neuron_morphology.snap_polygons.image_outputter module

class neuron_morphology.snap_polygons.image_outputter.ImageOutputter(native_geo: neuron_morphology.snap_polygons.geometries.Geometries, result_geo: neuron_morphology.snap_polygons.geometries.Geometries, image_specs: Optional[Sequence[Dict[KT, VT]]], alpha: float = 0.4, color_cycle: Optional[Sequence[T_co]] = None, savefig_kwargs: Optional[Dict[KT, VT]] = None)

Bases: object

Methods

draw_after(self, image, scale)	Display the post-fill polygons and surfaces overlaid on an image.
draw_before(self, image, scale)	Display the pre-fill polygons and surfaces overlaid on an image.
write_images(self)	For each image specified in this outputter and each overlay type requested for that image, produce and save an overlay.

DEFAULT_COLOR_CYCLE = ('c', 'm', 'y', 'k', 'r', 'g', 'b')

OVERLAY_TYPES = {'after': 'draw_after', 'before': 'draw_before'}

draw_after(self, image: numpy.ndarray, scale: float = 1.0)

Display the post-fill polygons and surfaces overlaid on an image.

Parameters:

image : onto which objects will be drawn

scale : required to transform from object space to image space

Returns:

A matplotlib figure containing the overlay

draw_before(self, image: numpy.ndarray, scale: float = 1.0)

Display the pre-fill polygons and surfaces overlaid on an image.

Parameters:

image : onto which objects will be drawn

scale : required to transform from object space to image space

Returns:

A matplotlib figure containing the overlay

write_images(self)

For each image specified in this outputter and each overlay type requested for that image, produce and save an overlay.

neuron_morphology.snap_polygons.image_outputter.fname_suffix(path: str, suffix: str)

Utility for adding a suffix to a path string. The suffix will be inserted before the extension.

neuron_morphology.snap_polygons.image_outputter.make_pathpatch(vertices: Sequence[Tuple[float, float]], **patch_kwargs) → matplotlib.patches.PathPatch

Utility for building a matplotlib pathpatch from an array of vertices

Parameters:

vertices : Defines the path. May be closed or open

**patch_kwargs : passed directly to pathpatch constructor

neuron_morphology.snap_polygons.image_outputter.read_image(path: str, decimate: int = 1)

Read an image. Dispatch to an appropriate library based on that image’s extension.

Parameters:

path : to the image

decimate : apply a decimation of this factor along each axis of the image

neuron_morphology.snap_polygons.image_outputter.read_jp2(path: str, decimate: int)

neuron_morphology.snap_polygons.image_outputter.read_with_ndimage(path: str, decimate: int)

neuron_morphology.snap_polygons.image_outputter.write_figure(fig: matplotlib.figure.Figure, *args, **kwargs)

Write a matplotlib figure without respect to the current figure.

Parameters:

fig : the figure to be writter

*args, **kwargs : passed to plt.savefig