Module PdmModule.utils.distances

from scipy.spatial.distance import cdist
from dtaidistance import dtw
from sklearn.metrics.pairwise import rbf_kernel
import numpy as np
# calculate all pair distances between two dataframes a and b
def calculate_distance_many_to_many(  a, b, metric):
    distances = []
    if metric == 'dtw':
        for s1 in a.values:
            distances.append([])
            for s2 in b.values:
                ddist = dtw.distance_fast(s1, s2)
                distances[-1].append(ddist)
    elif 'rbf_kernel' in metric:
        if metric == "rbf_kernel":
            gamma = 0.5
        else:
            gamma = float(metric.split("kernel")[-1])
        distances = 1 - rbf_kernel(a.values, b.values, gamma=gamma)
        distances = distances
    else:
        distances = cdist(a.values, b.values, metric)
    return distances

# calculate distance from point to all profile points
def calculate_distance_many_to_one(  a, b, metric):
    distances = []
    if metric == 'dtw':
        for s1 in a.values:
            ddist = dtw.distance_fast(s1, b)
            distances.append(ddist)
    elif 'rbf_kernel' in metric:
        if metric == "rbf_kernel":
            gamma = 0.5
        else:
            gamma = float(metric.split("kernel")[-1])
        distances = 1 - rbf_kernel(b.reshape(1, -1), a.values, gamma=gamma)
    else:
        distances = cdist(b.reshape(1, -1), a, metric)[0]
    return distances