Mailman 3 June 2017 - Matplotlib-users

animation in thread
by arash Aug. 7, 2017

Aug. 7, 2017

I am new to matplotlib and I am trying to get started with animation library.There is an example here for a simple strip chart:https://matplotlib.org/examples/animation/strip_chart_demo.htmlI tried to use this example in a thread. I created a simple *threading.Thread* class, and in it's* run() *method, called:ani = animation.FuncAnimation(fig, scope.update, emitter, interval=10,True)plt.show()here is class:class graph(threading.Thread): def __init__(self, feeder): threading.Thread.__init__(self) self.fig, self.ax = plt.subplots() self.scope = Scope(self.ax) self.feeder=feeder self.running=True def run(self): while self.running: ani = animation.FuncAnimation(self.fig, self.scope.update, self.feeder.emit_ch1(), interval=1, blit=True) plt.show() but when I start this thread, it never shows the windows. Isn't this right usage? -- View this message in context: http://matplotlib.1069221.n5.nabble.com/animation-in-thread-tp48055.html Sent from the matplotlib - users mailing list archive at Nabble.com.

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Problem of memory leak using FigureCanvasTkAgg
by GARCIA PIERRE SIMON p0904379 Aug. 7, 2017

Aug. 7, 2017

Hello, I'm PhD student in Bioinformatic and I'm working on a project using matplotlib and Tkinter but I've got a big problem of memory leak using these modules. I'll be very grateful if you could help me to solve this problem. Here is the link explaining what happends, with a reduced script: http://stackoverflow.com/questions/43097378/matplotlib-vs-tkinter-memory-le… Thank you in advance, Sincerly, Pierre Garcia, PhD Student --------- Bases Moléculaires et Structurales des Systèmes infectieux-UMR5086 Institut de Biologie et Chimie des Protéines 7 passage du Vercors 69 367 Lyon cedex 07 --------- Laboratoire de Biométrie et Biologie Evolutive-UMR5558 UCBL Lyon 1 -Bât. Grégory Mendel 43 bd du 11 novembre 1918 69622 VILLEURBANNE cedex

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Embedding, Drawing, Curser in Tkinter
by stefanxfg Aug. 5, 2017

Aug. 5, 2017

Hello to everyone. I develop a GUI and i want to embedd Matplotlib in a Tkinter Canvas. Theres is no problem until here. But i want to draw the lines and have a curser line in the diagram. In the code below i embedd the canvas in the INIT-Function. class BOStrab_Fahrzeugeinschraenkung: def __init__(self, top=None): ...... self.ya = np.array(ddd) self.yb = np.array(ddd) self.z = np.array(ddd) self.canvasframe11 = Frame(self.TPanedwindow4_f2) self.canvasframe11.place(x=0, y=0, relwidth=1.0, relheight=0.95, bordermode=INSIDE) self.canvasframe12 = Frame(self.TPanedwindow4_f2) self.canvasframe12.place(x=0, rely=0.95, relwidth=1.0, bordermode=INSIDE) global ax1 self.fig1 = Figure (figsize=(5,4), dpi=100) self.ax1 = self.fig1.add_subplot(111) #für 2d-Plot self.ax1.set_title('Definition der LRUGL') self.ax1.set_xlabel('Breite y [mm]') self.ax1.set_ylabel('Hoehe z [mm]') self.ax1.axis([-2000,2000,0, 5000]) self.ax1.grid(True) self.ax1.plot(self.ya,self.z, color='red', linestyle='--', marker='') self.ax1.plot(self.yb,self.z, color='red', linestyle='--', marker='') self.canvas1 = FigureCanvasTkAgg(self.fig1,self.canvasframe11) toolbar1 = NavigationToolbar2TkAgg(self.canvas1, self.canvasframe12) self.canvas1.get_tk_widget().pack(fill=BOTH, expand=TRUE, pady=2, padx=2, anchor="n") In several examples i saw the drawing in def's and the input for the drawing from root. So the following code is function then. def onMouseMove(event): ax1.lines = [ax1.lines[0]] ax1.axhline(y=event.ydata, color="k") ax1.axvline(x=event.xdata, color="k") def updateData(): global level1, val1 clamp = lambda n, minn, maxn: max(min(maxn, n), minn) yield 1 # FuncAnimation expects an iterator def visualize(i): lineVal1.set_ydata(val1) return lineVal1 My question is. Is my way to embedd the code in Tkinter right? Or its better to declare the diagram functionalities outside the class and only draw into the class? Best regards from Stefan -- View this message in context: http://matplotlib.1069221.n5.nabble.com/Embedding-Drawing-Curser-in-Tkinter… Sent from the matplotlib - users mailing list archive at Nabble.com.

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figsize wrong in Qt5Agg import
by David J Pine Aug. 5, 2017

Aug. 5, 2017

Using the qt5agg backend, I get plots that are 2 times too small unless I use pyplot. I just upgraded to matplotlib 2.01. I'm running on a Mac using the Anaconda installation: 4.3.17 py36_0 This two scripts produce plots that are the same size. Why do I have to double the figsize parameters when I do not use pyplot? Seems like a bug. I didn't need to do this for the Qt4Agg backend. # script 1 import matplotlib matplotlib.use('Qt5Agg') import matplotlib.pyplot as plt fig1, ax = plt.subplots(figsize=(6, 4)) ax.plot([1, 2, 3, 2, 3, 4, 3, 4, 5]) ax.set_title('A simple plot') ax.grid(True) ax.set_xlabel('time') ax.set_ylabel('volts') plt.savefig('test1.pdf') plt.show() # script 2 import matplotlib matplotlib.use('Qt5Agg') from matplotlib.backends.backend_qt5agg \ import FigureCanvasQTAgg as FigureCanvas from matplotlib.figure import Figure fig = Figure(figsize=(12, 8)) canvas = FigureCanvas(fig) ax = fig.add_subplot(111) ax.plot([1, 2, 3, 2, 3, 4, 3, 4, 5]) ax.set_title('A simple plot') ax.grid(True) ax.set_xlabel('time') ax.set_ylabel('volts') canvas.print_figure('test2.pdf') canvas.show()

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Polygon Selector Demo
by Tap, Frank Aug. 5, 2017

Aug. 5, 2017

Dear all, I try to run the Polygon Selector Demo (https://matplotlib.org/devdocs/gallery/widgets/polygon_selector_demo.html#s…) but I get the following error: ImportError: cannot import name PolygonSelector I am using matplotlib 2.0.2. Can anybody please tell me what I’m doing wrong? Regards, Frank dr. ir. Frank Tap | Software Engineer | Maritime Simulation & Software Group MARIN | T +31 317 49 32 11 | r.tap(a)marin.nl<mailto:r.tap@marin.nl> | www.marin.nl<http://www.marin.nl> [LinkedIn]<https://www.linkedin.com/company/marin> [YouTube] <http://www.youtube.com/marinmultimedia> [Twitter] <https://twitter.com/MARIN_nieuws> [Facebook] <https://www.facebook.com/marin.wageningen> MARIN news: ‘Hydrodynamics of Floating Offshore Structures’ course, Singapore & Houston<http://www.marin.nl/web/News/News-items/Hydrodynamics-of-Floating-Offshore-…>

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Matplotlib tkinter error
by Pooja Aug. 5, 2017

Aug. 5, 2017

Hi, I have been working on a piece of code and suddenly getting these errors: /Users/poojabhalode/.bash_profile: line 1: .bashrc: No such file or directory [[ 2 -1 0] [-1 2 -1] [ 0 -1 2]] [[ 3.41421356e+00 8.32667268e-17 -6.37995760e-17] [ 0.00000000e+00 2.00000000e+00 1.35170527e-16] [ 0.00000000e+00 0.00000000e+00 5.85786438e-01]] 8.32667268469e-17 8.32667268469e-17 -6.37995760397e-17 0.0 1.35170526715e-16 0.0 0.0 [[ 3.41421356 0. 0. ] [ 0. 2. 0. ] [ 0. 0. 0.58578644]] Traceback (most recent call last): File "/Users/poojabhalode/Google Drive/PYTHON/files/1sttest/May17.py", line 7, in <module> import matplotlib File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/__init__.py", line 947, in <module> rcParams = rc_params() File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/__init__.py", line 856, in rc_params fname = matplotlib_fname() File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/__init__.py", line 726, in matplotlib_fname configdir = _get_configdir() File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/__init__.py", line 597, in _get_configdir return _get_config_or_cache_dir(_get_xdg_config_dir()) File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/__init__.py", line 566, in _get_config_or_cache_dir if not _is_writable_dir(p): File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/__init__.py", line 228, in _is_writable_dir t = tempfile.TemporaryFile(dir=p) AttributeError: 'module' object has no attribute 'TemporaryFile' [Finished in 0.2s with exit code 1] [shell_cmd: python -u "/Users/poojabhalode/Google Drive/PYTHON/files/1sttest/May17.py"] [dir: /Users/poojabhalode/Google Drive/PYTHON/files/1sttest] [path: /usr/bin:/bin:/usr/sbin:/sbin] My code gives errors at the import statement itself: Code:: import matplotlib ERROR indicated here. matplotlib.use("TkAgg") from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg, NavigationToolbar2TkAgg from matplotlib.figure import Figure Can someone please let me know what is going wrong with this? Thank you. I would really appreciate it. Thanks! -- View this message in context: http://matplotlib.1069221.n5.nabble.com/Matplotlib-tkinter-error-tp48051.ht… Sent from the matplotlib - users mailing list archive at Nabble.com.

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Superimpose circles on a contourf plot
by SilverSurfer Aug. 5, 2017

Aug. 5, 2017

Dear all I am new to matplotlib and python. Up until now i was able to achieve what i wanted, but now i run into a weird problem. If i superimpose markers onto a countourf plot they change their size when i zoom into and area off the plot. The information i use to plot the positions of the circles is gathered from ASE (Atomic Simulation Environment ). I will first try to outline my code without suppling a MWE as this would be hard to do at the moment: __________________________ ..... from matplotlib import pyplot from matplotlib.patches import Circle from ase.io import read, write from ase import Atom from ase.atoms import Atoms import pylab #xarray,yarray are the x and y coordinates ,DATA contains a density at this point niso=1#min max value ncontours=512# number off contours ###ploting starts here myplot = pylab.contourf(xarray,yarray,DATA,ncontours,antialiased=False,cmap=my_cmap,vmin=-niso,vmax=niso) atoms=read('somedata', format="vasp") for atom in atoms color = my_colors_DCLN[atom.number] radius = radii[atom.number] struc = pylab.plot(atom.x, atom.y, color='black', linestyle='solid', marker='o', markerfacecolor=color, markersize=(1.2+radius*3.8),alpha=0.45) #circle = Circle((atom.x, atom.y), (radius/3.5), facecolor=color,edgecolor='k', linewidth=0.4)#alpha=10) #ax.add_patch(circle)) #ax.axis('equal') #ax.set_xticks([]) #ax.set_yticks([]) #ax.axis('off') density_plot pylab.axis('image') plt.Figure() plt.draw() pylab.show() _______________________ If i use the normal markers from matplotlib everything works correct. My DATA that i plot with contourf has the same dimensions as the atoms object. So i only need to have the xy coordinates of this object. I can plot the atoms object fine if i do it like this: ____________ import numpy as np from matplotlib import pyplot from ase.lattice.surface import fcc111 from ase import Atom from ase.data import covalent_radii as radii from ase.data.colors import jmol_colors from matplotlib.patches import Circle from ase.io import read, write fig, ax = pyplot.subplots() atoms = read('somedata', format="vasp") for atom in atoms: color = my_colors[atom.number] radius = radii[atom.number] circle = Circle((atom.x, atom.y), (radius), facecolor=color,edgecolor='k', linewidth=0.4) ax.add_patch(circle) # Enforce the circles are round (equal x and y scales) and turn off # tickmarks. ax.axis('equal') ax.set_xticks([]) ax.set_yticks([]) ax.axis('off') fig.savefig('out.png',dpi=300) pyplot.draw() pyplot.show() _____________________ But i do not know what "fig, ax = pyplot.subplots()" does and how i could incoporate this code in a way that i can supperimpose it to my contourf plot. The Contourf plot is the important information and i just want to show the positions of certian atoms ( circles) ontop of this plot. Thank you in advance fabian -- View this message in context: http://matplotlib.1069221.n5.nabble.com/Superimpose-circles-on-a-contourf-p… Sent from the matplotlib - users mailing list archive at Nabble.com.

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Combine two histogramm in one histogramm
by bellafkih Aug. 5, 2017

Aug. 5, 2017

Hello, I present a data of each month in histogram, so for each month, there two percentages: first the percentage of messages updates (example: 80 %) and the second, the percentage of non update messages (eg. 20%), i must divide the update messages into two parts: the first : important messages (eg. 70 %) and non important messages (eg 30%). My current solution is to create two histograms, but i ask if there is a possibility to create only graphic, so present the 70 % and 30 % in the part of 80% ? Thanks -- View this message in context: http://matplotlib.1069221.n5.nabble.com/Combine-two-histogramm-in-one-histo… Sent from the matplotlib - users mailing list archive at Nabble.com.

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Subplot x-axis shared with other subplots y-axis
by Juan Nunez-Iglesias June 27, 2017

June 27, 2017

Hello, I’m trying to build an orthogonal-views volume viewer in Matplotlib like this one: https://imagej.nih.gov/ij/docs/guide/images/OrthogonalViews.png For this to work, I need to share the y-axis of the YZ (right) view/subplot with the x-axis of the XZ (bottom) view/subplot. Is this possible? Juan.

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Problem animating a histogram and movie at the same time
by David J Pine June 14, 2017

June 14, 2017

I am having a problem animating a histogram and movie at the same time using matplotlib.animation.ArtistAnimation. The first program below, which makes an animated histogram using the "bar" routine works fine. If I substitute the two lines commented out for the two lines preceding those lines, it still works fine (using "plot" instead of 'bar"). For reasons that are not clear to me, I need make a list (ims) for animation for the histogram using the "bar" routine, and a list of lists for animation of the simple "plot" routine. There is a more serious problem with the second routine where I simultaneously animate a sequence of images using imshow and also try to make an animated histogram. It works fine if I plot the "histogram" using the "plot" routine but does not work if I use the "bar" routine. Can someone offer some help? I am running these on OSX 10.12.5, Python 3.5.2 or Python 3.6.1, and matplotlib 2.0.0 or 2.0.2 ---------------------------- import numpy as np import matplotlib.pyplot as plt import matplotlib.animation as animation fig, ax = plt.subplots() ims = [] xh = np.random.randn(10) for i in range(100): xh = np.append(xh, np.random.randn(10)) a, b = np.histogram(xh, bins=24, normed=True) xx = 0.5*(b[:-1]+b[1:]) ax.set_xlim(-3, 3) ax.set_ylim(0, 0.5) im = ax.bar(xx, a, width=0.9*(b[1]-b[0]), color='C1') ims.append(im) # im, = ax.plot(xx, a, '-oC0') # ims.append([im]) ani = animation.ArtistAnimation(fig, artists=ims, interval=50, repeat=False) plt.show() ---------------------------- import numpy as np import matplotlib.pyplot as plt import matplotlib.animation as animation def f(x, y): return np.sin(x) + np.cos(y) xm = np.linspace(0, 2 * np.pi, 120) ym = np.linspace(0, 2 * np.pi, 120).reshape(-1, 1) fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(8, 3.5)) ax1.axis('off') ims = [] xh = np.random.randn(10) for i in range(100): xm += np.pi / 20. ym += np.pi / 20. im1 = ax1.imshow(f(xm, ym), cmap=plt.get_cmap('plasma'), aspect='equal', animated=True) xh = np.append(xh, np.random.randn(10)) a, b = np.histogram(xh, bins=24, normed=True) xx = 0.5*(b[:-1]+b[1:]) ax2.set_xlim(-3, 3) ax2.set_ylim(0, 0.5) # im2 = ax2.bar(xx, a, width=0.9*(b[1]-b[0]), color='C1') im2, = ax2.plot(xx, a, '-oC0') ims.append([im1, im2]) ani = animation.ArtistAnimation(fig, artists=ims, interval=50, repeat=False) # ani.save('junk.mp4') plt.show() ----------------------------

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