Opened 8 years ago
Closed 5 years ago
#14973 closed enhancement (wontfix)
New functions for binary linear codes
Reported by:  veronica  Owned by:  

Priority:  major  Milestone:  sageduplicate/invalid/wontfix 
Component:  coding theory  Keywords:  binary codes 
Cc:  ppurka, dimpase  Merged in:  
Authors:  Reviewers:  
Report Upstream:  N/A  Work issues:  
Branch:  u/ppurka/ticket/14973 (Commits, GitHub, GitLab)  Commit:  743826b1c73c946be9b8ff4fdb97819879fc07ac 
Dependencies:  Stopgaps: 
Description (last modified by )
The idea of this work is to add some functions to linear_code.py and new decoding algorithms. Theory and algorithms are taken from: I. MarquezCorbella. A combinatorial Commutative Algebra Approach to Complete Decoding PhD thesis, University of Valladolid, 2013.
Apply to devel/sage: trac_14973new_decoding_functions.patch
Attachments (2)
Change History (33)
comment:1 Changed 8 years ago by
 Cc ppurka added
comment:2 Changed 8 years ago by
comment:3 Changed 8 years ago by
This is just a list of short comments, nothing like a comprehensive review. Anybody else looking at this should feel free to test the code and report problems.
Did you run the tests in this file? I get
Running doctests with ID 201307261031104d8b78a5. Doctesting 1 file. sage t devel/sage/sage/coding/linear_code.py ********************************************************************** File "devel/sage/sage/coding/linear_code.py", line 2996, in sage.coding.linear_code.LinearCode.newton_radius Failed example: H = matrix(GF(2),[[1,0,0,0,1,0,0,0,0,0],[1,0,1,1,0,1,0,0,0,0],[1,1,0,1,0,0,1,0,0,0], Exception raised: Traceback (most recent call last): File "/home/burcin/sage/sage5.11.beta3/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 485, in _run compileflags, 1) File "<doctest sage.coding.linear_code.LinearCode.newton_radius[0]>", line 1 H = matrix(GF(Integer(2)),[[Integer(1),Integer(0),Integer(0),Integer(0),Integer(1),Integer(0),Integer(0),Integer(0),Integer(0),Integer(0)],[Integer(1),Integer(0),Integer(1),Integer(1),Integer(0),Integer(1),Integer(0),Integer(0),Integer(0),Integer(0)],[Integer(1),Integer(1),Integer(0),Integer(1),Integer(0),Integer(0),Integer(1),Integer(0),Integer(0),Integer(0)], ^ SyntaxError: unexpected EOF while parsing ********************************************************************** File "devel/sage/sage/coding/linear_code.py", line 2998, in sage.coding.linear_code.LinearCode.newton_radius Failed example: C = LinearCodeFromCheckMatrix(H) Exception raised: Traceback (most recent call last): File "/home/burcin/sage/sage5.11.beta3/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 486, in _run self.execute(example, compiled, test.globs) File "/home/burcin/sage/sage5.11.beta3/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 845, in execute exec compiled in globs File "<doctest sage.coding.linear_code.LinearCode.newton_radius[1]>", line 1, in <module> C = LinearCodeFromCheckMatrix(H) NameError: name 'H' is not defined ********************************************************************** File "devel/sage/sage/coding/linear_code.py", line 3000, in sage.coding.linear_code.LinearCode.newton_radius Failed example: C.newton_radius(t) Exception raised: Traceback (most recent call last): File "/home/burcin/sage/sage5.11.beta3/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 486, in _run self.execute(example, compiled, test.globs) File "/home/burcin/sage/sage5.11.beta3/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 845, in execute exec compiled in globs File "<doctest sage.coding.linear_code.LinearCode.newton_radius[3]>", line 1, in <module> C.newton_radius(t) NameError: name 'C' is not defined ********************************************************************** 1 item had failures: 3 of 5 in sage.coding.linear_code.LinearCode.newton_radius [374 tests, 3 failures, 5.76 s]  sage t devel/sage/sage/coding/linear_code.py # 3 doctests failed  Total time for all tests: 5.9 seconds cpu time: 4.4 seconds cumulative wall time: 5.8 seconds
After fixing that problem, I still have:
Running doctests with ID 201307261031500e819b57. Doctesting 1 file. sage t devel/sage/sage/coding/linear_code.py ********************************************************************** File "devel/sage/sage/coding/linear_code.py", line 2999, in sage.coding.linear_code.LinearCode.newton_radius Failed example: C.newton_radius(t) Exception raised: Traceback (most recent call last): File "/home/burcin/sage/sage5.11.beta3/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 486, in _run self.execute(example, compiled, test.globs) File "/home/burcin/sage/sage5.11.beta3/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 845, in execute exec compiled in globs File "<doctest sage.coding.linear_code.LinearCode.newton_radius[3]>", line 1, in <module> C.newton_radius(t) TypeError: newton_radius() takes exactly 1 argument (2 given) ********************************************************************** 1 item had failures: 1 of 5 in sage.coding.linear_code.LinearCode.newton_radius [374 tests, 1 failure, 4.69 s]  sage t devel/sage/sage/coding/linear_code.py # 1 doctest failed  Total time for all tests: 4.9 seconds cpu time: 4.3 seconds cumulative wall time: 4.7 seconds
Please document and test __insert_nextnew()
as well. All new functions introduced in a patch should be tested.
You should rename covering_rad()
to covering_radius()
.
The documentation needs a spell check. Did you try building the documentation? I'm not sure if all of it is formatted properly.
The output of weight_distribution_coset()
and groebner_representation()
should be immutable, i.e., a tuple instead of a list. It might be better to reconsider the format of groebner_representation()
altogether. A list of lists is not very mathematical. There are quite a few possibilities in Sage to represent various mathematical structures.
Please run your code through a pep8 checker: https://pypi.python.org/pypi/pep8
In Python, you don't need to write CC[len(CC)  1]
to get the last element of a list. You can just say CC[1]
.
It seems that all your examples/tests use the same code. Can you add different examples which stress the code properly, covering corner cases, etc.?
comment:4 Changed 8 years ago by
Burcin, which structure would you consider appropriate for representing the groebner representation? Maybe a dictionary?
comment:5 Changed 8 years ago by
Are you sure you uploaded the last version of your patch? The version insert_nextnew does not have any doctest. And the function covering_rad should be merged with the existing covering_radius, providing an option to choose between the preexisting algorithm, and the one you implemented.
comment:6 Changed 8 years ago by
Here goes the real patch:
Right tests (Doctests already run)
_insert_nextnew()
documented and tested
The functions covering_rad()
was merged with covering_radius()
, this function was already implemented but required optional GAP package guava.
Now you can indicate which method use. Algorithm = "guava"
does the same that
the old covering_radius()
using guava. And Algorithm = None
is my implemented
function.
The output of weight_distribution_coset()
is now a tuple.
About making output of groebner_representation()
immutable: This function has been implemented
because in next step I'm going to use it for a decoding algorithm. And actually it's going to be more convenient
to change the output to a dictionary, though.
I'll document more examples. I'm testing coset_leaders()
to determinate how big can be the length and dimension of the code before
the algorithm gets slow.
comment:7 Changed 8 years ago by
With coding_theory.2.patch:
Running doctests with ID 2013072809332848923423. Doctesting 1 file. Traceback (most recent call last): File "/home/burcin/sage/sage5.11.beta3/local/bin/sageruntests", line 87, in <module> err = DC.run() File "/home/burcin/sage/sage5.11.beta3/local/lib/python2.7/sitepackages/sage/doctest/control.py", line 891, in run self.run_doctests() File "/home/burcin/sage/sage5.11.beta3/local/lib/python2.7/sitepackages/sage/doctest/control.py", line 661, in run_doctests self.dispatcher = DocTestDispatcher(self) File "/home/burcin/sage/sage5.11.beta3/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 1339, in __init__ init_sage() File "/home/burcin/sage/sage5.11.beta3/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 93, in init_sage import sage.all_cmdline File "/home/burcin/sage/sage5.11.beta3/local/lib/python2.7/sitepackages/sage/all_cmdline.py", line 18, in <module> from sage.all import * File "/home/burcin/sage/sage5.11.beta3/local/lib/python2.7/sitepackages/sage/all.py", line 124, in <module> from sage.coding.all import * File "/home/burcin/sage/sage5.11.beta3/local/lib/python2.7/sitepackages/sage/coding/__init__.py", line 1, in <module> import all File "/home/burcin/sage/sage5.11.beta3/local/lib/python2.7/sitepackages/sage/coding/all.py", line 1, in <module> from ag_code import ag_code File "/home/burcin/sage/sage5.11.beta3/local/lib/python2.7/sitepackages/sage/coding/ag_code.py", line 20, in <module> import linear_code File "/home/burcin/sage/sage5.11.beta3/local/lib/python2.7/sitepackages/sage/coding/linear_code.py", line 1266 F = self.base_ring() ^ IndentationError: expected an indented block
After fixing this, all tests pass.
comment:8 followup: ↓ 9 Changed 8 years ago by
Some comments:
 The indentation error is not only in the line
F = self.base_ring()
. All of the existing code in thecovering_radius
method needs to be indented.  The
@rename_keyword
should not be introduced at all in thecovering_radius
code. This is a new keyword to the covering radius method and so you can simply introduce it without any deprecation warnings.  Is all of your code only for linear codes over
GF(2)
? Then you need to check the inputs to make sure that if other parents are input then it either degrades gracefully and automatically to an older algorithm (for instance incovering_radius
), or it gives an error.  Do you have plans to use values of
order
other thandegrevlex
?
In fact, I don't understand why ETuple
is being used. The only place I am finding it really being used is in comparing of two lists (the compare_tuples_degrevlex
function). I raise this point because quite a bit of time would be spent in simply converting vectors to lists and then the lists to ETuple
s. Later on, you also need the ETuple
s to be converted back to vectors in the grobner_representation
function. If there is a more direct way of doing the comparison you are doing (without all these conversions to ETuple
and back), then that should speed up the computations a bit.
comment:9 in reply to: ↑ 8 Changed 8 years ago by
Replying to ppurka:
Some comments:
Thanks for your comments!!
 The indentation error is not only in the line
F = self.base_ring()
. All of the existing code in thecovering_radius
method needs to be indented.
Yes, it got moved after I runned the tests, I guess. I just fixed it.
 The
@rename_keyword
should not be introduced at all in thecovering_radius
code. This is a new keyword to the covering radius method and so you can simply introduce it without any deprecation warnings.
Ok I got it. Also fixed
 Is all of your code only for linear codes over
GF(2)
? Then you need to check the inputs to make sure that if other parents are input then it either degrades gracefully and automatically to an older algorithm (for instance incovering_radius
), or it gives an error.
So far it is only for linear codes over GF(2)
. I'll do the check in every function.
 Do you have plans to use values of
order
other thandegrevlex
?
degrevlex
in most of the cases reduce the number of operations to compute the grobner_basis
.
Even that I'd like to leave it as option to the user, but maybe I should do this only for the function groebner_basis()
(still at work)
In other cases like grobner_representation()
and coset_leaders()
I should use only degrevlex
.
In fact, I don't understand why
ETuple
is being used. The only place I am finding it really being used is in comparing of two lists (thecompare_tuples_degrevlex
function). I raise this point because quite a bit of time would be spent in simply converting vectors to lists and then the lists toETuple
s. Later on, you also need theETuple
s to be converted back to vectors in thegrobner_representation
function. If there is a more direct way of doing the comparison you are doing (without all these conversions toETuple
and back), then that should speed up the computations a bit.
You're right
Actually the set of coset leaders it doesn't depend on the order, so at least for this function I'm doing the implementation without using ETuple
. I also think that should speed up the computations.
grobner_representation()
is going to be used in one of the decoding algorithm, so maybe I can also only use degrevlex
, I'll discuss it with my mentors.
comment:10 Changed 8 years ago by
I will just add some comments about the last question: as Veronica already mentioned, for the decoding algorithm that Veronica is implementing (whose code will be public in the following days), the term ordering is important.
Note that for those cosets for which more than one coset leader exists the degree compatible ordering chosen will play an important role.
However, in general I will suggest to leave as default the "degrevlex" ordering for several reasons related to the preprocessing of the mentioned decoding algorithm.
comment:11 Changed 8 years ago by
Here is the patch with the last details fixed. And I added the GDDA algorithm. This algorithm with Hamming Codes and Random linear codes seems to be faster. For example I have tested(among others):
sage: C = HammingCode(5,GF(2)) sage: v = random_vector(GF(2),C.length()) sage: v (1,1,0,1,0,1,0,0,0,0,1,0,1,0,1,0,0,1,1,1,0,1,1,0,0,0,1,1,0,0,1) #using syndrome algorithm sage: %time C.decode(v) CPU times: user 847.37 s, sys: 4.45 s, total: 851.82 s Wall time: 868.36 s (1,1,0,0,0,1,0,0,0,0,1,0,1,0,1,0,0,1,1,1,0,1,1,0,0,0,1,1,0,0,1) #using nearest neighbor algorithm sage: %time C.decode(v,"nearest neighbor") CPU times: user 879.19 s, sys: 1.61 s, total: 880.80 s Wall time: 880.80 s (1,1,0,0,0,1,0,0,0,0,1,0,1,0,1,0,0,1,1,1,0,1,1,0,0,0,1,1,0,0,1) #using guava algorithm sage: %time C.decode(v,"guava") CPU times: user 0.07 s, sys: 0.02 s, total: 0.08 s Wall time: 1.00 s (1,1,0,0,0,1,0,0,0,0,1,0,1,0,1,0,0,1,1,1,0,1,1,0,0,0,1,1,0,0,1) #using GDDA algorithm (first time compute grobner representation) sage: %time C.decode_gdda(v) CPU times: user 0.73 s, sys: 0.06 s, total: 0.78 s Wall time: 0.84 s (1,1,0,0,0,1,0,0,0,0,1,0,1,0,1,0,0,1,1,1,0,1,1,0,0,0,1,1,0,0,1) #using GDDA algorithm (with grobner representation computed) sage: %time C.decode_gdda(v) CPU times: user 0.00 s, sys: 0.00 s, total: 0.00 s Wall time: 0.00 s (1,1,0,0,0,1,0,0,0,0,1,0,1,0,1,0,0,1,1,1,0,1,1,0,0,0,1,1,0,0,1)
I've been suggeste to use timeit
instead of time
for benchmarking, so that's next. But with this results of time we can appreciate the differences among the differents decoding algorithms
comment:12 Changed 8 years ago by
The next patch is presented as result of a GSoC project 2013.
The work contains implementation of new decoding algorithms for linear codes proposed in "Combinatorial Commutative Algebra Approach to Complete Decoding", PhD Thesis, University of Valladolid, 2013 by Irene MarquezCorbella.
Algorithms are called "groebner representation"
and "groebner basis"
and has been added to sage.coding.decoder.py
This algorithms has been hooked up with the decode
function in sage.coding.linear_code.py
, adding also a block of tests in which is explained the cases where this new algorithms performs better.
The patch contains functions added to sage.coding.linear_code.py
such as coset_leaders
, error_correcting_capacity
, newton_radius
, weight_distribution_coset
, and new algorithm to covering_radius
.
comment:13 Changed 8 years ago by
 Description modified (diff)
 Status changed from new to needs_review
Patchbot apply trac_14973new_decoding_functions.patch
comment:14 Changed 8 years ago by
Hmm.. I didn't notice these two issues before:
 The
syndrome()
function is (strangely) duplicated indecoder.py
 At some point during the GSOC, we made the output of
groebner_basis_singular
a list, to make the output similar to the output of the othergroebner_basis_fglm
function (which was probably named differently). Now, I feel that the generator itself should be returned, i.e., the return statement should bereturn I.groebner_basis('libsingular:stdfglm')
because the output of this function is used sequentially, and used only once. Consequently, all the doctests should be changed tolist(groebner_basis_singular..)
.
Changed 8 years ago by
comment:15 Changed 8 years ago by
I just changed the patch.
 The
syndrome
function duplicated has been deleted. groebner_basis_fglm
function output is now a generator iterable object.
comment:16 Changed 8 years ago by
 Cc dimpase added
comment:17 Changed 7 years ago by
 Milestone changed from sage6.1 to sage6.2
comment:18 Changed 7 years ago by
 Status changed from needs_review to needs_work
This needs to be turned into a git branch (and rebased)
comment:19 Changed 7 years ago by
 Milestone changed from sage6.2 to sage6.3
comment:20 Changed 7 years ago by
 Branch set to u/defeo/ticket/14973
 Created changed from 07/26/13 03:56:47 to 07/26/13 03:56:47
 Modified changed from 05/06/14 15:20:58 to 05/06/14 15:20:58
comment:21 Changed 7 years ago by
 Commit set to d21956ca00caf389801f84ecadc15059e1fb4f8e
 Status changed from needs_work to needs_review
Gitified, doctested and fixed some minor problems. sage/coding/decoder
didn't use to show up in the reference manual, I added it to the "Coding theory" section and fixed some docstring bugs.
There where conflicts while importing the mercurial patches. It'd be better if the original author could check the merge was done right.
New commits:
bbbdf5a  Add new decoding algorithms for linear codes.

fba788b  Fixed deprecation warnings

d21956c  Expose sage/coding/decoder in the ref manual, and doc fixes

comment:22 Changed 7 years ago by
 Status changed from needs_review to needs_work
 Work issues set to resolve merge conflict with 6.3b1
I am working on resolving the (seems trivial) conflict with 6.3beta1.
comment:23 Changed 7 years ago by
 Status changed from needs_work to needs_review
I added some commits to fix the merge conflicts and also clean up a bit.
Your changes looked ok to me except for just one change that was not present. You can look at the changes that you made and compare with the changes in the hg patch attached to this ticket, like so.
$ git diff develop d02a468 > coding.patch # alternatively, you can use your HEAD: d21956c $ <some visual diff tool> coding.patch trac_14973new_decoding_functions.patch
I used gvimdiff
as the visual diff tool. There are many available like meld, kdiff3, etc.
comment:24 Changed 7 years ago by
 Branch changed from u/defeo/ticket/14973 to u/ppurka/ticket/14973
comment:25 Changed 7 years ago by
 Commit changed from d21956ca00caf389801f84ecadc15059e1fb4f8e to b1850ba30e81c0772974187818c1c50b6e06d72c
 Work issues resolve merge conflict with 6.3b1 deleted
New commits:
d02a468  merge develop on to #14973; resolved merge conflicts

9f31603  fix docstrings in decoder.py

32d9c4f  fix some docstrings in linear_code.py

bf4094d  remove deprecation message about method to algorithm from sage/coding

eba4566  one more merge conflict that was missed

b1850ba  groebner > Groebner

comment:26 Changed 7 years ago by
 Commit changed from b1850ba30e81c0772974187818c1c50b6e06d72c to 743826b1c73c946be9b8ff4fdb97819879fc07ac
Branch pushed to git repo; I updated commit sha1. New commits:
743826b  fix some documentation build problems

comment:27 Changed 7 years ago by
 Milestone changed from sage6.3 to sage6.4
comment:29 Changed 5 years ago by
 Milestone changed from sage6.4 to sageduplicate/invalid/wontfix
See #21339 which is a readaptation of this ticket.
comment:30 Changed 5 years ago by
 Status changed from needs_work to positive_review
comment:31 Changed 5 years ago by
 Resolution set to wontfix
 Status changed from positive_review to closed
Determined to be invalid/duplicate/wontfix (closing as "wontfix" as a catchall resolution).
one quick comment: you should also add an example for the function insert_nextnew