void mcxDiagnosticsAttractor
( const char* ffn_attr
, const mclMatrix* clus2elem
, const mcxDumpParam dumpParam
)
{ int n_nodes = clus2elem->n_range
; int n_written = dumpParam->n_written
; mclMatrix* mtx_Ascore = mclxAllocZero(n_written, n_nodes)
; mcxIO* xfOut = mcxIOnew(ffn_atr, "w")
; dim d = 0
; if (mcxIOopen(xfOut, RETURN_ON_FAIL) == STATUS_FAIL)
{ mclxFree(&mtx_Ascore)
; mcxIOfree(&xfOut)
; return
; }
; for(d=0; d<n_written; d++)
{ mclMatrix* iterand = *(dumpParam->iterands+d)
; mclVector* vec_Ascore = NULL
; if (iterands->n_cols != n_nodes || iterand->n_range != n_nodes)
{ fprintf(stderr, "mcxDiagnosticsAttractor: dimension error\n")
; mcxExit(1)
; }
vec_Ascore = mcxAttractivityScale(iterand)
; mclvRenew((mtx_Ascore->cols+d), vec_Ascore->ivps, vec_Ascore->n_ivps)
; mclvFree(&vec_Ascore)
; }
mclxbWrite(mtx_Ascore, xfOut, RETURN_ON_FAIL)
; mclxFree(mtx_Ascore)
; }
static mcxstatus convertMain
( int argc_unused cpl__unused
, const char* argv[]
)
{ mclMatrix* mx
; mclxCat st
; xfin = mcxIOnew(argv[0], "r")
; xfout = mcxIOnew(argv[1], "w")
; mclxCatInit(&st)
; if (main_mode == 'l')
{ if (mclxCatRead(xfin, &st, catmax, NULL, NULL, 0))
mcxDie(1, me, "failure is, if not an option, the result after all")
; mclxCatWrite(xfout, &st, MCLXIO_VALUE_GETENV, EXIT_ON_FAIL)
; }
else if (main_mode == 'f')
{ int format
; mx = mclxRead(xfin, EXIT_ON_FAIL)
; format = mclxIOformat(xfin)
; if (!test_read)
{ mcxIOopen(xfout, EXIT_ON_FAIL)
; if (format == 'a')
mclxbWrite(mx, xfout, EXIT_ON_FAIL)
; else
mclxaWrite(mx, xfout, MCLXIO_VALUE_GETENV, EXIT_ON_FAIL)
; }
}
else
{ mcxbits bits
= main_mode == 'c'
? MCLX_REQUIRE_DOMTREE | MCLX_CATREAD_CLUSTERSTACK
: main_mode == 's'
? MCLX_REQUIRE_DOMSTACK | MCLX_CATREAD_CLUSTERTREE
: 0
; mcxIOopen(xfout, EXIT_ON_FAIL)
; if (mclxCatRead(xfin, &st, catmax, NULL, NULL, bits))
mcxDie(1, me, "failure is, if not an option, the result after all")
; mclxCatWrite(xfout, &st, MCLXIO_VALUE_NONE, EXIT_ON_FAIL)
; }
return 0
; }
int main
( int argc
, const char* argv[]
)
{ mcxIO* xfmx = mcxIOnew("-", "r"), *xfout = mcxIOnew("-", "w")
; mclx* mx = NULL
; mclv* mx_diag = NULL
; mcxstatus parseStatus = STATUS_OK
; mcxOption* opts, *opt
; dim N_edge = 0
; dim* offsets
; dim template_n_nodes = 0
; mcxbool plus = FALSE
; double e_min = 1.0
; double e_max = 0.0
; double skew = 0.0
; double radius = 0.0
; double n_sdev = 0.5
; double n_range = 2.0
; double g_radius = 0.0
; double g_mean = 0.0
; double g_sdev = 0.0
; double g_min = 1.0
; double g_max = 0.0
; mcxbool do_gaussian = FALSE
; dim i = 0
; dim N_remove = 0
; dim N_add = 0
; dim N_shuffle = 0
; unsigned long random_ignore = 0
; srandom(mcxSeed(2308947))
; mcxOptAnchorSortById(options, sizeof(options)/sizeof(mcxOptAnchor) -1)
; if
(!(opts = mcxOptParse(options, (char**) argv, argc, 1, 0, &parseStatus)))
exit(0)
; mcxLogLevel =
MCX_LOG_AGGR | MCX_LOG_MODULE | MCX_LOG_IO | MCX_LOG_GAUGE | MCX_LOG_WARN
; mclxIOsetQMode("MCLXIOVERBOSITY", MCL_APP_VB_YES)
; mclx_app_init(stderr)
; for (opt=opts;opt->anch;opt++)
{ mcxOptAnchor* anch = opt->anch
; switch(anch->id)
{ case MY_OPT_HELP
: case MY_OPT_APROPOS
: mcxOptApropos(stdout, me, syntax, 20, MCX_OPT_DISPLAY_SKIP, options)
; return 0
;
case MY_OPT_VERSION
: app_report_version(me)
; return 0
;
case MY_OPT_SKEW
: skew = atof(opt->val)
; break
;
case MY_OPT_GEN
: template_n_nodes = atoi(opt->val)
; break
;
case MY_OPT_IMX
: mcxIOrenew(xfmx, opt->val, NULL)
; break
;
case MY_OPT_PLUS
: case MY_OPT_WB
: plus = TRUE
; break
;
case MY_OPT_OUT
: mcxIOrenew(xfout, opt->val, NULL)
; break
;
case MY_OPT_E_MAX
: if (!strcmp(opt->val, "copy"))
e_max = -DBL_MAX
; else
e_max = atof(opt->val)
; break
;
case MY_OPT_E_MIN
: e_min = atof(opt->val)
; break
;
case MY_OPT_G_MIN
: g_min = atof(opt->val)
; break
;
case MY_OPT_G_MAX
: g_max = atof(opt->val)
; break
;
case MY_OPT_G_SDEV
: g_sdev = atof(opt->val)
; break
;
case MY_OPT_G_MEAN
: g_mean = atof(opt->val)
; do_gaussian = TRUE
; break
;
case MY_OPT_G_RADIUS
: g_radius = atof(opt->val)
; break
;
case MY_OPT_N_RANGE
: n_range = atof(opt->val)
; break
;
case MY_OPT_N_SDEV
: n_sdev = atof(opt->val)
; break
;
case MY_OPT_N_RADIUS
: radius = atof(opt->val)
; break
;
case MY_OPT_SHUFFLE
: N_shuffle = atoi(opt->val)
; break
;
case MY_OPT_ADD
: N_add = atoi(opt->val)
; break
;
case MY_OPT_REMOVE
: N_remove = atoi(opt->val)
; break
; }
}
/* hitting y% in vi tells me the size of this block */
{ if (template_n_nodes)
mx = mclxAllocZero
( mclvCanonical(NULL, template_n_nodes, 1.0)
, mclvCanonical(NULL, template_n_nodes, 1.0)
)
; else
mx = mclxReadx
( xfmx
, EXIT_ON_FAIL
, MCLX_REQUIRE_GRAPH
)
; mx_diag = mclxDiagValues(mx, MCL_VECTOR_COMPLETE)
; if (N_shuffle)
mclxAdjustLoops(mx, mclxLoopCBremove, NULL)
; else
mclxSelectUpper(mx)
/* ^ apparently we always work on single arc representation (docme andsoon) */
; offsets = mcxAlloc(sizeof offsets[0] * N_COLS(mx), EXIT_ON_FAIL)
; N_edge = 0
; for (i=0;i<N_COLS(mx);i++)
{ offsets[i] = N_edge
; N_edge += mx->cols[i].n_ivps
; }
if (N_edge < N_remove)
{ mcxErr
( me
, "removal count %ld exceeds edge count %ld"
, (long) N_remove
, (long) N_edge
)
; N_remove = N_edge
; }
random_ignore = RAND_MAX - (N_edge ? RAND_MAX % N_edge : 0)
; if (RAND_MAX / 2 < N_edge)
mcxDie(1, me, "graph too large!")
; if (N_shuffle)
{ do_the_shuffle(mx, N_shuffle, offsets, N_edge, random_ignore)
; mx_readd_diagonal(mx, mx_diag)
; mclxWrite(mx, xfout, MCLXIO_VALUE_GETENV, RETURN_ON_FAIL)
; exit(0)
; }
; if (N_remove)
{ dim n_remove = do_remove(mx, N_remove, offsets, N_edge, random_ignore)
/* Need to recompute N_edge and random_ignore.
* NOTE we work with *upper* matrix; this counts graph edges.
*/
; N_edge = mclxNrofEntries(mx) - n_remove
; random_ignore = RAND_MAX - (RAND_MAX % N_COLS(mx))
; }
if (g_mean)
{ if (!g_radius)
{ if (g_sdev)
g_radius = 2 * g_sdev
; mcxWarn(me, "set radius to %.5f\n", g_radius)
; }
}
; if (N_add)
N_edge += do_add
( mx
, N_add , N_edge
, do_gaussian ? &g_mean : NULL, g_radius , g_sdev , g_min , g_max
, skew
, e_min , e_max
)
; if (radius)
{ for (i=0;i<N_COLS(mx);i++)
{ mclp* ivp = mx->cols[i].ivps, *ivpmax = ivp + mx->cols[i].n_ivps
;if(DEBUG)fprintf(stderr, "here %d\n", (int) i)
; while (ivp < ivpmax)
{ double val = ivp->val
; double r = mcxNormalCut(n_range * n_sdev, n_sdev)
; double newval = val + radius * (r / (n_range * n_sdev))
; if (e_min < e_max && newval >= e_min && newval <= e_max)
; ivp->val = newval
; ivp++
; }
}
}
mclxUnary(mx, fltxCopy, NULL) /* remove zeroes */
; mclxAddTranspose(mx, 0.0)
; mx_readd_diagonal(mx, mx_diag)
; if (plus)
mclxbWrite(mx, xfout, RETURN_ON_FAIL)
; else
mclxWrite(mx, xfout, MCLXIO_VALUE_GETENV, RETURN_ON_FAIL)
; }
return 0
; }
static mcxstatus collectMain
( int argc
, const char* argv[]
)
{ aggr* collect = NULL
; int a
; dim i, collect_n = 0
; mclTab* tab = NULL
; double avg = 0.0
; mclx* aggr = NULL, *mx = NULL
/* mcxHash* map = NULL */
; mcxIO* xfout = mcxIOnew(out_g, "w")
; mcxIOopen(xfout, EXIT_ON_FAIL)
; if
( transform_spec
&& (!(transform = mclgTFparse(NULL, transform_spec)))
)
mcxDie(1, me, "input -tf spec does not parse")
; if (xftab_g)
tab = mclTabRead(xftab_g, NULL, EXIT_ON_FAIL)
/* map not used; perhaps someday we want to map labels to indexes?
* in that case, we could also simply reverse the tab when reading ..
, map = mclTabHash(tab)
*/
; if (!collect_g)
mcxDie(1, me, "require one of --paste, --add-column, --add-matrix")
; if (argc)
{ if (collect_g == 'm')
{ mcxIO* xf = mcxIOnew(argv[0], "r")
; mcxIOopen(xf, EXIT_ON_FAIL)
; aggr = mclxRead(xf, EXIT_ON_FAIL)
; mcxIOfree(&xf)
; }
else
collect_n = do_a_file(&collect, argv[0], 0)
; }
if (tab && collect_n != N_TAB(tab) + (header_g ? 1 : 0))
mcxErr
( me
, "tab has differing size (%lu vs %lu), continuing anyway"
, (ulong) N_TAB(tab)
, (ulong) (collect_n ? collect_n -1 : 0)
)
; for (a=1;a<argc;a++)
{ if (collect_g == 'm')
{ mcxIO* xf = mcxIOnew(argv[a], "r")
; mcxIOopen(xf, EXIT_ON_FAIL)
; mx = mclxRead(xf, EXIT_ON_FAIL)
; mclxAugment(aggr, mx, fltop_g)
; mcxIOfree(&xf)
; mclxFree(&mx)
; }
else
do_a_file(&collect, argv[a], collect_n)
; }
if (collect_g == 'm')
{ if (transform)
mclgTFexec(aggr, transform)
; if (mcx_wb_g)
mclxbWrite(aggr, xfout, EXIT_ON_FAIL)
; else
mclxWrite(aggr, xfout, MCLXIO_VALUE_GETENV, EXIT_ON_FAIL)
; mcxIOclose(xfout)
; exit(0)
; }
/* fimxe: dispatch on binary_g */
for (i=0;i<collect_n;i++)
{ const char* lb = collect[i].label
; if (!i && collect[i].columns && collect_g != 'p')
{ fprintf(xfout->fp, "%s\t%s\n", lb, collect[i].columns->str)
; continue
; }
if (tab && (!header_g || i > 0))
{ unsigned u = atoi(lb)
; lb = mclTabGet(tab, u, NULL)
; if (TAB_IS_NA(tab, lb))
mcxDie(1, me, "no label found for index %ld - abort", (long) u)
; }
if (summary_g)
avg += collect[i].val
; else
{ if (collect_g == 'p')
fprintf(xfout->fp, "%s%s\n", lb, collect[i].columns->str)
; else
fprintf(xfout->fp, "%s\t%.8g\n", lb, collect[i].val)
; }
}
if (summary_g && collect_n)
{ dim middle1 = (collect_n-1)/2, middle2 = collect_n/2
; qsort(collect, collect_n, sizeof collect[0], aggr_cmp_val)
; avg /= collect_n
; fprintf /* --summary option is a bit rubbish interface-wise */
( xfout->fp
, "%g %g %g %g\n"
, collect[0].val
, (collect[middle1].val + collect[middle2].val) / 2
, collect[collect_n-1].val
, avg
)
; }
return STATUS_OK
; }
