def make_rrl_finder_chart(target_stem, ra, dec):
target_stem = re.sub('\.', '_', target_stem)
target_stem = re.sub('-', '', target_stem)
target_stem = sgr_setup.get_target_stem(target_stem)
coords = str(ra) +' ' +str(dec)
ra= SkyCoord(coords, unit=(u.deg, u.deg)).ra
dec = SkyCoord(coords, unit=(u.deg, u.deg)).dec
fitsfile = target_stem + '_e1_3p6um.fits'
print ra, dec
inputfile = fitsfile
fitsdata = astropy.io.fits.open(fitsfile)[0].data
interval = ZScaleInterval()
zmin, zmax = interval.get_limits(fitsdata)
fig = mp.figure(figsize=(10,10))
mosaic = aplpy.FITSFigure(inputfile, figure = fig)
mosaic.show_grayscale(vmin=zmin,vmax=zmax, invert='true') ### manually implimenting zscale
mosaic.tick_labels.set_font(size='small')
mosaic.tick_labels.set_xformat("hh:mm:ss")
mosaic.set_theme('publication')
mosaic.show_markers(ra.deg, dec.deg, edgecolor='magenta', facecolor='magenta', marker='o', s=100, alpha=0.3)
mosaic.show_markers(ra.deg, dec.deg, edgecolor='magenta', facecolor='magenta', marker='o', s=300, alpha=0.1)
#mosaic.save(target_stem + '_location.pdf')
mp.show()
def make_rrl_finder_chart(target_stem, ra, dec):
target_stem = re.sub('\.', '_', target_stem)
target_stem = re.sub('-', '', target_stem)
target_stem = sgr_setup.get_target_stem(target_stem)
coords = str(ra) + ' ' + str(dec)
ra = SkyCoord(coords, unit=(u.deg, u.deg)).ra
dec = SkyCoord(coords, unit=(u.deg, u.deg)).dec
fitsfile = target_stem + '_e1_3p6um.fits'
print ra, dec
inputfile = fitsfile
fitsdata = astropy.io.fits.open(fitsfile)[0].data
interval = ZScaleInterval()
zmin, zmax = interval.get_limits(fitsdata)
fig = mp.figure(figsize=(10, 10))
mosaic = aplpy.FITSFigure(inputfile, figure=fig)
mosaic.show_grayscale(vmin=zmin, vmax=zmax,
invert='true') ### manually implimenting zscale
mosaic.tick_labels.set_font(size='small')
mosaic.tick_labels.set_xformat("hh:mm:ss")
mosaic.set_theme('publication')
mosaic.show_markers(ra.deg,
dec.deg,
edgecolor='magenta',
facecolor='magenta',
marker='o',
s=100,
alpha=0.3)
mosaic.show_markers(ra.deg,
dec.deg,
edgecolor='magenta',
facecolor='magenta',
marker='o',
s=300,
alpha=0.1)
#mosaic.save(target_stem + '_location.pdf')
mp.show()
target = sys.argv[4]
else:
target = target_name
outname = re.sub(' ', '_', target)
is_hrs = re.search(":", coords)
if (is_hrs != None):
ra = SkyCoord(coords, unit=(u.hourangle, u.deg)).ra
dec = SkyCoord(coords, unit=(u.hourangle, u.deg)).dec
is_deg = re.search("d", coords)
if (is_deg != None):
ra = SkyCoord(coords, unit=(u.deg, u.deg)).ra
dec = SkyCoord(coords, unit=(u.deg, u.deg)).dec
image_stem = sgr_setup.get_target_stem(target)
fitsfile = image_stem + '_e1_3p6um.fits'
print ra, dec, period
fig = aplpy.FITSFigure(fitsfile)
rr_x, rr_y = fig.world2pixel(ra, dec)
print rr_x, rr_y
mch_file = image_stem + '_3p6um_cal.mch'
phot_file = image_stem + '_3p6um.cal'
num_frames = len(glob.glob('*_dn.cal'))
file_list = []
mch_file = open(mch_file, 'r')
def robust_offset_calculator(row):
target_stem = row.ix[0, 'survey_ident']
target_stem = re.sub('\.', '_', target_stem)
target_stem = re.sub('-', '', target_stem)
target_stem = sgr_setup.get_target_stem(target_stem)
file_list = glob.glob('*.alf')
num_frames = len(file_list)
print num_frames
### Reading in the daomaster raw file here
if ((num_frames % 6) == 0):
n_lines_raw = num_frames / 6.0 + 1.0
else:
n_lines_raw = np.ceil(num_frames / 6.0)
print n_lines_raw
with open(target_stem + '_3p6um_cal.raw') as raw_file:
lines = []
## skip the 3 header lines if they exist
firstline = raw_file.readline()
isheader = re.search('NL', firstline)
if (isheader != None):
for count in np.arange(0, 2):
raw_file.readline()
else:
raw_file.seek(0)
while True:
line = list(itertools.islice(raw_file, n_lines_raw))
if line:
lines.append(line)
else:
break
num_stars = len(lines)
objects = np.zeros((num_stars, (num_frames * 2) + 3))
for star in np.arange(0, num_stars):
data = "".join(lines[star])
data = data.split()
objects[star][0] = data[0] ## ID
objects[star][1] = data[1] ## XC
objects[star][2] = data[2] ## YC
for epoch in np.arange(0, (num_frames * 2), 2):
objects[star][epoch + 3] = data[epoch + 3] ## mag
objects[star][epoch + 4] = data[epoch + 4] ## err
epoch1 = objects[:, 3]
epoch1_err = objects[:, 4]
min_epoch1 = min(epoch1)
offsets = np.zeros(num_frames)
sdev_offsets = np.zeros(num_frames)
for epoch in np.arange(
2, (num_frames * 2),
2): ## starting from 1 because don't match epoch 1 to itself
difference = epoch1 - objects[:, epoch + 3]
ediff = np.sqrt(epoch1_err**2 + objects[:, epoch + 4]**2)
clipped = sigma_clip(difference, sig=4., iters=100)
av_diff = np.ma.mean(clipped)
sdev_diff = np.ma.std(clipped)
offsets[(epoch / 2.)] = av_diff
sdev_offsets[(epoch / 2.)] = sdev_diff
print "Epoch " + str((epoch / 2.) + 1) + " offset " + str(
av_diff) + " sdev " + str(sdev_diff)
mp.close('all')
axp1 = mp.subplot(111)
mp.axis([min_epoch1, min_epoch1 + 8, av_diff - 1, av_diff + 1])
axp1.errorbar(epoch1, clipped, yerr=ediff, color='grey', ls='none')
axp1.plot(epoch1, clipped, 'k.', ls='none')
axp1.axhline(av_diff, color='r', ls='--')
axp1.axhline(av_diff + 2 * sdev_diff, color='b', ls='--')
axp1.axhline(av_diff - 2 * sdev_diff, color='b', ls='--')
mp.show()
def calibrate_and_plot(row):
directory_switcher(row, 0)
survey_ident = row['survey_ident']
ra = row['ra']
dec = row['dec']
period = row['period']
target_name = row['target_name']
channel = 1 ### hardwired to channel 1 here
if (channel == 1 or channel == '3p6um' or channel == '1'):
new_chan = '3p6um'
elif (channel == 2 or channel == '4p5um' or channel == '2'):
new_chan = '4p5um'
else:
print 'invalid channel'
exit(1)
if new_chan == '3p6um': num_chan = 1
if new_chan == '4p5um': num_chan = 2
target_stem = sgr_setup.get_target_stem(survey_ident)
dir_name = re.sub('\.', '_', survey_ident)
dir_name = re.sub('-', '', dir_name)
directory = '/Users/vs522/Dropbox/TRACCS/TRACCS_Output/' + dir_name + '/' + dir_name + '_' + new_chan
os.chdir(directory)
if (len(glob.glob(target_stem + '*' + new_chan + '*.alf')) == 0):
print 'You need to run ALLFRAME before you can calibrate the photometry'
print 'This is the CALIBRATION ONLY script'
print 'Run ``globular_pipeline_anychannel.py`` to do the combined photometry and calibration script'
exit(1)
flux_epoch_1 = target_stem + '_e1_' + new_chan
aperture_correction_photometry.apcor_photo(flux_epoch_1)
apcor, sdev_apcor = calculate_aperture_correction_testing.calc_apcor(
flux_epoch_1, 'apcor.raw', 3, target_stem, 0.3)
apply_aperture_correction.apply_apcor(
target_stem + '_e1_' + new_chan + '_dn.alf', apcor, num_chan)
calibrate_all_epochs.calibrate(target_stem + '_' + new_chan + '.mch')
all_location_corrections.location_corr(target_stem, new_chan)
robust_offset_calculator(row)
#make_rrl_finder_chart(target_stem, ra, dec)
mch_file = target_stem + '_3p6um_cal.mch'
phot_file = target_stem + '_3p6um.cal'
make_rrl_finder_chart(survey_ident, ra, dec)
mag, err = find_which_star(target_stem, ra, dec)
mjds = grab_mjds(mch_file)
#plot_a_lc(target_stem, target_name, period, mjds, mag, err)
#mosaic.save(target_stem + '_location.pdf')
offsets_df = pd.read_csv(target_stem + '_3p6um_cal.off_log',
delim_whitespace=True,
header=None,
names=('obs', 'offset', 'sdev', 'nstars'))
mp.close()
mp.clf()
mp.errorbar(offsets_df.obs,
offsets_df.offset,
yerr=offsets_df.sdev,
color='k',
ls='none')
mp.plot(offsets_df.obs, offsets_df.offset, 'ko', ls='none')
mp.axhline(offsets_df.offset.mean(), color='r', ls='--')
mp.axhline(offsets_df.offset.mean() - 2 * offsets_df.offset.std(),
color='b',
ls='--')
mp.show()
#plot_existing_lc(row, 1, 1.5/12.)
avmag1, sdev1 = plot_new_lc(row, mjds, mag, err, period, target_name, 1,
1.5 / 12.)
print avmag1, sdev1
row.av_3p6 = avmag1
row.sdev_3p6 = sdev1
return (row)
import all_location_corrections import os target_name = sys.argv[1] channel = sys.argv[2] if (channel == 1 or channel == '3p6um' or channel == '1'): new_chan = '3p6um' elif (channel == 2 or channel == '4p5um' or channel == '2'): new_chan = '4p5um' else: print 'invalid channel' exit(1) if new_chan == '3p6um': num_chan = 1 if new_chan == '4p5um': num_chan = 2 target_stem = sgr_setup.get_target_stem(target_name) if (len(glob.glob(target_stem + '*' + channel +'*.alf'))==0): print 'You need to run ALLFRAME before you can calibrate the photometry' print 'This is the CALIBRATION ONLY script' print 'Run ``globular_pipeline_anychannel.py`` to do the combined photometry and calibration script' exit(1) ## Convert the images to counts and give them sensible names ## Also cleans up old runs ## for omegaCen only - doesn't apply for Sgr stream, orphan stream etc: ## Aperture correction
def robust_offset_calculator(row):
target_stem = row.ix[0, 'survey_ident']
target_stem = re.sub('\.', '_', target_stem)
target_stem = re.sub('-', '', target_stem)
target_stem = sgr_setup.get_target_stem(target_stem)
file_list = glob.glob('*.alf')
num_frames = len(file_list)
print num_frames
### Reading in the daomaster raw file here
if ((num_frames % 6 ) == 0):
n_lines_raw = num_frames / 6.0 + 1.0
else:
n_lines_raw = np.ceil(num_frames / 6.0)
print n_lines_raw
with open(target_stem + '_3p6um_cal.raw') as raw_file:
lines = []
## skip the 3 header lines if they exist
firstline = raw_file.readline()
isheader = re.search('NL', firstline)
if (isheader!=None):
for count in np.arange(0,2): raw_file.readline()
else:
raw_file.seek(0)
while True:
line = list(itertools.islice(raw_file, n_lines_raw))
if line:
lines.append(line)
else:
break
num_stars = len(lines)
objects = np.zeros((num_stars, (num_frames*2) + 3))
for star in np.arange(0,num_stars):
data = "".join(lines[star])
data = data.split()
objects[star][0] = data[0] ## ID
objects[star][1] = data[1] ## XC
objects[star][2] = data[2] ## YC
for epoch in np.arange(0,(num_frames*2), 2):
objects[star][epoch + 3] = data[epoch + 3] ## mag
objects[star][epoch + 4] = data[epoch + 4] ## err
epoch1 = objects[:,3]
epoch1_err = objects[:,4]
min_epoch1 = min(epoch1)
offsets = np.zeros(num_frames)
sdev_offsets = np.zeros(num_frames)
for epoch in np.arange(2, (num_frames*2), 2): ## starting from 1 because don't match epoch 1 to itself
difference = epoch1 - objects[ : , epoch + 3]
ediff = np.sqrt(epoch1_err**2 + objects[ : , epoch + 4]**2)
clipped = sigma_clip(difference, sig = 4., iters=100)
av_diff = np.ma.mean(clipped)
sdev_diff = np.ma.std(clipped)
offsets[(epoch/2.)] = av_diff
sdev_offsets[(epoch/2.)] = sdev_diff
print "Epoch " + str((epoch/2.)+1) + " offset " +str(av_diff) + " sdev " + str(sdev_diff)
mp.close('all')
axp1 = mp.subplot(111)
mp.axis([min_epoch1, min_epoch1+8, av_diff - 1, av_diff + 1])
axp1.errorbar(epoch1, clipped, yerr = ediff, color='grey', ls='none')
axp1.plot(epoch1, clipped, 'k.', ls='none')
axp1.axhline(av_diff, color='r', ls='--')
axp1.axhline(av_diff+2*sdev_diff, color='b', ls='--')
axp1.axhline(av_diff-2*sdev_diff, color='b', ls='--')
mp.show()
def calibrate_and_plot(row):
directory_switcher(row, 0)
survey_ident = row['survey_ident']
ra = row['ra']
dec = row['dec']
period = row['period']
target_name = row['target_name']
channel = 1 ### hardwired to channel 1 here
if (channel == 1 or channel == '3p6um' or channel == '1'): new_chan = '3p6um'
elif (channel == 2 or channel == '4p5um' or channel == '2'): new_chan = '4p5um'
else:
print 'invalid channel'
exit(1)
if new_chan == '3p6um': num_chan = 1
if new_chan == '4p5um': num_chan = 2
target_stem = sgr_setup.get_target_stem(survey_ident)
dir_name = re.sub('\.', '_', survey_ident)
dir_name = re.sub('-', '', dir_name)
directory = '/Users/vs522/Dropbox/TRACCS/TRACCS_Output/' + dir_name + '/' + dir_name + '_' + new_chan
os.chdir(directory)
if (len(glob.glob(target_stem + '*' + new_chan +'*.alf'))==0):
print 'You need to run ALLFRAME before you can calibrate the photometry'
print 'This is the CALIBRATION ONLY script'
print 'Run ``globular_pipeline_anychannel.py`` to do the combined photometry and calibration script'
exit(1)
flux_epoch_1 = target_stem + '_e1_' + new_chan
aperture_correction_photometry.apcor_photo(flux_epoch_1)
apcor, sdev_apcor = calculate_aperture_correction_testing.calc_apcor(flux_epoch_1, 'apcor.raw', 3, target_stem, 0.3)
apply_aperture_correction.apply_apcor(target_stem + '_e1_' + new_chan + '_dn.alf', apcor, num_chan)
calibrate_all_epochs.calibrate(target_stem + '_' + new_chan + '.mch')
all_location_corrections.location_corr(target_stem, new_chan)
robust_offset_calculator(row)
#make_rrl_finder_chart(target_stem, ra, dec)
mch_file = target_stem + '_3p6um_cal.mch'
phot_file = target_stem + '_3p6um.cal'
make_rrl_finder_chart(survey_ident, ra, dec)
mag, err = find_which_star(target_stem, ra, dec)
mjds = grab_mjds(mch_file)
#plot_a_lc(target_stem, target_name, period, mjds, mag, err)
#mosaic.save(target_stem + '_location.pdf')
offsets_df = pd.read_csv(target_stem + '_3p6um_cal.off_log', delim_whitespace=True, header=None, names=('obs', 'offset', 'sdev', 'nstars'))
mp.close()
mp.clf()
mp.errorbar(offsets_df.obs, offsets_df.offset, yerr=offsets_df.sdev, color='k', ls='none')
mp.plot(offsets_df.obs, offsets_df.offset, 'ko', ls='none')
mp.axhline(offsets_df.offset.mean(), color='r', ls='--')
mp.axhline(offsets_df.offset.mean()- 2*offsets_df.offset.std(), color='b', ls='--')
mp.show()
#plot_existing_lc(row, 1, 1.5/12.)
avmag1, sdev1 = plot_new_lc(row, mjds, mag, err, period, target_name, 1, 1.5/12.)
print avmag1, sdev1
row.av_3p6 = avmag1
row.sdev_3p6 = sdev1
return(row)
import sgr_pre_allframe_matching
import traccs_master_image_phot
target_name = sys.argv[1]
channel = sys.argv[2]
if (channel == 1 or channel == '3p6um' or channel == '1'): new_chan = '3p6um'
elif (channel == 2 or channel == '4p5um' or channel == '2'): new_chan = '4p5um'
else:
print 'invalid channel'
exit(1)
if new_chan == '3p6um': num_chan = 1
if new_chan == '4p5um': num_chan = 2
target_stem = sgr_setup.get_target_stem(target_name)
print target_stem
### Checking that you've made a good psf for epoch 1
if ((os.path.isfile(target_stem + '_e1_' + new_chan + '_dn.psf') == False)
and os.path.isfile('master_' + new_chan + '.psf') == False):
print 'You need to make the master psf first!!'
exit(1)
## Now copy the psf to each epoch
if (os.path.isfile('master_' + new_chan + '.psf') == False):
shutil.copy(target_stem + '_e1_' + new_chan + '_dn.psf',
'master_' + new_chan + '.psf')