Define the conditional Jupyter cell - jupyter-notebook

I have Jupyter Notebook tutorials that I used Matplotlibe and ipywidgets(interact) to display video with NumPy 3D format.
class JupyterDisplay():
def __init__(self, video, median_filter_flag=False, color='gray', imgSizex=5, imgSizey=5, IntSlider_width='500px'):
self.color = color
self.video = video
self.imgSizex = imgSizex
self.imgSizey = imgSizey
self.median_filter_flag = median_filter_flag
interact(self.display, frame=widgets.IntSlider(min=0, max=self.video.shape[0] - 1, step=1, value=10,
layout=Layout(width=IntSlider_width),
readout_format='10', continuous_update=False,
description='Frame:'))
def display(self, frame):
fig = plt.figure(figsize=(self.imgSizex, self.imgSizey))
ax = fig.add_axes([0, 0, 1, 1])
if self.median_filter_flag:
frame_v = median_filter(self.video[int(frame), :, :], 3)
else:
frame_v = self.video[int(frame), :, :]
myplot = ax.imshow(frame_v, cmap=self.color)
divider = make_axes_locatable(ax)
cax = divider.append_axes("right", size="5%", pad=0.05)
plt.colorbar(myplot, cax=cax)
plt.show()
I want to create an HTML version from tutorials with sphinx make HTML. But the video is not visualized in the HTML version. What is the best way to display dynamic video in the HTML version?
I can create the mp4 from videos, but in this case, I need to have a conditional Jupyter cell to only run this part of the code when making HTML Sphinx used. Can you inform me how I should define this conditional cell?

Related

Is there a way to prevent scrolling of an iPython notebook, when calling 'mouse_scroll' event over a plot figure inside a cell?

Is there a way to prevent the entire notebook from scrolling, when scrolling over the figure to cycle through the images as shown in this example (and reproduced below): https://matplotlib.org/stable/gallery/event_handling/image_slices_viewer.html
import numpy as np
import matplotlib.pyplot as plt
# Fixing random state for reproducibility
np.random.seed(19680801)
class IndexTracker:
def __init__(self, ax, X):
self.ax = ax
ax.set_title('use scroll wheel to navigate images')
self.X = X
rows, cols, self.slices = X.shape
self.ind = self.slices//2
self.im = ax.imshow(self.X[:, :, self.ind])
self.update()
def on_scroll(self, event):
print("%s %s" % (event.button, event.step))
if event.button == 'up':
self.ind = (self.ind + 1) % self.slices
else:
self.ind = (self.ind - 1) % self.slices
self.update()
def update(self):
self.im.set_data(self.X[:, :, self.ind])
self.ax.set_ylabel('slice %s' % self.ind)
self.im.axes.figure.canvas.draw_idle()
def plot(X):
mpl.rc('image', cmap='gray')
fig, ax = plt.subplots(1, 1)
plot = IndexTracker(ax, X)
fig.canvas.mpl_connect('scroll_event', plot.scroll)
plt.show()
On VS Code, using the,
%matplotlib widget
backend, I call the following function in a new code cell:
X = np.random.rand(20, 20, 40)
plot(X)
I am able to successfully generate an interactive plot in an iPython notebook, whereby scrolling over the figure scrolls through the "image slices". The scroll event only works if I hover the cursor over the plot/figure (as it should), however the entire notebook scrolls as well, thereby moving the cursor out of the figure frame.
Is there a way to prevent the notebook from scrolling when the cursor is hovering over a figure in the cell output?

How compare two images using sikuli in robotframework

am totaly new to the sikuli with robotframework. I have some want idea of click and action of the window based but i dont have the concept of compare the image using sikuli with robotframework. Can any one help me?
This is RaiMan from SikuliX.
I recommend to use
https://github.com/rainmanwy/robotframework-SikuliLibrary
I have developed a python script for image comparison, which gets two images to compare the images and write the difference.
You can use this as robot keyword for image comparison. Challenge is that you have to crop the image from desktop application. you can able to do this using robot framework sikuli library keyword crop region by providing x,y, width and height values
compare images.py
# importing the necessary packages
#from skimage.measure import compare_ssim
from skimage.metrics import structural_similarity
import argparse
import imutils
import cv2
import time
import logging
def Compare_Image(image1,image2,Original_image_path,Modified_image_path):
# Reading images
imageA = cv2.imread(image1)
imageB = cv2.imread(image2)
# convert the images to grayscale
grayA = cv2.cvtColor(imageA, cv2.COLOR_BGR2GRAY)
grayB = cv2.cvtColor(imageB, cv2.COLOR_BGR2GRAY)
#getting the structural similarity between the images
(score, diff) = structural_similarity(grayA, grayB, full=True)
diff = (diff * 255).astype("uint8")
print("SSIM: {}".format(score))
#Threshold differences
thresh = cv2.threshold(diff, 0, 255,
cv2.THRESH_BINARY_INV | cv2.THRESH_OTSU)[1]
cnts = cv2.findContours(thresh.copy(), cv2.RETR_EXTERNAL,
cv2.CHAIN_APPROX_SIMPLE)
cnts = imutils.grab_contours(cnts)
# loop over the contours
for c in cnts:
#Displaying Rectangles on image difference
(x, y, w, h) = cv2.boundingRect(c)
cv2.rectangle(imageA, (x, y), (x + w, y + h), (0, 0, 255), 2)
cv2.rectangle(imageB, (x, y), (x + w, y + h), (0, 0, 255), 2)
# show the output images
image1=cv2.imshow("Original", imageA)
image2=cv2.imshow("Modified", imageB)
cv2.imwrite(Original_image_path, imageA)
cv2.imwrite(Modified_image_path, imageB)
# cv2.imshow("Diff", diff)
# cv2.imshow("Thresh", thresh)
#cv2.waitKey(0)
#cv2.destroyAllWindows()
#Validating and Logging Image Results
if score==1.0:
print("Reference and Test images are same")
else:
print("Reference and Test images are different")
Sample.robot
* Setting *
Library compare_Images.py
* Test Cases *
Check_Image_Compare
Compare Image path_to_image1\\img1.png path_to_image2\\image2.png
path_to_saveorginalimage1\\orgimage.png path_to_savemodifiedimage\\modifiedimage.png
Log <img src="path_to_saveorginalimage1\\orgimage.png"> HTML
Log <img src="path_to_savemodifiedimage\\modifiedimage.png"> HTML
On executing the python script it will give two images (original image- image1 to compare Modified image- image2 to compare) which will be saved in specified location and logged as in robot file above.

bokeh selected.on_change not working for my current setup

Basically, this is an interactive heatmap but the twist is that the source is updated by reading values from a file that gets updated regularly.
dont bother about the class "generator", it is just for keeping data and it runs regularly threaded
make sure a file named "Server_dump.txt" exists in the same directory of the script with a single number greater than 0 inside before u execute the bokeh script.
what basically happens is i change a number inside the file named "Server_dump.txt" by using echo 4 > Server_dump.txt on bash,
u can put any number other than 4 and the script automatically checks the file and plots the new point.
if u don't use bash, u could use a text editor , replace the number and save, and all will be the same.
the run function inside the generator class is the one which checks if this file was modified , reads the number, transforms it into x& y coords and increments the number of taps associated with these coords and gives the source x,y,taps values based on that number.
well that function works fine and each time i echo a number , the correct rectangle is plotted but,
now I want to add the functionality of that clicking on a certain rectangle triggers a callback to plot a second graph based on the coords of the clicked rectangle but i can't even get it to trigger even though i have tried other examples with selected.on_change in them and they worked fine.
*if i increase self.taps for a certain rect by writing the number to the file multiple times, color gets updated but if i hover over the rect it shows me the past values and not the latest value only .
my bokeh version is 1.0.4
from functools import partial
from random import random,randint
import threading
import time
from tornado import gen
from os.path import getmtime
from math import pi
import pandas as pd
from random import randint, random
from bokeh.io import show
from bokeh.models import LinearColorMapper, BasicTicker, widgets, PrintfTickFormatter, ColorBar, ColumnDataSource, FactorRange
from bokeh.plotting import figure, curdoc
from bokeh.layouts import row, column, gridplot
source = ColumnDataSource(data=dict(x=[], y=[], taps=[]))
doc = curdoc()
#sloppy data receiving function to change data to a plottable shape
class generator(threading.Thread):
def __init__(self):
super(generator, self).__init__()
self.chart_coords = {'x':[],'y':[],'taps':[]}
self.Pi_coords = {}
self.coord = 0
self.pos = 0
self.col = 0
self.row = 0
self.s = 0
self.t = 0
def chart_dict_gen(self,row, col):
self.col = col
self.row = row+1
self.chart_coords['x'] = [i for i in range(1,cla.row)]
self.chart_coords['y'] = [i for i in range(cla.col, 0, -1)] #reversed list because chart requires that
self.chart_coords['taps']= [0]*(row * col)
self.taps = [[0 for y in range(col)] for x in range(row)]
def Pi_dict_gen(self,row,col):
key = 1
for x in range(1,row):
for y in range(1,col):
self.Pi_coords[key] = (x,y)
key = key + 1
def Pi_to_chart(self,N):
x,y = self.Pi_coords[N][0], self.Pi_coords[N][1]
return x,y
def run(self):
while True:
if(self.t == 0):
self.t=1
continue
time.sleep(0.1)
h = getmtime("Server_dump.txt")
if self.s != h:
self.s = h
with open('Server_dump.txt') as f:
m = next(f)
y,x = self.Pi_to_chart(int(m))
self.taps[x][y] += 1
# but update the document from callback
doc.add_next_tick_callback(partial(update, x=x, y=y, taps=self.taps[x][y]))
cla = generator()
cla.chart_dict_gen(15,15)
cla.Pi_dict_gen(15, 15)
x = cla.chart_coords['x']
y = cla.chart_coords['y']
taps = cla.chart_coords['taps']
#gen.coroutine
def update(x, y, taps):
taps += taps
print(x,y,taps)
source.stream(dict(x=[x], y=[y], taps=[taps]))
colors = ["#CCEBFF","#B2E0FF","#99D6FF","#80CCFF","#66c2FF","#4DB8FF","#33ADFF","#19A3FF", "#0099FF", "#008AE6", "#007ACC","#006BB2", "#005C99", "#004C80", "#003D66", "#002E4C", "#001F33", "#000F1A", "#000000"]
mapper = LinearColorMapper(palette=colors, low= 0, high= 15) #low = min(cla.chart_coords['taps']) high = max(cla.chart_coords['taps'])
TOOLS = "hover,save,pan,box_zoom,reset,wheel_zoom"
p = figure(title="Tou",
x_range=list(map(str,x)),
y_range=list(map(str,reversed(y))),
x_axis_location="above",
plot_width=900, plot_height=400,
tools=TOOLS, toolbar_location='below',
tooltips=[('coords', '#y #x'), ('taps', '#taps%')])
p.grid.grid_line_color = "#ffffff"
p.axis.axis_line_color = "#ef4723"
p.axis.major_tick_line_color = "#af0a36"
p.axis.major_label_text_font_size = "7pt"
p.xgrid.grid_line_color = None
p.ygrid.grid_line_color = None
p.rect(x="x", y="y",
width=0.9, height=0.9,
source=source,
fill_color={'field': 'taps', 'transform': mapper},
line_color = "#ffffff",
)
color_bar = ColorBar(color_mapper=mapper,
major_label_text_font_size="7pt",
ticker=BasicTicker(desired_num_ticks=len(colors)),
formatter=PrintfTickFormatter(format="%d%%"),
label_standoff=6, border_line_color=None, location=(0, 0))
curdoc().theme = 'dark_minimal'
def ck(attr, old, new):
print('here') #doesn't even print hi in the terminal if i click anywhere
source.selected.on_change('indices', ck)
p.add_layout(color_bar, 'right')
doc.add_root(p)
thread = cla
thread.start()
i wanted even to get a printed hi in the terminal but nothing
You have not actually added any selection tool at all to your plot, so no selection is ever made. You have specified:
TOOLS = "hover,save,pan,box_zoom,reset,wheel_zoom"
Those are the only tools that will be added, and none of them make selections, there for nothing will cause source.selection.indices to ever be updated. If you are looking for selections based on tap, you must add a TapTool, e.g. with
TOOLS = "hover,save,pan,box_zoom,reset,wheel_zoom,tap"
Note that there will not be repeated callbacks if you tap the same rect multiple times. The callback only fires when the selection changes and clicking the same glyph twice in a row results in an identical selection.

How to update plotly plot in offline mode (Jupyter notebook)

I would like to build a simple interface with plotly and ipywidgets inside Jupyter Notebook (offline mode) and I am wondering how to update the plot if I want to add extra data. Here is my code:
import plotly
from plotly.offline import iplot
from plotly.graph_objs import graph_objs as go
import ipywidgets as widgets
from IPython.display import display
plotly.offline.init_notebook_mode(connected=True)
trace_high = go.Scatter(
x=[1,2,3,4],
y=[4,6,2,8],
name = "High",
line = dict(color = '#7F7F7F'),
opacity = 0.8)
data = [trace_high]
def plot_extra_data(drop):
if drop["new"] == "2":
trace_low = go.Scatter(
x=[1,2,3,4],
y=[1,7,3,5],
name = "Low",
line = dict(color = 'green'),
opacity = 0.8)
data.append(trace_low)
fig.update(data=data)
drop = widgets.Dropdown(
options=['1', '2', '3'],
value='1',
description='Number:',
disabled=False,
)
drop.observe(plot_extra_data, "value")
display(drop)
fig = dict(data=data)
iplot(fig)
Any comments/suggestions are highly appreciated.
Crazy how everyone seem to be confused about interacting with offline plotly charts!
Still it is fairly simple taking benefit of property assignment (e.g. see this documentation although it is now partly deprecated).
The naive snippet example below updates a plotly.graph_objs.FigureWidget() as user interacts via a dropdown widget. In fact, the pandas.DataFrame() containing the xaxis and yaxis data of the chart is sliced along a Commodity dimension the user wants to display the line chart of.
The most tedious part probably is getting all additional library requirements set if you are using jupyterlab
import pandas as pd
import plotly.graph_objs as go
import ipywidgets as widgets
df = pd.DataFrame({'cmdty' : ['beans', 'beans', 'beans', 'corn', 'corn', 'corn'],
'month' : [1, 2, 3, 1, 2, 3],
'value' : [10.5, 3.5, 8.0, 5.0, 8.75, 5.75]})
items = df.cmdty.unique().tolist()
cmdty = widgets.Dropdown(options=items,
description='Commodity')
def response(change):
c = cmdty.value
df_tmp = df[df.cmdty == c]
x0 = df_tmp['month'] # Useless here as x is equal for the 2 commodities
x1 = df_tmp['value']
fig.data[0].x = x0 # Useless here as x is equal for the 2 commodities
fig.data[0].y = x1
fig = go.FigureWidget(data=[{'type' : 'scatter'}])
cmdty.observe(response, names='value')
display(widgets.VBox([cmdty, fig]))

Bokeh Colorbar Vertical title to right of colorbar?

I'm trying to do something that I'd normally consider trivial but seems to be very difficult in bokeh: Adding a vertical colorbar to a plot and then having the title of the colorbar (a.k.a. the variable behind the colormapping) appear to one side of the colorbar but rotated 90 degrees clockwise from horizontal.
From what I can tell of the bokeh ColorBar() interface (looking at both documentation and using the python interpreter's help() function for this element), this is not possible. In desperation I have added my own Label()-based annotation. This works but is klunky and displays odd behavior when deployed in a bokeh serve situation--that the width of the data window on the plot varies inversely with the length of the title colorbar's title string.
Below I've included a modified version of the bokeh server mpg example. Apologies for its complexity, but I felt this was the best way to illustrate the problem using infrastructure/data that ships with bokeh. For those unfamiliar with bokeh serve, this code snippet needs to saved to a file named main.py that resides in a directory--for the sake of argument let's say CrossFilter2--and in the parent directory of CrossFilter2 one needs to invoke the command
bokeh serve --show CrossFilter2
this will then display in a browser window (localhost:5006/CrossFilter2) and if you play with the color selection widget you will see what I mean, namely that short variable names such as 'hp' or 'mpg' result in a wider data display windows than longer variable names such as 'accel' or 'weight'. I suspect that there may be a bug in how label elements are sized--that their x and y dimensions are swapped--and that bokeh has not understood that the label element has been rotated.
My questions are:
Must I really have to go to this kind of trouble to get a simple colorbar label feature that I can get with little-to-no trouble in matplotlib/plotly?
If I must go through the hassle you can see in my sample code, is there some other way I can do this that avoids the data window width problem?
import numpy as np
import pandas as pd
from bokeh.layouts import row, widgetbox
from bokeh.models import Select
from bokeh.models import HoverTool, ColorBar, LinearColorMapper, Label
from bokeh.palettes import Spectral5
from bokeh.plotting import curdoc, figure, ColumnDataSource
from bokeh.sampledata.autompg import autompg_clean as df
df = df.copy()
SIZES = list(range(6, 22, 3))
COLORS = Spectral5
# data cleanup
df.cyl = df.cyl.astype(str)
df.yr = df.yr.astype(str)
columns = sorted(df.columns)
discrete = [x for x in columns if df[x].dtype == object]
continuous = [x for x in columns if x not in discrete]
quantileable = [x for x in continuous if len(df[x].unique()) > 20]
def create_figure():
xs = df[x.value].tolist()
ys = df[y.value].tolist()
x_title = x.value.title()
y_title = y.value.title()
name = df['name'].tolist()
kw = dict()
if x.value in discrete:
kw['x_range'] = sorted(set(xs))
if y.value in discrete:
kw['y_range'] = sorted(set(ys))
kw['title'] = "%s vs %s" % (y_title, x_title)
p = figure(plot_height=600, plot_width=800,
tools='pan,box_zoom,wheel_zoom,lasso_select,reset,save',
toolbar_location='above', **kw)
p.xaxis.axis_label = x_title
p.yaxis.axis_label = y_title
if x.value in discrete:
p.xaxis.major_label_orientation = pd.np.pi / 4
if size.value != 'None':
groups = pd.qcut(df[size.value].values, len(SIZES))
sz = [SIZES[xx] for xx in groups.codes]
else:
sz = [9] * len(xs)
if color.value != 'None':
coloring = df[color.value].tolist()
cv_95 = np.percentile(np.asarray(coloring), 95)
mapper = LinearColorMapper(palette=Spectral5,
low=cv_min, high=cv_95)
mapper.low_color = 'blue'
mapper.high_color = 'red'
add_color_bar = True
ninety_degrees = pd.np.pi / 2.
color_bar = ColorBar(color_mapper=mapper, title='',
#title=color.value.title(),
title_text_font_style='bold',
title_text_font_size='20px',
title_text_align='center',
orientation='vertical',
major_label_text_font_size='16px',
major_label_text_font_style='bold',
label_standoff=8,
major_tick_line_color='black',
major_tick_line_width=3,
major_tick_in=12,
location=(0,0))
else:
c = ['#31AADE'] * len(xs)
add_color_bar = False
if add_color_bar:
source = ColumnDataSource(data=dict(x=xs, y=ys,
c=coloring, size=sz, name=name))
else:
source = ColumnDataSource(data=dict(x=xs, y=ys, color=c,
size=sz, name=name))
if add_color_bar:
p.circle('x', 'y', fill_color={'field': 'c',
'transform': mapper},
line_color=None, size='size', source=source)
else:
p.circle('x', 'y', color='color', size='size', source=source)
p.add_tools(HoverTool(tooltips=[('x', '#x'), ('y', '#y'),
('desc', '#name')]))
if add_color_bar:
color_bar_label = Label(text=color.value.title(),
angle=ninety_degrees,
text_color='black',
text_font_style='bold',
text_font_size='20px',
x=25, y=300,
x_units='screen', y_units='screen')
p.add_layout(color_bar, 'right')
p.add_layout(color_bar_label, 'right')
return p
def update(attr, old, new):
layout.children[1] = create_figure()
x = Select(title='X-Axis', value='mpg', options=columns)
x.on_change('value', update)
y = Select(title='Y-Axis', value='hp', options=columns)
y.on_change('value', update)
size = Select(title='Size', value='None',
options=['None'] + quantileable)
size.on_change('value', update)
color = Select(title='Color', value='None',
options=['None'] + quantileable)
color.on_change('value', update)
controls = widgetbox([x, y, color, size], width=200)
layout = row(controls, create_figure())
curdoc().add_root(layout)
curdoc().title = "Crossfilter"
You can add a vertical label to the Colorbar by plotting it on a separate axis and adding a title to this axis. To illustrate this, here's a modified version of Bokeh's standard Colorbar example (found here):
import numpy as np
from bokeh.plotting import figure, output_file, show
from bokeh.models import LogColorMapper, LogTicker, ColorBar
from bokeh.layouts import row
plot_height = 500
plot_width = 500
color_bar_height = plot_height + 11
color_bar_width = 180
output_file('color_bar.html')
def normal2d(X, Y, sigx=1.0, sigy=1.0, mux=0.0, muy=0.0):
z = (X-mux)**2 / sigx**2 + (Y-muy)**2 / sigy**2
return np.exp(-z/2) / (2 * np.pi * sigx * sigy)
X, Y = np.mgrid[-3:3:100j, -2:2:100j]
Z = normal2d(X, Y, 0.1, 0.2, 1.0, 1.0) + 0.1*normal2d(X, Y, 1.0, 1.0)
image = Z * 1e6
color_mapper = LogColorMapper(palette="Viridis256", low=1, high=1e7)
plot = figure(x_range=(0,1), y_range=(0,1), toolbar_location=None,
width=plot_width, height=plot_height)
plot.image(image=[image], color_mapper=color_mapper,
dh=[1.0], dw=[1.0], x=[0], y=[0])
Now, to make the Colorbar, create a separate dummy plot, add the Colorbar to the dummy plot and place it next to the main plot. Add the Colorbar label as the title of the dummy plot and center it appropriately.
color_bar = ColorBar(color_mapper=color_mapper, ticker=LogTicker(),
label_standoff=12, border_line_color=None, location=(0,0))
color_bar_plot = figure(title="My color bar title", title_location="right",
height=color_bar_height, width=color_bar_width,
toolbar_location=None, min_border=0,
outline_line_color=None)
color_bar_plot.add_layout(color_bar, 'right')
color_bar_plot.title.align="center"
color_bar_plot.title.text_font_size = '12pt'
layout = row(plot, color_bar_plot)
show(layout)
This gives the following output image:
One thing to look out for is that color_bar_width is set wide enough to incorporate both the Colorbar, its axes labels and the Colorbar label. If the width is set too small, you will get an error and the plot won't render.
As of Bokeh 0.12.10 there is no built in label available for colorbars. In addition to your approach or something like it, another possibility would be a custom extension, though that is similarly not trivial.
Offhand, a colobar label certainly seems like a reasonable thing to consider. Regarding the notion that it ought to be trivially available, if you polled all users about what they consider should be trivially available, there will be thousands of different suggestions for what to prioritize. As is very often the case in the OSS world, there are far more possible things to do, than there are people to do them (less than 3 in this case). So, would first suggest a GitHub Issue to request the feature, and second, if you have the ability, volunteering to help implement it. Your contribution would be valuable and appreciated by many.

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