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Updated to avoid masked column issues with astropy.
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@york-stsci
york-stsci committed Aug 20, 2021
1 parent 4b0c4ed commit 16c439f
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Showing 2 changed files with 214 additions and 55 deletions.
2 changes: 1 addition & 1 deletion stips/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@

__all__ = ['observation_module', 'scene_module']

__version__ = "1.0.9dev1"
__version__ = "1.0.8b"
version = __version__

# Local Definitions
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267 changes: 213 additions & 54 deletions stips/instruments/instrument.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@

from astropy import units as u
from astropy.io import fits as pyfits
from astropy.table import Table, Column
from astropy.table import Table, Column, MaskedColumn
from functools import wraps
from pandeia.engine.custom_exceptions import DataConfigurationError

Expand Down Expand Up @@ -453,15 +453,42 @@ def readPhoenixTable(self, table, bp, cached=-1):
if table is None:
return None
self._log("info","Converting Phoenix Table to Internal format")
ids = table['id']
datasets = table['dataset']
ras = table['ra']
decs = table['dec']
ages = table['age']
metallicities = table['metallicity']
masses = table['mass']
distances = table['distance']
binaries = table['binary']
if isinstance(table['id'], MaskedColumn):
ids = table['id'].filled()
else:
ids = table['id']
if isinstance(table['dataset'], MaskedColumn):
datasets = table['dataset'].filled()
else:
datasets = table['dataset']
if isinstance(table['ra'], MaskedColumn):
ras = table['ra'].filled()
else:
ras = table['ra']
if isinstance(table['dec'], MaskedColumn):
decs = table['dec'].filled()
else:
decs = table['dec']
if isinstance(table['age'], MaskedColumn):
ages = table['age'].filled()
else:
ages = table['age']
if isinstance(table['metallicity'], MaskedColumn):
metallicities = table['metallicity'].filled()
else:
metallicities = table['metallicity']
if isinstance(table['mass'], MaskedColumn):
masses = table['mass'].filled()
else:
masses = table['mass']
if isinstance(table['distance'], MaskedColumn):
distances = table['distance'].filled()
else:
distances = table['distance']
if isinstance(table['binary'], MaskedColumn):
binaries = table['binary'].filled()
else:
binaries = table['binary']
rates = np.zeros_like(ras)
all_datasets = np.unique(datasets)
self._log("info","{} datasets".format(len(all_datasets)))
Expand Down Expand Up @@ -514,13 +541,34 @@ def readPhoenixRealtimeTable(self, table, bp, cached=-1):
"""
if table is None:
return None
ids = table['id']
ras = table['ra']
decs = table['dec']
temps = table['teff']
gravs = table['log_g']
metallicities = table['metallicity']
apparents = table['apparent']
if isinstance(table['id'], MaskedColumn):
ids = table['id'].filled()
else:
ids = table['id']
if isinstance(table['ra'], MaskedColumn):
ras = table['ra'].filled()
else:
ras = table['ra']
if isinstance(table['dec'], MaskedColumn):
decs = table['dec'].filled()
else:
decs = table['dec']
if isinstance(table['teff'], MaskedColumn):
temps = table['teff'].filled()
else:
temps = table['teff']
if isinstance(table['log_g'], MaskedColumn):
gravs = table['log_g'].filled()
else:
gravs = table['log_g']
if isinstance(table['metallicity'], MaskedColumn):
metallicities = table['metallicity'].filled()
else:
metallicities = table['metallicity']
if isinstance(table['apparent'], MaskedColumn):
apparents = table['apparent'].filled()
else:
apparents = table['apparent']
norm_bp = table.meta['BANDPASS']
self._log("info", "Normalization Bandpass is {} ({})".format(norm_bp, type(norm_bp)))
if norm_bp == '' or norm_bp is None or norm_bp == 'None':
Expand Down Expand Up @@ -556,11 +604,26 @@ def readPandeiaTable(self, table, bp, cached=-1):
if table is None:
return None
from pandeia.engine.sed import SEDFactory
ids = table['id']
ras = table['ra']
decs = table['dec']
keys = table['key']
apparents = table['apparent']
if isinstance(table['id'], MaskedColumn):
ids = table['id'].filled()
else:
ids = table['id']
if isinstance(table['ra'], MaskedColumn):
ras = table['ra'].filled()
else:
ras = table['ra']
if isinstance(table['dec'], MaskedColumn):
decs = table['dec'].filled()
else:
decs = table['dec']
if isinstance(table['key'], MaskedColumn):
keys = table['key'].filled()
else:
keys = table['key']
if isinstance(table['apparent'], MaskedColumn):
apparents = table['apparent'].filled()
else:
apparents = table['apparent']
norm_bp = table.meta['BANDPASS']
self._log("info", "Normalization Bandpass is {} ({})".format(norm_bp, type(norm_bp)))
if norm_bp == '' or norm_bp is None or norm_bp == 'None':
Expand Down Expand Up @@ -605,21 +668,51 @@ def stringify(num):
self._log("info", "Converting BC95 Catalogue")
proflist = {"expdisk":1,"devauc":4}
distance_type = "redshift"
ids = table['id']
ras = table['ra']
decs = table['dec']
if isinstance(table['id'], MaskedColumn):
ids = table['id'].filled()
else:
ids = table['id']
if isinstance(table['ra'], MaskedColumn):
ras = table['ra'].filled()
else:
ras = table['ra']
if isinstance(table['dec'], MaskedColumn):
decs = table['dec'].filled()
else:
decs = table['dec']
try:
zs = table['redshift']
if isinstance(table['redshift'], MaskedColumn):
zs = table['redshift'].filled()
else:
zs = table['redshift']
except KeyError: #distances instead
zs = table['distance']
if isinstance(table['distance'], MaskedColumn):
zs = table['distance'].filled()
else:
zs = table['distance']
distance_type = "pc"
models = table['model']
ages = table['age']
profiles = table['profile']
if isinstance(table['model'], MaskedColumn):
models = table['model'].filled()
else:
models = table['model']
if isinstance(table['age'], MaskedColumn):
ages = table['age'].filled()
else:
ages = table['age']
if isinstance(table['profile'], MaskedColumn):
profiles = table['profile'].filled()
else:
profiles = table['profile']
radii = table['radius']/self.SCALE[0] #at some point, may want to figure out multiple scales.
ratios = table['axial_ratio']
if isinstance(table['axial_ratio'], MaskedColumn):
ratios = table['axial_ratio'].filled()
else:
ratios = table['axial_ratio']
pas = (table['pa'] + (self.pa*180./np.pi) )%360.
vmags = table['apparent_surface_brightness']
if isinstance(table['apparent_surface_brightness'], MaskedColumn):
vmags = table['apparent_surface_brightness'].filled()
else:
vmags = table['apparent_surface_brightness']
norm_bp = table.meta['BANDPASS']
self._log("info", "Normalization Bandpass is {} ({})".format(norm_bp, type(norm_bp)))
if norm_bp == '' or norm_bp is None or norm_bp == 'None':
Expand Down Expand Up @@ -672,18 +765,51 @@ def readMixedTable(self, table, bp, cached=-1):
"""
if table is None:
return None
ras = table['ra']
decs = table['dec']
types = table['type']
indices = table['n']
radii = table['re']
pas = table['phi']
ratios = table['ratio']
ids = table['id']
notes = table['notes']
if isinstance(table['ra'], MaskedColumn):
ras = table['ra'].filled()
else:
ras = table['ra']
if isinstance(table['dec'], MaskedColumn):
decs = table['dec'].filled()
else:
decs = table['dec']
if isinstance(table['type'], MaskedColumn):
types = table['type'].filled()
else:
types = table['type']
if isinstance(table['n'], MaskedColumn):
indices = table['n'].filled()
else:
indices = table['n']
if isinstance(table['re'], MaskedColumn):
radii = table['re'].filled()
else:
radii = table['re']
if isinstance(table['phi'], MaskedColumn):
pas = table['phi'].filled()
else:
pas = table['phi']
if isinstance(table['ratio'], MaskedColumn):
ratios = table['ratio'].filled()
else:
ratios = table['ratio']
if isinstance(table['id'], MaskedColumn):
ids = table['id'].filled()
else:
ids = table['id']
if isinstance(table['notes'], MaskedColumn):
notes = table['notes'].filled()
else:
notes = table['notes']

rates = table['flux']
units = table['units']
if isinstance(table['flux'], MaskedColumn):
rates = table['flux'].filled()
else:
rates = table['flux']
if isinstance(table['units'], MaskedColumn):
units = table['units'].filled()
else:
units = table['units']
idxp = np.where(units == 'p')
rates[idxp] *= self.convertToCounts('p')
idxe = np.where(units == 'e')
Expand All @@ -710,15 +836,39 @@ def readMultiTable(self, table, bp, cached=-1):
"""
if table is None:
return None
ras = table['ra']
decs = table['dec']
types = table['type']
indices = table['n']
if isinstance(table['ra'], MaskedColumn):
ras = table['ra'].filled()
else:
ras = table['ra']
if isinstance(table['dec'], MaskedColumn):
decs = table['dec'].filled()
else:
decs = table['dec']
if isinstance(table['type'], MaskedColumn):
types = table['type'].filled()
else:
types = table['type']
if isinstance(table['n'], MaskedColumn):
indices = table['n'].filled()
else:
indices = table['n']
radii = table['re']/self.SCALE[0] #at some point, may want to figure out multiple scales.
pas = table['phi']
ratios = table['ratio']
ids = table['id']
notes = table['notes']
if isinstance(table['phi'], MaskedColumn):
pas = table['phi'].filled()
else:
pas = table['phi']
if isinstance(table['ratio'], MaskedColumn):
ratios = table['ratio'].filled()
else:
ratios = table['ratio']
if isinstance(table['id'], MaskedColumn):
ids = table['id'].filled()
else:
ids = table['id']
if isinstance(table['notes'], MaskedColumn):
notes = table['notes'].filled()
else:
notes = table['notes']
rates = table[self.filter]
t = Table()
t['ra'] = Column(data=ras)
Expand All @@ -740,11 +890,20 @@ def readGenericTable(self, table, bp, cached=-1):
"""
if table is None:
return None
ras = table['ra']
decs = table['dec']
if isinstance(table['ra'], MaskedColumn):
ras = table['ra'].filled()
else:
ras = table['ra']
if isinstance(table['dec'], MaskedColumn):
decs = table['dec'].filled()
else:
decs = table['dec']
rates = table[self.filter.lower()]
if 'id' in table:
ids = table['id']
if isinstance(table['id'], MaskedColumn):
ids = table['id'].filled()
else:
ids = table['id']
else:
ids = np.arange(len(ras),dtype=int)
t = Table()
Expand Down

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