sleap.nn.config.outputs

class sleap.nn.config.outputs.CheckpointingConfig(initial_model: bool = False, best_model: bool = True, every_epoch: bool = False, latest_model: bool = False, final_model: bool = False)

Configuration of model checkpointing.

initial_model

If True, the initial model is saved before any training occurs. If the model was not pretrained, these will just be the model with random weights. This is mostly useful for comparisons to a random baseline. If enabled, the model will be serialized to:

“{run_folder}/initial_model.h5”

Type:

bool

best_model

If True, the model will be saved at the end of an epoch if the validation loss has improved. If enabled, the model will be serialized to:

“{run_folder}/best_model.h5”

Type:

bool

every_epoch

If True, the model will be saved at the end of every epoch, regardless of whether there was an improvement detected. If enabled, the models will be serialized to:

“{run_folder}/model.epoch{04d}.h5”

Type:

bool

latest_model

If True, the model will be saved at the end of every epoch, regardless of whether there was an improvement detected, but will overwrite the previous latest model. If enabled, the model will be serialized to:

“{run_folder}/latest_model.h5”

Type:

bool

final_model

If True, the model will be saved at the end of training, whether it was stopped early or finished all epochs. If enabled, the model will be serialized to:

“{run_folder}/final_model.h5”

Type:

bool

class sleap.nn.config.outputs.OutputsConfig(save_outputs: bool = True, run_name: Optional[str] = None, run_name_prefix: str = '', run_name_suffix: Optional[str] = None, runs_folder: str = 'models', tags: List[str] = _Nothing.NOTHING, save_visualizations: bool = True, keep_viz_images: bool = False, zip_outputs: bool = False, log_to_csv: bool = True, checkpointing: CheckpointingConfig = _Nothing.NOTHING, tensorboard: TensorBoardConfig = _Nothing.NOTHING, zmq: ZMQConfig = _Nothing.NOTHING)

Configuration of training outputs.

save_outputs

If True, file system-based outputs will be saved. If False, nothing will be written to disk, which may be useful for interactive training where no outputs are desired.

Type:

bool

run_name

Name of the training run. This is the name of the folder that all outputs related to the training job are stored. If not specified explicitly, this will be automatically generated from the configuration options and the timestamp of the start of the training job. Note that if this is specified rather than automatically generated, multiple runs can end up overwriting each other if run_name_prefix or run_name_suffix are not specified.

Type:

Optional[str]

run_name_prefix

String to prepend to the run name. This is useful to prevent multiple runs started at the same exact time to be mapped to the same folder, or when a fixed run name is specified.

Type:

str

run_name_suffix

String to append to the run name. This is useful to prevent multiple runs started at the same exact time to be mapped to the same folder, or when a fixed run name is specified. If set to None, this will be automatically set to a number (e.g., “_1”) that does not conflict with an existing folder, so sequential jobs with a fixed run name will have an increasing counter as the suffix. Warning: This can fail to prevent overwriting if multiple jobs are run in

parallel and attempt to detect the run name at the same time, especially over network storage which can have a short delay in updating the directory listing across clients.

Type:

Optional[str]

runs_folder

Path to the folder that run data should be stored in. All the data for a single run are stored in the path:

“{runs_folder}/{run_name_prefix}{run_name}{run_name_suffix}”

These are specified separately to allow the run_name to be auto-generated. This can be specified as an absolute or relative path. Relative paths specify a path with respect to the current working directory. Non-existing folders will be created if they do not already exist. Defaults to the “models” subdirectory of the current working directory.

Type:

str

tags

A list of strings to use as “tags” that can be used to organize multiple runs. These are not used for anything during training or inference, so they can be used to store arbitrary user-specified metadata.

Type:

List[str]

save_visualizations

If True, will render and save visualizations of the model predictions as PNGs to “{run_folder}/viz/{split}.{epoch:04d}.png”, where the split is one of “train”, “validation”, “test”.

Type:

bool

keep_viz_images

If True, keep the saved visualization images after training completes. This is useful unchecked to reduce the model folder size if you do not need to keep the visualization images.

Type:

bool

zip_outputs

If True, compress the run folder to a zip file. This will be named “{run_folder}.zip”.

Type:

bool

log_to_csv

If True, loss and metrics will be saved to a simple CSV after each epoch to “{run_folder}/training_log.csv”

Type:

bool

checkpointing

Configuration options related to model checkpointing.

Type:

sleap.nn.config.outputs.CheckpointingConfig

tensorboard

Configuration options related to TensorBoard logging.

Type:

sleap.nn.config.outputs.TensorBoardConfig

zmq

Configuration options related to ZeroMQ-based control and monitoring.

Type:

sleap.nn.config.outputs.ZMQConfig

property run_path: str

Return the complete run path where all training outputs are stored.

This path is determined by other attributes using the pattern:

{runs_folder}/{run_name_prefix}{run_name}{run_name_suffix}

If run_name_suffix is set to None, it will be ignored.

Raises:

ValueError – If run_name is not set.

Notes

This does not perform any checks for existence or validity and should only be used when the above fields are complete.

This path will not be updated if the files are moved. To ensure this path is valid, use a relative path for the runs_folder or manually update it.

class sleap.nn.config.outputs.TensorBoardConfig(write_logs: bool = False, loss_frequency: str = 'epoch', architecture_graph: bool = False, profile_graph: bool = False, visualizations: bool = True)

Configuration of TensorBoard-based monitoring of the training.

write_logs

If True, logging data will be written to disk within the run folder. TensorBoard can monitor either the specific run folder, or the parent runs folder that may contain multiple models/runs. Both will be displayed correctly in the dashboard.

Type:

bool

loss_frequency

How often loss and metrics will be written out to disk. This can be “epoch” to only write summaries at the end of every epoch, “batch” to write summaries after every batch. High frequency writing can considerably slow down training, so this is not recommended to be anything other than “epoch” if training interactively. This value only affects the monitored losses and metrics, not other summaries like visualizations.

Type:

str

architecture_graph

If True, the architecture of the model will be saved and can be viewed graphically in TensorBoard. This is only saved at the beginning of training, but can consume a lot of disk space for large models, as well as potentially freezing the browser tab when rendered.

Type:

bool

profile_graph

If True, profiles the second batch of examples to collect compute statistics.

Type:

bool

visualizations

If True, visualizations of the model predictions are rendered and logged for display in TensorBoard -> Images.

Type:

bool

class sleap.nn.config.outputs.ZMQConfig(subscribe_to_controller: bool = False, controller_address: str = 'tcp://127.0.0.1:9000', controller_polling_timeout: int = 10, publish_updates: bool = False, publish_address: str = 'tcp://127.0.0.1:9001')

Configuration of ZeroMQ-based monitoring of the training.

subscribe_to_controller

If True, will listen for commands broadcast over a socket or another messaging endpoint using the ZeroMQ SUB protocol. This allows for external/asynchronous control of the training loop from other programs, e.g., GUIs or job schedulers. Commands are expected to be JSON-serialized strings of dictionaries with a key named “command”. The endpoint is polled for messages at the end of each batch. Current commands are:

“stop”: Stops the training after the current batch. “set_lr”: Sets the optimizer’s learning rate after the current batch.

The new learning rate should be a float specified in the “lr” key.

Type:

bool

controller_address

IP address/hostname and port number of the endpoint to listen for command messages from. For TCP-based endpoints, this must be in the form of “tcp://{ip_address}:{port_number}”. Defaults to “tcp://127.0.0.1:9000”.

Type:

str

controller_polling_timeout

Polling timeout in microseconds specified as an integer. This controls how long the poller should wait to receive a response and should be set to a small value to minimize the impact on training speed.

Type:

int

publish_updates

If True, training summaries will be broadcast over a socket or another messaging endpoint using the ZeroMQ PUB protocol. This is useful for asynchronously monitoring training with external programs without writing to the file system and without requiring special dependencies like TensorBoard. All data will be broadcast as JSON serialized strings. TODO: Describe published message keys.

Type:

bool

publish_address

IP address/hostname and port number of the endpoint to publish updates to. For TCP-based endpoints, this must be in the form of “tcp://{ip_address}:{port_number}”. Defaults to “tcp://127.0.0.1:9001”.

Type:

str