neuron_morphology.snap_polygons.geometries module

class neuron_morphology.snap_polygons.geometries.Geometries

Bases: object

Attributes:

close_bounds

Methods

rasterize(self, box, NoneType] = None, …)	Rasterize one or more owned geometries.
register_polygon(self, name, path, …)	Adds a named polygon path to this object.
register_polygons(self, polygons, Union[str, …)	utility for registering multiple polygons.
register_surface(self, name, path, …)	Adds a line (e.g.
register_surfaces(self, surfaces, Union[str, …)	utility for registering multiple surfaces.
to_json(self)	Write contained polygons to a json-serializable format
transform(self, transform, float], …)	Apply a transform to each owned geometry.

close_bounds

rasterize(self, box: Union[neuron_morphology.snap_polygons.bounding_box.BoundingBox, NoneType] = None, polygons: Union[Sequence[str], bool] = True, surfaces: Union[Sequence[str], bool] = False) → Dict[str, numpy.ndarray]

Rasterize one or more owned geometries. Produce a mapping from object names to masks.

Parameters:

shape : if provided, the output image shape. Otherwise, use the rounded close bounding box shape

polygons : a list of names. Alternatively all (True) or none (False)

lines : a list of names. Alternatively all (True) or none (False)

Notes

uses rasterio.features.rasterize

register_polygon(self, name: str, path: Union[str, Sequence[Sequence[float]], shapely.geometry.polygon.Polygon, shapely.geometry.polygon.LinearRing])

Adds a named polygon path to this object. Updates the close bounding box.

Parameters:

name : identifier for this polygon

path : defines the exterior of this (simple) polygon

register_polygons(self, polygons: Union[Dict[str, Union[str, Sequence[Sequence[float]], shapely.geometry.polygon.Polygon, shapely.geometry.polygon.LinearRing]], Sequence[Dict[str, Union[str, Sequence[Sequence[float]], shapely.geometry.polygon.Polygon, shapely.geometry.polygon.LinearRing]]]])

utility for registering multiple polygons. See register_polygon

register_surface(self, name: str, path: Union[str, Sequence[Sequence[float]], shapely.geometry.linestring.LineString])

Adds a line (e.g. the pia/wm surfaces) to this object. Updates the bounding box.

Parameters:

name : identifier for this surface

path : defines the surface

register_surfaces(self, surfaces: Dict[str, Union[str, Sequence[Sequence[float]], shapely.geometry.linestring.LineString]])

utility for registering multiple surfaces. See register_surface

to_json(self) → Dict

Write contained polygons to a json-serializable format

transform(self, transform: Callable[[float, float], Tuple[float, float]]) → 'Geometries'

Apply a transform to each owned geometry. Return a new collection.

Parameters:

transform : A callable which maps (vertical, horizontal) coordinates to

new (vertical, horizontal) coordinates.

neuron_morphology.snap_polygons.geometries.clear_overlaps(stack: Dict[str, numpy.ndarray])

Given a stack of masks, remove all inter-mask overlaps inplace

Parameters:

stack : Keys are names, values are masks (of the same shape). 0 indicates

absence

neuron_morphology.snap_polygons.geometries.closest_from_stack(stack: Dict[str, numpy.ndarray])

Given a stack of images describing distance from several objects, find the closest object to each pixel.

Parameters:

stack : Keys are names, values are ndarrays (of the same shape). Each pixel

in the values describes the distance from that pixel to the named object

Returns:

closest : An integer array whose values are the closest object to each

pixel

names : A mapping from the integer codes in the “closest” array to names

neuron_morphology.snap_polygons.geometries.find_vertical_surfaces(polygons: Dict[str, shapely.geometry.polygon.Polygon], order: Sequence[str], pia: Union[shapely.geometry.linestring.LineString, NoneType] = None, wm: Union[shapely.geometry.linestring.LineString, NoneType] = None)

Given a set of polygons describing cortical layer boundaries, find the boundaries between each layer.

Parameters:

polygons : named layer polygons

order : A sequence of names defining the order of the layer polygons from

pia to white matter

pia : The upper pia surface.

wm : The lower white matter surface.

Returns:

dictionary whose keys are as “{name}_{side}” and whose values are

linestrings describing these boundaries.

neuron_morphology.snap_polygons.geometries.get_snapped_polys(closest: numpy.ndarray, name_lut: Dict[int, str]) → Dict[str, shapely.geometry.polygon.Polygon]

Obtains named shapes from a label image.

Parameters:

closest : label integer with integer codes

name_lut : look up table from integer codes to string names

Returns:

mapping from names to polygons describing each labelled region

neuron_morphology.snap_polygons.geometries.make_scale(scale: float = 1.0) → Callable[[float, float], Tuple[float, float]]

A utility for making a 2D scale transform, suitable for transforming bounding boxes and Geometries

Parameters:

scale : isometric scale factor

Returns:

A transform function

neuron_morphology.snap_polygons.geometries.rasterize(geometry: shapely.geometry.base.BaseGeometry, box: neuron_morphology.snap_polygons.bounding_box.BoundingBox) → <built-in function array>

Rasterize a shapely object to a grid defined by a provided bounding box.

Parameters:

geometry : to be rasterized

box : defines the window (in the same coordinate space as the geometry)

into which the geometry will be rasterized

Returns:

A mask, where 1 indicates presence and 0 absence