[Matplotlib-users] [matplotlib-users] Is it possible to show a fullscreen plot on windows?
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Re: [Matplotlib-users] specgram memory problem
On Sat, Feb 4, 2012 at 9:44 AM, Fabrice Silva si...@lma.cnrs-mrs.fr wrote: Le vendredi 03 février 2012 à 17:39 +, David Craig a écrit : sure how to get it to plot the outputs from specgram. I use specgram as follows, Pxx, freqs, bins, im = plt.specgram(..) what am I trying imshow?? plt.specgram computes the spectrogram and when calls imshow to display the resulting array into an image Please tell the shape of Pxx, and try the following import numpy as np import matplotlib.pyplot as plt a = np.empty((12000, 14400), dtype=float) plt.imshow(a) plt.show() Le samedi 04 février 2012 à 10:30 +, David Craig a écrit : Pxx has shape (6001, 1430) and when I tried the lines of code it returned the following memory error, Traceback (most recent call last): File /usr/lib/python2.7/site-packages/matplotlib/backends/backend_gtk.py, line 394, in expose_event self._render_figure(self._pixmap, w, h) File /usr/lib/python2.7/site-packages/matplotlib/backends/backend_gtkagg.py, line 75, in _render_figure FigureCanvasAgg.draw(self) File /usr/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py, line 394, in draw self.figure.draw(self.renderer) File /usr/lib/python2.7/site-packages/matplotlib/artist.py, line 55, in draw_wrapper draw(artist, renderer, *args, **kwargs) File /usr/lib/python2.7/site-packages/matplotlib/figure.py, line 798, in draw func(*args) File /usr/lib/python2.7/site-packages/matplotlib/artist.py, line 55, in draw_wrapper draw(artist, renderer, *args, **kwargs) File /usr/lib/python2.7/site-packages/matplotlib/axes.py, line 1946, in draw a.draw(renderer) File /usr/lib/python2.7/site-packages/matplotlib/artist.py, line 55, in draw_wrapper draw(artist, renderer, *args, **kwargs) File /usr/lib/python2.7/site-packages/matplotlib/image.py, line 354, in draw im = self.make_image(renderer.get_image_magnification()) File /usr/lib/python2.7/site-packages/matplotlib/image.py, line 569, in make_image transformed_viewLim) File /usr/lib/python2.7/site-packages/matplotlib/image.py, line 201, in _get_unsampled_image x = self.to_rgba(self._A, self._alpha) File /usr/lib/python2.7/site-packages/matplotlib/cm.py, line 193, in to_rgba x = self.norm(x) File /usr/lib/python2.7/site-packages/matplotlib/colors.py, line 802, in __call__ val = ma.asarray(value).astype(np.float) File /usr/lib/python2.7/site-packages/numpy/ma/core.py, line 2908, in astype output = self._data.astype(newtype).view(type(self)) MemoryError Please, answer on the mailing list, It confirms that the troubles lie in the rendering of images. Could you tell the versions of numpy and matplotlib you are using, and the characteristics of the computer you are working on ? -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Setting x scale manually, but letting y scale automatic within the current x-axis
Hi
I understand that it would be hard to implement, as it requires that all
the points are checked, which for a arbitrary plot is not easy.
Though is this not what is already done for the normal autoscale, or have I
misunderstood how the normal autoscale is done?
I would like to have this as a new feature, as it would prove useful for
analysing graphs, especially in scientific research.
Kind regards
Pål
On 3 February 2012 19:56, Eric Firing efir...@hawaii.edu wrote:
On 02/03/2012 06:07 AM, Benjamin Root wrote:
On Fri, Feb 3, 2012 at 9:15 AM, Pål Gunnar Ellingsen paa...@gmail.com
mailto:paa...@gmail.com wrote:
Hi
Thank you for trying to help me, though I can't see how aspect is
going
to help me. As I understand of the documentation, it would require
me to know the
relationship between x and y, which I don't.
I can calculate it, but since it varies between each change in
xlimits
and different plot, it would be the same as calculating the ylimits.
As for pyplot.xlim(xmin,xmax) (suggested by Ethan Swint), it does
the same as ax.set_xlim() for me.
Below is a sample code that will illustrate the problem.
Regards
Pål
### Start code
#!/usr/bin/env python
import matplotlib
matplotlib.use('Qt4Agg') # generate postscript output by default
import matplotlib.pyplot as plt
import numpy as np
# Creating a function to plot
x = np.linspace(-10, 10, 200)
p = np.poly1d([2, 3, 1, 4])
y = p(x) * np.sin(x)
# plotting the full figure
fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot(x, y)
ax.autoscale(tight=True)
plt.title('Full graph. (Press key for next plot)')
plt.draw()
plt.waitforbuttonpress()
# This is how I'm currently doing it
# x limits
xmin = 2
xmax = 6
# Calculating y limits
ymin = y[np.logical_and(xmin x, x xmax)].min()
ymax = y[np.logical_and(xmin x, x xmax)].max()
# Inserting some room
room = np.maximum(np.abs(ymin * 0.05), np.abs(ymax * 0.05))
ymin = ymin + room * np.sign(ymin)
ymax = ymax + room * np.sign(ymax)
# Setting the limits
ax.set_xlim([xmin, xmax])
ax.set_ylim([ymin, ymax])
plt.title('What I want (Press key for next plot)')
plt.draw()
plt.waitforbuttonpress()
# This is what pyplot does by default if I only set the limits
ax.autoscale(tight=True)
ax.set_xlim([2, 6])
plt.title('What I get if I only use set_xlim (Press key for exit)')
plt.draw()
plt.waitforbuttonpress()
plt.close()
### End code
Ok, I see what you want. You want the y-limits to automatically change
to fit only the data that is displayed for the x-domain you have chosen.
This has never been supported; it would have to be a new option. I
suspect it would be quite difficult to get this right in general, even
though the concept seems simple enough.
Eric
I have tried some tricks, and I am not sure that it is currently
possible. There might even be some sort of bug at play here because the
function ax.update_datalim() does not appear to update the internal data
used for autoscaling. We might have to look into this further.
Ben Root
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Re: [Matplotlib-users] Why pixel marker size is 4 pixels?
Thanks. Now I understand the situation. As far as I can see, marker=, is implemented as a rectangle path with width/height of 1 pixel, so this result in 2x2 pixel filled square. I tried to change the size of the rectangle, etc, to get a single pixel filled square, but did not get a satisfactory result. I think we need an Agg expert. I hope Mike or others take a look. Chris, if you do not get a response from others in this mailing list, I recommend you to open a new issue in our github page. Regards, -JJ On Mon, Feb 6, 2012 at 1:53 AM, Chris plut...@gmail.com wrote: Thanks JJ. The problem seems not to be a size issue -- markersize has no effect when use marker=, (pixel). I have also tried to turn off aa, and it doesn't help either. I also tried different backends. The PNG output from Agg and Cairo is slightly different: Agg's point has 4 solid pixel, while Cairo's has 4 pixel with random shade. Postscript output has the same problem. The pixel in an EPS file generated by mpl is significantly bigger than that from another drawing program I used. The problem occurs in all my plotting scripts, e.g., this basic one: [CODE] import numpy as np x=np.arange(100) y=np.random.randn(100) ioff() fig=gcf() fig.clf() ax=fig.add_axes(0.15,0.1,0.8, 0.85) ax.plot(x,y,k,) ion() fig.canvas.draw() [/CODE] Here is how I identify the problem: 1. use the above script to plot on screen 2. savefig(plot.png) 3. open plot.png in GIMP and check the pixel size. I also attached the two PNG files generated with Agg and Cairo backends. On Sun, Feb 5, 2012 at 6:45 AM, Jae-Joon Lee lee.j.j...@gmail.com wrote: How are you plotting your points. If you use *plot*, there is a *markersize* parameter. If you use *scatter*, the third argument controls the marker size. But you may actually complaining about other issues, e.g., antialiasing, etc. So, if above are not your answer, please post a complete example and describe your problem in more detail. Regards, -JJ On Sat, Feb 4, 2012 at 2:15 PM, Chris plut...@gmail.com wrote: I noticed this a few years back, but left it aside because most of the time I can live with it. Recently I need to make a few plots containing a few million points, and 4 pixels for a point is a disaster. So my question is why the pixel marker size is set at 4 pixels? And is there anyway to change it to a single pixel? Thanks, Chris -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Why pixel marker size is 4 pixels?
Chris, You might want to try a module written by Tom Robitaille (aka astrofrog) called rasterized_scatter. Look for it on github. Jon On Mon, 2012-02-06 at 21:28 +0900, Jae-Joon Lee wrote: Thanks. Now I understand the situation. As far as I can see, marker=, is implemented as a rectangle path with width/height of 1 pixel, so this result in 2x2 pixel filled square. I tried to change the size of the rectangle, etc, to get a single pixel filled square, but did not get a satisfactory result. I think we need an Agg expert. I hope Mike or others take a look. Chris, if you do not get a response from others in this mailing list, I recommend you to open a new issue in our github page. Regards, -JJ On Mon, Feb 6, 2012 at 1:53 AM, Chris plut...@gmail.com wrote: Thanks JJ. The problem seems not to be a size issue -- markersize has no effect when use marker=, (pixel). I have also tried to turn off aa, and it doesn't help either. I also tried different backends. The PNG output from Agg and Cairo is slightly different: Agg's point has 4 solid pixel, while Cairo's has 4 pixel with random shade. Postscript output has the same problem. The pixel in an EPS file generated by mpl is significantly bigger than that from another drawing program I used. The problem occurs in all my plotting scripts, e.g., this basic one: [CODE] import numpy as np x=np.arange(100) y=np.random.randn(100) ioff() fig=gcf() fig.clf() ax=fig.add_axes(0.15,0.1,0.8, 0.85) ax.plot(x,y,k,) ion() fig.canvas.draw() [/CODE] Here is how I identify the problem: 1. use the above script to plot on screen 2. savefig(plot.png) 3. open plot.png in GIMP and check the pixel size. I also attached the two PNG files generated with Agg and Cairo backends. On Sun, Feb 5, 2012 at 6:45 AM, Jae-Joon Lee lee.j.j...@gmail.com wrote: How are you plotting your points. If you use *plot*, there is a *markersize* parameter. If you use *scatter*, the third argument controls the marker size. But you may actually complaining about other issues, e.g., antialiasing, etc. So, if above are not your answer, please post a complete example and describe your problem in more detail. Regards, -JJ On Sat, Feb 4, 2012 at 2:15 PM, Chris plut...@gmail.com wrote: I noticed this a few years back, but left it aside because most of the time I can live with it. Recently I need to make a few plots containing a few million points, and 4 pixels for a point is a disaster. So my question is why the pixel marker size is set at 4 pixels? And is there anyway to change it to a single pixel? Thanks, Chris -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Change xaxis labels
Hi, I have a plot and the xaxis shows number of seconds after a start point. I would like to convert them to days anyone know how to do this. I have looked at the documentation but cant find what I need. -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Change xaxis labels
On Mon, Feb 6, 2012 at 9:23 AM, David Craig dcdavem...@gmail.com wrote: Hi, I have a plot and the xaxis shows number of seconds after a start point. I would like to convert them to days anyone know how to do this. I have looked at the documentation but cant find what I need. Couldn't you divide your data points by the conversion (86400) before plotting? E.g., 432,000 seconds then becomes 5 days. -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Why pixel marker size is 4 pixels?
I'm looking into the source of this bug now. Mike On 02/06/2012 09:19 AM, Jonathan Slavin wrote: Chris, You might want to try a module written by Tom Robitaille (aka astrofrog) called rasterized_scatter. Look for it on github. Jon On Mon, 2012-02-06 at 21:28 +0900, Jae-Joon Lee wrote: Thanks. Now I understand the situation. As far as I can see, marker=, is implemented as a rectangle path with width/height of 1 pixel, so this result in 2x2 pixel filled square. I tried to change the size of the rectangle, etc, to get a single pixel filled square, but did not get a satisfactory result. I think we need an Agg expert. I hope Mike or others take a look. Chris, if you do not get a response from others in this mailing list, I recommend you to open a new issue in our github page. Regards, -JJ On Mon, Feb 6, 2012 at 1:53 AM, Chrisplut...@gmail.com wrote: Thanks JJ. The problem seems not to be a size issue -- markersize has no effect when use marker=, (pixel). I have also tried to turn off aa, and it doesn't help either. I also tried different backends. The PNG output from Agg and Cairo is slightly different: Agg's point has 4 solid pixel, while Cairo's has 4 pixel with random shade. Postscript output has the same problem. The pixel in an EPS file generated by mpl is significantly bigger than that from another drawing program I used. The problem occurs in all my plotting scripts, e.g., this basic one: [CODE] import numpy as np x=np.arange(100) y=np.random.randn(100) ioff() fig=gcf() fig.clf() ax=fig.add_axes(0.15,0.1,0.8, 0.85) ax.plot(x,y,k,) ion() fig.canvas.draw() [/CODE] Here is how I identify the problem: 1. use the above script to plot on screen 2. savefig(plot.png) 3. open plot.png in GIMP and check the pixel size. I also attached the two PNG files generated with Agg and Cairo backends. On Sun, Feb 5, 2012 at 6:45 AM, Jae-Joon Leelee.j.j...@gmail.com wrote: How are you plotting your points. If you use *plot*, there is a *markersize* parameter. If you use *scatter*, the third argument controls the marker size. But you may actually complaining about other issues, e.g., antialiasing, etc. So, if above are not your answer, please post a complete example and describe your problem in more detail. Regards, -JJ On Sat, Feb 4, 2012 at 2:15 PM, Chrisplut...@gmail.com wrote: I noticed this a few years back, but left it aside because most of the time I can live with it. Recently I need to make a few plots containing a few million points, and 4 pixels for a point is a disaster. So my question is why the pixel marker size is set at 4 pixels? And is there anyway to change it to a single pixel? Thanks, Chris -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Setting x scale manually, but letting y scale automatic within the current x-axis
On Mon, Feb 6, 2012 at 4:47 AM, Pål Gunnar Ellingsen paa...@gmail.comwrote: Hi I understand that it would be hard to implement, as it requires that all the points are checked, which for a arbitrary plot is not easy. Though is this not what is already done for the normal autoscale, or have I misunderstood how the normal autoscale is done? I would like to have this as a new feature, as it would prove useful for analysing graphs, especially in scientific research. Kind regards Pål Pal, Normal autoscaling (when aspect is None, which is default) means to display all the data that has been plotted. This is possible because the plotting functions (which were given the data as input) updates the limits of the known data bounding box for the axes. This data is not stored except within each artist object, in their own form. It becomes difficult to then re-query that data in the general case. It isn't to say that it isn't possible to do, just that the architecture isn't set up to query subsets of collections. I hope this is clearer, Ben Root -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Setting x scale manually, but letting y scale automatic within the current x-axis
Hi That was a very nice explanation of how autoscale works, thank you very much :D After now understanding how the function autoscale function works, I see that this would be a major change in the code, as it would require the axes to know all of the bounding boxes, and not only one of them. As it, at least in my code, is easy to calculate the new limits on the unset axis, I would not put this up as something that should be a feature. Though I think the documentation for autoscale, section axis could be a bit clearer and state that autoscaling only one axis autoscales that axis with respect to everything plotted, even though xlim/ylim has been set. Regards Pål On 6 February 2012 18:02, Benjamin Root ben.r...@ou.edu wrote: On Mon, Feb 6, 2012 at 4:47 AM, Pål Gunnar Ellingsen paa...@gmail.comwrote: Hi I understand that it would be hard to implement, as it requires that all the points are checked, which for a arbitrary plot is not easy. Though is this not what is already done for the normal autoscale, or have I misunderstood how the normal autoscale is done? I would like to have this as a new feature, as it would prove useful for analysing graphs, especially in scientific research. Kind regards Pål Pal, Normal autoscaling (when aspect is None, which is default) means to display all the data that has been plotted. This is possible because the plotting functions (which were given the data as input) updates the limits of the known data bounding box for the axes. This data is not stored except within each artist object, in their own form. It becomes difficult to then re-query that data in the general case. It isn't to say that it isn't possible to do, just that the architecture isn't set up to query subsets of collections. I hope this is clearer, Ben Root -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Why pixel marker size is 4 pixels?
JJ, Thanks for the clarification. Now I understand why EPS outputs of pixel plot from mpl is a few times bigger than those from SuperMongo. I guess that mpl uses the square implementation for pixel so that it would use the same method to handle all marker types. I will file an issue report on git. Meanwhile, is there any easy workaround? Jonathan, Tom Robitaille's module does help reducing file size of postscript, but by rasterize a scalable plot. It doesn't really help my problem since the markers are still drawn with the same method as other plotting methods. Bests, Chris On Mon, Feb 6, 2012 at 4:28 AM, Jae-Joon Lee lee.j.j...@gmail.com wrote: Thanks. Now I understand the situation. As far as I can see, marker=, is implemented as a rectangle path with width/height of 1 pixel, so this result in 2x2 pixel filled square. I tried to change the size of the rectangle, etc, to get a single pixel filled square, but did not get a satisfactory result. I think we need an Agg expert. I hope Mike or others take a look. Chris, if you do not get a response from others in this mailing list, I recommend you to open a new issue in our github page. Regards, -JJ On Mon, Feb 6, 2012 at 6:19 AM, Jonathan Slavin jsla...@cfa.harvard.edu wrote: Chris, You might want to try a module written by Tom Robitaille (aka astrofrog) called rasterized_scatter. Look for it on github. Jon On Mon, 2012-02-06 at 21:28 +0900, Jae-Joon Lee wrote: Thanks. Now I understand the situation. As far as I can see, marker=, is implemented as a rectangle path with width/height of 1 pixel, so this result in 2x2 pixel filled square. I tried to change the size of the rectangle, etc, to get a single pixel filled square, but did not get a satisfactory result. I think we need an Agg expert. I hope Mike or others take a look. Chris, if you do not get a response from others in this mailing list, I recommend you to open a new issue in our github page. Regards, -JJ On Mon, Feb 6, 2012 at 1:53 AM, Chris plut...@gmail.com wrote: Thanks JJ. The problem seems not to be a size issue -- markersize has no effect when use marker=, (pixel). I have also tried to turn off aa, and it doesn't help either. I also tried different backends. The PNG output from Agg and Cairo is slightly different: Agg's point has 4 solid pixel, while Cairo's has 4 pixel with random shade. Postscript output has the same problem. The pixel in an EPS file generated by mpl is significantly bigger than that from another drawing program I used. The problem occurs in all my plotting scripts, e.g., this basic one: [CODE] import numpy as np x=np.arange(100) y=np.random.randn(100) ioff() fig=gcf() fig.clf() ax=fig.add_axes(0.15,0.1,0.8, 0.85) ax.plot(x,y,k,) ion() fig.canvas.draw() [/CODE] Here is how I identify the problem: 1. use the above script to plot on screen 2. savefig(plot.png) 3. open plot.png in GIMP and check the pixel size. I also attached the two PNG files generated with Agg and Cairo backends. On Sun, Feb 5, 2012 at 6:45 AM, Jae-Joon Lee lee.j.j...@gmail.com wrote: How are you plotting your points. If you use *plot*, there is a *markersize* parameter. If you use *scatter*, the third argument controls the marker size. But you may actually complaining about other issues, e.g., antialiasing, etc. So, if above are not your answer, please post a complete example and describe your problem in more detail. Regards, -JJ On Sat, Feb 4, 2012 at 2:15 PM, Chris plut...@gmail.com wrote: I noticed this a few years back, but left it aside because most of the time I can live with it. Recently I need to make a few plots containing a few million points, and 4 pixels for a point is a disaster. So my question is why the pixel marker size is set at 4 pixels? And is there anyway to change it to a single pixel? Thanks, Chris -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] specgram memory problem
I'm using a lenovo laptop with fedora 16. It has 2.9 GiB memory and 4 intel core CPUs @ 2.3GHz each. Available disk space is 147.9GiB. numpy 1.6.0 matplotlib 1.0.1 On 6 Feb 2012, at 10:29, Fabrice Silva wrote: On Sat, Feb 4, 2012 at 9:44 AM, Fabrice Silva si...@lma.cnrs- mrs.fr wrote: Le vendredi 03 février 2012 à 17:39 +, David Craig a écrit : sure how to get it to plot the outputs from specgram. I use specgram as follows, Pxx, freqs, bins, im = plt.specgram(..) what am I trying imshow?? plt.specgram computes the spectrogram and when calls imshow to display the resulting array into an image Please tell the shape of Pxx, and try the following import numpy as np import matplotlib.pyplot as plt a = np.empty((12000, 14400), dtype=float) plt.imshow(a) plt.show() Le samedi 04 février 2012 à 10:30 +, David Craig a écrit : Pxx has shape (6001, 1430) and when I tried the lines of code it returned the following memory error, Traceback (most recent call last): File /usr/lib/python2.7/site-packages/matplotlib/backends/ backend_gtk.py, line 394, in expose_event self._render_figure(self._pixmap, w, h) File /usr/lib/python2.7/site-packages/matplotlib/backends/ backend_gtkagg.py, line 75, in _render_figure FigureCanvasAgg.draw(self) File /usr/lib/python2.7/site-packages/matplotlib/backends/ backend_agg.py, line 394, in draw self.figure.draw(self.renderer) File /usr/lib/python2.7/site-packages/matplotlib/artist.py, line 55, in draw_wrapper draw(artist, renderer, *args, **kwargs) File /usr/lib/python2.7/site-packages/matplotlib/figure.py, line 798, in draw func(*args) File /usr/lib/python2.7/site-packages/matplotlib/artist.py, line 55, in draw_wrapper draw(artist, renderer, *args, **kwargs) File /usr/lib/python2.7/site-packages/matplotlib/axes.py, line 1946, in draw a.draw(renderer) File /usr/lib/python2.7/site-packages/matplotlib/artist.py, line 55, in draw_wrapper draw(artist, renderer, *args, **kwargs) File /usr/lib/python2.7/site-packages/matplotlib/image.py, line 354, in draw im = self.make_image(renderer.get_image_magnification()) File /usr/lib/python2.7/site-packages/matplotlib/image.py, line 569, in make_image transformed_viewLim) File /usr/lib/python2.7/site-packages/matplotlib/image.py, line 201, in _get_unsampled_image x = self.to_rgba(self._A, self._alpha) File /usr/lib/python2.7/site-packages/matplotlib/cm.py, line 193, in to_rgba x = self.norm(x) File /usr/lib/python2.7/site-packages/matplotlib/colors.py, line 802, in __call__ val = ma.asarray(value).astype(np.float) File /usr/lib/python2.7/site-packages/numpy/ma/core.py, line 2908, in astype output = self._data.astype(newtype).view(type(self)) MemoryError Please, answer on the mailing list, It confirms that the troubles lie in the rendering of images. Could you tell the versions of numpy and matplotlib you are using, and the characteristics of the computer you are working on ? -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] specgram memory problem
On Mon, Feb 6, 2012 at 11:59 AM, David Craig dcdavem...@gmail.com wrote: I'm using a lenovo laptop with fedora 16. It has 2.9 GiB memory and 4 intel core CPUs @ 2.3GHz each. Available disk space is 147.9GiB. numpy 1.6.0 matplotlib 1.0.1 32-bit or 64-bit OS? Please use 'uname -a' to tell us, because you can install a 32-bit OS on a 64-bit machine. Ben Root -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] (no subject)
what is the basic difference between the commands import pylab as * import matplotlib.pyplot as plt -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] (no subject)
On Mon, Feb 6, 2012 at 1:07 PM, Debashish Saha silid...@gmail.com wrote: what is the basic difference between the commands import pylab as * import matplotlib.pyplot as plt This page should help you out. Let us know if you have any further questions. http://matplotlib.sourceforge.net/faq/usage_faq.html#matplotlib-pylab-and-pyplot-how-are-they-related Ben Root -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Why pixel marker size is 4 pixels?
There is a pull request for this here: https://github.com/matplotlib/matplotlib/pull/695 If you're able to checkout and build that branch from git, I would appreciate hearing if it resolves your issue. Mike On 02/06/2012 12:58 PM, Chris wrote: JJ, Thanks for the clarification. Now I understand why EPS outputs of pixel plot from mpl is a few times bigger than those from SuperMongo. I guess that mpl uses the square implementation for pixel so that it would use the same method to handle all marker types. I will file an issue report on git. Meanwhile, is there any easy workaround? Jonathan, Tom Robitaille's module does help reducing file size of postscript, but by rasterize a scalable plot. It doesn't really help my problem since the markers are still drawn with the same method as other plotting methods. Bests, Chris On Mon, Feb 6, 2012 at 4:28 AM, Jae-Joon Leelee.j.j...@gmail.com wrote: Thanks. Now I understand the situation. As far as I can see, marker=, is implemented as a rectangle path with width/height of 1 pixel, so this result in 2x2 pixel filled square. I tried to change the size of the rectangle, etc, to get a single pixel filled square, but did not get a satisfactory result. I think we need an Agg expert. I hope Mike or others take a look. Chris, if you do not get a response from others in this mailing list, I recommend you to open a new issue in our github page. Regards, -JJ On Mon, Feb 6, 2012 at 6:19 AM, Jonathan Slavinjsla...@cfa.harvard.edu wrote: Chris, You might want to try a module written by Tom Robitaille (aka astrofrog) called rasterized_scatter. Look for it on github. Jon On Mon, 2012-02-06 at 21:28 +0900, Jae-Joon Lee wrote: Thanks. Now I understand the situation. As far as I can see, marker=, is implemented as a rectangle path with width/height of 1 pixel, so this result in 2x2 pixel filled square. I tried to change the size of the rectangle, etc, to get a single pixel filled square, but did not get a satisfactory result. I think we need an Agg expert. I hope Mike or others take a look. Chris, if you do not get a response from others in this mailing list, I recommend you to open a new issue in our github page. Regards, -JJ On Mon, Feb 6, 2012 at 1:53 AM, Chrisplut...@gmail.com wrote: Thanks JJ. The problem seems not to be a size issue -- markersize has no effect when use marker=, (pixel). I have also tried to turn off aa, and it doesn't help either. I also tried different backends. The PNG output from Agg and Cairo is slightly different: Agg's point has 4 solid pixel, while Cairo's has 4 pixel with random shade. Postscript output has the same problem. The pixel in an EPS file generated by mpl is significantly bigger than that from another drawing program I used. The problem occurs in all my plotting scripts, e.g., this basic one: [CODE] import numpy as np x=np.arange(100) y=np.random.randn(100) ioff() fig=gcf() fig.clf() ax=fig.add_axes(0.15,0.1,0.8, 0.85) ax.plot(x,y,k,) ion() fig.canvas.draw() [/CODE] Here is how I identify the problem: 1. use the above script to plot on screen 2. savefig(plot.png) 3. open plot.png in GIMP and check the pixel size. I also attached the two PNG files generated with Agg and Cairo backends. On Sun, Feb 5, 2012 at 6:45 AM, Jae-Joon Leelee.j.j...@gmail.com wrote: How are you plotting your points. If you use *plot*, there is a *markersize* parameter. If you use *scatter*, the third argument controls the marker size. But you may actually complaining about other issues, e.g., antialiasing, etc. So, if above are not your answer, please post a complete example and describe your problem in more detail. Regards, -JJ On Sat, Feb 4, 2012 at 2:15 PM, Chrisplut...@gmail.com wrote: I noticed this a few years back, but left it aside because most of the time I can live with it. Recently I need to make a few plots containing a few million points, and 4 pixels for a point is a disaster. So my question is why the pixel marker size is set at 4 pixels? And is there anyway to change it to a single pixel? Thanks, Chris -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now!
Re: [Matplotlib-users] specgram memory problem
uname -a gives, Linux David 3.2.2-1.fc16.i686 #1 SMP Thu Jan 26 03:38:31 UTC 2012 i686 i686 i386 GNU/Linux On Mon, Feb 6, 2012 at 6:07 PM, Benjamin Root ben.r...@ou.edu wrote: On Mon, Feb 6, 2012 at 11:59 AM, David Craig dcdavem...@gmail.com wrote: I'm using a lenovo laptop with fedora 16. It has 2.9 GiB memory and 4 intel core CPUs @ 2.3GHz each. Available disk space is 147.9GiB. numpy 1.6.0 matplotlib 1.0.1 32-bit or 64-bit OS? Please use 'uname -a' to tell us, because you can install a 32-bit OS on a 64-bit machine. Ben Root -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] How matplotlib got me a job
Alternate title: How I finally convinced my Dad that open-source can put food on the table. Since this entire story got started on this mailing list, I figured it would be appropriate to end it here. Last Friday, I signed a contract to begin working as a Senior Scientific Programmer for a research company. The company has recently begun making Python the preferred language for new development and has become heavily dependent upon NumPy, SciPy and matplotlib. They have been doing fairly well for a while now, but a few months ago, they ran into a problem with matplotlib. After spending a few weeks butting heads on it, they finally decided to post a question about it to the matplotlib-users list. After reading the question and seeing the code example, I replied with a one-line fix within half an hour of its posting and moved on. About a week later, I got a personal email from the original poster informing me that my solution worked perfectly. He also noticed that I was working in a neighboring building on campus and wondered just how much longer my PhD was going to take and if I had any interest in going into the private sector. (The company happened to deal with atmospheric science and my PhD is in meteorology). It turned out that the company realized the value of having on-staff a SciPy Guru (I still consider myself a beginner). After the usual visits and interviews, I was offered a position. At multiple times throughout the process, it was obvious to me that while it was good that I was an atmospheric scientist, what was most valuable to them was my knowledge, insight and expertise with Python and its tools. The lesson I hope everyone here can take in is that there are many companies out there that are using open-source tools and libraries for their purposes. Learning and using these tools for your own purposes not only solves your immediate needs, but also sets you up for future opportunities. Therefore, I would like to thank John Hunter for making matplotlib available for the community, and a hearty thanks to the rest of the community for their contributions to matplotlib. Without this, I doubt I would have found this job opportunity, nor have the value-added skills to have them consider hiring me. Lastly, a reminder to everyone on this list, I hope this encourages more of you to help each other out with answers. You never know if the person you help out is your future co-worker! Cheers! Ben Root -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] How matplotlib got me a job
Benjamin Root, on 2012-02-06 13:59, wrote: Alternate title: How I finally convinced my Dad that open-source can put food on the table. Since this entire story got started on this mailing list, I figured it would be appropriate to end it here. Last Friday, I signed a contract to begin working as a Senior Scientific Programmer for a research company. Congrats on the new job, Ben! Great story, I could say that it had me Root-ing for you - but that would make you groan from the number of times you've probably heard it before, so I'm not gonna do that ;) Lastly, a reminder to everyone on this list, I hope this encourages more of you to help each other out with answers. You never know if the person you help out is your future co-worker! Hope this doesn't mean you'll be posting less, now :) I want to second Ben's comments: I learned (and continue to learn) quite a bit about matplotlib by trying to answer the questions others have (with my trusty IPython tab-completion, and when necessary, doing what every Python Jedi does, and use the Source) - and by following along with the answers others provide. best, -- Paul Ivanov 314 address only used for lists, off-list direct email at: http://pirsquared.org | GPG/PGP key id: 0x0F3E28F7 -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] How matplotlib got me a job
On Mon, Feb 6, 2012 at 2:59 PM, Benjamin Root ben.r...@ou.edu wrote: Alternate title: How I finally convinced my Dad that open-source can put food on the table. Since this entire story got started on this mailing list, I figured it would be appropriate to end it here. Inspiring and uplifting story, Ben. I'm glad you posted it. Congratulations on your new job! (That's also interesting that your father even knows what open-source is). Che -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] rendering unicode using the PDF backend
Hi All, I am having trouble rendering my Unicode strings in matplotlib using the PDF backend. When I use certain fonts (like the Win 7 default), I get no complaints but the characters are not rendered When I use a font like Arial Unicode MS, that I know contains all the chars, then I get the error message below. I did in fact, find a tty file that would work with Chinese (Microsoft YaHei), but I would like to avoid trying to map font files to languages. Any info on this subject would be greatly appreciated. Here is a snippet that reproduces the error below... if you remove the fontproperties option to the PYLAB.xlabel() call then the error is avoided but the result is not rendered. Thanks so much! MJ import matplotlib.pyplot as PLT import pylab as PYLAB from matplotlib.backends.backend_pdf import PdfPages as PDF import matplotlib.font_manager as fm fontFile = r'C:\Windows\Fonts\ARIALUNI.TTF' fp1 = fm.FontProperties(fname=fontFile) reportFile = r'C:\Temp\TestUnicode.pdf' pdfOutput = PDF(reportFile) vals = range(100) PLT.plot(vals, vals, color = r, linestyle = -) mess = u'\u6B63\u5728\u8BFB\u53D6\u6570\u636E...' PYLAB.xlabel(mess, fontproperties = fp1) PLT.savefig(pdfOutput, format='pdf') PLT.close() pdfOutput.close() Traceback (most recent call last): File C:\Data\CRs\10.1\MemLeak\matplotlib\Scripts\matplotlib_unicode.py, line 27, in module PLT.savefig(pdfOutput, format='pdf') File C:\Python27\lib\site-packages\matplotlib\pyplot.py, line 472, in savefig return fig.savefig(*args, **kwargs) File C:\Python27\lib\site-packages\matplotlib\figure.py, line 1173, in savefig self.canvas.print_figure(*args, **kwargs) File C:\Python27\lib\site-packages\matplotlib\backend_bases.py, line 2027, in print_figure **kwargs) File C:\Python27\lib\site-packages\matplotlib\backends\backend_pdf.py, line 2181, in print_pdf self.figure.draw(renderer) File C:\Python27\lib\site-packages\matplotlib\artist.py, line 55, in draw_wrapper draw(artist, renderer, *args, **kwargs) File C:\Python27\lib\site-packages\matplotlib\figure.py, line 886, in draw func(*args) File C:\Python27\lib\site-packages\matplotlib\artist.py, line 55, in draw_wrapper draw(artist, renderer, *args, **kwargs) File C:\Python27\lib\site-packages\matplotlib\axes.py, line 1983, in draw a.draw(renderer) File C:\Python27\lib\site-packages\matplotlib\artist.py, line 55, in draw_wrapper draw(artist, renderer, *args, **kwargs) File C:\Python27\lib\site-packages\matplotlib\axis.py, line 1054, in draw self.label.draw(renderer) File C:\Python27\lib\site-packages\matplotlib\artist.py, line 55, in draw_wrapper draw(artist, renderer, *args, **kwargs) File C:\Python27\lib\site-packages\matplotlib\text.py, line 587, in draw ismath=ismath) File C:\Python27\lib\site-packages\matplotlib\backends\backend_pdf.py, line 1784, in draw_text return draw_text_woven(chunks) File C:\Python27\lib\site-packages\matplotlib\backends\backend_pdf.py, line 1754, in draw_text_woven glyph_name = font.get_glyph_name(gind) RuntimeError: Face has no glyph names PS. I cannot use a different backend. -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] How matplotlib got me a job
On Mon, Feb 6, 2012 at 1:59 PM, Benjamin Root ben.r...@ou.edu wrote: Alternate title: How I finally convinced my Dad that open-source can put food on the table. Since this entire story got started on this mailing list, I figured it would be appropriate to end it here. Love the alternate title. I'm sure we can all substitute dad|mom|wife|husband|significant_other in that one. About a week later, I got a personal email from the original poster informing me that my solution worked perfectly. He also noticed that I was working in a neighboring building on campus and wondered just how much longer my PhD was going to take and if I had any interest in going into the private sector. (The company happened to deal with atmospheric science and my PhD is in meteorology). I love that a tiny bit of altruism turned into a good job for you. Recently my wife, who is a criminal defense attorney, decided to transition from criminal law to family law, and took on a pro-bono case of a friend who was in a tough spot (he was accused of spousal battery by a mentally ill wife and they had several young kids in the middle). At a Halloween party, she met someone who worked at a family law firm and began telling him about her case, and that led to a job interview and soon she'll be having her third interview with the firm. I don't know how it will turn out, but I'm pretty sure that she wouldn't have gotten this opportunity had she not taken on this case pro-bono. I grew up pretty much accepting the US ethos that 'there is no such thing as free lunch and no one works for free. So it came as a great surprise to me, sometime in 1994-1995, when I posted a question on comp.lang.awk about a script I was developing mixing sed and awk which parsed BibTeX. Some kind soul responded withing 12 hours, you should really be using Perl for this, *and* wrote a non-trivial, several hundred line piece of Perl to solve my problem. I was dumbstruck that someone would stay up all night solving a problem for me, not looking for anything except perhaps for credit. What I learned next was that altruism is infectious. I began diving deeply into Perl, mastering it, and answering other people's questions on the Perl mailing list. At one point, I was one of the top ten posters on the Perl mailing list -- no mean feat at the time -- mainly obsessively answering people's questions. Of course when I discovered Python, I dropped Perl faster than a hot potato, but that spirit of contributing to and benefiting from a community of people motivated not by a payback but by contributing to and participating in something excellent persisted. That free help that guy gave me on comp.lang.awk probably caused me to spend 8,000 hours over the next decade helping other people. I guess there is no such thing as free lunch. It turned out that the company realized the value of having on-staff a SciPy Guru (I still consider myself a beginner). After the usual visits and interviews, I was offered a position. At multiple times throughout the process, it was obvious to me that while it was good that I was an atmospheric scientist, what was most valuable to them was my knowledge, insight and expertise with Python and its tools. The lesson I hope everyone here can take in is that there are many companies out there that are using open-source tools and libraries for their purposes. Learning and using these tools for your own purposes not only solves your immediate needs, but also sets you up for future opportunities. No doubt about this one. I have tried with mixed success on a number of occasions to hire people for a job in quantitative finance who possess skills in scientific python tools as well as statistics, and it is hard to find good matches. Whenever I meet other people like me who are trying to hire people, they all tell the same tale: it's hard to find talent. So if you have these skills and would like a job, contact me :-) I've been astounded by the degree of uptake of the scientific python toolset, and it is accelerating. As more and more people use these tools, more and more companies require them and most importantly, more and more talented developers put their energies into them. The amount of productivity being poured into not only the core tools but also pandas, scikits-learn, scikits-image, pystatsmodels and others is awesome, and is definitely taking the tool chain to the next level. Therefore, I would like to thank John Hunter for making matplotlib available for the community, and a hearty thanks to the rest of the community for their contributions to matplotlib. Without this, I doubt I would have found this job opportunity, nor have the value-added skills to have them consider hiring me. You're welcome, but I owe you a significant thanks as well. As my time for significant development has dwindled, the major contributions by you and the other developers has enabled the project to thrive. I hope that in your
