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    # -*- coding: utf-8 -*-
    """
    Updated Aug 7 2024
    
    @author: Qianliang Li (glia@dtu.dk)
    
    This is the main Python file containing the code that support the findings of
    https://doi.org/10.1101/2024.05.06.592342 
    
    The data used in this analysis was previously described and preprocessed
    by Zimmermann, M., Lomoriello, A. S., and Konvalinka, I.
    Intra-individual behavioural and neural signatures of audience effects and
    interactions in a mirror-game paradigm. Royal Society Open Science, 9(2) 2022
    """
    
    # %% Load libraries
    import os
    import numpy as np
    import pandas as pd
    import matplotlib.pyplot as plt
    import mne
    import pickle
    import mat73
    import time
    import seaborn as sns
    import nolds
    from tqdm import tqdm # progress bar
    
    # import Python script for microstates [von Wegner & Lauf, 2018]
    # originally downloaded from https://github.com/Frederic-vW/eeg_microstates
    # I modified the script for estimating two-brain microstates
    # by defining kmeans_return_all and kmeans_dualmicro
    from eeg_microstates3 import (kmeans_return_all, kmeans_dualmicro)
    # import helper functions
    from helper import (numpy_arr_to_pandas_df, time_now)
    
    from dualmicro_functions import (load_epoch_from_fieldtrip, prepare_1P_micro_arr,
                                     plot_microstates, reorder_microstate_results,
                                     single_micro_fit_all_feature_computation,
                                     interbrain_microstate_feature_computation,
                                     prepare_2P_micro_arr_collapsed_events,
                                     plot_dualmicro, sign_swap_microstates,
                                     dualmicro_fit_all_feature_computation,
                                     load_microstate_arrays, 
                                     get_synch_events_from_pseudo_pairs,
                                     combine_two_person_microstate_arrays,
                                     pseudo_pair_dualmicro_backfitting,
                                     dualmicro_fit_all_pseudo_pair_feature_computation,
                                     compute_dualmicro_DFA, compute_dualmicro_DFA_pseudo,
                                     shifted_interbrain_microstate_feature_computation)
    
    # Style for matplotlib/seaborn
    plt.style.use('default')
    
    # Root for project
    os.chdir("C:/Users/glia/Documents/MirrorGame")
    
    # Paths
    data_path = "./data/external/EEG/"
    mov_data_path = "./data/external/movement/"
    fig_save_path = "./reports/figures/"
    feat_save_path = "./data/features/"
    microstate_save_path = "./data/features/microstates2/"
    mov_save_path = "./data/features/movement/"
    
    
    # %% Load preprocessed EEG data
    # The data was originally preprocessed in Fieldtrip by Marius Zimmermann
    # Get filenames for the EEG data
    files = []
    for r, d, f in os.walk(data_path):
        for file in f:
            if (".mat" in file) & ("ppn" in file):
                files.append(os.path.join(r, file))
    # Sort the filenames
    files.sort()
    
    n_subjects = len(files)
    # Get Subject_id
    Subject_id = [0]*n_subjects
    for i in range(n_subjects):
        id_number = files[i].split("/")[-1].split(".")[0].split("pair")[-1].split("pair")[-1].replace("_ppn","")
        Subject_id[i] = int(id_number)+1000 # add 1000 to keep the first 0
    
    # There are data from 23 pairs
    # Pair 21 and 25 were excluded in the original analysis
    # After looking at the data, it seems pair 21, participant 1 and pair 25
    # participant 2 only had 1254 and 1440 epochs respectively.
    # Their data also do not end with resting-state condition
    # All the other EEG data have around 2400 1s epochs and start and ends with rest
    bad_subjects = [1211, 1212, 1251, 1252] # the whole pair is dropped
    good_subject_idx = [not i in bad_subjects for i in Subject_id]
    # Update Subject_id and files
    Subject_id = list(np.array(Subject_id)[good_subject_idx])
    n_subjects = len(Subject_id)
    files = list(np.array(files)[good_subject_idx])
    
    Pair_id = [0]*(n_subjects//2)
    for i in range(n_subjects//2):
        Pair_id[i] = int(str(Subject_id[2*i])[1:-1])
    # Add 100 to pair_id to fix sorting for 1 digit numbers, e.g. 03
    Pair_id = [ele+100 for ele in Pair_id]
    n_pairs = len(Pair_id)
    
    # Save the IDs as environmental variables to be used in functions
    # from dualmicro_functions.py
    os.environ["Subject_id"] = Subject_id
    os.environ["Pair_id"] = Pair_id
    
    event_id = {"rest":1, "uncoupled":2, "coupled": 3, "observe, actor": 4,
                "observe, observer": 6, "imitate, leader": 5, "imitate, follower": 7,
                "control": 8}
    
    # Clarification of the labels
    # Cond4: ppn1 is observer, ppn2 is actor
    # Cond6: ppn1 is actor, ppn2 is observer
    # Cond5: ppn1 is follower, ppn2 is leader
    # Cond5: ppn1 is leader, ppn2 is follower
    
    event_id_inv = {v: k for k, v in event_id.items()}
    
    # We collapsed condition 4 and 6 & 5 and 7 for two-brain microstates
    # By swapping the EEG of ppn1 and ppn2 so ppn1 is always observer/follower and
    # ppn2 actor/leader
    collapsed_event_id = {"rest":1, "uncoupled":2, "coupled": 3,
                          "observer_actor": 4, "follower_leader": 5, "control": 8}
    collapsed_event_id_inv = {v: k for k, v in collapsed_event_id.items()}
    
    # Load the first EEG to get info about sfreq and n_channels
    i = 0
    epoch, trialinfo = load_epoch_from_fieldtrip(0, files, event_id)
    n_channels = epoch.info["nchan"]
    sfreq = int(epoch.info["sfreq"])
    
    # Visualize the data
    # epoch.plot(scalings=40e-6, n_channels=32)
    # mne.viz.plot_events(epoch.events, sfreq = 1, event_id = event_id, first_samp=-3) # sfreq set to epoch length in s to reflect experiment time
    
    # We compute microstates for the three frequency ranges
    alpha_range = [8.0, 13.0]
    beta_range = [13.0, 30.0]
    broadband_range = None # Data is already 1 to 40 Hz broadband filtered
    freq_names = ["alpha","beta","broadband"]
    all_freq_ranges = [alpha_range, beta_range, broadband_range]
    
    # %% Intrabrain microstates fit all data
    # All subjects from all pairs are concatenated to find common microstates
    single_brain_event_id = {"rest":1, "uncoupled":2, "coupled": 3, "observer": 4,
                             "actor": 6, "follower": 5, "leader": 7, "control": 8}
    ppn2_correction = {6:4, 4:6, 7:5, 5:7}
    
    # Loop over frequencies
    for f in len(all_freq_ranges):
        ff = freq_names[f]
        freq_range0 = all_freq_ranges[f]
        # =========================================================================
        # First the microstate topographies are determined
        # It might be an advantage to run the estimation of microstates on a HPC
        # =========================================================================
        # Get data from all pairs before performing kmeans
        np.random.seed(1234)
        n_clusters=[3, 4, 5, 6, 7, 8, 9, 10]
        n_runs = 100 # increased to 100 runs!
        # Get current time
        c_time1 = time_now(); print(c_time1)
        # Save RAM by appending directly to array instead of making list and then array
        sub_arr_indices = [0]
        trialinfo_list = []
        for i in range(n_subjects):
            tmp_data, trialinfo = prepare_1P_micro_arr(i, ppn2_correction, sfreq,
                                                       freq_range=freq_range0, standardize=True)
            sub_arr_indices.append(len(tmp_data))
            trialinfo_list.append([Subject_id[i],trialinfo])
            if i == 0: # first run initiation
                micro_data_all = tmp_data
            else:
                micro_data_all = np.append(micro_data_all, tmp_data, axis=0)
            del tmp_data # clear up space
            print(f"Finished preparing microstate data for pair {Subject_id[i]}")
        
        # Use cumulative sum to determine indices for each subjects's data
        subject_indices = np.cumsum(sub_arr_indices)
        
        # Save the trialinfos from all subjects, for easier access in later steps
        with open(f"{microstate_save_path}Intrabrain_microstate_fit_all_{ff}_trialinfos.pkl", "wb") as filehandle:
            pickle.dump(trialinfo_list, filehandle)
        
        # # with args parser in hpc
        # n_maps = n_clusters[(args.map_idx-1)]
        # print(f"Running analysis for maps: {n_maps}")
        # print("Memory used by the micro data array (GB):",micro_data_all.nbytes*9.31e-10)
        
        # Run Kmeans
        for n_maps in n_clusters: # Don't use for loop on the HPC!
            # Run the 100 runs in batches of 10 to save underway in case the job script terminates
            best_cv_crit = 9999 # initialize unreasonably high value
            for r in range(10):
                microstate_results = list(kmeans_return_all(micro_data_all, n_maps,
                                                            n_runs=int(n_runs/10),maxiter=1000))
                # Overwrite the maps if a lower CV criterion was found for the initiation
                if microstate_results[4] < best_cv_crit:
                    microstate_results.append(subject_indices)
                    # Save results
                    with open(f"{microstate_save_path}Intrabrain_microstate_fit_all_{ff}{n_maps}.pkl", "wb") as filehandle:
                        pickle.dump(microstate_results, filehandle) # [maps, L, gfp_peaks, gev, cv_min, Subject_id]
                    print(f"Updated the microstates. Previous best CV: {best_cv_crit}",
                          f"new best CV criterion : {microstate_results[4]}")
                    # Update best cv criterion value
                    best_cv_crit = microstate_results[4]
        
                print(f"Finished sub-run {r+1} out of 10")
        
            print(f"Finished microstate analysis for n_maps = {n_maps}")
            print("Started", c_time1, "\nCurrent",time_now())
        
        # =========================================================================
        # Evaluate microstates fitted to all data
        # =========================================================================
        # Get summary results
        microstate_summary_results = []
        
        for n_maps in n_clusters:
            with open(f"{microstate_save_path}Intrabrain_microstate_fit_all_{ff}{n_maps}.pkl", "rb") as file:
                microstate_results = pickle.load(file)
            # Also save summary results across n_maps
            microstate_summary_results.append([microstate_results[0],microstate_results[3],microstate_results[4]])
        
        # Use CV criterion to estimate best number of microstates
        cv_gev_arr = np.zeros((len(n_clusters),2))
        for imap in range(len(n_clusters)):
            gev = np.sum(microstate_summary_results[imap][1])
            cv = microstate_summary_results[imap][2]
            cv_gev_arr[imap,:] = [cv, gev]
        
        # Convert to Pandas dataframe
        col_names = ["n_Microstates", "Fit_Criteria", "Value"]
        Fit_Criteria = ["CV Criterion", "Global Explained Variance"]
        dtypes = [int,str,"float64"]
        
        cv_gev_df = numpy_arr_to_pandas_df(cv_gev_arr, col_names = col_names,
                                           col_values = [n_clusters,Fit_Criteria],
                                           dtypes = dtypes)
        
        # Evaluate optimal n_Microstates
        h_order = Fit_Criteria
        g = sns.FacetGrid(data=cv_gev_df,row=None,
                          margin_titles=True, height=8, aspect=1.2)
        g = g.map(sns.pointplot,"n_Microstates", "Value", "Fit_Criteria",
                  dodge=0, capsize=0.18, errorbar=None, linestyles=["-", "-"],
                  markers=["o", "o"], hue_order=h_order, palette=sns.color_palette())
        g.add_legend()
        plt.subplots_adjust(top=0.9, right=0.85, left=0.1)
        g.fig.suptitle("Mean CV Criterion and GEV", fontsize=18)
        g.set_axis_labels(x_var="Number of Microstates",
                          y_var="GEV and CV",
                          fontsize=14)
        # The lower CV the better. Measure of residual variance
        # But the higher GEV the better.
        # Save file
        g.savefig(f"{fig_save_path}Microstates/Fit_all_{ff}/"+"Single_micro_fit_all_{ff}_CV_Criterion_GEV"+".png")
        
        # Count which number of microstates have the lowest cv criterion for each subject
        min_idx = np.argmin(cv_gev_df.loc[cv_gev_df["Fit_Criteria"]=="CV Criterion","Value"])
        cv_gev_df.loc[cv_gev_df["Fit_Criteria"]=="CV Criterion"].iloc[min_idx]
        
        # Visualize all microstates prior to re-ordering
        for ii in range(len(n_clusters)):
            plot_microstates(n_clusters[ii], microstate_summary_results[ii][0], microstate_summary_results[ii][1], epoch.info)
        
        # =========================================================================
        # # Re-order intrabrain microstates
        # =========================================================================
        # This is only run once, after microstates are created
        # The optimal number of microstates were 5, with 56% GEV
        n_maps = 5
        ii = n_clusters.index(n_maps)
        
        with open(f"{microstate_save_path}Intrabrain_microstate_fit_all_{ff}{n_maps}.pkl", "rb") as file:
            microstate_results = pickle.load(file)
        
        maps, m_labels, gfp_peaks, gev, cv_min, sub_idx = microstate_results
        
        plot_microstates(n_maps, maps, gev)
        
        # Make dictionary with n_maps and new order
        manual_reordering_template = {"5_alpha":[4,1,3,2,0],
                                      "5_beta":[3,2,1,4,0],
                                      "5_broadband":[3,2,4,1,0]}
        new_order = manual_reordering_template[f"{n_maps}_{ff}"]
        
        # Re-order the microstates
        maps, gev, m_labels = reorder_microstate_results(new_order, maps, gev, m_labels)
        
        # Plot again to check it worked
        plot_microstates(n_maps, maps, gev, epoch.info)
        
        # Since neuronal activity is often oscillating, this causes polarity inversions
        # Microstates ignores the sign, and hence the polarity in the map is arbitrary
        # It is only the relative difference within the plot that is interesting
        # depending on initiation. We can thus freely change the sign for visualization
        # For two-person microstates, each person's map is sign-changed separately
        manual_sign_correction = {"5_alpha":[1,-1,1,1,1],
                                  "5_beta":[1,1,1,-1,-1],
                                  "5_broadband":[-1,1,-1,1,1]}
        sign_swap = manual_sign_correction[f"{n_maps}_{ff}"]
        for m in range(n_maps):
            maps[m] *= sign_swap[m]
        
        # Plot a final time for last confirmation
        plot_microstates(n_maps, maps, gev, epoch.info)
        
        # Close all figures
        plt.close("all")
        
        ### Save reordered results
        n_maps = 5
        ii = n_clusters.index(n_maps)
        
        with open(f"{microstate_save_path}Intrabrain_microstate_fit_all_{ff}{n_maps}.pkl", "rb") as file:
            microstate_results = pickle.load(file)
        maps, m_labels, gfp_peaks, gev, cv, sub_indices = microstate_results
        # Re-order
        new_order = manual_reordering_template[str(n_maps)]
        maps, gev, m_labels = reorder_microstate_results(new_order, maps, gev, m_labels)
        # Sign swap
        for m in range(n_maps):
            maps[m] *= sign_swap[m]
        # Overwrite variable
        microstate_results = maps, m_labels, gfp_peaks, gev, cv, sub_indices
        # Save to new file
        with open(f"{microstate_save_path}Reordered/Intrabrain_microstate_fit_all_{ff}{n_maps}.pkl", "wb") as filehandle:
            pickle.dump(microstate_results, filehandle) # [maps, L, gfp_peaks, gev, cv_min, sub_idx]
        
        # Save topomaps for the microstates
        save_path = f"{fig_save_path}Microstates/Fit_all_{ff}/"
        with open(f"{microstate_save_path}Reordered/Intrabrain_microstate_fit_all_{ff}{n_maps}.pkl", "rb") as file:
            microstate_results = pickle.load(file)
        maps, m_labels, gfp_peaks, gev, cv_min, sub_idx = microstate_results
        fig = plot_microstates(n_maps, maps, gev, epoch.info)
        fig.savefig(save_path+f"Intrabrain_fit_all_{ff}_maps{n_maps}"+".png")
        # Save svg for Paper
        fig.savefig(save_path+f"Intrabrain_fit_all_{ff}_maps{n_maps}"+".svg")
        
        # =========================================================================
        # # Estimate one-person microstate metrics/features
        # # There might be a small error introduced due to gaps in the time series from
        # # dropped segments, e.g. when calculating the transition probability as
        # # the time series is discontinuous due to the gaps. But with the high sampling rate
        # # only a very small fraction of the samples have discontinuous neighbors
        # =========================================================================
        # The observer_actor and observer_observe conditions have been separated
        # So there are observer and actor conditions.
        # And the same for leader and follower.
        """
        Overview of common (intrabrain) microstate features:
            1. Average duration a given microstate remains stable (Dur)
            2. Frequency occurrence, independent of individual duration (Occ)
                Average number of times a microstate becomes dominant per second
            3. Ratio of total Time Covered (TCo)
            4. Transition probabilities (TMx)
            5. Ratio of shannon entropy relative to theoretical max chaos (Ent)
        """
        # Hard-coded the optimal number of microstates based on CV criterion and GEV for dualmicro
        n_maps = 5
        # Load all microstate results
        with open(f"{microstate_save_path}Reordered/Intrabrain_microstate_fit_all_{ff}{n_maps}.pkl", "rb") as file:
            microstate_results = pickle.load(file)
        # Load all trialinfos
        with open(f"{microstate_save_path}Intrabrain_microstate_fit_all_{ff}_trialinfos.pkl", "rb") as file:
            trialinfo_list = pickle.load(file)
        
        Microstate_names = [chr(ele) for ele in range(65,65+n_maps)]
        
        m_labels = [0]*n_subjects
        events = [0]*n_subjects
        m_feats = [0]*n_subjects
        
        for i in range(n_subjects):
            m_labels[i], events[i], m_feats[i] = single_micro_fit_all_feature_computation(i,
               n_maps, microstate_results, trialinfo_list, sfreq, event_id, single_brain_event_id)
            print(f"Finished computing microstate features for Subject {Subject_id[i]}")
        
        # Save the raw microstate features
        with open(f"{microstate_save_path}/raw_features_single_micro_fit_all_{ff}_maps{n_maps}.pkl", "wb") as filehandle:
            pickle.dump(m_feats, filehandle) # [Subject][Dur_arr,Occ_arr,TCo_arr,TMx_arr,Ent_arr] [Event, map*]
            # * the feature is calculated for each map, where applicable.
            # Transition matrix is calculated for each map -> map transition probability
        
        # with open(f"{microstate_save_path}/raw_features_single_micro_fit_all_{ff}_maps{n_maps}.pkl", "rb") as file:
        #     m_feats = pickle.load(file) # [Subject][Dur_arr,Occ_arr,TCo_arr,TMx_arr,Ent_arr] [Event, map*]
        
        ### Convert all features to dataframes for further processing
        col_names = ["Subject_ID", "Event_ID", "Microstate", "Value"]
        col_values = [Subject_id,list(single_brain_event_id.keys()),Microstate_names]
        dtypes = ["int64",str,str,"float64"]
        # Mean duration
        Dur_arr = np.stack([ele[0] for ele in m_feats]) # [Subject, event, n_map]
        Dur_df = numpy_arr_to_pandas_df(Dur_arr, col_names, col_values, dtypes)
        # Add dummy variable to enabling combining of dataframes
        measurement_id = ["Duration"]*len(Dur_df)
        Dur_df.insert(2, "Measurement", measurement_id)
        # Save df
        Dur_df.to_pickle(os.path.join(microstate_save_path,f"Single_micro_fit_all_{ff}_maps{n_maps}_duration_df.pkl"))
        
        # Frequency of occurrence per sec
        Occ_arr = np.stack([ele[1] for ele in m_feats]) # [Subject, event, n_map]
        Occ_df = numpy_arr_to_pandas_df(Occ_arr, col_names, col_values, dtypes)
        # Add dummy variable to enabling combining of dataframes
        measurement_id = ["Occurrence"]*len(Occ_df)
        Occ_df.insert(2, "Measurement", measurement_id)
        # Save df
        Occ_df.to_pickle(os.path.join(microstate_save_path,f"Single_micro_fit_all_{ff}_maps{n_maps}_occurrence_df.pkl"))
        
        # Ratio total Time Covered
        TCo_arr = np.stack([ele[2] for ele in m_feats]) # [Subject, event, n_map]
        TCo_df = numpy_arr_to_pandas_df(TCo_arr, col_names, col_values, dtypes)
        # Add dummy variable to enabling combining of dataframes
        measurement_id = ["Time_covered"]*len(TCo_df)
        TCo_df.insert(2, "Measurement", measurement_id)
        # Save df
        TCo_df.to_pickle(os.path.join(microstate_save_path,f"Single_micro_fit_all_{ff}_maps{n_maps}_ratio_time_covered_df.pkl"))
        
        # Transition matrix should be read as probability of row to column
        xi, xj = np.meshgrid(Microstate_names,Microstate_names)
        _, arrow = np.meshgrid(Microstate_names,["->"]*n_maps)
        
        transition_info = np.char.add(np.char.add(xj,arrow),xi)
        
        TMx_arr = np.stack([ele[3] for ele in m_feats]) # [Subject, event, n_map, n_map]
        TMx_arr = TMx_arr.reshape((n_subjects,len(single_brain_event_id),n_maps*n_maps)) # Flatten the maps to 1D
        
        col_names = ["Subject_ID", "Event_ID", "Transition", "Value"]
        col_values = [Subject_id,list(single_brain_event_id.keys()),transition_info.flatten()]
        TMx_df = numpy_arr_to_pandas_df(TMx_arr, col_names, col_values, dtypes)
        # Add dummy variable to enabling combining of dataframes
        measurement_id = ["Probability"]*len(TMx_df)
        TMx_df.insert(2, "Measurement", measurement_id)
        # Save df
        TMx_df.to_pickle(os.path.join(microstate_save_path,f"Single_micro_fit_all_{ff}_maps{n_maps}_transition_df.pkl"))
        
        # Entropy
        Ent_arr = np.stack([ele[4] for ele in m_feats]) # [Subject, event]
        col_names = ["Subject_ID", "Event_ID", "Value"]
        col_values = [Subject_id,list(single_brain_event_id.keys())]
        dtypes = ["int64",str,"float64"]
        Ent_df = numpy_arr_to_pandas_df(Ent_arr, col_names, col_values, dtypes)
        # Add dummy variable to enabling combining of dataframes
        measurement_id = ["Entropy"]*len(Ent_df)
        Ent_df.insert(2, "Measurement", measurement_id)
        # Save df
        Ent_df.to_pickle(os.path.join(microstate_save_path,f"Single_micro_fit_all_{ff}_maps{n_maps}_ratio_entropy_df.pkl"))
    
    # =========================================================================
    # We also did it for 8 alpha microstates to use the same number as
    # the two-brain microstates
    # =========================================================================
    # This is only run once, after microstates are created
    ff = "alpha"
    n_maps = 8
    ii = n_clusters.index(n_maps)
    
    with open(f"{microstate_save_path}Intrabrain_microstate_fit_all_{ff}{n_maps}.pkl", "rb") as file:
        microstate_results = pickle.load(file)
    
    maps, m_labels, gfp_peaks, gev, cv_min, sub_idx = microstate_results
    
    plot_microstates(n_maps, maps, gev)
    
    # Make dictionary with n_maps and new order
    manual_reordering_template = {"8":[6,0,5,1,7,2,3,4]}
    new_order = manual_reordering_template[str(n_maps)]
    
    # Re-order the microstates
    maps, gev, m_labels = reorder_microstate_results(new_order, maps, gev, m_labels)
    
    # Plot again to check it worked
    plot_microstates(n_maps, maps, gev, epoch.info)
    
    # Since neuronal activity is often oscillating, this causes polarity inversions
    # Microstates ignores the sign, and hence the polarity in the map is arbitrary
    # It is only the relative difference within the plot that is interesting
    # depending on initiation. We can thus freely change the sign for visualization
    # For two-person microstates, each person's map is sign-changed separately
    manual_sign_correction = {"8":[-1,1,-1,1,1,1,-1,-1]}
    sign_swap = manual_sign_correction[str(n_maps)]
    for m in range(n_maps):
        maps[m] *= sign_swap[m]
    
    # Plot a final time for last confirmation
    plot_microstates(n_maps, maps, gev, epoch.info)
    
    # Close all figures
    plt.close("all")
    
    ### Save reordered results
    n_maps = 8
    ii = n_clusters.index(n_maps)
    
    with open(f"{microstate_save_path}Intrabrain_microstate_fit_all_{ff}{n_maps}.pkl", "rb") as file:
        microstate_results = pickle.load(file)
    maps, m_labels, gfp_peaks, gev, cv, sub_indices = microstate_results
    # Re-order
    new_order = manual_reordering_template[str(n_maps)]
    maps, gev, m_labels = reorder_microstate_results(new_order, maps, gev, m_labels)
    # Sign swap
    for m in range(n_maps):
        maps[m] *= sign_swap[m]
    # Overwrite variable
    microstate_results = maps, m_labels, gfp_peaks, gev, cv, sub_indices
    # Save to new file
    with open(f"{microstate_save_path}Reordered/Intrabrain_microstate_fit_all_{ff}{n_maps}.pkl", "wb") as filehandle:
        pickle.dump(microstate_results, filehandle) # [maps, L, gfp_peaks, gev, cv_min, sub_idx]
    
    # Save topomaps for the microstates
    save_path = f"{fig_save_path}Microstates/Fit_all_{ff}/"
    with open(f"{microstate_save_path}Reordered/Intrabrain_microstate_fit_all_{ff}{n_maps}.pkl", "rb") as file:
        microstate_results = pickle.load(file)
    maps, m_labels, gfp_peaks, gev, cv_min, sub_idx = microstate_results
    fig = plot_microstates(n_maps, maps, gev, epoch.info)
    fig.savefig(save_path+f"Intrabrain_fit_all_{ff}_maps{n_maps}"+".png")
    # Save svg for Paper
    fig.savefig(save_path+f"Intrabrain_fit_all_{ff}_maps{n_maps}"+".svg")
    
    # =========================================================================
    # # Estimate one-person microstate metrics/features
    # # There might be a small error introduced due to gaps in the time series from
    # # dropped segments, e.g. when calculating the transition probability as
    # # the time series is discontinuous due to the gaps. But with the high sampling rate
    # # only a very small fraction of the samples have discontinuous neighbors
    # =========================================================================
    # The observer_actor and observer_observe conditions have been separated
    # So there are observer and actor conditions.
    # And the same for leader and follower.
    """
    Overview of common (intrabrain) microstate features:
        1. Average duration a given microstate remains stable (Dur)
        2. Frequency occurrence, independent of individual duration (Occ)
            Average number of times a microstate becomes dominant per second
        3. Ratio of total Time Covered (TCo)
        4. Transition probabilities (TMx)
        5. Ratio of shannon entropy relative to theoretical max chaos (Ent)
    """
    # Hard-coded the optimal number of microstates based on CV criterion and GEV for dualmicro
    n_maps = 8
    # Load all microstate results
    with open(f"{microstate_save_path}Reordered/Intrabrain_microstate_fit_all_{ff}{n_maps}.pkl", "rb") as file:
        microstate_results = pickle.load(file)
    # Load all trialinfos
    with open(f"{microstate_save_path}Intrabrain_microstate_fit_all_{ff}_trialinfos.pkl", "rb") as file:
        trialinfo_list = pickle.load(file)
    
    Microstate_names = [chr(ele) for ele in range(65,65+n_maps)]
    
    m_labels = [0]*n_subjects
    events = [0]*n_subjects
    m_feats = [0]*n_subjects
    
    for i in range(n_subjects):
        m_labels[i], events[i], m_feats[i] = single_micro_fit_all_feature_computation(i,
           n_maps, microstate_results, trialinfo_list, sfreq, event_id, single_brain_event_id)
        print(f"Finished computing microstate features for Subject {Subject_id[i]}")
    
    # Save the raw microstate features
    with open(f"{microstate_save_path}/raw_features_single_micro_fit_all_{ff}_maps{n_maps}.pkl", "wb") as filehandle:
        pickle.dump(m_feats, filehandle) # [Subject][Dur_arr,Occ_arr,TCo_arr,TMx_arr,Ent_arr] [Event, map*]
        # * the feature is calculated for each map, where applicable.
        # Transition matrix is calculated for each map -> map transition probability
    
    # with open(f"{microstate_save_path}/raw_features_single_micro_fit_all_{ff}_maps{n_maps}.pkl", "rb") as file:
    #     m_feats = pickle.load(file) # [Subject][Dur_arr,Occ_arr,TCo_arr,TMx_arr,Ent_arr] [Event, map*]
    
    ### Convert all features to dataframes for further processing
    col_names = ["Subject_ID", "Event_ID", "Microstate", "Value"]
    col_values = [Subject_id,list(single_brain_event_id.keys()),Microstate_names]
    dtypes = ["int64",str,str,"float64"]
    # Mean duration
    Dur_arr = np.stack([ele[0] for ele in m_feats]) # [Subject, event, n_map]
    Dur_df = numpy_arr_to_pandas_df(Dur_arr, col_names, col_values, dtypes)
    # Add dummy variable to enabling combining of dataframes
    measurement_id = ["Duration"]*len(Dur_df)
    Dur_df.insert(2, "Measurement", measurement_id)
    # Save df
    Dur_df.to_pickle(os.path.join(microstate_save_path,f"Single_micro_fit_all_{ff}_maps{n_maps}_duration_df.pkl"))
    
    # Frequency of occurrence per sec
    Occ_arr = np.stack([ele[1] for ele in m_feats]) # [Subject, event, n_map]
    Occ_df = numpy_arr_to_pandas_df(Occ_arr, col_names, col_values, dtypes)
    # Add dummy variable to enabling combining of dataframes
    measurement_id = ["Occurrence"]*len(Occ_df)
    Occ_df.insert(2, "Measurement", measurement_id)
    # Save df
    Occ_df.to_pickle(os.path.join(microstate_save_path,f"Single_micro_fit_all_{ff}_maps{n_maps}_occurrence_df.pkl"))
    
    # Ratio total Time Covered
    TCo_arr = np.stack([ele[2] for ele in m_feats]) # [Subject, event, n_map]
    TCo_df = numpy_arr_to_pandas_df(TCo_arr, col_names, col_values, dtypes)
    # Add dummy variable to enabling combining of dataframes
    measurement_id = ["Time_covered"]*len(TCo_df)
    TCo_df.insert(2, "Measurement", measurement_id)
    # Save df
    TCo_df.to_pickle(os.path.join(microstate_save_path,f"Single_micro_fit_all_{ff}_maps{n_maps}_ratio_time_covered_df.pkl"))
    
    # Transition matrix should be read as probability of row to column
    xi, xj = np.meshgrid(Microstate_names,Microstate_names)
    _, arrow = np.meshgrid(Microstate_names,["->"]*n_maps)
    
    transition_info = np.char.add(np.char.add(xj,arrow),xi)
    
    TMx_arr = np.stack([ele[3] for ele in m_feats]) # [Subject, event, n_map, n_map]
    TMx_arr = TMx_arr.reshape((n_subjects,len(single_brain_event_id),n_maps*n_maps)) # Flatten the maps to 1D
    
    col_names = ["Subject_ID", "Event_ID", "Transition", "Value"]
    col_values = [Subject_id,list(single_brain_event_id.keys()),transition_info.flatten()]
    TMx_df = numpy_arr_to_pandas_df(TMx_arr, col_names, col_values, dtypes)
    # Add dummy variable to enabling combining of dataframes
    measurement_id = ["Probability"]*len(TMx_df)
    TMx_df.insert(2, "Measurement", measurement_id)
    # Save df
    TMx_df.to_pickle(os.path.join(microstate_save_path,f"Single_micro_fit_all_{ff}_maps{n_maps}_transition_df.pkl"))
    
    # Entropy
    Ent_arr = np.stack([ele[4] for ele in m_feats]) # [Subject, event]
    col_names = ["Subject_ID", "Event_ID", "Value"]
    col_values = [Subject_id,list(single_brain_event_id.keys())]
    dtypes = ["int64",str,"float64"]
    Ent_df = numpy_arr_to_pandas_df(Ent_arr, col_names, col_values, dtypes)
    # Add dummy variable to enabling combining of dataframes
    measurement_id = ["Entropy"]*len(Ent_df)
    Ent_df.insert(2, "Measurement", measurement_id)
    # Save df
    Ent_df.to_pickle(os.path.join(microstate_save_path,f"Single_micro_fit_all_{ff}_maps{n_maps}_ratio_entropy_df.pkl"))
    
    # %% Inter-brain microstates fit all data
    # Based on the microstate topographies estimated on single-brian data
    """
    Interbrain features:
        1. Average duration of common interbrain microstates (IBDur)
        2. Frequency occurrence of common interbrain microstates in the pair (IBOcc)
        3. Ratio of total time covered by interbrain common microstates in the pair (IBCov)
        4. Transition probability towards common interbrain microstates in the pair (IBTMx)
        5. Ratio of joint shannon entropy relative to theoretical max chaos (IBEnt)
    """
    
    for f in len(all_freq_ranges):
        ff = freq_names[f]
        # Hard-coded the optimal number of microstates based on CV criterion and GEV
        n_maps = 5
        # Load all microstate results
        with open(f"{microstate_save_path}Reordered/Intrabrain_microstate_fit_all_{ff}{n_maps}.pkl", "rb") as file:
            microstate_results = pickle.load(file)
        # Load all trialinfos
        with open(f"{microstate_save_path}Intrabrain_microstate_fit_all_{ff}_trialinfos.pkl", "rb") as file:
            trialinfo_list = pickle.load(file)
        
        Microstate_names = [chr(ele) for ele in range(65,65+n_maps)]
        # Insert Z as the symbol for non common microstate
        Microstate_names.insert(0,"Z")
        
        m_labels = [0]*(n_subjects//2)
        events = [0]*(n_subjects//2)
        m_feats = [0]*(n_subjects//2)
        Pair_id = [0]*(n_subjects//2)
        
        for i in range(n_subjects//2):
            m_labels[i], events[i], m_feats[i] = interbrain_microstate_feature_computation(i,
               n_maps, microstate_results, trialinfo_list, sfreq, event_id, collapsed_event_id)
            Pair_id[i] = int(str(Subject_id[2*i])[1:-1])
            print(f"Finished computing interbrain microstate features for pair {Pair_id[i]}")
        
        Pair_id = [ele+100 for ele in Pair_id]
        
        # Save the raw microstate features
        with open(f"{microstate_save_path}/raw_interbrain_single_micro_fit_all_{ff}_maps{n_maps}.pkl", "wb") as filehandle:
            pickle.dump([Pair_id, m_feats], filehandle) # [Subject][Dur_arr,Occ_arr,TCo_arr,TMx_arr,Ent_arr] [Event, map*]
            # * the feature is calculated for each map, where applicable.
            # Transition matrix is calculated for each map -> map transition probability
            # The first row and column correspond to the non common microstate, i.e.
            # there is a different microstate in the pair
        
        # with open(f"{microstate_save_path}/raw_interbrain_single_micro_fit_all_{ff}_maps.pkl", "rb") as file:
        #     Pair_id, m_feats = pickle.load(file) # [Subject][Dur_arr,Occ_arr,TCo_arr,TMx_arr,Ent_arr] [Event, map*]
        
        n_pairs = len(Pair_id)
        
        ### Convert all features to dataframes for further processing
        col_names = ["Pair_ID", "Event_ID", "Microstate", "Value"]
        col_values = [Pair_id,list(collapsed_event_id.keys()),Microstate_names]
        dtypes = [int,str,str,"float64"]
        # Mean duration
        Dur_arr = np.stack([ele[0] for ele in m_feats]) # [Subject, event, n_map]
        Dur_df = numpy_arr_to_pandas_df(Dur_arr, col_names, col_values, dtypes)
        # Add dummy variable to enabling combining of dataframes
        measurement_id = ["Duration"]*len(Dur_df)
        Dur_df.insert(2, "Measurement", measurement_id)
        # Save df
        Dur_df.to_pickle(os.path.join(microstate_save_path,f"IB_Single_micro_fit_all_{ff}_maps{n_maps}_duration_df.pkl"))
        
        # Frequency of occurrence per sec
        Occ_arr = np.stack([ele[1] for ele in m_feats]) # [Subject, event, n_map]
        Occ_df = numpy_arr_to_pandas_df(Occ_arr, col_names, col_values, dtypes)
        # Add dummy variable to enabling combining of dataframes
        measurement_id = ["Occurrence"]*len(Occ_df)
        Occ_df.insert(2, "Measurement", measurement_id)
        # Save df
        Occ_df.to_pickle(os.path.join(microstate_save_path,f"IB_Single_micro_fit_all_{ff}_maps{n_maps}_occurrence_df.pkl"))
        
        # Ratio total Time Covered
        TCo_arr = np.stack([ele[2] for ele in m_feats]) # [Subject, event, n_map]
        TCo_df = numpy_arr_to_pandas_df(TCo_arr, col_names, col_values, dtypes)
        # Add dummy variable to enabling combining of dataframes
        measurement_id = ["Time_covered"]*len(TCo_df)
        TCo_df.insert(2, "Measurement", measurement_id)
        # Save df
        TCo_df.to_pickle(os.path.join(microstate_save_path,f"IB_Single_micro_fit_all_{ff}_maps{n_maps}_ratio_time_covered_df.pkl"))
        
        # Transition matrix should be read as probability of row to column
        xi, xj = np.meshgrid(Microstate_names,Microstate_names)
        _, arrow = np.meshgrid(Microstate_names,["->"]*(n_maps+1))
        
        transition_info = np.char.add(np.char.add(xj,arrow),xi)
        
        TMx_arr = np.stack([ele[3] for ele in m_feats]) # [Subject, event, n_map, n_map]
        TMx_arr = TMx_arr.reshape((n_pairs,len(collapsed_event_id),(n_maps+1)*(n_maps+1))) # Flatten the maps to 1D
        
        col_names = ["Pair_ID", "Event_ID", "Transition", "Value"]
        col_values = [Pair_id,list(collapsed_event_id.keys()),transition_info.flatten()]
        TMx_df = numpy_arr_to_pandas_df(TMx_arr, col_names, col_values, dtypes)
        # Add dummy variable to enabling combining of dataframes
        measurement_id = ["Probability"]*len(TMx_df)
        TMx_df.insert(2, "Measurement", measurement_id)
        # Save df
        TMx_df.to_pickle(os.path.join(microstate_save_path,f"IB_Single_micro_fit_all_{ff}_maps{n_maps}_transition_df.pkl"))
        
        # Entropy
        Ent_arr = np.stack([ele[4] for ele in m_feats]) # [Subject, event]
        col_names = ["Pair_ID", "Event_ID", "Value"]
        col_values = [Pair_id,list(collapsed_event_id.keys())]
        dtypes = [int, str, "float64"]
        Ent_df = numpy_arr_to_pandas_df(Ent_arr, col_names, col_values, dtypes)
        # Add dummy variable to enabling combining of dataframes
        measurement_id = ["Entropy"]*len(Ent_df)
        Ent_df.insert(2, "Measurement", measurement_id)
        # Save df
        Ent_df.to_pickle(os.path.join(microstate_save_path,f"IB_Single_micro_fit_all_{ff}_maps{n_maps}_ratio_joint_entropy_df.pkl"))
        
    # =========================================================================
    # Repeat for 8 alpha microstates
    # =========================================================================
    ff = "alpha"
    n_maps = 8
    # Load all microstate results
    with open(f"{microstate_save_path}Reordered/Intrabrain_microstate_fit_all_{ff}{n_maps}.pkl", "rb") as file:
        microstate_results = pickle.load(file)
    # Load all trialinfos
    with open(f"{microstate_save_path}Intrabrain_microstate_fit_all_{ff}_trialinfos.pkl", "rb") as file:
        trialinfo_list = pickle.load(file)
    
    Microstate_names = [chr(ele) for ele in range(65,65+n_maps)]
    # Insert Z as the symbol for non common microstate
    Microstate_names.insert(0,"Z")
    
    m_labels = [0]*(n_subjects//2)
    events = [0]*(n_subjects//2)
    m_feats = [0]*(n_subjects//2)
    Pair_id = [0]*(n_subjects//2)
    
    for i in range(n_subjects//2):
        m_labels[i], events[i], m_feats[i] = interbrain_microstate_feature_computation(i,
           n_maps, microstate_results, trialinfo_list, sfreq, event_id, collapsed_event_id)
        Pair_id[i] = int(str(Subject_id[2*i])[1:-1])
        print(f"Finished computing interbrain microstate features for pair {Pair_id[i]}")
    
    Pair_id = [ele+100 for ele in Pair_id]
    
    # Save the raw microstate features
    with open(f"{microstate_save_path}/raw_interbrain_single_micro_fit_all_{ff}_maps{n_maps}.pkl", "wb") as filehandle:
        pickle.dump([Pair_id, m_feats], filehandle) # [Subject][Dur_arr,Occ_arr,TCo_arr,TMx_arr,Ent_arr] [Event, map*]
        # * the feature is calculated for each map, where applicable.
        # Transition matrix is calculated for each map -> map transition probability
        # The first row and column correspond to the non common microstate, i.e.
        # there is a different microstate in the pair
    
    # with open(f"{microstate_save_path}/raw_interbrain_single_micro_fit_all_{ff}_maps.pkl", "rb") as file:
    #     Pair_id, m_feats = pickle.load(file) # [Subject][Dur_arr,Occ_arr,TCo_arr,TMx_arr,Ent_arr] [Event, map*]
    
    n_pairs = len(Pair_id)
    
    ### Convert all features to dataframes for further processing
    col_names = ["Pair_ID", "Event_ID", "Microstate", "Value"]
    col_values = [Pair_id,list(collapsed_event_id.keys()),Microstate_names]
    dtypes = [int,str,str,"float64"]
    # Mean duration
    Dur_arr = np.stack([ele[0] for ele in m_feats]) # [Subject, event, n_map]
    Dur_df = numpy_arr_to_pandas_df(Dur_arr, col_names, col_values, dtypes)
    # Add dummy variable to enabling combining of dataframes
    measurement_id = ["Duration"]*len(Dur_df)
    Dur_df.insert(2, "Measurement", measurement_id)
    # Save df
    Dur_df.to_pickle(os.path.join(microstate_save_path,f"IB_Single_micro_fit_all_{ff}_maps{n_maps}_duration_df.pkl"))
    
    # Frequency of occurrence per sec
    Occ_arr = np.stack([ele[1] for ele in m_feats]) # [Subject, event, n_map]
    Occ_df = numpy_arr_to_pandas_df(Occ_arr, col_names, col_values, dtypes)
    # Add dummy variable to enabling combining of dataframes
    measurement_id = ["Occurrence"]*len(Occ_df)
    Occ_df.insert(2, "Measurement", measurement_id)
    # Save df
    Occ_df.to_pickle(os.path.join(microstate_save_path,f"IB_Single_micro_fit_all_{ff}_maps{n_maps}_occurrence_df.pkl"))
    
    # Ratio total Time Covered
    TCo_arr = np.stack([ele[2] for ele in m_feats]) # [Subject, event, n_map]
    TCo_df = numpy_arr_to_pandas_df(TCo_arr, col_names, col_values, dtypes)
    # Add dummy variable to enabling combining of dataframes
    measurement_id = ["Time_covered"]*len(TCo_df)
    TCo_df.insert(2, "Measurement", measurement_id)
    # Save df
    TCo_df.to_pickle(os.path.join(microstate_save_path,f"IB_Single_micro_fit_all_{ff}_maps{n_maps}_ratio_time_covered_df.pkl"))
    
    # Transition matrix should be read as probability of row to column
    xi, xj = np.meshgrid(Microstate_names,Microstate_names)
    _, arrow = np.meshgrid(Microstate_names,["->"]*(n_maps+1))
    
    transition_info = np.char.add(np.char.add(xj,arrow),xi)
    
    TMx_arr = np.stack([ele[3] for ele in m_feats]) # [Subject, event, n_map, n_map]
    TMx_arr = TMx_arr.reshape((n_pairs,len(collapsed_event_id),(n_maps+1)*(n_maps+1))) # Flatten the maps to 1D
    
    col_names = ["Pair_ID", "Event_ID", "Transition", "Value"]
    col_values = [Pair_id,list(collapsed_event_id.keys()),transition_info.flatten()]
    TMx_df = numpy_arr_to_pandas_df(TMx_arr, col_names, col_values, dtypes)
    # Add dummy variable to enabling combining of dataframes
    measurement_id = ["Probability"]*len(TMx_df)
    TMx_df.insert(2, "Measurement", measurement_id)
    # Save df
    TMx_df.to_pickle(os.path.join(microstate_save_path,f"IB_Single_micro_fit_all_{ff}_maps{n_maps}_transition_df.pkl"))
    
    # Entropy
    Ent_arr = np.stack([ele[4] for ele in m_feats]) # [Subject, event]
    col_names = ["Pair_ID", "Event_ID", "Value"]
    col_values = [Pair_id,list(collapsed_event_id.keys())]
    dtypes = [int, str, "float64"]
    Ent_df = numpy_arr_to_pandas_df(Ent_arr, col_names, col_values, dtypes)
    # Add dummy variable to enabling combining of dataframes
    measurement_id = ["Entropy"]*len(Ent_df)
    Ent_df.insert(2, "Measurement", measurement_id)
    # Save df
    Ent_df.to_pickle(os.path.join(microstate_save_path,f"IB_Single_micro_fit_all_{ff}_maps{n_maps}_ratio_joint_entropy_df.pkl"))
    
    
    # %% Two-brain microstates fit all data
    """
    The two observe and imitate conditions are collapesed
    Instead of having ppn1 being observer/follower in 8 trials and actor/leader
    in 8 trials, we will fix the topomap from "ppn1, top row" to always be
    observer and follower. This means for condition 6 and 7, ppn2 will be treated
    as ppn1 so the first topomap is still being fitted to the observer/follower!
    So the first microstate (top row) will always correspond to the Observer and Follower
    And the 2nd paired microstate (bot row) will always correspond to Actor and Leader
    
    Additionally we compute features for 8 trials and then take the average instead
    of all 16. This is done in order to compute it for the asymmetrical trials
    without flipping, as the flip itself can create artefacts.
    
    And the same process is repeated for the symmetrical conditions to be consistent,,
    although it shouldn't have a big impact for those trials
    """
    
    # Compute two-person microstates for each pair, fitted for all data
    # We will concatenate the pairs along the channel axis
    # Loop over frequencies
    for f in len(all_freq_ranges):
        ff = freq_names[f]
        freq_range0 = all_freq_ranges[f]
        # =========================================================================
        # First the microstate topographies are determined
        # It might be an advantage to run the estimation of microstates on a HPC
        # =========================================================================
        # Get data from all pairs before performing kmeans
        np.random.seed(1234)
        n_clusters=[3, 4, 5, 6, 7, 8, 9, 10]
        n_runs = 100 # increased to 100 runs!
        # Get current time
        c_time1 = time_now(); print(c_time1)
        # Save RAM by appending directly to array instead of making list and then array
        pair_arr_indices = [0]
        trialinfo_list = []
        events_list = []
        for i in range(n_pairs):
            tmp_data, tmp_trialinfo, tmp_events = prepare_2P_micro_arr_collapsed_events(i, sfreq, event_id, freq_range=freq_range0, standardize=True)
            pair_arr_indices.append(len(tmp_data))
            trialinfo_list.append(tmp_trialinfo)
            events_list.append(tmp_events)
            if i == 0: # first run initiation
                micro_data_all = tmp_data
            else:
                micro_data_all = np.append(micro_data_all,tmp_data, axis=0)
            del tmp_data # clear up space
            print(f"Finished preparing microstate data for pair {Pair_id[i]}")
        
        # Use cumulative sum to determine indices for each pair's data
        pair_indices = np.cumsum(pair_arr_indices)
        
        # Save the trialinfos and events from all pairs, for easier access in later steps
        with open(f"{microstate_save_path}Dualmicro_fit_all_{ff}_trial_events_infos.pkl", "wb") as filehandle:
            pickle.dump([Pair_id,trialinfo_list,events_list], filehandle) # [maps, L, gfp_peaks, gev, cv_min, pair_idx]
        
    
        # # with args parser in hpc
        # n_maps = n_clusters[(args.map_idx-1)]
        # print(f"Running analysis for maps: {n_maps}")
        # print("Memory used by the micro data array (GB):",micro_data_all.nbytes*9.31e-10)
        
        for n_maps in n_clusters: # Don't use for loop on the HPC!
            # Run the 100 runs in batches of 10 to save underway in case the job script terminates
            best_cv_crit = 9999 # initialize unreasonably high value
            for r in range(10):
                microstate_results = list(kmeans_dualmicro(micro_data_all, n_maps,
                                                            n_runs=int(n_runs/10),maxiter=1000))
                # Overwrite the maps if a lower CV criterion was found for the initiation
                if microstate_results[4] < best_cv_crit:
                    microstate_results.append(pair_indices)
                    # Save results
                    with open(f"{microstate_save_path}Dualmicro_fit_all_{ff}_data_maps{n_maps}.pkl", "wb") as filehandle:
                        pickle.dump(microstate_results, filehandle) # [maps, L, gfp_peaks, gev, cv_min, pair_idx]
                    print(f"Updated the microstates. Previous best CV: {best_cv_crit}",
                          f"new best CV criterion : {microstate_results[4]}")
                    # Update best cv criterion value
                    best_cv_crit = microstate_results[4]
        
                print(f"Finished sub-run {r+1} out of 10")
        
            print(f"Finished microstate analysis for n_maps = {n_maps}")
            print("Started", c_time1, "\nCurrent",time_now())
        
        # =========================================================================
        # # Evaluate microstates fitted to all data
        # =========================================================================
        # Get summary results
        microstate_summary_results = []
        
        for n_maps in n_clusters:
            with open(f"{microstate_save_path}Dualmicro_fit_all_{ff}_data_maps{n_maps}.pkl", "rb") as file:
                microstate_results = pickle.load(file)
            # Also save summary results across n_maps
            microstate_summary_results.append([microstate_results[0],microstate_results[3],microstate_results[4]])
        
        # Use CV criterion to estimate best number of microstates
        cv_gev_arr = np.zeros((len(n_clusters),2))
        for imap in range(len(n_clusters)):
            gev = np.sum(microstate_summary_results[imap][1])
            cv = microstate_summary_results[imap][2]
            cv_gev_arr[imap,:] = [cv, gev]
        
        # Convert to Pandas dataframe
        col_names = ["n_Microstates", "Fit_Criteria", "Value"]
        Fit_Criteria = ["CV Criterion", "Global Explained Variance"]
        dtypes = [int,str,"float64"]
        
        cv_gev_df = numpy_arr_to_pandas_df(cv_gev_arr, col_names = col_names, col_values = [n_clusters,Fit_Criteria],
                                           dtypes = dtypes)
        # Evaluate optimal n_Microstates
        h_order = Fit_Criteria
        g = sns.FacetGrid(data=cv_gev_df,row=None,
                          margin_titles=True, height=8, aspect=1.5)
        g = g.map(sns.pointplot,"n_Microstates", "Value", "Fit_Criteria",
                  dodge=0, capsize=0.18, errorbar=None, linestyles=["-", "-"],
                  markers=["o", "o"], hue_order=h_order, palette=sns.color_palette())
        g.add_legend()
        plt.subplots_adjust(top=0.9, right=0.85, left=0.1)
        g.fig.suptitle("Mean CV Criterion and GEV", fontsize=18)
        g.set_axis_labels(x_var="Number of Microstates",
                          y_var="GEV and CV",
                          fontsize=14)
        # The lower CV the better. Measure of residual variance
        # But the higher GEV the better.
        # Save file
        g.savefig(f"{fig_save_path}Microstates/Fit_all_{ff}/"+"Dualmicro_fit_all_{ff}_CV_Criterion_GEV"+".png")
        
        # Count which number of microstates have the lowest cv criterion for each subject
        min_idx = np.argmin(cv_gev_df.loc[cv_gev_df["Fit_Criteria"]=="CV Criterion","Value"])
        cv_gev_df.loc[cv_gev_df["Fit_Criteria"]=="CV Criterion"].iloc[min_idx]
        
        # Visualize the microstates
        # Prior to re-ordering    
        for ii in range(len(n_clusters)):
            plot_dualmicro(n_clusters[ii], microstate_summary_results[ii][0], microstate_summary_results[ii][1], epoch.info)
        
        # =========================================================================
        # # Re-order two-person microstates
        # # This is only run once, after microstates are created
        # # We only do it for 8 microstates, which was the optimal number
        # =========================================================================
        n_maps = 8
        ii = n_clusters.index(n_maps)
        
        with open(f"{microstate_save_path}Dualmicro_fit_all_{ff}_data_maps{n_maps}.pkl", "rb") as file:
            microstate_results = pickle.load(file)
        
        maps, m_labels, gfp_peaks, gev, cv_min, pair_idx = microstate_results