[Matplotlib-users] fmt_xdata / fmt_ydata on polar plot?

[Alex Page]

Is there any way to do this?  The example here works in Cartesian
coordinates:

http://matplotlib.org/examples/pylab_examples/coords_report.html

but if you change

subplots()

to

subplots(subplot_kw={'polar':True})

Then the millions() function is never even called.

Thanks,
Alex
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[Matplotlib-users] Bug in matplotlib 1.4.2

[Alex Böhnert]

Dear all,

when plotting scattered data with the , marker, the data points do not
show up either on screen (Qt4Agg backend) or in saved bitmap images (tested
with png); they do show up if the plot is exported as pdf.

Example code (run in ipython --pylab for simplicity):

import numpy as np
a = np.random.standard_normal(500)
b = np.random.standard_normal(500)
plot(a,b,',')
savefig(testplot.png)
savefig(testplot.pdf)

Expected result: Scatter plot of random data points, both on screen and in
saved files.

Actual result: Empty-looking plot both on screen and in png, but plot as
expected in pdf.

System info: Arch linux, Kernel 3.17.6 (and 3.18.6), matplotlib version
1.4.2, Python 3.4.2, IPython 2.3.1., numpy version 1.9.1, Qt4Agg backend.

Related: I posted this to the arch-bugtracker (
https://bugs.archlinux.org/task/43392) and asked on stack overflow whether
anyone else saw this (
http://stackoverflow.com/questions/28112916/python-matplotlib-does-not-display-data-points-bug-or-something-else).
Apparently, the same thing happens in Ubuntu, too.

Hope this is the right place to report this.

Cheers,
Alex

P.S.: I sent the same mail to the list a few weeks ago without registering,
but it was never posted, nor replied to. It might be a good idea not to
suggest at http://matplotlib.org/faq/troubleshooting_faq.html#getting-help
that just sending a mail to the list will achieve anything...
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Re: [Matplotlib-users] One colorbar for many plot

[Alex Goodman]

I would consider using the AxesGrid toolkit [1], which makes it very easy
to have a single colorbar for multiple plots.

[1] - http://matplotlib.org/1.3.1/mpl_toolkits/axes_grid/users/overview.html

Thanks,
Alex


On Tue, May 20, 2014 at 8:04 PM, Alex Goodman alex.good...@colostate.eduwrote:

 I would consider using the AxesGrid toolkit [1], which makes it very easy
 to have a single colorbar for multiple plots.

 [1] -
 http://matplotlib.org/1.3.1/mpl_toolkits/axes_grid/users/overview.html

 Thanks,
 Alex


 On Tue, May 20, 2014 at 7:57 PM, Dyah rahayu martiningrum 
 dyahr...@gmail.com wrote:

 I am a newbie in python and I try to plot data like below :

 base_dir = 'C:/DATA2013/Day_E/'
 nc_fnames = ['20130203.faieb3p4g.nc', 
 '20130203.faieb3p4g.nc','20130203.faieb3p4g.nc']
 # beams
 ibeams = [0,1,2]
 # Change directory
 os.chdir(base_dir)
 for i, fname in enumerate(nc_fnames):

# Open file
 fd = nc.Dataset(fname, 'r')

 # Read variables
 beam = fd.variables['beam'][:]
 rng = fd.variables['range'][:]
 tim = fd.variables['time'][:]
 pwr = fd.variables['pwr'][:]
 nfft = fd.variables['nfft'][0]
 pn = fd.variables['pnoise'][:]

 # Close netCDF file
 fd.close()

 # Specify beam
 ibeam = ibeams[i]

 # Time convertion
 tim = tim/3600.0

 #Plot
 p_plot = pwr[ibeam]

 for it in range(len(tim)):
 p_plot[it] = p_plot[it] - pn[ibeam][it] - 10.*np.log10(nfft)

 p_plot = p_plot.transpose()
 #Specify subplot
 pl.subplot(311 + i)#Contour plot
 pl.contourf(tim, rng, p_plot)#Plot colorbar
 pl.colorbar()
 # Set X and Y axis lower/upper limit
 set_xy = range(4)
 set_xy[0] = 18.0 # x min
 set_xy[1] = 30.0 # x max
 set_xy[2] = 90.0 # y min
 set_xy[3] = 170.0 # y max
 pl.axis(set_xy)
 # Set labels
 pl.xlabel('time (hours)')
 pl.ylabel('range (km)')

 pl.show()


 The result looks like three panels with different colorbar for each
 panel. How do I make only one colorbar for all panels? Thank you in advance.


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Re: [Matplotlib-users] Can't plot NCEP reanalysis data

[Alex Goodman]

Hi Fadzil,

I am not sure if I fully understand your question. Are you simply trying to
write a general script that plots contours for atmospheric netcdf data? At
the very least, your error message has a very simple explanation in that
the third argument of contourf (in this case, pcpr or omg?) must be a 2D
array with shape (Xsize, Ysize). For data with one vertical level, it would
be reasonable to expect the script to work, but if you have multiple
vertical levels and don't select a specific one in your code, then you
can't use contourf, simple as that.

Does that help at all?
Alex



On Tue, Mar 4, 2014 at 8:22 PM, Fadzil Mnor fadzilmno...@gmail.com wrote:

 Hi all,
 I've been looking for solution on this for days, and seems like nothing
 works.
 I wrote this code to read TRMM data and it works, but somehow not working
 when I use the same script to read NCEP reanalysis data...which later I
 found out it worked for netCDF files with only 1 'level'  (Zsize=1), not
 multiple 'levels' (Zsize more than 1).
 I'm stuck at where went wrong, and I tried everything and lost of track
 what the error massages were.
 This is what I wrote to read and plot NCEP reanalysis data. (this omega
 data has Xsize=144, Ysize=73, Zsize=12, Tsize=792, Esize=1)

 ---
 *import netCDF4 as nc*
 *import matplotlib.pyplot as plt*
 *from mpl_toolkits.basemap import Basemap*
 *import numpy as np*

 *f = nc.Dataset('D:/data/omega.mon.mean.nc
 http://omega.mon.mean.nc','r')*
 *omg = f.variables['omega'][0]*
 *lon = f.variables['lon'][:]*
 *lat = f.variables['lat'][:]*
 *times = f.variables['time'][:]*

 *# Set up a map *
 *map =
 Basemap(projection='cyl',llcrnrlat=0.,urcrnrlat=10.,llcrnrlon=97.,urcrnrlon=110.,resolution='i')*
 *x,y=map(*np.meshgrid(lon,lat))*
 *map.drawcoastlines()*
 *map.drawcountries()*
 *map.drawparallels(np.arange(-90.,90.,3),labels=[1,0,0,0],fontsize=10)*
 *map.drawmeridians(np.arange(-180.,180.,3),labels=[0,0,0,1],fontsize=10)*

 *#contour data*
 *clevs=np.arange(0.,1.,0.1) # contour interval*
 *cs = map.contourf(x,y,pcpr,clevs,extent='both')*
 *cb = map.colorbar(cs,'bottom',size='2%',pad=5%) #plot the colorbar *

 *cb.set_label('m/s')*
 *plt.title('Omega-test')*

 *plt.show()*

 *f.close()*

 -

 Above code gave error: Input z must be a 2D array
 (that's at *cs = map.contourf(x,y,pcpr,clevs,extent='both')*...)

 Hopefully anyone can help.
 Thanks for your time reading this.

 Fadzil




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Re: [Matplotlib-users] Area averaged

[Alex Goodman]

Hi Fadzil,

All you actually need to do is use numpy.average(), which is numpy's
implementation of the weighted average. It can be shown geometrically that
using the cosine of the latitude as the weights in the weighted average
would give you approximately the area average, though if your SST data has
a grid cell area attribute in the netcdf file, that would be the most
suitable choice to use as your weights. Otherwise, you could determine the
area weighted average as follows:

# numpy is imported as np, lat are the latitudes extracted from the netcdf
file
# First we need to convert the latitudes to radians
latr = np.deg2rad(lat)

# Use the cosine of the converted latitudes as weights for the average
weights = np.cos(latr)

# Assuming the shape of your data array is (nTimes, nLats, nLons)
# First find the zonal mean SST by averaging along the latitude circles
sst = sstv[:]
sst_ave_zonal = sst.mean(axis=2)

# Then take the weighted average of those using the weights we calculated
earlier
sst_ave = np.average(sst_ave_zonal, axis=1, weights=weights)

This should give a time series of global mean SST. Is this what you wanted?

Thanks,
Alex


On Sun, Feb 23, 2014 at 10:28 AM, Fadzil Mnor fadzilmno...@gmail.comwrote:

 Hi,
 I just started using Python for the last few weeks, and previously been
 using GrADS for around 4 years.
 I have trouble looking for a simplest way to calculate area average, let
 say I need to calculate a SST over a region of 20S-10N and 130E-170E.
 I know how to get one point values of SST vs Time, as in:

 
 ...
 ...
 f = nc.Dataset('d:/data/sst.mon.mean.nc', 'r')
 sstv = f.variables['sst']
 timev = f.variables['time']
 sst = sstv[:, 35, 100]
 plt.plot(timev,sst)
 plt.show()
 ...
 ...
 ***
 but I couldn't figure out how to get an area average value (...and didn't
 get the right reference in the internet either)
 Something missing, probably because I don't understand enough about
 slicing or something else.
 Can anyone give me a hint ?

 Thanks.

 Fadzil.





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Re: [Matplotlib-users] Area averaged

[Alex Goodman]

Hi Fadzil,

Ah sorry, I glossed over that part of your question. There are actually two
solutions to this, one would be to actually find the indices where the
latitudes and longitudes are within your desired bounds using
numpy.where(). However I generally prefer to use numpy's built-in fancy
indexing for this type of problem. For example:

# lat and lon are extracted from the netcdf file, assumed to be 1D
# Determine which latitudes are between 20S and 10N
latidx = (lat = -20)  (lat = 10)

# Determine which longitudes are between 130E and 170E.
# The numbers here may differ depending on the longitude convention in your
data.
lonidx = (lon = 130)  (lon = 170)

# Now we will actually subset the data. We need to subset lat too to make
sure weights are consistent.
sst = sstv[:]
sst = sst[:, latidx][..., lonidx]
lat = lat[latidx]

Yes, the indexing does get a little tricky but it should work if you do it
this way, then follow the same procedure outlined in the previous email.

Thanks,
Alex

On Sun, Feb 23, 2014 at 6:02 PM, Fadzil Mnor fadzilmno...@gmail.com wrote:

 Thanks Alex for the reply.
 So, that script calculates the global SST. What if when we want to
 calculate for only in specific box? For example, SST over this area only:

 --- 10 N
 | |
 | |
 | |
 |   SST  |
 | |
 | |
 --- 20 S
 130 E 170E

 Thanks.

 Fadzil




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Re: [Matplotlib-users] [os x] Can't get IPython to use latest version of matplotlib

[Alex Goodman]

Hi Tim,

Whenever you have two python versions installed to one machine, it is
generally a good practice to set your PATH environment variable to the
directory where the python executable you want to use currently lies, and
make it permanent by adding it to your ~/.bash_profile file (on MacOSX).
Say your python.org version of python was installed in /something/bin. Then
add the following line to your ~/.bash_profile:

export PATH=/something/bin:$PATH

Then run these commands:
source ~/.bash_profile
which python
which pip

If the output is /something/bin, then you are good to go; pip should then
install matplotlib in the correct place. Hope that helps.

Thanks,
Alex


On Fri, Feb 21, 2014 at 4:58 PM, Timothy Duly timdu...@gmail.com wrote:

 Paul,

 Do you know how to to get pip install on python.org's version?

 Thanks,
 Tim


 On Fri, Feb 21, 2014 at 5:53 PM, Paul Hobson pmhob...@gmail.com wrote:

 It appears that you have two different version of python installed
 (Apple's 2.7.3 and python.org's 2.7.5). You have to install all
 third-party packages to the correct one. It appears pip in acting on
 Apple's python.


 On Fri, Feb 21, 2014 at 2:08 PM, Timothy Duly timdu...@gmail.com wrote:

 Hello,

 I recently upgraded matplotlib, which was relatively simple:

 sudo pip install matplotlib --upgrade

 I checked to make sure I did indeed upgrade:

 [~]$ python
 Python 2.7.3 (v2.7.3:70274d53c1dd, Apr  9 2012, 20:52:43)
 [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
 Type help, copyright, credits or license for more information.
  import matplotlib; matplotlib.__version__
 '1.3.1'

 Success.  However, when I do the same in IPython, I get the old version:

 [~]$ ipython --pylab
 Python 2.7.5 (default, Aug 25 2013, 00:04:04)
 Type copyright, credits or license for more information.
 IPython 1.2.0 -- An enhanced Interactive Python.
 ? - Introduction and overview of IPython's features.
 %quickref - Quick reference.
 help  - Python's own help system.
 object?   - Details about 'object', use 'object??' for extra details.
 Using matplotlib backend: MacOSX
 In [1]: import matplotlib; matplotlib.__version__
 Out[1]: '1.1.1'

 Anyone know why this is the case?  How do I point IPython to the newest
 version of matplotlib?

 I tried googling, but wasn't sure how to zero in on the answer with a
 search.  Also, I'm not sure if this question is best suited for IPython
 people.

 Thanks,
 Tim


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Re: [Matplotlib-users] could I get rid of the contour of Antarctica by using Basemap?

[Alex Goodman]

A quick apology for a typo in my previous message, the method in question
is drawcoastlines(), not drawcontinents(). The code snippet should still be
correct though!


On Mon, Dec 30, 2013 at 7:09 PM, Alex Goodman alex.good...@colostate.eduwrote:

 Hi Chao,

 Actually it is possible to remove the borders for Antarctica with basemap.
 The default method for drawing the continents in basemap, drawcontinents(),
 returns an instance of matplotlib.collections.LineCollection. What you will
 want to do is manually remove the line segments within the collection that
 correspond to Antarctica. For example,

 # m is a Basemap instance
 lcol = m.drawcoastlines()
 segs = lcol.get_segments()

 for i, seg in enumerate(segs):
  # The segments are lists of ordered pairs in spherical (lon, lat),
 coordinates.
  # We can filter out which ones correspond to Antarctica based on
 latitude using numpy.any()
  if np.any(seg[:, 1]  -60):
   segs.pop(i)

 lcol.set_segments(segs)

 This should do the trick unless I made a silly typo somewhere.

 Thanks,
 Alex


 On Mon, Dec 30, 2013 at 5:05 PM, Sterling Smith smit...@fusion.gat.comwrote:

 Chao,

 I know nothing of the Basemap toolkit so I can't comment on the removal
 of continents, but presumably the text command you are using takes some
 keywords to set the properties of the bounding box.  Try setting the
 background of the bounding box to white so that your words show up cleanly.
  Feel free to let me know that I'm barking up the wrong tree.

 -Sterling

 On Dec 30, 2013, at 3:46PM, Chao YUE wrote:

  Dear all,
 
  Happy new year!
 
  I am using Basemap toolkit to make some maps, I would like to
  write something at the bottom of the map, whose position is now
  taken by the contourf of Antarctica. Is there a way I can keep contours
  of other continents but suppressing the one for antarctica? I attached
  showing why I would like to have this.
 
  thanks for any help,
 
  Chao
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Re: [Matplotlib-users] Clipping a plot inside a polygon

[Alex Goodman]

Hi Phil,

Thanks, that is more or less what I was looking for. However, I still think
that generalizing this approach for other types of plotting functions that
don't return artists directly would be useful. Your solution gave me
another idea for doing this, which would be to iterate through all of the
child artists on the axes using the get_children() method and then calling
set_clip_path() on each artist. This would make the methodology very
general but I am not sure if there are any negative side effects to
resetting the clip path on the other artists besides the PatchCollections.
I modified my simple example script and it seems to work well for
contourf(), pcolor(), and imshow():

import numpy as np
import matplotlib.pyplot as plt
from matplotlib.patches import RegularPolygon

data = np.arange(100).reshape(10, 10)
fig = plt.figure()
ax = fig.add_subplot(111)
ax.contourf(data)
poly = RegularPolygon([ 0.5,  0.5], 6, 0.4, fc='none',
ec='k', transform=ax.transAxes)
for artist in ax.get_children():
artist.set_clip_path(poly)

ax.add_patch(poly)
ax.set_aspect('equal')
ax.axis('off')
plt.show()


Also, I appreciated the cartopy example. I think it has the potential to be
a good basemap replacement thanks to the more robust shapefile support
(which you have very elegantly shown), and I hope the development goes well.

Thanks,
Alex


On Mon, Sep 2, 2013 at 2:33 AM, Phil Elson pelson@gmail.com wrote:

 Great question. The contour set itself does not have a set_clip_path
 method but you can iterate over each of the contour collections and set
 their respective clip paths, i.e.:

 cs = plt.contourf(data)
 for collection in cs.collections:
 collection.set_clip_path(poly)

 Of course, you can use this approach in either Basemap or cartopy, but
 I've put together an example of doing it in cartopy to demonstrate the neat
 Shapely integration: http://nbviewer.ipython.org/6410510

 HTH,

 Phil


 On 2 September 2013 05:40, Alex Goodman alex.good...@colostate.eduwrote:

 Hi all,

 I want to be able to plot data on maps (using basemap or cartopy) inside
 specific regions, eg a single state, province or country. A similar
 question was asked a long time ago on the mailing list and the suggested
 solution back then was to read the bounding polygon from a shapefile and
 then check if each individual point was inside that polygon. Currently I
 have no problem doing this if I use matplotlib.path.Path.contains_points()
 to mask the original data array, but the disadvantage to this solution is
 that it is very slow. Another solution that I have discovered recently is
 to use the set_clip_path() method for artists. In addition to being much
 faster, this also makes the areas near the polygon boundary look much
 smoother since the actual items being clipped are individual pixels and not
 data points.

 Here is an example script that plots an image via imshow, but the only
 part of the image that gets shown is inside the hexagon.

 import numpy as np
 import matplotlib.pyplot as plt
 from matplotlib.patches import RegularPolygon

 data = np.arange(100).reshape(10, 10)
 fig = plt.figure()
 ax = fig.add_subplot(111)
 im = ax.imshow(data)
 poly = RegularPolygon([ 0.5,  0.5], 6, 0.4, fc='none',
   ec='k', transform=ax.transAxes)
 im.set_clip_path(poly)
 ax.add_patch(poly)
 ax.axis('off')
 plt.show()

 While this does seem like an ideal solution, it doesn't work for every
 type of plot. The most notable example is contourf(). It returns a
 QuadContourSet instance which does not inherit from Artist, so it does not
 contain the set_clip_path() method. My main question is whether there is a
 mechanism in matplotlib that can convert something like a QuadContourSet
 into an image so I can make use of this solution for contourf() as well. Or
 better yet, is there perhaps another artist within the axes that I can use
 the set_clip_path() method for and still get what I want?

 Thanks,
 Alex
 --
 Alex Goodman
 Graduate Research Assistant
 Department of Atmospheric Science
 Colorado State University


 --
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Re: [Matplotlib-users] Clipping a plot inside a polygon

[Alex Goodman]

Actually, it seems I have partially answered my own question. Since I am
calling axis('off'), I do not notice the effect of clipping the other
artists since I made a call to axis('off'). Without it the spines and axes
rectangle are still removed but the ticks are still visible. I suppose this
is fine for my own purposes of contouring within one country on a map since
I would want to use something like axis('off') anyway, but then it would
not work if I wanted to use the axes background. Another approach I have
tried is to use the clip_path keyword in the plotting functions themselves,
which works for imshow and pcolor, but not contourf. Any other ideas?

Alex


On Mon, Sep 2, 2013 at 12:18 PM, Alex Goodman alex.good...@colostate.eduwrote:

 Hi Phil,

 Thanks, that is more or less what I was looking for. However, I still
 think that generalizing this approach for other types of plotting functions
 that don't return artists directly would be useful. Your solution gave me
 another idea for doing this, which would be to iterate through all of the
 child artists on the axes using the get_children() method and then calling
 set_clip_path() on each artist. This would make the methodology very
 general but I am not sure if there are any negative side effects to
 resetting the clip path on the other artists besides the PatchCollections.
 I modified my simple example script and it seems to work well for
 contourf(), pcolor(), and imshow():

 import numpy as np
 import matplotlib.pyplot as plt
 from matplotlib.patches import RegularPolygon

 data = np.arange(100).reshape(10, 10)
 fig = plt.figure()
 ax = fig.add_subplot(111)
 ax.contourf(data)
 poly = RegularPolygon([ 0.5,  0.5], 6, 0.4, fc='none',
 ec='k', transform=ax.transAxes)
 for artist in ax.get_children():
 artist.set_clip_path(poly)

 ax.add_patch(poly)
 ax.set_aspect('equal')
 ax.axis('off')
 plt.show()


 Also, I appreciated the cartopy example. I think it has the potential to
 be a good basemap replacement thanks to the more robust shapefile support
 (which you have very elegantly shown), and I hope the development goes well.

 Thanks,
 Alex


 On Mon, Sep 2, 2013 at 2:33 AM, Phil Elson pelson@gmail.com wrote:

 Great question. The contour set itself does not have a set_clip_path
 method but you can iterate over each of the contour collections and set
 their respective clip paths, i.e.:

 cs = plt.contourf(data)
 for collection in cs.collections:
 collection.set_clip_path(poly)

 Of course, you can use this approach in either Basemap or cartopy, but
 I've put together an example of doing it in cartopy to demonstrate the neat
 Shapely integration: http://nbviewer.ipython.org/6410510

 HTH,

 Phil


 On 2 September 2013 05:40, Alex Goodman alex.good...@colostate.eduwrote:

 Hi all,

 I want to be able to plot data on maps (using basemap or cartopy) inside
 specific regions, eg a single state, province or country. A similar
 question was asked a long time ago on the mailing list and the suggested
 solution back then was to read the bounding polygon from a shapefile and
 then check if each individual point was inside that polygon. Currently I
 have no problem doing this if I use matplotlib.path.Path.contains_points()
 to mask the original data array, but the disadvantage to this solution is
 that it is very slow. Another solution that I have discovered recently is
 to use the set_clip_path() method for artists. In addition to being much
 faster, this also makes the areas near the polygon boundary look much
 smoother since the actual items being clipped are individual pixels and not
 data points.

 Here is an example script that plots an image via imshow, but the only
 part of the image that gets shown is inside the hexagon.

 import numpy as np
 import matplotlib.pyplot as plt
 from matplotlib.patches import RegularPolygon

 data = np.arange(100).reshape(10, 10)
 fig = plt.figure()
 ax = fig.add_subplot(111)
 im = ax.imshow(data)
 poly = RegularPolygon([ 0.5,  0.5], 6, 0.4, fc='none',
   ec='k', transform=ax.transAxes)
 im.set_clip_path(poly)
 ax.add_patch(poly)
 ax.axis('off')
 plt.show()

 While this does seem like an ideal solution, it doesn't work for every
 type of plot. The most notable example is contourf(). It returns a
 QuadContourSet instance which does not inherit from Artist, so it does not
 contain the set_clip_path() method. My main question is whether there is a
 mechanism in matplotlib that can convert something like a QuadContourSet
 into an image so I can make use of this solution for contourf() as well. Or
 better yet, is there perhaps another artist within the axes that I can use
 the set_clip_path() method for and still get what I want?

 Thanks,
 Alex
 --
 Alex Goodman
 Graduate Research Assistant
 Department of Atmospheric Science
 Colorado State University


 --
 Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
 Discover

Re: [Matplotlib-users] Clipping a plot inside a polygon

[Alex Goodman]

Actually, sorry for the triple post, but is there a reason why we can't do
something like pass in the keyword arguments directly from the call to
contourf when instantiating each collection? Then the keyword arguments for
contourf (and ContourSet) could be used for the collections directly,
including clip_path. I know a similar approach is taken for the keyword
arguments in plot, since those can be used to modify the properties of each
Line2D instance.

Thanks,
Alex


On Mon, Sep 2, 2013 at 1:09 PM, Alex Goodman alex.good...@colostate.eduwrote:

 Actually, it seems I have partially answered my own question. Since I am
 calling axis('off'), I do not notice the effect of clipping the other
 artists since I made a call to axis('off'). Without it the spines and axes
 rectangle are still removed but the ticks are still visible. I suppose this
 is fine for my own purposes of contouring within one country on a map since
 I would want to use something like axis('off') anyway, but then it would
 not work if I wanted to use the axes background. Another approach I have
 tried is to use the clip_path keyword in the plotting functions themselves,
 which works for imshow and pcolor, but not contourf. Any other ideas?

 Alex


 On Mon, Sep 2, 2013 at 12:18 PM, Alex Goodman 
 alex.good...@colostate.eduwrote:

 Hi Phil,

 Thanks, that is more or less what I was looking for. However, I still
 think that generalizing this approach for other types of plotting functions
 that don't return artists directly would be useful. Your solution gave me
 another idea for doing this, which would be to iterate through all of the
 child artists on the axes using the get_children() method and then calling
 set_clip_path() on each artist. This would make the methodology very
 general but I am not sure if there are any negative side effects to
 resetting the clip path on the other artists besides the PatchCollections.
 I modified my simple example script and it seems to work well for
 contourf(), pcolor(), and imshow():

 import numpy as np
 import matplotlib.pyplot as plt
 from matplotlib.patches import RegularPolygon

 data = np.arange(100).reshape(10, 10)
 fig = plt.figure()
 ax = fig.add_subplot(111)
 ax.contourf(data)
 poly = RegularPolygon([ 0.5,  0.5], 6, 0.4, fc='none',
 ec='k', transform=ax.transAxes)
 for artist in ax.get_children():
 artist.set_clip_path(poly)

 ax.add_patch(poly)
 ax.set_aspect('equal')
 ax.axis('off')
 plt.show()


 Also, I appreciated the cartopy example. I think it has the potential to
 be a good basemap replacement thanks to the more robust shapefile support
 (which you have very elegantly shown), and I hope the development goes well.

 Thanks,
 Alex


 On Mon, Sep 2, 2013 at 2:33 AM, Phil Elson pelson@gmail.com wrote:

 Great question. The contour set itself does not have a set_clip_path
 method but you can iterate over each of the contour collections and set
 their respective clip paths, i.e.:

 cs = plt.contourf(data)
 for collection in cs.collections:
 collection.set_clip_path(poly)

 Of course, you can use this approach in either Basemap or cartopy, but
 I've put together an example of doing it in cartopy to demonstrate the neat
 Shapely integration: http://nbviewer.ipython.org/6410510

 HTH,

 Phil


 On 2 September 2013 05:40, Alex Goodman alex.good...@colostate.eduwrote:

 Hi all,

 I want to be able to plot data on maps (using basemap or cartopy)
 inside specific regions, eg a single state, province or country. A similar
 question was asked a long time ago on the mailing list and the suggested
 solution back then was to read the bounding polygon from a shapefile and
 then check if each individual point was inside that polygon. Currently I
 have no problem doing this if I use matplotlib.path.Path.contains_points()
 to mask the original data array, but the disadvantage to this solution is
 that it is very slow. Another solution that I have discovered recently is
 to use the set_clip_path() method for artists. In addition to being much
 faster, this also makes the areas near the polygon boundary look much
 smoother since the actual items being clipped are individual pixels and not
 data points.

 Here is an example script that plots an image via imshow, but the only
 part of the image that gets shown is inside the hexagon.

 import numpy as np
 import matplotlib.pyplot as plt
 from matplotlib.patches import RegularPolygon

 data = np.arange(100).reshape(10, 10)
 fig = plt.figure()
 ax = fig.add_subplot(111)
 im = ax.imshow(data)
 poly = RegularPolygon([ 0.5,  0.5], 6, 0.4, fc='none',
   ec='k', transform=ax.transAxes)
 im.set_clip_path(poly)
 ax.add_patch(poly)
 ax.axis('off')
 plt.show()

 While this does seem like an ideal solution, it doesn't work for every
 type of plot. The most notable example is contourf(). It returns a
 QuadContourSet instance which does not inherit from Artist, so it does not
 contain the set_clip_path() method. My main question is whether there is a
 mechanism

[Matplotlib-users] Clipping a plot inside a polygon

[Alex Goodman]

Hi all,

I want to be able to plot data on maps (using basemap or cartopy) inside
specific regions, eg a single state, province or country. A similar
question was asked a long time ago on the mailing list and the suggested
solution back then was to read the bounding polygon from a shapefile and
then check if each individual point was inside that polygon. Currently I
have no problem doing this if I use matplotlib.path.Path.contains_points()
to mask the original data array, but the disadvantage to this solution is
that it is very slow. Another solution that I have discovered recently is
to use the set_clip_path() method for artists. In addition to being much
faster, this also makes the areas near the polygon boundary look much
smoother since the actual items being clipped are individual pixels and not
data points.

Here is an example script that plots an image via imshow, but the only part
of the image that gets shown is inside the hexagon.

import numpy as np
import matplotlib.pyplot as plt
from matplotlib.patches import RegularPolygon

data = np.arange(100).reshape(10, 10)
fig = plt.figure()
ax = fig.add_subplot(111)
im = ax.imshow(data)
poly = RegularPolygon([ 0.5,  0.5], 6, 0.4, fc='none',
  ec='k', transform=ax.transAxes)
im.set_clip_path(poly)
ax.add_patch(poly)
ax.axis('off')
plt.show()

While this does seem like an ideal solution, it doesn't work for every type
of plot. The most notable example is contourf(). It returns a
QuadContourSet instance which does not inherit from Artist, so it does not
contain the set_clip_path() method. My main question is whether there is a
mechanism in matplotlib that can convert something like a QuadContourSet
into an image so I can make use of this solution for contourf() as well. Or
better yet, is there perhaps another artist within the axes that I can use
the set_clip_path() method for and still get what I want?

Thanks,
Alex
-- 
Alex Goodman
Graduate Research Assistant
Department of Atmospheric Science
Colorado State University
attachment: clip_example.png--
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Re: [Matplotlib-users] subplots [xy]labels

[Alex Goodman]

Hi Giacomo,

Try using the set_ylabel() and set_xlabel() methods for each Axes instance
instead, eg:

a[0].set_ylabel('f1')
a[0].set_xlabel('t')

a[1].set_ylabel('f2')
a[1].set_xlabel('t')


On Fri, Jan 4, 2013 at 5:44 AM, giacomo.bo...@polimi.it wrote:

 two plots in a figure:
 
 from pylab import *
 ...
 f,a = subplots(nrows=2, sharex=False, sharey=False)
 a[0].plot(x,f0(x))
 ylabel('f1')
 xlabel('t')
 ...
 a[1].plot(x,f1(x))
 ylabel('f2')
 xlabel('t')
 ...
 show()
 
 but all i can get are labels for ONLY the lower subplot, what shoud I do?

 any help will be appreciated

 tia
 gb



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[Matplotlib-users] ANN: pythonpackages.com beta

[Alex Clark]

Hi matplotlib folks,


I am reaching out to various Python-related programming communities in 
order to offer my help packaging your software.

If you have ever struggled with packaging and releasing Python software 
(e.g. to PyPI), please check out my new service:


- http://pythonpackages.com


The basic idea is to automate packaging by checking out code, testing, 
and uploading (e.g. to PyPI) all through the web, as explained in this 
introduction:


- http://docs.pythonpackages.com/en/latest/introduction.html


Also, I will be available to answer your Python packaging questions most 
days/nights in #pythonpackages on irc.freenode.net. Hope to meet/talk 
with all of you soon.



Alex



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Re: [Matplotlib-users] Plot Fill with Jacobian Coordinates

[Alex Naysmith]

On Thu, Dec 15, 2011 at 9:32 PM, Benjamin Root ben.r...@ou.edu wrote:


 On Thu, Dec 15, 2011 at 3:18 PM, Alex Naysmith yeoman.pyt...@gmail.comwrote:



 On Tue, Dec 13, 2011 at 7:12 PM, Alex Naysmith 
 yeoman.pyt...@gmail.comwrote:



 On Mon, Dec 12, 2011 at 7:03 PM, Benjamin Root ben.r...@ou.edu wrote:

 On Sat, Dec 10, 2011 at 10:36 AM, Alex Naysmith 
 yeoman.pyt...@gmail.com wrote:

 Hello,

 I'm trying to plot the stresses in colour of a strained isoparametric
 element.

 I have a six noded triangle with vertice coordinates
 [(xa1,ya1),(xa2,ya2),(xa3,ya3)] = pos_a

 This triangle deforms and the new coordinate positions are
 [(xb1,yb1),(xa2,yb2),(xb3,yb3)] = pos_b

 The remaining nodes are mid nodes also with rest and deformed
 coordinate positions.

 To plot the edges of the triangle I use a Jacobian transformation
 function so that the coordinates of the triangle are in Jacobian
 coordinates xi1 and xi2 (with xi3 = 1 - xi1 - xi2). This is required as 
 the
 elements are quadratic with mid-nodes.

 Each interval is hard coded so that:
 xi1 = [1.0,0.9,0.8,0.7,0.6,0.5, etc..]
 xi2 = [0.0,0.1,0.2,0.3,0.4,0.5, etc..]

 I would like to plot the strains in colour so that the interior of the
 triangle is filled but I don't want to hard code the Jacobian intervals as
 this seems an awkward way of doing it.

 With strain as a function of xi1 and xi2, How can matplotlib provide a
 continuous interior strain plot of the triangle for all the xi1 and xi2
 values from 0 to 1?

 Regards

 Alex Naysmith


 Alex,

 Perhaps if you can provide an example figure, we might be able to
 better help you.  Right now, I am having trouble envisioning what you
 describe.

 Ben Root

 Ben,

 I have created a script that uses one isoparametric triangle as an
 example. The triangle nodes undergo a displacement, resulting in strains
 inside the triangle. The new script calculates the strains inside the
 triangle for a range of xi1 and xi2 barycentric coordinates and returns the
 global coordinates with the corresponding strain.

 I would like matplotlib to give me a nice interpolated colour plot of
 the strains inside the triangle, but as the output global coordinates are
 not aligned in neat rows and columns, I cannot do a straightforward
 meshgrid plot with imshow.

 http://bazaar.launchpad.net/~eckeroo/misc/mpl_scripts/files

 There are further comments in the script that may explain things better.

 I want a figure like this:

 http://matplotlib.sourceforge.net/examples/pylab_examples/animation_demo.html
 But for a 6 noded quadratic triangle instead of square. The intention is
 to have all the triangles in the mesh display their strains with
 interpolated colours.

 Regards

 Alex


 Hello,

 I tried using contour and now I have a figure!


 http://bazaar.launchpad.net/~eckeroo/misc/mpl_scripts/view/head:/figure.png

 I can now show clearly what I'm aiming for with this figure. I want the
 contour fill to remain inside the triangle. There will be a whole mesh of
 triangles to fill.

 The updated sample script is here:


 http://bazaar.launchpad.net/~eckeroo/misc/mpl_scripts/view/head:/triangle_fill_v2.py

 I arranged my data points into square X and Y arrays along with the
 strains in the Z array and then simply P.contourf(X, Y, Z)

 As the figure shows, it's not there yet as a couple of the corners aren't
 filled in and there's a big fill outside the triangle. I think this is due
 to difficulties in translating points from the natural triangle coordinates
 (barycentric) to the x,y coordinates. But the contour looks correct as it's
 interpolated between the strain points.

 Regards

 Alex


 Alex,

 Just curious, have you checked to see if tricontourf() meets your needs?


 http://matplotlib.sourceforge.net/api/axes_api.html?highlight=tricontourf#matplotlib.axes.Axes.tricontourf

 Ben Root

 Ben,

I've now succeeded in producing the plot I want using just contour(X,Y,Z):

http://bazaar.launchpad.net/~eckeroo/misc/mpl_scripts/view/head:/figure2.png

The script used to produce figure2 is here:

http://bazaar.launchpad.net/~eckeroo/misc/mpl_scripts/view/head:/triangle_fill_v3.py

For the X,Y and Z arrays, the upper triangle repeats the same data point.
This doesn't seem to be a problem for the contour(X,Y,Z) function.

The tricontourf() approach may be better, but it involves creating a
triangle mesh inside each element.

The next step will be to plot the strain contours for all the elements in
the mesh.

Regards

Alex Naysmith
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Re: [Matplotlib-users] Plot Fill with Jacobian Coordinates

[Alex Naysmith]

On Tue, Dec 13, 2011 at 7:12 PM, Alex Naysmith yeoman.pyt...@gmail.comwrote:



 On Mon, Dec 12, 2011 at 7:03 PM, Benjamin Root ben.r...@ou.edu wrote:

 On Sat, Dec 10, 2011 at 10:36 AM, Alex Naysmith 
 yeoman.pyt...@gmail.comwrote:

 Hello,

 I'm trying to plot the stresses in colour of a strained isoparametric
 element.

 I have a six noded triangle with vertice coordinates
 [(xa1,ya1),(xa2,ya2),(xa3,ya3)] = pos_a

 This triangle deforms and the new coordinate positions are
 [(xb1,yb1),(xa2,yb2),(xb3,yb3)] = pos_b

 The remaining nodes are mid nodes also with rest and deformed coordinate
 positions.

 To plot the edges of the triangle I use a Jacobian transformation
 function so that the coordinates of the triangle are in Jacobian
 coordinates xi1 and xi2 (with xi3 = 1 - xi1 - xi2). This is required as the
 elements are quadratic with mid-nodes.

 Each interval is hard coded so that:
 xi1 = [1.0,0.9,0.8,0.7,0.6,0.5, etc..]
 xi2 = [0.0,0.1,0.2,0.3,0.4,0.5, etc..]

 I would like to plot the strains in colour so that the interior of the
 triangle is filled but I don't want to hard code the Jacobian intervals as
 this seems an awkward way of doing it.

 With strain as a function of xi1 and xi2, How can matplotlib provide a
 continuous interior strain plot of the triangle for all the xi1 and xi2
 values from 0 to 1?

 Regards

 Alex Naysmith


 Alex,

 Perhaps if you can provide an example figure, we might be able to better
 help you.  Right now, I am having trouble envisioning what you describe.

 Ben Root

 Ben,

 I have created a script that uses one isoparametric triangle as an
 example. The triangle nodes undergo a displacement, resulting in strains
 inside the triangle. The new script calculates the strains inside the
 triangle for a range of xi1 and xi2 barycentric coordinates and returns the
 global coordinates with the corresponding strain.

 I would like matplotlib to give me a nice interpolated colour plot of the
 strains inside the triangle, but as the output global coordinates are not
 aligned in neat rows and columns, I cannot do a straightforward meshgrid
 plot with imshow.

 http://bazaar.launchpad.net/~eckeroo/misc/mpl_scripts/files

 There are further comments in the script that may explain things better.

 I want a figure like this:

 http://matplotlib.sourceforge.net/examples/pylab_examples/animation_demo.html
 But for a 6 noded quadratic triangle instead of square. The intention is
 to have all the triangles in the mesh display their strains with
 interpolated colours.

 Regards

 Alex


Hello,

I tried using contour and now I have a figure!

 http://bazaar.launchpad.net/~eckeroo/misc/mpl_scripts/view/head:/figure.png

I can now show clearly what I'm aiming for with this figure. I want the
contour fill to remain inside the triangle. There will be a whole mesh of
triangles to fill.

The updated sample script is here:

http://bazaar.launchpad.net/~eckeroo/misc/mpl_scripts/view/head:/triangle_fill_v2.py

I arranged my data points into square X and Y arrays along with the strains
in the Z array and then simply P.contourf(X, Y, Z)

As the figure shows, it's not there yet as a couple of the corners aren't
filled in and there's a big fill outside the triangle. I think this is due
to difficulties in translating points from the natural triangle coordinates
(barycentric) to the x,y coordinates. But the contour looks correct as it's
interpolated between the strain points.

Regards

Alex
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Re: [Matplotlib-users] Plot Fill with Jacobian Coordinates

[Alex Naysmith]

On Mon, Dec 12, 2011 at 7:03 PM, Benjamin Root ben.r...@ou.edu wrote:

 On Sat, Dec 10, 2011 at 10:36 AM, Alex Naysmith 
 yeoman.pyt...@gmail.comwrote:

 Hello,

 I'm trying to plot the stresses in colour of a strained isoparametric
 element.

 I have a six noded triangle with vertice coordinates
 [(xa1,ya1),(xa2,ya2),(xa3,ya3)] = pos_a

 This triangle deforms and the new coordinate positions are
 [(xb1,yb1),(xa2,yb2),(xb3,yb3)] = pos_b

 The remaining nodes are mid nodes also with rest and deformed coordinate
 positions.

 To plot the edges of the triangle I use a Jacobian transformation
 function so that the coordinates of the triangle are in Jacobian
 coordinates xi1 and xi2 (with xi3 = 1 - xi1 - xi2). This is required as the
 elements are quadratic with mid-nodes.

 Each interval is hard coded so that:
 xi1 = [1.0,0.9,0.8,0.7,0.6,0.5, etc..]
 xi2 = [0.0,0.1,0.2,0.3,0.4,0.5, etc..]

 I would like to plot the strains in colour so that the interior of the
 triangle is filled but I don't want to hard code the Jacobian intervals as
 this seems an awkward way of doing it.

 With strain as a function of xi1 and xi2, How can matplotlib provide a
 continuous interior strain plot of the triangle for all the xi1 and xi2
 values from 0 to 1?

 Regards

 Alex Naysmith


 Alex,

 Perhaps if you can provide an example figure, we might be able to better
 help you.  Right now, I am having trouble envisioning what you describe.

 Ben Root

 Ben,

I have created a script that uses one isoparametric triangle as an example.
The triangle nodes undergo a displacement, resulting in strains inside the
triangle. The new script calculates the strains inside the triangle for a
range of xi1 and xi2 barycentric coordinates and returns the global
coordinates with the corresponding strain.

I would like matplotlib to give me a nice interpolated colour plot of the
strains inside the triangle, but as the output global coordinates are not
aligned in neat rows and columns, I cannot do a straightforward meshgrid
plot with imshow.

http://bazaar.launchpad.net/~eckeroo/misc/mpl_scripts/files

There are further comments in the script that may explain things better.

I want a figure like this:
http://matplotlib.sourceforge.net/examples/pylab_examples/animation_demo.html
But for a 6 noded quadratic triangle instead of square. The intention is to
have all the triangles in the mesh display their strains with interpolated
colours.

Regards

Alex
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[Matplotlib-users] Plot Fill with Jacobian Coordinates

[Alex Naysmith]

Hello,

I'm trying to plot the stresses in colour of a strained isoparametric
element.

I have a six noded triangle with vertice coordinates
[(xa1,ya1),(xa2,ya2),(xa3,ya3)] = pos_a

This triangle deforms and the new coordinate positions are
[(xb1,yb1),(xa2,yb2),(xb3,yb3)] = pos_b

The remaining nodes are mid nodes also with rest and deformed coordinate
positions.

To plot the edges of the triangle I use a Jacobian transformation function
so that the coordinates of the triangle are in Jacobian coordinates xi1 and
xi2 (with xi3 = 1 - xi1 - xi2). This is required as the elements are
quadratic with mid-nodes.

Each interval is hard coded so that:
xi1 = [1.0,0.9,0.8,0.7,0.6,0.5, etc..]
xi2 = [0.0,0.1,0.2,0.3,0.4,0.5, etc..]

I would like to plot the strains in colour so that the interior of the
triangle is filled but I don't want to hard code the Jacobian intervals as
this seems an awkward way of doing it.

With strain as a function of xi1 and xi2, How can matplotlib provide a
continuous interior strain plot of the triangle for all the xi1 and xi2
values from 0 to 1?

Regards

Alex Naysmith

My finite element program can be downloaded from here:
http://www.pynw.org.uk/Talks?action=AttachFiledo=viewtarget=2D_FEA.zip
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[Matplotlib-users] saving PdfPages figure before closing

[Alex Flint]

I'm using the approach described the FAQ to save multiple figures to a
multi-page PDF:
http://matplotlib.sourceforge.net/faq/howto_faq.html#save-multiple-plots-to-one-pdf-file

The figures are produced at consecutive iterations of my algorithm, and
since each iteration takes a long time I'd like to save the PDF containing
the current figures at each iteration so that I can take a look. However, it
seems that I can only cause the PDF to be written to disk by calling
PdfPages.close(), after which I can't add any more figures. Is there any way
I can write a PdfPages object to file, then add more figures and write it to
file again later?

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Re: [Matplotlib-users] adding a subplot

[Alex Flint]

I'm using 0.99.3, which is from the ubuntu maverick repos.

This comes up mostly when I'm drawing plots interactively from ipython.

Cheers,
Alex



On Tue, Jun 28, 2011 at 10:44 AM, Benjamin Root ben.r...@ou.edu wrote:



 On Mon, Jun 27, 2011 at 5:09 PM, Alex Flint alex.fl...@gmail.com wrote:

 Hi there,

 I'm wondering whether there is an easy way to append an additional subplot
 to an existing figure without losing the subplots already drawn.

 Currently if I do something like
  subplot(211); plot(...); subplot(212); plot(...);

 Then I get inconsistent drawing results if I try something like:
  subplot(313); plot(...);

  Cheers,
 Alex


 Yes, it is possible, but it can be messy to do so.  Also, which version
 of matplotlib are you using?  Is there a particular reason why you don't
 know the number of plots ahead of time?

 Ben Root


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[Matplotlib-users] adding a subplot

[Alex Flint]

Hi there,

I'm wondering whether there is an easy way to append an additional subplot
to an existing figure without losing the subplots already drawn.

Currently if I do something like
 subplot(211); plot(...); subplot(212); plot(...);

Then I get inconsistent drawing results if I try something like:
 subplot(313); plot(...);

Cheers,
Alex
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[Matplotlib-users] matplotlibrc for [ieee] publications

[alex arsenovic]

 i was wondering if anyone had considered making a matplotlibrc which
generates plots suitable for ieee publications (specifically ieee
transactions)? 

or any other publications for that matter. like a set of matching
matplotlibrc's to journals (or some other way to achieve a similar
functionality)

if not, i think it would be a valuable thing to make, because it wouldnt
be very hard, and would save a lot of users time/effort. specifically it
would specify the dimension/dpi/font type/sizes/etc.  i have a
preliminary one for ieee we can use as a starting point, that can be
improved.


thanks 
alex 



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[Matplotlib-users] matplotlibrc for ieee publications

[alex arsenovic]

 i was wondering if anyone had considered making a matplotlibrc which
generates plots suitable for ieee publications (specifically ieee
transactions)? 

or any other publications for that matter. like a set of matching
matplotlibrc's to journals. 

if not, i think it would be a valuable thing to make, because it wouldnt
be very hard, and would save a lot of users time/effort. specifically it
would specify the dimension/dpi/font sizes/etc.  i have a preliminary
one  we can use as a starting point, that can be improved.


thanks 
alex 




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Re: [Matplotlib-users] Re : matplotlibrc for [ieee] publications

[alex arsenovic]

i like the module-based idea. its a bit overkill for the functionality
needed, but the concise call makes it very convenient. also,
installation and updating would be easy through pip/easy_install.

should i start a google-code project? or does someone have a preferred
way to start this?


alex



On Fri, 2011-04-15 at 14:09 -0400, Tony Yu wrote:
 
 
 On Fri, Apr 15, 2011 at 8:36 AM, Auré Gourrier
 aurelien.gourr...@yahoo.fr wrote:
 Good Idea !
 I'm also using mpl for other publications than ieee and it
 sounds like a small mplrc data base with targeted journal
 specifications would be worthwhile doing ! I would be ready to
 contribute.
 Cheers,
 Auré
 
 
 
 
 Is there any reason this needs to done with rc files? I prefer to put
 document-specific configuration into modules. For example, you could
 have a module that looks like:
 
 mplrc/
 __init__.py
 aps_fullpage.py
 aps_twocolumn.py
 ieee.py
 ...
 
 (`aps` could even be directory). And each module would set rc
 parameters using function calls; for example, aps_twocolumn.py might
 look like:
 
 import matplotlib.pyplot as plt
 plt.rc('axes', labelsize=10)
 plt.rc('text', fontsize=10)
 plt.rc('legend', fontsize=10)
 plt.rc('xtick', labelsize=8)
 plt.rc('ytick', labelsize=8)
 plt.rc('text', usetex=False)
 plt.rc('figure', figsize=(3.4039, 2.1037))
 
 (Alternatively, you could create a separate rc file and just have the
 module load that rc file). The advantage of this module-based approach
 is that you could simply import the module whenever you need it (e.g.,
 just add `import mplrc.aps_twocolumn` at the top of your script). If I
 used an rc file instead, I'd have to copy the rc file to my working
 directory each time, or somehow, manually load the rc file from a
 path.
 
 Just a suggestion.
 
 -Tony
 



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Re: [Matplotlib-users] Bug in `dviread.py'

[Alex]

On 07.02.2011 17:17, Jouni K. Seppänen wrote:
 Jouni Seppänenj...@iki.fi  writes:

 I filed this in the bug tracker: 
 https://sourceforge.net/tracker/?func=detailaid=3175113group_id=80706atid=560720

 I installed TeX Live 2010 on my Mac in order to test this, but
 mysteriously, the pdftex.map file does not have a line for pbkdo8y. The
 closest match is

 pbkdo8r URWBookmanL-DemiBold .167 SlantFont TeXBase1Encoding 
 ReEncodeFont8r.encubkd8a.pfb

 which is the same font but with another encoding. I wonder if this
 indicates a problem in the way Ubuntu sets up TeX Live?


Hi Jouni,

currently Ubuntu still uses Texlive 2009. I also got the same bug 
(http://article.gmane.org/gmane.comp.python.matplotlib.general/26110) 
with Texlive 2010 installed directly from tug.org.
I think it is unlikely that this is an Ubuntu specific problem, but I 
don't know for sure whether this file gets generated during the 
installation or is unmodified from the Texlive distribution.

Greetings
Alexander

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[Matplotlib-users] Bug in dviread?

[Alex]

Hello to all,

using a standard python install on Ubuntu 10.04 the example fails to 
produce a figure.

Python 2.6.5 (r265:79063, Apr 16 2010, 13:09:56)
[GCC 4.4.3] on linux2
Type help, copyright, credits or license for more information.
 import matplotlib
 matplotlib.__version__
'0.99.1.1'

Test case in python:

from numpy import sin, cos

import matplotlib
import matplotlib.pyplot as plt
plt.matplotlib.rc('text', usetex = True)
import pylab
fig = plt.figure()
ax = fig.add_subplot(111)
t = pylab.linspace(0,10,400)
ax.plot(t, sin(3*t), '-',
  t, sin(0.3*t**2), '--',
  t, cos(t), '-.')
ax.legend((r'$A^{\omega}$', r'$A^{2\omega}$', r'$A^{3\omega}$'),
  shadow = False, loc = (0.75, 0.1))
ax.set_xlabel(r'$\gamma_1 + \gamma_2$', {'fontsize'   : 20 })
ax.set_ylabel(r'$A^{n\omega}$ (dB)', {'fontsize'   : 20 })

fig.savefig(filename='test.pdf')

This leads to the following traceback:

Traceback (most recent call last):
   File test.py, line 18, in module
 fig.savefig(filename='test.pdf')
   File /usr/lib/pymodules/python2.6/matplotlib/figure.py, line 1032, 
in savefig
 self.canvas.print_figure(*args, **kwargs)
   File /usr/lib/pymodules/python2.6/matplotlib/backend_bases.py, line 
1476, in print_figure
 **kwargs)
   File /usr/lib/pymodules/python2.6/matplotlib/backend_bases.py, line 
1334, in print_pdf
 return pdf.print_pdf(*args, **kwargs)
   File 
/usr/lib/pymodules/python2.6/matplotlib/backends/backend_pdf.py, line 
2025, in print_pdf
 self.figure.draw(renderer)
   File /usr/lib/pymodules/python2.6/matplotlib/artist.py, line 46, in 
draw_wrapper
 draw(artist, renderer, *kl)
   File /usr/lib/pymodules/python2.6/matplotlib/figure.py, line 773, 
in draw
 for a in self.axes: a.draw(renderer)
   File /usr/lib/pymodules/python2.6/matplotlib/artist.py, line 46, in 
draw_wrapper
 draw(artist, renderer, *kl)
   File /usr/lib/pymodules/python2.6/matplotlib/axes.py, line 1735, in 
draw
 a.draw(renderer)
   File /usr/lib/pymodules/python2.6/matplotlib/artist.py, line 46, in 
draw_wrapper
 draw(artist, renderer, *kl)
   File /usr/lib/pymodules/python2.6/matplotlib/axis.py, line 742, in draw
 tick.draw(renderer)
   File /usr/lib/pymodules/python2.6/matplotlib/artist.py, line 46, in 
draw_wrapper
 draw(artist, renderer, *kl)
   File /usr/lib/pymodules/python2.6/matplotlib/axis.py, line 196, in draw
 self.label1.draw(renderer)
   File /usr/lib/pymodules/python2.6/matplotlib/text.py, line 553, in draw
 self._fontproperties, angle)
   File 
/usr/lib/pymodules/python2.6/matplotlib/backends/backend_pdf.py, line 
1431, in draw_tex
 psfont = self.tex_font_mapping(dvifont.texname)
   File 
/usr/lib/pymodules/python2.6/matplotlib/backends/backend_pdf.py, line 
1264, in tex_font_mapping
 dviread.PsfontsMap(dviread.find_tex_file('pdftex.map'))
   File /usr/lib/pymodules/python2.6/matplotlib/dviread.py, line 668, 
in __init__
 self._parse(file)
   File /usr/lib/pymodules/python2.6/matplotlib/dviread.py, line 701, 
in _parse
 self._register(words)
   File /usr/lib/pymodules/python2.6/matplotlib/dviread.py, line 727, 
in _register
 assert encoding is None
AssertionError

I assume that the errors happens during parsing of the file 8r.enc 
(http://tug.org/fontname/8r.enc). This file belongs to TexLive 2010 and 
can also be found identically in MikTeX 2.9. I could only reproduce the 
error in Linux so far. Any help would be appreciated.

Alexander

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[Matplotlib-users] (no subject)

[Alex Liberzon]

Hi,

While moving from Matlab to Numpy/Scipy/Matplotlib I need sometimes to work 
with Matlab figures. It would be nice if we could load Matlab figures in 
Python, extract the data and some basic parameters of how it was looking in 
Matlab and create its clone in matplotlib. At present the Matlab figures are 
MAT files and in the near future it will be HDF5, both formats are loadable. 
However, I have not found any reference for such attempts to load and parse the 
FIG files. As a beginner I find it difficult to write a large piece of code. 
However, if there are other  interested users that can cooperate on such, I'd 
gladly contribute some hours for this task. Meanwhile, to show the 
proof-of-concept attempt is attached below. All your useful comments and 
suggestions are very welcome. 

Thank you,
Alex 

# loadfig.py -- #
 Loadfig loads simple Matlab figures as MAT files and plots the lines using 
matplotlib


import numpy as np
from scipy.io import loadmat
import matplotlib.pyplot as plt


def lowest_order(d):
 
lowestsc_order(hgstruct) finds the handle of axes (i.e. children of 
figure handles, etc.)


while not 'graph2d.lineseries' in d['type']:
d = d['children'][0][0]
return d

def get_data(d):
 
get_data(hgstruct) extracts XData, YData, Color and Marker of each line 
in the 
given axis

Parameters
--
hgstruct : structure 
obtained from lowest_order(loadmat('matlab.fig'))


xd,yd,dispname,marker,colors = [],[],[],[],[]
for i in d:
if i['type'] == 'graph2d.lineseries':
xd.append(i['properties'][0][0]['XData'][0][0])
yd.append(i['properties'][0][0]['YData'][0][0])

dispname.append(i['properties'][0][0]['DisplayName'][0][0])
marker.append(i['properties'][0][0]['Marker'][0][0])
colors.append(i['properties'][0][0]['Color'][0][0])

return 
np.asarray(xd),np.asarray(yd),dispname,np.asarray(marker).astype('S1'),colors


def plot_data(xd,yd,dispname=None,marker=None,colors=None):

plot_data(xd,yd,dispname=None,marker=None,colors=None)

plots the data sets extracted by 
get_data(lowest_order(loadmat('matlab.fig')))  

Parameters
--
xd,yd : array_like
data arrays 
dispname : array of strings 
to be used in legend, optional
marker : array of characters
markers, e.g. ['o','x'], optional
colors : array of color sets 
in RGB, e.g. [[0,0,1],[1,0,0]], optional



for i,n in enumerate(xd):

plt.plot(xd[i].T,yd[i].T,color=tuple(colors[i]),marker=marker[i],linewidth=0)

plt.legend(dispname)
plt.show()

def main(filename):

main(filename) 

loads the filename (with the extension .fig) which is Matlab figure. At 
the moment only
simple 2D lines are supported. 

Examples
---
 loadfig('matlab.fig') # is equivalent to:

 d = loadmat(filename)
 d = d['hgS_07']
 xd,yd,dispname,marker,colors = get_data(lowest_order(d))
 plot_data(xd,yd,dispname,marker,colors)


d = loadmat(filename)
# ver 7.2 or lower:
d = d['hgS_07']
xd,yd,dispname,marker,colors = get_data(lowest_order(d))
plot_data(xd,yd,dispname,marker,colors)


if __name__ == __main__:
import sys
import os
try:
filename = sys.argv[1]
main(filename)
except:
print(Wrong file)
# - EOF loadfig.py --- # 

Alex Liberzon
Turbulence Structure Laboratory [http://www.eng.tau.ac.il/efdl]
School of Mechanical Engineering
Tel Aviv University
Ramat Aviv 69978
Israel
Tel: +972-3-640-8928
Lab: +972-3-640-6860 (telefax)
E-mail: alex...@eng.tau.ac.il





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Re: [Matplotlib-users] Font not carrying through Py2Exe

[Alex S]

Thank you very much for the help, I'm sorry I didn't reply to you.  I ended
up doing what you recommend against, which is I took my fontlist.cache and
copied it to the other computers C:\Documents and
Settings\username\.matplotlib folder.  This worked, maybe because all the
computers here have the same font that for some reason didn't get included
in the fontlist for everyone else.  I know it's not perfect and that if I
tried to get the program to work for anyone outside of work it would
probably crash horribly, but it works now so I think I'll just leave it.

Thank you very much Mike, you might not remember but you were the one that
taught me how to get it into New Century Schoolbook in the first place.  
http://old.nabble.com/Changing-the-font-td28111472.html#a28118916 Here it is
, for old times sake.




Michael Droettboom-3 wrote:
 
 On 01/13/2011 11:38 AM, Alex S wrote:
 Hi there,
 I've made a program that makes plots using New Century Schoolbook Lt Std
 font.  I did this by inserting this into the matplotlibrc file:

 font.family :  New Century Schoolbook LT Std # serif #sans-serif

 There's also a fontlist.cache file that I think points to it when it
 says:

 .
 .
 .
 (dp283
 g12
 g45
 sg14
 S'New Century Schoolbook LT Std'
 p284
 sg16
 I400
 sg17
 g13
 sg18
 .
 .
 .

 This all works fine on my computer.  But I'm trying to make it run on
 other
 people's computers (off a network drive) but when I do the plots all go
 back
 into Ariel font and all the spacing and stuff gets screwed up.  Running
 the
 exact same exe from the same place, my computer continues to make them
 with
 the correct font.  I have copied the matplotlibrc file and the
 fontlist.cache file from my hard drive (C:...Matplotlib) to the mpl-data
 folder in the dist folder (from py2exe) but that didn't work.

 Does anyone have any ideas for fixing this stuff?  I think it might just
 be
 a matter of including the right files in the Py2Exe setup file but I
 don't
 know which ones.  Or maybe changing how I select the font, which was a
 roundabout way of doing it from the start.
 The fontList.cache file maps from the properties (names, weights, 
 slants) etc. of the fonts available on a particular system to their file 
 path.  You should definitely not ship this file with the exe, but rather 
 allow it to be regenerated from scratch on each system, since the 
 selection and locations of fonts is very likely to be different.
 
 I think New Century Schoolbook is one of the fonts that ships with 
 Windows, so you can probably count on it being there.  If not, you need 
 to ship the font as part of the exe by adding it to mpl-data/fonts/ttf 
 and then following the instructions to include the fonts given here:
 
 http://www.py2exe.org/index.cgi/MatPlotLib
When I run the plots
 (successfully on my computer) it says this at one point:

 c:\Python26\lib\site-packages\matplotlib\backends\backend_pdf.py:982:
 UserWarning: 'newcenturyschlbkltstd-roman.otf' can not be subsetted into
 a
 Type 3 font. The entire font will be embedded in the output.

 Maybe that has somethign to do with what's going on?

 I don't think that's related.  All this means is that when it embeds the 
 font into the PDF file, it has to embed the entire thing rather than 
 only the characters that are being used.  (Resulting in a larger PDF 
 file, but otherwise fine.)  To avoid this message, you can set the 
 rcParam pdf.fonttype to 42.
 
 Cheers,
 Mike


 Thanks a lot,
 Alex

 
 
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[Matplotlib-users] Font not carrying through Py2Exe

[Alex S]

Hi there,
I've made a program that makes plots using New Century Schoolbook Lt Std
font.  I did this by inserting this into the matplotlibrc file:

font.family :  New Century Schoolbook LT Std # serif #sans-serif

There's also a fontlist.cache file that I think points to it when it says:

.
.
.
(dp283
g12
g45
sg14
S'New Century Schoolbook LT Std'
p284
sg16
I400
sg17
g13
sg18
.
.
.

This all works fine on my computer.  But I'm trying to make it run on other
people's computers (off a network drive) but when I do the plots all go back
into Ariel font and all the spacing and stuff gets screwed up.  Running the
exact same exe from the same place, my computer continues to make them with
the correct font.  I have copied the matplotlibrc file and the
fontlist.cache file from my hard drive (C:...Matplotlib) to the mpl-data
folder in the dist folder (from py2exe) but that didn't work.  

Does anyone have any ideas for fixing this stuff?  I think it might just be
a matter of including the right files in the Py2Exe setup file but I don't
know which ones.  Or maybe changing how I select the font, which was a
roundabout way of doing it from the start.  When I run the plots
(successfully on my computer) it says this at one point:

c:\Python26\lib\site-packages\matplotlib\backends\backend_pdf.py:982:
UserWarning: 'newcenturyschlbkltstd-roman.otf' can not be subsetted into a
Type 3 font. The entire font will be embedded in the output.

Maybe that has somethign to do with what's going on?



Thanks a lot,
Alex
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[Matplotlib-users] savefig eps error

[alex arsenovic]

today i produced an image that failed to save to eps. 
i can save the file in pdf, but i get the same error if i try to use
pdf2ps. png works too, but its not vector. 

not sure if its important, but the image has 401 lines, with 500 points
each.


the image is produced from a bunch of data files and im not sure how to
most effectively send this over email ( in case you all wanted to
re-produced the error).

the main error is 

Error: /nocurrentpoint in --lineto--

here is the whole error

thanks 
alex


--
In [774]: savefig ('output.eps', format='eps')
GPL Ghostscript 8.70: Unrecoverable error, exit code 1


RuntimeError: ghostscript was not able to process your image.
Here is the full report generated by ghostscript:

GPL Ghostscript 8.70 (2009-07-31)
Copyright (C) 2009 Artifex Software, Inc.  All rights reserved.
This software comes with NO WARRANTY: see the file PUBLIC for details.
Loading CenturySchL-Roma font
from /var/lib/defoma/gs.d/dirs/fonts/c059013l.pfb... 3081280 1718017
6003072 4188814 1 done.
Error: /nocurrentpoint in --lineto--
Operand stack:
   178.896   120.362
Execution stack:
   %interp_exit   .runexec2   --nostringval--   --nostringval--
--nostringval--   2   %stopped_push   --nostringval--   --nostringval--
--nostringval--   false   1   %stopped_push   1862   1   3   %
oparray_pop   1861   1   3   %oparray_pop   1845   1   3   %oparray_pop
1739   1   3   %oparray_pop   --nostringval--   %
errorexec_pop   .runexec2   --nostringval--   --nostringval--
--nostringval--   2   %stopped_push   --nostringval--
Dictionary stack:
   --dict:1154/1684(ro)(G)--   --dict:1/20(G)--   --dict:75/200(L)--
--dict:5/6(ro)(L)--   --dict:178/300(L)--   --dict:44/200(L)--
--dict:7/7(L)--
Current allocation mode is local
Last OS error: 2
Current file position is 34416








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[Matplotlib-users] Not using exponents on y-axis of log graphs

[Alex S]

Hi there,

I've got a program that generates a bunch of plots with logarithmic charts. 
Matplotlib handles them great, but it seems to by default label the y axis
ticks 10^0, 10^1, 10^2 etc.  Is there an way to make it spell out these
numbers instead (ie 1, 10, 100 etc)?  I guess I could make custom ticks for
every one, but the graph is not always the same and if it could do it
automatically it would be much better.

Thanks a lot,
Alex
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Re: [Matplotlib-users] Not using exponents on y-axis of log graphs

[Alex S]

Ah thank you very much, that works fine except for decimals... (.1, .01, .001
etc all show as 0).  Is there a way to show these as well (preferably
without showing all the rest of the numbers as 1.000, 10.000, 100.000)?  
Sorry if this is a very newbie question...  I don't know what symbol does
what on the string formatter, is there a web site somewhere that lays it all
out?  As per usual,  http://matplotlib.sourceforge.net/api/ticker_api.html
the manual  has just confused me...
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Re: [Matplotlib-users] Not using exponents on y-axis of log graphs

[Alex S]

Thanks again to Mike who explained my problems off list.  For other people
trying to do something similar, 
http://docs.python.org/library/stdtypes.html#string-formatting here  is the
page describing python string formats, and the format i was looking for to
show decimals was '%g' (rather than '%d' which was for integers and so
truncated decimals). 

Thanks guys,
Alex


Alex S wrote:
 
 Ah thank you very much, that works fine except for decimals... (.1, .01,
 .001 etc all show as 0).  Is there a way to show these as well (preferably
 without showing all the rest of the numbers as 1.000, 10.000, 100.000)?  
 Sorry if this is a very newbie question...  I don't know what symbol does
 what on the string formatter, is there a web site somewhere that lays it
 all out?  As per usual, 
 http://matplotlib.sourceforge.net/api/ticker_api.html the manual  has just
 confused me...
 

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Re: [Matplotlib-users] Changing the font

[Alex S]

I think I'm using MPL .99.1 (is there a command to check?) on Windows XP. 
Thanks for the debug tip, I don't think posting the whole thing is necessary
because this line seems to be the problem:

findfont: Could not match
:family=serif:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0.
Returning
C:\Python26\lib\site-packages\matplotlib\mpl-data\fonts\ttf\Vera.ttf

So I guess the font's missing from the folder.  Can I add it somehow?



Michael Droettboom-3 wrote:
 
 Can you set verbose.level to debug-annoying in your matplotlibrc 
 file, and then send the output to this list.  That may help us track 
 down where the font lookup is failing.  Also, what platform and version 
 of matplotlib are you running?
 
 Mike
 
 Alex S wrote:
 Hi, sorry I wasn't too clear... I changed that, but I don't seem to be
 able
 to choose between the different serif fonts, it just always gives me the
 default...



 Alex S wrote:
   
 Hi there,
 I'm trying to change the font default on my graph to New Century
 Schoolbook.  I'm trying to do this by editing the matplotlibrc file. 
 Unfortunately, although I'm able to change the font.family, I can't
 figure
 out how to make it use something other than the default in the family... 
 I tried changing the list further down to only include the font I want,
 like this:

 font.serif  : New Century Schoolbook #Bitstream Vera Serif, New
 Century Schoolbook, Century Schoolbook L, Utopia, ITC Bookman, Bookman,
 Nimbus Roman No9 L, Times New Roman, Times, Palatino, Charter, serif

 (note I commented out the other fonts, just rearranging the list to put
 New Century Schoolbook first didn't seem to work either)

 Could anyone tell me what I'm doing wrong?
 Thanks a lot!
 Alex


 

   
 
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 Operations and Engineering Division
 Space Telescope Science Institute
 Operated by AURA for NASA
 
 
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Re: [Matplotlib-users] Changing the font

[Alex S]

Ah ok, I've sent it on to you.  I've just tried setting font.family to New
Century Schoolbook directly but it generates something similar.  I'm
starting to think part of the problem is that I've set the home directory to
U: somehow, U: being a shared drive which doesn't have a font directory... 
I don't know how I set this, it's not mentioned in the rc file anywhere that
I can see...


Michael Droettboom-3 wrote:
 
 It would still be helpful to see the whole listing (send it to me 
 offlist) because that will indicate where fonts are being looked for, 
 and hopefully *why* this is failing.
 
 It should search for fonts in the standard Windows location (usually 
 C:\Windows\Fonts).  Have you tried setting font.family to New Century 
 Schoolbook directly?  (I wonder if the secondary lookup is failing).
 
 Cheers,
 Mike
 
 Alex S wrote:
 I think I'm using MPL .99.1 (is there a command to check?) on Windows XP. 
 Thanks for the debug tip, I don't think posting the whole thing is
 necessary
 because this line seems to be the problem:

 findfont: Could not match
 :family=serif:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0.
 Returning
 C:\Python26\lib\site-packages\matplotlib\mpl-data\fonts\ttf\Vera.ttf

 So I guess the font's missing from the folder.  Can I add it somehow?



 Michael Droettboom-3 wrote:
   
 Can you set verbose.level to debug-annoying in your matplotlibrc 
 file, and then send the output to this list.  That may help us track 
 down where the font lookup is failing.  Also, what platform and version 
 of matplotlib are you running?

 Mike

 Alex S wrote:
 
 Hi, sorry I wasn't too clear... I changed that, but I don't seem to be
 able
 to choose between the different serif fonts, it just always gives me
 the
 default...



 Alex S wrote:
   
   
 Hi there,
 I'm trying to change the font default on my graph to New Century
 Schoolbook.  I'm trying to do this by editing the matplotlibrc file. 
 Unfortunately, although I'm able to change the font.family, I can't
 figure
 out how to make it use something other than the default in the
 family... 
 I tried changing the list further down to only include the font I
 want,
 like this:

 font.serif  : New Century Schoolbook #Bitstream Vera Serif,
 New
 Century Schoolbook, Century Schoolbook L, Utopia, ITC Bookman,
 Bookman,
 Nimbus Roman No9 L, Times New Roman, Times, Palatino, Charter, serif

 (note I commented out the other fonts, just rearranging the list to
 put
 New Century Schoolbook first didn't seem to work either)

 Could anyone tell me what I'm doing wrong?
 Thanks a lot!
 Alex


 
 
   
   
 -- 
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 Operations and Engineering Division
 Space Telescope Science Institute
 Operated by AURA for NASA


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Re: [Matplotlib-users] Changing the font

[Alex S]

Yup, thanks for the help everyone


Michael Droettboom-3 wrote:
 
 For the benefit of future users Googling this problem --
 
 After an off-list discussion, we realized there were a couple of fonts 
 on Alex' system with the names Century Schoolbook and New Century 
 Schoolbook LT Std.  Using one of those names instead resolved the
 problem.
 
 Mike
 
 Alex S wrote:
 Ah ok, I've sent it on to you.  I've just tried setting font.family to
 New
 Century Schoolbook directly but it generates something similar.  I'm
 starting to think part of the problem is that I've set the home directory
 to
 U: somehow, U: being a shared drive which doesn't have a font
 directory... 
 I don't know how I set this, it's not mentioned in the rc file anywhere
 that
 I can see...


 Michael Droettboom-3 wrote:
   
 It would still be helpful to see the whole listing (send it to me 
 offlist) because that will indicate where fonts are being looked for, 
 and hopefully *why* this is failing.

 It should search for fonts in the standard Windows location (usually 
 C:\Windows\Fonts).  Have you tried setting font.family to New Century 
 Schoolbook directly?  (I wonder if the secondary lookup is failing).

 Cheers,
 Mike

 Alex S wrote:
 
 I think I'm using MPL .99.1 (is there a command to check?) on Windows
 XP. 
 Thanks for the debug tip, I don't think posting the whole thing is
 necessary
 because this line seems to be the problem:

 findfont: Could not match
 :family=serif:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0.
 Returning
 C:\Python26\lib\site-packages\matplotlib\mpl-data\fonts\ttf\Vera.ttf

 So I guess the font's missing from the folder.  Can I add it somehow?



 Michael Droettboom-3 wrote:
   
   
 Can you set verbose.level to debug-annoying in your matplotlibrc 
 file, and then send the output to this list.  That may help us track 
 down where the font lookup is failing.  Also, what platform and
 version 
 of matplotlib are you running?

 Mike

 Alex S wrote:
 
 
 Hi, sorry I wasn't too clear... I changed that, but I don't seem to
 be
 able
 to choose between the different serif fonts, it just always gives me
 the
 default...



 Alex S wrote:
   
   
   
 Hi there,
 I'm trying to change the font default on my graph to New Century
 Schoolbook.  I'm trying to do this by editing the matplotlibrc file. 
 Unfortunately, although I'm able to change the font.family, I can't
 figure
 out how to make it use something other than the default in the
 family... 
 I tried changing the list further down to only include the font I
 want,
 like this:

 font.serif  : New Century Schoolbook #Bitstream Vera Serif,
 New
 Century Schoolbook, Century Schoolbook L, Utopia, ITC Bookman,
 Bookman,
 Nimbus Roman No9 L, Times New Roman, Times, Palatino, Charter, serif

 (note I commented out the other fonts, just rearranging the list to
 put
 New Century Schoolbook first didn't seem to work either)

 Could anyone tell me what I'm doing wrong?
 Thanks a lot!
 Alex


 
 
 
   
   
   
 -- 
 Michael Droettboom
 Science Software Branch
 Operations and Engineering Division
 Space Telescope Science Institute
 Operated by AURA for NASA


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 -- 
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Re: [Matplotlib-users] Changing the font

[Alex S]

Hi, sorry I wasn't too clear... I changed that, but I don't seem to be able
to choose between the different serif fonts, it just always gives me the
default...



Alex S wrote:
 
 Hi there,
 I'm trying to change the font default on my graph to New Century
 Schoolbook.  I'm trying to do this by editing the matplotlibrc file. 
 Unfortunately, although I'm able to change the font.family, I can't figure
 out how to make it use something other than the default in the family... 
 I tried changing the list further down to only include the font I want,
 like this:
 
 font.serif  : New Century Schoolbook #Bitstream Vera Serif, New
 Century Schoolbook, Century Schoolbook L, Utopia, ITC Bookman, Bookman,
 Nimbus Roman No9 L, Times New Roman, Times, Palatino, Charter, serif
 
 (note I commented out the other fonts, just rearranging the list to put
 New Century Schoolbook first didn't seem to work either)
 
 Could anyone tell me what I'm doing wrong?
 Thanks a lot!
 Alex
 
 

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[Matplotlib-users] xlim with dates

[Alex S]

Hi there, does anyone know if there's a simple way to set an axis limit to a
date?  viewlim_to_dt() looks promising, but I can't figure out how to use
it...

Thanks a lot,
Alex
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Re: [Matplotlib-users] xlim with dates

[Alex S]

Ah perfect, thanks a lot, sorry for the mundane question :)
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[Matplotlib-users] Making tick marks of a secondary axis line up with the primary axis

[Alex S]

Hi there,
I'm trying to make a plot with two y axes.  I'm able to do that no problem,
but what I'd really like to do now is make the tick marks line up for them
both so that they both use the same grid.  Is there a simple way to do this?  
Basically, I want to force the number of tick marks on the right hand axis
to be the same as on the left hand axis, and I'd like it to select nice
numbers to do so (ie not intervals of .358 or something).  

Also, on a somewhat related note, is there a simple way to force the y ticks
to start at 0 rather than some other value?

Thanks a lot,
Alex
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Re: [Matplotlib-users] Making an Axis Label like a legend

[Alex S]

Hmm I think I could do this with TextWithDash, but I can't manage to use
it...  I go:

CumGasTxt = fig.text(0.5, 0.5, 'Cumulative Gas (MCF)', withdash=True)

and it says AttributeError: Unknown property withdash.

I tried changing fig to ax1, but although that doesn't spit out an
error, it doesn't display anything.

Does anyone know what I'm doing wrong?

Thanks a lot,
Alex


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[Matplotlib-users] Multiple Y Axes redux

[Alex S]

Hi there,
I know this has been discussed in the past, but I was looking through some
of the history and I'm not sure what the exact situation is.  I think
multiple y axes on the same side of the graph is unsupported officially, but
can be hacked together somehow, is that right?  Is there an example of such
a hacked together method somewhere that I could look at?

There may be a simpler way to do what I'm trying to do...  I'm not trying to
make several different axes, I'm trying to have a logarithmic axis on the
left, but have three different scales (ie 1, 10, 100 on one, 10, 100, 1000
on another, 100, 1000, 1 on the final one).  Is there a way to manually
label the ticks on the axis 1 10  1000 and so on?  I think that
might do in a pinch, then I could just divide the plotted values by the
correct scaling factor.  Do you guys think that would be the way to go?  And
if that is possible, is it possible to have the tick labels be different
colours for the different numbers so it shows which scale is for which line
on the graph?  I guess I'm not hopeful for that...  Instead could I put in a
bit at the bottom of the graph to highlight which markers go to which axis? 
Something like this (for x, o and * data markers on the chart):

|  |  |
|  |  |
|  |  |_*
|  |_o
|_x

Thanks a lot, sorry if this question is kind of hard to follow...  Please
let me know if more clarification is needed!

Alex
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[Matplotlib-users] Making an Axis Label like a legend

[Alex S]

Hello again,
I've got a question about axis labels, specifically y axis labels for
multiple lines.  What I'd ideally like to do is take something like the
legends shown in the attached picture, rotate them 90 degrees counter
clockwise, then stick them to the left of the Y axes to use it as a label
there.  I don't think there is any way to rotate the legend, but is there
anything I could do to get a similar effect?  Basically I'd like the legend
out of the plot area and into the y axis title, but it needs to show which
line is which.  Having the sample line and marker in the title would be
perfect, but I guess just having the words in the corresponding colour would
work too.

Thanks a lot!
Alex
http://old.nabble.com/file/p27826934/test.png 
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[Matplotlib-users] basemap Cairo exception

[Alex Stapleton]

Not sure if this is the right place to send this, can't seem to find a
dedicated bugs list or issue tracker. Or much discussion regarding the
basemap toolkit at all really.

Trying to savefig some Basemap instances causes the following
exception in the Cairo backend. Seems to work alright using the Agg
backend but the fill doesn't seem to come out properly. The sea gets
colored as well as the continents.

Traceback (most recent call last):
  File map.py, line 48, in module
plt.savefig(map.png, dpi=100)
  File /usr/lib/python2.5/site-packages/matplotlib/pyplot.py, line
286, in savefig
return fig.savefig(*args, **kwargs)
  File /usr/lib/python2.5/site-packages/matplotlib/figure.py, line
1033, in savefig
self.canvas.print_figure(*args, **kwargs)
  File /usr/lib/python2.5/site-packages/matplotlib/backend_bases.py,
line 1301, in print_figure
**kwargs)
  File /usr/lib/python2.5/site-packages/matplotlib/backends/backend_cairo.py,
line 406, in print_png
self.figure.draw (renderer)
  File /usr/lib/python2.5/site-packages/matplotlib/figure.py, line
833, in draw
for a in self.axes: a.draw(renderer)
  File /usr/lib/python2.5/site-packages/matplotlib/axes.py, line 1539, in draw
a.draw(renderer)
  File /usr/lib/python2.5/site-packages/matplotlib/patches.py, line
285, in draw
renderer.draw_path(gc, tpath, affine, rgbFace)
  File /usr/lib/python2.5/site-packages/matplotlib/backends/backend_cairo.py,
line 140, in draw_path
raise ValueError(The Cairo backend can not draw paths longer than
18980 points.)
ValueError: The Cairo backend can not draw paths longer than 18980 points.

Here's a short reduction

import matplotlib
matplotlib.use(Cairo)
from mpl_toolkits.basemap import Basemap
import matplotlib.pyplot as plt

map = Basemap(projection='ortho',
  llcrnrlon=-12.7, llcrnrlat=49,
  urcrnrlon=4.7,  urcrnrlat=61,
  lat_0 = 50, lon_0 = 0,
  lat_ts=50,
  resolution='i')
map.drawcoastlines(linewidth=0.5)
map.drawcountries(linewidth=0.5)
map.drawstates(linewidth=0.5)
map.drawmapboundary()
plt.savefig(map.png, dpi=100)

-- 
Alex Stapleton

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Re: [Matplotlib-users] basemap Cairo exception

[Alex Stapleton]

2008/7/16 Jeff Whitaker [EMAIL PROTECTED]:
 Alex Stapleton wrote:

 Not sure if this is the right place to send this, can't seem to find a
 dedicated bugs list or issue tracker. Or much discussion regarding the
 basemap toolkit at all really.

 Trying to savefig some Basemap instances causes the following
 exception in the Cairo backend. Seems to work alright using the Agg
 backend but the fill doesn't seem to come out properly. The sea gets
 colored as well as the continents.

 Traceback (most recent call last):
  File map.py, line 48, in module
plt.savefig(map.png, dpi=100)
  File /usr/lib/python2.5/site-packages/matplotlib/pyplot.py, line
 286, in savefig
return fig.savefig(*args, **kwargs)
  File /usr/lib/python2.5/site-packages/matplotlib/figure.py, line
 1033, in savefig
self.canvas.print_figure(*args, **kwargs)
  File /usr/lib/python2.5/site-packages/matplotlib/backend_bases.py,
 line 1301, in print_figure
**kwargs)
  File
 /usr/lib/python2.5/site-packages/matplotlib/backends/backend_cairo.py,
 line 406, in print_png
self.figure.draw (renderer)
  File /usr/lib/python2.5/site-packages/matplotlib/figure.py, line
 833, in draw
for a in self.axes: a.draw(renderer)
  File /usr/lib/python2.5/site-packages/matplotlib/axes.py, line 1539, in
 draw
a.draw(renderer)
  File /usr/lib/python2.5/site-packages/matplotlib/patches.py, line
 285, in draw
renderer.draw_path(gc, tpath, affine, rgbFace)
  File
 /usr/lib/python2.5/site-packages/matplotlib/backends/backend_cairo.py,
 line 140, in draw_path
raise ValueError(The Cairo backend can not draw paths longer than
 18980 points.)
 ValueError: The Cairo backend can not draw paths longer than 18980 points.

 Here's a short reduction

 import matplotlib
 matplotlib.use(Cairo)
 from mpl_toolkits.basemap import Basemap
 import matplotlib.pyplot as plt

 map = Basemap(projection='ortho',
  llcrnrlon=-12.7, llcrnrlat=49,
  urcrnrlon=4.7,  urcrnrlat=61,
  lat_0 = 50, lon_0 = 0,
  lat_ts=50,
  resolution='i')
 map.drawcoastlines(linewidth=0.5)
 map.drawcountries(linewidth=0.5)
 map.drawstates(linewidth=0.5)
 map.drawmapboundary()
 plt.savefig(map.png, dpi=100)



 Alex:  I don't have the Cairo backend installed, but I bet it would work if
 you changed resolution='i' to resolution='l'.  Seems like a pretty severe
 limitation of the backend though.

 -Jeff


I suppose it's not up to matplotlib to work around silly limits in
Cairo :) What about the fill issue with the Agg backend when doing
zoomed in ortho maps? Am I doing something wrong?

(actually hit reply all this time)

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Re: [Matplotlib-users] Problem with matplotlib and pdflatex

[Alex Coventry]

 I believe I have fixed the problem in the latest svn versions, both on
 the maintenance branch and on the trunk. Please try the latest version

Thanks for your help, Jouni.  That seems to have fixed the problem.

Best,
Alex

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[Matplotlib-users] Problem with matplotlib and pdflatex

[Alex Coventry]

I'm trying to use some matplotlib-generated pdfs in a pdflatex document,
and seeing some extremely weird and disruptive size effects.  The
resulting pdfs can be seen at

http://research.janelia.org/coventry/paper.pdf
http://research.janelia.org/coventry/paper-small.pdf

The first results from the code 

\begin{figure}
  \centering
  \subfigure[Prior distribution]{\label{fig:prior-graph}
\includegraphics[width=6in]{prior-example}
  }
  \subfigure[Posterior distribution]{\label{fig:posterior-graph}
\includegraphics[width=6in]{posterior-example}
  }
\end{figure}

and the second from the same code with width=5cm.  The two pdfs I'm
trying to include are at 

http://research.janelia.org/coventry/prior-example.pdf and
http://research.janelia.org/coventry/posterior-example.pdf

It doesn't matter what order I include them in, I get the same size
effects.  If I generate postscript files with matplotlib and convert
them to pdfs, I don't get this problem.  So I have a workaround, but I
would like to know how to create usable pdfs directly, and thought
reporting this might be useful to matplotlib development.

Best,
Alex

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Re: [Matplotlib-users] Looking for a way to save a graph

[Alex Pounds]

On Thu, August 23, 2007 5:33 pm, David Tremouilles wrote:
  I would like to save a matplotlib figure (data, title and axes label,
 plot properties, ...) to load it later on for modification.  Something
 like figure.savelall(file.matplot) and later on do a
 figure.loadall(file.matplot)  using an empty figure.

I am but a humble newbie, but why not simply take your figure
object/reference and Pickle it (see
http://docs.python.org/lib/module-pickle.html)?

-- 
Alex Pounds (Creature)  .~.   http://www.alexpounds.com/
/V\  http://www.ethicsgirls.com/
   // \\
Variables won't; Constants aren't   /(   )\
   ^`~'^


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[Matplotlib-users] pylib BaseHTTPRequestHandler

[Alex Davies]

Hi Everyone,

I am trying to find a way of producing a graph in pylib and then
returning it as a graphic via a simple BaseHTTPRequestHandler
webserver.

I don't appear to be able to find any documentation on this, although
I am sure it must be possible to achieve this!

I know that I can produce a temporary file in pylib and then load it
and output it in BaseHTTPRequestHandler but I am looking to avoid this
unnecessary step!

Many thanks,

Alex

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[Matplotlib-users] matplotlib + mpi4py on win32

[Alex Pletzer]

Hi,

Has anyone had experience running matplotlib in conjunction with 
mpi4py/mpich2 on Windows?

The following program hangs (python 2.4), even when running  with 
mpiexec -n 1 python test.py:

import pylab
from mpi4py import MPI

pylab.plot([1,2,3])
pylab.show()

but runs once the line pylab.show() is commented out. I haven't seen 
that behavior on Linux or Mac OS X. Thanks in advance for your help.

--Alex


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