def test_log():
# This is required for this test to pass!
Log.override_test_exclusion = True
lprint('Test')
with lsection('a section'):
lprint('a line')
lprint('another line')
lprint('we are done')
with lsection('a subsection'):
lprint('another line')
lprint('we are done')
with lsection('a subsection'):
lprint('another line')
lprint('we are done')
assert Log.depth == 3
with lsection('a subsection'):
lprint('another line')
lprint('we are done')
with lsection('a subsection'):
lprint('another line')
lprint('we are done')
assert Log.depth == 5
with lsection('a subsection'):
lprint('another line')
lprint('we are done')
with lsection('a subsection'):
lprint('another line')
lprint('we are done')
assert Log.depth == 7
with lsection('a subsection'):
lprint('another line')
lprint('we are done')
with lsection('a subsection'):
lprint('another line')
lprint('we are done')
with lsection('a subsection'):
lprint('another line')
lprint('we are done')
lprint('test is finished...')
assert Log.depth == 0
def test_log():
# This is required for this test to pass!
Log.override_test_exclusion = True
lprint("Test")
with lsection("a section"):
lprint("a line")
lprint("another line")
lprint("we are done")
with lsection("a subsection"):
lprint("another line")
lprint("we are done")
with lsection("a subsection"):
lprint("another line")
lprint("we are done")
assert Log.depth == 3
with lsection("a subsection"):
lprint("another line")
lprint("we are done")
with lsection("a subsection"):
lprint("another line")
lprint("we are done")
assert Log.depth == 5
with lsection("a subsection"):
lprint("another line")
lprint("we are done")
with lsection("a subsection"):
lprint("another line")
lprint("we are done")
assert Log.depth == 7
with lsection("a subsection"):
lprint("another line")
lprint("we are done")
with lsection("a subsection"):
lprint("another line")
lprint("we are done")
with lsection("a subsection"):
lprint("another line")
lprint("we are done")
lprint("test is finished...")
assert Log.depth == 0
def _train_loop(self, data_loader, optimizer, loss_function):
# Scheduler:
scheduler = ReduceLROnPlateau(
optimizer,
'min',
factor=self.reduce_lr_factor,
verbose=True,
patience=self.reduce_lr_patience,
)
best_val_loss_value = math.inf
best_model_state_dict = None
patience_counter = 0
with lsection(f"Training loop:"):
lprint(f"Maximum number of epochs: {self.max_epochs}")
lprint(
f"Training type: {'self-supervised' if self.self_supervised else 'supervised'}"
)
for epoch in range(self.max_epochs):
with lsection(f"Epoch {epoch}:"):
if hasattr(self, 'masked_model'):
self.masked_model.density = 0.005 * self.masking_density + 0.995 * self.masked_model.density
lprint(f"masking density: {self.masked_model.density}")
train_loss_value = 0
val_loss_value = 0
iteration = 0
for i, (input_images, target_images,
val_mask_images) in enumerate(data_loader):
lprint(f"index: {i}, shape:{input_images.shape}")
input_images_gpu = input_images.to(self.device,
non_blocking=True)
target_images_gpu = target_images.to(self.device,
non_blocking=True)
validation_mask_images_gpu = val_mask_images.to(
self.device, non_blocking=True)
# Adding training noise to input:
if self.training_noise > 0:
with torch.no_grad():
alpha = self.training_noise / (
1 + (10000 * epoch / self.max_epochs))
lprint(f"Training noise level: {alpha}")
training_noise = alpha * torch.randn_like(
input_images)
input_images_gpu += training_noise.to(
input_images_gpu.device)
# Clear gradients w.r.t. parameters
optimizer.zero_grad()
# Forward pass:
self.model.train()
if self.masking:
translated_images_gpu = self.masked_model(
input_images_gpu)
else:
translated_images_gpu = self.model(
input_images_gpu)
# apply forward model:
forward_model_images_gpu = self._forward_model(
translated_images_gpu)
# validation masking:
u = forward_model_images_gpu * (
1 - validation_mask_images_gpu)
v = target_images_gpu * (1 -
validation_mask_images_gpu)
# with napari.gui_qt():
# viewer = napari.Viewer()
# viewer.add_image(to_numpy(validation_mask_images_gpu), name='validation_mask_images_gpu')
# viewer.add_image(to_numpy(forward_model_images_gpu), name='forward_model_images_gpu')
# viewer.add_image(to_numpy(target_images_gpu), name='target_images_gpu')
# translation loss (per voxel):
if self.masking:
mask = self.masked_model.get_mask()
translation_loss = loss_function(u, v, mask)
else:
translation_loss = loss_function(u, v)
# loss value (for all voxels):
translation_loss_value = translation_loss.mean()
# Additional losses:
additional_loss_value = self._additional_losses(
translated_images_gpu, forward_model_images_gpu)
if additional_loss_value is not None:
translation_loss_value += additional_loss_value
# backpropagation:
translation_loss_value.backward()
# Updating parameters
optimizer.step()
# post optimisation -- if needed:
self.model.post_optimisation()
# update training loss_deconvolution for whole image:
train_loss_value += translation_loss_value.item()
iteration += 1
# Validation:
with torch.no_grad():
# Forward pass:
self.model.eval()
if self.masking:
translated_images_gpu = self.masked_model(
input_images_gpu)
else:
translated_images_gpu = self.model(
input_images_gpu)
# apply forward model:
forward_model_images_gpu = self._forward_model(
translated_images_gpu)
# validation masking:
u = forward_model_images_gpu * validation_mask_images_gpu
v = target_images_gpu * validation_mask_images_gpu
# translation loss (per voxel):
if self.masking:
translation_loss = loss_function(u, v, None)
else:
translation_loss = loss_function(u, v)
# loss values:
translation_loss_value = (
translation_loss.mean().cpu().item())
# update validation loss_deconvolution for whole image:
val_loss_value += translation_loss_value
iteration += 1
train_loss_value /= iteration
lprint(f"Training loss value: {train_loss_value}")
val_loss_value /= iteration
lprint(f"Validation loss value: {val_loss_value}")
# Learning rate schedule:
scheduler.step(val_loss_value)
if val_loss_value < best_val_loss_value:
lprint(f"## New best val loss!")
if val_loss_value < best_val_loss_value - self.patience_epsilon:
lprint(f"## Good enough to reset patience!")
patience_counter = 0
# Update best val loss value:
best_val_loss_value = val_loss_value
# Save model:
best_model_state_dict = OrderedDict({
k: v.to('cpu')
for k, v in self.model.state_dict().items()
})
else:
if (epoch % max(1, self.reload_best_model_period) == 0
and best_model_state_dict):
lprint(f"Reloading best models to date!")
self.model.load_state_dict(best_model_state_dict)
if patience_counter > self.patience:
lprint(f"Early stopping!")
break
# No improvement:
lprint(
f"No improvement of validation losses, patience = {patience_counter}/{self.patience} "
)
patience_counter += 1
lprint(f"## Best val loss: {best_val_loss_value}")
if self._stop_training_flag:
lprint(f"Training interupted!")
break
lprint(f"Reloading best models to date!")
self.model.load_state_dict(best_model_state_dict)
def train(
self,
input_image,
target_image=None,
batch_dims=None,
channel_dims=None,
tile_size=None,
train_valid_ratio=0.1,
callback_period=3,
jinv=None,
):
"""Train to translate a given input image to a given output image.
This has a lot of the machinery for batching and more...
"""
if target_image is None:
target_image = input_image
with lsection(
f"Learning to translate from image of dimensions {str(input_image.shape)} to {str(target_image.shape)} ."
):
lprint("Running garbage collector...")
gc.collect()
# If we use the same image for input and output then we are in a self-supervised setting:
self.self_supervised = input_image is target_image
if self.self_supervised:
lprint("Training is self-supervised.")
else:
lprint("Training is supervised.")
if batch_dims is None: # set default batch_dim value:
batch_dims = (False,) * len(input_image.shape)
self.input_normaliser = self.normalizer_class(
transform=self.normaliser_transform, clip=self.normaliser_clip
)
self.target_normaliser = (
self.input_normaliser
if self.self_supervised
else self.normalizer_class(
transform=self.normaliser_transform, clip=self.normaliser_clip
)
)
# Calibrates normaliser(s):
self.input_normaliser.calibrate(input_image)
if not self.self_supervised:
self.target_normaliser.calibrate(target_image)
# Intensity values normalisation:
normalised_input_image = self.input_normaliser.normalise(
input_image, batch_dims=batch_dims, channel_dims=channel_dims
)
normalised_target_image = (
normalised_input_image
if self.self_supervised
else self.target_normaliser.normalise(
target_image, batch_dims=batch_dims, channel_dims=channel_dims
)
)
# Let's pad the images to avoid border effects:
# If we do it for translation we also have to do it for training because of
# location-aware features such as large-scale features or spatial-features.
normalised_input_image = self._pad_norm_image(normalised_input_image)
normalised_target_image = self._pad_norm_image(normalised_target_image)
self._train(
normalised_input_image,
normalised_target_image,
tile_size=tile_size,
train_valid_ratio=train_valid_ratio,
callback_period=callback_period,
jinv=jinv,
)
def _get_tilling_strategy_and_margins(
self,
image,
max_voxels_per_tile,
min_margin,
max_margin,
suggested_tile_size=None,
):
# We will store the batch strategy as a list of integers representing the number of chunks per dimension:
with lsection(f"Determine tilling strategy:"):
suggested_tile_size = (
math.inf if suggested_tile_size is None else suggested_tile_size
)
# image shape:
shape = image.shape
num_spatio_temp_dim = num_spatiotemp_dim = len(shape) - 2
lprint(f"image shape = {shape}")
lprint(f"max_voxels_per_tile = {max_voxels_per_tile}")
# Estimated amount of memory needed for storing all features:
(
estimated_memory_needed,
total_memory_available,
) = self._estimate_memory_needed_and_available(image)
lprint(f"Estimated amount of memory needed: {estimated_memory_needed}")
# Available physical memory :
total_memory_available *= self.max_memory_usage_ratio
lprint(
f"Available memory (we reserve 10% for 'comfort'): {total_memory_available}"
)
# How much do we need to tile because of memory, if at all?
split_factor_mem = estimated_memory_needed / total_memory_available
lprint(
f"How much do we need to tile because of memory? : {split_factor_mem} times."
)
# how much do we have to tile because of the limit on the number of voxels per tile?
split_factor_max_voxels = image.size / max_voxels_per_tile
lprint(
f"How much do we need to tile because of the limit on the number of voxels per tile? : {split_factor_max_voxels} times."
)
# how much do we have to tile because of the suggested tile size?
split_factor_suggested_tile_size = image.size / (
suggested_tile_size ** num_spatio_temp_dim
)
lprint(
f"How much do we need to tile because of the suggested tile size? : {split_factor_suggested_tile_size} times."
)
# we keep the max:
desired_split_factor = max(
split_factor_mem,
split_factor_max_voxels,
split_factor_suggested_tile_size,
)
# We cannot split less than 1 time:
desired_split_factor = max(1, int(math.ceil(desired_split_factor)))
lprint(f"Desired split factor: {desired_split_factor}")
# Number of batches:
num_batches = shape[0]
# Does the number of batches split the data enough?
if num_batches < desired_split_factor:
# Not enough splitting happening along the batch dimension, we need to split further:
# how much?
rest_split_factor = desired_split_factor / num_batches
lprint(
f"Not enough splitting happening along the batch dimension, we need to split spatio-temp dims by: {rest_split_factor}"
)
# let's split the dimensions in a way proportional to their lengths:
split_per_dim = (rest_split_factor / numpy.prod(shape[2:])) ** (
1 / num_spatio_temp_dim
)
spatiotemp_tilling_strategy = tuple(
max(1, int(math.ceil(split_per_dim * s))) for s in shape[2:]
)
# correction_factor = numpy.prod(tuple(s for s in spatiotemp_tilling_strategy if s<1))
tilling_strategy = (num_batches, 1) + spatiotemp_tilling_strategy
lprint(f"Preliminary tilling strategy is: {tilling_strategy}")
# We correct for eventual oversplitting by favouring splitting over the front dimensions:
current_splitting_factor = 1
corrected_tilling_strategy = []
split_factor_reached = False
for i, s in enumerate(tilling_strategy):
if split_factor_reached:
corrected_tilling_strategy.append(1)
else:
corrected_tilling_strategy.append(s)
current_splitting_factor *= s
if current_splitting_factor >= desired_split_factor:
split_factor_reached = True
tilling_strategy = tuple(corrected_tilling_strategy)
else:
tilling_strategy = (desired_split_factor, 1) + tuple(
1 for s in shape[2:]
)
lprint(f"Tilling strategy is: {tilling_strategy}")
# Handles defaults:
if max_margin is None:
max_margin = math.inf
if min_margin is None:
min_margin = 0
# First we estimate the shape of a tile:
estimated_tile_shape = tuple(
int(round(s / ts)) for s, ts in zip(shape[2:], tilling_strategy[2:])
)
lprint(f"The estimated tile shape is: {estimated_tile_shape}")
# Limit margins:
# We automatically set the margin of the tile size:
# the max-margin factor guarantees that tilling will incur no more than a given max tiling overhead:
margin_factor = 0.5 * (
((1 + self.max_tilling_overhead) ** (1 / num_spatiotemp_dim)) - 1
)
margins = tuple(int(s * margin_factor) for s in estimated_tile_shape)
# Limit the margin to something reasonable (provided or automatically computed):
margins = tuple(min(max_margin, m) for m in margins)
margins = tuple(max(min_margin, m) for m in margins)
# We add the batch and channel dimensions:
margins = (0, 0) + margins
# We only need margins if we split a dimension:
margins = tuple(
(0 if split == 1 else margin)
for margin, split in zip(margins, tilling_strategy)
)
return tilling_strategy, margins
def translate(
self,
input_image,
translated_image=None,
batch_dims=None,
channel_dims=None,
tile_size=None,
denormalise_values=True,
leave_as_float=False,
clip=True,
):
"""
Translates an input image into an output image according to the learned function.
:param input_image:
:type input_image:
:param clip:
:type clip:
:return:
:rtype:
"""
with lsection(
f"Predicting output image from input image of dimension {input_image.shape}"
):
# set default batch_dim and channel_dim values:
if batch_dims is None:
batch_dims = (False,) * len(input_image.shape)
if channel_dims is None:
channel_dims = (False,) * len(input_image.shape)
# Number of spatio-temporal dimensions:
num_spatiotemp_dim = sum(
0 if b or c else 1 for b, c in zip(batch_dims, channel_dims)
)
# First we normalise the input values:
normalised_input_image = self.input_normaliser.normalise(
input_image, batch_dims=batch_dims, channel_dims=channel_dims
)
# When we trained supervised we need to update permutated image shape of target_normaliser
# This way we can accommodate different sizes of batch dimensions than batch dimensions used for training
if not self.self_supervised:
(
_,
_,
self.target_normaliser.permutated_image_shape,
) = self.target_normaliser.shape_normalize(
input_image, batch_dims=batch_dims, channel_dims=channel_dims
)
# Let's pad the input array so we avoid annoying border-effects:
normalised_input_image = self._pad_norm_image(normalised_input_image)
# Spatio-temporal shape:
spatiotemp_shape = normalised_input_image.shape[-num_spatiotemp_dim:]
normalised_translated_image = None
if tile_size == 0:
# we _force_ no tilling, this is _not_ the default.
# We translate:
normalised_translated_image = self._translate(
normalised_input_image,
whole_image_shape=normalised_input_image.shape,
)
else:
# We do need to do tiled inference because of a lack of memory
# or because a small batch size was requested:
normalised_input_shape = normalised_input_image.shape
# We get the tilling strategy:
# tile_size, shape, min_margin, max_margin
tilling_strategy, margins = self._get_tilling_strategy_and_margins(
normalised_input_image,
self.max_voxels_per_tile,
self.tile_min_margin,
self.tile_max_margin,
suggested_tile_size=tile_size,
)
lprint(f"Tilling strategy: {tilling_strategy}")
lprint(f"Margins for tiles: {margins} .")
# tile slice objects (with and without margins):
tile_slices_margins = list(
nd_split_slices(
normalised_input_shape, tilling_strategy, margins=margins
)
)
tile_slices = list(
nd_split_slices(normalised_input_shape, tilling_strategy)
)
# Number of tiles:
number_of_tiles = len(tile_slices)
lprint(f"Number of tiles (slices): {number_of_tiles}")
# We create slice list:
slicezip = zip(tile_slices_margins, tile_slices)
counter = 1
for slice_margin_tuple, slice_tuple in slicezip:
with lsection(
f"Current tile: {counter}/{number_of_tiles}, slice: {slice_tuple} "
):
# We first extract the tile image:
input_image_tile = normalised_input_image[
slice_margin_tuple
].copy()
# We do the actual translation:
lprint(f"Translating...")
translated_image_tile = self._translate(
input_image_tile,
image_slice=slice_margin_tuple,
whole_image_shape=normalised_input_image.shape,
)
# We compute the slice needed to cut out the margins:
lprint(f"Removing margins...")
remove_margin_slice_tuple = remove_margin_slice(
normalised_input_shape, slice_margin_tuple, slice_tuple
)
# We allocate -just in time- the translated array if needed:
# if the array is already provided, it must of course have the right dimensions...
if normalised_translated_image is None:
translated_image_shape = (
normalised_input_image.shape[:2] + spatiotemp_shape
)
normalised_translated_image = offcore_array(
shape=translated_image_shape,
dtype=translated_image_tile.dtype,
max_memory_usage_ratio=self.max_memory_usage_ratio,
)
# We plug in the batch without margins into the destination image:
lprint(f"Inserting translated batch into result image...")
normalised_translated_image[
slice_tuple
] = translated_image_tile[remove_margin_slice_tuple]
counter += 1
# Let's crop the padding:
normalised_translated_image = self._crop_norm_image(
normalised_translated_image
)
# Then we denormalise:
denormalised_translated_image = self.target_normaliser.denormalise(
normalised_translated_image,
# denormalise_values=denormalise_values,
leave_as_float=leave_as_float,
clip=clip,
)
if translated_image is None:
translated_image = denormalised_translated_image
else:
translated_image[...] = denormalised_translated_image
return translated_image
def offcore_array(
shape: Union[Tuple[int, ...], Generator[int, None, None]],
dtype: numpy.dtype,
force_memmap: bool = False,
zarr_allowed: bool = False,
no_memmap_limit: bool = True,
max_memory_usage_ratio: float = 0.9,
):
"""
Instanciates an array of given shape and dtype in 'off-core' fashion i.e. not in main memory.
Right now it simply uses memory mapping on temp file that is deleted after the file is closed
Parameters
----------
shape
dtype
force_memmap
zarr_allowed
no_memmap_limit
max_memory_usage_ratio
"""
with lsection(f"Array of shape: {shape} and dtype: {dtype} requested"):
size_in_bytes = numpy.prod(shape) * numpy.dtype(dtype).itemsize
lprint(f'Array requested will be {(size_in_bytes / 1E6)} MB.')
total_physical_memory_in_bytes = psutil.virtual_memory().total
total_swap_memory_in_bytes = psutil.swap_memory().total
total_mem_in_bytes = total_physical_memory_in_bytes + total_swap_memory_in_bytes
lprint(
f'There is {int(psutil.virtual_memory().total / 1E6)} MB of physical memory'
)
lprint(
f'There is {int(psutil.swap_memory().total / 1E6)} MB of swap memory'
)
lprint(f'There is {int(total_mem_in_bytes / 1E6)} MB of total memory')
is_enough_physical_memory = (size_in_bytes < max_memory_usage_ratio *
total_physical_memory_in_bytes)
is_enough_total_memory = (size_in_bytes <
max_memory_usage_ratio * total_mem_in_bytes)
if not force_memmap and is_enough_total_memory:
lprint(
f'There is enough physical+swap memory -- we do not need to use a mem mapped array or zarr-backed array.'
)
array = numpy.zeros(shape, dtype=dtype)
elif no_memmap_limit:
lprint(
f'There is not enough physical+swap memory -- we will use a mem mapped array.'
)
temp_file = tempfile.NamedTemporaryFile(
dir=OffCore.memmap_directory)
lprint(
f'The temporary memory mapped file is at: {temp_file.name} (but you might not be able to see it!)'
)
array = numpy.memmap(temp_file,
dtype=dtype,
mode='w+',
shape=shape)
elif zarr_allowed:
lprint(
f'There is not enough physical+swap memory -- we will use a zarr-backed array.'
)
import zarr
array = zarr.create(shape=shape,
dtype=dtype,
store=zarr.TempStore("output.zarr"))
# from numcodecs import Blosc
# compressor = Blosc(cname = 'zstd', clevel = 3, shuffle = Blosc.BITSHUFFLE)
# array = zarr.zeros((102_0, 200, 210), chunks = (100, 200, 210), compressor = compressor
return array
def _train_loop(self, data_loader, optimizer):
# Scheduler:
if self.scheduler == "plateau":
scheduler = ReduceLROnPlateau(
optimizer,
"min",
factor=self.reduce_lr_factor,
verbose=True,
patience=self.reduce_lr_patience,
)
elif self.scheduler == "cosine":
scheduler = CosineAnnealingLR(
optimizer, T_max=self.max_epochs, eta_min=1e-6
)
else:
raise ValueError(
f"Unknown scheduler: {self.scheduler}, supported: plateau, cosine"
)
self.best_val_loss_value = math.inf
self.best_model_state_dict = None
self.patience_counter = 0
with lsection(f"Training loop:"):
lprint(f"Maximum number of epochs: {self.max_epochs}")
lprint(
f"Training type: {'self-supervised' if self.self_supervised else 'supervised'}"
)
for epoch in range(self.max_epochs):
with lsection(f"Epoch {epoch}:"):
# One epoch of training
train_loss_value, val_loss_value, loss_log_epoch = self._epoch(
optimizer, data_loader, epoch
)
# Learning rate schedule:
if self.scheduler == "plateau":
scheduler.step(val_loss_value)
else:
scheduler.step()
# Logging:
loss_log_epoch["masking_density"] = self.masked_model.density
loss_log_epoch["lr"] = scheduler._last_lr[0]
if not self.check:
wandb.log(loss_log_epoch)
# Monitoring and saving:
if val_loss_value < self.best_val_loss_value:
lprint(f"## New best val loss!")
if (
val_loss_value
< self.best_val_loss_value - self.patience_epsilon
):
lprint(f"## Good enough to reset patience!")
self.patience_counter = 0
# Update best val loss value:
self.best_val_loss_value = val_loss_value
# Save model:
self.best_model_state_dict = OrderedDict(
{k: v.to("cpu") for k, v in self.model.state_dict().items()}
)
else:
if (
epoch % max(1, self.reload_best_model_period) == 0
and self.best_model_state_dict
):
lprint(f"Reloading best models to date!")
self.model.load_state_dict(self.best_model_state_dict)
if self.patience_counter > self.patience:
lprint(f"Early stopping!")
break
# No improvement:
lprint(
f"No improvement of validation losses, patience = {self.patience_counter}/{self.patience} "
)
self.patience_counter += 1
lprint(f"## Best val loss: {self.best_val_loss_value}")
if self._stop_training_flag:
lprint(f"Training interupted!")
break
lprint(f"Reloading best models to date!")
self.model.load_state_dict(self.best_model_state_dict)
