def create_folded_figured_based_on_clicks_in_unfolded_figure(
self, unfolded_figure):
# Setup empty period recording clicks for folding.
event_coordinates = []
event_coordinates_data_source = ColumnDataSource({
'Time (BTJD)': [],
'Relative flux': []
})
unfolded_figure.circle('Time (BTJD)',
'Relative flux',
source=event_coordinates_data_source,
color='red',
alpha=0.8) # Will be updated.
# Prepare the folded plot.
folded_data_source = ColumnDataSource({
'Relative flux': self.relative_fluxes,
'Folded time (days)': [],
'Time (BTJD)': self.times
})
folded_figure = Figure(x_axis_label='Folded time (days)',
y_axis_label='Relative flux',
title=f'Folded {self.title}')
self.plot_light_curve_source(folded_figure,
folded_data_source,
time_column_name='Folded time (days)')
folded_figure.sizing_mode = 'stretch_width'
self_ = self
def click_unfolded_figure_callback(
tap_event): # Setup what should happen when a click occurs.
event_coordinate = tap_event.x, tap_event.y
event_coordinates.append(event_coordinate)
event_coordinates_data_source.data = {
'Time (BTJD)':
[coordinate[0] for coordinate in event_coordinates],
'Relative flux':
[coordinate[1] for coordinate in event_coordinates]
}
if len(
event_coordinates
) > 1: # If we have more than 1 period click, we can start folding.
event_times = [
coordinate[0] for coordinate in event_coordinates
]
epoch, period = self.calculate_epoch_and_period_from_approximate_event_times(
event_times)
folded_times = self.fold_times(self_.times, epoch, period)
folded_data_source.data['Folded time (days)'] = folded_times
# folded_figure.x_range.start = -period/10
# folded_figure.x_range.end = period/10
self_.period = period
self_.transit_epoch = epoch
period_depths = [
coordinate[1] for coordinate in event_coordinates
]
self_.depth = np.abs(np.mean(period_depths))
unfolded_figure.on_event(Tap, click_unfolded_figure_callback)
return folded_figure
def create_unfolded_light_curve_figure(self, data_source):
figure = Figure(title='Unfolded light curve',
x_axis_label='Time (BTJD)',
y_axis_label='Normalized PDCSAP flux',
active_drag='box_zoom')
self.plot_folding_colored_light_curve_source(figure, data_source)
figure.sizing_mode = 'stretch_width'
return figure
def create_folded_figured_based_on_clicks_in_unfolded_figure(
self, unfolded_figure, data_source):
# Setup empty period recording clicks for folding.
unfolded_figure.circle('Time (BTJD)',
'Normalized PDCSAP flux',
source=self.fold_coordinate_data_source,
color='red',
alpha=0.8) # Will be updated.
# Prepare the folded plot.
folded_figure = Figure(x_axis_label='Folded time (days)',
y_axis_label='Normalized PDCSAP flux',
title=f'Folded light curve')
self.plot_folding_colored_light_curve_source(
folded_figure, data_source, time_column_name='Folded time (days)')
folded_figure.sizing_mode = 'stretch_width'
self_ = self
@gen.coroutine
def update_click_dots():
self.fold_coordinate_data_source.data = {
'Time (BTJD)':
[coordinate[0] for coordinate in self.event_coordinates],
'Normalized PDCSAP flux':
[coordinate[1] for coordinate in self.event_coordinates]
}
@gen.coroutine
def update_folded_figure(folded_times):
data_source.data['Folded time (days)'] = folded_times
@gen.coroutine
@without_document_lock
def click_unfolded_figure_callback(
tap_event): # Setup what should happen when a click occurs.
event_coordinate = tap_event.x, tap_event.y
self.event_coordinates.append(event_coordinate)
self.bokeh_document.add_next_tick_callback(update_click_dots)
if len(
self.event_coordinates
) > 1: # If we have more than 1 period click, we can start folding.
event_times = [
coordinate[0] for coordinate in self.event_coordinates
]
epoch, period = self.calculate_epoch_and_period_from_approximate_event_times(
event_times)
folded_times = self.fold_times(data_source.data['Time (BTJD)'],
epoch, period)
self.bokeh_document.add_next_tick_callback(
partial(update_folded_figure, folded_times=folded_times))
self_.period = period
self_.transit_epoch = epoch
period_depths = [
coordinate[1] for coordinate in self.event_coordinates
]
self_.depth = np.abs(np.mean(period_depths))
unfolded_figure.on_event(Tap, click_unfolded_figure_callback)
return folded_figure
def create_light_curve_figure(self):
figure = Figure(title=self.title,
x_axis_label='Time (BTJD)',
y_axis_label='Relative flux',
active_drag='box_zoom')
data_source = ColumnDataSource({
'Time (BTJD)': self.times,
'Relative flux': self.relative_fluxes
})
self.plot_light_curve_source(figure, data_source)
figure.sizing_mode = 'stretch_width'
return figure
def view_database_file(_id, file_type):
ds = load_file(_id, file_type)
d = {}
for data_var in ds.data_vars:
d[data_var] = [ds[data_var].values]
d["to_plot"] = [ds[list(ds.data_vars)[0]].values]
source = ColumnDataSource(d)
callback = CustomJS(
args=dict(source=source),
code="""
var data = source.data;
data['to_plot'] = data[cb_obj.value];
source.change.emit();
""",
)
select = Select(title="Variable:", options=list(ds.data_vars))
select.js_on_change("value", callback)
p = Figure(
x_range=(-180, 180),
y_range=(-90, 90),
aspect_ratio=2.5,
tools="pan,wheel_zoom,box_zoom,reset, hover",
)
p.sizing_mode = "scale_width"
p.image(
image="to_plot",
x=-180,
y=-90,
dw=360,
dh=180,
source=source,
palette="Viridis11",
)
script, div = components(
column(column(select), p, sizing_mode="stretch_width"))
return render_template(
"app/bokeh_plot.html",
script=script,
div=div,
data_file_id=_id,
title=file_type.capitalize(),
)
def show_light_curve(self, light_curve_path: Path):
"""
Shows a figure of the light curve at the passed path.
:param light_curve_path: The path of the light curve.
"""
fluxes, times = self.load_fluxes_and_times_from_fits_file(
light_curve_path)
figure = Figure(title=str(light_curve_path),
x_axis_label='Flux',
y_axis_label='Time',
active_drag='box_zoom')
color = 'mediumblue'
figure.line(times, fluxes, line_color=color, line_alpha=0.1)
figure.circle(times,
fluxes,
line_color=color,
line_alpha=0.4,
fill_color=color,
fill_alpha=0.1)
figure.sizing_mode = 'stretch_width'
show(figure)
def create_flux_comparison_light_curve_figure(
) -> (Figure, ColumnDataSource):
figure = Figure(title='Normalized flux comparison',
x_axis_label='Time (BTJD)',
y_axis_label='Normalized flux',
active_drag='box_zoom')
data_source = ColumnDataSource({
'Time (BTJD)': [],
'Normalized PDCSAP flux': [],
'Normalized SAP flux': [],
'Time (days)': [],
'Folded time (days)': []
})
def add_light_curve(times_column_name, fluxes_column_name,
legend_label, color):
"""Adds a light curve to the figure."""
figure.line(source=data_source,
x=times_column_name,
y=fluxes_column_name,
line_color=color,
line_alpha=0.1)
figure.circle(source=data_source,
x=times_column_name,
y=fluxes_column_name,
legend_label=legend_label,
line_color=color,
line_alpha=0.4,
fill_color=color,
fill_alpha=0.1)
add_light_curve('Time (BTJD)', 'Normalized PDCSAP flux', 'PDCSAP',
'firebrick')
add_light_curve('Time (BTJD)', 'Normalized SAP flux', 'SAP',
'mediumblue')
figure.sizing_mode = 'stretch_width'
return figure, data_source
def create_mcmc_fit_figures(self, run_fitting_button):
self_ = self
initial_fit_figure = Figure(x_axis_label='Folded time (days)',
y_axis_label='Relative flux',
title=f'Initial fit')
parameters_table_columns = [
TableColumn(field=column, title=column)
for column in ['parameter', 'mean', 'sd', 'r_hat']
]
parameters_table = DataTable(source=self.parameters_table_data_source,
columns=parameters_table_columns,
editable=True)
initial_fit_data_source = self.initial_fit_data_source
bokeh_document = self.bokeh_document
@gen.coroutine
def update_initial_fit_figure(fluxes, gp_pred, inds, lc_pred, map_soln,
relative_times, times, x_fold):
initial_fit_data_source.data['Time (BTJD)'] = times
initial_fit_data_source.data['Time (days)'] = relative_times
initial_fit_data_source.data['Folded time (days)'] = x_fold
initial_fit_data_source.data[
'Relative flux'] = fluxes - gp_pred - map_soln["mean"]
initial_fit_data_source.data[
'Fit'] = lc_pred[inds] - map_soln["mean"]
initial_fit_data_source.data['Fit time'] = x_fold[
inds] # TODO: This is terrible, you should be able to line them up *afterward* to not make a duplicate time column
@gen.coroutine
@without_document_lock
def fit(self, map_soln, model):
with model:
trace = pm.sample(
tune=2000,
draws=2000,
start=map_soln,
chains=4,
step=xo.get_dense_nuts_step(target_accept=0.9),
)
trace_summary = pm.summary(
trace, round_to='none'
) # Not a typo. PyMC3 wants 'none' as a string here.
epoch = round(
trace_summary['mean']['Transit epoch (BTJD)'],
3) # Round the epoch differently, as BTJD needs more digits.
trace_summary['mean'] = self_.round_series_to_significant_figures(
trace_summary['mean'], 5)
trace_summary['mean']['Transit epoch (BTJD)'] = epoch
self.bokeh_document.add_next_tick_callback(
partial(self.update_parameters_table, trace_summary))
with pd.option_context('display.max_columns', None,
'display.max_rows', None):
print(trace_summary)
print(f'Star radius: {self.star_radius}')
# TODO: This should not happen automatically. Only after a button click.
# scopes = ['https://spreadsheets.google.com/feeds', 'https://www.googleapis.com/auth/drive']
# credentials = Credentials.from_service_account_file(
# 'ramjet/analysis/google_spreadsheet_credentials.json', scopes=scopes)
# gc = gspread.authorize(credentials)
# sh = gc.open('Ramjet transit candidates shared for vetting')
# worksheet = sh.get_worksheet(0)
# # Find first empty row.
# empty_row_index = 1
# for row_index in itertools.count(start=1):
# row_values = worksheet.row_values(row_index)
# if len(row_values) == 0:
# empty_row_index = row_index
# break
# worksheet.update_cell(empty_row_index, 1, self_.tic_id)
# worksheet.update_cell(empty_row_index, 2, str(self_.sectors).replace('[', '').replace(']', '')),
# worksheet.update_cell(empty_row_index, 3, trace_summary['mean']['Transit epoch (BTJD)'])
# worksheet.update_cell(empty_row_index, 4, trace_summary['mean']['period'])
# worksheet.update_cell(empty_row_index, 5, trace_summary['mean']['Transit depth (relative flux)'])
# worksheet.update_cell(empty_row_index, 6, trace_summary['mean']['Transit duration (days)'])
# worksheet.update_cell(empty_row_index, 7, self_.star_radius)
# worksheet.update_cell(empty_row_index, 8, trace_summary['mean']['Planet radius (solar radii)'] * self_.star_radius)
@gen.coroutine
@without_document_lock
def run_fitting():
times = self.light_curve_data_source.data['Time (BTJD)'].astype(
np.float32)
flux_errors = self.light_curve_data_source.data[
'Normalized PDCSAP flux error']
fluxes = self.light_curve_data_source.data[
'Normalized PDCSAP flux']
relative_times = self.light_curve_data_source.data['Time (days)']
nan_indexes = np.union1d(
np.argwhere(np.isnan(fluxes)),
np.union1d(np.argwhere(np.isnan(times)),
np.argwhere(np.isnan(flux_errors))))
fluxes = np.delete(fluxes, nan_indexes)
flux_errors = np.delete(flux_errors, nan_indexes)
times = np.delete(times, nan_indexes)
relative_times = np.delete(relative_times, nan_indexes)
with pm.Model() as model:
# Stellar parameters
mean = pm.Normal("mean", mu=0.0, sigma=10.0 * 1e-3)
u = xo.distributions.QuadLimbDark("u")
star_params = [mean, u]
# Gaussian process noise model
sigma = pm.InverseGamma("sigma",
alpha=3.0,
beta=2 * np.nanmedian(flux_errors))
log_Sw4 = pm.Normal("log_Sw4", mu=0.0, sigma=10.0)
log_w0 = pm.Normal("log_w0",
mu=np.log(2 * np.pi / 10.0),
sigma=10.0)
kernel = xo.gp.terms.SHOTerm(log_Sw4=log_Sw4,
log_w0=log_w0,
Q=1.0 / 3)
noise_params = [sigma, log_Sw4, log_w0]
# Planet parameters
log_ror = pm.Normal("log_ror",
mu=0.5 * np.log(self_.depth),
sigma=10.0 * 1e-3)
ror = pm.Deterministic("ror", tt.exp(log_ror))
depth = pm.Deterministic('Transit depth (relative flux)',
tt.square(ror))
planet_radius = pm.Deterministic('Planet radius (solar radii)',
ror * self_.star_radius)
# Orbital parameters
log_period = pm.Normal("log_period",
mu=np.log(self_.period),
sigma=1.0)
t0 = pm.Normal('Transit epoch (BTJD)',
mu=self_.transit_epoch,
sigma=1.0)
log_dur = pm.Normal("log_dur", mu=np.log(0.1), sigma=10.0)
b = xo.distributions.ImpactParameter("b", ror=ror)
period = pm.Deterministic('Transit period (days)',
tt.exp(log_period))
dur = pm.Deterministic('Transit duration (days)',
tt.exp(log_dur))
# Set up the orbit
orbit = xo.orbits.KeplerianOrbit(period=period,
duration=dur,
t0=t0,
b=b,
r_star=self.star_radius)
# We're going to track the implied density for reasons that will become clear later
pm.Deterministic("rho_circ", orbit.rho_star)
# Set up the mean transit model
star = xo.LimbDarkLightCurve(u)
def lc_model(t):
return mean + tt.sum(star.get_light_curve(
orbit=orbit, r=ror * self.star_radius, t=t),
axis=-1)
# Finally the GP observation model
gp = xo.gp.GP(kernel,
times, (flux_errors**2) + (sigma**2),
mean=lc_model)
gp.marginal("obs", observed=fluxes)
# Double check that everything looks good - we shouldn't see any NaNs!
print(model.check_test_point())
# Optimize the model
map_soln = model.test_point
map_soln = xo.optimize(map_soln, [sigma])
map_soln = xo.optimize(map_soln, [log_ror, b, log_dur])
map_soln = xo.optimize(map_soln, noise_params)
map_soln = xo.optimize(map_soln, star_params)
map_soln = xo.optimize(map_soln)
with model:
gp_pred, lc_pred = xo.eval_in_model(
[gp.predict(), lc_model(times)], map_soln)
x_fold = (times - map_soln['Transit epoch (BTJD)'] +
0.5 * map_soln['Transit period (days)']
) % map_soln['Transit period (days)'] - 0.5 * map_soln[
'Transit period (days)']
inds = np.argsort(x_fold)
bokeh_document.add_next_tick_callback(
partial(update_initial_fit_figure, fluxes, gp_pred, inds,
lc_pred, map_soln, relative_times, times, x_fold))
self.bokeh_document.add_next_tick_callback(
partial(fit, self, map_soln, model))
run_fitting_button.on_click(run_fitting)
self.plot_folding_colored_light_curve_source(
initial_fit_figure,
self.initial_fit_data_source,
time_column_name='Folded time (days)',
flux_column_name='Relative flux')
initial_fit_figure.line('Fit time',
'Fit',
source=self.initial_fit_data_source,
color='black',
line_width=3)
initial_fit_figure.sizing_mode = 'stretch_width'
return initial_fit_figure, parameters_table