Re: [Matplotlib-users] Creating Dendrograms
On 9/12/06, John Hunter [EMAIL PROTECTED] wrote: Minor correction license. Fernando Perez did this with ipython, which was released under the LGPL and then re-released under a BSD license to ease integration with scipy and other enthought products. The LGPL is ^^^ matplotlib, scipy and... Integration and free back-and-forth code sharing with you was one of the main factors behind that decision. And just to provide a datapoint confirming John's argument, ipython was one of those cases where I chose LGPL out of pure ignorance and incomplete understanding. Regards, f - 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=lnkkid=120709bid=263057dat=121642 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] MPL/Pylab install woes (still)
Spot on. Thanks Charles - that did the trick (setting WX_CONFIG to point to the right place). I had the universal wxpython installed but unbeknownst to me there was a previous wx installation on my machine. (Possibly installed by some super-pack or along with some other library.) Setting the environmental variable WX_CONFIG to the correct location (/usr/local/lib/wxPython-unicode-2.6.3.3/bin/wx-config) before the build sorted things out.As an aside, the spurious error messages generated in the build stage (warning: "M_PI" redefined, /usr/local/lib/libgcc_s.10.4.dylib does not contain an architecture that matches the specified -arch flag: ppc, etc.) aren't helpful and may hide any genuine problems. It would be nice to have them go away.Thanks againp After some progress in installing matplotlib (after solving the numpyproblem, thanks), I've hit another obstacle. Again, perhaps someone willrecognise the symptoms or suggest the next place to look. The technical setup: OSX 10.4, MPL 0.87.5, numeric, numarray and numpy 1.0b5 installed,intel MacBook.The issue: matplotlib installs but when pylab is imported, I get: : 14:28:56: Debug: ../src/common/object.cpp(224): assert"sm_classTable-Get(m_className) == NULL" failed: classalready in RTTI table - have you used IMPLEMENT_DYNAMIC_CLASS() twice (maybe by linking some object module(s) twice)? ../src/common/object.cpp(224): assert"sm_classTable-Get(m_className) == NULL" failed: classalready in RTTI table - have you used IMPLEMENT_DYNAMIC_CLASS() twice (maybe by linking some object module(s) twice)? Trace/BPT trapand then dumped to the CLI. ``sm_classTable`` appears to be defined in thewxagg backend. Do you have the universal wxpython installed? If so, make sure youset WX_CONFIG to point to the correct wx-config executable. --Dr Paul-Michael Agapow, VieDigitale / Institute of Animal Health[EMAIL PROTECTED] / [EMAIL PROTECTED] - 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=lnkkid=120709bid=263057dat=121642___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Default dpi for savefig
Hi,
David == David Huard [EMAIL PROTECTED] writes:
David Hi, I'm a little bit lost with respect to setting the
David resolution of images saved in png. The matplotlibrc file
David sets the dpi to 80, but the default keyword argument of
David savefig is set to 150. Thus, changing the rc setting to
David dpi=300 does not modify savefig's default behaviour. Is
David there a way to set a default dpi that would be used when
David calling savefig ?
Have you tried modifying the rc setting
savefig.dpi : 100 # figure dots per inch
On a related issue: when exporting a figure from the tkagg backend
(using the appropriate button) to PNG, the dpi is arbitrirarily set to
300 (see backend_tkagg.py in NavigationToolbar2TkAgg.save_figure):
self.canvas.print_figure(fname, dpi=300)
I think it should honor the savefig.dpi rc setting:
self.canvas.print_figure(fname, dpi=rcParams['savefig.dpi'])
so that using savefig('toto.png') in the script or exporting it from the
window is equivalent. I dont't know if this happens w/ other 'GUI' backends.
Cheers.
--
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Re: [Matplotlib-users] Default dpi for savefig
Yannick == Yannick Copin [EMAIL PROTECTED] writes: Yannick Hi, David == David Huard [EMAIL PROTECTED] writes: David Hi, I'm a little bit lost with respect to setting the David resolution of images saved in png. The matplotlibrc file David sets the dpi to 80, but the default keyword argument of David savefig is set to 150. Thus, changing the rc setting to David dpi=300 does not modify savefig's default behaviour. Is David there a way to set a default dpi that would be used when David calling savefig ? Have you tried modifying the rc setting savefig.dpi : 100 # figure dots per inch Yannick On a related issue: when exporting a figure from the Yannick tkagg backend (using the appropriate button) to PNG, the Yannick dpi is arbitrirarily set to 300 (see backend_tkagg.py in Yannick NavigationToolbar2TkAgg.save_figure): Yannick self.canvas.print_figure(fname, dpi=300) Yannick I think it should honor the savefig.dpi rc setting: Yannick self.canvas.print_figure(fname, Yannick dpi=rcParams['savefig.dpi']) Yep -- this is a bug in my view. pylab.savefig and fig.avefig respect the setting, but canvas.print_figure did not. I updated the following backends: Sendingmatplotlib/lib/matplotlib/backend_bases.py Sendingmatplotlib/lib/matplotlib/backends/backend_agg.py Sendingmatplotlib/lib/matplotlib/backends/backend_fltkagg.py Sendingmatplotlib/lib/matplotlib/backends/backend_gtk.py Sendingmatplotlib/lib/matplotlib/backends/backend_gtkagg.py Sendingmatplotlib/lib/matplotlib/backends/backend_qt4agg.py Sendingmatplotlib/lib/matplotlib/backends/backend_qtagg.py Sendingmatplotlib/lib/matplotlib/backends/backend_template.py Sendingmatplotlib/lib/matplotlib/backends/backend_tkagg.py Sendingmatplotlib/lib/matplotlib/backends/backend_wx.py Sendingmatplotlib/lib/matplotlib/backends/backend_wxagg.py Sendingmatplotlib/lib/matplotlib/figure.py Those of you with svn access please give it a test drive on your favorite backends to make sure it is behaving properly. I was able to test several... JDH - 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=lnkkid=120709bid=263057dat=121642 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Creating Dendrograms
I chose the GPL because it was the open source license I was aware of and didn't realize that it would create problems with reusability of the code. It is not my intention to restrict people from reusing the code. Indeed, I'd much prefer that people did reuse the code. Since that appears to mean switching to a BSD style license, I'll make that switch. -- R. Padraic Springuel Teaching Assistant Department of Physics and Astronomy University of Maine Bennett 309 Office Hours: Wednesday 2-3pm - 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=lnkkid=120709bid=263057dat=121642 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Creating Dendrograms
Have you thought about combining the dendrogram with a heatmap/colormap (e.g. http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/python/heatmap/)? Could ClusterPlot be combined with pcolor() to do this? To be honest, I haven't thought about doing anything like this. While I'm using the Pycluster package to do my cluster analysis, I'm actually doing research in Physics Education, not genetics. As a result, I've never even seen diagrams like the one shown in the above link before. Looking at it, however, I imagine that with the judicious use of subplots, ClusterPlot could create the dendrograms in those images. Once direction control is added to ClusterPlot, that is. At this point I have thought about only two further extensions to ClusterPlot. The first is the afore mentioned one: allowing control of the direction of the dendrogram. Once that's implemented, I'd consider the code to be out of the beta stage. The other extension would be a modification to the coordinates function so that the vertical coordinates of the dendrogram don't have to follow the Pycluster distances in the tree. Pycluster doesn't support having anything other than a distance measure in that slot. Now, while Pycluster does have 8 different distance measures, I can imagine cases where one would prefer to spread the tree by a dissimilarity measure or some other metric. This modification should be simple enough to make, so it'll probably be included in the next update (which might come before full release). Finally, concerning the license discussion, I've posted version 0.6 which is released under the BSD-style license. Version 0.5, with its GPL license has been removed from the download site. http://www.umit.maine.edu/~r.springuel/000CCFE8-8018/ -- R. Padraic Springuel Teaching Assistant Department of Physics and Astronomy University of Maine Bennett 309 Office Hours: Wednesday 2-3pm - 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=lnkkid=120709bid=263057dat=121642 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] tooltips in matplotlib?
Martin Spacek wrote:
Attached is an example file of
what I've got running now. It should run on its own. A wx tooltip pops
up whenever the mouse is over the axes.
cool.
I had to make a change to get it to run:
mpl.use('WXAgg') has to come before import pylab
once running, it's not working quite right: the tooltip always is at the
bottom of the Window, though it does track the X location.
oddly it looks likeit's getting it's coords in figure units (0 to 1),
whcih shouldn't work with a wxWindow.
Also, I'm getting the tooltip even when the window doesnot have focus
and is under other windows -- at least when the mouse is over an exposed
part of the window. That's probably a wx issue.
Python 2.4.3
wx.__version__
'2.6.3.0'
matplotlib.__version__
'0.87.5'
wxGTK on on Fedora core 4 linux.
-Chris
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Re: [Matplotlib-users] MPL/Pylab install woes (still)
Paul-Michael Agapow wrote: there was a previous wx installation on my machine. (Possibly installed by some super-pack or along with some other library.) Apple put it there. they included a version of wxpython with their Python install. It's out of date, but pretty coll that they did it. -Chris -- Christopher Barker, Ph.D. Oceanographer NOAA/ORR/HAZMAT (206) 526-6959 voice 7600 Sand Point Way NE (206) 526-6329 fax Seattle, WA 98115 (206) 526-6317 main reception [EMAIL PROTECTED] - 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=lnkkid=120709bid=263057dat=121642 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] tooltips in matplotlib?
once running, it's not working quite right: the tooltip always is at the bottom of the Window, though it does track the X location. Hm, dunno. I'm running win32 (winxp), Python 2.4.3. Maybe try updating your wx install. I've tried with 2.6.3, same result. I think this is a platform issue: I expect that GTK is putting the tooltip at the bottom of the wx.Window it's on. this is really to bad, as with larger Windows, that might not be what you want. In fact, I have a need to add tooltips to a wx.lib.floatcanvas based app, a I need to be able to place them where I need. I guess I'll send a note to wxpython-users about this. I've enclosed a wxpython tiny test app, to isolate matplotlib issues. It has the same behavior. does the tooltip follow the mouse on Windows (or OS-X) -Chris -- Christopher Barker, Ph.D. Oceanographer NOAA/ORR/HAZMAT (206) 526-6959 voice 7600 Sand Point Way NE (206) 526-6329 fax Seattle, WA 98115 (206) 526-6317 main reception [EMAIL PROTECTED] #!/usr/bin/env python2.4 import wx class DemoPanel(wx.Panel): A very minimal Panel to test Tooltips. def __init__(self, *args, **kwargs): kwargs['size'] = (200,200) wx.Panel.__init__(self, *args, **kwargs) self.tooltip = wx.ToolTip(tip='A tool tip') # create an empty tooltip #self.tooltip = wx.TipWindow(self, text = A tip Window) #self.tooltip.Hide() self.tooltip.SetDelay(100) # set popup delay in ms self.SetToolTip(self.tooltip) # connect tooltip to canvas # self.Bind(wx.EVT_LEFT_DOWN, self.OnLeft) self.Bind(wx.EVT_MOTION, self.OnMove) self.MoveTip = None def OnMove(self, event=None): self.tooltip.SetTip(tip='x=%f, y=%f' % (event.GetX(), event.GetY())) class DemoFrame(wx.Frame): This window displays a button def __init__(self, title = Micro App): wx.Frame.__init__(self, None , -1, title) MenuBar = wx.MenuBar() FileMenu = wx.Menu() item = wx.MenuItem(FileMenu, text = Quit) FileMenu.AppendItem(item) self.Bind(wx.EVT_MENU, self.OnQuit, item) MenuBar.Append(FileMenu, File) self.SetMenuBar(MenuBar) P = DemoPanel(self) self.Fit() def OnQuit(self,Event): self.Destroy() app = wx.App() frame = DemoFrame() frame.Show() app.MainLoop() - 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=lnkkid=120709bid=263057dat=121642___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] tooltips in matplotlib?
Just gave it a try, and yes, the tooltip tracks the mouse perfectly for me on my win32 install. Martin Christopher Barker wrote: once running, it's not working quite right: the tooltip always is at the bottom of the Window, though it does track the X location. Hm, dunno. I'm running win32 (winxp), Python 2.4.3. Maybe try updating your wx install. I've tried with 2.6.3, same result. I think this is a platform issue: I expect that GTK is putting the tooltip at the bottom of the wx.Window it's on. this is really to bad, as with larger Windows, that might not be what you want. In fact, I have a need to add tooltips to a wx.lib.floatcanvas based app, a I need to be able to place them where I need. I guess I'll send a note to wxpython-users about this. I've enclosed a wxpython tiny test app, to isolate matplotlib issues. It has the same behavior. does the tooltip follow the mouse on Windows (or OS-X) -Chris - 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=lnkkid=120709bid=263057dat=121642 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
