Mailman 3 August 2019 - Matplotlib-users

wxmplot 0.9.38: interactive plotting with wxPython + matplotlib
by Matt Newville Aug. 29, 2019

Aug. 29, 2019

Hello matplotlib users, wxmplot 0.9.38 is now available and can be installed with `pip install wxmplot`. Docs are at https://newville.github.io/wxmplot/ and code at https://github.com/newville/wxmplot/. I suspect many people here are not aware of this module that combines wxPython and matplotlib. I also think that some of you may find it very useful for making 2D line plots and image displays because the displays created are highly configurable and interactive. With 0.9.38, interactive plotting from the Python command line (that is, from a plain Python terminal or a Jupyter qtconsole, notebook, or Juptyerlab) can be done with: >>> import wxmplot.interactive as wi >>> import numpy as np >>> x = np.linspace(-5, 5, 101) >>> wi.plot(x, np.sin(x), label='sine') At first look, the results are similar to `pyplot.plot()` : a new Plot Window with the 2D Line Plot. From this window, not only can the user zoom in, adjust the margins, and save an image as with the Navigation Toolbar, but they can also change the styling/theming, labels and titles, configure the legend, and so on. They can also change the color, marker, linewidth, label, and style of each trace. With the legend displayed, clicking on a legend label will toggle whether the corresponding trace is displayed. Additional functions such as `wi.plot_text()`, `wi.plot_marker()`, and `wi.plot_axhline()` allow the user to add annotations to the 2D line plot. For image displays, `wi.imshow(image_data)` will display a false-color image of data, similar to `pyplot.imshow(image_data)`, but with widgets, menu items, and keyboard shortcuts to allow the user to rotate, flip, or smooth the image, change color tables and contrast thresholds, display as a contour map, draw a scalebar, and show slices through the image. The `wxmplot.interactive` module does not use a blocking `show()` function - the results are drawn immediately and are interactive, and the shell is not frozen while the plot is displayed. This means that from the Python shell, the user can additional traces to an existing plot, replace the current plot, or draw to a second (or more) separate Plotting or Image Display windows. When run with `python myscript.py`, a script that uses the `wxmplot.interactive` functions will show the displays, and these will persist (and be interactive) until closed. That is, the script will not finish and kill the displays until all displays are closed or until the script is explicitly killed with Ctrl-C. There are some specialty displays available (see examples), but there are many aspects of matplotlib that have no equivalent in wxmplot. Still, I invite anyone interested to try out the basic plotting and image display as I think some of you may find it very useful for exploratory data analysis. Wxmplot 0.9.38 uses and MIT license and supports Python 2.7, 3.5, 3.6, and 3.7, and requires matplotlib 2.0+, wxPython 4.0.2+, numpy, and six. Support for Python 2 will be dropped for the next release. Feedback, suggestions, and improvements are most welcome. Cheers, --Matt Newville

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**Question post from Albert**
by JL Aug. 21, 2019

Aug. 21, 2019

Dear Matplotlib users, I am a matplotlib user from Leeds, UK. Recently, I struggle with a triangle surface plot (https://matplotlib.org/3.1.0/gallery/mplot3d/trisurf3d.html <https://matplotlib.org/3.1.0/gallery/mplot3d/trisurf3d.html>) problem in matplotlib. As we know, if you have data x, y, z, you can directly call ax.plot_trisurf(x, y, z). However, the data set I have is only three lists of data and if you direct call so, you will find surface losses in the z axis. In MATLAB, you can add a boundary (K = boundary(X, Y, Z, 1);) and then call the function trisurf(K, X, Y, Z), while I cannot find an suitable way in matplotlib or in Python since I do not want to use MATLAB any more :) The details (including data and some codes) are post as follows, please kindly check, https://stackoverflow.com/questions/57481995/how-to-generate-a-3d-triangle-… <https://stackoverflow.com/questions/57481995/how-to-generate-a-3d-triangle-…>. Thanks, Albert

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[ANN] "Scientific Visualization - Python & Matplotlib" book project
by Nicolas Rougier Aug. 19, 2019

Aug. 19, 2019

Dear all, The matplotlib cheat-sheet (https://github.com/rougier/matplotlib-cheatsheet) I posted a few days comes from a book project I’m starting, that is planned to be released (open access) on Summer 2020. You can follow the progress and support the project at: https://github.com/rougier/scientific-visualization-book Everything will be freely available at the end of the project (but the printed book). I hope this is not an inappropriate message for this mailing list. Nicolas Some teaser (made with matplotlib of course).

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Date/Time not displaying as expected.
by Mike Sacauskis Aug. 19, 2019

Aug. 19, 2019

Hi I'm new to Matplotlib, I'm going to be plotting some temperature data over time and wrote a test program to see with Matplotlab can do for me. When I plot the the date the date time does not display as I would expect, the date is output but the time is some type of counter not the time of day as expected. What am I doing wrong? I've attached the code, data and the resulting image. Any help would be greatly appreciated. Mike

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mplcairo multipage pdf and too many figures open
by Neal Becker Aug. 16, 2019

Aug. 16, 2019

I've been using mplcairo multipage pdf. The pattern I use is: from mplcairo.multipage import MultiPage cm = MultiPage(ap_args.output) with cm as pdf: fig,ax = plt.subplots() do something pdf.savefig(fig) fig2,ax2 = plt.subplots() do something pdf.savefig(fig2) ... after 20 figures: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`). What is the proper way to use mplcairo.multipage to avoid this issue? Thanks, Neal

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Re: [Matplotlib-users] Plot
by Partha Sinha Aug. 14, 2019

Aug. 14, 2019

I got the solution as suggested by scott. My new problem is: Lets say I will generate lets two pairs of 10 random numbers, say x and y. When first pair of x and y is generated, it will be plotted. Again when second set of number is generated, it will appear on the same graph and not on 2nd graph. This will continue till 10th pair. How to do this? Regards Parth On 3 Aug 2019 1:17 pm, "Scott Lasley" <selasley(a)icloud.com> wrote: This should do what you want. It works in a jupyter notebook but not in jupyterlab. It also works as a standalone python script if you comment out the %matplotlib notebook line. Best regards, Scott # based on https://matplotlib.org/gallery/animation/animate_ decay.html#sphx-glr-gallery-animation-animate-decay-py # but uses a zip iterator for the frames variable in FuncAnimation instead of the data_gen generator function # used in the example # comment out this line if you are not running this in a jupyter notebook %matplotlib notebook # %matplotlib nbagg import numpy as np from matplotlib import pyplot as plt from matplotlib.animation import FuncAnimation def init_plot(): # if you know the data ranges you can set fixed # xlim and ylim limits here, otherwise uncomment # the ax.relim and ax.autoscale_view calls in # draw_pts to rescale the axes based on the # last data point plotted ax.set(xlim=[0, 11], ylim=[0, 120]) return [] def update_pts(data): x.append(data[0]) y.append(data[1]) pts.set_data(x, y) # ax.relim() # ax.autoscale_view(scaley=True) return [pts] # data to plot. replace with your data values xvals = np.arange(1, 11) yvals = np.array([1, 4, 9, 16, 25, 36, 49, 64, 81, 100]) # zip xvals[1:] and yvals[1:] since we are plotting # xvals[0], yvals[0] at time 0 after we create the figure xy_points = zip(xvals[1:], yvals[1:]) # create x and y lists containing the first point to be plotted. # update_pts will append the next x and y values from the iterator xy_points # to x and y every 5000ms and update the pts being plotted x = [xvals[0]] y = [yvals[0]] # create a figure and plot the first x, y point at time 0 fig, ax = plt.subplots() pts = ax.plot(x, y, 'o')[0] # loop through the remaining points and update the plot every # 5000ms anim = FuncAnimation(fig=fig, func=update_pts, frames=xy_points, init_func=init_plot, interval=5000, blit=False, repeat=False) plt.show() > On Aug 3, 2019, at 1:04 AM, Partha Sinha <pnsinha68(a)gmail.com> wrote: > > I want to plot a list of 10 numbers. I want to plot each point after 5 secs (first point in o sec and 2nd point after 5 sec anf so on) and want to plot them in same graph. > How to do? > Regards > Parth > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users(a)python.org > https://mail.python.org/mailman/listinfo/matplotlib-users

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Re: [Matplotlib-users] Matplotlib-users Digest, Vol 48, Issue 2
by Animatore. TRPS03000X Aug. 13, 2019

Aug. 13, 2019

Dears all, I solved the issue changing the command 'ani = animation.FuncAnimation(fig, run, data_gen, blit=True, interval=5,repeat=True) ' and my Open Physics Laboratory works fine!! Thanks a bunch far all! Bye, Marco Il giorno mar 16 lug 2019 alle ore 18:02 < matplotlib-users-request(a)python.org> ha scritto: > Send Matplotlib-users mailing list submissions to > matplotlib-users(a)python.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.python.org/mailman/listinfo/matplotlib-users > or, via email, send a message with subject or body 'help' to > matplotlib-users-request(a)python.org > > You can reach the person managing the list at > matplotlib-users-owner(a)python.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Matplotlib-users digest..." > > > Today's Topics: > > 1. Help request serila data plot, Ubuntu 18 (Animatore. TRPS03000X) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 15 Jul 2019 21:05:16 +0200 > From: "Animatore. TRPS03000X" <animatore.trps03000x(a)didasca.org> > To: matplotlib-users(a)python.org > Subject: [Matplotlib-users] Help request serila data plot, Ubuntu 18 > Message-ID: > <CACxvrmM6QZKih4d5Zr_8s38Usf2kbEfhwkqw= > uo_-vD6AoN6hw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear matplot users, > > I have installed Ubuntu 18 on my computer and Matplotlib, I use it to graph > position vs. time of moving objects by serial data. > > The python script is the following: > > > import matplotlib > > matplotlib.use("Qt5Agg") > > import numpy as np > > import matplotlib.pyplot as plt > > import matplotlib.animation as animation > > from time import sleep > > import serial > > import time > > fine="c" > > pre="ciao" > > while (fine != "f"): > > raw_input("\n\n\n Premi Enter per far partire la registrazione dei > dati") > > xdata, ydata = [], [] > > ser = serial.Serial('/dev/ttyACM0', 9600) > > while (False): > > pre=ser.readline() > > pre=ser.readline() > > prec = float(pre) > > y=prec > > fig, ax = plt.subplots() > > line, = ax.plot([], [], lw=2) > > ax.set_ylim(0, 90) > > ax.set_xlim(0, 10) > > ax.grid() > > def data_gen(): > > t=0 > > y=0 > > cnt=0 > > p=0 > > a = ser.readline() > > while (True)&(t < 10): > > a = ser.readline() > > y = float(a) > > if (y != 0) : > > t = (time.time() - start) > > t = float(t) > > yield t, y > > def run(data): > > t,y = data > > xdata.append(t) > > ydata.append(y) > > ax.figure.canvas.draw() > > line.set_data(xdata, ydata) > > return line, > > data_gen.t = 0 > > while (abs(y-prec) < 2): > > if True: > > a = ser.readline() > > y = float(a) > > start = time.time() > > ani = animation.FuncAnimation(fig, run, data_gen, blit=True, > interval=5,repeat=False) > > plt.show() > > stop =0 > > fine=raw_input("Premi f per finire :") > > > It works fine, but after the plotting (10 seconds), there is a problem, I > cannnot use the tools of the matplot window, i.e. when I try to zoom, after > selecting the area, the plot desappear. > > Can you help me? >

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Matplotlib 3.1 cheat sheet
by Nicolas Rougier Aug. 11, 2019

Aug. 11, 2019

I just made a matplotlib cheat sheet that might come handy when you don’t remember the name of a function or a parameter. It’s available from https://github.com/rougier/matplotlib-cheatsheet Nicolas

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Why are these plots different?
by Henry Ekene Aug. 9, 2019

Aug. 9, 2019

Hello, Matplotlib Users, My challenge is that I saw this below image somewhere [image: Screenshot from 2019-08-09 15-24-34.png]and i decided to reproduce it using the same matplotlib codes but it turned out that my own image appear different as can be seen below [image: Screenshot from 2019-08-09 15-28-38.png]Please why is mine different in color, and what can I do to get the exact image as the other one? Thanks for your help. Henry

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Is there any way to get interactive matplotlib in Jupyterlab without conda-forge?
by Brendan Barnwell Aug. 9, 2019

Aug. 9, 2019

I was recently told ( file:///C:/Users/BrenBarn/AppData/Roaming/jupyter/runtime/nbserver-6156-open.html ) that Jupyterlab is supposed to be ready for prime time. For me that would include interactive use of Matplotlib. Apparently the way to do this in Jupyterlab is with ipympl, aka "jupyter-matplotlib" at https://github.com/matplotlib/jupyter-matplotlib . Looking at the instructions, I see it tells me to install from conda-forge. However, I have found several warnings (e.g., here https://github.com/conda/conda/issues/8920#issuecomment-519105949 ) that mixing conda defaults and conda-forge channels can cause problems. I have experienced this myself with conda going crazy upgrading and downgrading packages due to slight version differences between the packages in different channels. I am going to be teaching a class using Python. I do not want to use conda-forge because I want to keep installation of everything as simple as possible for the students and avoid the possibility of such problems. So my question is: is it possible to get fully functional interactive Matplotlib in Jupyterlab WITHOUT ever using conda-forge? If not, I would say that Jupyterlab is not really ready for primetime! (I realize that, if the answer is no, that may be more an Anaconda issue than a Matplotlib or Jupyter issue, but I'm just trying to figure out whether it's actually possible to replicate my working Jupyter notebook environment in Jupyterlab using only the conda defaults channel.) Thanks, -- Brendan Barnwell "Do not follow where the path may lead. Go, instead, where there is no path, and leave a trail." --author unknown

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