Merge remote-tracking branch 'origin/T_ref300' into dynamic-C
This commit is contained in:
Sharan Roongta
commit
8b06d97e84
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@ -1 +1 @@
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v3.0.0-alpha5-155-gbf76d9f3a
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v3.0.0-alpha5-164-gdc993bc6f
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@ -2,6 +2,9 @@ import os
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import json
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import functools
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import colorsys
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from pathlib import Path
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from typing import Sequence, Union, TextIO
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import numpy as np
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import matplotlib as mpl
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@ -39,20 +42,20 @@ class Colormap(mpl.colors.ListedColormap):
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"""
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def __add__(self,other):
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def __add__(self, other: "Colormap") -> "Colormap":
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"""Concatenate."""
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return Colormap(np.vstack((self.colors,other.colors)),
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f'{self.name}+{other.name}')
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def __iadd__(self,other):
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def __iadd__(self, other: "Colormap") -> "Colormap":
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"""Concatenate (in-place)."""
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return self.__add__(other)
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def __invert__(self):
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def __invert__(self) -> "Colormap":
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"""Reverse."""
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return self.reversed()
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def __repr__(self):
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def __repr__(self) -> str:
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"""Show as matplotlib figure."""
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fig = plt.figure(self.name,figsize=(5,.5))
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ax1 = fig.add_axes([0, 0, 1, 1])
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@ -64,7 +67,11 @@ class Colormap(mpl.colors.ListedColormap):
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@staticmethod
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def from_range(low,high,name='DAMASK colormap',N=256,model='rgb'):
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def from_range(low: Sequence[float],
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high: Sequence[float],
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name: str = 'DAMASK colormap',
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N: int = 256,
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model: str = 'rgb') -> "Colormap":
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"""
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Create a perceptually uniform colormap between given (inclusive) bounds.
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@ -145,7 +152,7 @@ class Colormap(mpl.colors.ListedColormap):
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@staticmethod
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def from_predefined(name,N=256):
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def from_predefined(name: str, N: int = 256) -> "Colormap":
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"""
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Select from a set of predefined colormaps.
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@ -185,7 +192,10 @@ class Colormap(mpl.colors.ListedColormap):
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return Colormap.from_range(definition['low'],definition['high'],name,N)
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def shade(self,field,bounds=None,gap=None):
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def shade(self,
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field: np.ndarray,
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bounds: Sequence[float] = None,
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gap: float = None) -> Image:
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"""
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Generate PIL image of 2D field using colormap.
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@ -226,7 +236,7 @@ class Colormap(mpl.colors.ListedColormap):
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mode='RGBA')
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def reversed(self,name=None):
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def reversed(self, name: str = None) -> "Colormap":
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"""
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Reverse.
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@ -251,7 +261,7 @@ class Colormap(mpl.colors.ListedColormap):
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return Colormap(np.array(rev.colors),rev.name[:-4] if rev.name.endswith('_r_r') else rev.name)
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def _get_file_handle(self,fname,extension):
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def _get_file_handle(self, fname: Union[TextIO, str, Path, None], suffix: str) -> TextIO:
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"""
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Provide file handle.
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@ -259,8 +269,7 @@ class Colormap(mpl.colors.ListedColormap):
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----------
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fname : file, str, pathlib.Path, or None
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Filename or filehandle, will be name of the colormap+extension if None.
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extension: str
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suffix: str
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Extension of the filename.
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Returns
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@ -270,17 +279,14 @@ class Colormap(mpl.colors.ListedColormap):
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"""
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if fname is None:
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fhandle = open(self.name.replace(' ','_')+'.'+extension,'w',newline='\n')
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return open(self.name.replace(' ','_')+suffix, 'w', newline='\n')
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elif isinstance(fname, (str, Path)):
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return open(fname, 'w', newline='\n')
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else:
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try:
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fhandle = open(fname,'w',newline='\n')
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except TypeError:
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fhandle = fname
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return fhandle
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return fname
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def save_paraview(self,fname=None):
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def save_paraview(self, fname: Union[TextIO, str, Path] = None):
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"""
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Save as JSON file for use in Paraview.
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@ -303,10 +309,10 @@ class Colormap(mpl.colors.ListedColormap):
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'RGBPoints':colors
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}]
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json.dump(out,self._get_file_handle(fname,'json'),indent=4)
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json.dump(out,self._get_file_handle(fname,'.json'),indent=4)
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def save_ASCII(self,fname=None):
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def save_ASCII(self, fname: Union[TextIO, str, Path] = None):
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"""
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Save as ASCII file.
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@ -319,10 +325,10 @@ class Colormap(mpl.colors.ListedColormap):
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"""
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labels = {'RGBA':4} if self.colors.shape[1] == 4 else {'RGB': 3}
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t = Table(self.colors,labels,f'Creator: {util.execution_stamp("Colormap")}')
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t.save(self._get_file_handle(fname,'txt'))
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t.save(self._get_file_handle(fname,'.txt'))
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def save_GOM(self,fname=None):
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def save_GOM(self, fname: Union[TextIO, str, Path] = None):
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"""
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Save as ASCII file for use in GOM Aramis.
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@ -340,10 +346,10 @@ class Colormap(mpl.colors.ListedColormap):
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+ ' '.join([f' 0 {c[0]} {c[1]} {c[2]} 255 1' for c in reversed((self.colors*255).astype(int))]) \
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+ '\n'
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self._get_file_handle(fname,'legend').write(GOM_str)
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self._get_file_handle(fname,'.legend').write(GOM_str)
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def save_gmsh(self,fname=None):
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def save_gmsh(self, fname: Union[TextIO, str, Path] = None):
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"""
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Save as ASCII file for use in gmsh.
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@ -358,11 +364,13 @@ class Colormap(mpl.colors.ListedColormap):
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gmsh_str = 'View.ColorTable = {\n' \
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+'\n'.join([f'{c[0]},{c[1]},{c[2]},' for c in self.colors[:,:3]*255]) \
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+'\n}\n'
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self._get_file_handle(fname,'msh').write(gmsh_str)
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self._get_file_handle(fname,'.msh').write(gmsh_str)
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@staticmethod
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def _interpolate_msh(frac,low,high):
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def _interpolate_msh(frac,
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low: np.ndarray,
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high: np.ndarray) -> np.ndarray:
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"""
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Interpolate in Msh color space.
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@ -439,31 +447,31 @@ class Colormap(mpl.colors.ListedColormap):
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@staticmethod
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def _hsv2rgb(hsv):
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def _hsv2rgb(hsv: np.ndarray) -> np.ndarray:
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"""H(ue) S(aturation) V(alue) to R(red) G(reen) B(lue)."""
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return np.array(colorsys.hsv_to_rgb(hsv[0]/360.,hsv[1],hsv[2]))
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@staticmethod
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def _rgb2hsv(rgb):
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def _rgb2hsv(rgb: np.ndarray) -> np.ndarray:
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"""R(ed) G(reen) B(lue) to H(ue) S(aturation) V(alue)."""
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h,s,v = colorsys.rgb_to_hsv(rgb[0],rgb[1],rgb[2])
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return np.array([h*360,s,v])
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@staticmethod
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def _hsl2rgb(hsl):
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def _hsl2rgb(hsl: np.ndarray) -> np.ndarray:
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"""H(ue) S(aturation) L(uminance) to R(red) G(reen) B(lue)."""
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return np.array(colorsys.hls_to_rgb(hsl[0]/360.,hsl[2],hsl[1]))
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@staticmethod
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def _rgb2hsl(rgb):
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def _rgb2hsl(rgb: np.ndarray) -> np.ndarray:
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"""R(ed) G(reen) B(lue) to H(ue) S(aturation) L(uminance)."""
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h,l,s = colorsys.rgb_to_hls(rgb[0],rgb[1],rgb[2])
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return np.array([h*360,s,l])
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@staticmethod
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def _xyz2rgb(xyz):
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def _xyz2rgb(xyz: np.ndarray) -> np.ndarray:
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"""
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CIE Xyz to R(ed) G(reen) B(lue).
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@ -483,7 +491,7 @@ class Colormap(mpl.colors.ListedColormap):
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return np.clip(rgb,0.,1.)
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@staticmethod
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def _rgb2xyz(rgb):
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def _rgb2xyz(rgb: np.ndarray) -> np.ndarray:
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"""
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R(ed) G(reen) B(lue) to CIE Xyz.
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@ -501,7 +509,7 @@ class Colormap(mpl.colors.ListedColormap):
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@staticmethod
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def _lab2xyz(lab,ref_white=None):
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def _lab2xyz(lab: np.ndarray, ref_white: np.ndarray = None) -> np.ndarray:
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"""
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CIE Lab to CIE Xyz.
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@ -520,7 +528,7 @@ class Colormap(mpl.colors.ListedColormap):
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])*(ref_white if ref_white is not None else _ref_white)
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@staticmethod
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def _xyz2lab(xyz,ref_white=None):
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def _xyz2lab(xyz: np.ndarray, ref_white: np.ndarray = None) -> np.ndarray:
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"""
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CIE Xyz to CIE Lab.
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@ -540,7 +548,7 @@ class Colormap(mpl.colors.ListedColormap):
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@staticmethod
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def _lab2msh(lab):
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def _lab2msh(lab: np.ndarray) -> np.ndarray:
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"""
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CIE Lab to Msh.
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@ -558,7 +566,7 @@ class Colormap(mpl.colors.ListedColormap):
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])
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@staticmethod
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def _msh2lab(msh):
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def _msh2lab(msh: np.ndarray) -> np.ndarray:
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"""
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Msh to CIE Lab.
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@ -575,29 +583,29 @@ class Colormap(mpl.colors.ListedColormap):
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])
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@staticmethod
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def _lab2rgb(lab):
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def _lab2rgb(lab: np.ndarray) -> np.ndarray:
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return Colormap._xyz2rgb(Colormap._lab2xyz(lab))
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@staticmethod
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def _rgb2lab(rgb):
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def _rgb2lab(rgb: np.ndarray) -> np.ndarray:
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return Colormap._xyz2lab(Colormap._rgb2xyz(rgb))
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@staticmethod
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def _msh2rgb(msh):
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def _msh2rgb(msh: np.ndarray) -> np.ndarray:
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return Colormap._lab2rgb(Colormap._msh2lab(msh))
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@staticmethod
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def _rgb2msh(rgb):
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def _rgb2msh(rgb: np.ndarray) -> np.ndarray:
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return Colormap._lab2msh(Colormap._rgb2lab(rgb))
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@staticmethod
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def _hsv2msh(hsv):
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def _hsv2msh(hsv: np.ndarray) -> np.ndarray:
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return Colormap._rgb2msh(Colormap._hsv2rgb(hsv))
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@staticmethod
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def _hsl2msh(hsl):
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def _hsl2msh(hsl: np.ndarray) -> np.ndarray:
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return Colormap._rgb2msh(Colormap._hsl2rgb(hsl))
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@staticmethod
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def _xyz2msh(xyz):
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def _xyz2msh(xyz: np.ndarray) -> np.ndarray:
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return Colormap._lab2msh(Colormap._xyz2lab(xyz))
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@ -77,6 +77,12 @@ class TestColormap:
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# xyz2msh
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assert np.allclose(Colormap._xyz2msh(xyz),msh,atol=1.e-6,rtol=0)
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@pytest.mark.parametrize('low,high',[((0,0,0),(1,1,1)),
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([0,0,0],[1,1,1])])
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def test_from_range_types(self,low,high):
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a = Colormap.from_range(low,high)
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b = Colormap.from_range(np.array(low),np.array(high))
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assert np.all(a.colors == b.colors)
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@pytest.mark.parametrize('format',['ASCII','paraview','GOM','gmsh'])
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@pytest.mark.parametrize('model',['rgb','hsv','hsl','xyz','lab','msh'])
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@ -4,6 +4,7 @@
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!> @details List of files needed by MSC.Marc
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!--------------------------------------------------------------------------------------------------
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#include "parallelization.f90"
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#include "constants.f90"
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#include "IO.f90"
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#include "YAML_types.f90"
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#include "YAML_parse.f90"
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@ -0,0 +1,15 @@
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!--------------------------------------------------------------------------------------------------
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!> @author Martin Diehl, KU Leuven
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!> @brief physical constants
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!--------------------------------------------------------------------------------------------------
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module constants
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use prec
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implicit none
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public
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real(pReal), parameter :: &
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T_ROOM = 300.0_pReal, & !< Room temperature in K
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kB = 1.38e-23_pReal !< Boltzmann constant in J/Kelvin
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end module constants
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@ -5,6 +5,7 @@
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!--------------------------------------------------------------------------------------------------
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module phase
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use prec
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use constants
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use math
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use rotations
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use IO
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@ -58,7 +58,7 @@ module function thermalexpansion_init(kinematics_length) result(myKinematics)
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associate(prm => param(kinematics_thermal_expansion_instance(p)))
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kinematic_type => kinematics%get(k)
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prm%T_ref = kinematic_type%get_asFloat('T_ref', defaultVal=0.0_pReal)
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prm%T_ref = kinematic_type%get_asFloat('T_ref', defaultVal=T_ROOM)
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prm%A(1,1,1) = kinematic_type%get_asFloat('A_11')
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prm%A(1,1,2) = kinematic_type%get_asFloat('A_11,T',defaultVal=0.0_pReal)
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@ -7,9 +7,6 @@
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!--------------------------------------------------------------------------------------------------
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submodule(phase:plastic) dislotungsten
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real(pReal), parameter :: &
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kB = 1.38e-23_pReal !< Boltzmann constant in J/Kelvin
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type :: tParameters
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real(pReal) :: &
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D = 1.0_pReal, & !< grain size
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@ -9,9 +9,6 @@
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!--------------------------------------------------------------------------------------------------
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submodule(phase:plastic) dislotwin
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real(pReal), parameter :: &
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kB = 1.38e-23_pReal !< Boltzmann constant in J/Kelvin
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type :: tParameters
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real(pReal) :: &
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Q_cl = 1.0_pReal, & !< activation energy for dislocation climb
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@ -31,7 +28,7 @@ submodule(phase:plastic) dislotwin
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delta_G = 1.0_pReal, & !< Free energy difference between austensite and martensite
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i_tr = 1.0_pReal, & !< adjustment parameter to calculate MFP for transformation
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h = 1.0_pReal, & !< Stack height of hex nucleus
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T_ref = 0.0_pReal, &
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T_ref = T_ROOM, &
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a_cI = 1.0_pReal, &
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a_cF = 1.0_pReal
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real(pReal), dimension(2) :: &
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@ -19,9 +19,6 @@ submodule(phase:plastic) nonlocal
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type(tGeometry), dimension(:), allocatable :: geom
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real(pReal), parameter :: &
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kB = 1.38e-23_pReal !< Boltzmann constant in J/Kelvin
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! storage order of dislocation types
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integer, dimension(*), parameter :: &
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sgl = [1,2,3,4,5,6,7,8] !< signed (single)
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