morph_tool.converter¶
A morphology converter that tries to keep the soma surface equal.
Functions
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Choose a target soma type based on the given output extension. |
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This follows the function in lib/hoc/import3d/import3d_gui.hoc. |
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Convert the simple contour into a cylinder. |
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Python implementation of NEURON code lib/hoc/import3d/import3d_sec.hoc. |
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Run the appropriate converter. |
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Convert the soma of the given neuron to the required soma type. |
Convert the cylinder into a simple contour that represents the same sphere. |
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We convert the cylinder into a circular contour that represents the same sphere. |
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Convert from ASC/H5. |
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Convert to SWC. |
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Circular permutation of the points. |
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Keep only points that make path convex. |
Single point soma to contour soma. |
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Surface preserving cylindrical soma to a single point sphere. |
- morph_tool.converter.choose_target_soma_type(neuron, output_ext)¶
Choose a target soma type based on the given output extension.
- morph_tool.converter.contour2centroid(mean, points)¶
This follows the function in lib/hoc/import3d/import3d_gui.hoc.
Most of the comments are from there, so if you want to follow along, it should break up the function the same way.
- morph_tool.converter.contour_to_cylinders(neuron)¶
Convert the simple contour into a cylinder.
- morph_tool.converter.contourcenter(xyz)¶
Python implementation of NEURON code lib/hoc/import3d/import3d_sec.hoc.
- morph_tool.converter.convert(input_file, output_file, recenter=False, nrn_order=False, single_point_soma=False, sanitize=False, ensure_NRN_area=False)¶
Run the appropriate converter.
- Parameters:
input_file (str) – path to input file
output_file (str) – path to output file
recenter (bool) – whether to recenter the morphology based on the
soma (center of gravity of the) –
nrn_order (bool) – whether to traverse the neuron in the NEURON fashion
single_point_soma (bool) – For SWC only
sanitize (bool) – whether to sanitize the morphology
ensure_NRN_area (bool) – to ensure area is preserved in NEURON from swc point soma
- morph_tool.converter.convert_soma(neuron, output_ext, ensure_NRN_area=False)¶
Convert the soma of the given neuron to the required soma type.
- morph_tool.converter.cylinder_stack_to_cylindrical_contour(neuron)¶
Convert the cylinder into a simple contour that represents the same sphere.
- morph_tool.converter.cylinder_to_cylindrical_contour(neuron)¶
We convert the cylinder into a circular contour that represents the same sphere.
- morph_tool.converter.from_h5_or_asc(neuron, output_ext, ensure_NRN_area=False)¶
Convert from ASC/H5.
- morph_tool.converter.from_swc(neuron, output_ext, ensure_NRN_area=False)¶
Convert to SWC.
- morph_tool.converter.get_sides(points, major, minor)¶
Circular permutation of the points.
So that the point with the largest coordinate along the major axis becomes the last point
tobj = major.c.mul(d.x[i])
###### unneeded? line 1191
- morph_tool.converter.make_convex(sides, rads)¶
Keep only points that make path convex.
- morph_tool.converter.single_point_sphere_to_circular_contour(neuron, ensure_NRN_area=False)¶
Single point soma to contour soma.
Transform a single point soma that represents a sphere into a circular contour that represents the same sphere.
With ensure_NRN_area=True, we perform a search on radius to ensure an equivalent soma surface area, as measured by NEURON with morph_tool.neuron_surface.get_NEURON_surface.
- morph_tool.converter.soma_to_single_point(soma)¶
Surface preserving cylindrical soma to a single point sphere.