tmd.view.view¶

Module for viewing neuronal morphologies.

Functions

`all_trunks`(nrn[, plane, new_fig, subplot, ...])	Generate a 2d figure of the neuron, that contains a soma and a list of trees.
`all_trunks3d`(nrn[, new_fig, new_axes, ...])	Generate a figure of the neuron, that contains a soma and a list of trees.
`density_cloud`(obj[, new_fig, subplot, ...])	View the neuron morphologies of a population as a density cloud.
`neuron`(nrn[, plane, new_fig, subplot, hadd, ...])	Generate a 2d figure of the neuron that contains a soma and a list of trees.
`neuron3d`(nrn[, new_fig, new_axes, subplot, ...])	Generate a figure of the neuron, that contains a soma and a list of trees.
`polar_plot`(pop[, neurite_type, bins])	Generate a polar plot of a neuron or population.
`population`(pop[, plane, new_fig, subplot, ...])	Generate a 2d figure of the population, that contains a soma and a list of trees.
`population3d`(pop[, new_fig, new_axes, subplot])	Generate a figure of the population, that contains the pop somata and a set of list of trees.
`soma`(sm[, plane, new_fig, subplot, hadd, vadd])	Generate a 2d figure of the soma.
`soma3d`(sm[, new_fig, new_axes, subplot])	Generate a 3d figure of the soma.
`tree`(tr[, plane, new_fig, subplot, hadd, vadd])	Generate a 2d figure of the tree.
`tree3d`(tr[, new_fig, new_axes, subplot])	Generate a figure of the tree in 3d.
`tree_barcode_colors`(tr[, plane, feature, cmap])	Generates a two panel figure with color-coded branches, bars.
`tree_full_persistence_colors`(tr[, plane, ...])	Generates a four panel figure with color-coded branches, bars.
`trunk`(tr[, plane, new_fig, subplot, hadd, ...])	Generate a 2d figure of the trunk = first N segments of the tree.
`trunk3d`(tr[, new_fig, new_axes, subplot, N])	Generate a figure of the trunk in 3d.

tmd.view.view.all_trunks(nrn, plane='xy', new_fig=True, subplot=False, hadd=0.0, vadd=0.0, neurite_type='all', N=10, **kwargs)¶

Generate a 2d figure of the neuron, that contains a soma and a list of trees.

Parameters:

nrn (Neuron) – A Neuron object.
plane (str) – Accepted values: Any sorted pair of xyz. Default value is ‘xy’.
new_fig (bool) – Defines if the neuron will be plotted in the current figure (False) or in a new figure (True). Default value is True.
subplot (matplotlib subplot value or False) – If False the default subplot 111 will be used. For any other value a matplotlib subplot will be generated. Default value is False.
hadd (float) – X shift.
vadd (float) – Y shift.
neurite_type (str) – The types of neurites that should be plotted.
N (float) – Half of the window size used if xlim and ylim are not given.

Keyword Arguments:

**kwargs – All keyword arguments will be passed to tmd.view.common.plot_style().

Returns:

A 3D matplotlib figure with a tree view, at the selected plane.

tmd.view.view.all_trunks3d(nrn, new_fig=True, new_axes=True, subplot=False, neurite_type='all', N=10, **kwargs)¶

Generate a figure of the neuron, that contains a soma and a list of trees.

Parameters:

neuron (Neuron) – A Neuron object.
new_fig (bool) – Defines if the neuron will be plotted in the current figure (False) or in a new figure (True).
new_axes (bool) – Defines if the neuron will be plotted in the current axes (False) or in new axes (True).
subplot (matplotlib subplot value or False) – If False the default subplot 111 will be used. For any other value a matplotlib subplot will be generated. Default value is False.
neurite_type (str) – The types of neurites that should be plotted.
N (float) – Half of the window size used if xlim and ylim are not given.

Keyword Arguments:

**kwargs – All keyword arguments will be passed to tmd.view.common.plot_style().

Returns:

A 3D matplotlib figure with a tree view.

tmd.view.view.density_cloud(obj, new_fig=True, subplot=111, new_axes=True, neurite_type='all', bins=100, plane='xy', color_map=<matplotlib.colors.LinearSegmentedColormap object>, alpha=0.8, centered=True, colorbar=True, plot_neuron=False, **kwargs)¶: View the neuron morphologies of a population as a density cloud.

tmd.view.view.neuron(nrn, plane='xy', new_fig=True, subplot=False, hadd=0.0, vadd=0.0, neurite_type='all', apical_alignment=False, plot_soma=True, new_axes=True, **kwargs)¶

Generate a 2d figure of the neuron that contains a soma and a list of trees.

Parameters:

nrn (Neuron) – A neuron object.
plane (str) – Accepted values: Any sorted pair of xyz. Default value is ‘xy’.
new_fig (bool) – Defines if the neuron will be plotted in the current figure (False) or in a new figure (True). Default value is True.
subplot (bool) – Create a subplot if set to True.
hadd (float) – X shift. Default value is 0.
vadd (float) – Y shift. Default value is 0.
neurite_type (str) – The types of neurites that should be plotted. Default value is ‘all’.
apical_alignment (bool) – Defines if the neuron will be automatically aligned toward the pia. Default value is False.
plot_soma (bool) – Defines if the soma will be plotted. Default value is True.
new_axes (bool) – Defines if the neuron will be plotted in the current axes (False) or in new axes (True). Default value is True.

Keyword Arguments:

**kwargs – All keyword arguments will be passed to tmd.view.view.soma(), tmd.view.view.tree() and tmd.view.common.plot_style().

Returns:

A 3D matplotlib figure with a tree view, at the selected plane.

tmd.view.view.neuron3d(nrn, new_fig=True, new_axes=True, subplot=False, neurite_type='all', **kwargs)¶

Generate a figure of the neuron, that contains a soma and a list of trees.

Parameters:

neuron (Neuron) – A Neuron object.
new_fig (bool) – Defines if the neuron will be plotted in the current figure (False) or in a new figure (True).
new_axes (bool) – Defines if the neuron will be plotted in the current axes (False) or in new axes (True).
subplot (matplotlib subplot value or False) – If False the default subplot 111 will be used. For any other value a matplotlib subplot will be generated. Default value is False.
neurite_type (str) – The types of neurites that should be plotted.

Keyword Arguments:

**kwargs – All keyword arguments will be passed to tmd.view.common.plot_style().

Returns:

A 3D matplotlib figure with a tree view.

tmd.view.view.polar_plot(pop, neurite_type='neurites', bins=20)¶: Generate a polar plot of a neuron or population.

tmd.view.view.population(pop, plane='xy', new_fig=True, subplot=False, hadd=0.0, vadd=0.0, neurite_type='all', **kwargs)¶

Generate a 2d figure of the population, that contains a soma and a list of trees.

Parameters:

pop (Population) – A Population object.
plane (str) – Accepted values: Any sorted pair of xyz. Default value is ‘xy’.
new_fig (bool) – Defines if the neuron will be plotted in the current figure (False) or in a new figure (True).
subplot (matplotlib subplot value or False) – If False the default subplot 111 will be used. For any other value a matplotlib subplot will be generated. Default value is False.
hadd (float) – X shift.
vadd (float) – Y shift.
neurite_type (str) – The types of neurites that should be plotted.
N (float) – Half of the window size used if xlim and ylim are not given.

Keyword Arguments:

**kwargs – All keyword arguments will be passed to soma(), tree() and tmd.view.common.plot_style().

Returns:

A 3D matplotlib figure with a tree view, at the selected plane.

tmd.view.view.population3d(pop, new_fig=True, new_axes=True, subplot=False, **kwargs)¶

Generate a figure of the population, that contains the pop somata and a set of list of trees.

Parameters:

pop (Population) – A Population object.
new_fig (bool) – Defines if the neuron will be plotted in the current figure (False) or in a new figure (True).
new_axes (bool) – Defines if the neuron will be plotted in the current axes (False) or in new axes (True).
subplot (matplotlib subplot value or False) – If False the default subplot 111 will be used. For any other value a matplotlib subplot will be generated. Default value is False.

Keyword Arguments:

**kwargs – All keyword arguments will be passed to tmd.view.common.plot_style().

Returns:

A 3D matplotlib figure with a population view.

tmd.view.view.soma(sm, plane='xy', new_fig=True, subplot=False, hadd=0.0, vadd=0.0, **kwargs)¶

Generate a 2d figure of the soma.

Parameters:

sm (Soma) – A Soma object.
plane (str) – The plane to consider.
new_fig (bool) – Create a new figure if set to True.
subplot (bool) – Create a subplot if set to True.
hadd (float) – X shift.
vadd (float) – Y shift.

tmd.view.view.soma3d(sm, new_fig=True, new_axes=True, subplot=False, **kwargs)¶

Generate a 3d figure of the soma.

Parameters:

soma (Soma) – A Soma object.
new_fig (bool) – Defines if the neuron will be plotted in the current figure (False) or in a new figure (True).
new_axes (bool) – Defines if the neuron will be plotted in the current axes (False) or in new axes (True).
subplot (matplotlib subplot value or False) – If False the default subplot 111 will be used. For any other value a matplotlib subplot will be generated. Default value is False.

Keyword Arguments:

**kwargs – All keyword arguments will be passed to tmd.view.common.plot_style().

Returns:

A 3D matplotlib figure with a tree view.

tmd.view.view.tree(tr, plane='xy', new_fig=True, subplot=False, hadd=0.0, vadd=0.0, **kwargs)¶

Generate a 2d figure of the tree.

Parameters:

tr (Tree) – A Tree object.
plane (str) – The plane to consider.
new_fig (bool) – Create a new figure if set to True.
subplot (bool) – Create a subplot if set to True.
hadd (float) – X shift.
vadd (float) – Y shift.

tmd.view.view.tree3d(tr, new_fig=True, new_axes=True, subplot=False, **kwargs)¶

Generate a figure of the tree in 3d.

Parameters:

tr (Tree) – A Tree object.
new_fig (bool) – Defines if the neuron will be plotted in the current figure (False) or in a new figure (True).
new_axes (bool) – Defines if the neuron will be plotted in the current axes (False) or in new axes (True).
subplot (matplotlib subplot value or False) – If False the default subplot 111 will be used. For any other value a matplotlib subplot will be generated. Default value is False.

Keyword Arguments:

**kwargs – All keyword arguments will be passed to tmd.view.common.plot_style().

Returns:

A 3D matplotlib figure with a tree view.

tmd.view.view.tree_barcode_colors(tr, plane='xy', feature='path_distances', cmap=<matplotlib.colors.LinearSegmentedColormap object>)¶

Generates a two panel figure with color-coded branches, bars.

Generates a 2d pic of the tree, each branch has a unique color. A persistence barcode with the same colors at each bar.

Parameters:

tr (Tree) – A Tree object.
plane (str) – Accepted values: Any sorted pair of xyz: (xy, xz, yx, yz, zx, zy) Default value is ‘xy’.
feature (str) – Accepted values: path_distances, radial_distances. Default value is ‘path_distances’.
cmap (matplotlib colormap) – Default value is jet.

Returns:

2d matplotlib figure, axes.

tmd.view.view.tree_full_persistence_colors(tr, plane='xy', feature='path_distances', cmap=<matplotlib.colors.LinearSegmentedColormap object>)¶

Generates a four panel figure with color-coded branches, bars.

Generates a 2d pic of the tree, each branch has a unique color. A persistence barcode with the same colors at each bar, A persistence diagram with the same colors, A persistence image with the same colormap.

Parameters:

tr (Tree) – A Tree object.
plane (str) – Accepted values: Any sorted pair of xyz: (xy, xz, yx, yz, zx, zy) Default value is ‘xy’.
feature (str) – Accepted values: path_distances, radial_distances. Default value is ‘path_distances’.
cmap (matplotlib colormap) – Default value is jet.

Returns:

2d matplotlib figure, axes.

tmd.view.view.trunk(tr, plane='xy', new_fig=True, subplot=False, hadd=0.0, vadd=0.0, N=10, **kwargs)¶

Generate a 2d figure of the trunk = first N segments of the tree.

Parameters:

tr (Tree) – A Tree object.
plane (str) – The plane to consider.
new_fig (bool) – Create a new figure if set to True.
subplot (bool) – Create a subplot if set to True.
hadd (float) – X shift.
vadd (float) – Y shift.
N (int) – Number of segments.

tmd.view.view.trunk3d(tr, new_fig=True, new_axes=True, subplot=False, N=10, **kwargs)¶

Generate a figure of the trunk in 3d.

Parameters:

tr (Tree) – A Tree object.
new_fig (bool) – Defines if the neuron will be plotted in the current figure (False) or in a new figure (True).
new_axes (bool) – Defines if the neuron will be plotted in the current axes (False) or in new axes (True).
subplot (matplotlib subplot value or False) – If False the default subplot 111 will be used. For any other value a matplotlib subplot will be generated. Default value is False.
N (int) – The number of segments to plot.

Keyword Arguments:

**kwargs – All keyword arguments will be passed to tmd.view.common.plot_style().

Returns:

A 3D matplotlib figure with a tree view.