TVSD/_code/lucent-things/npc.py

### Functions for plotting, storing and fitting MEIs
import torch
import torchvision.models as models 
import torchvision.transforms.functional as F
import torch.nn.functional as nnf
from torchvision import datasets, transforms

from lucent.optvis import render, param, transform, objectives
from lucent.modelzoo import inceptionv1, util, inceptionv1_avgPool

import numpy as np
import pickle
from scipy.io import savemat,loadmat
from pathlib import Path
from os import listdir
from os.path import isfile, join

import matplotlib.pyplot as plt
from matplotlib.patches import Ellipse
import shapely.affinity
import shapely.geometry
from skimage.draw import polygon
from skimage.morphology import convex_hull_image
from skimage.filters import gaussian as smoothing
from PIL import Image  

import math
from tqdm import tqdm

from helper import gaussian, moments, fitgaussian, load, gabor_patch, occlude_pic
from neural_model import Model

def load_trained_model(gen_path,name,roi,layer = None):
    if layer is None:
        data_filename = gen_path + name + '/snapshots/grid_search_array'+ roi + '.pkl'
        f = open(data_filename,"rb")
        cc = pickle.load(f)
        val_corrs = cc['val_corrs']
        params = cc['params']
        val_corrs = np.array(val_corrs)
        layer = params[np.where(val_corrs==val_corrs.max())[0][0].astype('int')][0]
    
    n_neurons = 0
    layer_filename = gen_path + 'val_corr_'+ name + roi + '_' + layer + '.pkl'
    if isfile(layer_filename):
        f = open(layer_filename,"rb")
        cc = pickle.load(f)
        val_corrs = cc['val_corrs']
        n_neurons = len(val_corrs)
                
    if n_neurons == 0:
        data_filename = gen_path + name + '/data_THINGS_array'+ roi +'_v1.pkl'
        f = open(data_filename,"rb")
        cc = pickle.load(f)
        val_data = cc['val_data']
        n_neurons = val_data.shape[1]

    pretrained_model = inceptionv1(pretrained=True)
    trained_model = Model(pretrained_model,layer,n_neurons,device='cpu')
    trained_model.load_state_dict(torch.load(gen_path + name + '/snapshots/'+ name + roi + '_' + layer + '_neural_model.pt',map_location=torch.device('cpu')))
    return trained_model,n_neurons#,good_neurons

def plot_layer_corrs(gen_path,name,layers,roi):
    all_corrs = []
    for layer in layers:
        layer_filename = gen_path + 'val_corr_'+ name + roi + '_' + layer + '.pkl'
        f = open(layer_filename,"rb")
        cc = pickle.load(f)
        val_corrs = cc['val_corrs']
        all_corrs.append(val_corrs)
        
    all_corrs = np.array(all_corrs)
    fig1, ax = plt.subplots()
    c = '#3399ff'
    ax.set_title('Layers:')
    ax.boxplot(all_corrs.transpose(), labels=layers, notch=True,
               widths=.5,showcaps=False, whis=[2.5,97.5],patch_artist=True,
               showfliers=False,boxprops=dict(facecolor=c, color=c),
               capprops=dict(color=c),whiskerprops=dict(color=c),
               flierprops=dict(color=c, markeredgecolor=c),medianprops=dict(color='w',linewidth=2))
    ax.set_ylabel('Cross-validated Pearson r')
    ax.set_ylim([0,1])
    ax.spines['top'].set_visible(False)
    ax.spines['right'].set_visible(False)
    plt.show()

    temp = np.median(all_corrs,axis=1)
    layer = layers[np.where(temp==temp.max())[0][0].astype('int')]
    
    return all_corrs, layer

def compute_val_corrs(gen_path,name,trained_model,roi):
    data_filename = gen_path + name + '/data_THINGS_array'+ roi +'_v1.pkl'
    f = open(data_filename,"rb")
    cc = pickle.load(f)

    val_img_data = cc['val_img_data']
    val_outputs = trained_model(val_img_data).squeeze()
    val_data = cc['val_data']
    corrs = []
    for n in range(val_outputs.shape[1]):
        corrs.append(np.corrcoef(val_outputs[:,n].cpu().detach().numpy(),val_data[:,n])[1,0])
    return corrs

def good_neurons(trained_model,n_neurons,corrs,make_plots=True):
    z = 1
    all_good_rfs = []
    goods = []
    for n in range(n_neurons):
        trained_model_rf = np.abs(np.reshape(trained_model.w_s[n].squeeze().detach().cpu().numpy(),
                          [np.sqrt(trained_model.w_s.shape[2]).astype('int'),np.sqrt(trained_model.w_s.shape[2]).astype('int')]))
        if corrs[n] > 0:
            z += 1
            goods.append(n)
            trained_model_rf_norm = (trained_model_rf+np.abs(trained_model_rf.min()))/(np.abs(trained_model_rf.max())+np.abs(trained_model_rf.min()))
            all_good_rfs.append(trained_model_rf_norm)
            if make_plots:
                print(z,corrs[n])
                plt.imshow(trained_model_rf, cmap='seismic')
                plt.colorbar()
                plt.show()
                plt.plot(trained_model.w_f[0,n].squeeze().detach().cpu().numpy())
                plt.show()

    goods = np.array(goods)
    all_good_rfs = np.array(all_good_rfs)
    return goods,all_good_rfs

def gaussian_RFs(gen_path,all_good_rfs,goods,corrs,all_corrs,pixperdeg,stim_size,mask_size,trained_model,name,roi,shift_x=0,shift_y=0):
    centrex = []
    centrey = []
    szx = []
    szy = []
    szdeg = []
    masks = []
    sparsity = []
    all_feats = []
    pixperdeg_reduced = all_good_rfs[0].shape[0]/all_good_rfs*pixperdeg
    scaling_f = stim_size/all_good_rfs[0].shape[0]
    scaling_mask = mask_size/all_good_rfs[0].shape[0]
    pixperdeg_reduced_mask = all_good_rfs[0].shape[0]/mask_size*pixperdeg
    fovea_x = stim_size/2 - shift_x
    fovea_y = stim_size/2 - shift_y
    ax = plt.gca()
    ax.set_title('Spatial RFs:')
    for n in range(len(goods)):

        # fit 2d Gaussian to W_s
        data = all_good_rfs[n]
        params = fitgaussian(data)
        fit = gaussian(*params)
        plt.imshow(data, cmap=plt.cm.gist_earth_r)
        (height, y, x, width_y, width_x) = params # x and y are shifted in img coords
        circle = Ellipse((x, y), 2*1.65*width_x, 2*1.65*width_y, edgecolor='r', facecolor='None', clip_on=True)
        ax.add_patch(circle)
        centrex.append(x*scaling_f-fovea_x)
        centrey.append(fovea_y-y*scaling_f)
        szx.append(2*1.65*width_x*scaling_f)
        szy.append(2*1.65*width_y*scaling_f)
        szdeg.append(np.mean((2*1.65*width_x/pixperdeg_reduced,2*1.65*width_y/pixperdeg_reduced)))

        # create binary mask summing up the estimated 2d Gaussians (95% CI)
        mask = np.zeros(shape=(mask_size,mask_size), dtype="bool")
        circ = shapely.geometry.Point((x*scaling_mask,y*scaling_mask)).buffer(1)
        ell  = shapely.affinity.scale(circ, 1.65*width_x*scaling_mask+pixperdeg_reduced_mask, 1.65*width_y*scaling_mask+pixperdeg_reduced_mask)
        ell_coords = np.array(list(ell.exterior.coords))
        cc, rr = polygon(ell_coords[:,0], ell_coords[:,1], mask.shape)
        mask[rr,cc] = True
        masks.append(mask)
        
        feats = trained_model.w_f[0,goods[n]].squeeze().detach().cpu().numpy()
        chn_spars = (1 - (((np.sum(np.abs(feats)) / len(feats)) ** 2) / (np.sum(np.abs(feats) ** 2) / len(feats)))) / (1 - (1 / len(feats)))
        sparsity.append(chn_spars)
        all_feats.append(feats)

    plt.show()
    masks = np.array(masks)
    centrex = np.array(centrex)
    centrey = np.array(centrey)
    szx = np.array(szx)
    szy = np.array(szy)
    szdeg = np.array(szdeg)
    sparsity = np.array(sparsity)
    all_feats = np.array(all_feats)

     # plot:
    labels = ['Sparsity index','Frequency (neurons)','']
    c = '#3399ff'
    xline = [np.nanmedian(sparsity)]
    fig1, ax = plt.subplots()
    ax.hist(sparsity,bins=10,color=c)
    if len(xline) != 0:
        plt.axvline(xline[0], color='k', linestyle='dashed')
    if len(labels) != 0:
        ax.set_xlabel(labels[0])
        ax.set_ylabel(labels[1])
        ax.set_title(labels[2])
    ax.set_xlim([0,1])
    ax.spines['top'].set_visible(False)
    ax.spines['right'].set_visible(False)
    ax.set_title('Feature sparsness:')
    plt.show()
    
    all_corrs = np.moveaxis(all_corrs,0,-1)
    
    output = {'goods':goods,
             'all_good_rfs':all_good_rfs,
             'cross_val_corr':corrs,
             'layers_cross_val_corr':all_corrs,
             'centrex':centrex,
             'centrey':centrey,
             'szx':szx,
             'szy':szy,
             'szdeg':szdeg,
             'all_feats':all_feats,
             'sparsity':sparsity}
    savemat(gen_path + name + roi + '_good_rfs' + '.mat', output)
    return masks

def generate_MEIS(gen_path,trained_model,name,goods=None,roi='',sign=1,batch_n=1):
    if sign == 1:
        sign_label = 'MEIs/'
    elif sign == -1:
        sign_label = 'MIIs/'
    else:
        raise Exception('The variable sign must be either 1 (for MEIs) or -1 (for MIIs)')
        
    Path(gen_path + sign_label + name + roi + '_fft_decorr_lr_1e-2_l2_1e-3/').mkdir(parents=True, exist_ok=True)

    if goods is None:
        goods = np.linspace(0, trained_model.n_neurons-1, trained_model.n_neurons).astype(int)
        
    device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
    trained_model.to(device).eval()
    all_transforms = [
        #transform.pad(2),
        transform.jitter(8),
        transform.random_scale([n/1000. for n in range(975, 1050)]),
        transform.random_rotate(list(range(-5,5))),
        transform.jitter(4)
       #transforms.Grayscale(3),
    ]
    batch_param_f = lambda: param.image(128, batch=batch_n, fft=True, decorrelate=True)
    cppn_opt = lambda params: torch.optim.Adam(params, 1e-2, weight_decay=1e-3)

    for chn in range(len(goods)):
        obj = objectives.channel("output", int(goods[chn]))*sign
        _ = render.render_vis(trained_model, obj, batch_param_f, cppn_opt, transforms=all_transforms, 
                              show_inline=True, thresholds=(50,))
        for n in range(_[0].shape[0]):
            filename = gen_path + sign_label + name + roi + '_fft_decorr_lr_1e-2_l2_1e-3/' + str(goods[chn]) + '_' + str(n) + '.bmp'
            temp = _[0][n]#*np.repeat(np.expand_dims(masks[chn],-1),3,axis=-1)+np.repeat((1-np.expand_dims(masks[chn],-1))*.5,3,axis=-1)
            temp_pic = Image.fromarray(np.uint8((temp)*255))
            temp_pic = temp_pic.resize((500,500),Image.BILINEAR)
            temp_pic.save(filename)

def generate_surround_MEIS(gen_path,trained_model,name,goods=None,roi=''):
    Path(gen_path + 'surrMEIs/' + name + roi + '_fft_decorr_lr_1e-2_l2_1e-3/').mkdir(parents=True, exist_ok=True)

    if goods is None:
        goods = np.linspace(0, trained_model.n_neurons-1, trained_model.n_neurons).astype(int)
        
    device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
    trained_model.to(device).eval()
    all_transforms = [
        transform.pad(2),
        transform.jitter(4),
        transform.random_scale([n/1000. for n in range(975, 1050)]),
        transform.random_rotate(list(range(-5,5))),
        transforms.Grayscale(3),
    ]
    batch_param_f = lambda: param.image(128, batch=1, fft=True, decorrelate=True)
    cppn_opt = lambda params: torch.optim.Adam(params, 1e-2, weight_decay=1e-3)

    for chn in range(len(goods)):
        obj = objectives.channel("output", int(goods[chn]))
        mei = render.render_vis(trained_model, obj, batch_param_f, cppn_opt, transforms=all_transforms, 
                              show_inline=True, thresholds=(50,))

        mask = trained_model.w_s[chn].squeeze()
        mask = torch.reshape(mask,(np.sqrt(mask.shape[0]).astype('int'),np.sqrt(mask.shape[0]).astype('int')))
        mask = np.abs(nnf.interpolate(mask[None,None,:],mei[0].shape[1]).squeeze().cpu().detach().numpy())
        mask = smoothing(mask>(np.std(mask)*3),1)
        mask = np.repeat(mask[:,:,np.newaxis],3,2)
   
        all_transforms = [
            occlude_pic(mei[0], mask,device),
            transform.pad(2),
            transform.jitter(4),
            transform.random_scale([n/1000. for n in range(975, 1050)]),
            transform.random_rotate(list(range(-5,5))),
            transforms.Grayscale(3),
        ]
    
        for i in range(2):
            if i:
                obj = objectives.channel("output", int(goods[chn]))
                filename = gen_path + 'surrMEIs/' + name + roi + '_fft_decorr_lr_1e-2_l2_1e-3/' + str(goods[chn]) + '_positive_Surround.bmp'
            else:
                obj = -objectives.channel("output", int(goods[chn]))
                filename = gen_path + 'surrMEIs/' + name + roi + '_fft_decorr_lr_1e-2_l2_1e-3/' + str(goods[chn]) + '_negative_Surround.bmp'


            _ = render.render_vis(trained_model, obj, batch_param_f, cppn_opt, transforms=all_transforms, 
                              show_inline=True, thresholds=(50,))
            temp = _[0][0]
            temp_pic = Image.fromarray(np.uint8((temp)*255))
            temp_pic = temp_pic.resize((500,500),Image.BILINEAR)
            temp_pic.save(filename)
                       
def ori_tuning(gen_path,stim_size,wavelengths,orientations,phases,contrasts,trained_model,name,goods,roi):
    # load data:
    data_path = gen_path + name + roi + '_good_rfs' + '.mat'
    data_dict = {}
    f = loadmat(data_path)
    for k, v in f.items():
        data_dict[k] = np.array(v)
    centrex = data_dict['centrex'].astype(int)[0]
    centrey = data_dict['centrey'].astype(int)[0]

    # define transforms:
    #transform = transforms.Compose([transforms.ToPILImage(),
    #                            transforms.Resize([224,224]),
    #                            transforms.ToTensor(),
    #                            transforms.Normalize(mean=[0.485, 0.456, 0.406],
    #                            std=[0.229, 0.224, 0.225])])
    
    transform = transforms.Compose([transforms.ToPILImage(),
                                transforms.Resize([224,224]),
                                transforms.ToTensor()])
    # RF center:
    px_x = np.median(centrex)
    px_y = np.median(centrey)

    # iterate gabors:
    stimuli = []
    all_params = []
    for w in range(len(wavelengths)):
        for o in range(len(orientations)):
            for p in range(len(phases)):
                for c in range(len(contrasts)):
                    
                    min_b = 0.5 - contrasts[c]/2
                    max_b = 0.5 + contrasts[c]/2

                    # create stimulus:
                    stimulus = gabor_patch([stim_size,stim_size], pos_yx = [px_y,px_x], 
                                           radius = stim_size, wavelength = wavelengths[w], 
                                           orientation = orientations[o], phase = phases[p],
                                           min_brightness = min_b, max_brightness = max_b)
                    stimuli.append(stimulus)
                    all_params.append([wavelengths[w],orientations[o],phases[p],contrasts[c]])

    all_params = np.array(all_params)

    # get response:
    stimuli = np.array(stimuli).squeeze()
    all_resps_tot = []
    for s in range(stimuli.shape[0]):
        temp = transform(np.moveaxis(stimuli[s]*255,0,-1).squeeze().astype(np.uint8))#.to('cpu')
        all_resps_tot.append(trained_model(temp[None,:,:,:]).squeeze()[goods].detach().numpy())

    all_resps_tot = np.array(all_resps_tot)

    OI_sel = []
    BEST_params = []
    TUN_curves = []
    SFS_curves = []
    CNTR_curves = []
    for n in range(len(goods)):
        # reshape the overall response:
        all_resps = all_resps_tot[:,n].reshape(len(wavelengths),len(orientations),len(phases),len(contrasts))

        # compute the orientation index OI:
        norm_resp = (all_resps - np.min(all_resps)) / (np.max(all_resps) - np.min(all_resps))
        max_idx = np.where(norm_resp == np.max(norm_resp))
        if len(max_idx)>1:
            max_idx = np.array(max_idx)
            max_idx = max_idx[:,-1]

        ortho_idx = np.where((180 * orientations / math.pi) == (180 * orientations / math.pi)[max_idx[1]] + 90)
        if np.array(ortho_idx).size == 0: 
            ortho_idx = np.where((180 * orientations / math.pi) == (180 * orientations / math.pi)[max_idx[1]] - 90)
        chn_sel = (norm_resp.max() - norm_resp[max_idx[0],ortho_idx,max_idx[2],max_idx[3]]) / (norm_resp.max() + norm_resp[max_idx[0],ortho_idx,max_idx[2],max_idx[3]])
        OI_sel.append(np.squeeze(chn_sel))
        
        # find best parameters (= max response)
        #print(np.where(all_resps_tot == np.max(all_resps))[0][0])
        par_max = all_params[np.int(np.where(all_resps_tot == np.max(all_resps))[0][0]),:]
        BEST_params.append(par_max)
        
        # output all tuning curve
        ori_curve = np.squeeze(norm_resp[max_idx[0],:,max_idx[2],max_idx[3]])
        TUN_curves.append(ori_curve)
        
        #sf_curve = np.squeeze(norm_resp[:,max_idx[1],max_idx[2],max_idx[3]])
        sf_curve = np.squeeze(all_resps[:,max_idx[1],max_idx[2],max_idx[3]])
        SFS_curves.append(sf_curve)
        
        con_curve = np.mean(norm_resp,axis=(0,1,2))
        CNTR_curves.append(con_curve)

    OI_sel = np.array(OI_sel)
    BEST_params = np.array(BEST_params)
    TUN_curves = np.array(TUN_curves)
    CNTR_curves = np.array(CNTR_curves)

    # plot:
    labels = ['Orientation selectivity index','Frequency (neurons)','']
    c = '#3399ff'
    xline = [np.nanmedian(OI_sel)]
    fig1, ax = plt.subplots()
    ax.hist(OI_sel,bins=10,color=c)
    if len(xline) != 0:
        plt.axvline(xline[0], color='k', linestyle='dashed')
    if len(labels) != 0:
        ax.set_xlabel(labels[0])
        ax.set_ylabel(labels[1])
        ax.set_title(labels[2])
    ax.set_xlim([0,1])
    ax.spines['top'].set_visible(False)
    ax.spines['right'].set_visible(False)
    ax.set_title('Orientation tuning:')
    plt.show()
    
    output = {'goods':goods,
              'OI_sel':OI_sel,
              'SFS_curves':SFS_curves,
              'TUN_curves':TUN_curves,
              'CNTR_curves':CNTR_curves,
              'BEST_params':BEST_params}
    savemat(gen_path + name + roi + '_ori_sel' + '.mat', output)
    
def size_tuning(gen_path,stim_size,radii,trained_model,name,goods,roi):
    # load data:
    data_path = gen_path + name + roi + '_good_rfs' + '.mat'
    data_dict = {}
    f = loadmat(data_path)
    for k, v in f.items():
        data_dict[k] = np.array(v)
    centrex = data_dict['centrex'].astype(int)[0]
    centrey = data_dict['centrey'].astype(int)[0]

    radii_f = radii.astype(int)

    data_path = gen_path + name + roi + '_ori_sel' + '.mat'
    data_dict = {}
    f = loadmat(data_path)
    for k, v in f.items():
        data_dict[k] = np.array(v)
    BEST_params = data_dict['BEST_params']

    # define transforms:
    transform = transforms.Compose([transforms.ToPILImage(),
                                transforms.Resize([224,224]),
                                transforms.ToTensor(),
                                transforms.Normalize(mean=[0.485, 0.456, 0.406],
                                std=[0.229, 0.224, 0.225])])
    
    SSI_sel = []
    BEST_size = []
    S_TUN_curves = []
    for n in tqdm(range(len(goods)), disable=False):
         # RF center:
        px_x = centrex[n]
        px_y = centrey[n]
        params = BEST_params[n,:]

        # iterate gabors:
        stimuli = []
        for r in range(len(radii_f)):
            # create stimulus:
            stimulus = gabor_patch([stim_size,stim_size], pos_yx = [px_y,px_x], 
                                   radius = radii_f[r], wavelength = params[0], 
                                   orientation = params[1], phase = params[2])
            stimuli.append(stimulus)

        # get response:
        stimuli = np.array(stimuli).squeeze()
        all_resps = []
        for s in range(stimuli.shape[0]):
            temp = transform(np.moveaxis(stimuli[s]*255,0,-1).squeeze().astype(np.uint8))#.to('cpu')
            all_resps.append(trained_model(temp[None,:,:,:]).squeeze()[goods[n]].detach().numpy())

        all_resps = np.array(all_resps)

        # find best size (= max response)
        index = np.where(all_resps == np.max(all_resps))[0]
        if len(index) > 1:
            index = index[0]
        rad_max = radii[np.int(index)]
        BEST_size.append(rad_max)
        

        # compute the surround suppression index SS:
        norm_resp = (all_resps - np.min(all_resps)) / (np.max(all_resps) - np.min(all_resps))
        max_resp = norm_resp[np.int(index)]
        fin_resp = norm_resp[-1]
        if max_resp == fin_resp:
            chn_sel = 0
        else:
            chn_sel = (max_resp - fin_resp) / (max_resp + fin_resp) 
        SSI_sel.append(np.squeeze(chn_sel))
        S_TUN_curves.append(norm_resp)

    SSI_sel = np.array(SSI_sel)
    BEST_size = np.array(BEST_size)
    S_TUN_curves = np.array(S_TUN_curves)

    # plot:
    labels = ['Surround suppression index','Frequency (neurons)','']
    c = '#3399ff'
    xline = [np.nanmedian(SSI_sel)]
    fig1, ax = plt.subplots()
    ax.hist(SSI_sel,bins=10,color=c)
    if len(xline) != 0:
        plt.axvline(xline[0], color='k', linestyle='dashed')
    if len(labels) != 0:
        ax.set_xlabel(labels[0])
        ax.set_ylabel(labels[1])
        ax.set_title(labels[2])
    ax.set_xlim([0,1])
    ax.spines['top'].set_visible(False)
    ax.spines['right'].set_visible(False)
    ax.set_title('Surround suppression:')
    plt.show()
    
    output = {'goods':goods,
              'SSI_sel':SSI_sel,
              'S_TUN_curves':S_TUN_curves,
              'BEST_size':BEST_size}
    savemat(gen_path + name + roi + '_size_sel' + '.mat', output)

def get_full_resps(gen_path,trained_model,goods,name,roi,folder):
    trained_model.to('cpu').eval()
    trained_model.w_s = torch.nn.Parameter(torch.ones(trained_model.w_s.shape),requires_grad=False)
    transform = transforms.Compose([transforms.Resize([224,224]),
                            transforms.ToTensor(),
                            transforms.Normalize(mean=[0.485, 0.456, 0.406],
                            std=[0.229, 0.224, 0.225])])
    dataset = datasets.ImageFolder(folder, transform=transform)
    dataloader = torch.utils.data.DataLoader(dataset, batch_size=len(dataset.imgs), shuffle=False)
    img_data, junk = next(iter(dataloader))
    resps = trained_model(img_data).squeeze().detach().numpy()[:,goods]
                
    output = {'goods':goods,
             'responses':resps}
    savemat(gen_path + name + roi + '_responses' + '.mat', output)
    return resps, img_data


def output(gen_path,name,roi,goods,good_neurons,resps=False):
    # the output must be re-arranged in the same format as the input files
    # but we applied two selections (one for reliability and one for val-corr)
    max_n = len(good_neurons)
    tot = np.array(np.where(good_neurons.squeeze()==1)).squeeze()
    goods_ok = tot[goods]
    
    data_dict = {}
    
    data_path = gen_path + name + roi + '_good_rfs' + '.mat'
    f = loadmat(data_path)
    for k, v in f.items():
        if k[0] != '_':
            temp = np.array(v).squeeze()
            #idx = np.array(np.where(np.array(temp.shape) == np.array(goods.shape[0]))).squeeze().astype(int)
            ts = np.array(temp.shape)
            ts[0] = max_n
            temp_r = np.empty(ts)
            temp_r.fill(np.nan)
            if np.array(temp.shape[0]) == np.array(goods.shape[0]):
                temp_r[goods_ok] = temp
            else:
                temp_r[tot] = temp
            data_dict[k] = temp_r
    
    data_path = gen_path + name + roi + '_ori_sel' + '.mat'
    f = loadmat(data_path)
    for k, v in f.items():
        if k[0] != '_':
            temp = np.array(v).squeeze()
            #idx = np.array(np.where(np.array(temp.shape) == np.array(goods.shape[0]))).squeeze().astype(int)
            ts = np.array(temp.shape)
            ts[0] = max_n
            temp_r = np.empty(ts)
            temp_r.fill(np.nan)
            if np.array(temp.shape[0]) == np.array(goods.shape[0]):
                temp_r[goods_ok] = temp
            else:
                temp_r[tot] = temp
            data_dict[k] = temp_r
            
    data_path = gen_path + name + roi + '_size_sel' + '.mat'
    f = loadmat(data_path)
    for k, v in f.items():
        if k[0] != '_':
            temp = np.array(v).squeeze()
            #idx = np.array(np.where(np.array(temp.shape) == np.array(goods.shape[0]))).squeeze().astype(int)
            ts = np.array(temp.shape)
            ts[0] = max_n
            temp_r = np.empty(ts)
            temp_r.fill(np.nan)
            if np.array(temp.shape[0]) == np.array(goods.shape[0]):
                temp_r[goods_ok] = temp
            else:
                temp_r[tot] = temp
            data_dict[k] = temp_r
    
    data_dict['good_chns'] = good_neurons
    if resps:
        data_path = gen_path + name + roi + '_responses' + '.mat'
        f = loadmat(data_path)
        for k, v in f.items():
            if k[0] != '_':
                temp = np.transpose(np.array(v).squeeze())
                ts = np.array(temp.shape)
                ts[0] = max_n
                temp_r = np.empty(ts)
                temp_r.fill(np.nan)
                if np.array(temp.shape[0]) == np.array(goods.shape[0]):
                    temp_r[goods_ok] = temp
                else:
                    temp_r[tot] = temp
                data_dict[k] = temp_r
    
    savemat(gen_path + name + roi + '_OUTPUT' + '.mat', data_dict)