def plot_countpix(qa_dict,outfile,plotconf=None,hardplots=False):
"""
Plot pixel counts above some threshold
Args:
qa_dict: qa dictionary from countpix qa
outfile: pdf file of the plot
"""
from desispec.util import set_backend
_matplotlib_backend = None
set_backend()
expid=qa_dict["EXPID"]
camera = qa_dict["CAMERA"]
paname=qa_dict["PANAME"]
#npix_amp=np.array(qa_dict["METRICS"]["NPIX_AMP"])
litfrac=np.array(qa_dict["METRICS"]["LITFRAC_AMP"])
cutthres=qa_dict["PARAMS"]["CUTPIX"]
fig=plt.figure()
if plotconf:
hardplots=ql_qaplot(fig,plotconf,qa_dict,camera,expid,outfile)
if not hardplots:
pass
else:
plt.suptitle("Fraction of pixels lit after {}, Camera: {}, ExpID: {}".format(paname,camera,expid),fontsize=10,y=0.99)
#ax1=fig.add_subplot(211)
#heatmap1=ax1.pcolor(npix_amp.reshape(2,2),cmap=plt.cm.OrRd)
##plt.title('Total Pixels > {:d} sigma = {:f}'.format(cutthres,countlo), fontsize=10)
#ax1.set_xlabel("# pixels > {:d} sigma (per Amp)".format(cutthres),fontsize=10)
#ax1.tick_params(axis='x',labelsize=10,labelbottom=False)
#ax1.tick_params(axis='y',labelsize=10,labelleft=False)
# ax1.annotate("Amp 1\n{:f}".format(npix_amp[0]),
# xy=(0.4,0.4),
# fontsize=10
# )
#ax1.annotate("Amp 2\n{:f}".format(npix_amp[1]),
# xy=(1.4,0.4),
# fontsize=10
# )
#ax1.annotate("Amp 3\n{:f}".format(npix_amp[2]),
# xy=(0.4,1.4),
# fontsize=10
# )
#ax1.annotate("Amp 4\n{:f}".format(npix_amp[3]),
# xy=(1.4,1.4),
# fontsize=10
# )
ax2=fig.add_subplot(111)
heatmap2=ax2.pcolor(litfrac.reshape(2,2),cmap=plt.cm.OrRd)
ax2.set_xlabel("Fraction over {:d} sigma read noise(per Amp)".format(cutthres),fontsize=10)
ax2.tick_params(axis='x',labelsize=10,labelbottom=False)
ax2.tick_params(axis='y',labelsize=10,labelleft=False)
ax2.annotate("Amp 1\n{:f}".format(litfrac[0]),
xy=(0.4,0.4),
fontsize=10
)
ax2.annotate("Amp 2\n{:f}".format(litfrac[1]),
xy=(1.4,0.4),
fontsize=10
)
ax2.annotate("Amp 3\n{:f}".format(litfrac[2]),
xy=(0.4,1.4),
fontsize=10
)
ax2.annotate("Amp 4\n{:f}".format(litfrac[3]),
xy=(1.4,1.4),
fontsize=10
)
plt.tight_layout()
fig.savefig(outfile)
def ql_main(args=None):
from desispec.util import set_backend
_matplotlib_backend = None
set_backend()
from desispec.quicklook import quicklook,qllogger,qlconfig
if args is None:
args = parse()
qlog=qllogger.QLLogger(name="QuickLook",loglevel=args.loglvl)
log=qlog.getlog()
# quiet down DESI logs. We don't want DESI_LOGGER to print messages unless they are important
# initalize singleton with WARNING level
quietDesiLogger(args.loglvl+10)
if args.config is not None:
#RS: have command line arguments for finding files via old datamodel
psfid=None
if args.psfid:
psfid=args.psfid
flatid=None
if args.flatid:
flatid=args.flatid
templateid=None
if args.templateid:
templateid=args.templateid
templatenight=None
if args.templatenight:
templatenight=args.templatenight
if args.rawdata_dir:
rawdata_dir = args.rawdata_dir
else:
if 'QL_SPEC_DATA' not in os.environ:
sys.exit("must set ${} environment variable or provide rawdata_dir".format('QL_SPEC_DATA'))
rawdata_dir=os.getenv('QL_SPEC_DATA')
if args.specprod_dir:
specprod_dir = args.specprod_dir
else:
if 'QL_SPEC_REDUX' not in os.environ:
sys.exit("must set ${} environment variable or provide specprod_dir".format('QL_SPEC_REDUX'))
specprod_dir=os.getenv('QL_SPEC_REDUX')
log.debug("Running Quicklook using configuration file {}".format(args.config))
if os.path.exists(args.config):
if "yaml" in args.config:
config=qlconfig.Config(args.config, args.night,args.camera, args.expid, args.singqa, rawdata_dir=rawdata_dir, specprod_dir=specprod_dir,psfid=psfid,flatid=flatid,templateid=templateid,templatenight=templatenight,qlplots=args.qlplots,store_res=args.resolution)
configdict=config.expand_config()
else:
log.critical("Can't open config file {}".format(args.config))
sys.exit("Can't open config file")
else:
sys.exit("File does not exist: {}".format(args.config))
else:
sys.exit("Must provide a valid config file. See desispec/data/quicklook for an example")
pipeline, convdict = quicklook.setup_pipeline(configdict)
res=quicklook.runpipeline(pipeline,convdict,configdict)
log.info("QuickLook Pipeline completed")
Utility functions to perform a quick calibration of DESI data
TODO:
1. Expand to r, i cameras
2. QA plots
3. Test with CR data
"""
from __future__ import print_function, absolute_import, division
import numpy as np
from desiutil.log import get_logger
from desispec import bootcalib as desiboot
from desiutil import funcfits as dufits
from desispec.util import set_backend
set_backend()
from matplotlib.backends.backend_pdf import PdfPages
import sys
import argparse
from astropy.io import fits
def parse(options=None):
parser = argparse.ArgumentParser(description="Bootstrap DESI PSF.")
parser.add_argument('--contfile', type = str, default = None, required=False,
help = 'path of DESI continuum fits file')
parser.add_argument('--arcfile', type = str, default = None, required=False,
def ql_main(args=None):
from desispec.util import set_backend
_matplotlib_backend = None
set_backend()
from desispec.quicklook import quicklook, qllogger, qlconfig
if args is None:
args = parse()
qlog = qllogger.QLLogger(name="QuickLook", loglevel=args.loglvl)
log = qlog.getlog()
# quiet down DESI logs. We don't want DESI_LOGGER to print messages unless they are important
# initalize singleton with WARNING level
quietDesiLogger(args.loglvl + 10)
if args.config is not None:
#RS: have command line arguments for finding files via old datamodel
psfid = None
if args.psfid:
psfid = args.psfid
flatid = None
if args.flatid:
flatid = args.flatid
templateid = None
if args.templateid:
templateid = args.templateid
templatenight = None
if args.templatenight:
templatenight = args.templatenight
if args.rawdata_dir:
rawdata_dir = args.rawdata_dir
else:
if 'QL_SPEC_DATA' not in os.environ:
sys.exit(
"must set ${} environment variable or provide rawdata_dir".
format('QL_SPEC_DATA'))
rawdata_dir = os.getenv('QL_SPEC_DATA')
if args.specprod_dir:
specprod_dir = args.specprod_dir
else:
if 'QL_SPEC_REDUX' not in os.environ:
sys.exit(
"must set ${} environment variable or provide specprod_dir"
.format('QL_SPEC_REDUX'))
specprod_dir = os.getenv('QL_SPEC_REDUX')
log.debug("Running Quicklook using configuration file {}".format(
args.config))
if os.path.exists(args.config):
if "yaml" in args.config:
config = qlconfig.Config(args.config,
args.night,
args.camera,
args.expid,
args.singqa,
rawdata_dir=rawdata_dir,
specprod_dir=specprod_dir,
psfid=psfid,
flatid=flatid,
templateid=templateid,
templatenight=templatenight,
qlplots=args.qlplots,
store_res=args.resolution)
configdict = config.expand_config()
else:
log.critical("Can't open config file {}".format(args.config))
sys.exit("Can't open config file")
else:
sys.exit("File does not exist: {}".format(args.config))
else:
sys.exit(
"Must provide a valid config file. See desispec/data/quicklook for an example"
)
pipeline, convdict = quicklook.setup_pipeline(configdict)
res = quicklook.runpipeline(pipeline, convdict, configdict)
log.info("QuickLook Pipeline completed")
