Mailman 3 June 2016 - Matplotlib-users

Real-time graph, redrawing a changing Y axis
by John Ladasky June 30, 2016

June 30, 2016

Hello everyone, Thomas Caswell has kindly directed me from the old Matplotlib-users mailing list on Sourceforge, to this address at Python.org. I submitted this post once before to this mailing list, yesterday, before I found the web page for subscribing. If a duplicate message should appear, please accept my apologies. I am using MPL 1.4.2, Python 3.4, and Ubuntu 15.04. I am developing a program which displays real-time data. On each update cycle, the graph needs to adjust the y-axis scale. I have code that mostly works, but when it re-renders the y-axis, it is not completely erasing the old one. I get tick labels written on top of each other, until everything is an unreadable smear, like this: [image: Inline image 1] Here is the relevant part of my update method: self.plot.set_data(self.x[:size], self.y[:size]) lo = self.y[:size].min() hi = self.y[:size].max() if hi - lo > 150: self.ax.set_ylim(lo-25, hi+25) else: mid = self.y[:size].mean() self.ax.set_ylim(mid-100, mid+100) self.ax.relim() self.ax.autoscale_view(None, False, True) self.ax.redraw_in_frame() # Something which erases the Y axis should go here? self.ax.get_yaxis().draw(self.parent.get_renderer()) I think that the details of setting the Y limits are unimportant, but I've included that code anyway, so that you can see my set_data() method call at the top, and you can also see that I'm continually adjusting the Y range to track the data. I think that I am searching for a method in the axis class which would erase the previously drawn tick marks and labels. So far, I haven't found one. It would replace the comment line in my code. I am trying to avoid redrawing the entire canvas on which this plot is embedded, since there are several other live data plots besides the one I have shown. The first version of my program did a full redraw, and it took over 150 milliseconds to complete an update call. That's too slow for my needs. Thanks for any help you can provide! -- *John J. Ladasky Jr., Ph.D.* *Research Scientist* *International Technological University* *2711 N. First St, San Jose, CA 95134 USA*

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Fwd: poor tick locator defaults in 2.0?
by Thomas Caswell June 29, 2016

June 29, 2016

Great to hear! ---------- Forwarded message --------- From: Mike Kaufman <mckauf(a)gmail.com> Date: Wed, Jun 29, 2016 at 3:28 PM Subject: Re: [Matplotlib-users] poor tick locator defaults in 2.0? To: Thomas Caswell <tcaswell(a)gmail.com>, Benjamin Root <ben.v.root(a)gmail.com > Freshening up my tree fixes things. Thanks guys. M On 6/28/16 2:28 PM, Thomas Caswell wrote: > https://github.com/matplotlib/matplotlib/pull/6584 Is the PR that should > ensure that there are always at least 2 ticks. > > If you have that commit in you tree, can you give us an example where it > fails? > > Tom > > On Tue, Jun 28, 2016 at 2:26 PM Benjamin Root <ben.v.root(a)gmail.com > <mailto:ben.v.root@gmail.com>> wrote: > > Yeah, we were experimenting with a modified ticker/autoscaling logic > and we aren't too happy with it either. How fresh is your v2.x > branch? I can't remember if we merged in some tweaks to the logic yet. > > Ben Root > > On Tue, Jun 28, 2016 at 2:23 PM, Mike Kaufman <mckauf(a)gmail.com > <mailto:mckauf@gmail.com>> wrote: > > Hi, > > When I switched over to the 2.x branch, I found that for shorter > plots (like when you have a set of vertically stacked subplots), > I am seeing y-axes with only a single tick label. This is > without doing any explicit tick locating. In 1.5.x I didn't see > this. > > This is bad as it makes the whole point of labeling the ticks > pointless because you can't get any sense of scale. > > M > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users(a)python.org <mailto:Matplotlib-users@python.org> > https://mail.python.org/mailman/listinfo/matplotlib-users > > > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users(a)python.org <mailto:Matplotlib-users@python.org> > https://mail.python.org/mailman/listinfo/matplotlib-users >

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poor tick locator defaults in 2.0?
by Mike Kaufman June 28, 2016

June 28, 2016

Hi, When I switched over to the 2.x branch, I found that for shorter plots (like when you have a set of vertically stacked subplots), I am seeing y-axes with only a single tick label. This is without doing any explicit tick locating. In 1.5.x I didn't see this. This is bad as it makes the whole point of labeling the ticks pointless because you can't get any sense of scale. M

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Need clarification on shiftgrid and addcylic
by ashwinD12 . June 24, 2016

June 24, 2016

Hello, I am just starting to learn how to plot NCEP reanalysis data using Python3 and matplotlib and basemap. I have some clarifications on how to go about doing it. My dataset is between latitude 5 N to 40 N and 65 E and 100 E. I am trying to plot geopotential height from NCEP reanalysis data. Here is my code - <code> level = 5 time = 0 meters_per_grid = 277830 d = Dataset("hgt_500_2014_12_5_00Z.nc") hgt = d.get_variables_by_attributes(axis="hgt") lon = d.get_variables_by_attributes(axis="lon") lat =d.get_variables_by_attributes(axis="lat") hgt = hgt[::-1] hgt, lon = shiftgrid(180, hgt, lon, start = False </code> Why do I get an IndexError: index out of range on shiftgrid call ? BR, Ashwin.

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fail to build matplotlib on smartos(like open solaris) system
by Frank Yu June 23, 2016

June 23, 2016

Hi there, I am trying build matplotlib on smartos(like open solaris) system. but failed with error. I am build the latest matplotlib. steps as below: # git describe v2.0.0b1-1699-g4b3350d # python setup.py install ============================================================================ Edit setup.cfg to change the build options BUILDING MATPLOTLIB matplotlib: yes [2.0.0b1+1699.g4b3350d] python: yes [2.7.11 (default, Jan 11 2016, 23:16:55) [GCC 4.9.3]] platform: yes [sunos5] REQUIRED DEPENDENCIES AND EXTENSIONS numpy: yes [version 1.11.0] six: yes [The installed version of six is 1.9.0 but a the minimum required version is 1.10. pip/easy install will attempt to install a newer version.] dateutil: yes [using dateutil version 2.4.0] functools32: yes [using functools32] pytz: yes [using pytz version 2014.10] cycler: yes [using cycler version 0.10.0] tornado: yes [using tornado version 4.3] pyparsing: yes [using pyparsing version 2.0.2] libagg: yes [pkg-config information for 'libagg' could not be found. Using local copy.] freetype: yes [version 2.5.5] png: yes [version 1.6.17] qhull: yes [pkg-config information for 'qhull' could not be found. Using local copy.] OPTIONAL SUBPACKAGES sample_data: yes [installing] toolkits: yes [installing] tests: yes [using nose version 1.3.7 / mock is required to run the matplotlib test suite. Please install it with pip or your preferred tool to run the test suite] toolkits_tests: yes [using nose version 1.3.7 / mock is required to run the matplotlib test suite. Please install it with pip or your preferred tool to run the test suite] OPTIONAL BACKEND EXTENSIONS macosx: no [Mac OS-X only] qt5agg: no [PySide2 not found; PyQt5 not found] qt4agg: no [PySide not found; PyQt4 not found] gtk3agg: no [Requires pygobject to be installed.] gtk3cairo: no [Requires pygobject to be installed.] gtkagg: no [Requires pygtk] tkagg: yes [installing; run-time loading from Python Tcl / Tk] wxagg: no [requires wxPython] gtk: no [Requires pygtk] agg: yes [installing] cairo: yes [installing, pycairo version 1.10.0] windowing: no [Microsoft Windows only] OPTIONAL LATEX DEPENDENCIES dvipng: no ghostscript: no latex: no pdftops: no OPTIONAL PACKAGE DATA dlls: no [skipping due to configuration] running install running bdist_egg running egg_info creating lib/matplotlib.egg-info writing requirements to lib/matplotlib.egg-info/requires.txt writing lib/matplotlib.egg-info/PKG-INFO writing namespace_packages to lib/matplotlib.egg-info/namespace_packages.txt writing top-level names to lib/matplotlib.egg-info/top_level.txt writing dependency_links to lib/matplotlib.egg-info/dependency_links.txt writing manifest file 'lib/matplotlib.egg-info/SOURCES.txt' reading manifest file 'lib/matplotlib.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'lib/matplotlib.egg-info/SOURCES.txt' installing library code to build/bdist.solaris-2.11-i86pc.64bit/egg running install_lib running build_py creating build creating build/lib.solaris-2.11-i86pc.64bit-2.7 copying lib/pylab.py -> build/lib.solaris-2.11-i86pc.64bit-2.7 creating build/lib.solaris-2.11-i86pc.64bit-2.7/matplotlib copying lib/matplotlib/_version.py -> build/lib.solaris-2.11-i86pc.64bit-2.7/matplotlib ............ running build_ext building 'matplotlib.ft2font' extension creating build/temp.solaris-2.11-i86pc.64bit-2.7 creating build/temp.solaris-2.11-i86pc.64bit-2.7/src gcc -fno-strict-aliasing -O2 -pipe -O2 -gdwarf-2 -DHAVE_DB_185_H -pthread -I/usr/include -I/opt/local/include -I/opt/local/include/db4 -I/opt/local/include/ncurses -DNDEBUG -O2 -pipe -O2 -gdwarf-2 -DHAVE_DB_185_H -pthread -I/usr/include -I/opt/local/include -I/opt/local/include/db4 -I/opt/local/include/ncurses -fPIC -DFREETYPE_BUILD_TYPE=system -DPY_ARRAY_UNIQUE_SYMBOL=MPL_matplotlib_ft2font_ARRAY_API -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -I/opt/local/lib/python2.7/site-packages/numpy/core/include -I/opt/local/include/libpng16 -I/opt/local/include -I/opt/local/include/freetype2 -I/usr/local/include -I. -I/opt/local/include/python2.7 -c src/ft2font.cpp -o build/temp.solaris-2.11-i86pc.64bit-2.7/src/ft2font.o gcc -fno-strict-aliasing -O2 -pipe -O2 -gdwarf-2 -DHAVE_DB_185_H -pthread -I/usr/include -I/opt/local/include -I/opt/local/include/db4 -I/opt/local/include/ncurses -DNDEBUG -O2 -pipe -O2 -gdwarf-2 -DHAVE_DB_185_H -pthread -I/usr/include -I/opt/local/include -I/opt/local/include/db4 -I/opt/local/include/ncurses -fPIC -DFREETYPE_BUILD_TYPE=system -DPY_ARRAY_UNIQUE_SYMBOL=MPL_matplotlib_ft2font_ARRAY_API -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -I/opt/local/lib/python2.7/site-packages/numpy/core/include -I/opt/local/include/libpng16 -I/opt/local/include -I/opt/local/include/freetype2 -I/usr/local/include -I. -I/opt/local/include/python2.7 -c src/ft2font_wrapper.cpp -o build/temp.solaris-2.11-i86pc.64bit-2.7/src/ft2font_wrapper.o In file included from /opt/local/include/python2.7/Python.h:44:0, from src/mplutils.h:21, from src/ft2font_wrapper.cpp:1: /usr/include/unistd.h:521:75: error: declaration of C function 'void swab(const void*, void*, ssize_t)' conflicts with In file included from /opt/local/include/python2.7/Python.h:42:0, from src/mplutils.h:21, from src/ft2font_wrapper.cpp:1: /usr/include/stdlib.h:170:13: error: previous declaration 'void swab(const char*, char*, ssize_t)' here error: command 'gcc' failed with exit status 1 The error is clear, swab was declared twice in both unistd.h and stdlib.h # sed -n 519,522p /usr/include/unistd.h #if defined(_XPG4) /* __EXTENSIONS__ makes the SVID Third Edition prototype in stdlib.h visible */ extern void swab(const void *_RESTRICT_KYWD, void *_RESTRICT_KYWD, ssize_t); #endif /* defined(_XPG4) */ # sed -n 170p /usr/include/stdlib.h extern void swab(const char *, char *, ssize_t); # sed -n 158,171p /usr/include/stdlib.h #if (defined(__EXTENSIONS__) || \ (!defined(_STRICT_STDC__) && !defined(_POSIX_C_SOURCE))) && \ (!defined(_XOPEN_SOURCE) || (defined(_XPG3) && !defined(_XPG4))) #ifndef _SSIZE_T #define _SSIZE_T #if defined(_LP64) || defined(_I32LPx) typedef long ssize_t; /* size of something in bytes or -1 */ #else typedef int ssize_t; /* (historical version) */ #endif #endif /* !_SSIZE_T */ extern void swab(const char *, char *, ssize_t); #endif /* defined(__EXTENSIONS__) || !defined(_STRICT_STDC) ... */ I saw someone has asked this question, but can't get a proper answer. -- Regards Frank Yu

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Re: [Matplotlib-users] When data is graphed with an offset
by Thomas Caswell June 23, 2016

June 23, 2016

John, This seems to be a common question ( http://stackoverflow.com/questions/14711655/how-to-prevent-numbers-being-ch… ) ax = plt.gca() ax.get_xaxis().get_major_formatter().set_useOffset(False) ax.get_yaxis().get_major_formatter().set_useOffset(False) will control a single axes To control it globally set `axes.formatter.useoffset: False` in rcparams. see http://matplotlib.org/users/customizing.html#a-sample-matplotlibrc-file Where would you have expected to look for this information in the documentation? Tom PS the sourceforge list is no longer used, please send future mail to matplotlib-users(a)python.org On Wed, Jun 22, 2016 at 8:30 PM John Ladasky <jladasky(a)itu.edu> wrote: > Hi there, > > I have been subscribed to matplotlib-users before. I have a new job, and > now I'm connecting from a new email address. I've been using Matplotlib > since before 1.0 was released. Currently, I'm using MPL 1.4.2 and Python > 3.5 on Ubuntu Linux 15.04 (if any of that matters). > > Please have a look at the following graph: > > [image: For matplotlib discussion.png] > > The values in the data set used to plot these two graphs range from 14942 > to 14948. In other words, the median of the data set is very far from > zero, but the range of the data is very small. With such a data set, MPL > subtracts a large offset value from the data points, choosing a value such > that the remaining differences are small, positive numbers. I understand > the logic behind this, it simplifies graph labeling on the x-axis of the > left graph, and the y-axis of the right graph. > > However, I do not like the way that MPL is displaying the offset value. > It is written in small text, and it does not show up in a consistent > place. On a figure with many adjacent axes, it sometimes isn't clear which > axes owns the annotation. I would prefer to incorporate the offset in the > axes title: for example, the title of the left graph could read "internal > thermistor (+14940)". > > So, what is this offset value called in Matplotlib? How do I retrieve > it? How can I override its display? I can obviously do this by wrapping > these particular plots in functions which apply the offset before giving > the data to MPL. But I would prefer to work with MPL itself, as I don't > always know when MPL will judge that a data offset value is needed. > > Thanks for your help! > -- > *John J. Ladasky Jr., Ph.D.* > *Research Scientist* > *International Technological University* > *2711 N. First St, San Jose, CA 95134 USA* > > ------------------------------------------------------------------------------ > Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San > Francisco, CA to explore cutting-edge tech and listen to tech luminaries > present their vision of the future. This family event has something for > everyone, including kids. Get more information and register today. > http://sdm.link/attshape_______________________________________________ > 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] fancy border for basemap's map?
by Jake Larson June 16, 2016

June 16, 2016

Maria Liukis <liukis@...> writes: > > Hello, > > I was wondering if there is an option in basemap to put “fancy“ (white and > black skinny rectangles) map > border like the one is available in GMT? Not a perfect fix but works for cylindrical projections. github.com/larsonjl/mapping/blob/master/fancy_map_borders.md

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Failing to install matplotlib with python 3
by Alan June 16, 2016

June 16, 2016

Hi there, I am not the admin so I have installed my own python 3.5.1 and I am using pip3 to install all modules I need. I got all but matplotlib :-( pip3 install -U matplotlib Collecting matplotlib Using cached matplotlib-1.5.1.tar.gz Complete output from command python setup.py egg_info: Traceback (most recent call last): File "<string>", line 1, in <module> File "/tmp/pip-build-6eka4_fr/matplotlib/setup.py", line 167, in <module> result = package.check() File "/tmp/pip-build-6eka4_fr/matplotlib/setupext.py", line 980, in check min_version='1.2', version=version) File "/tmp/pip-build-6eka4_fr/matplotlib/setupext.py", line 459, in _check_for_pkg_config if (not is_min_version(version, min_version)): File "/tmp/pip-build-6eka4_fr/matplotlib/setupext.py", line 179, in is_min_version return found_version >= expected_version File "/sw/arch/Test2/lib/python3.5/distutils/version.py", line 70, in __ge__ c = self._cmp(other) File "/sw/arch/Test2/lib/python3.5/distutils/version.py", line 337, in _cmp if self.version < other.version: TypeError: unorderable types: str() < int() ============================================================================ Edit setup.cfg to change the build options BUILDING MATPLOTLIB matplotlib: yes [1.5.1] python: yes [3.5.1 (default, Jun 16 2016, 11:03:02) [GCC 4.4.7 20120313 (Red Hat 4.4.7-11)]] platform: yes [linux] REQUIRED DEPENDENCIES AND EXTENSIONS numpy: yes [version 1.11.0] dateutil: yes [using dateutil version 2.5.3] pytz: yes [using pytz version 2016.4] cycler: yes [using cycler version 0.10.0] tornado: yes [using tornado version 4.3] pyparsing: yes [using pyparsing version 2.1.5] libagg: yes [pkg-config information for 'libagg' could not be found. Using local copy.] freetype: yes [version unknown] ---------------------------------------- Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-6eka4_fr/matplotlib/ What am I missing here please? Thanks, Alan PS. btw, with python 2.7.11 all went fine.

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Re: [Matplotlib-users] Failing to install matplotlib with python 3
by Eric Firing June 16, 2016

June 16, 2016

Alan, This mailing list is obsolete; please use matplotlib-users(a)python.org. Your traceback looks vaguely familiar as something that has come up before, but I don't have any more recollection than that. Suggestions: 1) Install your python environment the easy way via anaconda or miniconda: https://www.continuum.io/downloads 2) If you are *sure* you don't want to do it that way, make sure you have the most recent version of pip. 3) Likewise, install the most recent matplotlib. See attached message. Eric On 2016/06/16 6:07 AM, Alan wrote: > Hi there, > > I am not the admin so I have installed my own python 3.5.1 and I am > using pip3 to install all modules I need. I got all but matplotlib :-( > > pip3 install -U matplotlib > > Collecting matplotlib > Using cached matplotlib-1.5.1.tar.gz > Complete output from command python setup.py egg_info: > Traceback (most recent call last): > File "<string>", line 1, in <module> > File "/tmp/pip-build-6eka4_fr/matplotlib/setup.py", line 167, in > <module> > result = package.check() > File "/tmp/pip-build-6eka4_fr/matplotlib/setupext.py", line 980, > in check > min_version='1.2', version=version) > File "/tmp/pip-build-6eka4_fr/matplotlib/setupext.py", line 459, > in _check_for_pkg_config > if (not is_min_version(version, min_version)): > File "/tmp/pip-build-6eka4_fr/matplotlib/setupext.py", line 179, > in is_min_version > return found_version >= expected_version > File "/sw/arch/Test2/lib/python3.5/distutils/version.py", line 70, > in __ge__ > c = self._cmp(other) > File "/sw/arch/Test2/lib/python3.5/distutils/version.py", line > 337, in _cmp > if self.version < other.version: > TypeError: unorderable types: str() < int() > > ============================================================================ > Edit setup.cfg to change the build options > > BUILDING MATPLOTLIB > matplotlib: yes [1.5.1] > python: yes [3.5.1 (default, Jun 16 2016, 11:03:02) > [GCC > 4.4.7 20120313 (Red Hat 4.4.7-11)]] > platform: yes [linux] > > REQUIRED DEPENDENCIES AND EXTENSIONS > numpy: yes [version 1.11.0] > dateutil: yes [using dateutil version 2.5.3] > pytz: yes [using pytz version 2016.4] > cycler: yes [using cycler version 0.10.0] > tornado: yes [using tornado version 4.3] > pyparsing: yes [using pyparsing version 2.1.5] > libagg: yes [pkg-config information for 'libagg' > could not > be found. Using local copy.] > freetype: yes [version unknown] > > ---------------------------------------- > Command "python setup.py egg_info" failed with error code 1 in > /tmp/pip-build-6eka4_fr/matplotlib/ > > What am I missing here please? > > Thanks, > > Alan > > PS. btw, with python 2.7.11 all went fine. >

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patch and its border
by Matěj Týč June 7, 2016

June 7, 2016

Hello, consider a case when I want to draw a patch, but it is important how the border is drawn. For example, if I have an aerial photo and I would like to add a rectangle of given dimensions as a reference. Having the rectangle interior white and its border thick and black is good, because it ensures that the reference will be always clearly visible, regardless of whether the photo is dark or bright. However, as the border is thick, it may significantly overlap with the interior, which is highly unwanted, because it will look smaller. Therefore, in this case, I would like to draw the border, but all of it should be outside of the patch primary area. And I am sure that there are use cases for the opposite situation. TL;DR: Take a look at the attached picture to see what I have in mind - I would like to use "outer borders" (red) or "inner borders", or classical ones, depending on my needs. Is there a user possibility to influence how the border is drawn? If not, how difficult would it be to implement this in matplotlib?

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