def open(frame, event):
'''
open(frame, event) --> None
Event handler for opening a model file...
'''
# Check so the model is saved before quitting
if not frame.model.saved:
ans = ShowQuestionDialog(frame, 'If you continue any changes in'
'your model will not be saved.',
'Model not saved')
if not ans:
return
dlg = wx.FileDialog(frame, message="Open", defaultFile="",\
wildcard="GenX File (*.gx)|*.gx",\
style=wx.OPEN | wx.CHANGE_DIR
)
if dlg.ShowModal() == wx.ID_OK:
path = dlg.GetPath()
try:
io.load_gx(path, frame.model,\
frame.solver_control.optimizer,\
frame.config)
except modellib.IOError, e:
ShowModelErrorDialog(frame, e.__str__())
except Exception, e:
outp = StringIO.StringIO()
traceback.print_exc(200, outp)
val = outp.getvalue()
outp.close()
ShowErrorDialog(frame, 'Could not open the file. Python Error:'\
'\n%s'%(val,))
return
def open_model(frame, path):
frame.model.new_model()
# Update all components so all the traces are gone.
_post_new_model_event(frame, frame.model)
try:
io.load_gx(path, frame.model,\
frame.solver_control.optimizer,\
frame.config)
except modellib.IOError, e:
ShowModelErrorDialog(frame, e.__str__())
def open_model(frame, path):
frame.model.new_model()
# Update all components so all the traces are gone.
_post_new_model_event(frame, frame.model)
#io.load_gx(path, frame.model,\
# frame.solver_control.optimizer,\
# frame.config)
try:
io.load_gx(path, frame.model,\
frame.solver_control.optimizer,\
frame.config)
except modellib.IOError as e:
print(e.__str__())
ShowModelErrorDialog(frame, e.__str__())
except Exception as e:
#outp = StringIO.StringIO()
outp = StringIO()
traceback.print_exc(200, outp)
val = outp.getvalue()
outp.close()
ShowErrorDialog(frame, 'Could not open the file. Python Error:'\
'\n%s'%(val,))
return
try:
[p.ReadConfig() for p in get_pages(frame)]
except Exception as e:
outp = StringIO()
traceback.print_exc(200, outp)
val = outp.getvalue()
outp.close()
print(val)
ShowErrorDialog(
frame, 'Could not read the config for the'
' plots. Python Error:\n%s' % (val, ))
# Letting the plugin do their stuff...
try:
frame.plugin_control.OnOpenModel(None)
except Exception as e:
outp = StringIO()
traceback.print_exc(200, outp)
val = outp.getvalue()
outp.close()
ShowErrorDialog(frame, 'Problems when plugins processed model.'\
' Python Error:\n%s'%(val,))
frame.main_frame_statusbar.SetStatusText('Model loaded from file',\
1)
# Post an event to update everything else
_post_new_model_event(frame, frame.model)
# Needs to put it to saved since all the widgets will have
# been updated
frame.model.saved = True
set_title(frame)
def make_gx_file():
mod = model.Model()
config = io.Config()
opt = diffev.DiffEv()
par=parameters.Parameters()
make_par_file()
par.set_ascii_input_new(os.path.join(dump_path_locator(),'par_table.tab'))
io.load_gx('temp_DONOT_delete.gx',mod,opt,config)
mod.script=make_script_file()
mod.parameters=par
mod.data,num_ctr=make_data_file()
for i in range(len(mod.data.items)-num_ctr):
mod.data.items[i+num_ctr].use=False
io.save_gx(gx_file_name,mod,opt,config)
print('gx file is saved in the current workdir!\n')
print('##########Basic model info##########')
print('Resonant element: '+RAXR_EL)
print('Number of Gaussian peaks in CTR: '+str(NUMBER_GAUSSIAN_PEAK))
print('Number of Gaussian peaks in RAXR: '+str(NUMBER_GAUSSIAN_PEAK_FREEZE))
print('Number of RAXR datasets: '+str(NUMBER_RAXS_SPECTRA))
print('RAXR data fit mode: '+{'\'MI\''[1:3]:'Model independent fit','\'MD\''[1:3]:'Model dependent fit'}[RAXR_FIT_MODE[1:3]])
def make_gx_file():
mod = model.Model()
config = io.Config()
opt = diffev.DiffEv()
par = parameters.Parameters()
make_par_file()
par.set_ascii_input_new(os.path.join(dump_path_locator(), 'table.tab'))
io.load_gx('temp_DONOT_delete.gx', mod, opt, config)
mod.script = make_script_file()
mod.parameters = par
mod.data, num_ctr = make_data_file()
for i in range(len(mod.data.items) - num_ctr):
mod.data.items[i + num_ctr].use = False
io.save_gx(gx_file_name, mod, opt, config)
print('gx file is saved in the current workdir!\n')
print('##########Basic model info##########')
print('Domain number: ' + str(len(domain_setup_HLT)) +
' half layer domains and ' + str(len(domain_setup_FLT)) +
' full layer domains')
print('sorbate: ' + sorbate)
local_structure_db = eval(LOCAL_STRUCTURE_MATCH_LIB)
for key in local_structure_db.keys():
if sorbate in local_structure_db[key]:
print('local_structure: ' + key)
break
else:
pass
binding_mode_db = []
for i in range(len(binding_mode)):
if binding_mode[i][0].startswith('clean'):
binding_mode_db.append('Clean_surface')
elif binding_mode[i][0].startswith('CS'):
binding_mode_db.append('Corner-sharing')
elif binding_mode[i][0].startswith('ES'):
binding_mode_db.append('Edge-sharing')
elif binding_mode[i][0].startswith('TD'):
binding_mode_db.append('Tridentate-binding')
elif binding_mode[i][0].startswith('OS'):
binding_mode_db.append('Outersphere binding')
print('Binding_mode: ' + ','.join(binding_mode_db))
sys.path.append('P://apps//genx_pc_qiu//lib')
import numpy as np
import model,diffev
import filehandling as io
path='P://temp_model'
file_path_raxr_mi=os.path.join(path,'Pb_3domains_cmp_1_1_2_waterpair_bv_constrained_run1_May30_ran.gx')
scan_number=50
error_bar_level=1.05
mod_raxr_mi = model.Model()
config_raxr_mi = io.Config()
opt_raxr_mi = diffev.DiffEv()
io.load_gx(file_path_raxr_mi,mod_raxr_mi,opt_raxr_mi,config_raxr_mi)
first_grid_mi,first_grid_md=None,None
print 'scan number is ',scan_number
print 'error bar level is ',error_bar_level
mod_raxr_mi.simulate()
best_fom=mod_raxr_mi.fom
for i in range(len(mod_raxr_mi.parameters.data)):
if mod_raxr_mi.parameters.data[i][2]==True:
print 'scan ',mod_raxr_mi.parameters.data[i][0],' now'
left,right=float(mod_raxr_mi.parameters.data[i][3]),float(mod_raxr_mi.parameters.data[i][4])
values=np.arange(left,right,(right-left)/scan_number)
best=float(mod_raxr_mi.parameters.data[i][1])
tmp_fom=[]
tmp_trial_vec=[]
tmp_pop_vec=[]
tmp_fom_vec=[]
for pars in par_list:
trial=pars[0]
fom = pars[1]
km = pars[2][0] # km
kr = pars[2][1] # kr
pf=pars[2][2]
iter = pars[3]
# Load the model ...
if rank==0: print 'Loading model %s...'%infile
io.load_gx(infile, mod, opt, config)
# Simulate, this will also compile the model script
if rank==0: print 'Simulating model...'
mod.simulate()
# Setting up the solver
eval('mod.set_fom_func(fom_funcs.%s)' % fom)
# Lets set the solver parameters:
try:
opt.set_create_trial(trial)
except:
print 'Warning: create_trial is not defined in script.'
try:
opt.set_kr(kr)
except:
import os, sys
os.chdir("C:\\apps\\genx\\")
import model, diffev, time, fom_funcs
import filehandling as io
import glob
import numpy as np
mod = model.Model()
config = io.Config()
opt = diffev.DiffEv()
io.load_gx(sys.argv[1], mod, opt, config)
slopes = []
names, values, switch, low, high = [], [], [], [], []
for i in range(mod.parameters.get_len_rows()):
if (mod.parameters.get_value(i, 0) != '') & (mod.parameters.get_value(
i, 2) == True):
left, right = mod.parameters.get_value(i, 3), mod.parameters.get_value(
i, 4)
val_init = mod.parameters.get_value(i, 1)
temp_fom = []
for val in np.arange(left, right, (right - left) / 5):
mod.parameters.set_value(i, 1, val)
mod.simulate()
temp_fom.append(mod.fom)
fom_max, fom_min = max(temp_fom), min(temp_fom)
fom_max_index, fom_min_index = temp_fom.index(fom_max), temp_fom.index(
fom_min)
par_max, par_min = np.arange(
left, right, (right - left) / 5)[fom_max_index], np.arange(
left, right, (right - left) / 5)[fom_min_index]
for filename in sys.argv[1:]:
print "\n\n--------------------"
print "Now exporting: %s" %filename
name = os.path.basename(filename) # filename without path
name = os.path.splitext(name)[0] # remove the filename extension
mainpath = os.path.dirname(filename) # path of file withouth filename
import model, diffev, filehandling, time
mod = model.Model()
opt = diffev.DiffEv()
config = filehandling.Config()
# Load the model ...
print 'Loading model %s...'%filename
filehandling.load_gx(filename, mod, opt, config)
# Simulate, this will also compile the model script
print 'Simulating model...'
mod.simulate()
# Setting up the solver
#opt.pickle_load(mod.load_addition('optimizer'))
# export the fom as function of generation
if do_fom_log:
print 'saving fom log to file...'
exportfile = os.path.join(mainpath,name + '_fom_log.dat')
np.savetxt(exportfile, opt.fom_log)
# export the fom array of all individuals
import os, sys
os.chdir("C:\\apps\\genx\\")
import model, diffev, time, fom_funcs
import filehandling as io
import glob
import numpy as np
mod = model.Model()
config = io.Config()
opt = diffev.DiffEv()
io.load_gx(sys.argv[1], mod, opt, config)
slopes = []
names, values, switch, low, high = [], [], [], [], []
for i in range(mod.parameters.get_len_rows()):
if (mod.parameters.get_value(i, 0) != "") & (mod.parameters.get_value(i, 2) == True):
left, right = mod.parameters.get_value(i, 3), mod.parameters.get_value(i, 4)
val_init = mod.parameters.get_value(i, 1)
temp_fom = []
for val in np.arange(left, right, (right - left) / 5):
mod.parameters.set_value(i, 1, val)
mod.simulate()
temp_fom.append(mod.fom)
fom_max, fom_min = max(temp_fom), min(temp_fom)
fom_max_index, fom_min_index = temp_fom.index(fom_max), temp_fom.index(fom_min)
par_max, par_min = (
np.arange(left, right, (right - left) / 5)[fom_max_index],
np.arange(left, right, (right - left) / 5)[fom_min_index],
)
slopes.append(abs((fom_max - fom_min) / (par_max - par_min)))
import model,diffev
import filehandling as io
path='P:\\My stuff\\Models\\CTR models\\Zr models for final publication\\refit results\\GenX'
file_path_raxr_mi=os.path.join(path,'Good_MI_RAXR_refit_Zr_100mM_NaCl_6O_run2_Apr3combined_ran.gx')
file_path_raxr_md=os.path.join(path,'MD_RAXR_refit_Zr_100mM_NaCl_6O_run2_Apr3_best_1_bin_R1_weighted_2_kr0.90_km0.90_pf0.80_run1_ran.gx')
mod_raxr_mi = model.Model()
config_raxr_mi = io.Config()
opt_raxr_mi = diffev.DiffEv()
mod_raxr_md = model.Model()
config_raxr_md = io.Config()
opt_raxr_md = diffev.DiffEv()
io.load_gx(file_path_raxr_mi,mod_raxr_mi,opt_raxr_mi,config_raxr_mi)
io.load_gx(file_path_raxr_md,mod_raxr_md,opt_raxr_md,config_raxr_md)
first_grid_mi,first_grid_md=None,None
for i in range(len(mod_raxr_mi.parameters.data)):
if mod_raxr_mi.parameters.data[i][0]=='rgh_raxs.setA1':
first_grid_mi=i
break
else:
print mod_raxr_mi.parameters.data[i][0]
for i in range(len(mod_raxr_md.parameters.data)):
if mod_raxr_md.parameters.data[i][0]=='rgh_raxs.setA1':
first_grid_md=i
break
else:
sys.path.append('C:\\apps\\genx_pc_qiu')
sys.path.append('C:\\apps\\genx_pc_qiu\\lib')
sys.path.append('/u1/uaf/cqiu/genx_pc_qiu')
import model,diffev,time,fom_funcs
import filehandling as io
import glob
import numpy as np
first_grid=54
grid_gap=20
path='/import/c/w/cqiu/temp_gx_files/'
gx_files=glob.glob(path+'*_May8.gx')#file must be sortable to have the code work correctly
gx_files.sort()
mod = model.Model()
config = io.Config()
opt = diffev.DiffEv()
io.load_gx(gx_files[0],mod,opt,config)
for gx_file in gx_files[1:]:
print "processing ",gx_file
i=gx_files.index(gx_file)
begin_grid=first_grid+grid_gap*i
mod_temp = model.Model()
config_temp = io.Config()
opt_temp = diffev.DiffEv()
io.load_gx(gx_file,mod_temp,opt_temp,config_temp)
for grid_index in range(begin_grid,begin_grid+grid_gap):
for k in range(5):
mod.parameters.set_value(grid_index,k,mod_temp.parameters.get_value(grid_index,k))
io.save_gx(path+"combined_model_file.gx",mod,opt,config)
def extract_xy_2(data, i):
x, y, err, index_use = [], [], [], []
each = data[i]
x = x + list(each.x)
y = y + list(each.y)
err = err + list(each.error)
index_use.append(i)
return x, y, err, index_use
for i in i_container: #looping through 21 RAXR datasets normally
mod = model.Model()
config = io.Config()
opt = diffev.DiffEv()
if i == 0:
io.load_gx(infile, mod, opt, config)
else:
io.load_gx(outfile, mod, opt, config)
data_sets = mod.data.items
bounds = []
x, y, err, index_use = extract_xy_2(data_sets, i + 1)
bounds, best_vec, par_indx = extract_bounds_2(mod.parameters, i + 1)
#set the data used and the associated pars columns
for j in range(len(data_sets)):
if j not in index_use:
mod.data.items[j].use = False
else:
mod.data.items[j].use = True
for j in range(mod.parameters.get_len_rows()):
line_start_pos=loc
while str_text[loc]!='\n':
if str_text[loc]=='#':
comment_pos=loc
elif str_text[loc]=='=':
equal_sign_pos=loc
else:
pass
loc+=1
line_end_pos=loc
if comment_pos==None:
comment_pos=line_end_pos
text_to_be_feed=key_text+'='+str(replace_value)+str_text[comment_pos:line_end_pos]
str_text=str_text.replace(str_text[line_start_pos:line_end_pos],text_to_be_feed,1)
return str_text
if __name__=="__main__":
mod = model.Model()
config = io.Config()
opt = diffev.DiffEv()
io.load_gx(gx_file_path,mod,opt,config)
mod.script=replace_script_section(mod.script,'running_mode','0')
for i in range(len(mod.data.items)):
mod.data.items[i].use=True
print('Simulate and dump files now!')
mod.simulate()
print('Plot files are dumpt to pocket!')
print('Plot the results now!')
plot_all(plot_e_model=plot_e_model,plot_e_FS=plot_e_FS,plot_ctr=plot_ctr,plot_raxr=plot_raxr,plot_AP_Q=plot_AP_Q)
pyplot.show()
sys.path.append('C:\\apps\\genx_pc_qiu')
sys.path.append('C:\\apps\\genx_pc_qiu\\lib')
sys.path.append('/u1/uaf/cqiu/genx_pc_qiu')
import model,diffev,time,fom_funcs
import filehandling as io
import glob
import numpy as np
first_grid=54
grid_gap=20
path='/import/c/w/cqiu/temp_gx_files/'
gx_files=glob.glob(path+'*_May8.gx')#file must be sortable to have the code work correctly
gx_files.sort()
mod = model.Model()
config = io.Config()
opt = diffev.DiffEv()
io.load_gx(gx_files[0],mod,opt,config)
for gx_file in gx_files[1:]:
print "processing ",gx_file
i=gx_files.index(gx_file)
begin_grid=first_grid+grid_gap*i
mod_temp = model.Model()
config_temp = io.Config()
opt_temp = diffev.DiffEv()
io.load_gx(gx_file,mod_temp,opt_temp,config_temp)
for grid_index in range(begin_grid,begin_grid+grid_gap):
for k in range(5):
mod.parameters.set_value(grid_index,k,mod_temp.parameters.get_value(grid_index,k))
io.save_gx(path+"combined_model_file.gx",mod,opt,config)
if len(sys.argv)==2 and sys.argv[1].endswith('.gx'):
app = genx_gui.MyApp(False, 0)
# Create the window
app.Yield()
frame=app.TopWindow
# load a model on start
import filehandling as io
import StringIO, traceback
from event_handlers import ShowModelErrorDialog, ShowErrorDialog, get_pages, \
_post_new_model_event, set_title
import model as modellib
path = os.path.abspath(sys.argv[1])
try:
io.load_gx(path, frame.model,\
frame.solver_control.optimizer,\
frame.config)
except modellib.IOError, e:
ShowModelErrorDialog(frame, e.__str__())
except Exception, e:
outp = StringIO.StringIO()
traceback.print_exc(200, outp)
val = outp.getvalue()
outp.close()
ShowErrorDialog(frame, 'Could not open the file. Python Error:'\
'\n%s'%(val,))
else:
app.Yield()
try:
[p.ReadConfig() for p in get_pages(frame)]
except Exception, e:
if len(sys.argv) == 2 and sys.argv[1].endswith('.gx'):
app = genx_gui.MyApp(False, 0)
# Create the window
app.Yield()
frame = app.TopWindow
# load a model on start
import filehandling as io
import StringIO, traceback
from event_handlers import ShowModelErrorDialog, ShowErrorDialog, get_pages, \
_post_new_model_event, set_title
import model as modellib
path = os.path.abspath(sys.argv[1])
try:
io.load_gx(path, frame.model,\
frame.solver_control.optimizer,\
frame.config)
except modellib.IOError, e:
ShowModelErrorDialog(frame, e.__str__())
except Exception, e:
outp = StringIO.StringIO()
traceback.print_exc(200, outp)
val = outp.getvalue()
outp.close()
ShowErrorDialog(frame, 'Could not open the file. Python Error:'\
'\n%s'%(val,))
else:
app.Yield()
try:
[p.ReadConfig() for p in get_pages(frame)]
except Exception, e:
import os, sys
os.chdir("C:\\apps\\genx\\")
import model, diffev, time, fom_funcs
import filehandling as io
import glob
#python create_tab_files D:\\Google Drive\\modeling files\\GenX model file\\fitting with brute force\\RAXS\\ * RAXS
path = sys.argv[1]
files = glob.glob(path + sys.argv[2])
for file in files:
mod = model.Model()
config = io.Config()
opt = diffev.DiffEv()
io.load_gx(file, mod, opt, config)
content = mod.parameters.get_ascii_output()
file_list = file.rsplit('\\')[-1].rsplit('_')
tab_file_name = sys.argv[3] + '_' + file_list[4] + '_R' + file_list[-1][
-4] + '.tab'
f = open(path + tab_file_name, 'w')
f.write(content)
f.close()
tmp_fom = []
tmp_trial_vec = []
tmp_pop_vec = []
tmp_fom_vec = []
for pars in par_list:
trial = pars[0]
fom = pars[1]
km = pars[2][0] # km
kr = pars[2][1] # kr
pf = pars[2][2]
iter = pars[3]
# Load the model ...
if rank == 0: print 'Loading model %s...' % infile
io.load_gx(infile, mod, opt, config)
for spectra in spectras:
# Simulate, this will also compile the model script
if rank == 0: print 'Simulating model...'
mod.simulate()
# Setting up the solver
eval('mod.set_fom_func(fom_funcs.%s)' % fom)
# Lets set the solver parameters (same for all processors):
try:
opt.set_create_trial(trial)
except:
print 'Warning: create_trial is not defined in script.'
try:
tmp_fom=[]
tmp_trial_vec=[]
tmp_pop_vec=[]
tmp_fom_vec=[]
for pars in par_list:
trial=pars[0]
fom = pars[1]
km = pars[2][0] # km
kr = pars[2][1] # kr
pf=pars[2][2]
iter = pars[3]
# Load the model ...
if rank==0: print 'Loading model %s...'%infile
io.load_gx(infile, mod, opt, config)
for spectra in spectras:
# Simulate, this will also compile the model script
if rank==0: print 'Simulating model...'
mod.simulate()
# Setting up the solver
eval('mod.set_fom_func(fom_funcs.%s)' % fom)
# Lets set the solver parameters (same for all processors):
try:
opt.set_create_trial(trial)
except:
print 'Warning: create_trial is not defined in script.'