void mclvFree
( mclVector** vecpp
)
{ if (*vecpp)
{ mcxFree((*vecpp)->ivps)
; mcxFree(*vecpp)
; (*vecpp) = NULL
; }
; }
static void free_pars
( stream_state* iface
)
{ dim i
; for (i=0; i<iface->pars_n_alloc; i++)
mcxFree(iface->pars[i].ivps)
; mcxFree(iface->pars)
; iface->pars = NULL
; }
void mclpARfree
( mclpAR** mclparp
)
{ if (*mclparp)
{ mcxFree(mclparp[0]->ivps)
; mcxFree(*mclparp)
; *mclparp = NULL
; }
}
void mcxHeapFree
( mcxHeap** heap
)
{ if (*heap)
{ if ((*heap)->base)
mcxFree((*heap)->base)
; mcxFree(*heap)
; *heap = NULL
; }
}
void mcxGrimFree
( mcxGrim** srcp
)
{ grim_buf *this = (*srcp)->buf
; while (this)
{ grim_buf* tmp = this->prev
; mcxFree(this->units)
; mcxFree(this)
; this = tmp
; }
mcxFree(*srcp)
; *srcp = NULL
; }
void mclInterpretParamFree
( mclInterpretParam **ipp
)
{ if (*ipp)
mcxFree(*ipp)
; *ipp = NULL
; }
mcxHash* mcxHashNew
( dim n_buckets
, u32 (*hash)(const void *a)
, int (*cmp) (const void *a, const void *b)
)
{ mcxHash *h
; mcxbool ok = FALSE
; u8 n_bits = 0
; if (!n_buckets)
{ mcxErr("mcxHashNew strange", "void alloc request")
; n_buckets = 2
; }
if (!(h = mcxAlloc(sizeof(mcxHash), RETURN_ON_FAIL)))
return NULL
; while(n_buckets)
{ n_buckets >>= 1
; n_bits++
; }
h->load = 0.5
; h->n_entries = 0
; h->n_buckets = n_buckets = (1 << n_bits)
; h->cmp = cmp
; h->hash = hash
; h->options = MCX_HASH_OPT_DEFAULTS
; h->src_link = NULL
; while (1) /* fixme 2nd arg below, have better choice? */
{ h->src_link = mcxGrimNew(sizeof(hash_link), h->n_buckets, MCX_GRIM_ARITHMETIC)
; if (!h->src_link)
break
; if
(! ( h->buckets
= mcxNAlloc
( h->n_buckets
, sizeof(mcx_bucket)
, mcx_bucket_init
, RETURN_ON_FAIL
) ) )
break
; ok = TRUE
; break
; }
if (!ok)
{ mcxGrimFree(&(h->src_link))
; mcxFree(h)
; return NULL
; }
return h
; }
void mclpFree
( mclIvp** p_ivp
)
{ if (*p_ivp)
{ mcxFree(*p_ivp)
; *p_ivp = NULL
; }
}
void mclvRelease
( mclVector* vec
)
{ if (!vec)
return
; mcxFree(vec->ivps)
; vec->ivps = NULL
; vec->n_ivps = 0
; }
void mclgTFfree
( mclgTF** tfpp
)
{ mclgTF* tf = tfpp[0]
; if (tf)
{ mclpARfree(&(tf->par_edge))
; mcxFree(tf)
; tfpp[0] = NULL
; }
}
void mcxHeapRelease
( void* heapv
)
{ mcxHeap* heap = (mcxHeap*) heapv
; if (heap->base)
mcxFree(heap->base)
; heap->base = NULL
; heap->heapSize = 0
; }
void mcxIOrelease
( mcxIO* xf
)
{ if (xf)
{ mcxIOclose(xf)
; if (xf->fn)
mcxTingFree(&(xf->fn))
; if (xf->mode)
mcxFree(xf->mode)
; }
}
void mcxIOfree
( mcxIO** xfpp
)
{ if (*xfpp)
{ mcxIO* xf = *xfpp
; mcxIOrelease(xf)
; mcxTingFree(&(xf->buffer))
; if (xf->usr && xf->usr_free)
xf->usr_free(xf->usr)
; mcxFree(xf)
; *xfpp = NULL
; }
}
mclVector* mclvInstantiate
( mclVector* dst_vec
, dim new_n_ivps
, const mclIvp* src_ivps
)
{ mclIvp* new_ivps
; dim old_n_ivps
; if (!dst_vec && !(dst_vec = mclvInit(NULL))) /* create */
return NULL
; old_n_ivps = dst_vec->n_ivps
/* I've had a suspicion that some reallocs might be too lazy
* to reuse shrunk array space.
*/
; if (old_n_ivps / 2 > new_n_ivps)
{ new_ivps = mcxAlloc(new_n_ivps * sizeof new_ivps[0], ENQUIRE_ON_FAIL)
; if (new_ivps && !src_ivps)
memcpy(new_ivps, dst_vec->ivps, new_n_ivps * sizeof new_ivps[0])
; mcxFree(dst_vec->ivps)
; dst_vec->ivps = new_ivps
; }
else
dst_vec->ivps = mcxRealloc(dst_vec->ivps, new_n_ivps * sizeof new_ivps[0], ENQUIRE_ON_FAIL)
; if
( !dst_vec->ivps
&& new_n_ivps
)
{ mcxMemDenied(stderr, "mclvInstantiate", "mclIvp", new_n_ivps)
; return NULL
; }
/* ^ do not free; *dst_vec could be array element */
new_ivps = dst_vec->ivps
; if (!src_ivps) /* resize */
{ dim k = old_n_ivps
; while (k < new_n_ivps)
{ mclpInit(new_ivps + k)
; k++
; }
}
else if (src_ivps && new_n_ivps) /* copy */
memcpy(new_ivps, src_ivps, new_n_ivps * sizeof(mclIvp))
; dst_vec->n_ivps = new_n_ivps
; return dst_vec
; }
static mcxstatus get_interface
( mclAlgParam** mlpp
, const char* fn_input /* Use this as input or mx_input */
, const char* arg_shared
, const char* arg_extra
, mclx* mx_input /* Use this as input or fn_input */
, mcxbits CACHE
, mcxOnFail ON_FAIL
)
{ mcxTing* spec = mcxTingNew(arg_shared)
; int argc1 = 0
; char** argv1
; mcxstatus status
; mclAlgParam* mymlp = NULL
; mclAlgParam** mymlpp = mlpp ? mlpp : &mymlp
; if (arg_extra)
mcxTingPrintAfter(spec, " %s", arg_extra)
/* warning this clobbers spec->str */
; argv1 = mcxOptParseString(spec->str, &argc1, ' ')
; status
= mclAlgInterface
( mymlpp
, argv1
, argc1
, fn_input
, mx_input
, CACHE
)
; if (status && ON_FAIL == EXIT_ON_FAIL)
mcxExit(1)
; mcxFree(argv1)
; mcxTingFree(&spec)
/* fixfixfixmefixmefffixme: mclAlgInterface might use opt->val
* which points to somewhere in spec->str. Check.
*/
; if (!mlpp)
mclAlgParamFree(mymlpp, TRUE)
; return status
; }
void mclxInflateBoss
( mclMatrix* mx
, double power
, mclProcParam* mpp
)
{ int workLoad = N_COLS(mx) / mpp->n_ithreads
; int workTail = N_COLS(mx) % mpp->n_ithreads
; int i = 0
; pthread_attr_t pthread_custom_attr
; pthread_t *threads_inflate
= (pthread_t *) mcxAlloc
( mpp->n_ithreads*sizeof(pthread_t)
, EXIT_ON_FAIL
)
; pthread_attr_init(&pthread_custom_attr)
; for (i=0;i<mpp->n_ithreads;i++)
{
mclvInflateLine_arg *a
= (mclvInflateLine_arg *)
malloc(sizeof(mclvInflateLine_arg))
; a->id = i
; a->start = workLoad * i
; a->end = workLoad * (i+1)
; a->mx = mx
; a->power = power
; if (i+1==mpp->n_ithreads)
a->end += workTail
; pthread_create
( &threads_inflate[i]
, &pthread_custom_attr
, (void *(*)(void*)) mclvInflateLine
, (void *) a
)
; }
for (i = 0; i < mpp->n_ithreads; i++)
pthread_join(threads_inflate[i], NULL)
; mcxFree(threads_inflate)
; }
mcxGrim* mcxGrimNew
( dim sz_unit
, dim n_units
, mcxbits options
)
{ mcxGrim* src = mcxAlloc(sizeof(mcxGrim), RETURN_ON_FAIL)
; if (!src)
return NULL
; if (!(src->buf = grim_buf_new(sz_unit, n_units)))
{ mcxFree(src)
; return NULL
; }
src->buf->prev = NULL
; src->flags = options
; src->na = (void*) src->buf->units
; src->ct = 0
; src->sz_unit = sz_unit
; return src
; }
grim_buf* grim_buf_new
( dim sz_unit
, dim n_units
)
{ dim i
; grim_buf* buf
; char* units
; dim sz_load = sizeof(memnext) + sz_unit
; if (!(buf = mcxAlloc(sizeof(grim_buf), RETURN_ON_FAIL)))
return NULL
; if
( !(buf->units
= units
= mcxAlloc(n_units * sz_load, RETURN_ON_FAIL)
) )
{ mcxFree(buf)
; return NULL
; }
buf->prev = NULL
; buf->n_units = n_units
#if DEBUG
; fprintf (stderr, "Extending grim with <%lu> units\n", (ulong) n_units);
#endif
; for (i=0;i<n_units-1;i++)
((memnext*) (units + i * sz_load))->next
= (memnext*) (units + (i+1) * sz_load)
; ((memnext*) (buf->units + (n_units-1) * sz_load))->next = NULL
; return buf
; }
mclVector* mclvBinaryx
( const mclVector* vec1
, const mclVector* vec2
, mclVector* dst
, double (*op)(pval arg1, pval arg2, pval arg3)
, double arg3
)
{ mclIvp *ivp1, *ivp2, *ivp1max, *ivp2max, *ivpk, *ivpl
; long n1n2 = vec1->n_ivps+vec2->n_ivps
; if (vec1->n_ivps + vec2->n_ivps == 0)
return mclvInstantiate(dst, 0, NULL)
; ivpl = ivpk
= mcxAlloc
( n1n2 * sizeof(mclIvp)
, RETURN_ON_FAIL
)
; if (!ivpk)
{ mcxMemDenied(stderr, "mclvBinary", "mclIvp", n1n2)
; return NULL
; }
ivp1 = vec1->ivps
; ivp2 = vec2->ivps
; ivp1max = ivp1 + vec1->n_ivps
; ivp2max = ivp2 + vec2->n_ivps
;
{ double rval
; while (ivp1 < ivp1max && ivp2 < ivp2max)
{ pval val1 = 0.0
; pval val2 = 0.0
; long idx
; if (ivp1->idx < ivp2->idx)
{ idx = ivp1->idx
; val1 = (ivp1++)->val
; }
else if (ivp1->idx > ivp2->idx)
{ idx = ivp2->idx
; val2 = (ivp2++)->val
; }
else
{ idx = ivp1->idx
; val1 = (ivp1++)->val
; val2 = (ivp2++)->val
; }
if ((rval = op(val1, val2, arg3)) != 0.0)
{ ivpl->idx = idx
; (ivpl++)->val = rval
; }
}
while (ivp1 < ivp1max)
{ if ((rval = op(ivp1->val, 0.0, arg3)) != 0.0)
{ ivpl->idx = ivp1->idx
; (ivpl++)->val = rval
; }
ivp1++
; }
while (ivp2 < ivp2max)
{ if ((rval = op(0.0, ivp2->val, arg3)) != 0.0)
{ ivpl->idx = ivp2->idx
; (ivpl++)->val = rval
; }
ivp2++
; }
}
dst = mclvInstantiate(dst, ivpl-ivpk, ivpk)
; mcxFree(ivpk)
; return dst
; }
double mclvKBar
( mclVector *vec
, dim k
, double ignore /* ignore elements relative to this */
, int mode
)
{ int have_even = (k+1) % 2
; dim n_inserted = 0
; double ans = 0.0
; mclIvp * vecivp = vec->ivps
; mclIvp* vecmaxivp = vecivp + vec->n_ivps
; pval * heap
/* can select everything */
; if (k >= vec->n_ivps)
return mode == KBAR_SELECT_LARGE ? -FLT_MAX : FLT_MAX
/* let's select nothing, it might even help */
; if (!(heap = mcxAlloc ((k+have_even)*sizeof(pval), RETURN_ON_FAIL)))
return mode == KBAR_SELECT_LARGE ? FLT_MAX : -FLT_MAX
; if (mode == KBAR_SELECT_LARGE)
{ if (have_even)
*(heap+k) = PVAL_MAX
; while(vecivp < vecmaxivp)
{ pval val = vecivp->val
; if (val >= ignore)
NOTHING
; else if (n_inserted < k)
{ dim d = n_inserted
; while (d != 0 && *(heap+(d-1)/2) > val)
{ *(heap+d) = *(heap+(d-1)/2)
; d = (d-1)/2
; }
*(heap+d) = val
; n_inserted++
; }
else if (val > *heap)
{ dim root = 0
; dim d
; while((d = 2*root+1) < k)
{ if (*(heap+d) > *(heap+d+1))
d++
; if (val > *(heap+d))
{ *(heap+root) = *(heap+d)
; root = d
; }
else break
; }
*(heap+root) = val
; }
vecivp++
; }
}
else if (mode == KBAR_SELECT_SMALL)
{ if (have_even)
*(heap+k) = -PVAL_MAX
; while(vecivp < vecmaxivp)
{ pval val = vecivp->val
; if (val < ignore)
NOTHING
; else if (n_inserted < k)
{ dim d = n_inserted
; while (d != 0 && *(heap+(d-1)/2) < val)
{ *(heap+d) = *(heap+(d-1)/2)
; d = (d-1)/2
; }
*(heap+d) = val
; n_inserted++
; }
else if (val < *heap)
{ dim root = 0
; dim d
; while((d = 2*root+1) < k)
{ if (*(heap+d) < *(heap+d+1))
d++
; if (val < *(heap+d))
{ *(heap+root) = *(heap+d)
; root = d
; }
else break
; }
*(heap+root) = val
; }
vecivp++
; }
}
else
{ mcxErr("mclvKBar PBD", "invalid mode")
; mcxExit(1)
; }
ans = *heap
; mcxFree(heap)
; return ans
; }
mclgTF* mclgTFparse
( mcxLink* encoding_link
, mcxTing* thestring
)
{ mclgTF* gtf = mcxAlloc(sizeof gtf[0], EXIT_ON_FAIL)
; const char* me = "mclgTFparse"
; const char* a = thestring->str
; const char* z = thestring->str + thestring->len
; mcxTing* func = mcxTingEmpty(NULL, thestring->len)
; mcxTing* arg = mcxTingEmpty(NULL, thestring->len)
; int n = 0
; if (!(gtf->par_edge = mclpARensure(NULL, 10)))
return NULL /* +memleak gtf */
; if (!(gtf->par_graph = mclpARensure(NULL, 10)))
return NULL /* +memleak gtf, gtf->par_edge */
; if
( thestring
&& !mcxStrChrAint(thestring->str, isspace, thestring->len)
)
return gtf
; while (a < z)
{ const char* val, *key
; char* onw = NULL
; int tfe = -1, tfg = -1
; mcxbool nought = FALSE
; unsigned char k0
; double d
; int t
; mcxTingEmpty(arg, z-a)
; mcxTingEmpty(func, z-a)
; n = 0
; if ((t = sscanf(a, " %[a-z_#-] ( )%n", func->str, &n)) >= 1 && n > 0)
NOTHING
; else if ((t = sscanf(a, " %[a-z_#-] ( %[^)_ ] )%n", func->str, arg->str, &n)) >= 2 && n > 0)
NOTHING
; else
break
; a += n
; key= func->str
; val= arg->str
; k0 = key[0]
; d = strtod(val, &onw)
; if (!val || !strlen(val))
nought = TRUE
; else if (val == onw)
{ mcxErr(me, "failed to parse number <%s>", val)
; break
; }
if (k0 == '#')
{ if (!strcmp(key, "#ceilnb"))
tfg = MCLG_TF_CEILNB
; else if (!strcmp(key, "#knn"))
tfg = MCLG_TF_KNN
; else if (!strcmp(key, "#n"))
tfg = MCLG_TF_TOPN
; else if (!strcmp(key, "#ils"))
tfg = MCLG_TF_ILS
; else if (!strcmp(key, "#mcl"))
tfg = MCLG_TF_MCL
; else if (!strcmp(key, "#arcmcl"))
tfg = MCLG_TF_ARC_MCL
; else if (!strcmp(key, "#arcsub"))
tfg = MCLG_TF_ARCSUB
; else if (!strcmp(key, "#arcmax"))
tfg = MCLG_TF_ARCMAX
; else if (!strcmp(key, "#arcmingq"))
tfg = MCLG_TF_ARCMINGQ
; else if (!strcmp(key, "#arcmingt"))
tfg = MCLG_TF_ARCMINGT
; else if (!strcmp(key, "#arcmimlq"))
tfg = MCLG_TF_ARCMINLQ
; else if (!strcmp(key, "#arcminlt"))
tfg = MCLG_TF_ARCMINLT
; else if (!strcmp(key, "#arcdiffgq"))
tfg = MCLG_TF_ARCDIFFGQ
; else if (!strcmp(key, "#arcdiffgt"))
tfg = MCLG_TF_ARCDIFFGT
; else if (!strcmp(key, "#arcdifflq"))
tfg = MCLG_TF_ARCDIFFLQ
; else if (!strcmp(key, "#arcdifflt"))
tfg = MCLG_TF_ARCDIFFLT
; else if (!strcmp(key, "#arcmaxgq"))
tfg = MCLG_TF_ARCMAXGQ
; else if (!strcmp(key, "#arcmaxgt"))
tfg = MCLG_TF_ARCMAXGT
; else if (!strcmp(key, "#arcmaxlq"))
tfg = MCLG_TF_ARCMAXLQ
; else if (!strcmp(key, "#arcmaxlt"))
tfg = MCLG_TF_ARCMAXLT
; else if (!strcmp(key, "#selfrm"))
tfg = MCLG_TF_SELFRM
; else if (!strcmp(key, "#selfmax"))
tfg = MCLG_TF_SELFMAX
; else if (!strcmp(key, "#normself"))
tfg = MCLG_TF_NORMSELF
; else if (!strcmp(key, "#add"))
tfg = MCLG_TF_ADD
; else if (!strcmp(key, "#max"))
tfg = MCLG_TF_MAX
; else if (!strcmp(key, "#min"))
tfg = MCLG_TF_MIN
; else if (!strcmp(key, "#mul"))
tfg = MCLG_TF_MUL
; else if (!strcmp(key, "#tug"))
tfg = MCLG_TF_TUG
; else if (!strcmp(key, "#ssq"))
tfg = MCLG_TF_SSQ
; else if (!strcmp(key, "#qt"))
tfg = MCLG_TF_QT
; else if (!strcmp(key, "#tp") || !strcmp(key, "#rev"))
tfg = MCLG_TF_TRANSPOSE
; else if (!strcmp(key, "#step"))
tfg = MCLG_TF_STEP
; else if (!strcmp(key, "#thread"))
tfg = MCLG_TF_THREAD
; else if (!strcmp(key, "#shrug"))
tfg = MCLG_TF_SHRUG
; else if (!strcmp(key, "#shuffle"))
tfg = MCLG_TF_SHUFFLE
; }
else
{ if (!strcmp(key, "gq"))
tfe = MCLX_UNARY_GQ
; else if (!strcmp(key, "gt"))
tfe = MCLX_UNARY_GT
; else if (!strcmp(key, "lt"))
tfe = MCLX_UNARY_LT
; else if (!strcmp(key, "lq"))
tfe = MCLX_UNARY_LQ
; else if (!strcmp(key, "rand"))
tfe = MCLX_UNARY_RAND
; else if (!strcmp(key, "mul"))
tfe = MCLX_UNARY_MUL
; else if (!strcmp(key, "scale"))
tfe = MCLX_UNARY_SCALE
; else if (!strcmp(key, "add"))
tfe = MCLX_UNARY_ADD
; else if (!strcmp(key, "abs"))
tfe = MCLX_UNARY_ABS
; else if (!strcmp(key, "ceil"))
tfe = MCLX_UNARY_CEIL
; else if (!strcmp(key, "floor"))
tfe = MCLX_UNARY_FLOOR
; else if (!strcmp(key, "pow"))
tfe = MCLX_UNARY_POW
; else if (!strcmp(key, "exp"))
tfe = MCLX_UNARY_EXP
; else if (!strcmp(key, "log"))
tfe = MCLX_UNARY_LOG
; else if (!strcmp(key, "neglog"))
tfe = MCLX_UNARY_NEGLOG
; }
if (tfe < 0 && tfg < 0)
{ mcxErr(me, "unknown value transform <%s>", key)
; break
; }
if (tfe >= 0)
{ if (nought)
{ if
( tfe == MCLX_UNARY_LOG || tfe == MCLX_UNARY_ABS
|| tfe == MCLX_UNARY_EXP || tfe == MCLX_UNARY_NEGLOG
)
d = 0.0
; else
{ mcxErr(me, "transform <%s> needs value", key)
; break
; }
; }
mclpARextend(gtf->par_edge, tfe, d)
; }
else if (tfg >= 0)
{ if (nought)
{ if
( tfg >= MCLG_TF_DUMMY_NOVALUE_START
&& tfg <= MCLG_TF_DUMMY_NOVALUE_END
)
d = 0.0
; else if (tfg == MCLG_TF_TUG || tfg == MCLG_TF_SHRUG)
d = 1000.0
; else if (tfg == MCLG_TF_STEP)
d = 2.0
; else
{ mcxErr(me, "transform <%s> needs value", key)
; break
; }
; }
mclpARextend(gtf->par_edge, MCLX_UNARY_UNUSED, 0.0)
; mclpARextend(gtf->par_graph, tfg, d)
; }
a = mcxStrChrAint(a, isspace, z-a)
; if (!a || a[0] != ',')
break
; a++
; }
if (a)
{ mcxErr(me, "trailing part <%s> not matched", a)
; mclpARfree(&(gtf->par_edge))
; mcxFree(gtf)
; gtf = NULL
; }
return gtf
; }
static void vary_threshold
( mcxIO* xf
, FILE* fp
, int vary_a
, int vary_z
, int vary_s
, int vary_n
, unsigned mode
)
{ dim cor_i = 0, j
; int step
; mclx* mx
; unsigned long noe
; pval* allvals
; dim n_allvals = 0
; double sum_vals = 0.0
; mx = mclxRead(xf, EXIT_ON_FAIL)
; mcxIOclose(xf)
; if (transform)
mclgTFexec(mx, transform)
; noe = mclxNrofEntries(mx)
; allvals = mcxAlloc(noe * sizeof allvals[0], EXIT_ON_FAIL)
; if (!weight_scale)
{ if (mode == 'c')
weight_scale = 1.0
; else
weight_scale = vary_n
; }
n_allvals = get_n_sort_allvals(mx, allvals, noe, &sum_vals, FALSE)
; if (mode == 'c')
{ double smallest = n_allvals ? allvals[n_allvals-1] : -DBL_MAX
; if (vary_a * 1.0 / vary_n < smallest)
{ while (vary_a * 1.0 / vary_n < smallest)
vary_a++
; vary_a--
; }
mcxTell
( me
, "smallest correlation is %.2f, using starting point %.2f"
, smallest
, vary_a * 1.0 / vary_n
)
; }
if (output_flags & OUTPUT_TABLE)
{
;fprintf(fp, "L\tD\tR\tS\tcce\tEWmean\tEWmed\tEWiqr\tNDmean\tNDmed\tNDiqr\tCCF\t%s\n", mode == 'k' ? "kNN" : mode == 'l' ? "N" : "Cutoff")
;} else
{ if (output_flags & OUTPUT_KEY)
{
;fprintf(fp, "-------------------------------------------------------------------------------\n")
;fprintf(fp, " L Percentage of nodes in the largest component\n")
;fprintf(fp, " D Percentage of nodes in components of size at most %d [-div option]\n", (int) divide_g)
;fprintf(fp, " R Percentage of nodes not in L or D: 100 - L -D\n")
;fprintf(fp, " S Percentage of nodes that are singletons\n")
;fprintf(fp, " cce Expected size of component, nodewise [ sum(sz^2) / sum^2(sz) ]\n")
;fprintf(fp, "*EW Edge weight traits (mean, median and IQR, all scaled!)\n")
;fprintf(fp, " Scaling is used to avoid printing of fractional parts throughout.\n")
;fprintf(fp, " The scaling factor is %.2f [-report-scale option]\n", weight_scale)
;fprintf(fp, " ND Node degree traits [mean, median and IQR]\n")
;fprintf(fp, " CCF Clustering coefficient %s\n", compute_flags & COMPUTE_CLCF ? "(not computed; use --clcf to include this)" : "")
;fprintf(fp, " eff Induced component efficiency %s\n", compute_flags & COMPUTE_EFF ? "(not computed; use --eff to include this)" : "")
;if (mode == 'c')
fprintf(fp, "Cutoff The threshold used.\n")
;else if (mode == 't')
fprintf(fp, "*Cutoff The threshold with scale factor %.2f and fractional parts removed\n", weight_scale)
;else if (mode == 'k')
fprintf(fp, "k-NN The knn parameter\n")
;else if (mode == 'l')
fprintf(fp, "N The knn parameter (merge mode)\n")
;else if (mode == 'n')
fprintf(fp, "ceil The ceil parameter\n")
;fprintf(fp, "Total number of nodes: %lu\n", (ulong) N_COLS(mx))
;}
fprintf(fp, "-------------------------------------------------------------------------------\n")
;fprintf(fp, " L D R S cce *EWmean *EWmed *EWiqr NDmean NDmed NDiqr CCF eff %6s \n", mode == 'k' ? "k-NN" : mode == 'l' ? "N" : mode == 'n' ? "Ceil" : "Cutoff")
;fprintf(fp, "-------------------------------------------------------------------------------\n")
; }
for (step = vary_a; step <= vary_z; step += vary_s)
{ double cutoff = step * 1.0 / vary_n
; double eff = -1.0
; mclv* nnodes = mclvCanonical(NULL, N_COLS(mx), 0.0)
; mclv* degree = mclvCanonical(NULL, N_COLS(mx), 0.0)
; dim i, n_sample = 0
; double cor, y_prev, iqr = 0.0
; mclx* cc = NULL, *res = NULL
; mclv* sz, *ccsz = NULL
; int step2 = vary_z + vary_a - step
; sum_vals = 0.0
; if (mode == 't' || mode == 'c')
mclxSelectValues(mx, &cutoff, NULL, MCLX_EQT_GQ)
, res = mx
; else if (mode == 'k')
{ res = rebase_g ? mclxCopy(mx) : mx
; mclxKNNdispatch(res, step2, n_thread_l, 1)
; }
else if (mode == 'l')
{ res = mx
; mclxKNNdispatch(res, step2, n_thread_l, 0)
; }
else if (mode == 'n')
{ res = rebase_g ? mclxCopy(mx) : mx
; mclv* cv = mclgCeilNB(res, step2, NULL, NULL, NULL)
; mclvFree(&cv)
; }
sz = mclxColSizes(res, MCL_VECTOR_COMPLETE)
; mclvSortDescVal(sz)
; cc = clmUGraphComponents(res, NULL) /* fixme: user has to specify -tf '#max()' if graph is directed */
; if (cc)
{ ccsz = mclxColSizes(cc, MCL_VECTOR_COMPLETE)
; if (compute_flags & COMPUTE_EFF)
{ clmPerformanceTable pftable
; clmPerformance(mx, cc, &pftable)
; eff = pftable.efficiency
; }
}
if (mode == 't' || mode == 'c')
{ for
(
; n_allvals > 0 && allvals[n_allvals-1] < cutoff
; n_allvals--
)
; sum_vals = 0.0
; for (i=0;i<n_allvals;i++)
sum_vals += allvals[i]
; }
else if (mode == 'k' || mode == 'n' || mode == 'l')
{ n_allvals = get_n_sort_allvals(res, allvals, noe, &sum_vals, FALSE)
; }
levels[cor_i].sim_median= mcxMedian(allvals, n_allvals, sizeof allvals[0], pval_get_double, &iqr)
; levels[cor_i].sim_iqr = iqr
; levels[cor_i].sim_mean = n_allvals ? sum_vals / n_allvals : 0.0
; levels[cor_i].nb_median = mcxMedian(sz->ivps, sz->n_ivps, sizeof sz->ivps[0], ivp_get_double, &iqr)
; levels[cor_i].nb_iqr = iqr
; levels[cor_i].nb_mean = mclvSum(sz) / N_COLS(res)
; levels[cor_i].cc_exp = cc ? mclvPowSum(ccsz, 2.0) / N_COLS(res) : 0
; levels[cor_i].nb_sum = mclxNrofEntries(res)
; if (compute_flags & COMPUTE_CLCF)
{ mclv* clcf = mclgCLCFdispatch(res, n_thread_l)
; levels[cor_i].clcf = mclvSum(clcf) / N_COLS(mx)
; mclvFree(&clcf)
; }
else
levels[cor_i].clcf = 0.0
; levels[cor_i].threshold = mode == 'k' || mode == 'l' || mode == 'n' ? step2 : cutoff
; levels[cor_i].bigsize = cc ? cc->cols[0].n_ivps : 0
; levels[cor_i].n_single = 0
; levels[cor_i].n_edge = n_allvals
; levels[cor_i].n_lq = 0
; if (cc)
for (i=0;i<N_COLS(cc);i++)
{ dim n = cc->cols[N_COLS(cc)-1-i].n_ivps
; if (n == 1)
levels[cor_i].n_single++
; if (n <= divide_g)
levels[cor_i].n_lq += n
; else
break
; }
if (levels[cor_i].bigsize <= divide_g)
levels[cor_i].bigsize = 0
; y_prev = sz->ivps[0].val
/* wiki says:
A scale-free network is a network whose degree distribution follows a power
law, at least asymptotically. That is, the fraction P(k) of nodes in the
network having k connections to other nodes goes for large values of k as P(k)
~ k^−g where g is a constant whose value is typically in the range 2<g<3,
although occasionally it may lie outside these bounds.
*/
; for (i=1;i<sz->n_ivps;i++)
{ double y = sz->ivps[i].val
; if (y > y_prev - 0.5)
continue /* same as node degree seen last */
; nnodes->ivps[n_sample].val = log( (i*1.0) / (1.0*N_COLS(res))) /* x = #nodes >= k, as fraction */
; degree->ivps[n_sample].val = log(y_prev ? y_prev : 1) /* y = k = degree of node */
; n_sample++
;if(0)fprintf(stderr, "k=%.0f\tn=%d\t%.3f\t%.3f\n", (double) y_prev, (int) i, (double) nnodes->ivps[n_sample-1].val, (double) degree->ivps[n_sample-1].val)
; y_prev = y
; }
nnodes->ivps[n_sample].val = 0
; nnodes->ivps[n_sample++].val = log(y_prev ? y_prev : 1)
;if(0){fprintf(stderr, "k=%.0f\tn=%d\t%.3f\t%.3f\n", (double) sz->ivps[sz->n_ivps-1].val, (int) N_COLS(res), (double) nnodes->ivps[n_sample-1].val, (double) degree->ivps[n_sample-1].val)
;}
; mclvResize(nnodes, n_sample)
; mclvResize(degree, n_sample)
; cor = pearson(nnodes, degree, n_sample)
; levels[cor_i].degree_cor = cor * cor
;if(0)fprintf(stdout, "cor at cutoff %.2f %.3f\n\n", cutoff, levels[cor_i-1].degree_cor)
; mclvFree(&nnodes)
; mclvFree(°ree)
; mclvFree(&sz)
; mclvFree(&ccsz)
; mclxFree(&cc)
; if(output_flags & OUTPUT_TABLE)
{ fprintf
( fp
, "%lu\t%lu\t%lu\t%lu\t%lu"
"\t%6g\t%6g\t%6g"
"\t%6g\t%lu\t%6g"
, (ulong) levels[cor_i].bigsize
, (ulong) levels[cor_i].n_lq
, (ulong) N_COLS(mx) - levels[cor_i].bigsize - levels[cor_i].n_lq
, (ulong) levels[cor_i].n_single
, (ulong) levels[cor_i].cc_exp
, (double) levels[cor_i].sim_mean
, (double) levels[cor_i].sim_median
, (double) levels[cor_i].sim_iqr
, (double) levels[cor_i].nb_mean
, (ulong) levels[cor_i].nb_median
, (double) levels[cor_i].nb_iqr
)
; if (compute_flags & COMPUTE_CLCF) fprintf(fp, "\t%6g", levels[cor_i].clcf) ; else fputs("\tNA", fp)
; if (eff >= 0.0) fprintf(fp, "\t%4g", eff) ; else fputs("\tNA", fp)
; fprintf(fp, "\t%6g", (double) levels[cor_i].threshold)
; fputc('\n', fp)
; }
else
{ fprintf
( fp
, "%3d %3d %3d %3d %7d "
"%7.0f %7.0f %6.0f"
"%6.1f %6.0f %6.0f"
, 0 ? 1 : (int) (0.5 + (100.0 * levels[cor_i].bigsize) / N_COLS(mx))
, 0 ? 1 : (int) (0.5 + (100.0 * levels[cor_i].n_lq) / N_COLS(mx))
, 0 ? 1 : (int) (0.5 + (100.0 * (N_COLS(mx) - levels[cor_i].bigsize - levels[cor_i].n_lq)) / N_COLS(mx))
, 0 ? 1 : (int) (0.5 + (100.0 * levels[cor_i].n_single) / N_COLS(mx))
, 0 ? 1 : (int) (0.5 + levels[cor_i].cc_exp)
, 0 ? 1.0 : (double) (levels[cor_i].sim_mean * weight_scale)
, 0 ? 1.0 : (double) (levels[cor_i].sim_median * weight_scale)
, 0 ? 1.0 : (double) (levels[cor_i].sim_iqr * weight_scale)
, 0 ? 1.0 : (double) (levels[cor_i].nb_mean )
, 0 ? 1.0 : (double) (levels[cor_i].nb_median + 0.5 )
, 0 ? 1.0 : (double) (levels[cor_i].nb_iqr + 0.5 )
)
; if (compute_flags & COMPUTE_CLCF)
fprintf(fp, " %3d", 0 ? 1 : (int) (0.5 + (100.0 * levels[cor_i].clcf)))
; else
fputs(" -", fp)
; if (eff >= 0.0)
fprintf(fp, " %3d", (int) (0.5 + 1000 * eff))
; else
fputs(" -", fp)
; if (mode == 'c')
fprintf(fp, "%8.2f\n", (double) levels[cor_i].threshold)
; else if (mode == 't')
fprintf(fp, "%8.0f\n", (double) levels[cor_i].threshold * weight_scale)
; else if (mode == 'k' || mode == 'n' || mode == 'l')
fprintf(fp, "%8.0f\n", (double) levels[cor_i].threshold)
; }
; cor_i++
; if (res != mx)
mclxFree(&res)
; }
if (!(output_flags & OUTPUT_TABLE))
{ if (weefreemen)
{
fprintf(fp, "-------------------------------------------------------------------------------\n")
;fprintf(fp, "The graph below plots the R^2 squared value for the fit of a log-log plot of\n")
;fprintf(fp, "<node degree k> versus <#nodes with degree >= k>, for the network resulting\n")
;fprintf(fp, "from applying a particular %s cutoff.\n", mode == 'c' ? "correlation" : "similarity")
;fprintf(fp, "-------------------------------------------------------------------------------\n")
; for (j=0;j<cor_i;j++)
{ dim jj
; for (jj=30;jj<=100;jj++)
{ char c = ' '
; if (jj * 0.01 < levels[j].degree_cor && (jj+1.0) * 0.01 > levels[j].degree_cor)
c = 'X'
; else if (jj % 5 == 0)
c = '|'
; fputc(c, fp)
; }
if (mode == 'c')
fprintf(fp, "%8.2f\n", (double) levels[j].threshold)
; else
fprintf(fp, "%8.0f\n", (double) levels[j].threshold * weight_scale)
; }
fprintf(fp, "|----+----|----+----|----+----|----+----|----+----|----+----|----+----|--------\n")
;fprintf(fp, "| R^2 0.4 0.5 0.6 0.7 0.8 0.9 | 1.0 -o)\n")
;fprintf(fp, "+----+----+----+----+----+---------+----+----+----+----+----+----+----+ /\\\\\n")
;fprintf(fp, "| 2 4 6 8 2 4 6 8 | 2 4 6 8 | 2 4 6 8 | 2 4 6 8 | 2 4 6 8 | 2 4 6 8 | _\\_/\n")
;fprintf(fp, "+----+----|----+----|----+----|----+----|----+----|----+----|----+----+--------\n")
; }
else
fprintf(fp, "-------------------------------------------------------------------------------\n")
; }
mclxFree(&mx)
; mcxFree(allvals)
; }
mcxIO* mcxIOrenew
( mcxIO* xf
, const char* name
, const char* mode
)
{ mcxbool twas_stdio = xf && xf->stdio /* it was one of STD{IN,OUT,ERR} */
; if
( mode
&& !strstr(mode, "w") && !strstr(mode, "r") && !strstr(mode, "a")
)
{ mcxErr ("mcxIOrenew PBD", "unsupported open mode <%s>", mode)
; return NULL
; }
if
( getenv("TINGEA_PLUS_APPEND")
&& ( name && (uchar) name[0] == '+' )
&& ( mode && strchr(mode, 'w') )
)
{ name++ /* user can specify -o +foo to append to foo */
; mode = "a"
; }
if (!xf) /* case 1) create a new one */
{ if (!name || !mode)
{ mcxErr("mcxIOrenew PBD", "too few arguments")
; return NULL
; }
if (!(xf = (mcxIO*) mcxAlloc(sizeof(mcxIO), RETURN_ON_FAIL)))
return NULL
; if (!(xf->fn = mcxTingEmpty(NULL, 20)))
return NULL
; if (!(xf->buffer = mcxTingEmpty(NULL, getpagesize())))
return NULL
; xf->fp = NULL
; xf->mode = NULL
; xf->usr = NULL
; xf->usr_reset = NULL
; xf->buffer_consumed = 0
; }
else if (xf->stdio) /* case 2) have one, don't close */
NOTHING
; else if (mcxIOwarnOpenfp(xf, "mcxIOrenew"))
mcxIOclose(xf) /* case 3) have one, warn and close if open */
; mcxIOreset(xf)
; if (name && !mcxTingWrite(xf->fn, name))
return NULL
; if (mode)
{ if (xf->mode)
mcxFree(xf->mode)
; xf->mode = mcxStrDup(mode)
; }
xf->stdio = begets_stdio(xf->fn->str, xf->mode)
/* name changed, no longer stdio */
; if (twas_stdio && !xf->stdio)
xf->fp = NULL
; if (xf->stdio && mode && strchr(mode, 'a')) /* recently added */
{ if (xf->mode)
mcxFree(xf->mode)
; xf->mode = mcxStrDup("w")
; }
return xf
; }
int main
( int argc
, const char* argv[]
)
{ mcxIO
*xfcl = NULL
, *xfctrl = NULL
, *xfcoarse= NULL
, *xfbase = NULL
, *xfcone = NULL
, *xfstack = NULL
; mclx* mxbase, *cl, *cl_coarse, *clprev, *clctrl = NULL
; mcxTing* shared = mcxTingNew("-I 4 -overlap split")
; mcxbool root = TRUE
; mcxbool have_bootstrap = FALSE
; const char* plexprefix = NULL
; const char* stem = "mcl"
; mcxbool same = FALSE
; mcxbool plex = TRUE
; mcxbool add_transpose = FALSE
; const char* b2opts = NULL
; const char* b1opts = NULL
; mcxbits write_modes = 0
; mclAlgParam* mlp = NULL
; mcxstatus status = STATUS_OK
; mcxstatus parse_status = STATUS_OK
; int multiplex_idx = 1
; int N = 0
; int n_ite = 0
; dim n_components = 0, n_cls = 0
; int a = 1, i= 0
; int n_arg_read = 0
; int delta = 0
; mcxOption* opts, *opt
; mcxTing* cline = mcxOptArgLine(argv+1, argc-1, '\'')
; mclgTF* transform = NULL
; mcxTing* transform_spec = NULL
; double iaf = 0.84
; mclx_app_init(stderr)
; if (0)
mcxLogLevel =
MCX_LOG_AGGR | MCX_LOG_MODULE | MCX_LOG_IO | MCX_LOG_GAUGE | MCX_LOG_WARN
; else
mcxLogLevelSetByString("xf4g1")
; mcxOptAnchorSortById(options, sizeof(options)/sizeof(mcxOptAnchor) -1)
; if (argc == 2 && argv[1][0] == '-' && mcxOptIsInfo(argv[1], options))
delta = 1
; else if (argc < 2)
{ help(options, shared)
; exit(0)
; }
opts = mcxOptExhaust
(options, (char**) argv, argc, 2-delta, &n_arg_read, &parse_status)
; if (parse_status != STATUS_OK)
{ mcxErr(me, "initialization failed")
; exit(1)
; }
; for (opt=opts;opt->anch;opt++)
{ mcxOptAnchor* anch = opt->anch
; switch(anch->id)
{ case MY_OPT_HELP
: help(options, shared)
; exit(0)
;
case MY_OPT_APROPOS
: help(options, shared)
; exit(0)
; break
;
case MY_OPT_NMAX
: N = atoi(opt->val)
; break
;
case MY_OPT_Z
: help(NULL, shared)
; exit(0)
; break
;
case MY_OPT_SHARED
: mcxTingPrintAfter(shared, " %s", opt->val)
; break
;
case MY_OPT_TRANSFORM
: transform_spec = mcxTingNew(opt->val)
; break
;
case MY_OPT_B1
: b1opts = opt->val
; break
;
case MY_OPT_B2
: b2opts = opt->val
; break
;
case ALG_OPT_SETENV
: mcxSetenv(opt->val)
; break
;
case ALG_OPT_QUIET
: mcxLogLevelSetByString(opt->val)
; break
;
case MY_OPT_HDP
: hdp_g = atof(opt->val)
; break
;
case MY_OPT_ADDTP
: add_transpose = TRUE
; break
;
case MY_OPT_ANNOT /* only used in command-line copying */
: break
;
case MY_OPT_IAF
: iaf = atof(opt->val) / 100
; break
;
case MY_OPT_WRITE
: if (strstr(opt->val, "stack"))
write_modes |= OUTPUT_STACK
; if (strstr(opt->val, "cone"))
write_modes |= OUTPUT_CONE
; if (strstr(opt->val, "levels"))
write_modes |= OUTPUT_STEPS
; if (strstr(opt->val, "coarse"))
write_modes |= OUTPUT_COARSE
; if (strstr(opt->val, "base"))
write_modes |= OUTPUT_BASE
; break
;
case MY_OPT_BASENAME
: xfbase = mcxIOnew(opt->val, "w")
; break
;
case MY_OPT_COARSE
: xfcoarse = mcxIOnew(opt->val, "w")
; break
;
case MY_OPT_CONE
: xfcone = mcxIOnew(opt->val, "w")
; break
;
case MY_OPT_ROOT
: root = strchr("1yY", (u8) opt->val[0]) ? TRUE : FALSE
; break
;
case MY_OPT_STACK
: xfstack = mcxIOnew(opt->val, "w")
; break
;
case MY_OPT_STEM
: stem = opt->val
; break
;
case MY_OPT_MULTIPLEX
: plex = strchr("yY1", (unsigned char) opt->val[0]) ? TRUE : FALSE
; break
;
case MY_OPT_DISPATCH
: dispatch_g = TRUE
; break
;
case MY_OPT_INTEGRATE
: integrate_g = TRUE
; break
;
case MY_OPT_CONTRACT
: break
;
case MY_OPT_SUBCLUSTERX
: subclusterx_g = TRUE, subcluster_g = TRUE
; break
;
case MY_OPT_SUBCLUSTER
: subcluster_g = TRUE
; break
;
case MY_OPT_CONTROL
: xfctrl = mcxIOnew(opt->val, "r")
; break
;
case MY_OPT_CL
: xfcl = mcxIOnew(opt->val, "r")
; have_bootstrap = TRUE
; break
;
case MY_OPT_VERSION
: app_report_version(me)
; exit(0)
;
default
: mcxExit(1)
;
}
}
mcxOptFree(&opts)
; a = 2 + n_arg_read
; if (a < argc)
{ if (strcmp(argv[a], "--"))
mcxDie
( 1
, me
, "trailing %s options require standalone '--' separator (found %s)"
, integrate_g ? "integrate" : "mcl"
, argv[a]
)
; a++
; }
if (subcluster_g + dispatch_g + integrate_g > 1)
mcxDie(1, me, "too many modes!")
; if (N && N < argc-a)
mcxErr(me, "-n argument leaves spurious option specifications")
; srandom(mcxSeed(89315))
; signal(SIGALRM, mclSigCatch)
; if (dispatch_g)
plexprefix = "dis"
; else if (!write_modes || (write_modes & OUTPUT_STEPS))
plexprefix = stem
; { mcxTing* tg = mcxTingEmpty(NULL, 30)
; if ((write_modes & OUTPUT_COARSE) && !xfcoarse)
mcxTingPrint(tg, "%s.%s", stem, "coarse")
, xfcoarse = mcxIOnew(tg->str, "w")
; if ((write_modes & OUTPUT_BASE) && !xfbase)
mcxTingPrint(tg, "%s.%s", stem, "base")
, xfbase = mcxIOnew(tg->str, "w")
; if
( (!write_modes || (write_modes & OUTPUT_CONE))
&& !xfcone
)
{ mcxTingPrint(tg, "%s.%s", stem, "cone")
; xfcone = mcxIOnew(tg->str, "w")
; mcxIOopen(xfcone, EXIT_ON_FAIL)
; fprintf(xfcone->fp, "# %s %s\n", argv[0], cline->str)
; }
if ((write_modes & OUTPUT_STACK) && !xfstack)
{ mcxTingPrint(tg, "%s.%s", stem, "stack")
; xfstack = mcxIOnew(tg->str, "w")
; mcxIOopen(xfstack, EXIT_ON_FAIL)
; fprintf(xfstack->fp, "# %s %s\n", argv[0], cline->str)
; }
mcxTingFree(&tg)
; }
if (integrate_g)
{ for (i=a;i<argc;i++)
{ mcxIO* xf = mcxIOnew(argv[i], "r")
; mclx* cl = mclxRead(xf, EXIT_ON_FAIL)
; mclxCatPush(&stck_g, cl, NULL, NULL, mclxCBdomStack, NULL, "dummy-integrate", n_cls++)
; }
integrate_results(&stck_g)
; if (xfstack)
mclxCatWrite(xfstack, &stck_g, MCLXIO_VALUE_NONE, RETURN_ON_FAIL)
; if (xfcone)
mclxCatConify(&stck_g)
, mclxCatWrite(xfcone, &stck_g, MCLXIO_VALUE_NONE, RETURN_ON_FAIL)
; return 0
; }
for (i=a;i<argc;i++)
{ if (get_interface(NULL, argv[1], shared->str, argv[i], NULL, 0, RETURN_ON_FAIL))
mcxDie(1, me, "error while testing mcl options viability (%s)", argv[i])
; }
mcxLog(MCX_LOG_APP, me, "pid %ld", (long) getpid())
/* make sure clusters align with this cluster
* status: does not seem promising.
*/
; if (xfctrl)
clctrl = mclxRead(xfctrl, EXIT_ON_FAIL)
;
/*
* Below: compute cl and mxbase.
*/
; if (xfcl)
{ cl = mclxRead(xfcl, EXIT_ON_FAIL)
; write_clustering
(cl, NULL, xfcone, xfstack, plexprefix, multiplex_idx++, NULL)
; if (subcluster_g || dispatch_g)
mclxCatPush(&stck_g, cl, NULL, NULL, mclxCBdomStack, NULL, "dummy-mclcm", n_cls++)
; mcxIOfree(&xfcl)
; if (!b1opts && !b2opts)
b1opts = ""
; mxbase = get_base(argv[1], NULL, b1opts, b2opts)
; }
else
{ mcxbits CACHE = b1opts || b2opts
? ALG_CACHE_INPUT /* cache, transform later */
: ALG_CACHE_START
; get_interface
( &mlp
, argv[1]
, shared->str
, a < argc ? argv[a] : NULL
, NULL
, CACHE
, EXIT_ON_FAIL
)
; if (a < argc)
a++
; if ((status = mclAlgorithm(mlp)) == STATUS_FAIL)
{ mcxErr(me, "failed at initial run")
; exit(1)
; }
cl_coarse = mclAlgParamRelease(mlp, mlp->cl_result)
; cl_coarse = control_test(cl_coarse, clctrl)
; write_clustering
(cl_coarse, NULL, xfcone, xfstack, plexprefix, multiplex_idx++, mlp)
; if (subcluster_g || dispatch_g)
mclxCatPush(&stck_g, cl_coarse, NULL, NULL, mclxCBdomStack, NULL, "dummy-mclcm", n_cls++)
; cl = cl_coarse
; n_ite++
; if (b1opts || b2opts)
{ mclx* mx_input = mclAlgParamRelease(mlp, mlp->mx_input)
; mxbase = get_base(NULL, mx_input, b1opts, b2opts)
/* ^ get_base frees mx_input */
; }
else
mxbase = mclAlgParamRelease(mlp, mlp->mx_start)
; }
clprev = cl
; mclAlgParamFree(&mlp, TRUE)
; if (xfbase)
{ dim nre = mclxNrofEntries(mxbase)
; mcxLog(MCX_LOG_APP, me, "base has %lu entries", (ulong) nre)
; mclxaWrite(mxbase, xfbase, MCLXIO_VALUE_GETENV, EXIT_ON_FAIL)
; mcxIOclose(xfbase)
; }
if (subcluster_g || dispatch_g)
iaf = iaf ? 1/iaf : 1.414
; while
( (!dispatch_g && (!N || n_ite < N))
|| (dispatch_g && a < argc)
)
{ mclx* mx_coarse = NULL, *clnext = NULL
; dim dist_new_prev = 0, dist_prev_new = 0
; mclx* clnew = NULL
; mcxbool faith = FALSE
; double inflation = -1.0
; if (subcluster_g)
mx_coarse
= subclusterx_g
? mclxBlockPartition(mxbase, clprev, 50)
: mclxBlockUnion(mxbase, clprev)
/* have to copy mxbase as mx_coarse is freed.
* Even if it were not freed, it is probably transformed.
*/
; else if (dispatch_g)
mx_coarse = mclxCopy(mxbase)
; else
{ mx_coarse = get_coarse(mxbase, clprev, add_transpose)
; if (n_ite == 1)
{ mclx* cc = clmUGraphComponents(mx_coarse, NULL) /* fixme; mx_coarse garantueed UD ? */
; n_components = N_COLS(cc)
; mclxFree(&cc)
; }
}
if (xfcoarse)
write_coarse(xfcoarse, mx_coarse)
; get_interface
( &mlp
, NULL
, shared->str
, a < argc ? argv[a] : NULL
, mx_coarse
, ALG_CACHE_START
, EXIT_ON_FAIL
)
; inflation = mlp->mpp->mainInflation
; BIT_OFF(mlp->modes, ALG_DO_SHOW_PID | ALG_DO_SHOW_JURY)
; if ((status = mclAlgorithm(mlp)) == STATUS_FAIL)
{ mcxErr(me, "failed")
; mcxExit(1)
; }
cl_coarse = mclAlgParamRelease(mlp, mlp->cl_result)
; if (xfcoarse)
mclxaWrite(cl_coarse, xfcoarse, MCLXIO_VALUE_NONE, RETURN_ON_FAIL)
; if (dispatch_g || subcluster_g)
clnext = cl_coarse
; else
clnext = mclxCompose(clprev, cl_coarse, 0)
, clnext = control_test(clnext, clctrl)
, mclxFree(&cl_coarse)
; clmSJDistance
(clprev, clnext, NULL, NULL, &dist_prev_new, &dist_new_prev)
; if (dist_prev_new + dist_new_prev)
{ write_clustering
(clnext, clprev, xfcone, xfstack, plexprefix, multiplex_idx++, mlp)
; clnew = clnext
; if (subcluster_g || dispatch_g)
mclxCatPush(&stck_g, clnext, NULL, NULL, mclxCBdomStack, NULL, "dummy-mclcm", n_cls++)
; else
mclxFree(&clprev)
; clprev = clnew
; }
else if
( N_COLS(clnext) > n_components
&& inflation * iaf > 1.2
&& inflation * iaf < 10
)
{ mclxFree(&clnext)
; inflation *= iaf
; mcxTingPrintAfter(shared, " -I %.2f", inflation)
; mcxLog(MCX_LOG_APP, me, "setting inflation to %.2f", inflation)
; faith = TRUE
; }
/* i.e. vanilla mode, contraction */
else if (!subcluster_g && !dispatch_g)
{ mclx* cc
; mclxFree(&clnext)
; mclxAddTranspose(mx_coarse, 1.0)
; cc = clmUGraphComponents(mx_coarse, NULL)
; if (N_COLS(cc) < N_COLS(clprev))
{ mclx* ccback = mclxCompose(clprev, cc, 0)
; write_clustering
(ccback, clprev, xfcone, xfstack, plexprefix, multiplex_idx++, NULL)
; mclxFree(&clprev)
; clprev = ccback
; mcxTell(me, "connected components added as root clustering")
; }
if (root && N_COLS(cc) > 1)
{ mclx* root = mclxCartesian
( mclvCanonical(NULL, 1, 0)
, mclvCopy(NULL, mxbase->dom_cols)
, 1.0
)
; write_clustering
(root, clprev, xfcone, xfstack, plexprefix, multiplex_idx++, NULL)
; mclxFree(&clprev)
; mcxTell(me, "universe added as root clustering")
; clprev = root
; clnew = NULL
; }
mclxFree(&cc)
; }
else if (subcluster_g || dispatch_g)
mclxFree(&clnext)
; mclAlgParamFree(&mlp, TRUE) /* frees mx_coarse */
; if (!clnew && !faith)
{ same = TRUE
; break
; }
a++
; if (dispatch_g && a == argc)
break
; n_ite++
; }
if (same)
mcxLog(MCX_LOG_MODULE, me, "no further contraction: halting")
; if (dispatch_g)
integrate_results(&stck_g)
; else if (subcluster_g)
mclxCatReverse(&stck_g)
; if (dispatch_g || subcluster_g)
{ dim j
; if (xfstack)
mclxCatWrite(xfstack, &stck_g, MCLXIO_VALUE_NONE, RETURN_ON_FAIL)
; if (xfcone && ! mclxCatConify(&stck_g))
mclxCatWrite(xfcone, &stck_g, MCLXIO_VALUE_NONE, RETURN_ON_FAIL)
; for (j=0;j<stck_g.n_level;j++)
{ mclxAnnot* an = stck_g.level+j
; mclxFree(&an->mx)
; }
mcxFree(stck_g.level)
; }
mcxIOfree(&xfcoarse)
; mcxIOfree(&xfbase)
; mcxIOfree(&xfcone)
; mcxIOfree(&xfstack)
; mcxTingFree(&shared)
; if (!dispatch_g && !subcluster_g) /* fixme fixme fixme */
mclxFree(&clprev)
; mclxFree(&mxbase)
; mclvFree(&start_col_sums_g)
; mcxTingFree(&cline)
; helpful_reminder()
; return STATUS_OK
; }
static void mcxIOcleanpat
( mcxIOpat* md
)
{ mcxFree(md->circle)
; }
