def reduce(filename): _p = GMOSLongslit([astrodata.open(filename)]) _p.viewer = geminidr.dormantViewer(_p, None) _p.prepare() _p.addDQ(static_bpm=None) _p.addVAR(read_noise=True) _p.overscanCorrect() _p.ADUToElectrons() _p.addVAR(poisson_noise=True) _p.mosaicDetectors() _p.makeIRAFCompatible() _p.determineWavelengthSolution(suffix="_arc") return _p
def create_inputs_recipe(): """ Creates input data for tests using pre-processed standard star and its calibration files. The raw files will be downloaded and saved inside the path stored in the `$DRAGONS_TEST/raw_inputs` directory. Processed files will be stored inside a new folder called "dragons_test_inputs". The sub-directory structure should reflect the one returned by the `path_to_inputs` fixture. """ import os from astrodata.testing import download_from_archive from geminidr.gmos.tests.spect import CREATED_INPUTS_PATH_FOR_TESTS module_name, _ = os.path.splitext(os.path.basename(__file__)) path = os.path.join(CREATED_INPUTS_PATH_FOR_TESTS, module_name) os.makedirs(path, exist_ok=True) os.chdir(path) os.makedirs("inputs/", exist_ok=True) print('Current working directory:\n {:s}'.format(os.getcwd())) for filename in datasets: print('Downloading files...') basename = filename.split("_")[0] + ".fits" sci_path = download_from_archive(basename) sci_ad = astrodata.open(sci_path) data_label = sci_ad.data_label() print('Reducing pre-processed data:') logutils.config(file_name='log_{}.txt'.format(data_label)) p = GMOSLongslit([sci_ad]) p.prepare() p.addDQ(static_bpm=None) p.addVAR(read_noise=True) p.overscanCorrect() p.ADUToElectrons() p.addVAR(poisson_noise=True) p.mosaicDetectors() p.makeIRAFCompatible() os.chdir("inputs/") processed_ad = p.writeOutputs().pop() os.chdir("..") print("Wrote pre-processed file to:\n" " {:s}".format(processed_ad.filename))
def process_arc(filename, suffix="distortionDetermined"): """ Helper recipe to reduce the arc file. Returns ------- AstroData Processed arc. """ from astrodata.testing import download_from_archive from geminidr.gmos.primitives_gmos_longslit import GMOSLongslit processed_filename, ext = os.path.splitext(filename) processed_filename += "_{:s}{:s}".format(suffix, ext) if os.path.exists(processed_filename): ad = astrodata.open(processed_filename) else: if os.path.exists(filename): ad = astrodata.open(filename) else: ad = astrodata.open( download_from_archive(filename, path='', env_var='DRAGONS_TEST')) p = GMOSLongslit([ad]) p.prepare() p.addDQ(static_bpm=None) p.addVAR(read_noise=True) p.overscanCorrect() # p.biasCorrect() p.ADUToElectrons() p.addVAR(poisson_noise=True) p.mosaicDetectors() p.makeIRAFCompatible() p.determineWavelengthSolution() p.determineDistortion() ad = p.streams['main'][0] ad.write(overwrite=True) return ad
def create_inputs_recipe(): """ Creates input data for tests using pre-processed standard star and its calibration files. The raw files will be downloaded and saved inside the path stored in the `$DRAGONS_TEST/raw_inputs` directory. Processed files will be stored inside a new folder called "dragons_test_inputs". The sub-directory structure should reflect the one returned by the `path_to_inputs` fixture. """ import os from astrodata.testing import download_from_archive from recipe_system.reduction.coreReduce import Reduce from gempy.utils import logutils associated_calibrations = { "S20190808S0048.fits": { "arcs": ["S20190808S0167.fits"] }, "S20190808S0049.fits": { "arcs": ["S20190808S0168.fits"] }, # "S20190808S0052.fits": {"arcs": ["S20190808S0165.fits"]}, # Can't find aperture "S20190808S0053.fits": { "arcs": ["S20190808S0169.fits"] }, } root_path = os.path.join("./dragons_test_inputs/") module_path = "geminidr/gmos/spect/{}".format(__file__.split('.')[0]) path = os.path.join(root_path, module_path) os.makedirs(path, exist_ok=True) os.chdir(path) os.makedirs("./inputs", exist_ok=True) print('Current working directory:\n {:s}'.format(os.getcwd())) for filename, cals in associated_calibrations.items(): print('Downloading files...') sci_path = download_from_archive(filename) arc_path = [download_from_archive(f) for f in cals['arcs']] sci_ad = astrodata.open(sci_path) data_label = sci_ad.data_label() print('Reducing ARC for {:s}'.format(data_label)) logutils.config(file_name='log_arc_{}.txt'.format(data_label)) arc_reduce = Reduce() arc_reduce.files.extend(arc_path) arc_reduce.runr() arc = arc_reduce.output_filenames.pop() print('Reducing pre-processed data:') logutils.config(file_name='log_{}.txt'.format(data_label)) p = GMOSLongslit([sci_ad]) p.prepare() p.addDQ(static_bpm=None) p.addVAR(read_noise=True) p.overscanCorrect() p.ADUToElectrons() p.addVAR(poisson_noise=True) p.mosaicDetectors() p.distortionCorrect(arc=arc) p.findSourceApertures(max_apertures=1) p.skyCorrectFromSlit() p.traceApertures() p.extract1DSpectra() os.chdir("inputs/") _ = p.writeOutputs().pop() os.chdir("../")
def create_inputs_recipe(): """ Creates input data for tests using pre-processed standard star and its calibration files. The raw files will be downloaded and saved inside the path stored in the `$DRAGONS_TEST/raw_inputs` directory. Processed files will be stored inside a new folder called "dragons_test_inputs". The sub-directory structure should reflect the one returned by the `path_to_inputs` fixture. """ import os from astrodata.testing import download_from_archive from recipe_system.reduction.coreReduce import Reduce from gempy.utils import logutils from astrodata.testing import get_associated_calibrations associated_calibrations = { "S20190808S0048.fits": 'S20190808S0167.fits', "S20190808S0049.fits": 'S20190808S0168.fits', "S20190808S0053.fits": 'S20190808S0169.fits', "N20180106S0025.fits": 'N20180115S0264.fits', "N20180106S0026.fits": 'N20180115S0264.fits', "N20180106S0028.fits": 'N20180115S0264.fits', "N20180106S0029.fits": 'N20180115S0264.fits', } root_path = os.path.join("./dragons_test_inputs/") module_path = "geminidr/gmos/spect/{}".format(__file__.split('.')[0]) path = os.path.join(root_path, module_path) os.makedirs(path, exist_ok=True) os.chdir(path) os.makedirs("./inputs", exist_ok=True) print('Current working directory:\n {:s}'.format(os.getcwd())) for fname, arc_fname in associated_calibrations.items(): sci_path = download_from_archive(fname) arc_path = download_from_archive(arc_fname) sci_ad = astrodata.open(sci_path) data_label = sci_ad.data_label() print('Reducing ARC for {:s}'.format(data_label)) logutils.config(file_name='log_arc_{}.txt'.format(data_label)) if os.path.exists( arc_fname.replace('.fits', '_distortionDetermined.fits')): arc = astrodata.open( arc_fname.replace('.fits', '_distortionDetermined.fits')) else: p = GMOSLongslit([astrodata.open(arc_path)]) p.prepare() p.addDQ(static_bpm=None) p.addVAR(read_noise=True) p.overscanCorrect() p.ADUToElectrons() p.addVAR(poisson_noise=True) p.mosaicDetectors() p.makeIRAFCompatible() p.determineWavelengthSolution() p.determineDistortion() arc = p.writeOutputs().pop() print('Reducing pre-processed data:') logutils.config(file_name='log_{}.txt'.format(data_label)) p = GMOSLongslit([sci_ad]) p.prepare() p.addDQ(static_bpm=None) p.addVAR(read_noise=True) p.overscanCorrect() p.ADUToElectrons() p.addVAR(poisson_noise=True) p.mosaicDetectors() p.distortionCorrect(arc=arc) p.findSourceApertures(max_apertures=1) p.skyCorrectFromSlit() os.chdir("inputs/") _ = p.writeOutputs().pop() os.chdir("../")