def set_order(self,i):
"""
This modifies the currently active order to be plotted.
"""
import numpy as np
import tayph.functions as fun
import warnings
import tayph.util as ut
import copy
from tayph.vartests import typetest
typetest(i,int,'i in mask_maker.set_order()',)
self.wl = self.list_of_wls[i]
self.order = self.list_of_orders[i]
#Measure the shape of the current order
self.nexp = np.shape(self.order)[0]
self.npx = np.shape(self.order)[1]
#Compute the meanspec and the residuals, ignoring runtime warnings related to NaNs:
with warnings.catch_warnings():
warnings.simplefilter("ignore", category=RuntimeWarning)
self.meanspec = np.nanmean(self.list_of_orders[i],axis=0)
self.residual = self.order / self.meanspec
self.img_max = np.nanmean(self.meanspec[fun.selmax(self.meanspec,0.02,s=0.02)])*1.3
self.vmin = np.nanmedian(self.residual)-3.0*np.nanstd(self.residual)
self.vmax = np.nanmedian(self.residual)+3.0*np.nanstd(self.residual)
def envelope(wlm, fxm, binsize, selfrac=0.05, mode='top', threshold=''):
"""
This program measures the top or bottom envelope of a spectrum (wl,fx), by
chopping it up into bins of size binsze (unit of wl), and measuring the mean
of the top n % of values in that bin. Setting the mode to 'bottom' will do the
oppiste: The mean of the bottom n% of values. The output is the resulting wl
and flux points of these bins.
Example: wle,fxe = envelope(wl,fx,1.0,selfrac=3.0,mode='top')
"""
import numpy as np
import tayph.util as ut
import tayph.functions as fun
from tayph.vartests import typetest, dimtest, nantest, postest
from matplotlib import pyplot as plt
typetest(wlm, np.ndarray, 'wlm in ops.envelope()')
typetest(fxm, np.ndarray, 'fxm in ops.envelope()')
dimtest(wlm, [len(fxm)])
typetest(binsize, [int, float], 'binsize in ops.envelope()')
typetest(selfrac, float, 'percentage in ops.envelope()')
typetest(mode, str, 'mode in envelope')
nantest(fxm, 'fxm in ops.envelope()')
nantest(wlm, 'wlm in ops.envelope()')
postest(wlm, 'wlm in ops.envelope()')
postest(binsize, 'binsize in ops.envelope()')
if mode not in ['top', 'bottom']:
raise Exception(
f'RuntimeError in ops.envelope(): Mode should be set to "top" or "bottom" ({mode}).'
)
binsize = float(binsize)
if mode == 'bottom':
fxm *= -1.0
wlcs = np.array([]) #Center wavelengths
fxcs = np.array([]) #Flux at center wavelengths
i_start = 0
wlm_start = wlm[i_start]
for i in range(0, len(wlm) - 1):
if wlm[i] - wlm_start >= binsize:
wlsel = wlm[i_start:i]
fxsel = fxm[i_start:i]
maxsel = fun.selmax(fxsel, selfrac)
wlcs = np.append(wlcs, np.mean(wlsel[maxsel]))
fxcs = np.append(fxcs, np.mean(fxsel[maxsel]))
i_start = i + 1
wlm_start = wlm[i + 1]
if isinstance(threshold, float) == True:
#This means that the threshold value is set, and we set all bins less than
#that threshold to the threshold value:
if mode == 'bottom':
threshold *= -1.0
fxcs[(fxcs < threshold)] = threshold
if mode == 'bottom':
fxcs *= -1.0
fxm *= -1.0
return wlcs, fxcs
def set_spectrum(self, i):
"""This modifies the currently active spectrum to be plotted."""
import numpy as np
import tayph.functions as fun
from tayph.vartests import typetest
import matplotlib.pyplot as plt
typetest(i, int, 'i in molecfit_gui/set_order')
self.wl = self.wls[i]
self.spectrum = self.fxc[i]
self.Tspectrum = self.trans[i]
self.img_max = np.nanmean(self.spectrum[fun.selmax(
self.spectrum, 0.02, s=0.02)]) * 1.3