def read_valentini():
data1= asciitable.read(os.path.join(datadir,'arcs_a.dat'),
readme="../data/ReadMe",
Reader=asciitable.cds.Cds,
guess=False,
fill_values=[('', '-999')])
data2= asciitable.read(os.path.join(datadir,'arcs_b.dat'),
readme="../data/ReadMe",
Reader=asciitable.cds.Cds,
guess=False,
fill_values=[('', '-999')])
#Remove duplicates
indxarray1= numpy.zeros(len(data1),dtype='bool')+True
hipnums= []
for ii in range(len(data1)):
if data1['HIP'][ii] in hipnums:
indxarray1[ii]= False
continue
hipnums.append(data1['HIP'][ii])
data1= data1[indxarray1]
indxarray2= numpy.zeros(len(data2),dtype='bool')+True
hipnums= []
for ii in range(len(data2)):
if data2['HIP'][ii] in hipnums:
indxarray2[ii]= False
continue
hipnums.append(data2['HIP'][ii])
data2= data2[indxarray2]
return data2
def add_keys(file_list, keys=''):
"""Add keywords to a list of FITS files.
`file_list` should have one file per line.
`keylist` can be in any format easily readable by
asciitable. There needs to be a header line followed by, on each
line, a FITS keyword and its value.
All keywords in the `keylist` file are added to all of the files
in `file_list`.
A sample `keylist` file is:
Keyword Value
OBJCTDEC '+49 49 14'
OBJCTRA '09 02 21'
"""
files =at.read(file_list)
key_table = at.read(keys)
for fil in files:
fil_fits = pyfits.open(fil[0],mode='update')
hdr = fil_fits[0].header
for key, val in key_table:
print key, val
hdr.update(key, val)
fil_fits.close()
def fetch_12():
base_path = '/vega/astro/users/sd2706/'
if os.path.exists(base_path)==True:
my_bds = BDList('/vega/astro/users/sd2706/Ldwarf_sample2014.csv')
# Use Burgasser+08's spectrum from the SpeX Prism Library
oldfile = at.read('/vega/astro/users/sd2706/2MASSWJ0208+25_spex.dat')
else:
my_bds = BDList('/home/stephanie/ldwarfs/Ldwarf_sample2014.csv')
# Use Burgasser+08's spectrum from the SpeX Prism Library
oldfile = at.read('/home/stephanie/ldwarfs/summerAMNH/LdwarfSpectra/2MASSWJ0208+25_spex.dat')
old_spectrum = {'wavelength':oldfile['col1']*u.um,
'flux':oldfile['col2']*u.dimensionless_unscaled,
'unc':oldfile['col3']*u.dimensionless_unscaled}
my_bds.brown_dwarfs['U13079'].specs['low'] = old_spectrum
# select appropriate spectrum for GD 165 B //Should no longer be needed
#source_id = my_bds.brown_dwarfs['U40039'].sid
#my_bds.brown_dwarfs['U40039'].specs['low'] = spectrum_query(source_id,
# '','',filename='spex_prism_G196-3B_U40039.fits')
return my_bds
def test_first_sosa_update():
# for a plain update, sosa or not, nothing should be deleted
# and new entries should be inserted
db_loads = asciitable.read('t/pre_sosa_db_loads.txt')
want_load_rdb = asciitable.read('t/first_sosa.rdb')
want_loads = update_load_seg_db.rdb_to_db_schema(want_load_rdb)
to_delete, to_insert = update_load_seg_db.find_load_seg_changes(want_loads, db_loads, exclude=['id'])
assert len(to_delete) == 0
assert len(to_insert) == len(want_loads[want_loads['datestart'] >= '2011:335:13:44:41.368'])
assert to_insert[0]['datestart'] == '2011:335:13:44:41.368'
def test_load_update_truncate():
# if an old entry is now truncated, it and all after should be replaced
db_loads = asciitable.read('t/pre_sosa_db_loads.txt')
want_load_rdb = asciitable.read('t/first_sosa.rdb')
want_loads = update_load_seg_db.rdb_to_db_schema(want_load_rdb)
want_loads[10]['datestop'] = '2011:332:00:00:00.000'
to_delete, to_insert = update_load_seg_db.find_load_seg_changes(want_loads, db_loads, exclude=['id'])
assert len(to_delete) == len(db_loads[db_loads['datestart'] >= want_loads[10]['datestart']])
assert len(to_insert) == len(want_loads[want_loads['datestart'] >= want_loads[10]['datestart']])
assert to_delete[0]['datestart'] == want_loads[10]['datestart']
assert to_insert[0]['datestart'] == want_loads[10]['datestart']
def calc_final_eqws(file1,file2):
e1 = at.read(file1)
e2 = at.read(file2)
eqws = (e1["eqw"] + e2["eqw"]) / 2.0
diff = e1["eqw"] - e2["eqw"]
u_eqws = np.sqrt(e2["u_eqw"]**2 + diff**2)
return eqws,u_eqws
def test_load_update_sosa_truncate():
# if an old entry is now truncated, it and all after should be replaced
# but the first entry of a sosa pair should not be removed if it is before the difference
db_loads = asciitable.read('t/post_sosa_db_loads.txt')
want_load_rdb = asciitable.read('t/second_sosa.rdb')
want_loads = update_load_seg_db.rdb_to_db_schema(want_load_rdb)
want_loads[12]['datestop'] = '2011:338:00:00:00.000'
to_delete, to_insert = update_load_seg_db.find_load_seg_changes(want_loads, db_loads, exclude=['id'])
assert len(to_delete) == 11
assert len(to_insert) == 11
assert to_delete[0]['datestart'] == want_loads[12]['datestart']
assert to_insert[0]['datestart'] == want_loads[12]['datestart']
def test_load_update_weird():
# for a difference in the past on any column, the entry
# should be replaced
db_loads = asciitable.read('t/pre_sosa_db_loads.txt')
db_loads[5]['load_segment'] = 'CL324:0120'
want_load_rdb = asciitable.read('t/first_sosa.rdb')
want_loads = update_load_seg_db.rdb_to_db_schema(want_load_rdb)
to_delete, to_insert = update_load_seg_db.find_load_seg_changes(want_loads, db_loads, exclude=['id'])
assert len(to_delete) == len(db_loads[db_loads['datestart'] >= '2011:324:01:05:40.930'])
assert len(to_insert) == len(want_loads[want_loads['datestart'] >= '2011:324:01:05:40.930'])
assert to_delete[0]['datestart'] == '2011:324:01:05:40.930'
assert to_insert[0]['datestart'] == '2011:324:01:05:40.930'
def read_depthofcoverage(self, prefix, indir="."):
"""read depthofcoverage tables"""
## Read sample summary - skip last line since lacks columns
infile = os.path.abspath(os.path.join(indir, prefix + "." + self.ext["sample_summary"]))
with open(infile) as fp:
self.data["sample_summary"] = asciitable.read(infile, delimiter="\t", guess=False, data_end=-1)
## Read rest of tables
for k in self.ext_keys[0:(len(self.ext_keys) - 1)]:
infile = os.path.abspath(os.path.join(indir, prefix + "." + self.ext[k]))
tab = asciitable.read(self._sniff_table(infile), delimiter="\t", guess=False)
self.data[k] = tab
def convertCosmos(inName, outName):
inFile = open(inName, "r")
table = asciitable.read(inFile, Reader=asciitable.FixedWidthTwoLine, delimiter='|', header_start=0,
data_start=4, data_end=-1)
schema = pyfits.ColDefs([column for column in MAPPING.values()])
outHdu = pyfits.new_table(schema, nrows=len(table))
outData = outHdu.data
for name, column in MAPPING.items():
outData.field(column.name)[:] = table.field(name)
for f in FILTERS:
mag = outData.field(f)
err = outData.field(f + "_err")
indices = numpy.where(numpy.logical_or(mag < 0, mag > 50))
mag[indices] = numpy.NAN
err[indices] = numpy.NAN
outHdu.writeto(outName, clobber=True)
print "Wrote %s" % outName
print "To create an astrometry.net catalogue, execute:"
outBase = outName.replace(".fits", "")
print "build-index -i %s -o %s_and_0.fits -I 77770 -P0 -n 100 -S r -L 20 -E -M -j 0.4" % (inName, outBase)
for i in range(1, 5):
print "build-index -1 %s_and_0.fits -o %s_and_%d.fits -I 7777%d -P%d -n 100 -S r -L 10 -E -M -j 0.4 &" % (outBase, outBase, i, i, i)
def read_table_rg(filename):
# astropy.io.ascii.convert_numpy
converters = { 'col1': [asciitable.convert_list(str)],
'col2': [asciitable.convert_list(float)],
'col3': [asciitable.convert_list(float)],
'col4': [asciitable.convert_list(float)],
'col5': [asciitable.convert_list(float)],
'col6': [asciitable.convert_list(str)],
'col7': [asciitable.convert_list(str)],
'col8': [asciitable.convert_list(str)],
'col9': [asciitable.convert_list(str)],
'col10': [asciitable.convert_list(float)]}
names = ('POINT_NAME', 'RA_PNT', 'DEC_PNT', 'BACK','NH', 'MOS1FILTER', 'MOS2FILTER', 'PNFILTER', 'EXPOTIME')
data = asciitable.read(filename, delimiter='|', converters=converters)
npoint = data.size
name = data['col1'].tolist()
back = data['col4']
nh = data['col5']
m1filt = data['col6'].tolist()
m2filt = data['col7'].tolist()
pnfilt = data['col8'].tolist()
timestamp = data['col9']
area = data['col10']
return (name, back, nh, m1filt, m2filt, pnfilt, timestamp, area, npoint)
def readColHeight():
minhgt= 2.5 # Assumed minimum detection limit
fname = 'column_heights.txt' # File to read
table = asciitable.read(fname) # Read file
date0 = table.col1 # extract start date
time0 = table.col2 # extract start time
date1 = table.col3 # extract end date
time1 = table.col4 # extract end time
hgt = table.col5 # extract height
mass = table.col6 # extract mass release
name = table.col7 # extract name/comment
#TODO check if column 6 is missing, use power law to calc
# mass if that is the case.
for i in range(hgt.shape[0]): # For each column height
#for h in hgt:
h=hgt[i]
if h >=999: # Assume error
msg="column height greater than 999 km found, assuming error code"
warnings.warn(msg)
print "Row: %i, Height: %f",i,h
raise Exception("NOT SUPPORTED YET, ABORTING")
# Bundle date and time in same string
datestr0 = [date0[i]+time0[i] for i in range(date0.shape[0])]
datestr1 = [date1[i]+time1[i] for i in range(date1.shape[0])]
# Convert string date/time to python date format
date0_py = [datetime.strptime(t,"%Y-%m-%d%H:%M:%S") for t in datestr0]
date1_py = [datetime.strptime(t,"%Y-%m-%d%H:%M:%S") for t in datestr1]
# Make time relative to first start date:
dateBase = date0_py[0]
date0_py = [d-dateBase for d in date0_py]
date1_py = [d-dateBase for d in date1_py]
return date0_py,date1_py,hgt,mass,name
def print_table(self, data, title=None):
print("")
table = asciitable.read(data)
if title:
table.title = title
print(table.table)
print("")
def get_ifot(event_type, start=None, stop=None, props=[], columns=[], timeout=TIMEOUT, types={}):
start = DateTime('1998:001' if start is None else start)
stop = DateTime(stop)
event_props = '.'.join([event_type] + props)
params = odict(r='home',
t='qserver',
format='tsv',
tstart=start.date,
tstop=stop.date,
e=event_props,
ul='7',
)
if columns:
params['columns'] = ','.join(columns)
# Get the TSV data for the iFOT event table
url = ROOTURL + URLS['ifot']
response = requests.get(url, auth=get_auth(), params=params, timeout=timeout)
text = response.text.encode('ascii', 'ignore')
text = re.sub(r'\r\n', ' ', text)
lines = [x for x in text.split('\t\n') if x.strip()]
converters = {key: [asciitable.convert_numpy(getattr(np, type_))]
for key, type_ in types.items()}
dat = asciitable.read(lines, Reader=asciitable.Tab, guess=False, converters=converters)
return dat
def texes2fits(file):
detector_shape = (256,256)
data = np.fromfile(file,dtype='>i4')
header_raw = at.read(file+'.hd',delimiter='=')
header_dict = {}
for pair in header_raw:
key = pair[0]
try:
value=float(pair[1])
except:
value=pair[1]
header_dict[key] = value
nnods = header_dict['nnod']
try:
cube = np.reshape(-data,(nnods*2,detector_shape[0],detector_shape[1]))
except ValueError:
print "Failed reading ", file
return
hdu = pf.PrimaryHDU(cube)
hdu.header.extend(header_dict.items())
# for key in header_dict.keys():
# hdu.header[key] = header_dict[key]
hdu.writeto(file+'.fits',clobber=True)
print "successfully read ", file
def readRave():
data= asciitable.read(_DATAFILE,
readme=_DATAREADME,
Reader=asciitable.cds.Cds,
guess=False,
fill_values=[('', '-999')])
return data
def vivado_resources(self, report_file):
with open(report_file, 'r') as fp:
report_data = fp.read()
report_data = report_data.split('\n\n')
report = dict()
section = None
for d in report_data:
match = re.search(r'\n-+$', d)
if match is not None:
match = re.search(r'\n?[0-9\.]+ (.*)', d)
if match is not None:
section = match.groups()[0]
if d.startswith('+--'):
if section is not None:
# cleanup the table
d = re.sub(r'\+-.*-\+\n', '', d)
d = re.sub(r'\+-.*-\+$', '', d)
d = re.sub(r'^\|\s+', '', d, flags=re.M)
d = re.sub(r'\s\|\n', '\n', d)
report[section.lower()] = asciitable.read(
d,
delimiter='|',
guess=False,
comment=r'(\+.*)|(\*.*)',
numpy=False)
return report
def check_pop(sample_list, user_choices):
"""
Check the number of objects from each time in a given sample.
input: sample_list, str
list of objects raw data files.
user_choices, dict
output from read_user_input
output: pop, dict
keys are types and values are the number of objects in the sample
"""
# read raw data files names
flist = asciitable.read(sample_list)
# count types
pop = {}
for name in flist:
user_choices['path_to_lc'] = [name[0]]
raw = read_snana_lc(user_choices)
if raw['SIM_NON1a:'][0] not in pop.keys():
pop[raw['SIM_NON1a:'][0]] = 1
else:
pop[raw['SIM_NON1a:'][0]] = pop[raw['SIM_NON1a:'][0]] + 1
return pop
def main(args=None):
args = get_args()
tank_limit = 93.0
files = glob('*-*-{}.dat'.format(args.tank_start))
print files
dats = []
for fn in files:
dat = asciitable.read(fn,
guess=False,
Reader=asciitable.NoHeader,
names=['p0', 'p1', 'p2', 'p3', 't_max', 't_end'])
dats.append(dat)
colds = np.hstack([dat['p3'] for dat in dats])
hots = np.hstack([dat['p0'] + dat['p2'] for dat in dats])
t_maxes = np.hstack([dat['t_max'] for dat in dats])
t_ends = np.hstack([dat['t_end'] for dat in dats])
ok_colds = []
ok_hots = []
n_bin = 20
bins = np.linspace(0., 1., n_bin + 1)
t_50 = np.zeros((n_bin, n_bin), dtype=np.float) + 70.0
t_90 = np.zeros((n_bin, n_bin), dtype=np.float) + 70.0
frac_bad = np.zeros((n_bin, n_bin), dtype=np.float) - 0.5
for x0, x1 in zip(bins[:-1], bins[1:]):
ok_colds.append((colds > x0) & (colds <= x1))
ok_hots.append((hots > x0) & (hots <= x1))
for i in range(n_bin):
for j in range(n_bin):
ok = ok_colds[i] & ok_hots[j] # select realizations within bin
t_ends_ok = t_ends[ok]
if len(t_ends_ok) > 3:
t_50[i, j], t_90[i, j] = np.percentile(t_ends_ok, [50, 90])
t_maxes_ok = t_maxes[ok]
if len(t_maxes_ok) > 0:
n_bad = np.sum(t_maxes_ok > tank_limit)
frac_bad[i, j] = n_bad / len(t_maxes_ok)
x = (bins[1:] + bins[:-1]) / 2.0
y = x.copy()
for perc, t, pref in ((50, t_50, 'Median'), (90, t_90, '90%')):
title = '{} temp after 7 days, start={} F'.format(
pref, args.tank_start)
filename = None if args.no_save else 'tank_perc{}_start{}.png'.format(
perc, args.tank_start)
plot_t_img_contour(x, y, t, title, filename)
title = 'Fraction exceeding 93F limit, start={}'.format(args.tank_start)
filename = None if args.no_save else 'tank_bad_start{}.png'.format(
args.tank_start)
plot_frac_bad(x, y, frac_bad, title, filename)
title = 'blah start={}'.format(args.tank_start)
filename = None if args.no_save else 'tank_end_10_start{}.png'.format(
args.tank_start)
plot_t_50_at_frac_bad_10(args.tank_start, x, y, t_50, title, filename=None)
def save_female_height_np():
import asciitable
x = asciitable.read(
'/Users/pdh21/Documents/CFwork/Patient_link/Female_height_2_20_years.txt',
guess=False,
delimiter='\t',
fill_values=[('', '-999')])
age = []
height = []
for i in x:
age.append(i[0])
height_tmp = []
for j in range(1, 12):
height_tmp.append(i[j])
height.append(height_tmp)
age = np.array(age)
height = np.array(height)
age = np.append(age, np.arange(240, 960.0, 1))
height_extra = np.empty((960.0 - 240.0, height.shape[1]))
print
height[-1, :], height.shape, height_extra.shape
for i in np.arange(0, 960.0 - 240.0, 1):
print
i
height_extra[i, :] = height[-1, :]
height = np.concatenate((height, height_extra), axis=0)
import pylab as plt
for i in range(0, 11):
plt.plot(age, height[:, i])
plt.show()
np.savez('Female_height', age, height)
def survey_file_import(self,filename):
"""
A simple function to import the survey data (not a subsample)
"""
datafile = open(filename,"r")
self.survey_data = atab.read(datafile.read())
datafile.close()
def get_ECFSPR_data():
import asciitable
x = asciitable.read(
'/Users/pdh21/Documents/CFwork/Patient_link/2008_2009/db0809_protected.txt',
guess=False,
delimiter='\t',
fill_values=[('', '-999')])
# x=asciitable.read('db0809_protected.txt', guess=False,delimiter='\t',fill_values=[('', '-999')])
yy = map(int, x['birth_yy'])
year = map(int, x['year'])
gender = np.array(map(float, x['gender']))
mm = map(float, x['birth_mm'])
dd = map(float, x['birth_dd'])
ID = map(float, x['ID'])
bmi = map(float, x['bmiECFSPR'])
hgt = map(float, x['hgt'])
mut1 = np.array(x['mut1'])
mut2 = np.array(x['mut2'])
age_dia = np.array(x['age_dia'])
ID = np.array(ID)
BMI = np.array(bmi)
hgt = np.array(hgt)
year = np.array(year)
dob_j = np.empty_like(yy)
for i in range(0, len(yy)):
dob_j[i] = ((yy[i] - 1900) * 12) + mm[i]
# indices in dob_j for each year
ind_2008, = np.nonzero(np.less(year, 2009))
ind_2009, = np.nonzero(np.greater(year, 2008))
return BMI, hgt, ID, ind_2008, ind_2009, dob_j, gender, np.array(
[mut1, mut2]), age_dia
def parse_header(header_lines):
"""Parse VOTS header fields from 'header_lines', which should be an
iterable that returns lines of the VOTS table. Returns an dict
of header fields where all but 'description' are in turn a numpy
recarray table."""
header = {}
keywords = ('DESCRIPTION::', 'COOSYS::', 'PARAM::', 'FIELD::')
key = 'none'
for line in header_lines:
line = line.strip()
if line in keywords:
key = line[:-2].lower()
continue
if key not in header:
header[key] = []
header[key].append(line)
for key, lines in header.items():
# Flatten description key, otherwise parse lines as a table
if key == 'description':
header[key] = '\n'.join(lines)
else:
for quotechar in ['"', "'"]:
try:
header[key] = asciitable.read(lines, quotechar=quotechar)
break
except asciitable.InconsistentTableError, error:
pass
else:
raise asciitable.InconsistentTableError(error)
def texes2fits(file):
detector_shape = (256, 256)
data = np.fromfile(file, dtype='>i4')
header_raw = at.read(file + '.hd', delimiter='=')
header_dict = {}
for pair in header_raw:
key = pair[0]
try:
value = float(pair[1])
except:
value = pair[1]
header_dict[key] = value
nnods = header_dict['nnod']
try:
cube = np.reshape(-data,
(nnods * 2, detector_shape[0], detector_shape[1]))
except ValueError:
print("Failed reading ", file)
return
hdu = pf.PrimaryHDU(cube)
hdu.header.extend(header_dict.items())
# for key in header_dict.keys():
# hdu.header[key] = header_dict[key]
hdu.writeto(file + '.fits', clobber=True)
print("successfully read ", file)
def test_from_lines(numpy):
f = 't/simple.txt'
table = open(f).readlines()
testfile = get_testfiles(f)
data = asciitable.read(table, numpy=numpy, **testfile['opts'])
assert_equal(data.dtype.names, testfile['cols'])
assert_equal(len(data), testfile['nrows'])
def import_file(self, filename, camera_name): h = extract_headers(filename) T = asciitable.read(filename) table = convert_ascii(T) cam = Camera(camera_name, float(h['zp']), float(h['sky']), float(h['scale']), self.name) #create a camera from headers cam.add_data_table(table) #call add_table_data in camera self.camera_list.append(cam) self.ID = h['ID']
def interpUVB(model):
if model=='HM12':
data=asciitable.read("FIXME")
elif model=="OHL16": # this is our corrected model to match observations
data=asciitable.read("FIXME")
elif model=="P18":
data=asciitable.read("data/TREECOOL_P18.txt")
else:
print('ERROR, model not defined: %s'%(model))
lz = data['col1']
fpiHI=spi.interp1d(lz,data['col2'],kind='linear')
fpiHeI=spi.interp1d(lz,data['col3'],kind='linear')
fpiHeII=spi.interp1d(lz,data['col4'],kind='linear')
fphHI=spi.interp1d(lz,data['col5'],kind='linear')
fphHeI=spi.interp1d(lz,data['col6'],kind='linear')
fphHeII=spi.interp1d(lz,data['col7'],kind='linear')
return [lz,fpiHI,fpiHeI,fpiHeII,fphHI,fphHeI,fphHeII]
def test_set_converters(numpy):
converters = {'zabs1.nh': [asciitable.convert_numpy('int32'),
asciitable.convert_numpy('float32')],
'p1.gamma': [asciitable.convert_numpy('str')]
}
data = asciitable.read('t/test4.dat', converters=converters, numpy=numpy)
assert_equal(str(data['zabs1.nh'].dtype), 'float32')
assert_equal(data['p1.gamma'][0], '1.26764544642')
def read_ECFSPR_all():
import asciitable
x = asciitable.read(
'/Users/pdh21/Documents/CFwork/Patient_link/2008_2009/db0809_protected.txt',
guess=False,
delimiter='\t',
fill_values=[('', '-999')])
return x
def test_fill_values_list(numpy):
f = 't/fill_values.txt'
testfile = get_testfiles(f)
data = asciitable.read(f, numpy=numpy, fill_values=[('a','42'),('1','42','a')],
**testfile['opts'])
if numpy:
assert_true((data.data['a']==[42,42]).all())
else:
assert_equal(data['a'],[42,42])
def filter_bad_times(msid_self, start=None, stop=None, table=None):
"""Filter out intervals of bad data in the MSID object.
There are three usage options:
- Supply no arguments. This will use the global list of bad times read
in with fetch.read_bad_times().
- Supply both ``start`` and ``stop`` values where each is a single
value in a valid DateTime format.
- Supply an ``table`` parameter in the form of a 2-column table of
start and stop dates (space-delimited) or the name of a file with
data in the same format.
The ``table`` parameter must be supplied as a table or the name of a
table file, for example::
bad_times = ['2008:292:00:00:00 2008:297:00:00:00',
'2008:305:00:12:00 2008:305:00:12:03',
'2010:101:00:01:12 2010:101:00:01:25']
msid.filter_bad_times(table=bad_times)
msid.filter_bad_times(table='msid_bad_times.dat')
:param start: Start of time interval to exclude (any DateTime format)
:param stop: End of time interval to exclude (any DateTime format)
:param table: Two-column table (start, stop) of bad time intervals
"""
if table is not None:
bad_times = asciitable.read(table, Reader=asciitable.NoHeader,
names=['start', 'stop'])
elif start is None and stop is None:
raise ValueError('filter_times requires 2 args ')
elif start is None or stop is None:
raise ValueError('filter_times requires either 2 args '
'(start, stop) or no args')
else:
bad_times = [(start, stop)]
ok = np.ones(len(msid_self.times), dtype=bool)
for start, stop in bad_times:
tstart = DateTime(start).secs
tstop = DateTime(stop).secs
if tstart > tstop:
raise ValueError("Start time %s must be less than stop time %s"
% (start, stop))
if tstop < msid_self.times[0] or tstart > msid_self.times[-1]:
continue
i0, i1 = np.searchsorted(msid_self.times, [tstart, tstop])
ok[i0:i1 + 1] = False
colnames = (x for x in msid_self.colnames)
for colname in colnames:
attr = getattr(msid_self, colname)
if isinstance(attr, np.ndarray):
setattr(msid_self, colname, attr[ok])
def plotData():
""" PURPOSE: Read in the text file and plot the median efficiency """
medefffn="/Users/matt/projects/CHIRON/EFFICIENCY/data.txt"
medeff = asciitable.read(medefffn, data_start=0, delimiter=" ")
pylab.clf()
pylab.xlabel('Wavelength [$\AA$]')
pylab.ylabel('Efficiency (%)')
pylab.plot(medeff.wav, medeff.eff*100.,'ko')
pylab.savefig('fig_medeff.eps')
def plotData():
""" PURPOSE: Read in the text file and plot the median efficiency """
medefffn = "/Users/matt/projects/CHIRON/EFFICIENCY/data.txt"
medeff = asciitable.read(medefffn, data_start=0, delimiter=" ")
pylab.clf()
pylab.xlabel('Wavelength [$\AA$]')
pylab.ylabel('Efficiency (%)')
pylab.plot(medeff.wav, medeff.eff * 100., 'ko')
pylab.savefig('fig_medeff.eps')
def read_saga():
"""Read the SAGA data"""
filename= os.path.join('..','data','star_prop_uvby.dat')
readme= os.path.join('..','data','ReadMe.txt')
sagadata= asciitable.read(filename,
readme=readme,
Reader=asciitable.cds.Cds,
guess=False,
fill_values=[('', '-999')])
return sagadata
def ascii2pkl(name, phase):
table = asciitable.read(name, delimiter="\s")
points = numpy.zeros((len(table), 2))
for i in xrange(len(table)):
points[i] = (table.col1[i] - phase, table.col2[i])
values = table.col3
out = dict([('points', points), ('values', values)])
f = open(name + '.pkl', 'wb')
pickle.dump(out, f, pickle.HIGHEST_PROTOCOL)
f.close()
def plotLC(line, continuum):
lData = asc.read('values' + line + '.dat', numpy=True)
cData = asc.read('values' + continuum + '.dat', numpy=True)
lDist, lFlux, lIvar = lData['dist'], lData['flux'], lData['ivar']
cDist, cFlux, cIvar = cData['dist'], cData['flux'], cData['ivar']
if (len(lDist) > len(cDist)):
dist = lDist
flux = lFlux - np.interp(dist, cDist, cFlux)
err = np.sqrt(1.0 / lIvar) + np.sqrt(1.0 / np.interp(dist, cDist, cIvar))
else:
dist = cDist
flux = np.interp(dist, lDist, lFlux) - cFlux
err = np.sqrt(1.0 / np.interp(dist, lDist, lIvar)) + np.sqrt(1.0 / cIvar)
plt.subplot(212)
plt.xlabel("Distance along the slit (kpc)", fontsize=20)
plt.ylabel("Flux Difference", fontsize=20)
plt.tick_params(axis='both', which='major', labelsize=20)
plt.axhline(0, color='k')
plt.errorbar(dist, flux, err, marker='o')
def plotDataShort():
""" PURPOSE: Read in the text file with the removed "kinks"
and replot """
medefffn="/Users/matt/projects/CHIRON/EFFICIENCY/data_short.txt"
#medeff = asciitable.read(medefffn,delimiter=" ", data_start=2)
medeff = asciitable.read(medefffn, data_start=0, delimiter="\s")
pylab.clf()
pylab.xlabel('Wavelength [$\AA$]')
pylab.ylabel('Efficiency (%)')
pylab.plot(medeff.wav, medeff.eff*100.,'ko')
def plotDataShort():
""" PURPOSE: Read in the text file with the removed "kinks"
and replot """
medefffn = "/Users/matt/projects/CHIRON/EFFICIENCY/data_short.txt"
#medeff = asciitable.read(medefffn,delimiter=" ", data_start=2)
medeff = asciitable.read(medefffn, data_start=0, delimiter="\s")
pylab.clf()
pylab.xlabel('Wavelength [$\AA$]')
pylab.ylabel('Efficiency (%)')
pylab.plot(medeff.wav, medeff.eff * 100., 'ko')
def asciiWrite(stackedFluxes, asciiName):
flux = stackedFluxes[1] / stackedFluxes[2]
flux = flux / np.max(flux) # normalized meanFlux
ivar = (stackedFluxes[2] ** 2) / (np.max(flux) ** 2) # propagated inverse variance
data = Table([stackedFluxes[0], flux, ivar], names=['dist', 'flux', 'ivar'])
ascii.write(data, ('values' + asciiName + '.dat'))
readData = asc.read('values' + asciiName + '.dat', numpy=True)
dist, flux, ivar = readData['dist'], readData['flux'], readData['ivar']
return dist, flux, ivar
def ECFPR_data_BMI():
import asciitable
x = asciitable.read(
'/Users/pdh21/Documents/CFwork/Patient_link/2008_2009/db0809_protected.txt',
guess=False,
delimiter='\t',
fill_values=[('', '-999')])
yy = map(int, x['birth_yy'])
year = map(int, x['year'])
gender = np.array(map(float, x['gender']))
mm = map(float, x['birth_mm'])
dd = map(float, x['birth_dd'])
ID = map(float, x['ID'])
bmi = map(float, x['bmiECFSPR'])
hgt = map(float, x['hgt'])
hgt = np.array(hgt)
ID = np.array(ID)
BMI = np.array(bmi)
year = np.array(year)
dob_j = np.empty_like(yy)
for i in range(0, len(yy)):
dob_j[i] = ((yy[i] - 1900) * 12) + mm[i]
# indices in dob_j for each year
# first select patients which have a BMI and height measure
b = np.array([], dtype=int)
for i in range(0, len(BMI) - 1):
if BMI[i] >= 0:
if hgt[i] > 0:
b = np.append(b, [[i]])
BMI = BMI[b]
ID = ID[b]
year = year[b]
gender = gender[b]
dob_j = dob_j[b]
hgt[b]
# next, selet patients where there is a match in the database
a = np.array([], dtype=int)
for i in range(0, len(ID) - 1):
if ID[i] == ID[i + 1]:
a = np.append(a, [[i], [i + 1]])
BMI = BMI[a]
ID = ID[a]
year = year[a]
gender = gender[a]
dob_j = dob_j[a]
hgt = hgt[a]
ind_2008, = np.nonzero(np.less(year, 2009))
ind_2009, = np.nonzero(np.greater(year, 2008))
return BMI, hgt, ID, ind_2008, ind_2009, dob_j, gender
def test_masking_Cds(numpy):
f = 't/cds.dat'
testfile = get_testfiles(f)
data = asciitable.read(f, numpy=numpy,
**testfile['opts'])
if numpy:
assert_true(data['AK'].mask[0])
assert_true(not data['Fit'].mask[0])
else:
assert_true(isnan(data['AK'][0]))
assert_true(not isnan(data['Fit'][0]))
def _load(self):
filename = 'sedov.csv'
data = asciitable.read(filename)
L = data['col1']
R = data['col2']
R[np.abs(R) < 1e-8] = 0
V = data['col3']
P = data['col4']
self.R = interp1d(L, R)
self.V = interp1d(L, V)
self.P = interp1d(L, P)
def load_sb_curve(fname):
"""
Loads the surface brightness curve from file.
Arguments:
- `fname`: file name
"""
# FIXME: refactor to have a unified reading based on topcatformat
try:
# old format: headerstart=9
data = atab.read(table=fname,
data_start=0, data_end=None, header_start=9,
delimiter=' ', comment='#', quotechar='"')
except Exception, e:
# new format: headerstart=11
data = atab.read(table=fname,
data_start=0, data_end=None, header_start=11,
delimiter=' ', comment='#', quotechar='"')
def funReadBlast(sOutFileName,all_species,sARGOSID,nNumContig,nTotalAssemblySize,\
nN50,nLargestContig,lGC,lSize):
import asciitable
tblBlast = asciitable.read(sOutFileName, Reader = asciitable.NoHeader, delimiter ='\t')
"""Get Name of Contigs"""
lContigName = list(set(tblBlast['col1']))
tblComplete = [];
for j in range(0,len(lContigName)):
print('Processing BLAST Result for Contig')
iContigIndices = [i for i,x in enumerate(list(tblBlast['col1'])) if x == lContigName[j]]
lAccesions = list(set(tblBlast[iContigIndices]['col4']))
temp = all_species[j]
lTempRow = [sARGOSID] #0
lTempRow.append(str(nNumContig)) #1
lTempRow.append(str(nTotalAssemblySize)) #2
lTempRow.append(str(nN50)) #3
lTempRow.append(str(nLargestContig)) #4
lTempRow.append(lContigName[j]) #5
lTempRow.append(str(tblBlast[iContigIndices[0]][1])) #6
lTempRow.append(str(lGC[lSize.index(tblBlast[iContigIndices[0]][1])])) #7
lTempRow.append(temp[0:-3]) #8
lTempRow.append('Hit Name') #9
lTempRow.append('Hit ACC') #10
lTempRow.append('Hit Score') #11
lTempRow.append('Hit PIdent') #12
lTempRow.append('Hit PCOV') #13
lTempRow.append('Scientific_Names') #14
for k in range(0,len(lAccesions)):
iAccesionIndices = [i for i,x in enumerate(list(tblBlast['col4'])) if x == lAccesions[k]]
iAccesionIndices = list(set(iAccesionIndices).intersection(iContigIndices))
name = tblBlast[iAccesionIndices[0]]['col5']
name = name.replace(",","_")
lTempRow[9] = name
lTempRow[10] = lAccesions[k]
lTempRow[-2] = tblBlast[iAccesionIndices[0]]['col9']
lTempRow[-1] = tblBlast[iAccesionIndices[0]]['col3']
nPident = 0
nAsize = 0
nScore = 0
for l in range(0,len(iAccesionIndices)):
nPident = nPident + tblBlast[iAccesionIndices[l]]['col8']*tblBlast[iAccesionIndices[l]]['col6']
nAsize = nAsize + tblBlast[iAccesionIndices[l]]['col6']
nScore = nScore + tblBlast[iAccesionIndices[l]]['col7']
nPident = nPident/nAsize
lTempRow[11] = nScore
lTempRow[12] = nPident
tblComplete.append(lTempRow.copy())
return tblComplete
def read_multibench_results(read_path):
sample_sizes = []
samples_per_sample_size = []
column_keys = [None, "runtime", "memory", "disk_read", "disk_write", None]
file1 = open(read_path, 'r')
lines = file1.readlines()
table_ind = -1
table_keys = []
tables = []
for line in lines:
if (line[:2] == "->"):
table_ind += 1
table_keys.append(line[2:-1])
tables.append([])
else:
tables[table_ind].append(line)
multibench_results_per_key = []
for table in tables:
key_multibench_results = []
raw_rows = asciitable.read(table,
Reader=asciitable.FixedWidthTwoLine,
bookend=True,
delimiter="|",
quotechar="'")
raw_rows = list(raw_rows)
for raw_row in raw_rows:
multibench_result = {}
for ind, column_key in enumerate(column_keys):
if column_key is not None:
multibench_result[column_key] = raw_row[ind]
sample_sizes.append(raw_row[0])
samples_per_sample_size.append(
list(map(lambda word: word.strip(), raw_row[5].split(" "))))
key_multibench_results.append(multibench_result)
multibench_results_per_key.append(key_multibench_results)
multibench_results = []
for multibench_result_ind in range(len(multibench_results_per_key[0])):
multibench_result = {}
for key_ind, key_multibench_results in enumerate(
multibench_results_per_key):
multibench_result[table_keys[key_ind]] = key_multibench_results[
multibench_result_ind]
multibench_results.append(multibench_result)
return multibench_results, samples_per_sample_size
def convert_extinction(inputfile,outputfile): # from palomar table = asciitable.read(inputfile) abswave = [] abstemp = [] for i in range(len(table)): abswave.append(table[i][0]) abstemp.append(table[i][1]) with archive.archive(outputfile,'a') as ar: ar['/sky/extinction/wave'] = numpy.array(abswave) ar['/sky/extinction/power'] = numpy.array(abstemp)
def convert_sky_bkg(inputfile,outputfile): # from skybg_50_10 table = asciitable.read(inputfile) wave = [] power = [] for i in range(len(table)): wave.append(table[i][0]) power.append(table[i][1]) with archive.archive(outputfile,'a') as ar: ar['/sky/background/wave'] = numpy.array(wave) ar['/sky/background/power'] = numpy.array(power)
def read_lbt_spec(filename):
d = asciitable.read(filename, names=('wave', 'flux', 'err'))
waved = np.array(d['wave'])
fluxd = np.array(d['flux'])
g1 = ((waved > 7000) & (waved < 9000))
waved = waved[g1]
fluxd = fluxd[g1]
z = np.polyfit(waved, fluxd, 4)
f = np.poly1d(z)
fluxd = fluxd / f(waved)
#median(fluxd[g1])
data = Spectrum(waved, fluxd)
return data
def main():
data = asciitable.read('ringwaydata.txt', fill_values=('---', None))
data = data.filled()
data.dtype.names = ('year', 'mm', 'tmax_deg', 'tmin_deg', 'af_days',
'rain_mm', 'sun_hours')
max_deg = list(data['tmax_deg'])
max_deg = [float(x) for x in max_deg if x != 'N/A']
random.seed(42)
max_deg = [x + 0.01 * random.random() for x in max_deg]
m = Distribution(max_deg)
# m.show_histogram()
# m.kernel_density(1)
est = Estimator(max_deg)
est.divide_subset(3)
def f2c(res_tem="S", step_tem=100): # es el programa en si, todo en iraf
#valores para los template
if res_tem == "h" or res_tem == "H":
lit = "@template"
print("Working with template spectra in hihg resolution")
else:
lit = "@template"
print("Working with template spectra in low resolution")
#parametros de entrada
lio = "@objetos"
lit = "@template"
spa = "A"
spb = "B"
vo = 24.86
q1 = 0.1
q2 = 0.7
dq = 0.05
sam = "4120-4340,4360-4840,4880-5700"
flist = "tmp/lit"
#ejecuto fn2
iraf.fn2(lio=lio,
lit=lit,
spa=spa,
spb=spb,
vo=vo,
q1=q1,
q2=q2,
dq=dq,
sam=sam,
flist=flist)
os.chdir("tmp")
#recupero los datos de fn2
archivos = glob.glob("datT*") #archivos de salida de f2c
temps = []
pasos = []
intensidad = []
for archivo in archivos:
temp = float(archivo[4:])
data = asciitable.read(archivo)
for paso, inte in zip(
data["col1"],
data["col2"]): #recupero de los archivos la info que necesito
#print temp,paso,inte
temps.append(temp)
pasos.append(paso)
intensidad.append(inte)
return temps, pasos, intensidad
def pull_data(sampletable):
'''
Function that pulls data from the BDNYC database. Run this in the same directory
in which you have the Python Database stored!
Input:
ASCII table with unum, type, resolution, instrument, date,
and filter/order for each data set in the sample.
Outputs:
specData: list of arrays with wavelength in position 0, flux is position 1,
and uncertainty in position 2 if included in database.
targetinfo: lost of each target instance of the objects.
'''
f=open('BDNYCData.txt','rb')
bdnyc=pickle.load(f)
f.close()
objects = asciitable.read(sampletable)
specData = []
targetinfo = []
for x in range(len(objects)):
target = bdnyc.match_unum(objects.unum[x])
res = objects.res[x]
instrument = objects.inst[x]
filter = objects.filter[x]
date = objects.date[x]
if objects.type[x] == 'nir':
data = bdnyc.targets[target].nir[res][instrument][date][filter]
if objects.type[x] == 'mir':
data = bdnyc.targets[target].mir[res][instrument][date][filter]
if objects.type[x] == 'opt':
data = bdnyc.targets[target].opt[res][instrument][date][filter]
wl_array = data['wl']
flux_array = data['flux']
objData = [wl_array,flux_array]
if len(data.keys()) >= 3:
if data.keys()[2] == 'uncertainty':
uncertainty_array = data['uncertainty']
objData.append(uncertainty_array)
targetinfo.append(bdnyc.targets[target])
specData.append(objData)
return [specData,targetinfo]
def __init__(self, filter=None, sf10=True):
"""
NAME:
__init__
PURPOSE:
Initialize the Sale14 dust map
INPUT:
filter= filter to return the extinction in
sf10= (True) if True, use the Schlafly & Finkbeiner calibrations
OUTPUT:
object
HISTORY:
2015-03-08 - Started - Bovy (IAS)
"""
DustMap3D.__init__(self, filter=filter)
self._sf10 = sf10
#Read the maps
sys.stdout.write('\r' + "Reading Sale et al. (2014) data file ...\r")
sys.stdout.flush()
self._saledata = asciitable.read(os.path.join(_saledir, 'Amap.dat'),
readme=os.path.join(
_saledir, 'ReadMe'),
Reader=asciitable.cds.Cds,
guess=False,
fill_values=[('', '-999')])
sys.stdout.write('\r' + _ERASESTR + '\r')
sys.stdout.flush()
# Some summaries
self._dl = self._saledata['lmax'] - self._saledata['lmin']
self._db = self._saledata['b_max'] - self._saledata['b_min']
self._lmin = numpy.amin(self._saledata['lmin'])
self._lmax = numpy.amax(self._saledata['lmax'])
self._bmin = numpy.amin(self._saledata['b_min'])
self._bmax = numpy.amax(self._saledata['b_max'])
self._ndistbin = 150
self._ds = numpy.linspace(0.05, 14.95, self._ndistbin)
# For dust_vals
self._sintheta = numpy.sin((90. - self._saledata['GLAT']) * _DEGTORAD)
self._costheta = numpy.cos((90. - self._saledata['GLAT']) * _DEGTORAD)
self._sinphi = numpy.sin(self._saledata['GLON'] * _DEGTORAD)
self._cosphi = numpy.cos(self._saledata['GLON'] * _DEGTORAD)
self._intps = numpy.zeros(
len(self._saledata),
dtype='object') #array to cache interpolated extinctions
return None
def __init__(self, filename):
super(AsciiTable, self).__init__(filename, nommap=True)
import asciitable
table = asciitable.read(filename)
logger.debug("done parsing ascii table")
#import pdb
#pdb.set_trace()
#names = table.array.dtype.names
names = table.dtype.names
#data = table.array.data
for i in range(len(table.dtype)):
name = table.dtype.names[i]
type = table.dtype[i]
if type.kind in ["f", "i"]: # only store float and int
#datagroup.create_dataset(name, data=table.array[name].astype(np.float64))
#dataset.addMemoryColumn(name, table.array[name].astype(np.float64))
self.addColumn(name, array=table[name])
def __init__(self, filter=None, sf10=True):
"""
NAME:
__init__
PURPOSE:
Initialize the Marshall06 dust map
INPUT:
filter= filter to return the extinction in
sf10= (True) if True, use the Schlafly & Finkbeiner calibrations
OUTPUT:
object
HISTORY:
2013-11-24 - Started - Bovy (IAS)
"""
DustMap3D.__init__(self, filter=filter)
self._sf10 = sf10
#Read the maps
sys.stdout.write('\r' +
"Reading Marshall et al. (2006) data file ...\r")
sys.stdout.flush()
self._marshalldata = asciitable.read(
os.path.join(_marshalldir, 'table1.dat'),
readme=os.path.join(_marshalldir, 'ReadMe'),
Reader=asciitable.cds.Cds,
guess=False,
fill_values=[('', '-999')])
sys.stdout.write('\r' + _ERASESTR + '\r')
sys.stdout.flush()
#Sort the data on l and then b
negIndx = self._marshalldata['GLON'] > 180.
self._marshalldata['GLON'][
negIndx] = self._marshalldata['GLON'][negIndx] - 360.
sortIndx = numpy.arange(len(self._marshalldata))
keyArray = (self._marshalldata['GLON'] +
self._marshalldata['GLAT'] / 100.).data
sortIndx = sorted(sortIndx, key=lambda x: keyArray[x])
self._marshalldata = self._marshalldata[sortIndx]
self._dl = 0.25
self._db = 0.25
self._intps = numpy.zeros(
len(self._marshalldata),
dtype='object') #array to cache interpolated extinctions
return None
def get_iss_photos():
"""
Gets public photos from ISS missions and provide data input for tasks
:arg string size: Size of the image from ISS mission
:returns: A list of photos.
:rtype: list
http://eol.jsc.nasa.gov/sseop/images/ESC/small/ISS030/ISS030-E-67805.JPG
"""
photos = []
#asciitable.BaseReader.inconsistent_handler = skip_bad_lines
lista = asciitable.read('atlasOfNight.csv', guess=False, delimiter=",")
for i in lista:
tmpMission = i['ISS-ID'].split('-E-')
mission = tmpMission[0]
idIss = tmpMission[1]
pattern_s = "http://eol.jsc.nasa.gov/sseop/images/ESC/%s/%s/%s-E-%s.JPG" % (
"small", mission, mission, idIss)
pattern_b = "http://eol.jsc.nasa.gov/sseop/images/ESC/%s/%s/%s-E-%s.JPG" % (
'large', mission, mission, idIss)
linkData = "http://eol.jsc.nasa.gov/scripts/sseop/photo.pl?mission=%s&roll=E&frame=%s" % (
mission, idIss)
idISS = idIss
citylon2 = str(i['nlon'])
citylat2 = str(i['nlat'])
f = '50'
tmp = dict(link_small=pattern_s,
link_big=pattern_b,
linkData=linkData,
idISS=idISS,
citylon=citylon2,
citylat=citylat2,
focal=f)
photos.append(tmp)
return photos
def pytest_generate_tests(metafunc):
print metafunc.config.getoption('cmdopt')
# if linux test job get parmetrize from core_test.list
if metafunc.config.getoption('cmdopt') != "adb":
if 'testcase_dict' in metafunc.fixturenames:
test_path = metafunc.config.getoption('targetdir')
testcase_list=collections.OrderedDict()
print(test_path)
testlist=asciitable.read(test_path+'/jenkins/core_test.list')
for rec in testlist:
testcase_list[rec[0]]=rec[1]
pprint.pprint(dict(testcase_list.items()))
metafunc.parametrize("testcase_dict", testcase_list.keys())
else:
# If test job is for Android ,use the list of android_testlist to call
# testcases in testcasses.py
metafunc.parametrize("testcase_dict", android_testlist)
print(android_testlist)
def save_BMI_data_Female():
import asciitable
x = asciitable.read(
'/Users/pdh21/Documents/CFwork/Patient_link/BMI_Boelle2012.txt',
guess=False,
delimiter='\t',
fill_values=[('', '-999')])
age_tab = x['age_fe']
BMI_tab = x['female']
age = np.arange(3, 38, 1)
ind_90 = range(0, 10)
ind_75 = range(11, 24)
ind_50 = range(25, 39)
ind_25 = range(40, 51)
ind_10 = range(52, 64)
indices = [ind_10, ind_25, ind_50, ind_75, ind_90]
BMI = np.empty((35.0, 7))
ii = 0
for i in indices:
print
age_tab[i], BMI_tab[i]
f = interp1d(age_tab[i], BMI_tab[i], kind='slinear')
BMI[:, ii + 1] = f(age)
ii += 1
BMI[:, 0] = BMI[:, 1] / 1.5
BMI[:, -1] = BMI[:, -2] * 1.2
age = np.append(age, np.arange(38, 80.0, 1))
BMI_extra = np.empty((80 - 38, BMI.shape[1]))
for i in np.arange(0, 80 - 38, 1):
print
i
BMI_extra[i, :] = BMI[-1, :]
BMI = np.concatenate((BMI, BMI_extra), axis=0)
import pylab as plt
for i in range(0, 7):
plt.plot(age, BMI[:, i])
plt.show()
np.savez('Female_BMI', age, BMI)
def take_data(Burst='130427A'):
import asciitable
GRB = 'GRBs/' + Burst + '.csv'
burst = asciitable.read(GRB, delimiter=',')
start_time = []
stop_time = []
Flux_erg = []
for x_1 in burst['start time']:
start_time.append(x_1)
for x_2 in burst['stop time']:
stop_time.append(x_2)
for y in burst['Energy flux (erg/cm2/s)']:
Flux_erg.append(y)
time, time_err = zip(*[(((y - x) / 2) + x, (y - x) / 2)
for x, y in zip(start_time, stop_time)])
Flux_GeV = [624.150934 * x for x in Flux_erg]
fig2 = pyplot.figure(figsize=(16, 8))
fig2ax1 = fig2.add_subplot(111)
fig2ax1.set_ylabel(r'Differential Flux [cm$^{-2}$ s$^{-1}$ GeV$^{-1}$]')
fig2ax1.set_xlabel('Time [s]')
fig2ax1.errorbar(time, Flux_GeV, xerr=time_err, fmt='o')
fig2ax1.loglog(time, Flux_GeV)
pyplot.show()
ax.set_xlabel('t (Gyr)', fontsize=15)
ax.legend(loc=4, fontsize=10, frameon=True, facecolor='w')
ax1.set_ylim(2e5, 2e12)
ax1.set_ylabel('M* (M$_\odot$)', fontsize=15)
ax2.set_ylim(1e-3, 1e2)
ax2.set_ylabel('SFR (M$_\odot$/yr)', fontsize=15)
plt.tight_layout()
plt.show()
# =============================================================================
# Show ALdo and Ciesla in one Fig.
# =============================================================================
M_today = np.array([9.5, 10.0, 10.5, 10.75, 11.0])
Data_a = {}
for m in M_today.astype('str'):
table = asc.read('Aldo/galaxies/gal_%s.dat' % m)
t, z, lgMh, lgMs, SFR = table.col1, table.col2, table.col3, table.col4, table.col5
data = pd.DataFrame({
't': t,
'z': z,
'lgMh': lgMh,
'lgMs': lgMs,
'SFR': SFR
})
Data_a['%s' % m] = data
from matplotlib.collections import PatchCollection
from matplotlib.patches import Rectangle
import matplotlib.transforms as mtransforms
from matplotlib.patches import FancyBboxPatch
import asciitable
from context_def import ft, files
def get_options():
parser = optparse.OptionParser()
parser.add_option("--dry-run",
action="store_true",
help="Dry run (no actual file or database updatees)")
return parser.parse_args()
opt, args = get_options()
filetypes = asciitable.read('Ska/engarchive/filetypes.dat')
if len(args) > 0:
filetypes = filetypes[filetypes['content'] == args[0].upper()]
for filetype in filetypes:
# Update attributes of global ContextValue "ft". This is needed for
# rendering of "files" ContextValue.
print filetype.content
ft['content'] = filetype['content'].lower()
ft['msid'] = 'TIME'
# archive files
if not os.path.exists(files['oldmsid'].abs + '.bak'):
print 'Skipping', ft[
'content'], ' because there is no backup from fix_ingest_h5.py'
