def display(self, adinputs=None, **params):
"""
Displays an image on the ds9 display, using multiple frames if
there are multiple extensions. Saturated pixels can be displayed
in red, and overlays can also be shown.
Parameters
----------
extname: str
'SCI', 'VAR', or 'DQ': plane to display
frame: int
starting frame for display
ignore: bool
setting to True turns off the display
remove_bias: bool
attempt to subtract bias before displaying?
threshold: str='auto'/float
level above which to flag pixels as saturated
tile: bool
attempt to tile arrays before displaying?
zscale: bool
use zscale algorithm?
overlay: list
list of overlays for the display
"""
log = self.log
log.debug(gt.log_message("primitive", self.myself(), "starting"))
# No-op if ignore=True
if params["ignore"]:
log.warning("display turned off per user request")
return
threshold = params['threshold']
remove_bias = params.get('remove_bias', False)
extname = params['extname']
tile = params['tile']
zscale = params['zscale']
overlays = params['overlay']
frame = params['frame'] if params['frame'] else 1
overlay_index = 0
lnd = _localNumDisplay()
for ad in adinputs:
# Allows elegant break from nested loops
if frame > 16:
log.warning("Too many images; only the first 16 are displayed")
break
# Threshold and bias make sense only for SCI extension
if extname != 'SCI':
threshold = None
remove_bias = False
elif threshold == 'None':
threshold = None
elif threshold == 'auto':
mosaicked = ((ad.phu.get(self.timestamp_keys["mosaicDetectors"])
is not None) or
(ad.phu.get(self.timestamp_keys["tileArrays"])
is not None))
has_dq = all([ext.mask is not None for ext in ad])
if not has_dq:
if mosaicked:
log.warning("Cannot add DQ to mosaicked data; no "
"threshold mask will be applied to "
"{}".format(ad.filename))
threshold = None
else:
# addDQ operates in place so deepcopy to preserve input
ad = self.addDQ([deepcopy(ad)])[0]
if remove_bias:
if (ad.phu.get('BIASIM') or ad.phu.get('DARKIM') or
any(ad.hdr.get('OVERSCAN'))):
log.fullinfo("Bias level has already been removed from "
"data; no approximate correction will be "
"performed")
else:
try:
bias_level = get_bias_level(ad)
except NotImplementedError:
# For non-GMOS instruments
bias_level = None
if bias_level is not None:
ad = deepcopy(ad) # Leave original untouched!
log.stdinfo("Subtracting approximate bias level from "
"{} for display".format(ad.filename))
log.fullinfo("Bias levels used: {}".format(str(bias_level)))
for ext, bias in zip(ad, bias_level):
ext.subtract(np.float32(bias) if bias is not None
else 0)
else:
log.warning("Bias level not found for {}; approximate "
"bias will not be removed".format(ad.filename))
# Check whether data needs to be tiled before displaying
# Otherwise, flatten all desired extensions into a single list
if tile and len(ad) > 1:
log.fullinfo("Tiling extensions together before displaying")
# !! This is the replacement call for tileArrays() !!
# !! mosaicADdetectors handles both GMOS and GSAOI !!
# ad = self.mosaicADdetectors(tile=True)[0]
ad = self.tileArrays([ad], tile_all=True)[0]
# Each extension is an individual display item (if the data have been
# tiled, then there'll only be one extension per AD, of course)
for ext in ad:
if frame > 16:
break
# Squeeze the data to remove any empty dimensions (eg, raw F2 data)
ext.operate(np.squeeze)
# Get the data we're going to display. TODO Replace extname with attr?
data = getattr(ext, {'SCI':'data', 'DQ':'mask',
'VAR':'variance'}[extname], None)
dqdata = ext.mask
if data is None:
log.warning("No data to display in {}[{}]".format(ext.filename,
extname))
continue
# One-dimensional data (ie, extracted spectra)
if len(data.shape) == 1:
continue
# Make threshold mask if desired
masks = []
mask_colors = []
if threshold is not None:
if threshold != 'auto':
satmask = data > float(threshold)
else:
if dqdata is None:
log.warning("No DQ plane found; cannot make "
"threshold mask")
satmask = None
else:
satmask = (dqdata & (DQ.non_linear | DQ.saturated)) > 0
if satmask is not None:
masks.append(satmask)
mask_colors.append(204)
if overlays:
# Could be single overlay, or list. Replicate behaviour of
# gt.make_lists (which we can't use because we haven't
# made a complete list of displayed extensions at the start
# in order to avoid memory bloat)
try:
overlay = overlays[overlay_index]
except TypeError:
overlay = overlays
except IndexError:
if len(overlays) == 1:
overlay = overlays[0]
masks.append(overlay)
mask_colors.append(206)
# Define the display name
if tile and extname=='SCI':
name = ext.filename
elif tile:
name = '{}({})'.format(ext.filename, extname)
else:
name = '{}({},{})'.format(ext.filename, extname,
ext.hdr['EXTVER'])
try:
lnd.display(data, name=name, frame=frame, zscale=zscale,
bpm=None if extname=='DQ' else dqdata,
quiet=True, masks=masks, mask_colors=mask_colors)
except IOError:
log.warning("ds9 not found; cannot display input")
frame += 1
# Print from statistics for flats
if extname=='SCI' and {'GMOS', 'IMAGE', 'FLAT'}.issubset(ext.tags):
good_data = data[dqdata==0] if dqdata is not None else data
mean = np.mean(good_data)
median = np.median(good_data)
log.stdinfo("Twilight flat counts for {}:".format(ext.filename))
log.stdinfo(" Mean value: {:.0f}".format(mean))
log.stdinfo(" Median value: {:.0f}".format(median))
return adinputs
def display(self, adinputs=None, **params):
"""
Displays an image on the ds9 display, using multiple frames if
there are multiple extensions. Saturated pixels can be displayed
in red, and overlays can also be shown.
Parameters
----------
extname: str
'SCI', 'VAR', or 'DQ': plane to display
frame: int
starting frame for display
ignore: bool
setting to True turns off the display
remove_bias: bool
attempt to subtract bias before displaying?
threshold: str='auto'/float
level above which to flag pixels as saturated
tile: bool
attempt to tile arrays before displaying?
zscale: bool
use zscale algorithm?
overlay: list
list of overlays for the display
"""
log = self.log
log.debug(gt.log_message("primitive", self.myself(), "starting"))
# No-op if ignore=True
if params["ignore"]:
log.warning("display turned off per user request")
return
threshold = params['threshold']
remove_bias = params.get('remove_bias', False)
extname = params['extname']
tile = params['tile']
zscale = params['zscale']
overlays = params['overlay']
frame = params['frame'] if params['frame'] else 1
overlay_index = 0
lnd = _localNumDisplay()
for ad in adinputs:
# Allows elegant break from nested loops
if frame > 16:
log.warning("Too many images; only the first 16 are displayed")
break
# Threshold and bias make sense only for SCI extension
if extname != 'SCI':
threshold = None
remove_bias = False
elif threshold == 'None':
threshold = None
elif threshold == 'auto':
mosaicked = ((ad.phu.get(
self.timestamp_keys["mosaicDetectors"]) is not None)
or (ad.phu.get(self.timestamp_keys["tileArrays"])
is not None))
has_dq = all([ext.mask is not None for ext in ad])
if not has_dq:
if mosaicked:
log.warning("Cannot add DQ to mosaicked data; no "
"threshold mask will be applied to "
"{}".format(ad.filename))
threshold = None
else:
# addDQ operates in place so deepcopy to preserve input
ad = self.addDQ([deepcopy(ad)])[0]
if remove_bias:
if (ad.phu.get('BIASIM') or ad.phu.get('DARKIM')
or any(ad.hdr.get('OVERSCAN'))):
log.fullinfo("Bias level has already been removed from "
"data; no approximate correction will be "
"performed")
else:
try:
bias_level = get_bias_level(ad)
except NotImplementedError:
# For non-GMOS instruments
bias_level = None
if bias_level is not None:
ad = deepcopy(ad) # Leave original untouched!
log.stdinfo("Subtracting approximate bias level from "
"{} for display".format(ad.filename))
log.fullinfo("Bias levels used: {}".format(
str(bias_level)))
for ext, bias in zip(ad, bias_level):
ext.subtract(
np.float32(bias) if bias is not None else 0)
else:
log.warning("Bias level not found for {}; approximate "
"bias will not be removed".format(
ad.filename))
# Check whether data needs to be tiled before displaying
# Otherwise, flatten all desired extensions into a single list
if tile and len(ad) > 1:
log.fullinfo("Tiling extensions together before displaying")
# !! This is the replacement call for tileArrays() !!
# !! mosaicADdetectors handles both GMOS and GSAOI !!
# ad = self.mosaicADdetectors(tile=True)[0]
ad = self.tileArrays([ad], tile_all=True)[0]
# Each extension is an individual display item (if the data have been
# tiled, then there'll only be one extension per AD, of course)
for ext in ad:
if frame > 16:
break
# Squeeze the data to remove any empty dimensions (eg, raw F2 data)
ext.operate(np.squeeze)
# Get the data we're going to display. TODO Replace extname with attr?
data = getattr(ext, {
'SCI': 'data',
'DQ': 'mask',
'VAR': 'variance'
}[extname], None)
dqdata = ext.mask
if data is None:
log.warning("No data to display in {}[{}]".format(
ext.filename, extname))
continue
# One-dimensional data (ie, extracted spectra)
if len(data.shape) == 1:
continue
# Make threshold mask if desired
masks = []
mask_colors = []
if threshold is not None:
if threshold != 'auto':
satmask = data > float(threshold)
else:
if dqdata is None:
log.warning("No DQ plane found; cannot make "
"threshold mask")
satmask = None
else:
satmask = (dqdata &
(DQ.non_linear | DQ.saturated)) > 0
if satmask is not None:
masks.append(satmask)
mask_colors.append(204)
if overlays:
# Could be single overlay, or list. Replicate behaviour of
# gt.make_lists (which we can't use because we haven't
# made a complete list of displayed extensions at the start
# in order to avoid memory bloat)
try:
overlay = overlays[overlay_index]
except TypeError:
overlay = overlays
except IndexError:
if len(overlays) == 1:
overlay = overlays[0]
masks.append(overlay)
mask_colors.append(206)
# Define the display name
if tile and extname == 'SCI':
name = ext.filename
elif tile:
name = '{}({})'.format(ext.filename, extname)
else:
name = '{}({},{})'.format(ext.filename, extname,
ext.hdr['EXTVER'])
try:
lnd.display(data,
name=name,
frame=frame,
zscale=zscale,
bpm=None if extname == 'DQ' else dqdata,
quiet=True,
masks=masks,
mask_colors=mask_colors)
except IOError:
log.warning("ds9 not found; cannot display input")
frame += 1
# Print from statistics for flats
if extname == 'SCI' and {'GMOS', 'IMAGE', 'FLAT'}.issubset(
ext.tags):
good_data = data[dqdata ==
0] if dqdata is not None else data
mean = np.mean(good_data)
median = np.median(good_data)
log.stdinfo("Twilight flat counts for {}:".format(
ext.filename))
log.stdinfo(" Mean value: {:.0f}".format(mean))
log.stdinfo(" Median value: {:.0f}".format(median))
return adinputs
def standardizeInstrumentHeaders(self, adinputs=None, suffix=None):
"""
This primitive is used to make the changes and additions to the
keywords in the headers of GMOS data, specifically.
Parameters
----------
suffix: str
suffix to be added to output files
"""
log = self.log
log.debug(gt.log_message("primitive", self.myself(), "starting"))
timestamp_key = self.timestamp_keys[self.myself()]
for ad in adinputs:
if ad.phu.get(timestamp_key):
log.warning("No changes will be made to {}, since it has "
"already been processed by "
"standardizeInstrumentHeaders".format(ad.filename))
continue
# Standardize the headers of the input AstroData object. Update the
# keywords in the headers that are specific to GMOS.
log.status("Updating keywords that are specific to GMOS")
# #M Some of the header keywords are wrong for certain types of
# #M Hamamatsu data. This is temporary fix until GMOS-S DC is fixed
# if ad.detector_name(pretty=True) == "Hamamatsu-S":
# log.status("Fixing headers for GMOS-S Hamamatsu data")
# # Image extension headers appear to be correct - MS 2014-10-01
# # correct_image_extensions=Flase
# # As does the DATE-OBS but as this seemed to break even after
# # apparently being fixed, still perform this check. - MS
# hdulist = ad.to_hdulist()
# # correct_headers(hdulist, logger=log,
# # correct_image_extensions=False)
# # When we create the new AD object, it needs to retain the
# # filename information
# orig_path = ad.path
# ad = astrodata.open(hdulist)
# ad.path = orig_path
# KL Commissioning GMOS-N Hamamatsu. Headers are not fully
# KL settled yet.
if ad.detector_name(pretty=True) == "Hamamatsu-N":
log.status("Fixing headers for GMOS-N Hamamatsu data")
try:
ad.phu['DATE-OBS'] = ad.phu['DATE']
except KeyError:
pass
# Update keywords in the image extensions. The descriptors return
# the true values on unprepared data.
descriptors = ['pixel_scale', 'read_noise', 'gain_setting',
'gain', 'saturation_level']
for desc in descriptors:
keyword = ad._keyword_for(desc)
comment = self.keyword_comments[keyword]
dv = getattr(ad, desc)()
if isinstance(dv, list):
for ext, value in zip(ad, dv):
ext.hdr.set(keyword, value, comment)
else:
ad.hdr.set(keyword, dv, comment)
if 'SPECT' in ad.tags:
kw = ad._keyword_for('dispersion_axis')
ad.hdr.set(kw, 1, self.keyword_comments[kw])
# And the bias level too!
bias_level = get_bias_level(adinput=ad,
estimate='qa' in self.mode)
for ext, bias in zip(ad, bias_level):
if bias is not None:
ext.hdr.set('RAWBIAS', bias,
self.keyword_comments['RAWBIAS'])
# Timestamp and update filename
gt.mark_history(ad, primname=self.myself(), keyword=timestamp_key)
ad.update_filename(suffix=suffix, strip=True)
return adinputs