3rTm165PeuV27Pe9KZXbs965fY83rlNdm7FK7fn8c6teNPbuKtevHJ7HnfVJ97d8uJwDdn/KD2H23O4PYfbc7g965Xbs165PetNb3rl9qxXbs9605teuT3rldvzeOc22bkVr9yexzu34k1v46568crtedzVf/4LDINsdg==
<InformationKey name="L2_NORM_RANGE" location="vtkDataArray" length="2">
<Value index="0">
0.10871961483
</Value>
<Value index="1">
1.1607924027
</Value>
</InformationKey>
</DataArray>
</CellData>
<Coordinates>
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.6">
AQAAAACAAAAwAAAAJwAAAA==eF5jYICAHXKtrwN37LOH0Ofsua4vLrDlug7l37M3BoPH9gCdQxK6
</DataArray>
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="1">
AQAAAACAAAA4AAAAIgAAAA==eF5jYICAUDA4ag+hr9pDRB9A+U/tV4HBK6j4B3sAk7wQqg==
</DataArray>
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.5">
AQAAAACAAABAAAAALAAAAA==eF5jYICASSqeQLTJHkIfsr+9LReITkP5l+zB3NvXoOK37SG6HtgDANusGUo=
</DataArray>
</Coordinates>
</Piece>
</RectilinearGrid>
</VTKFile>

57
python/tests/test_VTK.py
View File

@ -6,11 +6,12 @@ import pytest
import numpy as np
from damask import VTK
from damask import grid_filters
@pytest.fixture
def reference_dir(reference_dir_base):
"""Directory containing reference results."""
return os.path.join(reference_dir_base,'Result')
return reference_dir_base/'VTK'
class TestVTK:
@ -20,22 +21,22 @@ class TestVTK:
origin = np.random.random(3)
v = VTK.from_rectilinearGrid(grid,size,origin)
string = v.__repr__()
v.write(os.path.join(tmp_path,'rectilinearGrid'),False)
vtr = VTK.from_file(os.path.join(tmp_path,'rectilinearGrid.vtr'))
with open(os.path.join(tmp_path,'rectilinearGrid.vtk'),'w') as f:
v.write(tmp_path/'rectilinearGrid',False)
vtr = VTK.from_file(tmp_path/'rectilinearGrid.vtr')
with open(tmp_path/'rectilinearGrid.vtk','w') as f:
f.write(string)
vtk = VTK.from_file(os.path.join(tmp_path,'rectilinearGrid.vtk'),'VTK_rectilinearGrid')
vtk = VTK.from_file(tmp_path/'rectilinearGrid.vtk','VTK_rectilinearGrid')
assert(string == vtr.__repr__() == vtk.__repr__())
def test_polyData(self,tmp_path):
points = np.random.rand(100,3)
v = VTK.from_polyData(points)
string = v.__repr__()
v.write(os.path.join(tmp_path,'polyData'),False)
vtp = VTK.from_file(os.path.join(tmp_path,'polyData.vtp'))
with open(os.path.join(tmp_path,'polyData.vtk'),'w') as f:
v.write(tmp_path/'polyData',False)
vtp = VTK.from_file(tmp_path/'polyData.vtp')
with open(tmp_path/'polyData.vtk','w') as f:
f.write(string)
vtk = VTK.from_file(os.path.join(tmp_path,'polyData.vtk'),'polyData')
vtk = VTK.from_file(tmp_path/'polyData.vtk','polyData')
assert(string == vtp.__repr__() == vtk.__repr__())
@pytest.mark.parametrize('cell_type,n',[
@ -50,19 +51,19 @@ class TestVTK:
connectivity = np.random.choice(np.arange(n),n,False).reshape(-1,n)
v = VTK.from_unstructuredGrid(nodes,connectivity,cell_type)
string = v.__repr__()
v.write(os.path.join(tmp_path,'unstructuredGrid'),False)
vtu = VTK.from_file(os.path.join(tmp_path,'unstructuredGrid.vtu'))
with open(os.path.join(tmp_path,'unstructuredGrid.vtk'),'w') as f:
v.write(tmp_path/'unstructuredGrid',False)
vtu = VTK.from_file(tmp_path/'unstructuredGrid.vtu')
with open(tmp_path/'unstructuredGrid.vtk','w') as f:
f.write(string)
vtk = VTK.from_file(os.path.join(tmp_path,'unstructuredGrid.vtk'),'unstructuredgrid')
vtk = VTK.from_file(tmp_path/'unstructuredGrid.vtk','unstructuredgrid')
assert(string == vtu.__repr__() == vtk.__repr__())
def test_parallel_out(self,tmp_path):
points = np.random.rand(102,3)
v = VTK.from_polyData(points)
fname_s = os.path.join(tmp_path,'single.vtp')
fname_p = os.path.join(tmp_path,'parallel.vtp')
fname_s = tmp_path/'single.vtp'
fname_p = tmp_path/'parallel.vtp'
v.write(fname_s,False)
v.write(fname_p,True)
for i in range(10):
@ -79,3 +80,29 @@ class TestVTK:
def test_invalid_dataset_type(self,dataset_type,name):
with pytest.raises(TypeError):
VTK.from_file('this_file_does_not_exist.vtk',dataset_type)
def test_compare_reference_polyData(self,update,reference_dir,tmp_path):
points=np.dstack((np.linspace(0.,1.,10),np.linspace(0.,2.,10),np.linspace(-1.,1.,10))).squeeze()
polyData = VTK.from_polyData(points)
polyData.add(points,'coordinates')
if update:
polyData.write(reference_dir/'polyData')
else:
reference = VTK.from_file(reference_dir/'polyData.vtp')
assert polyData.__repr__() == reference.__repr__()
def test_compare_reference_rectilinearGrid(self,update,reference_dir,tmp_path):
grid = np.array([5,6,7],int)
size = np.array([.6,1.,.5])
rectilinearGrid = VTK.from_rectilinearGrid(grid,size)
c = grid_filters.cell_coord0(grid,size).reshape(-1,3,order='F')
n = grid_filters.node_coord0(grid,size).reshape(-1,3,order='F')
rectilinearGrid.add(c,'cell')
rectilinearGrid.add(n,'node')
if update:
rectilinearGrid.write(reference_dir/'rectilinearGrid')
else:
reference = VTK.from_file(reference_dir/'rectilinearGrid.vtr')
assert rectilinearGrid.__repr__() == reference.__repr__()