Workaround for bad flux values #722
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sbailey
approved these changes
Nov 12, 2018
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I think this is ready to merge. I tested this with the redshift-database tutorial, which itself needed updates for 18.11++. |
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This fixes the bad flux values, but I'm still getting a crash from loading a full minitest production: basedir = '/global/cscratch1/sd/sjbailey/desi/dev/end2end'
targetdir = '/global/cscratch1/sd/sjbailey/desi/dev/end2end/targets'
reduxdir = '/global/cscratch1/sd/sjbailey/desi/dev/end2end/spectro/redux/mini'
fibassigndir = '/global/cscratch1/sd/sjbailey/desi/dev/end2end/fiberassign'
expfile = '/global/cscratch1/sd/sjbailey/desi/dev/end2end/survey/exposures.fits'
from argparse import Namespace
from desispec.database.redshift import (setup_db, dbSession, load_file, ObsList, Target, Truth, ZCat, FiberAssign,
load_fiberassign)
options = Namespace(overwrite=True, dbfile=os.path.join(os.getenv('SCRATCH'), 'minitest.db'), hostname=None, maxrows=0,
chunksize=50000, schema=None, username=None, verbose=False, datapath=basedir)
# We'll be using a SQLite database, ignore the return value of setup_db
postgresql = setup_db(options)
load_file(expfile, ObsList, hdu='EXPOSURES', expand={'PASS': 'passnum'})
load_file(os.path.join(targetdir, 'truth.fits'), Truth, hdu='TRUTH')
load_file(os.path.join(targetdir, 'targets.fits'), Target, hdu="TARGETS")
load_file(os.path.join(reduxdir, 'zcatalog-mini.fits'), ZCat, hdu='ZCATALOG',
expand={'COEFF': ('coeff_0', 'coeff_1', 'coeff_2', 'coeff_3', 'coeff_4',
'coeff_5', 'coeff_6', 'coeff_7', 'coeff_8', 'coeff_9',)},
rowfilter=lambda x: ((x['TARGETID'] != 0) & (x['TARGETID'] != -1)))
load_fiberassign(fibassigndir)Results in |
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@sbailey, you need to look at the redshift-database tutorial to see how to change the loading sequence. |
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@weaverba137 got it. For the record, this worked. I'll merge now and update the minitest notebook. from argparse import Namespace
from desispec.database.redshift import (setup_db, dbSession, load_file, ObsList, Target, Truth, ZCat, FiberAssign,
load_fiberassign, update_truth)
options = Namespace(overwrite=True, dbfile=os.path.join(basedir, 'minitest.db'), hostname=None, maxrows=0,
chunksize=50000, schema=None, username=None, verbose=False, datapath=basedir)
# We'll be using a SQLite database, ignore the return value of setup_db
postgresql = setup_db(options)
print('--- Loading exposure list')
load_file(expfile, ObsList, hdu='EXPOSURES', expand={'PASS': 'passnum'})
print('--- Loading truth tables')
load_file(os.path.join(targetdir, 'truth.fits'), Truth, hdu='TRUTH')
for h in ('BGS', 'ELG', 'LRG', 'QSO', 'STAR', 'WD'):
update_truth(os.path.join(targetdir, 'truth.fits'), 'TRUTH_' + h)
print('--- Loading targets')
load_file(os.path.join(targetdir, 'targets.fits'), Target, hdu='TARGETS',
expand={'DCHISQ': ('dchisq_psf', 'dchisq_rex', 'dchisq_dev', 'dchisq_exp', 'dchisq_comp',)})
print('--- loading redshift catalog')
load_file(os.path.join(reduxdir, 'zcatalog-mini.fits'), ZCat, hdu='ZCATALOG',
expand={'COEFF': ('coeff_0', 'coeff_1', 'coeff_2', 'coeff_3', 'coeff_4',
'coeff_5', 'coeff_6', 'coeff_7', 'coeff_8', 'coeff_9',)},
rowfilter=lambda x: ((x['TARGETID'] != 0) & (x['TARGETID'] != -1)))
print('--- loading fiber assignments')
load_fiberassign(fibassigndir)
print('--- done') |
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This PR is a workaround for desihub/desitarget#397.
Do not merge yet. I also need to review changes to the data model (for example, the target table has added about 60 columns).