def add_to_cmf_dict(bar=None, cieobs='indv', K=683, M=np.eye(3)):
"""
Add set of cmfs to _CMF dict.
Args:
:bar:
| None, optional
| Set of CMFs. None: initializes to empty ndarray.
:cieobs:
| 'indv' or str, optional
| Name of CMF set.
:K:
| 683 (lm/W), optional
| Conversion factor from radiometric to photometric quantity.
:M:
| np.eye, optional
| Matrix for lms to xyz conversion.
"""
if bar is None:
wl3 = getwlr(_WL3)
bar = np.vstack((wl3, np.empty((3, wl3.shape[0]))))
_CMF['types'].append(cieobs)
_CMF[cieobs] = {'bar': bar}
_CMF[cieobs]['K'] = K
_CMF[cieobs]['M'] = M
def mutation(Xp, options):
"""
Performs mutation in the individuals.
| The mutation is one of the operators responsible for random changes in
| the individuals. Each parent x will have a new individual, called trial
| vector u, after the mutation.
| To do that, pick up two random individuals from the population, x2 and
| x3, and creates a difference vector v = x2 - x3. Then, chooses another
| point, called base vector, xb, and creates the trial vector by
|
| u = xb + F*v = xb + F*(x2 - x3)
|
| wherein F is an internal parameter, called scale factor.
Args:
:Xp:
| a n x mu ndarray with mu "parents" and of dimension n
:options:
| the dict with the internal parameters
Returns:
:Xo:
| a n x mu ndarray with the mu mutated individuals (of dimension n)
"""
# Creates a mu x mu matrix of 1:n elements on each row
A = np.arange(options['mu']).repeat(options['mu']).reshape(options['mu'],options['mu']).T
# Now, one removes the diagonal of A, because it contains indexes that repeat
# the current i-th individual
A = np.reshape(A[(np.eye(A.shape[0]))==False],(options['mu'],options['mu']-1))
# Now, creates a matrix that permutes the elements of A randomly
J = np.argsort(np.random.rand(*A.shape), axis = 1)
# J = getdata('J.txt')-1
Ilin = J*options['mu'] + np.arange(options['mu'])[:,None]
A = A.T.flatten()[Ilin].reshape(A.shape)
# Chooses three random points (for each row)
xbase = Xp[:, A[:,0]] #base vectors
v = Xp[:, A[:,1]] - Xp[:, A[:,2]] #difference vector
# Performs the mutation
Xo = xbase + options['F']*v
return Xo
def mahalanobis2(x, y = None, z = None, mu = None, sigmainv = None):
"""
Evaluate the squared mahalanobis distance
Args:
:x:
| scalar or list or ndarray (.ndim = 1 or 2) with x(y)-coordinates
at which to evaluate the mahalanobis distance squared.
:y:
| None or scalar or list or ndarray (.ndim = 1) with y-coordinates
at which to evaluate the mahalanobis distance squared, optional.
| If :y: is None, :x: should be a 2d array.
:z:
| None or scalar or list or ndarray (.ndim = 1) with z-coordinates
at which to evaluate the mahalanobis distance squared, optional.
| If :z: is None & :y: is None, then :x: should be a 2d array.
:mu:
| None or ndarray (.ndim = 1) with center coordinates of the
mahalanobis ellipse, optional.
| None defaults to zeros(2) or zeros(3).
:sigmainv:
| None or ndarray with 'inverse covariance matrix', optional
| Determines the shape and orientation of the PD.
| None default to np.eye(2) or eye(3).
Returns:
:returns:
| ndarray with magnitude of mahalanobis2(x,y[,z])
"""
if (y is None) & (z is None):
p = x.shape[-1]
elif (z is None):
p = x.shape[-1] if (y is None) else 2
elif (z is not None):
p = 3 if (y is not None) else 2
if mu is None:
mu = np.zeros(p)
if sigmainv is None:
sigmainv = np.eye(p)
x = np2d(x)
mu = np2d(mu)
if (y is None) & (z is None):
x = x - mu
if p == 2:
x, y = asplit(x)
elif p==3:
x, y, z = asplit(x)
elif (z is None):
if y is None:
x = x - mu
x, y = asplit(x)
else:
x = x - mu[...,0] # center data on mu
y = np2d(y) - mu[...,1] # center data on mu
elif (z is not None):
if (y is not None):
x = x - mu[0] # center data on mu
y = np2d(y) - mu[...,1] # center data on mu
z = np2d(z) - mu[...,2] # center data on mu
else:
x = x - mu[...,0] # center data on mu
y = np2d(z) - mu[...,1] # center data on mu
if p == 2:
return (sigmainv[0,0] * (x**2.0) + sigmainv[1,1] * (y**2.0) + 2.0*sigmainv[0,1]*(x*y))
else:
return (sigmainv[0,0] * (x**2.0) + sigmainv[1,1] * (y**2.0) + 2.0*sigmainv[0,1]*(x*y) +
sigmainv[2,2] * (z**2.0) + 2.0*sigmainv[0,2]*(x*z) + 2.0*sigmainv[1,2]*(y*z))
def symmM_to_posdefM(A = None, atol = 1.0e-9, rtol = 1.0e-9, method = 'make', forcesymm = True):
"""
Convert a symmetric matrix to a positive definite one.
Args:
:A:
| ndarray
:atol:
| float, optional
| The absolute tolerance parameter (see Notes of numpy.allclose())
:rtol:
| float, optional
| The relative tolerance parameter (see Notes of numpy.allclose())
:method:
| 'make' or 'nearest', optional (see notes for more info)
:forcesymm:
| True or False, optional
| If A is not symmetric, force symmetry using:
| A = numpy.triu(A) + numpy.triu(A).T - numpy.diag(numpy.diag(A))
Returns:
:returns:
| ndarray with positive-definite matrix.
Notes on supported methods:
1. `'make': A Python/Numpy port of Muhammad Asim Mubeen's matlab function
Spd_Mat.m
<https://nl.mathworks.com/matlabcentral/fileexchange/45873-positive-definite-matrix>`_
2. `'nearest': A Python/Numpy port of John D'Errico's `nearestSPD`
MATLAB code.
<https://stackoverflow.com/questions/43238173/python-convert-matrix-to-positive-semi-definite>`_
"""
if A is not None:
A = np2d(A)
# Make sure matrix A is symmetric up to a certain tolerance:
sn = check_symmetric(A, atol = atol, rtol = rtol)
if ((A.shape[0] != A.shape[1]) | (sn != True)):
if (forcesymm == True) & (A.shape[0] == A.shape[1]):
A = np.triu(A) + np.triu(A).T - np.diag(np.diag(A))
else:
raise Exception('symmM_to_posdefM(): matrix A not symmetric.')
if check_posdef(A, atol = atol, rtol = rtol) == True:
return A
else:
if method == 'make':
# A Python/Numpy port of Muhammad Asim Mubeen's matlab function Spd_Mat.m
#
# See: https://nl.mathworks.com/matlabcentral/fileexchange/45873-positive-definite-matrix
Val, Vec = np.linalg.eig(A)
Val = np.real(Val)
Vec = np.real(Vec)
Val[np.where(Val==0)] = _EPS #making zero eigenvalues non-zero
p = np.where(Val<0)
Val[p] = -Val[p] #making negative eigenvalues positive
return np.dot(Vec,np.dot(np.diag(Val) , Vec.T))
elif method == 'nearest':
# A Python/Numpy port of John D'Errico's `nearestSPD` MATLAB code [1], which
# credits [2].
#
# [1] https://www.mathworks.com/matlabcentral/fileexchange/42885-nearestspd
#
# [2] N.J. Higham, "Computing a nearest symmetric positive semidefinite
# matrix" (1988): https://doi.org/10.1016/0024-3795(88)90223-6
#
# See: https://stackoverflow.com/questions/43238173/python-convert-matrix-to-positive-semi-definite
B = (A + A.T) / 2.0
_, s, V = np.linalg.svd(B)
H = np.dot(V.T, np.dot(np.diag(s), V))
A2 = (B + H) / 2.0
A3 = (A2 + A2.T) / 2.0
if check_posdef(A3, atol = atol, rtol = rtol) == True:
return A3
spacing = np.spacing(np.linalg.norm(A))
I = np.eye(A.shape[0])
k = 1
while not check_posdef(A3, atol = atol, rtol = rtol):
mineig = np.min(np.real(np.linalg.eigvals(A3)))
A3 += I * (-mineig * k**2.0+ spacing)
k += 1
return A3
def cam18sl(data,
datab=None,
Lb=[100],
fov=10.0,
inputtype='xyz',
direction='forward',
outin='Q,aS,bS',
parameters=None):
"""
Convert between CIE 2006 10° XYZ tristimulus values (or spectral data)
and CAM18sl color appearance correlates.
Args:
:data:
| ndarray of CIE 2006 10° absolute XYZ tristimulus values or spectral data
| or color appearance attributes of stimulus
:datab:
| ndarray of CIE 2006 10° absolute XYZ tristimulus values or spectral data
| of stimulus background
:Lb:
| [100], optional
| Luminance (cd/m²) value(s) of background(s) calculated using the CIE 2006 10° CMFs
| (only used in case datab == None and the background is assumed to be an Equal-Energy-White)
:fov:
| 10.0, optional
| Field-of-view of stimulus (for size effect on brightness)
:inputtpe:
| 'xyz' or 'spd', optional
| Specifies the type of input:
| tristimulus values or spectral data for the forward mode.
:direction:
| 'forward' or 'inverse', optional
| -'forward': xyz -> cam18sl
| -'inverse': cam18sl -> xyz
:outin:
| 'Q,aS,bS' or str, optional
| 'Q,aS,bS' (brightness and opponent signals for saturation)
| other options: 'Q,aM,bM' (colorfulness)
| (Note that 'Q,aW,bW' would lead to a Cartesian
| a,b-coordinate system centered at (1,0))
| Str specifying the type of
| input (:direction: == 'inverse') and
| output (:direction: == 'forward')
:parameters:
| None or dict, optional
| Set of model parameters.
| - None: defaults to luxpy.cam._CAM18SL_PARAMETERS
| (see references below)
Returns:
:returns:
| ndarray with color appearance correlates (:direction: == 'forward')
| or
| XYZ tristimulus values (:direction: == 'inverse')
Notes:
| * Instead of using the CIE 1964 10° CMFs in some places of the model,
| the CIE 2006 10° CMFs are used througout, making it more self_consistent.
| This has an effect on the k scaling factors (now different those in CAM15u)
| and the illuminant E normalization for use in the chromatic adaptation transform.
| (see future erratum to Hermans et al., 2018)
| * The paper also used an equation for the amount of white W, which is
| based on a Q value not expressed in 'bright' ('cA' = 0.937 instead of 123).
| This has been corrected for in the luxpy version of the model, i.e.
| _CAM18SL_PARAMETERS['cW'][0] has been changed from 2.29 to 1/11672.
| (see future erratum to Hermans et al., 2018)
| * Default output was 'Q,aW,bW' prior to March 2020, but since this
| is an a,b Cartesian system centered on (1,0), the default output
| has been changed to 'Q,aS,bS'.
References:
1. `Hermans, S., Smet, K. A. G., & Hanselaer, P. (2018).
"Color appearance model for self-luminous stimuli."
Journal of the Optical Society of America A, 35(12), 2000–2009.
<https://doi.org/10.1364/JOSAA.35.002000>`_
"""
if parameters is None:
parameters = _CAM18SL_PARAMETERS
outin = outin.split(',')
#unpack model parameters:
cA, cAlms, cHK, cM, cW, ca, calms, cb, cblms, cfov, cieobs, k, naka, unique_hue_data = [
parameters[x] for x in sorted(parameters.keys())
]
# precomputations:
Mlms2xyz = np.linalg.inv(_CMF[cieobs]['M'])
MAab = np.array([cAlms, calms, cblms])
invMAab = np.linalg.inv(MAab)
#-------------------------------------------------
# setup EEW reference field and default background field (Lr should be equal to Lb):
# Get Lb values:
if datab is not None:
if inputtype != 'xyz':
Lb = spd_to_xyz(datab, cieobs=cieobs, relative=False)[..., 1:2]
else:
Lb = datab[..., 1:2]
else:
if isinstance(Lb, list):
Lb = np2dT(Lb)
# Setup EEW ref of same luminance as datab:
if inputtype == 'xyz':
wlr = getwlr(_CAM18SL_WL3)
else:
if datab is None:
wlr = data[0] # use wlr of stimulus data
else:
wlr = datab[0] # use wlr of background data
datar = np.vstack((wlr, np.ones(
(Lb.shape[0], wlr.shape[0])))) # create eew
xyzr = spd_to_xyz(datar, cieobs=cieobs,
relative=False) # get abs. tristimulus values
datar[1:] = datar[1:] / xyzr[..., 1:2] * Lb
# Create datab if None:
if (datab is None):
if inputtype != 'xyz':
datab = datar.copy()
else:
datab = spd_to_xyz(datar, cieobs=cieobs, relative=False)
# prepare data and datab for loop over backgrounds:
# make axis 1 of datab have 'same' dimensions as data:
if (data.ndim == 2):
data = np.expand_dims(data, axis=1) # add light source axis 1
if inputtype == 'xyz':
datar = spd_to_xyz(datar, cieobs=cieobs,
relative=False) # convert to xyz!!
if datab.shape[
0] == 1: #make datab and datar have same lights source dimension (used to store different backgrounds) size as data
datab = np.repeat(datab, data.shape[1], axis=0)
datar = np.repeat(datar, data.shape[1], axis=0)
else:
if datab.shape[0] == 2:
datab = np.vstack(
(datab[0], np.repeat(datab[1:], data.shape[1], axis=0)))
if datar.shape[0] == 2:
datar = np.vstack(
(datar[0], np.repeat(datar[1:], data.shape[1], axis=0)))
# Flip light source/ background dim to axis 0:
data = np.transpose(data, axes=(1, 0, 2))
#-------------------------------------------------
#initialize camout:
dshape = list(data.shape)
dshape[-1] = len(outin) # requested number of correlates
if (inputtype != 'xyz') & (direction == 'forward'):
dshape[-2] = dshape[
-2] - 1 # wavelength row doesn't count & only with forward can the input data be spectral
camout = np.zeros(dshape)
camout.fill(np.nan)
for i in range(data.shape[0]):
# get rho, gamma, beta of background and reference white:
if (inputtype != 'xyz'):
xyzb = spd_to_xyz(np.vstack((datab[0], datab[i + 1:i + 2, :])),
cieobs=cieobs,
relative=False)
xyzr = spd_to_xyz(np.vstack((datar[0], datar[i + 1:i + 2, :])),
cieobs=cieobs,
relative=False)
else:
xyzb = datab[i:i + 1, :]
xyzr = datar[i:i + 1, :]
lmsb = np.dot(_CMF[cieobs]['M'], xyzb.T).T # convert to l,m,s
rgbb = (lmsb / _CMF[cieobs]['K']) * k # convert to rho, gamma, beta
#lmsr = np.dot(_CMF[cieobs]['M'],xyzr.T).T # convert to l,m,s
#rgbr = (lmsr / _CMF[cieobs]['K']) * k # convert to rho, gamma, beta
#rgbr = rgbr/rgbr[...,1:2]*Lb[i] # calculated EEW cone excitations at same luminance values as background
rgbr = np.ones(xyzr.shape) * Lb[
i] # explicitely equal EEW cone excitations at same luminance values as background
if direction == 'forward':
# get rho, gamma, beta of stimulus:
if (inputtype != 'xyz'):
xyz = spd_to_xyz(data[i], cieobs=cieobs, relative=False)
elif (inputtype == 'xyz'):
xyz = data[i]
lms = np.dot(_CMF[cieobs]['M'], xyz.T).T # convert to l,m,s
rgb = (lms / _CMF[cieobs]['K']) * k # convert to rho, gamma, beta
# apply von-kries cat with D = 1:
if (rgbb == 0).any():
Mcat = np.eye(3)
else:
Mcat = np.diag((rgbr / rgbb)[0])
rgba = np.dot(Mcat, rgb.T).T
# apply naka-rushton compression:
rgbc = naka_rushton(rgba,
n=naka['n'],
sig=naka['sig'](rgbr.mean()),
noise=naka['noise'],
scaling=naka['scaling'])
#rgbc = np.ones(rgbc.shape)*rgbc.mean() # test if eew ends up at origin
# calculate achromatic and color difference signals, A, a, b:
Aab = np.dot(MAab, rgbc.T).T
A, a, b = asplit(Aab)
a = ca * a
b = cb * b
# calculate colorfullness like signal M:
M = cM * ((a**2.0 + b**2.0)**0.5)
# calculate brightness Q:
Q = cA * (
A + cHK[0] * M**cHK[1]
) # last term is contribution of Helmholtz-Kohlrausch effect on brightness
# calculate saturation, s:
s = M / Q
S = s # make extra variable, jsut in case 'S' is called
# calculate amount of white, W:
W = 1 / (1.0 + cW[0] * (s**cW[1]))
# adjust Q for size (fov) of stimulus (matter of debate whether to do this before or after calculation of s or W, there was no data on s, M or W for different sized stimuli: after)
Q = Q * (fov / 10.0)**cfov
# calculate hue, h and Hue quadrature, H:
h = hue_angle(a, b, htype='deg')
if 'H' in outin:
H = hue_quadrature(h, unique_hue_data=unique_hue_data)
else:
H = None
# calculate cart. co.:
if 'aM' in outin:
aM = M * np.cos(h * np.pi / 180.0)
bM = M * np.sin(h * np.pi / 180.0)
if 'aS' in outin:
aS = s * np.cos(h * np.pi / 180.0)
bS = s * np.sin(h * np.pi / 180.0)
if 'aW' in outin:
aW = W * np.cos(h * np.pi / 180.0)
bW = W * np.sin(h * np.pi / 180.0)
if (outin != ['Q', 'as', 'bs']):
camout[i] = eval('ajoin((' + ','.join(outin) + '))')
else:
camout[i] = ajoin((Q, aS, bS))
elif direction == 'inverse':
# get Q, M and a, b depending on input type:
if 'aW' in outin:
Q, a, b = asplit(data[i])
Q = Q / (
(fov / 10.0)**cfov
) #adjust Q for size (fov) of stimulus back to that 10° ref
W = (a**2.0 + b**2.0)**0.5
s = (((1.0 / W) - 1.0) / cW[0])**(1.0 / cW[1])
M = s * Q
if 'aM' in outin:
Q, a, b = asplit(data[i])
Q = Q / (
(fov / 10.0)**cfov
) #adjust Q for size (fov) of stimulus back to that 10° ref
M = (a**2.0 + b**2.0)**0.5
if 'aS' in outin:
Q, a, b = asplit(data[i])
Q = Q / (
(fov / 10.0)**cfov
) #adjust Q for size (fov) of stimulus back to that 10° ref
s = (a**2.0 + b**2.0)**0.5
M = s * Q
if 'h' in outin:
Q, WsM, h = asplit(data[i])
Q = Q / (
(fov / 10.0)**cfov
) #adjust Q for size (fov) of stimulus back to that 10° ref
if 'W' in outin:
s = (((1.0 / WsM) - 1.0) / cW[0])**(1.0 / cW[1])
M = s * Q
elif 's' in outin:
M = WsM * Q
elif 'M' in outin:
M = WsM
# calculate achromatic signal, A from Q and M:
A = Q / cA - cHK[0] * M**cHK[1]
# calculate hue angle:
h = hue_angle(a, b, htype='rad')
# calculate a,b from M and h:
a = (M / cM) * np.cos(h)
b = (M / cM) * np.sin(h)
a = a / ca
b = b / cb
# create Aab:
Aab = ajoin((A, a, b))
# calculate rgbc:
rgbc = np.dot(invMAab, Aab.T).T
# decompress rgbc to (adapted) rgba :
rgba = naka_rushton(rgbc,
n=naka['n'],
sig=naka['sig'](rgbr.mean()),
noise=naka['noise'],
scaling=naka['scaling'],
direction='inverse')
# apply inverse von-kries cat with D = 1:
rgb = np.dot(np.diag((rgbb / rgbr)[0]), rgba.T).T
# convert rgb to lms to xyz:
lms = rgb / k * _CMF[cieobs]['K']
xyz = np.dot(Mlms2xyz, lms.T).T
camout[i] = xyz
camout = np.transpose(camout, axes=(1, 0, 2))
if camout.shape[1] == 1:
camout = np.squeeze(camout, axis=1)
return camout