crikit.utils package

Submodules

crikit.utils.breadcrumb module

crikit.utils.datacheck module

Functions to check and (if needed) convert input variables

Created on Sat Jun 18 00:16:27 2016

@author: chc

crikit.utils.general module

General utilities

expand_1d_to_ndim_data : Match 1D data array dimensionality to that of another array

expand_1d_to_ndim : Expand 1D data array dimensionality to ndim

find_nearestGiven a vector and a value, find the index and value

of the closest match

padWrapper around numpy.pad that also returns a window defining the

original signal

Notes

crikit.utils.general.arange_nonzero(start, stop, dtype=<class 'float'>)[source]

Similar to numpy arange but only returns non-zero elements

crikit.utils.general.expand_1d_to_ndim(data, ndim)[source]

Make 1D array into ndim dimensions

crikit.utils.general.expand_1d_to_ndim_data(data, data_to_match)[source]

Make 1D data array equal in dimensions to data_to_match

crikit.utils.general.find_nearest(np_vec, to_find=0)[source]

Given a vector and a value (or list/vector of values), find the index and value of the closest match

Parameters
  • np_vec (numpy.ndarray) – Numpy array (list) of values

  • to_find (int, float, numpy.ndarray, or list) –

Returns

out – Closest value (nearest_value) and index (index)

Return type

tuple (nearest_value(s), index(es))

crikit.utils.general.lin_from_row_col(row, col, sh)[source]

Convert a col and row counter to 1D linear count

crikit.utils.general.mean_nd_to_1d(data, axis=- 1)[source]

Take the mean of an nd array, except axis, returning a 1D array

crikit.utils.general.np_fcn_nd_to_1d(fcn, data, axis=- 1)[source]

Take in an n-dimensional array and return a 1D version operated on by fcn. Works with many numpy functions that can take an “axis” parameter

crikit.utils.general.pad(y, pad_width, mode)[source]

Pad array with either constants or edge values.

Note: For N-D arrays, pads the -1 axis

Parameters
  • y (ndarray) – Input array

  • pad_width (int) – Size of padding on each side of y

  • mode (str) – ‘constant’ (0), ‘edge’ currently accepted

Returns

Padded array and window. Window defines the region of the original signal

Return type

y_pad, window

crikit.utils.general.pad_dual(y, edge_pad_width, constant_pad_width)[source]

Pad array with edge values followed by constant 0’s.

Note: For N-D arrays, pads the -1 axis

Parameters
  • y (ndarray) – Input array

  • edge_pad_width (int) – Size of edge-value padding on each side of y

  • constant_pad_width (int) – Size of 0-padding on each side of y after edge-value padding

Returns

Padded array and window. Window defines the region of the original signal

Return type

y_pad, window

crikit.utils.general.pad_edge_mean(y, pad_width, n_edge=1, axis=- 1)[source]

Pad data y with edge-values or near-edge mean values along axis

Parameters
  • y (ndarray) – Input array

  • pad_width (int) – Size of padding on each side of y

  • n_edge (int) – Number of edge points to average for the pad value

  • axis (int) – Axis to pad

Returns

  • (y_pad, window)

  • y_pad (ndarray) – Padded y

  • window (ndarray (1D)) – Mask with 0’s for pad regions, 1’s for original size

crikit.utils.general.row_col_from_lin(ct, sh)[source]

Convert a 1D counter into a col and row counter

crikit.utils.general.std_nd_to_1d(data, axis=- 1)[source]

Take the mean of an nd array, except axis, returning a 1D array

crikit.utils.roi module

Created on Wed Jun 15 23:33:41 2016

@author: chc

crikit.utils.roi.pts_in_path(path)[source]

Return points (pixels) that fall within path (but not on boundary)

crikit.utils.roi.pts_to_verts(xvec, yvec)[source]

Convert points to vertices, i.e., convert from 2 1D arrays (or list) of x- and y-coordinates to a list-of-lists of [x,y] pairs

crikit.utils.roi.verts_to_path(verts, isclosed=True)[source]

Convert vertices to paths

crikit.utils.roi.verts_to_points_in_roi(verts)[source]

Vertice list defining ROI in, points within returned.

Module contents