def jwst_2d_det(result_dict, plot=True, output_file='det2d.html'):
"""Plot 2d detector image
Parameters
----------
result_dict : dict
Dictionary from pandexo output. If parameter space was run in run_pandexo
make sure to restructure the input as a list of dictionaries without they key words
that run_pandexo assigns.
plot : bool
(Optional) True renders plot, Flase does not. Default=True
output_file : str
(Optional) Default = 'det2d.html'
Return
------
numpy array
2D array of out of transit detector simulation
See Also
--------
jwst_1d_spec, jwst_1d_bkg, jwst_1d_flux, jwst_1d_snr, jwst_noise, jwst_2d_sat
"""
TOOLS = "pan,wheel_zoom,box_zoom,resize,reset,save"
out = result_dict['PandeiaOutTrans']
data = out['2d']['detector']
xr, yr = data.shape
plot_detector_2d = Figure(
tools="pan,wheel_zoom,box_zoom,resize,reset,hover,save",
x_range=[0, yr],
y_range=[0, xr],
x_axis_label='Pixel',
y_axis_label='Spatial',
title="2D Detector Image",
plot_width=800,
plot_height=300)
plot_detector_2d.image(image=[data],
x=[0],
y=[0],
dh=[xr],
dw=[yr],
palette="Spectral11")
if plot:
outputfile(output_file)
show(plot_detector_2d)
return data
def jwst_noise(result_dict, plot=True, output_file='noise.html'):
"""Plot background
Parameters
----------
result_dict : dict
Dictionary from pandexo output. If parameter space was run in run_pandexo
make sure to restructure the input as a list of dictionaries without they key words
that run_pandexo assigns.
plot : bool
(Optional) True renders plot, Flase does not. Default=True
output_file : str
(Optional) Default = 'noise.html'
Return
------
x : numpy array
micron
y : numpy array
1D noise (ppm)
See Also
--------
jwst_1d_spec, jwst_1d_bkg, jwst_1d_flux, jwst_1d_snr, jwst_2d_det, jwst_2d_sat
"""
TOOLS = "pan,wheel_zoom,box_zoom,reset,save" #saturation
x = result_dict['FinalSpectrum']['wave']
y = result_dict['FinalSpectrum']['error_w_floor'] * 1e6
x = x[~np.isnan(y)]
y = y[~np.isnan(y)]
ymed = np.median(y)
plot_noise_1d1 = Figure(
tools=TOOLS, #responsive=True,
x_axis_label='Wavelength (micron)',
y_axis_label='Error on Spectrum (PPM)',
title="Error Curve",
plot_width=800,
plot_height=300,
y_range=[0, 2.0 * ymed])
ymed = np.median(y)
plot_noise_1d1.circle(x, y, line_width=4, alpha=.7)
if plot:
outputfile(output_file)
show(plot_noise_1d1)
return x, y
def jwst_1d_flux(result_dict, plot=True, output_file='flux.html'):
"""Plot flux rate in e/s
Parameters
----------
result_dict : dict
Dictionary from pandexo output. If parameter space was run in run_pandexo
make sure to restructure the input as a list of dictionaries without they key words
that run_pandexo assigns.
plot : bool
(Optional) True renders plot, Flase does not. Default=True
output_file : str
(Optional) Default = 'flux.html'
Return
------
x : numpy array
micron
y : numpy array
1D flux rate in electrons/s
See Also
--------
jwst_1d_spec, jwst_1d_bkg, jwst_noise, jwst_1d_snr, jwst_2d_det, jwst_2d_sat
"""
TOOLS = "pan,wheel_zoom,box_zoom,reset,save"
out = result_dict['PandeiaOutTrans']
# Flux 1d
x, y = out['1d']['extracted_flux']
x = x[~np.isnan(y)]
y = y[~np.isnan(y)]
plot_flux_1d1 = Figure(tools=TOOLS,
x_axis_label='Wavelength [microns]',
y_axis_label='Flux (e/s)',
title="Out of Transit Flux Rate",
plot_width=800,
plot_height=300)
plot_flux_1d1.line(x, y, line_width=4, alpha=.7)
if plot:
outputfile(output_file)
show(plot_flux_1d1)
return x, y
def jwst_1d_snr(result_dict, plot=True, output_file='snr.html'):
"""Plot SNR
Parameters
----------
result_dict : dict
Dictionary from pandexo output. If parameter space was run in run_pandexo
make sure to restructure the input as a list of dictionaries without they key words
that run_pandexo assigns.
plot : bool
(Optional) True renders plot, Flase does not. Default=True
output_file : str
(Optional) Default = 'snr.html'
Return
------
x : numpy array
micron
y : numpy array
1D SNR
See Also
--------
jwst_1d_bkg, jwst_noise, jwst_1d_flux, jwst_1d_spec, jwst_2d_det, jwst_2d_sat
"""
TOOLS = "pan,wheel_zoom,box_zoom,reset,save"
# Flux 1d
x = result_dict['RawData']['wave']
electrons_out = result_dict['RawData']['electrons_out']
y = electrons_out / np.sqrt(result_dict['RawData']['var_out'])
x = x[~np.isnan(y)]
y = y[~np.isnan(y)]
plot_snr_1d1 = Figure(tools=TOOLS,
x_axis_label='Wavelength (micron)',
y_axis_label='SNR',
title="SNR Out of Trans",
plot_width=800,
plot_height=300)
plot_snr_1d1.line(x, y, line_width=4, alpha=.7)
if plot:
outputfile(output_file)
show(plot_snr_1d1)
return x, y
def jwst_2d_det(result_dict, plot=True, output_file='det2d.html'):
"""Plot 2d detector image
Parameters
----------
result_dict : dict
Dictionary from pandexo output. If parameter space was run in run_pandexo
make sure to restructure the input as a list of dictionaries without they key words
that run_pandexo assigns.
plot : bool
(Optional) True renders plot, Flase does not. Default=True
output_file : str
(Optional) Default = 'det2d.html'
Return
------
numpy array
2D array of out of transit detector simulation
See Also
--------
jwst_1d_spec, jwst_1d_bkg, jwst_1d_flux, jwst_1d_snr, jwst_noise, jwst_2d_sat
"""
TOOLS = "pan,wheel_zoom,box_zoom,resize,reset,save"
out = result_dict['PandeiaOutTrans']
data = out['2d']['detector']
xr, yr = data.shape
plot_detector_2d = Figure(tools="pan,wheel_zoom,box_zoom,resize,reset,hover,save",
x_range=[0, yr], y_range=[0, xr],
x_axis_label='Pixel', y_axis_label='Spatial',
title="2D Detector Image",
plot_width=800, plot_height=300)
plot_detector_2d.image(image=[data], x=[0], y=[0], dh=[xr], dw=[yr],
palette="Spectral11")
if plot:
outputfile(output_file)
show(plot_detector_2d)
return data
def jwst_noise(result_dict, plot=True, output_file= 'noise.html'):
"""Plot background
Parameters
----------
result_dict : dict
Dictionary from pandexo output. If parameter space was run in run_pandexo
make sure to restructure the input as a list of dictionaries without they key words
that run_pandexo assigns.
plot : bool
(Optional) True renders plot, Flase does not. Default=True
output_file : str
(Optional) Default = 'noise.html'
Return
------
x : numpy array
micron
y : numpy array
1D noise (ppm)
See Also
--------
jwst_1d_spec, jwst_1d_bkg, jwst_1d_flux, jwst_1d_snr, jwst_2d_det, jwst_2d_sat
"""
TOOLS = "pan,wheel_zoom,box_zoom,resize,reset,save" #saturation
x = result_dict['FinalSpectrum']['wave']
y = result_dict['FinalSpectrum']['error_w_floor']*1e6
x = x[~np.isnan(y)]
y = y[~np.isnan(y)]
ymed = np.median(y)
plot_noise_1d1 = Figure(tools=TOOLS,#responsive=True,
x_axis_label='Wavelength (micron)',
y_axis_label='Error on Spectrum (PPM)', title="Error Curve",
plot_width=800, plot_height=300, y_range = [0,2.0*ymed])
ymed = np.median(y)
plot_noise_1d1.circle(x, y, line_width = 4, alpha = .7)
if plot:
outputfile(output_file)
show(plot_noise_1d1)
return x,y
def jwst_1d_flux(result_dict, plot=True, output_file= 'flux.html'):
"""Plot flux rate in e/s
Parameters
----------
result_dict : dict
Dictionary from pandexo output. If parameter space was run in run_pandexo
make sure to restructure the input as a list of dictionaries without they key words
that run_pandexo assigns.
plot : bool
(Optional) True renders plot, Flase does not. Default=True
output_file : str
(Optional) Default = 'flux.html'
Return
------
x : numpy array
micron
y : numpy array
1D flux rate in electrons/s
See Also
--------
jwst_1d_spec, jwst_1d_bkg, jwst_noise, jwst_1d_snr, jwst_2d_det, jwst_2d_sat
"""
TOOLS = "pan,wheel_zoom,box_zoom,resize,reset,save"
out = result_dict['PandeiaOutTrans']
# Flux 1d
x, y = out['1d']['extracted_flux']
x = x[~np.isnan(y)]
y = y[~np.isnan(y)]
plot_flux_1d1 = Figure(tools=TOOLS,
x_axis_label='Wavelength [microns]',
y_axis_label='Flux (e/s)', title="Out of Transit Flux Rate",
plot_width=800, plot_height=300)
plot_flux_1d1.line(x, y, line_width = 4, alpha = .7)
if plot:
outputfile(output_file)
show(plot_flux_1d1)
return x,y
def jwst_1d_snr(result_dict, plot=True, output_file='snr.html'):
"""Plot SNR
Parameters
----------
result_dict : dict
Dictionary from pandexo output. If parameter space was run in run_pandexo
make sure to restructure the input as a list of dictionaries without they key words
that run_pandexo assigns.
plot : bool
(Optional) True renders plot, Flase does not. Default=True
output_file : str
(Optional) Default = 'snr.html'
Return
------
x : numpy array
micron
y : numpy array
1D SNR
See Also
--------
jwst_1d_bkg, jwst_noise, jwst_1d_flux, jwst_1d_spec, jwst_2d_det, jwst_2d_sat
"""
TOOLS = "pan,wheel_zoom,box_zoom,resize,reset,save"
# Flux 1d
x= result_dict['RawData']['wave']
electrons_out = result_dict['RawData']['electrons_out']
y = electrons_out/np.sqrt(result_dict['RawData']['var_out'])
x = x[~np.isnan(y)]
y = y[~np.isnan(y)]
plot_snr_1d1 = Figure(tools=TOOLS,
x_axis_label='Wavelength (micron)',
y_axis_label='SNR', title="SNR Out of Trans",
plot_width=800, plot_height=300)
plot_snr_1d1.line(x, y, line_width = 4, alpha = .7)
if plot:
outputfile(output_file)
show(plot_snr_1d1)
return x,y
def jwst_1d_spec(result_dict,
model=True,
title='Model + Data + Error Bars',
output_file='data.html',
legend=False,
R=False,
num_tran=False,
plot_width=800,
plot_height=400,
x_range=[1, 10],
y_range=None,
plot=True,
output_notebook=False):
"""Plots 1d simulated spectrum and rebin or rescale for more transits
Plots 1d data points with model in the background (if wanted). Designed to read in exact
output of run_pandexo.
Parameters
----------
result_dict : dict or list of dict
Dictionary from pandexo output. If parameter space was run in run_pandexo
make sure to restructure the input as a list of dictionaries without they key words
that run_pandexo assigns.
model : bool
(Optional) True is default. True plots model, False does not plot model
title : str
(Optional) Title of plot. Default is "Model + Data + Error Bars".
output_file : str
(Optional) name of html file for you bokeh plot. After bokeh plot is rendered you will
have the option to save as png.
legend : bool
(Optional) Default is False. True, plots legend.
R : float
(Optional) Rebin data from native instrument resolution to specified resolution. Dafult is False,
no binning. Here I adopt R as w[1]/(w[2] - w[0]) to maintain consistency with `pandeia.engine`
num_tran : float
(Optional) Scales data by number of transits to improve error by sqrt(`num_trans`)
plot_width : int
(Optional) Sets the width of the plot. Default = 800
plot_height : int
(Optional) Sets the height of the plot. Default = 400
y_range : list of int
(Optional) sets y range of plot. Defaut is +- 10% of max and min
x_range : list of int
(Optional) Sets x range of plot. Default = [1,10]
plot : bool
(Optional) Supresses the plot if not wanted (Default = True)
out_notebook : bool
(Optional) Output notebook. Default is false, if true, outputs in the notebook
Returns
-------
x,y,e : list of arrays
Returns wave axis, spectrum and associated error in list format. x[0] will be correspond
to the first dictionary input, x[1] to the second, etc.
Examples
--------
>>> jwst_1d_spec(result_dict, num_tran = 3, R = 35) #for a single plot
If you wanted to save each of the axis that were being plotted:
>>> x,y,e = jwst_1d_data([result_dict1, result_dict2], model=False, num_tran = 5, R = 100) #for multiple
See Also
--------
jwst_noise, jwst_1d_bkg, jwst_1d_flux, jwst_1d_snr, jwst_2d_det, jwst_2d_sat
"""
outx = []
outy = []
oute = []
TOOLS = "pan,wheel_zoom,box_zoom,reset,save"
if output_notebook:
outnotebook()
else:
outputfile(output_file)
colors = [
'black', 'blue', 'red', 'orange', 'yellow', 'purple', 'pink', 'cyan',
'grey', 'brown'
]
#make sure its iterable
if type(result_dict) != list:
result_dict = [result_dict]
if type(legend) != bool:
legend_keys = legend
legend = True
if type(legend_keys) != list:
legend_keys = [legend_keys]
i = 0
for dictt in result_dict:
ntran_old = dictt['timing']['Number of Transits']
to = dictt['timing']["Num Integrations Out of Transit"]
ti = dictt['timing']["Num Integrations In Transit"]
#remove any nans
y = dictt['FinalSpectrum']['spectrum_w_rand']
x = dictt['FinalSpectrum']['wave'][~np.isnan(y)]
err = dictt['FinalSpectrum']['error_w_floor'][~np.isnan(y)]
y = y[~np.isnan(y)]
if (R == False) & (num_tran == False):
x = x
y = y
elif (R != False) & (num_tran != False):
new_wave = bin_wave_to_R(x, R)
out = uniform_tophat_sum(
new_wave, x,
dictt['RawData']['electrons_out'] * num_tran / ntran_old)
inn = uniform_tophat_sum(
new_wave, x,
dictt['RawData']['electrons_in'] * num_tran / ntran_old)
vout = uniform_tophat_sum(
new_wave, x,
dictt['RawData']['var_out'] * num_tran / ntran_old)
vin = uniform_tophat_sum(
new_wave, x, dictt['RawData']['var_in'] * num_tran / ntran_old)
var_tot = (to / ti / out)**2.0 * vin + (inn * to / ti /
out**2.0)**2.0 * vout
if dictt['input']['Primary/Secondary'] == 'fp/f*':
fac = -1.0
else:
fac = 1.0
rand_noise = np.sqrt((var_tot)) * (np.random.randn(len(new_wave)))
raw_spec = (out / to - inn / ti) / (out / to)
sim_spec = fac * (raw_spec + rand_noise)
x = new_wave
y = sim_spec
err = np.sqrt(var_tot)
elif (R == False) & (num_tran != False):
out = dictt['RawData']['electrons_out'] * num_tran / ntran_old
inn = dictt['RawData']['electrons_in'] * num_tran / ntran_old
vout = dictt['RawData']['var_out'] * num_tran / ntran_old
vin = dictt['RawData']['var_in'] * num_tran / ntran_old
var_tot = (to / ti / out)**2.0 * vin + (inn * to / ti /
out**2.0)**2.0 * vout
if dictt['input']['Primary/Secondary'] == 'fp/f*':
fac = -1.0
else:
fac = 1.0
rand_noise = np.sqrt((var_tot)) * (np.random.randn(len(x)))
raw_spec = (out / to - inn / ti) / (out / to)
sim_spec = fac * (raw_spec + rand_noise)
x = x
y = sim_spec
err = np.sqrt(var_tot)
elif (R != False) & (num_tran == False):
new_wave = bin_wave_to_R(x, R)
out = uniform_tophat_sum(new_wave, x,
dictt['RawData']['electrons_out'])
inn = uniform_tophat_sum(new_wave, x,
dictt['RawData']['electrons_in'])
vout = uniform_tophat_sum(new_wave, x, dictt['RawData']['var_out'])
vin = uniform_tophat_sum(new_wave, x, dictt['RawData']['var_in'])
var_tot = (to / ti / out)**2.0 * vin + (inn * to / ti /
out**2.0)**2.0 * vout
if dictt['input']['Primary/Secondary'] == 'fp/f*':
fac = -1.0
else:
fac = 1.0
rand_noise = np.sqrt((var_tot)) * (np.random.randn(len(new_wave)))
raw_spec = (out / to - inn / ti) / (out / to)
sim_spec = fac * (raw_spec + rand_noise)
x = new_wave
y = sim_spec
err = np.sqrt(var_tot)
else:
print(
"Something went wrong. Cannot enter both resolution and ask to bin to new wave"
)
return
#create error bars for Bokeh's multi_line and drop nans
data = pd.DataFrame({'x': x, 'y': y, 'err': err}).dropna()
y_err = []
x_err = []
for px, py, yerr in zip(data['x'], data['y'], data['err']):
np.array(x_err.append((px, px)))
np.array(y_err.append((py - yerr, py + yerr)))
#initialize Figure
if i == 0:
#Define units for x and y axis
y_axis_label = dictt['input']['Primary/Secondary']
if y_axis_label == 'fp/f*': p = -1.0
else: y_axis_label = y_axis_label
if dictt['input']['Calculation Type'] == 'phase_spec':
x_axis_label = 'Time (secs)'
x_range = [min(x), max(x)]
else:
x_axis_label = 'Wavelength [microns]'
if y_range != None:
ylims = y_range
else:
ylims = [
min(dictt['OriginalInput']['model_spec']) -
0.1 * min(dictt['OriginalInput']['model_spec']),
0.1 * max(dictt['OriginalInput']['model_spec']) +
max(dictt['OriginalInput']['model_spec'])
]
fig1d = Figure(x_range=x_range,
y_range=ylims,
plot_width=plot_width,
plot_height=plot_height,
title=title,
x_axis_label=x_axis_label,
y_axis_label=y_axis_label,
tools=TOOLS,
background_fill_color='white')
#plot model, data, and errors
if model:
mxx = dictt['OriginalInput']['model_wave']
myy = dictt['OriginalInput']['model_spec']
my = uniform_tophat_mean(x, mxx, myy)
model_line = pd.DataFrame({'x': x, 'my': my}).dropna()
fig1d.line(model_line['x'],
model_line['my'],
color=colors[i],
alpha=0.2,
line_width=4)
if legend:
fig1d.circle(data['x'],
data['y'],
color=colors[i],
legend=legend_keys[i])
else:
fig1d.circle(data['x'], data['y'], color=colors[i])
outx += [data['x'].values]
outy += [data['y'].values]
oute += [data['err'].values]
fig1d.multi_line(x_err, y_err, color=colors[i])
i += 1
if plot:
show(fig1d)
return outx, outy, oute
def hst_simulated_lightcurve(result_dict,
plot=True,
output_file='hsttime.html',
model=True):
"""Plot simulated HST light curves (in fluece) for earliest and latest start times
Parameters
----------
result_dict : dict
Dictionary from pandexo output.
plot : bool
(Optional) True renders plot, False does not. Default=True
model : bool
(Optional) Plot model under data. Default=True
output_file : str
(Optional) Default = 'hsttime.html'
Return
------
obsphase1 : numpy array
earliest start time
counts1 : numpy array
white light curve in fluence (e/pixel)
obsphase2 : numpy array
latest start time
counts2 : numpy array
white light curve in fluence (e/pixel)
rms : numpy array
1D rms noise
See Also
--------
hst_spec
"""
TOOLS = "pan,wheel_zoom,box_zoom,reset,save"
# earliest and latest start times
obsphase1 = result_dict['light_curve']['obsphase1']
rms = result_dict['light_curve']['light_curve_rms']
obsphase2 = result_dict['light_curve']['obsphase2']
phase1 = result_dict['light_curve']['phase1']
phase2 = result_dict['light_curve']['phase2']
counts1 = result_dict['light_curve']['counts1']
counts2 = result_dict['light_curve']['counts2']
count_noise = result_dict['light_curve']['count_noise']
ramp_included = result_dict['light_curve']['ramp_included']
model_counts1 = result_dict['light_curve']['model_counts1']
model_counts2 = result_dict['light_curve']['model_counts2']
if isinstance(count_noise, float):
rms = np.zeros(len(counts1)) + count_noise
y_err1 = []
x_err1 = []
for px, py, yerr in zip(obsphase1, counts1, rms):
np.array(x_err1.append((px, px)))
np.array(y_err1.append((py - yerr, py + yerr)))
y_err2 = []
x_err2 = []
for px, py, yerr in zip(obsphase2, counts2, rms):
np.array(x_err2.append((px, px)))
np.array(y_err2.append((py - yerr, py + yerr)))
if ramp_included:
title_description = " (Ramp Included)"
else:
title_description = " (Ramp Removed)"
early = Figure(
plot_width=400,
plot_height=300,
tools=TOOLS, #responsive=True,
x_axis_label='Orbital Phase',
y_axis_label='Flux [electrons/pixel]',
title="Earliest Start Time" + title_description)
if model:
early.line(phase1,
model_counts1,
color='black',
alpha=0.5,
line_width=4)
early.circle(obsphase1, counts1, line_width=3, line_alpha=0.6)
early.multi_line(x_err1, y_err1)
late = Figure(
plot_width=400,
plot_height=300,
tools=TOOLS, # responsive=True,
x_axis_label='Orbital Phase',
y_axis_label='Flux [electrons/pixel]',
title="Latest Start Time" + title_description)
if model:
late.line(phase2,
model_counts2,
color='black',
alpha=0.5,
line_width=3)
late.circle(obsphase2, counts2, line_width=3, line_alpha=0.6)
late.multi_line(x_err2, y_err2)
start_time = row(early, late)
if plot:
outputfile(output_file)
show(start_time)
return obsphase1, counts1, obsphase2, counts2, rms
def hst_time(result_dict, plot=True, output_file='hsttime.html', model=True):
"""Plot earliest and latest start times for hst observation
Parameters
----------
result_dict : dict
Dictionary from pandexo output.
plot : bool
(Optional) True renders plot, False does not. Default=True
model : bool
(Optional) Plot model under data. Default=True
output_file : str
(Optional) Default = 'hsttime.html'
Return
------
obsphase1 : numpy array
earliest start time
obstr1 : numpy array
white light curve
obsphase2 : numpy array
latest start time
obstr2 : numpy array
white light curve
rms : numpy array
1D rms noise
See Also
--------
hst_spec
"""
TOOLS = "pan,wheel_zoom,box_zoom,reset,save"
#earliest and latest start times
obsphase1 = result_dict['calc_start_window']['obsphase1']
obstr1 = result_dict['calc_start_window']['obstr1']
rms = result_dict['calc_start_window']['light_curve_rms']
obsphase2 = result_dict['calc_start_window']['obsphase2']
obstr2 = result_dict['calc_start_window']['obstr2']
phase1 = result_dict['calc_start_window']['phase1']
phase2 = result_dict['calc_start_window']['phase2']
trmodel1 = result_dict['calc_start_window']['trmodel1']
trmodel2 = result_dict['calc_start_window']['trmodel2']
if isinstance(rms, float):
rms = np.zeros(len(obsphase1)) + rms
y_err1 = []
x_err1 = []
for px, py, yerr in zip(obsphase1, obstr1, rms):
np.array(x_err1.append((px, px)))
np.array(y_err1.append((py - yerr, py + yerr)))
y_err2 = []
x_err2 = []
for px, py, yerr in zip(obsphase2, obstr2, rms):
np.array(x_err2.append((px, px)))
np.array(y_err2.append((py - yerr, py + yerr)))
early = Figure(
plot_width=400,
plot_height=300,
tools=TOOLS, #responsive=True,
x_axis_label='Orbital Phase',
y_axis_label='Flux',
title="Earliest Start Time")
if model:
early.line(phase1, trmodel1, color='black', alpha=0.5, line_width=4)
early.circle(obsphase1, obstr1, line_width=3, line_alpha=0.6)
early.multi_line(x_err1, y_err1)
late = Figure(
plot_width=400,
plot_height=300,
tools=TOOLS, #responsive=True,
x_axis_label='Orbital Phase',
y_axis_label='Flux',
title="Latest Start Time")
if model:
late.line(phase2, trmodel2, color='black', alpha=0.5, line_width=3)
late.circle(obsphase2, obstr2, line_width=3, line_alpha=0.6)
late.multi_line(x_err2, y_err2)
start_time = row(early, late)
if plot:
outputfile(output_file)
show(start_time)
return obsphase1, obstr1, obsphase2, obstr2, rms
def hst_spec(result_dict, plot=True, output_file='hstspec.html', model=True):
"""Plot 1d spec with error bars for hst
Parameters
----------
result_dict : dict
Dictionary from pandexo output.
plot : bool
(Optional) True renders plot, False does not. Default=True
model : bool
(Optional) Plot model under data. Default=True
output_file : str
(Optional) Default = 'hstspec.html'
Return
------
x : numpy array
micron
y : numpy array
1D spec fp/f* or rp^2/r*^2
e : numpy array
1D rms noise
modelx : numpy array
micron
modely : numpy array
1D spec fp/f* or rp^2/r*^2
See Also
--------
hst_time
"""
TOOLS = "pan,wheel_zoom,box_zoom,reset,save"
#plot planet spectrum
mwave = result_dict['planet_spec']['model_wave']
mspec = result_dict['planet_spec']['model_spec']
binwave = result_dict['planet_spec']['binwave']
binspec = result_dict['planet_spec']['binspec']
error = result_dict['planet_spec']['error']
error = np.zeros(len(binspec)) + error
xlims = [
result_dict['planet_spec']['wmin'], result_dict['planet_spec']['wmax']
]
ylims = [
np.min(binspec) - 2.0 * error[0],
np.max(binspec) + 2.0 * error[0]
]
plot_spectrum = Figure(
plot_width=800,
plot_height=300,
x_range=xlims,
y_range=ylims,
tools=TOOLS, #responsive=True,
x_axis_label='Wavelength [microns]',
y_axis_label='Ratio',
title="Original Model with Observation")
y_err = []
x_err = []
for px, py, yerr in zip(binwave, binspec, error):
np.array(x_err.append((px, px)))
np.array(y_err.append((py - yerr, py + yerr)))
if model:
plot_spectrum.line(mwave,
mspec,
color="black",
alpha=0.5,
line_width=4)
plot_spectrum.circle(binwave, binspec, line_width=3, line_alpha=0.6)
plot_spectrum.multi_line(x_err, y_err)
if plot:
outputfile(output_file)
show(plot_spectrum)
return binwave, binspec, error, mwave, mspec
def hst_time(result_dict, plot=True, output_file ='hsttime.html', model = True):
"""Plot earliest and latest start times for hst observation
Parameters
----------
result_dict : dict
Dictionary from pandexo output.
plot : bool
(Optional) True renders plot, False does not. Default=True
model : bool
(Optional) Plot model under data. Default=True
output_file : str
(Optional) Default = 'hsttime.html'
Return
------
obsphase1 : numpy array
earliest start time
obstr1 : numpy array
white light curve
obsphase2 : numpy array
latest start time
obstr2 : numpy array
white light curve
rms : numpy array
1D rms noise
See Also
--------
hst_spec
"""
TOOLS = "pan,wheel_zoom,box_zoom,resize,reset,save"
#earliest and latest start times
obsphase1 = result_dict['calc_start_window']['obsphase1']
obstr1 = result_dict['calc_start_window']['obstr1']
rms = result_dict['calc_start_window']['light_curve_rms']
obsphase2 = result_dict['calc_start_window']['obsphase2']
obstr2 = result_dict['calc_start_window']['obstr2']
phase1 = result_dict['calc_start_window']['phase1']
phase2 = result_dict['calc_start_window']['phase2']
trmodel1 = result_dict['calc_start_window']['trmodel1']
trmodel2 = result_dict['calc_start_window']['trmodel2']
if isinstance(rms, float):
rms = np.zeros(len(obsphase1))+rms
y_err1 = []
x_err1 = []
for px, py, yerr in zip(obsphase1, obstr1, rms):
np.array(x_err1.append((px, px)))
np.array(y_err1.append((py - yerr, py + yerr)))
y_err2 = []
x_err2 = []
for px, py, yerr in zip(obsphase2, obstr2, rms):
np.array(x_err2.append((px, px)))
np.array(y_err2.append((py - yerr, py + yerr)))
early = Figure(plot_width=400, plot_height=300,
tools=TOOLS,#responsive=True,
x_axis_label='Orbital Phase',
y_axis_label='Flux',
title="Earliest Start Time")
if model: early.line(phase1, trmodel1, color='black',alpha=0.5, line_width = 4)
early.circle(obsphase1, obstr1, line_width=3, line_alpha=0.6)
early.multi_line(x_err1, y_err1)
late = Figure(plot_width=400, plot_height=300,
tools=TOOLS,#responsive=True,
x_axis_label='Orbital Phase',
y_axis_label='Flux',
title="Latest Start Time")
if model: late.line(phase2, trmodel2, color='black',alpha=0.5, line_width = 3)
late.circle(obsphase2, obstr2, line_width=3, line_alpha=0.6)
late.multi_line(x_err2, y_err2)
start_time = row(early, late)
if plot:
outputfile(output_file)
show(start_time)
return obsphase1, obstr1, obsphase2, obstr2,rms
def hst_spec(result_dict, plot=True, output_file ='hstspec.html', model = True):
"""Plot 1d spec with error bars for hst
Parameters
----------
result_dict : dict
Dictionary from pandexo output.
plot : bool
(Optional) True renders plot, False does not. Default=True
model : bool
(Optional) Plot model under data. Default=True
output_file : str
(Optional) Default = 'hstspec.html'
Return
------
x : numpy array
micron
y : numpy array
1D spec fp/f* or rp^2/r*^2
e : numpy array
1D rms noise
modelx : numpy array
micron
modely : numpy array
1D spec fp/f* or rp^2/r*^2
See Also
--------
hst_time
"""
TOOLS = "pan,wheel_zoom,box_zoom,resize,reset,save"
#plot planet spectrum
mwave = result_dict['planet_spec']['model_wave']
mspec = result_dict['planet_spec']['model_spec']
binwave = result_dict['planet_spec']['binwave']
binspec = result_dict['planet_spec']['binspec']
error = result_dict['planet_spec']['error']
error = np.zeros(len(binspec))+ error
xlims = [result_dict['planet_spec']['wmin'], result_dict['planet_spec']['wmax']]
ylims = [np.min(binspec)-2.0*error[0], np.max(binspec)+2.0*error[0]]
plot_spectrum = Figure(plot_width=800, plot_height=300, x_range=xlims,
y_range=ylims, tools=TOOLS,#responsive=True,
x_axis_label='Wavelength [microns]',
y_axis_label='Ratio',
title="Original Model with Observation")
y_err = []
x_err = []
for px, py, yerr in zip(binwave, binspec, error):
np.array(x_err.append((px, px)))
np.array(y_err.append((py - yerr, py + yerr)))
if model:
plot_spectrum.line(mwave,mspec, color= "black", alpha = 0.5, line_width = 4)
plot_spectrum.circle(binwave,binspec, line_width=3, line_alpha=0.6)
plot_spectrum.multi_line(x_err, y_err)
if plot:
outputfile(output_file)
show(plot_spectrum)
return binwave, binspec, error, mwave, mspec
def jwst_1d_spec(result_dict, model=True, title='Model + Data + Error Bars', output_file = 'data.html',legend = False,
R=False, num_tran = False, plot_width=800, plot_height=400,x_range=[1,10]):
"""Plots 1d simulated spectrum and rebin or rescale for more transits
Plots 1d data points with model in the background (if wanted). Designed to read in exact
output of run_pandexo.
Parameters
----------
result_dict : dict or list of dict
Dictionary from pandexo output. If parameter space was run in run_pandexo
make sure to restructure the input as a list of dictionaries without they key words
that run_pandexo assigns.
model : bool
(Optional) True is default. True plots model, False does not plot model
title : str
(Optional) Title of plot. Default is "Model + Data + Error Bars".
output_file : str
(Optional) name of html file for you bokeh plot. After bokeh plot is rendered you will
have the option to save as png.
legend : bool
(Optional) Default is False. True, plots legend.
R : float
(Optional) Rebin data from native instrument resolution to specified resolution. Dafult is False,
no binning.
num_tran : float
(Optional) Scales data by number of transits to improve error by sqrt(`num_trans`)
plot_width : int
(Optional) Sets the width of the plot. Default = 800
plot_height : int
(Optional) Sets the height of the plot. Default = 400
x_range : list of int
(Optional) Sets x range of plot. Default = [1,10]
Returns
-------
x,y,e : list of arrays
Returns wave axis, spectrum and associated error in list format. x[0] will be correspond
to the first dictionary input, x[1] to the second, etc.
Examples
--------
>>> jwst_1d_spec(result_dict, num_tran = 3, R = 35) #for a single plot
If you wanted to save each of the axis that were being plotted:
>>> x,y,e = jwst_1d_data([result_dict1, result_dict2], model=False, num_tran = 5, R = 100) #for multiple
See Also
--------
jwst_noise, jwst_1d_bkg, jwst_1d_flux, jwst_1d_snr, jwst_2d_det, jwst_2d_sat
"""
outx=[]
outy=[]
oute=[]
TOOLS = "pan,wheel_zoom,box_zoom,resize,reset,save"
outputfile(output_file)
colors = ['black','blue','red','orange','yellow','purple','pink','cyan','grey','brown']
#make sure its iterable
if type(result_dict) != list:
result_dict = [result_dict]
if type(legend)!=bool:
legend_keys = legend
legend = True
if type(legend_keys) != list:
legend_keys = [legend_keys]
i = 0
for dict in result_dict:
ntran_old = dict['timing']['Number of Transits']
to = dict['timing']["Num Integrations Out of Transit"]
ti = dict['timing']["Num Integrations In Transit"]
#remove any nans
y = dict['FinalSpectrum']['spectrum_w_rand']
x = dict['FinalSpectrum']['wave'][~np.isnan(y)]
err = dict['FinalSpectrum']['error_w_floor'][~np.isnan(y)]
y = y[~np.isnan(y)]
if (R == False) & (num_tran == False):
x=x
y=y
elif (R != False) & (num_tran != False):
new_wave = bin_wave_to_R(x, R)
out = uniform_tophat_sum(new_wave,x, dict['RawData']['electrons_out']*num_tran/ntran_old)
inn = uniform_tophat_sum(new_wave,x, dict['RawData']['electrons_in']*num_tran/ntran_old)
vout = uniform_tophat_sum(new_wave,x, dict['RawData']['var_out']*num_tran/ntran_old)
vin = uniform_tophat_sum(new_wave,x, dict['RawData']['var_in']*num_tran/ntran_old)
var_tot = (to/ti/out)**2.0 * vin + (inn*to/ti/out**2.0)**2.0 * vout
if dict['input']['Primary/Secondary']=='fp/f*':
fac = -1.0
else:
fac = 1.0
rand_noise = np.sqrt((var_tot))*(np.random.randn(len(new_wave)))
raw_spec = (out/to-inn/ti)/(out/to)
sim_spec = fac*(raw_spec + rand_noise )
x = new_wave
y = sim_spec
err = np.sqrt(var_tot)
elif (R == False) & (num_tran != False):
out = dict['RawData']['electrons_out']*num_tran/ntran_old
inn = dict['RawData']['electrons_in']*num_tran/ntran_old
vout = dict['RawData']['var_out']*num_tran/ntran_old
vin = dict['RawData']['var_in']*num_tran/ntran_old
var_tot = (to/ti/out)**2.0 * vin + (inn*to/ti/out**2.0)**2.0 * vout
if dict['input']['Primary/Secondary']=='fp/f*':
fac = -1.0
else:
fac = 1.0
rand_noise = np.sqrt((var_tot))*(np.random.randn(len(x)))
raw_spec = (out/to-inn/ti)/(out/to)
sim_spec = fac*(raw_spec + rand_noise )
x = x
y = sim_spec
err = np.sqrt(var_tot)
elif (R != False) & (num_tran == False):
new_wave = bin_wave_to_R(x, R)
out = uniform_tophat_sum(new_wave,x, dict['RawData']['electrons_out'])
inn = uniform_tophat_sum(new_wave,x, dict['RawData']['electrons_in'])
vout = uniform_tophat_sum(new_wave,x, dict['RawData']['var_out'])
vin = uniform_tophat_sum(new_wave,x, dict['RawData']['var_in'])
var_tot = (to/ti/out)**2.0 * vin + (inn*to/ti/out**2.0)**2.0 * vout
if dict['input']['Primary/Secondary']=='fp/f*':
fac = -1.0
else:
fac = 1.0
rand_noise = np.sqrt((var_tot))*(np.random.randn(len(new_wave)))
raw_spec = (out/to-inn/ti)/(out/to)
sim_spec = fac*(raw_spec + rand_noise )
x = new_wave
y = sim_spec
err = np.sqrt(var_tot)
else:
print("Something went wrong. Cannot enter both resolution and ask to bin to new wave")
return
#create error bars for Bokeh's multi_line
y_err = []
x_err = []
for px, py, yerr in zip(x, y, err):
np.array(x_err.append((px, px)))
np.array(y_err.append((py - yerr, py + yerr)))
#initialize Figure
if i == 0:
#Define units for x and y axis
y_axis_label = dict['input']['Primary/Secondary']
if y_axis_label == 'fp/f*': p = -1.0
else: y_axis_label = '('+y_axis_label+')^2'
if dict['input']['Calculation Type'] =='phase_spec':
x_axis_label='Time (secs)'
x_range = [min(x), max(x)]
else:
x_axis_label='Wavelength [microns]'
ylims = [min(dict['OriginalInput']['model_spec'])- 0.1*min(dict['OriginalInput']['model_spec']),
0.1*max(dict['OriginalInput']['model_spec'])+max(dict['OriginalInput']['model_spec'])]
xlims = [min(x), max(x)]
fig1d = Figure(x_range=x_range, y_range = ylims,
plot_width = plot_width, plot_height =plot_height,title=title,x_axis_label=x_axis_label,
y_axis_label = y_axis_label, tools=TOOLS, background_fill_color = 'white')
#plot model, data, and errors
if model:
mxx = dict['OriginalInput']['model_wave']
myy = dict['OriginalInput']['model_spec']
my = uniform_tophat_mean(x, mxx,myy)
fig1d.line(x,my, color='black',alpha=0.2, line_width = 4)
if legend:
fig1d.circle(x, y, color=colors[i], legend = legend_keys[i])
else:
fig1d.circle(x, y, color=colors[i])
outx += [x]
outy += [y]
oute += [err]
fig1d.multi_line(x_err, y_err,color=colors[i])
i += 1
show(fig1d)
return outx,outy,oute
