# Module for LRIS spectific codes
import numpy as np
import glob
import astropy.io.fits as pyfits
import armsgs
import arload
try:
from xastropy.xutils.xdebug import set_trace
# from xastropy.xutils import xdebug as xdb
except ImportError:
from pdb import set_trace
# Logging
msgs = armsgs.get_logger()
def read_lris(raw_file, det=None, TRIM=False):
"""
Read a raw LRIS data frame (one or more detectors)
Packed in a multi-extension HDU
Based on readmhdufits.pro
Parameters
----------
raw_file : str
Filename
det : int, optional
Detector number; Default = both
TRIM : bool, optional
Trim the image?
import numpy as np
import sys, os
import json
# Setup for PYPIT imports
this_file = os.path.realpath(__file__)
this_path = this_file[: this_file.rfind("/")]
sys.path.append(os.path.abspath(this_path + "/../src"))
import armsgs
import ardebug
debug = ardebug.init()
last_updated = "2 May 2016"
version = "0.1"
msgs = armsgs.get_logger((None, debug, last_updated, version, 1))
import arqa
from linetools.utils import loadjson
try:
from xastropy.xutils import xdebug as debugger
except:
import pdb as debugger
def main():
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
def PYPIT(redname, progname=__file__, quick=False, ncpus=1, verbose=1, logname=None):
"""
Main driver of the PYPIT code. Default settings and
user-specified changes are made, and passed to the
appropriate code for data reduction.
Parameters
----------
redname : string
Input reduction script
progname : string
Name of the program
quick : bool
If True, a quick reduction (but possibly less
accurate) will be performed. This flag is most
useful for observing at a telescope, but not
for publication quality results.
ncpus : int
Number of CPUs to use for multiprocessing the
data reduction (sometimes not used)
verbose : int (0,1,2)
Level of verbosity:
0 = No output
1 = Minimal output (default - suitable for the average user)
2 = All output
logname : string
The name of an ascii log file which is used to
save the output details of the reduction
---------------------------------------------------
"""
# Init logger
import armsgs
msgs = armsgs.get_logger((logname, debug, last_updated, version, verbose))
import arload
# First send all signals to messages to be dealt with (i.e. someone hits ctrl+c)
sigsignal(SIGINT, msgs.signal_handler)
# Ignore all warnings given by python
resetwarnings()
simplefilter("ignore")
# Record the starting time
tstart = time()
# Load the input file
parlines, datlines, spclines = arload.load_input(redname)
# Initialize the arguments and flags
argflag = arload.argflag_init()
argflag['run']['ncpus'] = ncpus
argflag['out']['verbose'] = verbose
# Determine the name of the spectrograph
specname = None
for i in range(len(parlines)):
parspl = parlines[i].split()
if len(parspl) < 3:
msgs.error("There appears to be a missing argument on the following input line" + msgs.newline() +
parlines[i])
if (parspl[0] == 'run') and (parspl[1] == 'spectrograph'):
specname = parspl[2]
if specname is None:
msgs.error("Please specify the spectrograph settings to be used with the command" + msgs.newline() +
"run spectrograph <name>")
msgs.info("Reducing data from the {0:s} spectrograph".format(specname))
# Load the Spectrograph settings
spect = arload.load_spect(progname, specname)
# Load default reduction arguments/flags, and set any command line arguments
#argflag = arload.optarg(argflag, cmdlnarg, spect['mosaic']['reduction'].lower())
# Load the default settings
prgn_spl = progname.split('/')
tfname = ""
for i in range(0,len(prgn_spl)-2): tfname += prgn_spl[i]+"/"
fname = tfname + prgn_spl[-2] + '/settings.' + spect['mosaic']['reduction'].lower()
argflag = arload.load_settings(fname, argflag)
argflag['run']['prognm'] = progname
argflag['run']['pypitdir'] = tfname
# Now update the settings based on the user input file
argflag = arload.set_params(parlines, argflag, setstr="Input ")
# Check the input file
arload.check_argflag(argflag)
# Load any changes to the spectrograph settings based on the user input file
spect = arload.load_spect(progname, specname, spect=spect, lines=spclines)
# If a quick reduction has been requested, make sure the requested pipeline
# is the quick implementation (if it exists), otherwise run the standard pipeline.
if quick:
# Change to a "quick" settings file
msgs.work("QUICK REDUCTION TO STILL BE DONE")
# Load the important information from the fits headers
fitsdict = arload.load_headers(argflag, spect, datlines)
# Reduce the data!
status = 0
msgs.work("Make appropriate changes to quick reduction")
if quick:
msgs.work("define what is needed here for quick reduction")
# Send the data away to be reduced
if spect['mosaic']['reduction'] == 'ARMLSD':
msgs.info("Data reduction will be performed using PYPIT-ARMLSD")
import armlsd
status = armlsd.ARMLSD(argflag, spect, fitsdict)
elif spect['mosaic']['reduction'] == 'ARMED':
msgs.info("Data reduction will be performed using PYPIT-ARMED")
import armed
status = armed.ARMED(argflag, spect, fitsdict)
# Check for successful reduction
if status == 0:
msgs.info("Data reduction complete")
else:
msgs.error("Data reduction failed with status ID {0:d}".format(status))
# Capture the end time and print it to user
tend = time()
codetime = tend-tstart
if codetime < 60.0:
msgs.info("Data reduction execution time: {0:.2f}s".format(codetime))
elif codetime/60.0 < 60.0:
mns = int(codetime/60.0)
scs = codetime - 60.0*mns
msgs.info("Data reduction execution time: {0:d}m {1:.2f}s".format(mns, scs))
else:
hrs = int(codetime/3600.0)
mns = int(60.0*(codetime/3600.0 - hrs))
scs = codetime - 60.0*mns - 3600.0*hrs
msgs.info("Data reduction execution time: {0:d}h {1:d}m {2:.2f}s".format(hrs, mns, scs))
return
import argparse
import numpy as np
import sys, os
import json
# Setup for PYPIT imports
this_file = os.path.realpath(__file__)
this_path = this_file[:this_file.rfind('/')]
sys.path.append(os.path.abspath(this_path+'/../src'))
import armsgs
import ardebug
debug = ardebug.init()
last_updated = "2 May 2016"
version = '0.1'
msgs = armsgs.get_logger((None, debug, last_updated, version, 1))
import arqa
from linetools.utils import loadjson
try:
from xastropy.xutils import xdebug as debugger
except:
import pdb as debugger
def main() :
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('wave_soln', type = str, default = None,
