method = 'least_squares' sp = EdiblesSpectrum(filename) print(sp.target) sp.getSpectrum(xmin=7661, xmax=7670) # ################################################################################# cont_model = ContinuumModel(n_anchors=4) cont_pars = cont_model.guess(sp.flux, x=sp.wave) model = cont_model pars = cont_pars result = model.fit(data=sp.flux, params=pars, x=sp.wave, method=method) out = cont_model.eval(data=sp.flux, params=result.params, x=sp.wave) resid = sp.flux - out # result.plot_fit() # plt.show() # ################################################################################# voigt1 = VoigtModel(prefix='voigt1_') voigt1_pars = voigt1.guess(resid, x=sp.wave) model = model * voigt1 pars = result.params + voigt1_pars result = model.fit(data=sp.flux, params=pars, x=sp.wave, method=method) out = model.eval(data=sp.flux, params=result.params, x=sp.wave)
from edibles.models import ContinuumModel
# #################################################################################
# Example 1
x = np.linspace(0, 3)
y = x**3 - 3 * x**2 + 1
cont_model = ContinuumModel(n_anchors=4)
cont_pars = cont_model.guess(y, x=x)
# ##############################
# Show initial model
out = cont_model.eval(data=y, params=cont_pars, x=x)
y_param_names = []
for i in range(cont_model.n_anchors):
y_param_names.append('y_' + str(i))
x_param_names = []
for i in range(cont_model.n_anchors):
x_param_names.append('x_' + str(i))
init_y = []
for par_name in y_param_names:
init_y.append(cont_pars[par_name].value)
init_x = []
for par_name in x_param_names:
def prebuilt_model(self, chosen_save_num=None, plot=False, verbose=0):
"""A function that generates continua based on data saved in csv files.
Args:
chosen_save_num (int): The 'save number' of the continuum data, default=None.
If None, the function will create all saved models and (possibly) plot them.
plot (bool): If True, plot the model(s) once it is created
verbose (int): If > 0, print more information about the data
"""
# assert self.num_saved_continua is not 0, otherwise there is no known continuum point
assert self.num_saved_continua > 0, "There is no saved continuum."
# read and parse file contents
saves_counter = 0
saves_dict = {}
with open(self.Spectrum.continuum_filename, mode="r") as f:
for line in f:
line = line.split("\n")[0]
# initialize new save group
if len(line) > 0:
if line == "######":
name = "save" + str(saves_counter)
saves_counter += 1
saves_dict[name] = {"x": None, "y": None}
# update dict
elif line[0:2] == "# ":
key, val = line.split("# ")[1].split("=")
if key == "n_anchors":
val = int(val)
if key == "datetime":
val = datetime.strptime(val, "%Y-%m-%d %H:%M:%S.%f")
saves_dict[name][key] = val
else:
if saves_dict[name]["x"] is None:
saves_dict[name]["x"] = [
float(item) for item in line.split(",")
]
else:
saves_dict[name]["y"] = [
float(item) for item in line.split(",")
]
if chosen_save_num is not None:
assert chosen_save_num < self.num_saved_continua, (
"There are only " + str(self.num_saved_continua) + " saved continua."
)
chosen_save = saves_dict["save" + str(chosen_save_num)]
if verbose > 0:
print("Number of saved continuum datasets: ", saves_counter)
print("Save chosen: save" + str(chosen_save_num))
pprint(chosen_save)
cont_model = ContinuumModel(n_anchors=chosen_save['n_anchors'])
params = cont_model.make_params()
for i in range(cont_model.n_anchors):
params['%sx_%i' % (cont_model.prefix, i)].set(value=chosen_save["x"][i], vary=False)
params['%sy_%i' % (cont_model.prefix, i)].set(value=chosen_save["y"][i], vary=False)
params = update_param_vals(params, cont_model.prefix)
out = cont_model.eval(params=params, x=self.Spectrum.wave)
if plot:
plt.plot(self.Spectrum.wave, self.Spectrum.flux)
plt.plot(self.Spectrum.wave, out)
plt.scatter(chosen_save["x"], chosen_save["y"], marker="x", s=80, color="k")
plt.show()
return out
else:
for j in range(saves_counter):
chosen_save = saves_dict["save" + str(j)]
try:
method = str(chosen_save["method"])
except:
method = "unknown"
try:
n_anchors = str(chosen_save["n_anchors"])
except:
n_anchors = "unknown"
try:
date_time = str(chosen_save["datetime"])
except:
date_time = "unknown"
try:
user = str(chosen_save["user"])
except:
user = "******"
try:
comments = str(chosen_save["comments"])
except:
comments = "None"
print("Continuum group {a}/{b}".format(a = j, b=saves_counter-1))
print("Method: " + method + ", n_anchors: " + n_anchors + ";")
print("Added by: " + user + ", at time:" + date_time + ";")
print("Comments: " + comments)
if plot:
cont_model = ContinuumModel(n_anchors=chosen_save['n_anchors'])
params = cont_model.make_params()
for i in range(cont_model.n_anchors):
params['%sx_%i' % (cont_model.prefix, i)].set(value=chosen_save["x"][i], vary=False)
params['%sy_%i' % (cont_model.prefix, i)].set(value=chosen_save["y"][i], vary=False)
params = update_param_vals(params, cont_model.prefix)
out = cont_model.eval(params=params, x=self.Spectrum.wave)
plt.plot(self.Spectrum.wave, self.Spectrum.flux)
plt.plot(self.Spectrum.wave, out)
plt.scatter(chosen_save["x"], chosen_save["y"], marker="x", s=80, color="k")
plt.show()
print("Please make your selection back in the script.")