Module src.ref.tracks_neighbor_features

Functions

def find_clathrin_neighbors(tracks, tracks_by_frame, distance, norm_ord)

function that populates the "neighbors" attribute of all clathrin signals

Input: tracks, tracks_by_frame: output of read_tracks distance: float norm_ord: np.inf or int this will be used for the ord argument of np.linalg.norm np.inf corresponds to square patches

Output

list of tracks, for each clathrin signal in each track, this computes all neighbors of that signal within distance (in norm_ord norm) smaller than elements in the "distance" argument

Expand source code

def find_clathrin_neighbors(tracks, tracks_by_frame, distance, norm_ord):
    
    """
    function that populates the "neighbors" attribute of all clathrin signals
    
    Input: 
        tracks, tracks_by_frame: output of read_tracks
        distance: float
        norm_ord: np.inf or int
            this will be used for the ord argument of np.linalg.norm
            np.inf corresponds to square patches
            
    Output:
        list of tracks, for each clathrin signal in each track, this computes all neighbors of that signal within distance
        (in norm_ord norm) smaller than elements in the "distance" argument
    """
    
    distance = [dist for dist in distance if dist not in tracks[0].clathrin_signals[0].neighbors]
    for track in tracks:
        for signal in track.clathrin_signals:
            for dist in distance:
                signal.neighbors[dist] = []
            for ss in tracks_by_frame[signal.frame]:
                ds = np.linalg.norm(np.array((signal.x - ss['cla'].x, signal.y - ss['cla'].y)), 
                                    ord=norm_ord)
                for dist in distance:
                    if ds <= dist and ds > 0.01:
                        signal.neighbors[dist].append(ss['cla'])
    return tracks