toc = pd.read_table(tocfilename)
# Estimate the model for one case to generate timing table with different regions of interest.
#for f in folderlist:
# path = 'ELBO/%s' %str(folderlist.index(f))
for dilution in np.unique(toc[toc.isRef == 'N'].Dilution):
logging.debug("Processing dilution: %0.1f" % dilution)
h5FileName = "Case%s.hdf5" % str(dilution).replace(".", "_", 1)
try:
with h5py.File(h5FileName, 'r') as f:
pass
except IOError as e:
dsample = 10000
region = "top_400_positions"
#caseFileList = ['./depth_chart/%s/%s/20100916_c3_p1.07_CGT.dc' % (dsample, region)] # For single file
caseFileList = [
"./depth_chart/10000/top_400_positions/%s" % filename
for filename in toc.Filename[toc.Dilution == dilution]
]
logging.info('Estimate %s' % caseFileList)
(r, n, loc, refb) = rvd3.load_depth(caseFileList)
casephi, caseq = rvd3.ELBO_opt(r,
n,
seed=19860522,
pool=60,
dsample=dsample,
region=region)
logging.debug("Saving model in %s" % h5FileName)
rvd3.save_model(h5FileName, r, n, casephi, caseq, loc, refb)
except IOError as e:
time_all = []
caseFileList = ["../2015-10-15_Plot_time_vs_region_length_rvd3_synthetic_data/depth_chart/100/top_400_positions/%s"\
% filename for filename in toc.Filename[toc.Dilution==dilution] ]
logging.info('Estimate %s' % caseFileList)
t0 = time.time()
(r, n, loc, refb) = rvd3.load_depth(caseFileList)
t1 = time.time()
time_load_depth = t1 - t0
time_all.extend([time_load_depth])
casephi, caseq, time_ini_model_para, time_ini_var_para, time_ini_ELBO, time_opt_gam, time_opt_delta, time_conv, \
time_opt_mu0, time_opt_M0, time_opt_M, time_update_ELBO = rvd3.ELBO_opt(r, n, seed = 19860522, pool=None)
time_all.extend([time_ini_model_para, time_ini_var_para, time_ini_ELBO, time_opt_gam, time_opt_delta, time_conv, \
time_opt_mu0, time_opt_M0, time_opt_M, time_update_ELBO])
logging.debug("Saving model in %s" % h5FileName)
t2 = time.time()
rvd3.save_model(h5FileName, r, n, casephi, caseq, loc, refb)
t3 = time.time()
time_save = t3 - t2
time_all.extend([time_save])
print time_all
items = "load_depth, ini_model_para, ini_var_para, ini_ELBO, opt_gamma, opt_delta, conv, opt_mu0, opt_M0, opt_M, update_ELBO, save_model"
np.savetxt("time_400_single.csv",
import multiprocessing as mp
import logging
import pdb
# <codecell>
logging.basicConfig(level=logging.DEBUG,
format='%(levelname)s:%(module)s:%(message)s')
rvddir = os.path.join('./')
sys.path.insert(0, rvddir)
import rvd3
##pool =None
pool = mp.Pool(processes=64)
# Estimate the model for the control
logging.debug("Processing control data.")
h5FileName = "c4-34_MTH1_M0times1000.hdf5"
try:
with h5py.File(h5FileName, 'r') as f:
pass
except IOError as e:
filename = "c4-34_MTH1.dc"
controlFileList = [
"../2016-01-12_Run_rvd3_Dan_data_regions/dc/E1/%s" % filename
]
(r, n, loc, refb) = rvd3.load_depth(controlFileList)
controlphi, controlq = rvd3.ELBO_opt(r, n, seed=20160210, pool=62)
logging.debug("Saving model in %s" % h5FileName)
rvd3.save_model(h5FileName, r, n, controlphi, controlq, loc, refb)
logging.debug("Processing control data.")
h5FileName = "Control.hdf5"
try:
with h5py.File(h5FileName, 'r') as f:
pass
except IOError as e:
controlFileList = ["../2015-09-28_Run_rvd3_synthetic_data_set/depth_chart/10/%s" % filename for filename in toc.Filename[toc.isRef=='Y']]
(r, n, loc, refb) = rvd3.load_depth(controlFileList)
controlphi, controlq = rvd3.ELBO_opt(r, n, seed = 1986, pool=60)
logging.debug("Saving model in %s" % h5FileName)
rvd3.save_model(h5FileName, r, n, controlphi, controlq, loc, refb)'''
# Estimate the model for the cases
for dilution in np.unique(toc[toc.isRef == 'N'].Dilution):
logging.debug("Processing dilution: %0.1f" % dilution)
h5FileName = "Case%s.hdf5" % str(dilution).replace(".", "_", 1)
try:
with h5py.File(h5FileName, 'r') as f:
pass
except IOError as e:
caseFileList = [
"../2015-09-28_Run_rvd3_synthetic_data_set/depth_chart/10/%s" %
filename for filename in toc.Filename[toc.Dilution == dilution]
]
(r, n, loc, refb) = rvd3.load_depth(caseFileList)
casephi, caseq = rvd3.ELBO_opt(r, n, seed=1986, pool=60, vaf=dilution)
logging.debug("Saving model in %s" % h5FileName)
rvd3.save_model(h5FileName, r, n, casephi, caseq, loc, refb)