def dont_test_load_save_fits_tables():
# The version of astropy on travis breaks on this!
# probably a bug that will be fixed by astropy later.
catalog = [OutputSource()]
cat.save_catalog('a.fits', catalog, meta=None)
if not os.path.exists('a_comp.fits'):
raise AssertionError()
os.remove('a_comp.fits')
def test_load_save_catalog():
"""Test that we can load and save various file formats"""
catalog = [OutputSource()]
for ext in ['csv', 'vot']:
fout = 'a.'+ext
cat.save_catalog(fout, catalog, meta=None)
fout = 'a_comp.'+ext
if not os.path.exists(fout):
raise AssertionError()
catin = cat.load_catalog(fout)
if not len(catin) == len(catalog):
raise AssertionError()
os.remove(fout)
# test the prefix is being written.
fout = 'a.csv'
cat.save_catalog(fout, catalog, meta=None, prefix='test')
fout = 'a_comp.csv'
if not os.path.exists(fout):
raise AssertionError()
if 'test_ra' not in open(fout).readlines()[0]:
raise AssertionError()
os.remove(fout)
for ext in ['reg', 'ann', 'bla']:
fout = 'a.'+ext
cat.save_catalog(fout, catalog, meta=None)
fout = 'a_comp.'+ext
if not os.path.exists(fout):
raise AssertionError()
os.remove(fout)
fout = 'a.db'
cat.save_catalog(fout, catalog, meta=None)
if not os.path.exists(fout):
raise AssertionError()
# again so that we trigger an overwrite
cat.save_catalog(fout, catalog, meta=None)
os.remove(fout)
badfile = open("file.fox", 'w')
print("ff 012.d", file=badfile)
badfile.close()
assert_raises(Exception, cat.load_catalog, 'file.fox')
badfile = open("file.fox", 'w')
print('1 1', file=badfile)
badfile.close()
catin = cat.load_catalog('file.fox')
print(catin)
if not len(catin) == 1:
raise AssertionError()
os.remove('file.fox')
def test_load_save_catalog():
"""Test that we can load and save various file formats"""
catalog = [ComponentSource()]
for ext in ['csv', 'vot']:
fout = 'a.' + ext
cat.save_catalog(fout, catalog, meta=None)
fout = 'a_comp.' + ext
if not os.path.exists(fout):
raise AssertionError()
catin = cat.load_catalog(fout)
if not len(catin) == len(catalog):
raise AssertionError()
os.remove(fout)
# test the prefix is being written.
fout = 'a.csv'
cat.save_catalog(fout, catalog, meta=None, prefix='test')
fout = 'a_comp.csv'
if not os.path.exists(fout):
raise AssertionError()
if 'test_ra' not in open(fout).readlines()[0]:
raise AssertionError()
os.remove(fout)
for ext in ['reg', 'ann', 'bla']:
fout = 'a.' + ext
cat.save_catalog(fout, catalog, meta=None)
fout = 'a_comp.' + ext
if not os.path.exists(fout):
raise AssertionError()
os.remove(fout)
fout = 'a.db'
cat.save_catalog(fout, catalog, meta=None)
if not os.path.exists(fout):
raise AssertionError()
# again so that we trigger an overwrite
cat.save_catalog(fout, catalog, meta=None)
os.remove(fout)
badfile = open("file.fox", 'w')
print("ff 012.d", file=badfile)
badfile.close()
assert_raises(Exception, cat.load_catalog, 'file.fox')
badfile = open("file.fox", 'w')
print('1 1', file=badfile)
badfile.close()
catin = cat.load_catalog('file.fox')
print(catin)
if not len(catin) == 1:
raise AssertionError()
os.remove('file.fox')
def dont_test_load_save_fits_tables():
"""Test that we can load and save fits tables"""
# The version of astropy on travis breaks on this!
# probably a bug that will be fixed by astropy later.
catalog = [OutputSource()]
cat.save_catalog('a.fits', catalog, meta=None)
if not os.path.exists('a_comp.fits'):
raise AssertionError()
os.remove('a_comp.fits')
def objdet(tele, lat, out_file0, fits_file, seed, flood, tab_file,
catalog_input_name, cellSize_string):
sources = []
# get latitude for telescope
# adding SMA and NOEMA to list
if tele == 'SMA':
lat = 19.8243
elif tele == 'NOEMA':
lat = 44.6339
else:
lat = scope2lat(tele)
out_file = open(out_file0, 'w')
sf = SourceFinder()
print 'Running Aegean Object Detection -->'
detections = sf.find_sources_in_image(fits_file,
outfile=out_file,
hdu_index=0,
rms=None,
max_summits=None,
innerclip=seed,
outerclip=flood,
cores=cpu_count(),
rmsin=None,
bkgin=None,
beam=None,
doislandflux=False,
nonegative=not False,
nopositive=False,
mask=None,
lat=lat,
imgpsf=None)
out_file.flush()
out_file.close()
if len(detections) == 0:
raise Exception(
'No sources detected by Aegean. Please check your inputs.')
sources.extend(detections)
# write detected source info to file
if len(sources) > 0:
save_catalog(catalog_input_name, sources)
# print detected sources fro user to choose from
src_l, ra_l, dec_l, maj_l, min_l, pos_l = run_aegean(
tab_file, cellSize_string)
print 'Number of Objects Detected is ', len(src_l)
print 'Objects Detected-->'
print 'Object, RA, DEC'
for i in range(0, len(src_l)):
print src_l[i], ra_l[i], dec_l[i]
return (src_l, ra_l, dec_l, maj_l, min_l, pos_l)
def objdet(tele,lat,out_file0,fits_file,seed,flood,tab_file,catalog_input_name,cellSize_string):
sources = []
# get latitude for telescope
# adding SMA and NOEMA to list
if tele == 'SMA':
lat = 19.8243
elif tele == 'NOEMA':
lat = 44.6339
else:
lat = scope2lat(tele)
out_file = open(out_file0, 'w')
sf = SourceFinder()
print 'Running Aegean Object Detection -->'
detections = sf.find_sources_in_image(fits_file,
outfile=out_file,
hdu_index=0,
rms=None,
max_summits=None,
innerclip=seed,
outerclip=flood,
cores=cpu_count(),
rmsin=None,
bkgin=None, beam=None,
doislandflux=False,
nonegative=not False,
nopositive=False,
mask=None, lat=lat, imgpsf=None)
out_file.flush()
out_file.close()
if len(detections) == 0:
raise Exception('No sources detected by Aegean. Please check your inputs.')
sources.extend(detections)
# write detected source info to file
if len(sources) > 0:
save_catalog(catalog_input_name, sources)
# print detected sources fro user to choose from
src_l, ra_l, dec_l, maj_l, min_l, pos_l = run_aegean(tab_file, cellSize_string)
print 'Number of Objects Detected is ', len(src_l)
print 'Objects Detected-->'
print 'Object, RA, DEC'
for i in range(0, len(src_l)):
print src_l[i], ra_l[i], dec_l[i]
return(src_l, ra_l, dec_l, maj_l, min_l, pos_l)
def aegean_format(catalogue, out):
"""
Save a catalogue in a format that Aegean will recognize
:param catalogue: Catalogue
:param out: Output filename
:return:
"""
sources = []
for i, c in enumerate(catalogue):
src = SimpleSource()
src.ra, src.dec, src.peak_flux = c
src.uuid = "injected_{0:04d}".format(i)
src.pa = 0
src.a = src.b = 0.0326580516349937 * 3600
sources.append(src)
save_catalog(out, sources)
print("Wrote to file {0}".format(out))
return
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
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 test_load_save_catalog():
catalog = [OutputSource()]
for ext in ['csv', 'vot']:
fout = 'a.'+ext
cat.save_catalog(fout, catalog, meta=None)
fout = 'a_comp.'+ext
if not os.path.exists(fout):
raise AssertionError()
catin = cat.load_catalog(fout)
if not len(catin) == len(catalog):
raise AssertionError()
os.remove(fout)
for ext in ['reg', 'ann', 'bla']:
fout = 'a.'+ext
cat.save_catalog(fout, catalog, meta=None)
fout = 'a_comp.'+ext
if not os.path.exists(fout):
raise AssertionError()
os.remove(fout)
fout = 'a.db'
cat.save_catalog(fout, catalog, meta=None)
if not os.path.exists(fout):
raise AssertionError()
os.remove(fout)
badfile = open("file.fox", 'w')
print("ff 012.d", file=badfile)
badfile.close()
assert_raises(Exception, cat.load_catalog, 'file.fox')
badfile = open("file.fox", 'w')
print('1 1', file=badfile)
badfile.close()
catin = cat.load_catalog('file.fox')
print(catin)
if not len(catin) == 1:
raise AssertionError()
os.remove('file.fox')
hdu = fits.open(fits_file)[0]
fits_data = hdu.data
fits_header = hdu.header
mywcs_helper = WCSHelper.from_file(fits_file)
log = logging.getLogger(bname)
sf = SourceFinder(log=log)
found = sf.find_sources_in_image( filename = fits_file,\
innerclip = innerclip,\
outerclip = outerclip,\
cores = 5,\
nonegative=False \
#nonegative=True \
)
save_catalog(catalog_file, found)
shape = fits_data.shape
m, n = shape
m0 = int(m * cuty0)
m1 = int(m * cuty1)
n0 = int(n * cutx0)
n1 = int(n * cutx1)
img = make_model(sf.sources, shape, mywcs_helper)
fig, axs = plt.subplots(2, 2, figsize=(10, 10))
axs[0, 0].imshow(fits_data, norm=mplc.LogNorm(), cmap=cm.jet)
#axs[0,1].imshow( fits_data, norm=mplc.LogNorm(), cmap=cm.jet )
axs[0, 1].imshow(img, norm=mplc.LogNorm(), cmap=cm.jet)
axs[1,0].imshow( fits_data[m0:m1, n0:n1],\
rms=None,
max_summits=None,
innerclip=seed,
outerclip=flood,
cores=cpu_count(),
rmsin=None,
bkgin=None,
beam=None,
doislandflux=False,
nonegative=not False,
nopositive=False,
mask=None,
lat=lat,
imgpsf=None)
out_file.flush()
out_file.close()
if len(detections) == 0:
raise Exception('No sources detected by Aegean. Please check your inputs.')
sources.extend(detections)
# write detected source info to file
if len(sources) > 0:
save_catalog(catalog_input_name, sources)
# print detected sources fro user to choose from
src_l, ra_l, dec_l, maj_l, min_l, pos_l = run_aegean(tab_file, cellSize)
print 'Number of Objects Detected is ', len(src_l)
print 'Objects Detected-->'
print 'Object, RA, DEC'
for i in range(0, len(src_l)):
print src_l[i], ra_l[i], dec_l[i]