def button2action(self, event=None, debug=False, subtract=True,
powerlaw=None, fit_original=False,
spline=False,
spline_sampling=None,
spline_downsampler=np.median,
baseline_fit_color='orange', **kwargs):
"""
Do the baseline fitting and save and plot the results.
"""
if debug: print "Button 2/3 Baseline. Subtract=",subtract
if self.subtracted:
self.unsubtract()
# interactive guesspeakwidth passes this on; it should be excised
if 'nwidths' in kwargs:
kwargs.pop('nwidths')
if powerlaw is None:
powerlaw = self.powerlaw
self.clear_highlights()
self._xfit_units = self.Spectrum.xarr.unit
log.debug("Fitting baseline: powerlaw={0} "
"spline={1}".format(self.powerlaw, spline))
self.fit(powerlaw=powerlaw, includemask=self.includemask,
order=self.order, spline=spline,
spline_sampling=spline_sampling,
spline_downsampler=spline_downsampler)
if subtract:
if self.subtracted and fit_original:
# use the spectrum with the old baseline added in (that's what we fit to)
self.Spectrum.data = self.spectofit - self.basespec
else:
self.Spectrum.data -= self.basespec
self.subtracted = True
else:
if self.subtracted:
self.unsubtract()
self.subtracted = False
if self.Spectrum.plotter.axis is not None:
if debug: print "Plotting baseline"
if event is not None:
# preserve frame if fitting interactively
kwargs.update({'use_window_limits':True})
self.plot_baseline(baseline_fit_color=baseline_fit_color, **kwargs)
# disconnect interactive window (and more importantly, reconnect to
# original interactive cmds)
self.clear_all_connections()
if hasattr(self.Spectrum,'header'):
history.write_history(self.Spectrum.header,
"BASELINE order=%i pars=%s" % (self.order,
",".join([str(s) for s in self.baselinepars])) +
"(powerlaw)" if self.powerlaw else "")
def crop(self, x1, x2, units=None, **kwargs):
"""
Replace the current spectrum with a subset from x1 to x2 in current
units
Fixes CRPIX1 and baseline and model spectra to match cropped data spectrum
"""
# do slice (this code is redundant... need to figure out how to fix that)
x1pix = np.argmin(np.abs(x1 - self.xarr.as_unit(units)))
x2pix = np.argmin(np.abs(x2 - self.xarr.as_unit(units)))
if x1pix > x2pix: x1pix, x2pix = x2pix, x1pix
if x1pix == x2pix:
raise IndexError("ERROR: Trying to crop to zero size.")
self = self.slice(x1pix, x2pix, units='pixels', copy=False, **kwargs)
# a baseline spectrum is always defined, even if it is all zeros
# this is needed to prevent size mismatches. There may be a more
# elegant way to do this...
# this is taken care of in Slice now self.baseline.crop(x1pix,x2pix)
# this is taken care of in Slice now self.specfit.crop(x1pix,x2pix)
if hasattr(self.specfit, 'fitter'):
self.specfit._full_model()
if hasattr(self, 'header'):
history.write_history(
self.header, "CROP: Cropped from %g to %g (pixel %i to %i)" %
(x1, x2, x1pix, x2pix))
if self.header.get('CRPIX1'):
self.header['CRPIX1'] = self.header.get('CRPIX1') - x1pix
history.write_history(
self.header, "CROP: Changed CRPIX1 from %f to %f" %
(self.header.get('CRPIX1') + x1pix,
self.header.get('CRPIX1')))
def crop(self, x1, x2, units=None, **kwargs):
"""
Replace the current spectrum with a subset from x1 to x2 in current
units
Fixes CRPIX1 and baseline and model spectra to match cropped data spectrum
"""
# do slice (this code is redundant... need to figure out how to fix that)
x1pix = np.argmin(np.abs(x1 - self.xarr.as_unit(units)))
x2pix = np.argmin(np.abs(x2 - self.xarr.as_unit(units)))
if x1pix > x2pix:
x1pix, x2pix = x2pix, x1pix
if x1pix == x2pix:
raise IndexError("ERROR: Trying to crop to zero size.")
self = self.slice(x1pix, x2pix, units="pixels", copy=False, **kwargs)
# a baseline spectrum is always defined, even if it is all zeros
# this is needed to prevent size mismatches. There may be a more
# elegant way to do this...
# this is taken care of in Slice now self.baseline.crop(x1pix,x2pix)
# this is taken care of in Slice now self.specfit.crop(x1pix,x2pix)
if hasattr(self.specfit, "fitter"):
self.specfit._full_model()
if hasattr(self, "header"):
history.write_history(self.header, "CROP: Cropped from %g to %g (pixel %i to %i)" % (x1, x2, x1pix, x2pix))
if self.header.get("CRPIX1"):
self.header.update("CRPIX1", self.header.get("CRPIX1") - x1pix)
history.write_history(
self.header,
"CROP: Changed CRPIX1 from %f to %f"
% (self.header.get("CRPIX1") + x1pix, self.header.get("CRPIX1")),
)
def execute_commands(self, user_input, raw_input):
if not user_input:
self.exit_code = 1
return
command = user_input[0]
write_history(command, raw_input)
if ("\\&&" not in raw_input and "\\||" not in raw_input
and ('&&' in raw_input or '||' in raw_input)):
if check_valid_operator(raw_input):
return self.logical_operator(raw_input)
else:
self.exit_code = 2
return
# check if command is a built-in
if command in self.builtins:
self.do_builtin(user_input)
# check if command is '!*'
elif command.startswith('!') and len(command) > 1:
self.do_exclamation(user_input)
self.should_write_history = False
# if command is not a built-in
else:
self.do_external(user_input)
def _smooth_header(self,smooth):
"""
Internal - correct the FITS header parameters when smoothing
"""
if self.header.get('CDELT1') is not None and self.header.get('CRPIX1') is not None:
self.header['CDELT1'] = self.header.get('CDELT1') * float(smooth)
self.header['CRPIX1'] = self.header.get('CRPIX1') / float(smooth)
history.write_history(self.header,"SMOOTH: Smoothed and downsampled spectrum by factor %i" % (smooth))
history.write_history(self.header,"SMOOTH: Changed CRPIX1 from %f to %f" % (self.header.get('CRPIX1')*float(smooth),self.header.get('CRPIX1')))
history.write_history(self.header,"SMOOTH: Changed CDELT1 from %f to %f" % (self.header.get('CRPIX1')/float(smooth),self.header.get('CRPIX1')))
def _smooth_header(self, smooth):
"""
Internal - correct the FITS header parameters when smoothing
"""
if self.header.get('CDELT1') is not None and self.header.get(
'CRPIX1') is not None:
self.header['CDELT1'] = self.header.get('CDELT1') * float(smooth)
self.header['CRPIX1'] = self.header.get('CRPIX1') / float(smooth)
history.write_history(
self.header,
"SMOOTH: Smoothed and downsampled spectrum by factor %i" %
(smooth))
history.write_history(
self.header, "SMOOTH: Changed CRPIX1 from %f to %f" %
(self.header.get('CRPIX1') * float(smooth),
self.header.get('CRPIX1')))
history.write_history(
self.header, "SMOOTH: Changed CDELT1 from %f to %f" %
(self.header.get('CRPIX1') / float(smooth),
self.header.get('CRPIX1')))
def button2action(self, event=None, debug=False, subtract=True, powerlaw=None,
fit_original=False, baseline_fit_color='orange', **kwargs):
"""
Do the baseline fitting and save and plot the results.
"""
if debug: print "Button 2/3 Baseline. Subtract=",subtract
if self.subtracted:
self.unsubtract()
# interactive guesspeakwidth passes this on; it should be excised
if 'nwidths' in kwargs:
kwargs.pop('nwidths')
if powerlaw is None:
powerlaw = self.powerlaw
self.clear_highlights()
self._xfit_units = self.Spectrum.xarr.units
if debug: print "Fitting baseline"
self.basespec, self.baselinepars = self._baseline(
self.spectofit,
xarr=self.Spectrum.xarr,
err=self.Spectrum.error,
order=self.order,
mask=(True-self.includemask),
powerlaw=powerlaw,
xarr_fit_units=self._xfit_units,
**kwargs)
self.set_basespec_frompars()
if subtract:
if self.subtracted and fit_original:
# use the spectrum with the old baseline added in (that's what we fit to)
self.Spectrum.data = self.spectofit - self.basespec
else:
self.Spectrum.data -= self.basespec
self.subtracted = True
else:
if self.subtracted:
self.unsubtract()
self.subtracted = False
if self.Spectrum.plotter.axis is not None:
if debug: print "Plotting baseline"
if event is not None:
# preserve frame if fitting interactively
kwargs.update({'use_window_limits':True})
self.plot_baseline(baseline_fit_color=baseline_fit_color, **kwargs)
# disconnect interactive window (and more importantly, reconnect to
# original interactive cmds)
self.clear_all_connections()
if hasattr(self.Spectrum,'header'):
history.write_history(self.Spectrum.header,
"BASELINE order=%i pars=%s" % (self.order,
",".join([str(s) for s in self.baselinepars])) +
"(powerlaw)" if self.powerlaw else "")
def button2action(
self,
event=None,
debug=False,
subtract=True,
powerlaw=None,
fit_original=False,
baseline_fit_color="orange",
**kwargs
):
"""
Do the baseline fitting and save and plot the results.
"""
if debug:
print "Button 2/3 Baseline. Subtract=", subtract
if self.subtracted:
self.unsubtract()
# interactive guesspeakwidth passes this on; it should be excised
if "nwidths" in kwargs:
kwargs.pop("nwidths")
if powerlaw is not None:
powerlaw = self.powerlaw
self.clear_highlights()
self._xfit_units = self.Spectrum.xarr.units
if debug:
print "Fitting baseline"
self.basespec, self.baselinepars = self._baseline(
self.spectofit,
xarr=self.Spectrum.xarr,
err=self.Spectrum.error,
order=self.order,
mask=(True - self.includemask),
powerlaw=powerlaw,
xarr_fit_units=self._xfit_units,
**kwargs
)
self.set_basespec_frompars()
if subtract:
if self.subtracted and fit_original:
# use the spectrum with the old baseline added in (that's what we fit to)
self.Spectrum.data = self.spectofit - self.basespec
else:
self.Spectrum.data -= self.basespec
self.subtracted = True
else:
if self.subtracted:
self.unsubtract()
self.subtracted = False
if self.Spectrum.plotter.axis is not None:
if debug:
print "Plotting baseline"
if event is not None:
# preserve frame if fitting interactively
kwargs.update({"use_window_limits": True})
self.plot_baseline(baseline_fit_color=baseline_fit_color, **kwargs)
# disconnect interactive window (and more importantly, reconnect to
# original interactive cmds)
self.clear_all_connections()
if hasattr(self.Spectrum, "header"):
history.write_history(
self.Spectrum.header,
"BASELINE order=%i pars=%s" % (self.order, ",".join([str(s) for s in self.baselinepars])) + "(powerlaw)"
if self.powerlaw
else "",
)
