Mailman 3 October 2017 - Matplotlib-users

Scientific notation digits at left-bottom corner of figure
by Ardeal LIANG Oct. 30, 2017

Oct. 30, 2017

Hi, If I put the mouse on the figure, x and y axis are displayed on the left-bottom corner of the figure. but the x axis is displayed as scientific notation, I want it to be displayed as decimal notation. how to make x axis or y axis values displayed as decimal notation on the left-bottom corner? [cid:image003.jpg@01D34F3B.58162F30] Best Regards, Ardeal Liang ________________________________ The information contained in this email may be confidential and/or legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this email is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original email.

4 15

loop through x and y axes
by Andrei Berceanu Oct. 27, 2017

Oct. 27, 2017

Hi all, Please consider this code: fig, (ax1, ax2) = plt.subplots(ncols=2, figsize=[14,4]) for ax in (ax1, ax2): ax.set_xlabel(labels[0]) ax.set_ylabel(labels[1]) This could be simplified if I could just loop though the x and y axes of each subplot, something like: for index, ax in enumerate((ax1, ax2)): ax.set_label[index](labels[index]) Is there some way of achieving this in Matplotlib? From what I found, it seems one can only refer to the axes using x and y, and so I don't know how to loop over both of them. Thank you, Andrei

3 2

Why is canvas.print_figure to a png reduce the real size of my image
by David Goldsmith Oct. 21, 2017

Oct. 21, 2017

Hi! I spent a good part of yesterday trying to figure this out on my own, without success, so I'm posting. I have a 3601x2401 pixel, 300 DPI figure I export to a png using print_figure; here's sample code: PLB.imshow(rslt) # rslt is a 3601x2401 int-valued array curfig = PLB.Figure fig = PLB.gcf() # next three lines are in my code; don't seem relevant, but I include them in case they are ax = fig.gca() ax.xaxis.set_ticks([]) ax.yaxis.set_ticks([]) fig.canvas.print_figure(fn + '.png', dpi=300, bbox_inches='tight', pad_inches=-1.0 / 72) The resulting png is neither the right number of pixels by pixels, nor the right number of inches by incheses; what's more the resulting png differs depending on whether I use imshow or matshow (which I also tried). What's going on, and how do I "fix" it? (If I really am getting the full resolution figure, despite what the png is telling me are the pixel counts, why are the physical dimensions off, and why is the png telling me that the pixel counts are different? If it has something to do with compression, is there some undocumented way to say "no compression" and will that have the desired effect?) Thanks! DLG

3 8

Re: [Matplotlib-users] Problem of memory leak using FigureCanvasTkAgg
by Thomas Caswell Oct. 20, 2017

Oct. 20, 2017

I think there was a bug in how you were capturing the clearing the children of the top level frame. Tweaking it a bit I can reproduce the leaking, but not on every cycle: from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg import matplotlib.patches as patches # from Tkinter import Tk, Canvas, Frame, Label, Button from six.moves import tkinter as Tk import gc import resource from matplotlib.figure import Figure import sys list_fig_g = [] list_wid_g = [] def launcher(list_wid, list_fig, frame): print('Memory usage: %s (kb)' % resource.getrusage(resource.RUSAGE_SELF).ru_maxrss,) for f in list_fig: f.clf() f.clear() f._master = None del f list_fig.clear() for i in list_wid: print(i, sys.getrefcount(i)) r = i.winfo_toplevel() i.grid_forget() i.destroy() for k in ('<MouseWheel>', '<Destroy>'): r.unbind(k) print(i, sys.getrefcount(i)) del i list_wid.clear() fig1 = Figure(figsize=(1, 1)) ax1 = fig1.add_subplot(111, aspect='equal') ax1.add_patch( patches.Arrow( 0, # x -0, # y 1, # dx 0, # dy width=1, ) ) list_fig.append(fig1) # this seems to be the first line that leaks memory # but not _always_ canvas = FigureCanvasTkAgg(fig1, master=None) t1, t2, w, h = fig1.bbox.bounds widget = canvas.get_tk_widget() # widget = Tk.Canvas( # master=frame, width=w, height=h, borderwidth=0, # highlightthickness=0) # w2 = Tk.PhotoImage( # master=widget, width=int(w), height=int(h)) # widget.create_image(w//2, h//2, image=w2) widget.grid(row=0, column=1) widget.focus_set() list_wid.extend(frame.winfo_children()) # print(w) # print('gc: ', gc.collect(2)) gc.collect(2) # canvas.draw() print('Memory usage: %s (kb)' % resource.getrusage(resource.RUSAGE_SELF).ru_maxrss) print() def bulk(list_wid, list_fig, frame): for j in range(100): launcher(list_wid, list_fig, frame) root = Tk.Tk() Entete5 = Tk.Label(root, width=20, height=1).grid(row=0, column=1) fond = Tk.Canvas(root, width=800, height=200) fond.grid(row=1, column=1) frame_g = Tk.Frame(fond, width=80, height=10) frame_g.grid(row=0, column=1) fond.create_window(0, 0, window=frame_g) Load = Tk.Button(root, text="Load", command=lambda: launcher(list_wid_g, list_fig_g, frame_g)) go = Tk.Button(root, text="bulk", command=lambda: bulk(list_wid_g, list_fig_g, frame_g)) Load.grid(row=7, column=4) go.grid(row=6, column=4) list_wid = frame_g.winfo_children() root.mainloop() (I also added a 'bulk' button to run 100 iterations). I tried just creating a FigureCanvasAgg object (the super-class of FigureCanvasTkAgg) and that seems not to leak. Doing most of the tk work that FigureCanvasTkAgg does not seem to leak. It looks like it is the callbacks that are registered to handle mouse and key board events, deleteing them from the __init__ seems to prevent the leak! Not sure what the right way to clean those up is though, but at least this is pointing the right direction! Tom On Thu, Oct 19, 2017 at 12:18 PM GARCIA PIERRE SIMON p0904379 < pierre.garcia(a)etu.univ-lyon1.fr> wrote: > Adding gc.collect() everywhere in the script doesn't change anything. Here > is a code that works and that is simpler: > > > #! /usr/bin/python2.7 > #-*- coding: utf-8 -*- > import matplotlib > matplotlib.use('Tkagg') > from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg > import matplotlib.patches as patches > from Tkinter import * > import gc > import resource > from matplotlib.figure import Figure > > list_fig_g = [] > list_wid_g = [] > > def Launcher(list_wid,list_fig,frame): > print 'Memory usage: %s (kb)' % > resource.getrusage(resource.RUSAGE_SELF).ru_maxrss, > for i in list_wid: > i.grid_forget() > i.destroy() > del i > try: > list_fig[0].clf()# other round > list_fig[0].clear() > del list_fig[0] > except: > print "",# first round > fig1 = Figure(figsize=(1,1)) > ax1 = fig1.add_subplot(111, aspect='equal') > ax1.add_patch( > patches.Arrow( > 0, # x > -0, # y > 1, # dx > 0, # dy > width=1, > ) > ) > list_fig.append(fig1) > canvas = FigureCanvasTkAgg(list_fig[0], master=frame) > canvas.get_tk_widget().grid(row=0,column=1) > list_wid = frame.winfo_children() > print 'Memory usage: %s (kb)' % > resource.getrusage(resource.RUSAGE_SELF).ru_maxrss > > root = Tk() > Entete5 = Label(root,width=20, height=1).grid(row=0,column=1) > fond = Canvas(root, width=800, height=200) > fond.grid(row=1, column=1) > frame_g = Frame(fond,width=80, height=10) > frame_g.grid(row=0,column=1) > fond.create_window(0, 0, window=frame_g) > Load = Button (root, text = "Load", command = lambda : > Launcher(list_wid_g,list_fig_g,frame_g)) > Load.grid(row=7,column=4) > list_wid = frame_g.winfo_children() > root.mainloop() > > > and here is the output: > > > Memory usage: 49516 (kb) Memory usage: 50824 (kb) > Memory usage: 51880 (kb) Memory usage: 52672 (kb) > Memory usage: 52936 (kb) Memory usage: 53728 (kb) > Memory usage: 53992 (kb) Memory usage: 54256 (kb) > Memory usage: 54520 (kb) Memory usage: 54520 (kb) > Memory usage: 54520 (kb) Memory usage: 55048 (kb) > Memory usage: 55312 (kb) Memory usage: 55840 (kb) > Memory usage: 55840 (kb) Memory usage: 55840 (kb) > Memory usage: 56104 (kb) Memory usage: 56104 (kb) > Memory usage: 56104 (kb) Memory usage: 56104 (kb) > Memory usage: 56368 (kb) Memory usage: 56368 (kb) > Memory usage: 56368 (kb) Memory usage: 56632 (kb) > Memory usage: 56896 (kb) Memory usage: 57424 (kb) > Memory usage: 57688 (kb) Memory usage: 57688 (kb) > Memory usage: 57688 (kb) Memory usage: 57952 (kb) > Memory usage: 58216 (kb) Memory usage: 59008 (kb) > Memory usage: 59008 (kb) Memory usage: 59008 (kb) > Memory usage: 59008 (kb) Memory usage: 59272 (kb) > Memory usage: 59536 (kb) Memory usage: 60328 (kb) > > Pierre > ------------------------------ > *De :* Thomas Caswell <tcaswell(a)gmail.com> > *Envoyé :* jeudi 19 octobre 2017 17:30 > *À :* GARCIA PIERRE SIMON p0904379; Benjamin Root > *Cc :* matplotlib-users(a)python.org > > *Objet :* Re: [Matplotlib-users] Problem of memory leak using > FigureCanvasTkAgg > Have you tried manually adding calls to `gc.collect(2)`? That may help to > clean up any circular reference cycles hanging around. > > Can you replicate this with a simpler script? The code on SO is hard to > follow. > > Tom > > On Thu, Oct 19, 2017 at 10:56 AM GARCIA PIERRE SIMON p0904379 < > pierre.garcia(a)etu.univ-lyon1.fr> wrote: > >> Here is the diagnostic for the old version : >> >> Memory usage: 39832 (kb) Memory usage: 45376 (kb)Memory usage: 46168 (kb) Memory usage: 46960 (kb)Memory usage: 47224 (kb) Memory usage: 47752 (kb)Memory usage: 47752 (kb) Memory usage: 48544 (kb)Memory usage: 48544 (kb) Memory usage: 48808 (kb)Memory usage: 48808 (kb) Memory usage: 49072 (kb)Memory usage: 49072 (kb) Memory usage: 49336 (kb)Memory usage: 49336 (kb) Memory usage: 49864 (kb)Memory usage: 49864 (kb) Memory usage: 50128 (kb)Memory usage: 50128 (kb) Memory usage: 50392 (kb)Memory usage: 50392 (kb) Memory usage: 50656 (kb) >> >> and here is the diagnostic for 2.1.0: >> >> Memory usage: 51808 (kb) Memory usage: 55504 (kb) >> Memory usage: 57088 (kb) Memory usage: 57352 (kb) >> Memory usage: 57880 (kb) Memory usage: 58144 (kb) >> Memory usage: 58672 (kb) Memory usage: 58936 (kb) >> Memory usage: 59464 (kb) Memory usage: 59464 (kb) >> Memory usage: 59992 (kb) Memory usage: 60256 (kb) >> Memory usage: 60520 (kb) Memory usage: 61048 (kb) >> Memory usage: 61312 (kb) Memory usage: 61576 (kb) >> Memory usage: 62104 (kb) Memory usage: 62368 (kb) >> Memory usage: 62632 (kb) Memory usage: 63160 (kb) >> Memory usage: 63424 (kb) Memory usage: 63688 (kb) >> Memory usage: 64216 (kb) Memory usage: 64480 (kb) >> >> It seems that the initial memory used is higher for 2.1.0. >> >> For the delta against n and n+1, the value varies at the begin >> and converge to 264 for 1.1.1 and 792 for 2.1.0. >> >> >> So globally, the rate of leak increases in 2.1.0.... >> >> >> Pierre >> ------------------------------ >> *De :* Benjamin Root <ben.v.root(a)gmail.com> >> *Envoyé :* jeudi 19 octobre 2017 16:32 >> *À :* GARCIA PIERRE SIMON p0904379 >> *Cc :* Thomas Caswell; matplotlib-users(a)python.org >> >> *Objet :* Re: [Matplotlib-users] Problem of memory leak using >> FigureCanvasTkAgg >> Did the rate of memory leak change? >> >> On Thu, Oct 19, 2017 at 10:26 AM, GARCIA PIERRE SIMON p0904379 < >> pierre.garcia(a)etu.univ-lyon1.fr> wrote: >> >>> Thank you for your answer but I updated MPL to 2.1.0 and the memory leak >>> is still there. Also, I skipped entirely pyplot and the result is strictly >>> the same. >>> >>> >>> Pierre >>> ------------------------------ >>> *De :* Benjamin Root <ben.v.root(a)gmail.com> >>> *Envoyé :* lundi 7 août 2017 19:27 >>> *À :* Thomas Caswell >>> *Cc :* GARCIA PIERRE SIMON p0904379; matplotlib-users(a)python.org >>> *Objet :* Re: [Matplotlib-users] Problem of memory leak using >>> FigureCanvasTkAgg >>> >>> The stackoverflow posting notes that mpl v1.1.1 was used, which is 5 >>> years old. I am pretty sure we have made a lot of memory leak fixes since >>> then. I noted as such on SO. >>> >>> Ben Root >>> >>> On Sat, Aug 5, 2017 at 7:48 PM, Thomas Caswell <tcaswell(a)gmail.com> >>> wrote: >>> >>>> It is likely there things are not being garbage collected due to either >>>> a missed reference surviving or the circular references between the various >>>> objects is delaying gc from collecting them (I do not recall the details >>>> exactly off the top of my head, but running gc manually with more >>>> generations may help). >>>> >>>> However, if you are embedding in a GUI you are probably better off just >>>> doing the embedding directly (and skipping `pyplot` entirely, see >>>> https://matplotlib.org/examples/user_interfaces/embedding_in_tk.html ). >>>> Re-using the Figures / Axes / Artists to update the data (rather than >>>> starting from scratch every time) may also prevent the memory leaks _and_ >>>> give you a performance boost. >>>> >>>> Please subscribe to the list so that you can post without moderation. >>>> >>>> Tom >>>> >>>> On Sat, Aug 5, 2017 at 12:36 PM GARCIA PIERRE SIMON p0904379 < >>>> pierre.garcia(a)etu.univ-lyon1.fr> wrote: >>>> >>>>> 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 >>>>> <https://maps.google.com/?q=7+passage+du+Vercors&entry=gmail&source=g> >>>>> 69 367 Lyon cedex 07 >>>>> --------- >>>>> Laboratoire de Biométrie et Biologie Evolutive-UMR5558 >>>>> UCBL Lyon 1 -Bât. Grégory Mendel >>>>> 43 bd du 11 novembre 1918 >>>>> <https://maps.google.com/?q=43+bd+du+11+novembre+1918&entry=gmail&source=g> >>>>> 69622 VILLEURBANNE cedex >>>>> >>>>> >>>>> _______________________________________________ >>>>> Matplotlib-users mailing list >>>>> Matplotlib-users(a)python.org >>>>> https://mail.python.org/mailman/listinfo/matplotlib-users >>>>> >>>> >>>> _______________________________________________ >>>> Matplotlib-users mailing list >>>> Matplotlib-users(a)python.org >>>> https://mail.python.org/mailman/listinfo/matplotlib-users >>>> >>>> >>> >>

1 0

Re: [Matplotlib-users] Obtaining the contour data in terms of latitude and longitude
by Slavin, Jonathan Oct. 19, 2017

Oct. 19, 2017

I'm wondering if we could make this easier by modifying contour/contourf so that the ContourSet object created had a paths object attribute. It doesn't seem like it'd be that hard. Maybe some would object that it would slow down the creation of contour plots? Jon On Wed, Oct 18, 2017 at 5:08 PM, <matplotlib-users-request(a)python.org> wrote: > > Date: Thu, 19 Oct 2017 02:29:11 +0530 > From: "ashwin .D" <winash12(a)gmail.com> > To: matplotlib-users(a)python.org > Subject: [Matplotlib-users] Obtaining the contour data in terms of > latitude and longitude > Message-ID: > <CAH0LXy4O++PS3morh4B1L-83TvDqRG64YMkDrDe3LKQewFUSiw@ > mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello, > I have data on a 2d lat lon grid(equal grid spacing) in terms of > laitude and longitude and heights as enclosed in the image. I need the > coordinates(in terms of latitude and longitude) of the contours( as shown > in red in the image). From this answer - > https://stackoverflow.com/questions/18304722/python- > find-contour-lines-from-matplotlib-pyplot-contour/ > will this give me what I am looking for or is there a scaling required to > latitude and longitude that I need to include? > > Best regards, > Ashwin. > > import numpy as np > def get_contour_verts(cn): > contours = [] > # for each contour line > for cc in cn.collections: > paths = [] > # for each separate section of the contour line > for pp in cc.get_paths(): > xy = [] > # for each segment of that section > for vv in pp.iter_segments(): > xy.append(vv[0]) > paths.append(np.vstack(xy)) > contours.append(paths) > > return contours >

2 1

Re: [Matplotlib-users] Problem of memory leak using FigureCanvasTkAgg
by Thomas Caswell Oct. 19, 2017

Oct. 19, 2017

Have you tried manually adding calls to `gc.collect(2)`? That may help to clean up any circular reference cycles hanging around. Can you replicate this with a simpler script? The code on SO is hard to follow. Tom On Thu, Oct 19, 2017 at 10:56 AM GARCIA PIERRE SIMON p0904379 < pierre.garcia(a)etu.univ-lyon1.fr> wrote: > Here is the diagnostic for the old version : > > Memory usage: 39832 (kb) Memory usage: 45376 (kb)Memory usage: 46168 (kb) Memory usage: 46960 (kb)Memory usage: 47224 (kb) Memory usage: 47752 (kb)Memory usage: 47752 (kb) Memory usage: 48544 (kb)Memory usage: 48544 (kb) Memory usage: 48808 (kb)Memory usage: 48808 (kb) Memory usage: 49072 (kb)Memory usage: 49072 (kb) Memory usage: 49336 (kb)Memory usage: 49336 (kb) Memory usage: 49864 (kb)Memory usage: 49864 (kb) Memory usage: 50128 (kb)Memory usage: 50128 (kb) Memory usage: 50392 (kb)Memory usage: 50392 (kb) Memory usage: 50656 (kb) > > and here is the diagnostic for 2.1.0: > > Memory usage: 51808 (kb) Memory usage: 55504 (kb) > Memory usage: 57088 (kb) Memory usage: 57352 (kb) > Memory usage: 57880 (kb) Memory usage: 58144 (kb) > Memory usage: 58672 (kb) Memory usage: 58936 (kb) > Memory usage: 59464 (kb) Memory usage: 59464 (kb) > Memory usage: 59992 (kb) Memory usage: 60256 (kb) > Memory usage: 60520 (kb) Memory usage: 61048 (kb) > Memory usage: 61312 (kb) Memory usage: 61576 (kb) > Memory usage: 62104 (kb) Memory usage: 62368 (kb) > Memory usage: 62632 (kb) Memory usage: 63160 (kb) > Memory usage: 63424 (kb) Memory usage: 63688 (kb) > Memory usage: 64216 (kb) Memory usage: 64480 (kb) > > It seems that the initial memory used is higher for 2.1.0. > > For the delta against n and n+1, the value varies at the begin > and converge to 264 for 1.1.1 and 792 for 2.1.0. > > > So globally, the rate of leak increases in 2.1.0.... > > > Pierre > ------------------------------ > *De :* Benjamin Root <ben.v.root(a)gmail.com> > *Envoyé :* jeudi 19 octobre 2017 16:32 > *À :* GARCIA PIERRE SIMON p0904379 > *Cc :* Thomas Caswell; matplotlib-users(a)python.org > > *Objet :* Re: [Matplotlib-users] Problem of memory leak using > FigureCanvasTkAgg > Did the rate of memory leak change? > > On Thu, Oct 19, 2017 at 10:26 AM, GARCIA PIERRE SIMON p0904379 < > pierre.garcia(a)etu.univ-lyon1.fr> wrote: > >> Thank you for your answer but I updated MPL to 2.1.0 and the memory leak >> is still there. Also, I skipped entirely pyplot and the result is strictly >> the same. >> >> >> Pierre >> ------------------------------ >> *De :* Benjamin Root <ben.v.root(a)gmail.com> >> *Envoyé :* lundi 7 août 2017 19:27 >> *À :* Thomas Caswell >> *Cc :* GARCIA PIERRE SIMON p0904379; matplotlib-users(a)python.org >> *Objet :* Re: [Matplotlib-users] Problem of memory leak using >> FigureCanvasTkAgg >> >> The stackoverflow posting notes that mpl v1.1.1 was used, which is 5 >> years old. I am pretty sure we have made a lot of memory leak fixes since >> then. I noted as such on SO. >> >> Ben Root >> >> On Sat, Aug 5, 2017 at 7:48 PM, Thomas Caswell <tcaswell(a)gmail.com> >> wrote: >> >>> It is likely there things are not being garbage collected due to either >>> a missed reference surviving or the circular references between the various >>> objects is delaying gc from collecting them (I do not recall the details >>> exactly off the top of my head, but running gc manually with more >>> generations may help). >>> >>> However, if you are embedding in a GUI you are probably better off just >>> doing the embedding directly (and skipping `pyplot` entirely, see >>> https://matplotlib.org/examples/user_interfaces/embedding_in_tk.html ). >>> Re-using the Figures / Axes / Artists to update the data (rather than >>> starting from scratch every time) may also prevent the memory leaks _and_ >>> give you a performance boost. >>> >>> Please subscribe to the list so that you can post without moderation. >>> >>> Tom >>> >>> On Sat, Aug 5, 2017 at 12:36 PM GARCIA PIERRE SIMON p0904379 < >>> pierre.garcia(a)etu.univ-lyon1.fr> wrote: >>> >>>> 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 >>>> <https://maps.google.com/?q=7+passage+du+Vercors&entry=gmail&source=g> >>>> 69 367 Lyon cedex 07 >>>> --------- >>>> Laboratoire de Biométrie et Biologie Evolutive-UMR5558 >>>> UCBL Lyon 1 -Bât. Grégory Mendel >>>> 43 bd du 11 novembre 1918 >>>> <https://maps.google.com/?q=43+bd+du+11+novembre+1918&entry=gmail&source=g> >>>> 69622 VILLEURBANNE cedex >>>> >>>> >>>> _______________________________________________ >>>> Matplotlib-users mailing list >>>> Matplotlib-users(a)python.org >>>> https://mail.python.org/mailman/listinfo/matplotlib-users >>>> >>> >>> _______________________________________________ >>> Matplotlib-users mailing list >>> Matplotlib-users(a)python.org >>> https://mail.python.org/mailman/listinfo/matplotlib-users >>> >>> >> >

1 0

Re: [Matplotlib-users] Problem of memory leak using FigureCanvasTkAgg
by Benjamin Root Oct. 19, 2017

Oct. 19, 2017

Did the rate of memory leak change? On Thu, Oct 19, 2017 at 10:26 AM, GARCIA PIERRE SIMON p0904379 < pierre.garcia(a)etu.univ-lyon1.fr> wrote: > Thank you for your answer but I updated MPL to 2.1.0 and the memory leak > is still there. Also, I skipped entirely pyplot and the result is strictly > the same. > > > Pierre > ------------------------------ > *De :* Benjamin Root <ben.v.root(a)gmail.com> > *Envoyé :* lundi 7 août 2017 19:27 > *À :* Thomas Caswell > *Cc :* GARCIA PIERRE SIMON p0904379; matplotlib-users(a)python.org > *Objet :* Re: [Matplotlib-users] Problem of memory leak using > FigureCanvasTkAgg > > The stackoverflow posting notes that mpl v1.1.1 was used, which is 5 years > old. I am pretty sure we have made a lot of memory leak fixes since then. I > noted as such on SO. > > Ben Root > > On Sat, Aug 5, 2017 at 7:48 PM, Thomas Caswell <tcaswell(a)gmail.com> wrote: > >> It is likely there things are not being garbage collected due to either a >> missed reference surviving or the circular references between the various >> objects is delaying gc from collecting them (I do not recall the details >> exactly off the top of my head, but running gc manually with more >> generations may help). >> >> However, if you are embedding in a GUI you are probably better off just >> doing the embedding directly (and skipping `pyplot` entirely, see >> https://matplotlib.org/examples/user_interfaces/embedding_in_tk.html ). >> Re-using the Figures / Axes / Artists to update the data (rather than >> starting from scratch every time) may also prevent the memory leaks _and_ >> give you a performance boost. >> >> Please subscribe to the list so that you can post without moderation. >> >> Tom >> >> On Sat, Aug 5, 2017 at 12:36 PM GARCIA PIERRE SIMON p0904379 < >> pierre.garcia(a)etu.univ-lyon1.fr> wrote: >> >>> 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-leak-using-figurecanvastkagg >>> >>> 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 >>> <https://maps.google.com/?q=7+passage+du+Vercors&entry=gmail&source=g> >>> 69 367 Lyon cedex 07 >>> --------- >>> Laboratoire de Biométrie et Biologie Evolutive-UMR5558 >>> UCBL Lyon 1 -Bât. Grégory Mendel >>> 43 bd du 11 novembre 1918 >>> <https://maps.google.com/?q=43+bd+du+11+novembre+1918&entry=gmail&source=g> >>> 69622 VILLEURBANNE cedex >>> >>> >>> _______________________________________________ >>> Matplotlib-users mailing list >>> Matplotlib-users(a)python.org >>> https://mail.python.org/mailman/listinfo/matplotlib-users >>> >> >> _______________________________________________ >> Matplotlib-users mailing list >> Matplotlib-users(a)python.org >> https://mail.python.org/mailman/listinfo/matplotlib-users >> >> >

1 0

Obtaining the contour data in terms of latitude and longitude
by ashwin .D Oct. 19, 2017

Oct. 19, 2017

Hello, I have data on a 2d lat lon grid(equal grid spacing) in terms of laitude and longitude and heights as enclosed in the image. I need the coordinates(in terms of latitude and longitude) of the contours( as shown in red in the image). From this answer - https://stackoverflow.com/questions/18304722/python-find-contour-lines-from… will this give me what I am looking for or is there a scaling required to latitude and longitude that I need to include? Best regards, Ashwin. import numpy as np def get_contour_verts(cn): contours = [] # for each contour line for cc in cn.collections: paths = [] # for each separate section of the contour line for pp in cc.get_paths(): xy = [] # for each segment of that section for vv in pp.iter_segments(): xy.append(vv[0]) paths.append(np.vstack(xy)) contours.append(paths) return contours

3 4

contourf with data frames
by nuncio Oct. 13, 2017

Oct. 13, 2017

I am trying to make a time height contour plot , here is the script used dates=mpl.dates.date2num(data.index.to_pydatetime()) xh=list(dates) dfX=pd.DataFrame(xh) date2= dfX.groupby(np.arange(len(dfX))//400).mean() dates=num2date(date2) dfT=pd.DataFrame(data.iloc[:,5].reshape(400,427).T) #dfT.insert(loc=0,column='',value=date) hgtl=data.iloc[0:400:,1] #plot(dates,dfT.iloc[:,0]) contourf(dates,hgtl,dfT.iloc[0:400:,0].T) this results in the following error TypeError Traceback (most recent call last) <ipython-input-140-d1e220b1ce6a> in <module>() 8 hgtl=data.iloc[0:400:,1] 9 #plot(dates,dfT.iloc[:,0]) ---> 10 contourf(dates,hgtl,dfT.iloc[0:400:,0].T) /home/nuncio/anaconda2/lib/python2.7/site-packages/matplotlib/pyplot.pyc in contourf(*args, **kwargs) 2781 ax.hold(hold) 2782 try: -> 2783 ret = ax.contourf(*args, **kwargs) 2784 finally: 2785 ax.hold(washold) /home/nuncio/anaconda2/lib/python2.7/site-packages/matplotlib/__init__.pyc in inner(ax, *args, **kwargs) 1810 warnings.warn(msg % (label_namer, func.__name__), 1811 RuntimeWarning, stacklevel=2) -> 1812 return func(ax, *args, **kwargs) 1813 pre_doc = inner.__doc__ 1814 if pre_doc is None: /home/nuncio/anaconda2/lib/python2.7/site-packages/matplotlib/axes/_axes.pyc in contourf(self, *args, **kwargs) 5650 self.cla() 5651 kwargs['filled'] = True -> 5652 return mcontour.QuadContourSet(self, *args, **kwargs) 5653 contourf.__doc__ = mcontour.QuadContourSet.contour_doc 5654 /home/nuncio/anaconda2/lib/python2.7/site-packages/matplotlib/contour.pyc in __init__(self, ax, *args, **kwargs) 1422 are described in QuadContourSet.contour_doc. 1423 """ -> 1424 ContourSet.__init__(self, ax, *args, **kwargs) 1425 1426 def _process_args(self, *args, **kwargs): /home/nuncio/anaconda2/lib/python2.7/site-packages/matplotlib/contour.pyc in __init__(self, ax, *args, **kwargs) 861 self._transform = kwargs.get('transform', None) 862 --> 863 self._process_args(*args, **kwargs) 864 self._process_levels() 865 /home/nuncio/anaconda2/lib/python2.7/site-packages/matplotlib/contour.pyc in _process_args(self, *args, **kwargs) 1443 self._corner_mask = mpl.rcParams['contour.corner_mask'] 1444 -> 1445 x, y, z = self._contour_args(args, kwargs) 1446 1447 _mask = ma.getmask(z) /home/nuncio/anaconda2/lib/python2.7/site-packages/matplotlib/contour.pyc in _contour_args(self, args, kwargs) 1526 args = args[1:] 1527 elif Nargs <= 4: -> 1528 x, y, z = self._check_xyz(args[:3], kwargs) 1529 args = args[3:] 1530 else: /home/nuncio/anaconda2/lib/python2.7/site-packages/matplotlib/contour.pyc in _check_xyz(self, args, kwargs) 1555 y = self.ax.convert_yunits(y) 1556 -> 1557 x = np.asarray(x, dtype=np.float64) 1558 y = np.asarray(y, dtype=np.float64) 1559 z = ma.asarray(args[2], dtype=np.float64) /home/nuncio/anaconda2/lib/python2.7/site-packages/numpy/core/numeric.pyc in asarray(a, dtype, order) 472 473 """ --> 474 return array(a, dtype, copy=False, order=order) 475 476 def asanyarray(a, dtype=None, order=None): * TypeError: float() argument must be a string or a number* I undesrstand the problem is with the dates however plot(dates,dfT.iloc[:,0]) runs perfectly Any suggestions to get around it THanks and regards nuncio -- Sent from: http://matplotlib.1069221.n5.nabble.com/matplotlib-users-f3.html

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MacOS matplotlib broken after `pip install matplotlib --upgrade` to version 2.1.0
by Victor Zhao Oct. 13, 2017

Oct. 13, 2017

My OS X python installation is through homebrew. I then add python software using pip. I recently upgraded matplotlib from version 1.4.3 to 2.1.0 via `pip install matplotlib --upgrade`, and now matplotlib gives me this error when I try to make a basic plot: In [1]: plt.plot(np.arange(10)) --------------------------------------------------------------------------- TypeError Traceback (most recent call last) <ipython-input-1-a81699eb47e8> in <module>() ----> 1 plt.plot(np.arange(10)) /usr/local/lib/python2.7/site-packages/matplotlib/pyplot.pyc in plot(*args, **kwargs) 3227 @_autogen_docstring(Axes.plot) 3228 def plot(*args, **kwargs): -> 3229 ax = gca() 3230 # Deprecated: allow callers to override the hold state 3231 # by passing hold=True|False /usr/local/lib/python2.7/site-packages/matplotlib/pyplot.pyc in gca(**kwargs) 957 matplotlib.figure.Figure.gca : The figure's gca method. 958 """ --> 959 return gcf().gca(**kwargs) 960 961 # More ways of creating axes: /usr/local/lib/python2.7/site-packages/matplotlib/pyplot.pyc in gcf() 586 return figManager.canvas.figure 587 else: --> 588 return figure() 589 590 /usr/local/lib/python2.7/site-packages/matplotlib/pyplot.pyc in figure(num, figsize, dpi, facecolor, edgecolor, frameon, FigureClass, clear, **kwargs) 554 # FigureManager base class. 555 if matplotlib.is_interactive(): --> 556 draw_if_interactive() 557 558 if _INSTALL_FIG_OBSERVER: /usr/local/lib/python2.7/site-packages/matplotlib/backend_bases.pyc in draw_if_interactive(cls) 183 manager = Gcf.get_active() 184 if manager: --> 185 cls.trigger_manager_draw(manager) 186 187 @classmethod TypeError: unbound method trigger_manager_draw() must be called with _BackendMac instance as first argument (got FigureManagerMac instance instead) I am not sure how to diagnose this. I do have a working Python 3 matplotlib however. Is this actually a bug within version 2.1.0 of matplotlib? Thanks

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