def extract_parameters(args):
"""Extracts the parameters to outfile"""
from genx import model
from genx import diffev
from genx import filehandling as io
# Open the genx file
mod = model.Model()
config = io.Config()
config.load_default(
os.path.split(os.path.abspath(__file__))[0] + 'genx.conf')
opt = diffev.DiffEv()
iprint("Loading file: %s " % args.infile)
io.load_file(args.infile, mod, opt, config)
iprint("File loaded")
names, values = mod.parameters.get_sim_pars()
if args.outfile == '':
outfile = sys.stdout
fout = open(outfile, 'w')
else:
outfile = args.outfile
if os.path.isfile(outfile):
fout = open(outfile, 'a')
else:
fout = open(outfile, 'w')
# Add header
fout.write('\t'.join([name for name in names]) + '\n')
fout.write('\t'.join(['%f' % val for val in values]) + '\n')
fout.close()
def create_simulated_data(args):
"""Function to create simulated data from the model and add it to data.y"""
from genx import model
from genx import diffev
from genx import filehandling as io
from scipy.stats import poisson
mod = model.Model()
config = io.Config()
config.load_default(
os.path.split(os.path.abspath(__file__))[0] + 'genx.conf')
opt = diffev.DiffEv()
iprint("Loading file: %s " % args.infile)
io.load_file(args.infile, mod, opt, config)
# io.load_opt_config(opt, config)
iprint("File loaded")
iprint("Simualting..")
mod.simulate()
iprint("Storing simualted data")
for data_set in mod.data:
data_set.y_raw = poisson.rvs(data_set.y_sim)
data_set.y_command = 'y'
data_set.run_y_command()
data_set.error_command = 'sqrt(where(y > 0, y, 1.0))'
data_set.run_error_command()
iprint('Saving the model to %s' % args.outfile)
io.save_file(args.outfile, mod, opt, config)
def load(fname, compile=True):
model = Model()
optimizer = DiffEv()
io.load_file(fname, model, optimizer, _config)
if compile:
model.compile_script()
optimizer.model = model
return model, optimizer
def modify_file(args):
"""Modify a GenX file given command line arguments"""
from genx import model
from genx import diffev
from genx import filehandling as io
# Open the genx file
mod = model.Model()
config = io.Config()
config.load_default(
os.path.split(os.path.abspath(__file__))[0] + 'genx.conf')
opt = diffev.DiffEv()
iprint("Loading file: %s " % args.infile)
io.load_file(args.infile, mod, opt, config)
iprint("File loaded")
if args.datafile:
datafile = os.path.abspath(args.datafile)
if 0 > args.data_set or args.data_set >= len(mod.data):
iprint(
"The selected data set does not exist - select one between 0 and %d"
% (len(mod.data) - 1))
return
iprint('Loading dataset %s into data set %d' %
(datafile, args.data_set))
mod.data[args.data_set].loadfile(datafile)
if args.outfile:
iprint('Saving the fit to %s' % args.outfile)
io.save_file(args.outfile, mod, opt, config)
elif args.save_datafile:
save_datafile = os.path.abspath(args.save_datafile)
iprint("Simualting..")
mod.simulate()
if 0 > args.data_set or args.data_set >= len(mod.data):
iprint(
"The selected data set does not exist - select one between 0 and %d"
% (len(mod.data) - 1))
return
iprint('Exporting data set %d into ASCII file %s' %
(args.data_set, save_datafile))
mod.data[args.data_set].save_file(save_datafile)
def open_model(frame, path):
#print "open_model"
frame.model.new_model()
frame.paramter_grid.PrepareNewModel()
# Update all components so all the traces are gone.
#_post_new_model_event(frame, frame.model)
try:
io.load_file(path, frame.model, frame.solver_control.optimizer,
frame.config)
except modellib.IOError as e:
ShowModelErrorDialog(frame, e.__str__())
except Exception as e:
outp = io.StringIO()
traceback.print_exc(200, outp)
val = outp.getvalue()
outp.close()
print('Error in loading the file ', path, '. Pyton traceback:\n ', val)
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 = io.StringIO()
traceback.print_exc(200, outp)
val = outp.getvalue()
outp.close()
print('Error in loading config for the plots. Pyton traceback:\n ',
val)
ShowErrorDialog(
frame,
'Could not read the config for the plots. Python Error:\n%s' %
(val, ))
try:
frame.paramter_grid.ReadConfig()
except Exception as e:
outp = io.StringIO()
traceback.print_exc(200, outp)
val = outp.getvalue()
outp.close()
print(
'Error in loading config for parameter grid. Pyton traceback:\n ',
val)
ShowErrorDialog(
frame,
'Could not read the config for the parameter grid. Python Error:\n%s'
% (val, ))
else:
# Update the Menu choice
frame.mb_view_grid_slider.Check(
frame.paramter_grid.GetValueEditorSlider())
# Letting the plugin do their stuff...
try:
frame.plugin_control.OnOpenModel(None)
except Exception as e:
outp = io.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 sld_mc(args):
""" Function to start fitting from the command line.
:param args:
:return:
"""
import genx.model
import genx.diffev
import genx.filehandling as io
mod = genx.model.Model()
config = io.Config()
config_loaded = False
for loc in appdirs.user_config_dir(
'genx',
'MattsBjorck'), os.path.expanduser("~"), appdirs.site_config_dir(
'genx', 'MattsBjorck').replace('xdg', ''):
try:
config.load_default(os.path.join(loc, 'genx.conf'))
except IOError:
pass
else:
config_loaded = True
break
if not config_loaded:
raise IOError('Could not load default config file', 'genx.conf')
opt = genx.diffev.DiffEv()
print('Loading model %s...' % args.infile)
io.load_file(args.infile, mod, opt, config)
io.load_opt_config(opt, config)
# Hack the script so that it simulates the SLD instead of the data
mod.script = re.sub(r"SimSpecular\((.*)\,(.*)\)",
r"SimSLD(data[0].x, None,\2)", mod.script)
print("Hacking the model script. Resulting script:")
print(mod.script)
# Simulate, this will also compile the model script
print('Compiling model...')
mod.compile_script()
(funcs, vals, minvals, maxvals) = mod.get_fit_pars()
vals = np.array(vals)
boundaries = [
row[5] for row in mod.parameters.data if not row[0] == '' and row[2]
]
print(boundaries)
boundaries = np.array([eval(s) for s in boundaries])
minvals, maxvals = boundaries[:, 0] + vals, boundaries[:, 1] + vals
min_SLD = []
max_SLD = []
z = np.arange(args.min, args.max, args.step)
# Change the x-data so that it contain the z values instead.
for d in mod.data:
d.x = z
def extreme_dict(cur, extreme, func):
"""Makes a comparison of cur and extreme through func (np.min or np.max) and returns the result as a dict"""
return_dic = {}
for key in extreme:
if key not in ['z', 'SLD unit']:
#print cur[key].shape
return_dic[key] = func(np.c_[cur[key], extreme[key]], axis=1)
else:
return_dic[key] = cur[key]
return return_dic
print("Calculating sld's...")
missed = 0
for i in range(args.runs):
current_vals = minvals + (maxvals - minvals) * np.random.random_sample(
len(funcs))
[func(val) for func, val in zip(funcs, current_vals)]
mod.script_module._sim = False
current_sld = mod.script_module.Sim(mod.data)
same_shape = all([
sld['z'].shape == msld['z'].shape
for sld, msld in zip(current_sld, min_SLD)
])
if i == 0:
min_SLD = [sld for sld in current_sld]
max_SLD = [sld for sld in current_sld]
elif same_shape:
min_SLD = [
extreme_dict(sld, msld, np.min)
for sld, msld in zip(current_sld, min_SLD)
]
max_SLD = [
extreme_dict(sld, msld, np.max)
for sld, msld in zip(current_sld, max_SLD)
]
else:
missed += 1
sys.stdout.write("\r Progress: %d%%" %
(float(i) * 100 / float(args.runs)))
sys.stdout.flush()
print(' ')
print(missed, " simulations was discarded due to wrong size.")
print("Saving the data to file...")
for sim in range(len(min_SLD)):
new_filename = (args.outfile + '%03d' % sim + '.dat')
save_array = np.array([min_SLD[sim]['z']])
header = 'z\t'
for key in min_SLD[sim]:
if key != 'z' and key != 'SLD unit':
save_array = np.r_[save_array, [min_SLD[sim][key].real],
[min_SLD[sim][key].imag],
[max_SLD[sim][key].real],
[max_SLD[sim][key].imag]]
header += 'min(%s.real)\tmin(%s.imag)\tmax(%s.real)\tmax(%s.imag)\t' % (
key, key, key, key)
f = open(new_filename, 'w')
f.write(
"# Monte Carlo estimation of SLD bounds with script sld_errorbars.py model taken from file: %s\n"
% args.infile)
f.write("# File created: %s\n" % time.ctime())
f.write("# Simulated SLD for data set: %s\n" % mod.data[sim].name)
f.write("# Headers: \n")
f.write('#' + header + '\n')
np.savetxt(f, save_array.transpose(), delimiter='\t')
f.close()
def start_fitting(args, rank=0):
""" Function to start fitting from the command line.
:param args:
:return:
"""
import time
from genx import model
from genx import diffev
from genx import filehandling as io
mod = model.Model()
config = io.Config()
config.load_default(
os.path.split(os.path.abspath(__file__))[0] + 'genx.conf')
opt = diffev.DiffEv()
if rank == 0:
def autosave():
# print 'Updating the parameters'
mod.parameters.set_value_pars(opt.best_vec)
if args.error:
iprint("Calculating error bars")
calc_errorbars(config, mod, opt)
if args.outfile:
iprint("Saving to %s" % args.outfile)
io.save_file(args.outfile, mod, opt, config)
opt.set_autosave_func(autosave)
if rank == 0:
iprint('Loading model %s...' % args.infile)
io.load_file(args.infile, mod, opt, config)
io.load_opt_config(opt, config)
# has to be used in order to save everything....
if args.esave:
config.set('solver', 'save all evals', True)
# Simulate, this will also compile the model script
if rank == 0:
iprint('Simulating model...')
mod.simulate()
# Sets up the fitting ...
if rank == 0:
iprint('Setting up the optimizer...')
set_optimiser_pars(opt, args)
opt.reset()
opt.init_fitting(mod)
opt.init_fom_eval()
opt.set_sleep_time(0.0)
if args.outfile and rank == 0:
iprint('Saving the initial model to %s' % args.outfile)
io.save_file(args.outfile, mod, opt, config)
# To start the fitting
if rank == 0:
iprint('Fitting starting...')
t1 = time.time()
# print opt.use_mpi, opt.use_parallel_processing
opt.optimize()
if rank == 0:
t2 = time.time()
iprint('Fitting finished!')
iprint('Time to fit: ', (t2 - t1) / 60., ' min')
if rank == 0:
iprint('Updating the parameters')
mod.parameters.set_value_pars(opt.best_vec)
if args.outfile and rank == 0:
if args.error:
iprint('Calculating errorbars')
calc_errorbars(config, mod, opt)
iprint('Saving the fit to %s' % args.outfile)
opt.set_use_mpi(False)
io.save_file(args.outfile, mod, opt, config)
if rank == 0:
iprint('Fitting successfully completed')
def start_interactive(args):
''' Start genx in interactive mode (with the gui)
:param args:
:return:
'''
debug('enter start_interactive')
activate_excepthook()
# Fix blurry text on Windows 10
import ctypes
try:
ctypes.windll.shcore.SetProcessDpiAwareness(True)
except:
pass
from genx import genx_gui
if args.infile.endswith('.gx') or args.infile.endswith('.hgx'):
debug('start GUI setup with file to load')
app = genx_gui.MyApp(False, 0)
# Create the window
app.Yield()
frame = app.TopWindow
# load a model on start
from genx import filehandling as io
import traceback
from io import StringIO
from genx.event_handlers import ShowModelErrorDialog, ShowErrorDialog, get_pages, \
_post_new_model_event, set_title
from genx import model as modellib
path = os.path.abspath(args.infile)
try:
io.load_file(path, frame.model, frame.solver_control.optimizer,
frame.config)
except modellib.IOError as e:
ShowModelErrorDialog(frame, e.__str__())
except Exception as e:
outp = 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 as e:
outp = StringIO()
traceback.print_exc(200, outp)
val = outp.getvalue()
outp.close()
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)
app.Yield()
# 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)
app.Yield()
# Just a force update of the data_list
frame.data_list.list_ctrl.SetItemCount(
frame.data_list.list_ctrl.data_cont.get_count())
# Updating the imagelist as well
frame.data_list.list_ctrl._UpdateImageList()
frame.plot_data.plot_data(frame.model.data)
frame.paramter_grid.SetParameters(frame.model.parameters)
debug('setup complete, start WX MainLoop')
app.MainLoop()
elif args.infile == '':
debug('start GUI setup')
app = genx_gui.MyApp(True, 0)
debug('setup complete, start WX MainLoop')
app.MainLoop()
else:
iprint('Wrong file ending on infile, should be .gx or .hgx. Exiting.')
debug('leave start_interactive')