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Use the same convetion for module import and export

This commit is contained in:
Tiago Gomes 2012-12-17 14:50:12 +00:00
parent 2738c0fb56
commit 409a230826
27 changed files with 632 additions and 614 deletions
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1
packages/CLPBN/clpbn.yap
View File

@ -116,7 +116,6 @@
:- use_module('clpbn/graphviz',
[clpbn2gviz/4]).
%
% avoid the overhead of using goal_expansion/2.
%

19
packages/CLPBN/clpbn/aggregates.yap
View File

@ -1,8 +1,8 @@
%
% generate explicit CPTs
%
:- module(clpbn_aggregates, [
check_for_agg_vars/2,
:- module(clpbn_aggregates,
[check_for_agg_vars/2,
cpt_average/6,
cpt_average/7,
cpt_max/6,
@ -10,7 +10,8 @@
avg_factors/5
]).
:- use_module(library(clpbn), [{}/1]).
:- use_module(library(clpbn),
[{}/1]).
:- use_module(library(lists),
[last/2,
@ -24,19 +25,21 @@
:- use_module(library(matrix),
[matrix_new/3,
matrix_to_list/2,
matrix_set/3]).
matrix_set/3
]).
:- use_module(library(clpbn/dists),
[
add_dist/6,
get_dist_domain_size/2]).
[add_dist/6,
get_dist_domain_size/2
]).
:- use_module(library(clpbn/matrix_cpt_utils),
[normalise_CPT_on_lines/3]).
:- use_module(library(pfl),
[skolem/2,
add_ground_factor/5]).
add_ground_factor/5
]).
:- use_module(library(bhash)).

1
packages/CLPBN/clpbn/bdd.yap
View File

@ -1064,4 +1064,3 @@ build_cnf(CNF, IVs, Indics, AllParms, AllParmValues, Val) :-
set_to_ones(Extra),
ddnnf_is(F, Val).

34
packages/CLPBN/clpbn/bnt.yap
View File

@ -1,20 +1,23 @@
:- module(bnt, [do_bnt/3,
:- module(bnt,
[do_bnt/3,
create_bnt_graph/2,
check_if_bnt_done/1]).
check_if_bnt_done/1
]).
:- use_module(library('clpbn/display'), [
clpbn_bind_vals/3]).
:- use_module(library('clpbn/display'),
[clpbn_bind_vals/3]).
:- use_module(library('clpbn/dists'), [
get_dist_domain_size/2,
:- use_module(library('clpbn/dists'),
[get_dist_domain_size/2,
get_dist_domain/2,
get_dist_params/2
]).
:- use_module(library('clpbn/discrete_utils'), [
reorder_CPT/5]).
:- use_module(library('clpbn/discrete_utils'),
[reorder_CPT/5]).
:- use_module(library(matlab), [start_matlab/1,
:- use_module(library(matlab),
[start_matlab/1,
close_matlab/0,
matlab_on/0,
matlab_eval_string/1,
@ -27,7 +30,8 @@
matlab_call/2
]).
:- use_module(library(dgraphs), [dgraph_new/1,
:- use_module(library(dgraphs),
[dgraph_new/1,
dgraph_add_vertices/3,
dgraph_add_edges/3,
dgraph_top_sort/2,
@ -35,11 +39,13 @@
dgraph_edges/2
]).
:- use_module(library(lists), [append/3,
member/2,nth/3]).
:- use_module(library(lists),
[append/3,
member/2,nth/3
]).
:- use_module(library(ordsets), [
ord_insert/3]).
:- use_module(library(ordsets),
[ord_insert/3]).
:- yap_flag(write_strings,on).

10
packages/CLPBN/clpbn/connected.yap
View File

@ -3,8 +3,8 @@
[influences/3,
factor_influences/4,
init_influences/3,
influences/4]
).
influences/4
]).
:- use_module(library(maplist)).
@ -14,13 +14,15 @@
dgraph_add_vertex/3,
dgraph_neighbors/3,
dgraph_edge/3,
dgraph_transpose/2]).
dgraph_transpose/2
]).
:- use_module(library(rbtrees),
[rb_new/1,
rb_lookup/3,
rb_insert/4,
rb_visit/2]).
rb_visit/2
]).
factor_influences(Vs, QVars, Ev, LV) :-
init_factor_influences(Vs, G, RG),

13
packages/CLPBN/clpbn/discrete_utils.yap
View File

@ -1,10 +1,14 @@
:- module(discrete_utils, [project_from_CPT/3,
:- module(discrete_utils,
[project_from_CPT/3,
reorder_CPT/5,
get_dist_size/2]).
get_dist_size/2
]).
:- use_module(library(clpbn/dists), [get_dist_domain_size/2,
get_dist_domain/2]).
:- use_module(library(clpbn/dists),
[get_dist_domain_size/2,
get_dist_domain/2
]).
%
% remove columns from a table
%
@ -143,4 +147,3 @@ get_sizes([V|Deps], [Sz|Sizes]) :-
get_dist_domain_size(Id,Sz),
get_sizes(Deps, Sizes).

14
packages/CLPBN/clpbn/display.yap
View File

@ -1,14 +1,14 @@
:- module(clpbn_display, [
clpbn_bind_vals/3]).
:- module(clpbn_display,
[clpbn_bind_vals/3]).
:- use_module(library(lists),
[
member/2
]).
[member/2]).
:- use_module(library(clpbn/dists), [get_dist_domain/2]).
:- use_module(library(clpbn/dists),
[get_dist_domain/2]).
:- use_module(library(clpbn), [use_parfactors/1]).
:- use_module(library(clpbn),
[use_parfactors/1]).
:- use_module(library(maplist)).

15
packages/CLPBN/clpbn/dists.yap
View File

@ -3,8 +3,7 @@
%
:- module(clpbn_dist,
[
dist/1,
[dist/1,
dist/4,
dists/1,
dist_new_table/2,
@ -30,7 +29,10 @@
additive_dists/6
]).
:- use_module(library(lists),[nth0/3,append/3]).
:- use_module(library(lists),
[nth0/3,
append/3
]).
:- use_module(library(clpbn),
[use_parfactors/1]).
@ -39,11 +41,13 @@
[matrix_new/4,
matrix_new/3,
matrix_to_list/2,
matrix_to_logs/1]).
matrix_to_logs/1
]).
:- use_module(library(clpbn/matrix_cpt_utils),
[random_CPT/2,
uniform_CPT/2]).
uniform_CPT/2
]).
/*
:- mode dist(+, -).
@ -365,3 +369,4 @@ reset_all_dists.
additive_dists(ip(Domain,Tabs1), ip(Domain,Tabs2), Parents1, Parents2, ip(Domain,Tabs), Parents) :-
append(Tabs1, Tabs2, Tabs),
append(Parents1, Parents2, Parents).

16
packages/CLPBN/clpbn/evidence.yap
View File

@ -4,26 +4,24 @@
%
:- module(clpbn_evidence,
[
store_evidence/1,
[store_evidence/1,
incorporate_evidence/2,
check_stored_evidence/2,
add_stored_evidence/2,
put_evidence/2
]).
:- use_module(library(clpbn), [
{}/1,
:- use_module(library(clpbn),
[{}/1,
clpbn_flag/3,
set_clpbn_flag/2
]).
:- use_module(library('clpbn/dists'), [
get_dist/4
]).
:- use_module(library('clpbn/dists'),
[get_dist/4]).
:- use_module(library(rbtrees), [
rb_new/1,
:- use_module(library(rbtrees),
[rb_new/1,
rb_lookup/3,
rb_insert/4
]).

41
packages/CLPBN/clpbn/gibbs.yap
View File

@ -11,48 +11,51 @@
[gibbs/3,
check_if_gibbs_done/1,
init_gibbs_solver/4,
run_gibbs_solver/3]).
run_gibbs_solver/3
]).
:- use_module(library(rbtrees),
[rb_new/1,
rb_insert/4,
rb_lookup/3]).
rb_lookup/3
]).
:- use_module(library(lists),
[member/2,
append/3,
delete/3,
max_list/2,
sum_list/2]).
sum_list/2
]).
:- use_module(library(ordsets),
[ord_subtract/3]).
:- use_module(library('clpbn/matrix_cpt_utils'), [
project_from_CPT/3,
:- use_module(library('clpbn/matrix_cpt_utils'),
[project_from_CPT/3,
reorder_CPT/5,
multiply_possibly_deterministic_factors/3,
column_from_possibly_deterministic_CPT/3,
normalise_possibly_deterministic_CPT/2,
list_from_CPT/2]).
list_from_CPT/2
]).
:- use_module(library('clpbn/utils'), [
check_for_hidden_vars/3]).
:- use_module(library('clpbn/utils'),
[check_for_hidden_vars/3]).
:- use_module(library('clpbn/dists'), [
get_possibly_deterministic_dist_matrix/5,
get_dist_domain_size/2]).
:- use_module(library('clpbn/dists'),
[get_possibly_deterministic_dist_matrix/5,
get_dist_domain_size/2
]).
:- use_module(library('clpbn/topsort'), [
topsort/2]).
:- use_module(library('clpbn/topsort'),
[topsort/2]).
:- use_module(library('clpbn/display'), [
clpbn_bind_vals/3]).
:- use_module(library('clpbn/display'),
[clpbn_bind_vals/3]).
:- use_module(library('clpbn/connected'),
[
influences/3
]).
[influences/3]).
:- dynamic gibbs_params/3.
@ -542,5 +545,3 @@ divide_list([C|Add], Sum, [P|Dist]) :-
P is C/Sum,
divide_list(Add, Sum, Dist).

15
packages/CLPBN/clpbn/graphs.yap
View File

@ -3,13 +3,14 @@
% Just output a graph with all the variables.
%
:- module(clpbn2graph, [clpbn2graph/1]).
:- module(clpbn2graph,
[clpbn2graph/1]).
:- use_module(library('clpbn/utils'), [
check_for_hidden_vars/3]).
:- use_module(library('clpbn/utils'),
[check_for_hidden_vars/3]).
:- use_module(library('clpbn/dists'), [
get_dist/4]).
:- use_module(library('clpbn/dists'),
[get_dist/4]).
:- attribute node/0.
@ -37,7 +38,3 @@ translate_vars([V|Vs],[K|Ks]) :-
clpbn:get_atts(V, [key(K)]),
translate_vars(Vs,Ks).

4
packages/CLPBN/clpbn/graphviz.yap
View File

@ -1,4 +1,6 @@
:- module(clpbn_gviz, [clpbn2gviz/4]).
:- module(clpbn_gviz,
[clpbn2gviz/4]).
clpbn2gviz(Stream, Name, Network, Output) :-
format(Stream, 'digraph ~w {

9
packages/CLPBN/clpbn/hmm.yap
View File

@ -1,8 +1,9 @@
:- module(hmm, [init_hmm/0,
:- module(hmm,
[init_hmm/0,
hmm_state/1,
emission/1]).
emission/1
]).
:- ensure_loaded(library(clpbn)).
@ -79,5 +80,3 @@ cvt_vals([A|B],[A|B]).
find_probs(Logs,Nth,Log) :-
arg(Nth,Logs,Log).

26
packages/CLPBN/clpbn/jt.yap
View File

@ -1,8 +1,9 @@
:- module(jt, [jt/3,
:- module(jt,
[jt/3,
init_jt_solver/4,
run_jt_solver/3]).
run_jt_solver/3
]).
:- use_module(library(dgraphs),
[dgraph_new/1,
@ -41,14 +42,16 @@
:- use_module(library(rbtrees),
[rb_new/1,
rb_insert/4,
rb_lookup/3]).
rb_lookup/3
]).
:- use_module(library(ordsets),
[ord_subset/2,
ord_insert/3,
ord_intersection/3,
ord_del_element/3,
ord_memberchk/2]).
ord_memberchk/2
]).
:- use_module(library(lists),
[reverse/2]).
@ -61,7 +64,8 @@
:- use_module(library('clpbn/dists'),
[get_dist_domain_size/2,
get_dist_domain/2,
get_dist_matrix/5]).
get_dist_matrix/5
]).
:- use_module(library('clpbn/matrix_cpt_utils'),
[project_from_CPT/3,
@ -74,14 +78,14 @@
get_CPT_sizes/2,
reset_CPT_that_disagrees/5,
sum_out_from_CPT/4,
list_from_CPT/2]).
list_from_CPT/2
]).
:- use_module(library('clpbn/display'), [
clpbn_bind_vals/3]).
:- use_module(library('clpbn/display'),
[clpbn_bind_vals/3]).
:- use_module(library('clpbn/connected'),
[
init_influences/3,
[init_influences/3,
influences/4
]).

6
packages/CLPBN/clpbn/matrix_cpt_utils.yap
View File

@ -21,7 +21,8 @@
random_CPT/2,
uniform_CPT/2,
uniform_CPT_as_list/2,
normalise_CPT_on_lines/3]).
normalise_CPT_on_lines/3
]).
:- use_module(library(matrix),
[matrix_new/4,
@ -45,7 +46,8 @@
matrix_agg_lines/3,
matrix_agg_cols/3,
matrix_op_to_lines/4,
matrix_column/3]).
matrix_column/3
]).
init_CPT(List, Sizes, TAB) :-
matrix_new(floats, Sizes, List, TAB),

5
packages/CLPBN/clpbn/numbers.yap
View File

@ -1,13 +1,13 @@
:- module(clpbn_numbers,
[
keys_to_numbers/7,
[keys_to_numbers/7,
keys_to_numbers/9,
lists_of_keys_to_ids/6
]).
:- use_module(library(bhash)).
:- use_module(library(maplist)).
:- use_module(library(pfl),
[skolem/2,
get_pfl_cpt/5
@ -60,4 +60,3 @@ evidence_to_id(Key=Ev, I0=Ev, Hash0, Hash, I0, I) :-
b_hash_insert(Hash0, Key, I0, Hash),
I is I0+1.

15
packages/CLPBN/clpbn/pgrammar.yap
View File

@ -2,24 +2,23 @@
:- style_check(all).
:- module(clpbn_pgrammar,[grammar_to_atts/1,
:- module(clpbn_pgrammar,
[grammar_to_atts/1,
grammar_prob/2,
grammar_mle/2,
init_pcg_solver/4,
run_pcg_solver/3,
pcg_init_graph/0]).
pcg_init_graph/0
]).
:- load_files([library(clpbn)],
[ if(not_loaded),
silent(true)
]).
[if(not_loaded), silent(true)]).
:- use_module([library(lists)],
[ sum_list/2
]).
[sum_list/2]).
:- use_module([library(matrix)],
[ matrix_new/3,
[matrix_new/3,
matrix_add/3,
matrix_get/3,
matrix_op/4,

13
packages/CLPBN/clpbn/table.yap
View File

@ -29,7 +29,8 @@
:- use_module(library(bhash),
[b_hash_new/4,
b_hash_lookup/3,
b_hash_insert/4]).
b_hash_insert/4
]).
:- meta_predicate clpbn_table(:),
clpbn_tabled_clause(:.?),
@ -43,14 +44,13 @@
clpbn_tabled_number_of_clauses(:,-),
clpbn_is_tabled(:).
:- use_module(library(terms), [
instantiated_term_hash/4,
:- use_module(library(terms),
[instantiated_term_hash/4,
variant/2
]).
:- use_module(evidence, [
put_evidence/2
]).
:- use_module(evidence,
[put_evidence/2]).
:- dynamic clpbn_table/3.
@ -364,4 +364,3 @@ clpbn_is_tabled(M:Clause, _) :- !,
clpbn_is_tabled(Head, M) :-
clpbn_table(Head, M, _).

7
packages/CLPBN/clpbn/topsort.yap
View File

@ -1,11 +1,13 @@
:- module(topsort, [topsort/2]).
:- module(topsort,
[topsort/2]).
:- use_module(library(dgraphs),
[dgraph_new/1,
dgraph_add_edges/3,
dgraph_add_vertices/3,
dgraph_top_sort/2]).
dgraph_top_sort/2
]).
/* simple implementation of a topological sorting algorithm */
/* graph is as Node-[Parents] */
@ -31,4 +33,3 @@ add_edges([], _V) --> [].
add_edges([P|Parents], V) --> [P-V],
add_edges(Parents, V).

9
packages/CLPBN/clpbn/utils.yap
View File

@ -1,9 +1,11 @@
:- module(clpbn_utils, [
clpbn_not_var_member/2,
:- module(clpbn_utils,
[clpbn_not_var_member/2,
clpbn_var_member/2,
check_for_hidden_vars/3,
sort_vars_by_key/3,
sort_vars_by_key_and_parents/3]).
sort_vars_by_key_and_parents/3
]).
%
% It may happen that variables from a previous query may still be around.
@ -113,4 +115,3 @@ transform_parents([P|Parents0],[P|NParents],KeyVarsF,KeyVars0) :-
transform_parents([P|Parents0],[V|NParents],[P-V|KeyVarsF],KeyVars0) :-
transform_parents(Parents0,NParents,KeyVarsF,KeyVars0).

36
packages/CLPBN/clpbn/ve.yap
View File

@ -14,41 +14,45 @@
*********************************/
:- module(clpbn_ve, [ve/3,
:- module(clpbn_ve,
[ve/3,
check_if_ve_done/1,
init_ve_solver/4,
run_ve_solver/3,
init_ve_ground_solver/5,
run_ve_ground_solver/3,
call_ve_ground_solver/6]).
call_ve_ground_solver/6
]).
:- use_module(library(atts)).
:- use_module(library(ordsets),
[ord_union/3,
ord_member/2]).
ord_member/2
]).
:- use_module(library('clpbn/xbif'), [clpbn2xbif/3]).
:- use_module(library('clpbn/xbif'),
[clpbn2xbif/3]).
:- use_module(library('clpbn/graphviz'), [clpbn2gviz/4]).
:- use_module(library('clpbn/graphviz'),
[clpbn2gviz/4]).
:- use_module(library('clpbn/dists'),
[
dist/4,
[dist/4,
get_dist_domain_size/2,
get_dist_params/2,
get_dist_domain_size/2,
get_dist_matrix/5]).
get_dist_matrix/5
]).
:- use_module(library('clpbn/utils'), [
clpbn_not_var_member/2]).
:- use_module(library('clpbn/utils'),
[clpbn_not_var_member/2]).
:- use_module(library('clpbn/display'), [
clpbn_bind_vals/3]).
:- use_module(library('clpbn/display'),
[clpbn_bind_vals/3]).
:- use_module(library('clpbn/connected'),
[
init_influences/3,
[init_influences/3,
influences/4,
factor_influences/4
]).
@ -58,8 +62,7 @@
:- use_module(library(clpbn/numbers)).
:- use_module(library(lists),
[
member/2,
[member/2,
append/3,
delete/3
]).
@ -474,4 +477,3 @@ multiply([F0|Fs], Vs, T) :-
multiply_factor(f(_,Vs1,T1), f(_,Vs0,T0), f(_,Vs,T)) :-
multiply_CPTs(T1, Vs1, T0, Vs0, T, Vs).

12
packages/CLPBN/clpbn/viterbi.yap
View File

@ -1,11 +1,13 @@
%:- style_check(all).
:- module(viterbi, [viterbi/4]).
:- module(viterbi,
[viterbi/4]).
:- use_module(library(lists),
[nth/3,
member/2]).
member/2
]).
:- use_module(library(assoc)).
@ -17,8 +19,8 @@
:- ensure_loaded(library('clpbn/hmm')).
:- use_module(library('clpbn/dists'), [
get_dist_params/2]).
:- use_module(library('clpbn/dists'),
[get_dist_params/2]).
:- meta_predicate viterbi(:,:,+,-).
@ -231,5 +233,3 @@ trace(L1,Next,Dump,Map,Trace0,Trace) :-
matrix_get(Dump,[NL,P],New),
trace(NL,New,Dump,Map,[Key|Trace0],Trace).

6
packages/CLPBN/clpbn/vmap.yap
View File

@ -1,7 +1,6 @@
:- module(clpbn_vmap,
[
init_vmap/1, % init_vmap(-Vmap)
[init_vmap/1, % init_vmap(-Vmap)
add_to_vmap/4, % add_to_vmap(+V,-I,+VMap0,VMapF)
get_from_vmap/3, % add_to_vmap(+V,-I,+VMap0)
vars_to_numbers/4, % vars_to_numbers(+Vs,-Is,+VMap0,VMapF)
@ -39,6 +38,3 @@ lvars_to_numbers(LVs, LIs, VMap0, VMap) :-
vmap_to_list(vmap(_,Map), L) :-
rb_visit(Map, L).

7
packages/CLPBN/clpbn/xbif.yap
View File

@ -2,10 +2,11 @@
% XMLBIF support for CLP(BN)
%
:- module(xbif, [clpbn2xbif/3]).
:- module(xbif,
[clpbn2xbif/3]).
:- use_module(library('clpbn/dists'), [
get_dist_domain/2]).
:- use_module(library('clpbn/dists'),
[get_dist_domain/2]).
clpbn2xbif(Stream, Name, Network) :-
format(Stream, '<?xml version="1.0" encoding="US-ASCII"?>