def do_snls_photo(catalog):
task_str = catalog.get_current_task_str()
snls_path = os.path.join(catalog.get_current_task_repo(), 'SNLS-ugriz.dat')
data = list(
csv.reader(
open(snls_path, 'r'),
delimiter=' ',
quotechar='"',
skipinitialspace=True))
for row in pbar(data, task_str):
counts = row[3]
err = row[4]
name = 'SNLS-' + row[0]
name = catalog.add_entry(name)
source = catalog.entries[name].add_source(
bibcode='2010A&A...523A...7G')
catalog.entries[name].add_quantity(SUPERNOVA.ALIAS, name, source)
# Conversion comes from SNLS-Readme
# NOTE: Datafiles avail for download suggest diff zeropoints than 30,
# but README states mags should be calculated assuming 30. Need to
# inquire.
zp = 30.0
photodict = {
PHOTOMETRY.TIME: row[2],
PHOTOMETRY.U_TIME: 'MJD',
PHOTOMETRY.BAND: row[1],
PHOTOMETRY.COUNT_RATE: counts,
PHOTOMETRY.E_COUNT_RATE: err,
PHOTOMETRY.ZERO_POINT: str(zp),
PHOTOMETRY.SOURCE: source,
PHOTOMETRY.TELESCOPE: 'CFHT',
PHOTOMETRY.INSTRUMENT: 'MegaCam',
PHOTOMETRY.BAND_SET: 'MegaCam',
PHOTOMETRY.SYSTEM: 'BD17'
}
set_pd_mag_from_counts(photodict, counts, ec=err, zp=zp, sig=5.0)
catalog.entries[name].add_photometry(**photodict)
catalog.journal_entries()
return
def do_snls_photo(catalog):
task_str = catalog.get_current_task_str()
snls_path = os.path.join(catalog.get_current_task_repo(), 'SNLS-ugriz.dat')
data = list(
csv.reader(open(snls_path, 'r'),
delimiter=' ',
quotechar='"',
skipinitialspace=True))
for row in pbar(data, task_str):
counts = row[3]
err = row[4]
name = 'SNLS-' + row[0]
name = catalog.add_entry(name)
source = catalog.entries[name].add_source(
bibcode='2010A&A...523A...7G')
catalog.entries[name].add_quantity(SUPERNOVA.ALIAS, name, source)
# Conversion comes from SNLS-Readme
# NOTE: Datafiles avail for download suggest diff zeropoints than 30,
# but README states mags should be calculated assuming 30. Need to
# inquire.
zp = 30.0
photodict = {
PHOTOMETRY.TIME: row[2],
PHOTOMETRY.U_TIME: 'MJD',
PHOTOMETRY.BAND: row[1],
PHOTOMETRY.COUNT_RATE: counts,
PHOTOMETRY.E_COUNT_RATE: err,
PHOTOMETRY.ZERO_POINT: str(zp),
PHOTOMETRY.SOURCE: source,
PHOTOMETRY.TELESCOPE: 'CFHT',
PHOTOMETRY.INSTRUMENT: 'MegaCam',
PHOTOMETRY.BAND_SET: 'MegaCam',
PHOTOMETRY.SYSTEM: 'BD17'
}
set_pd_mag_from_counts(photodict, counts, ec=err, zp=zp, sig=5.0)
catalog.entries[name].add_photometry(**photodict)
catalog.journal_entries()
return
def _first_event_first_source(catalog):
"""Try adding a single source, with some data.
"""
log = catalog.log
# Add Entry to Catalog
log.info("Calling: ``add_entry('{}')``".format(FAKE_ALIAS_1))
name = catalog.add_entry(FAKE_ALIAS_1)
log.debug("\t `name`: '{}'".format(name))
log.debug("\n{}\n".format(repr(catalog.entries[name])))
# Make sure entry exists
if FAKE_ALIAS_1 not in catalog.entries:
raise RuntimeError("`FAKE_ALIAS_1`: '{}' is not in entries".format(
FAKE_ALIAS_1))
# Make sure entry has the correct name
stored_name = catalog.entries[FAKE_ALIAS_1][ENTRY.NAME]
if stored_name != FAKE_ALIAS_1:
raise RuntimeError("`FAKE_ALIAS_1`[{}]: '{}' does not match".format(
ENTRY.NAME, stored_name, FAKE_ALIAS_1))
# Add source to entry
log.info("Calling: ``add_source('{}')``".format(FAKE_BIBCODE_1))
source = catalog.entries[name].add_source(
name=FAKE_NAME_1, bibcode=FAKE_BIBCODE_1)
log.debug("\t `source`: '{}'".format(source))
log.debug("\n{}\n".format(repr(catalog.entries[name])))
# Make sure source alias is correct
if source != '1':
raise RuntimeError("Returned `source`: '{}' is wrong.".format(source))
# Make sure source has the right properties
check_source_1(catalog, name)
# Add alias
log.info("Calling: ``add_quantity('alias', '{}', '{}')``".format(
FAKE_ALIAS_2, source))
catalog.entries[name].add_quantity(ENTRY.ALIAS, FAKE_ALIAS_2, source)
log.debug("\n{}\n".format(repr(catalog.entries[name])))
# Make sure source alias is correct
stored_aliases = catalog.entries[name][ENTRY.ALIAS]
if ((len(stored_aliases) != 1 or
stored_aliases[0]['value'] != FAKE_ALIAS_2 or
stored_aliases[0]['source'] != source)):
raise RuntimeError("Stored alias: '{}' looks wrong.".format(
stored_aliases[0]))
log.info("Calling: ``add_quantity('redshift', '{}', '{}')``".format(
FAKE_REDZ_1, source))
catalog.entries[name].add_quantity(
ENTRY.REDSHIFT, FAKE_REDZ_1, source, kind='spectroscopic')
log.debug("\n{}\n".format(repr(catalog.entries[name])))
# Add a fake photometric observation
log.info("Calling: ``add_photometry(...)``")
catalog.entries[name].add_photometry(
time='12345', magnitude='20.0', band='g', e_magnitude='0.01',
telescope='OWELTMT', instrument='UltraCam', observer='I. M. Fake',
observatory='Mt. Olympus', survey='Zeus Analog Sky Survey',
source=source)
log.debug("\n{}\n".format(repr(catalog.entries[name])))
# Add a fake photometric observation with mangled data
log.info("Calling: ``add_photometry(...)``")
catalog.entries[name].add_photometry(
time='oiasjdqw', magnitude='oihqwr', source=source)
log.debug("\n{}\n".format(repr(catalog.entries[name])))
# Add a fake photometric observation without required fields
log.info("Calling: ``add_photometry(...)``")
catalog.entries[name].add_photometry(e_magnitude='0.01')
log.debug("\n{}\n".format(repr(catalog.entries[name])))
# Add a fake photometric observation by counts
log.info("Calling: ``add_photometry(...)``")
photodict = {
PHOTOMETRY.TIME: '12345',
PHOTOMETRY.U_TIME: 'MJD',
PHOTOMETRY.BAND: 'r',
PHOTOMETRY.SOURCE: source
}
set_pd_mag_from_counts(photodict, str(100.0), ec=10.0, zp=30.0)
catalog.entries[name].add_photometry(**photodict)
log.debug("\n{}\n".format(repr(catalog.entries[name])))
log.info("Calling: ``journal_entries()``")
catalog.journal_entries()
log.debug("\n{}\n".format(repr(catalog.entries[name])))
# Make sure the remaining stub looks right
check_stub(catalog, name)
return
def _first_event_first_source(catalog):
"""Try adding a single source, with some data.
"""
log = catalog.log
# Add Entry to Catalog
log.info("Calling: ``add_entry('{}')``".format(FAKE_ALIAS_1))
name = catalog.add_entry(FAKE_ALIAS_1)
log.debug("\t `name`: '{}'".format(name))
log.debug("\n{}\n".format(repr(catalog.entries[name])))
# Make sure entry exists
if FAKE_ALIAS_1 not in catalog.entries:
raise RuntimeError(
"`FAKE_ALIAS_1`: '{}' is not in entries".format(FAKE_ALIAS_1))
# Make sure entry has the correct name
stored_name = catalog.entries[FAKE_ALIAS_1][ENTRY.NAME]
if stored_name != FAKE_ALIAS_1:
raise RuntimeError("`FAKE_ALIAS_1`[{}]: '{}' does not match".format(
ENTRY.NAME, stored_name, FAKE_ALIAS_1))
# Add source to entry
log.info("Calling: ``add_source('{}')``".format(FAKE_BIBCODE_1))
source = catalog.entries[name].add_source(name=FAKE_NAME_1,
bibcode=FAKE_BIBCODE_1)
log.debug("\t `source`: '{}'".format(source))
log.debug("\n{}\n".format(repr(catalog.entries[name])))
# Make sure source alias is correct
if source != '1':
raise RuntimeError("Returned `source`: '{}' is wrong.".format(source))
# Make sure source has the right properties
check_source_1(catalog, name)
# Add alias
log.info("Calling: ``add_quantity('alias', '{}', '{}')``".format(
FAKE_ALIAS_2, source))
catalog.entries[name].add_quantity(ENTRY.ALIAS, FAKE_ALIAS_2, source)
log.debug("\n{}\n".format(repr(catalog.entries[name])))
# Make sure source alias is correct
stored_aliases = catalog.entries[name][ENTRY.ALIAS]
if ((len(stored_aliases) != 1 or stored_aliases[0]['value'] != FAKE_ALIAS_2
or stored_aliases[0]['source'] != source)):
raise RuntimeError("Stored alias: '{}' looks wrong.".format(
stored_aliases[0]))
log.info("Calling: ``add_quantity('redshift', '{}', '{}')``".format(
FAKE_REDZ_1, source))
catalog.entries[name].add_quantity(ENTRY.REDSHIFT,
FAKE_REDZ_1,
source,
kind='spectroscopic')
log.debug("\n{}\n".format(repr(catalog.entries[name])))
# Add a fake photometric observation
log.info("Calling: ``add_photometry(...)``")
catalog.entries[name].add_photometry(time='12345',
magnitude='20.0',
band='g',
e_magnitude='0.01',
telescope='OWELTMT',
instrument='UltraCam',
observer='I. M. Fake',
observatory='Mt. Olympus',
survey='Zeus Analog Sky Survey',
source=source)
log.debug("\n{}\n".format(repr(catalog.entries[name])))
# Add a fake photometric observation with mangled data
log.info("Calling: ``add_photometry(...)``")
catalog.entries[name].add_photometry(time='oiasjdqw',
magnitude='oihqwr',
source=source)
log.debug("\n{}\n".format(repr(catalog.entries[name])))
# Add a fake photometric observation without required fields
log.info("Calling: ``add_photometry(...)``")
catalog.entries[name].add_photometry(e_magnitude='0.01')
log.debug("\n{}\n".format(repr(catalog.entries[name])))
# Add a fake photometric observation by counts
log.info("Calling: ``add_photometry(...)``")
photodict = {
PHOTOMETRY.TIME: '12345',
PHOTOMETRY.U_TIME: 'MJD',
PHOTOMETRY.BAND: 'r',
PHOTOMETRY.SOURCE: source
}
set_pd_mag_from_counts(photodict, str(100.0), ec=10.0, zp=30.0)
catalog.entries[name].add_photometry(**photodict)
log.debug("\n{}\n".format(repr(catalog.entries[name])))
log.info("Calling: ``journal_entries()``")
catalog.journal_entries()
log.debug("\n{}\n".format(repr(catalog.entries[name])))
# Make sure the remaining stub looks right
check_stub(catalog, name)
return
def generate_event_list(self, event_list):
"""Generate a list of events and/or convert events to JSON format."""
prt = self._printer
cidict = OrderedDict()
intro_shown = False
new_event_list = []
previous_file = None
for event in event_list:
rsource = {SOURCE.NAME: self._DEFAULT_SOURCE}
use_self_source = None
new_events = []
toffset = Decimal('0')
if ('.' in event and os.path.isfile(event) and
not event.endswith('.json')):
if not intro_shown:
prt.message('converter_info')
intro_shown = True
prt.message('converting_to_json', [event])
with open(event, 'r') as f:
ftxt = f.read()
# Try a couple of table formats from astropy.
table = None
try:
table = read(ftxt, Reader=Cds, guess=False)
except Exception:
pass
else:
prt.message('convert_cds')
flines = [table.colnames] + [
list(x) for x in np.array(table).tolist()]
for i in range(len(flines)):
flines[i] = [str(x) for x in flines[i]]
try:
table = read(ftxt, Reader=Latex, guess=False)
except Exception:
pass
else:
prt.message('convert_latex')
flines = [table.colnames] + [
list(x) for x in np.array(table).tolist()]
if table is None:
# Count to try and determine delimiter.
delims = [' ', '\t', ',', ';', '|', '&']
delimnames = [
'Space: ` `', 'Tab: `\t`', 'Comma: `,`',
'Semi-colon: `;`', 'Bar: `|`', 'Ampersand: `&`']
delim = None
delimcounts = [ftxt.count(x) for x in delims]
maxdelimcount = max(delimcounts)
delim = delims[delimcounts.index(maxdelimcount)]
# If two delimiter options are close in count, ask user.
for i, x in enumerate(delimcounts):
if x > 0.5 * maxdelimcount and delims[i] != delim:
delim = None
if delim is None:
odelims = list(np.array(delimnames)[
np.array(delimcounts) > 0])
delim = delims[prt.prompt(
'delim', kind='option', options=odelims) - 1]
ad = list(delims)
ad.remove(delim)
ad = ''.join(ad)
fsplit = ftxt.splitlines()
fsplit = [
x.replace('$', '').replace('\\pm', delim)
.replace('±', delim).replace('(', delim + '(')
.strip(ad + '()# ').replace('′', "'")
for x in fsplit]
flines = []
for fs in fsplit:
flines.append(list(
csv.reader([fs], delimiter=delim))[0])
flines = [[
x.strip(ad + '#$()\\')
for x in y] for y in flines]
# Find band columns if they exist and insert error columns
# if they don't exist.
for fi, fl in enumerate(list(flines)):
flcopy = list(fl)
offset = 0
if not any([is_number(x) for x in fl]):
for fci, fc in enumerate(fl):
if (fc in self._band_names and
(fci == len(fl) - 1 or
fl[fci + 1] not in self._emagstrs)):
flcopy.insert(fci + 1 + offset, 'e mag')
offset += 1
flines[fi] = flcopy
# Find the most frequent column count. These are probably
# the tables we wish to read.
flens = [len(x) for x in flines]
ncols = Counter(flens).most_common(1)[0][0]
newlines = []
potential_name = None
for fi, fl in enumerate(flines):
if (len(fl) and flens[fi] == 1 and
fi < len(flines) - 1 and
flens[fi + 1] == ncols and not len(newlines)):
potential_name = fl[0]
if flens[fi] == ncols:
if potential_name is not None and any(
[is_number(x) for x in fl]):
newlines.append([potential_name] + list(fl))
else:
newlines.append(list(fl))
flines = newlines
for fi, fl in enumerate(flines):
if len(fl) == ncols and potential_name is not None:
if not any([is_number(x) for x in fl]):
flines[fi] = ['name'] + list(fl)
# If none of the rows contain numeric data, the file
# is likely a list of transient names.
if (len(flines) and
(not any(any([is_number(x) or x == '' for x in y])
for y in flines) or
len(flines) == 1)):
new_events = [
it for s in flines for it in s]
# If last row is numeric, then likely this is a file with
# transient data.
elif (len(flines) > 1 and
any([is_number(x) for x in flines[-1]])):
# Check that each row has the same number of columns.
if len(set([len(x) for x in flines])) > 1:
print(set([len(x) for x in flines]))
raise ValueError(
'Number of columns in each row not '
'consistent!')
if len(cidict) and len(new_event_list):
msg = ('is_file_same' if
previous_file else 'is_event_same')
reps = [previous_file] if previous_file else [''.join(
new_event_list[-1].split('.')[:-1])]
text = prt.text(msg, reps)
is_same = prt.prompt(text, message=False,
kind='bool')
if not is_same:
cidict = OrderedDict()
# If the first row has no numbers it is likely a header.
if not len(cidict):
self.assign_columns(cidict, flines)
perms = 1
for key in cidict:
if isinstance(cidict[key], list) and not isinstance(
cidict[key], string_types):
if cidict[key][0] != 'j':
perms = len(cidict[key])
# Get event name (if single event) or list of names from
# table.
event_names = []
if ENTRY.NAME in cidict:
for fi, fl in enumerate(flines):
flines[fi][cidict[ENTRY.NAME]] = name_clean(
fl[cidict[ENTRY.NAME]])
event_names = list(sorted(set([
x[cidict[ENTRY.NAME]] for x in flines[
self._first_data:]])))
new_events = [x + '.json' for x in event_names]
else:
new_event_name = '.'.join(event.split(
'.')[:-1]).split('/')[-1]
text = prt.message(
'is_event_name', [new_event_name], prt=False)
is_name = prt.prompt(text, message=False,
kind='bool', default='y')
if not is_name:
new_event_name = ''
while new_event_name.strip() == '':
new_event_name = prt.prompt(
'enter_name', kind='string')
event_names.append(new_event_name)
new_events = [new_event_name + '.json']
# Create a new event, populate the photometry, and dump
# to a JSON file in the run directory.
entries = OrderedDict([(x, Entry(name=x))
for x in event_names])
# Clean up the data a bit now that we know the column
# identities.
# Strip common prefixes/suffixes from band names
if PHOTOMETRY.BAND in cidict:
bi = cidict[PHOTOMETRY.BAND]
for d in [True, False]:
if not isinstance(bi, (int, np.integer)):
break
strip_cols = []
lens = [len(x[bi])
for x in flines[self._first_data:]]
llen = min(lens)
ra = range(llen) if d else range(-1, -llen - 1, -1)
for li in ra:
letter = None
for row in list(flines[self._first_data:]):
if letter is None:
letter = row[bi][li]
elif row[bi][li] != letter:
letter = None
break
if letter is not None:
strip_cols.append(li)
else:
break
if len(strip_cols) == llen:
break
for ri in range(len(flines[self._first_data:])):
flines[self._first_data + ri][bi] = ''.join(
[c for i, c in enumerate(flines[
self._first_data + ri][bi])
if (i if d else i - len(flines[
self._first_data + ri][bi])) not in
strip_cols])
if (PHOTOMETRY.TIME in cidict and
(not isinstance(cidict[PHOTOMETRY.TIME], list) or
len(cidict[PHOTOMETRY.TIME]) <= 2)):
bi = cidict[PHOTOMETRY.TIME]
if isinstance(bi, list) and not isinstance(
bi, string_types) and isinstance(
bi[0], string_types) and bi[0] == 'jd':
bi = bi[-1]
mmtimes = [float(x[bi])
for x in flines[self._first_data:]]
mintime, maxtime = min(mmtimes), max(mmtimes)
if mintime < 10000:
while True:
try:
response = prt.prompt(
'small_time_offset', kind='string')
if response is not None:
toffset = Decimal(response)
break
except Exception:
pass
elif maxtime > 60000 and cidict[
PHOTOMETRY.TIME][0] != 'jd':
isjd = prt.prompt(
'large_time_offset',
kind='bool', default='y')
if isjd:
toffset = Decimal('-2400000.5')
for row in flines[self._first_data:]:
photodict = {}
rname = (row[cidict[ENTRY.NAME]]
if ENTRY.NAME in cidict else event_names[0])
for pi in range(perms):
sources = set()
for key in cidict:
if key in self._bool_keys:
rval = row[cidict[key]]
if rval in self._FALSE_VALS:
rval = False
elif rval in self._TRUE_VALS:
rval = True
if type(rval) != 'bool':
try:
rval = bool(rval)
except Exception:
pass
if type(rval) != 'bool':
try:
rval = bool(float(rval))
except Exception:
rval = True
if not rval:
continue
row[cidict[key]] = rval
elif key == 'reference':
if (isinstance(cidict[key],
string_types) and
len(cidict[key]) == 19):
new_src = entries[rname].add_source(
bibcode=cidict[key])
sources.update(new_src)
row[
cidict[key]] = new_src
elif key == ENTRY.NAME:
continue
elif (isinstance(key, Key) and
key.type == KEY_TYPES.TIME and
isinstance(cidict[key], list) and not
isinstance(cidict[key],
string_types)):
tval = np.array(row)[np.array(cidict[key][
1:], dtype=int)]
if cidict[key][0] == 'j':
date = '-'.join([x.zfill(2) for x in
tval])
date = self._month_rep.sub(
lambda x: self._MONTH_IDS[
x.group()], date)
photodict[key] = str(
astrotime(date, format='isot').mjd)
elif cidict[key][0] == 'jd':
photodict[key] = str(
jd_to_mjd(Decimal(tval[-1])))
continue
val = cidict[key]
if (isinstance(val, list) and not
isinstance(val, string_types)):
val = val[pi]
if isinstance(val, string_types):
if val != '':
photodict[key] = val
else:
photodict[key] = row[val]
else:
if isinstance(val, string_types):
if val != '':
photodict[key] = val
else:
photodict[key] = row[val]
if self._data_type == 2:
if self._zp:
photodict[PHOTOMETRY.ZERO_POINT] = self._zp
else:
photodict[PHOTOMETRY.ZERO_POINT] = (
row[cidict[PHOTOMETRY.ZERO_POINT][pi]]
if isinstance(cidict[
PHOTOMETRY.ZERO_POINT], list) else
row[cidict[PHOTOMETRY.ZERO_POINT]])
zpp = photodict[PHOTOMETRY.ZERO_POINT]
cc = (
row[cidict[PHOTOMETRY.COUNT_RATE][pi]] if
isinstance(cidict[
PHOTOMETRY.COUNT_RATE], list) else
row[cidict[PHOTOMETRY.COUNT_RATE]])
ecc = (
row[cidict[PHOTOMETRY.E_COUNT_RATE][pi]] if
isinstance(cidict[
PHOTOMETRY.E_COUNT_RATE], list) else
row[cidict[PHOTOMETRY.E_COUNT_RATE]])
if '<' in cc:
set_pd_mag_from_counts(
photodict, ec=cc.strip('<'), zp=zpp)
else:
set_pd_mag_from_counts(
photodict, c=cc, ec=ecc, zp=zpp)
elif self._data_type == 3:
photodict[
PHOTOMETRY.U_FLUX_DENSITY] = self._ufd
if PHOTOMETRY.U_FLUX_DENSITY in cidict:
photodict[PHOTOMETRY.U_FLUX_DENSITY] = (
row[cidict[
PHOTOMETRY.U_FLUX_DENSITY][pi]]
if isinstance(cidict[
PHOTOMETRY.
U_FLUX_DENSITY], list) else
row[cidict[PHOTOMETRY.U_FLUX_DENSITY]])
if photodict[
PHOTOMETRY.U_FLUX_DENSITY] == '':
photodict[
PHOTOMETRY.U_FLUX_DENSITY] = 'µJy'
fd = (
row[cidict[PHOTOMETRY.FLUX_DENSITY][pi]] if
isinstance(cidict[
PHOTOMETRY.FLUX_DENSITY], list) else
row[cidict[PHOTOMETRY.FLUX_DENSITY]])
efd = (
row[cidict[
PHOTOMETRY.E_FLUX_DENSITY][pi]] if
isinstance(cidict[
PHOTOMETRY.E_FLUX_DENSITY], list) else
row[cidict[PHOTOMETRY.E_FLUX_DENSITY]])
mult = Decimal('1')
ufd = photodict[PHOTOMETRY.U_FLUX_DENSITY]
if ufd.lower() in [
'mjy', 'millijy', 'millijansky']:
mult = Decimal('1e3')
elif ufd.lower() in ['jy', 'jansky']:
mult = Decimal('1e6')
if '<' in fd:
set_pd_mag_from_flux_density(
photodict, efd=str(
Decimal(fd.strip('<')) * mult))
else:
set_pd_mag_from_flux_density(
photodict, fd=Decimal(fd) * mult,
efd=Decimal(efd) * mult)
if not len(sources):
if use_self_source is None:
sopts = [
('Bibcode', 'b'), ('Last name', 'l')]
if self._require_source:
sel_str = 'must_select_source'
else:
sel_str = 'select_source'
text = prt.text(sel_str)
skind = prt.prompt(
text, kind='option',
options=sopts, default='b',
none_string=(
None if self._require_source else
'Neither, tag MOSFiT as source'))
if skind == 'b':
rsource = {}
bibcode = ''
while len(bibcode) != 19:
bibcode = prt.prompt(
'bibcode',
kind='string',
allow_blank=False
)
bibcode = bibcode.strip()
if (re.search(
'[0-9]{4}..........[\.0-9]{4}'
'[A-Za-z]', bibcode)
is None):
bibcode = ''
rsource[
SOURCE.BIBCODE] = bibcode
use_self_source = False
elif skind == 'l':
rsource = {}
last_name = prt.prompt(
'last_name', kind='string'
)
rsource[
SOURCE.NAME] = (
last_name.strip().title() +
' et al., in preparation')
use_self_source = False
elif skind == 'n':
use_self_source = True
photodict[
PHOTOMETRY.SOURCE] = entries[
rname].add_source(**rsource)
if any([x in photodict.get(
PHOTOMETRY.MAGNITUDE, '')
for x in ['<', '>']]):
photodict[PHOTOMETRY.UPPER_LIMIT] = True
photodict[
PHOTOMETRY.MAGNITUDE] = photodict[
PHOTOMETRY.MAGNITUDE].strip('<>')
if '<' in photodict.get(PHOTOMETRY.COUNT_RATE, ''):
photodict[PHOTOMETRY.UPPER_LIMIT] = True
photodict[
PHOTOMETRY.COUNT_RATE] = photodict[
PHOTOMETRY.COUNT_RATE].strip('<')
if PHOTOMETRY.E_COUNT_RATE in photodict:
del(photodict[PHOTOMETRY.E_COUNT_RATE])
if '<' in photodict.get(
PHOTOMETRY.FLUX_DENSITY, ''):
photodict[PHOTOMETRY.UPPER_LIMIT] = True
photodict[
PHOTOMETRY.FLUX_DENSITY] = photodict[
PHOTOMETRY.FLUX_DENSITY].strip('<')
if PHOTOMETRY.E_FLUX_DENSITY in photodict:
del(photodict[PHOTOMETRY.E_FLUX_DENSITY])
# Apply offset time if set.
if (PHOTOMETRY.TIME in photodict and
toffset != Decimal('0')):
photodict[PHOTOMETRY.TIME] = str(
Decimal(photodict[PHOTOMETRY.TIME]) +
toffset)
# Skip entries for which key values are not
# expected type.
if not all([
is_number(photodict.get(x, ''))
for x in photodict.keys() if
(PHOTOMETRY.get_key_by_name(x).type ==
KEY_TYPES.NUMERIC)]):
continue
# Skip placeholder values.
if float(photodict.get(
PHOTOMETRY.MAGNITUDE, 0.0)) > 50.0:
continue
# Add system if specified by user.
if (self._system is not None and
PHOTOMETRY.SYSTEM not in photodict):
photodict[PHOTOMETRY.SYSTEM] = self._system
# Remove keys not in the `PHOTOMETRY` class.
for key in list(photodict.keys()):
if key not in PHOTOMETRY.vals():
del(photodict[key])
# Add the photometry.
entries[rname].add_photometry(
**photodict)
merge_with_existing = None
for ei, entry in enumerate(entries):
entries[entry].sanitize()
if os.path.isfile(new_events[ei]):
if merge_with_existing is None:
merge_with_existing = prt.prompt(
'merge_with_existing', default='y')
if merge_with_existing:
existing = Entry.init_from_file(
catalog=None,
name=event_names[ei],
path=new_events[ei],
merge=False,
pop_schema=False,
ignore_keys=[ENTRY.MODELS],
compare_to_existing=False)
Catalog().copy_entry_to_entry(
existing, entries[entry])
oentry = entries[entry]._ordered(entries[entry])
entabbed_json_dump(
{entry: oentry}, open(new_events[ei], 'w'),
separators=(',', ':'))
self._converted.extend([
[event_names[x], new_events[x]]
for x in range(len(event_names))])
new_event_list.extend(new_events)
previous_file = event
else:
new_event_list.append(event)
return new_event_list
def do_essence_photo(catalog):
task_str = catalog.get_current_task_str()
ess_path = os.path.join(catalog.get_current_task_repo(), 'ESSENCE',
'obj_table.dat')
data = list(
csv.reader(open(ess_path, 'r'),
delimiter=' ',
quotechar='"',
skipinitialspace=True))
for row in pbar(data[1:], task_str):
etype = row[2]
if etype.upper().replace('?', '') in catalog.nonsnetypes:
continue
ess_name = 'ESSENCE ' + row[0]
name, source = catalog.new_entry(ess_name,
bibcode='2016ApJS..224....3N')
if row[1] != '---':
catalog.entries[name].add_quantity(SUPERNOVA.ALIAS, 'SN' + row[1],
source)
if etype != '---':
catalog.entries[name].add_quantity(SUPERNOVA.CLAIMED_TYPE, etype,
source)
catalog.entries[name].add_quantity(SUPERNOVA.RA, row[5], source)
catalog.entries[name].add_quantity(SUPERNOVA.DEC, row[6], source)
if is_number(row[11]):
quantdict = {
QUANTITY.VALUE: row[11],
QUANTITY.SOURCE: source,
QUANTITY.KIND: 'host'
}
if is_number(row[12]):
quantdict[QUANTITY.E_VALUE] = row[12]
catalog.entries[name].add_quantity(
[SUPERNOVA.REDSHIFT, SUPERNOVA.HOST_REDSHIFT], **quantdict)
files = glob(
os.path.join(catalog.get_current_task_repo(), 'ESSENCE',
'*clean*.dat'))
for pfile in pbar(files, task_str):
name = 'ESSENCE ' + pfile.split('/')[-1].split('.')[0]
name, source = catalog.new_entry(name, bibcode='2016ApJS..224....3N')
with open(pfile, 'r') as f:
rows = list(csv.reader(f, delimiter=' ', skipinitialspace=True))
for ri, row in enumerate(rows):
if ri == 1:
catalog.entries[name].add_quantity(
SUPERNOVA.REDSHIFT,
row[5],
source,
kind=['spectroscopic', 'heliocentric'])
catalog.entries[name].add_quantity(
SUPERNOVA.REDSHIFT,
row[6],
source,
kind=['spectroscopic', 'cmb'])
continue
if row[0].startswith('#'):
continue
counts = row[3][:6]
lerr = row[4][:6]
uerr = row[5][:6]
zp = 25.0
photodict = {
PHOTOMETRY.TIME: row[1],
PHOTOMETRY.U_TIME: 'MJD',
PHOTOMETRY.BAND: row[2][0],
PHOTOMETRY.COUNT_RATE: counts,
PHOTOMETRY.E_LOWER_COUNT_RATE: lerr,
PHOTOMETRY.E_UPPER_COUNT_RATE: uerr,
PHOTOMETRY.ZERO_POINT: str(zp),
PHOTOMETRY.SOURCE: source,
PHOTOMETRY.TELESCOPE: 'CTIO 4m',
PHOTOMETRY.SYSTEM: 'Natural'
}
set_pd_mag_from_counts(photodict,
counts,
ec='',
lec=lerr,
uec=uerr,
zp=zp,
sig=5.0)
catalog.entries[name].add_photometry(**photodict)
catalog.journal_entries()
return
def do_donated_photo(catalog):
"""Import donated photometry."""
task_str = catalog.get_current_task_str()
# Private donations here #
if not catalog.args.travis:
pass
# End private donations #
# Ponder 05-12-17 donation
with open(
os.path.join(catalog.get_current_task_repo(), 'Donations',
'Ponder-05-12-17', 'meta.json'), 'r') as f:
metadict = json.loads(f.read())
file_names = glob(
os.path.join(catalog.get_current_task_repo(), 'Donations',
'Ponder-05-12-17', '*.dat'))
for path in file_names:
with open(path, 'r') as f:
tsvin = list(csv.reader(f, delimiter=' ', skipinitialspace=True))
oname = path.split('/')[-1].split('.')[0]
name, source = catalog.new_entry(
oname, bibcode=metadict[oname]['bibcode'])
for row in pbar(tsvin, task_str + ': Ponder ' + oname):
if row[0][0] == '#' or not is_number(row[-1]):
continue
mjd = row[1]
bandinst = row[2].split('_')
band = bandinst[0]
inst = ''
if len(bandinst) > 1:
inst = bandinst[1]
mag = row[3]
uerr = row[4]
lerr = row[5]
photodict = {
PHOTOMETRY.TIME: mjd,
PHOTOMETRY.U_TIME: 'MJD',
PHOTOMETRY.BAND: band,
PHOTOMETRY.MAGNITUDE: mag,
PHOTOMETRY.E_LOWER_MAGNITUDE: lerr,
PHOTOMETRY.E_UPPER_MAGNITUDE: uerr,
PHOTOMETRY.SOURCE: source
}
if inst:
photodict[PHOTOMETRY.INSTRUMENT] = inst
catalog.entries[name].add_photometry(**photodict)
# Benetti 03-08-17 donation
path = os.path.join(catalog.get_current_task_repo(), 'Donations',
'Benetti-03-08-17', '1999E.dat')
with open(path, 'r') as f:
tsvin = list(csv.reader(f, delimiter=' ', skipinitialspace=True))
name, source = catalog.new_entry(
'SN1999E', bibcode='2003MNRAS.340..191R')
bands = None
for row in tsvin:
if not row or row[0][0] == '#':
continue
if not bands:
bands = row[2:-2]
continue
mjd = row[1]
tel = row[-1] if 'IAUC' not in row[-1] else None
for bi, band in enumerate(bands):
mag = row[2 + 2 * bi]
if mag == '9999':
continue
err = row[2 + 2 * bi + 1]
limit = row[6] == 'True'
photodict = {
PHOTOMETRY.TIME: mjd,
PHOTOMETRY.U_TIME: 'MJD',
PHOTOMETRY.TELESCOPE: tel,
PHOTOMETRY.BAND: band,
PHOTOMETRY.MAGNITUDE: mag,
PHOTOMETRY.SOURCE: source
}
if err != '.00':
photodict[PHOTOMETRY.E_MAGNITUDE] = str(Decimal(err))
if tel:
photodict[PHOTOMETRY.TELESCOPE] = tel
catalog.entries[name].add_photometry(**photodict)
# Nicholl 01-29-17 donation
with open(
os.path.join(catalog.get_current_task_repo(), 'Donations',
'Nicholl-01-29-17', 'meta.json'), 'r') as f:
metadict = json.loads(f.read())
file_names = glob(
os.path.join(catalog.get_current_task_repo(), 'Donations',
'Nicholl-01-29-17', '*.txt'))
for path in file_names:
data = read(path, format='cds')
oname = path.split('/')[-1].split('_')[0]
name, source = catalog.new_entry(
oname, bibcode=metadict[oname]['bibcode'])
for row in pbar(data, task_str + ': Nicholl ' + oname):
photodict = {
PHOTOMETRY.TIME: str(row['MJD']),
PHOTOMETRY.U_TIME: 'MJD',
PHOTOMETRY.MAGNITUDE: str(row['mag']),
PHOTOMETRY.BAND: row['Filter'],
PHOTOMETRY.SOURCE: source
}
if 'system' in metadict[oname]:
photodict[PHOTOMETRY.SYSTEM] = metadict[oname]['system']
if 'l_mag' in row.columns and row['l_mag'] == '>':
photodict[PHOTOMETRY.UPPER_LIMIT] = True
elif 'e_mag' in row.columns:
photodict[PHOTOMETRY.E_MAGNITUDE] = str(row['e_mag'])
if 'Telescope' in row.columns:
photodict[PHOTOMETRY.TELESCOPE] = row['Telescope']
catalog.entries[name].add_photometry(**photodict)
# Arcavi 2016gkg donation
path = os.path.join(catalog.get_current_task_repo(), 'Donations',
'Arcavi-01-24-17', 'SN2016gkg.txt')
with open(path, 'r') as f:
tsvin = list(csv.reader(f, delimiter=' ', skipinitialspace=True))
name, source = catalog.new_entry(
'SN2016gkg', bibcode='2016arXiv161106451A')
for row in tsvin:
if row[0][0] == '#':
continue
mjd = str(jd_to_mjd(Decimal(row[0])))
tel = row[1]
band = row[3]
mag = row[4]
err = row[5]
limit = row[6] == 'True'
photodict = {
PHOTOMETRY.TIME: mjd,
PHOTOMETRY.U_TIME: 'MJD',
PHOTOMETRY.TELESCOPE: tel,
PHOTOMETRY.BAND: band,
PHOTOMETRY.MAGNITUDE: mag,
PHOTOMETRY.SOURCE: source
}
if limit:
photodict[PHOTOMETRY.UPPER_LIMIT] = True
else:
photodict[PHOTOMETRY.E_MAGNITUDE] = err
catalog.entries[name].add_photometry(**photodict)
# Nicholl Gaia16apd donation
path = os.path.join(catalog.get_current_task_repo(), 'Donations',
'Nicholl-01-20-17', 'gaia16apd_phot.txt')
data = read(path, format='cds')
name, source = catalog.new_entry(
'Gaia16apd', bibcode='2017ApJ...835L...8N')
for row in pbar(data, task_str + ': Nicholl Gaia16apd'):
photodict = {
PHOTOMETRY.TIME: str(row['MJD']),
PHOTOMETRY.U_TIME: 'MJD',
PHOTOMETRY.MAGNITUDE: str(row['mag']),
PHOTOMETRY.BAND: row['Filter'],
PHOTOMETRY.TELESCOPE: row['Telescope'],
PHOTOMETRY.SOURCE: source
}
if row['l_mag'] == '>':
photodict[PHOTOMETRY.UPPER_LIMIT] = True
else:
photodict[PHOTOMETRY.E_MAGNITUDE] = str(row['e_mag'])
catalog.entries[name].add_photometry(**photodict)
# Kuncarayakti-01-09-17
datafile = os.path.join(catalog.get_current_task_repo(), 'Donations',
'Kuncarayakti-01-09-17', 'SN1978K.dat')
inpname = os.path.basename(datafile).split('.')[0]
with open(datafile, 'r') as f:
tsvin = csv.reader(f, delimiter=' ', skipinitialspace=True)
host = False
for ri, row in enumerate(tsvin):
if ri == 0:
continue
if row[0][0] == '#':
rsplit = [x.strip('# ') for x in ' '.join(row).split(',')]
bc = rsplit[0]
tel, ins = '', ''
if len(rsplit) > 1:
tel = rsplit[1]
if len(rsplit) > 2:
ins = rsplit[2]
continue
(name, source) = catalog.new_entry(inpname, bibcode=bc)
mag = row[4]
err = row[5]
mjd = str(astrotime('-'.join(row[:3]), format='iso').mjd)
photodict = {
PHOTOMETRY.BAND: row[3],
PHOTOMETRY.TIME: mjd,
PHOTOMETRY.U_TIME: 'MJD',
PHOTOMETRY.MAGNITUDE: mag.strip('>s'),
PHOTOMETRY.SOURCE: source
}
if is_number(err):
photodict[PHOTOMETRY.E_MAGNITUDE] = err
if tel:
photodict[PHOTOMETRY.TELESCOPE] = tel
if ins:
photodict[PHOTOMETRY.INSTRUMENT] = ins
if '>' in mag:
photodict[PHOTOMETRY.UPPER_LIMIT] = True
if 's' in mag:
photodict[PHOTOMETRY.SYNTHETIC] = True
catalog.entries[name].add_photometry(**photodict)
# Nugent 01-09-17 donation
file_names = glob(
os.path.join(catalog.get_current_task_repo(), 'Donations',
'Nugent-01-09-17', '*.dat'))
for datafile in pbar_strings(file_names, task_str + ': Nugent-01-09-17'):
inpname = os.path.basename(datafile).split('.')[0]
(name, source) = catalog.new_entry(
inpname, bibcode='2006ApJ...645..841N')
with open(datafile, 'r') as f:
tsvin = csv.reader(f, delimiter=' ', skipinitialspace=True)
host = False
for urow in tsvin:
row = list(filter(None, urow))
counts = row[2]
e_counts = row[3]
zp = row[4]
photodict = {
PHOTOMETRY.BAND: row[1],
PHOTOMETRY.TIME: row[0],
PHOTOMETRY.U_TIME: 'MJD',
PHOTOMETRY.COUNT_RATE: counts,
PHOTOMETRY.E_COUNT_RATE: e_counts,
PHOTOMETRY.ZERO_POINT: zp,
PHOTOMETRY.TELESCOPE: 'CFHT',
PHOTOMETRY.SURVEY: 'SNLS',
PHOTOMETRY.SOURCE: source
}
set_pd_mag_from_counts(photodict, counts, ec=e_counts, zp=zp,
sig=5.0)
catalog.entries[name].add_photometry(**photodict)
# Inserra 09-04-16 donation
file_names = glob(
os.path.join(catalog.get_current_task_repo(), 'Donations',
'Inserra-09-04-16', '*.txt'))
for datafile in pbar_strings(file_names, task_str + ': Inserra-09-04-16'):
inpname = os.path.basename(datafile).split('.')[0]
(name, source) = catalog.new_entry(
inpname, bibcode='2013ApJ...770..128I')
with open(datafile, 'r') as f:
tsvin = csv.reader(f, delimiter=' ', skipinitialspace=True)
host = False
for row in tsvin:
if row[0][0] == '#':
if row[0] == '#Host':
host = True
continue
host = False
bands = row[3:-1]
continue
for bi, ba in enumerate(bands):
mag = row[5 + 2 * bi]
if not is_number(mag):
continue
system = 'AB'
if ba in ['U', 'B', 'V', 'R', 'I', 'J', 'H', 'K']:
system = 'Vega'
photodict = {
PHOTOMETRY.TIME: row[3],
PHOTOMETRY.U_TIME: 'MJD',
PHOTOMETRY.BAND: ba,
PHOTOMETRY.MAGNITUDE: mag.strip('< '),
PHOTOMETRY.SOURCE: source,
PHOTOMETRY.SYSTEM: system
}
if 'ATel' not in row[-1]:
photodict[PHOTOMETRY.TELESCOPE] = row[-1]
if host:
photodict[PHOTOMETRY.HOST] = True
if '<' in mag:
photodict[PHOTOMETRY.UPPER_LIMIT] = True
e_mag = row[5 + 2 * bi + 1].strip('() ')
if is_number(e_mag):
photodict[PHOTOMETRY.E_MAGNITUDE] = e_mag
catalog.entries[name].add_photometry(**photodict)
# Nicholl 04-01-16 donation
with open(
os.path.join(catalog.get_current_task_repo(), 'Donations',
'Nicholl-04-01-16', 'bibcodes.json'), 'r') as f:
bcs = json.loads(f.read())
kcorrected = ['SN2011ke', 'SN2011kf', 'SN2012il', 'PTF10hgi', 'PTF11rks']
ignorephoto = ['PTF10hgi', 'PTF11rks', 'SN2011ke', 'SN2011kf', 'SN2012il']
file_names = glob(
os.path.join(catalog.get_current_task_repo(), 'Donations',
'Nicholl-04-01-16/*.txt'))
for datafile in pbar_strings(file_names, task_str + ': Nicholl-04-01-16'):
inpname = os.path.basename(datafile).split('_')[0]
isk = inpname in kcorrected
name = catalog.add_entry(inpname)
bibcode = ''
for bc in bcs:
if inpname in bcs[bc]:
bibcode = bc
if not bibcode:
raise ValueError('Bibcode not found!')
source = catalog.entries[name].add_source(bibcode=bibcode)
catalog.entries[name].add_quantity(SUPERNOVA.ALIAS, inpname, source)
if inpname in ignorephoto:
continue
with open(datafile, 'r') as f:
tsvin = csv.reader(f, delimiter='\t', skipinitialspace=True)
rtelescope = ''
for r, rrow in enumerate(tsvin):
row = list(filter(None, rrow))
if not row:
continue
if row[0] == '#MJD':
bands = [x for x in row[1:] if x and 'err' not in x]
elif row[0][0] == '#' and len(row[0]) > 1:
rtelescope = row[0][1:]
if row[0][0] == '#':
continue
mjd = row[0]
if not is_number(mjd):
continue
for v, val in enumerate(row[1::2]):
upperlimit = ''
mag = val.strip('>')
emag = row[2 * v + 2]
if '>' in val or (is_number(emag) and float(emag) == 0.0):
upperlimit = True
if (not is_number(mag) or isnan(float(mag)) or
float(mag) > 90.0):
continue
band = bands[v]
instrument = ''
survey = ''
system = ''
telescope = rtelescope
if telescope == 'LSQ':
instrument = 'QUEST'
elif telescope == 'PS1':
instrument = 'GPC'
elif telescope == 'NTT':
instrument = 'EFOSC'
elif telescope == 'GROND':
instrument = 'GROND'
telescope = 'MPI/ESO 2.2m'
else:
if band == 'NUV':
instrument = 'GALEX'
telescope = 'GALEX'
elif band in ['u', 'g', 'r', 'i', 'z']:
if inpname.startswith('PS1'):
instrument = 'GPC'
telescope = 'PS1'
survey = 'Pan-STARRS'
elif inpname.startswith('PTF'):
telescope = 'P60'
survey = 'PTF'
elif band.upper() in ['UVW2', 'UVW1', 'UVM2']:
instrument = 'UVOT'
telescope = 'Swift'
if inpname in ['PTF12dam']:
system = 'AB'
if inpname in ['SCP-06F6']:
system = 'Vega'
photodict = {
PHOTOMETRY.TIME: mjd,
PHOTOMETRY.U_TIME: 'MJD',
PHOTOMETRY.BAND: band,
PHOTOMETRY.MAGNITUDE: mag,
PHOTOMETRY.UPPER_LIMIT: upperlimit,
PHOTOMETRY.SOURCE: source
}
if instrument:
photodict[PHOTOMETRY.INSTRUMENT] = instrument
if telescope:
photodict[PHOTOMETRY.TELESCOPE] = telescope
if survey:
photodict[PHOTOMETRY.SURVEY] = survey
if system:
photodict[PHOTOMETRY.SYSTEM] = system
if (is_number(emag) and
not isnan(float(emag)) and float(emag) > 0.0):
photodict[PHOTOMETRY.E_MAGNITUDE] = emag
if isk:
photodict[PHOTOMETRY.KCORRECTED] = True
catalog.entries[name].add_photometry(**photodict)
catalog.journal_entries()
# Maggi 04-11-16 donation (MC SNRs)
with open(
os.path.join(catalog.get_current_task_repo(), 'Donations',
'Maggi-04-11-16', 'LMCSNRs_OpenSNe.csv')) as f:
tsvin = csv.reader(f, delimiter=',')
for row in pbar(list(tsvin), task_str + ': Maggi-04-11-16/LMCSNRs'):
name = 'MCSNR ' + row[0]
name = catalog.add_entry(name)
ra = row[2]
dec = row[3]
source = (catalog.entries[name]
.add_source(bibcode='2016A&A...585A.162M'))
catalog.entries[name].add_quantity(
SUPERNOVA.ALIAS,
'LMCSNR J' + rep_chars(ra, ' :.') + rep_chars(dec, ' :.'),
source)
catalog.entries[name].add_quantity(SUPERNOVA.ALIAS, name, source)
if row[1] != 'noname':
catalog.entries[name].add_quantity(SUPERNOVA.ALIAS, row[1],
source)
catalog.entries[name].add_quantity(SUPERNOVA.RA, row[2], source)
catalog.entries[name].add_quantity(SUPERNOVA.DEC, row[3], source)
catalog.entries[name].add_quantity(SUPERNOVA.HOST, 'LMC', source)
if row[4] == '1':
catalog.entries[name].add_quantity(SUPERNOVA.CLAIMED_TYPE,
'Ia', source)
elif row[4] == '2':
catalog.entries[name].add_quantity(SUPERNOVA.CLAIMED_TYPE,
'CC', source)
with open(
os.path.join(catalog.get_current_task_repo(), 'Donations',
'Maggi-04-11-16', 'SMCSNRs_OpenSNe.csv')) as f:
tsvin = csv.reader(f, delimiter=',')
for row in pbar(list(tsvin), task_str + ': Maggi-04-11-16/SMCSNRs'):
name = 'MCSNR ' + row[0]
name = catalog.add_entry(name)
source = catalog.entries[name].add_source(name='Pierre Maggi')
ra = row[3]
dec = row[4]
catalog.entries[name].add_quantity(
SUPERNOVA.ALIAS, 'SMCSNR J' + ra.replace(
':', '')[:6] + dec.replace(':', '')[:7], source)
catalog.entries[name].add_quantity(SUPERNOVA.ALIAS, name, source)
catalog.entries[name].add_quantity(SUPERNOVA.ALIAS, row[1], source)
catalog.entries[name].add_quantity(SUPERNOVA.ALIAS, row[2], source)
catalog.entries[name].add_quantity(SUPERNOVA.RA, row[3], source)
catalog.entries[name].add_quantity(SUPERNOVA.DEC, row[4], source)
catalog.entries[name].add_quantity(SUPERNOVA.HOST, 'SMC', source)
catalog.journal_entries()
# Galbany 04-18-16 donation
folders = next(
os.walk(
os.path.join(catalog.get_current_task_repo(), 'Donations',
'Galbany-04-18-16/')))[1]
bibcode = '2016AJ....151...33G'
for folder in folders:
infofiles = glob(
os.path.join(catalog.get_current_task_repo(), 'Donations',
'Galbany-04-18-16/') + folder + '/*.info')
photfiles = glob(
os.path.join(catalog.get_current_task_repo(), 'Donations',
'Galbany-04-18-16/') + folder + '/*.out*')
zhel = ''
zcmb = ''
zerr = ''
for path in infofiles:
with open(path, 'r') as f:
lines = f.read().splitlines()
for line in lines:
splitline = line.split(':')
field = splitline[0].strip().lower()
value = splitline[1].strip()
if field == 'name':
name = value[:6].upper()
name += (value[6].upper()
if len(value) == 7 else value[6:])
name = catalog.add_entry(name)
source = (catalog.entries[name]
.add_source(bibcode=bibcode))
catalog.entries[name].add_quantity(SUPERNOVA.ALIAS,
name, source)
elif field == 'type':
claimedtype = value.replace('SN', '')
catalog.entries[name].add_quantity(
SUPERNOVA.CLAIMED_TYPE, claimedtype, source)
elif field == 'zhel':
zhel = value
elif field == 'redshift_error':
zerr = value
elif field == 'zcmb':
zcmb = value
elif field == 'ra':
catalog.entries[name].add_quantity(
SUPERNOVA.RA,
value,
source,
u_value='floatdegrees')
elif field == 'dec':
catalog.entries[name].add_quantity(
SUPERNOVA.DEC,
value,
source,
u_value='floatdegrees')
elif field == 'host':
value = value.replace('- ', '-').replace('G ', 'G')
catalog.entries[name].add_quantity(SUPERNOVA.HOST,
value, source)
elif field == 'e(b-v)_mw':
catalog.entries[name].add_quantity(SUPERNOVA.EBV,
value, source)
catalog.entries[name].add_quantity(
SUPERNOVA.REDSHIFT,
zhel,
source,
e_value=zerr,
kind='heliocentric')
catalog.entries[name].add_quantity(
SUPERNOVA.REDSHIFT, zcmb, source, e_value=zerr, kind='cmb')
for path in photfiles:
with open(path, 'r') as f:
band = ''
lines = f.read().splitlines()
for li, line in enumerate(lines):
if li in [0, 2, 3]:
continue
if li == 1:
band = line.split(':')[-1].strip()
else:
cols = list(filter(None, line.split()))
if not cols:
continue
catalog.entries[name].add_photometry(
time=cols[0],
u_time='MJD',
magnitude=cols[1],
e_magnitude=cols[2],
band=band,
system=cols[3],
telescope=cols[4],
source=source)
catalog.journal_entries()
# Nicholl 05-03-16
files = glob(
os.path.join(catalog.get_current_task_repo(), 'Donations',
'Nicholl-05-03-16', '*.txt'))
name = catalog.add_entry('SN2015bn')
for fi in pbar(files, task_str + ': Nicholl-05-03-16'):
if 'late' in fi:
bc = '2016ApJ...828L..18N'
else:
bc = '2016ApJ...826...39N'
source = catalog.entries[name].add_source(bibcode=bc)
catalog.entries[name].add_quantity(SUPERNOVA.ALIAS, name, source)
catalog.entries[name].add_quantity(SUPERNOVA.ALIAS, 'PS15ae', source)
telescope = os.path.basename(fi).split('_')[1]
with open(fi, 'r') as f:
lines = f.read().splitlines()
for li, line in enumerate(lines):
if not line or (line[0] == '#' and li != 0):
continue
cols = list(filter(None, line.split()))
if not cols:
continue
if li == 0:
bands = cols[1:]
continue
mjd = cols[0]
for ci, col in enumerate(cols[1::2]):
if not is_number(col) or np.isnan(float(col)):
continue
band = bands[ci]
band_set = ''
system = 'Vega'
if bands[ci] in ["u'", "g'", "r'", "i'", "z'"]:
band_set = 'SDSS'
system = 'SDSS'
elif telescope == 'ASASSN':
band_set = 'ASASSN'
system = 'Vega'
photodict = {
PHOTOMETRY.TIME: mjd,
PHOTOMETRY.U_TIME: 'MJD',
PHOTOMETRY.MAGNITUDE: col,
PHOTOMETRY.BAND: bands[ci],
PHOTOMETRY.SOURCE: source,
PHOTOMETRY.TELESCOPE: telescope,
PHOTOMETRY.SYSTEM: system
}
if band_set:
photodict[PHOTOMETRY.BAND_SET] = band_set
emag = cols[2 * ci + 2]
if is_number(emag):
photodict[PHOTOMETRY.E_MAGNITUDE] = emag
else:
photodict[PHOTOMETRY.UPPER_LIMIT] = True
if telescope == 'Swift':
photodict[PHOTOMETRY.INSTRUMENT] = 'UVOT'
catalog.entries[name].add_photometry(**photodict)
catalog.journal_entries()
return
def do_donated_photo(catalog):
"""Import donated photometry."""
task_str = catalog.get_current_task_str()
# Private donations here #
if not catalog.args.travis:
pass
# End private donations #
# Ponder 05-12-17 donation
with open(
os.path.join(catalog.get_current_task_repo(), 'Donations',
'Ponder-05-12-17', 'meta.json'), 'r') as f:
metadict = json.loads(f.read())
file_names = glob(
os.path.join(catalog.get_current_task_repo(), 'Donations',
'Ponder-05-12-17', '*.dat'))
for path in file_names:
with open(path, 'r') as f:
tsvin = list(csv.reader(f, delimiter=' ', skipinitialspace=True))
oname = path.split('/')[-1].split('.')[0]
name, source = catalog.new_entry(oname,
bibcode=metadict[oname]['bibcode'])
for row in pbar(tsvin, task_str + ': Ponder ' + oname):
if row[0][0] == '#' or not is_number(row[-1]):
continue
mjd = row[1]
bandinst = row[2].split('_')
band = bandinst[0]
inst = ''
if len(bandinst) > 1:
inst = bandinst[1]
mag = row[3]
uerr = row[4]
lerr = row[5]
photodict = {
PHOTOMETRY.TIME: mjd,
PHOTOMETRY.U_TIME: 'MJD',
PHOTOMETRY.BAND: band,
PHOTOMETRY.MAGNITUDE: mag,
PHOTOMETRY.E_LOWER_MAGNITUDE: lerr,
PHOTOMETRY.E_UPPER_MAGNITUDE: uerr,
PHOTOMETRY.SOURCE: source
}
if inst:
photodict[PHOTOMETRY.INSTRUMENT] = inst
catalog.entries[name].add_photometry(**photodict)
# Benetti 03-08-17 donation
path = os.path.join(catalog.get_current_task_repo(), 'Donations',
'Benetti-03-08-17', '1999E.dat')
with open(path, 'r') as f:
tsvin = list(csv.reader(f, delimiter=' ', skipinitialspace=True))
name, source = catalog.new_entry('SN1999E',
bibcode='2003MNRAS.340..191R')
bands = None
for row in tsvin:
if not row or row[0][0] == '#':
continue
if not bands:
bands = row[2:-2]
continue
mjd = row[1]
tel = row[-1] if 'IAUC' not in row[-1] else None
for bi, band in enumerate(bands):
mag = row[2 + 2 * bi]
if mag == '9999':
continue
err = row[2 + 2 * bi + 1]
limit = row[6] == 'True'
photodict = {
PHOTOMETRY.TIME: mjd,
PHOTOMETRY.U_TIME: 'MJD',
PHOTOMETRY.TELESCOPE: tel,
PHOTOMETRY.BAND: band,
PHOTOMETRY.MAGNITUDE: mag,
PHOTOMETRY.SOURCE: source
}
if err != '.00':
photodict[PHOTOMETRY.E_MAGNITUDE] = str(Decimal(err))
if tel:
photodict[PHOTOMETRY.TELESCOPE] = tel
catalog.entries[name].add_photometry(**photodict)
# Nicholl 01-29-17 donation
with open(
os.path.join(catalog.get_current_task_repo(), 'Donations',
'Nicholl-01-29-17', 'meta.json'), 'r') as f:
metadict = json.loads(f.read())
file_names = glob(
os.path.join(catalog.get_current_task_repo(), 'Donations',
'Nicholl-01-29-17', '*.txt'))
for path in file_names:
data = read(path, format='cds')
oname = path.split('/')[-1].split('_')[0]
name, source = catalog.new_entry(oname,
bibcode=metadict[oname]['bibcode'])
for row in pbar(data, task_str + ': Nicholl ' + oname):
photodict = {
PHOTOMETRY.TIME: str(row['MJD']),
PHOTOMETRY.U_TIME: 'MJD',
PHOTOMETRY.MAGNITUDE: str(row['mag']),
PHOTOMETRY.BAND: row['Filter'],
PHOTOMETRY.SOURCE: source
}
if 'system' in metadict[oname]:
photodict[PHOTOMETRY.SYSTEM] = metadict[oname]['system']
if 'l_mag' in row.columns and row['l_mag'] == '>':
photodict[PHOTOMETRY.UPPER_LIMIT] = True
elif 'e_mag' in row.columns:
photodict[PHOTOMETRY.E_MAGNITUDE] = str(row['e_mag'])
if 'Telescope' in row.columns:
photodict[PHOTOMETRY.TELESCOPE] = row['Telescope']
catalog.entries[name].add_photometry(**photodict)
# Arcavi 2016gkg donation
path = os.path.join(catalog.get_current_task_repo(), 'Donations',
'Arcavi-01-24-17', 'SN2016gkg.txt')
with open(path, 'r') as f:
tsvin = list(csv.reader(f, delimiter=' ', skipinitialspace=True))
name, source = catalog.new_entry('SN2016gkg',
bibcode='2016arXiv161106451A')
for row in tsvin:
if row[0][0] == '#':
continue
mjd = str(jd_to_mjd(Decimal(row[0])))
tel = row[1]
band = row[3]
mag = row[4]
err = row[5]
limit = row[6] == 'True'
photodict = {
PHOTOMETRY.TIME: mjd,
PHOTOMETRY.U_TIME: 'MJD',
PHOTOMETRY.TELESCOPE: tel,
PHOTOMETRY.BAND: band,
PHOTOMETRY.MAGNITUDE: mag,
PHOTOMETRY.SOURCE: source
}
if limit:
photodict[PHOTOMETRY.UPPER_LIMIT] = True
else:
photodict[PHOTOMETRY.E_MAGNITUDE] = err
catalog.entries[name].add_photometry(**photodict)
# Nicholl Gaia16apd donation
path = os.path.join(catalog.get_current_task_repo(), 'Donations',
'Nicholl-01-20-17', 'gaia16apd_phot.txt')
data = read(path, format='cds')
name, source = catalog.new_entry('Gaia16apd',
bibcode='2017ApJ...835L...8N')
for row in pbar(data, task_str + ': Nicholl Gaia16apd'):
photodict = {
PHOTOMETRY.TIME: str(row['MJD']),
PHOTOMETRY.U_TIME: 'MJD',
PHOTOMETRY.MAGNITUDE: str(row['mag']),
PHOTOMETRY.BAND: row['Filter'],
PHOTOMETRY.TELESCOPE: row['Telescope'],
PHOTOMETRY.SOURCE: source
}
if row['l_mag'] == '>':
photodict[PHOTOMETRY.UPPER_LIMIT] = True
else:
photodict[PHOTOMETRY.E_MAGNITUDE] = str(row['e_mag'])
catalog.entries[name].add_photometry(**photodict)
# Kuncarayakti-01-09-17
datafile = os.path.join(catalog.get_current_task_repo(), 'Donations',
'Kuncarayakti-01-09-17', 'SN1978K.dat')
inpname = os.path.basename(datafile).split('.')[0]
with open(datafile, 'r') as f:
tsvin = csv.reader(f, delimiter=' ', skipinitialspace=True)
host = False
for ri, row in enumerate(tsvin):
if ri == 0:
continue
if row[0][0] == '#':
rsplit = [x.strip('# ') for x in ' '.join(row).split(',')]
bc = rsplit[0]
tel, ins = '', ''
if len(rsplit) > 1:
tel = rsplit[1]
if len(rsplit) > 2:
ins = rsplit[2]
continue
(name, source) = catalog.new_entry(inpname, bibcode=bc)
mag = row[4]
err = row[5]
mjd = str(astrotime('-'.join(row[:3]), format='iso').mjd)
photodict = {
PHOTOMETRY.BAND: row[3],
PHOTOMETRY.TIME: mjd,
PHOTOMETRY.U_TIME: 'MJD',
PHOTOMETRY.MAGNITUDE: mag.strip('>s'),
PHOTOMETRY.SOURCE: source
}
if is_number(err):
photodict[PHOTOMETRY.E_MAGNITUDE] = err
if tel:
photodict[PHOTOMETRY.TELESCOPE] = tel
if ins:
photodict[PHOTOMETRY.INSTRUMENT] = ins
if '>' in mag:
photodict[PHOTOMETRY.UPPER_LIMIT] = True
if 's' in mag:
photodict[PHOTOMETRY.SYNTHETIC] = True
catalog.entries[name].add_photometry(**photodict)
# Nugent 01-09-17 donation
file_names = glob(
os.path.join(catalog.get_current_task_repo(), 'Donations',
'Nugent-01-09-17', '*.dat'))
for datafile in pbar_strings(file_names, task_str + ': Nugent-01-09-17'):
inpname = os.path.basename(datafile).split('.')[0]
(name, source) = catalog.new_entry(inpname,
bibcode='2006ApJ...645..841N')
with open(datafile, 'r') as f:
tsvin = csv.reader(f, delimiter=' ', skipinitialspace=True)
host = False
for urow in tsvin:
row = list(filter(None, urow))
counts = row[2]
e_counts = row[3]
zp = row[4]
photodict = {
PHOTOMETRY.BAND: row[1],
PHOTOMETRY.TIME: row[0],
PHOTOMETRY.U_TIME: 'MJD',
PHOTOMETRY.COUNT_RATE: counts,
PHOTOMETRY.E_COUNT_RATE: e_counts,
PHOTOMETRY.ZERO_POINT: zp,
PHOTOMETRY.TELESCOPE: 'CFHT',
PHOTOMETRY.SURVEY: 'SNLS',
PHOTOMETRY.SOURCE: source
}
set_pd_mag_from_counts(photodict, counts, ec=e_counts, zp=zp)
catalog.entries[name].add_photometry(**photodict)
# Inserra 09-04-16 donation
file_names = glob(
os.path.join(catalog.get_current_task_repo(), 'Donations',
'Inserra-09-04-16', '*.txt'))
for datafile in pbar_strings(file_names, task_str + ': Inserra-09-04-16'):
inpname = os.path.basename(datafile).split('.')[0]
(name, source) = catalog.new_entry(inpname,
bibcode='2013ApJ...770..128I')
with open(datafile, 'r') as f:
tsvin = csv.reader(f, delimiter=' ', skipinitialspace=True)
host = False
for row in tsvin:
if row[0][0] == '#':
if row[0] == '#Host':
host = True
continue
host = False
bands = row[3:-1]
continue
for bi, ba in enumerate(bands):
mag = row[5 + 2 * bi]
if not is_number(mag):
continue
system = 'AB'
if ba in ['U', 'B', 'V', 'R', 'I', 'J', 'H', 'K']:
system = 'Vega'
photodict = {
PHOTOMETRY.TIME: row[3],
PHOTOMETRY.U_TIME: 'MJD',
PHOTOMETRY.BAND: ba,
PHOTOMETRY.MAGNITUDE: mag.strip('< '),
PHOTOMETRY.SOURCE: source,
PHOTOMETRY.SYSTEM: system
}
if 'ATel' not in row[-1]:
photodict[PHOTOMETRY.TELESCOPE] = row[-1]
if host:
photodict[PHOTOMETRY.HOST] = True
if '<' in mag:
photodict[PHOTOMETRY.UPPER_LIMIT] = True
e_mag = row[5 + 2 * bi + 1].strip('() ')
if is_number(e_mag):
photodict[PHOTOMETRY.E_MAGNITUDE] = e_mag
catalog.entries[name].add_photometry(**photodict)
# Nicholl 04-01-16 donation
with open(
os.path.join(catalog.get_current_task_repo(), 'Donations',
'Nicholl-04-01-16', 'bibcodes.json'), 'r') as f:
bcs = json.loads(f.read())
kcorrected = ['SN2011ke', 'SN2011kf', 'SN2012il', 'PTF10hgi', 'PTF11rks']
ignorephoto = ['PTF10hgi', 'PTF11rks', 'SN2011ke', 'SN2011kf', 'SN2012il']
file_names = glob(
os.path.join(catalog.get_current_task_repo(), 'Donations',
'Nicholl-04-01-16/*.txt'))
for datafile in pbar_strings(file_names, task_str + ': Nicholl-04-01-16'):
inpname = os.path.basename(datafile).split('_')[0]
isk = inpname in kcorrected
name = catalog.add_entry(inpname)
bibcode = ''
for bc in bcs:
if inpname in bcs[bc]:
bibcode = bc
if not bibcode:
raise ValueError('Bibcode not found!')
source = catalog.entries[name].add_source(bibcode=bibcode)
catalog.entries[name].add_quantity(SUPERNOVA.ALIAS, inpname, source)
if inpname in ignorephoto:
continue
with open(datafile, 'r') as f:
tsvin = csv.reader(f, delimiter='\t', skipinitialspace=True)
rtelescope = ''
for r, rrow in enumerate(tsvin):
row = list(filter(None, rrow))
if not row:
continue
if row[0] == '#MJD':
bands = [x for x in row[1:] if x and 'err' not in x]
elif row[0][0] == '#' and len(row[0]) > 1:
rtelescope = row[0][1:]
if row[0][0] == '#':
continue
mjd = row[0]
if not is_number(mjd):
continue
for v, val in enumerate(row[1::2]):
upperlimit = ''
mag = val.strip('>')
emag = row[2 * v + 2]
if '>' in val or (is_number(emag) and float(emag) == 0.0):
upperlimit = True
if (not is_number(mag) or isnan(float(mag))
or float(mag) > 90.0):
continue
band = bands[v]
instrument = ''
survey = ''
system = ''
telescope = rtelescope
if telescope == 'LSQ':
instrument = 'QUEST'
elif telescope == 'PS1':
instrument = 'GPC'
elif telescope == 'NTT':
instrument = 'EFOSC'
elif telescope == 'GROND':
instrument = 'GROND'
telescope = 'MPI/ESO 2.2m'
else:
if band == 'NUV':
instrument = 'GALEX'
telescope = 'GALEX'
elif band in ['u', 'g', 'r', 'i', 'z']:
if inpname.startswith('PS1'):
instrument = 'GPC'
telescope = 'PS1'
survey = 'Pan-STARRS'
elif inpname.startswith('PTF'):
telescope = 'P60'
survey = 'PTF'
elif band.upper() in ['UVW2', 'UVW1', 'UVM2']:
instrument = 'UVOT'
telescope = 'Swift'
if inpname in ['PTF12dam']:
system = 'AB'
if inpname in ['SCP-06F6']:
system = 'Vega'
photodict = {
PHOTOMETRY.TIME: mjd,
PHOTOMETRY.U_TIME: 'MJD',
PHOTOMETRY.BAND: band,
PHOTOMETRY.MAGNITUDE: mag,
PHOTOMETRY.UPPER_LIMIT: upperlimit,
PHOTOMETRY.SOURCE: source
}
if instrument:
photodict[PHOTOMETRY.INSTRUMENT] = instrument
if telescope:
photodict[PHOTOMETRY.TELESCOPE] = telescope
if survey:
photodict[PHOTOMETRY.SURVEY] = survey
if system:
photodict[PHOTOMETRY.SYSTEM] = system
if (is_number(emag) and not isnan(float(emag))
and float(emag) > 0.0):
photodict[PHOTOMETRY.E_MAGNITUDE] = emag
if isk:
photodict[PHOTOMETRY.KCORRECTED] = True
catalog.entries[name].add_photometry(**photodict)
catalog.journal_entries()
# Maggi 04-11-16 donation (MC SNRs)
with open(
os.path.join(catalog.get_current_task_repo(), 'Donations',
'Maggi-04-11-16', 'LMCSNRs_OpenSNe.csv')) as f:
tsvin = csv.reader(f, delimiter=',')
for row in pbar(list(tsvin), task_str + ': Maggi-04-11-16/LMCSNRs'):
name = 'MCSNR ' + row[0]
name = catalog.add_entry(name)
ra = row[2]
dec = row[3]
source = (catalog.entries[name].add_source(
bibcode='2016A&A...585A.162M'))
catalog.entries[name].add_quantity(
SUPERNOVA.ALIAS,
'LMCSNR J' + rep_chars(ra, ' :.') + rep_chars(dec, ' :.'),
source)
catalog.entries[name].add_quantity(SUPERNOVA.ALIAS, name, source)
if row[1] != 'noname':
catalog.entries[name].add_quantity(SUPERNOVA.ALIAS, row[1],
source)
catalog.entries[name].add_quantity(SUPERNOVA.RA, row[2], source)
catalog.entries[name].add_quantity(SUPERNOVA.DEC, row[3], source)
catalog.entries[name].add_quantity(SUPERNOVA.HOST, 'LMC', source)
if row[4] == '1':
catalog.entries[name].add_quantity(SUPERNOVA.CLAIMED_TYPE,
'Ia', source)
elif row[4] == '2':
catalog.entries[name].add_quantity(SUPERNOVA.CLAIMED_TYPE,
'CC', source)
with open(
os.path.join(catalog.get_current_task_repo(), 'Donations',
'Maggi-04-11-16', 'SMCSNRs_OpenSNe.csv')) as f:
tsvin = csv.reader(f, delimiter=',')
for row in pbar(list(tsvin), task_str + ': Maggi-04-11-16/SMCSNRs'):
name = 'MCSNR ' + row[0]
name = catalog.add_entry(name)
source = catalog.entries[name].add_source(name='Pierre Maggi')
ra = row[3]
dec = row[4]
catalog.entries[name].add_quantity(
SUPERNOVA.ALIAS, 'SMCSNR J' + ra.replace(':', '')[:6] +
dec.replace(':', '')[:7], source)
catalog.entries[name].add_quantity(SUPERNOVA.ALIAS, name, source)
catalog.entries[name].add_quantity(SUPERNOVA.ALIAS, row[1], source)
catalog.entries[name].add_quantity(SUPERNOVA.ALIAS, row[2], source)
catalog.entries[name].add_quantity(SUPERNOVA.RA, row[3], source)
catalog.entries[name].add_quantity(SUPERNOVA.DEC, row[4], source)
catalog.entries[name].add_quantity(SUPERNOVA.HOST, 'SMC', source)
catalog.journal_entries()
# Galbany 04-18-16 donation
folders = next(
os.walk(
os.path.join(catalog.get_current_task_repo(), 'Donations',
'Galbany-04-18-16/')))[1]
bibcode = '2016AJ....151...33G'
for folder in folders:
infofiles = glob(
os.path.join(catalog.get_current_task_repo(), 'Donations',
'Galbany-04-18-16/') + folder + '/*.info')
photfiles = glob(
os.path.join(catalog.get_current_task_repo(), 'Donations',
'Galbany-04-18-16/') + folder + '/*.out*')
zhel = ''
zcmb = ''
zerr = ''
for path in infofiles:
with open(path, 'r') as f:
lines = f.read().splitlines()
for line in lines:
splitline = line.split(':')
field = splitline[0].strip().lower()
value = splitline[1].strip()
if field == 'name':
name = value[:6].upper()
name += (value[6].upper()
if len(value) == 7 else value[6:])
name = catalog.add_entry(name)
source = (catalog.entries[name].add_source(
bibcode=bibcode))
catalog.entries[name].add_quantity(
SUPERNOVA.ALIAS, name, source)
elif field == 'type':
claimedtype = value.replace('SN', '')
catalog.entries[name].add_quantity(
SUPERNOVA.CLAIMED_TYPE, claimedtype, source)
elif field == 'zhel':
zhel = value
elif field == 'redshift_error':
zerr = value
elif field == 'zcmb':
zcmb = value
elif field == 'ra':
catalog.entries[name].add_quantity(
SUPERNOVA.RA,
value,
source,
u_value='floatdegrees')
elif field == 'dec':
catalog.entries[name].add_quantity(
SUPERNOVA.DEC,
value,
source,
u_value='floatdegrees')
elif field == 'host':
value = value.replace('- ', '-').replace('G ', 'G')
catalog.entries[name].add_quantity(
SUPERNOVA.HOST, value, source)
elif field == 'e(b-v)_mw':
catalog.entries[name].add_quantity(
SUPERNOVA.EBV, value, source)
catalog.entries[name].add_quantity(SUPERNOVA.REDSHIFT,
zhel,
source,
e_value=zerr,
kind='heliocentric')
catalog.entries[name].add_quantity(SUPERNOVA.REDSHIFT,
zcmb,
source,
e_value=zerr,
kind='cmb')
for path in photfiles:
with open(path, 'r') as f:
band = ''
lines = f.read().splitlines()
for li, line in enumerate(lines):
if li in [0, 2, 3]:
continue
if li == 1:
band = line.split(':')[-1].strip()
else:
cols = list(filter(None, line.split()))
if not cols:
continue
catalog.entries[name].add_photometry(
time=cols[0],
u_time='MJD',
magnitude=cols[1],
e_magnitude=cols[2],
band=band,
system=cols[3],
telescope=cols[4],
source=source)
catalog.journal_entries()
# Nicholl 05-03-16
files = glob(
os.path.join(catalog.get_current_task_repo(), 'Donations',
'Nicholl-05-03-16', '*.txt'))
name = catalog.add_entry('SN2015bn')
for fi in pbar(files, task_str + ': Nicholl-05-03-16'):
if 'late' in fi:
bc = '2016ApJ...828L..18N'
else:
bc = '2016ApJ...826...39N'
source = catalog.entries[name].add_source(bibcode=bc)
catalog.entries[name].add_quantity(SUPERNOVA.ALIAS, name, source)
catalog.entries[name].add_quantity(SUPERNOVA.ALIAS, 'PS15ae', source)
telescope = os.path.basename(fi).split('_')[1]
with open(fi, 'r') as f:
lines = f.read().splitlines()
for li, line in enumerate(lines):
if not line or (line[0] == '#' and li != 0):
continue
cols = list(filter(None, line.split()))
if not cols:
continue
if li == 0:
bands = cols[1:]
continue
mjd = cols[0]
for ci, col in enumerate(cols[1::2]):
if not is_number(col) or np.isnan(float(col)):
continue
band = bands[ci]
band_set = ''
system = 'Vega'
if bands[ci] in ["u'", "g'", "r'", "i'", "z'"]:
band_set = 'SDSS'
system = 'SDSS'
elif telescope == 'ASASSN':
band_set = 'ASASSN'
system = 'Vega'
photodict = {
PHOTOMETRY.TIME: mjd,
PHOTOMETRY.U_TIME: 'MJD',
PHOTOMETRY.MAGNITUDE: col,
PHOTOMETRY.BAND: bands[ci],
PHOTOMETRY.SOURCE: source,
PHOTOMETRY.TELESCOPE: telescope,
PHOTOMETRY.SYSTEM: system
}
if band_set:
photodict[PHOTOMETRY.BAND_SET] = band_set
emag = cols[2 * ci + 2]
if is_number(emag):
photodict[PHOTOMETRY.E_MAGNITUDE] = emag
else:
photodict[PHOTOMETRY.UPPER_LIMIT] = True
if telescope == 'Swift':
photodict[PHOTOMETRY.INSTRUMENT] = 'UVOT'
catalog.entries[name].add_photometry(**photodict)
catalog.journal_entries()
return
def do_essence_photo(catalog):
task_str = catalog.get_current_task_str()
ess_path = os.path.join(catalog.get_current_task_repo(), 'ESSENCE',
'obj_table.dat')
data = list(
csv.reader(
open(ess_path, 'r'),
delimiter=' ',
quotechar='"',
skipinitialspace=True))
for row in pbar(data[1:], task_str):
etype = row[2]
if etype.upper().replace('?', '') in catalog.nonsnetypes:
continue
ess_name = 'ESSENCE ' + row[0]
name, source = catalog.new_entry(
ess_name, bibcode='2016ApJS..224....3N')
if row[1] != '---':
catalog.entries[name].add_quantity(SUPERNOVA.ALIAS, 'SN' + row[1],
source)
if etype != '---':
catalog.entries[name].add_quantity(SUPERNOVA.CLAIMED_TYPE, etype,
source)
catalog.entries[name].add_quantity(SUPERNOVA.RA, row[5], source)
catalog.entries[name].add_quantity(SUPERNOVA.DEC, row[6], source)
if is_number(row[11]):
quantdict = {
QUANTITY.VALUE: row[11],
QUANTITY.SOURCE: source,
QUANTITY.KIND: 'host'
}
if is_number(row[12]):
quantdict[QUANTITY.E_VALUE] = row[12]
catalog.entries[name].add_quantity(
[SUPERNOVA.REDSHIFT, SUPERNOVA.HOST_REDSHIFT], **quantdict)
files = glob(
os.path.join(catalog.get_current_task_repo(), 'ESSENCE',
'*clean*.dat'))
for pfile in pbar(files, task_str):
name = 'ESSENCE ' + pfile.split('/')[-1].split('.')[0]
name, source = catalog.new_entry(name, bibcode='2016ApJS..224....3N')
with open(pfile, 'r') as f:
rows = list(csv.reader(f, delimiter=' ', skipinitialspace=True))
for ri, row in enumerate(rows):
if ri == 1:
catalog.entries[name].add_quantity(
SUPERNOVA.REDSHIFT,
row[5],
source,
kind=['spectroscopic', 'heliocentric'])
catalog.entries[name].add_quantity(
SUPERNOVA.REDSHIFT,
row[6],
source,
kind=['spectroscopic', 'cmb'])
continue
if row[0].startswith('#'):
continue
counts = row[3][:6]
lerr = row[4][:6]
uerr = row[5][:6]
zp = 25.0
photodict = {
PHOTOMETRY.TIME: row[1],
PHOTOMETRY.U_TIME: 'MJD',
PHOTOMETRY.BAND: row[2][0],
PHOTOMETRY.COUNT_RATE: counts,
PHOTOMETRY.E_LOWER_COUNT_RATE: lerr,
PHOTOMETRY.E_UPPER_COUNT_RATE: uerr,
PHOTOMETRY.ZERO_POINT: str(zp),
PHOTOMETRY.SOURCE: source,
PHOTOMETRY.TELESCOPE: 'CTIO 4m',
PHOTOMETRY.SYSTEM: 'Natural'
}
set_pd_mag_from_counts(
photodict, counts, ec='', lec=lerr, uec=uerr, zp=zp, sig=5.0)
catalog.entries[name].add_photometry(**photodict)
catalog.journal_entries()
return