Contents
Interactive Movie
This is an example widget for showing movies interactively.
# Widget for displaying movies interactively.
%matplotlib widget
from ipywidgets import Play, Checkbox, Dropdown, FloatRangeSlider, Layout, HBox, VBox
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import make_axes_locatable
from matplotlib.path import Path
from matplotlib.patches import PathPatch
from IPython.display import display
import numpy as np
import imageio.v3 as iio
plot_every_frame = 2
file_name = "data/45grains_compressed.mp4"
video_shape = iio.improps(file_name,plugin="pyav").shape
num_frames = video_shape[0] // plot_every_frame
dpi = 72
array = iio.imread(file_name,index=0,plugin='pyav')[:,:,0]
plt.close('all')
plt.ioff()
hist_range_plot = (-4,4)
hist_range_init = (-2,1)
hist_num_bins = 100
# Histogram visualization
def compute_histogram_values(array):
int_mean = np.mean(array)
int_std = np.sqrt(np.mean((array - int_mean)**2))
int_min = int_mean + hist_range_plot[0] * int_std
int_max = int_mean + hist_range_plot[1] * int_std
init_min = int_mean + hist_range_init[0] * int_std
init_max = int_mean + hist_range_init[1] * int_std
int_ranges = (int_mean, int_std, int_min, int_max,init_min,init_max)
hist_bins = np.linspace(
int_ranges[2],
int_ranges[3],
hist_num_bins+1,
endpoint=True)
hist_data, _ = np.histogram(
array.ravel(),
bins=hist_bins,
)
hist_data = hist_data.astype('float')
hist_data /= np.max(hist_data)
hist_bins = hist_bins[:-1] + (hist_bins[1] - hist_bins[0])/2
return hist_bins, hist_data, int_ranges
hist_bins, hist_data, int_ranges = compute_histogram_values(array)
fig_hist, ax_hist = plt.subplots(figsize=(180/dpi, 150/dpi), dpi=dpi)
hist_path = Path(np.array([hist_bins,hist_data]).T)
hist_patch = PathPatch(hist_path,visible=False,transform=ax_hist.transData)
cmap = plt.colormaps.get_cmap('gray')
im_hist = ax_hist.imshow(
hist_bins[None],
vmin=int_ranges[4],
vmax=int_ranges[5],
cmap=cmap,
origin='lower',
aspect="auto",
interpolation='bilinear',
clip_path=hist_patch,
extent=[int_ranges[2],int_ranges[3],0,np.quantile(hist_data,0.9)],
clip_on=True
)
h_vlines = ax_hist.vlines(
int_ranges[4:6],
ymin = 0,
ymax = 1.1,
colors = [cmap(cmap.N),cmap(0)],
)
ax_hist.set_xlim((int_ranges[2], int_ranges[3]));
ax_hist.set_ylim((0, np.quantile(hist_data,0.9)));
ax_hist.set(yticks=[])
ax_hist.set(yticklabels=[])
ax_hist.set_facecolor((0.9,0.85,0.85))
fig_hist.canvas.toolbar_visible = False
fig_hist.canvas.header_visible = False
fig_hist.canvas.footer_visible = False
fig_hist.canvas.resizable = False
fig_hist.tight_layout()
# Main visualization
fig, ax = plt.subplots(figsize=(420/dpi, 430/dpi), dpi=dpi)
fig.canvas.resizable = False
fig.canvas.header_visible = False
fig.canvas.footer_visible = False
fig.canvas.toolbar_visible = True
fig.canvas.layout.width = '430px'
fig.canvas.toolbar_position = 'bottom'
ax.axis('off')
fig.set_frameon(False)
fig_hist.set_frameon(False)
ax_hist.xaxis.set_tick_params(labelcolor=(0.4,0.4,0.4))
im=ax.imshow(array,cmap=cmap,vmin=int_ranges[4],vmax=int_ranges[5])
divider = make_axes_locatable(ax)
ax_cb = divider.append_axes("right", size="5%", pad="2.5%")
ax_cb.yaxis.set_tick_params(labelcolor=(0.4,0.4,0.4))
fig.add_axes(ax_cb)
fig.colorbar(im, cax=ax_cb)
fig.tight_layout()
scalebar_plot=ax.plot((20,70),(484-20,484-20),lw=5,color=cmap(0))
scalebar_text=ax.text((70+20)/2,484-20-10,"2 nm",color=cmap(0),ha='center')
def display_frame(change):
# main
index = change['new']
array = iio.imread(file_name,index=index*plot_every_frame,plugin='pyav')[:,:,0] # grayscale image
# array = 255 - array # reverse array
im.set_data(array)
fig.canvas.draw_idle()
# hist
hist_bins, hist_data, int_ranges = compute_histogram_values(array)
path = Path(np.array([hist_bins,hist_data]).T)
patch = PathPatch(path,visible=False,transform=ax_hist.transData)
im_hist.set_data(hist_bins[None])
im_hist.set_clip_path(patch)
fig_hist.canvas.draw_idle()
return None
def toggle_scalebar(change):
scalebar = change['new']
scalebar_plot[0].set_visible(scalebar)
scalebar_text.set_visible(scalebar)
fig.canvas.draw_idle()
return None
def update_colormap(change):
cmap_string = change['new']
cmap = plt.colormaps.get_cmap(cmap_string)
im.set_cmap(cmap)
im_hist.set_cmap(cmap)
h_vlines.set_colors([cmap(cmap.N),cmap(0)])
scalebar_plot[0].set_color(cmap(0))
scalebar_text.set_color(cmap(0))
fig.canvas.draw_idle()
fig_hist.canvas.draw_idle()
return None
def update_vlines(change):
min, max = change['new']
p = np.array([
[
[min, 0],
[min, 1.1],
],
[
[max, 0],
[max, 1.1],
]
])
h_vlines.set_segments(p)
fig_hist.canvas.draw_idle()
im.set_clim([min,max])
im_hist.set_clim([min,max])
fig.canvas.draw_idle()
fig_hist.canvas.draw_idle()
return None
index_widget = Play(value=0,min=0,max=num_frames-1,step=1,interval=50,layout=Layout(width='180px'))
index_widget.observe(display_frame,names='value')
scalebar_widget =Checkbox(value=True,description="Show scale bar",indent=False,layout=Layout(width='180px'))
scalebar_widget.observe(toggle_scalebar,names='value')
sequential_cmaps = [
'gray','viridis', 'plasma', 'inferno', 'magma', 'cividis','turbo',
'Purples_r', 'Blues_r', 'Greens_r', 'Oranges_r', 'Reds_r',
'YlOrBr_r', 'YlOrRd_r', 'OrRd_r', 'PuRd_r', 'RdPu_r', 'BuPu_r',
'GnBu_r', 'PuBu_r', 'YlGnBu_r', 'PuBuGn_r', 'BuGn_r', 'YlGn_r'
]
cmap_widget =Dropdown(
options=sequential_cmaps,
value='gray',description="Colormap",
indent=False,
layout=Layout(width=' 180px'))
cmap_widget.observe(update_colormap,names='value')
histogram_range_slider = FloatRangeSlider(
value=int_ranges[4:6],
min=int_ranges[2],
max=int_ranges[3],
continuous_update=False,
orientation='horizontal',
readout=False,
indent=True,
layout=Layout(width='180px')
)
histogram_range_slider.observe(update_vlines,names='value')
visualization_layout = Layout(
display='flex',
flex_flow='row',
align_items='center',
width='630px'
)
histogram_box_layout = Layout(
display='flex',
flex_flow='column',
align_items='center',
width='200px'
)
histogram_vbox = VBox([fig_hist.canvas,histogram_range_slider],layout=histogram_box_layout)
controls_vbox = VBox([histogram_vbox,index_widget,cmap_widget,scalebar_widget],layout=histogram_box_layout)
display(
HBox(
[
fig.canvas,
controls_vbox
],
layout=visualization_layout
)
)
HBox(children=(Canvas(footer_visible=False, header_visible=False, layout=Layout(width='430px'), resizable=Fals…