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Merge remote-tracking branch 'origin/increase-geom-test-coverage' into geom-out-of-place

This commit is contained in:
Philip Eisenlohr 2020-08-24 14:50:40 -04:00
parent 3738002e4a 9d505c8518
commit 2560f014a3
46 changed files with 1001 additions and 291 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.execution_stamp('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.execution_stamp("Colormap")}')
if fhandle is None:
with open(colormap.name.replace(' ','_')+'.txt', 'w') as f:

184
python/damask/_geom.py
View File

@ -1,13 +1,12 @@
import sys
import copy
from io import StringIO
import multiprocessing
from io import StringIO
from functools import partial
import numpy as np
from scipy import ndimage,spatial
from . import version
from . import environment
from . import Rotation
from . import VTK
@ -83,7 +82,7 @@ class Geom:
"""
if size is not None and autosize:
raise ValueError('Auto sizing conflicts with explicit size parameter.')
raise ValueError('Auto-sizing conflicts with explicit size parameter.')
grid_old = self.get_grid()
dup = self.copy()
@ -101,67 +100,6 @@ class Geom:
return dup
def update(self,microstructure=None,size=None,origin=None,autosize=False):
"""
Update microstructure and size.
Parameters
----------
microstructure : numpy.ndarray, optional
Microstructure array (3D).
size : list or numpy.ndarray, optional
Physical size of the microstructure in meter.
origin : list or numpy.ndarray, optional
Physical origin of the microstructure in meter.
autosize : bool, optional
Ignore size parameter and rescale according to change of grid points.
"""
grid_old = self.get_grid()
size_old = self.get_size()
origin_old = self.get_origin()
unique_old = self.N_microstructure
max_old = np.nanmax(self.microstructure)
if size is not None and autosize:
raise ValueError('Auto sizing conflicts with explicit size parameter.')
self.set_microstructure(microstructure)
self.set_origin(origin)
if size is not None:
self.set_size(size)
elif autosize:
self.set_size(self.get_grid()/grid_old*self.size)
message = [f'grid a b c: {util.srepr(grid_old," x ")}']
if np.any(grid_old != self.get_grid()):
message[-1] = util.delete(message[-1])
message.append(util.emph(f'grid a b c: {util.srepr(self.get_grid()," x ")}'))
message.append(f'size x y z: {util.srepr(size_old," x ")}')
if np.any(size_old != self.get_size()):
message[-1] = util.delete(message[-1])
message.append(util.emph(f'size x y z: {util.srepr(self.get_size()," x ")}'))
message.append(f'origin x y z: {util.srepr(origin_old," ")}')
if np.any(origin_old != self.get_origin()):
message[-1] = util.delete(message[-1])
message.append(util.emph(f'origin x y z: {util.srepr(self.get_origin()," ")}'))
message.append(f'# microstructures: {unique_old}')
if unique_old != self.N_microstructure:
message[-1] = util.delete(message[-1])
message.append(util.emph(f'# microstructures: {self.N_microstructure}'))
message.append(f'max microstructure: {max_old}')
if max_old != np.nanmax(self.microstructure):
message[-1] = util.delete(message[-1])
message.append(util.emph(f'max microstructure: {np.nanmax(self.microstructure)}'))
return util.return_message(message)
def diff(self,other):
"""
Report property differences of self relative to other.
@ -264,10 +202,7 @@ 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:
@ -348,16 +283,6 @@ 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):
"""
@ -422,31 +347,23 @@ 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
@ -495,10 +412,8 @@ class Geom:
else:
microstructure = microstructure.reshape(grid)
return Geom(microstructure+1,
size,
homogenization=1,
comments=f'geom.py:from_Laguerre_tessellation v{version}',
return Geom(microstructure+1,size,homogenization=1,
comments=util.execution_stamp('Geom','from_Laguerre_tessellation'),
)
@ -523,10 +438,8 @@ class Geom:
KDTree = spatial.cKDTree(seeds,boxsize=size) if periodic else spatial.cKDTree(seeds)
devNull,microstructure = KDTree.query(coords)
return Geom(microstructure.reshape(grid)+1,
size,
homogenization=1,
comments=f'geom.py:from_Voronoi_tessellation v{version}',
return Geom(microstructure.reshape(grid)+1,size,homogenization=1,
comments=util.execution_stamp('Geom','from_Voronoi_tessellation'),
)
@ -542,7 +455,12 @@ 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:
@ -574,7 +492,7 @@ 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':
@ -596,27 +514,28 @@ 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__())
def show(self):
"""Show raw content (as in file)."""
def as_ASCII(self):
"""Format geometry as human-readable ASCII."""
f = StringIO()
self.to_file(f)
f.seek(0)
@ -664,7 +583,7 @@ class Geom:
coords_rot = R.broadcast_to(tuple(self.grid))@coords
with np.errstate(over='ignore',under='ignore'):
mask = np.where(np.sum(np.abs(coords_rot/r)**(2.0**exponent),axis=-1) <= 1.0,False,True)
mask = np.where(np.linalg.norm(coords_rot/r,2.0**exponent,axis=-1) <= 1.0,False,True)
if periodic: # translate back to center
mask = np.roll(mask,((c-np.ones(3)*.5)*self.grid).astype(int),(0,1,2))
@ -673,7 +592,7 @@ class Geom:
ms = np.ma.MaskedArray(fill_,np.logical_not(mask) if inverse else mask)
return self.duplicate(ms,
comments=self.get_comments()+[f'geom.py:add_primitive v{version}'],
comments=self.get_comments()+[util.execution_stamp('Geom','add_primitive')],
)
@ -691,9 +610,7 @@ 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]
@ -707,7 +624,7 @@ class Geom:
ms = np.concatenate([ms,ms[limits[0]:limits[1]:-1,:,:]],0)
return self.duplicate(ms,
comments=self.get_comments()+[f'geom.py:mirror {set(directions)} v{version}'],
comments=self.get_comments()+[util.execution_stamp('Geom','mirror')],
autosize=True)
@ -739,11 +656,11 @@ class Geom:
ms = ms[limits[0]:limits[1]:-1,:,:]
return self.duplicate(ms,
comments=self.get_comments()+[f'geom.py:flip {set(directions)} v{version}'],
comments=self.get_comments()+[util.execution_stamp('Geom','flip')],
)
def scale(self,grid):
def scale(self,grid,periodic=True):
"""
Scale microstructure to new grid.
@ -751,6 +668,8 @@ 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.
"""
return self.duplicate(ndimage.interpolation.zoom(
@ -758,14 +677,14 @@ class Geom:
grid/self.get_grid(),
output=self.microstructure.dtype,
order=0,
mode='nearest',
mode=('wrap' if periodic else 'nearest'),
prefilter=False
),
comments=self.get_comments()+[f'geom.py:scale {grid} v{version}'],
comments=self.get_comments()+[util.execution_stamp('Geom','scale')],
)
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.
@ -773,11 +692,10 @@ 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):
@ -792,10 +710,10 @@ class Geom:
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),
comments=self.get_comments()+[f'geom.py:clean {stencil} {mode} v{version}'],
comments=self.get_comments()+[util.execution_stamp('Geom','clean')],
)
@ -806,7 +724,7 @@ class Geom:
renumbered = np.where(self.microstructure == oldID, i+1, renumbered)
return self.duplicate(renumbered,
comments=self.get_comments()+[f'geom.py:renumber v{version}'],
comments=self.get_comments()+[util.execution_stamp('Geom','renumber')],
)
@ -843,7 +761,7 @@ class Geom:
return self.duplicate(microstructure_in,
origin=origin,
comments=self.get_comments()+[f'geom.py:rotate {R.as_quaternion()} v{version}'],
comments=self.get_comments()+[util.execution_stamp('Geom','rotate')],
autosize=True,
)
@ -870,7 +788,7 @@ 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))
@ -879,7 +797,7 @@ class Geom:
return self.duplicate(canvas,
origin=self.origin+offset*self.size/self.grid,
comments=self.get_comments()+[f'geom.py:canvas {grid} {offset} {fill} v{version}'],
comments=self.get_comments()+[util.execution_stamp('Geom','canvas')],
autosize=True,
)
@ -901,7 +819,7 @@ class Geom:
substituted[self.microstructure==from_ms] = to_ms
return self.duplicate(substituted,
comments=self.get_comments()+[f'geom.py:substitute v{version}'],
comments=self.get_comments()+[util.execution_stamp('Geom','substitute')],
)
@ -948,5 +866,5 @@ class Geom:
microstructure = np.ma.MaskedArray(self.microstructure + offset_, np.logical_not(mask))
return self.duplicate(microstructure,
comments=self.get_comments()+[f'geom.py:vicinity_offset {vicinity} v{version}'],
comments=self.get_comments()+[util.execution_stamp('Geom','vicinity_offset')],
)

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.execution_stamp("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',
'execution_stamp'
]
####################################################################################################
@ -175,6 +178,13 @@ def scale_to_coprime(v):
return m
def execution_stamp(class_name,function_name=None):
"""Timestamp the execution of a (function within a) class."""
now = datetime.datetime.now().astimezone().strftime('%Y-%m-%d %H:%M:%S%z')
_function_name = '' if function_name is None else f'.{function_name}'
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 execution_stamp(monkeypatch):
"""Set damask.util.execution_stamp for reproducible tests results."""
def execution_stamp(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, 'execution_stamp', execution_stamp)
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_1_1+2+3_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 8 0 5 0 4">
<Piece Extent="0 8 0 5 0 4">
<PointData>
</PointData>
<CellData>
<DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
AQAAAACAAAAABQAAYwAAAA==eF7t0scBgkAAAEHBgBEwgDmBsf8GfTANCN/bzzSwUa8pCrYyZp8DDjliwjEnnHLGORdMmTHnkiuuuWHBklvuuOeBR5545oVX3nhnxZoPPvnimx9+GQc7GT5sqvjvhz+ZtAcJ
</DataArray>
</CellData>
<Coordinates>
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
AQAAAACAAABIAAAAOgAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2D3IeNxx9YfV6DiN+22x9tFGsbchco/sAMA/fQl6g==
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<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="1">
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</DataArray>
</CellData>
<Coordinates>
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</DataArray>
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="1">
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<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="1">
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</Coordinates>
</Piece>
</RectilinearGrid>
</VTKFile>

25
python/tests/reference/Geom/clean_4_None_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 8 0 5 0 4">
<Piece Extent="0 8 0 5 0 4">
<PointData>
</PointData>
<CellData>
<DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="2">
AQAAAACAAAAABQAAIAAAAA==eF5jZIAAxlF6lB4AmokAPdj1DzRNyP2jNH4aAMufANU=
</DataArray>
</CellData>
<Coordinates>
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
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<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
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<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
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</VTKFile>

25
python/tests/reference/Geom/clean_4_None_True.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 8 0 5 0 4">
<Piece Extent="0 8 0 5 0 4">
<PointData>
</PointData>
<CellData>
<DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="2">
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</DataArray>
</CellData>
<Coordinates>
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
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<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
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<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
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</Coordinates>
</Piece>
</RectilinearGrid>
</VTKFile>

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
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
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
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
2 2 2 2 1 1 1 1
2 2 2 2 1 1 1 1
2 2 2 2 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

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 _execution_stamp(self, execution_stamp):
print('patched damask.util.execution_stamp')
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:

74
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
@ -41,15 +45,6 @@ class TestGeom:
print(modified)
assert geom_equal(default,modified)
def test_update(self,default):
modified = default.copy()
modified.update(
default.get_microstructure(),
default.get_size(),
default.get_origin()
)
print(modified)
assert geom_equal(default,modified)
@pytest.mark.parametrize('masked',[True,False])
def test_set_microstructure(self,default,masked):
@ -71,16 +66,34 @@ class TestGeom:
new = Geom.from_file(f)
assert geom_equal(default,new)
def test_write_show(self,default,tmpdir):
def test_write_as_ASCII(self,default,tmpdir):
with open(tmpdir/'str.geom','w') as f:
f.write(default.show())
f.write(default.as_ASCII())
with open(tmpdir/'str.geom') as f:
new = Geom.from_file(f)
assert geom_equal(default,new)
def test_export_import_vtk(self,default,tmpdir):
default.to_vtk(tmpdir/'default')
assert geom_equal(default,Geom.from_vtk(tmpdir/'default.vtr'))
default.to_vtr(tmpdir/'default')
assert geom_equal(default,Geom.from_vtr(tmpdir/'default.vtr'))
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])
@ -91,25 +104,25 @@ class TestGeom:
def test_invalid_combination(self,default):
with pytest.raises(ValueError):
default.update(default.microstructure[1:,1:,1:],size=np.ones(3), autosize=True)
default.duplicate(default.microstructure[1:,1:,1:],size=np.ones(3), autosize=True)
def test_invalid_size(self,default):
with pytest.raises(ValueError):
default.update(default.microstructure[1:,1:,1:],size=np.ones(2))
default.duplicate(default.microstructure[1:,1:,1:],size=np.ones(2))
def test_invalid_origin(self,default):
with pytest.raises(ValueError):
default.update(default.microstructure[1:,1:,1:],origin=np.ones(4))
default.duplicate(default.microstructure[1:,1:,1:],origin=np.ones(4))
def test_invalid_microstructure_size(self,default):
microstructure = np.ones((3,3))
with pytest.raises(ValueError):
default.update(microstructure)
default.duplicate(microstructure)
def test_invalid_microstructure_type(self,default):
microstructure = np.random.randint(1,300,(3,4,5))==1
with pytest.raises(TypeError):
default.update(microstructure)
default.duplicate(microstructure)
def test_invalid_homogenization(self,default):
with pytest.raises(TypeError):
@ -145,14 +158,25 @@ class TestGeom:
assert geom_equal(Geom.from_file(reference),
modified)
@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.clean(stencil)
tag = f'stencil={stencil}'
reference = reference_dir/f'clean_{tag}.geom'
if update: modified.to_file(reference)
assert geom_equal(Geom.from_file(reference),
modified)
@pytest.mark.parametrize('selection',[None,[1],[1,2,3]])
@pytest.mark.parametrize('periodic',[True,False])
def test_clean(self,default,update,reference_dir,stencil,selection,periodic):
current = default.clean(stencil,selection,periodic)
reference = reference_dir/f'clean_{stencil}_{"+".join(map(str,[None] if selection is None else 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(Geom.from_vtr(reference) if stencil > 1 else default,
current
)
@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 \