def __init__(self,
label: str,
metric: str,
label_mapping: Optional[Dict[str, Any]] = None,
bounds: Union[None, str, Iterable[Union[str, None]]] = "std",
mode: Union[None, str, Iterable[str]] = "eval",
ds_id: Union[None, str, Iterable[str]] = None,
outputs: Optional[str] = None):
super().__init__(inputs=[label, metric],
outputs=outputs or f"{metric}_by_{label}",
mode=mode,
ds_id=ds_id)
self.points = []
self.label_summaries = DefaultKeyDict(
default=lambda x: Summary(name=x))
self.label_mapping = {val: key
for key, val in label_mapping.items()
} if label_mapping else None
bounds = to_set(bounds)
if not bounds:
bounds.add(None)
for option in bounds:
if option not in (None, "std", "range"):
raise ValueError(
f"'interval' must be either None, 'std', or 'range', but got '{bounds}'."
)
self.bounds = bounds
def __init__(self, root_log_dir: str, time_stamp: str,
network: TFNetwork) -> None:
super().__init__(root_log_dir=root_log_dir,
time_stamp=time_stamp,
network=network)
self.tf_summary_writers = DefaultKeyDict(
lambda key: (tf.summary.create_file_writer(
os.path.join(root_log_dir, time_stamp, key))))
def __setstate__(self, state: Dict[str, Any]) -> None:
"""Set this objects internal state from a dictionary of variables.
This method is invoked by pickle.
Args:
state: The saved state to be used by this object.
"""
label_summaries = DefaultKeyDict(default=lambda x: Summary(name=x))
label_summaries.update(state.get('label_summaries', {}))
state['label_summaries'] = label_summaries
self.__dict__.update(state)
def on_end(self, data: Data) -> None:
index_summaries = DefaultKeyDict(default=lambda x: Summary(name=x))
for mode in self.mode:
final_scores = sorted([(idx, elem[-1][1]) for idx, elem in self.index_history[mode].items()],
key=lambda x: x[1])
max_idx_list = {elem[0] for elem in final_scores[-1:-self.n_max_to_keep - 1:-1]}
min_idx_list = {elem[0] for elem in final_scores[:self.n_min_to_keep]}
target_idx_list = Set.union(min_idx_list, max_idx_list, self.idx_to_keep)
for idx in target_idx_list:
for step, score in self.index_history[mode][idx]:
index_summaries[idx].history[mode][self.metric_key][step] = score
self.system.add_graph(self.outputs[0], list(index_summaries.values())) # So traceability can draw it
data.write_without_log(self.outputs[0], list(index_summaries.values()))
class _TfWriter(_BaseWriter):
"""A class to write various TensorFlow data into TensorBoard summary files.
This class is intentionally not @traceable.
Args:
root_log_dir: The directory into which to store a new directory corresponding to this experiment's summary data
time_stamp: The timestamp of this experiment (used as a folder name within `root_log_dir`).
network: The network associated with the current experiment.
"""
tf_summary_writers: Dict[str, tf.summary.SummaryWriter]
def __init__(self, root_log_dir: str, time_stamp: str, network: TFNetwork) -> None:
super().__init__(root_log_dir=root_log_dir, time_stamp=time_stamp, network=network)
self.tf_summary_writers = DefaultKeyDict(
lambda key: (tf.summary.create_file_writer(os.path.join(root_log_dir, time_stamp, key))))
def write_epoch_models(self, mode: str) -> None:
with self.tf_summary_writers[mode].as_default(), summary_ops_v2.always_record_summaries():
summary_ops_v2.graph(backend.get_graph(), step=0)
for model in self.network.epoch_models:
summary_writable = (model.__class__.__name__ == 'Sequential'
or (hasattr(model, '_is_graph_network') and model._is_graph_network))
if summary_writable:
summary_ops_v2.keras_model(model.model_name, model, step=0)
def write_weights(self, mode: str, models: Iterable[Model], step: int, visualize: bool) -> None:
# Similar to TF implementation, but multiple models
with self.tf_summary_writers[mode].as_default(), summary_ops_v2.always_record_summaries():
for model in models:
for layer in model.layers:
for weight in layer.weights:
weight_name = weight.name.replace(':', '_')
weight_name = "{}_{}".format(model.model_name, weight_name)
with tfops.init_scope():
weight = backend.get_value(weight)
summary_ops_v2.histogram(weight_name, weight, step=step)
if visualize:
weight = self._weight_to_image(weight=weight, kernel_channels_last=True)
if weight is not None:
summary_ops_v2.image(weight_name, weight, step=step, max_images=weight.shape[0])
def close(self) -> None:
super().close()
modes = list(self.tf_summary_writers.keys()) # break connection with dictionary so can delete in iteration
for mode in modes:
self.tf_summary_writers[mode].close()
del self.tf_summary_writers[mode]
def __init__(self, root_log_dir: str, time_stamp: str,
network: BaseNetwork) -> None:
self.summary_writers = DefaultKeyDict(lambda key: (SummaryWriter(
log_dir=os.path.join(root_log_dir, time_stamp, key))))
self.network = network
class _BaseWriter:
"""A class to write various types of data into TensorBoard summary files.
This class is intentionally not @traceable.
Args:
root_log_dir: The directory into which to store a new directory corresponding to this experiment's summary data
time_stamp: The timestamp of this experiment (used as a folder name within `root_log_dir`).
network: The network associated with the current experiment.
"""
summary_writers: Dict[str, SummaryWriter]
network: BaseNetwork
def __init__(self, root_log_dir: str, time_stamp: str,
network: BaseNetwork) -> None:
self.summary_writers = DefaultKeyDict(lambda key: (SummaryWriter(
log_dir=os.path.join(root_log_dir, time_stamp, key))))
self.network = network
def write_epoch_models(self, mode: str) -> None:
"""Write summary graphs for all of the models in the current epoch.
Args:
mode: The current mode of execution ('train', 'eval', 'test', 'infer').
"""
raise NotImplementedError
def write_weights(self, mode: str, models: Iterable[Model], step: int,
visualize: bool) -> None:
"""Write summaries of all of the weights of a given collection of `models`.
Args:
mode: The current mode of execution ('train', 'eval', 'test', 'infer').
models: A list of models compiled with fe.build whose weights should be recorded.
step: The current training step.
visualize: Whether to attempt to paint graphical representations of the weights in addition to the default
histogram summaries.
"""
raise NotImplementedError
def write_scalars(self, mode: str, scalars: Iterable[Tuple[str, Any]],
step: int) -> None:
"""Write summaries of scalars to TensorBoard.
Args:
mode: The current mode of execution ('train', 'eval', 'test', 'infer').
scalars: A collection of pairs like [("key", val), ("key2", val2), ...].
step: The current training step.
"""
for key, val in scalars:
self.summary_writers[mode].add_scalar(tag=key,
scalar_value=to_number(val),
global_step=step)
def write_images(self, mode: str, images: Iterable[Tuple[str, Any]],
step: int) -> None:
"""Write images to TensorBoard.
Args:
mode: The current mode of execution ('train', 'eval', 'test', 'infer').
images: A collection of pairs like [("key", image1), ("key2", image2), ...].
step: The current training step.
"""
for key, img in images:
if isinstance(img, ImgData):
img = img.paint_figure()
if isinstance(img, plt.Figure):
self.summary_writers[mode].add_figure(tag=key,
figure=img,
global_step=step)
else:
self.summary_writers[mode].add_images(
tag=key,
img_tensor=to_number(img),
global_step=step,
dataformats='NCHW'
if isinstance(img, torch.Tensor) else 'NHWC')
def write_embeddings(
self,
mode: str,
embeddings: Iterable[Tuple[str, Tensor, Optional[List[Any]],
Optional[Tensor]]],
step: int,
):
"""Write embeddings (like UMAP) to TensorBoard.
Args:
mode: The current mode of execution ('train', 'eval', 'test', 'infer').
embeddings: A collection of quadruplets like [("key", <features>, [<label1>, ...], <label_images>)].
Features are expected to be batched, and if labels and/or label images are provided they should have the
same batch dimension as the features.
step: The current training step.
"""
for key, features, labels, label_imgs in embeddings:
flat = to_number(reshape(features, [features.shape[0], -1]))
if not isinstance(label_imgs, (torch.Tensor, type(None))):
label_imgs = to_tensor(label_imgs, 'torch')
if len(label_imgs.shape) == 4:
label_imgs = permute(label_imgs, [0, 3, 1, 2])
self.summary_writers[mode].add_embedding(mat=flat,
metadata=labels,
label_img=label_imgs,
tag=key,
global_step=step)
def close(self) -> None:
"""A method to flush and close all connections to the files on disk.
"""
modes = list(self.summary_writers.keys(
)) # break connection with dictionary so can delete in iteration
for mode in modes:
self.summary_writers[mode].close()
del self.summary_writers[mode]
@staticmethod
def _weight_to_image(
weight: Tensor,
kernel_channels_last: bool = False) -> Optional[Tensor]:
"""Logs a weight as a TensorBoard image.
Implementation from TensorFlow codebase, would have invoked theirs directly but they didn't make it a static
method.
"""
w_img = squeeze(weight)
shape = backend.int_shape(w_img)
if len(shape) == 1: # Bias case
w_img = reshape(w_img, [1, shape[0], 1, 1])
elif len(shape) == 2: # Dense layer kernel case
if shape[0] > shape[1]:
w_img = permute(w_img, [0, 1])
shape = backend.int_shape(w_img)
w_img = reshape(w_img, [1, shape[0], shape[1], 1])
elif len(shape) == 3: # ConvNet case
if kernel_channels_last:
# Switch to channels_first to display every kernel as a separate images
w_img = permute(w_img, [2, 0, 1])
w_img = expand_dims(w_img, axis=-1)
elif len(shape) == 4: # Conv filter with multiple input channels
if kernel_channels_last:
# Switch to channels first to display kernels as separate images
w_img = permute(w_img, [3, 2, 0, 1])
w_img = reduce_sum(
abs(w_img),
axis=1) # Sum over the each channel within the kernel
w_img = expand_dims(w_img, axis=-1)
shape = backend.int_shape(w_img)
# Not possible to handle 3D convnets etc.
if len(shape) == 4 and shape[-1] in [1, 3, 4]:
return w_img
class LabelTracker(Trace):
"""A Trace to track metrics grouped by labels, for example per-class loss over time during training.
Use this in conjunction with ImageViewer or ImageSaver to see the graph at training end. This also automatically
integrates with Traceability reports.
Args:
label: The key of the labels by which to group data.
metric: The key of the metric by which to score data.
label_mapping: A mapping of {DisplayName: LabelValue} to use when generating the graph. This can also be used to
limit which label values are graphed, since any label values not included here will not be graphed. A None
value will monitor all label values.
bounds: What error bounds should be graphed around the mean value. Options include None, 'std' for standard
deviation, and 'range' to plot (min_value, mean, max_value). Multiple values can be specified, ex.
['std', 'range'] to generate multiple graphs.
mode: What mode(s) to execute this Trace in. For example, "train", "eval", "test", or "infer". To execute
regardless of mode, pass None. To execute in all modes except for a particular one, you can pass an argument
like "!infer" or "!train".
ds_id: What dataset id(s) to execute this Trace in. To execute regardless of ds_id, pass None. To execute in all
ds_ids except for a particular one, you can pass an argument like "!ds1".
outputs: The name of the output which will be generated by this trace at the end of training. If None then it
will default to "<metric>_by_<label>".
Raises:
ValueError: If `bounds` is not one of the allowed options.
"""
def __init__(self,
label: str,
metric: str,
label_mapping: Optional[Dict[str, Any]] = None,
bounds: Union[None, str, Iterable[Union[str, None]]] = "std",
mode: Union[None, str, Iterable[str]] = "eval",
ds_id: Union[None, str, Iterable[str]] = None,
outputs: Optional[str] = None):
super().__init__(inputs=[label, metric],
outputs=outputs or f"{metric}_by_{label}",
mode=mode,
ds_id=ds_id)
self.points = []
self.label_summaries = DefaultKeyDict(
default=lambda x: Summary(name=x))
self.label_mapping = {val: key
for key, val in label_mapping.items()
} if label_mapping else None
bounds = to_set(bounds)
if not bounds:
bounds.add(None)
for option in bounds:
if option not in (None, "std", "range"):
raise ValueError(
f"'interval' must be either None, 'std', or 'range', but got '{bounds}'."
)
self.bounds = bounds
@property
def label_key(self) -> str:
return self.inputs[0]
@property
def metric_key(self) -> str:
return self.inputs[1]
def on_batch_end(self, data: Data) -> None:
self.points.append((to_number(data[self.label_key]),
to_number(data[self.metric_key])))
def on_epoch_end(self, data: Data) -> None:
label_scores = defaultdict(list)
for batch in self.points:
for label, metric in ((batch[0][i], batch[1][i])
for i in range(len(batch[0]))):
label_scores[label.item()].append(metric.item())
for label, metric in label_scores.items():
if self.label_mapping:
if label in self.label_mapping:
label = self.label_mapping[label]
else:
# Skip labels which the user does not want to inspect
continue
if 'std' in self.bounds:
mean, std = stats.mean(metric), stats.stdev(
metric) if len(metric) > 1 else 0.0
val = ValWithError(mean - std, mean, mean + std)
key = f"{self.metric_key} ($\\mu \\pm \\sigma$)"
# {label: {mode: {key: {step: value}}}}
self.label_summaries[label].history[self.system.mode][key][
self.system.global_step] = val
if 'range' in self.bounds:
val = ValWithError(min(metric), stats.mean(metric),
max(metric))
key = f"{self.metric_key} ($min, \\mu, max$)"
self.label_summaries[label].history[self.system.mode][key][
self.system.global_step] = val
if None in self.bounds:
val = stats.mean(metric)
key = self.metric_key
self.label_summaries[label].history[self.system.mode][key][
self.system.global_step] = val
self.points = []
def on_end(self, data: Data) -> None:
self.system.add_graph(
self.outputs[0],
list(self.label_summaries.values())) # So traceability can draw it
data.write_without_log(self.outputs[0],
list(self.label_summaries.values()))
def __getstate__(self) -> Dict[str, Any]:
"""Get a representation of the state of this object.
This method is invoked by pickle.
Returns:
The information to be recorded by a pickle summary of this object.
"""
state = self.__dict__.copy()
state['label_summaries'] = dict(state['label_summaries'])
return state
def __setstate__(self, state: Dict[str, Any]) -> None:
"""Set this objects internal state from a dictionary of variables.
This method is invoked by pickle.
Args:
state: The saved state to be used by this object.
"""
label_summaries = DefaultKeyDict(default=lambda x: Summary(name=x))
label_summaries.update(state.get('label_summaries', {}))
state['label_summaries'] = label_summaries
self.__dict__.update(state)
def _draw_diagram(self, mode: str, epoch: int, ds_id: str) -> pydot.Dot:
"""Draw a summary diagram of the FastEstimator Ops / Traces.
Args:
mode: The execution mode to summarize ('train', 'eval', 'test', or 'infer').
epoch: The epoch to summarize.
ds_id: The ds_id to summarize.
Returns:
A pydot digraph representing the execution flow.
"""
ds = self.system.pipeline.data[mode][ds_id]
if isinstance(ds, Scheduler):
ds = ds.get_current_value(epoch)
pipe_ops = get_current_items(
self.system.pipeline.ops, run_modes=mode, epoch=epoch,
ds_id=ds_id) if isinstance(ds, Dataset) else []
net_ops = get_current_items(self.system.network.ops,
run_modes=mode,
epoch=epoch,
ds_id=ds_id)
net_post = get_current_items(self.system.network.postprocessing,
run_modes=mode,
epoch=epoch,
ds_id=ds_id)
traces = sort_traces(get_current_items(self.system.traces,
run_modes=mode,
epoch=epoch,
ds_id=ds_id),
ds_ids=self.system.pipeline.get_ds_ids(
epoch=epoch, mode=mode))
diagram = pydot.Dot(
compound='true'
) # Compound lets you draw edges which terminate at sub-graphs
diagram.set('rankdir', 'TB')
diagram.set('dpi', 300)
diagram.set_node_defaults(shape='box')
# Make the dataset the first of the pipeline ops
pipe_ops.insert(0, ds)
label_last_seen = DefaultKeyDict(
lambda k: str(id(ds))) # Where was this key last generated
batch_size = ""
if isinstance(ds, Dataset):
if hasattr(ds, "fe_batch") and ds.fe_batch:
batch_size = ds.fe_batch
else:
batch_size = self.system.pipeline.batch_size
if isinstance(batch_size, Scheduler):
batch_size = batch_size.get_current_value(epoch)
if isinstance(batch_size, dict):
batch_size = batch_size[mode]
if batch_size is not None:
batch_size = f" (Batch Size: {batch_size})"
self._draw_subgraph(diagram, diagram, label_last_seen,
f'Pipeline{batch_size}', pipe_ops, ds_id)
self._draw_subgraph(diagram, diagram, label_last_seen, 'Network',
net_ops + net_post, ds_id)
self._draw_subgraph(diagram, diagram, label_last_seen, 'Traces',
traces, ds_id)
return diagram