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DAMASK_EICMD
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whitespace cleaning and other polishing

This commit is contained in:
Martin Diehl 2020-03-14 21:53:48 +01:00
parent 38b755740b
commit b4679fabfc
6 changed files with 535 additions and 525 deletions
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26
python/damask/colormaps.py
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@ -1,6 +1,6 @@
import numpy as np import numpy as np
class Color(): class Color:
"""Color representation in and conversion between different color-spaces.""" """Color representation in and conversion between different color-spaces."""
__slots__ = [ __slots__ = [
@ -97,7 +97,6 @@ class Color():
return self.__class__(self.model,self.color).convert_to(asModel) return self.__class__(self.model,self.color).convert_to(asModel)
def _HSV2HSL(self): def _HSV2HSL(self):
""" """
Convert H(ue) S(aturation) V(alue or brightness) to H(ue) S(aturation) L(uminance). Convert H(ue) S(aturation) V(alue or brightness) to H(ue) S(aturation) L(uminance).
@ -202,7 +201,6 @@ class Color():
self.color = converted.color self.color = converted.color
def _RGB2XYZ(self): def _RGB2XYZ(self):
""" """
Convert R(ed) G(reen) B(lue) to CIE XYZ. Convert R(ed) G(reen) B(lue) to CIE XYZ.
@ -223,7 +221,6 @@ class Color():
else: RGB_lin[i] = self.color[i] /12.92 else: RGB_lin[i] = self.color[i] /12.92
XYZ = np.dot(convert,RGB_lin) XYZ = np.dot(convert,RGB_lin)
for i in range(3): for i in range(3):
XYZ[i] = max(XYZ[i],0.0) XYZ[i] = max(XYZ[i],0.0)
converted = Color('XYZ', XYZ) converted = Color('XYZ', XYZ)
@ -231,7 +228,6 @@ class Color():
self.color = converted.color self.color = converted.color
def _XYZ2RGB(self): def _XYZ2RGB(self):
""" """
Convert CIE XYZ to R(ed) G(reen) B(lue). Convert CIE XYZ to R(ed) G(reen) B(lue).
@ -239,8 +235,7 @@ class Color():
All values are in the range [0,1] All values are in the range [0,1]
from http://www.cs.rit.edu/~ncs/color/t_convert.html from http://www.cs.rit.edu/~ncs/color/t_convert.html
""" """
if self.model != 'XYZ': if self.model != 'XYZ': return
return
convert = np.array([[ 3.240479,-1.537150,-0.498535], convert = np.array([[ 3.240479,-1.537150,-0.498535],
[-0.969256, 1.875992, 0.041556], [-0.969256, 1.875992, 0.041556],
@ -263,7 +258,6 @@ class Color():
self.color = converted.color self.color = converted.color
def _CIELAB2XYZ(self): def _CIELAB2XYZ(self):
""" """
Convert CIE Lab to CIE XYZ. Convert CIE Lab to CIE XYZ.
@ -352,7 +346,7 @@ class Color():
self.color = converted.color self.color = converted.color
class Colormap(): class Colormap:
"""Perceptually uniform diverging or sequential colormap.""" """Perceptually uniform diverging or sequential colormap."""
__slots__ = [ __slots__ = [
@ -403,7 +397,7 @@ class Colormap():
} }
# ------------------------------------------------------------------ # ------------------------------------------------------------------
def __init__(self, def __init__(self,
left = Color('RGB',[1,1,1]), left = Color('RGB',[1,1,1]),
right = Color('RGB',[0,0,0]), right = Color('RGB',[0,0,0]),
@ -440,32 +434,32 @@ class Colormap():
self.interpolate = interpolate self.interpolate = interpolate
# ------------------------------------------------------------------ # ------------------------------------------------------------------
def __repr__(self): def __repr__(self):
"""Left and right value of colormap.""" """Left and right value of colormap."""
return 'Left: %s Right: %s'%(self.left,self.right) return 'Left: %s Right: %s'%(self.left,self.right)
# ------------------------------------------------------------------ # ------------------------------------------------------------------
def invert(self): def invert(self):
"""Switch left/minimum with right/maximum.""" """Switch left/minimum with right/maximum."""
(self.left, self.right) = (self.right, self.left) (self.left, self.right) = (self.right, self.left)
return self return self
# ------------------------------------------------------------------ # ------------------------------------------------------------------
def show_predefined(self): def show_predefined(self):
"""Show the labels of the predefined colormaps.""" """Show the labels of the predefined colormaps."""
print('\n'.join(self.__predefined__.keys())) print('\n'.join(self.__predefined__.keys()))
# ------------------------------------------------------------------ # ------------------------------------------------------------------
def color(self,fraction = 0.5): def color(self,fraction = 0.5):
def interpolate_Msh(lo, hi, frac): def interpolate_Msh(lo, hi, frac):
def rad_diff(a,b): def rad_diff(a,b):
return abs(a[2]-b[2]) return abs(a[2]-b[2])
# if saturation of one of the two colors is too less than the other, hue of the less # if saturation of one of the two colors is too less than the other, hue of the less
def adjust_hue(Msh_sat, Msh_unsat): def adjust_hue(Msh_sat, Msh_unsat):
if Msh_sat[0] >= Msh_unsat[0]: if Msh_sat[0] >= Msh_unsat[0]:
return Msh_sat[2] return Msh_sat[2]
@ -507,7 +501,7 @@ class Colormap():
else: else:
raise NameError('unknown color interpolation method') raise NameError('unknown color interpolation method')
# ------------------------------------------------------------------ # ------------------------------------------------------------------
def export(self,name = 'uniformPerceptualColorMap',\ def export(self,name = 'uniformPerceptualColorMap',\
format = 'paraview',\ format = 'paraview',\
steps = 2,\ steps = 2,\

24
python/damask/geom.py
View File

@ -49,6 +49,7 @@ class Geom():
'max microstructure: {}'.format(np.nanmax(self.microstructure)), 'max microstructure: {}'.format(np.nanmax(self.microstructure)),
]) ])
def update(self,microstructure=None,size=None,origin=None,rescale=False): def update(self,microstructure=None,size=None,origin=None,rescale=False):
""" """
Updates microstructure and size. Updates microstructure and size.
@ -111,6 +112,7 @@ class Geom():
return util.return_message(message) return util.return_message(message)
def set_comments(self,comments): def set_comments(self,comments):
""" """
Replaces all existing comments. Replaces all existing comments.
@ -124,6 +126,7 @@ class Geom():
self.comments = [] self.comments = []
self.add_comments(comments) self.add_comments(comments)
def add_comments(self,comments): def add_comments(self,comments):
""" """
Appends comments to existing comments. Appends comments to existing comments.
@ -136,6 +139,7 @@ class Geom():
""" """
self.comments += [str(c) for c in comments] if isinstance(comments,list) else [str(comments)] self.comments += [str(c) for c in comments] if isinstance(comments,list) else [str(comments)]
def set_microstructure(self,microstructure): def set_microstructure(self,microstructure):
""" """
Replaces the existing microstructure representation. Replaces the existing microstructure representation.
@ -154,6 +158,7 @@ class Geom():
else: else:
self.microstructure = np.copy(microstructure) self.microstructure = np.copy(microstructure)
def set_size(self,size): def set_size(self,size):
""" """
Replaces the existing size information. Replaces the existing size information.
@ -173,6 +178,7 @@ class Geom():
else: else:
self.size = np.array(size) self.size = np.array(size)
def set_origin(self,origin): def set_origin(self,origin):
""" """
Replaces the existing origin information. Replaces the existing origin information.
@ -189,6 +195,7 @@ class Geom():
else: else:
self.origin = np.array(origin) self.origin = np.array(origin)
def set_homogenization(self,homogenization): def set_homogenization(self,homogenization):
""" """
Replaces the existing homogenization index. Replaces the existing homogenization index.
@ -205,34 +212,42 @@ class Geom():
else: else:
self.homogenization = homogenization self.homogenization = homogenization
@property @property
def grid(self): def grid(self):
return self.get_grid() return self.get_grid()
def get_microstructure(self): def get_microstructure(self):
"""Return the microstructure representation.""" """Return the microstructure representation."""
return np.copy(self.microstructure) return np.copy(self.microstructure)
def get_size(self): def get_size(self):
"""Return the physical size in meter.""" """Return the physical size in meter."""
return np.copy(self.size) return np.copy(self.size)
def get_origin(self): def get_origin(self):
"""Return the origin in meter.""" """Return the origin in meter."""
return np.copy(self.origin) return np.copy(self.origin)
def get_grid(self): def get_grid(self):
"""Return the grid discretization.""" """Return the grid discretization."""
return np.array(self.microstructure.shape) return np.array(self.microstructure.shape)
def get_homogenization(self): def get_homogenization(self):
"""Return the homogenization index.""" """Return the homogenization index."""
return self.homogenization return self.homogenization
def get_comments(self): def get_comments(self):
"""Return the comments.""" """Return the comments."""
return self.comments[:] return self.comments[:]
def get_header(self): def get_header(self):
"""Return the full header (grid, size, origin, homogenization, comments).""" """Return the full header (grid, size, origin, homogenization, comments)."""
header = ['{} header'.format(len(self.comments)+4)] + self.comments header = ['{} header'.format(len(self.comments)+4)] + self.comments
@ -242,6 +257,7 @@ class Geom():
header.append('homogenization {}'.format(self.get_homogenization())) header.append('homogenization {}'.format(self.get_homogenization()))
return header return header
@staticmethod @staticmethod
def from_file(fname): def from_file(fname):
""" """
@ -470,8 +486,8 @@ class Geom():
if 'x' in directions: if 'x' in directions:
ms = np.concatenate([ms,ms[limits[0]:limits[1]:-1,:,:]],0) ms = np.concatenate([ms,ms[limits[0]:limits[1]:-1,:,:]],0)
#self.add_comments('geom.py:mirror v{}'.format(version)
return self.update(ms,rescale=True) return self.update(ms,rescale=True)
#self.add_comments('tbd')
def scale(self,grid): def scale(self,grid):
@ -484,6 +500,7 @@ class Geom():
new grid dimension new grid dimension
""" """
#self.add_comments('geom.py:scale v{}'.format(version)
return self.update( return self.update(
ndimage.interpolation.zoom( ndimage.interpolation.zoom(
self.microstructure, self.microstructure,
@ -494,7 +511,6 @@ class Geom():
prefilter=False prefilter=False
) )
) )
#self.add_comments('tbd')
def clean(self,stencil=3): def clean(self,stencil=3):
@ -511,13 +527,13 @@ class Geom():
unique, inverse = np.unique(arr, return_inverse=True) unique, inverse = np.unique(arr, return_inverse=True)
return unique[np.argmax(np.bincount(inverse))] return unique[np.argmax(np.bincount(inverse))]
#self.add_comments('geom.py:clean v{}'.format(version)
return self.update(ndimage.filters.generic_filter( return self.update(ndimage.filters.generic_filter(
self.microstructure, self.microstructure,
mostFrequent, mostFrequent,
size=(stencil,)*3 size=(stencil,)*3
).astype(self.microstructure.dtype) ).astype(self.microstructure.dtype)
) )
#self.add_comments('tbd')
def renumber(self): def renumber(self):
@ -526,5 +542,5 @@ 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)
#self.add_comments('geom.py:renumber v{}'.format(version)
return self.update(renumbered) return self.update(renumbered)
#self.add_comments('tbd')

4
python/damask/mechanics.py
View File

@ -11,7 +11,7 @@ def Cauchy(P,F):
F : numpy.ndarray of shape (:,3,3) or (3,3) F : numpy.ndarray of shape (:,3,3) or (3,3)
Deformation gradient. Deformation gradient.
P : numpy.ndarray of shape (:,3,3) or (3,3) P : numpy.ndarray of shape (:,3,3) or (3,3)
1. Piola-Kirchhoff stress. First Piola-Kirchhoff stress.
""" """
if np.shape(F) == np.shape(P) == (3,3): if np.shape(F) == np.shape(P) == (3,3):
@ -136,7 +136,7 @@ def PK2(P,F):
Parameters Parameters
---------- ----------
P : numpy.ndarray of shape (:,3,3) or (3,3) P : numpy.ndarray of shape (:,3,3) or (3,3)
1. Piola-Kirchhoff stress. First Piola-Kirchhoff stress.
F : numpy.ndarray of shape (:,3,3) or (3,3) F : numpy.ndarray of shape (:,3,3) or (3,3)
Deformation gradient. Deformation gradient.

4
python/damask/table.py
View File

@ -287,7 +287,7 @@ class Table:
Parameters Parameters
---------- ----------
other : Table other : Table
Table to append Table to append.
""" """
if self.shapes != other.shapes or not self.data.columns.equals(other.data.columns): if self.shapes != other.shapes or not self.data.columns.equals(other.data.columns):
@ -305,7 +305,7 @@ class Table:
Parameters Parameters
---------- ----------
other : Table other : Table
Table to join Table to join.
""" """
if set(self.shapes) & set(other.shapes) or self.data.shape[0] != other.data.shape[0]: if set(self.shapes) & set(other.shapes) or self.data.shape[0] != other.data.shape[0]:

6
python/damask/util.py
View File

@ -66,7 +66,7 @@ def croak(what, newline = True):
Parameters Parameters
---------- ----------
what : str or iterable what : str or iterable
Content to be displayed Content to be displayed.
newline : bool, optional newline : bool, optional
Separate items of what by newline. Defaults to True. Separate items of what by newline. Defaults to True.
@ -122,8 +122,8 @@ def execute(cmd,
Input (via pipe) for executed process. Input (via pipe) for executed process.
wd : str, optional wd : str, optional
Working directory of process. Defaults to ./ . Working directory of process. Defaults to ./ .
env : env : dict, optional
Environment Environment for execution.
""" """
initialPath = os.getcwd() initialPath = os.getcwd()