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(self, slits=True, wcs_match=True):
"""
Show all of the flat field products
Args:
slits (bool, optional):
wcs_match (bool, optional):
"""
viewer, ch = ginga.show_image(self.mspixelflat,
chname='pixeflat',
cuts=(0.9, 1.1),
wcs_match=wcs_match,
clear=True)
viewer, ch = ginga.show_image(self.msillumflat,
chname='illumflat',
cuts=(0.9, 1.1),
wcs_match=wcs_match)
viewer, ch = ginga.show_image(self.rawflatimg,
chname='flat',
wcs_match=wcs_match)
viewer, ch = ginga.show_image(self.flat_model,
chname='flat_model',
wcs_match=wcs_match)
if slits:
if self.tslits_dict is not None:
slit_ids = [
trace_slits.get_slitid(self.rawflatimg.shape,
self.tslits_dict['slit_left'],
self.tslits_dict['slit_righ'],
ii)[0]
for ii in range(self.tslits_dict['slit_left'].shape[1])
]
ginga.show_slits(viewer, ch, self.tslits_dict['slit_left'],
self.tslits_dict['slit_righ'], slit_ids)
def main(args):
# List only?
hdu = fits.open(args.file)
head0 = hdu[0].header
if args.list:
hdu.info()
return
# Setup for PYPIT imports
msgs.reset(verbosity=2)
# Init
sdet = get_dnum(args.det, prefix=False)
# One detector, sky sub for now
names = [hdu[i].name for i in range(len(hdu))]
try:
exten = names.index('DET{:s}-PROCESSED'.format(sdet))
except: # Backwards compatability
msgs.error(
'Requested detector {:s} was not processed.\n'
'Maybe you chose the wrong one to view?\n'
'Set with --det= or check file contents with --list'.format(sdet))
sciimg = hdu[exten].data
try:
exten = names.index('DET{:s}-SKY'.format(sdet))
except: # Backwards compatability
msgs.error(
'Requested detector {:s} has no sky model.\n'
'Maybe you chose the wrong one to view?\n'
'Set with --det= or check file contents with --list'.format(sdet))
skymodel = hdu[exten].data
try:
exten = names.index('DET{:s}-MASK'.format(sdet))
except ValueError: # Backwards compatability
msgs.error(
'Requested detector {:s} has no bit mask.\n'
'Maybe you chose the wrong one to view?\n'
'Set with --det= or check file contents with --list'.format(sdet))
mask = hdu[exten].data
try:
exten = names.index('DET{:s}-IVARMODEL'.format(sdet))
except ValueError: # Backwards compatability
msgs.error(
'Requested detector {:s} has no IVARMODEL.\n'
'Maybe you chose the wrong one to view?\n' +
'Set with --det= or check file contents with --list'.format(sdet))
ivarmodel = hdu[exten].data
# Read in the object model for residual map
try:
exten = names.index('DET{:s}-OBJ'.format(sdet))
except ValueError: # Backwards compatability
msgs.error(
'Requested detector {:s} has no object model.\n'
'Maybe you chose the wrong one to view?\n' +
'Set with --det= or check file contents with --list'.format(sdet))
objmodel = hdu[exten].data
# Get waveimg
mdir = head0['PYPMFDIR'] + '/'
if not os.path.exists(mdir):
mdir_base = os.path.basename(os.path.dirname(mdir)) + '/'
msgs.warn('Master file dir: {0} does not exist. Using ./{1}'.format(
mdir, mdir_base))
mdir = mdir_base
trace_key = '{0}_{1:02d}'.format(head0['TRACMKEY'], args.det)
trc_file = os.path.join(
mdir, MasterFrame.construct_file_name('Trace', trace_key))
wave_key = '{0}_{1:02d}'.format(head0['ARCMKEY'], args.det)
waveimg = os.path.join(mdir,
MasterFrame.construct_file_name('Wave', wave_key))
tslits_dict = TraceSlits.load_from_file(trc_file)[0]
slitmask = pixels.tslits2mask(tslits_dict)
shape = (tslits_dict['nspec'], tslits_dict['nspat'])
slit_ids = [
trace_slits.get_slitid(shape, tslits_dict['slit_left'],
tslits_dict['slit_righ'], ii)[0]
for ii in range(tslits_dict['slit_left'].shape[1])
]
# Show the bitmask?
mask_in = mask if args.showmask else None
# Object traces
spec1d_file = args.file.replace('spec2d', 'spec1d')
det_nm = 'DET{:s}'.format(sdet)
if os.path.isfile(spec1d_file):
hdulist_1d = fits.open(spec1d_file)
else:
hdulist_1d = []
msgs.warn('Could not find spec1d file: {:s}'.format(spec1d_file) +
msgs.newline() +
' No objects were extracted.')
# Unpack the bitmask
bitMask = bitmask()
bpm, crmask, satmask, minmask, offslitmask, nanmask, ivar0mask, ivarnanmask, extractmask \
= bitMask.unpack(mask)
# Now show each image to a separate channel
# SCIIMG
image = sciimg # Raw science image
(mean, med, sigma) = sigma_clipped_stats(image[mask == 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=waveimg,
bitmask=mask_in,
clear=True)
#, cuts=(cut_min, cut_max), wcs_match=True)
ginga.show_slits(viewer, ch, tslits_dict['slit_left'],
tslits_dict['slit_righ'], slit_ids)
#, args.det)
# SKYSUB
image = (sciimg - skymodel) * (mask == 0) # sky subtracted image
(mean, med, sigma) = sigma_clipped_stats(image[mask == 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=waveimg,
bitmask=mask_in) #, cuts=(cut_min, cut_max),wcs_match=True)
show_trace(hdulist_1d, det_nm, viewer, ch)
ginga.show_slits(viewer, ch, tslits_dict['slit_left'],
tslits_dict['slit_righ'], slit_ids)
#, args.det)
# SKRESIDS
chname_skyresids = 'sky_resid-det{:s}'.format(sdet)
image = (sciimg - skymodel) * np.sqrt(ivarmodel) * (mask == 0
) # sky residual map
viewer, ch = ginga.show_image(image,
chname_skyresids,
waveimg=waveimg,
cuts=(-5.0, 5.0),
bitmask=mask_in) #,wcs_match=True)
show_trace(hdulist_1d, det_nm, viewer, ch)
ginga.show_slits(viewer, ch, tslits_dict['slit_left'],
tslits_dict['slit_righ'], slit_ids)
#, args.det)
# RESIDS
chname_resids = 'resid-det{:s}'.format(sdet)
# full model residual map
image = (sciimg - skymodel - objmodel) * np.sqrt(ivarmodel) * (mask == 0)
viewer, ch = ginga.show_image(image,
chname=chname_resids,
waveimg=waveimg,
cuts=(-5.0, 5.0),
bitmask=mask_in) #,wcs_match=True)
show_trace(hdulist_1d, det_nm, viewer, ch)
ginga.show_slits(viewer, ch, tslits_dict['slit_left'],
tslits_dict['slit_righ'], slit_ids)
#, args.det)
# 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:
IPython.embed()
def show(self, attr, image=None, showmask=False, sobjs=None, chname=None, slits=False,clear=False):
"""
Show one of the internal images
.. todo::
Should probably put some of these in ProcessImages
Parameters
----------
attr : str
global -- Sky model (global)
sci -- Processed science image
rawvar -- Raw variance image
modelvar -- Model variance image
crmasked -- Science image with CRs set to 0
skysub -- Science image with global sky subtracted
image -- Input image
display : str, optional
image : ndarray, optional
User supplied image to display
Returns
-------
"""
if showmask:
mask_in = self.mask
bitmask_in = self.bitmask
else:
mask_in = None
bitmask_in = None
if attr == 'global':
# global sky subtraction
if self.sciimg is not None and self.global_sky is not None and self.mask is not None:
# sky subtracted image
image = (self.sciimg - self.global_sky)*(self.mask == 0)
mean, med, sigma = stats.sigma_clipped_stats(image[self.mask == 0], sigma_lower=5.0,
sigma_upper=5.0)
cut_min = mean - 1.0 * sigma
cut_max = mean + 4.0 * sigma
ch_name = chname if chname is not None else 'global_sky_{}'.format(self.det)
viewer, ch = ginga.show_image(image, chname=ch_name, bitmask=bitmask_in,
mask=mask_in, clear=clear, wcs_match=True)
#, cuts=(cut_min, cut_max))
elif attr == 'local':
# local sky subtraction
if self.sciimg is not None and self.skymodel is not None and self.mask is not None:
# sky subtracted image
image = (self.sciimg - self.skymodel)*(self.mask == 0)
mean, med, sigma = stats.sigma_clipped_stats(image[self.mask == 0], sigma_lower=5.0,
sigma_upper=5.0)
cut_min = mean - 1.0 * sigma
cut_max = mean + 4.0 * sigma
ch_name = chname if chname is not None else 'local_sky_{}'.format(self.det)
viewer, ch = ginga.show_image(image, chname=ch_name, bitmask=bitmask_in,
mask=mask_in, clear=clear, wcs_match=True)
#, cuts=(cut_min, cut_max))
elif attr == 'sky_resid':
# sky residual map with object included
if self.sciimg is not None and self.skymodel is not None \
and self.objmodel is not None and self.ivarmodel is not None \
and self.mask is not None:
image = (self.sciimg - self.skymodel) * np.sqrt(self.ivarmodel)
image *= (self.mask == 0)
ch_name = chname if chname is not None else 'sky_resid_{}'.format(self.det)
viewer, ch = ginga.show_image(image, chname=ch_name, cuts=(-5.0, 5.0),
bitmask=bitmask_in, mask=mask_in, clear=clear,
wcs_match=True)
elif attr == 'resid':
# full residual map with object model subtractede
if self.sciimg is not None and self.skymodel is not None \
and self.objmodel is not None and self.ivarmodel is not None \
and self.mask is not None:
# full model residual map
image = (self.sciimg - self.skymodel - self.objmodel) * np.sqrt(self.ivarmodel)
image *= (self.mask == 0)
ch_name = chname if chname is not None else 'resid_{}'.format(self.det)
viewer, ch = ginga.show_image(image, chname=ch_name, cuts=(-5.0, 5.0),
bitmask=bitmask_in, mask=mask_in, clear=clear,
wcs_match=True)
elif attr == 'image':
ch_name = chname if chname is not None else 'image'
viewer, ch = ginga.show_image(image, chname=ch_name, clear=clear, wcs_match=True)
else:
msgs.warn("Not an option for show")
if sobjs is not None:
for spec in sobjs:
color = 'magenta' if spec.hand_extract_flag else 'orange'
ginga.show_trace(viewer, ch, spec.trace_spat, spec.idx, color=color)
if slits:
if self.tslits_dict is not None:
slit_ids = [trace_slits.get_slitid(
self.mask.shape, self.tslits_dict['slit_left'],
self.tslits_dict['slit_righ'], ii)[0] for ii in range(self.tslits_dict['slit_left'].shape[1])]
ginga.show_slits(viewer, ch, self.tslits_dict['slit_left'], self.tslits_dict['slit_righ'],
slit_ids) # , args.det)
def main(args):
# List only?
hdu = fits.open(args.file)
head0 = hdu[0].header
if args.list:
hdu.info()
return
# Init
sdet = get_dnum(args.det, prefix=False)
# One detector, sky sub for now
names = [hdu[i].name for i in range(len(hdu))]
try:
exten = names.index('DET{:s}-PROCESSED'.format(sdet))
except: # Backwards compatability
msgs.error('Requested detector {:s} was not processed.\n'
'Maybe you chose the wrong one to view?\n'
'Set with --det= or check file contents with --list'.format(sdet))
sciimg = hdu[exten].data
try:
exten = names.index('DET{:s}-SKY'.format(sdet))
except: # Backwards compatability
msgs.error('Requested detector {:s} has no sky model.\n'
'Maybe you chose the wrong one to view?\n'
'Set with --det= or check file contents with --list'.format(sdet))
skymodel = hdu[exten].data
try:
exten = names.index('DET{:s}-MASK'.format(sdet))
except ValueError: # Backwards compatability
msgs.error('Requested detector {:s} has no bit mask.\n'
'Maybe you chose the wrong one to view?\n'
'Set with --det= or check file contents with --list'.format(sdet))
mask = hdu[exten].data
frame = (sciimg - skymodel) * (mask == 0)
mdir = head0['PYPMFDIR']
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
trace_key = '{0}_{1:02d}'.format(head0['TRACMKEY'], args.det)
trc_file = os.path.join(mdir, MasterFrame.construct_file_name('Trace', trace_key))
# TODO -- Remove this once the move to Edges is complete
if args.old:
tslits_dict = TraceSlits.load_from_file(trc_file)[0]
else:
trc_file = trc_file.replace('Trace', 'Edges')+'.gz'
tslits_dict = edgetrace.EdgeTraceSet.from_file(trc_file).convert_to_tslits_dict()
shape = (tslits_dict['nspec'], tslits_dict['nspat'])
slit_ids = [trace_slits.get_slitid(shape, tslits_dict['slit_left'], tslits_dict['slit_righ'], ii)[0]
for ii in range(tslits_dict['slit_left'].shape[1])]
# Object traces
spec1d_file = args.file.replace('spec2d', 'spec1d')
det_nm = 'DET{:s}'.format(sdet)
if os.path.isfile(spec1d_file):
hdulist_1d = fits.open(spec1d_file)
else:
hdulist_1d = []
msgs.warn('Could not find spec1d file: {:s}'.format(spec1d_file) + msgs.newline() +
' No objects were extracted.')
tslits_dict['objtrc'] = parse_traces(hdulist_1d, det_nm)
# TODO :: Need to include standard star trace in the spec2d files
std_trace = None
# Extract some trace models
fwhm = 2 # Start with some default value
# Brightest object on slit
trace_model_obj = None
trace_model_dict = dict()
if len(tslits_dict['objtrc']['pkflux']) > 0:
smash_peakflux = tslits_dict['objtrc']['pkflux']
ibri = smash_peakflux.argmax()
trace_model_obj = tslits_dict['objtrc']['traces'][ibri]
fwhm = tslits_dict['objtrc']['fwhm'][ibri]
trace_model_dict['object'] = dict(trace_model=trace_model_obj, fwhm=fwhm)
# Standard star trace
trace_model_dict['std'] = dict(trace_model=std_trace, fwhm=fwhm)
# Trace of the slit edge
trace_model_dict['slit'] = dict(trace_model=tslits_dict['slit_left'].copy(), fwhm=fwhm)
tslits_dict['trace_model'] = trace_model_dict
# Finally, initialise the GUI
gui_object_find.initialise(args.det, frame, tslits_dict, None, printout=True, slit_ids=slit_ids)