def main(args=None):
parser = argparse.ArgumentParser(description="SkyPy pipeline driver")
parser.add_argument('--version', action='version', version=skypy_version)
parser.add_argument('config', help='Config file name')
parser.add_argument('-f',
'--format',
required=False,
choices=['fits', 'hdf5'],
help='Table file format')
parser.add_argument('-o',
'--overwrite',
action='store_true',
help='Whether to overwrite existing files')
# get system args if none passed
if args is None:
args = sys.argv[1:]
args = parser.parse_args(args or ['--help'])
pipeline = Pipeline.read(args.config)
pipeline.execute()
pipeline.write(file_format=args.format, overwrite=args.overwrite)
return (0)
def test_pipeline_read():
# Test reading config from a file
filename = get_pkg_data_filename('data/test_config.yml')
pipeline = Pipeline.read(filename)
pipeline.execute()
assert isinstance(pipeline['test_int'], int)
assert isinstance(pipeline['test_float'], float)
assert isinstance(pipeline['test_str'], str)
assert isinstance(pipeline['cosmology'], Cosmology)
assert isinstance(pipeline['test_table_1'], Table)
assert isinstance(pipeline['test_table_1']['test_column_3'], Column)
def setup(options):
module_name = options['pipeline', 'current_module']
filename = options.get_string(option_section, 'pipeline')
pipeline = Pipeline.read(filename)
for parameter_name, parameter_value in pipeline.parameters.items():
register_new_parameter(options,
module_name,
parameter_name,
*parameter_expand(parameter_value))
results = options.get_string(option_section, 'results')
results_map = {}
for line in results.splitlines():
section_name, skypy_label = tuple(map(str.strip, line.split('=')))
section, _, name = section_name.partition('--')
results_map[section, name] = skypy_label
return module_name, pipeline, results_map
# SDSS Photometry
# ---------------
#
# Here we compare the apparent magnitude distributions of our simulated
# galaxies with data from a :math:`10 \, \mathrm{deg^2}` region of the Sloan
# Digital Sky Survey [3]_. The binned SDSS magnitude distributions were
# generated from a query of the DR7 data release and can be downloaded
# :download:`here <../../../examples/galaxies/sdss_dered_10deg2.ecsv>`.
from astropy.table import Table, vstack
from matplotlib import pyplot as plt
import numpy as np
from skypy.pipeline import Pipeline
# Execute SkyPy galaxy photometry simulation pipeline
pipeline = Pipeline.read("sdss_photometry.yml")
pipeline.execute()
skypy_galaxies = vstack([pipeline['blue_galaxies'], pipeline['red_galaxies']])
# SDSS magnitude distributions for a 10 degree^2 region
sdss_data = Table.read("sdss_dered_10deg2.ecsv", format='ascii.ecsv')
# Plot magnitude distributions for SkyPy simulation and SDSS data
bins = np.linspace(14.95, 25.05, 102)
plt.hist(skypy_galaxies['mag_r'],
bins=bins,
alpha=0.5,
color='r',
label='SkyPy-r')
plt.hist(skypy_galaxies['mag_u'],
bins=bins,
from astropy.table import Table
from astropy.utils.data import download_file
from skypy.pipeline import Pipeline
# survey parameters
cosmology = FlatLambdaCDM(Om0=0.3, H0=70)
survey_area = u.Quantity('2.38 deg2')
# download catalogue
alhambra = download_file(
'http://svo2.cab.inta-csic.es/vocats/alhambra/download/alhambra.csv.gz',
cache=True)
# simulate with SkyPy
sim = Pipeline.read('fig_9.yml')
sim.execute()
# the model
def schechter_SF(M, z):
M_star = -21.00 - 1.03 * (z - 0.5)
phi_star = 10.**(-2.51 - 0.01 * (z - 0.5))
alpha = -1.29
M = np.reshape(M, (-1, 1))
return 0.4 * np.log(10) * phi_star * 10.**(
-0.4 * (M - M_star) * (alpha + 1)) * np.exp(-10.**(-0.4 *
(M - M_star)))
# four redshift bins