def reduce_exposure(self, frames, bg_frames=None, std_outfile=None):
"""
Reduce a single exposure
Args:
frame (:obj:`int`):
0-indexed row in :attr:`fitstbl` with the frame to
reduce.
bg_frames (:obj:`list`, optional):
List of frame indices for the background.
std_outfile (:obj:`str`, optional):
File with a previously reduced standard spectrum from
PypeIt.
Returns:
dict: The dictionary containing the primary outputs of
extraction.
"""
# TODO:
# - bg_frames should be None by default
# - change doc string to reflect that more than one frame can be
# provided
# if show is set, clear the ginga channels at the start of each new sci_ID
if self.show:
# TODO: Put this in a try/except block?
ginga.clear_all()
has_bg = True if bg_frames is not None and len(
bg_frames) > 0 else False
# Is this an IR reduction?
# TODO: Why specific to IR?
self.ir_redux = True if has_bg else False
# TODO: JFH Why does this need to be ordered?
sci_dict = OrderedDict() # This needs to be ordered
sci_dict['meta'] = {}
sci_dict['meta']['ir_redux'] = self.ir_redux
# Print status message
msgs_string = 'Reducing target {:s}'.format(
self.fitstbl['target'][frames[0]]) + msgs.newline()
# TODO: Print these when the frames are actually combined,
# backgrounds are used, etc?
msgs_string += 'Combining frames:' + msgs.newline()
for iframe in frames:
msgs_string += '{0:s}'.format(
self.fitstbl['filename'][iframe]) + msgs.newline()
msgs.info(msgs_string)
if has_bg:
bg_msgs_string = ''
for iframe in bg_frames:
bg_msgs_string += '{0:s}'.format(
self.fitstbl['filename'][iframe]) + msgs.newline()
bg_msgs_string = msgs.newline(
) + 'Using background from frames:' + msgs.newline(
) + bg_msgs_string
msgs.info(bg_msgs_string)
# Find the detectors to reduce
detectors = PypeIt.select_detectors(detnum=self.par['rdx']['detnum'],
ndet=self.spectrograph.ndet)
if len(detectors) != self.spectrograph.ndet:
msgs.warn('Not reducing detectors: {0}'.format(' '.join([
str(d) for d in set(np.arange(self.spectrograph.ndet)) -
set(detectors)
])))
# Loop on Detectors
for self.det in detectors:
msgs.info("Working on detector {0}".format(self.det))
sci_dict[self.det] = {}
# Calibrate
#TODO Is the right behavior to just use the first frame?
self.caliBrate.set_config(frames[0], self.det,
self.par['calibrations'])
self.caliBrate.run_the_steps()
# Extract
# TODO: pass back the background frame, pass in background
# files as an argument. extract one takes a file list as an
# argument and instantiates science within
sci_dict[self.det]['sciimg'], sci_dict[self.det]['sciivar'], \
sci_dict[self.det]['skymodel'], sci_dict[self.det]['objmodel'], \
sci_dict[self.det]['ivarmodel'], sci_dict[self.det]['outmask'], \
sci_dict[self.det]['specobjs'], \
= self.extract_one(frames, self.det, bg_frames,
std_outfile=std_outfile)
# JFH TODO write out the background frame?
# Return
return sci_dict
def reduce_exposure(self, frames, bg_frames=[], std_outfile=None):
"""
Reduce a single exposure
Args:
frame (:obj:`int`):
0-indexed row in :attr:`fitstbl` with the frame to
reduce
bgframes (:obj:`list`, optional):
List of frame indices for the background
std_outfile (:obj:`str`, optional):
the name of a file with a previously PypeIt-reduced standard spectrum.
Returns:
dict: The dictionary containing the primary outputs of extraction
"""
# if show is set, clear the ginga channels at the start of each new sci_ID
if self.show:
ginga.clear_all()
# Save the frame
self.frames = frames
self.bg_frames = bg_frames
# Is this an IR reduction?
self.ir_redux = True if len(bg_frames) > 0 else False
# JFH Why does this need to be ordered?
sci_dict = OrderedDict() # This needs to be ordered
sci_dict['meta'] = {}
sci_dict['meta']['vel_corr'] = 0.
sci_dict['meta']['ir_redux'] = self.ir_redux
# Print status message
msgs_string = 'Reducing target {:s}'.format(self.fitstbl['target'][self.frames[0]]) + msgs.newline()
msgs_string += 'Combining frames:' + msgs.newline()
for iframe in self.frames:
msgs_string += '{0:s}'.format(self.fitstbl['filename'][iframe]) + msgs.newline()
msgs.info(msgs_string)
if len(bg_frames) > 0:
bg_msgs_string = ''
for iframe in self.bg_frames:
bg_msgs_string += '{0:s}'.format(self.fitstbl['filename'][iframe]) + msgs.newline()
bg_msgs_string = msgs.newline() + 'Using background from frames:' + msgs.newline() + bg_msgs_string
msgs.info(bg_msgs_string)
# Find the detectors to reduce
detectors = self.select_detectors()
if len(detectors) != self.spectrograph.ndet:
msgs.warn('Not reducing detectors: {0}'.format(' '.join([ str(d) for d in
set(np.arange(self.spectrograph.ndet))-set(detectors)])))
# Loop on Detectors
for self.det in detectors:
msgs.info("Working on detector {0}".format(self.det))
sci_dict[self.det] = {}
# Calibrate
#TODO Is the right behavior to just use the first frame?
self.caliBrate.set_config(self.frames[0], self.det, self.par['calibrations'])
self.caliBrate.run_the_steps()
# Extract
# TODO: pass back the background frame, pass in background
# files as an argument. extract one takes a file list as an
# argument and instantiates science within
sci_dict[self.det]['sciimg'], sci_dict[self.det]['sciivar'], sci_dict[self.det]['skymodel'], \
sci_dict[self.det]['objmodel'], sci_dict[self.det]['ivarmodel'], sci_dict[self.det]['outmask'], \
sci_dict[self.det]['specobjs'], vel_corr \
= self.extract_one(self.frames, self.det, bg_frames = self.bg_frames, std_outfile = std_outfile)
if vel_corr is not None:
sci_dict['meta']['vel_corr'] = vel_corr
# JFH TODO write out the background frame?
# Return
return sci_dict
def reduce_exposure(self, frames, bg_frames=None, std_outfile=None):
"""
Reduce a single exposure
Args:
frame (:obj:`int`):
0-indexed row in :attr:`fitstbl` with the frame to
reduce.
bg_frames (:obj:`list`, optional):
List of frame indices for the background.
std_outfile (:obj:`str`, optional):
File with a previously reduced standard spectrum from
PypeIt.
Returns:
dict: The dictionary containing the primary outputs of
extraction.
"""
# TODO:
# - bg_frames should be None by default
# - change doc string to reflect that more than one frame can be
# provided
# if show is set, clear the ginga channels at the start of each new sci_ID
if self.show:
# TODO: Put this in a try/except block?
ginga.clear_all()
has_bg = True if bg_frames is not None and len(
bg_frames) > 0 else False
# Is this an IR reduction?
# TODO: Why specific to IR?
self.ir_redux = True if has_bg else False
# Container for all the Spec2DObj
all_spec2d = spec2dobj.AllSpec2DObj()
all_spec2d['meta']['ir_redux'] = self.ir_redux
# TODO -- Should we reset/regenerate self.slits.mask for a new exposure
all_specobjs = specobjs.SpecObjs()
# Print status message
msgs_string = 'Reducing target {:s}'.format(
self.fitstbl['target'][frames[0]]) + msgs.newline()
# TODO: Print these when the frames are actually combined,
# backgrounds are used, etc?
msgs_string += 'Combining frames:' + msgs.newline()
for iframe in frames:
msgs_string += '{0:s}'.format(
self.fitstbl['filename'][iframe]) + msgs.newline()
msgs.info(msgs_string)
if has_bg:
bg_msgs_string = ''
for iframe in bg_frames:
bg_msgs_string += '{0:s}'.format(
self.fitstbl['filename'][iframe]) + msgs.newline()
bg_msgs_string = msgs.newline(
) + 'Using background from frames:' + msgs.newline(
) + bg_msgs_string
msgs.info(bg_msgs_string)
# Find the detectors to reduce
detectors = PypeIt.select_detectors(
detnum=self.par['rdx']['detnum'],
slitspatnum=self.par['rdx']['slitspatnum'],
ndet=self.spectrograph.ndet)
if len(detectors) != self.spectrograph.ndet:
msgs.warn('Not reducing detectors: {0}'.format(' '.join([
str(d) for d in set(np.arange(self.spectrograph.ndet)) -
set(detectors)
])))
# Loop on Detectors
# TODO: Attempt to put in a multiprocessing call here?
for self.det in detectors:
msgs.info("Working on detector {0}".format(self.det))
# Instantiate Calibrations class
self.caliBrate = calibrations.Calibrations.get_instance(
self.fitstbl,
self.par['calibrations'],
self.spectrograph,
self.calibrations_path,
qadir=self.qa_path,
reuse_masters=self.reuse_masters,
show=self.show,
slitspat_num=self.par['rdx']['slitspatnum'])
# These need to be separate to accomodate COADD2D
self.caliBrate.set_config(frames[0], self.det,
self.par['calibrations'])
self.caliBrate.run_the_steps()
# Extract
# TODO: pass back the background frame, pass in background
# files as an argument. extract one takes a file list as an
# argument and instantiates science within
all_spec2d[self.det], tmp_sobjs \
= self.reduce_one(frames, self.det, bg_frames, std_outfile=std_outfile)
# Hold em
if tmp_sobjs.nobj > 0:
all_specobjs.add_sobj(tmp_sobjs)
# JFH TODO write out the background frame?
# TODO -- Save here? Seems like we should. Would probably need to use update_det=True
# Return
return all_spec2d, all_specobjs