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Merge branch 'increase-geom-test-coverage' into 'development' 

Increase geom test coverage

See merge request damask/DAMASK!204
This commit is contained in:
Franz Roters 2020-08-25 14:40:42 +02:00
parent a1f1b91c7f 279d43ccc6
commit cdc9f07838
36 changed files with 728 additions and 219 deletions
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6
python/damask/_colormap.py
View File

@ -10,7 +10,7 @@ import matplotlib.pyplot as plt
from matplotlib import cm
from PIL import Image
import damask
from . import util
from . import Table
_eps = 216./24389.
@ -280,7 +280,7 @@ class Colormap(mpl.colors.ListedColormap):
colors+=[i]+c
out = [{
'Creator':f'damask.Colormap v{damask.version}',
'Creator':util.version_date('Colormap'),
'ColorSpace':'RGB',
'Name':colormap.name,
'DefaultMap':True,
@ -296,7 +296,7 @@ class Colormap(mpl.colors.ListedColormap):
def _export_ASCII(colormap,fhandle=None):
"""Write colormap to ASCII table."""
labels = {'RGBA':4} if colormap.colors.shape[1] == 4 else {'RGB': 3}
t = Table(colormap.colors,labels,f'Creator: damask.Colormap v{damask.version}')
t = Table(colormap.colors,labels,f'Creator: {util.version_date("Colormap")}')
if fhandle is None:
with open(colormap.name.replace(' ','_')+'.txt', 'w') as f:

111
python/damask/_geom.py
View File

@ -1,7 +1,7 @@
import sys
import copy
from io import StringIO
import multiprocessing
from io import StringIO
from functools import partial
import numpy as np
@ -48,8 +48,8 @@ class Geom:
f'grid a b c: {util.srepr(self.get_grid ()," x ")}',
f'size x y z: {util.srepr(self.get_size ()," x ")}',
f'origin x y z: {util.srepr(self.get_origin()," ")}',
f'# microstructures: {self.N_microstructure}',
f'max microstructure: {np.nanmax(self.microstructure)}',
f'# materialpoints: {self.N_microstructure}',
f'max materialpoint: {np.nanmax(self.microstructure)}',
])
@ -188,10 +188,7 @@ class Geom:
physical size of the microstructure in meter.
"""
if size is None:
grid = np.asarray(self.microstructure.shape)
self.size = grid/np.max(grid)
else:
if size is not None:
if len(size) != 3 or any(np.array(size) <= 0):
raise ValueError(f'Invalid size {size}')
else:
@ -272,16 +269,6 @@ class Geom:
return self.comments[:]
def get_header(self):
"""Return the full header (grid, size, origin, homogenization, comments)."""
header = [f'{len(self.comments)+4} header'] + self.comments
header.append('grid a {} b {} c {}'.format(*self.get_grid()))
header.append('size x {} y {} z {}'.format(*self.get_size()))
header.append('origin x {} y {} z {}'.format(*self.get_origin()))
header.append(f'homogenization {self.get_homogenization()}')
return header
@staticmethod
def from_file(fname):
"""
@ -346,31 +333,23 @@ class Geom:
@staticmethod
def from_vtk(fname):
def from_vtr(fname):
"""
Read a geom from a VTK file.
Read a VTK rectilinear grid.
Parameters
----------
fname : str or file handle
fname : str or or pathlib.Path
Geometry file to read.
Valid extension is .vtr, it will be appended if not given.
"""
g = VTK.from_file(fname).geom
N_cells = g.GetNumberOfCells()
microstructure = np.zeros(N_cells)
grid = np.array(g.GetDimensions())-1
bbox = np.array(g.GetBounds()).reshape(3,2).T
v = VTK.from_file(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr')
grid = np.array(v.geom.GetDimensions())-1
bbox = np.array(v.geom.GetBounds()).reshape(3,2).T
size = bbox[1] - bbox[0]
celldata = g.GetCellData()
for a in range(celldata.GetNumberOfArrays()):
if celldata.GetArrayName(a) == 'microstructure':
array = celldata.GetArray(a)
for c in range(N_cells):
microstructure[c] = array.GetValue(c)
return Geom(microstructure.reshape(grid,order='F'),size,bbox[0])
return Geom(v.get('materialpoint').reshape(grid,order='F'),size,bbox[0])
@staticmethod
@ -419,8 +398,8 @@ class Geom:
else:
microstructure = microstructure.reshape(grid)
#ToDo: comments = 'geom.py:from_Laguerre_tessellation v{}'.format(version)
return Geom(microstructure+1,size,homogenization=1)
creator = util.version_date('Geom','from_Laguerre_tessellation')
return Geom(microstructure+1,size,homogenization=1,comments=creator)
@staticmethod
@ -444,8 +423,8 @@ class Geom:
KDTree = spatial.cKDTree(seeds,boxsize=size) if periodic else spatial.cKDTree(seeds)
devNull,microstructure = KDTree.query(coords)
#ToDo: comments = 'geom.py:from_Voronoi_tessellation v{}'.format(version)
return Geom(microstructure.reshape(grid)+1,size,homogenization=1)
creator = util.version_date('Geom','from_Voronoi_tessellation')
return Geom(microstructure.reshape(grid)+1,size,homogenization=1,comments=creator)
def to_file(self,fname,pack=None):
@ -460,7 +439,12 @@ class Geom:
Compress geometry with 'x of y' and 'a to b'.
"""
header = self.get_header()
header = [f'{len(self.comments)+4} header'] + self.comments
header.append('grid a {} b {} c {}'.format(*self.get_grid()))
header.append('size x {} y {} z {}'.format(*self.get_size()))
header.append('origin x {} y {} z {}'.format(*self.get_origin()))
header.append(f'homogenization {self.get_homogenization()}')
grid = self.get_grid()
if pack is None:
@ -492,7 +476,7 @@ class Geom:
reps += 1
else:
if compressType is None:
f.write('\n'.join(self.get_header())+'\n')
f.write('\n'.join(header)+'\n')
elif compressType == '.':
f.write(f'{former}\n')
elif compressType == 'to':
@ -514,21 +498,22 @@ class Geom:
f.write(f'{reps} of {former}\n')
def to_vtk(self,fname=None):
def to_vtr(self,fname=None):
"""
Generates vtk file.
Generates vtk rectilinear grid.
Parameters
----------
fname : str, optional
Vtk file to write. If no file is given, a string is returned.
Filename to write. If no file is given, a string is returned.
Valid extension is .vtr, it will be appended if not given.
"""
v = VTK.from_rectilinearGrid(self.grid,self.size,self.origin)
v.add(self.microstructure.flatten(order='F'),'microstructure')
v.add(self.microstructure.flatten(order='F'),'materialpoint')
if fname:
v.write(fname)
v.write(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr')
else:
sys.stdout.write(v.__repr__())
@ -590,6 +575,7 @@ class Geom:
fill_ = np.full_like(self.microstructure,np.nanmax(self.microstructure)+1 if fill is None else fill)
ms = np.ma.MaskedArray(fill_,np.logical_not(mask) if inverse else mask)
self.add_comments(util.version_date('Geom','add_primitive'))
return self.update(ms)
@ -607,9 +593,7 @@ class Geom:
"""
valid = {'x','y','z'}
if not all(isinstance(d, str) for d in directions):
raise TypeError('Directions are not of type str.')
elif not set(directions).issubset(valid):
if not set(directions).issubset(valid):
raise ValueError(f'Invalid direction {set(directions).difference(valid)} specified.')
limits = [None,None] if reflect else [-2,0]
@ -622,11 +606,11 @@ class Geom:
if 'x' in directions:
ms = np.concatenate([ms,ms[limits[0]:limits[1]:-1,:,:]],0)
#ToDo: self.add_comments('geom.py:mirror v{}'.format(version)
self.add_comments(util.version_date('Geom','mirror'))
return self.update(ms,rescale=True)
def scale(self,grid):
def scale(self,grid,periodic=True):
"""
Scale microstructure to new grid.
@ -634,22 +618,24 @@ class Geom:
----------
grid : numpy.ndarray of shape (3)
Number of grid points in x,y,z direction.
periodic : Boolean, optional
Assume geometry to be periodic. Defaults to True.
"""
#ToDo: self.add_comments('geom.py:scale v{}'.format(version)
self.add_comments(util.version_date('Geom','scale'))
return self.update(
ndimage.interpolation.zoom(
self.microstructure,
grid/self.get_grid(),
output=self.microstructure.dtype,
order=0,
mode='nearest',
mode=('wrap' if periodic else 'nearest'),
prefilter=False
)
)
def clean(self,stencil=3,mode='nearest',selection=None):
def clean(self,stencil=3,selection=None,periodic=True):
"""
Smooth microstructure by selecting most frequent index within given stencil at each location.
@ -657,11 +643,10 @@ class Geom:
----------
stencil : int, optional
Size of smoothing stencil.
mode : string, optional
The mode parameter determines how the input array is extended beyond its boundaries.
Default is 'nearest'. See scipy.ndimage.generic_filter for all options.
selection : list, optional
Field values that can be altered. Defaults to all.
periodic : Boolean, optional
Assume geometry to be periodic. Defaults to True.
"""
def mostFrequent(arr,selection=None):
@ -672,12 +657,12 @@ class Geom:
else:
return me
#ToDo: self.add_comments('geom.py:clean v{}'.format(version)
self.add_comments(util.version_date('Geom','clean'))
return self.update(ndimage.filters.generic_filter(
self.microstructure,
mostFrequent,
size=(stencil if selection is None else stencil//2*2+1,)*3,
mode=mode,
mode=('wrap' if periodic else 'nearest'),
extra_keywords=dict(selection=selection),
).astype(self.microstructure.dtype)
)
@ -689,7 +674,7 @@ class Geom:
for i, oldID in enumerate(np.unique(self.microstructure)):
renumbered = np.where(self.microstructure == oldID, i+1, renumbered)
#ToDo: self.add_comments('geom.py:renumber v{}'.format(version)
self.add_comments(util.version_date('Geom','renumber'))
return self.update(renumbered)
@ -724,7 +709,7 @@ class Geom:
origin = self.origin-(np.asarray(microstructure_in.shape)-self.grid)*.5 * self.size/self.grid
#ToDo: self.add_comments('geom.py:rotate v{}'.format(version)
self.add_comments(util.version_date('Geom','rotate'))
return self.update(microstructure_in,origin=origin,rescale=True)
@ -750,14 +735,14 @@ class Geom:
np.nanmax(self.microstructure)+1 if fill is None else fill,
dtype)
LL = np.clip( offset, 0,np.minimum(self.grid, grid+offset)) # noqa
LL = np.clip( offset, 0,np.minimum(self.grid, grid+offset))
UR = np.clip( offset+grid, 0,np.minimum(self.grid, grid+offset))
ll = np.clip(-offset, 0,np.minimum( grid,self.grid-offset))
ur = np.clip(-offset+self.grid,0,np.minimum( grid,self.grid-offset))
canvas[ll[0]:ur[0],ll[1]:ur[1],ll[2]:ur[2]] = self.microstructure[LL[0]:UR[0],LL[1]:UR[1],LL[2]:UR[2]]
#ToDo: self.add_comments('geom.py:canvas v{}'.format(version)
self.add_comments(util.version_date('Geom','canvas'))
return self.update(canvas,origin=self.origin+offset*self.size/self.grid,rescale=True)
@ -777,7 +762,7 @@ class Geom:
for from_ms,to_ms in zip(from_microstructure,to_microstructure):
substituted[self.microstructure==from_ms] = to_ms
#ToDo: self.add_comments('geom.py:substitute v{}'.format(version)
self.add_comments(util.version_date('Geom','substitute'))
return self.update(substituted)
@ -823,5 +808,5 @@ class Geom:
extra_keywords={'trigger':trigger})
microstructure = np.ma.MaskedArray(self.microstructure + offset_, np.logical_not(mask))
#ToDo: self.add_comments('geom.py:vicinity_offset v{}'.format(version)
self.add_comments(util.version_date('Geom','vicinity_offset'))
return self.update(microstructure)

7
python/damask/_table.py
View File

@ -3,7 +3,6 @@ import re
import pandas as pd
import numpy as np
from . import version
from . import util
class Table:
@ -49,7 +48,9 @@ class Table:
def _add_comment(self,label,shape,info):
if info is not None:
self.comments.append(f'{label}{" "+str(shape) if np.prod(shape,dtype=int) > 1 else ""}: {info}')
specific = f'{label}{" "+str(shape) if np.prod(shape,dtype=int) > 1 else ""}: {info}'
general = util.version_date('Table')
self.comments.append(f'{specific} / {general}')
@staticmethod
@ -135,7 +136,7 @@ class Table:
content = f.readlines()
comments = [f'table.py:from_ang v{version}']
comments = [util.version_date('Table','from_ang')]
for line in content:
if line.startswith('#'):
comments.append(line.strip())

88
python/damask/_vtk.py
View File

@ -6,8 +6,10 @@ 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
import damask
from . import util
from . import environment
from . import Table
@ -204,7 +206,18 @@ class VTK:
# Check https://blog.kitware.com/ghost-and-blanking-visibility-changes/ for missing data
# Needs support for pd.DataFrame and/or table
def add(self,data,label=None):
"""Add data to either cells or points."""
"""
Add data to either cells or points.
Parameters
----------
data : numpy.ndarray
Data to add. First dimension need to match either
number of cells or number of points
label : str
Data label.
"""
N_points = self.geom.GetNumberOfPoints()
N_cells = self.geom.GetNumberOfCells()
@ -232,10 +245,77 @@ class VTK:
raise TypeError
def get(self,label):
"""
Get either cell or point data.
Cell data takes precedence over point data, i.e. this
function assumes that labels are unique among cell and
point data.
Parameters
----------
label : str
Data label.
"""
celldata = self.geom.GetCellData()
for a in range(celldata.GetNumberOfArrays()):
if celldata.GetArrayName(a) == label:
return vtk_to_np(celldata.GetArray(a))
pointdata = self.geom.GetPointData()
for a in range(celldata.GetNumberOfArrays()):
if pointdata.GetArrayName(a) == label:
return vtk_to_np(pointdata.GetArray(a))
raise ValueError(f'array "{label}" not found')
def get_comments(self):
"""Return the comments."""
fielddata = self.geom.GetFieldData()
for a in range(fielddata.GetNumberOfArrays()):
if fielddata.GetArrayName(a) == 'comments':
comments = fielddata.GetAbstractArray(a)
return [comments.GetValue(i) for i in range(comments.GetNumberOfValues())]
return []
def set_comments(self,comments):
"""
Set Comments.
Parameters
----------
comments : str or list of str
Comments.
"""
s = vtk.vtkStringArray()
s.SetName('comments')
for c in [comments] if isinstance(comments,str) else comments:
s.InsertNextValue(c)
self.geom.GetFieldData().AddArray(s)
def add_comments(self,comments):
"""
Add Comments.
Parameters
----------
comments : str or list of str
Comments to add.
"""
self.set_comments(self.get_comments + ([comments] if isinstance(comments,str) else comments))
def __repr__(self):
"""ASCII representation of the VTK data."""
writer = vtk.vtkDataSetWriter()
writer.SetHeader(f'# damask.VTK v{damask.version}')
writer.SetHeader(f'# {util.version_date("VTK")}')
writer.WriteToOutputStringOn()
writer.SetInputData(self.geom)
writer.Write()
@ -261,7 +341,7 @@ class VTK:
ren.AddActor(actor)
ren.SetBackground(0.2,0.2,0.2)
window.SetSize(damask.environment.screen_size[0],damask.environment.screen_size[1])
window.SetSize(environment.screen_size[0],environment.screen_size[1])
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(window)

10
python/damask/solver/_marc.py
View File

@ -3,12 +3,12 @@ import shlex
import string
from pathlib import Path
import damask
from .. import environment
class Marc:
"""Wrapper to run DAMASK with MSCMarc."""
def __init__(self,version=damask.environment.options['MARC_VERSION']):
def __init__(self,version=environment.options['MARC_VERSION']):
"""
Create a Marc solver object.
@ -24,7 +24,7 @@ class Marc:
@property
def library_path(self):
path_MSC = damask.environment.options['MSC_ROOT']
path_MSC = environment.options['MSC_ROOT']
path_lib = Path(f'{path_MSC}/mentat{self.version}/shlib/linux64')
return path_lib if path_lib.is_dir() else None
@ -33,7 +33,7 @@ class Marc:
@property
def tools_path(self):
path_MSC = damask.environment.options['MSC_ROOT']
path_MSC = environment.options['MSC_ROOT']
path_tools = Path(f'{path_MSC}/marc{self.version}/tools')
return path_tools if path_tools.is_dir() else None
@ -49,7 +49,7 @@ class Marc:
):
usersub = damask.environment.root_dir/'src/DAMASK_marc'
usersub = environment.root_dir/'src/DAMASK_marc'
usersub = usersub.parent/(usersub.name + ('.f90' if compile else '.marc'))
if not usersub.is_file():
raise FileNotFoundError("DAMASK4Marc ({}) '{}' not found".format(('source' if compile else 'binary'),usersub))

10
python/damask/util.py
View File

@ -9,6 +9,8 @@ from optparse import Option
import numpy as np
from . import version
# limit visibility
__all__=[
'srepr',
@ -20,6 +22,7 @@ __all__=[
'scale_to_coprime',
'return_message',
'extendableOption',
'version_date'
]
####################################################################################################
@ -175,6 +178,13 @@ def scale_to_coprime(v):
return m
def version_date(class_name,function_name=None):
"""tbd."""
_function_name = '' if function_name is None else f'.{function_name}'
now = datetime.datetime.now().astimezone().strftime('%Y-%m-%d %H:%M:%S%z')
return f'damask.{class_name}{_function_name} v{version} ({now})'
####################################################################################################
# Classes
####################################################################################################

35
python/tests/conftest.py
View File

@ -1,11 +1,38 @@
from pathlib import Path
import numpy as np
import datetime
import numpy as np
import pytest
# Use to monkeypatch damask.version (for comparsion to reference files that contain version information)
def pytest_configure():
pytest.dummy_version = '99.99.99-9999-pytest'
import damask
patched_version = '99.99.99-9999-pytest'
@pytest.fixture
def patch_damask_version(monkeypatch):
"""Set damask.version for reproducible tests results."""
monkeypatch.setattr(damask, 'version', patched_version)
patched_date = datetime.datetime(2019, 11, 2, 11, 58, 0)
@pytest.fixture
def patch_datetime_now(monkeypatch):
"""Set datetime.datetime.now for reproducible tests results."""
class mydatetime:
@classmethod
def now(cls):
return patched_date
monkeypatch.setattr(datetime, 'datetime', mydatetime)
@pytest.fixture
def version_date(monkeypatch):
"""Set damask.util.version_date for reproducible tests results."""
def version_date(class_name,function_name=None):
_function_name = '' if function_name is None else f'.{function_name}'
return f'damask.{class_name}{_function_name} v{patched_version} ({patched_date})'
monkeypatch.setattr(damask.util, 'version_date', version_date)
def pytest_addoption(parser):

2
python/tests/reference/Colormap/binary.json
View File

@ -1,6 +1,6 @@
[
{
"Creator": "damask.Colormap v99.99.99-9999-pytest",
"Creator": "damask.Colormap v99.99.99-9999-pytest (2019-11-02 11:58:00)",
"ColorSpace": "RGB",
"Name": "binary",
"DefaultMap": true,

2
python/tests/reference/Colormap/binary.txt
View File

@ -1,4 +1,4 @@
# Creator: damask.Colormap v99.99.99-9999-pytest
# Creator: damask.Colormap v99.99.99-9999-pytest (2019-11-02 11:58:00)
1_RGBA 2_RGBA 3_RGBA 4_RGBA
1.0 1.0 1.0 1.0
0.996078431372549 0.996078431372549 0.996078431372549 1.0

25
python/tests/reference/Geom/clean.vtr Normal file
View File

@ -0,0 +1,25 @@
<?xml version="1.0"?>
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<RectilinearGrid WholeExtent="0 20 0 18 0 8">
<Piece Extent="0 20 0 18 0 8">
<PointData>
</PointData>
<CellData>
<DataArray type="Int32" Name="materialpoint" format="binary" RangeMin="1" RangeMax="2">
AQAAAACAAAAALQAANQAAAA==eF7t1CECACAMxLBj/380fhYwIyK2spWkmnWgt6b3AF65/avfegAAAAAAAAAAAMy0AfYtC2k=
</DataArray>
</CellData>
<Coordinates>
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="1">
AQAAAACAAACoAAAAVQAAAA==eF5jYICAWTNBYKU9hN5pb2IMAoeh/JP2EFUXoOKX7dPTQOAaVP6m/dkzIHAHqu4BVPwhVP1jqPwTqL5nUHUvoOpeQtW9hqp7A1X3Dqrugz0ASSZF3Q==
</DataArray>
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="1">
AQAAAACAAACYAAAAVgAAAA==eF5jYIAAmeOFQLTGHkLvsQ8Fg6NQ/hn7IjDjIlT8qr1F32MgugGVv2MPMeUBVN1D+8cQBVD1T+3BymSeQ/W9sF8FBq+g+t/Yg4Ut3kHN+WAPAAVdQE4=
</DataArray>
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="1">
AQAAAACAAABIAAAAIgAAAA==eF5jYEAGB+wh9AUofQNKP4DST6D0Cyj9Bkp/sAcAAU8I6Q==
</DataArray>
</Coordinates>
</Piece>
</RectilinearGrid>
</VTKFile>

25
python/tests/reference/Geom/clean_2_1_False.vtr Normal file
View File

@ -0,0 +1,25 @@
<?xml version="1.0"?>
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<RectilinearGrid WholeExtent="0 20 0 18 0 8">
<Piece Extent="0 20 0 18 0 8">
<PointData>
</PointData>
<CellData>
<DataArray type="Int32" Name="materialpoint" format="binary" RangeMin="1" RangeMax="2">
AQAAAACAAAAALQAANQAAAA==eF7t1CECACAMxLBj/380fhYwIyK2spWkmnWgt6b3AF65/avfegAAAAAAAAAAAMy0AfYtC2k=
</DataArray>
</CellData>
<Coordinates>
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="1">
AQAAAACAAACoAAAAVQAAAA==eF5jYICAWTNBYKU9hN5pb2IMAoeh/JP2EFUXoOKX7dPTQOAaVP6m/dkzIHAHqu4BVPwhVP1jqPwTqL5nUHUvoOpeQtW9hqp7A1X3Dqrugz0ASSZF3Q==
</DataArray>
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="1">
AQAAAACAAACYAAAAVgAAAA==eF5jYIAAmeOFQLTGHkLvsQ8Fg6NQ/hn7IjDjIlT8qr1F32MgugGVv2MPMeUBVN1D+8cQBVD1T+3BymSeQ/W9sF8FBq+g+t/Yg4Ut3kHN+WAPAAVdQE4=
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25
python/tests/reference/Geom/clean_4_2_False.vtr Normal file
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25
python/tests/reference/Geom/clean_4_None_False.vtr Normal file
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25
python/tests/reference/Geom/clean_stencil=1.geom
View File

@ -1,25 +0,0 @@
4 header
grid a 8 b 5 c 4
size x 8e-06 y 5e-06 z 4e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
2 3 4 5 6 7 8 9
10 11 12 13 14 15 16 17
18 19 20 21 22 23 24 25
26 27 28 29 30 31 32 33
34 35 36 37 38 39 40 41
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
1 2 3 4 5 6 7 8
9 10 11 12 13 14 15 16
17 18 19 20 21 22 23 24
25 26 27 28 29 30 31 32
33 34 35 36 37 38 39 40

25
python/tests/reference/Geom/clean_stencil=2.geom
View File

@ -1,25 +0,0 @@
4 header
grid a 8 b 5 c 4
size x 8e-06 y 5e-06 z 4e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
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2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
1 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2

25
python/tests/reference/Geom/clean_stencil=3.geom
View File

@ -1,25 +0,0 @@
4 header
grid a 8 b 5 c 4
size x 8e-06 y 5e-06 z 4e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
2 2 1 1 1 1 1 1
2 2 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2

25
python/tests/reference/Geom/clean_stencil=4.geom
View File

@ -1,25 +0,0 @@
4 header
grid a 8 b 5 c 4
size x 8e-06 y 5e-06 z 4e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
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2 2 2 2 1 1 1 1
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2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2

10
python/tests/test_Colormap.py
View File

@ -7,7 +7,6 @@ import pytest
from PIL import Image
from PIL import ImageChops
import damask
from damask import Colormap
@pytest.fixture
@ -17,8 +16,11 @@ def reference_dir(reference_dir_base):
class TestColormap:
def test_conversion(self):
@pytest.fixture(autouse=True)
def _version_date(self, version_date):
print('patched damask.util.version_date')
def test_conversion(self):
specials = np.array([[0.,0.,0.],
[1.,0.,0.],
[0.,1.,0.],
@ -29,7 +31,6 @@ class TestColormap:
[1.,1.,1.]
])
rgbs = np.vstack((specials,np.random.rand(100,3)))
pass # class not integrated
for rgb in rgbs:
print('rgb',rgb)
@ -150,8 +151,7 @@ class TestColormap:
('GOM','.legend'),
('Gmsh','.msh')
])
def test_compare_reference(self,format,ext,tmpdir,reference_dir,update,monkeypatch):
monkeypatch.setattr(damask, 'version', pytest.dummy_version)
def test_compare_reference(self,format,ext,tmpdir,reference_dir,update):
name = 'binary'
c = Colormap.from_predefined(name)
if update:

64
python/tests/test_Geom.py
View File

@ -1,6 +1,10 @@
import os
import time
import pytest
import numpy as np
from damask import VTK
from damask import Geom
from damask import Rotation
from damask import util
@ -47,31 +51,47 @@ class TestGeom:
def test_write_read_str(self,default,tmpdir):
default.to_file(str(tmpdir.join('default.geom')))
new = Geom.from_file(str(tmpdir.join('default.geom')))
default.to_file(str(tmpdir/'default.geom'))
new = Geom.from_file(str(tmpdir/'default.geom'))
assert geom_equal(new,default)
def test_write_read_file(self,default,tmpdir):
with open(tmpdir.join('default.geom'),'w') as f:
with open(tmpdir/'default.geom','w') as f:
default.to_file(f)
with open(tmpdir.join('default.geom')) as f:
with open(tmpdir/'default.geom') as f:
new = Geom.from_file(f)
assert geom_equal(new,default)
def test_write_show(self,default,tmpdir):
with open(tmpdir.join('str.geom'),'w') as f:
with open(tmpdir/'str.geom','w') as f:
f.write(default.show())
with open(tmpdir.join('str.geom')) as f:
with open(tmpdir/'str.geom') as f:
new = Geom.from_file(f)
assert geom_equal(new,default)
def test_export_vtk(self,default,tmpdir):
default.to_vtk(str(tmpdir.join('default')))
def test_read_write_vtr(self,default,tmpdir):
default.to_vtr(tmpdir/'default')
for _ in range(10):
time.sleep(.2)
if os.path.exists(tmpdir/'default.vtr'): break
new = Geom.from_vtr(tmpdir/'default.vtr')
assert geom_equal(new,default)
def test_invalid_vtr(self,tmpdir):
v = VTK.from_rectilinearGrid(np.random.randint(5,10,3)*2,np.random.random(3) + 1.0)
v.write(tmpdir/'no_materialpoint.vtr')
for _ in range(10):
time.sleep(.2)
if os.path.exists(tmpdir/'no_materialpoint.vtr'): break
with pytest.raises(ValueError):
Geom.from_vtr(tmpdir/'no_materialpoint.vtr')
@pytest.mark.parametrize('pack',[True,False])
def test_pack(self,default,tmpdir,pack):
default.to_file(tmpdir.join('default.geom'),pack=pack)
new = Geom.from_file(tmpdir.join('default.geom'))
default.to_file(tmpdir/'default.geom',pack=pack)
new = Geom.from_file(tmpdir/'default.geom')
assert geom_equal(new,default)
def test_invalid_combination(self,default):
@ -115,14 +135,24 @@ class TestGeom:
if update: modified.to_file(reference)
assert geom_equal(modified,Geom.from_file(reference))
@pytest.mark.parametrize('directions',[(1,2,'y'),('a','b','x'),[1]])
def test_mirror_invalid(self,default,directions):
with pytest.raises(ValueError):
default.mirror(directions)
@pytest.mark.parametrize('stencil',[1,2,3,4])
def test_clean(self,default,update,reference_dir,stencil):
modified = default.copy()
modified.clean(stencil)
tag = f'stencil={stencil}'
reference = reference_dir/f'clean_{tag}.geom'
if update: modified.to_file(reference)
assert geom_equal(modified,Geom.from_file(reference))
@pytest.mark.parametrize('selection',[None,1,2])
@pytest.mark.parametrize('periodic',[True,False])
def test_clean(self,update,reference_dir,stencil,selection,periodic):
current = Geom.from_vtr((reference_dir/'clean').with_suffix('.vtr'))
current.clean(stencil,None if selection is None else [selection],periodic)
reference = reference_dir/f'clean_{stencil}_{selection}_{periodic}'
if update and stencil !=1:
current.to_vtr(reference)
for _ in range(10):
time.sleep(.2)
if os.path.exists(reference.with_suffix('.vtr')): break
assert geom_equal(current,Geom.from_vtr(reference if stencil !=1 else reference_dir/'clean'))
@pytest.mark.parametrize('grid',[
(10,11,10),

12
python/tests/test_Orientation.py
View File

@ -4,7 +4,7 @@ from itertools import permutations
import pytest
import numpy as np
import damask
from damask import Table
from damask import Rotation
from damask import Orientation
from damask import Lattice
@ -68,7 +68,7 @@ class TestOrientation:
{'label':'blue', 'RGB':[0,0,1],'direction':[1,1,1]}])
@pytest.mark.parametrize('lattice',['fcc','bcc'])
def test_IPF_cubic(self,color,lattice):
cube = damask.Orientation(damask.Rotation(),lattice)
cube = Orientation(Rotation(),lattice)
for direction in set(permutations(np.array(color['direction']))):
assert np.allclose(cube.IPF_color(np.array(direction)),np.array(color['RGB']))
@ -104,15 +104,15 @@ class TestOrientation:
eu = np.array([o.rotation.as_Eulers(degrees=True) for o in ori.related(model)])
if update:
coords = np.array([(1,i+1) for i,x in enumerate(eu)])
table = damask.Table(eu,{'Eulers':(3,)})
table = Table(eu,{'Eulers':(3,)})
table.add('pos',coords)
table.to_ASCII(reference)
assert np.allclose(eu,damask.Table.from_ASCII(reference).get('Eulers'))
assert np.allclose(eu,Table.from_ASCII(reference).get('Eulers'))
@pytest.mark.parametrize('lattice',Lattice.lattices)
def test_disorientation360(self,lattice):
R_1 = Orientation(Rotation(),lattice)
R_2 = Orientation(damask.Rotation.from_Eulers([360,0,0],degrees=True),lattice)
R_2 = Orientation(Rotation.from_Eulers([360,0,0],degrees=True),lattice)
assert np.allclose(R_1.disorientation(R_2).as_matrix(),np.eye(3))
@pytest.mark.parametrize('lattice',Lattice.lattices)
@ -127,6 +127,6 @@ class TestOrientation:
def test_from_average(self,lattice):
R_1 = Orientation(Rotation.from_random(),lattice)
eqs = [r for r in R_1.equivalent]
R_2 = damask.Orientation.from_average(eqs)
R_2 = Orientation.from_average(eqs)
assert np.allclose(R_1.rotation.quaternion,R_2.rotation.quaternion)

7
python/tests/test_Result.py
View File

@ -8,8 +8,9 @@ import pytest
import numpy as np
import h5py
import damask
from damask import Result
from damask import Rotation
from damask import Orientation
from damask import mechanics
from damask import grid_filters
@ -174,7 +175,7 @@ class TestResult:
crystal_structure = default.get_crystal_structure()
in_memory = np.empty((qu.shape[0],3),np.uint8)
for i,q in enumerate(qu):
o = damask.Orientation(q,crystal_structure).reduced
o = Orientation(q,crystal_structure).reduced
in_memory[i] = np.uint8(o.IPF_color(np.array(d))*255)
in_file = default.read_dataset(loc['color'])
assert np.allclose(in_memory,in_file)
@ -233,7 +234,7 @@ class TestResult:
default.add_pole('orientation',pole,polar)
loc = {'orientation': default.get_dataset_location('orientation'),
'pole': default.get_dataset_location('p^{}_[1 0 0)'.format(u'rφ' if polar else 'xy'))}
rot = damask.Rotation(default.read_dataset(loc['orientation']).view(np.double))
rot = Rotation(default.read_dataset(loc['orientation']).view(np.double))
rotated_pole = rot * np.broadcast_to(pole,rot.shape+(3,))
xy = rotated_pole[:,0:2]/(1.+abs(pole[2]))
in_memory = xy if not polar else \