analyse module

Package for dealing with analysis methods of the ampObject and generating reports Copyright: Joshua Steer 2020, Joshua.Steer@soton.ac.uk

CMapOut(amp, colors)

Colour Map with 4 views (copied Josh’s code)

MeasurementsOut(amp, pos)

Calculates perimeter of limb/cast at intervals from mid-patella to the end of stump Takes position of mid-patella (x,y,z) coordinates as input Also creates images of limb views and graphs of CSA/Widths, which are used in the PDF. Calls the function responsible for adding the information to the PDF template. TODO: Split this into functions for each part i.e. Volume measure, CSA, widths

Return type

The path to the output file

calc_csa(polys)

Calculate the cross sectional area of each polygon from the slicing of the AmpObject

Parameters

polys (list) – A list of numpy arrays, each array contains the vertices of the polygon generated from the slice. Generate using ampscan.analyse.create_slices()

Returns

csa – Returns the cross-sectional area of the limb in mm^2 along the axis

Return type

array_like

calc_perimeter(polys)

Calculate the perimeter of each polygon from the slicing of the AmpObject

Parameters

polys (list) – A list of numpy arrays, each array contains the vertices of the polygon generated from the slice. Generate using ampscan.analyse.create_slices()

Returns

perimeter – Returns the perimeter of the limb in mm along the axis

Return type

array_like

calc_volume_closed(amp_in, return_closed=False)

Calculates the volume of a closed surface. If the surface is not closed the algorithm fills in the holes using a simple hole filling algorithm, the surface without holes can be accessed if return_closed is set to True.

Parameters

  • amp (AmpObject) – The AmpObject to analyse

  • return_closed (bool, default False) – Indicate whether to return the shape with holes filled in

Returns

  • vol (float) – The volume of the AmpObject

  • amp (AmpObject) – If return_closed is True, then the closed shape is returned

calc_widths(polys)

Calculate the coronal and sagittal widths of each polygon from the slicing of the AmpObject

Assumes that coronal width corresponds with the x-axis

Parameters

polys (list) – A list of numpy arrays, each array contains the vertices of the polygon generated from the slice. Generate using ampscan.analyse.create_slices()

Returns

  • cor_width (array_like) – Returns the coronal width in mm along the axis

  • sag_width (array_like) – Returns the sagittal width in mm along the axis

create_slices(amp, *args, typ='slices', axis=2, order=True)

Generate polygons from planar slices through the AmpObject. The slices are either defined as a list of positions in some axis

Parameters

  • amp (AmpObject) – The AmpObject to analyse

  • slices (array_like) – An array of the slice positions to take in the specified axis

  • limits (array_like) – The limits of the slices, either in real world units or normalised depending on that specified in typ

  • intervals (float) – The distance between slices, use in conjunction with

  • typ (str, 'slices', 'real_intervals', 'norm_intervals') – The height of the slice planes

  • axis (int, default 2) – The index of the axis to take the slices along

Returns

polys – A list of numpy arrays, each array contains the vertices of the polygon generated from the slice

Return type

list

Examples

>>> amp = AmpObject(filename)
>>> polys = create_slices(amp, [0.05, 0.95], 0.01, typ='norm_intervals', axis=2)
>>> polys = create_slices(amp, [-150, -100, -50, 0], typ='slices', axis=2)
>>> polys = create_slices(amp, [-150, 0], 10, typ='real_intervals', axis=2)
est_volume(polys)

Estimate the volume of the limb using bounds of the slices

Parameters

polys (list) – A list of numpy arrays, each array contains the vertices of the polygon generated from the slice. Generate using ampscan.analyse.create_slices()

Returns

Volume – Returns the estimated volume of the limb in mm^3 along the axis

Return type

float

logEuPath(arr)

Calculate the eularian path for an array of edges so the vertices all connect

planeEdgeIntersect_cy(arr, plane, axisInd)

Calculate the intersection between a an array of edges and a plane

Parameters

  • edges (array_like) – The edge array which have been calculated to cross the plane

  • plane (float) – The height of the plane

  • axis (int, default 2) – The index of the axis of the slice

Returns

intersectPoints – The intersection points between the edges and the plane

Return type

ndarray

planeEdgeintersect(edges, plane, axis=2)

Calculate the intersection between a an array of edges and a plane

Parameters

  • edges (array_like) – The edge array which have been calculated to cross the plane

  • plane (float) – The height of the plane

  • axis (int, default 2) – The index of the axis of the slice

Returns

intersectPoints – The intersection points between the edges and the plane

Return type

ndarray

plot_slices(amp, axis=2, slWidth=10)

Generate a mpl figure with information about the AmpObject

Top Left - Slices Top Right - Change in cross sectional area through slices Bottom Left - Rendering of shape Bottom Right - Rendering of shape with values

TODO: Split this up so each figure is it’s own function, top level function to tailor figure to user

Parameters

  • axis (int, default 2) – Axis along which to take slices

  • slWidth (float, default 10) – Distance between slices

Returns

  • fig (mpl figure) – The mpl figure generated by the function

  • ax (tuple) – A tuple of axes used for each subplot in the figure

visualise_slices(amp)

Create an mpl figure with the 3D rendering, slices, slice height and cross sectional area