Opened 10 years ago
Closed 4 years ago
#10775 closed enhancement (fixed)
streamline plots
Reported by:  jason  Owned by:  jason, was 

Priority:  major  Milestone:  sage7.4 
Component:  graphics  Keywords:  
Cc:  kcrisman, alauve, jakobkroeker, paulmasson, jhonrubia6  Merged in:  
Authors:  Paul Masson  Reviewers:  Travis Scrimshaw 
Report Upstream:  Completely fixed; Fix reported upstream  Work issues:  
Branch:  640cb6a (Commits)  Commit:  640cb6aad1a6b6380adabcb2c4d24d10eca3e718 
Dependencies:  Stopgaps: 
Description
Recently there was a thread on the matplotlib list where someone posted matplotlib code for a streamline plot. It looks very nice. If the code doesn't get included in matplotlib, we could still ask about including it in Sage to do streamline plots.
Mailing list message: http://permalink.gmane.org/gmane.comp.python.matplotlib.general/26362
Mailing list thread: http://comments.gmane.org/gmane.comp.python.matplotlib.general/26354
Example code: http://web.mit.edu/speth/Public/streamlines.py
Example plot: http://web.mit.edu/speth/Public/streamlines.png
Attachments (3)
Change History (43)
comment:1 Changed 10 years ago by
Changed 10 years ago by
Changed 10 years ago by
comment:2 Changed 10 years ago by
I've attached both code files so that we have them even if the above links go down for whatever reason.
comment:3 Changed 9 years ago by
See http://sagenb.org/home/pub/3237/ for a short example and rough Sage code (posted at http://sage.math.washington.edu/home/jason/sagefieldplots/)
comment:4 Changed 8 years ago by
 Report Upstream changed from N/A to Fixed upstream, but not in a stable release.
Yo, this is now in mpl!
I'm not sure how to figure out which release it's in, if it's in a release yet. It looks like it will probably be in 1.1.1, as 1.1.0 has been out for longer than this was in.
comment:5 Changed 8 years ago by
See also http://sage.cs.drake.edu/home/pub/60/ for another example.
Changed 8 years ago by
comment:6 Changed 8 years ago by
I attached the example I pointed out in the sage.cs.drake.edu server.
comment:7 Changed 8 years ago by
#13693 is for the appropriate mpl upgrade for this.
comment:8 Changed 7 years ago by
 Milestone changed from sage5.11 to sage5.12
comment:9 Changed 7 years ago by
 Milestone changed from sage6.1 to sage6.2
comment:10 Changed 7 years ago by
 Milestone changed from sage6.2 to sage6.3
comment:11 Changed 6 years ago by
 Milestone changed from sage6.3 to sage6.4
comment:12 Changed 6 years ago by
Here are some upstream examples.
Here is another example from somewhere in this discussion, allowing phase plots. Not directly related but looks nice with such things.
# based on code from oddrobot, http://sagenb.org/home/pub/1532/ from sage.calculus.desolvers import desolve_system_rk4 x,y,t=var('x y t') class DESolution: def __init__(self,system,time_range,initial,stepsize=0.05): self.tvar=time_range[0] self._times=srange(time_range[1],time_range[2],stepsize) self.vars=[v for v,_ in initial] self.dim=len(self.vars) self._soln=desolve_odeint(system, ics=[v for _,v in initial], times=self._times, dvars=self.vars, ivar=self.tvar) def phase_plot(self,vars=None,color='blue',**kwargs): # find which indices the specified variables are if vars is not None: vars_index=[self.vars.index(v) for v in vars] elif self.dim<=3: vars_index=range(self.dim) else: vars_index=range(2) p=line(self._soln[:,vars_index],color=color,**kwargs) # add an arrow head showing which way we are going around the phase line half=int(self._soln.shape[0]/2) p+=arrow(self._soln[half,vars_index], self._soln[half+1,vars_index],color=color) if len(vars_index)==2: p.axes_labels([str(self.vars[v]) for v in vars_index]) return p def coordinates(self,colors=None,**kwargs): if colors is None: colors=rainbow(len(self.vars)) p=Graphics() p+=sum(line(zip(self._times,self._soln[:,i]), color=colors[i], legend_label=str(self.vars[i]),**kwargs) for i in range(self.dim)) return p
comment:13 Changed 4 years ago by
 Cc alauve jakobkroeker paulmasson jhonrubia6 added
 Milestone changed from sage6.4 to sage7.4
 Report Upstream changed from Fixed upstream, but not in a stable release. to Completely fixed; Fix reported upstream
I was hoping we could resurrect this ticket as I am teaching a class on ODE's this semester and would like to plot streamlines on top of the slope fields. Does someone have some time to work on this? Alas, I don't know how much time I might have to do so.
So streamlines are included in matplotlib: http://matplotlib.org/examples/images_contours_and_fields/streamplot_demo_features.html
There is also another plot package I came across that is opensource python that does streamlines: https://plot.ly/python/streamlineplots/
comment:14 Changed 4 years ago by
Since I spent too much time today reading graphics code, I can take a crack at this. It looks like a new class is needed, modeled on PlotField
but calling the pyplot
method streamplot
instead of quiver
. It shouldn't be too difficult but won't happen overnight.
Travis, if you see a way to avoid a new class, then let me know before I dive in tomorrow.
comment:15 Changed 4 years ago by
To clarify: by new class I mean an individual file like scatter_plot.py
, which calls the pyplot
method scatter
.
comment:16 Changed 4 years ago by
Yes, this is exactly how you should do it. You could even keep it in the same module as the vector field plots, you can see that e.g. contour and density plots are in the same file.
comment:17 Changed 4 years ago by
Thank you for taking point on this Paul!
I agree with KarlDieter, you should definitely create a new class. However, contour and density plots are in separate files. Although, I have no preference whether or not you put in a separate file; it fits very well with plot_field.py
.
comment:18 Changed 4 years ago by
 Branch set to u/paulmasson/10775
comment:19 Changed 4 years ago by
 Commit set to 9576ba7abe47606fdf7667ea88e4bf8cf6dbefad
 Status changed from new to needs_review
This was surprisingly easy to get working! I copied over plot_field.py
and left variable names the same for consistency. Then it was a matter of rearranging how the data arrays were assembled and changing the pyplot
function name.
Doctests and useful examples have been updated. I left the _allowed_options
untouched because they might be relevant.
New commits:
852c719  Initial commit

e6094a3  Initial working commit

188b3c7  Update doctests

4c2ff90  Add streamline_plot

9576ba7  Update documentation

comment:20 Changed 4 years ago by
Sorry to ask for a bit more. Could we add a way to input an initial point, allow input as a single function to treat it as a slope field, and an option to display the vector/slope field? If this is too much trouble, I am okay with positive reviewing this ticket asis.
comment:21 followup: ↓ 22 Changed 4 years ago by
Travis, if by "initial point" you mean initial conditions, aren't those just part of the function arguments given to the plot? What more do you intend with this feature?
The idea of a convenience function that switches between streamline and vector/slope plots is interesting, but shouldn't be part of streamline_plot
itself. That one should stand alone, partly because the streamplot
function it uses behaves differently from the quiver
function used by the others. Some of the examples from plot_field.py
had to be left out of this new file because streamplot
returned errors for them.
Would this convenience function be used regularly by others, or just you for one class? What's the rule of thumb for adding those sorts of features to Sage?
If you still want an additional convenience function added to this file, give me a name for it and its options.
comment:22 in reply to: ↑ 21 Changed 4 years ago by
Replying to paulmasson:
Travis, if by "initial point" you mean initial conditions, aren't those just part of the function arguments given to the plot?
Yes, but how I am reading the code, it looks like it does streamlines starting at each integer point.
What more do you intend with this feature?
Plot a solution for a given IVP.
The idea of a convenience function that switches between streamline and vector/slope plots is interesting, but shouldn't be part of
streamline_plot
itself. That one should stand alone, partly because thestreamplot
function it uses behaves differently from thequiver
function used by the others. Some of the examples fromplot_field.py
had to be left out of this new file becausestreamplot
returned errors for them.
If you look at the slope plot, it redirects to the vector plot with special options. We should be able to automate this by looking at the input, a tuple for a vector plot and otherwise consider it a slope plot.
Would this convenience function be used regularly by others, or just you for one class? What's the rule of thumb for adding those sorts of features to Sage?
I would be surprised if this did not get significant uptake in a variety of other classes. One of my first forays into Python was plotting a single streamline for the Lorenz attractor. However, there are a number of things in Sage that are likely only used by a few people, so the rule is it gets added if someone is willing to positively review it.
If you still want an additional convenience function added to this file, give me a name for it and its options.
Granted, I would eventually like a 3d version, but that can most certainly be a followup ticket.
I should have time next week to actually directly work on this (i.e. write code).
comment:23 Changed 4 years ago by
 Commit changed from 9576ba7abe47606fdf7667ea88e4bf8cf6dbefad to 9201066f0ce6d2aab310a875b00a2eeeb4ec75e3
comment:24 followup: ↓ 25 Changed 4 years ago by
Travis, I went through the existing options, removed those that are not accepted by streamplot
and added one that is, density
. This value must be a single float or a pair of floats in a list, although I haven't added any validation for input values. It will at least allow you to see more streamlines and verify that they do not always start at integers.
There is another streamplot
option I though might be interesting called start_points
, but all it does is restrict streamlines to only those passing through an input list of points. You can test it by adding an option start_points=[[0,.1],[0,.1]]
or the like. Doesn't look too interesting to me.
comment:25 in reply to: ↑ 24 Changed 4 years ago by
 Branch changed from u/paulmasson/10775 to u/tscrim/streamline_plot10775
 Commit changed from 9201066f0ce6d2aab310a875b00a2eeeb4ec75e3 to 584486bf675c0c4b813ca2a75f745369f55f65a6
 Reviewers set to Travis Scrimshaw
Replying to paulmasson:
Travis, I went through the existing options, removed those that are not accepted by
streamplot
and added one that is,density
. This value must be a single float or a pair of floats in a list, although I haven't added any validation for input values. It will at least allow you to see more streamlines and verify that they do not always start at integers.
I added some input checking, but density
will still need to be documented.
There is another
streamplot
option I though might be interesting calledstart_points
, but all it does is restrict streamlines to only those passing through an input list of points. You can test it by adding an optionstart_points=[[0,.1],[0,.1]]
or the like. Doesn't look too interesting to me.
It is useful for showing numerical solutions to initial value problems (IVPs) of (nonlinear) ODEs. Also useful for seeing how stable solutions are. Although it is very annoying that it can't plot start points that are too close together:
sage: x,y = var('x,y') sage: f = (x + y) / sqrt(x^2 + y^2) sage: pts = [[1., 2.+val/8] for val in range(10)] sage: streamline_plot((cos(x), sin(x+y)), (x,3,3), (y,3,3), start_points=pts) /home/travis/sagebuild/local/lib/python2.7/sitepackages/sage/repl/rich_output/display_manager.py:590: RichReprWarning: Exception in _rich_repr_ while displaying object: RichReprWarning, Graphics object consisting of 1 graphics primitive
Although this is not something that would (nor should) block this getting a positive review.
New commits:
c443cc4  Merge branch 'u/paulmasson/10775' of git://trac.sagemath.org/sage into u/paulmasson/10775

584486b  Adding start points option and slope field input.

comment:26 Changed 4 years ago by
 Branch changed from u/tscrim/streamline_plot10775 to u/paulmasson/streamline_plot10775
comment:27 Changed 4 years ago by
 Commit changed from 584486bf675c0c4b813ca2a75f745369f55f65a6 to 9f3a5c25cd924b53bb8c4cb58fe6bd992440e40a
Ah, so that's what you had in mind for the additions.
The documentation would not build without some fixes. Sphinx plots do not allow ^
for exponentiation, needs to be **
, and variable declarations do not carry over between them. Documentation now builds.
New commits:
9f3a5c2  Fix Sphinx plots

comment:28 Changed 4 years ago by
Don't know if you noticed, Travis, but in the example with start_points
the streamlines come close to the start points but do not pass through them. I thought it might be because you didn't process the start points as in this example
http://matplotlib.org/examples/images_contours_and_fields/streamplot_demo_start_points.html
but even with setting up a numpy array as indicated and transposing it, the streamlines still do not pass through the start points. In fact the resulting graph is exactly the same as not bothering to process the points, so apparently that isn't necessary.
Problem with streamplot
? Thought you should know before any students ask what's going on.
comment:29 Changed 4 years ago by
Thanks for fixing that Paul. I guess we should add a note and example about the behavior of start_points
. Also, do you want me to document the density
option?
Actually, I think I should not be normalizing the input when we want to consider it as a slope field, which makes sense when considering plotting the tangent lines. I believe it just adds a unnecessary computation that cancels when considering splitting dy / dx
to (dx, dy)
.
comment:30 Changed 4 years ago by
 Commit changed from 9f3a5c25cd924b53bb8c4cb58fe6bd992440e40a to 478b1e19adc03befdc57d983aea8a09fc6e3e4dd
comment:31 Changed 4 years ago by
Documentation for implemented plot options now included. I also updated your language for start_points
using that from the matplotlib website and added the note.
I'm including a commented code block for the official way to handle start_points
in the event it is useful later.
comment:32 followup: ↓ 33 Changed 4 years ago by
I disagree with adding start_points
to the @options
, where if that is changed, it is perpetuated in all future plots, which is not what we want. I will revert this back when I make my next round of changes.
Does the "official way" for start_points
make any difference?
comment:33 in reply to: ↑ 32 Changed 4 years ago by
Replying to tscrim:
Does the "official way" for
start_points
make any difference?
Not that I can tell. xpos_array
and ypos_array
need to be explicit numpy arrays to avoid errors. The documentation says that start_points
is also supposed to be a numpy array, so I added this block of commented code in case that is ever enforced, but you can remove it if you feel that is more appropriate.
comment:34 Changed 4 years ago by
Let's use the official way. Also (not that it makes any real difference), you don't need to pop off the option:
if 'start_points' in options: xstart_array, ystart_array = [], [] for point in options['start_points']: xstart_array.append(point[0]) ystart_array.append(point[1]) options['start_points'] = numpy.array([xstart_array, ystart_array]).T
comment:35 Changed 4 years ago by
 Commit changed from 478b1e19adc03befdc57d983aea8a09fc6e3e4dd to 79e879535dc2096ed3e15a77f4ff276253e72e44
Branch pushed to git repo; I updated commit sha1. New commits:
79e8795  Update start_points handling

comment:36 Changed 4 years ago by
 Status changed from needs_review to positive_review
Thank you for all your work on this.
comment:37 Changed 4 years ago by
Not sure what Volker will find in his current run but I am failing to build the documentation in sageongentoo
[plotting ] /scratch2/portage/scimathematics/sage9999/work/sage9999/srcpython2_7/build/lib/sage/plot/streamline_plot.py:docstring of sage.plot.streamline_plot.streamline_plot:35: WARNING: Exception occurred in plotting streamline_plot1 [plotting ] from /scratch2/portage/scimathematics/sage9999/work/sage9999/srcpython2_7/doc/en/reference/plotting/sage/plot/streamline_plot.rst: [plotting ] Traceback (most recent call last): [plotting ] File "/usr/lib64/python2.7/sitepackages/matplotlib/sphinxext/plot_directive.py", line 517, in run_code [plotting ] six.exec_(code, ns) [plotting ] File "/usr/lib64/python2.7/sitepackages/matplotlib/externals/six.py", line 672, in exec_ [plotting ] exec("""exec _code_ in _globs_, _locs_""") [plotting ] File "<string>", line 1, in <module> [plotting ] File "<string>", line 2, in <module> [plotting ] File "/scratch2/portage/scimathematics/sage9999/work/sage9999/srcpython2_7/build/lib/sage/misc/decorators.py", line 554, in wrapper [plotting ] return func(*args, **options) [plotting ] File "/scratch2/portage/scimathematics/sage9999/work/sage9999/srcpython2_7/build/lib/sage/plot/streamline_plot.py", line 316, in streamline_plot [plotting ] for point in options['start_points']: [plotting ] TypeError: 'NoneType' object is not iterable
I have this several times. I note that the bots have a similar problem in their logs.
comment:38 Changed 4 years ago by
 Branch changed from u/paulmasson/streamline_plot10775 to u/tscrim/streamline_plot10775
 Commit changed from 79e879535dc2096ed3e15a77f4ff276253e72e44 to 640cb6aad1a6b6380adabcb2c4d24d10eca3e718
 Status changed from positive_review to needs_review
I had thought the first part of comment:32 was done by Paul. I removed start_points
from the @options
and did some little doc tweaking. Paul, can you make a quick check of my changes?
New commits:
1e2b2d0  Merge branch 'u/paulmasson/10775' of git://trac.sagemath.org/sage into u/tscrim/streamline_plot10775

fa8cda9  Merge branch 'u/paulmasson/streamline_plot10775' of git://trac.sagemath.org/sage into u/tscrim/streamline_plot10775

640cb6a  Some last little touchups.

comment:39 Changed 4 years ago by
 Status changed from needs_review to positive_review
Documentation now builds. Setting back to positive review.
comment:40 Changed 4 years ago by
 Branch changed from u/tscrim/streamline_plot10775 to 640cb6aad1a6b6380adabcb2c4d24d10eca3e718
 Resolution set to fixed
 Status changed from positive_review to closed
And here is another file from the same message with some fantastically nice plots:
Code: http://www.atm.damtp.cam.ac.uk/people/tjf37/streamplot.py
Result: http://www.atm.damtp.cam.ac.uk/people/tjf37/streamlines1.png
Result 2: http://www.atm.damtp.cam.ac.uk/people/tjf37/streamlines2.png