Skip to content

Commit

Permalink
SN --> transient in code
Browse files Browse the repository at this point in the history
  • Loading branch information
@alexandergagliano
alexandergagliano committed Feb 10, 2024
1 parent 1bf4814 commit 289055e
Show file tree
Hide file tree
Showing 2 changed files with 36 additions and 36 deletions.
56 changes: 28 additions & 28 deletions astro_ghost/ghostHelperFunctions.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -556,15 +556,15 @@ def fullData(GHOSTpath=''):
fullTable = pd.read_csv(GHOSTpath+"/database/GHOST.csv")
return fullTable

def getTransientHosts(transientName=[''], snCoord=[''], snClass=[''], verbose=False, starcut='normal', ascentMatch=False, GLADE=True, px=800, savepath='./', GHOSTpath='', redo_search=True):
def getTransientHosts(transientName=[''], transientCoord=[''], snClass=[''], verbose=False, starcut='normal', ascentMatch=False, GLADE=True, px=800, savepath='./', GHOSTpath='', redo_search=True):
"""The wrapper function for the main host association pipeline. The function first
searches the pre-existing GHOST database by transient name, then by transient coordinates, and finally
associates the remaining transients not found.
:param transientName: List of transients to associate.
:type transientName: array-like
:param snCoord: List of astropy SkyCoord transient positions.
:type snCoord: array-like
:param transientCoord: List of astropy SkyCoord transient positions.
:type transientCoord: array-like
:param snClass: List of transient classifications (if they exist).
:type snClass: array-like
:param verbose: If True, print logging information.
Expand Down Expand Up @@ -592,20 +592,20 @@ def getTransientHosts(transientName=[''], snCoord=[''], snClass=[''], verbose=Fa
if len(transientName) < 1:
transientName = []
print("No transient names listed, adding placeholder names...")
for i in np.arange(len(snCoord)):
for i in np.arange(len(transientCoord)):
transientName.append("Transient_%i" % (i+1))
hostDB = None
tempHost1 = tempHost2 = tempHost3 = None
found_by_name = found_by_coord = found_by_manual = 0
if not isinstance(snCoord, list) and not isinstance(snCoord, np.ndarray):
snCoord = [snCoord]
if not isinstance(transientCoord, list) and not isinstance(transientCoord, np.ndarray):
transientCoord = [transientCoord]
transientName = [transientName]
snClass = [snClass]
if len(snClass) != len(transientName):
snClass = ['']*len(transientName)

transientName = [x.replace(" ", "") for x in transientName]
df_transients = pd.DataFrame({'Name':np.array(transientName), 'snCoord':np.array(snCoord), 'snClass':np.array(snClass)})
df_transients = pd.DataFrame({'Name':np.array(transientName), 'transientCoord':np.array(transientCoord), 'snClass':np.array(snClass)})

tempHost1, notFoundNames = getDBHostFromTransientName(transientName, GHOSTpath)
found_by_name = len(transientName) - len(notFoundNames)
Expand All @@ -616,41 +616,41 @@ def getTransientHosts(transientName=[''], snCoord=[''], snClass=[''], verbose=Fa

df_transients_remaining = df_transients[df_transients['Name'].isin(notFoundNames)]

snCoord_remaining = df_transients_remaining['snCoord'].values
transientCoord_remaining = df_transients_remaining['transientCoord'].values

tempHost2, notFoundCoords = getDBHostFromTransientCoords(snCoord_remaining, GHOSTpath);
tempHost2, notFoundCoords = getDBHostFromTransientCoords(transientCoord_remaining, GHOSTpath);
found_by_coord = len(transientName) - len(notFoundCoords) - found_by_name
if tempHost2 is None or len(notFoundCoords) > 0:
if verbose:
print("%i transients not found in GHOST by name or coordinates, manually associating..."% len(notFoundCoords))

df_transients_remaining = df_transients_remaining[df_transients_remaining['snCoord'].isin(notFoundCoords)]
df_transients_remaining = df_transients_remaining[df_transients_remaining['transientCoord'].isin(notFoundCoords)]

transientName_remaining = df_transients_remaining['Name'].values
snCoord_remaining = df_transients_remaining['snCoord'].values
transientCoord_remaining = df_transients_remaining['transientCoord'].values
snClass_remaining = df_transients_remaining['snClass'].values

tempHost3 = findNewHosts(transientName_remaining, snCoord_remaining, snClass_remaining, verbose, starcut, ascentMatch, px, savepath, GLADE=GLADE)
tempHost3 = findNewHosts(transientName_remaining, transientCoord_remaining, snClass_remaining, verbose, starcut, ascentMatch, px, savepath, GLADE=GLADE)

if (len(transientName_remaining) > 0) and (len(tempHost3)==0) and (redo_search):
#bump up the search radius to 150 arcsec for extremely low-redshift hosts...
if verbose:
print("Couldn't find any hosts! Trying again with a search radius of 150''.")
tempHost3 = findNewHosts(transientName_remaining, snCoord_remaining, snClass_remaining, verbose, starcut, ascentMatch, px, savepath, 150)
tempHost3 = findNewHosts(transientName_remaining, transientCoord_remaining, snClass_remaining, verbose, starcut, ascentMatch, px, savepath, 150)
found_by_manual = len(tempHost3)
hostDB = pd.concat([tempHost1, tempHost2, tempHost3], ignore_index=True)
hostDB.replace(-999.0, np.nan, inplace=True)
if verbose:
print("%i transients found by name, %i transients found by coordinates, %i transients manually associated."% (found_by_name, found_by_coord, found_by_manual))
return hostDB

def findNewHosts(transientName, snCoord, snClass, verbose=False, starcut='gentle', ascentMatch=False, px=800, savepath='./', rad=60, GLADE=True):
def findNewHosts(transientName, transientCoord, snClass, verbose=False, starcut='gentle', ascentMatch=False, px=800, savepath='./', rad=60, GLADE=True):
"""Associates hosts of transients not in the GHOST database.
:param transientName: List of transients to associate.
:type transientName: array-like
:param snCoord: List of astropy SkyCoord transient positions.
:type snCoord: array-like
:param transientCoord: List of astropy SkyCoord transient positions.
:type transientCoord: array-like
:param snClass: List of transient classifications (if they exist).
:type snClass: array-like
:param verbose: If True, print logging information.
Expand All @@ -673,18 +673,18 @@ def findNewHosts(transientName, snCoord, snClass, verbose=False, starcut='gentle

if isinstance(transientName, str):
transientName = transientName.replace(" ", "")
snRA = snCoord.ra.degree
snDEC = snCoord.dec.degree
transientRA = transientCoord.ra.degree
transientDEC = transientCoord.dec.degree
elif isinstance(transientName, list) or isinstance(transientName, np.ndarray):
transientName = [x.replace(" ", "") for x in transientName]
snRA = [x.ra.degree for x in snCoord]
snDEC = [x.dec.degree for x in snCoord]
transientRA = [x.ra.degree for x in transientCoord]
transientDEC = [x.dec.degree for x in transientCoord]
else:
print("Error! Please pass in your transient name as either a string or a list/array of strings.\n")

transientName_arr = np.array(transientName)
snRA_arr = np.array(snRA)
snDEC_arr = np.array(snDEC)
transientRA_arr = np.array(transientRA)
transientDEC_arr = np.array(transientDEC)
snClass_arr = np.array(snClass)

dateStr = str(datetime.today()).replace("-", '').replace(".", '').replace(":", "").replace(" ", '')
Expand All @@ -700,8 +700,8 @@ def findNewHosts(transientName, snCoord, snClass, verbose=False, starcut='gentle
path = savepath+dir_name+'/'

#create temp dataframe with RA and DEC corresponding to the transient
snDF = pd.DataFrame({'Name':transientName_arr, 'RA':snRA_arr, 'DEC':snDEC_arr, 'HostName':['']*len(snDEC_arr), 'Obj. Type':snClass_arr})
snDF.to_csv(path+fn_transients, index=False)
transientDF = pd.DataFrame({'Name':transientName_arr, 'RA':transientRA_arr, 'DEC':transientDEC_arr, 'HostName':['']*len(transientDEC_arr), 'Obj. Type':snClass_arr})
transientDF.to_csv(path+fn_transients, index=False)

#new low-z method (beta) - before we do anything else, find and associate with GLADE
if GLADE:
Expand All @@ -712,17 +712,17 @@ def findNewHosts(transientName, snCoord, snClass, verbose=False, starcut='gentle
print("Successfully read in GWGC catalog.\n")

fn_glade = "gladeDLR.txt"
foundGladeHosts, noGladeHosts = chooseByGladeDLR(path, fn_glade, snDF, verbose=verbose, todo="r", GWGC=GWGC)
foundGladeHosts, noGladeHosts = chooseByGladeDLR(path, fn_glade, transientDF, verbose=verbose, todo="r", GWGC=GWGC)

#open transients df and drop the transients already found in GLADE. We'll add these back in at the end
snDF = snDF[snDF['Name'].isin(noGladeHosts)]
transientDF = transientDF[transientDF['Name'].isin(noGladeHosts)]
fn_transients_preGLADE = fn_transients
fn_transients = 'transients_%s_postGlade.csv' % dateStr
snDF.to_csv(path+fn_transients, index=False)
transientDF.to_csv(path+fn_transients, index=False)

else:
foundGladeHosts = []
noGladeHosts = snDF['Name'].values
noGladeHosts = transientDF['Name'].values
fn_transients_preGLADE = fn_transients

if len(noGladeHosts) < 1:
Expand Down
16 changes: 8 additions & 8 deletions tests/test_tutorial.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -37,16 +37,16 @@ def test_NED():

def test_associate():
#create a list of the supernova names, their skycoords, and their classes (these three are from TNS)
snName = ['SN 2012dt', 'SN 1998bn', 'SN 1957B']
transientName = ['SN 2012dt', 'SN 1998bn', 'SN 1957B']

snCoord = [SkyCoord(14.162*u.deg, -9.90253*u.deg, frame='icrs'), \
transientCoord = [SkyCoord(14.162*u.deg, -9.90253*u.deg, frame='icrs'), \
SkyCoord(187.32867*u.deg, -23.16367*u.deg, frame='icrs'), \
SkyCoord(186.26125*u.deg, +12.899444*u.deg, frame='icrs')]

snClass = ['SN IIP', 'SN', 'SN Ia']
transientClass = ['SN IIP', 'SN', 'SN Ia']

# run the association algorithm with the DLR method!
hosts = getTransientHosts(snName, snCoord, snClass, verbose=verbose, starcut='gentle', ascentMatch=False)
hosts = getTransientHosts(transientName, transientCoord, transientClass, verbose=verbose, starcut='gentle', ascentMatch=False)

correctHosts = [SkyCoord(14.1777425*u.deg, -9.9138756*u.deg, frame='icrs'),
SkyCoord(187.3380517*u.deg, -23.1666716*u.deg, frame='icrs'),
Expand Down Expand Up @@ -89,12 +89,12 @@ def test_plotLocus():
assert len(glob.glob(os.path.join(os.getcwd(), 'PS1_Gals_StellarLocus_.pdf'))) > 0

def test_skymapper_associate():
snName = ['AT2023hri']
snCoord = [SkyCoord(288.5964917*u.deg, -54.5636583*u.deg, frame='icrs')]
snClass = ['AT']
transientName = ['AT2023hri']
transientCoord = [SkyCoord(288.5964917*u.deg, -54.5636583*u.deg, frame='icrs')]
transientClass = ['AT']

# run the association algorithm with the DLR method!
hosts = getTransientHosts(snName, snCoord, snClass, verbose=verbose, starcut='gentle', ascentMatch=False)
hosts = getTransientHosts(transientName, transientCoord, transientClass, verbose=verbose, starcut='gentle', ascentMatch=False)
assert hosts['NED_name'].values[0] == 'ESO 184- G 042'

def test_resolve():
Expand Down

0 comments on commit 289055e

Please sign in to comment.