def merge_cells(angle_indices):
def connection(index_a, index_b):
if (index_a == 0 or index_a == 2) and (index_b == 0 or index_b == 2):
angle_difference = min((index_a - index_b) % 180, (index_b - index_a) % 180)
return abs(angle_difference) <= 0
else:
return False
grid_size = len(angle_indices)
num_grid_elements = grid_size * grid_size
graph = np.zeros((num_grid_elements, num_grid_elements))
for i in range(grid_size):
for j in range(grid_size):
index = np.ravel_multi_index((i, j), (grid_size, grid_size))
if i > 0 and connection(angle_indices[i, j], angle_indices[i - 1, j]):
graph[index, np.ravel_multi_index((i - 1, j), (grid_size, grid_size))] = 1
if i < (grid_size - 1) and connection(angle_indices[i, j], angle_indices[i + 1, j]):
graph[index, np.ravel_multi_index((i + 1, j), (grid_size, grid_size))] = 1
if j > 0 and connection(angle_indices[i, j], angle_indices[i, j - 1]):
graph[index, np.ravel_multi_index((i, j - 1), (grid_size, grid_size))] = 1
if j < (grid_size - 1) and connection(angle_indices[i, j], angle_indices[i, j + 1]):
graph[index, np.ravel_multi_index((i, j + 1), (grid_size, grid_size))] = 1
n_components, labels = connected_components(graph, directed=False, return_labels=True)
return (labels + 1).reshape(grid_size, grid_size)
def generateGridAdj(nrows, ncols):
Adj = np.zeros((nrows * ncols,nrows * ncols))
for i in range(ncols):
for j in range(nrows):
k = np.ravel_multi_index((i,j), dims=(ncols, nrows), order='F')
if i > 0:
ii = i-1
jj = j
kk = np.ravel_multi_index((ii,jj), dims=(ncols, nrows), order='F')
Adj[k,kk] = 1
if i<ncols-1:
ii=i+1
jj=j
kk = np.ravel_multi_index((ii,jj), dims=(ncols, nrows), order='F')
Adj[k,kk] = 1
if j>0:
ii=i
jj=j-1
kk = np.ravel_multi_index((ii,jj), dims=(ncols, nrows), order='F')
Adj[k,kk] = 1
if j<nrows-1:
ii=i
jj=j+1
kk = np.ravel_multi_index((ii,jj), dims=(ncols, nrows), order='F')
Adj[k,kk] = 1
return Adj
def create_sparse_pre_rate_matrix(state_space_shape, row, col, rate):
"""
Create the pre-rate matrix with empty diagonal.
"""
# check conformability of input arrays
ndim = len(state_space_shape)
assert_equal(len(row.shape), 2)
assert_equal(len(col.shape), 2)
assert_equal(len(rate.shape), 1)
assert_equal(row.shape[0], rate.shape[0])
assert_equal(col.shape[0], rate.shape[0])
assert_equal(row.shape[1], ndim)
assert_equal(col.shape[1], ndim)
# Define the transition rate matrix after the multivariate process
# is collapsed to a univariate process.
nstates = np.prod(state_space_shape)
mrow = np.ravel_multi_index(row.T, state_space_shape)
mcol = np.ravel_multi_index(col.T, state_space_shape)
# Diagonal entries are allowed for computing dwell times,
# but they are not allowed for transition expectations.
#assert_(not np.any(mrow == mcol))
# create the sparse pre_Q matrix from the sparse arrays
return coo_matrix((rate, (mrow, mcol)), (nstates, nstates))
def reverse_interpolate_two_array(value1, array1, value2, array2, delta1=0.1, delta2=0.1):
"""
Tries to reverse interpolate two vales from two arrays with the same dimensions, and finds a common index
for value1 and value2 in their respective arrays. the deltas define the search radius for a close value match
to the arrays.
:return: index1, index2
"""
tth_ind = np.argwhere(np.abs(array1 - value1) < delta1)
azi_ind = np.argwhere(np.abs(array2 - value2) < delta2)
tth_ind_ravel = np.ravel_multi_index((tth_ind[:, 0], tth_ind[:, 1]), dims=array1.shape)
azi_ind_ravel = np.ravel_multi_index((azi_ind[:, 0], azi_ind[:, 1]), dims=array2.shape)
common_ind_ravel = np.intersect1d(tth_ind_ravel, azi_ind_ravel)
result_ind = np.unravel_index(common_ind_ravel, dims=array1.shape)
while len(result_ind[0]) > 1:
if np.max(np.diff(array1)) > 0:
delta1 = np.max(np.diff(array1[result_ind]))
if np.max(np.diff(array2)) > 0:
delta2 = np.max(np.diff(array2[result_ind]))
tth_ind = np.argwhere(np.abs(array1[result_ind] - value1) < delta1)
azi_ind = np.argwhere(np.abs(array2[result_ind] - value2) < delta2)
print(result_ind)
common_ind = np.intersect1d(tth_ind, azi_ind)
result_ind = (result_ind[0][common_ind], result_ind[1][common_ind])
return result_ind[0], result_ind[1]
def map_to_phon(self):
'''decibel are converted into phon which are a logarithmic unit to human loudness sensation'''
# number of bark bands, matrix length in time dim
n_bands = self.processed.shape[0]
t = self.processed.shape[1]
# DB-TO-PHON BARK-SCALE-LIMIT TABLE
# introducing 1 level more with level(1) being infinite
# to avoid (levels - 1) producing errors like division by 0
table_dim = n_bands;
cbv = np.concatenate((np.tile(np.inf,(table_dim,1)),
self.loudn_bark[:,0:n_bands].transpose()),1)
# the matrix 'levels' stores the correct Phon level for each datapoint
# init lowest level = 2
levels = np.tile(2,(n_bands,t))
for lev in range(1,6):
db_thislev = np.tile(np.asarray([cbv[:,lev]]).transpose(),(1,t))
levels[np.where(self.processed > db_thislev)] = lev + 2
#ok here we compute indexes that match the cbv array such that when indexing the cbv array we get back an matrix with the proper dimensions
#this indices match the upper or lower phon level according to the current value of spl in our matrix
cbv_ind_hi = np.ravel_multi_index(dims=(table_dim,7), multi_index=np.array([np.tile(np.array([range(0,table_dim)]).transpose(),(1,t)), levels-1]), order='F')
cbv_ind_lo = np.ravel_multi_index(dims=(table_dim,7), multi_index=np.array([np.tile(np.array([range(0,table_dim)]).transpose(),(1,t)), levels-2]), order='F')
#for each datapoint in our matrix a interpolation factor 0 < f < 1 is calculated
ifac = (self.processed[:,0:t] - cbv.transpose().ravel()[cbv_ind_lo]) / (cbv.transpose().ravel()[cbv_ind_hi] - cbv.transpose().ravel()[cbv_ind_lo])
ifac[np.where(levels==2)] = 1 # keeps the upper phon value;
ifac[np.where(levels==8)] = 1 # keeps the upper phon value;
#finally the interpolation is computed here
self.processed[:,0:t] = AudioAnalytics.phons.transpose().ravel()[levels - 2] + (ifac * (AudioAnalytics.phons.transpose().ravel()[levels - 1] - AudioAnalytics.phons.transpose().ravel()[levels - 2])) # OPT: pre-calc diff
def TwoPeriodSun(constant,delta,slope,slopedir,lat):
# First derive A1 and A2 from the normal procedure
A1,A2 = SunHours(delta,slope,slopedir,lat)
# Then calculate the other two functions.
# Initialize function
a,b,c = Constants(delta,slope,slopedir,lat)
riseSlope, setSlope = BoundsSlope(a,b,c)
B1 = np.maximum(riseSlope,setSlope)
B2 = np.minimum(riseSlope,setSlope)
Angle_B1 = AngleSlope(a,b,c,B1)
Angle_B2 = AngleSlope(a,b,c,B2)
B1[abs(Angle_B1) > 0.001] = np.pi - B1[abs(Angle_B1) > 0.001]
B2[abs(Angle_B2) > 0.001] = -np.pi - B2[abs(Angle_B2) > 0.001]
# Check if two periods really exist
ID = np.ravel_multi_index(np.where(np.logical_and(B2 >= A1, B1 >= A2) == True),a.shape)
Val = IntegrateSlope(constant,B2.flat[ID],B1.flat[ID],delta,slope.flat[ID],slopedir.flat[ID],lat.flat[ID])
ID = ID[Val < 0]
# Finally calculate resulting values
Vals = np.zeros(B1.shape)
Vals.flat[ID] = (IntegrateSlope(constant,A1.flat[ID],B2.flat[ID],delta,slope.flat[ID],slopedir.flat[ID],lat.flat[ID]) +
IntegrateSlope(constant,B1.flat[ID],A2.flat[ID],delta,slope.flat[ID],slopedir.flat[ID],lat.flat[ID]))
ID = np.ravel_multi_index(np.where(Vals == 0),a.shape)
Vals.flat[ID] = IntegrateSlope(constant,A1.flat[ID],A2.flat[ID],delta,slope.flat[ID],slopedir.flat[ID],lat.flat[ID])
return(Vals)
def setInSlot(self, slot, key, value):
shape = self.inputs["shape"].value
eraseLabel = self.inputs["eraser"].value
neutralElement = 0
self.lock.acquire()
#fix slicing of single dimensions:
start, stop = sliceToRoi(key, shape, extendSingleton = False)
start = start.floor()
stop = stop.floor()
tempKey = roiToSlice(start-start, stop-start, hardBind = True)
stop += numpy.where(stop-start == 0,1,0)
key = roiToSlice(start,stop)
updateShape = tuple(stop-start)
update = self._denseArray[key].copy()
update[tempKey] = value
startRavel = numpy.ravel_multi_index(numpy.array(start, numpy.int32),shape)
#insert values into dict
updateNZ = numpy.nonzero(numpy.where(update != neutralElement,1,0))
updateNZRavelSmall = numpy.ravel_multi_index(updateNZ, updateShape)
if isinstance(value, numpy.ndarray):
valuesNZ = value.ravel()[updateNZRavelSmall]
else:
valuesNZ = value
updateNZRavel = numpy.ravel_multi_index(updateNZ, shape)
updateNZRavel += startRavel
self._denseArray.ravel()[updateNZRavel] = valuesNZ
valuesNZ = self._denseArray.ravel()[updateNZRavel]
self._denseArray.ravel()[updateNZRavel] = valuesNZ
td = blist.sorteddict(zip(updateNZRavel.tolist(),valuesNZ.tolist()))
self._sparseNZ.update(td)
#remove values to be deleted
updateNZ = numpy.nonzero(numpy.where(update == eraseLabel,1,0))
if len(updateNZ)>0:
updateNZRavel = numpy.ravel_multi_index(updateNZ, shape)
updateNZRavel += startRavel
self._denseArray.ravel()[updateNZRavel] = neutralElement
for index in updateNZRavel:
self._sparseNZ.pop(index)
self.lock.release()
self.outputs["Output"].setDirty(key)
def transform2phon(matrix):
# number of bark bands, matrix length in time dim
n_bands = matrix.shape[0]
t = matrix.shape[1]
# DB-TO-PHON BARK-SCALE-LIMIT TABLE
# introducing 1 level more with level(1) being infinite
# to avoid (levels - 1) producing errors like division by 0
#%%table_dim = size(CONST_loudn_bark,2);
table_dim = n_bands; # OK
cbv = np.concatenate((np.tile(np.inf,(table_dim,1)), loudn_bark[:,0:n_bands].transpose()),1) # OK
# init lowest level = 2
levels = np.tile(2,(n_bands,t)) # OK
for lev in range(1,6): # OK
db_thislev = np.tile(np.asarray([cbv[:,lev]]).transpose(),(1,t))
levels[np.where(matrix > db_thislev)] = lev + 2
# the matrix 'levels' stores the correct Phon level for each data point
cbv_ind_hi = np.ravel_multi_index(dims=(table_dim,7), multi_index=np.array([np.tile(np.array([range(0,table_dim)]).transpose(),(1,t)), levels-1]), order='F')
cbv_ind_lo = np.ravel_multi_index(dims=(table_dim,7), multi_index=np.array([np.tile(np.array([range(0,table_dim)]).transpose(),(1,t)), levels-2]), order='F')
# interpolation factor % OPT: pre-calc diff
ifac = (matrix[:,0:t] - cbv.transpose().ravel()[cbv_ind_lo]) / (cbv.transpose().ravel()[cbv_ind_hi] - cbv.transpose().ravel()[cbv_ind_lo])
ifac[np.where(levels==2)] = 1 # keeps the upper phon value;
ifac[np.where(levels==8)] = 1 # keeps the upper phon value;
# phons has been initialized globally above
matrix[:,0:t] = phons.transpose().ravel()[levels - 2] + (ifac * (phons.transpose().ravel()[levels - 1] - phons.transpose().ravel()[levels - 2])) # OPT: pre-calc diff
return(matrix)
def __init__(self, model):
""" Initialize the filtered stim model
"""
self.model = model
N = model['N']
prms = model['network']['weight']
self.prior = create_prior(prms['prior'])
# Implement refractory period by having negative mean on self loops
if 'refractory_prior' in prms:
#self.mu[np.diag_indices(N)] = prms['mu_refractory']
self.refractory_prior = create_prior(prms['refractory_prior'])
# Get the upper and lower diagonal indices so that we can evaluate
# the log prob of the refractory weights separately from the
# log prob of the regular weights
self.diags = np.ravel_multi_index(np.diag_indices(N), (N,N))
lower = np.ravel_multi_index(np.tril_indices(N,k=-1), (N,N))
upper = np.ravel_multi_index(np.triu_indices(N,k=1), (N,N))
self.nondiags = np.concatenate((lower, upper))
# Define weight matrix
self.W_flat = T.dvector(name='W')
self.W = T.reshape(self.W_flat,(N,N))
if hasattr(self, 'refractory_prior'):
self.log_p = self.prior.log_p(self.W.take(self.nondiags)) + \
self.refractory_prior.log_p(self.W.take(self.diags))
else:
self.log_p = self.prior.log_p(self.W)
def _offsets_to_raveled_neighbors(image_shape, structure, center):
"""Compute offsets to a samples neighbors if the image would be raveled.
Parameters
----------
image_shape : tuple
The shape of the image for which the offsets are computed.
structure : ndarray
A structuring element determining the neighborhood expressed as an
n-D array of 1's and 0's.
center : sequence
Tuple of indices specifying the center of `selem`.
Returns
-------
offsets : ndarray
Linear offsets to a samples neighbors in the raveled image, sorted by
their Euclidean distance from the center.
Examples
--------
>>> _offsets_to_raveled_neighbors((4, 5), np.ones((4, 3)), (1, 1))
array([-5, -1, 1, 5, -6, -4, 4, 6, 10, 9, 11])
"""
structure = structure.copy() # Don't modify original input
structure[tuple(center)] = 0 # Ignore the center; it's not a neighbor
connection_indices = np.transpose(np.nonzero(structure))
offsets = (np.ravel_multi_index(connection_indices.T, image_shape) -
np.ravel_multi_index(center, image_shape))
squared_distances = np.sum((connection_indices - center) ** 2, axis=1)
return offsets[np.argsort(squared_distances)]
def _init_indices(self):
# Moore neighbourhood for now. Will see others later.
self.n_neighbours = 8 # Moore
cols, rows = map(np.ndarray.flatten, np.meshgrid(*self._valid_range()))
self.inner_indices = np.ravel_multi_index((rows, cols),
self.dims,
order='C')
left_cols, right_cols = cols - 1, cols + 1
up_rows, down_rows = rows - 1, rows + 1
neighbour_pix_locs = [(up_rows, left_cols), (up_rows, cols),
(up_rows, right_cols),
(rows, left_cols), (rows, cols),
(rows, right_cols),
(down_rows, left_cols), (down_rows, cols),
(down_rows, right_cols)]
self.indices = np.empty((self.inner_indices.size,
self.n_neighbours + 1),
dtype=np.int)
for i in xrange(len(neighbour_pix_locs)):
self.indices[:,i] \
= np.ravel_multi_index(neighbour_pix_locs[i],
self.dims,
mode='wrap',
order='C')
def test_rmi():
I1 = _rmi([3, 4], [10, 10])
assert_equal(I1, 34)
I1 = _rmi([0, 0], [10, 10])
assert_equal(I1, 0)
assert_raises(ValueError, _rmi, [10, 0], [10, 10])
try:
from numpy import ravel_multi_index
except ImportError:
raise nose.SkipTest()
# Dtype of random integers is system dependent
A, B, C, D = np.random.randint(0, 1000, size=[4, 100])
I1 = _rmi([A, B], dims=[1000, 1000])
I2 = ravel_multi_index([A, B], dims=[1000, 1000])
assert_array_equal(I1, I2)
I1 = _rmi([A, B, C, D], dims=[1000]*4)
I2 = ravel_multi_index([A, B, C, D], dims=[1000]*4)
assert_array_equal(I1, I2)
# Check for overflow with small int types
indices = np.random.randint(0, 255, size=(2, 100))
dims = (1000, 1000)
I1 = _rmi(indices, dims=dims)
I2 = ravel_multi_index(indices, dims=dims)
assert_array_equal(I1, I2)
def create_sparse_rate_matrix(state_space_shape, row, col, rate):
"""
Create the rate matrix.
"""
# check conformability of input arrays
ndim = len(state_space_shape)
assert_equal(len(row.shape), 2)
assert_equal(len(col.shape), 2)
assert_equal(len(rate.shape), 1)
assert_equal(row.shape[0], rate.shape[0])
assert_equal(col.shape[0], rate.shape[0])
assert_equal(row.shape[1], ndim)
assert_equal(col.shape[1], ndim)
# create the sparse Q matrix from the sparse arrays
nstates = np.prod(state_space_shape)
mrow = np.ravel_multi_index(row.T, state_space_shape)
mcol = np.ravel_multi_index(col.T, state_space_shape)
Q = coo_matrix((rate, (mrow, mcol)), (nstates, nstates))
# get the dense array of exit rates, and set the diagonal
exit_rates = Q.sum(axis=1).A.flatten()
Q.setdiag(-exit_rates)
return Q
def dig(this, next):
# first select active mesh from next level, aligned to this level
next.data = next.data[activemask(next, this.Nmesh)]
# calculate the index of the covered mesh on this level
index_from_next = numpy.ravel_multi_index(
next.data["gps"].T // (next.Nmesh // this.Nmesh), (this.Nmesh, this.Nmesh, this.Nmesh)
)
# index this level
index = numpy.ravel_multi_index(this.data["gps"].T, (this.Nmesh, this.Nmesh, this.Nmesh))
preserve_mask2 = exist(index, index_from_next)
next.data = next.data[preserve_mask2]
if next.DownSample > 1:
# downsample levels need to carry on the interpolation
# of previous level
next.data["delta"] += trilinearinterp(
next.data["gps"] * (1.0 * this.Nmesh / next.Nmesh),
this.data["gps"],
this.data["delta"],
(next.Nmesh, next.Nmesh, next.Nmesh),
)
next.data["disp"] += trilinearinterp(
next.data["gps"] * (1.0 * this.Nmesh / next.Nmesh),
this.data["gps"],
this.data["disp"],
(next.Nmesh, next.Nmesh, next.Nmesh),
)
# locate those to be removed
covered_mask = exist(index_from_next, index)
preserve_mask = ~covered_mask
this.data = this.data[preserve_mask]
def test_dtypes(self):
# Test with different data types
for dtype in [np.int16, np.uint16, np.int32,
np.uint32, np.int64, np.uint64]:
coords = np.array(
[[1, 0, 1, 2, 3, 4], [1, 6, 1, 3, 2, 0]], dtype=dtype)
shape = (5, 8)
uncoords = 8*coords[0]+coords[1]
assert_equal(np.ravel_multi_index(coords, shape), uncoords)
assert_equal(coords, np.unravel_index(uncoords, shape))
uncoords = coords[0]+5*coords[1]
assert_equal(
np.ravel_multi_index(coords, shape, order='F'), uncoords)
assert_equal(coords, np.unravel_index(uncoords, shape, order='F'))
coords = np.array(
[[1, 0, 1, 2, 3, 4], [1, 6, 1, 3, 2, 0], [1, 3, 1, 0, 9, 5]],
dtype=dtype)
shape = (5, 8, 10)
uncoords = 10*(8*coords[0]+coords[1])+coords[2]
assert_equal(np.ravel_multi_index(coords, shape), uncoords)
assert_equal(coords, np.unravel_index(uncoords, shape))
uncoords = coords[0]+5*(coords[1]+8*coords[2])
assert_equal(
np.ravel_multi_index(coords, shape, order='F'), uncoords)
assert_equal(coords, np.unravel_index(uncoords, shape, order='F'))
def compute_offsets(self):
# Compute neighbor offsets index.
mask_coords = self.mask_coords
vol_num = self.vol_num
nb_num = self.nb_num
dims = self.dims
mask_idx = np.ravel_multi_index(self.mask_coords.T, dims)
offsets = self.nb_shape.compute_off()
ds_idx = np.arange(vol_num)
volid = np.zeros(nb_num*vol_num)
nbid = np.zeros(nb_num*vol_num)
is_nb = np.zeros(nb_num*vol_num)
count = 0
for v in range(self.vol_num):
v3d = mask_coords[v,:]
nb3d = v3d + offsets.T
imgnb = is_in_image(nb3d, dims)
nb1d = np.ravel_multi_index(nb3d[imgnb, :].T, dims)
is_in_mask = np.in1d(nb1d,mask_idx)
nb1d = nb1d[is_in_mask]
nb_idx_in_mask = np.in1d(mask_idx,nb1d)
nb1d = mask_idx[nb_idx_in_mask]
nb_idx_in_ds = np.nonzero(nb_idx_in_mask)[0]
volnb_num = len(nb1d)
volid[ count: count + volnb_num]= np.tile(v, volnb_num)
nbid[ count: count + volnb_num] = nb_idx_in_ds
is_nb[ count: count + volnb_num] = 1
count = count + volnb_num
neighbor_sparse_matrix = sparse.csc_matrix((is_nb,(volid,nbid)),shape = (vol_num,vol_num))
return neighbor_sparse_matrix
def unpack_array_c(input_data, output_shape):
"""Unpack an array."""
input_data = np.asarray(input_data)
output_data = _prepare_arrays(input_data, output_shape)
input_shape = input_data.shape
# Total number of elements in each type of array.
nft = np.prod(input_shape)
nn = np.prod(output_shape)
# Extract single dimension parameters, where relevant.
ny = output_shape[0]
nf = input_shape[-1]
nx = output_shape[-1]
# Determine the central element.
nfo = nf - 1 if nx % 2 == 0 else nf
for i in range(nft):
# Extract the cartesian coordinates in the original grid.
y = i // nf
x = i % nf
# re-map onto the wider grid.
io = (y * nx) + x
ii = (y * nf) + x
output_data.flat[io] = input_data.flat[ii]
# Check our indexing math with numpy's version.
assert np.allclose([y,x], np.unravel_index(ii, input_shape))
assert np.allclose([io], np.ravel_multi_index([y, x], output_shape))
# If we are at y=0, flip around center.
if y == 0 and 0 < x < nfo:
yo = 0
xo = nx - x
io = (yo * nx) + xo
# Check our math!
assert np.allclose([io], np.ravel_multi_index([yo, xo], output_shape))
assert np.allclose([yo, xo], np.unravel_index(io, output_shape))
# Insert data.
output_data.flat[io] = np.conj(input_data.flat[ii])
# If we are beyond y=0, flip in both axes.
if y > 0 and 0 < x < nfo:
yo = ny - y
xo = nx - x
io = (yo * nx) + xo
# Check our math!
assert np.allclose([io], np.ravel_multi_index([yo, xo], output_shape))
assert np.allclose([yo, xo], np.unravel_index(io, output_shape))
# Insert data.
output_data.flat[io] = np.conj(input_data.flat[ii])
return output_data
def test_clipmodes(self):
# Test clipmodes
assert_equal(np.ravel_multi_index([5,1,-1,2], (4,3,7,12), mode='wrap'),
np.ravel_multi_index([1,1,6,2], (4,3,7,12)))
assert_equal(np.ravel_multi_index([5,1,-1,2], (4,3,7,12),
mode=('wrap','raise','clip','raise')),
np.ravel_multi_index([1,1,0,2], (4,3,7,12)))
assert_raises(ValueError, np.ravel_multi_index, [5,1,-1,2], (4,3,7,12))
def build_diff_matrix(int_band, dxvec, shape):
"""Builds a Laplacian matrix"""
# TODO: generalize this!
shape = shape.astype(np.int64)
dim = len(shape)
if dim == 3:
# Assume now that band is not a linear index, but a 3D index (ie, int_band)
dx, dy, dz = dxvec
weights = np.array([-2/dx**2 -2/dy**2 -2/dz**2,
1/dx**2, 1/dx**2,
1/dy**2, 1/dy**2,
1/dz**2, 1/dz**2])
offsets = np.array([[ 0, 0, 0],
[ 1, 0, 0],
[-1, 0, 0],
[ 0, 1, 0],
[ 0,-1, 0],
[ 0, 0, 1],
[ 0, 0,-1]])
Li = np.tile(np.arange(int_band.shape[0])[:, np.newaxis], weights.size)
Lj = np.zeros_like(Li)
Ls = np.zeros_like(Li, dtype=np.float)
i, j, k = int_band.T #np.ravel_multi_index(band.T, shape)
for c in xrange(weights.size):
ii = i + offsets[c, 0]
jj = j + offsets[c, 1]
kk = k + offsets[c, 2]
Ls[:, c] = weights[c]
Lj[:, c] = np.ravel_multi_index((ii, jj, kk), shape)
L = coo_matrix((Ls.ravel(), (Li.ravel(), Lj.ravel())),
(int_band.shape[0], shape[0] * shape[1] * shape[2])).tocsr()
return L[:, np.ravel_multi_index(int_band.T, shape)]
elif dim == 2:
dx, dy, dz = dxvec
weights = np. array([-2/dx**2 -2/dy**2,
1/dx**2, 1/dx**2,
1/dy**2, 1/dy**2])
offsets = np.array([[ 0, 0],
[ 1, 0],
[-1, 0],
[ 0, 1],
[ 0,-1]])
Li = np.tile(np.arange(int_band.shape[0])[:, np.newaxis], weights.size)
Lj = np.zeros_like(Li)
Ls = np.zeros_like(Li, dtype=np.float)
i, j = int_band.T #np.ravel_multi_index(band.T, shape)
for c in xrange(weights.size):
ii = i + offsets[c, 0]
jj = j + offsets[c, 1]
Ls[:, c] = weights[c]
Lj[:, c] = np.ravel_multi_index((ii, jj), shape)
L = coo_matrix((Ls.ravel(), (Li.ravel(), Lj.ravel())),
(int_band.shape[0], shape[0] * shape[1])).tocsr()
return L[:, np.ravel_multi_index(int_band.T, shape)]
def _inpaint_biharmonic_single_channel(mask, out, limits):
# Initialize sparse matrices
matrix_unknown = sparse.lil_matrix((np.sum(mask), out.size))
matrix_known = sparse.lil_matrix((np.sum(mask), out.size))
# Find indexes of masked points in flatten array
mask_i = np.ravel_multi_index(np.where(mask), mask.shape)
# Find masked points and prepare them to be easily enumerate over
mask_pts = np.array(np.where(mask)).T
# Iterate over masked points
for mask_pt_n, mask_pt_idx in enumerate(mask_pts):
# Get bounded neighborhood of selected radius
b_lo, b_hi = _get_neighborhood(mask_pt_idx, 2, out.shape)
# Create biharmonic coefficients ndarray
neigh_coef = np.zeros(b_hi - b_lo)
neigh_coef[tuple(mask_pt_idx - b_lo)] = 1
neigh_coef = laplace(laplace(neigh_coef))
# Iterate over masked point's neighborhood
it_inner = np.nditer(neigh_coef, flags=['multi_index'])
for coef in it_inner:
if coef == 0:
continue
tmp_pt_idx = np.add(b_lo, it_inner.multi_index)
tmp_pt_i = np.ravel_multi_index(tmp_pt_idx, mask.shape)
if mask[tuple(tmp_pt_idx)]:
matrix_unknown[mask_pt_n, tmp_pt_i] = coef
else:
matrix_known[mask_pt_n, tmp_pt_i] = coef
# Prepare diagonal matrix
flat_diag_image = sparse.dia_matrix((out.flatten(), np.array([0])),
shape=(out.size, out.size))
# Calculate right hand side as a sum of known matrix's columns
matrix_known = matrix_known.tocsr()
rhs = -(matrix_known * flat_diag_image).sum(axis=1)
# Solve linear system for masked points
matrix_unknown = matrix_unknown[:, mask_i]
matrix_unknown = sparse.csr_matrix(matrix_unknown)
result = spsolve(matrix_unknown, rhs)
# Handle enormous values
result = np.clip(result, *limits)
result = result.ravel()
# Substitute masked points with inpainted versions
for mask_pt_n, mask_pt_idx in enumerate(mask_pts):
out[tuple(mask_pt_idx)] = result[mask_pt_n]
return out
def _make_hdu_sparse(data, npix, hdu, header):
shape = data.shape
# We make a copy, because below we modify `data` to handle non-finite entries
# TODO: The code below could probably be simplified to use expressions
# that create new arrays instead of in-place modifications
# But first: do we want / need the non-finite entry handling at all and always cast to 64-bit float?
data = data.copy()
if len(shape) == 2:
data_flat = np.ravel(data)
data_flat[~np.isfinite(data_flat)] = 0
nonzero = np.where(data_flat > 0)
value = data_flat[nonzero].astype(float)
cols = [
fits.Column('PIX', 'J', array=nonzero[0]),
fits.Column('VALUE', 'E', array=value),
]
elif npix[0].size == 1:
shape_flat = shape[:-2] + (shape[-1] * shape[-2],)
data_flat = np.ravel(data).reshape(shape_flat)
data_flat[~np.isfinite(data_flat)] = 0
nonzero = np.where(data_flat > 0)
channel = np.ravel_multi_index(nonzero[:-1], shape[:-2])
value = data_flat[nonzero].astype(float)
cols = [
fits.Column('PIX', 'J', array=nonzero[-1]),
fits.Column('CHANNEL', 'I', array=channel),
fits.Column('VALUE', 'E', array=value),
]
else:
data_flat = []
channel = []
pix = []
for i, _ in np.ndenumerate(npix[0]):
data_i = np.ravel(data[i[::-1]])
data_i[~np.isfinite(data_i)] = 0
pix_i = np.where(data_i > 0)
data_i = data_i[pix_i]
data_flat += [data_i]
pix += pix_i
channel += [np.ones(data_i.size, dtype=int) *
np.ravel_multi_index(i[::-1], shape[:-2])]
pix = np.concatenate(pix)
channel = np.concatenate(channel)
value = np.concatenate(data_flat).astype(float)
cols = [
fits.Column('PIX', 'J', array=pix),
fits.Column('CHANNEL', 'I', array=channel),
fits.Column('VALUE', 'E', array=value),
]
return fits.BinTableHDU.from_columns(cols, header=header, name=hdu)
def symmetrize(self, method=None, copy=False):
'''Symmetrizes (ignores method). Returns a copy if copy=True.'''
if copy:
return SymmEdgePairGraph(self._pairs.copy(),
num_vertices=self._num_vertices)
shape = (self._num_vertices, self._num_vertices)
flat_inds = np.union1d(np.ravel_multi_index(self._pairs.T, shape),
np.ravel_multi_index(self._pairs.T[::-1], shape))
self._pairs = np.transpose(np.unravel_index(flat_inds, shape))
return self
def row_extents(cube, dim_order=None):
if dim_order is None:
dim_order = MS_DIM_ORDER
shape = cube.dim_global_size(*dim_order)
lower = cube.dim_lower_extent(*dim_order)
upper = tuple(u-1 for u in cube.dim_upper_extent(*dim_order))
return (np.ravel_multi_index(lower, shape),
np.ravel_multi_index(upper, shape) + 1)
def getVectorField(Map, sign=True, colorMatrix=None):
X,Y,cardinal = Map.shape
uMatrix = getUmatrix(Map)
uMatrix_ravel = uMatrix.flatten()
distanceMatrix = scipy.spatial.distance.squareform(scipy.spatial.distance.pdist(Map.reshape(X*Y,cardinal)))
vectorsField = numpy.zeros((X,Y,2))
vectors_unit = [(-1/numpy.sqrt(2),-1/numpy.sqrt(2)),(-1,0),(-1/numpy.sqrt(2),1/numpy.sqrt(2)),(0,-1),(0,1),(1/numpy.sqrt(2),-1/numpy.sqrt(2)),(1,0),(1/numpy.sqrt(2),1/numpy.sqrt(2))]
for i in range(X):
for j in range(Y):
iRef = numpy.ravel_multi_index((i%X,j%Y),(X,Y))
jRef1 = numpy.ravel_multi_index(((i-1)%X,(j-1)%Y),(X,Y))
jRef2 = numpy.ravel_multi_index(((i-1)%X,(j)%Y),(X,Y))
jRef3 = numpy.ravel_multi_index(((i-1)%X,(j+1)%Y),(X,Y))
jRef4 = numpy.ravel_multi_index(((i)%X,(j-1)%Y),(X,Y))
jRef5 = numpy.ravel_multi_index(((i)%X,(j+1)%Y),(X,Y))
jRef6 = numpy.ravel_multi_index(((i+1)%X,(j-1)%Y),(X,Y))
jRef7 = numpy.ravel_multi_index(((i+1)%X,(j)%Y),(X,Y))
jRef8 = numpy.ravel_multi_index(((i+1)%X,(j+1)%Y),(X,Y))
norms = [distanceMatrix[iRef,jRef1], distanceMatrix[iRef,jRef2], distanceMatrix[iRef,jRef3], distanceMatrix[iRef,jRef4], distanceMatrix[iRef,jRef5], distanceMatrix[iRef,jRef6], distanceMatrix[iRef,jRef7], distanceMatrix[iRef,jRef8]]
if sign:
signs = [numpy.sign(uMatrix_ravel[iRef]-uMatrix_ravel[e]) for e in [jRef1,jRef2,jRef3,jRef4,jRef5,jRef6,jRef7,jRef8]]
norms = numpy.array(signs)*numpy.array(norms)
vectors = numpy.atleast_2d(norms).T*numpy.array(vectors_unit)
vectorsField[i,j] = vectors.sum(axis=0)
if colorMatrix == None:
vectorsFieldPlot = matplotlib.pyplot.quiver(vectorsField[:,:,1], vectorsField[:,:,0], uMatrix, units='xy', pivot='tail')
else:
vectorsFieldPlot = matplotlib.pyplot.quiver(vectorsField[:,:,1], vectorsField[:,:,0], colorMatrix, units='xy', pivot='tail')
return vectorsField
def _random_correlated_image(mean, sigma, image_shape, alpha=0.3, rng=None):
"""
Creates a random image with correlated neighbors.
pixel covariance is sigma^2, direct neighors pixel covariance is alpha * sigma^2.
Parameters
----------
mean : the mean value of the image pixel values.
sigma : the std dev of image pixel values.
image_shape : tuple, shape = (3, )
alpha : the neighbors correlation factor.
rng : random number generator (a numpy.random.RandomState instance).
"""
dim_x, dim_y, dim_z = image_shape
dim_image = dim_x * dim_y * dim_z
correlated_image = 0
for neighbor in [(1, 0, 0), (0, 1, 0), (0, 0, 1)]:
corr_data = []
corr_i = []
corr_j = []
for i, j, k in [(0, 0, 0), neighbor]:
d2 = 1.0 * (i*i + j*j + k*k)
ind = np.asarray(np.mgrid[0:dim_x-i, 0:dim_y-j, 0:dim_z-k], dtype=np.int)
ind = ind.reshape((3, (dim_x - i) * (dim_y - j) * (dim_z - k)))
corr_i.extend(np.ravel_multi_index(ind, (dim_x, dim_y, dim_z)).tolist())
corr_j.extend(np.ravel_multi_index(ind + np.asarray([i, j, k])[:, None],
(dim_x, dim_y, dim_z)).tolist())
if i>0 or j>0 or k>0:
corr_i.extend(np.ravel_multi_index(ind + np.asarray([i, j, k])[:, None],
(dim_x, dim_y, dim_z)).tolist())
corr_j.extend(np.ravel_multi_index(ind, (dim_x, dim_y, dim_z)).tolist())
if i==0 and j==0 and k==0:
corr_data.extend([3.0] * ind.shape[1])
else:
corr_data.extend([alpha * 3.0] * 2 * ind.shape[1])
correlation = scisp.csc_matrix((corr_data, (corr_i, corr_j)), shape=(dim_image, dim_image))
factor = cholesky(correlation)
L = factor.L()
P = factor.P()[None, :]
P = scisp.csc_matrix((np.ones(dim_image),
np.vstack((P, np.asarray(range(dim_image))[None, :]))),
shape=(dim_image, dim_image))
sq_correlation = P.dot(L)
X = rng.normal(0, 1, dim_image)
Y = sq_correlation.dot(X)
Y = Y.reshape((dim_x, dim_y, dim_z))
X = X.reshape((dim_x, dim_y, dim_z))
correlated_image += Y
correlated_image /= 3
return correlated_image * sigma + mean
def numpy_run_cut(self, cut, coords):
batch, y1, x1, ch, out_y, out_x = coords
cut_index = self.numpy_run_cut_offset(
cut, numpy.ravel_multi_index((batch, out_y, out_x, ch),
self.output.shape))
i, j = numpy.unravel_index(cut_index, cut.shape)
idx = numpy.ravel_multi_index((batch, y1 + i, x1 + j, ch),
self.input.shape)
val = numpy.ravel(self.input.mem)[idx]
self.input_offset.mem[batch, out_y, out_x, ch] = idx
return val
def adding_to_gridbit(bit, gridtf, dims):
refbit = bit.copy()
adding = False
for i in refbit:
for delta in zip(adj_x, adj_y):
j = np.array(delta) + np.unravel_index(i, dims)
if gridtf[np.ravel_multi_index(j, dims, 'wrap')]:
gridtf[np.ravel_multi_index(j, dims, 'wrap')] = False
bit.add(np.ravel_multi_index(j, dims, 'wrap'))
adding = True
return adding
def test_clipmodes(self):
# Test clipmodes
assert_equal(
np.ravel_multi_index([5, 1, -1, 2], (4, 3, 7, 12), mode="wrap"),
np.ravel_multi_index([1, 1, 6, 2], (4, 3, 7, 12)),
)
assert_equal(
np.ravel_multi_index([5, 1, -1, 2], (4, 3, 7, 12), mode=("wrap", "raise", "clip", "raise")),
np.ravel_multi_index([1, 1, 0, 2], (4, 3, 7, 12)),
)
assert_raises(ValueError, np.ravel_multi_index, [5, 1, -1, 2], (4, 3, 7, 12))
def basis_span(self, i):
self.check_index(i)
indx = np.unravel_index(i, self.shape)
min_indices = []
max_indices = []
for j in range(len(self.shape)):
min_indices.append(np.min(self.space_list[j].basis_span(indx[j])))
max_indices.append(np.max(self.space_list[j].basis_span(indx[j])))
i1 = np.ravel_multi_index(min_indices, self.shape)
i2 = np.ravel_multi_index(max_indices, self.shape)
return (i1, i2)
def skeleton_to_gt_graph(skeleton, with_coordinates = True, verbose = True):
"""Converts a binary skeleton image to a networkx graph
Arguments:
skeleton (array): 2d/3d binary skeleton image
Returns:
dict: dict of adjacency information with entries node_id : [neighbours]
"""
dim = skeleton.ndim;
shape =skeleton.shape;
coords, nh = skeleton_to_list(skeleton, with_neighborhoods = True);
nnodes = coords.shape[0];
coordids = np.ravel_multi_index(coords.T, shape);
coordids2ids = { k:i for i,k in enumerate(coordids) };
# create graph
if verbose:
print('creating graph...');
g = gt.Graph(directed = False);
g.add_vertex(nnodes);
if with_coordinates:
if verbose:
print('creating coordinate properties...')
vp = g.new_vertex_property('int', coords[:,0]);
g.vertex_properties['x'] = vp;
vp = g.new_vertex_property('int', coords[:,1]);
g.vertex_properties['y'] = vp;
if dim > 2:
vp = g.new_vertex_property('int', coords[:,2]);
g.vertex_properties['z'] = vp;
for i, pos in enumerate(coords):
if verbose and i % 1000 == 0:
print('%d/%d nodes constructed...' % (i, len(coords)));
#print 'nh'
#print nh[i]
posnh = np.transpose(np.where(nh[i]));
#print 'pos'
#print pos
#print posnh
if len(posnh) > 0:
posnh = np.array(posnh + pos - 1);
#print posnh
#print posnh.shape
ids = np.ravel_multi_index(posnh.T, shape);
#print ids
for j in [coordids2ids[k] for k in ids]:
if i < j:
g.add_edge(i,j);
return g
except ValueError:
print '--> Please enter an integer'
while True:
try:
hifac = float(raw_input('--> Nyquist range factor: '))
break
except ValueError:
print '--> Please enter a float'
print ' '
print ' '
### ETC ###
# dynamic variable names
for (j, k), img in np.ndenumerate(temp2d):
index = np.ravel_multi_index((j, k), table2.shape)
exec("pixel%d_flux = np.array(None)" % index)
exec("pixel%d_time = np.array(None)" % index)
# filling the flux array
for l in range(stitchcounter):
m = l + 1
exec("second_flux%d = np.zeros([xsize, ysize%d])" % (m, m))
exec("flux = flux%d" % m)
for (i, j, k), val in np.ndenumerate(flux):
index = (j + 1) * k + (x - k) * j
exec("second_flux%d[index, i] = val" % m)
exp = raw_input('--> Export data for each pixel? (y/n) ')
while exp != "y" and exp != "n":
exp = raw_input('--> Please enter y or n: ')
def grid_coordinates_to_indices(self, coordinates=None):
# pdb.set_trace()
if coordinates is None:
return np.arange(self.size)
return np.ravel_multi_index(coordinates, self.shape)
def create_adr_features(features,
durations,
id2idx,
k,
feature_grid,
kmeans=True):
pca = PCA(n_components=1)
print("Num features: ", len(features))
if durations is not None:
durations = np.array(durations)
#normalize
np_features = np.array(features)
print("Feature shape", np_features.shape)
if kmeans:
clustering = KMeans(n_clusters=min(k, len(np_features)),
random_state=0).fit(np_features)
labels = clustering.labels_
centroids = clustering.cluster_centers_
else:
clustering = MiniSom(k,
k,
np_features.shape[1],
sigma=0.5,
learning_rate=0.2,
neighborhood_function='gaussian',
random_seed=10)
clustering.train_batch(features, 500, verbose=True)
labels = np.array([clustering.winner(x) for x in features]).T
labels = np.ravel_multi_index(labels, (k, k))
print("Labels shape", labels.shape)
print("Labels count:", len(Counter(labels)))
data = []
for id, idxs in id2idx.items():
doc_distrib = labels[idxs]
doc_embeds = np_features[idxs]
if kmeans:
centroid_velocities = np.zeros((len(doc_distrib) - 1))
embed_velocities = np.zeros((len(doc_distrib) - 1))
for i in range(1, len(doc_distrib)):
len(doc_distrib)
label1 = doc_distrib[i]
label2 = doc_distrib[i - 1]
cs_centroids = cosine_similarity([centroids[label1]],
[centroids[label2]])[0][0]
cs_embeds = cosine_similarity([doc_embeds[i]],
[doc_embeds[i - 1]])[0][0]
embed_velocities[i - 1] = cs_embeds
centroid_velocities[i - 1] = cs_centroids
if len(centroid_velocities) > 128:
centroid_velocities = centroid_velocities[:128]
embed_velocities = embed_velocities[:128]
else:
centroid_velocities = np.pad(
centroid_velocities, (0, 128 - len(centroid_velocities)),
'constant',
constant_values=(0, 0))
embed_velocities = np.pad(embed_velocities,
(0, 128 - len(embed_velocities)),
'constant',
constant_values=(0, 0))
centroid_embeds = np.zeros((len(doc_distrib), doc_embeds.shape[1]))
for i in range(len(doc_distrib)):
label = doc_distrib[i]
centroid_embed = centroids[label]
centroid_embeds[i, :] = centroid_embed
centroid_embeds = pca.fit_transform(centroid_embeds).squeeze()
if len(centroid_embeds) > 128:
centroid_embeds = centroid_embeds[:128]
else:
centroid_embeds = np.pad(centroid_embeds,
(0, 128 - len(centroid_embeds)),
'constant',
constant_values=(0, 0))
label_velocities = []
for i in range(1, len(doc_distrib)):
diff_labels = doc_distrib[i] - doc_distrib[i - 1]
label_velocities.append(diff_labels)
label_acceleration = []
for i in range(1, len(label_velocities)):
diff_labels = label_velocities[i] - label_velocities[i - 1]
label_acceleration.append(diff_labels)
#get count features
c = Counter(doc_distrib)
num_all = len(doc_distrib)
counts = []
for i in range(k):
if i in c:
counts.append(c[i])
else:
counts.append(0)
counts = [x / num_all for x in counts]
#get embedding features
embeds = pca.fit_transform(doc_embeds).squeeze()
if len(embeds) > 128:
embeds = embeds[:128]
else:
embeds = np.pad(embeds, (0, 128 - len(embeds)),
'constant',
constant_values=(0, 0))
#duration
if durations is not None:
doc_dur = durations[idxs]
dur_dict = defaultdict(int)
all_dur = sum(doc_dur)
for l, dur in zip(doc_distrib, doc_dur):
dur_dict[l] += dur
doc_durations = []
for i in range(k):
if i in dur_dict:
doc_durations.append(dur_dict[i] / all_dur)
else:
doc_durations.append(0)
#print(id, doc_durations)
features = id.split('-')
if 'duration' in feature_grid and durations is not None:
features = features + doc_durations
if 'counts' in feature_grid:
features = features + counts
if 'embeds' in feature_grid:
features = features + list(embeds)
if 'centroid_embeds' in feature_grid:
features = features + list(centroid_embeds)
if 'embed_velocity' in feature_grid:
features = features + list(embed_velocities)
if 'centroid_velocity' in feature_grid and kmeans:
features = features + list(centroid_velocities)
data.append(features)
return data
def _get_sparse_rpn_targets(self, coords, anchors, anchor_coords, gt_boxes, gt_rotations,
gt_classes, rpn_strides):
def _split_layer(target, num_layer_anchors):
assert num_layer_anchors[-1] == target.shape[0]
return np.split(target, num_layer_anchors)
num_layer_anchors = np.cumsum([x.shape[0] for x in anchor_coords])
# Precompute anchors that may potentially hit based on input coordinates.
anchor_dcoords = np.floor(np.concatenate(anchor_coords) / rpn_strides[-1]).astype(int)
anchor_ddim = anchor_dcoords.max(0) - anchor_dcoords.min(0) + 2
anchor_idxs = np.ravel_multi_index((anchor_dcoords - anchor_dcoords.min(0)).T, anchor_ddim)
anchor_kernel_perm = np.array(list(itertools.product(*[range(-1, 2)] * 3)))
anchor_masks = []
for coord in coords:
anchor_hit = np.full(np.prod(anchor_ddim), False)
coords_dcoords = np.unique(np.floor(coord / rpn_strides[-1]).astype(int), axis=0)
coords_perm = (np.tile(np.expand_dims(coords_dcoords, 0), (3 ** 3, 1, 1))
+ np.expand_dims(anchor_kernel_perm, 1)).reshape(-1, 3)
coords_idxs = np.ravel_multi_index((coords_perm - anchor_dcoords.min(0)).T, anchor_ddim)
anchor_hit[coords_idxs] = True
anchor_masks.append(anchor_hit[anchor_idxs])
rpn_match, rpn_bbox, rpn_rotation, rpn_cls = self._get_rpn_targets(
anchors, gt_boxes, gt_rotations, gt_classes, anchor_masks=anchor_masks)
# Split dense regression targets based on layer index.
anchors = _split_layer(anchors, num_layer_anchors)
num_anchors = self.anchor_ratios.shape[0]
num_batch = len(rpn_match)
anchors_layer = []
anchor_coords_layer = []
rpn_match_layer = []
rpn_bbox_layer = []
rpn_cls_layer = []
rpn_rot_layer = []
for batch_idx in range(num_batch):
mask_layer = _split_layer(anchor_masks[batch_idx], num_layer_anchors)
batch_layer_anchors = np.cumsum([i.sum() for i in mask_layer][:-1])
rpn_positive_mask = np.where(rpn_match[batch_idx] == 1)
rpn_aligned_positive_mask = np.where(~np.all(rpn_bbox[batch_idx] == 0, -1))
anchors_layer.append([ac[ml] for ac, ml in zip(anchors, mask_layer)])
anchor_coords_layer.append([ac[ml] for ac, ml in zip(anchor_coords, mask_layer)])
rpn_match_layer.append(_split_layer(rpn_match[batch_idx], batch_layer_anchors))
rpn_bbox_aligned = np.zeros_like(rpn_bbox[batch_idx])
rpn_bbox_aligned[rpn_positive_mask] = rpn_bbox[batch_idx][rpn_aligned_positive_mask]
rpn_bbox_aligned = _split_layer(rpn_bbox_aligned, batch_layer_anchors)
rpn_bbox_layer.append(rpn_bbox_aligned)
rpn_cls_aligned = np.ones_like(rpn_cls[batch_idx]) * -1
rpn_cls_aligned[rpn_positive_mask] = rpn_cls[batch_idx][rpn_aligned_positive_mask]
rpn_cls_aligned = _split_layer(rpn_cls_aligned, batch_layer_anchors)
rpn_cls_layer.append(rpn_cls_aligned)
if rpn_rotation is not None:
rpn_rotation_aligned = np.zeros_like(rpn_rotation[batch_idx])
rpn_rotation_aligned[rpn_positive_mask] = rpn_rotation[batch_idx][rpn_aligned_positive_mask]
rpn_rotation_aligned = _split_layer(rpn_rotation_aligned, batch_layer_anchors)
rpn_rot_layer.append(rpn_rotation_aligned)
anchors_layer = list(zip(*anchors_layer))
anchor_coords_layer = list(zip(*anchor_coords_layer))
rpn_match_layer = list(zip(*rpn_match_layer))
rpn_bbox_layer = list(zip(*rpn_bbox_layer))
rpn_cls_layer = list(zip(*rpn_cls_layer))
rpn_rot_layer = None if rpn_rotation is None else list(zip(*rpn_rot_layer))
# Accumulate regression target in sparse tensor format.
sparse_anchor_centers = []
sparse_anchor_coords = []
sparse_rpn_matches = []
sparse_rpn_bboxes = []
sparse_rpn_cls = []
sparse_rpn_rotations = [] if rpn_rotation is not None else None
for layer_idx in range(len(anchor_coords)):
tensor_stride = rpn_strides[layer_idx]
sparse_anchor_centers.append(
torch.from_numpy(np.vstack(anchors_layer[layer_idx]).reshape(-1, num_anchors * 6)))
sub_anchor_coords = ME.utils.batched_coordinates([ac[::num_anchors] for ac
in anchor_coords_layer[layer_idx]])
sub_anchor_coords[:, 1:] -= tensor_stride // 2
sparse_anchor_coords.append(sub_anchor_coords)
sparse_rpn_matches.append(
torch.from_numpy(np.concatenate(rpn_match_layer[layer_idx]).reshape(-1, num_anchors)))
sparse_rpn_bboxes.append(
torch.from_numpy(np.concatenate(rpn_bbox_layer[layer_idx]).reshape(-1, num_anchors * 6)))
sparse_rpn_cls.append(
torch.from_numpy(np.concatenate(rpn_cls_layer[layer_idx]).reshape(-1, num_anchors)))
if sparse_rpn_rotations is not None:
sparse_rpn_rotations.append(
torch.from_numpy(np.concatenate(rpn_rot_layer[layer_idx]).reshape(-1, num_anchors)))
# Precompute positive/ambiguous target coordinates for sparse generative RPN.
anchor_match_coords = []
for batch_idx in range(num_batch):
batch_match_coords = []
for layer_idx in range(len(anchor_coords)):
layer_match = rpn_match_layer[layer_idx][batch_idx]
layer_coords = anchor_coords_layer[layer_idx][batch_idx]
positive_match = np.where(layer_match == 1)
if np.any(positive_match):
positive_coords = np.unique(layer_coords[positive_match], axis=0)
else:
positive_coords = np.zeros((0, 3))
ambiguous_match = np.where(layer_match == 0)
if np.any(ambiguous_match):
ambiguous_coords = np.unique(layer_coords[ambiguous_match], axis=0)
else:
ambiguous_coords = np.zeros((0, 3))
batch_match_coords.append((positive_coords, ambiguous_coords))
anchor_match_coords.append(batch_match_coords)
return (anchor_match_coords, sparse_anchor_centers, sparse_anchor_coords, sparse_rpn_matches,
sparse_rpn_bboxes, sparse_rpn_rotations, sparse_rpn_cls)
print(np.max(a))
print(count)
a = np.array(a)[np.array(a)>0].astype(np.int)
count+=1
img_mont_ = all_masks_gt[np.array(a)].squeeze()
shps_img = img_mont_.shape
img_mont = montage2d(img_mont_)
shps_img_mont = np.array(img_mont.shape)//50
pl.figure(figsize=(20,30))
pl.imshow(img_mont)
inp = pl.ginput(n=0,timeout = -100000)
imgs_to_exclude = []
inp = np.ceil(np.array(inp)/50).astype(np.int)-1
if len(inp)>0:
imgs_to_exclude = img_mont_[np.ravel_multi_index([inp[:,1],inp[:,0]],shps_img_mont)]
# pl.imshow(montage2d(imgs_to_exclude))
wrong.append(np.array(a)[np.ravel_multi_index([inp[:,1],inp[:,0]],shps_img_mont)])
np.save('temp_label_pos_minions.npy',wrong)
pl.close()
#%%
pl.imshow(montage2d(all_masks_gt[np.concatenate(wrong)].squeeze()))
#%%
lab_pos_wrong = np.load('temp_label_pos_minions.npy')
lab_neg_wrong = np.load('temp_label_neg_plus_minions.npy')
labels_gt_cur = labels_gt.copy()
labels_gt_cur[np.concatenate(lab_pos_wrong)] = 0
labels_gt_cur[np.concatenate(lab_neg_wrong)] = 1
np.savez('ground_truth_comoponents_curated_minions.npz',all_masks_gt = all_masks_gt,labels_gt_cur = labels_gt_cur)
def _action_from_move(move: chess.Move) -> Action:
return np.ravel_multi_index(
(move.from_square, move.to_square, move.promotion != None),
_action_shape)
def getIndex(self, s):
return np.ravel_multi_index(s, self.state_shape)
def bincount_app(a):
a2D = a.reshape(-1, a.shape[-1])
col_range = (256, 256, 256) # generically : a2D.max(0)+1
a1D = np.ravel_multi_index(a2D.T, col_range)
return np.unravel_index(np.bincount(a1D).argmax(), col_range)
def frontalize(img, proj_matrix, ref_U, eyemask):
ACC_CONST = 800
img = img.astype('float32')
print("query image shape:", img.shape)
bgind = np.sum(np.abs(ref_U), 2) == 0
# count the number of times each pixel in the query is accessed
threedee = np.reshape(ref_U, (-1, 3), order='F').transpose()
temp_proj = proj_matrix * np.vstack(
(threedee, np.ones((1, threedee.shape[1]))))
temp_proj2 = np.divide(temp_proj[0:2, :], np.tile(temp_proj[2, :], (2, 1)))
bad = np.logical_or(
temp_proj2.min(axis=0) < 1, temp_proj2[1, :] > img.shape[0])
bad = np.logical_or(bad, temp_proj2[0, :] > img.shape[1])
bad = np.logical_or(bad, bgind.reshape((-1), order='F'))
bad = np.asarray(bad).reshape((-1), order='F')
temp_proj2 -= 1
badind = np.nonzero(bad > 0)[0]
temp_proj2[:, badind] = 0
ind = np.ravel_multi_index(
(np.asarray(temp_proj2[1, :].round(), dtype='int64'),
np.asarray(temp_proj2[0, :].round(), dtype='int64')),
dims=img.shape[:-1],
order='F')
synth_frontal_acc = np.zeros(ref_U.shape[:-1])
ind_frontal = np.arange(0, ref_U.shape[0] * ref_U.shape[1])
c, ic = np.unique(ind, return_inverse=True)
bin_edges = np.r_[-np.Inf, 0.5 * (c[:-1] + c[1:]), np.Inf]
count, bin_edges = np.histogram(ind, bin_edges)
synth_frontal_acc = synth_frontal_acc.reshape(-1, order='F')
synth_frontal_acc[ind_frontal] = count[ic]
synth_frontal_acc = synth_frontal_acc.reshape((320, 320), order='F')
synth_frontal_acc[bgind] = 0
synth_frontal_acc = cv2.GaussianBlur(synth_frontal_acc, (15, 15),
30.,
borderType=cv2.BORDER_REPLICATE)
#remap
mapX = temp_proj2[0, :].astype(np.float32)
mapY = temp_proj2[1, :].astype(np.float32)
mapX = np.reshape(mapX, (-1, 320), order='F')
mapY = np.reshape(mapY, (-1, 320), order='F')
frontal_raw = cv2.remap(img, mapX, mapY, cv2.INTER_CUBIC)
frontal_raw = frontal_raw.reshape((-1, 3), order='F')
frontal_raw[badind, :] = 0
frontal_raw = frontal_raw.reshape((320, 320, 3), order='F')
# which side has more occlusions?
midcolumn = np.round(ref_U.shape[1] / 2)
sumaccs = synth_frontal_acc.sum(axis=0)
sum_left = sumaccs[0:midcolumn].sum()
sum_right = sumaccs[midcolumn + 1:].sum()
sum_diff = sum_left - sum_right
if np.abs(sum_diff) > ACC_CONST: # one side is ocluded
ones = np.ones((ref_U.shape[0], midcolumn))
zeros = np.zeros((ref_U.shape[0], midcolumn))
if sum_diff > ACC_CONST: # left side of face has more occlusions
weights = np.hstack((zeros, ones))
else: # right side of face has more occlusions
weights = np.hstack((ones, zeros))
weights = cv2.GaussianBlur(weights, (33, 33),
60.5,
borderType=cv2.BORDER_REPLICATE)
# apply soft symmetry to use whatever parts are visible in ocluded side
synth_frontal_acc /= synth_frontal_acc.max()
weight_take_from_org = 1. / np.exp(0.5 + synth_frontal_acc)
weight_take_from_sym = 1 - weight_take_from_org
weight_take_from_org = np.multiply(weight_take_from_org,
np.fliplr(weights))
weight_take_from_sym = np.multiply(weight_take_from_sym,
np.fliplr(weights))
weight_take_from_org = np.tile(
weight_take_from_org.reshape(320, 320, 1), (1, 1, 3))
weight_take_from_sym = np.tile(
weight_take_from_sym.reshape(320, 320, 1), (1, 1, 3))
weights = np.tile(weights.reshape(320, 320, 1), (1, 1, 3))
denominator = weights + weight_take_from_org + weight_take_from_sym
frontal_sym = np.multiply(frontal_raw, weights) + np.multiply(
frontal_raw, weight_take_from_org) + np.multiply(
np.fliplr(frontal_raw), weight_take_from_sym)
frontal_sym = np.divide(frontal_sym, denominator)
# exclude eyes from symmetry
frontal_sym = np.multiply(frontal_sym, 1 - eyemask) + np.multiply(
frontal_raw, eyemask)
frontal_raw[frontal_raw > 255] = 255
frontal_raw[frontal_raw < 0] = 0
frontal_raw = frontal_raw.astype('uint8')
frontal_sym[frontal_sym > 255] = 255
frontal_sym[frontal_sym < 0] = 0
frontal_sym = frontal_sym.astype('uint8')
else: # both sides are occluded pretty much to the same extent -- do not use symmetry
frontal_sym = frontal_raw
return frontal_raw, frontal_sym
def _get_multi_index(self, arr, indices):
"""Mimic multi dimensional indexing.
Parameters
----------
arr : ndarray
Array to be indexed.
indices : tuple of index objects
Returns
-------
out : ndarray
An array equivalent to the indexing operation (but always a copy).
`arr[indices]` should be identical.
no_copy : bool
Whether the indexing operation requires a copy. If this is `True`,
`np.may_share_memory(arr, arr[indicies])` should be `True` (with
some exceptions for scalars and possibly 0-d arrays).
Notes
-----
While the function may mostly match the errors of normal indexing this
is generally not the case.
"""
in_indices = list(indices)
indices = []
# if False, this is a fancy or boolean index
no_copy = True
# number of fancy/scalar indexes that are not consecutive
num_fancy = 0
# number of dimensions indexed by a "fancy" index
fancy_dim = 0
# NOTE: This is a funny twist (and probably OK to change).
# The boolean array has illegal indexes, but this is
# allowed if the broadcast fancy-indices are 0-sized.
# This variable is to catch that case.
error_unless_broadcast_to_empty = False
# We need to handle Ellipsis and make arrays from indices, also
# check if this is fancy indexing (set no_copy).
ndim = 0
ellipsis_pos = None # define here mostly to replace all but first.
for i, indx in enumerate(in_indices):
if indx is None:
continue
if isinstance(indx, np.ndarray) and indx.dtype == bool:
no_copy = False
if indx.ndim == 0:
raise IndexError
# boolean indices can have higher dimensions
ndim += indx.ndim
fancy_dim += indx.ndim
continue
if indx is Ellipsis:
if ellipsis_pos is None:
ellipsis_pos = i
continue # do not increment ndim counter
raise IndexError
if isinstance(indx, slice):
ndim += 1
continue
if not isinstance(indx, np.ndarray):
# This could be open for changes in numpy.
# numpy should maybe raise an error if casting to intp
# is not safe. It rejects np.array([1., 2.]) but not
# [1., 2.] as index (same for ie. np.take).
# (Note the importance of empty lists if changing this here)
indx = np.array(indx, dtype=np.intp)
in_indices[i] = indx
elif indx.dtype.kind != 'b' and indx.dtype.kind != 'i':
raise IndexError(
'arrays used as indices must be of integer (or boolean) type'
)
if indx.ndim != 0:
no_copy = False
ndim += 1
fancy_dim += 1
if arr.ndim - ndim < 0:
# we can't take more dimensions then we have, not even for 0-d arrays.
# since a[()] makes sense, but not a[(),]. We will raise an error
# later on, unless a broadcasting error occurs first.
raise IndexError
if ndim == 0 and None not in in_indices:
# Well we have no indexes or one Ellipsis. This is legal.
return arr.copy(), no_copy
if ellipsis_pos is not None:
in_indices[ellipsis_pos:ellipsis_pos +
1] = [slice(None, None)] * (arr.ndim - ndim)
for ax, indx in enumerate(in_indices):
if isinstance(indx, slice):
# convert to an index array
indx = np.arange(*indx.indices(arr.shape[ax]))
indices.append(['s', indx])
continue
elif indx is None:
# this is like taking a slice with one element from a new axis:
indices.append(['n', np.array([0], dtype=np.intp)])
arr = arr.reshape((arr.shape[:ax] + (1, ) + arr.shape[ax:]))
continue
if isinstance(indx, np.ndarray) and indx.dtype == bool:
if indx.shape != arr.shape[ax:ax + indx.ndim]:
raise IndexError
try:
flat_indx = np.ravel_multi_index(np.nonzero(indx),
arr.shape[ax:ax +
indx.ndim],
mode='raise')
except:
error_unless_broadcast_to_empty = True
# fill with 0s instead, and raise error later
flat_indx = np.array([0] * indx.sum(), dtype=np.intp)
# concatenate axis into a single one:
if indx.ndim != 0:
arr = arr.reshape(
(arr.shape[:ax] +
(np.prod(arr.shape[ax:ax + indx.ndim]), ) +
arr.shape[ax + indx.ndim:]))
indx = flat_indx
else:
# This could be changed, a 0-d boolean index can
# make sense (even outside the 0-d indexed array case)
# Note that originally this is could be interpreted as
# integer in the full integer special case.
raise IndexError
else:
# If the index is a singleton, the bounds check is done
# before the broadcasting. This used to be different in <1.9
if indx.ndim == 0:
if indx >= arr.shape[ax] or indx < -arr.shape[ax]:
raise IndexError
if indx.ndim == 0:
# The index is a scalar. This used to be two fold, but if fancy
# indexing was active, the check was done later, possibly
# after broadcasting it away (1.7. or earlier). Now it is always
# done.
if indx >= arr.shape[ax] or indx < -arr.shape[ax]:
raise IndexError
if len(indices
) > 0 and indices[-1][0] == 'f' and ax != ellipsis_pos:
# NOTE: There could still have been a 0-sized Ellipsis
# between them. Checked that with ellipsis_pos.
indices[-1].append(indx)
else:
# We have a fancy index that is not after an existing one.
# NOTE: A 0-d array triggers this as well, while
# one may expect it to not trigger it, since a scalar
# would not be considered fancy indexing.
num_fancy += 1
indices.append(['f', indx])
if num_fancy > 1 and not no_copy:
# We have to flush the fancy indexes left
new_indices = indices[:]
axes = list(range(arr.ndim))
fancy_axes = []
new_indices.insert(0, ['f'])
ni = 0
ai = 0
for indx in indices:
ni += 1
if indx[0] == 'f':
new_indices[0].extend(indx[1:])
del new_indices[ni]
ni -= 1
for ax in range(ai, ai + len(indx[1:])):
fancy_axes.append(ax)
axes.remove(ax)
ai += len(indx) - 1 # axis we are at
indices = new_indices
# and now we need to transpose arr:
arr = arr.transpose(*(fancy_axes + axes))
# We only have one 'f' index now and arr is transposed accordingly.
# Now handle newaxis by reshaping...
ax = 0
for indx in indices:
if indx[0] == 'f':
if len(indx) == 1:
continue
# First of all, reshape arr to combine fancy axes into one:
orig_shape = arr.shape
orig_slice = orig_shape[ax:ax + len(indx[1:])]
arr = arr.reshape(
(arr.shape[:ax] + (np.prod(orig_slice).astype(int), ) +
arr.shape[ax + len(indx[1:]):]))
# Check if broadcasting works
if len(indx[1:]) != 1:
res = np.broadcast(*indx[1:]) # raises ValueError...
else:
res = indx[1]
# unfortunately the indices might be out of bounds. So check
# that first, and use mode='wrap' then. However only if
# there are any indices...
if res.size != 0:
if error_unless_broadcast_to_empty:
raise IndexError
for _indx, _size in zip(indx[1:], orig_slice):
if _indx.size == 0:
continue
if np.any(_indx >= _size) or np.any(_indx < -_size):
raise IndexError
if len(indx[1:]) == len(orig_slice):
if np.product(orig_slice) == 0:
# Work around for a crash or IndexError with 'wrap'
# in some 0-sized cases.
try:
mi = np.ravel_multi_index(indx[1:],
orig_slice,
mode='raise')
except:
# This happens with 0-sized orig_slice (sometimes?)
# here it is a ValueError, but indexing gives a:
raise IndexError('invalid index into 0-sized')
else:
mi = np.ravel_multi_index(indx[1:],
orig_slice,
mode='wrap')
else:
# Maybe never happens...
raise ValueError
arr = arr.take(mi.ravel(), axis=ax)
arr = arr.reshape(
(arr.shape[:ax] + mi.shape + arr.shape[ax + 1:]))
ax += mi.ndim
continue
# If we are here, we have a 1D array for take:
arr = arr.take(indx[1], axis=ax)
ax += 1
return arr, no_copy
if rand == 1:
d_x = d_y = (snr * m)**0.5
hat_r_s = hat_r_s_naive_fixed_stim(r_n, r_s, d_x, d_y, n_x, n_y, n,
m)
else:
hat_r_s = hat_r_s_naive_rand_stim(r_n, r_s, d_x, d_y, n_x, n_y, n)
da.loc[snr, n, r_s, r_n] = hat_r_s
das.append(da)
plt.figure(figsize=(5.6, 5.6))
ticks = np.linspace(-1, 1, 9)
#tick_labels = ['' , '-0.5', '' , '-1'][::-1]+['0', '', '0.5', '', '1']
for i in range(3):
for j in range(3):
dat = da[:, i, j]
k = np.ravel_multi_index((i, j), dims=(3, 3))
plt.subplot(3, 3, k + 1)
for q in range(3):
plt.plot(dat.coords['r_n'].values, dat[q], color=colors[q])
plt.axis('square')
plt.ylim(-1, 1)
plt.xlim(-1, 1)
plt.xticks(ticks)
plt.yticks(ticks)
#plt.grid()
if i == 0:
plt.title('\n \n' + '$r_s$=' + str(dat.coords['r_s'].values))
if j == 2:
plt.ylabel('$n=$' + str(dat.coords['n'].values),
def dwel_image_random_sampling(maskfile, outfile, classes=None, numsamples=100, \
maskb=1, ancfile=None, ancb=1, \
maskcircle=None):
"""
Generate random samples from a mask image file of DWEL data. Currently only
support simply random sampling design.
Args:
maskfile: mask image file. 1 (not 0) is valid pixels where random
samples will be drawn from.
maskb (int): band index of mask in the mask file, with first band being
1.
ancb (int): band index of anciilary attribute to attach to random
samples, with first band being 1.
maskcircle (tuple): 3-element tuple giving (center_x, center_y, radius)
of a circle within which random samples are drawn from.
Returns:
"""
# read mask file
maskds = gdal.Open(maskfile, gdal.GA_ReadOnly)
maskband = maskds.GetRasterBand(maskb)
mask = maskband.ReadAsArray(0, 0, maskband.XSize, maskband.YSize).astype(np.int)
# read ancillary attribute band if it is given
addatt = False
if not (ancfile is None):
ancds = gdal.Open(ancfile, gdal.GA_ReadOnly)
ancband = ancds.GetRasterBand(ancb)
if (ancband.XSize != maskband.XSize) or (ancband.YSize != maskband.YSize):
print "Warning: Dimension of ancillary attribute image differs from input mask image."
print "No attribute will be added"
else:
ancatt = ancband.ReadAsArray(0, 0, ancband.XSize, ancband.YSize)
addatt = True
ancds = None
maskds = None
validx, validy = np.nonzero(mask)
# if a circle is given to define the area for random samples
if maskcircle is not None:
tmpflag = (validx - maskcircle[0])**2 + (validy - maskcircle[1])**2 <= maskcircle[2]**2
validx = validx[tmpflag]
validy = validy[tmpflag]
# get the indices of valid samples for all classes
validind = np.ravel_multi_index((validx, validy), \
(maskband.YSize, maskband.XSize))
if classes is None:
if len(validind) >= numsamples:
randind = np.random.permutation(len(validind))[:numsamples]
else:
print "Error: number of valid pixels is fewer than requested number of samples"
print "No samples are generated. Exit"
maskds = None
return ()
sampleind = validind[randind]
else:
numclass = len(classes)
if numclass != len(numsamples):
maskds = None
raise RuntimeError('Number of classes is {0:d} while only {1:d} numbers for sample counts are given!'.format(numclass, len(numsamples)))
else:
mask_vec = mask.flatten()[validind]
sampleind = [ draw_samples(validind[mask_vec==cls], ns) for cls, ns in zip(classes, numsamples) ]
sampleind = np.hstack(sampleind)
if addatt:
ancatt = np.ravel(ancatt, order='C')
sampleatt = ancatt[sampleind]
samplepos = np.unravel_index(sampleind, (maskband.YSize, maskband.XSize), order='C')
# convert pixel location to default coordinates for a raster in QGIS.
ypos = samplepos[0].astype(float)*(-1) - 0.5
xpos = samplepos[1].astype(float) + 0.5
# write sampels to output file and attribute if they are supplied
headerstr = \
"Random samples from " + maskfile + "\n" + \
"Band of mask = {0:d}\n".format(maskb) + \
"Class code = "
for cls in classes:
headerstr += "{0:d}, ".format(cls)
headerstr = headerstr.rstrip(', ') + "\nNumber of samples = "
for ns in numsamples:
headerstr += "{0:d}, ".format(ns)
headerstr = headerstr.rstrip(', ') + "\n"
numsamples = len(sampleind)
if addatt:
outmat = np.hstack(( xpos.reshape(numsamples, 1), \
ypos.reshape(numsamples, 1), \
sampleatt.reshape(numsamples, 1) ))
headerstr = headerstr + \
"Attributes from " + ancfile + "\n" + \
"Band of attribute = {0:d}\n".format(ancb) + \
"X, Y, Attribute"
fmtstr = ['%.3f', '%.3f', '%.3f']
else:
outmat = np.hstack(( xpos.reshape(numsamples, 1), \
ypos.reshape(numsamples, 1) ))
headerstr = headerstr + \
"Attributes None\n" + \
"Band of attribute = None\n" + \
"X, Y"
fmtstr = ['%.3f', '%.3f']
np.savetxt(outfile, outmat, fmt=fmtstr, delimiter=',', header=headerstr, comments="")
def lonlat_2_ind(lon,lat,extent,cellsize,dims):
row,col = lonlat_2_rowcol(lon,lat,extent,cellsize)
ind = np.ravel_multi_index((row, col), dims)
return ind
def precomputed_analysis_vote_cls(self, num_fts=4096, dense=True):
def lambda_func(arr, patch_size):
res = skimage.util.view_as_windows(
arr, (patch_size, patch_size, patch_size, patch_size, 2))
res = np.squeeze(res, 4)
return res
#print("Starting Analysis")
assert not self.auto_close_sess, "Need to keep sess open"
feature_response = self.run_ft(num_fts=num_fts)
flattened_features = feature_response.reshape((num_fts, -1)).T
# Use np.unravel_index to recover x,y coordinate
spread = max(1, self.patch_size // self.stride)
responses = np.zeros(
(self.max_h_ind + spread - 1, self.max_w_ind + spread - 1,
self.max_h_ind + spread - 1, self.max_w_ind + spread - 1),
dtype=np.float32)
vote_counts = np.zeros(
(self.max_h_ind + spread - 1, self.max_w_ind + spread - 1,
self.max_h_ind + spread - 1, self.max_w_ind + spread - 1)) + 1e-4
t0 = time.time()
# Get all possible combinations of patches
iterator = self.argless_extract_inds(dense=dense)
futures = []
inds_cpy = []
# responses_vote_count_as_patches = self.pool.submit(lambda_func,responses,spread)
for inds in iterator:
# print(inds.shape)
patch_a_inds = inds[:, :2]
patch_b_inds = inds[:, 2:]
a_ind = np.ravel_multi_index(patch_a_inds.T,
[self.max_h_ind, self.max_w_ind])
b_ind = np.ravel_multi_index(patch_b_inds.T,
[self.max_h_ind, self.max_w_ind])
futures.append(
self.pool.submit(self.solver.sess.run,
self.solver.net.pc_cls_pred,
feed_dict={
self.net.precomputed_features:
flattened_features,
self.net.im_a_index: a_ind,
self.net.im_b_index: b_ind
}))
inds_cpy.append(inds)
# responses_vote_count_as_patches = responses_vote_count_as_patches.result()
for idx, future in enumerate(futures):
preds_ = future.result()
inds = inds_cpy[idx]
t = time.time()
# responses_vote_count_as_patches[inds] += [preds_[i],1]
for i in range(preds_.shape[0]):
responses[inds[i][0]:(inds[i][0] + spread),
inds[i][1]:(inds[i][1] + spread),
inds[i][2]:(inds[i][2] + spread),
inds[i][3]:(inds[i][3] + spread)] += preds_[i]
vote_counts[inds[i][0]:(inds[i][0] + spread),
inds[i][1]:(inds[i][1] + spread),
inds[i][2]:(inds[i][2] + spread),
inds[i][3]:(inds[i][3] + spread)] += 1
#print('precomputed analysis time : {}'.format(time.time() - t))
if self.auto_close_sess:
self.solver.sess.close()
out = (responses / vote_counts)
# self.cr.queue.close()
return out
def step(self, action):
"""
Updates the environment with the given action
Takes as inputs
- action : array of value € [0,1] representing an action
Returns
- observable : 3d numpy array of shape (height, width, channels) representing the new state of the environment
- reward : reward given to the agent for the performed action
- done : boolean indicating if new state is a terminal state
- infos : dictionary of informations (for debugging purpose)
"""
assert self.target is not None, "The target not define, to do so reset the environment"
if self.state.step_type == environment.StepType.LAST:
return (self.getObservable(),
1 / ((LibMyPaintInterface._distance_l2(self.state.observation["canvas"], self.target) + 1e-9) / self.max_norm),
True,
{"info": "To continue reset the environment"})
self.actions.append(action)
action_spec = self.env.action_spec()
# extract the values
if self.coord_type == "cart":
x_start, y_start, x_control, y_control, x_end, y_end, brush_pressure, brush_size, color_1, color_2, color_3 = action
# map the coordinates to the right interval
x_start = LibMyPaintInterface._map_to_int_interval(x_start, 0, self.grid_size - 1)
y_start = LibMyPaintInterface._map_to_int_interval(y_start, 0, self.grid_size - 1)
x_control = LibMyPaintInterface._map_to_int_interval(x_control, 0, self.grid_size - 1)
y_control = LibMyPaintInterface._map_to_int_interval(y_control, 0, self.grid_size - 1)
x_end = LibMyPaintInterface._map_to_int_interval(x_end, 0, self.grid_size - 1)
y_end = LibMyPaintInterface._map_to_int_interval(y_end, 0, self.grid_size - 1)
elif self.coord_type == "hilb":
start, control, end, brush_pressure, brush_size, color_1, color_2, color_3 = action
# map the coordonates to the right interval
start = int(LibMyPaintInterface._map_to_int_interval(start, 0, pow(2, m.log(self.grid_size, 2) * 2) - 1))
control = int(LibMyPaintInterface._map_to_int_interval(control, 0, pow(2, m.log(self.grid_size, 2) * 2) - 1))
end = int(LibMyPaintInterface._map_to_int_interval(end, 0, pow(2, m.log(self.grid_size, 2) * 2) - 1))
x_start, y_start = self.hilbert_curve.coordinates_from_distance(start)
x_control, y_control = self.hilbert_curve.coordinates_from_distance(control)
x_end, y_end = self.hilbert_curve.coordinates_from_distance(end)
brush_pressure = LibMyPaintInterface._map_to_int_interval(brush_pressure,
action_spec["pressure"].minimum,
action_spec["pressure"].maximum)
brush_size = LibMyPaintInterface._map_to_int_interval(brush_size,
action_spec["size"].minimum,
action_spec["size"].maximum)
color_1 = LibMyPaintInterface._map_to_int_interval(color_1,
action_spec[self.color_name[0]].minimum,
action_spec[self.color_name[1]].maximum)
color_2 = LibMyPaintInterface._map_to_int_interval(color_2,
action_spec[self.color_name[1]].minimum,
action_spec[self.color_name[1]].maximum)
color_3 = LibMyPaintInterface._map_to_int_interval(color_3,
action_spec[self.color_name[2]].minimum,
action_spec[self.color_name[2]].maximum)
# go to the start of the curve
move = {"control": np.ravel_multi_index((x_start, y_start),
(self.grid_size, self.grid_size)).astype("int32"),
"end": np.ravel_multi_index((x_start, y_start),
(self.grid_size, self.grid_size)).astype("int32"),
"flag": np.int32(0),
"pressure": np.int32(brush_pressure),
"size": np.int32(brush_size),
self.color_name[0]: np.int32(color_1),
self.color_name[1]: np.int32(color_2),
self.color_name[2]: np.int32(color_3)}
self.state = self.env.step(move)
if self.state.step_type == environment.StepType.LAST:
return (self.getObservable(),
1 / ((LibMyPaintInterface._distance_l2(self.state.observation["canvas"], self.target) + 1e-9) / self.max_norm),
True,
{})
# draw the curve
draw = {"control": np.ravel_multi_index((x_control, y_control),
(self.grid_size, self.grid_size)).astype("int32"),
"end": np.ravel_multi_index((x_end, y_end),
(self.grid_size, self.grid_size)).astype("int32"),
"flag": np.int32(1),
"pressure": np.int32(brush_pressure),
"size": np.int32(brush_size),
self.color_name[0]: np.int32(color_1),
self.color_name[1]: np.int32(color_2),
self.color_name[2]: np.int32(color_3)}
self.state = self.env.step(draw)
if self.state.step_type == environment.StepType.LAST:
return (self.getObservable(),
1 / ((LibMyPaintInterface._distance_l2(self.state.observation["canvas"], self.target) + 1e-9) / self.max_norm),
True,
{})
return (self.getObservable(),
0,
False,
{})
def bin_to_idx(bin_loc, resolution):
return np.ravel_multi_index((bin_loc[0], bin_loc[1]), resolution)
def matlab_compat_ravel_multi_index(*xyz, shape):
return 1 + np.ravel_multi_index(xyz, shape, order='F')
def marginal_prob(self, prob, wires=None):
r"""Return the marginal probability of the computational basis
states by summing the probabiliites on the non-specified wires.
If no wires are specified, then all the basis states representable by
the device are considered and no marginalization takes place.
.. note::
If the provided wires are not in the order as they appear on the device,
the returned marginal probabilities take this permutation into account.
For example, if the addressable wires on this device are ``Wires([0, 1, 2])`` and
this function gets passed ``wires=[2, 0]``, then the returned marginal
probability vector will take this 'reversal' of the two wires
into account:
.. math::
\mathbb{P}^{(2, 0)}
= \left[
|00\rangle, |10\rangle, |01\rangle, |11\rangle
\right]
Args:
prob: The probabilities to return the marginal probabilities
for
wires (Iterable[Number, str], Number, str, Wires): wires to return
marginal probabilities for. Wires not provided
are traced out of the system.
Returns:
array[float]: array of the resulting marginal probabilities.
"""
if wires is None:
# no need to marginalize
return prob
wires = Wires(wires)
# determine which subsystems are to be summed over
inactive_wires = Wires.unique_wires([self.wires, wires])
# translate to wire labels used by device
device_wires = self.map_wires(wires)
inactive_device_wires = self.map_wires(inactive_wires)
# reshape the probability so that each axis corresponds to a wire
prob = self._reshape(prob, [2] * self.num_wires)
# sum over all inactive wires
prob = self._flatten(
self._reduce_sum(prob, inactive_device_wires.labels))
# The wires provided might not be in consecutive order (i.e., wires might be [2, 0]).
# If this is the case, we must permute the marginalized probability so that
# it corresponds to the orders of the wires passed.
basis_states = np.array(
list(itertools.product([0, 1], repeat=len(device_wires))))
perm = np.ravel_multi_index(
basis_states[:, np.argsort(np.argsort(device_wires))].T,
[2] * len(device_wires))
return self._gather(prob, perm)
def chaccum(A,
radiusRange,
method='phasecode',
objPolarity='bright',
edgeThresh=[]):
maxNumElemNHoodMat = 1e6
# all(A(:) == A(1));
# Assume that image is not flat
# Get the input image in the correct format
A = getGrayImage(A)
## Calculate gradient
Gx, Gy, gradientImg = imgradient(A)
Ex, Ey = getEdgePixels(gradientImg, edgeThresh)
E = np.stack((Ey, Ex))
# Not sure np.ravel_multi_index is equivalent with Matlab Function sub2ind
idxE = np.ravel_multi_index(E,
tuple(gradientImg.shape),
mode='raise',
order='C')
# Adding 0.0001 is to include end point of the radius
radiusRange = np.arange(radiusRange[0], radiusRange[1] + 0.0001, 0.5)
if objPolarity == 'bright':
RR = radiusRange
elif objPolarity == 'dark':
RR = -radiusRange
### This implementation only includes 'phasecode' mode
lnR = np.log(radiusRange)
phi = ((lnR - lnR[0]) / (lnR[-1] - lnR[0]) * 2 * np.pi) - np.pi
# Modified form of Log-coding from Eqn. 8 in [3]
Opca = np.exp(np.sqrt(-1 + 0j) * phi)
w0 = Opca / (2 * np.pi * radiusRange)
xcStep = int(maxNumElemNHoodMat // RR.shape[0])
lenE = Ex.shape[0]
M, N = A.shape[0], A.shape[1]
accumMatrix = np.zeros((M, N))
for i in range(0, lenE + 1, xcStep):
Ex_chunk = Ex[i:int(np.min((i + xcStep - 1, lenE)))]
Ey_chunk = Ey[i:int(np.min((i + xcStep - 1, lenE)))]
idxE_chunk = idxE[i:int(np.min((i + xcStep - 1, lenE)))]
chunckX = np.divide(
Gx[np.unravel_index(idxE_chunk, Gx.shape, 'C')],
gradientImg[np.unravel_index(idxE_chunk, gradientImg.shape, 'C')])
chunckY = np.divide(
Gy[np.unravel_index(idxE_chunk, Gy.shape, 'C')],
gradientImg[np.unravel_index(idxE_chunk, gradientImg.shape, 'C')])
# Eqns. 10.3 & 10.4 from Machine Vision by E. R. Davies
xc = matlib.repmat(Ex_chunk, RR.shape[0], 1).T + bsxfun_1d(
-RR, chunckX)
yc = matlib.repmat(Ey_chunk, RR.shape[0], 1).T + bsxfun_1d(
-RR, chunckY)
xc = np.round(xc)
yc = np.round(yc)
w = matlib.repmat(w0, xc.shape[0], 1)
## Determine which edge pixel votes are within the image domain
# Record which candidate center positions are inside the image rectangle.
M, N = A.shape[0], A.shape[1]
inside = (xc >= 1) & (xc <= N) & (yc >= 1) & (yc < M)
# Keep rows that have at least one candidate position inside the domain.
rows_to_keep = np.any(inside, 1)
xc = xc[rows_to_keep, :]
yc = yc[rows_to_keep, :]
w = w[rows_to_keep, :]
inside = inside[rows_to_keep, :]
## Accumulate the votes in the parameter plane
xc = xc[inside]
yc = yc[inside]
xyc = np.asarray(np.stack((xc[:], yc[:])), dtype=np.int64)
accumMatrix = accumMatrix + accum(xyc.T, w[inside], size=[M, N])
del xc, yc, w # These are cleared to create memory space for the next loop. Otherwise out-of-memory at xc = bsxfun... in the next loop.
return accumMatrix, gradientImg
def df_add_counts(df, cols): arr_slice = df[cols].values unq, unqtags, counts = np.unique(np.ravel_multi_index(arr_slice.T, arr_slice.max(0) + 1), return_inverse=True, return_counts=True) df["_".join(cols)+'_count'] = counts[unqtags]
def project_to_basis(y3d, edges, los=[0, 0, 1], poles=[]):
"""
Project a 3D statistic on to the specified basis. The basis will be one
of:
- 2D (`x`, `mu`) bins: `mu` is the cosine of the angle to the line-of-sight
- 2D (`x`, `ell`) bins: `ell` is the multipole number, which specifies
the Legendre polynomial when weighting different `mu` bins
.. note::
The 2D (`x`, `mu`) bins will be computed only if `poles` is specified.
See return types for further details.
Notes
-----
* the `mu` range extends from 0.0 to 1.0
* the `mu` bins are half-inclusive half-exclusive, except the last bin
is inclusive on both ends (to include `mu = 1.0`)
Parameters
----------
y3d : RealField or ComplexField
the 3D array holding the statistic to be projected to the specified basis
edges : list of arrays, (2,)
list of arrays specifying the edges of the desired `x` bins and `mu` bins
los : array_like,
the line-of-sight direction to use, which `mu` is defined with
respect to; default is [0, 0, 1] for z.
poles : list of int, optional
if provided, a list of integers specifying multipole numbers to
project the 2d `(x, mu)` bins on to
hermitian_symmetric : bool, optional
Whether the input array `y3d` is Hermitian-symmetric, i.e., the negative
frequency terms are just the complex conjugates of the corresponding
positive-frequency terms; if ``True``, the positive frequency terms
will be explicitly double-counted to account for this symmetry
Returns
-------
result : tuple
the 2D binned results; a tuple of ``(xmean_2d, mumean_2d, y2d, N_2d)``, where:
- xmean_2d : array_like, (Nx, Nmu)
the mean `x` value in each 2D bin
- mumean_2d : array_like, (Nx, Nmu)
the mean `mu` value in each 2D bin
- y2d : array_like, (Nx, Nmu)
the mean `y3d` value in each 2D bin
- N_2d : array_like, (Nx, Nmu)
the number of values averaged in each 2D bin
pole_result : tuple or `None`
the multipole results; if `poles` supplied it is a tuple of ``(xmean_1d, poles, N_1d)``,
where:
- xmean_1d : array_like, (Nx,)
the mean `x` value in each 1D multipole bin
- poles : array_like, (Nell, Nx)
the mean multipoles value in each 1D bin
- N_1d : array_like, (Nx,)
the number of values averaged in each 1D bin
"""
comm = y3d.pm.comm
x3d = y3d.x
hermitian_symmetric = numpy.iscomplexobj(y3d)
from scipy.special import legendre
# setup the bin edges and number of bins
xedges, muedges = edges
x2edges = xedges**2
Nx = len(xedges) - 1
Nmu = len(muedges) - 1
# always make sure first ell value is monopole, which
# is just (x, mu) projection since legendre of ell=0 is 1
do_poles = len(poles) > 0
_poles = [0]+sorted(poles) if 0 not in poles else sorted(poles)
legpoly = [legendre(l) for l in _poles]
ell_idx = [_poles.index(l) for l in poles]
Nell = len(_poles)
# valid ell values
if any(ell < 0 for ell in _poles):
raise ValueError("in `project_to_basis`, multipole numbers must be non-negative integers")
# initialize the binning arrays
musum = numpy.zeros((Nx+2, Nmu+2))
xsum = numpy.zeros((Nx+2, Nmu+2))
ysum = numpy.zeros((Nell, Nx+2, Nmu+2), dtype=y3d.dtype) # extra dimension for multipoles
Nsum = numpy.zeros((Nx+2, Nmu+2), dtype='i8')
# if input array is Hermitian symmetric, only half of the last
# axis is stored in `y3d`
symmetry_axis = -1 if hermitian_symmetric else None
# iterate over y-z planes of the coordinate mesh
for slab in SlabIterator(x3d, axis=0, symmetry_axis=symmetry_axis):
# the square of coordinate mesh norm
# (either Fourier space k or configuraton space x)
xslab = slab.norm2()
# if empty, do nothing
if len(xslab.flat) == 0: continue
# get the bin indices for x on the slab
dig_x = numpy.digitize(xslab.flat, x2edges)
# make xslab just x
xslab **= 0.5
# get the bin indices for mu on the slab
mu = slab.mu(los) # defined with respect to specified LOS
dig_mu = numpy.digitize(abs(mu).flat, muedges)
# make the multi-index
multi_index = numpy.ravel_multi_index([dig_x, dig_mu], (Nx+2,Nmu+2))
# sum up x in each bin (accounting for negative freqs)
xslab[:] *= slab.hermitian_weights
xsum.flat += numpy.bincount(multi_index, weights=xslab.flat, minlength=xsum.size)
# count number of modes in each bin (accounting for negative freqs)
Nslab = numpy.ones_like(xslab) * slab.hermitian_weights
Nsum.flat += numpy.bincount(multi_index, weights=Nslab.flat, minlength=Nsum.size)
# compute multipoles by weighting by Legendre(ell, mu)
for iell, ell in enumerate(_poles):
# weight the input 3D array by the appropriate Legendre polynomial
weighted_y3d = legpoly[iell](mu) * y3d[slab.index]
# add conjugate for this kx, ky, kz, corresponding to
# the (-kx, -ky, -kz) --> need to make mu negative for conjugate
# Below is identical to the sum of
# Leg(ell)(+mu) * y3d[:, nonsingular] (kx, ky, kz)
# Leg(ell)(-mu) * y3d[:, nonsingular].conj() (-kx, -ky, -kz)
# or
# weighted_y3d[:, nonsingular] += (-1)**ell * weighted_y3d[:, nonsingular].conj()
# but numerically more accurate.
if hermitian_symmetric:
if ell % 2: # odd, real part cancels
weighted_y3d.real[slab.nonsingular] = 0.
weighted_y3d.imag[slab.nonsingular] *= 2.
else: # even, imag part cancels
weighted_y3d.real[slab.nonsingular] *= 2.
weighted_y3d.imag[slab.nonsingular] = 0.
# sum up the weighted y in each bin
weighted_y3d *= (2.*ell + 1.)
ysum[iell,...].real.flat += numpy.bincount(multi_index, weights=weighted_y3d.real.flat, minlength=Nsum.size)
if numpy.iscomplexobj(ysum):
ysum[iell,...].imag.flat += numpy.bincount(multi_index, weights=weighted_y3d.imag.flat, minlength=Nsum.size)
# sum up the absolute mag of mu in each bin (accounting for negative freqs)
mu[:] *= slab.hermitian_weights
musum.flat += numpy.bincount(multi_index, weights=abs(mu).flat, minlength=musum.size)
# sum binning arrays across all ranks
xsum = comm.allreduce(xsum)
musum = comm.allreduce(musum)
ysum = comm.allreduce(ysum)
Nsum = comm.allreduce(Nsum)
# add the last 'internal' mu bin (mu == 1) to the last visible mu bin
# this makes the last visible mu bin inclusive on both ends.
ysum[..., -2] += ysum[..., -1]
musum[:, -2] += musum[:, -1]
xsum[:, -2] += xsum[:, -1]
Nsum[:, -2] += Nsum[:, -1]
# reshape and slice to remove out of bounds points
sl = slice(1, -1)
with numpy.errstate(invalid='ignore'):
# 2D binned results
y2d = (ysum[0,...] / Nsum)[sl,sl] # ell=0 is first index
xmean_2d = (xsum / Nsum)[sl,sl]
mumean_2d = (musum / Nsum)[sl, sl]
N_2d = Nsum[sl,sl]
# 1D multipole results (summing over mu (last) axis)
if do_poles:
N_1d = Nsum[sl,sl].sum(axis=-1)
xmean_1d = xsum[sl,sl].sum(axis=-1) / N_1d
poles = ysum[:, sl,sl].sum(axis=-1) / N_1d
poles = poles[ell_idx,...]
# return y(x,mu) + (possibly empty) multipoles
result = (xmean_2d, mumean_2d, y2d, N_2d)
pole_result = (xmean_1d, poles, N_1d) if do_poles else None
return result, pole_result
def integrate_visibility_from_rays(origins, directions, alpha_grid,
visibility_grid, scene_params, grid_params):
"""Ray marches rays through a grid and marks visited voxels as visible.
This function adds the visibility value (1-accumulated_alpha) into the
visibility_grid passed as a parameter.
Args:
origins: An np.array [N, 3] of the ray origins.
directions: An np.array [N, 3] of ray directions.
alpha_grid: A [cW, cH, cD, 1] numpy array for the alpha values in the
low-res culling grid.
visibility_grid: A [cW, cH, cD, 1] numpy array for the visibility values in
the low-res culling grid. Note that this function will be adding
visibility values into this grid.
scene_params: A dict for scene specific params (bbox, rotation, resolution).
grid_params: A dict with parameters describing the high-res voxel grid which
the atlas is representing.
"""
# Extract the relevant parameters from the dictionaries.
min_xyz = scene_params['min_xyz']
worldspace_t_opengl = scene_params['worldspace_T_opengl']
voxel_size = grid_params['_voxel_size']
grid_size = grid_params['_grid_size']
# Set up the rays and transform them to the voxel grid coordinate space.
num_rays = origins.shape[0]
opengl_t_worldspace = np.linalg.inv(worldspace_t_opengl)
directions_norm = np.linalg.norm(directions, axis=-1, keepdims=True)
directions /= directions_norm
origins_hom = np.concatenate(
[origins, np.ones_like(origins[Ellipsis, 0:1])], axis=-1)
origins_hom = origins_hom.reshape((-1, 4)).dot(opengl_t_worldspace)
origins_opengl = origins_hom[Ellipsis, 0:3].reshape(origins.shape)
directions_opengl = directions.dot(opengl_t_worldspace[0:3, 0:3])
origins_grid = (origins_opengl - min_xyz) / voxel_size
directions_grid = directions_opengl
inv_directions_grid = 1.0 / directions_grid
# Now set the near and far distance of each ray to match the cube which
# the voxel grid is defined in.
min_distances, max_distances = rays_aabb_intersection(
np.zeros_like(min_xyz), grid_size, origins_grid, inv_directions_grid)
invalid_mask = min_distances > max_distances
min_distances[invalid_mask] = 0
max_distances[invalid_mask] = 0
# The NeRF near/far bounds have been set for unnormalized ray directions, so
# we need to scale our bounds here to compensate for normalizing.
near_in_voxels = directions_norm[Ellipsis, 0] * scene_params['near'] / voxel_size
far_in_voxels = directions_norm[Ellipsis, 0] * scene_params['far'] / voxel_size
min_distances = np.maximum(near_in_voxels, min_distances)
max_distances = np.maximum(near_in_voxels, max_distances)
max_distances = np.minimum(far_in_voxels, max_distances)
num_steps = int(0.5 + max_distances.max() - min_distances.min())
# Finally, set up the accumulation buffers we need for ray marching.
raveled_alpha = alpha_grid.ravel()
total_visibility = np.ones((1, num_rays, 1), dtype=np.float32)
min_distances = np.expand_dims(min_distances, -1)
for i in range(num_steps):
visibility_mask = (total_visibility >= 0.01)[0]
if not visibility_mask.max():
break
current_distances = min_distances + 0.5 + i
active_current_distances = current_distances[visibility_mask]
active_max_distances = max_distances[visibility_mask[Ellipsis, 0]]
if active_current_distances.min() >= active_max_distances.max():
break
positions_grid = origins_grid + directions_grid * current_distances
epsilon = 0.1
valid_mask = (positions_grid[Ellipsis, 0] < grid_size[Ellipsis, 0] - 0.5 - epsilon)
valid_mask *= (positions_grid[Ellipsis, 1] < grid_size[Ellipsis, 1] - 0.5 - epsilon)
valid_mask *= (positions_grid[Ellipsis, 2] < grid_size[Ellipsis, 2] - 0.5 - epsilon)
valid_mask *= (positions_grid[Ellipsis, 0] > 0.5 + epsilon)
valid_mask *= (positions_grid[Ellipsis, 1] > 0.5 + epsilon)
valid_mask *= (positions_grid[Ellipsis, 2] > 0.5 + epsilon)
invalid_mask = np.logical_not(valid_mask)
if not valid_mask.max():
continue
invalid_mask = np.logical_not(valid_mask)
positions_grid -= 0.5
alpha = np.zeros((1, num_rays, 1), dtype=np.float32)
# Use trilinear interpolation for smoother results.
offsets_xyz = [(x, y, z) # pylint: disable=g-complex-comprehension
for x in [0.0, 1.0]
for y in [0.0, 1.0]
for z in [0.0, 1.0]]
for dx, dy, dz in offsets_xyz:
grid_indices = np.floor(positions_grid + np.array([dx, dy, dz])).astype(
np.int32)
weights = 1 - np.abs(grid_indices - positions_grid)
weights = weights.prod(axis=-1).reshape(alpha.shape)
grid_indices[invalid_mask] = 0
grid_indices = grid_indices.reshape(-1, 3).T
trilinear_alpha = np.take(
raveled_alpha, np.ravel_multi_index(grid_indices, alpha_grid.shape))
alpha += weights * trilinear_alpha.reshape(alpha.shape)
# Splat the visibility value into the visibility grid.
weighted_visibilities = weights * total_visibility
weighted_visibilities[0, invalid_mask] = 0.0
visibility_grid.ravel()[np.ravel_multi_index(
grid_indices, visibility_grid.shape)] += (
weighted_visibilities[0, :, 0])
alpha[0, invalid_mask] = 0.0
total_visibility *= 1.0 - alpha
def get_flattened_index(self, voxel: Voxel) -> int:
"""Return the flattened index of a voxel inside the grid.
This is a convenience method that wraps numpy.ravel_multi_index.
"""
return np.ravel_multi_index(voxel, self.shape)
def __init__(self, dem="", auxtopo=False, filled=False, verbose=False, verb_func=print):
"""
Class that define a network object (topologically sorted giver-receiver cells)
Parameters:
===========
dem : *DEM object* or *str*
topopy.DEM instance with the input Digital Elevation Model, or path to a previously saved Flow object. If the
parameter is an empty string, it will create an empty Flow instance.
filled : boolean
Boolean to check if input DEM was already pit-filled. The fill algoritm implemented in the DEM object,
althoug fast, consumes a lot of memory. In some cases could be necessary fill the DEM with alternative GIS tools.
auxtopo : boolean
Boolean to determine if a auxiliar topography is used (much slower). The auxiliar topography is calculated with
elevation differences between filled and un-filled dem. If filled is True, auxtopo is ignored (cannot compute differences)
verbose : boolean
Boolean to show processing messages in console to known the progress. Usefull with large DEMs to se the evolution.
References:
-----------
The algoritm to created the topologically sorted network has been adapted to Python from FLOWobj.m
by Wolfgang Schwanghart (version of 17. August, 2017) included in TopoToolbox matlab codes (really
smart algoritms there!). If use, please cite:
Schwanghart, W., Scherler, D., 2014. Short Communication: TopoToolbox 2 -
MATLAB-based software for topographic analysis and modeling in Earth
surface sciences. Earth Surf. Dyn. 2, 1–7. https://doi.org/10.5194/esurf-2-1-2014
"""
if dem == "":
# Creates an empty Flow object
self._size = (1, 1)
self._dims = (1, 1)
self._geot = (0., 1., 0., 0., 0., -1.)
self._cellsize = (self._geot[1], self._geot[5])
self._proj = ""
self._ncells = 1
self._nodata_pos = np.array([], dtype=np.int32)
self._ix = np.array([], dtype=np.int32)
self._ixc = np.array([], dtype=np.int32)
elif type(dem) == str:
# Loads the Flow object in GeoTiff format
try:
self.load_gtiff(dem)
except:
raise FlowError("Error opening the Geotiff")
else:
try:
# Set Network properties
self._size = dem.get_size()
self._dims = dem.get_dims()
self._geot = dem.get_geotransform()
self._cellsize = dem.get_cellsize()
self._proj = dem.get_projection()
self._ncells = dem.get_ncells()
self._nodata_pos = np.ravel_multi_index(dem.get_nodata_pos(), self._dims)
# Get topologically sorted nodes (ix - givers, ixc - receivers)
self._ix, self._ixc = sort_pixels(dem, auxtopo=auxtopo, filled=filled, verbose=verbose, verb_func=verb_func)
# Recalculate NoData values
self._nodata_pos = self._get_nodata_pos()
except:
raise FlowError("Unexpected Error creating the Flow object")
def grid_coordinates_to_indices(self, coordinates=None):
# Annoyingly, this doesn't work for negative indices.
# The mode='wrap' parameter only works on positive indices.
if coordinates is None:
return np.arange(self.size)
return np.ravel_multi_index(coordinates, self.shape)
def tt_construct_layer7(filename, feature_x):
mat_dict = {}
mat_dict.update(scipy.io.loadmat(filename))
a = mat_dict['TT_mat']
dim_arr = a['d'][0][0][0, 0]
#n_arr = a['n'][0][0][0:,0]
#ps_arr = a['ps'][0][0][0:,0]
#core_arr = a['core'][0][0][0:,0]
ranks = a['r'][0][0][0:, 0]
bias = a['bias'][0][0]
right_modes = a['right_modes'][0][0][0, 0:]
right_modes = np.array(right_modes, dtype=np.int32)
left_modes = a['left_modes'][0][0][0, 0:]
left_modes = np.array(left_modes, dtype=np.int32)
L = np.prod(left_modes)
R = np.prod(right_modes)
core_tensor_0 = a['tensor'][0][0][0, 0]
core_tensor_1 = a['tensor'][0][0][0, 1]
core_tensor_2 = a['tensor'][0][0][0, 2]
core_tensor_3 = a['tensor'][0][0][0, 3]
column_len = L
row_len = R
if dim_arr > 2:
shape = left_modes * right_modes.ravel()
else:
shape = [left_modes[0], right_modes[0]]
tensor_column_len = shape[0]
tensor_row_len = shape[1]
tensor_depth_len = shape[2]
tensor_channel_len = shape[3]
y_out = np.zeros((L, 1), dtype=float, order='F')
#t0 = time.time()
for i in range(0, tensor_row_len):
core_mat_0 = np.reshape(core_tensor_0[:, i, :], [ranks[0], ranks[1]],
order='F')
for j in range(0, tensor_column_len):
core_mat_1 = np.reshape(core_tensor_1[:, j, :],
[ranks[1], ranks[2]],
order='F')
tmp1 = np.dot(core_mat_0, core_mat_1)
for k in range(0, tensor_depth_len):
core_mat_2 = np.reshape(core_tensor_2[:, k, :],
[ranks[2], ranks[3]],
order='F')
tmp2 = np.dot(tmp1, core_mat_2)
ind1 = np.zeros(tensor_channel_len) + i
ind2 = np.zeros(tensor_channel_len) + j
ind3 = np.zeros(tensor_channel_len) + k
ind4 = np.arange(tensor_channel_len)
indy = np.ravel_multi_index([
ind1.astype('int64'),
ind2.astype('int64'),
ind3.astype('int64'),
ind4.astype('int64')
], (tensor_row_len, tensor_column_len, tensor_depth_len,
tensor_channel_len),
order='F')
row_index = np.mod(indy, column_len)
column_index = np.floor(indy / column_len).astype('int64')
tmp3 = np.dot(
tmp2,
core_tensor_3.reshape([ranks[3], tensor_channel_len],
order='F'))
tmp4 = np.multiply(
tmp3,
feature_x[[column_index]].reshape([1, tensor_channel_len],
order='F'))
for l in range(0, tensor_channel_len):
y_out[row_index[l]] = y_out[row_index[l]] + tmp4[0, l]
#t1 = time.time()
#print(y_out)
#frameinfo = getframeinfo(currentframe())
#print(frameinfo.filename, frameinfo.lineno)
#print(t1-t0)
y_out = y_out + bias
return y_out
def _get_facet_chunk(store, varname, iternum, nfacet, klevels, nx, nz, nfaces,
dtype, mask_override, domain, pad_before, pad_after):
fs, path = store.get_fs_and_full_path(varname, iternum)
assert (nfacet >= 0) & (nfacet < _nfacets)
file = fs.open(path)
# insert singleton axis for time (if not grid var) and k level
facet_shape = (1, ) + _facet_shape(nfacet, nx, nfaces)
facet_shape = (1, ) + facet_shape if iternum is not None else facet_shape
level_data = []
if (store.shrunk and iternum is not None) or \
(store.shrunk_grid and iternum is None):
# the store tells us whether we need a mask or not
point = _get_variable_point(varname, mask_override)
mykey = nx if domain == 'global' else f'{domain}_{nx}'
index = all_index_data[mykey][point]
zgroup = store.open_mask_group()
mask = zgroup['mask_' + point].astype('bool')
else:
index = None
mask = None
# Offset start/end read position due to padding facet before me
pre_pad = np.cumsum([x + y for x, y in zip(pad_before, pad_after)])
pre_pad = shift_and_pad(pre_pad, left=False).compute()
tot_pad = pre_pad[-1] + pad_after[-1]
for k in klevels:
assert (k >= 0) & (k < nz)
# figure out where in the file we have to read to get the data
# for this level and facet
if index:
i = np.ravel_multi_index((k, nfacet), (nz, _nfacets))
start = index[i]
end = index[i + 1]
else:
level_start = k * (nx**2 * nfaces - nx * tot_pad)
facet_start, facet_end = _uncompressed_facet_index(
nfacet, nx, nfaces)
start = level_start + facet_start
end = level_start + facet_end - nx * pad_after[nfacet]
end = end - nx * (pad_before[nfacet]) if k * nfacet == 0 else end
start, end = [
x - nx * pre_pad[nfacet] if k + nfacet != 0 else x
for x in [start, end]
]
read_offset = start * dtype.itemsize # in bytes
read_length = (end - start) * dtype.itemsize # in bytes
file.seek(read_offset)
buffer = file.read(read_length)
data = np.frombuffer(buffer, dtype=dtype)
assert len(data) == (end - start)
if mask:
mask_level = mask[k]
mask_facets = _faces_to_facets(mask_level, nfaces)
this_mask = mask_facets[nfacet]
data = _decompress(data, this_mask, dtype)
elif pad_before[nfacet] + pad_after[nfacet] > 0:
# Extra care for pad after with rotated fields
data = _pad_facet(data, facet_shape, _facet_reshape[nfacet],
pad_before[nfacet], pad_after[nfacet], dtype)
# this is the shape this facet is supposed to have
data.shape = facet_shape
level_data.append(data)
out = np.concatenate(level_data, axis=-4)
return out
# args = sys.argv
# Loading in Machine Learning models
#####################################
y_regress = joblib.load('modeldump\sc4k_yreg.pkl')
y_estimator = joblib.load('modeldump\sc4k_xaxis_class.pkl')
x_regress = joblib.load('modeldump\sc4k_xreg.pkl')
x_class = joblib.load('modeldump\sc4k_target_xaxisrestricted.pkl')
#####################################
# Initialising the Heart structure
a = ps.Heart(nu=0.2, delta=0.0, fakedata=True)
# Randomises the rotor x,y position
cp_x_pos = randint(30, 169)
cp_y_pos = randint(0, 199)
a.set_circuit(np.ravel_multi_index([cp_y_pos,cp_x_pos],(200,200)))
tissue_reset = False
# Initialising ECG recording (randomises the probe x,y position)
current_ecg_x_pos = randint(30, 169)
current_ecg_y_pos = randint(0, 199)
ecg_processing = at.ECG(centre=(current_ecg_y_pos, current_ecg_x_pos), m='g_single')
# Initialising the animation window
app = QtGui.QApplication([])
win = pg.GraphicsWindow(border=True)
win.show()
win.setWindowTitle('animation')
w1 = win.addLayout()
view = w1.addViewBox()
img = pg.ImageItem()
def compute_edt(self, msk=None, limits=None, verbose=True):
"""
Compute the Euclidean distance transform for the given ROI binary mask.
Keyword arguments:
:msK: edge mask
:limits:
"""
import time
if msk is None:
msk = self.mask
if msk is None:
return None
ND = len(msk.data.shape) # Number of Dimensions
edt = np.empty_like(msk.data, dtype=np.float)
edt.fill(np.inf)
root = np.zeros(msk.data.shape + (ND, ), dtype=np.uint16)
idx = Index(np.nonzero(msk.data))
edt[idx] = 0
root[idx] = idx.array
counter = 0
total_voxels = 0
while idx:
counter += 1
total_voxels += idx.array.shape[0]
t0 = time.clock()
newidx = None
if verbose:
print('Iteration {0}: {1} voxels, {2} total voxels, '.format(
counter, idx.array.shape[0], total_voxels))
for dim in range(ND):
for offset in [-1, 1]:
(idx_off, inbounds) = idx.offset(dim, offset, msk)
idx_inbounds = idx.apply_mask(inbounds)
idx_off = idx_off.apply_mask(inbounds)
dist = idx_off.array - root[idx_inbounds]
for dim2 in range(ND):
dist[:, dim2] *= msk.spacing[dim2]
dist = np.sum(np.square(dist), axis=1)
update_edt = (dist < edt[idx_off])
idx_update = idx_inbounds.apply_mask(update_edt)
idx_off = idx_off.apply_mask(update_edt)
edt[idx_off] = dist[update_edt]
root[idx_off] = root[idx_update]
if idx_off.array.size:
if newidx is None:
newidx = idx_off.array
else:
newidx = np.vstack((newidx, idx_off.array))
if newidx is None:
idx = None
else:
unique_idx = np.unique(
np.ravel_multi_index(tuple(newidx.T), msk.data.shape))
idx = Index(np.unravel_index(unique_idx, msk.data.shape))
if verbose:
print(time.clock() - t0, 'seconds')
if verbose:
print('Total iterations:', counter)
print('Total voxels:', total_voxels)
edt_out = image.Image()
edt_out.copy_information(msk)
edt_out.set_image(np.sqrt(edt))
return edt_out
def _as_1d(dense_shape, *edges):
edges = np.concatenate(edges, axis=0)
edges = np.ravel_multi_index(edges.T, dense_shape)
edges.sort()
return edges