def test_standards_present():
for s in list(STDS_DWARF_SPEX_KEYS.keys()):
sp = splat.Spectrum(STDS_DWARF_SPEX_KEYS[s])
assert type(sp) == splat.Spectrum
for s in list(STDS_SD_SPEX_KEYS.keys()):
sp = splat.Spectrum(STDS_SD_SPEX_KEYS[s])
assert type(sp) == splat.Spectrum
for s in list(STDS_ESD_SPEX_KEYS.keys()):
sp = splat.Spectrum(STDS_ESD_SPEX_KEYS[s])
assert type(sp) == splat.Spectrum
return
def readSpectrum(**kwargs):
""" Simple demo for plotting Apogee spectra, including visits
HDU0: master header with target information
HDU1: spectra: combined and individual
(Each spectrum has 8575 columns with the spectra, and 2+NVISITS rows.
The first two rows are both combined spectra, with different weighting:
first row uses pixel-based weighting, while second uses a more "global" weighting)
HDU2: error spectra
HDU3: mask spectra
HDU4: sky spectra
HDU5: sky error spectra
HDU6: telluric spectra
HDU7: telluric error spectra
HDU8: table with LSF coefficients
HDU9: table with RV/binary information
According to https://goo.gl/rLXEuc
"""
#not sure
" conversion from pixel to wavelength, info available in the hdu header"
crval = spectra.header['CRVAL1']
cdelt = spectra.header['CDELT1']
wave = np.array(
pow(10, crval + cdelt * np.arange(spectra.header['NAXIS1'])) /
10000) * u.micron #microns
# convert fluxes from (10^-17 erg/s/cm^2/Ang) to ( erg/s/cm^2/Mircon)
spectras = [
1e-13 * np.array(f) * u.erg / u.s / u.centimeter**2 / u.micron
for f in spectra.data
]
noises = [
1e-13 * np.array(f) * u.erg / u.s / u.centimeter**2 / u.micron
for f in noise.data
]
skys = [
1e-13 * np.array(f) * u.erg / u.s / u.centimeter**2 / u.micron
for f in sky.data
]
#create a splat Spectrum object just for the combine
combined = splat.Spectrum(wave=wave,
flux=spectra.data[0],
noise=noise.data[0])
#create APOGEE spectrum object
sp= Spectrum(wave=combined.wave, combined=combined, noise=noises, sky=skys, visits= spectras, \
nvisits = len(spectra.data))
print
return sp
def test_plotBatch():
data_folder = '/Users/adam/projects/splat/adddata/done/daniella/'
files = glob.glob(data_folder + '*.fits')
plotBatch(files,
classify=True,
output=out_folder + 'plotBatch_test1.pdf',
telluric=True)
plotBatch(data_folder + '*.fits',
classify=True,
output=out_folder + 'plotBatch_test2.pdf',
noise=True)
splist = [splat.Spectrum(file=f) for f in files]
plotBatch(splist,
classify=True,
output=out_folder + 'plotBatch_test3.pdf',
features=['h2o', 'feh', 'co'],
legend=[s.name for s in splist])
return
def test_plotSequence():
sp = splat.Spectrum(10001)
splat.plotSequence(sp, output=out_folder + 'plotSequence_test1.pdf')
splat.plotSequence(sp,
type_range=3,
output=out_folder + 'plotSequence_test2.png')
data_folder = '/Users/adam/projects/splat/adddata/done/daniella/'
files = glob.glob(data_folder + '*.fits')
splat.plotSequence(files[0],
telluric=True,
stack=0.7,
spt='M0',
output=out_folder + 'plotSequence_test3.eps')
sp = splat.getSpectrum(shortname='0415-0935')[0]
splat.plotSequence(sp,
telluric=True,
stack=0.3,
output=out_folder + 'plotSequence_test4.eps')
splat.plotSequence(sp, telluric=True, stack=0.3)
return
def test_catalog():
"""" a bunch of scripts """
table = ascii.read('apogee_reduced.csv')
for ind, locid, coords in zip(table['ASPCAP_ID'], table['LOCATION_ID'],
table['APOGEE_ID']):
downloadSpectra(ind, locid, coords)
smaller = table['CATALOG', 'CATALOG_NAME', 'SPTYPE', 'APOGEE_ID', 'GLAT',
'J', 'TEFF']
# for row in smaller:
# print row
l2 = readSpectrum(filename=HOME + 'apStar-r6-2M00452143+1634446.fits')
m7 = readSpectrum(filename=HOME + 'apStar-r6-' + '2M07140394+3702459.fits')
m6 = readSpectrum(filename=HOME + 'apStar-r6-' + '2M22400144+0532162.fits')
# m4=readSpectrum(filename=HOME+'apStar-r6-'+'2M05420897+1229252.fits')
#m3=readSpectrum(filename=HOME+'apStar-r6-'+'2M10121768-0344441.fits')
# m2=readSpectrum(filename=HOME+'apStar-r6-'+'2M11052903+4331357.fits')
l1 = readSpectrum(filename=HOME + 'apStar-r6-' + '2M06154934-0100415.fits')
#f=plt.figure()
#ax= f.add_subplot(111)
#ax.set_xlim([1.5, 1.7])
#ax.plot(l2.combined.wave, l2.combined.flux, label='$L2$)
#sp=smooth(l2.combined, l2.sky)
#splat.plotSpectrum(sp, xrange=[1.5, 1.55])
spectra = [l2.combined, l1.combined, m7.combined, m6.combined]
labels = [
'$L2 \gamma $ J00452143+1634446', '$L1$ J06154934-0100415',
r'$M7 \beta $ J07140394+3702459', '$M6$ J22400144+0532162'
]
colors = ['r', 'g', 'b', 'k']
counter = 0
for f in glob.glob(HOME + '/*'):
if counter < 8:
try:
sp = readSpectrum(filename=f)
c = 'c'
spectra.append(sp.combined)
colors.append(c)
labels.append('unknown')
except:
continue
counter = counter + 1
splat.plotSpectrum(spectra, filename='apogee_lines.pdf',\
labels=labels, colors=colors,xrange=[1.603, 1.608], yrange=[0, 0],
labelLocation='outside', ylabel='Normalized Flux+c', figsize=(12, 6))
fig = plt.figure(figsize=(10, 6))
ax1 = fig.add_subplot(111)
#ax2 =fig.add_subplot(222)
plot = ax1.scatter(table['J'] - table['H'],
table['J'],
c=table['GLAT'],
s=50,
cmap='rainbow')
ax1.set_xlabel('J-H')
ax1.set_ylabel('J')
ax1.set_xlim(0.0, 1.5)
ax1.set_ylim(4, 17)
ax = plt.gca()
ax.invert_yaxis()
clb = fig.colorbar(plot)
clb.ax.set_title('GLAT')
plt.title('SAMPLE')
#ax2.scatter(table['GLAT'], table['GLON'], s=50)
plt.show()
#smaller.more()
# for ind, locid, coords in zip(table['ASPCAP_ID'], table['LOCATION_ID'], table['APOGEE_ID']):
# downloadSpectra(ind,locid, coords)
splat_names = [
'J03444306+3137338', 'J05420897+1229252', 'J10121791-0344435',
'J10285555+0050275', 'J11052903+4331357'
]
#short_names=[createShortname(s) for s in splat_names]
#print short_names
tables = vstack(
[splat.searchLibrary(designation=s)[0] for s in splat_names])
spectra = [splat.Spectrum(s) for s in tables['DATA_FILE']]
print tables['SPEX_TYPE']
#=[splat.Spectrum(s) for s in spectra]
#splat.plotSpectrum(spcs)
# print short_names
# print spectra
return
def __init__(self, **kwargs):
self._wave = kwargs.get('wave', None)
self._flux = kwargs.get('flux', None)
self._contam = kwargs.get('contam', None)
self._noise = kwargs.get('noise', None)
self._snr = None
self._empty_flag = None
self._splat_spectrum = None
self._filename = None
self._filepath = None
self._snr_histogram = None
self._spectrum_image_path = None
self.two_d_spectrum = None
self._survey = None
self._sensitivity = None
self._spectrum_image_path = None
self._indices = None
self._spectral_type = kwargs.get('spt', None)
self._best_fit_line = None
self.is_ucd = kwargs.get('is_ucd', False) #flag for UCD candidates
#load spectrum if given filename
if 'filepath' in kwargs: self._filepath = kwargs.get('filepath', None)
if 'filename' in kwargs: self._filename = kwargs.get('filename', None)
if 'name' in kwargs: self._filename = kwargs.get('name', None)
#print (return_path(self._filename))
if (self._filename is not None):
self.filename = self._filename
if (self._filepath is not None):
self.filepath = self._filepath
if (self._wave
is not None) and (self.filepath is None) and (not self.is_ucd):
self._compute_snr()
self._splat_spectrum = splat.Spectrum(wave=self._wave,
flux=self._flux,
noise=self._noise,
instrument='WFC3')
self._best_fit_line = fit_a_line(self)
ftest = f_test(self)
for key in ftest.keys():
setattr(self, key, ftest[key])
self.normalize()
if self._spectral_type is not None:
self.spectral_type = self._spectral_type
#keep a copy of this object as an attribute
#read the file locallly for UCDs
if (self._wave is None) and self.is_ucd:
row = (UCD_SPECTRA[UCD_SPECTRA.grism_id == self._filename]).iloc[0]
self._wave = row.wave
self._flux = row.flux
self._noise = row.noise
self._contam = row.contam
self._compute_snr()
self._splat_spectrum = splat.Spectrum(wave=self._wave,
flux=self._flux,
noise=self._noise,
instrument='WFC3')
self._best_fit_line = fit_a_line(self)
ftest = f_test(self)
for key in ftest.keys():
setattr(self, key, ftest[key])
self.normalize()
self.original = copy.deepcopy(self)
def splat_spectrum(self):
return splat.Spectrum(wave=self._wave,
flux=self._flux,
noise=self._noise,
instrument='WFC3-G141')
def load_spectra():
#'/Users/guillaumeshippee/Desktop/splat-master/reference/Spectra/10001_10443.fits' #change
if request.method == 'GET':
return render_template('input.html', error='')
else:
# for k in list(request.form.keys()):
# print(k,request.form[k])
# search by file "upload"
if request.form['submit'] == 'Load File':
try:
path = request.form['path']
sp = splat.Spectrum(file=str(path))
sp = [sp]
except:
return render_template(
'input.html', error="\n\nProblem with file upload button")
# search by file path specification
if request.form['submit'] == 'Load File ':
try:
path = request.form['path']
sp = splat.Spectrum(file=str(path))
sp = [sp]
except:
return render_template(
'input.html',
error="\n\nProblem with file path specification")
# search by spectrum key
if request.form['submit'] == 'Load by ID':
try:
sp = splat.Spectrum(int(str(request.form['key'])))
sp = [sp]
except:
return render_template(
'input.html', error="\n\nProblem with key specification")
# search by date observed
if request.form['submit'] == 'Load by Date':
try:
sp = splat.getSpectrum(date=str(request.form['date']))
except:
return render_template(
'input.html', error="\n\nProblem with key specification")
# search by shortname
elif request.form['submit'] == 'Load by Shortname':
try:
sp = splat.getSpectrum(
shortname=str(request.form['shortname']))
except:
return render_template(
'input.html',
error="\n\nProblem with specifying file by shortname")
# search by name
elif request.form['submit'] == 'Load by Name':
try:
sp = splat.getSpectrum(name=str(request.form['name']))
except:
return render_template(
'input.html',
error="\n\nProblem with specifying file by name")
# search by options
elif request.form['submit'] == 'Load by Options':
sp1 = request.form['sp1']
sp2 = request.form['sp2']
mag1 = request.form['mag1']
mag2 = request.form['mag2']
if sp2 == '':
sp = sp1
elif sp1 == '':
sp2 = sp1
elif sp1 == '' and sp2 == '':
sp = ''
else:
sp = [sp1, sp2]
if mag2 == '':
mag = mag1
elif sp1 == '':
mag2 = mag1
elif sp1 == '' and sp2 == '':
mag = ''
else:
mag = [mag1, mag2]
kwargs = {
'spt': sp,
'jmag': mag,
'snr': request.form['snr'],
'date': request.form['date']
}
kwargs = {k: v for k, v in kwargs.items() if v}
try:
sp = splat.getSpectrum(**kwargs)
except:
return render_template('input.html',
error="\n\nProblem with option search")
# lucky pull
elif request.form['submit'] == 'Get Lucky!':
sp = splat.getSpectrum(lucky=True)
if len(sp) == 0:
return render_template(
'input.html',
error="\n\nNo spectra matched search constratins")
try:
tab = []
for s in sp:
spectral_type = splat.classifyByStandard(s)[0]
mpl_fig = splot.plotSpectrum(s, web=True, uncertainty=True)[0]
bokehfig = mpl.to_bokeh(fig=mpl_fig)
bokehfig.set(x_range=Range1d(.8, 2.4),
y_range=Range1d(0,
s.fluxMax().value * 1.2))
# sys.stdout = open("out1.txt", "w")
# sys.stdout = sys.__stdout__
# with open("out1.txt", "r") as f:
# content = f.read()
content = s.info(printout=False)
# print(content)
p = Paragraph(text=content)
widget = VBox(bokehfig, p)
tab.append(Panel(child=widget, title=str(s.name)))
# tab.append(Panel(child=widget, title=str(spectral_type)+ " Star"))
plottabs = Tabs(tabs=tab)
script, div_dict = components({"plot": tab})
except:
return render_template('input.html',
error="\n\nProblem Plotting Spectra")
return render_template('output.html',
star_type=spectral_type,
script=script,
div=div_dict)
def plotSequence(*args, **kwargs):
'''
:Purpose: Compares a spectrum to a sequence of standards a batch of spectra into a 2x2 set of PDF files, with options of overplotting comparison spectra, including best-match spectral standards.
:param input: A single or list of Spectrum objects or filenames, or the glob search string for a set of files (e.g., '/Data/myspectra/*.fits').
:type input: required
:param type_range: Number of subtypes to consider above and below best-fit spectral type
:type type_range: optional, default = 2
:param spt: Default spectral type for source; this input skips classifyByStandard
:type spt: optional, default = None
:param output: Filename for output; full path should be include if not saving to current directory. If blank, plot is shown on screen
:type output: optional, default = None (screen display)
Relevant parameters for plotSpectrum may also be passed
:Example:
>>> import glob, splat
>>> files = glob.glob('/home/mydata/*.fits')
>>> sp = splat.plotBatch(files,classify=True,output='comparison.pdf')
>>> sp = splat.plotBatch('/home/mydata/*.fits',classify=True,output='comparison.pdf')
>>> sp = splat.plotBatch([splat.Spectrum(file=f) for f in files],classify=True,output='comparison.pdf')
All three of these commands produce the same result
'''
# check inputs
if len(args) == 0:
raise ValueError(
'\nNeed to provide a spectrum object or filename for plotStandardSequence'
)
parameters = ['type_range']
splat.checkKeys(kwargs, parameters, forcekey=False)
type_range = kwargs.get('type_range', 2)
kwargs['stack'] = kwargs.get('stack', 0.5)
# kwargs['legendLocation']=kwargs.get('legendLocation','outside')
kwargs['telluric'] = kwargs.get('telluric', True)
kwargs['method'] = kwargs.get('method', 'kirkpatrick')
# kwargs['color']=kwargs.get('color','r')
kwargs['colorComparison'] = kwargs.get('colorComparison', 'k')
kwargs['colorScheme'] = kwargs.get('colorScheme', 'winter')
kwargs['figsize'] = kwargs.get('figsize',
[10, 10 * type_range * kwargs['stack']])
kwargs['fontscale'] = kwargs.get('fontscale', 1.5)
# process input
if isinstance(args[0], str):
if len(glob.glob(args[0])) == 0:
raise ValueError(
'\nCannot find input file {} - make sure full path is included'
.format(args[0]))
try:
sp = splat.Spectrum(file=args[0])
except:
raise ValueError(
'\nCould not read in file {} - make sure the file is correctly formatted'
.format(args[0]))
elif isinstance(args[0], splat.Spectrum):
sp = copy.deepcopy(args[0])
else:
raise ValueError('\nInput should be a Spectrum object or filename')
sp.normalize()
# classify by comparison to standards
spt = kwargs.get('spt', splat.classifyByStandard(sp, **kwargs)[0])
if not isinstance(spt, str):
spt = splat.typeToNum(spt)
# produce range of standards for plot
stdnum = numpy.arange(numpy.floor(splat.typeToNum(spt) - type_range),
numpy.ceil(splat.typeToNum(spt) + type_range) + 1)
if numpy.max(stdnum) > 39:
stdnum -= (numpy.max(stdnum) - 39)
if numpy.min(stdnum) < 10:
stdnum += (10 - numpy.min(stdnum))
stdspt = [splat.typeToNum(i) for i in stdnum]
stds = [splat.SPEX_STDS[s] for s in stdspt]
stdlabels = ['{} Standard'.format(s) for s in stdspt]
plotlist = []
labels = []
colors = []
for i, stdsp in enumerate(stds):
plotlist.append([stdsp, sp])
labels.extend([])
fig = splat.plotSpectrum(stds, comparison=sp, labels=stdlabels, **kwargs)
return fig
def plotBatch(*args, **kwargs):
'''
:Purpose: Plots a batch of spectra into a 2x2 set of PDF files, with options of overplotting comparison spectra, including best-match spectral standards.
:param input: A single or list of Spectrum objects or filenames, or the glob search string for a set of files (e.g., '/Data/myspectra/*.fits').
:type input: required
:param output: Filename for PDF file output; full path should be include if not saving to current directory
:type output: optional, default = 'spectra_plot.pdf'
:param comparisons: list of Spectrum objects or filenames for comparison spectra. If comparisons list is shorter than source list, then last comparison source will be repeated. If the comparisons list is longer, the list will be truncated.
:type comparisons: optional, default = None
:param classify: Set to True to classify sources based on comparison to MLT spectral standards following the method of `Kirkpatrick et al. (2010) <http://adsabs.harvard.edu/abs/2010ApJS..190..100K>`_. This option normalizes the spectra by default
:type classify: optional, default = False
:param normalize: Set to True to normalize source and (if passed) comparison spectra.
:type normalize: optional, default = False
:param legend: Set to list of legends for plots. The number of legends should equal the number of sources and comparisons (if passed) in an alternating sequence. T
:type legend: optional, default = displays file name for source and object name for comparison (if passed)
Relevant parameters for plotSpectrum may also be passed
:Example:
>>> import glob, splat
>>> files = glob.glob('/home/mydata/*.fits')
>>> sp = splat.plotBatch(files,classify=True,output='comparison.pdf')
>>> sp = splat.plotBatch('/home/mydata/*.fits',classify=True,output='comparison.pdf')
>>> sp = splat.plotBatch([splat.Spectrum(file=f) for f in files],classify=True,output='comparison.pdf')
All three of these commands produce the same result
'''
# keyword check
parameters = ['output', 'comparisons', 'classify', 'normalize', 'legend']
splat.checkKeys(kwargs, parameters, forcekey=False)
kwargs['layout'] = kwargs.get('layout', [2, 2])
kwargs['fontscale'] = kwargs.get('fontscale', 0.7)
# input check
if len(args) == 0:
print(
'\nNeed to provide a list of spectra or filenames, or a file search string, to use plotBatch'
)
return
kwargs['output'] = kwargs.get('output', 'spectra_plot.pdf')
# break out a list
if isinstance(args[0], list):
inputlist = args[0]
else:
inputlist = args
# if filenames, read in each file to a spectrum object
if isinstance(inputlist[0], str):
# try a glob search string
files = glob.glob(inputlist[0])
if len(files) > 1 or (len(files) == 1
and inputlist[0].find('*') != -1):
inputlist = files
# try reading in files into Spectrum object
try:
splist = [splat.Spectrum(file=f) for f in inputlist]
except:
raise ValueError(
'\nCould not read in list of files - make sure the full path is specified and the files are correctly formatted'
)
# if filenames, read in each file to a spectrum object
elif isinstance(inputlist[0], splat.Spectrum):
splist = copy.deepcopy(inputlist)
else:
print('\nInput should be list of Spectra objects or filenames')
return
# comparison files are present
compflag = False
complist = []
if kwargs.get('comparisons', False) != False:
comp = kwargs.get('comparisons')
if not isinstance(comp, list):
comp = [comp]
if len(comp) < len(splist):
while len(comp) < len(splist):
comp.append(comp[-1])
if isinstance(comp[0], str):
try:
complist = [splat.Spectrum(file=f) for f in comp]
compflag = True
except:
print(
'\nCould not read in comparison files: ignoring comparisons'
)
if isinstance(comp[0], splat.Spectrum):
complist = comp
compflag = True
# set comparison files to be standards for spectral classification
if kwargs.get('classify', False):
complist = []
for sp in splist:
spt = splat.classifyByStandard(sp, method='kirkpatrick')
complist.append(splat.SPEX_STDS[spt[0]])
compflag = True
kwargs['normalize'] = kwargs.get('normalize', True)
# normalize if desired
if kwargs.get('normalize', False):
tmp = [sp.normalize() for sp in splist]
if compflag == True:
tmp = [sp.normalize() for sp in complist]
# prep for plotting
plotlist = []
clist = []
for i, sp in enumerate(splist):
if compflag == True:
plotlist.append([sp, complist[i]])
clist.extend(['k', 'r'])
else:
plotlist.append([sp])
clist.extend(['k'])
# manage legends
if kwargs.get('legend', False) != False:
legends = kwargs.get('legend')
if not isinstance(legends, list):
legends = [legends]
if len(legends) < (len(splist) + len(complist)):
# guess: just left out the comparison legends
if len(complist) > 0 and len(legends) == len(splist):
legtmp = []
for i, l in enumerate(legends):
legtmp.extend([l, '{}'.format(complist[i].name)])
legends = legtmp
else:
# otherwise: pad the remaining legends with the last legend (pairs)
while len(legends) < (len(splist) + len(complist)):
if compflag:
legends.extend([legends[-2], legends[-1]])
else:
legends.extend([legends[-1]])
if len(legends) > (len(splist) + len(complist)):
legends = legends[0:(len(splist) + len(complist))]
else:
legends = []
for i, sp in enumerate(splist):
if compflag == True:
legends.extend([
'{}'.format(os.path.basename(sp.filename)),
'{}'.format(complist[i].name)
])
else:
legends.extend(['{}'.format(os.path.basename(sp.filename))])
# generate pdf
splat.plotSpectrum(plotlist,
multiplot=True,
multipage=True,
legends=legends,
colors=clist,
**kwargs)
return
