tmd.view.view¶
Module for viewing neuronal morphologies.
Functions
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Generate a 2d figure of the neuron, that contains a soma and a list of trees. |
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Generate a figure of the neuron, that contains a soma and a list of trees. |
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View the neuron morphologies of a population as a density cloud. |
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Generate a 2d figure of the neuron that contains a soma and a list of trees. |
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Generate a figure of the neuron, that contains a soma and a list of trees. |
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Generate a polar plot of a neuron or population. |
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Generate a 2d figure of the population, that contains a soma and a list of trees. |
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Generate a figure of the population, that contains the pop somata and a set of list of trees. |
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Generate a 2d figure of the soma. |
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Generate a 3d figure of the soma. |
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Generate a 2d figure of the tree. |
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Generate a figure of the tree in 3d. |
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Generates a two panel figure with color-coded branches, bars. |
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Generates a four panel figure with color-coded branches, bars. |
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Generate a 2d figure of the trunk = first N segments of the tree. |
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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()
andtmd.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()
andtmd.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.
- 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.
- 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:
- 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:
- 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.
- 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.