tmd.Topology.analysis¶

TMD Topology analysis algorithms implementation.

Functions

`barcode_bin_centers`(ph[, num_bins, min_bin, ...])	Calculate how many barcode lines are found in each bin.
`closest_ph`(ph_list, target_extent[, method])	Get index of the persistent homology in the ph_list closest to a target extent.
`collapse`(ph_list)	Collapses a list of ph diagrams into a single instance for plotting.
`distance_horizontal`(ph1, ph2[, normalized, bins])	Calculate distance between two ph diagrams.
`distance_horizontal_unnormed`(ph1, ph2[, ...])	Calculate unnormed distance between two ph diagrams.
`distance_stepped`(ph1, ph2[, order])	Calculate step distance difference between two ph.
`find_apical_point_distance`(ph)	Finds the apical distance (measured from the soma) based on the variation of the barcode.
`find_apical_point_distance_smoothed`(ph[, ...])	Finds the apical distance (measured from the soma) based on the variation of the barcode.
`get_average_persistence_image`(ph_list[, ...])	Plot the gaussian kernel of a population as an average of the ph diagrams that are given.
`get_image_add_data`(Z1, Z2[, normalized])	Get the sum of two images from the gaussian kernel plotting function.
`histogram_horizontal`(ph[, num_bins, ...])	Calculate how many barcode lines are found in each bin.
`histogram_stepped`(ph1)	Calculate step distance of ph data.
`load_file`(filename[, delimiter])	Load PH file in a np.array.
`matching_munkress_modified`(p1, p2[, use_diag])	Find matching components and the corresponding distance between the two input diagrams.
`sort_ph`(ph)	Sorts barcode according to decreasing length of bars.

tmd.Topology.analysis.barcode_bin_centers(ph, num_bins=100, min_bin=None, max_bin=None)¶

Calculate how many barcode lines are found in each bin.

Returns the bin centers and the number of bars that fall within a bin.

tmd.Topology.analysis.closest_ph(ph_list, target_extent, method='from_above')¶

Get index of the persistent homology in the ph_list closest to a target extent.

For each ph the maximum extent is computed and compared to the target_extent according to the selected method:

from_above: smallest maximum extent that is greater or equal than target_extent.
from_below: biggest maximum extent that is smaller or equal than target_extent.
nearest: closest by absolute value.

tmd.Topology.analysis.collapse(ph_list)¶: Collapses a list of ph diagrams into a single instance for plotting.

tmd.Topology.analysis.distance_horizontal(ph1, ph2, normalized=True, bins=100)¶

Calculate distance between two ph diagrams.

Distance definition: TODO

tmd.Topology.analysis.distance_horizontal_unnormed(ph1, ph2, normalized=True, bins=100)¶: Calculate unnormed distance between two ph diagrams.

tmd.Topology.analysis.distance_stepped(ph1, ph2, order=1)¶: Calculate step distance difference between two ph.

tmd.Topology.analysis.find_apical_point_distance(ph)¶: Finds the apical distance (measured from the soma) based on the variation of the barcode.

tmd.Topology.analysis.find_apical_point_distance_smoothed(ph, threshold=0.1)¶

Finds the apical distance (measured from the soma) based on the variation of the barcode.

This algorithm always computes a distance, even if there is no obvious apical point. The threshold corresponds to percent of minimum derivative variation that is used to select the minima.

tmd.Topology.analysis.get_average_persistence_image(ph_list, xlim=None, ylim=None, norm_factor=None, weighted=False)¶: Plot the gaussian kernel of a population as an average of the ph diagrams that are given.

tmd.Topology.analysis.get_image_add_data(Z1, Z2, normalized=True)¶: Get the sum of two images from the gaussian kernel plotting function.

tmd.Topology.analysis.histogram_horizontal(ph, num_bins=100, min_bin=None, max_bin=None)¶: Calculate how many barcode lines are found in each bin.

tmd.Topology.analysis.histogram_stepped(ph1)¶: Calculate step distance of ph data.

tmd.Topology.analysis.load_file(filename, delimiter=' ')¶: Load PH file in a np.array.

tmd.Topology.analysis.matching_munkress_modified(p1, p2, use_diag=True)¶: Find matching components and the corresponding distance between the two input diagrams.

tmd.Topology.analysis.sort_ph(ph)¶: Sorts barcode according to decreasing length of bars.