ui Package

class MayaViRenderer(morph=None, morphs=None, scalefactor=1.0)[source]

Bases: object

Display a morphology using the MayaVi interface

__init__(morph=None, morphs=None, scalefactor=1.0)[source]

classmethod dummy_test()[source]

Does not plot neuron - code copied from enthought website and only used to make sure that MayaVi is install propery for testing purposes.

make_video()[source]

Slightly more complex plotting - plot each section as a cylinders.

showSimpleCylinders()[source]

Slightly more complex plotting - plot each section as a cylinders.

show_as_points()[source]

Very simple plotting for speed with complex neurons - plot each section as a sphere about its endpoint. Only works for neurons with very small section lengths compared to radii

show_as_points_interpolated(lToRRatio=2.0)[source]

Draws the points as spheres, but also interpolates inbetween the points, so the structure looks more ‘whole’

class MatPlotLibViewer(morph, use_pca=True, fig_kwargs=None)[source]

Bases: object

Plot Projections of a morphology onto XY, XZ, and YZ axes.

__init__(morph, use_pca=True, fig_kwargs=None)[source]

_figure_labels = {0: ('X', 'Y'), 1: ('Z', 'Y'), 2: ('X', 'Z')}

_figure_positions = {0: 221, 1: 222, 2: 223}

_figure_projections = {0: <Mock object at 0x7f0ab1d4b9d0>, 1: <Mock object at 0x7f0ab1d4ba10>, 2: <Mock object at 0x7f0ab1d4ba90>}

_figure_titles = {0: 'View From Above', 1: 'View From Side', 2: 'View From Front'}

_projMatXY

_projMatXZ

_projMatYZ

build_draw_sub_plot(rotatedSectionDict, fig, i, plotLims)[source]

build_plot(usePCA)[source]

plot_views = [0, 1, 2]

matplotlibviewer Module

class MatPlotLibViewer(morph, use_pca=True, fig_kwargs=None)[source]

Bases: object

Plot Projections of a morphology onto XY, XZ, and YZ axes.

__init__(morph, use_pca=True, fig_kwargs=None)[source]

_figure_labels = {0: ('X', 'Y'), 1: ('Z', 'Y'), 2: ('X', 'Z')}

_figure_positions = {0: 221, 1: 222, 2: 223}

_figure_projections = {0: <Mock object at 0x7f0ab1d4b9d0>, 1: <Mock object at 0x7f0ab1d4ba10>, 2: <Mock object at 0x7f0ab1d4ba90>}

_figure_titles = {0: 'View From Above', 1: 'View From Side', 2: 'View From Front'}

_projMatXY

_projMatXZ

_projMatYZ

build_draw_sub_plot(rotatedSectionDict, fig, i, plotLims)[source]

build_plot(usePCA)[source]

plot_views = [0, 1, 2]

mayavirenderer Module

class MayaViRenderer(morph=None, morphs=None, scalefactor=1.0)[source]

Bases: object

Display a morphology using the MayaVi interface

__init__(morph=None, morphs=None, scalefactor=1.0)[source]

classmethod dummy_test()[source]

Does not plot neuron - code copied from enthought website and only used to make sure that MayaVi is install propery for testing purposes.

make_video()[source]

Slightly more complex plotting - plot each section as a cylinders.

showSimpleCylinders()[source]

Slightly more complex plotting - plot each section as a cylinders.

show_as_points()[source]

Very simple plotting for speed with complex neurons - plot each section as a sphere about its endpoint. Only works for neurons with very small section lengths compared to radii

show_as_points_interpolated(lToRRatio=2.0)[source]

Draws the points as spheres, but also interpolates inbetween the points, so the structure looks more ‘whole’

morphmaths Module

class MorphologyForRenderingOperator(morph, usePCA=True)[source]

Bases: morphforge.morphology.ui.morphmaths.PointOperator

__init__(morph, usePCA=True)[source]

class MorphologyMeanCenterer(morph, PtSrc=None)[source]

Bases: morphforge.morphology.ui.morphmaths.Pointtranslater

__init__(morph, PtSrc=None)[source]

class MorphologyPCARotator(morph)[source]

Bases: morphforge.morphology.ui.morphmaths.PointRotator

__init__(morph)[source]

class PCAAxes(morph)[source]

Bases: object

__init__(morph)[source]

class PointOperator(operations=None)[source]

Bases: object

__call__(pt)[source]

__init__(operations=None)[source]

class PointRotator(transMatrix)[source]

Bases: object

__call__(pt)[source]

__init__(transMatrix)[source]

class Pointtranslater(offset)[source]

Bases: object

__call__(pt)[source]

__init__(offset)[source]

_pca(X)[source]