def get_num_image(self, order_array_flat):
'''
This gennerates the image with information of how many times a pixel
was the best match.
:param order_array_flat:
'''
order_image = Image.new(
'L',
np.flipud(self.shape) * np.flipud(self.neighbor_shape))
max_E4 = np.max(order_array_flat)
min_E4 = np.min(order_array_flat)
for c in coords_iterate(self.shape):
# find index in flat array
k = self.estimator.flattening.cell2index[c]
E3_local_flat = order_array_flat[k]
E3_local_flat_normalized = 1 - (E3_local_flat - min_E4) / (max_E4 -
min_E4)
E3_local = E3_local_flat_normalized.reshape(self.neighbor_shape)
# find the upper left corner to paste
p0 = tuple(np.flipud(np.array(c) * self.neighbor_shape))
# calculate the box to past into
box = p0 + tuple(p0 + self.neighbor_shape)
order_image.paste(
Image.fromarray((E3_local * 255).astype('uint8')), box)
return order_image
def get_num_image(self, order_array_flat):
'''
This gennerates the image with information of how many times a pixel
was the best match.
:param order_array_flat:
'''
order_image = Image.new('L', np.flipud(self.shape) * np.flipud(self.neighbor_shape))
max_E4 = np.max(order_array_flat)
min_E4 = np.min(order_array_flat)
for c in coords_iterate(self.shape):
# find index in flat array
k = self.estimator.flattening.cell2index[c]
E3_local_flat = order_array_flat[k]
E3_local_flat_normalized = 1 - (E3_local_flat - min_E4) / (max_E4 - min_E4)
E3_local = E3_local_flat_normalized.reshape(self.neighbor_shape)
# find the upper left corner to paste
p0 = tuple(np.flipud(np.array(c) * self.neighbor_shape))
# calculate the box to past into
box = p0 + tuple(p0 + self.neighbor_shape)
order_image.paste(Image.fromarray((E3_local * 255).astype('uint8')), box)
return order_image
def get_order_image(self, order_array_flat):
'''
This gennerates an image search_area*image_size with the order
array (E4 error) for each pixel.
:param order_array_flat:
'''
order_image = Image.new(
'L',
np.flipud(self.shape) * np.flipud(self.neighbor_shape))
max_E4 = np.max(order_array_flat)
min_E4 = np.min(order_array_flat)
for c in coords_iterate(self.shape):
# find index in flat array
k = self.estimator.flattening.cell2index[c]
E4_local_flat = order_array_flat[k]
'''
Data is normalized such that 1 is no error and 0 is max error.
This can easily be inverted by the commented line below
'''
E4_local_flat_normalized = 1 - (E4_local_flat - min_E4) / (max_E4 -
min_E4)
# E4_local_flat_normalized = (E4_local_flat - min_E4) / (max_E4 - min_E4)
E4_local = E4_local_flat_normalized.reshape(self.neighbor_shape)
if c in c_peak_list:
fig = plt.figure()
ax = fig.gca(projection='3d')
X, Y = np.meshgrid(range(self.neighbor_shape[0]),
range(self.neighbor_shape[1]))
ax.plot_surface(
X,
Y,
E4_local,
rstride=1,
cstride=1,
cmap=cm.jet, #@UndefinedVariable
linewidth=0,
antialiased=False)
if not os.path.exists(self.folder + self.name + '/peaks'):
os.makedirs(self.folder + self.name + '/peaks')
plt.savefig(self.folder + self.name + '/peaks/order' + str(c) +
'.png')
plt.savefig(self.folder + self.name + '/peaks/order' + str(c) +
'.pdf')
# find the upper left corner to paste
p0 = tuple(np.flipud(np.array(c) * self.neighbor_shape))
# calculate the box to past into
box = p0 + tuple(p0 + self.neighbor_shape)
order_image.paste(
Image.fromarray((E4_local * 255).astype('uint8')), box)
return order_image
def get_similarity_image(self, sim_array):
'''
This gennerates a image with the simmilarity function E1 for each pixel.
:param sim_array:
'''
sim_image = Image.new(
'L',
np.flipud(self.shape) * np.flipud(self.neighbor_shape))
max_sim = np.max(sim_array)
min_sim = np.min(sim_array)
for c in coords_iterate(self.shape):
# find index in flat array
k = self.estimator.flattening.cell2index[c]
sim_local_flat = sim_array[k]
'''
Data is normalized such that 1 is no error and 0 is max error.
This can easily be inverted by the commented line below
'''
sim_local_flat_normalized = 1 - (sim_local_flat -
min_sim) / (max_sim - min_sim)
# sim_local_flat_normalized = (sim_local_flat - min_sim) / (max_sim - min_sim)
sim_local = sim_local_flat_normalized.reshape(self.neighbor_shape)
if c in c_peak_list:
fig = plt.figure()
ax = fig.gca(projection='3d')
X, Y = np.meshgrid(range(self.neighbor_shape[0]),
range(self.neighbor_shape[1]))
ax.plot_surface(
X,
Y,
sim_local,
rstride=1,
cstride=1,
cmap=cm.jet, #@UndefinedVariable
linewidth=0,
antialiased=False)
if not os.path.exists(self.folder + self.name + '/peaks'):
os.makedirs(self.folder + self.name + '/peaks')
plt.savefig(self.folder + self.name + '/peaks/sim' + str(c) +
'.png')
plt.savefig(self.folder + self.name + '/peaks/sim' + str(c) +
'.pdf')
# find the upper left corner to paste
p0 = tuple(np.flipud(np.array(c) * self.neighbor_shape))
# calculate the box to past into
box = p0 + tuple(p0 + self.neighbor_shape)
sim_image.paste(Image.fromarray((sim_local * 255).astype('uint8')),
box)
return sim_image
def get_order_image(self, order_array_flat):
'''
This gennerates an image search_area*image_size with the order
array (E4 error) for each pixel.
:param order_array_flat:
'''
order_image = Image.new('L', np.flipud(self.shape) * np.flipud(self.neighbor_shape))
max_E4 = np.max(order_array_flat)
min_E4 = np.min(order_array_flat)
for c in coords_iterate(self.shape):
# find index in flat array
k = self.estimator.flattening.cell2index[c]
E4_local_flat = order_array_flat[k]
'''
Data is normalized such that 1 is no error and 0 is max error.
This can easily be inverted by the commented line below
'''
E4_local_flat_normalized = 1 - (E4_local_flat - min_E4) / (max_E4 - min_E4)
# E4_local_flat_normalized = (E4_local_flat - min_E4) / (max_E4 - min_E4)
E4_local = E4_local_flat_normalized.reshape(self.neighbor_shape)
if c in c_peak_list:
fig = plt.figure()
ax = fig.gca(projection='3d')
X, Y = np.meshgrid(range(self.neighbor_shape[0]), range(self.neighbor_shape[1]))
ax.plot_surface(X, Y, E4_local, rstride=1, cstride=1, cmap=cm.jet, #@UndefinedVariable
linewidth=0, antialiased=False)
if not os.path.exists(self.folder + self.name + '/peaks'):
os.makedirs(self.folder + self.name + '/peaks')
plt.savefig(self.folder + self.name + '/peaks/order' + str(c) + '.png')
plt.savefig(self.folder + self.name + '/peaks/order' + str(c) + '.pdf')
# find the upper left corner to paste
p0 = tuple(np.flipud(np.array(c) * self.neighbor_shape))
# calculate the box to past into
box = p0 + tuple(p0 + self.neighbor_shape)
order_image.paste(Image.fromarray((E4_local * 255).astype('uint8')), box)
return order_image
def get_similarity_image(self, sim_array):
'''
This gennerates a image with the simmilarity function E1 for each pixel.
:param sim_array:
'''
sim_image = Image.new('L', np.flipud(self.shape) * np.flipud(self.neighbor_shape))
max_sim = np.max(sim_array)
min_sim = np.min(sim_array)
for c in coords_iterate(self.shape):
# find index in flat array
k = self.estimator.flattening.cell2index[c]
sim_local_flat = sim_array[k]
'''
Data is normalized such that 1 is no error and 0 is max error.
This can easily be inverted by the commented line below
'''
sim_local_flat_normalized = 1 - (sim_local_flat - min_sim) / (max_sim - min_sim)
# sim_local_flat_normalized = (sim_local_flat - min_sim) / (max_sim - min_sim)
sim_local = sim_local_flat_normalized.reshape(self.neighbor_shape)
if c in c_peak_list:
fig = plt.figure()
ax = fig.gca(projection='3d')
X, Y = np.meshgrid(range(self.neighbor_shape[0]), range(self.neighbor_shape[1]))
ax.plot_surface(X, Y, sim_local, rstride=1, cstride=1, cmap=cm.jet, #@UndefinedVariable
linewidth=0, antialiased=False)
if not os.path.exists(self.folder + self.name + '/peaks'):
os.makedirs(self.folder + self.name + '/peaks')
plt.savefig(self.folder + self.name + '/peaks/sim' + str(c) + '.png')
plt.savefig(self.folder + self.name + '/peaks/sim' + str(c) + '.pdf')
# find the upper left corner to paste
p0 = tuple(np.flipud(np.array(c) * self.neighbor_shape))
# calculate the box to past into
box = p0 + tuple(p0 + self.neighbor_shape)
sim_image.paste(Image.fromarray((sim_local * 255).astype('uint8')), box)
return sim_image
def diffeo_from_function_viewport(diffeo, manifold, viewport, shape):
domain = SquareDomain([[0, shape[0]], [0, shape[1]]])
domain2viewport = LinearCoordinateChange(domain.bounds, viewport.bounds)
viewport2domain = domain2viewport.get_inverse()
# Prepare the grid
M = shape[0]
N = shape[1]
D = np.zeros((M, N, 2), dtype='int32')
# Uncertainty (here, 0 or 1)
info = np.zeros((M, N), dtype='float32')
# Iterate at each cell
for coords in coords_iterate(shape):
# coords = (i,j)
# coordinates of the center of the cell
center_offset = np.array([0.5, 0.5])
cell_center = coords + center_offset
# the domain is ([0,M]x[0,N]) so it is still inside
assert domain.belongs(cell_center)
# transform to the "world"
world = domain2viewport(cell_center)
# apply the diffeomorphism
world2 = manifold.normalize(diffeo(world))
# Are we inside the viewport?
if viewport.belongs(world2):
cell2 = viewport2domain(world2)
assert domain.belongs(cell2)
new_cell = np.floor(cell2)
approx = np.linalg.norm(cell2 - (new_cell + center_offset))
quality = np.exp(-approx)
quality = 1
info[coords[0], coords[1]] = quality
D[coords[0], coords[1], 0] = new_cell[0]
D[coords[0], coords[1], 1] = new_cell[1]
else:
# we don't know
info[coords[0], coords[1]] = 0
# we put the identity as a dummy value
D[coords[0], coords[1], 0] = coords[0]
D[coords[0], coords[1], 1] = coords[1]
return D, info
def diffeo_from_function_viewport(diffeo, manifold, viewport, shape):
domain = SquareDomain([[0, shape[0]], [0, shape[1]]])
domain2viewport = LinearCoordinateChange(domain.bounds, viewport.bounds)
viewport2domain = domain2viewport.get_inverse()
# Prepare the grid
M = shape[0]
N = shape[1]
D = np.zeros((M, N, 2), dtype='int32')
# Uncertainty (here, 0 or 1)
info = np.zeros((M, N), dtype='float32')
# Iterate at each cell
for coords in coords_iterate(shape):
# coords = (i,j)
# coordinates of the center of the cell
center_offset = np.array([0.5, 0.5])
cell_center = coords + center_offset
# the domain is ([0,M]x[0,N]) so it is still inside
assert domain.belongs(cell_center)
# transform to the "world"
world = domain2viewport(cell_center)
# apply the diffeomorphism
world2 = manifold.normalize(diffeo(world))
# Are we inside the viewport?
if viewport.belongs(world2):
cell2 = viewport2domain(world2)
assert domain.belongs(cell2)
new_cell = np.floor(cell2)
approx = np.linalg.norm(cell2 - (new_cell + center_offset))
quality = np.exp(-approx)
quality = 1
info[coords[0], coords[1]] = quality
D[coords[0], coords[1], 0] = new_cell[0]
D[coords[0], coords[1], 1] = new_cell[1]
else:
# we don't know
info[coords[0], coords[1]] = 0
# we put the identity as a dummy value
D[coords[0], coords[1], 0] = coords[0]
D[coords[0], coords[1], 1] = coords[1]
return D, info