API reference: Datasets¶

The Dataset bundle and the exported singletons.

Dataset¶

Dataset ¶

Dataset(name, transform_fn, streamline_fn)

Bases: object

Bundle of a transform and a streamline for a single dataset.

The recommended entry points are the exported minnie_ds and v1dd_ds singletons. Use :meth:transform and :meth:streamline, each of which takes a resolution ("nm" (default), "vx", or an [x, y, z] list) and an optional version.

Parameters:

Name	Type	Description	Default
`name`	`str`	Dataset name; must match a key in the version registries.	required
`transform_fn`	`callable`	Factories with signature `(resolution="nm", version=None)` returning the transform / streamline for this dataset.	required
`streamline_fn`	`callable`	Factories with signature `(resolution="nm", version=None)` returning the transform / streamline for this dataset.	required

Source code in standard_transform/datasets.py

def __init__(self, name, transform_fn, streamline_fn):
    self.name = name
    self._transform_fn = transform_fn
    self._streamline_fn = streamline_fn
    # Streamlines may load a data file (the tangent field), so cache built ones.
    self._streamline_cache = {}

transform ¶

transform(
    resolution="nm", version=None
) -> TransformSequence

Transform into oriented microns for input at resolution.

Parameters:

Name	Type	Description	Default
`resolution`	`str or array - like`	`"nm"` (default), `"vx"`, or an explicit `[x, y, z]` resolution.	`'nm'`
`version`	`str`	Transform version; by default the latest. See :meth:`available_versions`.	`None`

Source code in standard_transform/datasets.py

def transform(self, resolution="nm", version=None) -> TransformSequence:
    """Transform into oriented microns for input at ``resolution``.

    Parameters
    ----------
    resolution : str or array-like, optional
        ``"nm"`` (default), ``"vx"``, or an explicit ``[x, y, z]`` resolution.
    version : str, optional
        Transform version; by default the latest. See :meth:`available_versions`.
    """
    return self._transform_fn(resolution, version=version)

streamline ¶

streamline(resolution='nm', version=None) -> Streamline

Streamline for input at resolution (data-derived field where available).

Parameters:

Name	Type	Description	Default
`resolution`	`str or array - like`	`"nm"` (default), `"vx"`, or an explicit `[x, y, z]` resolution.	`'nm'`
`version`	`str`	Streamline version; by default the latest. See :meth:`available_versions`.	`None`

Source code in standard_transform/datasets.py

def streamline(self, resolution="nm", version=None) -> Streamline:
    """Streamline for input at ``resolution`` (data-derived field where available).

    Parameters
    ----------
    resolution : str or array-like, optional
        ``"nm"`` (default), ``"vx"``, or an explicit ``[x, y, z]`` resolution.
    version : str, optional
        Streamline version; by default the latest. See :meth:`available_versions`.
    """
    key = (self._res_key(resolution), version)
    if key not in self._streamline_cache:
        self._streamline_cache[key] = self._streamline_fn(resolution, version=version)
    return self._streamline_cache[key]

available_versions ¶

available_versions()

Available transform and streamline versions. See :func:available_versions.

Source code in standard_transform/datasets.py

def available_versions(self):
    """Available transform and streamline versions. See :func:`available_versions`."""
    return available_versions(self.name)

Singletons¶

standard_transform.minnie_ds — the Minnie65 dataset bundle.
standard_transform.v1dd_ds — the V1dd dataset bundle.

Both are instances of Dataset. See Datasets for a task-oriented overview.