py-neuromodulation 0.0.4__py3-none-any.whl → 0.0.5__py3-none-any.whl

py_neuromodulation/nm_stats.py

@@ -1,480 +1,464 @@
-import random
-import copy
-
-import matplotlib.pyplot as plt
-
-# from numba import njit
-import numpy as np
-import pandas as pd
-import scipy.stats as stats
-
-
-from skimage import measure
-from sklearn.linear_model import LinearRegression
-from sklearn.model_selection import KFold
-import statsmodels.api as sm
-
-
-def fitlm(x, y):
-    return sm.OLS(y, sm.add_constant(x)).fit()
-
-
-def fitlm_kfold(x, y, kfold_splits=5):
-    model = LinearRegression()
-    if isinstance(x, type(np.array([]))) or isinstance(x, type([])):
-        x = pd.DataFrame(x)
-    if isinstance(y, type(np.array([]))) or isinstance(y, type([])):
-        y = pd.DataFrame(y)
-    scores, coeffs = [], np.zeros(x.shape[1])
-    kfold = KFold(n_splits=kfold_splits, shuffle=True, random_state=42)
-    for i, (train, test) in enumerate(kfold.split(x, y)):
-        model.fit(x.iloc[train, :], y.iloc[train, :])
-        score = model.score(x.iloc[test, :], y.iloc[test, :])
-        # mdl = fitlm(np.squeeze(y.iloc[test,:].transpose()), np.squeeze(model.predict(x.iloc[test, :])))
-        scores.append(score)
-        coeffs = np.vstack((coeffs, model.coef_))
-    coeffs = list(np.delete(coeffs, 0))
-    return scores, coeffs, model, ["scores", "coeffs", "model"]
-
-
-def zscore(data):
-    return (data - data.mean()) / data.std()
-
-
-def permutationTestSpearmansRho(x, y, plot_distr=True, x_unit=None, p=5000):
-    """
-    Calculate permutation test for multiple repetitions of Spearmans Rho
-    https://towardsdatascience.com/how-to-assess-statistical-significance-in-your-data-with-permutation-tests-8bb925b2113d
-
-    x (np array) : first distibution e.g. R^2
-    y (np array) : second distribution e.g. UPDRS
-    plot_distr (boolean) : if True: permutation histplot and ground truth will be
-    plotted
-    x_unit (str) : histplot xlabel
-    p (int): number of permutations
-
-    returns:
-    gT (float) : estimated ground truth, here spearman's rho
-    p (float) : p value of permutation test
-    """
-
-    # compute ground truth difference
-    gT = stats.spearmanr(x, y)[0]
-    #
-    pV = np.array((x, y))
-    # Initialize permutation:
-    pD = []
-    # Permutation loop:
-    args_order = np.arange(0, pV.shape[1], 1)
-    args_order_2 = np.arange(0, pV.shape[1], 1)
-    for i in range(0, p):
-        # Shuffle the data:
-        random.shuffle(args_order)
-        random.shuffle(args_order_2)
-        # Compute permuted absolute difference of your two sampled
-        # distributions and store it in pD:
-        pD.append(stats.spearmanr(pV[0, args_order], pV[1, args_order_2])[0])
-
-    # calculate p value
-    if gT < 0:
-        p_val = len(np.where(pD <= gT)[0]) / p
-    else:
-        p_val = len(np.where(pD >= gT)[0]) / p
-
-    if plot_distr is True:
-        plt.hist(pD, bins=30, label="permutation results")
-        plt.axvline(gT, color="orange", label="ground truth")
-        plt.title("ground truth " + x_unit + "=" + str(gT) + " p=" + str(p_val))
-        plt.xlabel(x_unit)
-        plt.legend()
-        plt.show()
-    return gT, p_val
-
-
-def permutationTest(x, y, plot_distr=True, x_unit=None, p=5000):
-    """
-    Calculate permutation test
-    https://towardsdatascience.com/how-to-assess-statistical-significance-in-your-data-with-permutation-tests-8bb925b2113d
-
-    x (np array) : first distr.
-    y (np array) : first distr.
-    plot_distr (boolean) : if True: plot permutation histplot and ground truth
-    x_unit (str) : histplot xlabel
-    p (int): number of permutations
-
-    returns:
-    gT (float) : estimated ground truth, here absolute difference of
-    distribution means
-    p (float) : p value of permutation test
-
-    """
-    # Compute ground truth difference
-    gT = np.abs(np.average(x) - np.average(y))
-
-    pV = np.concatenate((x, y), axis=0)
-    pS = copy.copy(pV)
-    # Initialize permutation:
-    pD = []
-    # Permutation loop:
-    for i in range(0, p):
-        # Shuffle the data:
-        random.shuffle(pS)
-        # Compute permuted absolute difference of your two sampled
-        # distributions and store it in pD:
-        pD.append(
-            np.abs(
-                np.average(pS[0 : int(len(pS) / 2)])
-                - np.average(pS[int(len(pS) / 2) :])
-            )
-        )
-
-    # Calculate p-value
-    if gT < 0:
-        p_val = len(np.where(pD <= gT)[0]) / p
-    else:
-        p_val = len(np.where(pD >= gT)[0]) / p
-
-    if plot_distr is True:
-        plt.hist(pD, bins=30, label="permutation results")
-        plt.axvline(gT, color="orange", label="ground truth")
-        plt.title("ground truth " + x_unit + "=" + str(gT) + " p=" + str(p_val))
-        plt.xlabel(x_unit)
-        plt.legend()
-        plt.show()
-    return gT, p_val
-
-
-def permutationTest_relative(x, y, plot_distr=True, x_unit=None, p=5000):
-    """
-    Calculate permutation test
-    https://towardsdatascience.com/how-to-assess-statistical-significance-in-your-data-with-permutation-tests-8bb925b2113d
-
-    x (np array) : first distr.
-    y (np array) : first distr.
-    plot_distr (boolean) : if True: plot permutation histplot and ground truth
-    x_unit (str) : histplot xlabel
-    p (int): number of permutations
-
-    returns:
-    gT (float) : estimated ground truth, here absolute difference of
-    distribution means
-    p (float) : p value of permutation test
-
-    """
-    gT = np.abs(np.average(x) - np.average(y))
-    pD = []
-    for i in range(0, p):
-        l_ = []
-        for i in range(x.shape[0]):
-            if random.randint(0, 1) == 1:
-                l_.append((x[i], y[i]))
-            else:
-                l_.append((y[i], x[i]))
-        pD.append(
-            np.abs(
-                np.average(np.array(l_)[:, 0]) - np.average(np.array(l_)[:, 1])
-            )
-        )
-    if gT < 0:
-        p_val = len(np.where(pD <= gT)[0]) / p
-    else:
-        p_val = len(np.where(pD >= gT)[0]) / p
-
-    if plot_distr is True:
-        plt.hist(pD, bins=30, label="permutation results")
-        plt.axvline(gT, color="orange", label="ground truth")
-        plt.title("ground truth " + x_unit + "=" + str(gT) + " p=" + str(p_val))
-        plt.xlabel(x_unit)
-        plt.legend()
-        plt.show()
-
-    return gT, p_val
-
-
-# @njit
-def permutation_numba_onesample(x, y, n_perm, two_tailed=True):
-    """Perform permutation test with one-sample distribution.
-
-    Parameters
-    ----------
-    x : array_like
-        First distribution
-    y : int or float
-        Baseline against which to check for statistical significane
-    n_perm : int
-        Number of permutations
-    two_tailed : bool, default: True
-        Set to False if you would like to perform a one-sampled permutation
-        test, else True
-    two_tailed : bool, default: True
-        Set to False if you would like to perform a one-tailed permutation
-        test, else True
-
-    Returns
-    -------
-    float
-        Estimated difference of distribution from baseline
-    float
-        P-value of permutation test
-    """
-    if two_tailed is True:
-        zeroed = x - y
-        z = np.abs(np.mean(zeroed))
-        p = np.empty(n_perm)
-        # Run the simulation n_perm times
-        for i in np.arange(n_perm):
-            sign = np.random.choice(
-                a=np.array([-1.0, 1.0]), size=len(x), replace=True
-            )
-            p[i] = np.abs(np.mean(zeroed * sign))
-    else:
-        zeroed = x - y
-        z = np.mean(zeroed)
-        p = np.empty(n_perm)
-        # Run the simulation n_perm times
-        for i in np.arange(n_perm):
-            sign = np.random.choice(
-                a=np.array([-1.0, 1.0]), size=len(x), replace=True
-            )
-            p[i] = np.mean(zeroed * sign)
-        # Return p-value
-    return z, (np.sum(p >= z)) / n_perm
-
-
-# @njit
-def permutation_numba_twosample(x, y, n_perm, two_tailed=True):
-    """Perform permutation test.
-
-    Parameters
-    ----------
-    x : array_like
-        First distribution
-    y : array_like
-        Second distribution
-    n_perm : int
-        Number of permutations
-    two_tailed : bool, default: True
-        Set to False if you would like to perform a one-sampled permutation
-        test, else True
-    two_tailed : bool, default: True
-        Set to False if you would like to perform a one-tailed permutation
-        test, else True
-
-    Returns
-    -------
-    float
-        Estimated difference of distribution means
-    float
-        P-value of permutation test
-    """
-    if two_tailed is True:
-        z = np.abs(np.mean(x) - np.mean(y))
-        pS = np.concatenate((x, y), axis=0)
-        half = int(len(pS) / 2)
-        p = np.empty(n_perm)
-        # Run the simulation n_perm times
-        for i in np.arange(0, n_perm):
-            # Shuffle the data
-            np.random.shuffle(pS)
-            # Compute permuted absolute difference of the two sampled
-            # distributions
-            p[i] = np.abs(np.mean(pS[:half]) - np.mean(pS[half:]))
-    else:
-        z = np.mean(x) - np.mean(y)
-        pS = np.concatenate((x, y), axis=0)
-        half = int(len(pS) / 2)
-        p = np.empty(n_perm)
-        # Run the simulation n_perm times
-        for i in np.arange(0, n_perm):
-            # Shuffle the data
-            np.random.shuffle(pS)
-            # Compute permuted absolute difference of the two sampled
-            # distributions
-            p[i] = np.mean(pS[:half]) - np.mean(pS[half:])
-    return z, (np.sum(p >= z)) / n_perm
-
-
-def cluster_wise_p_val_correction(p_arr, p_sig=0.05, num_permutations=10000):
-    """Obtain cluster-wise corrected p values.
-
-    Based on: https://github.com/neuromodulation/wjn_toolbox/blob/4745557040ad26f3b8498ca5d0c5d5dece2d3ba1/mypcluster.m
-    https://garstats.wordpress.com/2018/09/06/cluster/
-
-    Arguments
-    ---------
-    p_arr (np.array) : ndim, can be time series or image
-    p_sig (float) : significance level
-    num_permutations (int) : no. of random permutations of cluster comparisons
-
-    Returns
-    -------
-    p (float) : significance level of highest cluster
-    p_min_index : indices of significant samples
-    """
-    labels, num_clusters = measure.label(p_arr <= p_sig, return_num=True)
-
-    # loop through clusters of p_val series or image
-    index_cluster = {}
-    p_cluster_sum = np.zeros(num_clusters)
-    for cluster_i in np.arange(num_clusters):
-        # first cluster is assigned to be 1 from measure.label
-        index_cluster[cluster_i] = np.where(labels == cluster_i + 1)[0]
-        p_cluster_sum[cluster_i] = np.sum(
-            np.array(1 - p_arr)[index_cluster[cluster_i]]
-        )
-    # p_min corresponds to the most unlikely cluster
-    p_min = np.max(p_cluster_sum)
-
-    p_min_index = index_cluster[np.argmax(p_cluster_sum)]
-
-    # loop through random permutation cycles
-    r_per_arr = np.zeros(num_permutations)
-    for r in range(num_permutations):
-        r_per = np.random.randint(
-            low=0, high=p_arr.shape[0], size=p_arr.shape[0]
-        )
-
-        labels, num_clusters = measure.label(
-            p_arr[r_per] <= p_sig, return_num=True
-        )
-
-        index_cluster = {}
-        if num_clusters == 0:
-            r_per_arr[r] = 0
-        else:
-            p_cluster_sum = np.zeros(num_clusters)
-            for cluster_i in np.arange(num_clusters):
-                index_cluster[cluster_i] = np.where(labels == cluster_i + 1)[
-                    0
-                ]  # first cluster is assigned to be 1 from measure.label
-                p_cluster_sum[cluster_i] = np.sum(
-                    np.array(1 - p_arr[r_per])[index_cluster[cluster_i]]
-                )
-            # corresponds to the most unlikely cluster
-            r_per_arr[r] = np.max(p_cluster_sum)
-
-    sorted_r = np.sort(r_per_arr)
-
-    def find_arg_nearest(array, value):
-        array = np.asarray(array)
-        idx = (np.abs(array - value)).argmin()
-        return idx
-
-    p = 1 - find_arg_nearest(sorted_r, p_min) / num_permutations
-
-    return p, p_min_index
-
-
-# @njit
-def cluster_wise_p_val_correction_numba(p_arr, p_sig, n_perm):
-    """Calculate significant clusters and their corresponding p-values.
-
-    Based on:
-    https://github.com/neuromodulation/wjn_toolbox/blob/4745557040ad26f3b8498ca5d0c5d5dece2d3ba1/mypcluster.m
-    https://garstats.wordpress.com/2018/09/06/cluster/
-
-    Arguments
-    ---------
-    p_arr :  array-like
-        Array of p-values. WARNING: MUST be one-dimensional
-    p_sig : float
-        Significance level
-    n_perm : int
-        No. of random permutations for building cluster null-distribution
-
-    Returns
-    -------
-    p : list of floats
-        List of p-values for each cluster
-    p_min_index : list of numpy array
-        List of indices of each significant cluster
-    """
-
-    def cluster(iterable):
-        """Cluster 1-D array of boolean values.
-
-        Parameters
-        ----------
-        iterable : array-like of bool
-            Array to be clustered.
-
-        Returns
-        -------
-        cluster_labels : np.array
-            Array of shape (len(iterable), 1), where each value indicates the
-            number of the cluster. Values are 0 if the item does not belong to
-            a cluster
-        cluster_count : int
-            Number of detected cluster. Corresponds to the highest value in
-            cluster_labels
-        """
-        cluster_labels = np.zeros((len(iterable), 1))
-        cluster_count = 0
-        cluster_len = 0
-        for idx, item in enumerate(iterable):
-            if item:
-                cluster_labels[idx] = cluster_count + 1
-                cluster_len += 1
-            elif cluster_len == 0:
-                pass
-            else:
-                cluster_len = 0
-                cluster_count += 1
-        if cluster_len >= 1:
-            cluster_count += 1
-        return cluster_labels, cluster_count
-
-    def calculate_null_distribution(p_arr_, p_sig_, n_perm_):
-        """Calculate null distribution of clusters.
-
-        Parameters
-        ----------
-        p_arr_ :  numpy array
-            Array of p-values
-        p_sig_ : float
-            Significance level (p-value)
-        n_perm_ : int
-            No. of random permutations
-
-        Returns
-        -------
-        r_per_arr : numpy array
-            Null distribution of shape (n_perm_)
-        """
-        # loop through random permutation cycles
-        r_per_arr = np.zeros(n_perm_)
-        for r in range(n_perm_):
-            r_per = np.random.randint(
-                low=0, high=p_arr_.shape[0], size=p_arr_.shape[0]
-            )
-            labels_, n_clusters = cluster(p_arr_[r_per] <= p_sig_)
-
-            cluster_ind = {}
-            if n_clusters == 0:
-                r_per_arr[r] = 0
-            else:
-                p_sum = np.zeros(n_clusters)
-                for ind in range(n_clusters):
-                    cluster_ind[ind] = np.where(labels_ == ind + 1)[0]
-                    p_sum[ind] = np.sum(
-                        np.asarray(1 - p_arr_[r_per])[cluster_ind[ind]]
-                    )
-                r_per_arr[r] = np.max(p_sum)
-        return r_per_arr
-
-    labels, num_clusters = cluster(p_arr <= p_sig)
-
-    null_distr = calculate_null_distribution(p_arr, p_sig, n_perm)
-    # Loop through clusters of p_val series or image
-    clusters = []
-    p_vals = [np.float64(x) for x in range(0)]
-    # Cluster labels start at 1
-    for cluster_i in range(num_clusters):
-        index_cluster = np.where(labels == cluster_i + 1)[0]
-        p_cluster_sum = np.sum(np.asarray(1 - p_arr)[index_cluster])
-        p_val = 1 - np.sum(p_cluster_sum >= null_distr) / n_perm
-        if p_val <= p_sig:
-            clusters.append(index_cluster)
-            p_vals.append(p_val)
-
-    return p_vals, clusters
+import random
+import copy
+
+import matplotlib.pyplot as plt
+
+# from numba import njit
+import numpy as np
+import pandas as pd
+import scipy.stats as stats
+
+
+def fitlm(x, y):
+    import statsmodels.api as sm
+    return sm.OLS(y, sm.add_constant(x)).fit()
+
+
+def fitlm_kfold(x, y, kfold_splits=5):
+    from sklearn.linear_model import LinearRegression
+    from sklearn.model_selection import KFold
+
+    model = LinearRegression()
+    if isinstance(x, type(np.array([]))) or isinstance(x, type([])):
+        x = pd.DataFrame(x)
+    if isinstance(y, type(np.array([]))) or isinstance(y, type([])):
+        y = pd.DataFrame(y)
+    scores, coeffs = [], np.zeros(x.shape[1])
+    kfold = KFold(n_splits=kfold_splits, shuffle=True, random_state=42)
+    for i, (train, test) in enumerate(kfold.split(x, y)):
+        model.fit(x.iloc[train, :], y.iloc[train, :])
+        score = model.score(x.iloc[test, :], y.iloc[test, :])
+        # mdl = fitlm(np.squeeze(y.iloc[test,:].transpose()), np.squeeze(model.predict(x.iloc[test, :])))
+        scores.append(score)
+        coeffs = np.vstack((coeffs, model.coef_))
+    coeffs = list(np.delete(coeffs, 0))
+    return scores, coeffs, model, ["scores", "coeffs", "model"]
+
+
+def zscore(data):
+    return (data - data.mean()) / data.std()
+
+
+def permutationTestSpearmansRho(x, y, plot_distr=True, x_unit=None, p=5000):
+    """
+    Calculate permutation test for multiple repetitions of Spearmans Rho
+    https://towardsdatascience.com/how-to-assess-statistical-significance-in-your-data-with-permutation-tests-8bb925b2113d
+
+    x (np array) : first distibution e.g. R^2
+    y (np array) : second distribution e.g. UPDRS
+    plot_distr (boolean) : if True: permutation histplot and ground truth will be
+    plotted
+    x_unit (str) : histplot xlabel
+    p (int): number of permutations
+
+    returns:
+    gT (float) : estimated ground truth, here spearman's rho
+    p (float) : p value of permutation test
+    """
+
+    # compute ground truth difference
+    gT = stats.spearmanr(x, y)[0]
+    #
+    pV = np.array((x, y))
+    # Initialize permutation:
+    pD = []
+    # Permutation loop:
+    args_order = np.arange(0, pV.shape[1], 1)
+    args_order_2 = np.arange(0, pV.shape[1], 1)
+    for i in range(0, p):
+        # Shuffle the data:
+        random.shuffle(args_order)
+        random.shuffle(args_order_2)
+        # Compute permuted absolute difference of your two sampled
+        # distributions and store it in pD:
+        pD.append(stats.spearmanr(pV[0, args_order], pV[1, args_order_2])[0])
+
+    # calculate p value
+    if gT < 0:
+        p_val = len(np.where(pD <= gT)[0]) / p
+    else:
+        p_val = len(np.where(pD >= gT)[0]) / p
+
+    if plot_distr:
+        plt.hist(pD, bins=30, label="permutation results")
+        plt.axvline(gT, color="orange", label="ground truth")
+        plt.title("ground truth " + x_unit + "=" + str(gT) + " p=" + str(p_val))
+        plt.xlabel(x_unit)
+        plt.legend()
+        plt.show()
+    return gT, p_val
+
+
+def permutationTest(x, y, plot_distr=True, x_unit=None, p=5000):
+    """
+    Calculate permutation test
+    https://towardsdatascience.com/how-to-assess-statistical-significance-in-your-data-with-permutation-tests-8bb925b2113d
+
+    x (np array) : first distr.
+    y (np array) : first distr.
+    plot_distr (boolean) : if True: plot permutation histplot and ground truth
+    x_unit (str) : histplot xlabel
+    p (int): number of permutations
+
+    returns:
+    gT (float) : estimated ground truth, here absolute difference of
+    distribution means
+    p (float) : p value of permutation test
+
+    """
+    # Compute ground truth difference
+    gT = np.abs(np.average(x) - np.average(y))
+
+    pV = np.concatenate((x, y), axis=0)
+    pS = copy.copy(pV)
+    # Initialize permutation:
+    pD = []
+    # Permutation loop:
+    for i in range(0, p):
+        # Shuffle the data:
+        random.shuffle(pS)
+        # Compute permuted absolute difference of your two sampled
+        # distributions and store it in pD:
+        pD.append(
+            np.abs(
+                np.average(pS[0 : int(len(pS) / 2)])
+                - np.average(pS[int(len(pS) / 2) :])
+            )
+        )
+
+    # Calculate p-value
+    if gT < 0:
+        p_val = len(np.where(pD <= gT)[0]) / p
+    else:
+        p_val = len(np.where(pD >= gT)[0]) / p
+
+    if plot_distr:
+        plt.hist(pD, bins=30, label="permutation results")
+        plt.axvline(gT, color="orange", label="ground truth")
+        plt.title("ground truth " + x_unit + "=" + str(gT) + " p=" + str(p_val))
+        plt.xlabel(x_unit)
+        plt.legend()
+        plt.show()
+    return gT, p_val
+
+
+def permutationTest_relative(x, y, plot_distr=True, x_unit=None, p=5000):
+    """
+    Calculate permutation test
+    https://towardsdatascience.com/how-to-assess-statistical-significance-in-your-data-with-permutation-tests-8bb925b2113d
+
+    x (np array) : first distr.
+    y (np array) : first distr.
+    plot_distr (boolean) : if True: plot permutation histplot and ground truth
+    x_unit (str) : histplot xlabel
+    p (int): number of permutations
+
+    returns:
+    gT (float) : estimated ground truth, here absolute difference of
+    distribution means
+    p (float) : p value of permutation test
+
+    """
+    gT = np.abs(np.average(x) - np.average(y))
+    pD = []
+    for i in range(0, p):
+        l_ = []
+        for i in range(x.shape[0]):
+            if random.randint(0, 1) == 1:
+                l_.append((x[i], y[i]))
+            else:
+                l_.append((y[i], x[i]))
+        pD.append(
+            np.abs(np.average(np.array(l_)[:, 0]) - np.average(np.array(l_)[:, 1]))
+        )
+    if gT < 0:
+        p_val = len(np.where(pD <= gT)[0]) / p
+    else:
+        p_val = len(np.where(pD >= gT)[0]) / p
+
+    if plot_distr:
+        plt.hist(pD, bins=30, label="permutation results")
+        plt.axvline(gT, color="orange", label="ground truth")
+        plt.title("ground truth " + x_unit + "=" + str(gT) + " p=" + str(p_val))
+        plt.xlabel(x_unit)
+        plt.legend()
+        plt.show()
+
+    return gT, p_val
+
+
+# @njit
+def permutation_numba_onesample(x, y, n_perm, two_tailed=True):
+    """Perform permutation test with one-sample distribution.
+
+    Parameters
+    ----------
+    x : array_like
+        First distribution
+    y : int or float
+        Baseline against which to check for statistical significane
+    n_perm : int
+        Number of permutations
+    two_tailed : bool, default: True
+        Set to False if you would like to perform a one-sampled permutation
+        test, else True
+    two_tailed : bool, default: True
+        Set to False if you would like to perform a one-tailed permutation
+        test, else True
+
+    Returns
+    -------
+    float
+        Estimated difference of distribution from baseline
+    float
+        P-value of permutation test
+    """
+    if two_tailed:
+        zeroed = x - y
+        z = np.abs(np.mean(zeroed))
+        p = np.empty(n_perm)
+        # Run the simulation n_perm times
+        for i in np.arange(n_perm):
+            sign = np.random.choice(a=np.array([-1.0, 1.0]), size=len(x), replace=True)
+            p[i] = np.abs(np.mean(zeroed * sign))
+    else:
+        zeroed = x - y
+        z = np.mean(zeroed)
+        p = np.empty(n_perm)
+        # Run the simulation n_perm times
+        for i in np.arange(n_perm):
+            sign = np.random.choice(a=np.array([-1.0, 1.0]), size=len(x), replace=True)
+            p[i] = np.mean(zeroed * sign)
+        # Return p-value
+    return z, (np.sum(p >= z)) / n_perm
+
+
+# @njit
+def permutation_numba_twosample(x, y, n_perm, two_tailed=True):
+    """Perform permutation test.
+
+    Parameters
+    ----------
+    x : array_like
+        First distribution
+    y : array_like
+        Second distribution
+    n_perm : int
+        Number of permutations
+    two_tailed : bool, default: True
+        Set to False if you would like to perform a one-sampled permutation
+        test, else True
+    two_tailed : bool, default: True
+        Set to False if you would like to perform a one-tailed permutation
+        test, else True
+
+    Returns
+    -------
+    float
+        Estimated difference of distribution means
+    float
+        P-value of permutation test
+    """
+    if two_tailed:
+        z = np.abs(np.mean(x) - np.mean(y))
+        pS = np.concatenate((x, y), axis=0)
+        half = int(len(pS) / 2)
+        p = np.empty(n_perm)
+        # Run the simulation n_perm times
+        for i in np.arange(0, n_perm):
+            # Shuffle the data
+            np.random.shuffle(pS)
+            # Compute permuted absolute difference of the two sampled
+            # distributions
+            p[i] = np.abs(np.mean(pS[:half]) - np.mean(pS[half:]))
+    else:
+        z = np.mean(x) - np.mean(y)
+        pS = np.concatenate((x, y), axis=0)
+        half = int(len(pS) / 2)
+        p = np.empty(n_perm)
+        # Run the simulation n_perm times
+        for i in np.arange(0, n_perm):
+            # Shuffle the data
+            np.random.shuffle(pS)
+            # Compute permuted absolute difference of the two sampled
+            # distributions
+            p[i] = np.mean(pS[:half]) - np.mean(pS[half:])
+    return z, (np.sum(p >= z)) / n_perm
+
+
+def cluster_wise_p_val_correction(p_arr, p_sig=0.05, num_permutations=10000):
+    """Obtain cluster-wise corrected p values.
+
+    Based on: https://github.com/neuromodulation/wjn_toolbox/blob/4745557040ad26f3b8498ca5d0c5d5dece2d3ba1/mypcluster.m
+    https://garstats.wordpress.com/2018/09/06/cluster/
+
+    Arguments
+    ---------
+    p_arr (np.array) : ndim, can be time series or image
+    p_sig (float) : significance level
+    num_permutations (int) : no. of random permutations of cluster comparisons
+
+    Returns
+    -------
+    p (float) : significance level of highest cluster
+    p_min_index : indices of significant samples
+    """
+    from skimage.measure import label as measure_label
+
+    labels, num_clusters = measure_label(p_arr <= p_sig, return_num=True)
+
+    # loop through clusters of p_val series or image
+    index_cluster = {}
+    p_cluster_sum = np.zeros(num_clusters)
+    for cluster_i in np.arange(num_clusters):
+        # first cluster is assigned to be 1 from measure.label
+        index_cluster[cluster_i] = np.where(labels == cluster_i + 1)[0]
+        p_cluster_sum[cluster_i] = np.sum(np.array(1 - p_arr)[index_cluster[cluster_i]])
+    # p_min corresponds to the most unlikely cluster
+    p_min = np.max(p_cluster_sum)
+
+    p_min_index = index_cluster[np.argmax(p_cluster_sum)]
+
+    # loop through random permutation cycles
+    r_per_arr = np.zeros(num_permutations)
+    for r in range(num_permutations):
+        r_per = np.random.randint(low=0, high=p_arr.shape[0], size=p_arr.shape[0])
+
+        labels, num_clusters = measure_label(p_arr[r_per] <= p_sig, return_num=True)
+
+        index_cluster = {}
+        if num_clusters == 0:
+            r_per_arr[r] = 0
+        else:
+            p_cluster_sum = np.zeros(num_clusters)
+            for cluster_i in np.arange(num_clusters):
+                index_cluster[cluster_i] = np.where(labels == cluster_i + 1)[
+                    0
+                ]  # first cluster is assigned to be 1 from measure.label
+                p_cluster_sum[cluster_i] = np.sum(
+                    np.array(1 - p_arr[r_per])[index_cluster[cluster_i]]
+                )
+            # corresponds to the most unlikely cluster
+            r_per_arr[r] = np.max(p_cluster_sum)
+
+    sorted_r = np.sort(r_per_arr)
+
+    def find_arg_nearest(array, value):
+        array = np.asarray(array)
+        idx = (np.abs(array - value)).argmin()
+        return idx
+
+    p = 1 - find_arg_nearest(sorted_r, p_min) / num_permutations
+
+    return p, p_min_index
+
+
+# @njit
+def cluster_wise_p_val_correction_numba(p_arr, p_sig, n_perm):
+    """Calculate significant clusters and their corresponding p-values.
+
+    Based on:
+    https://github.com/neuromodulation/wjn_toolbox/blob/4745557040ad26f3b8498ca5d0c5d5dece2d3ba1/mypcluster.m
+    https://garstats.wordpress.com/2018/09/06/cluster/
+
+    Arguments
+    ---------
+    p_arr :  array-like
+        Array of p-values. WARNING: MUST be one-dimensional
+    p_sig : float
+        Significance level
+    n_perm : int
+        No. of random permutations for building cluster null-distribution
+
+    Returns
+    -------
+    p : list of floats
+        List of p-values for each cluster
+    p_min_index : list of numpy array
+        List of indices of each significant cluster
+    """
+
+    def cluster(iterable):
+        """Cluster 1-D array of boolean values.
+
+        Parameters
+        ----------
+        iterable : array-like of bool
+            Array to be clustered.
+
+        Returns
+        -------
+        cluster_labels : np.ndarray
+            Array of shape (len(iterable), 1), where each value indicates the
+            number of the cluster. Values are 0 if the item does not belong to
+            a cluster
+        cluster_count : int
+            Number of detected cluster. Corresponds to the highest value in
+            cluster_labels
+        """
+        cluster_labels = np.zeros((len(iterable), 1))
+        cluster_count = 0
+        cluster_len = 0
+        for idx, item in enumerate(iterable):
+            if item:
+                cluster_labels[idx] = cluster_count + 1
+                cluster_len += 1
+            elif cluster_len == 0:
+                pass
+            else:
+                cluster_len = 0
+                cluster_count += 1
+        if cluster_len >= 1:
+            cluster_count += 1
+        return cluster_labels, cluster_count
+
+    def calculate_null_distribution(p_arr_, p_sig_, n_perm_):
+        """Calculate null distribution of clusters.
+
+        Parameters
+        ----------
+        p_arr_ :  numpy array
+            Array of p-values
+        p_sig_ : float
+            Significance level (p-value)
+        n_perm_ : int
+            No. of random permutations
+
+        Returns
+        -------
+        r_per_arr : numpy array
+            Null distribution of shape (n_perm_)
+        """
+        # loop through random permutation cycles
+        r_per_arr = np.zeros(n_perm_)
+        for r in range(n_perm_):
+            r_per = np.random.randint(low=0, high=p_arr_.shape[0], size=p_arr_.shape[0])
+            labels_, n_clusters = cluster(p_arr_[r_per] <= p_sig_)
+
+            cluster_ind = {}
+            if n_clusters == 0:
+                r_per_arr[r] = 0
+            else:
+                p_sum = np.zeros(n_clusters)
+                for ind in range(n_clusters):
+                    cluster_ind[ind] = np.where(labels_ == ind + 1)[0]
+                    p_sum[ind] = np.sum(np.asarray(1 - p_arr_[r_per])[cluster_ind[ind]])
+                r_per_arr[r] = np.max(p_sum)
+        return r_per_arr
+
+    labels, num_clusters = cluster(p_arr <= p_sig)
+
+    null_distr = calculate_null_distribution(p_arr, p_sig, n_perm)
+    # Loop through clusters of p_val series or image
+    clusters = []
+    p_vals = [np.float64(x) for x in range(0)]
+    # Cluster labels start at 1
+    for cluster_i in range(num_clusters):
+        index_cluster = np.where(labels == cluster_i + 1)[0]
+        p_cluster_sum = np.sum(np.asarray(1 - p_arr)[index_cluster])
+        p_val = 1 - np.sum(p_cluster_sum >= null_distr) / n_perm
+        if p_val <= p_sig:
+            clusters.append(index_cluster)
+            p_vals.append(p_val)
+
+    return p_vals, clusters