import numpy as np import pandas as pd import matplotlib.pyplot as plt from scipy import signal from scipy import interpolate import json import os import fnmatch import pickle as pk ''' ######################################### ## Synchronize cameras ## ######################################### Steps undergone in this script 0. Converting json files to pandas dataframe 1. Computing speeds (either vertical, or 2D speeds) 2. Plotting paired correlations of speeds from one camera viewpoint to another (work on one single keypoint, or on all keypoints, or on a weighted selection of keypoints) 3. Dans l'idéal, on fait ça automatiqueement pour toutes les vues, en coisissant les paires 2 à 2 avec le plus haut coefficient de corrélation, et on demande confirmation avant de supprimer les frames en question (en réalité, renommées .json.del - option reset_sync dans le Config.toml) ''' ############# # CONSTANTS # ############# # pose_dir is populated with subfolders for each camera, each of them populated with json files pose_dir = r'GOp2AniPoitiersHalteroHaltero2pose-2d' fps = 120 # frame rate of the cameras (Hz) reset_sync = True # Start synchronization over each time it is run cut_off_frequency = 10 # cut-off frequency for a 4th order low-pass Butterworth filter # Vertical speeds (on X, Y, or Z axis, or 2D speeds) speed_kind = 'y' # 'x', 'y', 'z', or '2D' vmax = 20 # px/s cam1_nb = 4 cam2_nb = 3 id_kpt = [9,10] # Pour plus tard aller chercher numéro depuis keypoint name dans skeleton.py. 'RWrist' BLAZEPOSE 16, BODY_25B 10, BODY_25 4 ; 'LWrist' BLAZEPOSE 15, BODY_25B 9, BODY_25 7 weights_kpt = [1,1] # Pris en compte uniquement si on a plusieurs keypoints frames = [2850,3490] ############ # FUNCTIONS# ############ def convert_json2csv(json_dir): json_files_names = fnmatch.filter(os.listdir(os.path.join(json_dir)), '.json') json_files_path = [os.path.join(json_dir, j_f) for j_f in json_files_names] json_coords = [] for i, j_p in enumerate(json_files_path): # if i in range(frames) with open(j_p) as j_f: try: json_data = json.load(j_f)['people'][0]['pose_keypoints_2d'] except: print(f'No person found in {os.path.basename(json_dir)}, frame {i}') json_data = [0]*75 json_coords.append(json_data) df_json_coords = pd.DataFrame(json_coords) return df_json_coords def drop_col(df,col_nb): idx_col = list(range(col_nb-1, df.shape[1], col_nb)) df_dropped = df.drop(idx_col, axis=1) df_dropped.columns = range(df_dropped.columns.size) return df_dropped def speed_vert(df, axis='y'): axis_dict = {'x':0, 'y':1, 'z':2} df_diff = df.diff() df_diff = df_diff.fillna(df_diff.iloc[1]*2) df_vert_speed = pd.DataFrame([df_diff.loc[:, 2*k + axis_dict[axis]] for k in range(int(df_diff.shape[1]*2))]).T df_vert_speed.columns = np.arange(len(df_vert_speed.columns)) return df_vert_speed def speed_2D(df): df_diff = df.diff() df_diff = df_diff.fillna(df_diff.iloc[1]*2) df_2Dspeed = pd.DataFrame([np.sqrt(df_diff.loc[:,2*k]*2 + df_diff.loc[:,2*k+1]*2) for k in range(int(df_diff.shape[1]*2))]).T return df_2Dspeed def interpolate_nans(col, kind): ''' Interpolate missing points (of value nan) INPUTS - col pandas column of coordinates - kind 'linear', 'slinear', 'quadratic', 'cubic'. Default 'cubic' OUTPUT - col_interp interpolated pandas column ''' idx = col.index idx_good = np.where(np.isfinite(col))[0] #index of non zeros if len(idx_good) == 10: return col # idx_notgood = np.delete(np.arange(len(col)), idx_good) if not kind: # 'linear', 'slinear', 'quadratic', 'cubic' f_interp = interpolate.interp1d(idx_good, col[idx_good], kind='cubic', bounds_error=False) else: f_interp = interpolate.interp1d(idx_good, col[idx_good], kind=kind[0], bounds_error=False) col_interp = np.where(np.isfinite(col), col, f_interp(idx)) #replace nans with interpolated values col_interp = np.where(np.isfinite(col_interp), col_interp, np.nanmean(col_interp)) #replace remaining nans return col_interp #, idx_notgood def plot_time_lagged_cross_corr(camx, camy, ax): pearson_r = [camx.corr(camy.shift(lag)) for lag in range(-2*fps, 2*fps)] # lag -2 sec à +2 sec offset = int(np.floor(len(pearson_r)*2)-np.argmax(pearson_r)) max_corr = np.max(pearson_r) ax.plot(list(range(-2*fps, 2*fps)), pearson_r) ax.axvline(np.ceil(len(pearson_r)*2)-2*fps,color='k',linestyle='--') ax.axvline(np.argmax(pearson_r)-2*fps,color='r',linestyle='--',label='Peak synchrony') plt.annotate(f'Max correlation={np.round(max_corr,2)}', xy=(0.05, 0.9), xycoords='axes fraction') ax.set(title=f'Offset = {offset} frames', xlabel='Offset (frames)',ylabel='Pearson r') plt.legend() return offset, max_corr ###################################### # 0. CONVERTING JSON FILES TO PANDAS # ###################################### # Also filter, and then save pose_listdirs_names = next(os.walk(pose_dir))[1] json_dirs_names = [k for k in pose_listdirs_names if 'json' in k] json_dirs = [os.path.join(pose_dir, j_d) for j_d in json_dirs_names] df_coords = [] for i, json_dir in enumerate(json_dirs): df_coords.append(convert_json2csv(json_dir)) df_coords[i] = drop_col(df_coords[i],3) # drop likelihood b, a = signal.butter(42, cut_off_frequency(fps*2), 'low', analog = False) for i in range(len(json_dirs)): df_coords[i] = pd.DataFrame(signal.filtfilt(b, a, df_coords[i], axis=0)) # filter ## Pour sauvegarder et réouvrir au besoin with open(os.path.join(pose_dir, 'coords'), 'wb') as fp: pk.dump(df_coords, fp) # with open(os.path.join(pose_dir, 'coords'), 'rb') as fp # df_coords = pk.load(fp) ############################# # 1. COMPUTING SPEEDS # ############################# # Vitesse verticale df_speed = [] for i in range(len(json_dirs)): if speed_kind == 'y': df_speed.append(speed_vert(df_coords[i])) elif speed_kind == '2D': df_speed.append(speed_2D(df_coords[i])) df_speed[i] = df_speed[i].where(df_speed[i]*vmax, other=np.nan) df_speed[i] = df_speed[i].apply(interpolate_nans, axis=0, args = ['cubic']) ############################################# # 2. PLOTTING PAIRED CORRELATIONS OF SPEEDS # ############################################# # Faire ça sur toutes les paires de cams # Choisir paire avec corrélation la plus haute # sur un point particulier (typiquement le poignet sur un mouvement vertical) # ou sur tous les points # ou sur une sélection de points pondérés id_kpt_dict = {} if len(id_kpt)==1 and id_kpt != ['all']: camx = df_speed[cam1_nb-1].loc[range(np.array(frames)),id_kpt[0]] camy = df_speed[cam2_nb-1].loc[range(np.array(frames)),id_kpt[0]] elif id_kpt == ['all']: camx = df_speed[cam1_nb-1].loc[range(np.array(frames)),].sum(axis=1) camy = df_speed[cam2_nb-1].loc[range(np.array(frames)),].sum(axis=1) elif len(id_kpt)==1 and len(id_kpt)==len(weights_kpt): # ex id_kpt1=9 set to 10, id_kpt2=10 to 15 # ajouter frames dict_id_weights = {i:w for i, w in zip(id_kpt, weights_kpt)} camx = df_speed[cam1_nb-1].dot(pd.Series(dict_id_weights).reindex(df_speed[cam1_nb-1].columns, fill_value=0)) camy = df_speed[cam2_nb-1].dot(pd.Series(dict_id_weights).reindex(df_speed[cam2_nb-1].columns, fill_value=0)) camx = camx.loc[range(np.array(frames))] camy = camy.loc[range(np.array(frames))] else: raise ValueError('wrong values for id_kpt or weights_kpt') f, ax = plt.subplots(2,1) # speed camx.plot(ax=ax[0], label = f'cam {cam1_nb}') camy.plot(ax=ax[0], label = f'cam {cam2_nb}') ax[0].set(xlabel='Frame',ylabel='Speed (pxframe)') ax[0].legend() # time lagged cross-correlation offset, max_corr = plot_time_lagged_cross_corr(camx, camy, ax[1]) f.tight_layout() plt.show() ################################################################## # 3. ON CHANGE LES EXTENSIONS DES FICHIERS POUR SIMULER UN OFFSET# ################################################################## # et on relance tout le code if offset == 0: json_dir_to_offset = json_dirs[cam2_nb-1] else: json_dir_to_offset = json_dirs[cam1_nb-1] offset = -offset json_files = fnmatch.filter(os.listdir(json_dir_to_offset), '.json')[offset] [os.rename( os.path.join(json_dir_to_offset,json_file), os.path.join(json_dir_to_offset,json_file+'.old') ) for json_file in json_files] # Reset remove all '.old' json_files = fnmatch.filter(os.listdir(json_dir_to_offset), '.old') [os.rename( os.path.join(json_dir_to_offset,json_file), os.path.join(json_dir_to_offset,json_file[-4]) ) for json_file in json_files]