DAMASK_EICMD/python/damask/_colormap.py

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import os
import json
import functools
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import colorsys
from typing import Optional, Union
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from itertools import chain
import numpy as np
import scipy.interpolate as interp
import matplotlib as mpl
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if os.name == 'posix' and 'DISPLAY' not in os.environ:
mpl.use('Agg')
import matplotlib.pyplot as plt
from matplotlib import cm
from PIL import Image
from ._typehints import FloatSequence, FileHandle
from . import util
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from . import Table
_EPS = 216./24389.
_KAPPA = 24389./27.
_REF_WHITE = np.array([.95047, 1.00000, 1.08883]) # Observer = 2, Illuminant = D65
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# ToDo (if needed)
# - support alpha channel (paraview/ASCII/input)
# - support NaN color (paraview)
class Colormap(mpl.colors.ListedColormap):
"""
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Enhance matplotlib colormap functionality for use within DAMASK.
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Colors are internally stored as R(ed) G(green) B(lue) values.
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A colormap can be used in matplotlib, seaborn, etc., or can be
exported to file for external use.
References
----------
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K. Moreland, Proceedings of the 5th International Symposium on Advances in Visual Computing, 2009
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https://doi.org/10.1007/978-3-642-10520-3_9
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P. Eisenlohr et al., International Journal of Plasticity 46:3753, 2013
https://doi.org/10.1016/j.ijplas.2012.09.012
Matplotlib colormaps overview
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https://matplotlib.org/stable/tutorials/colors/colormaps.html
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"""
def __init__(self,
colors: np.ndarray, name: str):
"""
New colormap.
Parameters
----------
colors : numpy.ndarray, shape (:,3) or (:,4)
Color specifications as RGB(A) values.
name : str
String to identify the colormap.
"""
super().__init__(colors,name)
self.colors: np.ndarray = np.asarray(colors)
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def __eq__(self,
other: object) -> bool:
"""
Return self==other.
Test equality of other.
"""
if not isinstance(other, Colormap):
return NotImplemented
return np.array_equal(self.colors,other.colors)
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def __add__(self,
other: 'Colormap') -> 'Colormap':
"""
Return self+other.
Concatenate.
"""
return Colormap(np.vstack((self.colors,other.colors)),
f'{self.name}+{other.name}')
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def __iadd__(self,
other: 'Colormap') -> 'Colormap':
"""
Return self+=other.
Concatenate (in-place).
"""
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return self.__add__(other)
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def __mul__(self,
factor: int) -> 'Colormap':
"""
Return self*other.
Repeat.
"""
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return Colormap(np.vstack([self.colors]*factor),f'{self.name}*{factor}')
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def __imul__(self,
factor: int) -> 'Colormap':
"""
Return self*=other.
Repeat (in-place).
"""
return self.__mul__(factor)
def __invert__(self) -> 'Colormap':
"""
Return ~self.
Reverse.
"""
return self.reversed()
def __repr__(self) -> str:
"""
Return repr(self).
Show as matplotlib figure.
"""
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fig = plt.figure(self.name,figsize=(5,.5))
ax1 = fig.add_axes((0, 0, 1, 1))
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ax1.set_axis_off()
ax1.imshow(np.linspace(0,1,self.N).reshape(1,-1),
aspect='auto', cmap=self, interpolation='nearest')
plt.show(block=False)
return f'Colormap: {self.name}'
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@staticmethod
def from_range(low: FloatSequence,
high: FloatSequence,
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name: str = 'DAMASK colormap',
N: int = 256,
model: str = 'rgb') -> 'Colormap':
"""
Create a perceptually uniform colormap between given (inclusive) bounds.
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Parameters
----------
low : sequence of float, len (3)
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Color definition for minimum value.
high : sequence of float, len (3)
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Color definition for maximum value.
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name : str, optional
Name of the colormap. Defaults to 'DAMASK colormap'.
N : int, optional
Number of color quantization levels. Defaults to 256.
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model : {'rgb', 'hsv', 'hsl', 'xyz', 'lab', 'msh'}
Color model used for input color definitions. Defaults to 'rgb'.
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The available color models are:
- 'rgb': Red Green Blue.
- 'hsv': Hue Saturation Value.
- 'hsl': Hue Saturation Luminance.
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- 'xyz': CIE Xyz.
- 'lab': CIE Lab.
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- 'msh': Msh (for perceptually uniform interpolation).
Returns
-------
new : damask.Colormap
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Colormap spanning given bounds.
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Examples
--------
>>> import damask
>>> damask.Colormap.from_range((0,0,1),(0,0,0),'blue_to_black')
"""
toMsh = dict(
rgb=Colormap._rgb2msh,
hsv=Colormap._hsv2msh,
hsl=Colormap._hsl2msh,
xyz=Colormap._xyz2msh,
lab=Colormap._lab2msh,
msh=lambda x:x,
)
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if model.lower() not in toMsh:
raise ValueError(f'invalid color model "{model}"')
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low_high = np.vstack((low,high)).astype(float)
out_of_bounds = np.bool_(False)
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if model.lower() == 'rgb':
out_of_bounds = np.any(low_high<0) or np.any(low_high>1)
elif model.lower() == 'hsv':
out_of_bounds = np.any(low_high<0) or np.any(low_high>[360,1,1])
elif model.lower() == 'hsl':
out_of_bounds = np.any(low_high<0) or np.any(low_high>[360,1,1])
elif model.lower() == 'lab':
out_of_bounds = np.any(low_high[:,0]<0)
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if out_of_bounds:
raise ValueError(f'{model.upper()} colors {low_high[0]} | {low_high[1]} are out of bounds')
low_,high_ = map(toMsh[model.lower()],low_high)
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msh = map(functools.partial(Colormap._interpolate_msh,low=low_,high=high_),np.linspace(0,1,N))
rgb = np.array(list(map(Colormap._msh2rgb,msh)))
return Colormap(rgb,name=name)
@staticmethod
def from_predefined(name: str,
N: int = 256) -> 'Colormap':
"""
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Select from a set of predefined colormaps.
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Predefined colormaps (Colormap.predefined) include
native matplotlib colormaps and common DAMASK colormaps.
Parameters
----------
name : str
Name of the colormap.
N : int, optional
Number of color quantization levels. Defaults to 256.
This parameter is not used for matplotlib colormaps
that are of type `ListedColormap`.
Returns
-------
new : damask.Colormap
Predefined colormap.
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Examples
--------
>>> import damask
>>> damask.Colormap.from_predefined('strain')
"""
try:
# matplotlib presets
colormap = cm.__dict__[name]
return Colormap(np.array(list(map(colormap,np.linspace(0,1,N)))
if isinstance(colormap,mpl.colors.LinearSegmentedColormap) else
colormap.colors),
name=name)
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except KeyError:
# DAMASK presets
definition = Colormap._predefined_DAMASK[name]
return Colormap.from_range(definition['low'],definition['high'],name,N)
def at(self,
fraction : Union[float,FloatSequence]) -> np.ndarray:
"""
Interpolate color at fraction.
Parameters
----------
fraction : (sequence of) float
Fractional coordinate(s) to evaluate Colormap at.
Returns
-------
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color : numpy.ndarray, shape(...,4)
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RGBA values of interpolated color(s).
Examples
--------
>>> import damask
>>> cmap = damask.Colormap.from_predefined('gray')
>>> cmap.at(0.5)
array([0.5, 0.5, 0.5, 1. ])
>>> 'rgb({},{},{})'.format(*cmap.at(0.5))
'rgb(0.5,0.5,0.5)'
"""
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return interp.interp1d(np.linspace(0,1,self.N),
self.colors,
axis=0,
assume_sorted=True)(fraction)
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def shade(self,
field: np.ndarray,
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bounds: Optional[FloatSequence] = None,
gap: Optional[float] = None) -> Image.Image:
"""
Generate PIL image of 2D field using colormap.
Parameters
----------
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field : numpy.ndarray, shape (:,:)
Data to be shaded.
bounds : sequence of float, len (2), optional
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Value range (left,right) spanned by colormap.
gap : field.dtype, optional
Transparent value. NaN will always be rendered transparent.
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Defaults to None.
Returns
-------
PIL.Image
RGBA image of shaded data.
"""
mask = np.logical_not(np.isnan(field) if gap is None else
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np.logical_or(np.isnan(field), field == gap)) # mask NaN (and gap if present)
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l,r = (field[mask].min(),field[mask].max()) if bounds is None else \
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(bounds[0],bounds[1])
if abs(delta := r-l) * 1e8 <= (avg := 0.5*abs(r+l)): # delta is similar to numerical noise
l,r = (l-0.5*avg*np.sign(delta),r+0.5*avg*np.sign(delta)) # extend range to have actual data centered within
field_ = np.nan_to_num(field, nan=(l+r)/2, posinf=r, neginf=l)
return Image.fromarray(
(np.dstack((
self.colors[np.round(np.clip((field_-l)/(r-l),0.0,1.0)*(self.N-1)).astype(np.uint16),:3],
mask.astype(float)
)
)*255
).astype(np.uint8),
mode='RGBA')
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def reversed(self,
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name: Optional[str] = None) -> 'Colormap':
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"""
Reverse.
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Parameters
----------
name : str, optional
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Name of the reversed colormap.
Defaults to parent colormap name + '_r'.
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Returns
-------
damask.Colormap
Reversed colormap.
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Examples
--------
>>> import damask
>>> damask.Colormap.from_predefined('stress').reversed()
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Colormap: stress_r
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"""
rev = super().reversed(name)
return Colormap(np.array(rev.colors),rev.name[:-4] if rev.name.endswith('_r_r') else rev.name)
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def save_paraview(self,
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fname: Optional[FileHandle] = None):
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"""
Save as JSON file for use in Paraview.
Parameters
----------
fname : file, str, or pathlib.Path, optional
File to store results. Defaults to colormap name + '.json'.
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"""
out = [{
'Creator':util.execution_stamp('Colormap'),
'ColorSpace':'RGB',
'Name':self.name,
'DefaultMap':True,
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'RGBPoints':list(chain.from_iterable([(i,*c) for i,c in enumerate(self.colors.round(6))]))
}]
with util.open_text(self.name.replace(' ','_')+'.json' if fname is None else fname, 'w') as fhandle:
json.dump(out,fhandle,indent=4)
fhandle.write('\n')
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def save_ASCII(self,
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fname: Optional[FileHandle] = None):
"""
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Save as ASCII file.
Parameters
----------
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fname : file, str, or pathlib.Path, optional
File to store results. Defaults to colormap name + '.txt'.
"""
labels = {'RGBA':4} if self.colors.shape[1] == 4 else {'RGB': 3}
t = Table(labels,self.colors,[f'Creator: {util.execution_stamp("Colormap")}'])
with util.open_text(self.name.replace(' ','_')+'.txt' if fname is None else fname, 'w') as fhandle:
t.save(fhandle)
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def save_GOM(self, fname: Optional[FileHandle] = None):
"""
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Save as ASCII file for use in GOM Aramis.
Parameters
----------
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fname : file, str, or pathlib.Path, optional
File to store results. Defaults to colormap name + '.legend'.
"""
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# ToDo: test in GOM
GOM_str = '1 1 {name} 9 {name} '.format(name=self.name.replace(" ","_")) \
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+ '0 1 0 3 0 0 -1 9 \\ 0 0 0 255 255 255 0 0 255 ' \
+ f'30 NO_UNIT 1 1 64 64 64 255 1 0 0 0 0 0 0 3 0 {self.N}' \
+ ' '.join([f' 0 {c[0]} {c[1]} {c[2]} 255 1' for c in reversed((self.colors*255).astype(np.int64))]) \
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+ '\n'
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with util.open_text(self.name.replace(' ','_')+'.legend' if fname is None else fname, 'w') as fhandle:
fhandle.write(GOM_str)
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def save_gmsh(self,
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fname: Optional[FileHandle] = None):
"""
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Save as ASCII file for use in gmsh.
Parameters
----------
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fname : file, str, or pathlib.Path, optional
File to store results. Defaults to colormap name + '.msh'.
"""
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# ToDo: test in gmsh
gmsh_str = 'View.ColorTable = {\n' \
+'\n'.join([f'{c[0]},{c[1]},{c[2]},' for c in self.colors[:,:3]*255]) \
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+'\n}\n'
with util.open_text(self.name.replace(' ','_')+'.msh' if fname is None else fname, 'w') as fhandle:
fhandle.write(gmsh_str)
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@staticmethod
def _interpolate_msh(frac: float,
low: np.ndarray,
high: np.ndarray) -> np.ndarray:
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"""
Interpolate in Msh color space.
This interpolation gives a perceptually uniform colormap.
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References
----------
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| https://www.kennethmoreland.com/color-maps/ColorMapsExpanded.pdf
| https://www.kennethmoreland.com/color-maps/diverging_map.py
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"""
def rad_diff(a,b):
return abs(a[2]-b[2])
def adjust_hue(msh_sat, msh_unsat):
"""If saturation of one of the two colors is much less than the other, hue of the less."""
if msh_sat[0] >= msh_unsat[0]:
return msh_sat[2]
hSpin = msh_sat[1]/np.sin(msh_sat[1])*np.sqrt(msh_unsat[0]**2.0-msh_sat[0]**2)/msh_sat[0]
if msh_sat[2] < - np.pi/3.0: hSpin *= -1.0
return msh_sat[2] + hSpin
lo = np.array(low)
hi = np.array(high)
if (lo[1] > 0.05 and hi[1] > 0.05 and rad_diff(lo,hi) > np.pi/3.0):
M_mid = max(lo[0],hi[0],88.0)
if frac < 0.5:
hi = np.array([M_mid,0.0,0.0])
frac *= 2.0
else:
lo = np.array([M_mid,0.0,0.0])
frac = 2.0*frac - 1.0
if lo[1] < 0.05 < hi[1]:
lo[2] = adjust_hue(hi,lo)
elif hi[1] < 0.05 < lo[1]:
hi[2] = adjust_hue(lo,hi)
return (1.0 - frac) * lo + frac * hi
_predefined_mpl= {'Perceptually Uniform Sequential': [
'viridis', 'plasma', 'inferno', 'magma', 'cividis'],
'Sequential': [
'Greys', 'Purples', 'Blues', 'Greens', 'Oranges', 'Reds',
'YlOrBr', 'YlOrRd', 'OrRd', 'PuRd', 'RdPu', 'BuPu',
'GnBu', 'PuBu', 'YlGnBu', 'PuBuGn', 'BuGn', 'YlGn'],
'Sequential (2)': [
'binary', 'gist_yarg', 'gist_gray', 'gray', 'bone', 'pink',
'spring', 'summer', 'autumn', 'winter', 'cool', 'Wistia',
'hot', 'afmhot', 'gist_heat', 'copper'],
'Diverging': [
'PiYG', 'PRGn', 'BrBG', 'PuOr', 'RdGy', 'RdBu',
'RdYlBu', 'RdYlGn', 'Spectral', 'coolwarm', 'bwr', 'seismic'],
'Cyclic': ['twilight', 'twilight_shifted', 'hsv'],
'Qualitative': [
'Pastel1', 'Pastel2', 'Paired', 'Accent',
'Dark2', 'Set1', 'Set2', 'Set3',
'tab10', 'tab20', 'tab20b', 'tab20c'],
'Miscellaneous': [
'flag', 'prism', 'ocean', 'gist_earth', 'terrain', 'gist_stern',
'gnuplot', 'gnuplot2', 'CMRmap', 'cubehelix', 'brg',
'gist_rainbow', 'rainbow', 'jet', 'nipy_spectral', 'gist_ncar']}
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_predefined_DAMASK = {'orientation': {'low': [0.933334,0.878432,0.878431], # noqa
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'high': [0.250980,0.007843,0.000000]},
'strain': {'low': [0.941177,0.941177,0.870588],
'high': [0.266667,0.266667,0.000000]},
'stress': {'low': [0.878432,0.874511,0.949019],
'high': [0.000002,0.000000,0.286275]}}
predefined = dict(**{'DAMASK':list(_predefined_DAMASK)},**_predefined_mpl)
@staticmethod
def _hsv2rgb(hsv: np.ndarray) -> np.ndarray:
"""
Hue Saturation Value to Red Green Blue.
Parameters
----------
hsv : numpy.ndarray, shape (3)
HSV values.
Returns
-------
rgb : numpy.ndarray, shape (3)
RGB values.
"""
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return np.array(colorsys.hsv_to_rgb(hsv[0]/360.,hsv[1],hsv[2]))
@staticmethod
def _rgb2hsv(rgb: np.ndarray) -> np.ndarray:
"""
Red Green Blue to Hue Saturation Value.
Parameters
----------
rgb : numpy.ndarray, shape (3)
RGB values.
Returns
-------
hsv : numpy.ndarray, shape (3)
HSV values.
"""
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h,s,v = colorsys.rgb_to_hsv(rgb[0],rgb[1],rgb[2])
return np.array([h*360,s,v])
@staticmethod
def _hsl2rgb(hsl: np.ndarray) -> np.ndarray:
"""
Hue Saturation Luminance to Red Green Blue.
Parameters
----------
hsl : numpy.ndarray, shape (3)
HSL values.
Returns
-------
rgb : numpy.ndarray, shape (3)
RGB values.
"""
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return np.array(colorsys.hls_to_rgb(hsl[0]/360.,hsl[2],hsl[1]))
@staticmethod
def _rgb2hsl(rgb: np.ndarray) -> np.ndarray:
"""
Red Green Blue to Hue Saturation Luminance.
Parameters
----------
rgb : numpy.ndarray, shape (3)
RGB values.
Returns
-------
hsl : numpy.ndarray, shape (3)
HSL values.
"""
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h,l,s = colorsys.rgb_to_hls(rgb[0],rgb[1],rgb[2])
return np.array([h*360,s,l])
@staticmethod
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def _xyz2rgb(xyz: np.ndarray) -> np.ndarray:
"""
CIE Xyz to Red Green Blue.
Parameters
----------
xyz : numpy.ndarray, shape (3)
CIE Xyz values.
Returns
-------
rgb : numpy.ndarray, shape (3)
RGB values.
References
----------
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https://www.easyrgb.com/en/math.php
"""
rgb_lin = np.dot(np.array([
[ 3.240969942,-1.537383178,-0.498610760],
[-0.969243636, 1.875967502, 0.041555057],
[ 0.055630080,-0.203976959, 1.056971514]
]),xyz)
with np.errstate(invalid='ignore'):
rgb = np.where(rgb_lin>0.0031308,rgb_lin**(1.0/2.4)*1.0555-0.0555,rgb_lin*12.92)
return np.clip(rgb,0.,1.)
@staticmethod
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def _rgb2xyz(rgb: np.ndarray) -> np.ndarray:
"""
Red Green Blue to CIE Xyz.
Parameters
----------
rgb : numpy.ndarray, shape (3)
RGB values.
Returns
-------
xyz : numpy.ndarray, shape (3)
CIE Xyz values.
References
----------
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https://www.easyrgb.com/en/math.php
"""
rgb_lin = np.where(rgb>0.04045,((rgb+0.0555)/1.0555)**2.4,rgb/12.92)
return np.dot(np.array([
[0.412390799,0.357584339,0.180480788],
[0.212639006,0.715168679,0.072192315],
[0.019330819,0.119194780,0.950532152]
]),rgb_lin)
@staticmethod
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def _lab2xyz(lab: np.ndarray,
ref_white: np.ndarray = _REF_WHITE) -> np.ndarray:
"""
CIE Lab to CIE Xyz.
Parameters
----------
lab : numpy.ndarray, shape (3)
CIE lab values.
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ref_white : numpy.ndarray, shape (3)
Reference white, default value is the standard 2° observer for D65.
Returns
-------
xyz : numpy.ndarray, shape (3)
CIE Xyz values.
References
----------
http://www.brucelindbloom.com/index.html?Eqn_Lab_to_XYZ.html
"""
f_x = (lab[0]+16.)/116. + lab[1]/500.
f_z = (lab[0]+16.)/116. - lab[2]/200.
return np.array([
f_x**3. if f_x**3. > _EPS else (116.*f_x-16.)/_KAPPA,
((lab[0]+16.)/116.)**3 if lab[0]>_KAPPA*_EPS else lab[0]/_KAPPA,
f_z**3. if f_z**3. > _EPS else (116.*f_z-16.)/_KAPPA
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])*ref_white
@staticmethod
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def _xyz2lab(xyz: np.ndarray,
ref_white: np.ndarray = _REF_WHITE) -> np.ndarray:
"""
CIE Xyz to CIE Lab.
Parameters
----------
xyz : numpy.ndarray, shape (3)
CIE Xyz values.
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ref_white : numpy.ndarray, shape (3)
Reference white, default value is the standard 2° observer for D65.
Returns
-------
lab : numpy.ndarray, shape (3)
CIE lab values.
References
----------
http://www.brucelindbloom.com/index.html?Eqn_Lab_to_XYZ.html
"""
f = np.where(xyz/ref_white > _EPS,(xyz/ref_white)**(1./3.),(_KAPPA*xyz/ref_white+16.)/116.)
return np.array([
116.0 * f[1] - 16.0,
500.0 * (f[0] - f[1]),
200.0 * (f[1] - f[2])
])
@staticmethod
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def _lab2msh(lab: np.ndarray) -> np.ndarray:
"""
CIE Lab to Msh.
Parameters
----------
lab : numpy.ndarray, shape (3)
CIE lab values.
Returns
-------
msh : numpy.ndarray, shape (3)
Msh values.
References
----------
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| https://www.kennethmoreland.com/color-maps/ColorMapsExpanded.pdf
| https://www.kennethmoreland.com/color-maps/diverging_map.py
"""
M = np.linalg.norm(lab)
return np.array([
M,
np.arccos(lab[0]/M) if M>1e-8 else 0.,
np.arctan2(lab[2],lab[1]) if M>1e-8 else 0.,
])
@staticmethod
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def _msh2lab(msh: np.ndarray) -> np.ndarray:
"""
Msh to CIE Lab.
Parameters
----------
msh : numpy.ndarray, shape (3)
Msh values.
Returns
-------
lab : numpy.ndarray, shape (3)
CIE lab values.
References
----------
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| https://www.kennethmoreland.com/color-maps/ColorMapsExpanded.pdf
| https://www.kennethmoreland.com/color-maps/diverging_map.py
"""
return np.array([
msh[0] * np.cos(msh[1]),
msh[0] * np.sin(msh[1]) * np.cos(msh[2]),
msh[0] * np.sin(msh[1]) * np.sin(msh[2])
])
@staticmethod
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def _lab2rgb(lab: np.ndarray) -> np.ndarray:
return Colormap._xyz2rgb(Colormap._lab2xyz(lab))
@staticmethod
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def _rgb2lab(rgb: np.ndarray) -> np.ndarray:
return Colormap._xyz2lab(Colormap._rgb2xyz(rgb))
@staticmethod
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def _msh2rgb(msh: np.ndarray) -> np.ndarray:
return Colormap._lab2rgb(Colormap._msh2lab(msh))
@staticmethod
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def _rgb2msh(rgb: np.ndarray) -> np.ndarray:
return Colormap._lab2msh(Colormap._rgb2lab(rgb))
@staticmethod
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def _hsv2msh(hsv: np.ndarray) -> np.ndarray:
return Colormap._rgb2msh(Colormap._hsv2rgb(hsv))
@staticmethod
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def _hsl2msh(hsl: np.ndarray) -> np.ndarray:
return Colormap._rgb2msh(Colormap._hsl2rgb(hsl))
@staticmethod
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def _xyz2msh(xyz: np.ndarray) -> np.ndarray:
return Colormap._lab2msh(Colormap._xyz2lab(xyz))