Hello, I am relatively new to Python, numpy, matplotlib, etc., with a reasonable amount of Matlab experience. I am trying to do some simple array visualizations before moving on to specific work. e.g. I have a 5x5x10 array and I'd like to see each 5x5 piece as a "frame" with a short pause in between. I realize there are animation methods and such but I think the code below ought to work and don't understand what I'm getting. Expect: A figure window with the first 5x5 piece of the array, a short pause, a new figure window overwriting the old one with the second 5x5 piece, and so on. Equivalent code in Matlab does this. Result: Figure window opens, nothing gets drawn in it, there's a pause, the window closes, and another window opens in the same location with nothing in it, and so on. If I refresh the kernel, create the 3D array, and manually show one slice, it works. As soon as I run the loop, all I get from then on is blank windows whether I do it within a loop or type the matshow, show commands. This happens in iPython with and without the notebook interface. I'm trying to understand Matplotlib in some detail and am watching the SciPy2014 videos along with RTFM. https://www.youtube.com/watch?v=A2adyFMsut0 et.seq. So far, I've come up empty in figuring out what I'm doing wrong. I have Python 2.7.8/Anaconda 2.0.1 Thanks, JBB ===== Test code import numpy as np from matplotlib.pylab import * import time as time # Create a 3D array of "frames" A = np.random.rand(5,5,10) #Turn on interactive mode ion() # Turn off interactive mode # ioff() # Attempt to show each frame with a short delay between frames for k in range(10): matshow(A[:,:,k]) show() time.sleep(1) close()
On 2014年07月29日, 7:04 PM, JBB wrote: > Hello, > > I am relatively new to Python, numpy, matplotlib, etc., with a > reasonable amount of Matlab experience. > > I am trying to do some simple array visualizations before moving on to > specific work. > > e.g. I have a 5x5x10 array and I'd like to see each 5x5 piece as a > "frame" with a short pause in between. I realize there are animation > methods and such but I think the code below ought to work and don't > understand what I'm getting. > > Expect: A figure window with the first 5x5 piece of the array, a short > pause, a new figure window overwriting the old one with the second 5x5 > piece, and so on. Equivalent code in Matlab does this. > > Result: Figure window opens, nothing gets drawn in it, there's a pause, > the window closes, and another window opens in the same location with > nothing in it, and so on. > > If I refresh the kernel, create the 3D array, and manually show one > slice, it works. As soon as I run the loop, all I get from then on is > blank windows whether I do it within a loop or type the matshow, show > commands. > > This happens in iPython with and without the notebook interface. > > I'm trying to understand Matplotlib in some detail and am watching the > SciPy2014 videos along with RTFM. > https://www.youtube.com/watch?v=A2adyFMsut0 et.seq. > > So far, I've come up empty in figuring out what I'm doing wrong. > > I have Python 2.7.8/Anaconda 2.0.1 > > Thanks, > > JBB > ===== Test code > > import numpy as np > from matplotlib.pylab import * > import time as time > > # Create a 3D array of "frames" > A = np.random.rand(5,5,10) > > #Turn on interactive mode > ion() > # Turn off interactive mode > # ioff() > > # Attempt to show each frame with a short delay between frames > for k in range(10): > matshow(A[:,:,k]) > show() > time.sleep(1) > close() > First, at least initially for this sort of thing, run in "ipython --pylab", and don't use any "ion()" or "ioff()". Second, replace the "show(); time.sleep(1)" with "pause(1)". I think that will do it. Eric > > ------------------------------------------------------------------------------ > Infragistics Professional > Build stunning WinForms apps today! > Reboot your WinForms applications with our WinForms controls. > Build a bridge from your legacy apps to the future. > http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk > _______________________________________________ > Matplotlib-users mailing list > Mat...@li... > https://lists.sourceforge.net/lists/listinfo/matplotlib-users >
On 7/29/14, 10:49 PM, Eric Firing wrote: > On 2014年07月29日, 7:04 PM, JBB wrote: >> Hello, >> >> I am relatively new to Python, numpy, matplotlib, etc., with a >> reasonable amount of Matlab experience. ...[ Problem and test code trimmed ] > > First, at least initially for this sort of thing, run in "ipython > --pylab", and don't use any "ion()" or "ioff()". > > Second, replace the "show(); time.sleep(1)" with "pause(1)". > > I think that will do it. > > Eric > Thank you, very much. It did indeed work. Is there a pointer to why this worked when my initial approach did not? I thought from the documentation/videos that preparing a plot with relevant commands then issuing the show() command was the preferred approach within Python/Matplotlib. JBB
I think it is mostly an issue with how IPython interfaces with matplotlib. If you were running from a pure python prompt, then I would suspect it to work (haven't tried myself, though). Note that the --pylab option to ipython is now highly discouraged. Instead, I would try the "%matplotlib interactive" cell magic instead (I think that is the right incantation). On Wed, Jul 30, 2014 at 2:15 AM, JBB <jea...@gm...> wrote: > On 7/29/14, 10:49 PM, Eric Firing wrote: > > On 2014年07月29日, 7:04 PM, JBB wrote: > >> Hello, > >> > >> I am relatively new to Python, numpy, matplotlib, etc., with a > >> reasonable amount of Matlab experience. > > ...[ Problem and test code trimmed ] > > > > > First, at least initially for this sort of thing, run in "ipython > > --pylab", and don't use any "ion()" or "ioff()". > > > > Second, replace the "show(); time.sleep(1)" with "pause(1)". > > > > I think that will do it. > > > > Eric > > > > Thank you, very much. It did indeed work. > > Is there a pointer to why this worked when my initial approach did not? > I thought from the documentation/videos that preparing a plot with > relevant commands then issuing the show() command was the preferred > approach within Python/Matplotlib. > > JBB > > > > > > ------------------------------------------------------------------------------ > Infragistics Professional > Build stunning WinForms apps today! > Reboot your WinForms applications with our WinForms controls. > Build a bridge from your legacy apps to the future. > > http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk > _______________________________________________ > Matplotlib-users mailing list > Mat...@li... > https://lists.sourceforge.net/lists/listinfo/matplotlib-users >
Hi, On Wed, Jul 30, 2014 at 9:30 AM, Benjamin Root <ben...@ou...> wrote: > I think it is mostly an issue with how IPython interfaces with matplotlib. > If you were running from a pure python prompt, then I would suspect it to > work (haven't tried myself, though). Note that the --pylab option to ipython > is now highly discouraged. Instead, I would try the "%matplotlib > interactive" cell magic instead (I think that is the right incantation). Sorry for being slightly off-topic, but what is the current recommendation then for interactive plots from the console, if --pylab is discouraged? Cheers, Matthew
There is no change to the recommendations for interactive plots from the console, if by console you mean the normal python REPL. There is no --pylab for that. If you mean from the IPython console, then it is the cell magic I mentioned previously. On Wed, Jul 30, 2014 at 1:19 PM, Matthew Brett <mat...@gm...> wrote: > Hi, > > On Wed, Jul 30, 2014 at 9:30 AM, Benjamin Root <ben...@ou...> wrote: > > I think it is mostly an issue with how IPython interfaces with > matplotlib. > > If you were running from a pure python prompt, then I would suspect it to > > work (haven't tried myself, though). Note that the --pylab option to > ipython > > is now highly discouraged. Instead, I would try the "%matplotlib > > interactive" cell magic instead (I think that is the right incantation). > > Sorry for being slightly off-topic, but what is the current > recommendation then for interactive plots from the console, if --pylab > is discouraged? > > Cheers, > > Matthew >
On 2014年07月30日, 7:26 AM, Benjamin Root wrote: > There is no --pylab for that. I don't know what development version you are using, but for 2.1.0, it is still there--and it does what needs to be done.
On 2014年07月30日 14:51, Eric Firing wrote: > On 2014年07月30日, 7:26 AM, Benjamin Root wrote: >> There is no --pylab for that. > > I don't know what development version you are using, but for 2.1.0, it > is still there--and it does what needs to be done. He was talking about the normal Python interpreter, not IPython. -- Brendan Barnwell "Do not follow where the path may lead. Go, instead, where there is no path, and leave a trail." --author unknown
I've followed up on several suggestions and here is what I've done/found. (I know I don't use mlab or pylab but I pulled the import lines from another source and am leaving them in for the heck of it) Code A: import numpy as np import matplotlib import time from matplotlib import pylab, mlab, pyplot A = np.random.rand(5,5,10) for j in range(10): pyplot.matshow(A[:,:,j]) # pyplot.pause(.5) pyplot.show() time.sleep(0.5) pyplot.close() Code B: import numpy as np import matplotlib import time from matplotlib import pylab, mlab, pyplot A = np.random.rand(5,5,10) for j in range(10): pyplot.matshow(A[:,:,j]) pyplot.pause(.5) # pyplot.show() # time.sleep(0.5) pyplot.close() ================ 1) Code A: Spyder Python (Mac) - A blank figure window is generated, closed, and repeated over ten iterations. No user intervention needed to allow loop to continue. Adding a pyplot.ioff() line after the from matplotlib line gives the expected/hoped behavior: Ten arrays appear, one after the other, no intervention needed. --- Ipython Notebook (no --pylab) - A figure window with an array appears. I have to close it using the Window Close titlebar button, then the next one appears, waits for close action, etc. Adding a pyplot.ion() statement after the from matplotlib line yields the same result as Spyder Python w/o the pyplot.ioff() line. 10 blank windows appear one after the other. Code B: Spyder Python and Ipython Notebook (no --pylab) - Both display expected/hoped behavior. Figure window appears, figure displays, closes, and then opens with next piece of data So, there's something about the pause command that's special, at least in this case, and I'd like to understand what that is. 2) Additional interactive test following code runs: pyplot.matshow(A[:,:,6)] Spyder Python - Figure pops up, plot is displayed. Zoom, pan, back/forth, home buttons all work Ipython notebook (no --pylab) - Figure pops up, no plot displays. Adding pause(x) causes figure to display. Plot is interactive for x seconds. Zoom, pan, etc. work for that time. Notebook shows In[*] for x seconds. After x seconds, In[*] <-- In[Cell number]. Plot is no longer interactive, mousing over plot shows spinning Mac rainbow ball. Can't even close window using titlebar icons. pyplot.close() from a cell required to close. I would like to stay with the Notebook as I learn matplotlib but I'm not sure how to get around the plot being interactive for only a defined time period, spinning rainbow balls, etc. JBB On 7/30/14, 9:30 AM, Benjamin Root wrote: > I think it is mostly an issue with how IPython interfaces with > matplotlib. If you were running from a pure python prompt, then I would > suspect it to work (haven't tried myself, though). Note that the --pylab > option to ipython is now highly discouraged. Instead, I would try the > "%matplotlib interactive" cell magic instead (I think that is the right > incantation). > > > On Wed, Jul 30, 2014 at 2:15 AM, JBB > <jea...@gm... > <mailto:jea...@gm...>> wrote: > > On 7/29/14, 10:49 PM, Eric Firing wrote: > > On 2014年07月29日, 7:04 PM, JBB wrote: > >> Hello, > >> > >> I am relatively new to Python, numpy, matplotlib, etc., with a > >> reasonable amount of Matlab experience. > > ...[ Problem and test code trimmed ] > > > > > First, at least initially for this sort of thing, run in "ipython > > --pylab", and don't use any "ion()" or "ioff()". > > > > Second, replace the "show(); time.sleep(1)" with "pause(1)". > > > > I think that will do it. > > > > Eric > > > > Thank you, very much. It did indeed work. > > Is there a pointer to why this worked when my initial approach did not? > I thought from the documentation/videos that preparing a plot with > relevant commands then issuing the show() command was the preferred > approach within Python/Matplotlib. > > JBB > > > > > ------------------------------------------------------------------------------ > Infragistics Professional > Build stunning WinForms apps today! > Reboot your WinForms applications with our WinForms controls. > Build a bridge from your legacy apps to the future. > http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk > _______________________________________________ > Matplotlib-users mailing list > Mat...@li... > <mailto:Mat...@li...> > https://lists.sourceforge.net/lists/listinfo/matplotlib-users > > > > > ------------------------------------------------------------------------------ > Infragistics Professional > Build stunning WinForms apps today! > Reboot your WinForms applications with our WinForms controls. > Build a bridge from your legacy apps to the future. > http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk > > > > _______________________________________________ > Matplotlib-users mailing list > Mat...@li... > https://lists.sourceforge.net/lists/listinfo/matplotlib-users >
Exec. summary - I was having strange behavior with matshow in a loop and
also with discrepancies between how iPython Notebook and Python via IDE
displayed plots.
Solutions:
1) Using pause instead of show fixed matshow in a loop
2) Explicitly invoking %matplotblib qt or generally %matplotlib
{backend} before importing or using matplotlib fixed various problems
with plots in notebooks. Now when I create a plot in a notebook, it
appears, I can work with it, close it when appropriate, and
simultaneously be able to do other work in notebook cells.
Thanks to everyone for the rapid responses.
JBB
On 7/30/14, 10:04 PM, JBB wrote:
> I've followed up on several suggestions and here is what I've done/found.
>
> (I know I don't use mlab or pylab but I pulled the import lines from
> another source and am leaving them in for the heck of it)
[ Woe/intrigue trimmed ]
>> Is there a pointer to why this worked when my initial approach did not?
>> I thought from the documentation/videos that preparing a plot with
>> relevant commands then issuing the show() command was the preferred
>> approach within Python/Matplotlib.
>>
>> JBB
>>
You would use "%matplotlib inline" if you want the plots to show up inline in the notebook. If you want to use one of the gui backends, it would be "%matplotlib <backend>". More detail here: http://ipython.org/ipython-doc/2/api/generated/IPython.core.magics.pylab.html#IPython.core.magics.pylab.PylabMagics.matplotlib Pylab is going to be removed in IPython 3.0 (in fact it's already gone in master) since it has several bad interactions with the rest of the numpy/scipy universe and leads to un-reproducible code. See this blog post for more detail on why using pylab is a bad idea: https://carreau.github.io/posts/10-No-PyLab-Thanks.ipynb.html On Wed, Jul 30, 2014 at 10:19 AM, Matthew Brett <mat...@gm...> wrote: > Hi, > > On Wed, Jul 30, 2014 at 9:30 AM, Benjamin Root <ben...@ou...> wrote: > > I think it is mostly an issue with how IPython interfaces with > matplotlib. > > If you were running from a pure python prompt, then I would suspect it to > > work (haven't tried myself, though). Note that the --pylab option to > ipython > > is now highly discouraged. Instead, I would try the "%matplotlib > > interactive" cell magic instead (I think that is the right incantation). > > Sorry for being slightly off-topic, but what is the current > recommendation then for interactive plots from the console, if --pylab > is discouraged? > > Cheers, > > Matthew > > > ------------------------------------------------------------------------------ > Infragistics Professional > Build stunning WinForms apps today! > Reboot your WinForms applications with our WinForms controls. > Build a bridge from your legacy apps to the future. > > http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk > _______________________________________________ > Matplotlib-users mailing list > Mat...@li... > https://lists.sourceforge.net/lists/listinfo/matplotlib-users >
right, thank you, it is "inline", not "interactive". I really need a memory upgrade... Cheers! Ben Root On Wed, Jul 30, 2014 at 1:26 PM, Nathan Goldbaum <nat...@gm...> wrote: > You would use "%matplotlib inline" if you want the plots to show up inline > in the notebook. If you want to use one of the gui backends, it would be > "%matplotlib <backend>". More detail here: > > > http://ipython.org/ipython-doc/2/api/generated/IPython.core.magics.pylab.html#IPython.core.magics.pylab.PylabMagics.matplotlib > > Pylab is going to be removed in IPython 3.0 (in fact it's already gone in > master) since it has several bad interactions with the rest of the > numpy/scipy universe and leads to un-reproducible code. See this blog post > for more detail on why using pylab is a bad idea: > > https://carreau.github.io/posts/10-No-PyLab-Thanks.ipynb.html > > > On Wed, Jul 30, 2014 at 10:19 AM, Matthew Brett <mat...@gm...> > wrote: > >> Hi, >> >> On Wed, Jul 30, 2014 at 9:30 AM, Benjamin Root <ben...@ou...> wrote: >> > I think it is mostly an issue with how IPython interfaces with >> matplotlib. >> > If you were running from a pure python prompt, then I would suspect it >> to >> > work (haven't tried myself, though). Note that the --pylab option to >> ipython >> > is now highly discouraged. Instead, I would try the "%matplotlib >> > interactive" cell magic instead (I think that is the right incantation). >> >> Sorry for being slightly off-topic, but what is the current >> recommendation then for interactive plots from the console, if --pylab >> is discouraged? >> >> Cheers, >> >> Matthew >> >> >> ------------------------------------------------------------------------------ >> Infragistics Professional >> Build stunning WinForms apps today! >> Reboot your WinForms applications with our WinForms controls. >> Build a bridge from your legacy apps to the future. >> >> http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk >> _______________________________________________ >> Matplotlib-users mailing list >> Mat...@li... >> https://lists.sourceforge.net/lists/listinfo/matplotlib-users >> > >
Hi, On Wed, Jul 30, 2014 at 10:26 AM, Nathan Goldbaum <nat...@gm...> wrote: > You would use "%matplotlib inline" if you want the plots to show up inline > in the notebook. If you want to use one of the gui backends, it would be > "%matplotlib <backend>". More detail here: > > http://ipython.org/ipython-doc/2/api/generated/IPython.core.magics.pylab.html#IPython.core.magics.pylab.PylabMagics.matplotlib > > Pylab is going to be removed in IPython 3.0 (in fact it's already gone in > master) since it has several bad interactions with the rest of the > numpy/scipy universe and leads to un-reproducible code. See this blog post > for more detail on why using pylab is a bad idea: > > https://carreau.github.io/posts/10-No-PyLab-Thanks.ipynb.html I personally use the IPython console for my just-checking interactive work, rather than the notebook. Checking now, '%matplotlib inline' in the console raises an error, understandably enough, but this works: %matplotlib osx import matplotlib.pyplot as plt plt.plot(range(10)) I know that's what you said, it's just to give a complete snippet for Googlers, Cheers, Matthew
On Wed, Jul 30, 2014 at 10:26 AM, Nathan Goldbaum <nat...@gm...> wrote: > Pylab is going to be removed in IPython 3.0 (in fact it's already gone in > master) since it has several bad interactions with the rest of the > numpy/scipy universe and leads to un-reproducible code. Quick clarifications: - `--pylab` as a command-line flag is strongly discouraged and we will likely remove it (having it in that location requires really awkward special-case code everywhere). But we'll probably keep the %pylab magic indefinitely, since it's useful for quick-and-dirty command-line work where you don't care about namespace pollution, just about minimizing typing and namespace access for convenience. - The %matplotlib magic can also be used without args, case in which it works like %pylab used to, and will pick up the user's default backend: In [1]: %matplotlib Using matplotlib backend: TkAgg In [2]: import matplotlib.pyplot as plt In [3]: plt.plot([1,2,3]) Out[3]: [<matplotlib.lines.Line2D at 0x4b90ed0>] Cheers f -- Fernando Perez (@fperez_org; http://fperez.org) fperez.net-at-gmail: mailing lists only (I ignore this when swamped!) fernando.perez-at-berkeley: contact me here for any direct mail
Thanks for all the responses. I'll try pure Python via the Spyder IDE vs. Ipython/Ipython Notebook for this and report back. The 'No Pylab Thanks' was enlightening. I am confused about the role of the Notebook interface. I've been using it to learn the language, do experiments, and preserve tips/tricks I pick up along the way. I've also seen it used in many online presentations and courses on Python, numpy, matplotlib, and other packages. I've found it very helpful so far and would like to stick with it. But, it sounds like it there are some hidden issues in how the notebook i/f interacts with matplotlib? Is it not the best choice for learning plotting? If not, what's recommended - IDE? Python from a terminal window? ... ? JBB
Hi, On Wed, Jul 30, 2014 at 5:14 PM, JBB <jea...@gm...> wrote: > Thanks for all the responses. I'll try pure Python via the Spyder IDE > vs. Ipython/Ipython Notebook for this and report back. The 'No Pylab > Thanks' was enlightening. > > I am confused about the role of the Notebook interface. I've been using > it to learn the language, do experiments, and preserve tips/tricks I > pick up along the way. I've also seen it used in many online > presentations and courses on Python, numpy, matplotlib, and other > packages. I've found it very helpful so far and would like to stick with it. > > But, it sounds like it there are some hidden issues in how the notebook > i/f interacts with matplotlib? Is it not the best choice for learning > plotting? If not, what's recommended - IDE? Python from a terminal > window? ... ? I think the notebook is pretty good for all those things. I have got out of the habit of using the notebook when I'm writing code, because it can be hard to switch between the notebook and my usual development tools - in my case vim and bash and occasionally the IPython console. But - for exploring plotting, I would say it was a good choice. Cheers, Matthew
On Wed, Jul 30, 2014 at 6:11 PM, Matthew Brett <mat...@gm...> wrote: > But - for exploring plotting, I would say it was a good choice. Yup, I'm obviously as biased as they come, but I think that the immediate feedback and the ability to keep plots together with their source code, makes learning and experimenting with mpl (or other plotting libs) an ideal use case for the notebook. The only catch to be aware of is that, in order for a simple plot(x) to produce a figure without having to manually call show(), we do a bit of magic behind the scenes. And that magic can occasionally lead to duplicate figures when you start manually calling display(fig) yourself. So in that more advanced scenario, you will need to add the occasional plt.close() call. HTH, f -- Fernando Perez (@fperez_org; http://fperez.org) fperez.net-at-gmail: mailing lists only (I ignore this when swamped!) fernando.perez-at-berkeley: contact me here for any direct mail