jLM.JupyterDisplay#

SpatialModel mixins for rich display in Jupyter

Functions

showVolumeStack(vol[, plane, cmap, scl, ...])

Display slices volumetric data interactively

Classes

FileJupyterMixin()

JupyterDisplayMixin()

class jLM.JupyterDisplay.FileJupyterMixin[source]#

Bases: object

class jLM.JupyterDisplay.JupyterDisplayMixin[source]#

Bases: object

construct()[source]#

Track newly created model objects and display in Notebook.

Context manager which tracks new species, reactions, etc., and displays a HTML summary when used in Jupyter

displayGeometry(**kwargs)[source]#
showAllParameters(**kwargs)[source]#
showAllSpecies(**kwargs)[source]#
showDiffusionConstants(**kwargs)[source]#
showRateConstants(**kwargs)[source]#
showReactions(**kwargs)[source]#
showRegion(**kwargs)[source]#
showRegionStack(**kwargs)[source]#
showSpecies(**kwargs)[source]#
jLM.JupyterDisplay.showVolumeStack(vol, plane='xz', cmap='inferno', scl=None, maxWidth=600, maxHeight=600)[source]#

Display slices volumetric data interactively

Parameters:

vol (numpy.ndarray) – 3-D data

Keyword Arguments:

  • cmap (str) – Name of matplotlib colormap

  • plane (str) – Viewing plane, e.g. “xy”

  • scl (int) – Scale pixels by this amount

  • maxWidth (int) – Maximum width of image

  • maxHeight (int) – Maximum height of image