def ensure_utc(tm, str_allowed):
'''
Helper function to convert a time object (Time, datetime, or UTC string
if str_allowed == True) into UTC before passing it to WWT.
str_allowed is True for wwt.set_current_time (core.py) and False for TableLayer's 'time_att' implementation (layers.py).
'''
if tm is None:
utc_tm = datetime.utcnow().astimezone(pytz.UTC).isoformat()
elif isinstance(tm, datetime):
if tm.tzinfo is None:
utc_tm = pytz.utc.localize(tm).isoformat()
elif tm.tzinfo == pytz.UTC:
utc_tm = tm.isoformat()
else: # has a non-UTC time zone
utc_tm = tm.astimezone(pytz.UTC).isoformat()
elif isinstance(tm, Time):
utc_tm = tm.to_datetime(pytz.UTC).isoformat()
else:
if str_allowed: # is an ISOT string
dt = Time(tm, format='isot').to_datetime(pytz.UTC)
utc_tm = dt.isoformat()
else:
raise ValueError('Time must be a datetime or astropy.Time object')
return utc_tm
def standardizeMetadata(self):
run = self.header["RUN"].strip()
field = self.header["FIELD"].strip()
filter = self.header["COLOUR"].strip()
chip = self.header["CHIP"]
sciProg = f"{run}-{field}-{filter}-{chip}"
# TODO: Fix datetimes
# There is a timesys key but I have no idea how to generically instantiate
# timezone aware datetime and astropy Time seems not to work well with
# Django - the astrometadata is also broken!
if "UTC" in self.header["TIMESYS"].upper():
tzinfo = timezone.utc
else:
raise ValueError("Can not recognize time scale system that is used?")
jdstart = Time(self.header["JDSTART"], format="jd", scale="utc")
jdstart = jdstart.utc.datetime
jdstart = jdstart.replace(tzinfo=tzinfo)
jdend = Time(self.header["JDSTART"], format="jd", scale="utc")
jdend = jdend.utc.datetime
jdend = jdend.replace(tzinfo=tzinfo)
# TODO: filter out what is the filter standardization here?
meta = Metadata(
obs_lon=self.header["LOGITUD"],
obs_lat=self.header["LATITUD"],
obs_height=self.header["HEIGHT"],
datetime_begin=jdstart.isoformat(),
datetime_end=jdend.isoformat(),
telescope=self.header["OBSTEL"].strip(),
instrument=self.header["CAMERA"].strip(),
science_program=sciProg,
exposure_duration=self.header["EXPTIME"],
filter_name=self.header["COLOUR"].strip()
)
return meta
def main(pem_file,
app_id_file,
repo_owner,
repo_name,
time_window,
all_issues=False):
t1 = Time.now()
# templates are stored relative to the script dir
# stored one level up, find the parent directory
# and split the parent directory away
script_dir = os.path.dirname(os.path.realpath(__file__))
split_dir = os.path.split(script_dir)
template_dir = os.path.join(split_dir[0], "templates")
env = Environment(loader=FileSystemLoader(template_dir), trim_blocks=True)
jd_today = int(np.floor(t1.jd))
jd_list = []
if sys.version_info[0] < 3:
# py2
computer_hostname = os.uname()[1]
else:
# py3
computer_hostname = os.uname().nodename
all_tables = []
table = {}
table["title"] = "Commissioning Daily Logs"
table[
"div_style"] = 'style="max-height: 82%; text-align: center; overflow-x: auto; overflow-y: scroll;"'
table["colsize"] = "12"
table["headers"] = [
"Julian Date",
"Related Issues",
"Log Labels",
"Nightly Notebook",
"RFI Notebook",
"New Issues Opened<br>On This Day",
"Total Open Issues<br>On This Day",
]
table["rows"] = []
with open(pem_file, "r") as key_file:
key = key_file.read()
with open(app_id_file, "r") as id_file:
app_id = int(id_file.read())
gh = github3.github.GitHub()
if args.repo_name == "HERA_Commissioning":
gh.login_as_app(key.encode(), app_id)
app = gh.authenticated_app()
inst = gh.app_installation_for_repository(repo_owner, repo_name)
gh.login_as_app_installation(key.encode(), app.id, inst.id)
else:
gh = github3.github.GitHub()
repo = gh.repository(repo_owner, repo_name)
if all_issues:
if args.repo_name == "HERA_Commissioning":
issues = repo.issues(labels="Daily", )
else:
issues = repo.issues(state="open", )
else:
if args.repo_name == "HERA_Commissioning":
issues = repo.issues(labels="Daily",
since=datetime.now(timezone.utc) -
timedelta(days=30))
else:
issues = repo.issues(state="open",
since=datetime.now(timezone.utc) -
timedelta(days=30))
notebook_link = ("https://github.com/HERA-Team/H3C_plots"
"/blob/master/data_inspect_{}.ipynb")
rfi_link = ("https://github.com/alphatangojuliett/HERA_daily_RFI"
"/blob/herapost-master/daily_RFI_report_{}.ipynb")
label_issue_link = ("https://github.com/{owner}/{repo}".format(
owner=repo_owner, repo=repo_name) +
'/issues?q=is%3Aissue+is%3Aopen+label%3A"{url}"')
# replace the github.com with nbviwer.juptyer.org/github for actual
# viewing link
notebook_view = notebook_link.replace("github.com",
"nbviewer.jupyter.org/github")
rfi_view = rfi_link.replace("github.com", "nbviewer.jupyter.org/github")
full_issue_iter = repo.issues(state="all")
for cnt, issue in enumerate(issues):
row = {}
try:
jd = int(issue.title.split(" ")[-1])
obs_date = Time(jd, format="jd")
except ValueError:
obs_date = Time(2458750 - cnt * 5, format="jd")
jd = int(np.floor(obs_date.jd))
jd_list.insert(0, jd)
obs_date = dateparser.parse(obs_date.iso).astimezone(timezone.utc)
obs_end = obs_date + timedelta(days=1)
# count the number of issues opened in this day
# cound the number of total issues on this day
num_opened = 0
num_open_on_day = 0
for _iss in full_issue_iter:
if obs_date <= _iss.created_at.astimezone(timezone.utc) <= obs_end:
num_opened += 1
if _iss.created_at.astimezone(timezone.utc) <= obs_end:
if (_iss.closed_at is not None and
_iss.closed_at.astimezone(timezone.utc) >= obs_end):
num_open_on_day += 1
elif _iss.closed_at is None:
num_open_on_day += 1
else:
pass
# See if the nightly notebook is up for that day
request = requests.get(notebook_link.format(jd))
if request.status_code == 200:
url = notebook_view.format(jd)
notebook = '<a target="_blank" href={url}>View</a>'.format(url=url)
else:
notebook = "N/A"
request_date = obs_date.isoformat().split("T")[0].replace("-", "")
# See if the RFI notebook is up for that day
request = requests.get(rfi_link.format(request_date))
if request.status_code == 200:
url = rfi_view.format(request_date)
rfi_notebook = '<a target="_blank" href={url}>View</a>'.format(
url=url)
else:
rfi_notebook = "N/A"
link = issue.url.replace("api.", "").replace("repos/", "")
other_labels = [
lab.name for lab in issue.labels() if lab.name != "Daily"
]
other_labels = [('<a target="_blank" href=' + label_issue_link +
">{label}</a>").format(url=label.replace(" ", "+"),
label=label)
for label in other_labels]
display_text = '<a target="_blank" href={url}>{number}</a>'.format(
url=link, number=jd)
iss_urls = re.findall(github_link_regex, issue.body_html)
related_issues = []
for url in iss_urls:
url = url
num = url.split("/")[-1]
related_issues.append(
'<a target="_blank" href={url}>{num}</a>'.format(url=url,
num=num))
related_issues = [
iss + "<br>" * (iss_cnt % 3 == 2)
for iss_cnt, iss in enumerate(related_issues)
]
row["text"] = [
display_text,
" ".join(related_issues),
"<br>".join(other_labels),
notebook,
rfi_notebook,
num_opened,
num_open_on_day,
]
table["rows"].append(row)
jd_list = np.sort(jd_list)
full_jd_range = np.arange(jd_today - time_window, jd_today + 1)
for jd in full_jd_range:
if jd not in jd_list:
row = {}
# See if the nightly notebook is up for that day
request = requests.get(notebook_link.format(jd))
if request.status_code == 200:
url = notebook_view.format(jd)
notebook = '<a target="_blank" href={url}>View</a>'.format(
url=url)
else:
notebook = "N/A"
obs_date = Time(jd, format="jd")
request_date = obs_date.isot.split("T")[0].replace("-", "")
# See if the RFI notebook is up for that day
request = requests.get(rfi_link.format(request_date))
if request.status_code == 200:
url = rfi_view.format(request_date)
rfi_notebook = '<a target="_blank" href={url}>View</a>'.format(
url=url)
else:
rfi_notebook = "N/A"
log_url = ("https://github.com/HERA-Team/HERA_Commissioning/issues"
"/new?assignees=&labels=Daily&template=daily-log.md"
"&title=Observing+report+{}").format(jd)
display_text = '<a target="_blank" href={url}>{jd} No Entry</a>'.format(
url=log_url, jd=jd)
row["text"] = [
display_text, "", "", notebook, rfi_notebook, "-", "-"
]
# bisect assumes monotonically increasing
# but we want descending so we'll flip
# the index around the length of the list
index = bisect.bisect_left(jd_list, jd)
table["rows"].insert(len(jd_list) - index, row)
all_tables.append(table)
html_template = env.get_template("tables_with_footer.html")
rendered_html = html_template.render(
tables=all_tables,
gen_date=Time.now().iso,
gen_time_unix_ms=Time.now().unix * 1000,
scriptname=os.path.basename(__file__),
hostname=computer_hostname,
)
with open("issue_log.html", "w") as h_file:
h_file.write(rendered_html)
print("Execution Length: ", (Time.now() - t1).to("min"))
return
def mjdToDate(mjd):
dt = Time(mjd, format='mjd').datetime
str = dt.isoformat()
str = str.replace('-', '/')
return str
# SDSS 082346.00+201557.13
starRA = ephem.hours('08:23:46.00')
starDec = ephem.degrees('+20:15:57.13')
observatory_minHorizon = '25:00:00'
apo = ephem.Observer()
apo.lat = '32.0:46.0:49.0'
apo.long = '-105.0:49.0:13.0'
apo.elevation = 2788.0 # m
apo.temp = 10.0 ## Celsius
apo.horizon = observatory_minHorizon
airmass = np.zeros_like(times)
for i, t in enumerate(times):
t_dt = Time(t, format='jd', scale='utc').datetime
apo.date = t_dt.isoformat(' ')
star = ephem.FixedBody()
star._ra = ephem.hours(starRA)
star._dec = ephem.degrees(starDec)
star.compute(apo)
z = np.pi/2 - float(star.alt)
airmass[i] = 1./np.cos(z)
####################################
# Fit airmass to the light curve
def amtrend(p, t, airmass=airmass):
'''p = [OOT flux, airmass coeff]'''
return p[0]*(1 + p[1]*(airmass-1))
def errfunc(p, t, y, airmass=airmass):
# SDSS 082346.00+201557.13
starRA = ephem.hours('08:23:46.00')
starDec = ephem.degrees('+20:15:57.13')
observatory_minHorizon = '25:00:00'
apo = ephem.Observer()
apo.lat = '32.0:46.0:49.0'
apo.long = '-105.0:49.0:13.0'
apo.elevation = 2788.0 # m
apo.temp = 10.0 ## Celsius
apo.horizon = observatory_minHorizon
airmass = np.zeros_like(times)
for i, t in enumerate(times):
t_dt = Time(t, format='jd', scale='utc').datetime
apo.date = t_dt.isoformat(' ')
star = ephem.FixedBody()
star._ra = ephem.hours(starRA)
star._dec = ephem.degrees(starDec)
star.compute(apo)
z = np.pi / 2 - float(star.alt)
airmass[i] = 1. / np.cos(z)
####################################
# Fit airmass to the light curve
def amtrend(p, t, airmass=airmass):
'''p = [OOT flux, airmass coeff]'''
return p[0] * (1 + p[1] * (airmass - 1))
def errfunc(p, t, y, airmass=airmass):
