def main(pargs):
import time
from pypeit import ginga
from pypeit import flatfield
import subprocess
# Load up
flatField = flatfield.FlatField.from_master_file(pargs.master_file)
try:
ginga.connect_to_ginga(raise_err=True)
except ValueError:
subprocess.Popen(['ginga', '--modules=RC'])
time.sleep(3)
# Show RawFlatImage
viewer, ch = ginga.show_image(flatField.rawflatimg.image,
chname='Raw Flat')
# PixelFlat
if flatField.mspixelflat is not None:
viewer, ch = ginga.show_image(flatField.mspixelflat,
chname='Pixel Flat')
# Illumination flat
if flatField.msillumflat is not None:
viewer, ch = ginga.show_image(flatField.msillumflat,
chname='Illumination Flat')
# Illumination flat
if flatField.flat_model is not None:
viewer, ch = ginga.show_image(flatField.flat_model,
chname='Flat Model')
print("Check your Ginga viewer")
def main(pargs):
import pdb as debugger
import time
from pypeit import ginga
from pypeit import wavetilts
import subprocess
# Load up
wTilts = wavetilts.WaveTilts.from_master_files(pargs.setup)
# Launch ginga if need be
try:
ginga.connect_to_ginga(raise_err=True)
except ValueError:
subprocess.Popen(['ginga', '--modules=RC'])
time.sleep(3)
# Show
if pargs.slit is not None:
cname = 'Slit{:03d}'.format(pargs.slit)
else:
cname = None
wTilts.show(pargs.option, slit=pargs.slit, cname=cname)
def test_chk_flat():
mstrace_root = os.path.join(os.getenv('PYPEIT_DEV'), 'Cooked',
'shane_kast_blue', 'MasterFlat_A_1_01.fits')
# Ginga needs to be open in RC mode
ginga.connect_to_ginga(raise_err=True, allow_new=True)
#
pargs = chk_flats.parser([mstrace_root])
chk_flats.main(pargs)
def test_chk_edges():
mstrace_root = os.path.join(os.getenv('PYPEIT_DEV'), 'Cooked', 'Trace',
'MasterEdges_KeckLRISr_400_8500_det1.fits.gz')
# Ginga needs to be open in RC mode
ginga.connect_to_ginga(raise_err=True, allow_new=True)
#
pargs = chk_edges.parser([mstrace_root])
chk_edges.main(pargs)
def main(pargs):
import pdb as debugger
import time
from pypeit import ginga
from pypeit import traceslits
from pypeit.core.trace_slits import get_slitid
import subprocess
# Load up
tslits_dict, mstrace = traceslits.load_tslits(pargs.root)
import pdb
pdb.set_trace()
try:
ginga.connect_to_ginga(raise_err=True)
except ValueError:
subprocess.Popen(['ginga', '--modules=RC'])
time.sleep(3)
# This is deprecated since the class is not stored to disk anymore. You can just debug to achieve this functionality
#if pargs.show is not None:
# Tslits.show(pargs.show)
# print("Check your Ginga viewer")
# return
# Show Image
viewer, ch = ginga.show_image(mstrace, chname=pargs.chname)
nslits = tslits_dict['nslits']
# Get slit ids
stup = (mstrace.shape, tslits_dict['slit_left'], tslits_dict['slit_righ'])
if pargs.dumb_ids:
slit_ids = range(nslits)
else:
slit_ids = [
get_slitid(stup[0], stup[1], stup[2], ii)[0]
for ii in range(nslits)
]
ginga.show_slits(viewer,
ch,
tslits_dict['slit_left'],
tslits_dict['slit_righ'],
slit_ids,
pstep=50)
print("Check your Ginga viewer")
def show_alignment(alignframe, align_traces=None, slits=None, clear=False):
"""
Show one of the class internals
Parameters
----------
alignframe : `numpy.ndarray`_
Image to be plotted (i.e. the master align frame)
align_traces : list, optional
The align traces
slits : :class:`pypeit.slittrace.SlitTraceSet`, optional
properties of the slits, including traces.
clear : bool, optional
Clear the plotting window in ginga?
Returns
-------
"""
ginga.connect_to_ginga(raise_err=True, allow_new=True)
ch_name = 'alignment'
viewer, channel = ginga.show_image(alignframe,
chname=ch_name,
clear=clear,
wcs_match=False)
# Display the slit edges
if slits is not None and viewer is not None:
left, right, mask = slits.select_edges()
ginga.show_slits(viewer, channel, left, right)
# Display the alignment traces
if align_traces is not None and viewer is not None:
for bar in range(align_traces.shape[1]):
for slt in range(align_traces.shape[2]):
# Alternate the colors of the slits
color = 'orange'
if slt % 2 == 0:
color = 'magenta'
# Display the trace
ginga.show_trace(viewer,
channel,
align_traces[:, bar, slt],
trc_name="",
color=color)
def test_show_2dspec():
droot = os.path.join(os.getenv('PYPEIT_DEV'), 'Cooked')
spec2d_file = os.path.join(
droot, 'Science',
'spec2d_b27-J1217p3905_KASTb_2015May20T045733.560.fits')
# Ginga needs to be open in RC mode
ginga.connect_to_ginga(raise_err=True, allow_new=True)
# Save
cdir = os.getcwd()
os.chdir(droot)
# List
pargs = show_2dspec.parser([spec2d_file, '--list'])
show_2dspec.main(pargs)
# Show
pargs = show_2dspec.parser([spec2d_file])
show_2dspec.main(pargs)
# Go back
os.chdir(cdir)
def show_flats(pixelflat, illumflat, procflat, flat_model, wcs_match=True, slits=None):
"""
Interface to ginga to show a set of flat images
Args:
pixelflat (`numpy.ndarray`_):
illumflat (`numpy.ndarray`_ or None):
procflat (`numpy.ndarray`_):
flat_model (`numpy.ndarray`_):
wcs_match (bool, optional):
slits (:class:`pypeit.slittrace.SlitTraceSet`, optional):
Returns:
"""
ginga.connect_to_ginga(raise_err=True, allow_new=True)
if slits is not None:
left, right, mask = slits.select_edges()
gpm = mask == 0
# Loop me
clear = True
for img, name, cut in zip([pixelflat, illumflat, procflat, flat_model],
['pixelflat', 'illumflat', 'flat', 'flat_model'],
[(0.9, 1.1), (0.9, 1.1), None, None]):
if img is None:
continue
# TODO: Add an option that shows the relevant stuff in a
# matplotlib window.
viewer, ch = ginga.show_image(img, chname=name, cuts=cut,
wcs_match=wcs_match, clear=clear)
if slits is not None:
ginga.show_slits(viewer, ch, left[:, gpm], right[:, gpm],
slit_ids=slits.spat_id[gpm])
# Turn off clear
if clear:
clear = False
def main(args):
# List only?
if args.list:
hdu = fits.open(args.file)
hdu.info()
return
# Load it up
spec2DObj = spec2dobj.Spec2DObj.from_file(args.file, args.det)
# Setup for PYPIT imports
msgs.reset(verbosity=2)
# Init
# TODO: get_dnum needs to be deprecated...
sdet = get_dnum(args.det, prefix=False)
# if not os.path.exists(mdir):
# mdir_base = os.path.join(os.getcwd(), os.path.basename(mdir))
# msgs.warn('Master file dir: {0} does not exist. Using {1}'.format(mdir, mdir_base))
# mdir=mdir_base
# Slits
# slits_key = '{0}_{1:02d}'.format(spec2DObj.head0['TRACMKEY'], args.det)
# slit_file = os.path.join(mdir, masterframe.construct_file_name(slittrace.SlitTraceSet, slits_key))
# slits = slittrace.SlitTraceSet.from_file(slit_file)
# Grab the slit edges
slits = spec2DObj.slits
if spec2DObj.sci_spat_flexure is not None:
msgs.info("Offseting slits by {}".format(spec2DObj.sci_spat_flexure))
all_left, all_right, mask = slits.select_edges(
flexure=spec2DObj.sci_spat_flexure)
# TODO -- This may be too restrictive, i.e. ignore BADFLTCALIB??
gpm = mask == 0
left = all_left[:, gpm]
right = all_right[:, gpm]
slid_IDs = spec2DObj.slits.slitord_id[gpm]
bitMask = ImageBitMask()
# Object traces from spec1d file
spec1d_file = args.file.replace('spec2d', 'spec1d')
if os.path.isfile(spec1d_file):
sobjs = specobjs.SpecObjs.from_fitsfile(spec1d_file)
else:
sobjs = None
msgs.warn('Could not find spec1d file: {:s}'.format(spec1d_file) +
msgs.newline() +
' No objects were extracted.')
ginga.connect_to_ginga(raise_err=True, allow_new=True)
# Now show each image to a separate channel
# Show the bitmask?
mask_in = None
if args.showmask:
viewer, ch = ginga.show_image(spec2DObj.bpmmask,
chname="BPM",
waveimg=spec2DObj.waveimg,
clear=True)
#bpm, crmask, satmask, minmask, offslitmask, nanmask, ivar0mask, ivarnanmask, extractmask \
# SCIIMG
image = spec2DObj.sciimg # Processed science image
mean, med, sigma = sigma_clipped_stats(image[spec2DObj.bpmmask == 0],
sigma_lower=5.0,
sigma_upper=5.0)
cut_min = mean - 1.0 * sigma
cut_max = mean + 4.0 * sigma
chname_skysub = 'sciimg-det{:s}'.format(sdet)
# Clear all channels at the beginning
viewer, ch = ginga.show_image(image,
chname=chname_skysub,
waveimg=spec2DObj.waveimg,
clear=True)
if sobjs is not None:
show_trace(sobjs, args.det, viewer, ch)
ginga.show_slits(viewer, ch, left, right, slit_ids=slid_IDs)
# SKYSUB
if args.ignore_extract_mask:
# TODO -- Is there a cleaner way to do this?
gpm = (spec2DObj.bpmmask == 0) | (spec2DObj.bpmmask == 2**
bitMask.bits['EXTRACT'])
else:
gpm = spec2DObj.bpmmask == 0
image = (spec2DObj.sciimg - spec2DObj.skymodel
) * gpm #(spec2DObj.mask == 0) # sky subtracted image
mean, med, sigma = sigma_clipped_stats(image[spec2DObj.bpmmask == 0],
sigma_lower=5.0,
sigma_upper=5.0)
cut_min = mean - 1.0 * sigma
cut_max = mean + 4.0 * sigma
chname_skysub = 'skysub-det{:s}'.format(sdet)
# Clear all channels at the beginning
# TODO: JFH For some reason Ginga crashes when I try to put cuts in here.
viewer, ch = ginga.show_image(
image,
chname=chname_skysub,
waveimg=spec2DObj.waveimg,
bitmask=bitMask,
mask=mask_in) #, cuts=(cut_min, cut_max),wcs_match=True)
if not args.removetrace and sobjs is not None:
show_trace(sobjs, args.det, viewer, ch)
ginga.show_slits(viewer, ch, left, right, slit_ids=slid_IDs)
# SKRESIDS
chname_skyresids = 'sky_resid-det{:s}'.format(sdet)
image = (spec2DObj.sciimg - spec2DObj.skymodel) * np.sqrt(
spec2DObj.ivarmodel) * (spec2DObj.bpmmask == 0) # sky residual map
viewer, ch = ginga.show_image(image,
chname_skyresids,
waveimg=spec2DObj.waveimg,
cuts=(-5.0, 5.0),
bitmask=bitMask,
mask=mask_in)
if not args.removetrace and sobjs is not None:
show_trace(sobjs, args.det, viewer, ch)
ginga.show_slits(viewer, ch, left, right, slit_ids=slid_IDs)
# RESIDS
chname_resids = 'resid-det{:s}'.format(sdet)
# full model residual map
image = (spec2DObj.sciimg - spec2DObj.skymodel - spec2DObj.objmodel
) * np.sqrt(spec2DObj.ivarmodel) * (spec2DObj.bpmmask == 0)
viewer, ch = ginga.show_image(image,
chname=chname_resids,
waveimg=spec2DObj.waveimg,
cuts=(-5.0, 5.0),
bitmask=bitMask,
mask=mask_in)
if not args.removetrace and sobjs is not None:
show_trace(sobjs, args.det, viewer, ch)
ginga.show_slits(viewer, ch, left, right, slit_ids=slid_IDs)
# After displaying all the images sync up the images with WCS_MATCH
shell = viewer.shell()
out = shell.start_global_plugin('WCSMatch')
out = shell.call_global_plugin_method('WCSMatch', 'set_reference_channel',
[chname_resids], {})
if args.embed:
embed()
