lumicks.pylake.kymotracker.kymoline.KymoLine¶

class KymoLine(time_idx, coordinate_idx, image_data=None)¶

A line on a kymograph

__init__(time_idx, coordinate_idx, image_data=None)¶: Initialize self. See help(type(self)) for accurate signature.

Methods

`__init__`(time_idx, coordinate_idx[, image_data])	Initialize self.
`append`(time_idx, coordinate_idx)	Append time, coordinate pair to the KymoLine
`extrapolate`(forward, n_estimate, …)	This function linearly extrapolates a track segment towards positive time.
`in_rect`(rect)	Check whether any point of this KymoLine falls in the rect given in rect.
`interpolate`()	Interpolate Kymoline to whole pixel values
`sample_from_image`(num_pixels[, reduce])	Sample from image using coordinates from this KymoLine.
`with_offset`(time_offset, coordinate_offset)	Returns an offset version of the KymoLine

Attributes

`coordinate_idx`
`image_data`
`time_idx`

append(time_idx, coordinate_idx)¶: Append time, coordinate pair to the KymoLine

extrapolate(forward, n_estimate, extrapolation_length)¶

This function linearly extrapolates a track segment towards positive time.

Parameters:	forward: boolean extrapolate forward (True) or backward in time (False) n_estimate: int Number of points to use for linear regression. extrapolation_length: float How far to extrapolate.

in_rect(rect)¶

Check whether any point of this KymoLine falls in the rect given in rect.

Parameters:	rect : Tuple[Tuple[float, float], Tuple[float, float]] Only perform tracking over a subset of the image. Pixel coordinates should be given as: ((min_time, min_coord), (max_time, max_coord)).

interpolate()¶: Interpolate Kymoline to whole pixel values

sample_from_image(num_pixels, reduce=<function sum>)¶

Sample from image using coordinates from this KymoLine.

This function samples data from the image given in data based on the points in this KymoLine. It samples from [time, position - num_pixels : position + num_pixels + 1] and then applies the function sum.

Parameters:	num_pixels : int Number of pixels in either direction to include in the sample reduce : callable Function evaluated on the sample. (Default: np.sum which produces sum of photon counts).

with_offset(time_offset, coordinate_offset)¶: Returns an offset version of the KymoLine