def test_library_file(test_directory):
"""Download and save locally a segment PSF library file from Box for testing
Yields
-------
test_lib_filename : str
Path to test library used for testing
"""
# Download file and yield its name
test_lib_filename = os.path.join(test_directory, 'test_library',
'nircam_nrca3_f212n_fovp1024_samp1_npsf1_seg12.fits')
ensure_dir_exists(os.path.dirname(test_lib_filename))
url = "https://stsci.box.com/shared/static/4c0em1yhb1qsvrpku7j0jw1tztucvkih.fits"
with fits.open(url) as hdulist:
hdulist.writeto(test_lib_filename)
yield test_lib_filename
def path_check():
"""Check that the CRDS_PATH environment variable is set. This will be
the location to which CRDS reference files are downloaded. If the env
variable is not set, default to use $HOME/crds_cache/
Returns
-------
crds_path : str
Full path to the location of the CRDS reference files
"""
crds_path = os.environ.get('CRDS_PATH')
if crds_path is None:
reffile_dir = '{}/crds_cache'.format(os.environ.get('HOME'))
os.environ["CRDS_PATH"] = reffile_dir
ensure_dir_exists(reffile_dir)
print('CRDS_PATH environment variable not set. Setting to {}'.format(reffile_dir))
return reffile_dir
else:
return crds_path
def test_directory(test_dir=TEMP_TEST_DIRECTORY):
"""Create a test directory.
Parameters
----------
test_dir : str
Path to directory used for testing
Yields
-------
test_dir : str
Path to directory used for testing
"""
# Create directory and yield its name
ensure_dir_exists(test_dir) # creates directory with default mode=511
yield test_dir
# Remove directory
if os.path.isdir(test_dir):
shutil.rmtree(test_dir)
def download_reffiles(directory,
instrument='all',
dark_type='linearized',
skip_darks=False,
skip_cosmic_rays=False,
skip_psfs=False):
"""Download tarred and gzipped reference files. Expand, unzip and
organize into the necessary directory structure such that Mirage
can use them.
Parameters
----------
directory : str
Directory into which the reference files are placed. This will
be the directory set to the MIRAGE_DATA environment variable
instrument : str
Instruments for which to download data. Single string with
comma-separated instrument names.
If ``all``: download files for NIRCam, NIRISS, and FGS.
If the name of an individual instrument (e.g. 'nircam'),
download only the data for that instrument.
If a list of instrument names, (e.g. 'nircam, niriss') download
all data for those instruments.
dark_type : str
Type of dark current files to download. Options are:
'linearized': download linearize dark current ramps
'raw': download raw dark current ramps
'both': download both raw and linearized dark current ramps
skip_darks : bool
If False (default), download the requested darks. If True,
do not download the darks
skip_comsic_rays : bool
If False (default), download the requested cosmic ray libraries.
If True, do not download the cosmic ray library.
skip_psfs : bool
If False (default), download the requested PSF libraries.
If True, do not download the libraries.
"""
# Be sure the input instrument is a list
file_list = get_file_list(instrument.lower(),
dark_type.lower(),
skip_darks=skip_darks,
skip_cosmic_rays=skip_cosmic_rays,
skip_psfs=skip_psfs)
# Download everything first
for file_url in file_list:
filename = os.path.split(file_url)[-1]
local_file = os.path.join(directory, filename)
download_file(file_url, filename, directory)
# Now untar/organize. This way if the download is interrupted, it can
# pick up where it left off, since no downloaded files will have been
# moved yet.
for file_url in file_list:
filename = os.path.split(file_url)[-1]
local_file = os.path.join(directory, filename)
# Unzip and untar file
if 'tar.gz' in local_file:
print('Unzipping/extracting {}'.format(filename))
file_object = tarfile.open(name=local_file, mode='r:gz')
file_object.extractall(path=directory)
else:
# Darks need to be unzipped into the correct directory
if 'linearized' in filename.lower():
cal = 'linearized'
else:
cal = 'raw'
# Determine directory
if 'NRCNRC' in filename:
det_str = filename.split('NRCNRC')[1].split('-')[0]
if 'LONG' in det_str:
det_str.replace('LONG', '5')
darks_dir = os.path.join(directory, 'mirage_data', 'nircam',
'darks')
sub_directory = os.path.join(darks_dir, cal, det_str)
elif 'NIRISS' in filename:
darks_dir = os.path.join(directory, 'mirage_data', 'niriss',
'darks')
sub_directory = os.path.join(darks_dir, cal)
#sub_directory = os.path.join(directory, 'mirage_data', 'niriss', 'darks', cal)
elif 'FGS' in filename:
darks_dir = os.path.join(directory, 'mirage_data', 'fgs',
'darks')
sub_directory = os.path.join(darks_dir, cal)
# Create the directory if it does not yet exist
ensure_dir_exists(darks_dir)
ensure_dir_exists(os.path.join(darks_dir, cal))
ensure_dir_exists(sub_directory)
final_location = os.path.join(sub_directory, filename)
# Move the zipped file into the correct subdirectory
if not os.path.isfile(final_location):
print('Moving {} to {}'.format(filename, sub_directory))
shutil.move(local_file, final_location)
# Unzip
unzipped_filename = final_location.replace('.gz', '')
if not os.path.isfile(unzipped_filename):
unzip_file(final_location)
else:
print(
'Unzipped file {} already exists. Skipping unzip.'.format(
unzipped_filename))
full_dir = os.path.abspath(directory)
print(('Mirage reference files downloaded and extracted. \nBefore '
'using Mirage, be sure to set the MIRAGE_DATA environment '
'variable to point to:\n{}/mirage_data'.format(full_dir)))
print('In bash: ')
print('export MIRAGE_DATA="{}"'.format(
os.path.join(full_dir, 'mirage_data')))
from mirage.catalogs.catalog_generator import GrismTSOCatalog, ImagingTSOCatalog, PointSourceCatalog
from mirage.catalogs.catalog_generator import TSO_GRISM_INDEX
from mirage.grism_tso_simulator import GrismTSO
from mirage.imaging_simulator import ImgSim
from mirage.seed_image.catalog_seed_image import Catalog_seed
from mirage.utils.utils import ensure_dir_exists
from mirage.yaml import yaml_generator
# ---------- Define Paths to organize Inputs and Outputs ----------
input_data_path = os.path.abspath(
'/home/anadkarni/NIRCam_AZ_TSO_Data_Challenge/GJ436_apt_data/')
output_dir = '/home/anadkarni/NIRCam_AZ_TSO_Data_Challenge/GJ436_2102/'
output_yaml_dir = os.path.abspath(
'/home/anadkarni/NIRCam_AZ_TSO_Data_Challenge/GJ436_2102/GJ436_yaml_data/')
ensure_dir_exists(output_yaml_dir)
output_data_dir = os.path.abspath(
'/home/anadkarni/NIRCam_AZ_TSO_Data_Challenge/GJ436_2102/GJ436_sim_data/')
ensure_dir_exists(output_data_dir)
tsdir = '/home/anadkarni/NIRCam_AZ_TSO_Data_Challenge/GJ436_LC_TS_Params/'
# ---------- Prepare Inputs ----------
xml_file = os.path.join(input_data_path, 'GJ436.xml')
pointing_file = xml_file.replace('.xml', '.pointing')
# ---------- Stellar Spectrum ----------
t_eff = 3500 # surface temperature
metallicity = 0.02 # Fe/H
log_g = 5.0 # surface gravity = 182 m/s^2