def plot_SpikeSlab(parameterized, fignum=None, ax=None, colors=None, side_by_side=True):
"""
Plot latent space X in 1D:
- if fig is given, create input_dim subplots in fig and plot in these
- if ax is given plot input_dim 1D latent space plots of X into each `axis`
- if neither fig nor ax is given create a figure with fignum and plot in there
colors:
colors of different latent space dimensions input_dim
"""
if ax is None:
if side_by_side:
fig = pb.figure(num=fignum, figsize=(16, min(12, (2 * parameterized.mean.shape[1]))))
else:
fig = pb.figure(num=fignum, figsize=(8, min(12, (2 * parameterized.mean.shape[1]))))
if colors is None:
from ..Tango import mediumList
from itertools import cycle
colors = cycle(mediumList)
pb.clf()
else:
colors = iter(colors)
plots = []
means, variances, gamma = parameterized.mean, parameterized.variance, parameterized.binary_prob
x = np.arange(means.shape[0])
for i in range(means.shape[1]):
if side_by_side:
sub1 = (means.shape[1],2,2*i+1)
sub2 = (means.shape[1],2,2*i+2)
else:
sub1 = (means.shape[1]*2,1,2*i+1)
sub2 = (means.shape[1]*2,1,2*i+2)
# mean and variance plot
a = fig.add_subplot(*sub1)
a.plot(means, c='k', alpha=.3)
plots.extend(a.plot(x, means.T[i], c=colors.next(), label=r"$\mathbf{{X_{{{}}}}}$".format(i)))
a.fill_between(x,
means.T[i] - 2 * np.sqrt(variances.T[i]),
means.T[i] + 2 * np.sqrt(variances.T[i]),
facecolor=plots[-1].get_color(),
alpha=.3)
a.legend(borderaxespad=0.)
a.set_xlim(x.min(), x.max())
if i < means.shape[1] - 1:
a.set_xticklabels('')
# binary prob plot
a = fig.add_subplot(*sub2)
a.bar(x,gamma[:,i],bottom=0.,linewidth=1.,width=1.0,align='center')
a.set_xlim(x.min(), x.max())
a.set_ylim([0.,1.])
pb.draw()
fig.tight_layout(h_pad=.01) # , rect=(0, 0, 1, .95))
return fig
def plot_SpikeSlab(parameterized, fignum=None, ax=None, colors=None, side_by_side=True):
"""
Plot latent space X in 1D:
- if fig is given, create input_dim subplots in fig and plot in these
- if ax is given plot input_dim 1D latent space plots of X into each `axis`
- if neither fig nor ax is given create a figure with fignum and plot in there
colors:
colors of different latent space dimensions input_dim
"""
if ax is None:
if side_by_side:
fig = pb.figure(num=fignum, figsize=(16, min(12, (2 * parameterized.mean.shape[1]))))
else:
fig = pb.figure(num=fignum, figsize=(8, min(12, (2 * parameterized.mean.shape[1]))))
if colors is None:
colors = pb.gca()._get_lines.color_cycle
pb.clf()
else:
colors = iter(colors)
plots = []
means, variances, gamma = parameterized.mean, parameterized.variance, parameterized.binary_prob
x = np.arange(means.shape[0])
for i in range(means.shape[1]):
if side_by_side:
sub1 = (means.shape[1],2,2*i+1)
sub2 = (means.shape[1],2,2*i+2)
else:
sub1 = (means.shape[1]*2,1,2*i+1)
sub2 = (means.shape[1]*2,1,2*i+2)
# mean and variance plot
a = fig.add_subplot(*sub1)
a.plot(means, c='k', alpha=.3)
plots.extend(a.plot(x, means.T[i], c=colors.next(), label=r"$\mathbf{{X_{{{}}}}}$".format(i)))
a.fill_between(x,
means.T[i] - 2 * np.sqrt(variances.T[i]),
means.T[i] + 2 * np.sqrt(variances.T[i]),
facecolor=plots[-1].get_color(),
alpha=.3)
a.legend(borderaxespad=0.)
a.set_xlim(x.min(), x.max())
if i < means.shape[1] - 1:
a.set_xticklabels('')
# binary prob plot
a = fig.add_subplot(*sub2)
a.bar(x,gamma[:,i],bottom=0.,linewidth=0,width=1.0,align='center')
a.set_xlim(x.min(), x.max())
a.set_ylim([0.,1.])
pb.draw()
fig.tight_layout(h_pad=.01) # , rect=(0, 0, 1, .95))
return fig
def plot(parameterized, fignum=None, ax=None, colors=None, figsize=(12, 6)):
"""
Plot latent space X in 1D:
- if fig is given, create input_dim subplots in fig and plot in these
- if ax is given plot input_dim 1D latent space plots of X into each `axis`
- if neither fig nor ax is given create a figure with fignum and plot in there
colors:
colors of different latent space dimensions input_dim
"""
if ax is None:
fig = pb.figure(num=fignum, figsize=figsize)
if colors is None:
from ..Tango import mediumList
from itertools import cycle
colors = cycle(mediumList)
pb.clf()
else:
colors = iter(colors)
lines = []
fills = []
bg_lines = []
means, variances = parameterized.mean.values, parameterized.variance.values
x = np.arange(means.shape[0])
for i in range(means.shape[1]):
if ax is None:
a = fig.add_subplot(means.shape[1], 1, i + 1)
elif isinstance(ax, (tuple, list)):
a = ax[i]
else:
raise ValueError("Need one ax per latent dimension input_dim")
bg_lines.append(a.plot(means, c='k', alpha=.3))
lines.extend(
a.plot(x,
means.T[i],
c=next(colors),
label=r"$\mathbf{{X_{{{}}}}}$".format(i)))
fills.append(
a.fill_between(x,
means.T[i] - 2 * np.sqrt(variances.T[i]),
means.T[i] + 2 * np.sqrt(variances.T[i]),
facecolor=lines[-1].get_color(),
alpha=.3))
a.legend(borderaxespad=0.)
a.set_xlim(x.min(), x.max())
if i < means.shape[1] - 1:
a.set_xticklabels('')
pb.draw()
a.figure.tight_layout(h_pad=.01) # , rect=(0, 0, 1, .95))
return dict(lines=lines, fills=fills, bg_lines=bg_lines)
def plotIsoStaImpedance(ax, loc, array, flag, par='abs',
pSym='s', pColor=None, addLabel='', zorder=1):
appResFact = 1/(8*np.pi**2*10**(-7))
treshold = 1.0 # 1 meter
indUniSta = np.sqrt(np.sum((array[['x','y']].view((float,2))-loc)**2,axis=1)) < treshold
freq = array['freq'][indUniSta]
if par == 'abs':
zPlot = np.abs(array[flag][indUniSta])
elif par == 'real':
zPlot = np.real(array[flag][indUniSta])
elif par == 'imag':
zPlot = np.imag(array[flag][indUniSta])
elif par == 'res':
zPlot = (appResFact/freq)*np.abs(array[flag][indUniSta])**2
elif par == 'phs':
zPlot = np.arctan2(array[flag][indUniSta].imag,array[flag][indUniSta].real)*(180/np.pi)
if not pColor:
if 'xx' in flag:
lab = 'XX'
pColor = 'g'
elif 'xy' in flag:
lab = 'XY'
pColor = 'r'
elif 'yx' in flag:
lab = 'YX'
pColor = 'b'
elif 'yy' in flag:
lab = 'YY'
pColor = 'y'
ax.plot(freq,zPlot,color=pColor,marker=pSym,label=flag+addLabel,zorder=zorder)
def plot(parameterized, fignum=None, ax=None, colors=None, figsize=(12, 6)):
"""
Plot latent space X in 1D:
- if fig is given, create input_dim subplots in fig and plot in these
- if ax is given plot input_dim 1D latent space plots of X into each `axis`
- if neither fig nor ax is given create a figure with fignum and plot in there
colors:
colors of different latent space dimensions input_dim
"""
if ax is None:
fig = pb.figure(num=fignum, figsize=figsize)
if colors is None:
colors = pb.gca()._get_lines.color_cycle
pb.clf()
else:
colors = iter(colors)
lines = []
fills = []
bg_lines = []
means, variances = parameterized.mean.values, parameterized.variance.values
x = np.arange(means.shape[0])
for i in range(means.shape[1]):
if ax is None:
a = fig.add_subplot(means.shape[1], 1, i + 1)
elif isinstance(ax, (tuple, list)):
a = ax[i]
else:
raise ValueError("Need one ax per latent dimension input_dim")
bg_lines.append(a.plot(means, c='k', alpha=.3))
lines.extend(a.plot(x, means.T[i], c=colors.next(), label=r"$\mathbf{{X_{{{}}}}}$".format(i)))
fills.append(a.fill_between(x,
means.T[i] - 2 * np.sqrt(variances.T[i]),
means.T[i] + 2 * np.sqrt(variances.T[i]),
facecolor=lines[-1].get_color(),
alpha=.3))
a.legend(borderaxespad=0.)
a.set_xlim(x.min(), x.max())
if i < means.shape[1] - 1:
a.set_xticklabels('')
pb.draw()
a.figure.tight_layout(h_pad=.01) # , rect=(0, 0, 1, .95))
return dict(lines=lines, fills=fills, bg_lines=bg_lines)
def fitting_variables_calculating_parameters(dict_of_data):
x = dict_of_data.get(x)
dx = dict_of_data.get(dx)
y = dict_of_data.get(y)
dy = dict_of_data.get(dy)
N = len(x)
x_roof, x_square_roof, x_roof_square, y_roof, xy_roof, xy_square_roof, dy_square_roof, dy_power_minus2 = 0, 0, 0, 0, 0, 0, 0, 0
#now to assign the data to the variables
for k in range(0, N):
x_roof = x_roof + (x[k] / (dy[k]**2))
y_roof = y_roof + (y[k] / (dy[k]**2))
xy_roof = xy_roof + ((x[k] * y[k]) / (dy[k]**2))
x_square_roof += ((x[k]**2) / (dy[k]**2))
dy_square_roof += 1
dy_power_minus2 += (dy[k]**(-2))
x_roof = x_roof / dy_power_minus2
y_roof = y_roof / dy_power_minus2
xy_roof = xy_roof / dy_power_minus2
x_roof_square = x_roof**2
x_square_roof = x_square_roof / dy_power_minus2
dy_square_roof = dy_square_roof / dy_power_minus2
#now we calculate the fitting parameters
A = (xy_roof - (x_roof * y_roof)) / (x_square_roof - x_roof_square)
dA = numpy.sqrt((dy_square_roof) / (N * (x_square_roof - x_roof_square)))
B = y_roof - (A * x_roof)
dB = numpy.sqrt((dy_square_roof * x_square_roof) /
(N * (x_square_roof - x_roof_square)))
#chi square calculation
chi_square = 0
for i in range(0, N):
chi_square += ((y[i] - (A * x[i] + B)) / dy[i])**2
chi_square_red = chi_square / (N - 2)
#print and return the parameters calculated:
print('a =', A, '+-', dA)
print('b =', B, '+-', dB)
print('chi2 =', chi_square)
print('chi2_reduced =', chi_square_red)
return A, B
def plotIsoStaImpedance(ax,
loc,
array,
flag,
par="abs",
pSym="s",
pColor=None,
addLabel="",
zorder=1):
appResFact = 1 / (8 * np.pi**2 * 10**(-7))
treshold = 1.0 # 1 meter
indUniSta = (np.sqrt(
np.sum((array[["x", "y"]].copy().view(
(float, 2)) - loc)**2, axis=1)) < treshold)
freq = array["freq"][indUniSta]
if par == "abs":
zPlot = np.abs(array[flag][indUniSta])
elif par == "real":
zPlot = np.real(array[flag][indUniSta])
elif par == "imag":
zPlot = np.imag(array[flag][indUniSta])
elif par == "res":
zPlot = (appResFact / freq) * np.abs(array[flag][indUniSta])**2
elif par == "phs":
zPlot = np.arctan2(array[flag][indUniSta].imag,
array[flag][indUniSta].real) * (180 / np.pi)
if not pColor:
if "xx" in flag:
lab = "XX"
pColor = "g"
elif "xy" in flag:
lab = "XY"
pColor = "r"
elif "yx" in flag:
lab = "YX"
pColor = "b"
elif "yy" in flag:
lab = "YY"
pColor = "y"
ax.plot(freq,
zPlot,
color=pColor,
marker=pSym,
label=flag + addLabel,
zorder=zorder)
def plotIsoStaImpedance(ax,
loc,
array,
flag,
par='abs',
pSym='s',
pColor=None,
addLabel='',
zorder=1):
appResFact = 1 / (8 * np.pi**2 * 10**(-7))
treshold = 1.0 # 1 meter
indUniSta = np.sqrt(
np.sum((array[['x', 'y']].view(
(float, 2)) - loc)**2, axis=1)) < treshold
freq = array['freq'][indUniSta]
if par == 'abs':
zPlot = np.abs(array[flag][indUniSta])
elif par == 'real':
zPlot = np.real(array[flag][indUniSta])
elif par == 'imag':
zPlot = np.imag(array[flag][indUniSta])
elif par == 'res':
zPlot = (appResFact / freq) * np.abs(array[flag][indUniSta])**2
elif par == 'phs':
zPlot = np.arctan2(array[flag][indUniSta].imag,
array[flag][indUniSta].real) * (180 / np.pi)
if not pColor:
if 'xx' in flag:
lab = 'XX'
pColor = 'g'
elif 'xy' in flag:
lab = 'XY'
pColor = 'r'
elif 'yx' in flag:
lab = 'YX'
pColor = 'b'
elif 'yy' in flag:
lab = 'YY'
pColor = 'y'
ax.plot(freq,
zPlot,
color=pColor,
marker=pSym,
label=flag + addLabel,
zorder=zorder)
def cannyEdgeDetectorFilter(self, img, sigma=1, t_low=0.01, t_high=0.2):
im = img.convert('L')
img = np.array(im, dtype=float)
# 1) Convolve gaussian kernel with gradient
# gaussian kernel
halfSize = 3 * sigma
maskSize = 2 * halfSize + 1
mat = np.ones((maskSize, maskSize)) / (float)(2 * np.pi * (sigma**2))
xyRange = np.arange(-halfSize, halfSize + 1)
xx, yy = np.meshgrid(xyRange, xyRange)
x2y2 = (xx**2 + yy**2)
exp_part = np.exp(-(x2y2 / (2.0 * (sigma**2))))
gSig = mat * exp_part
gx, gy = self.drogEdgeDetectorFilter(gSig, ret_grad=True, pillow=False)
# 2) Magnitude and Angles
# apply kernels for Ix & Iy
Ix = cv2.filter2D(img, -1, gx)
Iy = cv2.filter2D(img, -1, gy)
# compute magnitude
mag = np.sqrt(Ix**2 + Iy**2)
# normalize magnitude image
normMag = my_Normalize(mag)
# compute orientation of gradient
orient = np.arctan2(Iy, Ix)
# round elements of orient
orientRows = orient.shape[0]
orientCols = orient.shape[1]
# 3) Non maximum suppression
for i in range(0, orientRows):
for j in range(0, orientCols):
if normMag[i, j] > t_low:
# case 0
if (orient[i, j] > (-np.pi / 8) and orient[i, j] <=
(np.pi / 8)):
orient[i, j] = 0
elif (orient[i, j] > (7 * np.pi / 8)
and orient[i, j] <= np.pi):
orient[i, j] = 0
elif (orient[i, j] >= -np.pi and orient[i, j] <
(-7 * np.pi / 8)):
orient[i, j] = 0
# case 1
elif (orient[i, j] > (np.pi / 8) and orient[i, j] <=
(3 * np.pi / 8)):
orient[i, j] = 3
elif (orient[i, j] >= (-7 * np.pi / 8) and orient[i, j] <
(-5 * np.pi / 8)):
orient[i, j] = 3
# case 2
elif (orient[i, j] > (3 * np.pi / 8) and orient[i, j] <=
(5 * np.pi / 8)):
orient[i, j] = 2
elif (orient[i, j] >= (-5 * np.pi / 4) and orient[i, j] <
(-3 * np.pi / 8)):
orient[i, j] = 2
# case 3
elif (orient[i, j] > (5 * np.pi / 8) and orient[i, j] <=
(7 * np.pi / 8)):
orient[i, j] = 1
elif (orient[i, j] >= (-3 * np.pi / 8) and orient[i, j] <
(-np.pi / 8)):
orient[i, j] = 1
mag = normMag
mag_thin = np.zeros(mag.shape)
for i in range(mag.shape[0] - 1):
for j in range(mag.shape[1] - 1):
if mag[i][j] < t_low:
continue
if orient[i][j] == 0:
if mag[i][j] > mag[i][j - 1] and mag[i][j] >= mag[i][j +
1]:
mag_thin[i][j] = mag[i][j]
if orient[i][j] == 1:
if mag[i][j] > mag[i - 1][j + 1] and mag[i][j] >= mag[
i + 1][j - 1]:
mag_thin[i][j] = mag[i][j]
if orient[i][j] == 2:
if mag[i][j] > mag[i - 1][j] and mag[i][j] >= mag[i +
1][j]:
mag_thin[i][j] = mag[i][j]
if orient[i][j] == 3:
if mag[i][j] > mag[i - 1][j - 1] and mag[i][j] >= mag[
i + 1][j + 1]:
mag_thin[i][j] = mag[i][j]
# 4) Thresholding and edge linking
result_binary = np.zeros(mag_thin.shape)
tHigh = t_high
tLow = t_low
# forward scan
for i in range(0, mag_thin.shape[0] - 1): # rows
for j in range(0, mag_thin.shape[1] - 1): # columns
if mag_thin[i][j] >= tHigh:
if mag_thin[i][j + 1] >= tLow: # right
mag_thin[i][j + 1] = tHigh
if mag_thin[i + 1][j + 1] >= tLow: # bottom right
mag_thin[i + 1][j + 1] = tHigh
if mag_thin[i + 1][j] >= tLow: # bottom
mag_thin[i + 1][j] = tHigh
if mag_thin[i + 1][j - 1] >= tLow: # bottom left
mag_thin[i + 1][j - 1] = tHigh
# backwards scan
for i in range(mag_thin.shape[0] - 2, 0, -1): # rows
for j in range(mag_thin.shape[1] - 2, 0, -1): # columns
if mag_thin[i][j] >= tHigh:
if mag_thin[i][j - 1] > tLow: # left
mag_thin[i][j - 1] = tHigh
if mag_thin[i - 1][j - 1]: # top left
mag_thin[i - 1][j - 1] = tHigh
if mag_thin[i - 1][j] > tLow: # top
mag_thin[i - 1][j] = tHigh
if mag_thin[i - 1][j + 1] > tLow: # top right
mag_thin[i - 1][j + 1] = tHigh
# fill in result_binary
for i in range(0, mag_thin.shape[0] - 1): # rows
for j in range(0, mag_thin.shape[1] - 1): # columns
if mag_thin[i][j] >= tHigh:
result_binary[i][j] = 255 # set to 255 for >= tHigh
img = Image.fromarray(result_binary)
return img