def _run_mscale(cdir, animation=ANIMATION):
outdir = "%s_viz/" % (cdir)
tl.mkdir("%s" % outdir)
#--------------------------------#
# (1) load modelDBs, Snaps
mdbHs = {}
SnapsHs = {}
CGHs = {}
outdirHs = {}
for i in range(0, MSCALE_H):
outdirHs[i] = "%s_Level%d/" % (outdir, i)
tl.mkdir("%s" % outdirHs[i])
mdbHs[i] = tl.load_obj('%s_Level%d/MDB.obj' % (cdir, i))
SnapsHs[i] = tl.load_mat('%s_Level%d/Snaps.mat' % (cdir, i))
CGHs[i] = tl.load_obj('%s_Level%d/CGs.obj' % (cdir, i))
#--------------------------------#
# (2) save multi-scale (LOCAL)
arg_list = []
for i in range(0, MSCALE_H):
arg_list.append([SnapsHs[i], mdbHs[i], CGHs[i], outdirHs[i]])
if (MULTI):
_multi_save_all_L(arg_list)
else:
for i in range(0, MSCALE_H):
_save_all_L(SnapsHs[i], mdbHs[i], CGHs[i], outdirHs[i])
#--------------------------------#
# (3) save Xorg-cast (GLOBAL)
Xorg = tl.loadsq('%sXorg.txt' % cdir).T # load Xorg
Snaps = _save_all_G(Xorg, outdir, SnapsHs, mdbHs, outdir)
def _create_multiscale_seqs(Xorg, lstep, mscale_h, outdir):
tl.msg("_create_multiscale_seq (lstep: %d, mscale_h: %d)"%(lstep, mscale_h))
tl.save_seq_txt_pdf(Xorg, "%sXorg"%outdir)
# multi-scale sequences
XHs={}; Xagg=tl.dcopy(Xorg); outdirHs={}
wdHs={} # window size list
for i in range(0,mscale_h):
# window size at i-th level
if(i<mscale_h-1): wdHs[i]=lstep*(2**(mscale_h-1-i)) # if HT=4: 3,2,1 ... (i.e., 8xlstep, 4xlstep, 2xlstep, 1)
#if(i<mscale_h-1): wdHs[i]=lstep*(2**(mscale_h-2-i)) # if HT=4: 2,1,0 ... (i.e., 4xlstep, 2xlstep, lstep, 1)
#if(i<mscale_h-1): wdHs[i]=lstep*(2**(mscale_h-3-i)) # if HT=4: 1,0,-1 ... (i.e., 2xlstep, lstep, 1/2xlstep, 1
else: wdHs[i]=1 # if, last seq
for i in range(0,mscale_h):
XHs[i]=tl.smoothWMAo(Xagg, wdHs[i]) # compute i-th level
Xagg=Xagg-XHs[i] # delete current scale
for i in range(0,mscale_h):
#XHs[i]= XHs[i][int(wdHs[0]):,:] # delete longest-window
XHs[i][0:int(wdHs[0]),:]=tl.NAN # delete longest-window
outdirHs[i]='%s_Level%d/'%(outdir,i); tl.mkdir(outdirHs[i]) # directory
# save sequence at i-th level
tl.save_txt(XHs[i], '%sXorg.txt'%(outdirHs[i])) # save data
tl.plt.clf(); tl.plt.plot(XHs[i]) # plot and save figure
tl.savefig("%sXorg"%(outdirHs[i]), 'pdf')
tl.msg("wdHs: ")
tl.msg(wdHs)
return (XHs, wdHs, outdirHs)
def _run_single(cdir, animation=ANIMATION):
outdir = "%s_viz/" % (cdir)
tl.mkdir("%s" % outdir)
#--------------------------------#
# (1) load modelDBs, Snaps
mdb = tl.load_obj('%sMDB.obj' % (cdir))
Snaps = tl.load_mat('%sSnaps.mat' % (cdir))
CG = tl.load_obj('%sCGs.obj' % (cdir))
# (2) save results
_save_all_L(Snaps, mdb, CG, outdir)
for i in range(para['dup']):
print('-------start {}-------'.format(i))
tmp = simulation1(para)
res1.append(tmp[0])
res2.append(tmp[1])
res3.append(tmp[2])
res4.append(tmp[3])
print('-------end {}-------'.format(i))
print(' ')
"""
统计数据所用，保存成csv
"""
res1 = np.array(res1).reshape(-1, 1)
res2 = np.array(res2).reshape(-1, 1)
res3 = np.array(res3)
res4 = np.array(res4)
res = np.hstack((res1, res2, res3, res4))
res = pd.DataFrame(res, columns=['pro_RE', 'ori_RE', 'pro_A', 'pro_B', 'pro_C', 'ori_A', 'ori_B', 'ori_C'])
print(res.mean())
save_path = 'result/Non supervision/'
tool.mkdir(save_path)
res.to_csv(save_path + 'size{}.csv'.format(para['I1']), sep=',', index=False)
print('Done!')
def run_est_single(Xorg, lstep, outdir, wd_level=1):
#--------------------------------#
want_refinement = tl.YES
#--------------------------------#
mdb_cb = om_mdb.MDB('%s' % outdir) # create modelDB
Snaps_cb = init_Snaps(Xorg, lstep, wd_level) # SnapShots
mdb_cb = mdb_cb.update_Xminmax(Xorg)
errF_cb = tl.INF #; Snaps_cb=[];
if (RHO_INIT == -1): rho_iter = _compute_rho_min(Xorg, lstep)
else: rho_iter = RHO_INIT
ERRs_full = []
ERRs_cb_i = []
outdir_tr = "%s_trials/" % outdir
if (SAVE_TRIALS): tl.mkdir(outdir_tr) # create directory
tl.msg("(%d) run_est_single: start trial (find opt rho) ..." % wd_level)
for i_trial in range(0, MAXTRIAL):
#--------------------------------#
mdb_i = tl.dcopy(mdb_cb)
Snaps_i = tl.dcopy(Snaps_cb)
#--------------------------------#
# set rho, cleansing (e.g., remove inappropriate regimes), etc.
mdb_i.update_rho(rho_iter)
(mdb_i, Snaps_i) = mdb_i.update_apoptosis(Snaps_i, AP_MD, AP_MS,
want_refinement)
mdb_i = mdb_i.init_objects()
#--------------------------------#
# start OrbitMap
(mdb_i, Snaps_i) = _OrbitMap(Xorg, lstep, wd_level, mdb_i,
"%sTrial_%d_" % (outdir_tr, i_trial),
SAVE_TRIALS,
SAVE_TRIALS) #tl.YES) #tl.NO)
#--------------------------------#
if (i_trial > 0 and Snaps_i['errF_half'] <
errF_cb): # update best-fit (if trial > 0)
errF_cb = Snaps_i['errF_half']
mdb_cb = tl.dcopy(mdb_i)
Snaps_cb = tl.dcopy(Snaps_i)
#--------------------------------#
tl.msg(
"(mscale-wd: %d) Trial %d rho=%f, c=%d, errE: %f, errF(half):%f, errF(full):%f"
% (wd_level, i_trial, rho_iter, mdb_i.get_c(), Snaps_i['errE'],
Snaps_i['errF_half'], Snaps_i['errF']))
ERRs_full.append([
i_trial, rho_iter,
mdb_i.get_c(), Snaps_i['errE'], Snaps_i['errF_half'],
Snaps_i['errF']
])
tl.save_txt(ERRs_full, "%s_trials_results.txt" % (outdir))
#--------------------------------#
if (EARLYSTOP and Snaps_i['errF_half'] >= errF_cb
and i_trial >= MINTRIAL):
break # if, no more better-fit, break
if (mdb_i.get_c() <= 1 and i_trial > 0):
break # if, # of regimes is less than one, then, stop
#--------------------------------#
#--------------------------------#
rho_iter *= RHO_ITER_R_BU # rho: try larger value
#--------------------------------#
# final-best-fit
(mdb_cb, Snaps_cb) = mdb_cb.update_apoptosis(Snaps_cb, AP_MD, AP_MS,
want_refinement)
mdb_cb = mdb_cb.init_objects()
if (Snaps_cb['errF_half'] > Snaps_cb['errS']):
mdb_cb.CC = tl.NO # if, not approp. (no causalchain), ignore model
(mdb_cb, Snaps_cb) = _OrbitMap(Xorg, lstep, wd_level, mdb_cb,
"%s" % (outdir), tl.YES, tl.YES)
tl.msg("best est: c=%d, errE: %f, errF(half):%f, errF(full):%f" %
(mdb_cb.get_c(), Snaps_cb['errE'], Snaps_cb['errF_half'],
Snaps_cb['errF']))
return (mdb_cb, Snaps_cb)
#---------------#
# main #
#---------------#
if __name__ == "__main__":
tl.msg("om_trans")
(DIR, st, wd, ncast, smin, cid) = _syn()
#(DIR, st, wd, ncast, smin, cid) = _mocap_c()
#(DIR, st, wd, ncast, smin, cid) = _mocap_c2()
mdbfn = "%sMDB.obj" % (DIR)
seqfn = "%sXorg.txt" % (DIR)
OUTDIR = "%sout/" % (DIR)
tl.mkdir(OUTDIR)
tl.eprint(OUTDIR)
mdb = tl.load_obj(mdbfn)
#
Xorg = tl.loadsq(seqfn).T
#snapsfn="%sSnaps.mat"%(DIR)
#Snaps=tl.load_mat(snapsfn)
#print(len(mdb.MS))
#tl.eprint(Snaps['Re_full'])
#tl.eprint(np.shape(Snaps['Re_full']))
#'''
for k in mdb.MS:
#print(mdb.MS)
print(k)
print(mdb.MS[k][0]['medoid']['cpt'])
mscale = args.mscale
else:
mscale = 1 # single-scale
#--- print args ---#
tl.comment('main_om.py - args')
tl.msg("-------------------------")
tl.msg("input-seqfn: [%s]" % iseqfn)
tl.msg("ls-step-ahead: [%d]" % lstep)
tl.msg("multi-scale: [%d]" % mscale)
tl.msg("outdir: [%s]" % outdir)
tl.msg("model dir (scan): [%s]" % mdir)
tl.msg("t_st (opt): [%s]" % my_tst)
tl.msg("duration (opt): [%s]" % my_n)
tl.msg("-------------------------")
try:
tl.mkdir("%s" % outdir)
except:
tl.error("cannot find: %s" % outdir)
#------------------------------#
# LOAD DATA
#------------------------------#
data = tl.loadsq(iseqfn).T
data = data[my_tst:, :]
(n, d) = np.shape(data)
#--- set data length (my_n) optional ---#
if (my_n < n):
data = data[0:my_n, :]
(n, d) = np.shape(data)
tl.msg("(n,d)=(%d,%d)" % (n, d))
Xorg = data # original data