Develop Reference

Image not updating in python plot during animation

The Problem:
I'm trying to simulate a live video by cycling through a series of still images I have saved in a directory, but when I add the animation and update functions my plot is displayed empty.
Background on why I'm doing this:
I believe its important for me to do it this way rather than a complete change of approach, say turning the images into a video first then displaying that, because what I really want to test is the image analysis I will be adding and then overlaying on each frame. The final application will be receiving frames one by one from a camera and will need to do some processing, display the image + annotations + output the data as .csv etc... I'm simulating this for now because I do not have any of the hardware to generate the images and will not have it for several months during which time I need to get the image processing set up, but I do have access to some sets of stills that are approximately what will be produced. In case its relevant my simulation images are 1680x1220 and are 1.88 Mb TIFFs, though I could covert and compress them if needed, and in the final form the resolution will be a bit higher and probably the image format could be adjusted if needed.
What I have tried:
I followed an example to list all files in a folder, and an example
to update a plot. However, the plot displays blank when I run the
code.
I added a line to print the current file name, and I can see this
cycling as expected.
I also made sure the images will display in the plot if I just create
a plot and add one image, and they do. But, when combined with the
animation function the plot is blank and I'm not sure what I've done
wrong/failed to include.
I also tried adding a plt.pause() in the update, but again this
didn't work.
I increased the interval up to 2000 to give it more time, but that didn't work. I believe 2000 is extreme, I'm expecting it should work with more like 20-30fps. Going to 0.5fps tells me the code is wrong or incomplete, rather than it just being a question of needing time to read the image file.
I appreciate no one else has my images, but they are nothing special. I'm using 60 images but I guess it could be tested with any 2 random images and setting range(60) to range(2) instead?
The example I copied originally demonstrated the animation function by making a random array, and if I do that it will show a plot that updates with random squares as expected.
Replacing:
A = np.random.randn(10,10)
im.set_array(A)
...with my image instead...
im = cv2.imread(files[i],0)
...and the plot remains empty/blank. I get a window shown called "Figure1" (like when using the random array), but unlike with the array there is nothing in this window.
Full code:
import matplotlib.pyplot as plt
from matplotlib.animation import FuncAnimation
import os
import cv2
def update(i):
im = cv2.imread(files[i],0)
print(files[i])
#plt.pause(0.1)
return im
path = 'C:\\Test Images\\'
files = []
# r=root, d=directories, f = files
for r, d, f in os.walk(path):
for file in f:
if '.TIFF' in file:
files.append(os.path.join(r, file))
ani = FuncAnimation(plt.gcf(), update, frames=range(60), interval=50, blit=False)
plt.show()
I'm a python and a programming novice so have relied on adjusting examples others have given online but I have only a simplistic understanding of how they are working and end up with a lot of trial and error on the syntax. I just can't figure out anything to make this one work though.
Cheers for any help!

The main reason nothing is showing up is because you never add the images to the plot. I've provided some code below to do what you want, be sure to look up anything you are curious about or don't understand!
import glob
import os
from matplotlib import animation
import matplotlib.image as mpimg
import matplotlib.pyplot as plt
IMG_DIRPATH = 'C:\\Test Images\\' # the folder with your images (be careful about
# putting spaces in directory names!)
IMG_EXT = '.TIFF' # the file extension of your images
# Create a figure, and set to the desired size.
fig = plt.figure(figsize=[5, 5])
# Create axes for the current figure so that images can be sized appropriately.
# Passing in [0, 0, 1, 1] makes the axes fill the whole figure.
# frame_on=False means we won't have a bounding box, and setting xticks=[] and
# yticks=[] means that we won't have pesky tick marks along our image.
ax_props = {'frame_on': False, 'xticks': [], 'yticks': []}
ax = plt.axes([0, 0, 1, 1], **ax_props)
# Get all image filenames.
img_filepaths = glob.glob(os.path.join(IMG_DIRPATH, '*' + IMG_EXT))
def update_image(img_filepath):
# Remove all existing images on the axes, and restore our settings.
ax.clear()
ax.update(ax_props)
# Read the current image.
img = mpimg.imread(img_filepath)
# Add the current image to the plot axes.
ax.imshow(img)
anim = animation.FuncAnimation(fig, update_image, frames=img_filepaths, interval=250)
plt.show()

Plotly world Choropleth Map offline in python?

I'm trying to recreate the world Choropleth map given in plotlys example page here: https://plot.ly/python/choropleth-maps/ with the intention of reusing some of the code, but changing the column which informs the shadings and the labelling.
However when I run the exact code given in the example I receive the following error.
plotly.exceptions.PlotlyError: Because you didn't supply a 'file_id' in the call, we're assuming you're trying to snag a figure from a url. You supplied the url, '', we expected it to start with 'https://plot.ly'.
Run help on this function for more information.
I have no idea where this error arises from and my question really is how do I adapt the code so that it produces the said figure offline? Secondly is there a simple method for saving the figure directly to a png? Apologies if this is trivial I'm completely new to the package.
Here is the code:
import plotly.plotly as py
import pandas as pd
df = pd.read_csv('https://raw.githubusercontent.com/plotly/datasets/master/2014_world_gdp_with_codes.csv')
data = [dict(
type='choropleth',
locations=df['CODE'],
z=df['GDP (BILLIONS)'],
text=df['COUNTRY'],
colorscale=[[0, "rgb(5, 10, 172)"], [0.35, "rgb(40, 60, 190)"], [0.5, "rgb(70, 100, 245)"],\
[0.6, "rgb(90, 120, 245)"], [0.7, "rgb(106, 137, 247)"], [1, "rgb(220, 220, 220)"]],
autocolorscale=False,
reversescale=True,
marker=dict(
line=dict(
color='rgb(180,180,180)',
width=0.5
)),
colorbar=dict(
autotick=False,
tickprefix='$',
title='GDP<br>Billions US$'),
)]
layout = dict(
title='2014 Global GDP<br>Source:\
<a href="https://www.cia.gov/library/publications/the-world-factbook/fields/2195.html">\
CIA World Factbook</a>',
geo=dict(
showframe=False,
showcoastlines=False,
projection=dict(
type='Mercator'
)
)
)
fig = dict(data=data, layout=layout)
py.iplot(fig,validate=False, filename='d3-world-map')

You need to import the offline specific functions, which allow you to plot inline in a jupyter notebook:
import plotly.figure_factory as ff
from plotly.offline import download_plotlyjs, init_notebook_mode, plot, iplot
init_notebook_mode(connected=True)
# All of your code
# ....
# Just change the last line from py.iplot to iplot
iplot(fig,validate=False, filename='d3-world-map')
This renders the image inline in a jupyter notebook, and there's a button that allows you to Download plot as a png in the upper right, along with other functionality.
If you need to save the image as a png, you can try changing the last line to:
plot(fig, validate=False, filename='d3-world-map.html', image='png')
This actually creates an .html file and will open a browser. You can then manually save this as a .png. The last step can be automated with other libraries like selenium, but not sure there is a simple way around it given their documentation:
Note that you must generate the graph and open the file to save the
image.

Big data multiple plots, multiple web pages Plotly

I am trying to work with big data plotting around 20 plots on plotly and embed them on web page. I can very well plot individual plots with username and one api_key that found in the profile.
The Problem comes is when: I have to rerun all the 20 plots with python program after interval of every 15 mins and every time I am getting new windows. Instead I need the same plot to update/redraw.
How do I get that? I tried reading the plot.ly document and also few tutorials outside. Cannot find how to get it done. Can anyone please help me with steps or refer me to some document where I can know how to work with multiple plots that will update at same time.
I am following the steps given in plotly tutorial not sure if I should use stream_ids ? Or can I create a new api_key for every plot ?Confused !!! Thanks in Advance for the suggestions.
Edit: I could make access tokens and Initiate the credentials from the following tutorial.
The code below works perfect: But now I am looking for required fixing in the below code by trying to minimize the code with annotations and where to include the streaming API Access Tokens while having sizable scatter plots ?
import plotly.plotly as py
import plotly.tools as tls
from plotly.graph_objs import *
import csv
import pandas as pd
import numpy as np
df = pd.read_csv('finally.csv')
df1=df[['NAME','COUNT']]
sizemode='area'
sizeref=df1['COUNT'].max()/1000
def Trace(X,PLACE,sizes):
return Scatter(
x=X['NAME'],
y=X['COUNT'].sum(),
name=PLACE,
mode='marker',
marker=Marker(
line=Line(width=0.9),
size=sizes,
sizeref=sizeref,
opacity=0.9,
)
)
data=Data()
for PLACE, X in df1.groupby('NAME'):
sizes=X['COUNT'].sum()/1000
data.append(Trace(X,PLACE,sizes))
title = "Fig 1.1 : All NAMES"
x_title = "Names".format()
y_title = "Count"
# Define a dictionary of axis style options
axis_style = dict(
zeroline=False, # remove thick zero line
gridcolor='#FFFFFF', # white grid lines
ticks='outside', # draw ticks outside axes
ticklen=8, # tick length
tickwidth=1.5 # and width
)
# Make layout object
layout = Layout(
title=title, # set plot title
plot_bgcolor='#EFECEA', # set plot color to grey
xaxis=XAxis(
axis_style, # add axis style dictionary
title=x_title, # x-axis title
),
yaxis=YAxis(
axis_style, # add axis style dictionary
title=y_title, # y-axis title
),
showlegend=False,
)
fig = Figure(data=data,layout=layout)
plot_url=py.plot(fig,filename=' plotting')

In plot/ iplot there is 'fileopt' option which should help you. For example, if you would want to add new traces to your existing data you can run
plot_url = py.plot(fig, filename='my-file', fileopt='append')
You're right it is not well documented yet. But if you run help(py.plot) you would get a small document on it as follow:
plot(figure_or_data, validate=True, **plot_options)
Create a unique url for this plot in Plotly and optionally open url.
plot_options keyword agruments:
filename (string) -- the name that will be associated with this figure
fileopt ('new' | 'overwrite' | 'extend' | 'append') -- 'new' creates a
'new': create a new, unique url for this plot
'overwrite': overwrite the file associated with `filename` with this
'extend': add additional numbers (data) to existing traces
'append': add additional traces to existing data lists
world_readable (default=True) -- make this figure private/public
auto_open (default=True) -- Toggle browser options
True: open this plot in a new browser tab
False: do not open plot in the browser, but do return the unique url

displaying charts from python executables in shell

I'm using python 2.7 on Ubuntu to draw charts from text files containing data.
My point is, when using python executables in shell, I have no problem recording plots, but if I want them shown on my screen instead I have to go through the graphic interface. If possible, I would very much like to skip that part and get a dynamic display that I can interact with (as if I were to run my script from a python shell)!!
a MWE of what i'm doing is :
MWE
import numpy as np
import matplotlib.pyplot as plt
with open('filename','r') as myfile:
DATA = np.genfromtxt(myfile,unpack=True)
fig = plt.figure()
... my plot configuration ...
plt.savefig("image_name"+'.png')
plt.close()
end of MWE
Using this script image_name.png appears in my repertory. I tried replacing the last 2 lines with plt.plot() and plt.draw() but nothing happened.
Many thanks!
Michel
(edited)

Python matlplotlib add hyperlink to text

I've created a plot in Python using matplotlib. After annotating each line, I'd like to make the label a hyperlink (or alternatively, make the line itself a hyperlink). The text item has a property called 'url', but I've tried it and I can't figure out what, if anything, it does.
Is it possible to make text or line objects into hyperlinks?

This example shows how to set hyperlinks if you're outputting an SVG. Note that this only makes sense for SVG. If the plot is just an image, it's just an image, and images can't have hyperlinks in them.
If you want to be able to click on the object in the interactive plotting window and have that act like a hyperlink, you could create an event handler to handle the "pick" event, and have that open a browser or whatever. See this example for how to do pick events. Matplotlib plots aren't web pages or even really documents, they're just windows with graphics displayed in them, so they don't support hyperlinks as such; using a pick event you can emulate a hyperlink by opening a web browser when an object is clicked.
Edit: You are right, it doesn't work. It seems that the URL property is only read and used for certain types of objects. Googling, I see some old matplotlib mailing list discussion of it, where it seems the idea was to gradually add URL support to different artist types, but I guess they never got around to it. I would suggest you raise a bug about this on the matplotlib bug tracker.
In the meantime, there is a way to do it, but it is somewhat roundabout. The URL is drawn for PathCollection objects, so you could make a Path out of your text, then make a PathCollection out of that path, and then add that PathCollection to your plot. Here's an example:
pyplot.scatter([1, 2, 3], [4, 5, 6])
t = mpl.text.TextPath((2, 4), 'This is text', size=0.1)
pc = mpl.collections.PathCollection([t])
pc.set_urls(['http://www.google.com'])
ax = pyplot.gca()
ax.add_collection(pc)
pyplot.draw()
f = pyplot.gcf()
f.canvas.print_figure('fig.svg')
Note that you must use set_urls and not set_url. This method produces an SVG with clickable text, but it has some drawbacks. Most notably, it seems you have to set the text size manually in data coordinates, so it may take some fiddling to find a text size that isn't too ridiculously huge or tiny relative to the magnitude of your plotted data.

Adding a hyperlink makes sense when e.g. using an SVG file.
The url property works in newer matplotlib versions:
text = plt.annotate("Link", xy=(2,5), xytext=(2.2,5.5),
url='http://matplotlib.org',
bbox=dict(color='w', alpha=1e-6, url='http://matplotlib.org'))
For example, in a Jupyter notebook, which runs in a browser anyways, one could display an SVG with hyperlinks like this:
import matplotlib.pyplot as plt
from IPython.display import set_matplotlib_formats
set_matplotlib_formats("svg")
fig, ax = plt.subplots()
ax.scatter([1, 2, 3], [4, 5, 6])
text = ax.annotate("Link", xy=(2,5), xytext=(2.2,5.5),
url='http://matplotlib.org',
bbox=dict(color='w', alpha=1e-6, url='http://matplotlib.org'))
In the figure produced this way you may click on the link and be directed to matplotlib.org.

This is possible with pgf backend:
#!/usr/bin/env python3
import matplotlib
matplotlib.use("pgf")
pgf_with_custom_preamble = {
"text.usetex": True,
"pgf.preamble": [
r"\usepackage{hyperref}"
]
}
matplotlib.rcParams.update(pgf_with_custom_preamble)
from matplotlib import pyplot as plt
x = range(5)
y = range(5)
fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot(x, y, "r-", label=r"Hyperlink: \url{http://google.com}")
ax.legend()
fig.savefig("mwe.pdf")