def calc_phase_resids(self, weighted_mean=True, set_pulse_nums=False):
"""Return timing model residuals in pulse phase."""
rs = self.model.phase(self.toas)
rs -= Phase(rs.int[0], rs.frac[0])
try:
delta_pulse_numbers = Phase(self.toas.table["delta_pulse_number"])
except:
self.toas.table["delta_pulse_number"] = np.zeros(len(self.toas.get_mjds()))
delta_pulse_numbers = Phase(self.toas.table["delta_pulse_number"])
if set_pulse_nums:
self.toas.table["delta_pulse_number"] = np.zeros(len(self.toas.get_mjds()))
delta_pulse_numbers = Phase(self.toas.table["delta_pulse_number"])
full = Phase(np.zeros_like(rs.frac), rs.frac) + delta_pulse_numbers
full = full.int + full.frac
# Track on pulse numbers, if necessary
if getattr(self.model, "TRACK").value == "-2":
pulse_num = self.toas.get_pulse_numbers()
if pulse_num is None:
raise ValueError(
"Pulse numbers missing from TOAs but TRACK -2 requires them"
)
pn_act = np.trunc(full)
addPhase = pn_act - pulse_num
full -= pn_act
full += addPhase
if not weighted_mean:
full -= full.mean()
else:
w = 1.0 / (np.array(self.toas.get_errors()) ** 2)
wm = (full * w).sum() / w.sum()
full -= wm
return full
if not weighted_mean:
full -= full.mean()
else:
# Errs for weighted sum. Units don't matter since they will
# cancel out in the weighted sum.
if np.any(self.toas.get_errors() == 0):
raise ValueError("TOA errors are zero - cannot calculate residuals")
w = 1.0 / (np.array(self.toas.get_errors()) ** 2)
wm = (full * w).sum() / w.sum()
full -= wm
return full
def calc_phase_resids(self, weighted_mean=True, set_pulse_nums=False):
"""Return timing model residuals in pulse phase."""
# Please define what set_pulse_nums means!
# Read any delta_pulse_numbers that are in the TOAs table.
# These are for PHASE statements, -padd flags, as well as user-inserted phase jumps
# Check for the column, and if not there then create it as zeros
try:
delta_pulse_numbers = Phase(self.toas.table["delta_pulse_number"])
except:
self.toas.table["delta_pulse_number"] = np.zeros(len(self.toas.get_mjds()))
delta_pulse_numbers = Phase(self.toas.table["delta_pulse_number"])
# I have no idea what this is trying to do. It just sets delta_pulse_number to zero
# This will wipe out any PHASE or -padd commands from the .tim file!!!
if set_pulse_nums:
self.toas.table["delta_pulse_number"] = np.zeros(len(self.toas.get_mjds()))
delta_pulse_numbers = Phase(self.toas.table["delta_pulse_number"])
# Compute model phase
rs = self.model.phase(self.toas)
# Track on pulse numbers, if requested
if getattr(self.model, "TRACK").value == "-2":
pulse_num = self.toas.get_pulse_numbers()
if pulse_num is None:
raise ValueError(
"Pulse numbers missing from TOAs but TRACK -2 requires them"
)
# Compute model phase. For pulse numbers tracking
# we need absolute phases, since TZRMJD serves as the pulse
# number reference.
rs = self.model.phase(self.toas, abs_phase=True) + delta_pulse_numbers
# First assign each TOA to the correct relative pulse number
rs -= Phase(pulse_num, np.zeros_like(pulse_num))
# Then subtract the constant offset since that is irrelevant
rs -= Phase(rs.int[0], rs.frac[0])
full = rs.int + rs.frac
# If not tracking then do the usual nearest pulse number calculation
else:
# Compute model phase
rs = self.model.phase(self.toas) + delta_pulse_numbers
# Here it subtracts the first phase, so making the first TOA be the
# reference. Not sure this is a good idea.
rs -= Phase(rs.int[0], rs.frac[0])
# What exactly is full?
full = Phase(np.zeros_like(rs.frac), rs.frac)
# This converts full from a Phase object to a np.float128
full = full.int + full.frac
# If we are using pulse numbers, do we really want to subtract any kind of mean?
# Perhaps there should be an option to not subtract any mean?
if not weighted_mean:
full -= full.mean()
else:
# Errs for weighted sum. Units don't matter since they will
# cancel out in the weighted sum.
if np.any(self.toas.get_errors() == 0):
raise ValueError(
"Some TOA errors are zero - cannot calculate residuals"
)
w = 1.0 / (np.array(self.toas.get_errors()) ** 2)
wm = (full * w).sum() / w.sum()
full -= wm
return full