#8431 closed task (fixed)
Substitutions over unit cube faces (Rauzy fractals)
Reported by: | vdelecroix | Owned by: | tjolivet |
---|---|---|---|
Priority: | major | Milestone: | sage-4.6.1 |
Component: | combinatorics | Keywords: | word morphism unit face generalized substitution rauzy fractal |
Cc: | sage-combinat, slabbe, abmasse, tmonteil | Merged in: | sage-4.6.1.alpha2 |
Authors: | Vincent Delecroix, Timo Jolivet, Franco Saliola, Štěpán Starosta | Reviewers: | Sébastien Labbé, Alexandre Blondin Massé |
Report Upstream: | N/A | Work issues: | |
Branch: | Commit: | ||
Dependencies: | Stopgaps: |
Description (last modified by )
This patch introduces unit cube faces and substitutions over them, as defined in the article Pisot substitutions and Rauzy fractals by Arnoux and Ito.
Three new classes are defined:
Face
-- models a unit cube facePatch
-- models a finite collection of facesE1Star
-- models the the E_1^*(sigma) substitution (over faces) defined by a unimodular substitutionsigma
The plotting features enable us draw approximations of Rauzy fractals, or to generate patches of discrete planes.
The dimension of the faces can be of any dimension (and the substitutions work accordingly), but the plotting features work only in dimension three (with three-letter alphabet substitutions).
Attachments (13)
Change History (63)
comment:1 Changed 8 years ago by
- Description modified (diff)
comment:2 Changed 8 years ago by
- Description modified (diff)
- Type changed from defect to task
comment:3 Changed 8 years ago by
- Cc slabbe added
- Description modified (diff)
Changed 8 years ago by
comment:4 Changed 8 years ago by
- Description modified (diff)
- Keywords unit face generalized substitution rauzy fractal added
- Owner changed from vdelecroix to tjolivet
- Summary changed from Rauzy fractal (discrete planes and broken lines) to Substitutions over unit cube faces (Rauzy fractals)
comment:5 Changed 8 years ago by
- Status changed from new to needs_review
comment:6 Changed 8 years ago by
- Cc abmasse added
comment:7 Changed 8 years ago by
I feel like Patch
, Face
, E1Star
might be too domain specific to import into the global namespace.
comment:8 Changed 8 years ago by
- Status changed from needs_review to needs_work
Cher Timo,
Thanks a lot for your recent effort in polishing that code. I am actually needing it rigth now!! It will be of great help to me.
I just read through the patch from my web browser and got those comments :
- As Mike Hanson, I think those three classes should not be in the global namespace. To create a E1Star, I recommand to add a method in the
WordMorphism
class. - Add the file to the documentation. To do this you must edit the file sage-your-branch/doc/en/reference/combinat.rst
- Each sage block must be preceded by ::.
- No example using color in Face
__init__
function. - Examples of all the possible drawings.
- Rename
_image_by_substitution
to_apply_substitution
in Face class. - Face._image_by_substitution should only accept E1Star object. If not, it should raise an
TypeError
and not try to coerce the input to an E1Star object. - Patch.translate method forgets the color of the faces.
- Patch.apply_substitution should only accept E1Star object. If not, it should raise an
TypeError
and not try to coerce the input to an E1Star object. _M
and_inv_M
should becomelazy_attributes
_inv_M
should be computed from _M- For the matrix method of E1Star, should
_inv_M
be the "matrix associated with self" more than_M
? - When I used these classes last week, I needed the method
__eq__
for Patch. Here is my code :
def __eq__(self, other): r""" EXAMPLES:: TODO!! """ return (isinstance(other, Patch) and set(self) == set(other) )
I am going to download, apply and use the patch real soon...and I guess I will have more comments...
comment:9 Changed 8 years ago by
I suggest to add this example for the method __eq__
for Patch class :
def __eq__(self, other): r""" EXAMPLES:: sage: from sage.combinat.e_one_star import E1Star, Face, Patch sage: x = WordMorphism('0->02,1->012,2->2') sage: y = WordMorphism('0->012,1->12,2->2') sage: p = Patch([Face((0,0,0),1), Face((0,0,0),2), Face((0,0,0),3)]) sage: E1Star(x) (p) == E1Star(y) (p) False sage: E1Star(x * y) (p) == E1Star(y) (E1Star(x) (p)) True """ return (isinstance(other, Patch) and set(self) == set(other) )
I also suggest to add a __len__
method and change the __repr__
to behave like Graphs (Graph of 45 vertices).
def __repr__(self): r""" String representation of a patch. EXAMPLES: sage: x = [Face((0,0,0),t) for t in [1,2,3]] sage: P = Patch(x) sage: P Patch of 3 faces """ return "Patch of %s faces"%len(self) def __len__(self): r""" Returns the number of faces. EXAMPLES:: sage: x = [Face((0,0,0),t) for t in [1,2,3]] sage: P = Patch(x) sage: len(P) #indirect doctest 3 """ return len(self._faces)
comment:10 Changed 8 years ago by
The method __call__
of E1Star should pass the possible kwds to apply_substitution method
:
def __call__(self, patch, **kwds): r""" EXAMPLES: sage: p = Patch([Face((0,0,0),t) for t in [1,2,3]]) sage: sigma = WordMorphism('1->12,2->13,3->1') sage: E = E1Star(sigma) sage: E(p) Patch: [[(1, 0, -1), 1]*, [(0, 1, -1), 2]*, [(0, 0, 0), 3]*, [(0, 0, 0), 1]*, [(0, 0, 0), 2]*] """ patch = Patch(patch) patch.apply_substitution(self, **kwds) return patch
comment:11 Changed 8 years ago by
The last lines of plot_tikz should be :
s += '\\end{tikzpicture}\n' return LatexExpr(s)
Make sure to add the following line in the beginning of the file :
from sage.misc.latex import LatexExpr
This is to avoid latex(a_patch.plot_tikz())
be edited wrongly.
comment:12 Changed 8 years ago by
The function plot_tikz
should be renamed _latex_
.
A graph in Sage has methods plot
, plot3d
and _latex_
and I think we can follow the same behavior.
comment:13 Changed 8 years ago by
- Description modified (diff)
- Status changed from needs_work to needs_review
comment:14 in reply to: ↑ description Changed 8 years ago by
EDIT (2010-09-19): a new version of the patch is attached (
trac_8431_e_one_star.patch
), taking into account the suggestions given in the comments. Documentation compiles fine, except for the following warning, which I don't think comes from an error ine_one_star.py
:
/home/timo/sage-4.5.3/local/lib/python2.6/site-packages/sage/combinat/e_one_star.py:docstring of sage.combinat.e_one_star:56: (WARNING/2) Literal block expected; none found.
Actually, it does. If you don't write a sage block after the line EXAMPLES:
, then you must write only one colon:
EXAMPLES: We start by drawing a simple three-face patch::
instead of
EXAMPLES:: We start by drawing a simple three-face patch::
One more detail about ReST :
This module implements the `E_1^*(\sigma)` substitution associated with a one-dimensional substitution `\sigma`, that acts on unit faces of dimension `(d-1)` in `\mathbb R^d`.
The macro \RR
, as well as \ZZ
and \QQ
is defined to get the doc more readable in the terminal, so the following should work : `\RR^d`
.
Changed 8 years ago by
comment:15 Changed 8 years ago by
Okay, thanks again for the useful comments!
I've updated the patch.
comment:16 Changed 8 years ago by
- Status changed from needs_review to needs_work
I just uploaded a patch which fixes some syntax stuff but I did a little bit more than that. More importantly, I :
- moved
Face._apply_substitution
to the methodE1Star._call_on_face
because that is where that code belongs. - reworked
Patch.apply_substitution
and moved the code that was repainting the faces to a method calledPatch.repaint
- moved the code of
Patch.apply_substitution
toE1Star.__call__
because it *was* creating a copy anyway.Patch.apply_substitution
works as before.E1Star.__call__
works twice as fast as before because it doesn't do two copies but only one. - added some cached method and lazy attributes in
E1Star
class
I still see one possible problem before giving a positive review, but didn't have time enough to test/fix it. The attribute E1Star._base_iter
seems to assume some conditions on the values of faces types. That they are integer for instance. Haven't tested it.
For the tikz output code, I think the \newcommand
in the code is not compatible with sagetex package. If I am not mistaken, \newcommand
are not possible in an input file.
Timo, now that I uploaded a new patch, you will have to create a new separate patch that applies over yours and mine if you want to modify anything.
comment:17 Changed 8 years ago by
Okay, I just re-uploaded my review patch. The faces type is now considered as an arbitrary object. It can be any hashable object. Doing this, the code is more readable (e.g. the method _base_iter
) and more versatile (no such type + 1
assuming type is an integer).
In order to do so, I changed the way E1Star._base_iter
behave. It now returns a dict.
And now, the domain alphabet of the substitution used must correspond to the type of faces. No more '1' -> rank('1') = 0 -> + 1 -> 1 = type of a face. The type of faces iff domain alphabet. If one wants to use integer type of faces, he must define a substitution on integers which is possible using dictionary.
I also moved orig_coords
to an attribute of Patch called face_contour
. Code gets cleaner that way also. face_contour
now gets assigned at the creation of a Patch.
I also added #not tested
to many plot test so that the time of testing for that file is decreased from 24s to 7s on my computer. I kept some plot tested at minimum.
My very last concern about the actual state of the ticket is about the methods outputting tikz code. I want to make sure that they work well. I will do more test later (I'm done for the day). The necessity of \newcommand
needs to be studied.
Sorry Timo, I am very serious on the review. But I think it is better and easier to do changes now than after inclusion in Sage.
Cheers,
comment:18 follow-up: ↓ 19 Changed 8 years ago by
Okay I'll continue working on it! Thanks again for all you advices and improvements!
I'll do the remaining things we talked about and upload a new patch.
As for the tikz code, I am sure that it compiles fine (with a normal texlive installation). The \newcommand is nice because then one face is reprensented by a small line instead of three bulky ones. It could be two lines, but in tikz there is no other way to specify an RGB color than using \definecolor, which takes one more line. (Something similar to black!30!green
for RGB would be the great...)
comment:19 in reply to: ↑ 18 ; follow-up: ↓ 20 Changed 8 years ago by
Hello, Timo and Sébastien !
Replying to tjolivet:
As for the tikz code, I am sure that it compiles fine (with a normal texlive installation). The \newcommand is nice because then one face is reprensented by a small line instead of three bulky ones. It could be two lines, but in tikz there is no other way to specify an RGB color than using \definecolor, which takes one more line. (Something similar to
black!30!green
for RGB would be the great...)
I agree with you that the \newcommand
makes the output much lighter. On the other hand, it doesn't compile correctly... I tried it with a normal Latex distribution, but I had to move the three \newcommand
statements outside the tikzpicture environment.
I might have a solution that would avoid using them, but which is not as neat. You could use
\foreach \x / \y / \z / \c1 / \c2 / \c3 in {...}
and replace the ...
by the appropriate very long list of parameters for each face and then put in the body of the \foreach
command the 3-lines Latex statement that draws the face with these parameters.
What do you say? Do you understand what I'm talking about (I don't feel my explanation is very clear)?
comment:20 in reply to: ↑ 19 ; follow-up: ↓ 21 Changed 8 years ago by
Replying to abmasse:
I agree with you that the
\newcommand
makes the output much lighter. On the other hand, it doesn't compile correctly... I tried it with a normal Latex distribution, but I had to move the three\newcommand
statements outside the tikzpicture environment. I might have a solution that would avoid using them, but which is not as neat. You could use {{{ \foreach \x / \y / \z / \c1 / \c2 / \c3 in {...} }}} and replace the...
by the appropriate very long list of parameters for each face and then put in the body of the\foreach
command the 3-lines Latex statement that draws the face with these parameters. What do you say? Do you understand what I'm talking about (I don't feel my explanation is very clear)?
Yes, you made yourself clear, and it seems like a good idea. I'll try it on big instances, and if it works, I'll make it that way in the new patch. Otherwise, moving the \newcommand outside the tikzpicture is not a problem at all (it should have been that way, I probably made a ``typo''...).
comment:21 in reply to: ↑ 20 ; follow-up: ↓ 22 Changed 8 years ago by
Replying to tjolivet:
Replying to abmasse:
Yes, you made yourself clear, and it seems like a good idea. I'll try it on big instances, and if it works, I'll make it that way in the new patch. Otherwise, moving the \newcommand outside the tikzpicture is not a problem at all (it should have been that way, I probably made a ``typo''...).
The problem is that if you use the tikz_plot
twice in the document with sagetex
there will be a compilation problem (since you can't use \newcommand
on an already define command (you need local variables!).
There might be another solution, using \def\loza#1#2#3#4#5#6
(which is local when included in a tikzpicture
environment), but I haven't tried it out.
comment:22 in reply to: ↑ 21 Changed 8 years ago by
Replying to abmasse:
The problem is that if you use the
tikz_plot
twice in the document withsagetex
there will be a compilation problem (since you can't use\newcommand
on an already define command (you need local variables!). There might be another solution, using\def\loza#1#2#3#4#5#6
(which is local when included in atikzpicture
environment), but I haven't tried it out.
Okay, so I'll get rid of the \newcommand
in any case, and use either the \foreach
or the \def
solution; I admit I also like the idea of outputing a tikzpicture
that works ``out of the box''. Thanks for the suggestions and comments.
comment:23 follow-up: ↓ 24 Changed 8 years ago by
- Description modified (diff)
Hello, I uploaded a new patch (that applies over ``e_one_star and `` and ``review-sl``).
- It changes the
plot_tikz
function. There are no more\newcommand
's, but only\def
's that are inside thetikzpicture
environment. (No more global annoyance, and it should work fine withsagetex
now.) Also, RGB colors a printed with two decimals only.
- In response to "the domain alphabet of the substitution used must correspond to the type of faces": now, every substitution defining an
E1Star
object is converted to an equivalent substitution on alphabet'1'
, ...,'d'
. The type of a face can be specified by a positive integer or a string representing a positive integer, and is converted to a string when theFace
object is created. This allows us to assume that the type of a face in 3D is in {'1'
,'2'
,'3'
}, which is very useful for plotting functions.
- An option to color face according to their type has been added.
- It is possible to choose whether to (or not to) print the
tikzpicture
environment definition, and the\def
macros.
- Some other minor fixes, and small documentation fixes.
comment:24 in reply to: ↑ 23 Changed 8 years ago by
Salut Timo,
I look at the patch and still have comments.
- It changes the
plot_tikz
function. There are no more\newcommand
's, but only\def
's that are inside thetikzpicture
environment. (No more global annoyance, and it should work fine withsagetex
now.) Also, RGB colors a printed with two decimals only.
Great for the \def
instead of \newcommand
.
- In response to "the domain alphabet of the substitution used must correspond to the type of faces":
When I wrote that comment, I was meaning that I fixed it in my patch. In fact, I removed the coercion of the face type into the integer ring which allows the user to use the type of object he wants for the face types.
now, every substitution defining an
E1Star
object is converted to an equivalent substitution on alphabet'1'
, ...,'d'
. The type of a face can be specified by a positive integer or a string representing a positive integer, and is converted to a string when theFace
object is created.
I do not agree with this. I do not want the type face to be converted to an integer nor to a str. I want it to stays as it is given by the user. I want the correspondance between the faces type and the domain alphabet of the morphism to be clean. I do not want the correspondance appear by coincidence. Here are three examples to clarify my point :
GOOD (integer faces type with integers for the domain of the substitution) :
sage: from sage.combinat.e_one_star import E1Star, Face, Patch sage: x = [Face((0,0,0),1), Face((0,0,0),2), Face((0,0,0),3)] sage: P = Patch(x) sage: sigma = WordMorphism({1:[1,2], 2:[1,3], 3:[1]}) sage: E = E1Star(sigma) sage: E(P) Patch: [[(1, 0, -1), 1]*, [(0, 1, -1), 2]*, [(0, 0, 0), 3]*, [(0, 0, 0), 1]*, [(0, 0, 0), 2]*]
GOOD (str faces type with str for the domain of the substitution) :
sage: from sage.combinat.e_one_star import E1Star, Face, Patch sage: x = [Face((0,0,0),'1'), Face((0,0,0),'2'), Face((0,0,0),'3')] sage: P = Patch(x) sage: sigma = WordMorphism('1->12,2->13,3->1') sage: E = E1Star(sigma) sage: E(P) Patch: [[(1, 0, -1), 1]*, [(0, 1, -1), 2]*, [(0, 0, 0), 3]*, [(0, 0, 0), 1]*, [(0, 0, 0), 2]*]
BAD (integer faces type with str for the domain of the substitution). Correspondance is lost. If the following is suppported, it makes the code less usable for potential future uses by others.
sage: from sage.combinat.e_one_star import E1Star, Face, Patch sage: x = [Face((0,0,0),1), Face((0,0,0),2), Face((0,0,0),3)] sage: P = Patch(x) sage: sigma = WordMorphism('1->12,2->13,3->1') sage: E = E1Star(sigma) sage: E(P) Patch: [[(1, 0, -1), 1]*, [(0, 1, -1), 2]*, [(0, 0, 0), 3]*, [(0, 0, 0), 1]*, [(0, 0, 0), 2]*]
The reason is that the code we write is *always* used differently by the others. And the coercion of the face type to a str object is an unneccessary restriction. Do you agree with me?
This allows us to assume that the type of a face in 3D is in {
'1'
,'2'
,'3'
}, which is very useful for plotting functions.
Can you explain me why it is useful for plotting functions? Is it because digits can not be used in a definition like \def\loz1{...}
? But then, I don't understand why '1'
is better than 1
. I am sure we can find a solution for the plotting problem that will not restrict the usability of the code.
- An option to color face according to their type has been added.
Thanks for fixing this in the __call__
method. Small suggestions : coloring='color_from_type' is redundant. I suggest that the following
- ``color_from_type`` - boolean (default: False). Colors the faces according to their type.
becomes
- ``'face_type'`` - boolean (default: False). Colors the faces according to their type.
For the repaint
method. I dislike the addition of a new argument to the function. The reason is that the user should never use the argument cmap
at the same time as the argument color_from_type
. Hence, inconstencies in the arguments can happen and should be considered. This tells us that it should be only one argument that plays the role for either one or the other. Python is great for that because it is not a typed language. Moreover, I was disappointed that it is not possible for the user to specify which color he can give to each faces type. Hence, I suggest to do the following which should fix all the problems I mention::
def repaint(self, cmap='hsv'): r""" Repaint all the faces of self from the given color map. This changes self. INPUT: - ``cmap`` - color map (default: 'hsv'). It can be one of the following : - string - A color map. For available color map names type: ``import matplotlib.cm; matplotlib.cm.datad.keys()``. Each face will be given a color according to their rank in the patch. - list - a list of color to assign to the faces in order. - dict - a dict of faces type mapped to colors. - ``{}``, the empty dict - the dict ``{'1':'red', '2':'green', '3':'blue'}`` is used.
- It is possible to choose whether to (or not to) print the
tikzpicture
environment definition, and the\def
macros.
Ok. And by default, they are printed : great.
- Some other minor fixes, and small documentation fixes.
Great.
Finally, lines like
if print_macros == True:
should be replaced by
if print_macros:
That is it for now.
If you rework on it, you can reload your last patch or add a new one. It is as you wish. I do not have any local modifications.
Cheers!
Changed 8 years ago by
comment:25 follow-up: ↓ 26 Changed 8 years ago by
Hi Sébastien and the others,
[We had a long discussion on skype with Sébastien regarding his last reply.]
I just uploaded a new version of the last patch. The face types are now integers, and only integers (from 1 to d), and the WordMorphism associated with an E1Star object is also defined on integers.
Some other things I changed:
- I removed the
coloring
option inapply_substitution
. Why? Because we can userepaint
, and it is better that all the "color business" is taken care of byrepaint
. The colors of a face in an image by a substitution is automatically the color of its preimage (which enables to get the interesting coloring given by the substitution). If we want to change the color of a patch obtained by iteration,repaint
!
- I took care of the above remarks concerning
color_from_preimage
, and used the clever solution suggested by Sébastien: dictionaries{types:colors}
.
- Some small fixes.
Now, a last and important remark. Writing
sigma = WordMorphism('1->12,2->13,3->1')
is less painful than writing
sigma = WordMorphism({1:[1,2], 2:[1,3], 3:[1]})
Since all the face types are integers and the WordMorphism defining an E1Star
must be on integers, we are supposed to use the latter way to define sigma
. However, I find it very inconvenient, so we allow the user to give a sigma
defined on an arbitrary alphabet. When E1Star
is defined, it is converted and stored as a substitution on the alphabet [1, ..., d]
(so that there is a correspondence between the types of the faces and the alphabet of the substitutions). It really makes the definitions much more convenient and I don't think that it harms sage
so much.
Also, I don't think that it would be useful to allow the user to specify an arbitrary alphabet for the faces, since they are not used as the letters of a word, but as three-dimensional objects, which we call of type 1
, 2
or 3
. (This is why all the types are represented by integers.) It corresponds to the mathematical definition of the object.
I strongly insist on this last remark!
comment:26 in reply to: ↑ 25 ; follow-up: ↓ 27 Changed 8 years ago by
Hi, Timo and Sébastien !
Replying to tjolivet:
Hi Sébastien and the others,
Now, a last and important remark. Writing
sigma = WordMorphism('1->12,2->13,3->1')is less painful than writing
sigma = WordMorphism({1:[1,2], 2:[1,3], 3:[1]})
I agree with you on that one. This is something I've noticed too when using WordMorphism
's. The thing is: the problem comes from the object WordMorphism?, and it's where it should be solved, in my opinion, and not in the class E1Star
.
Since all the face types are integers and the WordMorphism defining an
E1Star
must be on integers, we are supposed to use the latter way to definesigma
. However, I find it very inconvenient, so we allow the user to give asigma
defined on an arbitrary alphabet. WhenE1Star
is defined, it is converted and stored as a substitution on the alphabet[1, ..., d]
(so that there is a correspondence between the types of the faces and the alphabet of the substitutions). It really makes the definitions much more convenient and I don't think that it harmssage
so much.Also, I don't think that it would be useful to allow the user to specify an arbitrary alphabet for the faces, since they are not used as the letters of a word, but as three-dimensional objects, which we call of type
1
,2
or3
. (This is why all the types are represented by integers.) It corresponds to the mathematical definition of the object.
I disagree. If I'm not mistaken, the integer meaning of 1, 2, 3 is never used in the construction of patches and discrete plane. I mean, we could use a,b,c and everything would work the same, there is no gain from encoding it with integers, since no additive group structure is used (correct me if I'm wrong, though, that could be a good argument).
In fact, I think it's quite the opposite. It would be better to allow the user to have any alphabet, so that he can use any structure he wants (additive group, for instance, or any other operation that might encode interesting discrete plane construction).
I strongly insist on this last remark!
What I propose you is that either Sébastien or I work on the improvement of the construction of WordMorphism
in order to offer something like
sigma = WordMorphism('1->12,2->13,3->1', type='integer')
Does that seem reasonable?
P.S. I'm following your discussion and I see the progress... Keep the good work!
comment:27 in reply to: ↑ 26 Changed 8 years ago by
Thanks for you answer and hello!
Replying to abmasse:
I disagree. If I'm not mistaken, the integer meaning of 1, 2, 3 is never used in the construction of patches and discrete plane. I mean, we could use a,b,c and everything would work the same, there is no gain from encoding it with integers, since no additive group structure is used (correct me if I'm wrong, though, that could be a good argument). In fact, I think it's quite the opposite. It would be better to allow the user to have any alphabet, so that he can use any structure he wants (additive group, for instance, or any other operation that might encode interesting discrete plane construction).
Yes, the types are just names, so anything else could be used. But I'm not sure that it would be very useful, it's not comparable to allowing any choice of letters for words, for example. If you (or anybody else) want to implement it, it's OK, but please make sure that if integer faces are given, it works as in the current patch by default (to make it "easy-usable").
What I propose you is that either Sébastien or I work on the improvement of the construction of
WordMorphism
in order to offer something likesigma = WordMorphism('1->12,2->13,3->1', type='integer')
Does that seem reasonable? P.S. I'm following your discussion and I see the progress... Keep the good work!
This a good idea, even with respect to WordMorphism only. I'm just a bit saddened that we will have to add "type='integer'
") when specifying a substitution to work with the default integers, but I can live with it!
---
I think that apart from the possible option to leave the choice of the alphabet, and the "type='integer'
" feature to be added to WordMorphism, the work on this patch is over. Do you agree? I leave these two last points up to you.
Thanks for all your help, work and comments on this (it's my first patch, as you know), I'm learning a lot. And I'm ready to work more if there is something more that I forgot!
comment:28 Changed 8 years ago by
Hi Timo,
- I removed the
coloring
option inapply_substitution
. Why? Because we can userepaint
, and it is better that all the "color business" is taken care of byrepaint
. The colors of a face in an image by a substitution is automatically the color of its preimage (which enables to get the interesting coloring given by the substitution). If we want to change the color of a patch obtained by iteration,repaint
!
Great idea! Very very good. That is really upgrading the quality of the code. The design is converging!
- I took care of the above remarks concerning
color_from_preimage
, and used the clever solution suggested by Sébastien: dictionaries{types:colors}
.
Great. I am just wondering if we could avoid to use a list of one color to change the color of every faces. If their is no intersection between the list of available color and the list of available color map, then simply a color string could be used for coloring every faces the same color.
Now, a last and important remark. Writing
sigma = WordMorphism('1->12,2->13,3->1')is less painful than writing
sigma = WordMorphism({1:[1,2], 2:[1,3], 3:[1]})
I agree.
Since all the face types are integers and the WordMorphism defining an
E1Star
must be on integers, we are supposed to use the latter way to definesigma
. However, I find it very inconvenient, so we allow the user to give asigma
defined on an arbitrary alphabet. WhenE1Star
is defined, it is converted and stored as a substitution on the alphabet[1, ..., d]
(so that there is a correspondence between the types of the faces and the alphabet of the substitutions). It really makes the definitions much more convenient and I don't think that it harmssage
so much.Also, I don't think that it would be useful to allow the user to specify an arbitrary alphabet for the faces, since they are not used as the letters of a word, but as three-dimensional objects, which we call of type
1
,2
or3
. (This is why all the types are represented by integers.) It corresponds to the mathematical definition of the object.I strongly insist on this last remark!
One solution is to allow face type '1', '2' and '3' which would work easily with such expressions : WordMorphism('1->12,2->13,3->1')
. But I know you don't like this solution.
On the other side, as I already explained, I dislike the solution you propose because (1) it is getting the code less efficient for those who specify a WordMorphism? already defined on integers, (2) because those translation of object gets the code less versatile and reusable by others and (3) it may leads to conceptual problems for the user when letters gets translated not in the way he expected.
Personnaly, I can not give a positive review with this translation of alphabet.
I think Alexandre's ideas for improving the definition of WordMorphism
might be a good compromise.
Moreover, in the code of plot_tikz
, I suggest to use the following ideas :
sage: P = Patch([Face((0,0,0),t) for t in [1,2,3]]) sage: d = P._face_contour sage: ' -- '.join(map(str, d[1])) + ' -- cycle;\n' '(0, 0, 0) -- (0, 1, 0) -- (0, 1, 1) -- (0, 0, 1) -- cycle;\n'
rather than hardcoding the face contour points:
if print_macros: s += '\\def\\loza#1#2#3#4#5#6{\n' s += ' \\definecolor{facecolor}{rgb}{#4,#5,#6}\n' s += ' \\fill[fill=facecolor, draw=black, shift={(#1, #2, #3)}]\n' s += ' (0,0,0) -- (0,1,0) -- (0,1,1) -- (0,0,1) -- cycle;\n' s += '}\n'
comment:29 Changed 8 years ago by
Just added a patch that improves the color map manipulations and tikz code. I removed the Face._plot_tikz
method that was not really usable on its own and moved its code into the Patch.plot_tikz
.
Patches apply in this order :
- trac_8431_e_one_star.patch
- trac_8431_review-sl.patch
- trac_8431_might_be_final_tj.patch
- trac_8431_colors_tikz-sl.patch
Earlier, I wrote :
Great. I am just wondering if we could avoid to use a list of one color to change the color of every faces. If their is no intersection between the list of available color and the list of available color map, then simply a color string could be used for coloring every faces the same color.
Forget about that, I was wrong. I like the way it is.
comment:30 Changed 8 years ago by
So, now, I can say that I give a positive review to this ticket if the following 5 lines of E1Star.__init__
are removed.
# changing the alphabet of sigma to [1, ..., d] A = sigma.domain().alphabet() change_alphabet = WordMorphism(dict([(A[i], [Integer(i+1)]) for i in range(len(A))])) D = dict([(change_alphabet(a)[0], list(change_alphabet(sigma(a)))) for a in A]) sigma = WordMorphism(D)
Of course, my two patches also have to get a positive review by Timo or Alexandre (preferably both) before the ticket be ready to be merged into Sage.
comment:31 follow-up: ↓ 33 Changed 8 years ago by
OK, I uploaded a last patch to fix the type of the WordMorphism. The __init__
method of E1Star
accepts only integer substitutions. I have changed the doc accordingly. I hope that the type='integer'
option of WordMosphim will be available soon!
The patch seems to be ready. How do we give positive review of an individual patch, and not to the whole ticket? How long will it take before it is integrated to sage?
To recap, the patches apply in this order:
- trac_8431_e_one_star.patch
- trac_8431_review-sl.patch
- trac_8431_might_be_final_tj.patch
- trac_8431_colors_tikz-sl.patch
- trac_8431_sigma_type_fix.patch
(Can we remove the useless trac_8431_E1Star.patch patch?)
comment:32 Changed 8 years ago by
- Cc tmonteil added
comment:33 in reply to: ↑ 31 Changed 8 years ago by
Replying to tjolivet:
The patch seems to be ready. How do we give positive review of an individual patch, and not to the whole ticket? How long will it take before it is integrated to sage?
Normally, when two people work on the same ticket and both of them provide patches, the last person cannot make the final positive review, so in that case, it's Sébastien that should do it. However, I will probably do it this week since both you and Sébastien worked on it. This way, it will give a different point of view. The patch probably won't be merged in sage-4.6 as it is already in its alpha stage, but should be included in the next version.
To recap, the patches apply in this order:
- trac_8431_e_one_star.patch
- trac_8431_review-sl.patch
- trac_8431_might_be_final_tj.patch
- trac_8431_colors_tikz-sl.patch
- trac_8431_sigma_type_fix.patch
(Can we remove the useless trac_8431_E1Star.patch patch?)
Unfortunately, you can't.
comment:34 Changed 8 years ago by
- Reviewers set to Sébastien Labbé, Alexandre Blondin-Massé
- Status changed from needs_work to needs_review
Just added a new patch that adds two methods that might be useful : E1Star.__mul__
and WordMorphism.dual_map
.
Patches need to be applied in this order:
- trac_8431_e_one_star.patch
- trac_8431_review-sl.patch
- trac_8431_might_be_final_tj.patch
- trac_8431_colors_tikz-sl.patch
- trac_8431_sigma_type_fix.patch
- trac_8431-wordmorphism-sl.patch
comment:35 Changed 8 years ago by
- Reviewers changed from Sébastien Labbé, Alexandre Blondin-Massé to Sébastien Labbé, Alexandre Blondin Massé
comment:36 follow-up: ↓ 37 Changed 7 years ago by
Hi,
This patch (trac_8431-smallfixes-tj.patch) corrects three bugs and adds three minor features:
- in
.plot_tikz
, the optionedgecolor='facecolor'
didnt't work - in
.plot_tikz
, the optionprint_tikz_env=False
caused an error message - in
.plot3d
, the plot was rotated uselessly (it was confusing) - patches can now be added (which gives their union)
E1Star
morphisms can now be multiplied (according to the rule E1Star(s*t) = E1Star(t)*E1Star(s))
Patches need to be applied in this order:
- trac_8431_e_one_star.patch
- trac_8431_review-sl.patch
- trac_8431_might_be_final_tj.patch
- trac_8431_colors_tikz-sl.patch
- trac_8431_sigma_type_fix.patch
- trac_8431-wordmorphism-sl.patch
- trac_8431-smallfixes-tj.patch
comment:37 in reply to: ↑ 36 Changed 7 years ago by
Replying to tjolivet:
- in
.plot3d
, the plot was rotated uselessly (it was confusing)
A precision about the .plot3d
fix, the removal of these two lines:
911 P.aspect_ratio((1,1,1))
912 P = P.rotateY(pi/2).rotateX(pi/2)
The first line doesn't change anything. The only way to control the aspect ratio of the rendered object in Jmol is to include it into a cube that contains everything, because Jmol will automatically take the smallest 3D rectangle that contains the object, and deform it to a cube (hence changing the aspect ratio). If a cube bounds everything, we get an actual aspect ratio of (1,1,1).
The second line was initally written to "turn" the patch so that it faces the viewer when Jmol opens. The problem is that rotate
does not change the point of view, but rotates the object itself, which is very confusing when we want to plot something else with the Patch (normal vectors or contracting planes, for example).
Changed 7 years ago by
comment:38 Changed 7 years ago by
I just added a new patch (trac_8431-alphaset-tj.patch) that applies over the previous ones, and that allows to set the alpha
parameter in the .plot
method. It is useful if we want to plot fractals without seeing the unit cube edges.
comment:39 Changed 7 years ago by
Hi, Timo !
I tried applying the various patches on a sage-4.6 clone and the patch trac_8431-smallfixes-tj.patch fails. Here's what I get.
labo [~/Applications/sage/devel/sage-t8431/sage/combinat] $ hg qseries trac_8431_e_one_star.patch trac_8431_review-sl.patch trac_8431_might_be_final_tj.patch trac_8431_colors_tikz-sl.patch trac_8431_sigma_type_fix.patch trac_8431-wordmorphism-sl.patch trac_8431-smallfixes-tj.patch labo [~/Applications/sage/devel/sage-t8431/sage/combinat] $ hg qtop trac_8431-smallfixes-tj.patch labo [~/Applications/sage/devel/sage-t8431/sage/combinat] $ hg qpop now at: trac_8431-wordmorphism-sl.patch labo [~/Applications/sage/devel/sage-t8431/sage/combinat] $ hg qpush applying trac_8431-smallfixes-tj.patch patching file sage/combinat/e_one_star.py Hunk #6 FAILED at 1337 1 out of 7 hunks FAILED -- saving rejects to file sage/combinat/e_one_star.py.rej patch failed, unable to continue (try -v) patch failed, rejects left in working dir errors during apply, please fix and refresh trac_8431-smallfixes-tj.patch
Could you please fix it? Or is it because the order is not correct? Here's the output for the rejected hunk:
labo [~/Applications/sage/devel/sage-t8431/sage/combinat] $ cat e_one_star.py.rej --- e_one_star.py +++ e_one_star.py @@ -1230,49 +1338,6 @@ X[letter].append((v, k)) return X - def __call__(self, patch, iterations=1): - r""" - Apply a generalized substitution to a Patch; this returns a new - object. - - The color of every new face in the image is given the same color as its preimage. - - INPUT: - - - ``patch`` - a patch - - ``iterations`` - integer (optional, default: 1) number of iterations - - OUTPUT: - - a patch - - EXAMPLES:: - - sage: from sage.combinat.e_one_star import E1Star, Face, Patch - sage: P = Patch([Face((0,0,0),t) for t in [1,2,3]]) - sage: sigma = WordMorphism({1:[1,2], 2:[1,3], 3:[1]}) - sage: E = E1Star(sigma) - sage: R = E(P) - sage: len(R) - 5 - - :: - - sage: x = (0,0,0) - sage: p = Patch([Face(x, 1, 'red'), Face(x, 2, 'yellow'), Face(x, 3, 'green')]) - sage: p = E(p, iterations=4) - sage: p - Patch of 31 faces - """ - old_faces = patch - for i in xrange(iterations): - new_faces = [] - for f in old_faces: - new_faces.extend(self._call_on_face(f, color=f.color())) - old_faces = new_faces - - return Patch(new_faces) - def _call_on_face(self, face, color=None): r""" Returns an iterator of faces obtained by applying self on the face.
comment:40 Changed 7 years ago by
Hi !
Well, that's very strange: I just compiled 4.6, made a fresh clone, and I could apply all the patches without any problem:
timo@ukko:~/sage-4.6/devel/sage-haha$ ../../sage -hg qseries trac_8431_e_one_star.patch trac_8431_review-sl.patch trac_8431_might_be_final_tj.patch trac_8431_colors_tikz-sl.patch trac_8431_sigma_type_fix.patch trac_8431-wordmorphism-sl.patch trac_8431-smallfixes-tj.patch trac_8431-alphaset-tj.patch timo@ukko:~/sage-4.6/devel/sage-haha$ ../../sage -hg qtop trac_8431-alphaset-tj.patch timo@ukko:~/sage-4.6/devel/sage-haha$ ../../sage -hg qpop now at: trac_8431-smallfixes-tj.patch timo@ukko:~/sage-4.6/devel/sage-haha$ ../../sage -hg qpop now at: trac_8431-wordmorphism-sl.patch timo@ukko:~/sage-4.6/devel/sage-haha$ ../../sage -hg qpush applying trac_8431-smallfixes-tj.patch now at: trac_8431-smallfixes-tj.patch timo@ukko:~/sage-4.6/devel/sage-haha$ ../../sage -hg qpush applying trac_8431-alphaset-tj.patch now at: trac_8431-alphaset-tj.patch
Could you try it again? There's no reason that it works for me but not for you!
(And don't forget the last patch trac_8431-alphaset-tj.patch
!)
To recap, the order is:
- trac_8431_e_one_star.patch
- trac_8431_review-sl.patch
- trac_8431_might_be_final_tj.patch
- trac_8431_colors_tikz-sl.patch
- trac_8431_sigma_type_fix.patch
- trac_8431-wordmorphism-sl.patch
- trac_8431-smallfixes-tj.patch
- trac_8431-alphaset-tj.patch
[BTW, a question: when I need to apply such a sequence of patches, do I have to do "import, qpush, import, qpush, import, qpush, ...
", with an import
and a qpush
for each patch ?]
Changed 7 years ago by
comment:41 Changed 7 years ago by
Hi. Sorry, this error message was because of a manipulation error from my part. (I misapplied the wordmorphism-sl patch, and my two last patches were based on this misapplying.)
I made a new patch that applies correctly over wordmorphism-sl, and that takes into account my two last patches (which should now be ignored; it's a shame that we can't delete patches from the ticket!).
Patches should be applied in this order:
- trac_8431_e_one_star.patch
- trac_8431_review-sl.patch
- trac_8431_might_be_final_tj.patch
- trac_8431_colors_tikz-sl.patch
- trac_8431_sigma_type_fix.patch
- trac_8431-wordmorphism-sl.patch
- trac_new-fixes-final-tj.patch
(Sorry for misnaming the last patch, I forgot "8431"... And sorry if this made you lose some time!)
Changed 7 years ago by
comment:42 Changed 7 years ago by
Thanks for you final remarks. The last patch is trac_8431_typos-docfix-tj.patch, and the sequence is:
- trac_8431_e_one_star.patch
- trac_8431_review-sl.patch
- trac_8431_might_be_final_tj.patch
- trac_8431_colors_tikz-sl.patch
- trac_8431_sigma_type_fix.patch
- trac_8431-wordmorphism-sl.patch
- trac_new-fixes-final-tj.patch
- trac_8431_typos-docfix-tj.patch
comment:43 follow-up: ↓ 45 Changed 7 years ago by
Hi Timo and Sébastien !
I just uploaded a (I hope last) patch that fixes a minor doctest failure (decimal number, on my computer but not Timo's).
I tested all of it on sage-4.6. I'm satisfied with the code and the documentation looks good (no warning neither).
Before setting this ticket to "positive review", I want to know if Sébastien is ok with it, since he reviewed big parts, and if Timo agrees with my last patch (Timo, just make sure it still passes on your machine).
comment:44 Changed 7 years ago by
Yes, the patch applies fine, and the doctest passes. Everything seems to be fine now.
Just a recap:
- trac_8431_e_one_star.patch
- trac_8431_review-sl.patch
- trac_8431_might_be_final_tj.patch
- trac_8431_colors_tikz-sl.patch
- trac_8431_sigma_type_fix.patch
- trac_8431-wordmorphism-sl.patch
- trac_new-fixes-final-tj.patch
- trac_8431_typos-docfix-tj.patch
- trac_8431_doctest_fix-abm.patch
comment:45 in reply to: ↑ 43 Changed 7 years ago by
- Status changed from needs_review to positive_review
Before setting this ticket to "positive review", I want to know if Sébastien is ok with it, since he reviewed big parts, and if Timo agrees with my last patch (Timo, just make sure it still passes on your machine).
All test pass on my machine. Coverage is 100%. Documentation builds fine. Positive review!
I just folded the 9 patches into one : trac_8431_folded.patch. It might be easier for the release manager.
Great work!
comment:46 follow-up: ↓ 47 Changed 7 years ago by
- Status changed from positive_review to needs_work
1) Please update the commit message of the folded patch (use hg qrefresh -e
for that). Make sure the first line contains the ticket number and a short summary of the whole patch. The next lines can contain a longer description.
2) The copyright message in the files MUST be changed to state
# Distributed under the terms of the GNU General Public License (GPL) # as published by the Free Software Foundation; either version 2 of # the License, or (at your option) any later version. # http://www.gnu.org/licenses/ #*****************************************************************************
comment:47 in reply to: ↑ 46 Changed 7 years ago by
- Status changed from needs_work to needs_review
I just re-uploaded the folded patch.
1) Please update the commit message of the folded patch (use
hg qrefresh -e
for that).
Done.
2) The copyright message in the files MUST be changed to state
Done. I did not know the copyright message changed.
Needs review.
comment:48 Changed 7 years ago by
- Status changed from needs_review to positive_review
I just checked that the fixes required by the release manager have indeed been done.
All tests still pass.
Positive review.
comment:49 Changed 7 years ago by
- Merged in set to sage-4.6.1.alpha2
- Resolution set to fixed
- Status changed from positive_review to closed
I add myself in cc because I am interested.