def wavecal(self):
if not self.linelist:
popup = WarningDialog(text="Please select a line list first.")
popup.open()
return
calfile = self.paths['cal'] + self.speclist[self.spec_index]
if self.ids.lampcal.state == 'down':
calfile += '-lamp.fits'
else:
calfile += '-sky.fits'
try:
calib = ExtractedSpectrum(calfile)
except:
popup = WarningDialog(text="You don't have a calibration of this type...")
popup.open()
return
niter = self.ids.numiter.text
if self.linelist in self.linelists:
#lldb = shelve.open('storage/linelists')
#linelist_path = ird.deserialize(linelistdb[self.lineslist])
linelist_path = linelistdb[self.linelist]
#lldb.close()
else:
linelist_path = self.linelist
self.calibration = calibrate_wavelength(calib, linelist_path, (self.wmin, self.wmax), niter)
for i, w in self.calibration.parameters:
self.current_spectrum.header['WAVECAL%i'%i] = (w, 'Wavelength calibration coefficient')
self.current_spectrum.wav = self.calibration(range(len(self.current_spectrum.spec)))
self.wmin = self.current_spectrum.wav.min()
self.wmax = self.current_spectrum.wav.max()
self.current_spectrum.plot.points = zip(self.current_spectrum.wav, self.current_spectrum.spec)
def fix_distort(self):
if not (self.fit_params.get('pmodel',False) or \
self.fit_params.get('nmodel',False)):
popup = WarningDialog(text='Make sure you fit the trace centers first!')
popup.open()
return
pdistort, ndistort = draw_trace(self.extractregion, self.xx, self.fit_params['pmodel'], \
self.fit_params['nmodel'], fixdistort = True, fitdegree = self.fit_params['deg'])
im1, im2 = [x for x in copy.deepcopy(self.theapp.extract_pairs[self.pair_index])]
im1.load(); im2.load()
#if self.current_flats:
# im1 = im_divide(im1, self.current_flats)
# im2 = im_divide(im2, self.current_flats)
im1.data_array = undistort_imagearray(im1.data_array, pdistort)
im2.data_array = undistort_imagearray(im2.data_array, ndistort)
im_subtract(im1, im2, outputfile=self.current_impair.fitsfile)
tmp = self.current_impair
self.current_impair = FitsImage(self.current_impair.fitsfile)
self.current_impair.header['EXREGX1'] = (tmp.get_header_keyword('EXREGX1'), 'extraction region coordinate X1')
self.current_impair.header['EXREGY1'] = (tmp.get_header_keyword('EXREGY1'), 'extraction region coordinate Y1')
self.current_impair.header['EXREGX2'] = (tmp.get_header_keyword('EXREGX2'), 'extraction region coordinate X2')
self.current_impair.header['EXREGY2'] = (tmp.get_header_keyword('EXREGY2'), 'extraction region coordinate Y2')
self.current_impair.update_fits(header_only = True)
self.set_imagepair(self.pairstrings[self.pair_index])
self.fit_params['nmodel'] = None
self.fit_params['pmodel'] = None
def check_filestub(self, stub):
placeholder = '#'
reg = placeholder+'+'
if len(re.findall(reg, stub)) != 1:
popup = WarningDialog(text = "File format is not valid; must use '#' as placeholder only")
popup.open()
return
self.current_obsnight = self.current_obsnight._replace(filestub=stub)
def extract_spectrum(self):
if not (self.fit_params.get('pmodel',False) or \
self.fit_params.get('nmodel',False)):
popup = WarningDialog(text='Make sure you fit the trace centers first!')
popup.open()
return
#need a calibration, too
self.lamp = None
if theapp.current_night.cals:
self.lamp = theapp.current_night.cals.data_array if not self.current_flats \
else im_divide(theapp.current_night.cals, self.current_flats).data_array
self.lamp = self.lamp[self.region[1]:self.region[3]+1,self.region[0]:self.region[2]+1]
im1, im2 = [x for x in copy.deepcopy(the_app.extract_pairs[self.pair_index])]
im1.load(); im2.load()
#if self.current_flats:
# im1 = im_divide(im1, self.current_flats)
# im2 = im_divide(im2, self.current_flats)
im1.data_array = undistort_imagearray(im1.data_array, pdistort)
im2.data_array = undistort_imagearray(im2.data_array, ndistort)
self.tell = make_region(im1, im2, self.region, flat=self.current_flats, telluric=True)
#tmp, self.tell = im_minimum(im1.data_array, im2.data_array)
#self.tell = self.tell[self.region[1]:self.region[3]+1,self.region[0]:self.region[2]+1]
self.pextract = extract(self.fit_params['pmodel'], self.extractregion, self.tell, 'pos', lamp = self.lamp)
self.nextract = extract(self.fit_params['nmodel'], self.extractregion, self.tell, 'neg', lamp = self.lamp)
#write uncalibrated spectra to fits files (will update after calibration)
pstub = self.paths['out'] + re.sub('.fits','-ap%i',im1.fitsfile)
ext = ('.fits','-sky.fits','-lamp.fits')
h = im1.header
for i, p_ap in enumerate(self.pextract):
for j in range(p_ap.shape[1]):
spec = p_ap[:,j]
write_fits((pstub + ext[i]) % j, h, spec)
nstub = self.paths['out'] + re.sub('.fits','-ap%i',im2.fitsfile)
h = im2.header
for i, n_ap in enumerate(self.nextract):
for j in range(n_ap.shape[1]):
spec = n_ap[:,j]
write_fits((nstub + ext[i]) % j, h, spec)
def set_spectrum(self, spec):
self.spec_index = self.speclist.index(spec)
try:
tmp = ExtractedSpectrum(self.paths['out']+self.speclist[self.spec_index] + '.fits')
except:
popup = WarningDialog(text="You haven't extracted that spectrum yet!")
popup.open()
return
if self.current_spectrum:
self.ids.specdisplay.remove_plot(self.current_spectrum.plot)
self.current_spectrum = tmp
self.current_spectrum.plot = MeshLinePlot(color=[.9,1,1,1])
if not self.current_spectrum.wav:
self.wmin = 0
self.wmax = len(self.current_spectrum.spec)-1
self.current_spectrum.wav = range(self.wmax)
else:
self.wmin = self.current_spectrum.wav.min()
self.wmax = self.current_spectrum.wav.max()
self.dmin, self.dmax = minmax(self.current_spectrum.spec)
self.current_spectrum.plot.points = zip(self.current_spectrum.wav, self.current_spectrum.spec)
self.ids.specdisplay.add_plot(self.current_spectrum.plot)
def fit_trace(self):
if not self.fit_params or self.fit_params['shape'] not in ('Gaussian','Lorentzian'):
popup = WarningDialog(text='Make sure you set up your fit parameters!')
popup.open()
return
pos = {'pos':[x.slider.value for x in self.apertures['pos']], \
'neg':[x.slider.value for x in self.apertures['neg']]}
for x in self.trace_lines:
if x in self.ids.the_graph.plots:
self.ids.the_graph.remove_plot(x)
if self.fit_params.get('man',False):
popup = DefineTrace(npos=len(self.apertures['pos']), \
nneg=len(self.apertures['neg']), imtexture = self.iregion)
popup.bind(on_dismiss = self.manual_trace(popup.tracepoints))
popup.open()
return
self.xx, self.fit_params['pmodel'], self.fit_params['nmodel'] = \
fit_multipeak(self.tracepoints, pos = pos, wid = self.fit_params['wid'], \
ptype = self.fit_params['shape'])
self.trace_lines[0].points = zip(self.xx, self.fit_params['pmodel'](self.xx))
self.trace_lines[1].points = zip(self.xx, self.fit_params['nmodel'](self.xx))
self.ids.the_graph.add_plot(self.trace_lines[0])
self.ids.the_graph.add_plot(self.trace_lines[1])
def set_imagepair(self, val):
if not self.theapp.current_target:
popup = WarningDialog(text='You need to select a target (on the Observing Screen) before proceeding!')
popup.open()
return
pair_index = self.pairstrings.index(val)
fitsfile = self.paths['out']+re.sub(' ','',re.sub('.fits','',val))+'.fits'
if not path.isfile(fitsfile):
im1, im2 = [x for x in copy.deepcopy(self.extract_pairs[pair_index])]
im1.load(); im2.load()
#if self.current_flats:
# tmp = im_divide(im1, self.current_flats)
# im1.header, im1.data_array = tmp
# tmp = im_divide(im2, self.current_flats)
# im2.header, im2.data_array = tmp
im_subtract(im1, im2, outputfile=path.join(self.paths['out'],fitsfile))
self.current_impair = FitsImage(path.join(self.paths['out'],fitsfile), load=True)
self.ids.ipane.load_data(self.current_impair)
self.imwid, self.imht = self.current_impair.dimensions
if self.current_impair.get_header_keyword('EXREGX1'):
for x in ['x1', 'y1', 'x2', 'y2']:
tmp = self.current_impair.get_header_keyword('EXREG'+x.upper())
if tmp[0] is not None:
self.set_coord(x, tmp[0])
def set_imagepair(self, val):
if not self.theapp.current_target:
popup = WarningDialog(text='You need to select a target (on the Observing Screen) before proceeding!')
popup.open()
return
self.pair_index = self.pairstrings.index(val)
fitsfile = self.paths['out']+re.sub(' ','',re.sub('.fits','',val))+'.fits'
if not path.isfile(fitsfile):
popup = WarningDialog(text='You have to select an extraction'\
'region for this image pair \nbefore you can move on to this step.')
popup.open()
return
self.current_impair = FitsImage(fitsfile)
self.region = self.current_impair.get_header_keyword(*('EXREG' + x for x in ['X1','Y1','X2','Y2']))
if not any(self.region):
popup = WarningDialog(text='You have to select an extraction'\
'region for this image pair \nbefore you can move on to this step.')
popup.open()
return
self.current_impair.load()
idata = ''.join(map(chr,self.current_impair.scaled))
self.itexture.blit_buffer(idata, colorfmt='luminance', bufferfmt='ubyte', \
size = self.current_impair.dimensions)
self.trace_axis = 0 if get_tracedir(self.current_target.instrument_id) == 'vertical' else 1
#tmp = self.current_impair.data_array[self.region[1]:self.region[3]+1,self.region[0]:self.region[2]+1]
#self.extractregion = med_normal(tmp)
tmp = self.theapp.extract_pairs[self.pair_index]
if self.trace_axis:
#self.trace_axis = 1
reg = [self.region[x] for x in [1, 0, 3, 2]]
self.extractregion = make_region(tmp[0], tmp[1], reg, self.current_flats)#.transpose()
else:
self.extractregion = make_region(tmp[0], tmp[1], self.region, self.current_flats).transpose()
reg = self.region[:]
reg[2] = reg[2] - reg[0]
reg[3] = reg[3] - reg[1]
self.iregion = self.itexture.get_region(*reg)
dims = [[0,0],list(self.extractregion.shape)]
dims[0][self.trace_axis] = 0.4 * self.extractregion.shape[self.trace_axis]
dims[1][self.trace_axis] = 0.6 * self.extractregion.shape[self.trace_axis]
self.tracepoints = robm(self.extractregion[dims[0][0]:dims[1][0]+1,\
dims[0][1]:dims[1][1]+1], axis = self.trace_axis)
self.tplot.points = interp_nan(list(enumerate(self.tracepoints)))
pxs, self.tracepoints = zip(*self.tplot.points)
self.drange = minmax(self.tracepoints)
self.ids.the_graph.add_plot(self.tplot)