All geom methods are now out-of-place, i.e. return an updated duplicate (to allow for daisy chaining).
* Added comments when methods acted. * Added diff method * Added flip method * Fixed add_primitive inversion bug (again...) * Fixed cell centering bug in add_primitive * Added missing tests
This commit is contained in:
Philip Eisenlohr
parent
a1f1b91c7f
commit
446ac03b07
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@ -7,6 +7,7 @@ from functools import partial
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import numpy as np
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import numpy as np
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from scipy import ndimage,spatial
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from scipy import ndimage,spatial
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from . import version
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from . import environment
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from . import environment
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from . import Rotation
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from . import Rotation
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from . import VTK
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from . import VTK
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@ -24,15 +25,15 @@ class Geom:
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Parameters
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Parameters
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----------
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----------
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microstructure : numpy.ndarray
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microstructure : numpy.ndarray
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microstructure array (3D)
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Microstructure array (3D)
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size : list or numpy.ndarray
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size : list or numpy.ndarray
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physical size of the microstructure in meter.
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Physical size of the microstructure in meter.
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origin : list or numpy.ndarray, optional
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origin : list or numpy.ndarray, optional
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physical origin of the microstructure in meter.
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Physical origin of the microstructure in meter.
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homogenization : int, optional
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homogenization : int, optional
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homogenization index.
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Homogenization index.
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comments : list of str, optional
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comments : list of str, optional
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comments lines.
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Comment lines.
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"""
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"""
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self.set_microstructure(microstructure)
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self.set_microstructure(microstructure)
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@ -50,7 +51,7 @@ class Geom:
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f'origin x y z: {util.srepr(self.get_origin()," ")}',
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f'origin x y z: {util.srepr(self.get_origin()," ")}',
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f'# microstructures: {self.N_microstructure}',
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f'# microstructures: {self.N_microstructure}',
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f'max microstructure: {np.nanmax(self.microstructure)}',
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f'max microstructure: {np.nanmax(self.microstructure)}',
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])
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]+self.get_comments())
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def __copy__(self):
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def __copy__(self):
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@ -63,20 +64,57 @@ class Geom:
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return self.__copy__()
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return self.__copy__()
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def update(self,microstructure=None,size=None,origin=None,rescale=False):
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def duplicate(self,microstructure=None,size=None,origin=None,comments=None,autosize=False):
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"""
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Create a duplicate having updated microstructure, size, and origin.
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Parameters
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----------
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microstructure : numpy.ndarray, optional
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Microstructure array (3D).
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size : list or numpy.ndarray, optional
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Physical size of the microstructure in meter.
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origin : list or numpy.ndarray, optional
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Physical origin of the microstructure in meter.
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comments : list of str, optional
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Comment lines.
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autosize : bool, optional
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Ignore size parameter and rescale according to change of grid points.
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"""
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if size is not None and autosize:
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raise ValueError('Auto sizing conflicts with explicit size parameter.')
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grid_old = self.get_grid()
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dup = self.copy()
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dup.set_microstructure(microstructure)
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dup.set_origin(origin)
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if comments is not None:
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dup.set_comments(comments)
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if size is not None:
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dup.set_size(size)
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elif autosize:
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dup.set_size(dup.get_grid()/grid_old*self.get_size())
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return dup
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def update(self,microstructure=None,size=None,origin=None,autosize=False):
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"""
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"""
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Update microstructure and size.
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Update microstructure and size.
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Parameters
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Parameters
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----------
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----------
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microstructure : numpy.ndarray, optional
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microstructure : numpy.ndarray, optional
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microstructure array (3D).
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Microstructure array (3D).
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size : list or numpy.ndarray, optional
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size : list or numpy.ndarray, optional
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physical size of the microstructure in meter.
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Physical size of the microstructure in meter.
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origin : list or numpy.ndarray, optional
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origin : list or numpy.ndarray, optional
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physical origin of the microstructure in meter.
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Physical origin of the microstructure in meter.
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rescale : bool, optional
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autosize : bool, optional
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ignore size parameter and rescale according to change of grid points.
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Ignore size parameter and rescale according to change of grid points.
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"""
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"""
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grid_old = self.get_grid()
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grid_old = self.get_grid()
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@ -85,15 +123,15 @@ class Geom:
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unique_old = self.N_microstructure
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unique_old = self.N_microstructure
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max_old = np.nanmax(self.microstructure)
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max_old = np.nanmax(self.microstructure)
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if size is not None and rescale:
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if size is not None and autosize:
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raise ValueError('Either set size explicitly or rescale automatically')
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raise ValueError('Auto sizing conflicts with explicit size parameter.')
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self.set_microstructure(microstructure)
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self.set_microstructure(microstructure)
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self.set_origin(origin)
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self.set_origin(origin)
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if size is not None:
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if size is not None:
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self.set_size(size)
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self.set_size(size)
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elif rescale:
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elif autosize:
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self.set_size(self.get_grid()/grid_old*self.size)
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self.set_size(self.get_grid()/grid_old*self.size)
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message = [f'grid a b c: {util.srepr(grid_old," x ")}']
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message = [f'grid a b c: {util.srepr(grid_old," x ")}']
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@ -124,6 +162,40 @@ class Geom:
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return util.return_message(message)
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return util.return_message(message)
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def diff(self,other):
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"""
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Report property differences of self relative to other.
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Parameters
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----------
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other : Geom
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Geometry to compare self against.
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"""
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message = []
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if np.any(other.get_grid() != self.get_grid()):
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message.append(util.delete(f'grid a b c: {util.srepr(other.get_grid()," x ")}'))
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message.append(util.emph( f'grid a b c: {util.srepr( self.get_grid()," x ")}'))
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if np.any(other.get_size() != self.get_size()):
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message.append(util.delete(f'size x y z: {util.srepr(other.get_size()," x ")}'))
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message.append(util.emph( f'size x y z: {util.srepr( self.get_size()," x ")}'))
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if np.any(other.get_origin() != self.get_origin()):
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message.append(util.delete(f'origin x y z: {util.srepr(other.get_origin()," ")}'))
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message.append(util.emph( f'origin x y z: {util.srepr( self.get_origin()," ")}'))
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if other.N_microstructure != self.N_microstructure:
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message.append(util.delete(f'# microstructures: {other.N_microstructure}'))
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message.append(util.emph( f'# microstructures: { self.N_microstructure}'))
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if np.nanmax(other.microstructure) != np.nanmax(self.microstructure):
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message.append(util.delete(f'max microstructure: {np.nanmax(other.microstructure)}'))
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message.append(util.emph( f'max microstructure: {np.nanmax( self.microstructure)}'))
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return util.return_message(message)
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def set_comments(self,comments):
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def set_comments(self,comments):
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"""
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"""
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Replace all existing comments.
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Replace all existing comments.
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@ -131,7 +203,7 @@ class Geom:
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Parameters
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Parameters
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----------
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----------
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comments : list of str
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comments : list of str
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new comments.
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All comments.
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"""
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"""
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self.comments = []
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self.comments = []
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@ -145,7 +217,7 @@ class Geom:
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Parameters
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Parameters
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----------
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----------
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comments : list of str
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comments : list of str
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new comments.
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New comments.
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"""
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"""
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self.comments += [str(c) for c in comments] if isinstance(comments,list) else [str(comments)]
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self.comments += [str(c) for c in comments] if isinstance(comments,list) else [str(comments)]
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@ -172,6 +244,10 @@ class Geom:
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else:
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else:
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self.microstructure = np.copy(microstructure)
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self.microstructure = np.copy(microstructure)
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if self.microstructure.dtype == float and \
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np.all(self.microstructure == self.microstructure.astype(int).astype(float)):
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self.microstructure = self.microstructure.astype(int)
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if len(self.microstructure.shape) != 3:
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if len(self.microstructure.shape) != 3:
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raise ValueError(f'Invalid microstructure shape {microstructure.shape}')
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raise ValueError(f'Invalid microstructure shape {microstructure.shape}')
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elif self.microstructure.dtype not in np.sctypes['float'] + np.sctypes['int']:
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elif self.microstructure.dtype not in np.sctypes['float'] + np.sctypes['int']:
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@ -185,7 +261,7 @@ class Geom:
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Parameters
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Parameters
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----------
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----------
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size : list or numpy.ndarray
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size : list or numpy.ndarray
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physical size of the microstructure in meter.
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Physical size of the microstructure in meter.
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"""
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"""
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if size is None:
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if size is None:
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@ -205,7 +281,7 @@ class Geom:
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Parameters
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Parameters
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----------
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----------
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origin : list or numpy.ndarray
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origin : list or numpy.ndarray
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physical origin of the microstructure in meter
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Physical origin of the microstructure in meter.
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"""
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"""
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if origin is not None:
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if origin is not None:
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@ -222,12 +298,12 @@ class Geom:
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Parameters
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Parameters
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----------
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----------
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homogenization : int
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homogenization : int
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homogenization index
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Homogenization index.
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"""
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"""
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if homogenization is not None:
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if homogenization is not None:
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if not isinstance(homogenization,int) or homogenization < 1:
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if not isinstance(homogenization,int) or homogenization < 1:
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raise TypeError(f'Invalid homogenization {homogenization}')
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raise TypeError(f'Invalid homogenization {homogenization}.')
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else:
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else:
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self.homogenization = homogenization
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self.homogenization = homogenization
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@ -419,8 +495,11 @@ class Geom:
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else:
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else:
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microstructure = microstructure.reshape(grid)
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microstructure = microstructure.reshape(grid)
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#ToDo: comments = 'geom.py:from_Laguerre_tessellation v{}'.format(version)
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return Geom(microstructure+1,
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return Geom(microstructure+1,size,homogenization=1)
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size,
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homogenization=1,
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comments=f'geom.py:from_Laguerre_tessellation v{version}',
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)
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@staticmethod
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@staticmethod
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@ -444,8 +523,11 @@ class Geom:
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KDTree = spatial.cKDTree(seeds,boxsize=size) if periodic else spatial.cKDTree(seeds)
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KDTree = spatial.cKDTree(seeds,boxsize=size) if periodic else spatial.cKDTree(seeds)
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devNull,microstructure = KDTree.query(coords)
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devNull,microstructure = KDTree.query(coords)
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#ToDo: comments = 'geom.py:from_Voronoi_tessellation v{}'.format(version)
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return Geom(microstructure.reshape(grid)+1,
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return Geom(microstructure.reshape(grid)+1,size,homogenization=1)
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size,
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homogenization=1,
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comments=f'geom.py:from_Voronoi_tessellation v{version}',
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)
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def to_file(self,fname,pack=None):
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def to_file(self,fname,pack=None):
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@ -535,7 +617,7 @@ class Geom:
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def show(self):
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def show(self):
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"""Show raw content (as in file)."""
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"""Show raw content (as in file)."""
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f=StringIO()
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f = StringIO()
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self.to_file(f)
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self.to_file(f)
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f.seek(0)
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f.seek(0)
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return ''.join(f.readlines())
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return ''.join(f.readlines())
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@ -565,10 +647,10 @@ class Geom:
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R : damask.Rotation, optional
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R : damask.Rotation, optional
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Rotation of primitive. Defaults to no rotation.
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Rotation of primitive. Defaults to no rotation.
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inverse : Boolean, optional
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inverse : Boolean, optional
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Retain original microstructure within primitive and fill
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Retain original microstructure within primitive and fill outside.
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outside. Defaults to False.
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Defaults to False.
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periodic : Boolean, optional
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periodic : Boolean, optional
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Repeat primitive over boundaries. Defaults to False.
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Repeat primitive over boundaries. Defaults to True.
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"""
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"""
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# normalized 'radius' and center
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# normalized 'radius' and center
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@ -578,11 +660,11 @@ class Geom:
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(np.array(center) - self.origin)/self.size
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(np.array(center) - self.origin)/self.size
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coords = grid_filters.cell_coord0(self.grid,np.ones(3)) \
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coords = grid_filters.cell_coord0(self.grid,np.ones(3)) \
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- (np.ones(3)*0.5 if periodic else c) # center if periodic
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- ((np.ones(3)-(1./self.grid if np.array(center).dtype in np.sctypes['int'] else 0))*0.5 if periodic else c) # periodic center is always at CoG
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coords_rot = R.broadcast_to(tuple(self.grid))@coords
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coords_rot = R.broadcast_to(tuple(self.grid))@coords
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with np.errstate(over='ignore',under='ignore'):
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with np.errstate(over='ignore',under='ignore'):
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mask = np.where(np.sum(np.abs(coords_rot/r)**(2.0**exponent),axis=-1) < 1,True,False)
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mask = np.where(np.sum(np.abs(coords_rot/r)**(2.0**exponent),axis=-1) <= 1.0,False,True)
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if periodic: # translate back to center
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if periodic: # translate back to center
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mask = np.roll(mask,((c-np.ones(3)*.5)*self.grid).astype(int),(0,1,2))
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mask = np.roll(mask,((c-np.ones(3)*.5)*self.grid).astype(int),(0,1,2))
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@ -590,7 +672,9 @@ class Geom:
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fill_ = np.full_like(self.microstructure,np.nanmax(self.microstructure)+1 if fill is None else fill)
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fill_ = np.full_like(self.microstructure,np.nanmax(self.microstructure)+1 if fill is None else fill)
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ms = np.ma.MaskedArray(fill_,np.logical_not(mask) if inverse else mask)
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ms = np.ma.MaskedArray(fill_,np.logical_not(mask) if inverse else mask)
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return self.update(ms)
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return self.duplicate(ms,
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comments=self.get_comments()+[f'geom.py:add_primitive v{version}'],
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)
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def mirror(self,directions,reflect=False):
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def mirror(self,directions,reflect=False):
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@ -622,8 +706,41 @@ class Geom:
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if 'x' in directions:
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if 'x' in directions:
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ms = np.concatenate([ms,ms[limits[0]:limits[1]:-1,:,:]],0)
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ms = np.concatenate([ms,ms[limits[0]:limits[1]:-1,:,:]],0)
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#ToDo: self.add_comments('geom.py:mirror v{}'.format(version)
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return self.duplicate(ms,
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return self.update(ms,rescale=True)
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comments=self.get_comments()+[f'geom.py:mirror {set(directions)} v{version}'],
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autosize=True)
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def flip(self,directions):
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"""
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Flip microstructure along given directions.
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Parameters
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----------
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directions : iterable containing str
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Direction(s) along which the microstructure is flipped.
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Valid entries are 'x', 'y', 'z'.
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"""
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valid = {'x','y','z'}
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if not all(isinstance(d, str) for d in directions):
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raise TypeError('Directions are not of type str.')
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elif not set(directions).issubset(valid):
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raise ValueError(f'Invalid direction {set(directions).difference(valid)} specified.')
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limits = [None,None]
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ms = self.get_microstructure()
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if 'z' in directions:
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ms = ms[:,:,limits[0]:limits[1]:-1]
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if 'y' in directions:
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ms = ms[:,limits[0]:limits[1]:-1,:]
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if 'x' in directions:
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ms = ms[limits[0]:limits[1]:-1,:,:]
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return self.duplicate(ms,
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|
comments=self.get_comments()+[f'geom.py:flip {set(directions)} v{version}'],
|
||||||
|
)
|
||||||
|
|
||||||
|
|
||||||
def scale(self,grid):
|
def scale(self,grid):
|
||||||
|
|
@ -636,17 +753,16 @@ class Geom:
|
||||||
Number of grid points in x,y,z direction.
|
Number of grid points in x,y,z direction.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
#ToDo: self.add_comments('geom.py:scale v{}'.format(version)
|
return self.duplicate(ndimage.interpolation.zoom(
|
||||||
return self.update(
|
self.microstructure,
|
||||||
ndimage.interpolation.zoom(
|
grid/self.get_grid(),
|
||||||
self.microstructure,
|
output=self.microstructure.dtype,
|
||||||
grid/self.get_grid(),
|
order=0,
|
||||||
output=self.microstructure.dtype,
|
mode='nearest',
|
||||||
order=0,
|
prefilter=False
|
||||||
mode='nearest',
|
),
|
||||||
prefilter=False
|
comments=self.get_comments()+[f'geom.py:scale {grid} v{version}'],
|
||||||
)
|
)
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
def clean(self,stencil=3,mode='nearest',selection=None):
|
def clean(self,stencil=3,mode='nearest',selection=None):
|
||||||
|
|
@ -672,15 +788,15 @@ class Geom:
|
||||||
else:
|
else:
|
||||||
return me
|
return me
|
||||||
|
|
||||||
#ToDo: self.add_comments('geom.py:clean v{}'.format(version)
|
return self.duplicate(ndimage.filters.generic_filter(
|
||||||
return self.update(ndimage.filters.generic_filter(
|
self.microstructure,
|
||||||
self.microstructure,
|
mostFrequent,
|
||||||
mostFrequent,
|
size=(stencil if selection is None else stencil//2*2+1,)*3,
|
||||||
size=(stencil if selection is None else stencil//2*2+1,)*3,
|
mode=mode,
|
||||||
mode=mode,
|
extra_keywords=dict(selection=selection),
|
||||||
extra_keywords=dict(selection=selection),
|
).astype(self.microstructure.dtype),
|
||||||
).astype(self.microstructure.dtype)
|
comments=self.get_comments()+[f'geom.py:clean {stencil} {mode} v{version}'],
|
||||||
)
|
)
|
||||||
|
|
||||||
|
|
||||||
def renumber(self):
|
def renumber(self):
|
||||||
|
|
@ -689,8 +805,9 @@ class Geom:
|
||||||
for i, oldID in enumerate(np.unique(self.microstructure)):
|
for i, oldID in enumerate(np.unique(self.microstructure)):
|
||||||
renumbered = np.where(self.microstructure == oldID, i+1, renumbered)
|
renumbered = np.where(self.microstructure == oldID, i+1, renumbered)
|
||||||
|
|
||||||
#ToDo: self.add_comments('geom.py:renumber v{}'.format(version)
|
return self.duplicate(renumbered,
|
||||||
return self.update(renumbered)
|
comments=self.get_comments()+[f'geom.py:renumber v{version}'],
|
||||||
|
)
|
||||||
|
|
||||||
|
|
||||||
def rotate(self,R,fill=None):
|
def rotate(self,R,fill=None):
|
||||||
|
|
@ -724,8 +841,11 @@ class Geom:
|
||||||
|
|
||||||
origin = self.origin-(np.asarray(microstructure_in.shape)-self.grid)*.5 * self.size/self.grid
|
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)
|
return self.duplicate(microstructure_in,
|
||||||
return self.update(microstructure_in,origin=origin,rescale=True)
|
origin=origin,
|
||||||
|
comments=self.get_comments()+[f'geom.py:rotate {R.as_quaternion()} v{version}'],
|
||||||
|
autosize=True,
|
||||||
|
)
|
||||||
|
|
||||||
|
|
||||||
def canvas(self,grid=None,offset=None,fill=None):
|
def canvas(self,grid=None,offset=None,fill=None):
|
||||||
|
|
@ -757,8 +877,11 @@ class Geom:
|
||||||
|
|
||||||
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]]
|
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)
|
return self.duplicate(canvas,
|
||||||
return self.update(canvas,origin=self.origin+offset*self.size/self.grid,rescale=True)
|
origin=self.origin+offset*self.size/self.grid,
|
||||||
|
comments=self.get_comments()+[f'geom.py:canvas {grid} {offset} {fill} v{version}'],
|
||||||
|
autosize=True,
|
||||||
|
)
|
||||||
|
|
||||||
|
|
||||||
def substitute(self,from_microstructure,to_microstructure):
|
def substitute(self,from_microstructure,to_microstructure):
|
||||||
|
|
@ -777,8 +900,9 @@ class Geom:
|
||||||
for from_ms,to_ms in zip(from_microstructure,to_microstructure):
|
for from_ms,to_ms in zip(from_microstructure,to_microstructure):
|
||||||
substituted[self.microstructure==from_ms] = to_ms
|
substituted[self.microstructure==from_ms] = to_ms
|
||||||
|
|
||||||
#ToDo: self.add_comments('geom.py:substitute v{}'.format(version)
|
return self.duplicate(substituted,
|
||||||
return self.update(substituted)
|
comments=self.get_comments()+[f'geom.py:substitute v{version}'],
|
||||||
|
)
|
||||||
|
|
||||||
|
|
||||||
def vicinity_offset(self,vicinity=1,offset=None,trigger=[],periodic=True):
|
def vicinity_offset(self,vicinity=1,offset=None,trigger=[],periodic=True):
|
||||||
|
|
@ -819,9 +943,10 @@ class Geom:
|
||||||
mask = ndimage.filters.generic_filter(self.microstructure,
|
mask = ndimage.filters.generic_filter(self.microstructure,
|
||||||
tainted_neighborhood,
|
tainted_neighborhood,
|
||||||
size=1+2*vicinity,
|
size=1+2*vicinity,
|
||||||
mode=('wrap' if periodic else 'nearest'),
|
mode='wrap' if periodic else 'nearest',
|
||||||
extra_keywords={'trigger':trigger})
|
extra_keywords={'trigger':trigger})
|
||||||
microstructure = np.ma.MaskedArray(self.microstructure + offset_, np.logical_not(mask))
|
microstructure = np.ma.MaskedArray(self.microstructure + offset_, np.logical_not(mask))
|
||||||
|
|
||||||
#ToDo: self.add_comments('geom.py:vicinity_offset v{}'.format(version)
|
return self.duplicate(microstructure,
|
||||||
return self.update(microstructure)
|
comments=self.get_comments()+[f'geom.py:vicinity_offset {vicinity} v{version}'],
|
||||||
|
)
|
||||||
|
|
|
||||||
|
|
@ -28,6 +28,19 @@ def reference_dir(reference_dir_base):
|
||||||
|
|
||||||
class TestGeom:
|
class TestGeom:
|
||||||
|
|
||||||
|
@pytest.mark.parametrize('flavor',['plain','explicit'])
|
||||||
|
def test_duplicate(self,default,flavor):
|
||||||
|
if flavor == 'plain':
|
||||||
|
modified = default.duplicate()
|
||||||
|
elif flavor == 'explicit':
|
||||||
|
modified = default.duplicate(
|
||||||
|
default.get_microstructure(),
|
||||||
|
default.get_size(),
|
||||||
|
default.get_origin()
|
||||||
|
)
|
||||||
|
print(modified)
|
||||||
|
assert geom_equal(default,modified)
|
||||||
|
|
||||||
def test_update(self,default):
|
def test_update(self,default):
|
||||||
modified = default.copy()
|
modified = default.copy()
|
||||||
modified.update(
|
modified.update(
|
||||||
|
|
@ -36,7 +49,7 @@ class TestGeom:
|
||||||
default.get_origin()
|
default.get_origin()
|
||||||
)
|
)
|
||||||
print(modified)
|
print(modified)
|
||||||
assert geom_equal(modified,default)
|
assert geom_equal(default,modified)
|
||||||
|
|
||||||
@pytest.mark.parametrize('masked',[True,False])
|
@pytest.mark.parametrize('masked',[True,False])
|
||||||
def test_set_microstructure(self,default,masked):
|
def test_set_microstructure(self,default,masked):
|
||||||
|
|
@ -47,36 +60,38 @@ class TestGeom:
|
||||||
|
|
||||||
|
|
||||||
def test_write_read_str(self,default,tmpdir):
|
def test_write_read_str(self,default,tmpdir):
|
||||||
default.to_file(str(tmpdir.join('default.geom')))
|
default.to_file(tmpdir/'default.geom')
|
||||||
new = Geom.from_file(str(tmpdir.join('default.geom')))
|
new = Geom.from_file(tmpdir/'default.geom')
|
||||||
assert geom_equal(new,default)
|
assert geom_equal(default,new)
|
||||||
|
|
||||||
def test_write_read_file(self,default,tmpdir):
|
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)
|
default.to_file(f)
|
||||||
with open(tmpdir.join('default.geom')) as f:
|
with open(tmpdir/'default.geom') as f:
|
||||||
new = Geom.from_file(f)
|
new = Geom.from_file(f)
|
||||||
assert geom_equal(new,default)
|
assert geom_equal(default,new)
|
||||||
|
|
||||||
def test_write_show(self,default,tmpdir):
|
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())
|
f.write(default.show())
|
||||||
with open(tmpdir.join('str.geom')) as f:
|
with open(tmpdir/'str.geom') as f:
|
||||||
new = Geom.from_file(f)
|
new = Geom.from_file(f)
|
||||||
assert geom_equal(new,default)
|
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'))
|
||||||
|
|
||||||
def test_export_vtk(self,default,tmpdir):
|
|
||||||
default.to_vtk(str(tmpdir.join('default')))
|
|
||||||
|
|
||||||
@pytest.mark.parametrize('pack',[True,False])
|
@pytest.mark.parametrize('pack',[True,False])
|
||||||
def test_pack(self,default,tmpdir,pack):
|
def test_pack(self,default,tmpdir,pack):
|
||||||
default.to_file(tmpdir.join('default.geom'),pack=pack)
|
default.to_file(tmpdir/'default.geom',pack=pack)
|
||||||
new = Geom.from_file(tmpdir.join('default.geom'))
|
new = Geom.from_file(tmpdir/'default.geom')
|
||||||
assert geom_equal(new,default)
|
assert geom_equal(new,default)
|
||||||
|
|
||||||
def test_invalid_combination(self,default):
|
def test_invalid_combination(self,default):
|
||||||
with pytest.raises(ValueError):
|
with pytest.raises(ValueError):
|
||||||
default.update(default.microstructure[1:,1:,1:],size=np.ones(3), rescale=True)
|
default.update(default.microstructure[1:,1:,1:],size=np.ones(3), autosize=True)
|
||||||
|
|
||||||
def test_invalid_size(self,default):
|
def test_invalid_size(self,default):
|
||||||
with pytest.raises(ValueError):
|
with pytest.raises(ValueError):
|
||||||
|
|
@ -108,21 +123,36 @@ class TestGeom:
|
||||||
]
|
]
|
||||||
)
|
)
|
||||||
def test_mirror(self,default,update,reference_dir,directions,reflect):
|
def test_mirror(self,default,update,reference_dir,directions,reflect):
|
||||||
modified = default.copy()
|
modified = default.mirror(directions,reflect)
|
||||||
modified.mirror(directions,reflect)
|
|
||||||
tag = f'directions={"-".join(directions)}_reflect={reflect}'
|
tag = f'directions={"-".join(directions)}_reflect={reflect}'
|
||||||
reference = reference_dir/f'mirror_{tag}.geom'
|
reference = reference_dir/f'mirror_{tag}.geom'
|
||||||
if update: modified.to_file(reference)
|
if update: modified.to_file(reference)
|
||||||
assert geom_equal(modified,Geom.from_file(reference))
|
assert geom_equal(Geom.from_file(reference),
|
||||||
|
modified)
|
||||||
|
|
||||||
|
@pytest.mark.parametrize('directions',[
|
||||||
|
['x'],
|
||||||
|
['x','y','z'],
|
||||||
|
['z','x','y'],
|
||||||
|
['y','z'],
|
||||||
|
]
|
||||||
|
)
|
||||||
|
def test_flip(self,default,update,reference_dir,directions):
|
||||||
|
modified = default.flip(directions)
|
||||||
|
tag = f'directions={"-".join(directions)}'
|
||||||
|
reference = reference_dir/f'flip_{tag}.geom'
|
||||||
|
if update: modified.to_file(reference)
|
||||||
|
assert geom_equal(Geom.from_file(reference),
|
||||||
|
modified)
|
||||||
|
|
||||||
@pytest.mark.parametrize('stencil',[1,2,3,4])
|
@pytest.mark.parametrize('stencil',[1,2,3,4])
|
||||||
def test_clean(self,default,update,reference_dir,stencil):
|
def test_clean(self,default,update,reference_dir,stencil):
|
||||||
modified = default.copy()
|
modified = default.clean(stencil)
|
||||||
modified.clean(stencil)
|
|
||||||
tag = f'stencil={stencil}'
|
tag = f'stencil={stencil}'
|
||||||
reference = reference_dir/f'clean_{tag}.geom'
|
reference = reference_dir/f'clean_{tag}.geom'
|
||||||
if update: modified.to_file(reference)
|
if update: modified.to_file(reference)
|
||||||
assert geom_equal(modified,Geom.from_file(reference))
|
assert geom_equal(Geom.from_file(reference),
|
||||||
|
modified)
|
||||||
|
|
||||||
@pytest.mark.parametrize('grid',[
|
@pytest.mark.parametrize('grid',[
|
||||||
(10,11,10),
|
(10,11,10),
|
||||||
|
|
@ -134,33 +164,29 @@ class TestGeom:
|
||||||
]
|
]
|
||||||
)
|
)
|
||||||
def test_scale(self,default,update,reference_dir,grid):
|
def test_scale(self,default,update,reference_dir,grid):
|
||||||
modified = default.copy()
|
modified = default.scale(grid)
|
||||||
modified.scale(grid)
|
|
||||||
tag = f'grid={util.srepr(grid,"-")}'
|
tag = f'grid={util.srepr(grid,"-")}'
|
||||||
reference = reference_dir/f'scale_{tag}.geom'
|
reference = reference_dir/f'scale_{tag}.geom'
|
||||||
if update: modified.to_file(reference)
|
if update: modified.to_file(reference)
|
||||||
assert geom_equal(modified,Geom.from_file(reference))
|
assert geom_equal(Geom.from_file(reference),
|
||||||
|
modified)
|
||||||
|
|
||||||
def test_renumber(self,default):
|
def test_renumber(self,default):
|
||||||
modified = default.copy()
|
microstructure = default.get_microstructure()
|
||||||
microstructure = modified.get_microstructure()
|
|
||||||
for m in np.unique(microstructure):
|
for m in np.unique(microstructure):
|
||||||
microstructure[microstructure==m] = microstructure.max() + np.random.randint(1,30)
|
microstructure[microstructure==m] = microstructure.max() + np.random.randint(1,30)
|
||||||
modified.update(microstructure)
|
modified = default.duplicate(microstructure)
|
||||||
assert not geom_equal(modified,default)
|
assert not geom_equal(modified,default)
|
||||||
modified.renumber()
|
assert geom_equal(default,
|
||||||
assert geom_equal(modified,default)
|
modified.renumber())
|
||||||
|
|
||||||
def test_substitute(self,default):
|
def test_substitute(self,default):
|
||||||
modified = default.copy()
|
|
||||||
microstructure = modified.get_microstructure()
|
|
||||||
offset = np.random.randint(1,500)
|
offset = np.random.randint(1,500)
|
||||||
microstructure += offset
|
modified = default.duplicate(default.get_microstructure() + offset)
|
||||||
modified.update(microstructure)
|
|
||||||
assert not geom_equal(modified,default)
|
assert not geom_equal(modified,default)
|
||||||
modified.substitute(np.arange(default.microstructure.max())+1+offset,
|
assert geom_equal(default,
|
||||||
np.arange(default.microstructure.max())+1)
|
modified.substitute(np.arange(default.microstructure.max())+1+offset,
|
||||||
assert geom_equal(modified,default)
|
np.arange(default.microstructure.max())+1))
|
||||||
|
|
||||||
@pytest.mark.parametrize('axis_angle',[np.array([1,0,0,86.7]), np.array([0,1,0,90.4]), np.array([0,0,1,90]),
|
@pytest.mark.parametrize('axis_angle',[np.array([1,0,0,86.7]), np.array([0,1,0,90.4]), np.array([0,0,1,90]),
|
||||||
np.array([1,0,0,175]),np.array([0,-1,0,178]),np.array([0,0,1,180])])
|
np.array([1,0,0,175]),np.array([0,-1,0,178]),np.array([0,0,1,180])])
|
||||||
|
|
@ -168,38 +194,35 @@ class TestGeom:
|
||||||
modified = default.copy()
|
modified = default.copy()
|
||||||
for i in range(np.rint(360/axis_angle[3]).astype(int)):
|
for i in range(np.rint(360/axis_angle[3]).astype(int)):
|
||||||
modified.rotate(Rotation.from_axis_angle(axis_angle,degrees=True))
|
modified.rotate(Rotation.from_axis_angle(axis_angle,degrees=True))
|
||||||
assert geom_equal(modified,default)
|
assert geom_equal(default,modified)
|
||||||
|
|
||||||
@pytest.mark.parametrize('Eulers',[[32.0,68.0,21.0],
|
@pytest.mark.parametrize('Eulers',[[32.0,68.0,21.0],
|
||||||
[0.0,32.0,240.0]])
|
[0.0,32.0,240.0]])
|
||||||
def test_rotate(self,default,update,reference_dir,Eulers):
|
def test_rotate(self,default,update,reference_dir,Eulers):
|
||||||
modified = default.copy()
|
modified = default.rotate(Rotation.from_Eulers(Eulers,degrees=True))
|
||||||
modified.rotate(Rotation.from_Eulers(Eulers,degrees=True))
|
|
||||||
tag = f'Eulers={util.srepr(Eulers,"-")}'
|
tag = f'Eulers={util.srepr(Eulers,"-")}'
|
||||||
reference = reference_dir/f'rotate_{tag}.geom'
|
reference = reference_dir/f'rotate_{tag}.geom'
|
||||||
if update: modified.to_file(reference)
|
if update: modified.to_file(reference)
|
||||||
assert geom_equal(modified,Geom.from_file(reference))
|
assert geom_equal(Geom.from_file(reference),
|
||||||
|
modified)
|
||||||
|
|
||||||
def test_canvas(self,default):
|
def test_canvas(self,default):
|
||||||
|
grid = default.grid
|
||||||
grid_add = np.random.randint(0,30,(3))
|
grid_add = np.random.randint(0,30,(3))
|
||||||
modified = default.copy()
|
modified = default.canvas(grid + grid_add)
|
||||||
modified.canvas(modified.grid + grid_add)
|
assert np.all(modified.microstructure[:grid[0],:grid[1],:grid[2]] == default.microstructure)
|
||||||
e = default.grid
|
|
||||||
assert np.all(modified.microstructure[:e[0],:e[1],:e[2]] == default.microstructure)
|
|
||||||
|
|
||||||
@pytest.mark.parametrize('center1,center2',[(np.random.random(3)*.5,np.random.random(3)),
|
@pytest.mark.parametrize('center1,center2',[(np.random.random(3)*.5,np.random.random(3)),
|
||||||
(np.random.randint(4,8,(3)),np.random.randint(9,12,(3)))])
|
(np.random.randint(4,8,(3)),np.random.randint(9,12,(3)))])
|
||||||
@pytest.mark.parametrize('diameter',[np.random.random(3)*.5,
|
@pytest.mark.parametrize('diameter',[np.random.random(3)*.5,
|
||||||
np.random.randint(4,10,(3))])
|
np.random.randint(4,10,(3))])
|
||||||
def test_add_primitive(self,diameter,center1,center2):
|
def test_add_primitive(self,diameter,center1,center2):
|
||||||
"""Same volume fraction for periodic microstructures and different center."""
|
"""Same volume fraction for periodic microstructures and different center."""
|
||||||
o = np.random.random(3)-.5
|
o = np.random.random(3)-.5
|
||||||
g = np.random.randint(8,32,(3))
|
g = np.random.randint(8,32,(3))
|
||||||
s = np.random.random(3)+.5
|
s = np.random.random(3)+.5
|
||||||
G_1 = Geom(np.ones(g,'i'),s,o)
|
G_1 = Geom(np.ones(g,'i'),s,o).add_primitive(diameter,center1,1)
|
||||||
G_2 = Geom(np.ones(g,'i'),s,o)
|
G_2 = Geom(np.ones(g,'i'),s,o).add_primitive(diameter,center2,1)
|
||||||
G_1.add_primitive(diameter,center1,1)
|
|
||||||
G_2.add_primitive(diameter,center2,1)
|
|
||||||
assert np.count_nonzero(G_1.microstructure!=2) == np.count_nonzero(G_2.microstructure!=2)
|
assert np.count_nonzero(G_1.microstructure!=2) == np.count_nonzero(G_2.microstructure!=2)
|
||||||
|
|
||||||
@pytest.mark.parametrize('trigger',[[1],[]])
|
@pytest.mark.parametrize('trigger',[[1],[]])
|
||||||
|
|
@ -218,8 +241,7 @@ class TestGeom:
|
||||||
if len(trigger) > 0:
|
if len(trigger) > 0:
|
||||||
m2[m==1] = 1
|
m2[m==1] = 1
|
||||||
|
|
||||||
geom = Geom(m,np.random.rand(3))
|
geom = Geom(m,np.random.rand(3)).vicinity_offset(vicinity,offset,trigger=trigger)
|
||||||
geom.vicinity_offset(vicinity,offset,trigger=trigger)
|
|
||||||
|
|
||||||
assert np.all(m2==geom.microstructure)
|
assert np.all(m2==geom.microstructure)
|
||||||
|
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue