def __init__(self,
psc_file,
variable_names,
v_name,
ranges,
psc_string=None):
self.psc_file = psc_file
self.psc_string = psc_string
self.variable_names = variable_names
self.v_name = 'J_{0}'.format(v_name) if v_name[0:2] != 'J_' else v_name
self.ranges = ranges
import pysces
if self.psc_string is None:
self.mod = pysces.model(self.psc_file)
else:
self.mod = pysces.model(self.psc_file,
loader='string',
fString=self.psc_string)
self.mod.SetQuiet()
self.variables = None
self.v = numpy.array([])
self.scanner = pysces.Scanner(self.mod)
for n, r in zip(self.variable_names, self.ranges):
self.scanner.addScanParameter(n, r[0], r[1], r[2])
self.scanner.addUserOutput(self.v_name)
self.scanner.Run()
results = self.scanner.getResultMatrix()
self.variables = results[:, 0:-1]
self.v = results[:, -1]
def P_SCAN(self, *args):
"""Args: (par, out, par*[str(p),float(start),float(end),int(points),
log=(int(0/1)),follower=(int(0/1))], [out*str(o)])
"""
self.setStatus('SCANNING')
args = args[0]
print('Args', args)
commands = []
cpoint = 1
shift = 0
for set in range(int(args[0])):
ctmp = []
for t in range(2, 8):
cpoint += 1
ctmp.append(args[t + shift].strip())
commands.append(ctmp)
shift += 6
output = []
for out in range(int(args[1])):
cpoint += 1
output.append(args[cpoint].strip())
print('\n', commands)
print(output, '\n')
scan = pysces.Scanner(self.model)
scan.quietRun = True
for gen in commands:
print(gen)
print(
gen[0],
float(gen[1]),
float(gen[2]),
int(gen[3]),
bool(int(gen[4])),
bool(int(gen[5])),
)
scan.addGenerator(
gen[0],
float(gen[1]),
float(gen[2]),
int(gen[3]),
log=bool(int(gen[4])),
follower=bool(int(gen[5])),
)
scan.addUserOutput(*output)
scan.Run()
self.RESULT = scan.UserOutputResults
self.setStatus('DONE_SCAN')
del scan
return True
def do_mca_scan(self):
ecs = []
ccs = []
prc_names = []
rc_names = []
rc_pos = []
reagent_of = [each[2:] for each in self.scan_results.flux_names]
all_reactions = reagent_of + \
getattr(self._model_map,
self.scan_results.fixed).isModifierOf()
arl = len(all_reactions)
strt = 0
stp = arl
for flux_reaction in self.scan_results.flux_names:
reaction = flux_reaction[2:]
rc_names.append('rcJ%s_%s' % (reaction, self.scan_results.fixed))
rc_pos.append(range(strt, stp))
strt += arl
stp += arl
for route_reaction in all_reactions:
ec = 'ec' + route_reaction + '_' + self.scan_results.fixed
cc = 'ccJ' + reaction + '_' + route_reaction
name = 'prcJ%s_%s_%s' % (reaction,
self.scan_results.fixed,
route_reaction)
# ecs.append(ec)
if ec not in ecs:
ecs.append(ec)
ccs.append(cc)
prc_names.append(name)
ec_len = len(ecs)
user_output = [self.scan_results.fixed] + ecs + ccs
scanner = pysces.Scanner(self.mod)
scanner.quietRun = True
scanner.addScanParameter(self.scan_results.fixed,
self.scan_results.scan_min,
self.scan_results.scan_max,
self.scan_results.scan_points,
log=True)
scanner.addUserOutput(*user_output)
scanner.Run()
ax_properties = {'ylabel': 'Coefficient Value',
'xlabel': '[%s]' %
self.scan_results.fixed.replace('_', ' '),
'xscale': 'log',
'yscale': 'linear',
'xlim': [self.scan_results.scan_min,
self.scan_results.scan_max]}
cc_ec_data_obj = Data2D(mod=self.mod,
column_names=user_output,
data_array=scanner.UserOutputResults,
ltxe=self._ltxe,
analysis_method=self._analysis_method,
ax_properties=ax_properties,
file_name='cc_ec_scan',
num_of_groups=ec_len,
working_dir=path.split(self._working_dir)[0])
rc_data = []
all_outs = scanner.UserOutputResults[:, 1:]
ec_outs = all_outs[:, :ec_len]
cc_outs = all_outs[:, ec_len:]
ec_positions = range(ec_len) * (len(prc_names)/ec_len)
for i, prc_name in enumerate(prc_names):
ec_col_data = ec_outs[:, ec_positions[i]]
cc_col_data = cc_outs[:, i]
# ec_col_data = outs[:, i]
# cc_col_data = outs[:, i + cc_s_pos]
col = ec_col_data * cc_col_data
rc_data.append(col)
temp = numpy.vstack(rc_data).transpose()
rc_data += [numpy.sum(temp[:, rc_pos[i]], axis=1) for i in
range(len(rc_names))]
rc_out_arr = [scanner.UserOutputResults[:, 0]] + rc_data
rc_out_arr = numpy.vstack(rc_out_arr).transpose()
rc_data_obj = Data2D(mod=self.mod,
column_names=[self.scan_results.fixed] + prc_names + rc_names,
data_array=rc_out_arr,
ltxe=self._ltxe,
analysis_method=self._analysis_method,
ax_properties=ax_properties,
file_name='prc_scan',
num_of_groups=ec_len,
working_dir=path.split(self._working_dir)[0])
#rc_data_obj._working_dir = path.split(self._working_dir)[0]
#cc_ec_data_obj._working_dir = path.split(self._working_dir)[0]
return rc_data_obj, cc_ec_data_obj
#!/usr/bin/env python
# Testing the new parallel scanner class
import os
backupdir = os.getcwd()
import numpy as np
import pysces
tbox=pysces.PyscesUtils.TimerBox()
import time
m=pysces.model('isola2a')
ser = pysces.Scanner(m)
print("Serial execution...")
print("Start: ", tbox.normal_timer('SER'))
print(next(tbox.SER))
t1=time.time()
ser.quietRun = True
ser.addScanParameter('V4',60,100,11)
ser.addScanParameter('V1',100,160,16)
ser.addScanParameter('V2',100,130,16,slave=True)
ser.addScanParameter('V3',80,90,6)
ser.addUserOutput('J_R1', 'A', 'ecR4_X','ccJR1_R1')
#ser.addUserOutput('J_R1', 'A')
ser.Run()
print("Done: ", next(tbox.SER))
t2=time.time()
print("Duration: %.2f seconds" % (t2-t1))