def load_sources(filename):
"""
Open a file, read contents, return a list of all the sources in that file.
Parameters
----------
filename : str
Filename to be read
Return
------
catalog : [`class:AegeanTools.models.ComponentSource`, ...]
A list of source components
"""
table = catalogs.load_table(filename)
required_cols = ['ra', 'dec', 'peak_flux', 'a', 'b', 'pa']
good = True
for c in required_cols:
if c not in table.colnames:
logging.error("Column {0} not found".format(c))
good = False
if not good:
logging.error("Some required columns missing")
return None
catalog = catalogs.table_to_source_list(table)
logging.info("read {0} sources from {1}".format(len(catalog), filename))
return catalog
def load_sources(filename):
"""
Open a file, read contents, return a list of all the sources in that file.
@param filename:
@return: list of OutputSource objects
"""
catalog = catalogs.table_to_source_list(catalogs.load_table(filename))
logging.info("read {0} sources from {1}".format(len(catalog), filename))
return catalog
def test_load_sources_missing_columns():
filename = 'tests/test_files/1904_comp.fits'
table = catalogs.load_table(filename)
table.rename_column('ra', 'RAJ2000')
table.write('dlme.fits')
cat = ar.load_sources('dlme.fits')
if os.path.exists('dlme.fits'):
os.remove('dlme.fits')
if cat is not None:
raise AssertionError("Missing columns should be caught, but weren't")
return
def test_load_table_write_table():
catalog = [OutputSource()]
for fmt in ['csv', 'vo']:
fout = 'a.'+fmt
cat.save_catalog(fout, catalog, meta=None)
fout = 'a_comp.'+fmt
tab = cat.load_table(fout)
if not len(tab) == len(catalog):
raise AssertionError()
os.remove(fout)
cat.save_catalog('a.csv', catalog, meta=None)
tab = cat.load_table('a_comp.csv')
cat.write_table(tab, 'a.csv')
if not os.path.exists('a.csv'):
raise AssertionError()
os.remove('a.csv')
assert_raises(Exception, cat.write_table, tab, 'bla.fox')
assert_raises(Exception, cat.load_table, 'file.fox')
def test_load_table_write_table():
"""Test that we can write and load tables with various file formats"""
catalog = [OutputSource()]
for fmt in ['csv', 'vo']:
fout = 'a.'+fmt
cat.save_catalog(fout, catalog, meta=None)
fout = 'a_comp.'+fmt
tab = cat.load_table(fout)
if not len(tab) == len(catalog):
raise AssertionError()
# by keeping this out of the loop, we make use of the internal remove function
os.remove(fout)
cat.save_catalog('a.csv', catalog, meta=None)
tab = cat.load_table('a_comp.csv')
cat.write_table(tab, 'a.csv')
if not os.path.exists('a.csv'):
raise AssertionError()
os.remove('a.csv')
assert_raises(Exception, cat.write_table, tab, 'bla.fox')
assert_raises(Exception, cat.load_table, 'file.fox')
def test_load_table_write_table():
"""Test that we can write and load tables with various file formats"""
catalog = [ComponentSource()]
for fmt in ['csv', 'vo']:
fout = 'a.' + fmt
cat.save_catalog(fout, catalog, meta=None)
fout = 'a_comp.' + fmt
tab = cat.load_table(fout)
if not len(tab) == len(catalog):
raise AssertionError()
# by keeping this out of the loop, we make use of the internal remove function
os.remove(fout)
cat.save_catalog('a.csv', catalog, meta=None)
tab = cat.load_table('a_comp.csv')
cat.write_table(tab, 'a.csv')
if not os.path.exists('a.csv'):
raise AssertionError()
os.remove('a.csv')
assert_raises(Exception, cat.write_table, tab, 'bla.fox')
assert_raises(Exception, cat.load_table, 'file.fox')
def load_sources(filename,
ra_col='ra',
dec_col='dec',
peak_col='peak_flux',
a_col='a',
b_col='b',
pa_col='pa'):
"""
Open a file, read contents, return a list of all the sources in that file.
Parameters
----------
filename : str
Filename to be read
ra_col, dec_col, peak_col, a_col, b_col, pa_col : str
The column names for each of the parameters.
Default = ['ra', 'dec', 'peak_flux', 'a', 'b', 'pa']
Return
------
catalog : [`class:AegeanTools.models.ComponentSource`, ...]
A list of source components
"""
table = catalogs.load_table(filename)
required_cols = [ra_col, dec_col, peak_col, a_col, b_col, pa_col]
#required_cols = ['ra','dec','peak_flux','a','b','pa']
good = True
for c in required_cols:
if c not in table.colnames:
logging.error("Column {0} not found".format(c))
good = False
if not good:
logging.error("Some required columns missing or mis-labeled")
return None
# rename the table columns
for old, new in zip([ra_col, dec_col, peak_col, a_col, b_col, pa_col],
['ra', 'dec', 'peak_flux', 'a', 'b', 'pa']):
table.rename_column(old, new)
catalog = catalogs.table_to_source_list(table)
logging.info("read {0} sources from {1}".format(len(catalog), filename))
return catalog
def test_write_fits_table_variable_uuid_lengths():
"""Test that the length of the UUID column is appropriate"""
catalog = []
for l in range(10):
c = ComponentSource()
c.ra_str = c.dec_str = "hello!"
c.uuid = 'source-{0:d}'.format(2**l)
catalog.append(c)
cat.save_catalog('a.fits', catalog, meta={'Purpose': 'Testing'})
if not os.path.exists('a_comp.fits'):
raise AssertionError()
rcat = cat.load_table('a_comp.fits')
for src1, src2 in zip(rcat, catalog):
if len(src1['uuid']) != len(src2.uuid):
print("len mismatch for source {0}".format(src1))
print("uuid should be len={0}".format(len(src2.uuid)))
raise AssertionError("UUID col is of wrong length")
os.remove('a_comp.fits')
return
save_append = '_src_table_comp.vot' # Create a string that stores the location of the Stokes Q image Sto_Q_file = data_loc + 'Sto_Q_' + mosaic_area + '.fits' # Create a string that stores the location of the Stokes U image Sto_U_file = data_loc + 'Sto_U_' + mosaic_area + '.fits' # Create a string that stores the location of the Stokes Q source table. Sto_Q_table_loc = data_loc + 'Sto_Q_' + mosaic_area + save_append # Create a string that stores the location of the Stokes U source table. Sto_U_table_loc = data_loc + 'Sto_U_' + mosaic_area + save_append # Obtain a source list for Stokes Q, from the catalogue Q_srclist = catalogs.table_to_source_list(catalogs.load_table(Sto_Q_table_loc)) # Obtain a source list for Stokes U, from the catalogue U_srclist = catalogs.table_to_source_list(catalogs.load_table(Sto_U_table_loc)) # Open the Stokes Q FITS file, and extract its data and header Q_hdulist = fits.open(Sto_Q_file) Q_data = Q_hdulist[0].data Q_hdr = Q_hdulist[0].header # Create two empty matrices, one to hold the first mask, and the other to hold # the second mask first_mask = np.zeros(np.shape(Q_data), dtype=bool) second_mask = np.zeros(np.shape(Q_data), dtype=bool) # Run the generate mask function on Stokes Q, to create a mask that covers
save_append = '_src_table_comp.vot' # Create a string that stores the location of the Stokes Q image Sto_Q_file = data_loc + 'Sto_Q_' + mosaic_area + '.fits' # Create a string that stores the location of the Stokes U image Sto_U_file = data_loc + 'Sto_U_' + mosaic_area + '.fits' # Create a string that stores the location of the Stokes Q source table. Sto_Q_table_loc = data_loc + 'Sto_Q_' + mosaic_area + save_append # Create a string that stores the location of the Stokes U source table. Sto_U_table_loc = data_loc + 'Sto_U_' + mosaic_area + save_append # Obtain a source list for Stokes Q, from the catalogue Q_srclist = catalogs.table_to_source_list(catalogs.load_table(Sto_Q_table_loc)) # Obtain a source list for Stokes U, from the catalogue U_srclist = catalogs.table_to_source_list(catalogs.load_table(Sto_U_table_loc)) # Open the Stokes Q FITS file, and extract its data and header Q_hdulist = fits.open(Sto_Q_file) Q_data = Q_hdulist[0].data Q_hdr = Q_hdulist[0].header # Create two empty matrices, one to hold the first mask, and the other to hold # the second mask first_mask = np.zeros(np.shape(Q_data), dtype = bool) second_mask = np.zeros(np.shape(Q_data), dtype = bool) # Run the generate mask function on Stokes Q, to create a mask that covers
def load(filename):
print "load", filename
table = catalogs.load_table(filename)
return table