pyhealth.datasets.BaseSignalDataset#

This is the basic Signal dataset class. Any specific Signal dataset will inherit from this class.

class pyhealth.datasets.BaseSignalDataset(root, dataset_name=None, dev=False, refresh_cache=False, **kwargs)[source]#

Bases: ABC

Abstract base Signal dataset class.

This abstract class defines a uniform interface for all EEG datasets (e.g., SleepEDF, SHHS).

Each specific dataset will be a subclass of this abstract class, which can then be converted to samples dataset for different tasks by calling self.set_task().

Parameters

  • dataset_name (Optional[str]) – name of the dataset.

  • root (str) – root directory of the raw data (should contain many csv files).

  • dev (bool) – whether to enable dev mode (only use a small subset of the data). Default is False.

  • refresh_cache (bool) – whether to refresh the cache; if true, the dataset will be processed from scratch and the cache will be updated. Default is False.

stat()[source]#

Returns some statistics of the base dataset.

Return type

str

static info()[source]#

Prints the output format.

set_task(task_fn, task_name=None)[source]#

Processes the base dataset to generate the task-specific sample dataset.

This function should be called by the user after the base dataset is initialized. It will iterate through all patients in the base dataset and call task_fn which should be implemented by the specific task.

Parameters

  • task_fn (Callable) – a function that takes a single patient and returns a list of samples (each sample is a dict with patient_id, visit_id, and other task-specific attributes as key). The samples will be concatenated to form the sample dataset.

  • task_name (Optional[str]) – the name of the task. If None, the name of the task function will be used.

Returns

the task-specific sample (Base) dataset.

Return type

sample_dataset

Note

In task_fn, a patient may be converted to multiple samples, e.g.,

a patient with three visits may be converted to three samples ([visit 1], [visit 1, visit 2], [visit 1, visit 2, visit 3]). Patients can also be excluded from the task dataset by returning an empty list.