def fit(self, selected, iters=1):
"""
Run a fit using the specified fitter
"""
# Select all the TOAs if none are explicitly set
if not any(selected):
selected = ~selected
"""JUMP check, TODO: put in fitter?"""
if "PhaseJump" in self.prefit_model.components:
# if attempted fit (selected)
# A) contains only jumps, don't do the fit and return an error
# B) excludes a jump, turn that jump off
# C) partially contains a jump, redefine that jump only with the overlap
fit_jumps = []
for param in self.prefit_model.params:
if getattr(self.prefit_model,
param).frozen == False and param.startswith("JUMP"):
fit_jumps.append(int(param[4:]))
numjumps = self.prefit_model.components[
"PhaseJump"].get_number_of_jumps()
if numjumps == 0:
log.warn(
"There are no jumps (maskParameter objects) in PhaseJump. Please delete the PhaseJump object and try again. "
)
return None
# boolean array to determine if all selected toas are jumped
jumps = [
True if "jump" in dict.keys() and dict["jump"] in fit_jumps
else False for dict in self.all_toas.table["flags"][selected]
]
# check if par file jumps in PhaseJump object
if not any(jumps):
# for every jump, set appropriate flag for TOAs it jumps
for jump_par in self.prefit_model.components[
"PhaseJump"].get_jump_param_objects():
# find TOAs jump applies to
mask = jump_par.select_toa_mask(self.all_toas)
# apply to dictionaries for future use
for dict in self.all_toas.table["flags"][mask]:
dict["jump"] = jump_par.index
jumps = [
True if "jump" in dict.keys() and dict["jump"] in fit_jumps
else False
for dict in self.all_toas.table["flags"][selected]
]
if all(jumps):
log.warn(
"toas being fit must not all be jumped. Remove or uncheck at least one jump in the selected toas before fitting."
)
return None
# numerical array of selected jump flags
sel_jump_nums = [
dict["jump"] if "jump" in dict.keys() else np.nan
for dict in self.all_toas.table["flags"][selected]
]
# numerical array of all jump flags
full_jump_nums = [
dict["jump"] if "jump" in dict.keys() else np.nan
for dict in self.all_toas.table["flags"]
]
for num in range(1, numjumps + 1):
num = int(num)
if num not in sel_jump_nums:
getattr(self.prefit_model, "JUMP" + str(num)).frozen = True
continue
jump_select = [num == jump_num for jump_num in full_jump_nums]
overlap = [a and b for a, b in zip(jump_select, selected)]
# remove the jump flags for that num
for dict in self.all_toas.table["flags"]:
if "jump" in dict.keys() and dict["jump"] == num:
del dict["jump"]
# re-add the jump using overlap as 'selected'
for dict in self.all_toas.table["flags"][overlap]:
dict["jump"] = num
if self.fitted:
self.prefit_model = self.postfit_model
self.prefit_resids = self.postfit_resids
if self.fitter == Fitters.POWELL:
fitter = pint.fitter.PowellFitter(self.selected_toas,
self.prefit_model)
elif self.fitter == Fitters.WLS:
fitter = pint.fitter.WLSFitter(self.selected_toas,
self.prefit_model)
elif self.fitter == Fitters.GLS:
fitter = pint.fitter.GLSFitter(self.selected_toas,
self.prefit_model)
chi2 = self.prefit_resids.chi2
wrms = np.sqrt(chi2 / self.selected_toas.ntoas)
print("Pre-Fit Chi2:\t\t%.8g us^2" % chi2)
print("Pre-Fit Weighted RMS:\t%.8g us" % wrms)
fitter.fit_toas(maxiter=1)
self.postfit_model = fitter.model
self.postfit_resids = Residuals(self.all_toas, self.postfit_model)
self.fitted = True
self.write_fit_summary()
# TODO: delta_pulse_numbers need some work. They serve both for PHASE and -padd functions from the TOAs
# as well as for phase jumps added manually in the GUI. They really should not be zeroed out here because
# that will wipe out preexisting values
self.fulltoas.table["delta_pulse_numbers"] = np.zeros(
self.fulltoas.ntoas)
self.selected_toas.table["delta_pulse_number"] = np.zeros(
self.selected_toas.ntoas)
# plot the prefit without jumps
pm_no_jumps = copy.deepcopy(self.postfit_model)
for param in pm_no_jumps.params:
if param.startswith("JUMP"):
getattr(pm_no_jumps, param).value = 0.0
getattr(pm_no_jumps, param).frozen = True
self.prefit_resids_no_jumps = Residuals(self.selected_toas,
pm_no_jumps)
f = copy.deepcopy(fitter)
no_jumps = [
False if "jump" in dict.keys() else True
for dict in f.toas.table["flags"]
]
f.toas.select(no_jumps)
selectedMJDs = self.selected_toas.get_mjds()
if all(no_jumps):
q = list(self.all_toas.get_mjds())
index = q.index([
i for i in self.all_toas.get_mjds() if i > selectedMJDs.min()
][0])
rs_mean = (Residuals(
self.all_toas,
f.model).phase_resids[index:index + len(selectedMJDs)].mean())
else:
rs_mean = self.prefit_resids_no_jumps.phase_resids[no_jumps].mean()
# determines how far on either side fake toas go
# TODO: hard limit on how far fake toas can go --> can get clkcorr
# errors if go before GBT existed, etc.
minMJD, maxMJD = selectedMJDs.min(), selectedMJDs.max()
spanMJDs = maxMJD - minMJD
if spanMJDs < 30 * u.d:
redge = ledge = 4
npoints = 400
elif spanMJDs < 90 * u.d:
redge = ledge = 2
npoints = 300
elif spanMJDs < 200 * u.d:
redge = ledge = 1
npoints = 300
elif spanMJDs < 400 * u.d:
redge = ledge = 0.5
npoints = 200
else:
redge = ledge = 0.2
npoints = 150
# Check to see if too recent
nowish = (Time.now().mjd - 40) * u.d
if maxMJD + spanMJDs * redge > nowish:
redge = (nowish - maxMJD) / spanMJDs
if redge < 0.0:
redge = 0.0
f_toas, rs, mrands = random_models(
f,
rs_mean=rs_mean,
redge_multiplier=redge,
ledge_multiplier=ledge,
npoints=npoints,
iter=10,
)
self.random_resids = rs
self.fake_toas = f_toas
def fit(self, selected, iters=1):
"""
Run a fit using the specified fitter
"""
# Select all the TOAs if none are explicitly set
if not any(selected):
selected = ~selected
"""JUMP check, TODO: put in fitter?"""
if "PhaseJump" in self.prefit_model.components:
# if attempted fit (selected)
# A) contains only jumps, don't do the fit and return an error
# B) excludes a jump, turn that jump off
# C) partially contains a jump, redefine that jump only with the overlap
fit_jumps = []
for param in self.prefit_model.params:
if getattr(self.prefit_model,
param).frozen == False and param.startswith("JUMP"):
fit_jumps.append(int(param[4:]))
jumps = [
True if "jump" in dict.keys() and dict["jump"] in fit_jumps
else False for dict in self.selected_toas.table["flags"]
]
if all(jumps):
log.warn(
"toas being fit must not all be jumped. Remove or uncheck at least one jump in the selected toas before fitting."
)
return None
sel_jump_nums = [
dict["jump"] if "jump" in dict.keys() else np.nan
for dict in self.selected_toas.table["flags"]
]
full_jump_nums = [
dict["jump"] if "jump" in dict.keys() else np.nan
for dict in self.all_toas.table["flags"]
]
for num in range(1, int(np.nanmax(full_jump_nums) + 1)):
num = int(num)
if num not in sel_jump_nums:
getattr(self.prefit_model, "JUMP" + str(num)).frozen = True
continue
jump_select = [num == jump_num for jump_num in full_jump_nums]
overlap = [a and b for a, b in zip(jump_select, selected)]
# remove the jump flags for that num
for dict in self.all_toas.table["flags"]:
if "jump" in dict.keys() and dict["jump"] == num:
del dict["jump"]
# re-add the jump using overlap as 'selected'
for dict in self.all_toas.table["flags"][overlap]:
dict["jump"] = num
if self.fitted:
self.prefit_model = self.postfit_model
self.prefit_resids = self.postfit_resids
if self.fitter == Fitters.POWELL:
fitter = pint.fitter.PowellFitter(self.selected_toas,
self.prefit_model)
elif self.fitter == Fitters.WLS:
fitter = pint.fitter.WLSFitter(self.selected_toas,
self.prefit_model)
elif self.fitter == Fitters.GLS:
fitter = pint.fitter.GLSFitter(self.selected_toas,
self.prefit_model)
chi2 = self.prefit_resids.chi2
wrms = np.sqrt(chi2 / self.selected_toas.ntoas)
print("Pre-Fit Chi2:\t\t%.8g us^2" % chi2)
print("Pre-Fit Weighted RMS:\t%.8g us" % wrms)
fitter.fit_toas(maxiter=1)
self.postfit_model = fitter.model
self.postfit_resids = Residuals(self.all_toas,
self.postfit_model,
set_pulse_nums=True)
self.fitted = True
self.write_fit_summary()
# TODO: set pulse nums above not working to reset delta pulse nums, have to force it here
# self.fulltoas.table['delta_pulse_numbers'] = np.zeros(self.fulltoas.ntoas)
self.selected_toas.table["delta_pulse_number"] = np.zeros(
self.selected_toas.ntoas)
# plot the prefit without jumps
pm_no_jumps = copy.deepcopy(self.postfit_model)
for param in pm_no_jumps.params:
if param.startswith("JUMP"):
getattr(pm_no_jumps, param).value = 0.0
getattr(pm_no_jumps, param).frozen = True
self.prefit_resids_no_jumps = Residuals(self.all_toas,
pm_no_jumps,
set_pulse_nums=True)
f = copy.deepcopy(fitter)
no_jumps = [
False if "jump" in dict.keys() else True
for dict in f.toas.table["flags"]
]
f.toas.select(no_jumps)
selectedMJDs = self.selected_toas.get_mjds()
if all(no_jumps):
q = list(self.all_toas.get_mjds())
index = q.index([
i for i in self.all_toas.get_mjds() if i > selectedMJDs.min()
][0])
rs_mean = (Residuals(
self.all_toas, f.model,
set_pulse_nums=True).phase_resids[index:index +
len(selectedMJDs)].mean())
else:
rs_mean = self.prefit_resids_no_jumps.phase_resids[no_jumps].mean()
# determines how far on either side fake toas go
# TODO: hard limit on how far fake toas can go --> can get clkcorr
# errors if go before GBT existed, etc.
minMJD, maxMJD = selectedMJDs.min(), selectedMJDs.max()
spanMJDs = maxMJD - minMJD
if spanMJDs < 30 * u.d:
redge = ledge = 4
npoints = 400
elif spanMJDs < 90 * u.d:
redge = ledge = 2
npoints = 300
elif spanMJDs < 200 * u.d:
redge = ledge = 1
npoints = 300
elif spanMJDs < 400 * u.d:
redge = ledge = 0.5
npoints = 200
else:
redge = ledge = 0.2
npoints = 150
# Check to see if too recent
nowish = (Time.now().mjd - 40) * u.d
if maxMJD + spanMJDs * redge > nowish:
redge = (nowish - maxMJD) / spanMJDs
if redge < 0.0:
redge = 0.0
f_toas, rs = random_models(
f,
rs_mean=rs_mean,
redge_multiplier=redge,
ledge_multiplier=ledge,
npoints=npoints,
iter=10,
)
self.random_resids = rs
self.fake_toas = f_toas