def build_filter_library():
if not file_existing_and_readable(os.path.join(get_speclite_filter_path(),'filter_lib.yml')):
print ('Downloading optical filters. This will take a while.\n')
if internet_connection_is_active():
filter_dict={}
filter_dict = download_SVO_filters(filter_dict)
filter_dict = download_grond(filter_dict)
# Ok, finally, we want to keep track of the SVO filters we have
# so we will save this to a YAML file for future reference
with open(os.path.join(get_speclite_filter_path(),'filter_lib.yml'), 'w') as f:
yaml.safe_dump(filter_dict, f, default_flow_style=False)
return True
else:
print ("You do not have the 3ML filter library and you do not have an active internet connection.")
print ("Please connect to the internet to use the 3ML filter library.")
print ("pyspeclite filter library is still available.")
return False
else:
return True
def build_filter_library():
if not file_existing_and_readable(os.path.join(get_speclite_filter_path(),'filter_lib.yml')):
print ('Downloading optical filters. This will take a while.\n')
if internet_connection_is_active():
filter_dict={}
filter_dict = download_SVO_filters(filter_dict)
filter_dict = download_grond(filter_dict)
# Ok, finally, we want to keep track of the SVO filters we have
# so we will save this to a YAML file for future reference
with open(os.path.join(get_speclite_filter_path(),'filter_lib.yml'), 'w') as f:
yaml.safe_dump(filter_dict, f, default_flow_style=False)
return True
else:
print ("You do not have the 3ML filter library and you do not have an active internet connection.")
print ("Please connect to the internet to use the 3ML filter library.")
print ("pyspeclite filter library is still available.")
return False
else:
return True
def cone_search(self, ra, dec, radius):
"""
Searches for sources in a cone of given radius and center
:param ra: decimal degrees, R.A. of the center of the cone
:param dec: decimal degrees, Dec. of the center of the cone
:param radius: radius in degrees
:return: a table with the list of sources
"""
skycoord = SkyCoord(ra=ra * u.degree, dec=dec * u.degree, frame='icrs')
# First check that we have an active internet connection
if not internet_connection_is_active(): # pragma: no cover
raise ConeSearchFailed("It looks like you don't have an active internet connection. Cannot continue.")
with warnings.catch_warnings():
#Ignore all warnings, which are many from the conesearch module
warnings.simplefilter('ignore')
try:
votable = conesearch.conesearch(skycoord, radius,
catalog_db=self.catalog,
verb=3, verbose=True,
cache=False)
except VOSError as exc: # Pragma: no cover
# Download failed
raise ConeSearchFailed("Cone search failed. Reason: %s" % exc.message)
else:
# Download successful
table = votable.to_table()
self._last_query_results = table.to_pandas().set_index('name').sort_values("Search_Offset")
out = self.apply_format(table)
#This is needed to avoid strange errors
del votable
del table
# Save coordinates of center of cone search
self._ra = ra
self._dec = dec
# Make a DataFrame with the name of the source as index
return out
def compute_fermi_relative_mission_times(trigger_time):
"""
If the user has the requests library, this function looks
online to the HEASARC xtime utility and computes other mission
times relative to the input MET
:param trigger_time: a fermi MET
:return: mission time in a python dictionary
"""
mission_dict = collections.OrderedDict()
if trigger_time == 0:
return None
# Complements to Volodymyr Savchenko
xtime_url = "https://heasarc.gsfc.nasa.gov/cgi-bin/Tools/xTime/xTime.pl"
pattern = """<tr>.*?<th scope=row><label for="(.*?)">(.*?)</label></th>.*?<td align=center>.*?</td>.*?<td>(.*?)</td>.*?</tr>"""
args = dict(
time_in_sf=trigger_time,
timesys_in="u",
timesys_out="u",
apply_clock_offset="yes")
if internet_connection_is_active():
content = requests.get(xtime_url, params=args).content
mission_info = re.findall(pattern, content, re.S)
mission_dict['UTC'] = mission_info[0][-1]
mission_dict[mission_info[7][1]] = mission_info[7][2] # LIGO
mission_dict[mission_info[8][1]] = mission_info[8][2] # NUSTAR
mission_dict[mission_info[12][1]] = mission_info[12][2] # RXTE
mission_dict[mission_info[16][1]] = mission_info[16][2] # SUZAKU
mission_dict[mission_info[20][1]] = mission_info[20][2] # SWIFT
mission_dict[mission_info[24][1]] = mission_info[24][2] # CHANDRA
return mission_dict
else:
return None
def compute_fermi_relative_mission_times(trigger_time):
"""
If the user has the requests library, this function looks
online to the HEASARC xtime utility and computes other mission
times relative to the input MET
:param trigger_time: a fermi MET
:return: mission time in a python dictionary
"""
mission_dict = collections.OrderedDict()
if trigger_time == 0:
return None
# Complements to Volodymyr Savchenko
xtime_url = "https://heasarc.gsfc.nasa.gov/cgi-bin/Tools/xTime/xTime.pl"
pattern = """<tr>.*?<th scope=row><label for="(.*?)">(.*?)</label></th>.*?<td align=center>.*?</td>.*?<td>(.*?)</td>.*?</tr>"""
args = dict(
time_in_sf=trigger_time,
timesys_in="u",
timesys_out="u",
apply_clock_offset="yes",
)
if internet_connection_is_active():
content = requests.get(xtime_url, params=args).content
mission_info = re.findall(pattern, content, re.S)
mission_dict["UTC"] = mission_info[0][-1]
mission_dict[mission_info[7][1]] = mission_info[7][2] # LIGO
mission_dict[mission_info[8][1]] = mission_info[8][2] # NUSTAR
mission_dict[mission_info[12][1]] = mission_info[12][2] # RXTE
mission_dict[mission_info[16][1]] = mission_info[16][2] # SUZAKU
mission_dict[mission_info[20][1]] = mission_info[20][2] # SWIFT
mission_dict[mission_info[24][1]] = mission_info[24][2] # CHANDRA
return mission_dict
else:
return None
import shutil
import pytest
from threeML import *
from threeML.io.network import internet_connection_is_active
from threeML.exceptions.custom_exceptions import TriggerDoesNotExist
skip_if_internet_is_not_available = pytest.mark.skipif(
not internet_connection_is_active(),
reason="No active internet connection")
@skip_if_internet_is_not_available
@pytest.mark.xfail
def test_download_GBM_data():
# test good trigger names
good_triggers = ['080916009', 'bn080916009', 'GRB080916009']
which_detector = 'n1'
for i, trigger in enumerate(good_triggers):
temp_dir = '_download_temp'
dl_info = download_GBM_trigger_data(trigger_name=trigger,
detectors=[which_detector],
destination_directory=temp_dir)
assert os.path.exists(dl_info[which_detector]['rsp'])
assert os.path.exists(dl_info[which_detector]['tte'])
import pytest
from threeML import *
from threeML.io.network import internet_connection_is_active
skip_if_internet_is_not_available = pytest.mark.skipif(not internet_connection_is_active(),
reason="No active internet connection")
@skip_if_internet_is_not_available
#@pytest.mark.xfail
def test_gbm_catalog():
gbm_catalog = FermiGBMBurstCatalog()
_ = gbm_catalog.cone_search(0.0, 0.0, 5.0)
assert gbm_catalog.ra_center == 0.0
assert gbm_catalog.dec_center == 0.0
gbm_catalog.search_around_source('Crab', 5.0)
models = ['band','comp','plaw','sbpl']
intervals = ['peak','fluence']
for model in models:
for interval in intervals:
_ = gbm_catalog.get_model(model=model,interval=interval)
gbm_catalog.query('t90 >2')
import shutil
import pytest
from threeML import *
from threeML.io.network import internet_connection_is_active
from threeML.exceptions.custom_exceptions import TriggerDoesNotExist
skip_if_internet_is_not_available = pytest.mark.skipif(not internet_connection_is_active(),
reason="No active internet connection")
@skip_if_internet_is_not_available
@pytest.mark.xfail
def test_download_LAT_data():
# Crab
ra = 83.6331
dec = 22.0199
tstart = '2010-01-01 00:00:00'
tstop = '2010-01-02 00:00:00'
temp_dir = '_download_temp'
ft1, ft2 = download_LAT_data(ra, dec, 20.0,
tstart, tstop, time_type='Gregorian',
destination_directory=temp_dir)
assert os.path.exists(ft1)
assert os.path.exists(ft2)
def cone_search(self, ra, dec, radius):
"""
Searches for sources in a cone of given radius and center
:param ra: decimal degrees, R.A. of the center of the cone
:param dec: decimal degrees, Dec. of the center of the cone
:param radius: radius in degrees
:return: a table with the list of sources
"""
skycoord = SkyCoord(ra=ra * u.degree, dec=dec * u.degree, frame="icrs")
# First check that we have an active internet connection
if not internet_connection_is_active(): # pragma: no cover
raise ConeSearchFailed(
"It looks like you don't have an active internet connection. Cannot continue."
)
with warnings.catch_warnings():
# Ignore all warnings, which are many from the conesearch module
warnings.simplefilter("ignore")
try:
votable = conesearch.conesearch(
skycoord,
radius,
catalog_db=self.catalog,
verb=3,
verbose=True,
cache=False,
)
except VOSError as exc: # Pragma: no cover
# Download failed
raise ConeSearchFailed("Cone search failed. Reason: %s" %
exc.message)
else:
# Download successful
table = votable
# Workaround to comply with newer versions of astroquery
if isinstance(votable, astropy.io.votable.tree.Table):
table = votable.to_table()
if table is None:
log.error("Your search returned nothing")
return None
table.convert_bytestring_to_unicode()
pandas_df = (table.to_pandas().set_index("name").sort_values(
"Search_Offset"))
str_df = pandas_df.select_dtypes([object])
if astropy_old:
str_df = str_df.stack().str.decode("utf-8").unstack()
for col in str_df:
pandas_df[col] = str_df[col]
if astropy_old:
new_index = [x.decode("utf-8") for x in pandas_df.index]
pandas_df.index = new_index
self._last_query_results = pandas_df
out = self.apply_format(table)
# This is needed to avoid strange errors
del votable
del table
# Save coordinates of center of cone search
self._ra = ra
self._dec = dec
# Make a DataFrame with the name of the source as index
return out
import shutil
import os
import pytest
from threeML import *
from threeML.exceptions.custom_exceptions import TriggerDoesNotExist
from threeML.io.network import internet_connection_is_active
skip_if_internet_is_not_available = pytest.mark.skipif(
not internet_connection_is_active(), reason="No active internet connection"
)
try:
import GtApp
except ImportError:
has_Fermi = False
else:
has_Fermi = True
# This defines a decorator which can be applied to single tests to
# skip them if the condition is not met
skip_if_LAT_is_not_available = pytest.mark.skipif(not has_Fermi,
reason="Fermi Science Tools not installed",
)
def cone_search(self, ra, dec, radius):
"""
Searches for sources in a cone of given radius and center
:param ra: decimal degrees, R.A. of the center of the cone
:param dec: decimal degrees, Dec. of the center of the cone
:param radius: radius in degrees
:return: a table with the list of sources
"""
skycoord = SkyCoord(ra=ra * u.degree, dec=dec * u.degree, frame='icrs')
# First check that we have an active internet connection
if not internet_connection_is_active(): # pragma: no cover
raise ConeSearchFailed(
"It looks like you don't have an active internet connection. Cannot continue."
)
with warnings.catch_warnings():
#Ignore all warnings, which are many from the conesearch module
warnings.simplefilter('ignore')
try:
votable = conesearch.conesearch(skycoord,
radius,
catalog_db=self.catalog,
verb=3,
verbose=True,
cache=False)
except VOSError as exc: # Pragma: no cover
# Download failed
raise ConeSearchFailed("Cone search failed. Reason: %s" %
exc.message)
else:
# Download successful
table = votable.to_table()
self._last_query_results = table.to_pandas().set_index(
'name').sort_values("Search_Offset")
out = self.apply_format(table)
#This is needed to avoid strange errors
del votable
del table
# Save coordinates of center of cone search
self._ra = ra
self._dec = dec
# Make a DataFrame with the name of the source as index
return out
