def setUp(self):
self.ftk = fityk.Fityk()
self.ftk.set_option_as_number("verbosity", -1)
xx = [(n-5)/2. for n in range(25)]
yy = [-7+3*x for x in xx]
self.ftk = fityk.Fityk()
self.ftk.set_option_as_number("verbosity", -1)
self.ftk.load_data(0, xx, yy, [1]*len(xx), "line")
self.ftk.execute("F = Linear(~0, ~0[:2.5])")
self.methods = ["mpfit"]
if self.ftk.get_info("compiler"):
self.methods += ["nlopt_lbfgs", "nlopt_nm", "nlopt_bobyqa",
"nlopt_sbplx"]
def setUp(self):
self.ftk = fityk.Fityk()
self.ftk.set_option_as_number("verbosity", -1)
f = tempfile.NamedTemporaryFile(delete=False)
f.write("M=1\n X[0]=1.1, Y[0]=-5, S[0]=0.8")
f.close()
self.filename = f.name
def setUp(self):
self.x = [(n - 5) / 2. for n in range(20)]
self.y = [x * (x - 3.1) for x in self.x]
self.sigma = [1 for n in self.y]
self.ftk = fityk.Fityk()
self.ftk.set_option_as_number("verbosity", -1)
self.ftk.load_data(0, self.x, self.y, self.sigma, "test-data")
def setUp(self):
self.ftk = fityk.Fityk()
self.ftk.set_option_as_number("verbosity", -1)
self.voigt = "Voigt(926, 43.2, 0.144, 0.1)"
self.splitvoigt = "SplitVoigt(926, 43.2, 0.144, 0.143, 0.1, 0.13)"
self.splitvoigt_formula = ('x < 43.2 ? Voigt(926, 43.2, 0.144, 0.1) '
': Voigt(926, 43.2, 0.143, 0.13)')
def add_guessability_tests():
all_types = fityk.Fityk().get_info('types')
for func_type in all_types.split():
if func_type not in ['FCJAsymm']:
test = create_guessability_test(func_type)
test.__name__ = 'test_' + func_type
setattr(TestGuessability, test.__name__, test)
def setUp(self):
self.ftk = fityk.Fityk()
self.ftk.set_option_as_number("verbosity", -1)
f = tempfile.NamedTemporaryFile(suffix='.gz', delete=False)
self.filename = f.name
gf = gzip.GzipFile(fileobj=f)
gf.write("M=1\n X[0]=1.1, Y[0]=-5, S[0]=0.8")
gf.close()
def setUp(self):
xx = [(n - 5) / 2. for n in range(25)]
yy = [
11.2 / (1 + (x - 3.3)**2) + math.sin(40 * x) / 40 - x / 10.
for x in xx
]
self.ftk = fityk.Fityk()
self.ftk.set_option_as_number("verbosity", -1)
self.ftk.load_data(0, xx, yy, [1] * len(xx), "loren")
def setUp(self):
self.ftk = fityk.Fityk()
self.ftk.set_option_as_number("verbosity", -1)
f = tempfile.NamedTemporaryFile(delete=False)
self.data = [(random.uniform(-100, 100), random.gauss(10, 20))
for _ in range(30)]
for d in self.data:
f.write(self.line_format(d))
f.close()
self.data.sort()
self.filename = f.name
def setUp(self):
self.ftk = fityk.Fityk()
self.ftk.set_option_as_number("verbosity", -1)
prefix = getattr(self, 'file_prefix', 'tmp')
f = tempfile.NamedTemporaryFile(prefix=prefix, delete=False)
self.data = self.generate_data()
for d in self.data:
f.write(self.line_format(d))
f.close()
self.data.sort()
self.filename = f.name
def setUp(self):
self.ftk = fityk.Fityk()
self.ftk.set_option_as_number("verbosity", -1)
self.ftk.execute("$a = ~3.14 [-1:4.5]")
def setUp(self):
self.ftk = fityk.Fityk()
self.ftk.set_option_as_number("verbosity", -1)
def main():
config_dir = os.path.join(os.path.expanduser("~"), fityk.config_dirname())
if readline:
histfile = os.path.join(config_dir, "history")
if hasattr(readline, "read_history_file"):
try:
readline.read_history_file(histfile)
except IOError:
pass
atexit.register(readline.write_history_file, histfile)
fityk.interrupt_computations_on_sigint()
parser = OptionParser("Usage: %prog [-h] [-V] [-c <str>]"
" [script or data file...]")
parser.add_option("-V",
"--version",
action="store_true",
help="output version information and exit")
parser.add_option("-c",
"--cmd",
action="append",
default=[],
help="script passed in as string")
parser.add_option("-I",
"--no-init",
action="store_true",
help="don't process $HOME/.fityk/init file")
parser.add_option("-q",
"--quit",
action="store_true",
help="don't enter interactive shell")
(options, args) = parser.parse_args()
f = fityk.Fityk()
ui = f.get_ui_api()
ui.connect_draw_plot_py(functools.partial(plot_in_gnuplot, f))
if options.version:
print("cfityk.py %s" % f.get_info("version").split()[-1])
return
if not options.no_init:
init_file = os.path.join(config_dir, fityk.startup_commands_filename())
if os.path.exists(init_file):
sys.stderr.write(" -- init file: %s --\n" % init_file)
ui.exec_fityk_script(init_file)
sys.stderr.write(" -- end of init file --\n")
if readline:
readline.parse_and_bind("tab: complete")
readline.set_completer_delims(" \t\n\"\\'`@$><=;|&{(:") # default+":"
completer = Completer(f)
readline.set_completer(completer.complete)
try:
for s in options.cmd:
ui.exec_and_log(s)
for arg in args:
f.process_cmd_line_arg(arg)
if not options.quit:
while True:
line = read_line()
ui.exec_and_log(line)
print("")
except fityk.ExitRequestedException:
sys.stderr.write("\nbye...\n")
def run(data_name, fit_method, easy=True):
uses_gradient = (fit_method in ("mpfit", "levenberg_marquardt"))
if uses_gradient:
tolerance = {"wssr": 1e-10, "param": 4e-7, "err": 5e-3}
else:
tolerance = {"wssr": 1e-7, "param": 1e-4}
if fit_method == "nelder_mead_simplex":
tolerance["err"] = 5e-5
#if fit_method in ("mpfit", "levenberg_marquardt"):
if VERBOSE > 0:
print "Testing %s (start%s) on %-10s" % (fit_method, easy + 1,
data_name),
if VERBOSE > 1:
print
ref = read_reference_data(data_name)
if VERBOSE > 2:
print ref.model
ftk = fityk.Fityk()
if VERBOSE < 3:
ftk.execute("set verbosity=-1")
y, x = zip(*ref.data)
ftk.load_data(0, x, y, [1] * len(x), data_name)
par_names = [p.name for p in ref.parameters]
par_inits = [
"~%g" % (p.start2 if easy else p.start1) for p in ref.parameters
]
ftk.execute("define OurFunc(%s) = %s" % (", ".join(par_names), ref.model))
ftk.execute("F = OurFunc(%s)" % ", ".join(par_inits))
ftk.execute("set fitting_method=" + fit_method)
ftk.execute("set pseudo_random_seed=1234567")
#ftk.execute("set numeric_format='%.10E'")
ftk.execute("set lm_stop_rel_change=1e-16")
#ftk.execute("set lm_max_lambda=1e+50")
ftk.execute("set nm_convergence=1e-10")
if fit_method == "mpfit":
ftk.execute("set ftol_rel=1e-18")
ftk.execute("set xtol_rel=1e-18")
if fit_method == "genetic_algorithms":
ftk.execute("set max_wssr_evaluations=5e5")
elif not uses_gradient:
ftk.execute("set max_wssr_evaluations=2e4")
try:
ftk.execute("fit")
#ftk.execute("set fitting_method=levenberg_marquardt")
#ftk.execute("fit")
except fityk.ExecuteError as e:
print "fityk.ExecuteError: %s" % e
return False
ssr = ftk.get_ssr()
ssr_diff = (ssr - ref.ssr) / ref.ssr
# Lanczos1 and Lanczos2 have near-zero SSR, we need to be more tolerant
if ssr < 1e-20:
tolerance["wssr"] *= 1e8
elif ssr < 1e-10:
tolerance["wssr"] *= 1e2
ok = (abs(ssr_diff) < tolerance["wssr"])
if ref.ssr > 1e-10 and ssr_diff < -1e-10:
print "Eureka! %.10E < %.10E" % (ssr, ref.ssr)
fmt = " %8s %13E %13E %+.1E"
if VERBOSE > 2 or (VERBOSE == 2 and not ok):
print fmt % ("SSR", ssr, ref.ssr, ssr_diff)
our_func = ftk.all_functions()[0]
for par in ref.parameters:
calc_value = our_func.get_param_value(par.name)
val_diff = (calc_value - par.value) / par.value
param_ok = (abs(val_diff) < tolerance["param"])
err_ok = True
if "err" in tolerance:
vname = our_func.var_name(par.name)
calc_err = ftk.calculate_expr("$%s.error" % vname)
err_diff = (calc_err - par.stddev) / par.stddev
err_ok = (abs(err_diff) < tolerance["err"])
if VERBOSE > 2 or (VERBOSE == 2 and (not param_ok or not err_ok)):
print fmt % (par.name, calc_value, par.value, val_diff)
if "err" in tolerance:
print fmt % ("+/-", calc_err, par.stddev, err_diff)
ok = (ok and param_ok and err_ok)
if VERBOSE == 1:
print("OK" if ok else "FAILED")
return ok
def has_nlopt():
ftk = fityk.Fityk()
return "NLopt" in ftk.get_info("compiler")
def setUp(self):
self.ftk = fityk.Fityk()
self.ftk.set_option_as_number("verbosity", -1)
self.ftk.execute("%f = Quadratic(~1, 2, ~3)")
self.ftk.execute("%g = Constant(7.5)")
self.ftk.execute("F = %f + %g")
