# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
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"""Tools to visualize neuron morphological objects.
Examples:
>>> from neurom import viewer
>>> nrn = ... # load a neuron
>>> viewer.draw(nrn) # 2d plot
>>> viewer.draw(nrn, mode='3d') # 3d plot
>>> viewer.draw(nrn.neurites[0]) # 2d plot of neurite tree
>>> viewer.draw(nrn, mode='dendrogram') # dendrogram plot
"""
from .view import (plot_neuron, plot_neuron3d,
plot_tree, plot_tree3d,
plot_soma, plot_soma3d,
plot_dendrogram)
from .view import common
from .core import Tree, Neurite, Soma, Neuron
MODES = ('2d', '3d', 'dendrogram')
_VIEWERS = {
'neuron_3d': plot_neuron3d,
'neuron_2d': plot_neuron,
'neuron_dendrogram': plot_dendrogram,
'tree_3d': plot_tree3d,
'tree_2d': plot_tree,
'tree_dendrogram': plot_dendrogram,
'soma_3d': plot_soma3d,
'soma_2d': plot_soma
}
[docs]class ViewerError(Exception):
"""Base class for viewer exceptions."""
[docs]class InvalidDrawModeError(ViewerError):
"""Exception class to indicate invalid draw mode."""
[docs]class NotDrawableError(Exception):
"""Exception class for things that aren't drawable."""
[docs]def draw(obj, mode='2d', **kwargs):
"""Draw a morphology object.
Arguments:
obj: morphology object to be drawn (neuron, tree, soma).
mode (Optional[str]): drawing mode ('2d', '3d', 'dendrogram'). Defaults to '2d'.
**kwargs: keyword arguments for underlying neurom.view.view functions.
Raises:
InvalidDrawModeError if mode is not valid
NotDrawableError if obj is not drawable
NotDrawableError if obj type and mode combination is not drawable
Examples:
>>> nrn = ... # load a neuron
>>> fig, _ = viewer.draw(nrn) # 2d plot
>>> fig.show()
>>> fig3d, _ = viewer.draw(nrn, mode='3d') # 3d plot
>>> fig3d.show()
>>> fig, _ = viewer.draw(nrn.neurites[0]) # 2d plot of neurite tree
>>> dend, _ = viewer.draw(nrn, mode='dendrogram')
"""
if mode not in MODES:
raise InvalidDrawModeError('Invalid drawing mode %s' % mode)
if 'realistic_diameters' in kwargs and mode == '3d':
if kwargs['realistic_diameters']:
raise NotImplementedError('Option realistic_diameter not implemented for 3D plots')
del kwargs['realistic_diameters']
fig, ax = (common.get_figure() if mode in ('2d', 'dendrogram')
else common.get_figure(params={'projection': '3d'}))
if isinstance(obj, Neuron):
tag = 'neuron'
elif isinstance(obj, (Tree, Neurite)):
tag = 'tree'
elif isinstance(obj, Soma):
tag = 'soma'
else:
raise NotDrawableError('draw not implemented for %s' % obj.__class__)
viewer = '%s_%s' % (tag, mode)
try:
plotter = _VIEWERS[viewer]
except KeyError:
raise NotDrawableError('No drawer for class %s, mode=%s' % (obj.__class__, mode))
output_path = kwargs.pop('output_path', None)
plotter(ax, obj, **kwargs)
if mode != 'dendrogram':
common.plot_style(fig=fig, ax=ax, **kwargs)
if output_path:
common.save_plot(fig=fig, output_path=output_path, **kwargs)
return fig, ax