Object matching module

OpFlowLab.functions.object_matching.calculate_contour(label_image)

Calculates the contour of the object

Parameters

label_imagendarray

Local image of each object

Returns

contourarray_like

List of points describing the contour of the object

OpFlowLab.functions.object_matching.calculate_distance(x, y, circular=True)

Calculates distances between consecutive points in the list

Parameters

x, yarray_like

List of x, y position to calculate the Euclidean distances from

circularbool, optional

Determine if the distance between the last and first point should be calculated

Returns

distarray_like

List of distances between consecutive points

OpFlowLab.functions.object_matching.calculate_matched_velocities(initial_properties, target_properties, reverse_pair_list, forward_index, forward_unique, forward_bincount, reverse_unique, reverse_bincount, diff_search, matched_flow_x, matched_flow_y, selected_initial_mask, selected_target_mask, label_pos=0)

Calculates the velocities between matched pairs

Parameters

initial_propertiesarray_like

List of properties for each object in the initial image

target_propertiesarray_like

List of properties for each object in the target image

reverse_pair_listarray_like

List of pairs between the target image and the warped initial image

forward_indexarray_like

Indices of the first occurrence of the pairs

forward_uniquearray_like

Label of the corresponding pair

forward_bincountarray_like

Number of times that the pair is returned

reverse_uniquearray_like

Label of the corresponding pair in the reverse time direction

reverse_bincountarray_like

Number of times that the pair is returned in the reverse time direction

diff_searchint

Difference between the largest value of the labelled image and the length of the target property. Used to reduce the number of items used in the search to find a match

matched_flow_xndarray

Calculated velocities in the x direction

matched_flow_yndarray

Calculated velocities in the y direction

selected_initial_maskarray_like

Mask to track which objects in the initial image have been paired

selected_target_maskarray_like

Mask to track which objects in the target image have been paired

label_posint, optional

Index indicating the position of the labels inside properties

Returns

matched_flow_xndarray

Calculated velocities in the x direction

matched_flow_yndarray

Calculated velocities in the y direction

selected_initial_maskarray_like

Mask to track which objects in the initial image have been paired

selected_target_maskarray_like

Mask to track which objects in the target image have been paired

OpFlowLab.functions.object_matching.estimate_affine(pt1_perimeter, pt2_perimeter)

Calculates the affine matrix needed to transform the points in the perimeter of the first object to the second object

Parameters

pt1_perimeterarray_like

List of coordinates on the perimeter of the first object

pt2_perimeterfloat

List of coordinates on the perimeter of the second object

Returns

solutionarray_like

Affine matrix used to describe the transformation between the two sets of points

OpFlowLab.functions.object_matching.fast_distance_function(centroids, pos)

Calculates pairwise Euclidean distances between two array of coordinates

Parameters

centroidsarray_like

List of centroid coordinates of shape (n,2)

posarray_like

List of position coordinates of shape (m,2)

Returns

darray_like

Pairwise distance between coordinates

OpFlowLab.functions.object_matching.get_pairs(properties, remapped_target_image, coord_pos=5)

Identifies potential pairs from a warped image based on the centroid positions

Parameters

propertiesarray_like

List of properties for each object in the image

remapped_target_imagendarray

Remapped image that has been warped with a velocity field

coord_posint, optional

Index indicating the position of the coordinates inside properties

Returns

forward_pair_listarray_like

Array containing the list of pairs

OpFlowLab.functions.object_matching.obtain_perimeter_points(local_centroid, orientation, major_axis, contour)

Obtain points on the object perimeter starting from the top most point on the long axis of the fitted ellipse

Parameters

local_centroidarray_like

Local centroid position of the object

orientationfloat

Orientation of the object

major_axisfloat

Length of the major axis of the object

contourarray_like

List of points on the contour of the object

Returns

pt_listarray_like

Sorted coordinates of the perimeter points starting from the top most point on the long axis

OpFlowLab.functions.object_matching.remove_items(properties, mask)

Removes objects from the list of properties based on a binary mask

Parameters

propertiesarray_like

List of object properties

maskarray_like

Binary mask indicating which objects should be removed

Returns

outputarray_like

Shortened list of properties with objects removed based on mask

OpFlowLab.functions.object_matching.reslice_positions(x, y, num_points=21)

Interpolates a list of x, y positions to a list of evenly spaced points

Parameters

x, yarray_like

List of x, y position to interpolate from

num_pointsint, optional

Number of points with which to generate from the list

Returns

output_x, output_yarray_like

List of interpolated points

OpFlowLab.functions.object_matching.single_object_velocity(object1_properties, object2_properties, local_centroid_pos=1, centroid_pos=2, orientation_pos=3, major_axis_pos=4, coords_pos=5, contour_pos=6)

Calculated the velocity of the object between two time frames

Parameters

object1_propertiesarray_like

List of properties for the object in time frame 1

object2_propertiesarray_like

List of properties for the object in time frame 2

local_centroid_posint, optional

Index indicating the position of the local centroid potision inside properties

centroid_posint, optional

Index indicating the position of the centroid position inside properties

orientation_posint, optional

Index indicating the position of the orientation inside properties

major_axis_posint, optional

Index indicating the position of the major axis length inside properties

coords_posint, optional

Index indicating the position of the coordinates inside properties

contour_posint, optional

Index indicating the position of the contour inside properties

Returns

pt1_coordsarray_like

Coordinates of all the pixels in the object

output_velocityarray_like

Velocity for each pixel in the object

Interpolation module Tracer module