neuron_morphology.snap_polygons.image_outputter

Utilites for writing diagnostic overlay images

Module Contents

Classes

ImageOutputter Overlays polygons and surfaces on provided images. Writes the

Functions

write_figure(fig: plt.Figure, *args, **kwargs) Write a matplotlib figure without respect to the current figure.
read_image(path: str, decimate: int = 1) Read an image. Dispatch to an appropriate library based on that
read_with_ndimage(path: str, decimate: int) Read (and symmetrically decimate) an image file into a numpy array
read_jp2(path: str, decimate: int) Read (and symmetrically decimate) a jp2 file into a numpy array
fname_suffix(path: str, suffix: str) Utility for adding a suffix to a path string. The suffix will be
make_pathpatch(vertices: Sequence[Tuple[float, float]], **patch_kwargs) → mpl.patches.PathPatch Utility for building a matplotlib pathpatch from an array of vertices
class neuron_morphology.snap_polygons.image_outputter.ImageOutputter(native_geo: Geometries, result_geo: Geometries, image_specs: Optional[Sequence[Dict]], alpha: float = 0.4, color_cycle: Optional[Sequence] = None, savefig_kwargs: Optional[Dict] = None)

Overlays polygons and surfaces on provided images. Writes the results to files.

Parameters:
native_geo : Layer geometries before gaps are filled
result_geo : Layer geometries after gaps are filled
image_specs : Each is a dictionary defining a single image. Must
provide string keys:
  • input_path : read from here
  • output_path : write to (siblings of) this path
  • downsample : the image will be scaled by this factor in each
    dimension
  • overlay_types : produce these kinds of overlay for this image
alpha : of the transparent overlays
color_cycle : as polygon fills are drawn, cycle through these colors
savefig_kwargs : Passed directly to pyplot’s savefig, use to specify

e.g dpi.
DEFAULT_COLOR_CYCLE = ['c', 'm', 'y', 'k', 'r', 'g', 'b']
OVERLAY_TYPES
_draw_geometries(self, geometries: Geometries, image: np.ndarray)

Utility for overlaying polygons and surfaces on an image. See draw_before and draw_after for more details.

draw_before(self, image: np.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
draw_after(self, image: np.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
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.write_figure(fig: plt.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
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_with_ndimage(path: str, decimate: int)

Read (and symmetrically decimate) an image file into a numpy array

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

Read (and symmetrically decimate) a jp2 file into a numpy array

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) → mpl.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