Geometry module
This module is a direct copy of the SENeC package
PyNCulture.
Therefore, in the examples below, you will have to import nngt instead of
PyNCulture and replace pnc by nngt.geometry.
Overview
Principle
Module dedicated to the description of the spatial boundaries of neuronal
cultures.
This allows for the generation of neuronal networks that are embedded in space.
The shapely library is used to
generate and deal with the spatial environment of the neurons.
Examples
Basic features
The module provides a backup Shape object, which can be used with only
the numpy and scipy libraries.
It allows for the generation of simple rectangle, disk and ellipse shapes.
import matplotlib.pyplot as plt
import PyNCulture as nc
fig, ax = plt.subplots()
''' Choose a shape (uncomment the desired line) '''
# culture = nc.Shape.rectangle(15, 20, (5, 0))
culture = nc.Shape.disk(20, (5, 0))
# culture = nc.Shape.ellipse((20, 5), (5, 0))
''' Generate the neurons inside '''
pos = culture.seed_neurons(neurons=1000, xmax=0., ymax=0.)
''' Plot '''
nc.plot_shape(culture, ax, show=False)
ax.scatter(pos[:, 0], pos[:, 1], s=2, zorder=2)
plt.show()
All these features are of course still available with the more advanced
Shape object which inherits from shapely.geometry.Polygon.
Complex shapes from files
import matplotlib.pyplot as plt
import PyNCulture as nc
''' Choose a file '''
culture_file = "culture_from_filled_polygons.svg"
# culture_file = "culture_with_holes.svg"
# culture_file = "culture.dxf"
shapes = nc.shapes_from_file(culture_file, min_x=-5000., max_x=5000.)
''' Plot the shapes '''
fig, ax = plt.subplots()
fig.suptitle("shapes")
for p in shapes:
nc.plot_shape(p, ax, show=False)
plt.show()
''' Make a culture '''
fig2, ax2 = plt.subplots()
plt.title("culture")
culture = nc.culture_from_file(culture_file, min_x=-5000., max_x=5000.)
nc.plot_shape(culture, ax2)
''' Add neurons '''
fig3, ax3 = plt.subplots()
plt.title("culture with neurons")
culture_bis = nc.culture_from_file(culture_file, min_x=-5000., max_x=5000.)
pos = culture_bis.seed_neurons(neurons=1000, xmax=0)
nc.plot_shape(culture_bis, ax3, show=False)
ax3.scatter(pos[:, 0], pos[:, 1], s=2, zorder=3)
plt.show()
Content
-
nngt.geometry.Shape
alias of nngt.geometry.backup_shape.BackupShape
-
nngt.geometry.culture_from_file(*args, **kwargs)[source]
-
nngt.geometry.pop_largest(shapes)[source]
Returns the largest shape, removing it from the list.
If shapes is a shapely.geometry.MultiPolygon, returns the
largest shapely.geometry.Polygon without modifying the object.
| Parameters: | shapes (list of Shape objects or MultiPolygon.) |
|---|
-
nngt.geometry.shapes_from_file(*args, **kwargs)[source]
-
nngt.geometry.plot_shape(shape, axis=None, m='', mc='#999999', fc='#8888ff', ec='#444444', alpha=0.5, brightness='height', show=True, **kwargs)[source]
Plot a shape (set the axis aspect to 1 to respect the proportions).
| Parameters: |
- shape (
Shape) – Shape to plot.
- axis (
matplotlib.axes.Axes instance, optional (default: None)) – Axis on which the shape should be plotted. By default, a new figure
is created.
- m (str, optional (default: invisible)) – Marker to plot the shape’s vertices, matplotlib syntax.
- mc (str, optional (default: “#999999”)) – Color of the markers.
- fc (str, optional (default: “#8888ff”)) – Color of the shape’s interior.
- ec (str, optional (default: “#444444”)) – Color of the shape’s edges.
- alpha (float, optional (default: 0.5)) – Opacity of the shape’s interior.
- brightness (str, optional (default: height)) – Show how different other areas are from the ‘default_area’ (lower
values are darker, higher values are lighter).
Difference can concern the ‘height’, or any of the properties of the
Area objects.
- kwargs (keywords arguments for
matplotlib.patches.PathPatch)
|
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