pyfibre.utilities module

ColECM: Collagen ExtraCellular Matrix Simulation UTILITIES ROUTINE

Created by: Frank Longford Created on: 01/11/2015

Last Modified: 12/04/2018

exception pyfibre.utilities.NoiseError(noise, thresh)

Bases: Exception

exception pyfibre.utilities.NotSupportedError

Bases: Exception

message = 'Method not supported by class'

pyfibre.utilities.clear_border(image, thickness=1)

pyfibre.utilities.flatten_list(list_of_lists)

Returned a flattened version of a list of lists

pyfibre.utilities.label_set(labels, background=0)

Return a unique set of non-background values in labels

pyfibre.utilities.load_plugins()

Load PyFibre plugins via Stevedore.

pyfibre.utilities.log_time(message)

Use as a decorator around a callable to automatically record elapsed time to the log. Can be personalised with an extra string message argument

Example

>>> @log_time(name='TEST')
>>> def function(x, y):
>>>     return x * y
>>> ...
>>>
>>> function(2, 3)
6

Will produce a log message:

>>>
INFO: TOTAL TEST TIME .. s

pyfibre.utilities.logo(version)

pyfibre.utilities.matrix_split(matrix, nrows, ncols)

Split a matrix into sub-matrices

pyfibre.utilities.nanmean(array_like, weights=None)

pyfibre.utilities.numpy_remove(list1, list2)

Deletes overlapping elements of list2 from list1

pyfibre.utilities.ring(image, index, sizes, value)

pyfibre.utilities.unit_vector(vector, axis=-1)

Returns unit vector of vector