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Merge pull request #1798 from pypeit/gmoss_ccdupdate
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GMOS SOUTH CCD upgrade and some other fixes
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@debora-pe
debora-pe authored Apr 18, 2024
2 parents dbf2a60 + f131b07 commit 235a571
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1 change: 1 addition & 0 deletions doc/releases/1.15.1dev.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@ Instrument-specific Updates

- Added example of improved wavelength solution for GEMINI/GMOS
- Expanded the template for `shane_kast_red` and the 1200/5000 grating
- Updated Gemini/GMOS-S with the new detector parameters for the Hamamatsu CCDs replaced on 2023-12-14

Script Changes
--------------
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4 changes: 2 additions & 2 deletions pypeit/manual_extract.py
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Original file line number Diff line number Diff line change
Expand Up @@ -85,15 +85,15 @@ def by_fitstbl_input(cls, frame: str, inp: str, spectrograph):
m_es = inp.split(';')
for m_e in m_es:
parse = m_e.split(':')
# det_strip will be a list of a single number (no mosaic) or 2 numbers (mosaic)
# det_strip will be a list of a single number (no mosaic) or >= 2 numbers (mosaic)
det_strip = [int(d) for d in parse[0].strip('()').split(',')]
# check if it's negative object (i.e., if the det number is negative)
if np.all([item < 0 for item in det_strip]):
idict['neg'] += [True]
det_strip = [item * -1 for item in det_strip]
else:
idict['neg'] += [False]
if len(det_strip) == 2 and tuple(det_strip) in spectrograph.allowed_mosaics:
if len(det_strip) >= 2 and tuple(det_strip) in spectrograph.allowed_mosaics:
# we use detname, which is a string (e.g., 'DET01', 'MSC01')
idict['detname'] += [spectrograph.get_det_name(tuple(det_strip))]
elif len(det_strip) == 1:
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189 changes: 170 additions & 19 deletions pypeit/spectrographs/gemini_gmos.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
from astropy.table import Table
from astropy.coordinates import SkyCoord
from astropy import units
from astropy import time
from astropy.wcs import wcs
from astropy.io import fits

Expand Down Expand Up @@ -89,6 +90,14 @@ class GeminiGMOSMosaicLookUp:
(4096, 0): {'shift': (2109., -0.73),
'rotation': 0.}
},
'BI11-41-4k-2,BI13-19-4k-3,BI12-34-4k-1': {'default_shape': (2048, 4224),
(0, 0): {'shift': (-2112.5, -1.1),
'rotation': 0.},
(2048, 0): {},
(4096, 0): {
'shift': (2110.8, 1.05),
'rotation': 0.}
},
}


Expand All @@ -98,9 +107,12 @@ class GeminiGMOSSpectrograph(spectrograph.Spectrograph):
should not be instantiated.
"""
ndet = 3
detid = None
url = 'http://www.gemini.edu/instrumentation/gmos'

def __init__(self):
super().__init__()
self.detid = None

def init_meta(self):
"""
Define how metadata are derived from the spectrograph files.
Expand All @@ -116,7 +128,7 @@ def init_meta(self):
self.meta['decker'] = dict(ext=0, card='MASKNAME')
self.meta['binning'] = dict(card=None, compound=True) # Uses CCDSUM

self.meta['mjd'] = dict(ext=0, card='OBSEPOCH')
self.meta['mjd'] = dict(card=None, compound=True)
self.meta['exptime'] = dict(ext=0, card='EXPTIME')
self.meta['airmass'] = dict(ext=0, card='AIRMASS')
# Extras for config and frametyping
Expand Down Expand Up @@ -145,14 +157,21 @@ def compound_meta(self, headarr, meta_key):
# binning in the raw frames
ccdsum = headarr[1].get('CCDSUM')
if ccdsum is not None:
binspatial, binspec = parse.parse_binning(ccdsum)
binspec, binspatial = parse.parse_binning(ccdsum)
binning = parse.binning2string(binspec, binspatial)
else:
# binning in the spec2d file
binning = headarr[0].get('BINNING')
if binning is None:
msgs.error('Binning not found')
return binning
elif meta_key == 'mjd':
obsepoch = headarr[0].get('OBSEPOCH')
if obsepoch is not None:
return time.Time(obsepoch, format='jyear').mjd
else:
msgs.warn('OBSEPOCH header keyword not found. Using today as the date.')
return time.Time.now().mjd

def config_independent_frames(self):
"""
Expand Down Expand Up @@ -511,7 +530,9 @@ def get_mosaic_par(self, mosaic, hdu=None, msc_order=0):
for i, d in enumerate([det-1 for det in mosaic]):
msc_sft[i] = shift[d]
msc_rot[i] = rotation[d]
msc_tfm[i] = build_image_mosaic_transform(shape, msc_sft[i], msc_rot[i], binning)
# binning is here in the PypeIt convention of (binspec, binspat), but the mosaic tranformations
# occur in the raw data frame, which has spatial in y and spectral in x
msc_tfm[i] = build_image_mosaic_transform(shape, msc_sft[i], msc_rot[i], tuple(reversed(binning)))

return Mosaic(mosaic_id, detectors, shape, np.array(msc_sft), np.array(msc_rot),
np.array(msc_tfm), msc_order)
Expand Down Expand Up @@ -738,7 +759,6 @@ class GeminiGMOSSHamSpectrograph(GeminiGMOSSpectrograph):
telescope = telescopes.GeminiSTelescopePar()
supported = True
comment = 'Hamamatsu detector (R400, B600, R831); see :doc:`gemini_gmos`'
detid = 'BI5-36-4k-2,BI11-33-4k-1,BI12-34-4k-1'

def hdu_read_order(self):
"""
Expand Down Expand Up @@ -784,8 +804,8 @@ def get_detector_par(self, det, hdu=None):
nonlinear = 0.95,
mincounts = -1e10,
numamplifiers = 4,
gain = np.atleast_1d([1.83]*4),
ronoise = np.atleast_1d([3.98]*4),
gain = np.atleast_1d([1.86]*4), # Slow Readout, Low Gain
ronoise = np.atleast_1d([4.19]*4), # Slow Readout, Low Gain
)
# Detector 2
detector_dict2 = dict(
Expand All @@ -801,8 +821,8 @@ def get_detector_par(self, det, hdu=None):
nonlinear = 0.95,
mincounts = -1e10,
numamplifiers = 4,
gain = np.atleast_1d([1.83]*4),
ronoise = np.atleast_1d([3.98]*4),
gain = np.atleast_1d([1.89]*4), # Slow Readout, Low Gain
ronoise = np.atleast_1d([4.13]*4), # Slow Readout, Low Gain
)
# Detector 3
detector_dict3 = dict(
Expand All @@ -818,13 +838,77 @@ def get_detector_par(self, det, hdu=None):
nonlinear = 0.95,
mincounts = -1e10,
numamplifiers = 4,
gain = np.atleast_1d([1.83]*4),
ronoise = np.atleast_1d([3.98]*4),
gain = np.atleast_1d([1.74]*4), # Slow Readout, Low Gain
ronoise = np.atleast_1d([3.75]*4), # Slow Readout, Low Gain
)

# account for the CCD upgrade happened on 2023-12-14
if hdu is not None:
# date upgrade
t_upgrade = time.Time("2023-12-14", format='isot')
obs_date = time.Time(self.get_meta_value(self.get_headarr(hdu), 'mjd'), format='mjd')

if obs_date >= t_upgrade:
# These values are taken from
# https://github.com/GeminiDRSoftware/DRAGONS/blob/v3.2.0/gemini_instruments/gmos/lookup.py
# For each detector, we use the values averaged over the 4 amps for Slow Readout+Low Gain
detector_dict1['gain'] = np.atleast_1d([2.00]*4)
detector_dict2['gain'] = np.atleast_1d([1.78]*4)
detector_dict3['gain'] = np.atleast_1d([1.69]*4)
detector_dict1['ronoise'] = np.atleast_1d([4.19]*4)
detector_dict2['ronoise'] = np.atleast_1d([3.82]*4)
detector_dict3['ronoise'] = np.atleast_1d([3.50]*4)
# TODO: we may need to update the saturation values

detectors = [detector_dict1, detector_dict2, detector_dict3]
# Return
return detector_container.DetectorContainer(**detectors[det-1])

def get_mosaic_par(self, mosaic, hdu=None, msc_order=0):
"""
Return the hard-coded parameters needed to construct detector mosaics
from unbinned images.
The parameters expect the images to be trimmed and oriented to follow
the PypeIt shape convention of ``(nspec,nspat)``. For returned
lists, the length of the list is the same as the number of detectors in
the mosaic, and they are ordered by the detector number.
Args:
mosaic (:obj:`tuple`):
Tuple of detector numbers used to construct the mosaic. Must be
one among the list of possible mosaics as hard-coded by the
:func:`allowed_mosaics` function.
hdu (`astropy.io.fits.HDUList`_, optional):
The open fits file with the raw image of interest. If not
provided, frame-dependent detector parameters are set to a
default. BEWARE: If ``hdu`` is not provided, the binning is
assumed to be `1,1`, which will cause faults if applied to
binned images!
msc_order (:obj:`int`, optional):
Order of the interpolation used to construct the mosaic.
Returns:
:class:`~pypeit.images.mosaic.Mosaic`: Object with the mosaic *and*
detector parameters."""

# get self.detid
# Detector ID (it is used to identify the correct mosaic geometry)
if hdu is not None:
# account for the CCD upgrade happened on 2023-12-14
# date upgrade
t_upgrade = time.Time("2023-12-14", format='isot')
obs_date = time.Time(self.get_meta_value(self.get_headarr(hdu), 'mjd'), format='mjd')

if obs_date >= t_upgrade:
self.detid = 'BI11-41-4k-2,BI13-19-4k-3,BI12-34-4k-1'
msgs.info(f'Using the detector parameters for GMOS-S Hamamatsu after the upgrade on '
f'{t_upgrade.iso.split(" ")[0]}')
else:
self.detid = 'BI5-36-4k-2,BI11-33-4k-1,BI12-34-4k-1'

return super().get_mosaic_par(mosaic, hdu=hdu, msc_order=msc_order)

@classmethod
def default_pypeit_par(cls):
"""
Expand Down Expand Up @@ -884,7 +968,7 @@ def bpm(self, filename, det, shape=None, msbias=None):
# TODO: We're opening the file too many times...
hdrs = self.get_headarr(filename)
binning = self.get_meta_value(hdrs, 'binning')
obs_epoch = self.get_meta_value(hdrs, 'mjd')
obs_epoch = time.Time(self.get_meta_value(hdrs, 'mjd'), format='mjd').jyear
bin_spec, bin_spat= parse.parse_binning(binning)

# Add the detector-specific, hard-coded bad columns
Expand All @@ -906,7 +990,7 @@ def bpm(self, filename, det, shape=None, msbias=None):
_bpm_img[i,badr,:] = 1
# Bad amp as of January 28, 2022
# https://gemini.edu/sciops/instruments/gmos/GMOS-S_badamp5_ops_3.pdf
if obs_epoch > 2022.07:
if 2022.07 < obs_epoch < time.Time("2023-12-14", format='isot').jyear:
badr = (768*2)//bin_spec
_bpm_img[i,badr:,:] = 1
if 3 in _det:
Expand Down Expand Up @@ -945,16 +1029,15 @@ def config_specific_par(self, scifile, inp_par=None):
par['calibrations']['wavelengths']['method'] = 'reidentify'

# The bad amp needs a larger follow_span for slit edge tracing
obs_epoch = self.get_meta_value(scifile, 'mjd')
obs_epoch = time.Time(self.get_meta_value(scifile, 'mjd'), format='mjd').jyear
binning = self.get_meta_value(scifile, 'binning')
bin_spec, bin_spat= parse.parse_binning(binning)
if obs_epoch > 2022.07:
if 2022.07 < obs_epoch < time.Time("2023-12-14", format='isot').jyear:
par['calibrations']['slitedges']['follow_span'] = 290*bin_spec
#
return par



class GeminiGMOSNSpectrograph(GeminiGMOSSpectrograph):
"""
Child to handle Gemini/GMOS-N instrument
Expand All @@ -972,7 +1055,6 @@ class GeminiGMOSNHamSpectrograph(GeminiGMOSNSpectrograph):
name = 'gemini_gmos_north_ham'
supported = True
comment = 'Hamamatsu detector (R400, B600, R831); Used since Feb 2017; see :doc:`gemini_gmos`'
detid = 'BI13-20-4k-1,BI12-09-4k-2,BI13-18-4k-2'

def hdu_read_order(self):
"""
Expand Down Expand Up @@ -1056,9 +1138,44 @@ def get_detector_par(self, det, hdu=None):
ronoise = np.atleast_1d([4.14]*4),
)
detectors = [detector_dict1, detector_dict2, detector_dict3]

# Return
return detector_container.DetectorContainer(**detectors[det-1])

def get_mosaic_par(self, mosaic, hdu=None, msc_order=0):
"""
Return the hard-coded parameters needed to construct detector mosaics
from unbinned images.
The parameters expect the images to be trimmed and oriented to follow
the PypeIt shape convention of ``(nspec,nspat)``. For returned
lists, the length of the list is the same as the number of detectors in
the mosaic, and they are ordered by the detector number.
Args:
mosaic (:obj:`tuple`):
Tuple of detector numbers used to construct the mosaic. Must be
one among the list of possible mosaics as hard-coded by the
:func:`allowed_mosaics` function.
hdu (`astropy.io.fits.HDUList`_, optional):
The open fits file with the raw image of interest. If not
provided, frame-dependent detector parameters are set to a
default. BEWARE: If ``hdu`` is not provided, the binning is
assumed to be `1,1`, which will cause faults if applied to
binned images!
msc_order (:obj:`int`, optional):
Order of the interpolation used to construct the mosaic.
Returns:
:class:`~pypeit.images.mosaic.Mosaic`: Object with the mosaic *and*
detector parameters."""

# get self.detid
# Detector ID (it is used to identify the correct mosaic geometry)
self.detid = 'BI13-20-4k-1,BI12-09-4k-2,BI13-18-4k-2'

return super().get_mosaic_par(mosaic, hdu=hdu, msc_order=msc_order)

def config_specific_par(self, scifile, inp_par=None):
"""
Modify the PypeIt parameters to hard-wired values used for
Expand Down Expand Up @@ -1202,8 +1319,6 @@ class GeminiGMOSNE2VSpectrograph(GeminiGMOSNSpectrograph):
name = 'gemini_gmos_north_e2v'
supported = True
comment = 'E2V detector; see :doc:`gemini_gmos`'
# TODO: Check this is correct
detid = 'e2v 10031-23-05,10031-01-03,10031-18-04'

def hdu_read_order(self):
"""
Expand Down Expand Up @@ -1287,9 +1402,45 @@ def get_detector_par(self, det, hdu=None):
ronoise = np.atleast_1d([3.32]*2),
)
detectors = [detector_dict1, detector_dict2, detector_dict3]

# Return
return detector_container.DetectorContainer(**detectors[det-1])

def get_mosaic_par(self, mosaic, hdu=None, msc_order=0):
"""
Return the hard-coded parameters needed to construct detector mosaics
from unbinned images.
The parameters expect the images to be trimmed and oriented to follow
the PypeIt shape convention of ``(nspec,nspat)``. For returned
lists, the length of the list is the same as the number of detectors in
the mosaic, and they are ordered by the detector number.
Args:
mosaic (:obj:`tuple`):
Tuple of detector numbers used to construct the mosaic. Must be
one among the list of possible mosaics as hard-coded by the
:func:`allowed_mosaics` function.
hdu (`astropy.io.fits.HDUList`_, optional):
The open fits file with the raw image of interest. If not
provided, frame-dependent detector parameters are set to a
default. BEWARE: If ``hdu`` is not provided, the binning is
assumed to be `1,1`, which will cause faults if applied to
binned images!
msc_order (:obj:`int`, optional):
Order of the interpolation used to construct the mosaic.
Returns:
:class:`~pypeit.images.mosaic.Mosaic`: Object with the mosaic *and*
detector parameters."""

# get self.detid
# Detector ID (it is used to identify the correct mosaic geometry)
# TODO: Check this is correct
self.detid = 'e2v 10031-23-05,10031-01-03,10031-18-04'

return super().get_mosaic_par(mosaic, hdu=hdu, msc_order=msc_order)

def config_specific_par(self, scifile, inp_par=None):
"""
Modify the PypeIt parameters to hard-wired values used for
Expand Down

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