Mailman 3 August 2015 - Matplotlib-users

Re: [Matplotlib-users] matplotlib documentation from python notebook?
by Thomas Caswell Aug. 31, 2015

Aug. 31, 2015

A tad dry, but through, example of what the notebook backend can do is to look at the UAT at https://github.com/matplotlib/matplotlib/blob/master/lib/matplotlib/backend… Tom On Mon, Jun 8, 2015 at 5:28 PM Jody Klymak <jklymak(a)uvic.ca> wrote: > Hi Ben, > > My idea was to just make the notebook the “example”. But nbconvert-ing > the notebook makes static images that then need to be checked into the > repository, and take space, so I wasn’t sure how desirable that was. > > It would be fun to have the documentation script accept ipython notebooks > and run nbconvert on them. Being able to save state as you work through > examples is quite nice, versus creating five or six standalone *.py files > that then get run at build time. Of course you are adding a dependency to > anyone who has wants to build the docs. > > Thanks, Jody > > > > On 8 Jun 2015, at 13:35 PM, Benjamin Root <ben.root(a)ou.edu> wrote: > > No, there isn't an accepted way to do that AFAIK. However, it doesn't seem > like it is all that far off. Our doc-build process will create the images > from the examples automatically, so you don't need to include the image > tag. It is sort of a way to make sure the examples work and that the image > matches the code correctly. > > On Mon, Jun 8, 2015 at 1:06 PM, Jody Klymak <jklymak(a)uvic.ca> wrote: > >> >> Hi all, >> >> If I want to contribute *.rst files to the matplotlib documentation, I >> can see a few styles already contributed, at least one of which makes >> extensive use of ipython (http://matplotlib.org/users/image_tutorial.html). >> However, even it makes use of `.. sourcecode:: python` and `.. plot::` >> blocks. >> >> If I convert an ipython notebook to rst, it formats as: `.. code:: >> python` and instead of making plots it loads images: >> `.. image:: MyExample_files/MyExample_1_0.png` >> >> So, is there an acceptable way to directly make matplotlib documentation >> directly from a notebook? I didn’t see anything, but wanted to check, as >> that would by far be the easiest way to make a *.rst that had structured >> text, code, and plots. >> >> Thanks, Jody >> >> -- >> Jody Klymak >> http://web.uvic.ca/~jklymak/ >> >> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> _______________________________________________ >> Matplotlib-users mailing list >> Matplotlib-users(a)lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/matplotlib-users >> > > > -- > Jody Klymak > http://web.uvic.ca/~jklymak/ > > > > > > > ------------------------------------------------------------------------------ > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users(a)lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/matplotlib-users >

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Re: [Matplotlib-users] TrueType font is missing table
by Thomas Caswell Aug. 31, 2015

Aug. 31, 2015

I am having trouble reproducing this, you might want to raise this issue with the Fedora folks as they do some funny stuff with fonts + packaging mpl. Tom PS this list has moved to matplotlib-users(a)python.org On Mon, Jul 6, 2015 at 8:43 AM Neal Becker <ndbecker2(a)gmail.com> wrote: > Neal Becker wrote: > > > Using mpl 1.4.3 on Fedora 22, I'm trying to use stix font (so I can > render > > the unicode lambda label on the x-axis). I have every fedora package > > related to 'stix', I think. It displays ok in qtagg4, but if I try to > save > > to pdf if fails with > > > > RuntimeError Traceback (most recent call > > last) <ipython-input-2-7dee58c07264> in <module>() > > ----> 1 exec(open(r'/usr/tmp/python-8710q1Y.py').read()) # PYTHON-MODE > > > > <string> in <module>() > > > > /usr/lib64/python3.4/site-packages/matplotlib/pyplot.py in savefig(*args, > > **kwargs) > > 575 def savefig(*args, **kwargs): > > 576 fig = gcf() > > --> 577 res = fig.savefig(*args, **kwargs) > > 578 draw() # need this if 'transparent=True' to reset colors > > 579 return res > > > > /usr/lib64/python3.4/site-packages/matplotlib/figure.py in savefig(self, > > *args, **kwargs) > > 1474 self.set_frameon(frameon) > > 1475 > > -> 1476 self.canvas.print_figure(*args, **kwargs) > > 1477 > > 1478 if frameon: > > > > /usr/lib64/python3.4/site-packages/matplotlib/backend_bases.py in > > print_figure(self, filename, dpi, facecolor, edgecolor, orientation, > > format, **kwargs) > > 2209 orientation=orientation, > > 2210 bbox_inches_restore=_bbox_inches_restore, > > -> 2211 **kwargs) > > 2212 finally: > > 2213 if bbox_inches and restore_bbox: > > > > /usr/lib64/python3.4/site-packages/matplotlib/backends/backend_pdf.py in > > print_pdf(self, filename, **kwargs) > > 2489 file.endStream() > > 2490 else: # we opened the file above; now > > finish > > it off > > -> 2491 file.close() > > 2492 > > 2493 > > > > /usr/lib64/python3.4/site-packages/matplotlib/backends/backend_pdf.py in > > close(self) > > 523 self.endStream() > > 524 # Write out the various deferred objects > > --> 525 self.writeFonts() > > 526 self.writeObject(self.alphaStateObject, > > 527 dict([(val[0], val[1]) > > > > /usr/lib64/python3.4/site-packages/matplotlib/backends/backend_pdf.py in > > writeFonts(self) > > 626 chars = self.used_characters.get(stat_key) > > 627 if chars is not None and len(chars[1]): > > --> 628 fonts[Fx] = self.embedTTF(realpath, chars[1]) > > 629 self.writeObject(self.fontObject, fonts) > > 630 > > > > /usr/lib64/python3.4/site-packages/matplotlib/backends/backend_pdf.py in > > embedTTF(self, filename, characters) > > 1101 > > 1102 if fonttype == 3: > > -> 1103 return embedTTFType3(font, characters, descriptor) > > 1104 elif fonttype == 42: > > 1105 return embedTTFType42(font, characters, descriptor) > > > > /usr/lib64/python3.4/site-packages/matplotlib/backends/backend_pdf.py in > > embedTTFType3(font, characters, descriptor) > > 887 # actual outlines) > > 888 rawcharprocs = ttconv.get_pdf_charprocs( > > --> 889 filename.encode(sys.getfilesystemencoding()), > > glyph_ids) > > 890 charprocs = {} > > 891 for charname, stream in six.iteritems(rawcharprocs): > > > > RuntimeError: TrueType font is missing table > > > > forgot to attach the code. > > > #!/usr/bin/python > # -*- coding: utf-8 -*- > data='''carriers,lambda,per > 1,7,1.3e-4 > 1,8,3.0e-4 > 1,9,.0014 > 8,7,4.8e-4 > 8,8,1.3e-3 > 8,9,.0075 > ''' > > import pandas as pd > try: > from StringIO import StringIO > except ImportError: > from io import StringIO > df = pd.read_csv (StringIO (data)) > g = df.groupby ('carriers') > import matplotlib.pyplot as plt > > import matplotlib as mpl > #mpl.rcParams['font.family'] = 'stix' > mpl.rc('font', family='DejaVu Sans') > #mpl.rc('font', family='stix') > > import itertools > markers = itertools.cycle(['o','s','v']) > > fig = plt.figure() > ax = fig.add_subplot(111) > for c, stuff in g: > plt.semilogy (stuff['lambda'].values, stuff['per'].values, > label='carriers=%s'%c, marker=next(markers)) > > plt.legend (loc='best') > ax.set_xlabel (' ') > ax.set_ylabel ('per') > plt.grid(which='major', linestyle='solid') > plt.grid(which='minor', linestyle='dashed') > plt.savefig ('per_vs_lambda.pdf') > > > > > > > > ------------------------------------------------------------------------------ > Don't Limit Your Business. Reach for the Cloud. > GigeNET's Cloud Solutions provide you with the tools and support that > you need to offload your IT needs and focus on growing your business. > Configured For All Businesses. Start Your Cloud Today. > https://www.gigenetcloud.com/ > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users(a)lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/matplotlib-users >

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Graphic tests working with single files but not at package level
by Fabien Aug. 30, 2015

Aug. 30, 2015

Folks, I have two test files for a small personnal project. Both make use of the @image_comparison decorator to compare expected images to the outcome. When run on single files as follows, everything works fine: (py2) $ nosetests cleo/tests/test_colors.py .. ---------------------------------------------------------------------- Ran 2 tests in 0.414s OK (py2) $ nosetests cleo/tests/test_graphics.py ..... ---------------------------------------------------------------------- Ran 5 tests in 2.781s OK But when I run nose at the package level, I get an error: (py2) $ nosetests . ..F.... ====================================================================== FAIL: cleo.tests.test_graphics.test_DataLevels_graphics.test ---------------------------------------------------------------------- (...) ImageComparisonFailure: images not close: /home/mowglie/Documents/git/cleo/result_images/test_graphics/test_DataLevels.png vs. /home/mowglie/Documents/git/cleo/result_images/test_graphics/test_DataLevels-expected.png (RMS 25.865) ---------------------------------------------------------------------- Ran 7 tests in 3.685s FAILED (failures=1) An inspection of the failing test shows that the title and axis characters are slightly shifted, while the image plots (made with imshow) look exact same. I am pretty sure that I made no change to matplotlib's defaut params or whatsoever. I have the same behavior with python 2 and 3. Any idea what I could have done wrong? Thanks a lot, Fabien

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Re: [Matplotlib-users] ConnectionPatch axesA has to be the "latest" axes
by Thomas Caswell Aug. 30, 2015

Aug. 30, 2015

Sorry for the late response. The mailing list is now at matplotlib-users(a)python.org In your second case the issue is that axes are drawn one at a time so in that case the left axes with the line is drawn, then then right axes is drawn which overlays the line. If you do `ax22.set_zorder(-1)` that example will render correctly. This is a limitation of the compositing draw scheme that we use with the Agg. In the other two examples the issue is the check in https://github.com/matplotlib/matplotlib/blob/master/lib/matplotlib/patches… which is called as part of the draw logic of the ConnectionPatch. This checks that the starting point of the connection patch is with in the confines of the axes which it belongs to. However, in your case 1 and 4 you have added the artist to the Axes in which the _end_ belongs so the starting point will never fall within they axes the artist belongs to, and hence will never draw. The two things that need to be true for this to work as expected: - the Axes which the correction patch is added to needs to have a higher zorder than the other axes (or be added later, the z-order sort is stable to falls back to the order in which the elements were added to break ties) - the connection patch must start in the Axes it belongs to. It would probably be better if `ConnectionPatch` was a child of the Figure instead of the Axes. Tom On Thu, Aug 20, 2015 at 11:55 AM Oliver <oliver.willekens(a)gmail.com> wrote: > It would seem the `axesA` keyword always has to be the "latest" axes. If > not, the connector does not get added to the figure. > > Minimal, complete and verifiable example: > ###### > from matplotlib.patches import ConnectionPatch > import matplotlib.pyplot as plt > import matplotlib as mpl > import platform > > print(mpl.__version__) > print(platform.python_version()) > > xya = (.5,.5) > xyb = (.6,.7) > > # shows nothing > f1, (ax11, ax12) = plt.subplots(1,2, sharey=False) > con1 = ConnectionPatch(xyA=xya, xyB=xyb , coordsA='data', coordsB='data', > axesA=ax12, axesB=ax11) > ax11.add_artist(con1) > > # shows clipped line > f2, (ax21, ax22) = plt.subplots(1,2, sharey=False) > con2 = ConnectionPatch(xyA=xyb, xyB=xya , coordsA='data', coordsB='data', > axesA=ax21, axesB=ax22) > ax21.add_artist(con2) > > # shows desired result > f3, (ax31, ax32) = plt.subplots(1,2, sharey=False) > con3 = ConnectionPatch(xyA=xya, xyB=xyb , coordsA='data', coordsB='data', > axesA=ax32, axesB=ax31) > ax32.add_artist(con3) > > # shows nothing > f4, (ax41, ax42) = plt.subplots(1,2, sharey=False) > con4 = ConnectionPatch(xyA=xyb, xyB=xya , coordsA='data', coordsB='data', > axesA=ax41, axesB=ax42) > ax42.add_artist(con4) > > plt.draw() > plt.show() > > ###### > > While reference to clipping is made in the user guide[1], the seemingly > forced choice of `axesA` had me stumped for quite some time. While I > understand that the choice of the axes to add the connector is important to > avoid overlap (in other words, on which axes one should call the > `add_artist` method), it seems unimportant whether xyA or xyB are > referenced in ax1 or ax2. > > To clarify: I was expecting example 4 above to show a similar line as > example 3. > > > [1]: > http://matplotlib.org/users/annotations_guide.html#using-connectorpatch > > > > > ------------------------------------------------------------------------------ > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users(a)lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/matplotlib-users >

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Matplotlib tutorial
by Nicolas P. Rougier Aug. 21, 2015

Aug. 21, 2015

I've updated the matplotlib tutorial available from: https://github.com/rougier/matplotlib-tutorial http://www.labri.fr/perso/nrougier/teaching/matplotlib/matplotlib.html with a new section on animation (rain effect and earthquakes from last 30 days). Still plenty of English errors, but I'm working on it (or if someone is willing to review it...). Nicolas

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Basemap and counties
by Tommy Grav Aug. 19, 2015

Aug. 19, 2015

I am trying to use matplotlib and basemap to show a map of the State of Indiana and highlight a few different counties. As a newbie I started with the code below, but I am having trouble with how to identify and fill specific counties. Anyone have any suggestions? from mpl_toolkits.basemap import Basemap import matplotlib.pyplot as plt import numpy as np # make sure the value of resolution is a lowercase L, # for 'low', not a numeral 1 map = Basemap(projection='merc', lat_0=39.1622, lon_0=-86.5292, resolution = 'h', area_thresh = 0.1, llcrnrlon=-88.53, llcrnrlat=37.16, urcrnrlon=-84.53, urcrnrlat=41.16) map.drawcoastlines() map.drawcountries() map.drawstates(linewidth=0.5, linestyle="solid", color="r", antialiased=1, ax=None, zorder=None) map.drawcounties(linewidth=0.1,linestyle="solid", color="k", antialiased=1, ax=None, zorder=None, drawbounds=False) #map.fillcontinents(color='coral') map.drawmapboundary() map.drawmeridians(np.arange(0, 360, 30)) map.drawparallels(np.arange(-90, 90, 30)) plt.show()

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Re: [Matplotlib-users] Problem: AttributeError: 'module' object has no attribute '_string_to_bool'
by Adam Spannaus Aug. 18, 2015

Aug. 18, 2015

Thanks, it all works now. On 08/18/2015 12:53 PM, Thomas Caswell wrote: > Also, please use the new mailing list at matplotlib-users(a)python.org > <mailto:matplotlib-users@python.org> > > > > On Tue, Aug 18, 2015 at 12:53 PM Thomas Caswell <tcaswell(a)gmail.com > <mailto:tcaswell@gmail.com>> wrote: > > This is related to files from the previous implementation still > being around. Please make sure you have fully removed the old mpl > installation before installing the new one. Be aware that there > is some difference in the way pip/setuptools/distutils deal with > namespace packages so look for both `matplotlib` and > `mpl_toolkits` directories. > > Tom > > On Tue, Aug 18, 2015 at 12:49 PM Bob Dobalina <aspannaus(a)gmail.com > <mailto:aspannaus@gmail.com>> wrote: > > When trying to create a 3D axes, I receive this error: > > /usr/lib/pymodules/python2.7/mpl_toolkits/mplot3d/axes3d.pyc > in grid(self, > b, **kwargs) > 1254 if len(kwargs) : > 1255 b = True > -> 1256 self._draw_grid = maxes._string_to_bool(b) > 1257 > 1258 def ticklabel_format(self, **kwargs) : > > AttributeError: 'module' object has no attribute '_string_to_bool' > > I'm running matplotlib 1.4.3 on linux (ubuntu-based), and was > able to create > 3D axes until I updated last week. > > Thanks in advance. > > > > > -- > View this message in context: > http://matplotlib.1069221.n5.nabble.com/Problem-AttributeError-module-objec… > Sent from the matplotlib - users mailing list archive at > Nabble.com. > > ------------------------------------------------------------------------------ > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users(a)lists.sourceforge.net > <mailto:Matplotlib-users@lists.sourceforge.net> > https://lists.sourceforge.net/lists/listinfo/matplotlib-users >

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baseman and counties
by Tommy Grav Aug. 18, 2015

Aug. 18, 2015

I am trying to use matplotlib and basemap to show a map of the State of Indiana and highlight a few different counties. As a newbie I started with the code below, but I am having trouble with how to identify and fill specific counties. Anyone have any suggestions? from mpl_toolkits.basemap import Basemap import matplotlib.pyplot as plt import numpy as np # make sure the value of resolution is a lowercase L, # for 'low', not a numeral 1 map = Basemap(projection='merc', lat_0=39.1622, lon_0=-86.5292, resolution = 'h', area_thresh = 0.1, llcrnrlon=-88.53, llcrnrlat=37.16, urcrnrlon=-84.53, urcrnrlat=41.16) map.drawcoastlines() map.drawcountries() map.drawstates(linewidth=0.5, linestyle="solid", color="r", antialiased=1, ax=None, zorder=None) map.drawcounties(linewidth=0.1,linestyle="solid", color="k", antialiased=1, ax=None, zorder=None, drawbounds=False) #map.fillcontinents(color='coral') map.drawmapboundary() map.drawmeridians(np.arange(0, 360, 30)) map.drawparallels(np.arange(-90, 90, 30)) plt.show()

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Re: [Matplotlib-users] Marker size in pixels
by Where Where Aug. 16, 2015

Aug. 16, 2015

Good question! I'm only saving my graphs to file (via an animation), and not displaying them to the screen. I have the dpi I'm using in a variable. On Sun, Aug 16, 2015 at 5:03 PM, William Ray Wing <wrw(a)mac.com> wrote: > How will you know in advance what conversion factor to use, that is, how > will you know what your users are equipped with? Display devices with 72 > pixels/in, 225 pixels/in, and 300 pixels/in would have very different > conversion factors. > > Bill > > > > On Aug 15, 2015, at 8:46 PM, Where Where <wherewp(a)gmail.com> wrote: > > Apologies; I didn't include enough information. I see that matplotlib > allows you to set the marker size in points. My quest is to convert pixels > to points. > > On Sat, Aug 15, 2015 at 7:38 PM, Where Where <wherewp(a)gmail.com> wrote: > >> Salutations, community. >> >> I'd like to plot a circular marker with, say, a 10 pixel radius. Is it >> possible to do this in matplotlib? >> >> Daniel >> > > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users(a)python.org > https://mail.python.org/mailman/listinfo/matplotlib-users > > >

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Ann: mpldatacursor v0.6 - Interactive annotation boxes for Matplotlib
by Joe Kington Aug. 16, 2015

Aug. 16, 2015

Hi folks, mpldatacursor version 0.6 has been released (it's long overdue). mpldatacursor provides interactive “data cursors” (clickable annotation boxes) for matplotlib. Major Changes in v0.6 Version 0.6 adds: - Better handling of date-formatted axes. - “Popup” text boxes can be interactively hidden by right-clicking (controllable through the hide_button and display_button kwargs). - Proper support for twinned axes. - Better unicode support for the formatter function. Note that this makes mpldatacursor incompatibile with early 3.x versions (3.0, 3.1, and 3.2). However, it remains compatible with Python >= 3.3 (e.g. 3.3, 3.4, and 3.5) as well as 2.6 and 2.7. - Annotation boxes will now try to stay visible inside the figure by default. Specify keep_inside=False to disable this. - Added basic support for extracting the z-value of 3D artists. - Made the precision of the default x & y formatting depend on the range of the axes. - Full support for interactive IPython notebooks through the nbagg backend. Note that the performance on the nbagg may be very poor. - Workarounds for annotation issues in Matplotlib v1.4.3 - Numerous bugfixes (Thanks to everyone for the reports!). Basic Usage mpldatacursor offers a few different styles of interaction through the datacursor function. As an example, this displays the x, y coordinates of the selected artist in an annotation box: import matplotlib.pyplot as plt import numpy as np from mpldatacursor import datacursor data = np.outer(range(10), range(1, 5)) fig, ax = plt.subplots() lines = ax.plot(data) ax.set_title('Click somewhere on a line') datacursor(lines) plt.show() <https://github.com/joferkington/mpldatacursor/blob/master/examples/basic.py> Installation mpldatacursor can be installed from PyPi using easy_install/pip/etc. (e.g. pip install mpldatacursor) or you may download the source and install it directly with python setup.py install. Thanks, -Joe

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