def recv_signal(self):
n_atoms, n_channels, *atom_support = self.D.shape
comm = MPI.Comm.Get_parent()
X_info = comm.bcast(None, root=0)
self.has_z0 = X_info['has_z0']
self.valid_support = X_info['valid_support']
self.workers_topology = X_info['workers_topology']
self.size_msg = len(self.workers_topology) + 2
self.workers_segments = Segmentation(n_seg=self.workers_topology,
signal_support=self.valid_support,
overlap=self.overlap)
# Receive X and z from the master node.
worker_support = self.workers_segments.get_seg_support(self.rank)
X_shape = (n_channels, ) + get_full_support(worker_support,
atom_support)
z0_shape = (n_atoms, ) + worker_support
if self.has_z0:
z0 = self.recv_array(z0_shape)
else:
z0 = None
X_worker = self.recv_array(X_shape)
# Compute the local segmentation for LGCD algorithm
# If n_seg is not specified, compute the shape of the local segments
# as the size of an interfering zone.
n_atoms, _, *atom_support = self.D.shape
n_seg = self.n_seg
local_seg_support = None
if self.n_seg == 'auto':
n_seg = None
local_seg_support = 2 * np.array(atom_support) - 1
# Get local inner bounds. First, compute the seg_bound without overlap
# in local coordinates and then convert the bounds in the local
# coordinate system.
inner_bounds = self.workers_segments.get_seg_bounds(self.rank,
inner=True)
inner_bounds = np.transpose([
self.workers_segments.get_local_coordinate(self.rank, bound)
for bound in np.transpose(inner_bounds)
])
worker_support = self.workers_segments.get_seg_support(self.rank)
self.local_segments = Segmentation(n_seg=n_seg,
seg_support=local_seg_support,
inner_bounds=inner_bounds,
full_support=worker_support)
self.synchronize_workers(with_main=True)
return X_worker, z0
def test_padding_to_overlap():
n_seg = (4, 4)
sig_shape = (504, 504)
overlap = (12, 7)
seg = Segmentation(n_seg=n_seg, signal_shape=sig_shape, overlap=overlap)
seg_shape_all = seg.get_seg_shape(n_seg[1] + 1)
for i_seg in range(np.prod(n_seg)):
seg_shape = seg.get_seg_shape(i_seg)
z = np.empty(seg_shape)
overlap = seg.get_padding_to_overlap(i_seg)
z = np.pad(z, overlap, mode='constant')
assert z.shape == seg_shape_all
def test_change_coordinate():
sig_support = (505, 407)
overlap = (12, 7)
n_seg = (4, 4)
segments = Segmentation(n_seg=n_seg, signal_support=sig_support,
overlap=overlap)
for i_seg in range(segments.effective_n_seg):
seg_bound = segments.get_seg_bounds(i_seg)
seg_support = segments.get_seg_support(i_seg)
origin = tuple([start for start, _ in seg_bound])
assert segments.get_global_coordinate(i_seg, (0, 0)) == origin
assert segments.get_local_coordinate(i_seg, origin) == (0, 0)
corner = tuple([end for _, end in seg_bound])
assert segments.get_global_coordinate(i_seg, seg_support) == corner
assert segments.get_local_coordinate(i_seg, corner) == seg_support
def test_segmentation_coverage_overlap():
sig_support = (505, 407)
for overlap in [(3, 0), (0, 5), (3, 5), (12, 7)]:
for h_seg in [5, 7, 9, 13, 15, 17]:
for w_seg in [3, 11]:
segments = Segmentation(n_seg=(h_seg, w_seg),
signal_support=sig_support,
overlap=overlap)
z = np.zeros(sig_support)
for i_seg in range(segments.effective_n_seg):
seg_slice = segments.get_seg_slice(i_seg, inner=True)
z[seg_slice] += 1
i_seg = segments.increment_seg(i_seg)
non_overlapping = np.prod(sig_support)
assert np.sum(z == 1) == non_overlapping
z = np.zeros(sig_support)
for i_seg in range(segments.effective_n_seg):
seg_slice = segments.get_seg_slice(i_seg)
z[seg_slice] += 1
i_seg = segments.increment_seg(i_seg)
h_ov, w_ov = overlap
h_seg, w_seg = segments.n_seg_per_axis
expected_overlap = ((h_seg - 1) * sig_support[1] * 2 * h_ov)
expected_overlap += ((w_seg - 1) * sig_support[0] * 2 * w_ov)
# Compute the number of pixel where there is more than 2
# segments overlappping.
corner_overlap = 4 * (h_seg - 1) * (w_seg - 1) * h_ov * w_ov
expected_overlap -= 2 * corner_overlap
non_overlapping -= expected_overlap + corner_overlap
assert non_overlapping == np.sum(z == 1)
assert expected_overlap == np.sum(z == 2)
assert corner_overlap == np.sum(z == 4)
def recv_task(self):
# Retrieve different constants from the base communicator and store
# then in the class.
params = self.get_params()
if self.timeout:
self.timeout *= 3
self.random_state = params['random_state']
if isinstance(self.random_state, int):
self.random_state += self.rank
self.size_msg = len(params['valid_shape']) + 2
# Compute the shape of the worker segment.
self.D = self.get_D()
n_atoms, n_channels, *atom_support = self.D.shape
self.overlap = np.array(atom_support) - 1
self.workers_segments = Segmentation(
n_seg=params['workers_topology'],
signal_shape=params['valid_shape'],
overlap=self.overlap)
# Receive X and z from the master node.
worker_shape = self.workers_segments.get_seg_shape(self.rank)
X_shape = (n_channels, ) + get_full_shape(worker_shape, atom_support)
if params['has_z0']:
z0_shape = (n_atoms, ) + worker_shape
self.z0 = self.get_signal(z0_shape, params['debug'])
else:
self.z0 = None
self.X_worker = self.get_signal(X_shape, params['debug'])
# Compute the local segmentation for LGCD algorithm
# If n_seg is not specified, compute the shape of the local segments
# as the size of an interfering zone.
n_seg = self.n_seg
local_seg_shape = None
if self.n_seg == 'auto':
n_seg = None
local_seg_shape = 2 * np.array(atom_support) - 1
# Get local inner bounds. First, compute the seg_bound without overlap
# in local coordinates and then convert the bounds in the local
# coordinate system.
inner_bounds = self.workers_segments.get_seg_bounds(self.rank,
inner=True)
inner_bounds = np.transpose([
self.workers_segments.get_local_coordinate(self.rank, bound)
for bound in np.transpose(inner_bounds)
])
self.local_segments = Segmentation(n_seg=n_seg,
seg_shape=local_seg_shape,
inner_bounds=inner_bounds,
full_shape=worker_shape)
# Initialize the solution
n_atoms = self.D.shape[0]
seg_shape = self.workers_segments.get_seg_shape(self.rank)
if self.z0 is None:
self.z_hat = np.zeros((n_atoms, ) + seg_shape)
else:
self.z_hat = self.z0
self.info(
"Start DICOD with {} workers, strategy '{}', soft_lock"
"={} and n_seg={}({})",
self.n_jobs,
self.strategy,
self.soft_lock,
self.n_seg,
self.local_segments.effective_n_seg,
global_msg=True)
self.synchronize_workers()
class DICODWorker:
"""Worker for DICOD, running LGCD locally and using MPI for communications
Parameters
----------
backend: str
Backend used to communicate between workers. Available backends are
{ 'mpi' }.
"""
def __init__(self, backend):
self._backend = backend
def recv_task(self):
# Retrieve different constants from the base communicator and store
# then in the class.
params = self.get_params()
if self.timeout:
self.timeout *= 3
self.random_state = params['random_state']
if isinstance(self.random_state, int):
self.random_state += self.rank
self.size_msg = len(params['valid_shape']) + 2
# Compute the shape of the worker segment.
self.D = self.get_D()
n_atoms, n_channels, *atom_support = self.D.shape
self.overlap = np.array(atom_support) - 1
self.workers_segments = Segmentation(
n_seg=params['workers_topology'],
signal_shape=params['valid_shape'],
overlap=self.overlap)
# Receive X and z from the master node.
worker_shape = self.workers_segments.get_seg_shape(self.rank)
X_shape = (n_channels, ) + get_full_shape(worker_shape, atom_support)
if params['has_z0']:
z0_shape = (n_atoms, ) + worker_shape
self.z0 = self.get_signal(z0_shape, params['debug'])
else:
self.z0 = None
self.X_worker = self.get_signal(X_shape, params['debug'])
# Compute the local segmentation for LGCD algorithm
# If n_seg is not specified, compute the shape of the local segments
# as the size of an interfering zone.
n_seg = self.n_seg
local_seg_shape = None
if self.n_seg == 'auto':
n_seg = None
local_seg_shape = 2 * np.array(atom_support) - 1
# Get local inner bounds. First, compute the seg_bound without overlap
# in local coordinates and then convert the bounds in the local
# coordinate system.
inner_bounds = self.workers_segments.get_seg_bounds(self.rank,
inner=True)
inner_bounds = np.transpose([
self.workers_segments.get_local_coordinate(self.rank, bound)
for bound in np.transpose(inner_bounds)
])
self.local_segments = Segmentation(n_seg=n_seg,
seg_shape=local_seg_shape,
inner_bounds=inner_bounds,
full_shape=worker_shape)
# Initialize the solution
n_atoms = self.D.shape[0]
seg_shape = self.workers_segments.get_seg_shape(self.rank)
if self.z0 is None:
self.z_hat = np.zeros((n_atoms, ) + seg_shape)
else:
self.z_hat = self.z0
self.info(
"Start DICOD with {} workers, strategy '{}', soft_lock"
"={} and n_seg={}({})",
self.n_jobs,
self.strategy,
self.soft_lock,
self.n_seg,
self.local_segments.effective_n_seg,
global_msg=True)
self.synchronize_workers()
def compute_z_hat(self):
# Initialization of the algorithm variables
random_state = check_random_state(self.random_state)
i_seg = -1
n_coordinate_updates = 0
accumulator = 0
k0, pt0 = 0, None
self.n_paused_worker = 0
# compute the number of coordinates
n_atoms, *_ = self.D.shape
seg_in_shape = self.workers_segments.get_seg_shape(self.rank,
inner=True)
n_coordinates = n_atoms * np.prod(seg_in_shape)
self.init_cd_variables()
diverging = False
if flags.INTERACTIVE_PROCESSES and self.n_jobs == 1:
import ipdb
ipdb.set_trace() # noqa: E702
self.t_start = t_start = time.time()
if self.timeout is not None:
deadline = t_start + self.timeout
else:
deadline = None
for ii in range(self.max_iter):
# Display the progress of the algorithm
self.progress(ii, max_ii=self.max_iter, unit="iterations")
# Process incoming messages
self.process_messages()
# Increment the segment and select the coordinate to update
try:
i_seg = self.local_segments.increment_seg(i_seg)
except ZeroDivisionError:
print(self.local_segments.signal_shape,
self.local_segments.n_seg_per_axis)
raise
if self.local_segments.is_active_segment(i_seg):
k0, pt0, dz = _select_coordinate(self.dz_opt,
self.dE,
self.local_segments,
i_seg,
strategy=self.strategy,
random_state=random_state)
assert self.workers_segments.is_contained_coordinate(
self.rank, pt0, inner=True), pt0
else:
k0, pt0, dz = None, None, 0
# update the accumulator for 'random' strategy
accumulator = max(abs(dz), accumulator)
# If requested, check that the update chosen only have an impact on
# the segment and its overlap area.
if flags.CHECK_UPDATE_CONTAINED and pt0 is not None:
self.workers_segments.check_area_contained(
self.rank, pt0, self.overlap)
# Check if the coordinate is soft-locked or not.
soft_locked = False
if (pt0 is not None and abs(dz) > self.tol
and self.soft_lock != 'none'):
n_lock = 1 if self.soft_lock == "corner" else 0
lock_slices = self.workers_segments.get_touched_overlap_slices(
self.rank, pt0,
np.array(self.overlap) + 1)
# Only soft lock in the corners
if len(lock_slices) > n_lock:
max_on_lock = 0
for u_slice in lock_slices:
max_on_lock = max(
abs(self.dz_opt[u_slice]).max(), max_on_lock)
soft_locked = max_on_lock > abs(dz)
# Update the selected coordinate and beta, only if the update is
# greater than the convergence tolerance and is contained in the
# worker. If the update is not in the worker, this will
# effectively work has a soft lock to prevent interferences.
if abs(dz) > self.tol and not soft_locked:
n_coordinate_updates += 1
# update the selected coordinate and beta
self.coordinate_update(k0, pt0, dz)
# Notify neighboring workers of the update if needed.
pt_global = self.workers_segments.get_global_coordinate(
self.rank, pt0)
workers = self.workers_segments.get_touched_segments(
pt=pt_global, radius=np.array(self.overlap) + 1)
msg = np.array([k0, *pt_global, dz], 'd')
self.notify_neighbors(msg, workers)
if self.timing:
t_update = time.time() - t_start
self._log_updates.append(
(t_update, ii, self.rank, k0, pt_global, dz))
# Inactivate the current segment if the magnitude of the update is
# too small. This only work when using LGCD.
if abs(dz) <= self.tol and self.strategy == "greedy":
self.local_segments.set_inactive_segments(i_seg)
# When workers are diverging, finish the worker to avoid having to
# wait until max_iter for stopping the algorithm.
if abs(dz) >= 1e3:
self.info("diverging worker")
self.wait_status_changed(status=constants.STATUS_FINISHED)
diverging = True
break
# Check the stopping criterion and if we have locally converged,
# wait either for an incoming message or for full convergence.
if _check_convergence(self.local_segments,
self.tol,
ii,
self.dz_opt,
n_coordinates,
self.strategy,
accumulator=accumulator):
if flags.CHECK_ACTIVE_SEGMENTS:
inner_slice = (Ellipsis, ) + tuple([
slice(start, end)
for start, end in self.local_segments.inner_bounds
])
assert np.all(abs(self.dz_opt[inner_slice]) <= self.tol)
if self.check_no_transitting_message():
status = self.wait_status_changed()
if status == constants.STATUS_STOP:
self.debug(
"LGCD converged with {} coordinate "
"updates", n_coordinate_updates)
break
# Check is we reach the timeout
if deadline is not None and time.time() >= deadline:
self.stop_before_convergence("Reached timeout",
n_coordinate_updates)
break
else:
self.stop_before_convergence("Reached max_iter",
n_coordinate_updates)
self.synchronize_workers()
assert diverging or self.check_no_transitting_message()
runtime = time.time() - t_start
comm = MPI.Comm.Get_parent()
comm.gather([n_coordinate_updates, runtime], root=0)
return n_coordinate_updates, runtime
def run(self):
self.recv_task()
n_coordinate_updates, runtime = self.compute_z_hat()
self.send_result(n_coordinate_updates, runtime)
def stop_before_convergence(self, msg, n_coordinate_updates):
self.info("{}. Done {} coordinate updates. Max of |dz|={}.", msg,
n_coordinate_updates,
abs(self.dz_opt).max())
self.wait_status_changed(status=constants.STATUS_FINISHED)
def init_cd_variables(self):
t_start = time.time()
# Pre-compute some quantities
constants = {}
constants['norm_atoms'] = compute_norm_atoms(self.D)
constants['DtD'] = compute_DtD(self.D)
self.constants = constants
# List of all pending messages sent
self.messages = []
# Log all updates for logging purpose
self._log_updates = []
# Avoid printing progress too often
self._last_progress = 0
# Initialization of the auxillary variable for LGCD
return_dE = self.strategy == "gs-q"
self.beta, self.dz_opt, self.dE = _init_beta(
self.X_worker,
self.D,
self.reg,
z_i=self.z0,
constants=constants,
z_positive=self.z_positive,
return_dE=return_dE)
# Make sure all segments are activated
self.local_segments.reset()
if self.z0 is not None:
self.freezed_support = None
self.correct_beta_z0()
if flags.CHECK_WARM_BETA:
pt_global = self.workers_segments.get_seg_shape(0, inner=True)
pt = self.workers_segments.get_local_coordinate(
self.rank, pt_global)
if self.workers_segments.is_contained_coordinate(self.rank, pt):
_, _, *atom_support = self.D.shape
beta_slice = (Ellipsis, ) + tuple([
slice(v - size_ax + 1, v + size_ax - 1)
for v, size_ax in zip(pt, atom_support)
])
sum_beta = np.array(self.beta[beta_slice].sum(), dtype='d')
self.return_array(sum_beta)
if self.freeze_support:
assert self.z0 is not None
self.freezed_support = self.z0 == 0
self.dz_opt[self.freezed_support] = 0
else:
self.freezed_support = None
self.synchronize_workers()
t_local_init = time.time() - t_start
self.info("End local initialization in {:.2f}s",
t_local_init,
global_msg=True)
def coordinate_update(self, k0, pt0, dz, coordinate_exist=True):
self.beta, self.dz_opt, self.dE = coordinate_update(
k0,
pt0,
dz,
beta=self.beta,
dz_opt=self.dz_opt,
dE=self.dE,
z_hat=self.z_hat,
D=self.D,
reg=self.reg,
constants=self.constants,
z_positive=self.z_positive,
freezed_support=self.freezed_support,
coordinate_exist=coordinate_exist)
# Re-activate the segments where beta have been updated to ensure
# convergence.
touched_segments = self.local_segments.get_touched_segments(
pt=pt0, radius=self.overlap)
n_changed_status = self.local_segments.set_active_segments(
touched_segments)
# If requested, check that all inactive segments have no coefficients
# to update over the tolerance.
if flags.CHECK_ACTIVE_SEGMENTS and n_changed_status:
self.local_segments.test_active_segments(self.dz_opt, self.tol)
def process_messages(self, worker_status=constants.STATUS_RUNNING):
mpi_status = MPI.Status()
while MPI.COMM_WORLD.Iprobe(status=mpi_status):
src = mpi_status.source
tag = mpi_status.tag
if tag == constants.TAG_DICOD_UPDATE_BETA:
if worker_status == constants.STATUS_PAUSED:
self.notify_worker_status(
constants.TAG_DICOD_RUNNING_WORKER, wait=True)
worker_status = constants.STATUS_RUNNING
elif tag == constants.TAG_DICOD_STOP:
worker_status = constants.STATUS_STOP
elif tag == constants.TAG_DICOD_PAUSED_WORKER:
self.n_paused_worker += 1
assert self.n_paused_worker <= self.n_jobs
elif tag == constants.TAG_DICOD_RUNNING_WORKER:
self.n_paused_worker -= 1
assert self.n_paused_worker >= 0
msg = np.empty(self.size_msg, 'd')
MPI.COMM_WORLD.Recv([msg, MPI.DOUBLE], source=src, tag=tag)
if tag == constants.TAG_DICOD_UPDATE_BETA:
self.message_update_beta(msg)
if self.n_paused_worker == self.n_jobs:
worker_status = constants.STATUS_STOP
return worker_status
def message_update_beta(self, msg):
k0, *pt_global, dz = msg
k0 = int(k0)
pt_global = tuple([int(v) for v in pt_global])
pt0 = self.workers_segments.get_local_coordinate(self.rank, pt_global)
assert not self.workers_segments.is_contained_coordinate(
self.rank, pt0, inner=True), (pt_global, pt0)
coordinate_exist = self.workers_segments.is_contained_coordinate(
self.rank, pt0, inner=False)
self.coordinate_update(k0, pt0, dz, coordinate_exist=coordinate_exist)
if flags.CHECK_BETA and np.random.rand() > 0.99:
# Only check beta 1% of the time to avoid the check being too long
inner_slice = (Ellipsis, ) + tuple([
slice(start, end)
for start, end in self.local_segments.inner_bounds
])
beta, *_ = _init_beta(self.X_worker,
self.D,
self.reg,
z_i=self.z_hat,
constants=self.constants,
z_positive=self.z_positive)
assert np.allclose(beta[inner_slice], self.beta[inner_slice])
def notify_neighbors(self, msg, neighbors):
assert self.rank in neighbors
for i_neighbor in neighbors:
if i_neighbor != self.rank:
req = self.send_message(msg,
constants.TAG_DICOD_UPDATE_BETA,
i_neighbor,
wait=False)
self.messages.append(req)
def notify_worker_status(self, tag, i_worker=0, wait=False):
# handle the messages from Worker0 to himself.
if self.rank == 0 and i_worker == 0:
if tag == constants.TAG_DICOD_PAUSED_WORKER:
self.n_paused_worker += 1
assert self.n_paused_worker <= self.n_jobs
elif tag == constants.TAG_DICOD_RUNNING_WORKER:
self.n_paused_worker -= 1
assert self.n_paused_worker >= 0
elif tag == constants.TAG_DICOD_INIT_DONE:
pass
else:
raise ValueError("Got tag {}".format(tag))
return
# Else send the message to the required destination
msg = np.empty(self.size_msg, 'd')
self.send_message(msg, tag, i_worker, wait=wait)
def wait_status_changed(self, status=constants.STATUS_PAUSED):
if status == constants.STATUS_FINISHED:
# Make sure to flush the messages
while not self.check_no_transitting_message():
self.process_messages(worker_status=status)
time.sleep(0.001)
self.notify_worker_status(constants.TAG_DICOD_PAUSED_WORKER)
self.debug("paused worker")
# Wait for all sent message to be processed
count = 0
while status not in [constants.STATUS_RUNNING, constants.STATUS_STOP]:
time.sleep(.005)
status = self.process_messages(worker_status=status)
if (count % 500) == 0:
self.progress(self.n_paused_worker,
max_ii=self.n_jobs,
unit="done workers")
if self.rank == 0 and status == constants.STATUS_STOP:
for i_worker in range(1, self.n_jobs):
self.notify_worker_status(constants.TAG_DICOD_STOP,
i_worker,
wait=True)
elif status == constants.STATUS_RUNNING:
self.debug("wake up")
else:
assert status == constants.STATUS_STOP
return status
def compute_sufficient_statistics(self):
_, _, *atom_support = self.D.shape
z_slice = (Ellipsis, ) + tuple([
slice(start, end)
for start, end in self.local_segments.inner_bounds
])
X_slice = (Ellipsis, ) + tuple([
slice(start, end + size_atom_ax - 1)
for (start, end), size_atom_ax in zip(
self.local_segments.inner_bounds, atom_support)
])
ztX = compute_ztX(self.z_hat[z_slice], self.X_worker[X_slice])
padding_shape = self.workers_segments.get_padding_to_overlap(self.rank)
ztz = compute_ztz(self.z_hat,
atom_support,
padding_shape=padding_shape)
return np.array(ztz, dtype='d'), np.array(ztX, dtype='d')
def correct_beta_z0(self):
# Send coordinate updates to neighbors for all nonzero coordinates in
# z0
msg_send, msg_recv = [0] * self.n_jobs, [0] * self.n_jobs
for k0, *pt0 in zip(*self.z0.nonzero()):
# Notify neighboring workers of the update if needed.
pt_global = self.workers_segments.get_global_coordinate(
self.rank, pt0)
workers = self.workers_segments.get_touched_segments(
pt=pt_global, radius=np.array(self.overlap) + 1)
msg = np.array([k0, *pt_global, self.z0[(k0, *pt0)]], 'd')
self.notify_neighbors(msg, workers)
for i in workers:
msg_send[i] += 1
n_init_done = 0
done_pt = set()
no_msg, init_done = False, False
mpi_status = MPI.Status()
while not init_done:
if n_init_done == self.n_jobs:
for i_worker in range(1, self.n_jobs):
self.notify_worker_status(constants.TAG_DICOD_INIT_DONE,
i_worker=i_worker)
init_done = True
if not no_msg:
if self.check_no_transitting_message(check_incoming=False):
self.notify_worker_status(constants.TAG_DICOD_INIT_DONE)
if self.rank == 0:
n_init_done += 1
assert len(self.messages) == 0
no_msg = True
if MPI.COMM_WORLD.Iprobe(status=mpi_status):
tag = mpi_status.tag
src = mpi_status.source
if tag == constants.TAG_DICOD_INIT_DONE:
if self.rank == 0:
n_init_done += 1
else:
init_done = True
msg = np.empty(self.size_msg, 'd')
MPI.COMM_WORLD.Recv([msg, MPI.DOUBLE], source=src, tag=tag)
if tag == constants.TAG_DICOD_UPDATE_BETA:
msg_recv[src] += 1
k0, *pt_global, dz = msg
k0 = int(k0)
pt_global = tuple([int(v) for v in pt_global])
pt0 = self.workers_segments.get_local_coordinate(
self.rank, pt_global)
pt_exist = self.workers_segments.is_contained_coordinate(
self.rank, pt0, inner=False)
if not pt_exist and (k0, *pt0) not in done_pt:
done_pt.add((k0, *pt0))
self.coordinate_update(k0,
pt0,
dz,
coordinate_exist=False)
else:
time.sleep(.001)
def compute_cost(self):
X_hat_worker = reconstruct(self.z_hat, self.D)
inner_bounds = self.local_segments.inner_bounds
inner_slice = tuple(
[Ellipsis] +
[slice(start_ax, end_ax) for start_ax, end_ax in inner_bounds])
X_hat_slice = list(inner_slice)
i_seg = self.rank
ax_rank_offset = self.workers_segments.effective_n_seg
for ax, n_seg_ax in enumerate(self.workers_segments.n_seg_per_axis):
ax_rank_offset //= n_seg_ax
ax_i_seg = i_seg // ax_rank_offset
i_seg % ax_rank_offset
if (ax_i_seg + 1) % n_seg_ax == 0:
s = inner_slice[ax + 1]
X_hat_slice[ax + 1] = slice(s.start, None)
X_hat_slice = tuple(X_hat_slice)
diff = (X_hat_worker[X_hat_slice] - self.X_worker[X_hat_slice]).ravel()
cost = .5 * np.dot(diff, diff)
return cost + self.reg * abs(self.z_hat[inner_slice]).sum()
def return_z_hat(self):
if flags.GET_OVERLAP_Z_HAT:
res_slice = (Ellipsis, )
else:
res_slice = (Ellipsis, ) + tuple([
slice(start, end)
for start, end in self.local_segments.inner_bounds
])
z_worker = self.z_hat[res_slice].ravel()
self.return_array(z_worker)
def return_z_nnz(self):
res_slice = (Ellipsis, ) + tuple([
slice(start, end)
for start, end in self.local_segments.inner_bounds
])
z_nnz = self.z_hat[res_slice] != 0
z_nnz = np.sum(z_nnz, axis=tuple(range(1, z_nnz.ndim)))
self.reduce_sum_array(z_nnz)
def return_sufficient_statistics(self):
ztz, ztX = self.compute_sufficient_statistics()
self.reduce_sum_array(ztz)
self.reduce_sum_array(ztX)
def return_cost(self):
cost = self.compute_cost()
cost = np.array(cost, dtype='d')
self.reduce_sum_array(cost)
###########################################################################
# Display utilities
###########################################################################
def progress(self, ii, max_ii, unit):
t_progress = time.time()
if t_progress - self._last_progress < 1:
return
self._last_progress = t_progress
self._log("{:.0f}s - progress : {:7.2%} {}",
time.time() - self.t_start,
ii / max_ii,
unit,
level=1,
level_name="PROGRESS",
global_msg=True,
endline=False)
def info(self, msg, *fmt_args, global_msg=False, **fmt_kwargs):
self._log(msg,
*fmt_args,
level=1,
level_name="INFO",
global_msg=global_msg,
**fmt_kwargs)
def debug(self, msg, *fmt_args, global_msg=False, **fmt_kwargs):
self._log(msg,
*fmt_args,
level=5,
level_name="DEBUG",
global_msg=global_msg,
**fmt_kwargs)
def _log(self,
msg,
*fmt_args,
level=0,
level_name="None",
global_msg=False,
endline=True,
**fmt_kwargs):
if self.verbose >= level:
if global_msg:
if self.rank != 0:
return
msg_fmt = constants.GLOBAL_OUTPUT_TAG + msg
identity = self.n_jobs
else:
msg_fmt = constants.WORKER_OUTPUT_TAG + msg
identity = self.rank
if endline:
kwargs = {}
else:
kwargs = {'end': '', 'flush': True}
msg_fmt = msg_fmt.ljust(80)
print(
msg_fmt.format(
*fmt_args,
identity=identity,
level_name=level_name,
**fmt_kwargs,
), **kwargs)
###########################################################################
# Communication primitives
###########################################################################
def synchronize_workers(self):
if self._backend == "mpi":
self._synchronize_workers_mpi()
else:
raise NotImplementedError("Backend {} is not implemented".format(
self._backend))
def get_params(self):
"""Receive the parameter of the algorithm from the master node."""
if self._backend == "mpi":
self.rank, self.n_jobs, params = self._get_params_mpi()
else:
raise NotImplementedError("Backend {} is not implemented".format(
self._backend))
self.tol = params['tol']
self.reg = params['reg']
self.n_seg = params['n_seg']
self.timing = params['timing']
self.timeout = params['timeout']
self.verbose = params['verbose']
self.strategy = params['strategy']
self.max_iter = params['max_iter']
self.soft_lock = params['soft_lock']
self.z_positive = params['z_positive']
self.return_ztz = params['return_ztz']
self.freeze_support = params['freeze_support']
self.debug("tol updated to {:.2e}", self.tol, global_msg=True)
return params
def get_signal(self, X_shape, debug=False):
"""Receive the part of the signal to encode from the master node."""
if self._backend == "mpi":
return self._get_signal_mpi(X_shape, debug=debug)
else:
raise NotImplementedError("Backend {} is not implemented".format(
self._backend))
def send_message(self, msg, tag, i_worker, wait=False):
"""Send a message to a specified worker."""
assert self.rank != i_worker
if self._backend == "mpi":
return self._send_message_mpi(msg, tag, i_worker, wait=wait)
else:
raise NotImplementedError("Backend {} is not implemented".format(
self._backend))
def send_result(self, iterations, runtime):
if self._backend == "mpi":
self._send_result_mpi(iterations, runtime)
else:
raise NotImplementedError("Backend {} is not implemented".format(
self._backend))
def get_D(self):
"""Receive a dictionary D"""
if self._backend == "mpi":
comm = MPI.Comm.Get_parent()
self.D = recv_broadcasted_array(comm)
return self.D
else:
raise NotImplementedError("Backend {} is not implemented".format(
self._backend))
def return_array(self, sig):
if self._backend == "mpi":
self._return_array_mpi(sig)
else:
raise NotImplementedError("Backend {} is not implemented".format(
self._backend))
def reduce_sum_array(self, arr):
if self._backend == "mpi":
self._reduce_sum_array_mpi(arr)
else:
raise NotImplementedError("Backend {} is not implemented".format(
self._backend))
def shutdown(self):
if self._backend == "mpi":
self._shutdown_mpi()
else:
raise NotImplementedError("Backend {} is not implemented".format(
self._backend))
###########################################################################
# mpi4py implementation
###########################################################################
def _synchronize_workers_mpi(self):
comm = MPI.Comm.Get_parent()
comm.Barrier()
def check_no_transitting_message(self, check_incoming=True):
"""Check no message is in waiting to complete to or from this worker"""
if check_incoming and MPI.COMM_WORLD.Iprobe():
return False
while self.messages:
if not self.messages[0].Test() or (check_incoming
and MPI.COMM_WORLD.Iprobe()):
return False
self.messages.pop(0)
assert len(self.messages) == 0, len(self.messages)
return True
def _get_params_mpi(self):
comm = MPI.Comm.Get_parent()
rank = comm.Get_rank()
n_jobs = comm.Get_size()
params = comm.bcast(None, root=0)
return rank, n_jobs, params
def _get_signal_mpi(self, sig_shape, debug):
comm = MPI.Comm.Get_parent()
rank = comm.Get_rank()
sig_worker = np.empty(sig_shape, dtype='d')
comm.Recv([sig_worker.ravel(), MPI.DOUBLE],
source=0,
tag=constants.TAG_ROOT + rank)
if debug:
X_alpha = 0.25 * np.ones(sig_shape)
self.return_array(X_alpha)
return sig_worker
def _send_message_mpi(self, msg, tag, i_worker, wait=False):
if wait:
return MPI.COMM_WORLD.Ssend([msg, MPI.DOUBLE], i_worker, tag=tag)
else:
return MPI.COMM_WORLD.Issend([msg, MPI.DOUBLE], i_worker, tag=tag)
def _send_result_mpi(self, iterations, runtime):
comm = MPI.Comm.Get_parent()
self.info("Reducing the distributed results", global_msg=True)
self.return_z_hat()
if self.return_ztz:
self.return_sufficient_statistics()
self.return_cost()
if self.timing:
comm.send(self._log_updates, dest=0)
comm.Barrier()
def _return_array_mpi(self, arr):
comm = MPI.Comm.Get_parent()
arr.astype('d')
comm.Send([arr, MPI.DOUBLE],
dest=0,
tag=constants.TAG_ROOT + self.rank)
def _reduce_sum_array_mpi(self, arr):
comm = MPI.Comm.Get_parent()
arr = np.array(arr, dtype='d')
comm.Reduce([arr, MPI.DOUBLE], None, op=MPI.SUM, root=0)
def _shutdown_mpi(self):
comm = MPI.Comm.Get_parent()
self.debug("clean shutdown")
comm.Barrier()
comm.Disconnect()
def test_touched_segments():
"""Test detection of touched segments and records of active segments
"""
rng = np.random.RandomState(42)
H, W = sig_support = (108, 53)
n_seg = (9, 3)
for h_radius in [5, 7, 9]:
for w_radius in [3, 11]:
for _ in range(20):
h0 = rng.randint(-h_radius, sig_support[0] + h_radius)
w0 = rng.randint(-w_radius, sig_support[1] + w_radius)
z = np.zeros(sig_support)
segments = Segmentation(n_seg, signal_support=sig_support)
touched_slice = (
slice(max(0, h0 - h_radius), min(H, h0 + h_radius + 1)),
slice(max(0, w0 - w_radius), min(W, w0 + w_radius + 1))
)
z[touched_slice] = 1
touched_segments = segments.get_touched_segments(
(h0, w0), (h_radius, w_radius))
segments.set_inactive_segments(touched_segments)
n_active_segments = segments._n_active_segments
expected_n_active_segments = segments.effective_n_seg
for i_seg in range(segments.effective_n_seg):
seg_slice = segments.get_seg_slice(i_seg)
is_touched = np.any(z[seg_slice] == 1)
expected_n_active_segments -= is_touched
assert segments.is_active_segment(i_seg) != is_touched
assert n_active_segments == expected_n_active_segments
# Check an error is returned when touched radius is larger than seg_size
segments = Segmentation(n_seg, signal_support=sig_support)
with pytest.raises(ValueError, match="too large"):
segments.get_touched_segments((0, 0), (30, 2))
def test_segmentation_coverage():
sig_support = (108, 53)
for h_seg in [5, 7, 9, 13, 17]:
for w_seg in [3, 11]:
z = np.zeros(sig_support)
segments = Segmentation(n_seg=(h_seg, w_seg),
signal_support=sig_support)
assert tuple(segments.n_seg_per_axis) == (h_seg, w_seg)
seg_slice = segments.get_seg_slice(0)
seg_support = segments.get_seg_support(0)
assert seg_support == z[seg_slice].shape
z[seg_slice] += 1
i_seg = segments.increment_seg(0)
while i_seg != 0:
seg_slice = segments.get_seg_slice(i_seg)
seg_support = segments.get_seg_support(i_seg)
assert seg_support == z[seg_slice].shape
z[seg_slice] += 1
i_seg = segments.increment_seg(i_seg)
assert np.all(z == 1)
z = np.zeros(sig_support)
inner_bounds = [(8, 100), (3, 50)]
inner_slice = tuple([slice(start, end) for start, end in inner_bounds])
segments = Segmentation(n_seg=7, inner_bounds=inner_bounds,
full_support=sig_support)
for i_seg in range(segments.effective_n_seg):
seg_slice = segments.get_seg_slice(i_seg)
z[seg_slice] += 1
assert np.all(z[inner_slice] == 1)
z[inner_slice] = 0
assert np.all(z == 0)
def test_touched_overlap_area():
sig_support = (505, 407)
overlap = (11, 9)
n_seg = (8, 4)
segments = Segmentation(n_seg=n_seg, signal_support=sig_support,
overlap=overlap)
for i_seg in range(segments.effective_n_seg):
seg_support = segments.get_seg_support(i_seg)
seg_slice = segments.get_seg_slice(i_seg)
seg_inner_slice = segments.get_seg_slice(i_seg, inner=True)
if i_seg != 0:
with pytest.raises(AssertionError):
segments.check_area_contained(i_seg, (0, 0), overlap)
for pt0 in [overlap, (overlap[0], 25), (25, overlap[1]), (25, 25),
(seg_support[0] - overlap[0] - 1, 25),
(25, seg_support[1] - overlap[1] - 1),
(seg_support[0] - overlap[0] - 1,
seg_support[1] - overlap[1] - 1)
]:
assert segments.is_contained_coordinate(i_seg, pt0, inner=True)
segments.check_area_contained(i_seg, pt0, overlap)
z = np.zeros(sig_support)
pt_global = segments.get_global_coordinate(i_seg, pt0)
update_slice = tuple([
slice(max(v - r, 0), v + r + 1)
for v, r in zip(pt_global, overlap)])
z[update_slice] += 1
z[seg_inner_slice] = 0
# The returned slice are given in local coordinates. Take the
# segment in z to use local coordinate.
z_seg = z[seg_slice]
updated_slices = segments.get_touched_overlap_slices(i_seg, pt0,
overlap)
# Assert that all selected coordinate are indeed in the update area
for u_slice in updated_slices:
assert np.all(z_seg[u_slice] == 1)
# Assert that all coordinate updated in the overlap area have been
# selected with at least one slice.
for u_slice in updated_slices:
z_seg[u_slice] *= 0
assert np.all(z == 0)
def test_inner_coordinate():
sig_support = (505, 407)
overlap = (11, 11)
n_seg = (4, 4)
segments = Segmentation(n_seg=n_seg, signal_support=sig_support,
overlap=overlap)
for h_rank in range(n_seg[0]):
for w_rank in range(n_seg[1]):
i_seg = h_rank * n_seg[1] + w_rank
seg_support = segments.get_seg_support(i_seg)
assert segments.is_contained_coordinate(i_seg, overlap,
inner=True)
if h_rank == 0:
assert segments.is_contained_coordinate(i_seg, (0, overlap[1]),
inner=True)
else:
assert not segments.is_contained_coordinate(
i_seg, (overlap[0] - 1, overlap[1]), inner=True)
if w_rank == 0:
assert segments.is_contained_coordinate(i_seg, (overlap[0], 0),
inner=True)
else:
assert not segments.is_contained_coordinate(
i_seg, (overlap[0], overlap[1] - 1), inner=True)
if h_rank == 0 and w_rank == 0:
assert segments.is_contained_coordinate(i_seg, (0, 0),
inner=True)
else:
assert not segments.is_contained_coordinate(
i_seg, (overlap[0] - 1, overlap[1] - 1), inner=True)
if h_rank == n_seg[0] - 1:
assert segments.is_contained_coordinate(
i_seg,
(seg_support[0] - 1, seg_support[1] - overlap[1] - 1),
inner=True)
else:
assert not segments.is_contained_coordinate(
i_seg, (seg_support[0] - overlap[0],
seg_support[1] - overlap[1] - 1), inner=True)
if w_rank == n_seg[1] - 1:
assert segments.is_contained_coordinate(
i_seg,
(seg_support[0] - overlap[0] - 1, seg_support[1] - 1),
inner=True)
else:
assert not segments.is_contained_coordinate(
i_seg, (seg_support[0] - overlap[0] - 1,
seg_support[1] - overlap[1]), inner=True)
if h_rank == n_seg[0] - 1 and w_rank == n_seg[1] - 1:
assert segments.is_contained_coordinate(
i_seg, (seg_support[0] - 1, seg_support[1] - 1),
inner=True)
else:
assert not segments.is_contained_coordinate(
i_seg, (seg_support[0] - overlap[0],
seg_support[1] - overlap[1]), inner=True)
atom_support = (16, 16)
run_args = (n_atoms, atom_support, reg, tol, n_workers, random_state)
if args.no_cache:
X_hat, pobj = run_without_soft_lock.call(*run_args)[0]
else:
X_hat, pobj = run_without_soft_lock(*run_args)
file_name = f"soft_lock_M{n_workers}_support{atom_support[0]}"
np.save(f"benchmarks_results/{file_name}_X_hat.npy", X_hat)
# Compute the worker segmentation for the image,
n_channels, *sig_support = X_hat.shape
valid_support = get_valid_support(sig_support, atom_support)
workers_segments = Segmentation(n_seg=(w_world, w_world),
signal_support=valid_support,
overlap=0)
fig = plt.figure("recovery")
fig.patch.set_alpha(0)
ax = plt.subplot()
ax.imshow(X_hat.swapaxes(0, 2))
for i_seg in range(workers_segments.effective_n_seg):
seg_bounds = np.array(workers_segments.get_seg_bounds(i_seg))
seg_bounds = seg_bounds + np.array(atom_support) / 2
ax.vlines(seg_bounds[1], *seg_bounds[0], linestyle='--')
ax.hlines(seg_bounds[0], *seg_bounds[1], linestyle='--')
ax.axis('off')
plt.tight_layout()
def coordinate_descent(X_i, D, reg, z0=None, DtD=None, n_seg='auto',
strategy='greedy', tol=1e-5, max_iter=100000,
timeout=None, z_positive=False, freeze_support=False,
return_ztz=False, timing=False,
random_state=None, verbose=0):
"""Coordinate Descent Algorithm for 2D convolutional sparse coding.
Parameters
----------
X_i : ndarray, shape (n_channels, *sig_support)
Image to encode on the dictionary D
D : ndarray, shape (n_atoms, n_channels, *atom_support)
Current dictionary for the sparse coding
reg : float
Regularization parameter
z0 : ndarray, shape (n_atoms, *valid_support) or None
Warm start value for z_hat. If not present, z_hat is initialized to 0.
DtD : ndarray, shape (n_atoms, n_atoms, 2 * valid_support - 1) or None
Warm start value for DtD. If not present, it is computed on init.
n_seg : int or 'auto'
Number of segments to use for each dimension. If set to 'auto' use
segments of twice the size of the dictionary.
strategy : str in {strategies}
Coordinate selection scheme for the coordinate descent. If set to
'greedy'|'gs-r', the coordinate with the largest value for dz_opt is
selected. If set to 'random, the coordinate is chosen uniformly on the
segment. If set to 'gs-q', the value that reduce the most the cost
function is selected. In this case, dE must holds the value of this
cost reduction.
tol : float
Tolerance for the minimal update size in this algorithm.
max_iter : int
Maximal number of iteration run by this algorithm.
z_positive : boolean
If set to true, the activations are constrained to be positive.
freeze_support : boolean
If set to True, only update the coefficient that are non-zero in z0.
return_ztz : boolean
If True, returns the constants ztz and ztX, used to compute D-updates.
timing : boolean
If set to True, log the cost and timing information.
random_state : None or int or RandomState
current random state to seed the random number generator.
verbose : int
Verbosity level of the algorithm.
Return
------
z_hat : ndarray, shape (n_atoms, *valid_support)
Activation associated to X_i for the given dictionary D
"""
n_channels, *sig_support = X_i.shape
n_atoms, n_channels, *atom_support = D.shape
valid_support = get_valid_support(sig_support, atom_support)
if strategy not in STRATEGIES:
raise ValueError("'The coordinate selection strategy should be in "
"{}. Got '{}'.".format(STRATEGIES, strategy))
# compute sizes for the segments for LGCD. Auto gives segments of size
# twice the support of the atoms.
if n_seg == 'auto':
n_seg = np.array(valid_support) // (2 * np.array(atom_support) - 1)
n_seg = tuple(np.maximum(1, n_seg))
segments = Segmentation(n_seg, signal_support=valid_support)
# Pre-compute constants for maintaining the auxillary variable beta and
# compute the coordinate update values.
constants = {}
constants['norm_atoms'] = compute_norm_atoms(D)
if DtD is None:
constants['DtD'] = compute_DtD(D)
else:
constants['DtD'] = DtD
# Initialization of the algorithm variables
i_seg = -1
accumulator = 0
if z0 is None:
z_hat = np.zeros((n_atoms,) + valid_support)
else:
z_hat = np.copy(z0)
n_coordinates = z_hat.size
# Get a random number genator from the given random_state
rng = check_random_state(random_state)
order = None
if strategy in ['cyclic', 'cyclic-r', 'random']:
order = get_order_iterator(z_hat.shape, strategy=strategy,
random_state=rng)
t_start_init = time.time()
return_dE = strategy == "gs-q"
beta, dz_opt, dE = _init_beta(X_i, D, reg, z_i=z0, constants=constants,
z_positive=z_positive, return_dE=return_dE)
if strategy == "gs-q":
raise NotImplementedError("This is still WIP")
if freeze_support:
freezed_support = z0 == 0
dz_opt[freezed_support] = 0
else:
freezed_support = None
p_obj, next_log_iter = [], 1
t_init = time.time() - t_start_init
if timing:
p_obj.append((0, t_init, 0, compute_objective(X_i, z_hat, D, reg)))
n_coordinate_updates = 0
t_run = 0
t_select_coord, t_update_coord = [], []
t_start = time.time()
if timeout is not None:
deadline = t_start + timeout
else:
deadline = None
for ii in range(max_iter):
if ii % 1000 == 0 and verbose > 0:
print("\r[LGCD:PROGRESS] {:.0f}s - {:7.2%} iterations"
.format(t_run, ii / max_iter), end='', flush=True)
i_seg = segments.increment_seg(i_seg)
if segments.is_active_segment(i_seg):
t_start_selection = time.time()
k0, pt0, dz = _select_coordinate(dz_opt, dE, segments, i_seg,
strategy=strategy, order=order)
selection_duration = time.time() - t_start_selection
t_select_coord.append(selection_duration)
t_run += selection_duration
else:
dz = 0
accumulator = max(abs(dz), accumulator)
# Update the selected coordinate and beta, only if the update is
# greater than the convergence tolerance.
if abs(dz) > tol:
t_start_update = time.time()
# update the current solution estimate and beta
beta, dz_opt, dE = coordinate_update(
k0, pt0, dz, beta=beta, dz_opt=dz_opt, dE=dE, z_hat=z_hat, D=D,
reg=reg, constants=constants, z_positive=z_positive,
freezed_support=freezed_support)
touched_segs = segments.get_touched_segments(
pt=pt0, radius=atom_support)
n_changed_status = segments.set_active_segments(touched_segs)
# Logging of the time and the cost function if necessary
update_duration = time.time() - t_start_update
n_coordinate_updates += 1
t_run += update_duration
t_update_coord.append(update_duration)
if timing and ii + 1 >= next_log_iter:
p_obj.append((ii + 1, t_run, np.sum(t_select_coord),
compute_objective(X_i, z_hat, D, reg)))
next_log_iter = next_log_iter * 1.3
# If debug flag CHECK_ACTIVE_SEGMENTS is set, check that all
# inactive segments should be inactive
if flags.CHECK_ACTIVE_SEGMENTS and n_changed_status:
segments.test_active_segment(dz_opt, tol)
elif strategy in ["greedy", 'gs-r']:
segments.set_inactive_segments(i_seg)
# check stopping criterion
if _check_convergence(segments, tol, ii, dz_opt, n_coordinates,
strategy, accumulator=accumulator):
assert np.all(abs(dz_opt) <= tol)
if verbose > 0:
print("\r[LGCD:INFO] converged in {} iterations ({} updates)"
.format(ii + 1, n_coordinate_updates))
break
# Check is we reach the timeout
if deadline is not None and time.time() >= deadline:
if verbose > 0:
print("\r[LGCD:INFO] Reached timeout. Done {} iterations "
"({} updates). Max of |dz|={}."
.format(ii + 1, n_coordinate_updates, abs(dz_opt).max()))
break
else:
if verbose > 0:
print("\r[LGCD:INFO] Reached max_iter. Done {} coordinate "
"updates. Max of |dz|={}."
.format(n_coordinate_updates, abs(dz_opt).max()))
print(f"\r[LGCD:{strategy}] "
f"t_select={np.mean(t_select_coord):.3e}s "
f"t_update={np.mean(t_update_coord):.3e}s"
)
runtime = time.time() - t_start
if verbose > 0:
print("\r[LGCD:INFO] done in {:.3f}s ({:.3f}s)"
.format(runtime, t_run))
ztz, ztX = None, None
if return_ztz:
ztz = compute_ztz(z_hat, atom_support)
ztX = compute_ztX(z_hat, X_i)
p_obj.append([n_coordinate_updates, t_run,
compute_objective(X_i, z_hat, D, reg)])
run_statistics = dict(iterations=ii + 1, runtime=runtime, t_init=t_init,
t_run=t_run, n_updates=n_coordinate_updates,
t_select=np.mean(t_select_coord),
t_update=np.mean(t_update_coord))
return z_hat, ztz, ztX, p_obj, run_statistics
def coordinate_descent(X_i,
D,
reg,
z0=None,
n_seg='auto',
strategy='greedy',
tol=1e-5,
max_iter=100000,
timeout=None,
z_positive=False,
freeze_support=False,
return_ztz=False,
timing=False,
random_state=None,
verbose=0):
"""Coordinate Descent Algorithm for 2D convolutional sparse coding.
Parameters
----------
X_i : ndarray, shape (n_channels, *sig_shape)
Image to encode on the dictionary D
z_i : ndarray, shape (n_atoms, *valid_shape)
Warm start value for z_hat
D : ndarray, shape (n_atoms, n_channels, *atom_shape)
Current dictionary for the sparse coding
reg : float
Regularization parameter
n_seg : int or { 'auto' }
Number of segments to use for each dimension. If set to 'auto' use
segments of twice the size of the dictionary.
tol : float
Tolerance for the minimal update size in this algorithm.
strategy : str in { 'greedy' | 'random' | 'gs-r' | 'gs-q' }
Coordinate selection scheme for the coordinate descent. If set to
'greedy'|'gs-r', the coordinate with the largest value for dz_opt is
selected. If set to 'random, the coordinate is chosen uniformly on the
segment. If set to 'gs-q', the value that reduce the most the cost
function is selected. In this case, dE must holds the value of this
cost reduction.
max_iter : int
Maximal number of iteration run by this algorithm.
z_positive : boolean
If set to true, the activations are constrained to be positive.
freeze_support : boolean
If set to True, only update the coefficient that are non-zero in z0.
timing : boolean
If set to True, log the cost and timing information.
random_state : None or int or RandomState
current random state to seed the random number generator.
verbose : int
Verbosity level of the algorithm.
Return
------
z_hat : ndarray, shape (n_atoms, *valid_shape)
Activation associated to X_i for the given dictionary D
"""
n_channels, *sig_shape = X_i.shape
n_atoms, n_channels, *atom_shape = D.shape
valid_shape = tuple([
size_ax - size_atom_ax + 1
for size_ax, size_atom_ax in zip(sig_shape, atom_shape)
])
# compute sizes for the segments for LGCD
if n_seg == 'auto':
n_seg = []
for axis_size, atom_size in zip(valid_shape, atom_shape):
n_seg.append(max(axis_size // (2 * atom_size - 1), 1))
segments = Segmentation(n_seg, signal_shape=valid_shape)
# Pre-compute some quantities
constants = {}
constants['norm_atoms'] = compute_norm_atoms(D)
constants['DtD'] = compute_DtD(D)
# Initialization of the algorithm variables
i_seg = -1
p_obj, next_cost = [], 1
accumulator = 0
if z0 is None:
z_hat = np.zeros((n_atoms, ) + valid_shape)
else:
z_hat = np.copy(z0)
n_coordinates = z_hat.size
t_update = 0
t_start_update = time.time()
return_dE = strategy == "gs-q"
beta, dz_opt, dE = _init_beta(X_i,
D,
reg,
z_i=z0,
constants=constants,
z_positive=z_positive,
return_dE=return_dE)
if strategy == "gs-q":
raise NotImplementedError("This is still WIP")
if freeze_support:
freezed_support = z0 == 0
dz_opt[freezed_support] = 0
else:
freezed_support = None
t_start = time.time()
n_coordinate_updates = 0
if timeout is not None:
deadline = t_start + timeout
else:
deadline = None
for ii in range(max_iter):
if ii % 1000 == 0 and verbose > 0:
print("\r[LGCD:PROGRESS] {:.0f}s - {:7.2%} iterations".format(
t_update, ii / max_iter),
end='',
flush=True)
i_seg = segments.increment_seg(i_seg)
if segments.is_active_segment(i_seg):
k0, pt0, dz = _select_coordinate(dz_opt,
dE,
segments,
i_seg,
strategy=strategy,
random_state=random_state)
else:
k0, pt0, dz = None, None, 0
accumulator = max(abs(dz), accumulator)
# Update the selected coordinate and beta, only if the update is
# greater than the convergence tolerance.
if abs(dz) > tol:
n_coordinate_updates += 1
# update beta
beta, dz_opt, dE = coordinate_update(
k0,
pt0,
dz,
beta=beta,
dz_opt=dz_opt,
dE=dE,
z_hat=z_hat,
D=D,
reg=reg,
constants=constants,
z_positive=z_positive,
freezed_support=freezed_support)
touched_segs = segments.get_touched_segments(pt=pt0,
radius=atom_shape)
n_changed_status = segments.set_active_segments(touched_segs)
if flags.CHECK_ACTIVE_SEGMENTS and n_changed_status:
segments.test_active_segment(dz_opt, tol)
t_update += time.time() - t_start_update
if timing:
if ii >= next_cost:
p_obj.append(
(ii, t_update, compute_objective(X_i, z_hat, D, reg)))
next_cost = next_cost * 2
t_start_update = time.time()
elif strategy in ["greedy", 'gs-r']:
segments.set_inactive_segments(i_seg)
# check stopping criterion
if _check_convergence(segments,
tol,
ii,
dz_opt,
n_coordinates,
strategy,
accumulator=accumulator):
assert np.all(abs(dz_opt) <= tol)
if verbose > 0:
print("\r[LGCD:INFO] converged after {} iterations".format(ii +
1))
break
# Check is we reach the timeout
if deadline is not None and time.time() >= deadline:
if verbose > 0:
print("\r[LGCD:INFO] Reached timeout. Done {} coordinate "
"updates. Max of |dz|={}.".format(
n_coordinate_updates,
abs(dz_opt).max()))
break
else:
if verbose > 0:
print("\r[LGCD:INFO] Reached max_iter. Done {} coordinate "
"updates. Max of |dz|={}.".format(n_coordinate_updates,
abs(dz_opt).max()))
runtime = time.time() - t_start
if verbose > 0:
print("\r[LGCD:INFO] done in {:.3}s".format(runtime))
ztz, ztX = None, None
if return_ztz:
ztz = compute_ztz(z_hat, atom_shape)
ztX = compute_ztX(z_hat, X_i)
p_obj.append([n_coordinate_updates, t_update, None])
return z_hat, ztz, ztX, p_obj, None
