Re: [Matplotlib-users] ANN: Michael Droettboom, matplotlib lead developer
On Aug 2, 2012, at 5:25 PM, John Hunter wrote: > > I also extend my heartfelt thanks to Perry Greenfield and STScI. They > have been supporting matplotlib since 2004 with ideas, code and > developer resources. They employ Michael currently, and are part of > the reason why he is able to take on the leadership of this large > project. > John, it has been our great fortune have joined the matplotlib effort. It saved us an enormous effort. It has been an incredible pleasure working with you. I'm not sure you realize how very much Mike and I hope you can rejoin the matplotlib effort. It will always be there for you. Perry -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] [AstroPy] import problem (matplotlib ? numpy ?) on Mac Intel, python 2.6
matplotlib or numpy aren't going to work with jython.
On May 16, 2011, at 11:02 AM, Jean-Baptiste Marquette wrote:
> Dear matplotlib/numpy gurus,
>
> This is my first attempt to use matplotlib & numpy, with the
> following small piece of code:
>
> #!/usr/bin/env jython jython because of the import of stilts
> from starjava
>
> # Fabrique les figures des champs du papier Catalogue
>
>
> __author__="marquett"
> __date__ ="$16 mai 2011 12:17:08$"
>
> import sys
> sys.path.append('/star/starjava/etc/ttools')
> sys.path.append('/Library/Frameworks/Python.framework//Versions/2.6/
> lib/python2.6/site-packages')
> import stilts
> import glob
> import matplotlib.pyplot as plt
>
> I got the following trace:
>
> Traceback (most recent call last):
> File "/Users/marquett/Downloads/FigCat/src/figcat.py", line 14, in
>
> import matplotlib.pyplot as plt
> File "/Library/Frameworks/Python.framework/Versions/2.6/lib/
> python2.6/site-packages/matplotlib/__init__.py", line 135, in
> from matplotlib.rcsetup import (defaultParams,
> File "/Library/Frameworks/Python.framework/Versions/2.6/lib/
> python2.6/site-packages/matplotlib/rcsetup.py", line 19, in
> from matplotlib.colors import is_color_like
> File "/Library/Frameworks/Python.framework/Versions/2.6/lib/
> python2.6/site-packages/matplotlib/colors.py", line 52, in
> import numpy as np
> File "/Library/Frameworks/Python.framework/Versions/2.6/lib/
> python2.6/site-packages/numpy/__init__.py", line 137, in
> import add_newdocs
> File "/Library/Frameworks/Python.framework/Versions/2.6/lib/
> python2.6/site-packages/numpy/add_newdocs.py", line 9, in
> from numpy.lib import add_newdoc
> File "/Library/Frameworks/Python.framework/Versions/2.6/lib/
> python2.6/site-packages/numpy/lib/__init__.py", line 4, in
> from type_check import *
> File "/Library/Frameworks/Python.framework/Versions/2.6/lib/
> python2.6/site-packages/numpy/lib/type_check.py", line 8, in
> import numpy.core.numeric as _nx
> File "/Library/Frameworks/Python.framework/Versions/2.6/lib/
> python2.6/site-packages/numpy/core/__init__.py", line 5, in
> import multiarray
> ImportError: No module named multiarray
>
> I use the latest 1.6.0 version of numpy and 1.0.0 one of matplotlib.
>
> My so little experience tells me that this is a deep numpy issue
> rather than a matplotlib one.
>
> Any hint welcome, thanks.
>
> JB Marquette
>
> ___
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> astr...@scipy.org
> http://mail.scipy.org/mailman/listinfo/astropy
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Re: [Matplotlib-users] Memory issues with imshow
On Dec 15, 2009, at 12:30 PM, Wellenreuther, Gerd wrote: > Hi Perry, > > to clarify what I am doing - maybe the error lies in here: > > * First I am building up a list of the corrected+rotated images > > * After that is done I am creating the figure > > * Then looping over every image, creating proper axes for each > individual image and finally: > >>pylab.imshow(rotated_images[i],aspect='auto') >>rotated_images[i]=[] >>gc.collect(2) > > So I am trying to immediately delete the now obsolete image-data, by > removing the reference and forcing garbage collection. No idea whether > this is the proper/best way to do it ... but at least I hope my > intention is clear :). > > Anyone an idea how to improve? if the above code is in a loop, and there is no figure clearing in the loop, then rotated_images[i] = [] gc.collect(2) will have no effect since matplotlib will still have references to the array (and generally, you never need to call gc.collect by the way). What isn't clear to me in this is how you handle the offsetting and combining of images. Normally imshow will just display one image right over the other. Can you just insert the appropriate subsampled image into one output image, and then display that. After the insertion, you can delete the input image inside the loop. Perry -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Memory issues with imshow
On Dec 15, 2009, at 1:09 PM, Gerd Wellenreuther wrote: > > > Perry Greenfield schrieb: >> if the above code is in a loop, and there is no figure clearing in >> the loop, then >> >> rotated_images[i] = [] >> gc.collect(2) >> >> will have no effect since matplotlib will still have references to >> the array (and generally, you never need to call gc.collect by the >> way). > I do / did not know whether matplotlib is actually refering to my > array (in that context dereferencing it will not free memory), or > actually copying the data at one instance (in that case it should > help). So, as you can see I am lacking the inside-knowledge of > matplotlib, and was just trying some things which were not doing any > harm (at least this is what I suppose). > To give an idea, when you ask matplotlib to render an image, it processes it (resamples, rescales, maps to colors, etc) in order to actually display it. Since it may redo all that if you resize or otherwise re-render the figure, it needs to keep a reference to the original image. Even if you delete your reference to it, it still has it, and thus it won't be deleted until the figure is cleared. So if the input to the imshow call is the full size array, you will have that around. You may want to downsample that image to lower resolution (and make sure that the downsampled version is a copy, not a view of the original array). Then you can get rid of the original image, and instead display the smaller version. Keeping that around won't impact memory. > But I would expect that figure clearing would not only free memory, > but also erase the formerly inserted images, right? *That* would > harm ;). Yes, it would erase it :-) Perry -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Plotting large images
On Jun 30, 2009, at 7:54 PM, Tommy Grav wrote: > That is what I was assuming, but it still seems a little odd that > matplotlib generates > that large of a memory footprint. Loading the fits file into the > program using pyfits, > with the code only uses 19MB of real memory and 600MB of virtual > memory (strangly > adding the line img = hdu[1].data, increases this to 208MB/800MB). > The reason for this is that pyfits doesn't actually load the data until you 'touch' the data attribute (to minimize memory, particularly if you just are interested in the header information). As for the memory footprint of matplotlib, in order to be able to resize and handle interactive updates, it has to retain references to the original image, perhaps as well to intermediate products (and these references won't be memory collected until you clear the figure (e.g., clf()). It's one of the prices for flexibility and generality. It probably would take a lot of complexity to optimize it for large images (but John is better suited to answer this conclusively). Perry > Displaying images of various sizes I get these > numbers from Activity Monitor > > Size Real Mem Virtual > 3k x 3k 0.68GB1.57GB > 4k x 4k 0.92GB1.80GB > 5k x 5k 1.20GB2.10GB > 5.5k x 5.5k 1.38GB2.28GB > > And the limit seems to be somewhere just above 5.5k by 5.5k (darn :( ) > > Cheers > Tommy > -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Plotting large images
Because the image is so large, and matplotlib carries out various
operations on the image (scaling, resampling, etc), it uses a lot of
memory. This is one area where a specialized display program will be
more efficient. If you need to use matplotlib, decide whether you
really only want to display a subsection, or only need a lower
resolution version (e.g., boxcar smooth and subsample) before
displaying. I've found that image sizes well over 1kx1k can take some
time to display, and those that are much larger can cause you to run
out of memory. At least, that's what I think is happening.
Perry
On Jun 30, 2009, at 7:20 PM, Tommy Grav wrote:
> I am trying to use imshow to plot some semi-large fits images.
> Here is the code:
>
> from math import *
> import numpy as np
> from matplotlib import pyplot as plt
> from matplotlib import cm as cm
> import pyfits
>
> cat = "/Volumes/Sweden/PS1SC/Data/PS20090603-3/MD09/skycell.092/"
> fname = "o4985g0263o.warp.MD09.skycell.092"
>
> hdu = pyfits.open(cat+fname+".fits")
> print hdu.info()
> img = hdu[1].data.astype("int")
>
> plt.figure(figsize=[12,12])
> plt.imshow(img,cmap=cm.cool)
> plt.savefig("test.png")
>
> Which gives the result:
>
> Filename: /Volumes/Sweden/PS1SC/Data/PS20090603-3/MD09/skycell.092/
> o4985g0263o.warp.MD09.skycell.092.fits
> No.Name Type Cards Dimensions Format
> 0PRIMARY PrimaryHDU 6 ()int16
> 1CompImageHDU 101 (6000, 6000) float32
> None
> Python(23117,0xa04f2720) malloc: *** mmap(size=115200) failed
> (error code=12)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> Traceback (most recent call last):
> File "quick_look.py", line 16, in
> plt.savefig("test.png")
> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> python2.5/site-packages/matplotlib/pyplot.py", line 345, in savefig
> return fig.savefig(*args, **kwargs)
> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> python2.5/site-packages/matplotlib/figure.py", line 990, in savefig
> self.canvas.print_figure(*args, **kwargs)
> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> python2.5/site-packages/matplotlib/backend_bases.py", line 1419, in
> print_figure
> **kwargs)
> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> python2.5/site-packages/matplotlib/backends/backend_agg.py", line 323,
> in print_png
> FigureCanvasAgg.draw(self)
> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> python2.5/site-packages/matplotlib/backends/backend_agg.py", line 279,
> in draw
> self.figure.draw(self.renderer)
> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> python2.5/site-packages/matplotlib/figure.py", line 772, in draw
> for a in self.axes: a.draw(renderer)
> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> python2.5/site-packages/matplotlib/axes.py", line 1545, in draw
> im.draw(renderer)
> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> python2.5/site-packages/matplotlib/image.py", line 233, in draw
> im = self.make_image(renderer.get_image_magnification())
> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> python2.5/site-packages/matplotlib/image.py", line 180, in make_image
> x = self.to_rgba(self._A, self._alpha)
> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> python2.5/site-packages/matplotlib/cm.py", line 79, in to_rgba
> x = self.cmap(x, alpha=alpha, bytes=bytes)
> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> python2.5/site-packages/matplotlib/colors.py", line 501, in __call__
> rgba = np.empty(shape=xa.shape+(4,), dtype=lut.dtype)
> MemoryError
>
> I found the earlier thread of
> http://www.mail-archive.com/matplotlib-users@lists.sourceforge.net/msg11216.html
> but that didn't seem to produce any fixes or good explanations.
>
> I am on a Mac Pro Intel machine running 10.5.7 and
> [Heimdall:tgrav ~/Work/myCode/Python/pyPS1SC]> python
> ActivePython 2.5.4.3 (ActiveState Software Inc.) based on
> Python 2.5.4 (r254:67916, Jan 20 2009, 14:11:42)
> [GCC 4.0.1 (Apple Computer, Inc. build 5250)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
import numpy
numpy.__version__
> '1.3.0rc2'
import pyfits
pyfits.__version__
> '2.1.1dev462'
import matplotlib
matplotlib.__version__
> '0.98.5.2'
>
> Cheers
> Tommy
>
>
> --
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Re: [Matplotlib-users] Polygon masking possible?
Note that numdisplay can display numpy arrays directly to ds9 without saving to a file. (http://stsdas.stsci.edu/numdisplay). Perry On Mar 14, 2008, at 12:44 PM, Chiara Caronna wrote: > Hi, > I tried ds9 and It looks like this is what I would like to do > (though I couldn't try funtools, but what you describe is good). DO > you think it is possible to make something like this with matplotlib? > Thanks a lot for your help, > Chiara > > > Date: Wed, 12 Mar 2008 02:55:55 -0400 > > From: [EMAIL PROTECTED] > > To: [EMAIL PROTECTED] > > Subject: Re: [Matplotlib-users] Polygon masking possible? > > CC: matplotlib-users@lists.sourceforge.net > > > > Hi, > > > > I often do this with ds9 and funtools. > > ds9 is an astronomy-oriented image viewer (http://hea- > www.harvard.edu/RD/ds9/) > > but you can also use it with numpy array. > > Within ds9, you can define regions (ellipse, polynomial, etc) easily > > with a mouse. > > After you define a region (and save it as a file), you can > convert it > > to a mask image > > with funtools (funtools is a name of an astronomy-oriented image > > utility pacakge). > > funtools only support fits file (image format in astronomy) so this > > can be a bit tricky, but if you're > > interested i'll send my python wrapper code for it. > > > > So, take a look at ds9 and see it fits your need. > > To view numpy array in ds9, > > *. From python, save the array as a file (tofile method, better use > > "arr" as an extension) > > * in ds9, file-> open others -> open array. You need to select > > array dimension, type and endianness of the array. > > > > Regards, > > > > -JJ > > > > > > > > > > > > On Sat, Mar 8, 2008 at 11:17 AM, Chiara Caronna > > <[EMAIL PROTECTED]> wrote: > > > > > > Hello, > > > I am also interested in masking polygons and defining the > polygon by > > > 'clicking' on the image... but I do not know anything about > GUI does > > > anyone can help? Is there already something implemented? > > > Thanks! > > > Chiara > > > > > > > Date: Wed, 23 Jan 2008 13:50:15 +1300 > > > > From: [EMAIL PROTECTED] > > > > To: matplotlib-users@lists.sourceforge.net > > > > Subject: Re: [Matplotlib-users] Polygon masking possible? > > > > > > > > > > > > > > Hi Søren, > > > > > > > > I've put this back on the list in case it's useful to anyone > else, or > > > > if there are better suggestions or improvements around. Hope > you don't > > > > mind. > > > > > > > > On 22/01/2008, Søren Nielsen <[EMAIL PROTECTED]> > wrote: > > > > > Yeah i'd like to see your code if I can.. > > > > > > > > import numpy as n > > > > > > > > def get_poly_pts(x, y, shape): > > > > """Creates convex polygon mask from list of corners. > > > > > > > > Parameters > > > > -- > > > > x : array_like > > > > x co-ordinates of corners > > > > y : array_like > > > > y co-ordinates of corners, in order corresponding to x > > > > shape : array_like > > > > dimension sizes of result > > > > > > > > Returns > > > > --- > > > > build : ndarray > > > > 2-D array of shape shape with values True inside polygon > > > > > > > > Notes > > > > - > > > > Code is constrained to convex polygons by "inside" > > > > assessment criterion. > > > > > > > > """ > > > > x = n.asarray(x) > > > > y = n.asarray(y) > > > > shape = n.asarray(shape) > > > > npts = x.size # should probably assert x.size == y.size > > > > inds = n.indices( shape ) > > > > xs = inds[0] > > > > ys = inds[1] > > > > xav = n.round(x.mean()).astype(int) > > > > yav = n.round(y.mean()).astype(int) > > > > for i in xrange(npts): # iterate over pairs of co-ordinates > > > > j = (i + 1) % npts > > > > m = (y[j] - y[i])/(x[j] - x[i]) > > > > c = (x[j] * y[i] - x[i] * y[j])/(x[j] - x[i]) > > > > thisone = ( ys > m * xs + c ) > > > > if thisone[xav, yav] == False: > > > > thisone = ~thisone > > > > if i == 0: > > > > build = thisone > > > > else: > > > > build &= thisone > > > > return build > > > > > > > > (released under BSD licence) > > > > > > > > > I just needed the push over the edge to know how to draw on > the canvas, > > > > > mapping clicks etc. since i'm still fairly new to > matplotlib, so I think > > > > > your code will be helpfull. > > > > > > > > I hope so. As you can see this code doesn't do any of the > drawing or > > > > click collecting, but the cookbook page should be able to > guide you > > > > there. Ask again on the list if you have any further > questions and > > > > we'll see if we can help. > > > > > > > > Also, the code assumes that the average co-ordinate is inside > the > > > > shape - that's true for convex polygons, but not necessarily for > > > > arbitrary ones. I use if after taking a convex hull of a > greater list > > > > of points (using the delaunay module in scipy (now in scikits, I > > > > hear)), which ensures convexity. You just need to be aware of > that > > > > limitation. > > > > > > > > Cheers, > > > > > > > > A. > > > > -- > > > > AJC McMorland, PhD candidate > > > > Physiolog
Re: [Matplotlib-users] histogram question
On Sep 24, 2007, at 2:32 PM, Tommy Grav wrote: > I need to generate a set of histograms, but would like to plot only > the "skyline" > of the histogram, and leave out the vertical lines where adjencent > bars touch. > I have looked at the docs, but nothing jumped out at me as the right > keyword > for this. Is this possible? and if so, how? I believe that you can do the same thing using the regular plot command with linestyles='steps' (but I think you need to fiddle with the x values so that the steps are aligned properly. But it would be nice if hist could do this too. Perry - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] numpy version of Interactive Data Analysis tutorial available
I have updated the "Using Python for Interactive Data Analysis" tutorial to use numpy instead of numarray (finally!). There are further improvements I would like to make in its organization and formatting (in the process including suggestions others have made to that end), but I'd rather get this version out, which I believe addresses all the content changes needed to make it useful for numpy, without delaying it any further. The tutorial, as well as other supporting material and information, can be obtained from: http://www.scipy.org/wikis/topical_software/Tutorial I'm sure errors remain; please let me know of any you find. Perry - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] job opportunity at Space Telescope Science Institute
We are looking for someone to fill a position at the Space Telescope Science Institute (in Baltimore, MD) to work on Python tools for astronomical data processing and analysis. Details can be found at: http://www.stsci.edu/institute/brc/hr/co/external/Req559.html - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Native file format
On Feb 7, 2007, at 10:21 AM, John Hunter wrote: > On 2/7/07, Edin Salkovic <[EMAIL PROTECTED]> wrote: > >> Why can't mpl's figures be pickled? > > The main thing is we need to add pickle support for all of mpl's > extension code > > http://docs.python.org/lib/node321.html > > In earlier attempts people got stuck with trying to pickle the > CXX extension code, which was causing some problems, but these > problems may be fixed in more recent versions of CXX. Todd Miller was > the last person to look at this in some detail, I think. > I think Todd did get it to work, but I'll copy him on this just to make sure. > Other hinderances may come from the GUI layer, since figures store > pointers to their canvases which in some cases come from GUI extension > code that may not support pickling. But we can fairly easy decouple > the figure from the canvas at pickle time and deal with pure mpl, > numpy and python objects. The main work is to add pickle > serialization to the mpl extension code. > > -- > --- > Using Tomcat but need to do more? Need to support web services, > security? > Get stuff done quickly with pre-integrated technology to make your > job easier. > Download IBM WebSphere Application Server v.1.0.1 based on Apache > Geronimo > http://sel.as-us.falkag.net/sel? > cmd=lnk&kid=120709&bid=263057&dat=121642 > ___ > Matplotlib-users mailing list > Matplotlib-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/matplotlib-users - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier. Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
