From 4260418786f1ef828039c8f8a5989a49511044eb Mon Sep 17 00:00:00 2001
From: Vincent Danjean <Vincent.Danjean@ens-lyon.org>
Date: Wed, 31 Oct 2012 16:35:57 +0000
Subject: [PATCH] memory managed outside inner functions
outer functions can choose to allocate memory
with malloc or on their stack
git-svn-id: svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@466 cf695345-040a-0410-a956-b889e835fe2e
---
CUtils/CUtils.xs | 8 +++++--
CUtils/c_sources/double_permutation.c | 12 +++++++++++
CUtils/c_sources/resampling.c | 10 ++++++---
CUtils/c_sources/stats.c | 30 +++++++++++++--------------
CUtils/c_sources/stats.h | 14 ++++++++-----
5 files changed, 48 insertions(+), 26 deletions(-)
diff --git a/CUtils/CUtils.xs b/CUtils/CUtils.xs
index 61a7253..9c977dd 100644
--- a/CUtils/CUtils.xs
+++ b/CUtils/CUtils.xs
@@ -263,6 +263,7 @@ CalculChi2(tabnodes, ddl, test_results, sign_util)
int sign_util
INIT:
struct cc *nodes;
+ struct cc *th;
int nb_nodes;
struct calcul_chi2_res res;
int i;
@@ -273,6 +274,7 @@ CalculChi2(tabnodes, ddl, test_results, sign_util)
XSRETURN_UNDEF;
}
nodes=(struct cc*)malloc(nb_nodes*sizeof(struct cc));
+ th=(struct cc*)malloc(nb_nodes*sizeof(struct cc));
for (i=0; i<nb_nodes; i++) {
SV* ref=*av_fetch(tabnodes, i, 0);
@@ -288,7 +290,7 @@ CalculChi2(tabnodes, ddl, test_results, sign_util)
nodes[i].controls=SvNV(*svp);
}
- res=calcul_chi2(nb_nodes, nodes, sign_util, 1);
+ res=calcul_chi2(nb_nodes, nodes, sign_util, 1, th);
if (res.texte) {
hv_store(test_results, "texte", 5,
@@ -312,6 +314,7 @@ CalculChi2(tabnodes, ddl, test_results, sign_util)
}
free(nodes);
+ free(th);
EXTEND(SP, 2);
PUSHs(sv_2mortal(newSVnv(res.p_val)));
@@ -390,8 +393,9 @@ ReechChi2(sum_case, sum_control, nb_nodes, chi2_reel, clades)
case_avail=0;
}
}
+ struct cc th[nb_nodes];
- RETVAL=reech_chi2(sum_case, sum_control, nb_nodes, chi2_reel, nodes);
+ RETVAL=reech_chi2(sum_case, sum_control, nb_nodes, chi2_reel, nodes, th);
free(nodes);
OUTPUT:
diff --git a/CUtils/c_sources/double_permutation.c b/CUtils/c_sources/double_permutation.c
index 4cc4ae8..ea53dcd 100644
--- a/CUtils/c_sources/double_permutation.c
+++ b/CUtils/c_sources/double_permutation.c
@@ -151,6 +151,18 @@ datatype_t double_permutation(int nb_sample, int nb_chi2, matrice_t mat,
datatype_t min;
datatype_t local[nb_chi2];
+ FILE*out=fopen("/tmp/out.txt", "w+");
+ fprintf(out, "nb_sample=%d nb_chi2=%d\n", nb_sample, nb_chi2);
+ for(i=0; i<nb_sample; i++) {
+ for(j=0; j<nb_chi2; j++) {
+ fprintf(out, "\t%.12g", mat[j][i]);
+ }
+ fprintf(out,"\n");
+ }
+ fclose(out);
+
+
+
i=0;
for (j=0; j<nb_chi2; j++) {
rep[j]=CALC_PVAL(count_superieur(mat[j], mat[j][i], nb_sample),
diff --git a/CUtils/c_sources/resampling.c b/CUtils/c_sources/resampling.c
index f7feab5..fbe1b0f 100644
--- a/CUtils/c_sources/resampling.c
+++ b/CUtils/c_sources/resampling.c
@@ -7,13 +7,15 @@
struct chi2s {
int nb_leaves;
struct cc*leaves;
+ struct cc*th;
int nb_nodes;
int *stashed_nodes;
int *next_nodes;
struct cc*nodes;
};
-static void compute_chi2s(struct tree *tree, struct cc *lcc, struct chi2s *temp,
+static void compute_chi2s(const struct tree *tree, const struct cc *lcc,
+ struct chi2s *temp,
int prolonge, datatype_t *results)
{
int first_leaf=0;
@@ -32,7 +34,6 @@ static void compute_chi2s(struct tree *tree, struct cc *lcc, struct chi2s *temp,
int depth;
for (depth=tree->max_depth; depth>0; depth--){
- struct cc *leaves=temp->leaves;
int nb_leaves=0;
int next_first_leaf;
@@ -75,7 +76,8 @@ static void compute_chi2s(struct tree *tree, struct cc *lcc, struct chi2s *temp,
first_leaf=next_first_leaf;
//debug("depth=%i, ddl=%i", depth, nb_leaves-1);
- struct calcul_chi2_res r=calcul_chi2(nb_leaves, leaves, 0, 0);
+ struct calcul_chi2_res r=calcul_chi2(nb_leaves, temp->leaves,
+ 0, 0, temp->th);
assert(r.error==0);
results[depth-1]=r.chi2;
}
@@ -88,12 +90,14 @@ int resampling_chi2(struct tree *tree, struct cc *lcc, int prolonge,
struct cc rand_lcc[tree->nb_leaves];
struct cc leaves[tree->nb_leaves];
+ struct cc th[tree->nb_leaves];
struct cc nodes[tree->nb_nodes];
int stashed_nodes[tree->nb_nodes];
int next_nodes[tree->nb_nodes];
struct chi2s temp={
.nb_leaves=tree->nb_leaves,
.leaves=leaves,
+ .th=th,
.nb_nodes=tree->nb_nodes,
.stashed_nodes=stashed_nodes,
.next_nodes=next_nodes,
diff --git a/CUtils/c_sources/stats.c b/CUtils/c_sources/stats.c
index 4b3c4dd..8b3ec14 100644
--- a/CUtils/c_sources/stats.c
+++ b/CUtils/c_sources/stats.c
@@ -10,7 +10,8 @@
#include <strings.h>
#include <string.h>
-struct classical_chi2_res classical_chi2(int nb_nodes, struct cc *nodes) {
+struct classical_chi2_res classical_chi2(int nb_nodes,
+ const struct cc *nodes) {
struct classical_chi2_res res={
.chi2=0.0,
.chi2invalid=0,
@@ -80,8 +81,8 @@ struct classical_chi2_res classical_chi2(int nb_nodes, struct cc *nodes) {
ch; \
})
-struct calcul_chi2_res calcul_chi2(int nb_nodes, struct cc *nodes,
- int sign_util, int texte)
+struct calcul_chi2_res calcul_chi2(int nb_nodes, const struct cc *nodes,
+ int sign_util, int texte, struct cc *th)
{
struct classical_chi2_res r=
classical_chi2(nb_nodes, nodes);
@@ -141,7 +142,7 @@ struct calcul_chi2_res calcul_chi2(int nb_nodes, struct cc *nodes,
}
} else {
p_value = reech_chi2(r.sum_case, r.sum_control,
- nb_nodes, r.chi2, nodes);
+ nb_nodes, r.chi2, nodes, th);
res.warning=msprintfcat(res.warning," (%.6g)",p_value);
if (sign_util) {
res.significatif = reech_significatif(p_value);
@@ -196,19 +197,16 @@ int chi2_fisher_significatif(datatype_t pvalue)
return pvalue < chi2_p;
}
-datatype_t reech_chi2(int sum_case, int sum_control,
- int nb_nodes, int chi2_reel, struct cc *nodes)
+datatype_t reech_chi2(int sum_case, int sum_control, int nb_nodes,
+ int chi2_reel, const struct cc *nodes, struct cc *th)
{
int sum_total=sum_case+sum_control;
datatype_t p_val=0.0;
- datatype_t th_c[nb_nodes];
- datatype_t th_m[nb_nodes];
-
int i,k;
for(i=0; i<nb_nodes; i++) {
- th_c[i]=((datatype_t)(sum_control*(nodes[i].cases+nodes[i].controls)))/sum_total;
- th_m[i]=((datatype_t)(sum_case*(nodes[i].cases+nodes[i].controls)))/sum_total;
+ th[i].controls=((datatype_t)(sum_control*(nodes[i].cases+nodes[i].controls)))/sum_total;
+ th[i].cases=((datatype_t)(sum_case*(nodes[i].cases+nodes[i].controls)))/sum_total;
}
struct cc clades[nb_nodes];
@@ -218,10 +216,10 @@ datatype_t reech_chi2(int sum_case, int sum_control,
datatype_t chi2=0.0;
for(i=0; i<nb_nodes; i++) {
datatype_t t;
- t=clades[i].cases - th_m[i];
- chi2 += t*t/th_m[i];
- t=clades[i].controls - th_c[i];
- chi2 += t*t/th_c[i];
+ t=clades[i].cases - th[i].cases;
+ chi2 += t*t/th[i].cases;
+ t=clades[i].controls - th[i].controls;
+ chi2 += t*t/th[i].controls;
}
if (chi2 >= chi2_reel){
p_val++;
@@ -236,7 +234,7 @@ int reech_significatif(datatype_t p_val)
return (p_val<=chi2_p);
}
-void random_clades(int nb_nodes, struct cc *nodes,
+void random_clades(int nb_nodes, const struct cc *nodes,
int cases, int controls, struct cc *clades)
{
bzero(clades, nb_nodes*sizeof(struct cc));
diff --git a/CUtils/c_sources/stats.h b/CUtils/c_sources/stats.h
index 18e140e..c747528 100644
--- a/CUtils/c_sources/stats.h
+++ b/CUtils/c_sources/stats.h
@@ -29,15 +29,19 @@ struct calcul_chi2_res {
char *warning;
};
-struct classical_chi2_res classical_chi2(int nb_nodes, struct cc *nodes);
-struct calcul_chi2_res calcul_chi2(int nb_nodes, struct cc *nodes, int sign_util, int texte);
+struct classical_chi2_res classical_chi2(int nb_nodes, const struct cc *nodes);
+struct calcul_chi2_res calcul_chi2(int nb_nodes, const struct cc *nodes,
+ int sign_util, int texte, struct cc *th);
void definition_p_chi2(datatype_t p, datatype_t pprop);
int chi2_significatif(int ddl, datatype_t chi2);
int chi2_fisher_significatif(datatype_t pvalue);
-datatype_t reech_chi2(int sum_case, int sum_control,
- int nb_nodes, int chi2_reel, struct cc *nodes);
+/* nodes and th: array of size nb_nodes.
+ nodes is input only, th is used internally
+*/
+datatype_t reech_chi2(int sum_case, int sum_control, int nb_nodes,
+ int chi2_reel, const struct cc *nodes, struct cc *th);
int reech_significatif(datatype_t p_val);
-void random_clades(int nb_nodes, struct cc *nodes,
+void random_clades(int nb_nodes, const struct cc *nodes,
int cases, int controls, struct cc *clades);
#endif
--
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