Exemple #1
0
def plot_trajectories_from_dataset(dataset, keys, interpolated_data='hide'):
    '''
    interpolated_data - if trajectories contain interpolated data, use 'hide' to hide that data, 'dotted' to show it as a dotted line, or 'show' to show it in its entirety
    '''
    import fly_plot_lib.plot as fpl # download at: https://github.com/florisvb/FlyPlotLib
    from fly_plot_lib.colormaps import viridis as viridis
    
    path = dataset.config.path
    bgimg_filename = get_filename(path, 'bgimg_N1.png')
    bgimg = plt.imread(bgimg_filename)
    
    fig = plt.figure()
    ax = fig.add_subplot(111)
    ax.set_aspect('equal')
    
    ax.imshow(bgimg, cmap='gray')
    
    for key in keys: 
        trajec = dataset.trajec(key)
        if 'interpolated' in trajec.__dict__.keys():
            interpolated_indices = np.where(trajec.interpolated==1)[0]
            if interpolated_data == 'dotted':
                r = np.arange(0, len(interpolated_indices), 5)
                interpolated_indices = interpolated_indices[r]
            if interpolated_data != 'show':
                trajec.position_x[interpolated_indices] = np.nan
                trajec.position_y[interpolated_indices] = np.nan
        l = -1
        fpl.colorline(ax, trajec.position_x[0:l], trajec.position_y[0:l], trajec.time_epoch[0:l]-trajec.time_epoch[0:l][0], linewidth=2, colormap='none', norm=None, zorder=1, alpha=1, linestyle='solid', cmap=viridis)
    
    fpl.adjust_spines(ax, [])
    ax.set_frame_on(False)
Exemple #2
0
def plot_trajectories_from_dataset(dataset, keys, interpolated_data='hide'):
    '''
    interpolated_data - if trajectories contain interpolated data, use 'hide' to hide that data, 'dotted' to show it as a dotted line, or 'show' to show it in its entirety
    '''
    import matplotlib.pyplot as plt

    # download at: https://github.com/florisvb/FlyPlotLib
    import fly_plot_lib.plot as fpl 
    from fly_plot_lib.colormaps import viridis as viridis
    
    path = dataset.config.path
    bgimg_filename = get_filename(path, 'bgimg_N1.png')
    bgimg = plt.imread(bgimg_filename)
    
    fig = plt.figure()
    ax = fig.add_subplot(111)
    ax.set_aspect('equal')
    
    ax.imshow(bgimg, cmap='gray')
    
    for key in keys: 
        trajec = dataset.trajec(key)
        if 'interpolated' in trajec.__dict__.keys():
            interpolated_indices = np.where(trajec.interpolated==1)[0]
            if interpolated_data == 'dotted':
                r = np.arange(0, len(interpolated_indices), 5)
                interpolated_indices = interpolated_indices[r]
            if interpolated_data != 'show':
                trajec.position_x[interpolated_indices] = np.nan
                trajec.position_y[interpolated_indices] = np.nan
        l = -1
        fpl.colorline(ax, trajec.position_x[0:l], trajec.position_y[0:l], trajec.time_epoch[0:l]-trajec.time_epoch[0:l][0], linewidth=2, colormap='none', norm=None, zorder=1, alpha=1, linestyle='solid', cmap=viridis)
    
    fpl.adjust_spines(ax, [])
    ax.set_frame_on(False)
def cartesian_spagetti(ax, dataset, axes=[0,1], keys=None, nkeys=300, start_key=0, show_saccades=False, keys_to_highlight=[], colormap='jet', color='gray', color_attribute=None, norm=None, show_start=True):
    if keys is None:
        keys = dataset.trajecs.keys()
    else:
        if type(keys) is not list:
            keys = [keys]
            
    if nkeys < len(keys):
        last_key = np.min([len(keys), start_key+nkeys])
        keys = keys[start_key:last_key]
        keys.extend(keys_to_highlight)
            
    for key in keys:
        trajec = dataset.trajecs[key]    
        
        frames = np.arange(trajec.frame_range_roi[0], trajec.frame_range_roi[-1])
        
        if key in keys_to_highlight:
            alpha = 1
            linewidth = 1
            color = 'black'
            zorder = 500
            ax.plot(trajec.positions[frames,axes[0]], trajec.positions[frames,axes[1]], '-', color='black', alpha=1, linewidth=linewidth, zorder=zorder)
        else:
            alpha = 1
            linewidth = 0.5
            color = color
            zorder = 100

            if color_attribute is not None:
                c = trajec.__getattribute__(color_attribute)                
                fpl.colorline(ax,trajec.positions[frames,axes[0]], trajec.positions[frames,axes[1]], c[frames], colormap=colormap, linewidth=linewidth, alpha=alpha, zorder=zorder, norm=norm)
            else:
                ax.plot(trajec.positions[frames,axes[0]], trajec.positions[frames,axes[1]], '-', color=color, alpha=1, linewidth=linewidth, zorder=zorder)
            
        if show_saccades:
            if len(trajec.sac_ranges) > 0:
                for sac_range in trajec.sac_ranges:
                    angle_subtended = trajec.angle_subtended_by_post[sac_range[0]]
                    if sac_range[0] in frames and angle_subtended < 100.*np.pi/180.:
                    #if 1:
                        ax.plot(trajec.positions[sac_range,0], trajec.positions[sac_range,1], '-', color='red', alpha=1, linewidth=linewidth, zorder=zorder+1)
                        #sac = patches.Circle( (trajec.positions[sac_range[0],0], trajec.positions[sac_range[0],1]), radius=0.001, facecolor='red', edgecolor='none', alpha=alpha2, zorder=zorder+1)
                        #ax.add_artist(sac)
            
        if show_start:
            start = patches.Circle( (trajec.positions[frames[0],axes[0]], trajec.positions[frames[0],axes[1]]), radius=0.004, facecolor='green', edgecolor='none', linewidth=0, alpha=1, zorder=zorder+1)
            ax.add_artist(start)
def calc_positions_normalized_by_speed(trajec, normspeed=0.2, plot=False):
    
    distance_travelled = np.cumsum(trajec.speed)
    distance_travelled_normalized = np.arange(distance_travelled[0], distance_travelled[-1], normspeed)
    warped_time = np.interp(distance_travelled_normalized, distance_travelled, trajec.time_fly)
    
    trajec.positions_normalized_by_speed = np.zeros([len(warped_time), 3])
    for i in range(3):
        trajec.positions_normalized_by_speed[:,i] = np.interp(warped_time, trajec.time_fly, trajec.positions[:,i])
    
    trajec.time_normalized_by_speed = warped_time
    
    if plot:
        fig = plt.figure()
        ax = fig.add_subplot(111)
        x = trajec.positions[:,0]
        y = trajec.positions[:,1]
        speed = trajec.speed
        fpl.colorline(ax,x,y,speed)    
        
        x_warped = trajec.positions_normalized_by_speed[:,0]
        y_warped = trajec.positions_normalized_by_speed[:,1]
        ax.plot(x_warped, y_warped, '.')