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mp_lcfind.py
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mp_lcfind.py
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from __future__ import division
import numpy as np
import astropy
from astroquery.simbad import Simbad
from astroquery.mast import Observations
from astropy.coordinates import SkyCoord
import astropy.coordinates as coord
from astropy import units as u
import os
from astropy.io import fits as pyfits
import time
import traceback
import socket
from urllib.request import urlretrieve
import requests
from mp_tools import *
import copy
import subprocess
import shutil
#moonpydir = os.getcwd()
moonpydir = os.path.realpath(__file__)
moonpydir = moonpydir[:moonpydir.find('/mp_lcfind.py')]
curlscript_dir = moonpydir+'/tess_sector_curlscripts'
if os.path.exists(curlscript_dir) == False:
os.system('mkdir '+curlscript_dir)
#### move existing curlscripts into this directory!
os.system('mv '+moonpydir+'/*curlscript.txt '+curlscript_dir+'/')
hostname = socket.gethostname()
if ('tethys' in hostname) and ('sinica' in hostname):
#moonpydir = '/data/tethys/Documents/Software/MoonPy'
central_data_dir = '/data/tethys/Documents/Central_Data'
elif ('Alexs-MacBook') in hostname:
#moonpydir = '/Users/hal9000/Documents/Software/MoonPy'
central_data_dir = '/Users/hal9000/Documents/Central_Data'
elif 'umbriel' in hostname:
#moonpydir = '/home/cal/ateachey/Documents/MoonPy'
central_data_dir = '/home/cal/ateachey/Documents/Central_Data'
else:
#moonpydir = input('Please specify the MoonPy directory (or hard-code this into moonpy.py): ')
#central_data_dir = input("Please specify a 'central data' directory (or hard-code this into moonpy.py): ")
### store central_data within MoonPy directory
if os.path.exists(moonpydir+'/Central_Data'):
pass
else:
os.system('mkdir '+moonpydir+'/Central_Data')
central_data_dir = moonpydir+'/Central_Data'
#print('moonpydir = ', moonpydir)
#print('Light curves will be stored in '+central_data_dir)
#### THIS IS A MAJOR REWORKING OF THE ORIGINAL mp_lcfind.py (eventually mp_lcfind_deprecated.py).
#### THE KEY IS, The Kplr and k2plr packages are old, not available through conda, and cause all kinds of problems.
#### So this short_cadenceript will get around them entirely, doing it all under the hood, the way you want it.
#### (Note that you'll want to continue structuring the light curves as kplr does it.)
####
#### WILL NEED TO FOLLOW THESE INSTRUCTIONS: https://astroquery.readthedocs.io/en/latest/mast/mast.html
#####################################
# XXXXXXXXXX ALIAS FINDING XXXXXXXX #
#####################################
def Simbad_query(ra, dec, coord_format='degrees', telescope='kepler'):
print('calling mp_lcfind.py/Simbad_query().')
if 'h' in ra or ':' in ra:
coord_format == 'sexagesimal'
ra = ra.replace(' ', '') ### remove the spaces
dec = dec.replace(' ', '') ### remove the spaces
if coord_format=='degrees':
nearby_objects = Simbad.query_region(coord.SkyCoord(ra, dec, unit=(u.deg, u.deg), frame='icrs'), radius='0d0m5s')
elif coord_format=='sexagesimal':
nearby_objects = Simbad.query_region(coord.SkyCoord(str(ra)+' '+str(dec), frame='icrs'), radius='0d0m'+str(search_radius)+'s')
print(nearby_objects)
best_hit = nearby_objects[0][0].decode('UTF-8')
print("best_hit = ", best_hit)
if (telescope.lower() == 'kepler') and (best_hit.lower().startswith('koi') == False) and (best_hit.lower().startswith('kepler') == False) and (best_hit.lower().startswith("kic") == False):
### look for aliases
alias_query = Simbad.query_objectids(str(best_hit))['ID']
search_idx = 0
while search_idx < 10: ### maximum tries
try:
alias = alias_query[search_idx]
if alias.lower().startswith('koi') or alias.lower().statswith('kepler') or alias.lower().startswith("kic"):
best_hit = alias
break
else:
search_idx += 1
except:
break
print("alias = ", alias)
best_hit = alias
if best_hit.lower().startswith('koi'):
object_number = float(best_hit[4:]) ### strips off "KOI-"
### it's valuable to keep the quarters separated like this, because they should be detrended separately!
targtype = 'koi'
object_name = "KOI-"+str(object_number)
elif best_hit.lower().startswith('kepler'):
object_number = str(int(best_hit[7:]))+'b' ### strips off "Kepler-", adds b because we don't care which planet it is.
#object_number = object_number+'b'
targtype = 'planet'
object_name = 'Kepler-'+str(object_number)
elif best_hit.lower().startswith("kic"):
object_number = int(best_hit[4:])
targtype = 'kic'
object_name = 'KIC'+str(object_number)
print("object_number = ", object_number)
elif (telscope.lower() == 'tess') and (best_hit.lower().startswith('toi') == False) and (best_hit.lower().startswith('tic') == False):
### look for aliases if TOI or TIC number was not listed to start.
alias_query = Simbad.query_objectids(str(best_hit))['ID']
search_idx = 0
while search_idx < 10: ### maximum tries
try:
alias = alias_query[search_idx]
print('potential alias: ', alias)
if alias.lower().startswith('toi') or alias.lower().startswith('tic'):
best_hit = alias
break
else:
search_idx += 1
except:
break
print("alias = ", alias)
best_hit = alias
if best_hit.lower().startswith('toi'):
object_number = float(best_hit[4:]) ### strips off "KOI-"
### it's valuable to keep the quarters separated like this, because they should be detrended separately!
targtype = 'toi'
object_name = "TOI-"+str(object_number)
elif best_hit.lower().startswith("tic"):
object_number = int(best_hit[4:])
targtype = 'tic'
object_name = 'TIC'+str(object_number)
try:
print("object_number = ", object_number)
except:
pass
return object_name, object_number
def find_KIC_alias(target_name):
print('calling mp_lcfind.py/find_KIC_alias().')
#### FOR USE WITH KEPLER LIGHT CURVES.
### in order to return a KIC number, you need to remove final letters and decimals.
star_number = target_name
if '.' in star_number:
star_number = star_number[:star_number.find('.')] ### this will remove the decimal and final numbers
if star_number[-1] in ['b', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'j', 'k', 'l']:
star_number = star_number[:-1]
target_aliases = []
alias_search_results = Simbad.query_objectids(star_number)
if type(alias_search_results) != type(None):
for alidx in np.arange(0,np.array(alias_search_results).shape[0],1):
target_alias = alias_search_results[alidx][0]
target_aliases.append(target_alias)
if target_alias.lower().startswith('kic'):
kic_number = target_alias
break
else:
kic_number = target_name
try:
return kic_number
except:
return target_aliases
def find_TIC_alias(target_name):
print('calling mp_lcfind.py/find_TIC_alias().')
#### FOR USE WITH TESS LIGHT CURVES
### in order to return a KIC number, you need to remove final letters and decimals.
star_number = target_name
if '.' in star_number:
star_number = star_number[:star_number.find('.')] ### this will remove the decimal and final numbers
if star_number[-1] in ['b', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'j', 'k', 'l']:
star_number = star_number[:-1]
target_aliases = []
try:
alias_search_results = Simbad.query_objectids(star_number)
print('len(alias_search_results): ', len(alias_search_results))
for alidx in np.arange(0,np.array(alias_search_results).shape[0],1):
target_alias = alias_search_results[alidx][0]
target_aliases.append(target_alias)
if target_alias.lower().startswith('tic'):
tic_number = target_alias
self.ticnum = tic_number
break
except:
print('SIMBAD WAS UNABLE TO FIND THE TARGET.')
try:
target_aliases.np.array([self.ticnum])
tic_number = self.ticnum
print("TIC# LOCATED WITHIN EXOFOP.")
except:
try:
find_planet_row()
target_aliases.np.array([self.ticnum])
tic_number = self.ticnum
print("TIC# LOCATED WITHIN EXOFOP.")
except:
try:
tic_number = 'TIC '+np.array([self.exofop_data[self.exofop_rowidx]])[0]
except:
print('TARGET ALIAS IS JUST ORIGINAL TARGET NAME INPUT.')
target_aliases = np.array([target_name])
try:
return tic_number
except:
return target_aliases
def find_EPIC_alias(target_name):
print('calling mp_lcfind.py/find_EPIC_alias().')
#### FOR USE WITH k2 LIGHT CURVES.
### in order to return a EPIC number, you need to remove final letters and decimals.
star_number = target_name
if '.' in star_number:
star_number = star_number[:star_number.find('.')] ### this will remove the decimal and final numbers
if star_number[-1] in ['b', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'j', 'k', 'l']:
star_number = star_number[:-1]
target_aliases = []
alias_search_results = Simbad.query_objectids(star_number)
for alidx in np.arange(0,np.array(alias_search_results).shape[0],1):
target_alias = alias_search_results[alidx][0]
target_aliases.append(target_alias)
if target_alias.lower().startswith('epic'):
kic_number = target_alias
break
try:
return kic_number
except:
return target_aliases
#####################################
# XXXXXXXXXX URL GENERATION XXXXXXXX #
#####################################
def kepler_URL_generator(KIC, short_cadence=False):
print('calling mp_lcfind.py/kepler_URL_generator()')
### this function takes in a KIC number (with or without a prefix) and produces a URL and wget script.
"""
Kepler data may be retrieved without submitting a batch request.
Both lightcurve and target pixel files are online and stored in two directory trees.
For the browser paths below KKKKKKKKK is the KIC ID and XXXX is the first 4 digits
of the KIC ID including the initial zeros.
Lightcurves
http://archive.stsci.edu/pub/kepler/lightcurves/XXXX/KKKKKKKKK
http://archive.stsci.edu/pub/kepler/lightcurves/0014/001429092/
"""
query_format_number = KIC
#### you need to take the kic number, remove kic, and add zeroes until length = 9.
if query_format_number.lower().startswith('kic'):
query_format_number = query_format_number[3:]
while (query_format_number.startswith('-')) or (query_format_number.startswith(' ')):
query_format_number = query_format_number[1:]
### now it should be just a bunch of numbers:
while len(query_format_number) < 9:
query_format_number = '0'+query_format_number
assert len(query_format_number) == 9
first_four_numbers = query_format_number[:4]
#http://archive.stsci.edu/pub/kepler/lightcurves/0047/004760478/kplr004760478-2010078095331_llc.fits
final_URL = 'http://archive.stsci.edu/pub/kepler/lightcurves/'+first_four_numbers+'/'+query_format_number+'/'
if os.path.exists(central_data_dir+'/Kepler_lightcurves') == False:
os.system('mkdir '+central_data_dir+'/Kepler_lightcurves')
download_directory = central_data_dir+'/Kepler_lightcurves/KIC'+str(query_format_number)
if os.path.exists(download_directory):
pass
else:
os.system('mkdir '+download_directory)
if short_cadence == True:
wget_command = "wget -q -nH --cut-dirs=6 -r -l0 -c -N -np -R --reject tar --accept fits 'index*' -erobots=off "+final_URL+" -P "+download_directory+"/"
else:
wget_command = "wget -q -nH --cut-dirs=6 -r -l0 -c -N -np -R --reject tar --accept llc.fits 'index*' -erobots=off "+final_URL+" -P "+download_directory+"/"
return final_URL, wget_command, download_directory
def k2_URL_generator(EPIC):
print('calling mp_lcfind.py/k2_URL_generator()')
### this function takes in a EPIC number (with or without a prefix) and produces a URL and wget script.
"""
https://archive.stsci.edu/k2/download_options.html
Lightcurves
Individual files may be downloaded via FTP or through your browser (HTTPS) to download K2 data and catalogs.
For FTP, connect to archive.stsci.edu anonymously and cd to pub/k2 You will see the available directories
using ls. For HTTP, just go to https://archive.stsci.edu/pub/k2/. Examples for the browser paths to light
curves and target pixel files are shown below, where XXXXYYZZZ is the EPIC ID and N is the campaign number.
Files are available online in subdirectories in the form:
https://archive.stsci.edu/pub/k2/lightcurves/cN/XXXX00000/YY000. For example:
https://archive.stsci.edu/pub/k2/lightcurves/c3/212200000/35000/
### THEN THE FILE IS https://archive.stsci.edu/pub/k2/lightcurves/c3/212200000/35000/ktwo212235321-c03_llc.fits
"""
query_format_number = EPIC
#### you need to take the kic number, remove kic, and add zeroes until length = 9.
if query_format_number.lower().startswith('epic'):
query_format_number = query_format_number[4:] ### take off the epic
while (query_format_number.startswith('-')) or (query_format_number.startswith(' ')):
query_format_number = query_format_number[1:] #### remove initial "-" or " "
### now it should be just a bunch of numbers:
#### THE ACTION BELOW IS UNNECCESSARY FOR K2, I THINK.
#while len(query_format_number) < 9:
# query_format_number = '0'+query_format_number
assert len(query_format_number) == 9
XXXX = str(query_format_number[:4])
YY = str(query_format_number[4:6])
#final_URL = 'http://archive.stsci.edu/pub/kepler/lightcurves/'+first_four_numbers+'/'+query_format_number+'/'
#final_URL = 'https://archive.stsci.edu/pub/k2/lightcurves/c3/212200000/35000/'
download_directory = central_data_dir+'/K2_lightcurves/EPIC'+str(query_format_number)
if os.path.exists(download_directory):
pass
else:
os.system('mkdir '+download_directory)
#### since you don't know which campaign it's in, generate a list of final_URLs, a list of wget_commands,
final_URLs = []
wget_commands = []
filepaths = []
for campaign_number in np.arange(0,19,1):
print('campaign # ', campaign_number)
if campaign_number < 10:
filename = 'ktwo'+str(query_format_number)+'-c0'+str(campaign_number)+'_llc.fits'
final_URL = 'https://archive.stsci.edu/pub/k2/lightcurves/c'+str(campaign_number)+'/'+XXXX+'00000/'+YY+'000/'+filename #ktwo'+str(query_format_number)+'-c0'+str(campaign_number)+'_llc.fits'
else:
filename = 'ktwo'+str(query_format_number)+'-c'+str(campaign_number)+'_llc.fits'
final_URL = 'https://archive.stsci.edu/pub/k2/lightcurves/c'+str(campaign_number)+'/'+XXXX+'00000/'+YY+'000/'+filename #ktwo'+str(query_format_number)+'-c'+str(campaign_number)+'_llc.fits'
final_URLs.append(final_URL)
filepath = download_directory+'/'+filename
filepaths.append(filepath)
#wget_command = "wget -q -nH --cut-dirs=6 -r -l0 -c -N -np -R 'index*' -erobots=off "+final_URL+" -P "+download_directory+"/"
#wget_command = 'wget -nH --cut-dirs=6 -r -l0 -c -N -np -R "index*" -erobots=off '+final_URL+' -P '+download_directory+'/'
#os.system('wget --tries=1 "https://exoplanetarchive.ipac.caltech.edu/cgi-bin/nstedAPI/nph-nstedAPI?table=cumulative&select=kepid,kepoi_name,kepler_name,koi_disposition,koi_period,koi_period_err1,koi_period_err2,koi_sma,koi_sma_err1,koi_sma_err2,koi_insol,koi_insol_err1,koi_insol_err2,koi_time0bk,koi_time0bk_err1,koi_time0bk_err2,koi_impact,koi_impact_err1,koi_impact_err2,koi_duration,koi_duration_err1,koi_duration_err2,koi_eccen,koi_eccen_err1,koi_eccen_err2,koi_longp,koi_longp_err1,koi_longp_err2,koi_ror,koi_ror_err1,koi_ror_err2,koi_incl,koi_incl_err1,koi_incl_err2,koi_prad,koi_prad_err1,koi_prad_err2,koi_ldm_coeff2,koi_ldm_coeff1,ra,dec&order=kepoi_name&format=ascii" -O "'+kep_mast_address+'"')
wget_command = 'wget --tries=1 -N "'+final_URL+'" -P '+download_directory+'/'
wget_commands.append(wget_command)
return final_URLs, wget_commands, download_directory, filepaths
#####################################
# XXXXXXXXXX DOWNLOADING XXXXXXXX #
#####################################
def kepler_fits_download(target_name, clobber='n'):
print('calling mp_lcfind.py/kepler_fits_downloader().')
### first extract the KIC number
try:
KIC_name = find_KIC_alias(target_name)
print('KIC alias = ', KIC_name)
KIC_URL, KIC_wget, KIC_download_dir = functimer(kepler_URL_generator(KIC_name))
#print("KIC wget = ", KIC_wget)
#### check if KIC_download_dir files already exist... if they do, skip it!
if (len(os.listdir(KIC_download_dir)) > 0) and (clobber == 'n'):
print('light curve files already exist, no need to re-download.')
else:
print('wgetting KIC light curves...')
os.system(KIC_wget)
print('done.')
except:
traceback.print_exc()
raise Exception("something went wrong in 'kepler_fits_download()' (see traceback).")
def k2_fits_download(target_name, clobber='n'):
print('calling mp_lcfind.py/k2_fits_download().')
try:
EPIC_name = find_EPIC_alias(target_name)
EPIC_URLs, EPIC_wgets, EPIC_download_dir, EPIC_filepaths = k2_URL_generator(EPIC_name) ### EPIC_URLs and EPIC_wgets are LISTS!!!!
if (len(os.listdir(EPIC_download_dir)) > 0) and (clobber == 'n'):
print("light curve files already exist, no need to download again.")
else:
##### build a list of the EPIC_URLs that have been tried before.
unobserved_campaigns = []
if os.path.exists(EPIC_download_dir+'/unobserved_campaigns.txt'):
#### open it
unobserved_campaigns_file = open(EPIC_download_dir+'/unobserved_campaigns.txt', mode='r')
for nline,line in enumerate(unobserved_campaigns_file):
unobserved_campaigns.append(line[:line.find('\n')]) ### make sure you have just the EPIC_URL, not those final \n's.
unobserved_campaigns_file.close()
else:
#### start a new list.
unobserved_campaigns = []
print('wgetting EPIC light curves...')
for EPIC_URL, EPIC_wget, EPIC_filepath in zip(EPIC_URLs, EPIC_wgets, EPIC_filepaths):
if EPIC_URL in unobserved_campaigns:
print('target is known to not be observed in this campaign.')
else:
print('looking for ', EPIC_URL)
os.system(EPIC_wget)
print('done.')
print('EPIC filepath: ', EPIC_filepath)
if os.path.exists(EPIC_filepath) == False:
unobserved_campaigns_file = open(EPIC_download_dir+'/unobserved_campaigns.txt', mode='a')
unobserved_campaigns_file.write(EPIC_URL+'\n')
unobserved_campaigns_file.close()
print('added to the unobserved_campaigns.txt file.')
#### check to see if the file exists -- if it doesn't... add it to the unobserved_campaigns file.
except:
traceback.print_exc()
raise Exception("something went wrong in 'k2_fits_download()' (see traceback).")
#####################################
# XXXXXXXXXX UNPACK FITS XXXXXXXX #
#####################################
def kepler_unpack_fits(target_name, short_cadence=False, long_cadence=True):
print('calling mp_lcfind.py/kepler_unpack_fits().')
#### first thing you have to do is make sure the damn thing exists!
KIC_directory = functimer(kepler_URL_generator(find_KIC_alias(target_name))[2])
try:
#### use kepler_fits_download() to grab the KIC_download_dir and unpack these fits.
#KIC_directory = kepler_fits_download(target_name, download=download)
KIC_directory_files = os.listdir(KIC_directory)
print("KIC_directory_files = '", KIC_directory_files)
### start a dictionary with quarters, times, fluxes, errors, flags
kic_quarters_dict = {}
KIC_fits_files = []
### if short_cadence=True, you need to check whether there is a slc version!
### if short_cadence=False, reject slcs!
reject_wrong_cadence_files = []
for i,ki in enumerate(KIC_directory_files):
if ('slc.fits' in ki) and (short_cadence == False):
reject_wrong_cadence_files.append(ki)
if ('llc.fits' in ki) and (long_cadence == False):
reject_wrong_cadence_files.append(ki)
elif (short_cadence == True) and (long_cadence == True):
##### now we need to give preference for short_cadence over long_cadence
if 'llc.fits' in ki:
filename_before_suffix = ki[:ki.find('_llc.fits')]
continue
elif 'slc.fits' in ki:
filename_before_suffix = ki[:ki.find('_slc.fits')]
reject_wrong_cadence_files.append(filename_before_suffix+'_llc.fits')
print('reject wrong cadence files: ', reject_wrong_cadence_files)
for Kdf in KIC_directory_files:
if Kdf in reject_wrong_cadence_files:
continue
if ('.fits' in Kdf) and (Kdf not in reject_wrong_cadence_files):
print('reading ', Kdf)
KIC_fits_files.append(Kdf)
kdf_path = KIC_directory+'/'+Kdf
kdf_file = pyfits.open(kdf_path)
header = kdf_file[0].header
data = kdf_file[1].data
quarter = header['QUARTER']
kic_times = data['TIME']
kic_sap_flux = data['SAP_FLUX']
kic_sap_err = data['SAP_FLUX_ERR']
kic_pdc_flux = data['PDCSAP_FLUX']
kic_pdc_err = data['PDCSAP_FLUX_ERR']
kic_sap_qual = data['SAP_QUALITY']
#### create a dictionary JUST FOR THIS QUARTER
kic_quarter_dict = {}
kic_quarter_dict['TIME'] = kic_times
kic_quarter_dict['SAP_FLUX'] = kic_sap_flux
kic_quarter_dict['SAP_FLUX_ERR'] = kic_sap_err
kic_quarter_dict['PDCSAP_FLUX'] = kic_pdc_flux
kic_quarter_dict['PDCSAP_FLUX_ERR'] = kic_pdc_err
kic_quarter_dict['SAP_QUALITY'] = kic_sap_qual
### now add this dictionary to the kic_quarter_dict
kic_quarters_dict[quarter] = kic_quarter_dict
### output the kic_quarters_dict
return kic_quarters_dict
except:
traceback.print_exc()
raise Exception("Something went wrong in 'kepler_unpack_fits()' (see traceback).")
def k2_unpack_fits(target_name):
print('calling mp_lcfind.py/k2_unpack_fits()')
#### first thing you have to do is make sure the damn thing exists!
EPIC_directory = k2_URL_generator(find_EPIC_alias(target_name))[2]
try:
#### use kepler_fits_download() to grab the KIC_download_dir and unpack these fits.
#KIC_directory = kepler_fits_download(target_name, download=download)
EPIC_directory_files = os.listdir(EPIC_directory)
### start a dictionary with quarters, times, fluxes, errors, flags
epic_quarters_dict = {}
epic_fits_files = []
for Edf in EPIC_directory_files:
if '.fits' in Edf:
epic_fits_files.append(Edf)
edf_path = EPIC_directory+'/'+Edf
edf_file = pyfits.open(edf_path)
header = edf_file[0].header
data = edf_file[1].data
quarter = header['CAMPAIGN']
epic_times = data['TIME']
epic_sap_flux = data['SAP_FLUX']
epic_sap_err = data['SAP_FLUX_ERR']
epic_pdc_flux = data['PDCSAP_FLUX']
epic_pdc_err = data['PDCSAP_FLUX_ERR']
epic_sap_qual = data['SAP_QUALITY']
#### create a dictionary JUST FOR THIS QUARTER
epic_quarter_dict = {}
epic_quarter_dict['TIME'] = epic_times
epic_quarter_dict['SAP_FLUX'] = epic_sap_flux
epic_quarter_dict['SAP_FLUX_ERR'] = epic_sap_err
epic_quarter_dict['PDCSAP_FLUX'] = epic_pdc_flux
epic_quarter_dict['PDCSAP_FLUX_ERR'] = epic_pdc_err
epic_quarter_dict['SAP_QUALITY'] = epic_sap_qual
### now add this dictionary to the kic_quarter_dict
epic_quarters_dict[quarter] = epic_quarter_dict
### output the kic_quarters_dict
return epic_quarters_dict
except:
traceback.print_exc()
raise Exception("Something went wrong in 'k2_unpack_fits()' (see traceback).")
def kplr_target_download(targID, targtype='koi', quarters='all', lc_format='pdc', telescope='kepler', clobber='n', short_cadence=False):
print('calling mp_lcfind.py/kplr_target_download().')
#### using the functions developed above
### first, try unpacking without downloading.
### FOR MOONPY COMPATIBILITY, THIS REQUIRES SUPPORT FOR BOTH KEPLER AND K2 LIGHT CURVES.
if telescope.lower() == 'kepler':
kepler_fits_download(targID, clobber=clobber)
try:
kepler_lc_dictionary = kepler_unpack_fits(targID, short_cadence=short_cadence)
except:
print('first except triggered.')
time.sleep(2)
try:
print('lc may not have been downloaded. Attempting to download...')
kepler_fits_download(targID, clobber=clobber)
### after it's been downloaded, you can try to unpack again.
kepler_lc_dictionary = kepler_unpack_fits(targID, short_cadence=short_cadence)
except:
print('second except triggered.')
time.sleep(2)
traceback.print_exc()
raise Exception("Something went wrong in 'kplr_target_download()' (see traceback).")
elif telescope.lower() == 'k2':
k2_fits_download(targID, clobber=clobber)
try:
kepler_lc_dictionary = k2_unpack_fits(targID)
except:
print('first except triggered.')
time.sleep(2)
try:
print('lc may not have been downloaded. Attempting to download...')
k2_fits_download(targID, clobber=clobber)
### after it's been downloaded, you can try to unpack again.
kepler_lc_dictionary = k2_unpack_fits(targID)
except:
print('second except triggered.')
time.sleep(2)
traceback.print_exc()
raise Exception("Something went wrong in 'kplr_target_download()' (see traceback).")
### now you should have kepler_lc_dictionary, that's ready to return to spit out in the original format.
### first, sort the quarters
sorted_quarters = np.sort(list(kepler_lc_dictionary.keys()))
if quarters == 'all':
output_quarters = np.array(sorted_quarters)
else:
output_quarters = quarters
### make a bunch of lists -- this kinda sucks, but it's backwards compatible with the old kplr output.
kobj_times, kobj_pdc_fluxes, kobj_pdc_errors, kobj_flags, kobj_quarters, kobj_sap_fluxes, kobj_sap_errors = [], [], [], [], [], [], []
for oq in output_quarters:
quarter_entry = kepler_lc_dictionary[int(oq)]
#### need to find finite_idxs
times_finite = np.where(np.isfinite(quarter_entry['TIME']))[0]
pdc_flux_finite = np.where(np.isfinite(quarter_entry['PDCSAP_FLUX']))[0]
pdc_fluxerr_finite = np.where(np.isfinite(quarter_entry['PDCSAP_FLUX_ERR']))[0]
pdc_flags_finite = np.where(np.isfinite(quarter_entry['SAP_QUALITY']))[0]
sap_flux_finite = np.where(np.isfinite(quarter_entry['SAP_FLUX']))[0]
sap_fluxerr_finite = np.where(np.isfinite(quarter_entry['SAP_FLUX_ERR']))[0]
finite_idxs, finite_idx_counts = np.unique(np.concatenate((times_finite, pdc_flux_finite, pdc_fluxerr_finite, pdc_flags_finite, sap_flux_finite, sap_fluxerr_finite)), return_counts=True)
#### there are six arrays being concatenated... therefore, you only want the indices finite_idx_counts == 6.
finite_idxs = finite_idxs[finite_idx_counts == 6]
#print('len(finite_idxs) = ', len(finite_idxs))
#raise Exception("Look what you've done!")
kobj_times.append(quarter_entry['TIME'][finite_idxs])
kobj_pdc_fluxes.append(quarter_entry['PDCSAP_FLUX'][finite_idxs])
kobj_pdc_errors.append(quarter_entry['PDCSAP_FLUX_ERR'][finite_idxs])
kobj_flags.append(quarter_entry['SAP_QUALITY'][finite_idxs])
kobj_sap_fluxes.append(quarter_entry['SAP_FLUX'][finite_idxs])
kobj_sap_errors.append(quarter_entry['SAP_FLUX_ERR'][finite_idxs])
kobj_quarters.append(oq)
kobj_times = np.array(kobj_times, dtype=object)
kobj_pdc_fluxes = np.array(kobj_pdc_fluxes, dtype=object)
kobj_pdc_errors = np.array(kobj_pdc_errors, dtype=object)
kobj_flags = np.array(kobj_flags, dtype=object)
kobj_sap_fluxes = np.array(kobj_sap_fluxes, dtype=object)
kobj_sap_errors = np.array(kobj_sap_errors, dtype=object)
kobj_quarters = np.array(kobj_quarters, dtype=object)
print('kobj_quarters = ', kobj_quarters)
print('len(kobj_quarters) = ', len(kobj_quarters))
### it's valuable to keep the quarters separated like this, because they should be detrended separately!
if lc_format == 'pdc':
return kobj_times, kobj_pdc_fluxes, kobj_pdc_errors, kobj_flags, kobj_quarters
elif lc_format == 'sap':
return kobj_times, kobj_sap_fluxes, kobj_sap_errors, kobj_flags, kobj_quarters
elif lc_format == 'both':
return kobj_times, kobj_sap_fluxes, kobj_sap_errors, kobj_pdc_fluxes, kobj_pdc_errors, kobj_flags, kobj_quarters
def kplr_coord_download(ra, dec, coord_format='degrees', quarters='all', search_radius=5, lc_format='pdc', clobber='n', short_cadence=False):
print('calling mp_lcfind.py/kplr_coord_download().')
### find the object in Simbad using it's coordinates, and call kplr_target_download
print('ra,dec = ', ra, dec)
object_name, object_number = Simbad_query(ra=ra, dec=dec, coord_format=coord_format, telescope=self.telescope)
if lc_format == 'pdc':
kobj_times, kobj_pdc_fluxes, kobj_pdc_errors, kobj_flags, kobj_quarters = kplr_target_download(object_number, targtype=targtype, quarters=quarters, lc_format=lc_format, short_cadence=short_cadence)
elif lc_format == 'sap':
kobj_times, kobj_sap_fluxes, kobj_sap_errors, kobj_flags, kobj_quarters = kplr_target_download(object_number, targtype=targtype, quarters=quarters, lc_format=lc_format, short_cadence=short_cadence)
elif lc_format == 'both':
kobj_times, kobj_sap_fluxes, kobj_sap_errors, kobj_pdc_fluxes, kobj_pdc_errors, kobj_flags, kobj_quarters = kplr_target_download(object_number, targtype=targtype, quarters=quarters, lc_format=lc_format, short_cadence=short_cadence, clobber=clobber)
### it's valuable to keep the quarters separated like this, because they should be detrended separately!
if lc_format == 'pdc':
return kobj_times, kobj_pdc_fluxes, kobj_pdc_errors, kobj_flags, kobj_quarters, object_name
elif lc_format == 'sap':
return kobj_times, kobj_sap_fluxes, kobj_sap_errors, kobj_flags, kobj_quarters, object_name
elif lc_format == 'both':
return kobj_times, kobj_sap_fluxes, kobj_sap_errors, kobj_pdc_fluxes, kobj_pdc_errors, kobj_flags, kobj_quarters, object_name
def tess_coord_download(ra, dec, coord_format='degrees', quarters='all', search_radius=5, lc_format='pdc', short_cadence=False):
print('calling mp_lcfind.py/tess_coord_download().')
### find the object in Simbad using it's coordinates, and call kplr_target_download
print('ra,dec = ', ra, dec)
try:
object_name, object_number = Simbad_query(ra=ra, dec=dec, coord_format=coord_format, telescope=self.telescope)
except:
print('SIMBAD QUERY FAILED.')
#### try to find TIC number another way
try:
ticnumber = self.ticnum
object_name, object_number = ticnumber, ticnumber[4:]
except:
try:
ticnumber = np.array(self.exofop_data['TIC ID'][self.exofop_rowidx])[0]
object_name, object_number = ticnumber, ticnumber[4:]
except:
print('EXHAUSTED ALL TRIES TO FIND TIC.')
if lc_format == 'pdc':
kobj_times, kobj_pdc_fluxes, kobj_pdc_errors, kobj_flags, kobj_quarters = tess_target_download(object_number, targtype=targtype, quarters=quarters, lc_format=lc_format, short_cadence=short_cadence)
elif lc_format == 'sap':
kobj_times, kobj_sap_fluxes, kobj_sap_errors, kobj_flags, kobj_quarters = tess_target_download(object_number, targtype=targtype, quarters=quarters, lc_format=lc_format, short_cadence=short_cadence)
elif lc_format == 'both':
kobj_times, kobj_sap_fluxes, kobj_sap_errors, kobj_pdc_fluxes, kobj_pdc_errors, kobj_flags, kobj_quarters = tess_target_download(object_number, targtype=targtype, quarters=quarters, lc_format=lc_format, short_cadence=short_cadence)
### it's valuable to keep the quarters separated like this, because they should be detrended separately!
if lc_format == 'pdc':
return kobj_times, kobj_pdc_fluxes, kobj_pdc_errors, kobj_flags, kobj_quarters, object_name
elif lc_format == 'sap':
return kobj_times, kobj_sap_fluxes, kobj_sap_errors, kobj_flags, kobj_quarters, object_name
elif lc_format == 'both':
return kobj_times, kobj_sap_fluxes, kobj_sap_errors, kobj_pdc_fluxes, kobj_pdc_errors, kobj_flags, kobj_quarters, object_name
def tess_target_download(targID, sectors='all', short_cadence=True, lc_format='pdc', delete_fits='n', is_neighbor='n'):
print('calling mp_lcfind.py/tess_target_download().')
### this function interfaces with MASS to download light curves based on the TIC #.
print('targID: ', targID)
print('type(targID): ', type(targID))
if type(targID) != str:
targID = targID[0]
if os.path.exists(moonpydir+'/TESS_lcs'):
pass
else:
os.system('mkdir '+moonpydir+'/TESS_lcs')
### first try a simple curl script!
all_times = []
all_fluxes = []
all_errors = []
all_flags = []
sectors = []
lcfiles = []
try:
if targID.lower().startswith('tic'):
ticnum = str(targID)[3:]
if ticnum.startswith(' '):
ticnum = str(ticnum)[1:]
elif ticnum.startswith('-'):
ticnum = str(ticnum)[1:]
else:
#if targID.lower().startswith('toi'):
#### find it in exofop!
ticnum = self.exofop_data['TIC ID'][self.exofop_rowidx] #### I'm not sure where the self comes from, but it works! (for known TOIs)
#ticnum = exofop_data['TIC ID'][exofop_rowidx]
#ticnum = str(targID) ### you've already handled the TOI already!
if ticnum.startswith(' '):
ticnum = ticnum[1:]
#### now we have the ticnum, we can establish the download directory.
download_directory = central_data_dir+'/TESS_lightcurves/TIC'+str(ticnum)
if os.path.exists(download_directory):
pass
else:
os.system('mkdir '+download_directory)
### prepare for the query
query_num = ticnum
while len(query_num) < 16:
query_num = '0'+query_num
assert len(query_num) == 16
sector_prefixes, sector_suffixes = {}, {}
### these can be found at archive.stsci.edu/tess/bulk_downloads/bulk_downloads_ffi-tp-lc-dv.html,
### in the tesscurl_sector_NN_lc.sh files.
nsectors = 99
nactual_sectors = 0
last_existing_sector = 1
nempty_in_a_row = 0
sector_numbers = []
empty_curlscript_sectors = []
sector_filename = 'tess_sectors.txt'
if os.path.exists(moonpydir+'/'+sector_filename):
#### see if it is more than one day old:
current_time = time.time()
sectorfile_createtime = os.path.getctime(moonpydir+'/'+sector_filename)
if current_time - sectorfile_createtime > 86400: #### more than one day
### we're going to make a new one
create_new_sectorfile = True
else:
create_new_sectorfile = False
else:
#### just create it
create_new_sectorfile = True
os.system('touch '+moonpydir+'/'+sector_filename)
if create_new_sectorfile == True:
sectorfile = open(moonpydir+'/'+sector_filename, mode='w')
for sector in np.arange(1,nsectors,1):
### get the curl script... then extract the prefixes and suffixes from the first line.
print('looking for sector: ', sector)
try:
if os.path.exists(curlscript_dir+'/sector'+str(sector)+"_curlscript.txt"):
print('curlscript exists.')
pass
else:
print('attempting to download curlscript for the first time.')
sector_curl_URL = 'http://archive.stsci.edu/missions/tess/download_scripts/sector/tesscurl_sector_'+str(sector)+'_lc.sh'
print('sector_curl_URL')
os.system('wget --tries=1 -N "'+sector_curl_URL+'" -O '+curlscript_dir+'/sector'+str(sector)+"_curlscript.txt")
curltxt = open(curlscript_dir+'/sector'+str(sector)+'_curlscript.txt', mode='r')
first_line = curltxt.readline()
second_line = curltxt.readline()
sector_prefix = second_line[16:40]
sector_suffix = second_line[56:71]
### now read the first line of that
sector_prefixes[sector], sector_suffixes[sector] = sector_prefix, sector_suffix
print('sector_prefix = ', sector_prefix)
print('len(sector_prefix) = ', len(sector_prefix))
if len(sector_prefix) > 0:
#print("sector_prefix, sector_suffix = ", sector_prefix, sector_suffix)
nactual_sectors += 1
#last_existing_sector = copy.copy(sector)
nsectors = sector
### reset nempty_in_a_row
nempty_in_a_row = 0
sectorfile.write('sector '+str(sector)+'\n')
else:
print('sector '+str(sector)+' curlscript file was empty...')
print("REMOVING!")
empty_curlscript_sectors.append(sector)
nempty_in_a_row += 1
#### remove it!
os.system('rm -rf '+curlscript_dir+'/sector'+str(sector)+'_curlscript.txt')
#break
#continue
if nempty_in_a_row == 5:
break
else:
continue
except:
traceback.print_exc()
break_loop = input('Do you want to break loop? y/n: ')
if break_loop == 'y':
break
sectorfile.close()
elif create_new_sectorfile == False:
##### means you already queried the database once today, no need to do it again!
sector_numbers = []