def _get_uncertainties(self, star_group_size):
"""
Retrieve uncertainties on fitted parameters from the fitter
object.
Parameters
----------
star_group_size : int
Number of stars in the given group.
Returns
-------
unc_tab : `~astropy.table.QTable`
A table which contains uncertainties on the fitted parameters.
The uncertainties are reported as one standard deviation.
"""
unc_tab = QTable()
for param_name in self.psf_model.param_names:
if not self.psf_model.fixed[param_name]:
unc_tab.add_column(
Column(name=param_name + "_unc",
data=np.empty(star_group_size)))
k = 0
n_fit_params = len(unc_tab.colnames)
param_cov = self.fitter.fit_info.get('param_cov', None)
for i in range(star_group_size):
unc_tab[i] = np.sqrt(np.diag(param_cov))[k:k + n_fit_params]
k = k + n_fit_params
return unc_tab
def load_mage_z3(cls, sample='all'):
""" Load the LLS table from the z~3 MagE survey
(Fumagalli et al. 2013, ApJ, 775, 78)
Parameters
----------
sample : str
Survey sample
* all -- All
* non-color -- Restricts to quasars that were *not* color-selected
* color -- Restricts to quasars that were color-selected
Returns
-------
lls_survey : IGMSurvey
Includes all quasars observed in the survey
And all the LLS
"""
# LLS File
survey_fil = pyigm_path + '/data/LLS/HD-LLS/fumagalli13_apj775_78_tab1+2.fits'
tab = Table.read(survey_fil)
# Rename some columns
tab.rename_column('RAJ2000', 'RA')
tab['RA'].unit = u.deg
tab.rename_column('DEJ2000', 'DEC')
tab['DEC'].unit = u.deg
tab.rename_column('zqso', 'Z_QSO')
tab.rename_column('zlls', 'Z_LLS')
tab.rename_column('zend', 'Z_START') # F13 was opposite of POW10
tab.rename_column('zstart', 'Z_END') # F13 was opposite of POW10
# Cut table
if sample == 'all':
pass
elif sample == 'non-color':
NC = np.array(
[True if row['n_Name'][0] == 'N' else False for row in tab])
tab = tab[NC]
elif sample == 'color':
Clr = [True if row['n_Name'][0] == 'C' else False for row in tab]
tab = tab[Clr]
# Good LLS
lls = tab['Z_LLS'] >= tab['Z_START']
lls_tab = QTable(tab[lls])
nlls = np.sum(lls)
# Set NHI to 17.8 (tau>=2)
lls_tab.add_column(Column([17.8] * nlls, name='NHI'))
lls_tab.add_column(Column([99.9] * nlls, name='SIGNHI'))
# Generate survey
lls_survey = cls.from_sfits(lls_tab)
lls_survey.ref = 'z3_MagE'
lls_survey.sightlines = tab
return lls_survey
def load_mage_z3(cls, sample='all'):
""" Load the LLS table from the z~3 MagE survey
(Fumagalli et al. 2013, ApJ, 775, 78)
Parameters
----------
sample : str
Survey sample
* all -- All
* non-color -- Restricts to quasars that were *not* color-selected
* color -- Restricts to quasars that were color-selected
Returns
-------
lls_survey : IGMSurvey
Includes all quasars observed in the survey
And all the LLS
"""
# LLS File
survey_fil = pyigm_path+'/data/LLS/HD-LLS/fumagalli13_apj775_78_tab1+2.fits'
tab = Table.read(survey_fil)
# Rename some columns
tab.rename_column('RAJ2000', 'RA')
tab['RA'].unit = u.deg
tab.rename_column('DEJ2000', 'DEC')
tab['DEC'].unit = u.deg
tab.rename_column('zqso', 'Z_QSO')
tab.rename_column('zlls', 'Z_LLS')
tab.rename_column('zend', 'Z_START') # F13 was opposite of POW10
tab.rename_column('zstart', 'Z_END') # F13 was opposite of POW10
# Cut table
if sample == 'all':
pass
elif sample == 'non-color':
NC = np.array([True if row['n_Name'][0] == 'N' else False for row in tab])
tab = tab[NC]
elif sample == 'color':
Clr = [True if row['n_Name'][0] == 'C' else False for row in tab]
tab = tab[Clr]
# Good LLS
lls = tab['Z_LLS'] >= tab['Z_START']
lls_tab = QTable(tab[lls])
nlls = np.sum(lls)
# Set NHI to 17.8 (tau>=2)
lls_tab.add_column(Column([17.8]*nlls, name='NHI'))
lls_tab.add_column(Column([99.9]*nlls, name='SIGNHI'))
# Generate survey
lls_survey = cls.from_sfits(lls_tab)
lls_survey.ref = 'z3_MagE'
lls_survey.sightlines = tab
return lls_survey
def add_column(tbl: table.QTable, colname: str, dtype, unit):
if colname not in tbl.colnames:
if isinstance(dtype, str):
dtype = str
val = dtype("0" * 32)
else:
val = dtype(-999)
tbl.add_column([val] * len(tbl), name=colname)
if unit is not None:
tbl[colname] *= unit
def fetch_LCO_weather(site_code,
start=None,
end=None,
interval=600,
dbg=False):
"""Fetch LCO weather (temperature and pressure) for LCO <site_code> (e.g. 'ogg')
between [start] and [end] (defaults to start of current year and now) interpolated
to a spacing of [interval] seconds (defaults to 600s).
Returns an AstroPy QTable of UTC datetime and temperature and pressure"""
site_code = site_code.lower()
start = start or datetime(datetime.utcnow().year, 1, 1)
end = end or datetime.utcnow().replace(
hour=0, minute=0, second=0, microsecond=0)
nrows = int((end - start) / timedelta(seconds=interval))
# Construct a Q(uantity)Table and a column of datetime64's from <start> to
# <end> with [interval] spacing
table = QTable()
dt = np.arange(start, end, step=interval, dtype='datetime64[s]')
aa = Column(dt, name='UTC Datetime')
table.add_column(aa)
for quantity in ['temperature', 'pressure']:
datum = map_quantity_to_LCO_datum(quantity)
data = query_LCO_telemetry(site_code, start, end, datum)
if len(data) > 0:
interp_timestamps, interp_values = interpolate_LCO_telemetry(
data, interval)
unit = interp_values[0].unit
if dbg:
print(quantity, interp_timestamps[0], interp_timestamps[-1],
len(interp_timestamps), len(interp_values))
# Check if the interpolated dataset starts late or ends early and pad
# accordingly
num_before = max(
int((interp_timestamps[0] - start) /
timedelta(seconds=interval)), 0)
num_after = max(
int((end - interp_timestamps[-1]) /
timedelta(seconds=interval)), 0)
pad_values = np.pad(interp_values, (num_before, num_after), 'edge')
# Put units back
pad_values = pad_values * unit
if dbg:
print("Padding by {} before, {} after, new length={}".format(
num_before, num_after, len(pad_values)))
# Trim padded array to right length, turn into a column and add to table
col = Column(pad_values[0:nrows], name=quantity)
table.add_column(col)
else:
print("Found no data for {} at {} between {}->{}".format(
datum, site_code, start, end))
return table
def build_table(self):
"""Generate an astropy QTable out of the component.
Returns
-------
comp_tbl : QTable
"""
if len(self._abslines) == 0:
return
comp_tbl = QTable()
comp_tbl.add_column(Column([iline.wrest.to(u.AA).value for iline in self._abslines]*u.AA, name='wrest'))
for attrib in ['z', 'flag_N', 'logN', 'sig_logN']:
comp_tbl.add_column(Column([iline.attrib[attrib] for iline in self._abslines], name=attrib))
# Return
return comp_tbl
def _model_params2table(self, fit_model, star_group):
"""
Place fitted parameters into an astropy table.
Parameters
----------
fit_model : `astropy.modeling.Fittable2DModel` instance
PSF or PRF model to fit the data. Could be one of the models
in this package like `~photutils.psf.sandbox.DiscretePRF`,
`~photutils.psf.IntegratedGaussianPRF`, or any other
suitable 2D model.
star_group : `~astropy.table.Table`
the star group instance.
Returns
-------
param_tab : `~astropy.table.QTable`
A table that contains the fitted parameters.
"""
param_tab = QTable()
for param_tab_name in self._pars_to_output.keys():
param_tab.add_column(
Column(name=param_tab_name, data=np.empty(len(star_group))))
if len(star_group) > 1:
for i in range(len(star_group)):
for param_tab_name, param_name in self._pars_to_output.items():
# get sub_model corresponding to star with index i as name
# name was set in utils.get_grouped_psf_model()
# we can't use model['name'] here as that only
# searches leaves and we might want a intermediate
# node of the tree
sub_models = [
model for model in fit_model.traverse_postorder()
if model.name == i
]
if len(sub_models) != 1:
raise ValueError('sub_models must have a length of 1')
sub_model = sub_models[0]
param_tab[param_tab_name][i] = getattr(
sub_model, param_name).value
else:
for param_tab_name, param_name in self._pars_to_output.items():
param_tab[param_tab_name] = getattr(fit_model,
param_name).value
return param_tab
def read_in_galaxy(filename, index):
print "attempting to read in",filename
if ".pkl" in filename:
print "assuming that",filename,"is a pickle file with only a dict of galaxies in it"
galaxies = pickle.load(open(filename,"r"))
print "for now we're only dealing with one galaxy at a time; taking galaxy #",index
assert(index in galaxies.keys()), "index %i not in file :-(" % index
galaxy = galaxies[index]
col_z = Column(name='z',data=galaxies['z'])
galaxy.add_column(col_z,0)
elif "peter" in filename:
print "assuming that",filename,"is an ascii file from peter behroozi and gergo popping with Mh,Ms,dMhdt,sfr,Mg,Mhi,Mh2"
print "also assuming that",filename,"only has one iteration"
z,Mh,Ms,dMhdt,sfr,Mg,Mhi,Mh2 = np.loadtxt(filename,usecols=(0,7*index+1,7*index+2,7*index+3,7*index+4,7*index+5,7*index+6,7*index+7),unpack=True)
galaxy = QTable([z,Mh,Ms,dMhdt,sfr,Mg,Mhi,Mh2],names=('z','Mh','Ms','dMhdt','sfr','Mg','Mhi','Mh2'))
## need to add units
galaxy['Mh'].unit = u.Msun
galaxy['Ms'].unit = u.Msun
galaxy['Mg'].unit = u.Msun
galaxy['Mhi'].unit = u.Msun
galaxy['Mh2'].unit = u.Msun
galaxy['dMhdt'].unit = u.Msun / u.yr
if 'dMrdt' in galaxy.colnames:
galaxy['dMrdt'].unit = u.Msun / u.yr
galaxy['sfr'].unit = u.Msun / u.yr
### Helium is not included in the gas masses!!
galaxy['Mg'] = galaxy['Mg'] * HELIUM_CORR
### Let's make a CGM! ###
galaxy['Mcgm'] = galaxy['Mh']*cosmo.Ob0/cosmo.Om0 - galaxy['Ms'] - galaxy['Mg']
age = cosmo.age(galaxy['z'])
col_age = Column(name='age', data=age)
galaxy.add_column(col_age,1)
tlb = cosmo.lookback_time(galaxy['z'])
col_tlb = Column(name='lookback', data=tlb)
galaxy.add_column(col_tlb,2)
## check to make sure sorted so earlier is earlier
galaxy.sort('age')
return galaxy
def write_to_ascii(self, outfil, format='ascii.ecsv'):
""" Write to a text file.
Parameters
----------
outfil: str
Filename.
"""
# Convert to astropy Table
table = QTable([self.wavelength, self.flux],
names=('WAVE', 'FLUX'))
if self.sig_is_set:
sigclm = Column(self.sig, name='ERROR')
table.add_column(sigclm)
if self.co_is_set:
coclm = Column(self.co, name='CO')
table.add_column(coclm)
# Write
table.write(outfil, format=format)
def build_table(self):
"""Generate an astropy QTable out of the abs lines
Returns
-------
comp_tbl : QTable
"""
if len(self._abslines) == 0:
return
comp_tbl = QTable()
comp_tbl.add_column(Column([iline.wrest.to(u.AA).value for iline in self._abslines]*u.AA, name='wrest'))
comp_tbl.add_column(Column([iline.z for iline in self._abslines], name='z'))
for attrib in ['flag_N', 'logN', 'sig_logN']:
comp_tbl.add_column(Column([iline.attrib[attrib] for iline in self._abslines], name=attrib))
# Return
return comp_tbl
def find_peaks(data,
threshold,
box_size=3,
footprint=None,
mask=None,
border_width=None,
npeaks=np.inf,
centroid_func=None,
error=None,
wcs=None):
"""
Find local peaks in an image that are above above a specified
threshold value.
Peaks are the maxima above the ``threshold`` within a local region.
The local regions are defined by either the ``box_size`` or
``footprint`` parameters. ``box_size`` defines the local region
around each pixel as a square box. ``footprint`` is a boolean array
where `True` values specify the region shape.
If multiple pixels within a local region have identical intensities,
then the coordinates of all such pixels are returned. Otherwise,
there will be only one peak pixel per local region. Thus, the
defined region effectively imposes a minimum separation between
peaks unless there are identical peaks within the region.
If ``centroid_func`` is input, then it will be used to calculate a
centroid within the defined local region centered on each detected
peak pixel. In this case, the centroid will also be returned in the
output table.
Parameters
----------
data : array_like
The 2D array of the image.
threshold : float or array-like
The data value or pixel-wise data values to be used for the
detection threshold. A 2D ``threshold`` must have the same shape
as ``data``. See `~photutils.segmentation.detect_threshold` for
one way to create a ``threshold`` image.
box_size : scalar or tuple, optional
The size of the local region to search for peaks at every point
in ``data``. If ``box_size`` is a scalar, then the region shape
will be ``(box_size, box_size)``. Either ``box_size`` or
``footprint`` must be defined. If they are both defined, then
``footprint`` overrides ``box_size``.
footprint : `~numpy.ndarray` of bools, optional
A boolean array where `True` values describe the local footprint
region within which to search for peaks at every point in
``data``. ``box_size=(n, m)`` is equivalent to
``footprint=np.ones((n, m))``. Either ``box_size`` or
``footprint`` must be defined. If they are both defined, then
``footprint`` overrides ``box_size``.
mask : array_like, bool, optional
A boolean mask with the same shape as ``data``, where a `True`
value indicates the corresponding element of ``data`` is masked.
border_width : bool, optional
The width in pixels to exclude around the border of the
``data``.
npeaks : int, optional
The maximum number of peaks to return. When the number of
detected peaks exceeds ``npeaks``, the peaks with the highest
peak intensities will be returned.
centroid_func : callable, optional
A callable object (e.g., function or class) that is used to
calculate the centroid of a 2D array. The ``centroid_func``
must accept a 2D `~numpy.ndarray`, have a ``mask`` keyword, and
optionally an ``error`` keyword. The callable object must return
a tuple of two 1D `~numpy.ndarray` objects, representing the x
and y centroids, respectively.
error : array_like, optional
The 2D array of the 1-sigma errors of the input ``data``.
``error`` is used only if ``centroid_func`` is input (the
``error`` array is passed directly to the ``centroid_func``).
wcs : `None` or WCS object, optional
A world coordinate system (WCS) transformation that
supports the `astropy shared interface for WCS
<https://docs.astropy.org/en/stable/wcs/wcsapi.html>`_
(e.g., `astropy.wcs.WCS`, `gwcs.wcs.WCS`). If `None`, then
the sky coordinates will not be returned in the output
`~astropy.table.Table`.
Returns
-------
output : `~astropy.table.Table` or `None`
A table containing the x and y pixel location of the peaks and
their values. If ``centroid_func`` is input, then the table
will also contain the centroid position. If no peaks are found
then `None` is returned.
"""
from scipy.ndimage import maximum_filter
data = np.asanyarray(data)
if np.all(data == data.flat[0]):
warnings.warn('Input data is constant. No local peaks can be found.',
NoDetectionsWarning)
return None
if not np.isscalar(threshold):
threshold = np.asanyarray(threshold)
if data.shape != threshold.shape:
raise ValueError('A threshold array must have the same shape as '
'the input data.')
# remove NaN values to avoid runtime warnings
nan_mask = np.isnan(data)
if np.any(nan_mask):
data = np.copy(data) # ndarray
data[nan_mask] = np.nanmin(data)
if footprint is not None:
data_max = maximum_filter(data,
footprint=footprint,
mode='constant',
cval=0.0)
else:
data_max = maximum_filter(data,
size=box_size,
mode='constant',
cval=0.0)
peak_goodmask = (data == data_max) # good pixels are True
if mask is not None:
mask = np.asanyarray(mask)
if data.shape != mask.shape:
raise ValueError('data and mask must have the same shape')
peak_goodmask = np.logical_and(peak_goodmask, ~mask)
if border_width is not None:
for i in range(peak_goodmask.ndim):
peak_goodmask = peak_goodmask.swapaxes(0, i)
peak_goodmask[:border_width] = False
peak_goodmask[-border_width:] = False
peak_goodmask = peak_goodmask.swapaxes(0, i)
peak_goodmask = np.logical_and(peak_goodmask, (data > threshold))
y_peaks, x_peaks = peak_goodmask.nonzero()
peak_values = data[y_peaks, x_peaks]
nxpeaks = len(x_peaks)
if nxpeaks > npeaks:
idx = np.argsort(peak_values)[::-1][:npeaks]
x_peaks = x_peaks[idx]
y_peaks = y_peaks[idx]
peak_values = peak_values[idx]
if nxpeaks == 0:
warnings.warn('No local peaks were found.', NoDetectionsWarning)
return None
# construct the output table
meta = {'version': _get_version_info()}
colnames = ['x_peak', 'y_peak', 'peak_value']
coldata = [x_peaks, y_peaks, peak_values]
table = QTable(coldata, names=colnames, meta=meta)
if wcs is not None:
skycoord_peaks = wcs.pixel_to_world(x_peaks, y_peaks)
table.add_column(skycoord_peaks, name='skycoord_peak', index=2)
# perform centroiding
if centroid_func is not None:
from ..centroids import centroid_sources # prevents circular import
if not callable(centroid_func):
raise TypeError('centroid_func must be a callable object')
x_centroids, y_centroids = centroid_sources(
data,
x_peaks,
y_peaks,
box_size=box_size,
footprint=footprint,
error=error,
mask=mask,
centroid_func=centroid_func)
table['x_centroid'] = x_centroids
table['y_centroid'] = y_centroids
if wcs is not None:
skycoord_centroids = wcs.pixel_to_world(x_centroids, y_centroids)
idx = table.colnames.index('y_centroid') + 1
table.add_column(skycoord_centroids,
name='skycoord_centroid',
index=idx)
return table
def read_ascii(filepath, dbg=False):
"""Read single parameter ASCII format files extracted from the GrADS server e.g.
https://goldsmr4.gesdisc.eosdis.nasa.gov/dods/M2T1NXSLV.ascii?tqv
or from the output of fetch_merra2_ascii_timeseries()"""
with open(filepath, 'r') as foo_fh:
first_line = foo_fh.readline()
if 'Dataset:' in first_line.strip():
# JD for 2002-01-01, starting point of aggregation values
t0 = 2452275.5
# OpenDAP format file
data = {}
for line in foo_fh:
line = line.rstrip()
if len(line) == 0:
continue
if dbg: print(line)
if '[' not in line:
chunks = line.split(',')
if len(chunks) == 2:
quantity = chunks[0]
value = chunks[1]
try:
value = float(value)
except ValueError:
pass
value = [
value,
]
else:
quantity = chunks[0]
value = [float(x.strip()) for x in chunks[1:]]
data[quantity] = value
else:
chunks = line.split(',')
array_name = chunks[0]
value = chunks[1]
try:
value = float(value)
except ValueError:
pass
index = array_name.find('[')
if index > 0:
array_name = array_name[0:index]
if array_name not in data:
# New quantity
data[array_name] = []
data[array_name].append(value)
else:
# GDS format file
t0 = 1721423.5
status = foo_fh.seek(0)
in_data = False
data = {}
for line in foo_fh:
line = line.rstrip()
if len(line) == 0:
continue
if dbg: print(line, in_data)
if line.count(',') == 1:
if line[0] != '[':
if in_data is True:
data[array_name] = array
array = []
array_name = line.split(',')[0]
else:
in_data = True
array = []
array_name = line.split(',')[0]
if dbg: print("Created array_name", array_name)
else:
value = float(line.split(',')[1].strip())
array.append(value)
elif line.count(',') >= 1 and in_data is True:
values = [float(x.strip()) for x in line.split(',')]
data[array_name] = values
in_data = False
foo_fh.close()
if data.get('time', None) is not None:
times = np.array(time_index_to_dt(data['time'], t0),
dtype='datetime64[s]')
data['datetime'] = times
table = QTable()
for key in data.keys():
if dbg: print(key, len(data[key]))
if type(data[key]) != float and len(data[key]) > 1:
# Skip 1D values such as latitude or longitude
aa = Column(data[key], name=key)
table.add_column(aa)
return table
def get_nuv_cand(outfil=None, known_fil=None):
'''
Generate a list of NUV AGN candidates from WISE + GALEX
Paramaeters:
-----------
known_fil: string (None)
Filename for a Table of NUV candidates with known redshifts
'''
# Read photometry
z1_galex_nuv, z1_wise_nuv = uvqs_cand.load_phot(use_NUV=True)
# COLOR CUTS
gdc = color_cut(z1_galex_nuv, z1_wise_nuv)
srt = np.argsort(z1_wise_nuv[gdc]['RA'])
gdc = gdc[srt]
w1mw2 = z1_wise_nuv[gdc]['W1MPRO'] - z1_wise_nuv[gdc]['W2MPRO']
# Generate the QTable
z1_cand_nuv = QTable(
[Column(z1_wise_nuv[gdc]['RA'], name='RA', unit=u.degree)])
z1_cand_nuv.add_column(
Column(z1_wise_nuv[gdc]['DEC'], name='DEC', unit=u.degree))
z1_cand_nuv.add_column(Column(z1_wise_nuv[gdc]['W1MPRO'], name='W1'))
z1_cand_nuv.add_column(Column(z1_wise_nuv[gdc]['W2MPRO'], name='W2'))
z1_cand_nuv.add_column(
Column(z1_wise_nuv[gdc]['W1MPRO'] - z1_wise_nuv[gdc]['W2MPRO'],
name='W1-W2'))
z1_cand_nuv.add_column(Column(z1_galex_nuv[gdc]['FUV'], name='FUV'))
z1_cand_nuv.add_column(Column(z1_galex_nuv[gdc]['NUV'], name='NUV'))
z1_cand_nuv.add_column(
Column(z1_galex_nuv[gdc]['FUV'] - z1_galex_nuv[gdc]['NUV'],
name='FUV-NUV'))
msk = z1_cand_nuv['RA'] == z1_cand_nuv['RA']
c_z1_cand = SkyCoord(ra=z1_cand_nuv['RA'], dec=z1_cand_nuv['DEC'])
# Check against z1QSO
cut_z1qso = uvqs_io.new_z1qso() # z1QSO with good z, not in milliq
c_zq = SkyCoord(ra=cut_z1qso['RA'], dec=cut_z1qso['DEC'])
idx, d2d, d3d = coords.match_coordinates_sky(c_z1_cand,
c_zq,
nthneighbor=1)
bad = np.where(d2d.to('arcsec') < (5. * u.arcsec))[0]
print('z1q_nuv: Rejecting {:d} quasars from z1QSO'.format(len(bad)))
msk[bad] = False
# Check against Flesch+15
milliq = uvqs_io.load_milliq(good_z=True, good_FUV=True)
c_mq = SkyCoord(ra=milliq['RA'] * u.degree, dec=milliq['DEC'] * u.degree)
idx, d2d, d3d = coords.match_coordinates_sky(c_z1_cand,
c_mq,
nthneighbor=1)
# Fill in z
z = np.zeros(len(c_z1_cand))
mt = np.where((d2d.to('arcsec') < (5. * u.arcsec)))[0]
z[mt] = milliq['Z'][idx][mt]
z1_cand_nuv.add_column(Column(z, name='Z'))
# Write?
if known_fil is not None:
import pdb
pdb.set_trace()
xxf.table_to_fits(Table(z1_cand_nuv[mt]),
known_fil,
compress=True,
comment='Known NUV Candidates')
print('z1qso_nuv.get_cand: Writing {:d} candidates to {:s}'.format(
len(z1_cand_nuv), outfil))
# Parse out low-z
bad = np.where((d2d.to('arcsec') < (5. * u.arcsec))
& (milliq['Z'][idx] < 0.5))[0]
print('z1q_nuv: Rejecting {:d} quasars from Flesch+15'.format(len(bad)))
msk[bad] = False
# Add priority flags
z1_cand_nuv = z1_cand_nuv[msk]
priority = np.zeros(len(z1_cand_nuv), dtype='int')
gd1 = np.where(z1_cand_nuv['NUV'] < 16.5)[0]
priority[gd1] = 1
gd2 = np.where((z1_cand_nuv['NUV'] < 17.0) & priority == 0)[0]
priority[gd2] = 2
gd3 = np.where(z1_cand_nuv['NUV'] > 17.0)[0]
priority[gd3] = 3
z1_cand_nuv.add_column(Column(priority, name='PRI'))
# Fill in z1qso observed
z1qso, cand = z1qa.load_z1qso() # z1QSO with good z, not in milliq
c_zn = SkyCoord(ra=z1_cand_nuv['RA'], dec=z1_cand_nuv['DEC'])
c_zq = SkyCoord(ra=z1qso['RA'] * u.degree, dec=z1qso['DEC'] * u.degree)
idx, d2d, d3d = coords.match_coordinates_sky(c_zn, c_zq, nthneighbor=1)
mt = np.where((d2d.to('arcsec') < (5. * u.arcsec)))[0]
spec_qual = np.zeros(len(z1_cand_nuv), dtype='int')
z_qual = np.zeros(len(z1_cand_nuv), dtype='int')
spec_qual[mt] = z1qso['SPEC_QUAL'][idx[mt]]
z_qual[mt] = z1qso['Z_QUAL'][idx[mt]]
z1_cand_nuv.add_column(Column(spec_qual, name='SPEC_QUAL'))
z1_cand_nuv.add_column(Column(z_qual, name='Z_QUAL'))
# Names
names = []
for jj, z1c in enumerate(z1_cand_nuv):
name = 'z1c_J{:s}{:s}'.format(
c_zn[jj].ra.to_string(unit=u.hour, pad=True, sep='', precision=2),
c_zn[jj].dec.to_string(pad=True,
alwayssign=True,
sep='',
precision=2))
names.append(str(name))
z1_cand_nuv.add_column(Column(names, name='NAME'))
# Sort
srt = np.argsort(z1_cand_nuv['RA'])
z1_cand_nuv = z1_cand_nuv[srt]
# Write?
if not outfil is None:
xxf.table_to_fits(Table(z1_cand_nuv),
outfil,
compress=True,
comment='z1QSO NUV Candidates')
print('z1qso_nuv.get_cand: Writing {:d} candidates to {:s}'.format(
len(z1_cand_nuv), outfil))
# Return
return z1_cand_nuv
def mk_summary(dlas, prefix, outfil, specpath=None, htmlfil=None):
""" Loops through the DLA list and generates a Table
Also pushes the 1D spectra into the folder
Parameters
----------
dlas : DLASurvey
prefix : str
outfil : str
Name of the output FITS summary file
htmlfil : str, optional
Returns
-------
"""
#
if htmlfil is None:
htmlfil = 'tmp.html'
# # Constructing
# QSO, RA/DEC
cqso = Column(dlas.qso, name='QSO')
ra = dlas.coord.ra.degree[0]
dec = dlas.coord.dec.degree[0]
jname = []
for abs_sys in dlas._abs_sys:
jname.append(survey_name(prefix, abs_sys))
cjname = Column(jname, name='Name')
cra = Column(ra, name='RA', unit=u.degree)
cdec = Column(dec, name='DEC', unit=u.degree)
czem = Column(dlas.zem, name='Z_QSO')
# Begin the Table
dla_table = QTable( [cjname, cqso, cra, cdec, czem] )
# LLS properties
czabs = Column(dlas.zabs, name='ZABS')
cNHI = Column(dlas.NHI, name='logNHI')
csigNHI = Column(dlas.sig_NHI, name='sig(logNHI)')
# Add to Table
dla_table.add_columns([czabs, cNHI, csigNHI])
# Spectra files
all_sfiles = []
for jj,ills in enumerate(dlas._abs_sys):
sub_spec = mk_1dspec(ills, name=cjname[jj], outpath=specpath)
# Pad
while len(sub_spec) < 5:
sub_spec.append(str('NULL'))
# Append
all_sfiles.append(sub_spec)
cspec = Column(np.array(all_sfiles), name='SPEC_FILES')
dla_table.add_column( cspec )
# Sort
dla_table.sort('RA')
# Write
print('Writing {:s}'.format(outfil))
xxf.table_to_fits(dla_table,outfil)
print('Writing {:s}'.format(htmlfil))
Table(dla_table).write(htmlfil)
return dla_table
def stackLines(galaxy,
velocity,
binmap,
binedge,
bintype,
binunit,
cubeCO=None,
cubeHCN=None,
cubeHCOp=None,
cube13CO=None,
cubeC18O=None,
sfrmap=None,
ltirmap=None,
maxAbsVel=250.0):
'''
Actually do the stacking.
cube: data we are stacking (SpectralCube)
galaxy: line from degas_base.fits table with galaxy information.
velocity: velocity map to stack data using
binmap: bin map
binedge: bin edges
binlabel: bin labels
bintype: type of bin
cubeCO: CO cube
cubeHCN: HCN cube
cubeHCOp: HCO+ cube
cube13CO: 13CO cube
cubeC18O: C18O cube
sfrmap: star formation rate map
ltirmap: LTIR map
maxAbsVel: absolute maximum velocity to include in spectral in km/s.
Assumes line is centered at zero (which should be true for stacking).
Date Programmer Description of Changes
----------------------------------------------------------------------
10/29/2020 Yiqing Song Original Code
12/03/2020 A.A. Kepley Added comments and moved bin creation up
a level to simplify code.
12/10/2020 A.A. Kepley added LTIR calculation
5/6/2021 A.A. Kepley modified to fit all lines for one galaxy at
once so I can use CO FWHM to calculate upper
limits for other lines
'''
from signal_id.stacking import bin_by_label as BinByLabel
# get the relevant info on the galaxy and cube
D = galaxy['DIST_MPC'] * u.Mpc
pix_area = (np.radians(np.abs(cubeCO.header['CDELT1'])) *
D.to(u.kpc))**2 #kpc^2 ## TODO CHECK THIS CONVERSION
# do the individual line stacks.
# -----------------------------
stack = {}
if cubeCO:
## fill in nans with 0 to avoid fft shift issue with nans
#cubeCO_nonan = cubeCO.with_fill_value(0)
# do the stack -- making sure the units work out right.
stack['CO'], labelvals = BinByLabel(cubeCO,
binmap.value,
velocity,
weight_map=None,
return_weights=True)
if cubeHCN:
## fill in nans with 0 to avoid fft shift issue with nans
#cubeHCN_nonan = cubeHCN.with_fill_value(0)
# do the stack -- making sure the units work out right.
stack['HCN'], labelvals = BinByLabel(cubeHCN,
binmap.value,
velocity,
weight_map=None,
return_weights=True)
if cubeHCOp:
#cubeHCOp_nonan = cubeHCOp.with_fill_value(0)
# do the stack -- making sure the units work out right.
stack['HCOp'], labelvals = BinByLabel(cubeHCOp,
binmap.value,
velocity,
weight_map=None,
return_weights=True)
if cube13CO:
#cube13CO_nonan = cube13CO.with_fill_value(0)
# do the stack -- making sure the units work out right.
stack['13CO'], labelvals = BinByLabel(cube13CO,
binmap.value,
velocity,
weight_map=None,
return_weights=True)
if cubeC18O:
#cubeC18O_nonan = cubeC18O.with_fill_value(0)
# do the stack -- making sure the units work out right.
stack['C18O'], labelvals = BinByLabel(cubeC18O,
binmap.value,
velocity,
weight_map=None,
return_weights=True)
# putting the table together
# -------------------------
# first add bins
t = {
'bin_lower': binedge[0:-1],
'bin_upper': binedge[1:],
'bin_mean': (binedge[0:-1] + binedge[1:]) / 2.0
}
total_stack = QTable(t)
# Then set up the structures for the bin-based profiles, etc.
spectral_profile = {}
stack_weights = {}
for line in ['CO', 'HCN', 'HCOp', '13CO', 'C18O']:
spectral_profile[line] = np.zeros(
(len(labelvals), len(stack['CO'][0]['spectral_axis'])))
stack_weights[line] = np.zeros((len(labelvals)))
bin_label = np.zeros(len(labelvals))
bin_area = np.zeros(len(labelvals)) * pix_area.unit
sfr_mean = np.zeros(len(labelvals)) * sfrmap.unit
ltir_mean = np.zeros(len(labelvals)) * ltirmap.unit
spectral_axis = np.zeros(
(len(labelvals), len(stack['CO'][0]['spectral_axis'])
)) * stack['CO'][0]['spectral_axis'].unit
for i in range(len(labelvals)):
spectral_axis[i, :] = stack['CO'][i]['spectral_axis']
bin_label[i] = stack['CO'][i]['label']
## TODO CHECK THE CALCULATION BELOW FOR BINAREA
bin_area[i] = float(sum(
binmap[binmap == bin_label[i]].flatten())) * pix_area
# calculating the mean SFR as requested
if sfrmap is not None:
sfr_mean[i] = np.nanmean(sfrmap[binmap == bin_label[i]])
# calculate the mean LTIR as request
if ltirmap is not None:
ltir_mean[i] = np.nanmean(ltirmap[binmap == bin_label[i]])
# get the spectral profiles
for line in ['CO', 'HCN', 'HCOp', '13CO', 'C18O']:
if line in stack.keys():
spectral_profile[line][i, :] = stack[line][i]['spectrum']
stack_weights[line][i] = stack[line][i]['weights']
else:
spectral_profile[line][i, :] = np.full(
len(stack['CO'][0]['spectral_axis']), np.nan)
stack_weights[line][i] = np.nan
# add above items to the table
total_stack.add_column(Column(spectral_axis), name='spectral_axis')
for line in ['CO', 'HCN', 'HCOp', '13CO', 'C18O']:
total_stack.add_column(
Column(spectral_profile[line],
name='stack_profile_' + line,
unit=cubeCO.unit))
total_stack.add_column(
Column(stack_weights[line], name='stack_weights_' + line))
# TODO CHECK UNITS HERE
total_stack.add_column(Column(bin_area, name='bin_area'))
total_stack.add_column(Column(
sfr_mean, name='sfr_mean')) # Msun/yr/kpc^2 -- units from input image
total_stack.add_column(Column(sfr_mean * bin_area),
name='sfr_total') # Msun/yr/kpc^2 * kpc^2 = Msun/Yr
total_stack.add_column(
Column(ltir_mean),
name='ltir_mean') # Lsun/pc^2 -- units from input image
total_stack.add_column(
Column(ltir_mean * 1000.0**2 * bin_area),
name='ltir_total') # Lsun/pc^2 * (1000 pc/kpc)^2 * kpc^2 = Lsun
return total_stack
def nstar(self, image, star_groups):
"""
Fit, as appropriate, a compound or single model to the given
``star_groups``. Groups are fitted sequentially from the
smallest to the biggest. In each iteration, ``image`` is
subtracted by the previous fitted group.
Parameters
----------
image : numpy.ndarray
Background-subtracted image.
star_groups : `~astropy.table.Table`
This table must contain the following columns: ``id``,
``group_id``, ``x_0``, ``y_0``, ``flux_0``. ``x_0`` and
``y_0`` are initial estimates of the centroids and
``flux_0`` is an initial estimate of the flux. Additionally,
columns named as ``<param_name>_0`` are required if any
other parameter in the psf model is free (i.e., the
``fixed`` attribute of that parameter is ``False``).
Returns
-------
result_tab : `~astropy.table.QTable`
Astropy table that contains photometry results.
image : numpy.ndarray
Residual image.
"""
result_tab = QTable()
for param_tab_name in self._pars_to_output.keys():
result_tab.add_column(Column(name=param_tab_name))
unc_tab = QTable()
for param, isfixed in self.psf_model.fixed.items():
if not isfixed:
unc_tab.add_column(Column(name=param + "_unc"))
y, x = np.indices(image.shape)
star_groups = star_groups.group_by('group_id')
for n in range(len(star_groups.groups)):
group_psf = get_grouped_psf_model(self.psf_model,
star_groups.groups[n],
self._pars_to_set)
usepixel = np.zeros_like(image, dtype=bool)
for row in star_groups.groups[n]:
usepixel[overlap_slices(large_array_shape=image.shape,
small_array_shape=self.fitshape,
position=(row['y_0'], row['x_0']),
mode='trim')[0]] = True
fit_model = self.fitter(group_psf, x[usepixel], y[usepixel],
image[usepixel])
param_table = self._model_params2table(fit_model,
star_groups.groups[n])
result_tab = vstack([result_tab, param_table])
param_cov = self.fitter.fit_info.get('param_cov', None)
if param_cov is not None:
unc_tab = vstack([
unc_tab,
self._get_uncertainties(len(star_groups.groups[n]))
])
# do not subtract if the fitting did not go well
try:
image = subtract_psf(image,
self.psf_model,
param_table,
subshape=self.fitshape)
except NoOverlapError:
pass
if param_cov is not None:
result_tab = hstack([result_tab, unc_tab])
return result_tab, image
def apply(self, data, name, unit=None):
"""Apply an arbitrarily shaped sequence as additional column to a
`~sbpy.data.DataClass` object and reshape it accordingly.
Parameters
----------
data : list or iterable `~astropy.units.Quantity` object
Data to be added in a new column in form of a one-dimensional
list or a two-dimensional nested sequence. Each element in
``data``
corresponds to one of the rows in the existing data table. If
an element
of ``data`` is a list, the corresponding data table row is
repeated the same the number of times as there are elements in
this sublist. If ``data`` is
provided as a flat list and has the same length as the current
data table, ``data`` will be simply added as a column to the data
table and the length of the data table will not change. If
``data`` is provided as a `~astropy.units.Quantity` object (only
possible for flat lists), its
unit is adopted, unless ``unit`` is specified (not None).
name : str
Name of the new data column.
unit : `~astropy.units` object or str, optional
Unit to be applied to the new column. Default:
`None`
Returns
-------
None
Note
----
As a result of this method, the length of the underlying data table
will be the same as the length of the flattened `data` parameter.
Examples
--------
Imagine the following scenario: you obtain photometric measurements
of the same asteroid over a number of nights. The following
`~sbpy.data.Ephem` object summarizes the observations:
>>> from sbpy.data import Ephem
>>> import astropy.units as u
>>> obs = Ephem.from_columns([[2451223, 2451224, 2451226]*u.d,
... [120.1, 121.3, 124.9]*u.deg,
... [12.4, 12.2, 10.8]*u.deg],
... names=('JD', 'RA', 'DEC'))
>>> obs
<QTable length=3>
JD RA DEC
d deg deg
float64 float64 float64
--------- ------- -------
2451223.0 120.1 12.4
2451224.0 121.3 12.2
2451226.0 124.9 10.8
After analyzing the observations, you would like to add the
measured apparent V-band magnitudes to this object. You have
one observation from the first night, two from the second night,
and three from the third night. Instead of re-creating ``obs``,
`~sbpy.data.DataClass.apply` offers a convenient way to
supplement ``obs``:
>>> obs.apply([[12.1], [12.5, 12.6], [13.5, 13.4, 13.5]],
... name='V', unit='mag')
>>> obs
<QTable length=6>
JD RA DEC V
d deg deg mag
float64 float64 float64 float64
--------- ------- ------- -------
2451223.0 120.1 12.4 12.1
2451224.0 121.3 12.2 12.5
2451224.0 121.3 12.2 12.6
2451226.0 124.9 10.8 13.5
2451226.0 124.9 10.8 13.4
2451226.0 124.9 10.8 13.5
Note how the data table has been re-arranged and rows have been
duplicated in order to provide the expected shape.
"""
_newtable = None
# strip units off Quantity objects
if isinstance(data, u.Quantity):
unit = data.unit
data = data.value
if len(data) != len(self.table):
raise DataClassError('Data parameter must have '
'same length as self._table')
_newcolumn = array([])
for i, val in enumerate(data):
if not isinstance(val, (list, tuple, ndarray)):
val = [val]
_newcolumn = hstack([_newcolumn, val])
# add corresponding row from _table for each element in val
for j in range(len(val)):
# initialize new QTable object
if _newtable is None:
_newtable = QTable(self.table[0])
continue
_newtable.add_row(self.table[i])
# add new column
_newtable.add_column(Column(_newcolumn, name=name, unit=unit))
self._table = _newtable
class DataClass():
"""`~sbpy.data.DataClass` serves as the base class for all data
container classes in `sbpy` in order to provide consistent
functionality throughout all these classes.
The core of `~sbpy.data.DataClass` is an `~astropy.table.QTable`
object (referred to as the `data table` below) - a type of
`~astropy.table.Table` object that supports the `~astropy.units`
formalism on a per-column base - which already provides most of
the required functionality. `~sbpy.data.DataClass` objects can be
manually generated from dictionaries
(`~sbpy.data.DataClass.from_dict`), `~numpy.array`-like
(`~sbpy.data.DataClass.from_array`) objects, or directly from
another `~astropy.table.QTable` object.
A few high-level functions for table data access or modification
are provided; other, more complex modifications can be applied to
the underlying table object (`~sbpy.data.DataClass.table`) directly.
"""
def __init__(self, data):
self._table = QTable()
# self.altkeys = {} # dictionary for alternative column names
if (len(data.items()) == 1 and 'table' in data.keys()):
# single item provided named 'table' -> already Table object
self._table = QTable(data['table'])
else:
# treat kwargs as dictionary
for key, val in data.items():
try:
unit = val.unit
val = val.value
except AttributeError:
unit = None
# check if val is already list-like
try:
val[0]
except (TypeError, IndexError):
val = [val]
self._table[key] = Column(val, unit=unit)
@classmethod
def from_dict(cls, data):
"""Create `~sbpy.data.DataClass` object from dictionary or list of
dictionaries.
Parameters
----------
data : `~collections.OrderedDict`, dictionary or list (or similar) of
dictionaries Data that will be ingested in
`~sbpy.data.DataClass` object. Each dictionary creates a
row in the data table. Dictionary keys are used as column
names; corresponding values must be scalar (cannot be
lists or arrays). If a list of dictionaries is provided,
all dictionaries have to provide the same set of keys
(and units, if used at all).
Returns
-------
`DataClass` object
Examples
--------
>>> import astropy.units as u
>>> from sbpy.data import Orbit
>>> orb = Orbit.from_dict({'a': 2.7674*u.au,
... 'e': 0.0756,
... 'i': 10.59321*u.deg})
Since dictionaries have no specific order, the ordering of the
column in the example above is not defined. If your data table
requires a specific order, use an ``OrderedDict``:
>>> from collections import OrderedDict
>>> orb = Orbit.from_dict(OrderedDict([('a', 2.7674*u.au),
... ('e', 0.0756),
... ('i', 10.59321*u.deg)]))
>>> print(orb)
<QTable length=1>
a e i
AU deg
float64 float64 float64
------- ------- --------
2.7674 0.0756 10.59321
>>> print(orb.column_names) # doctest: +SKIP
<TableColumns names=('a','e','i')>
>>> print(orb.table['a', 'e', 'i'])
a e i
AU deg
------ ------ --------
2.7674 0.0756 10.59321
"""
if isinstance(data, (dict, OrderedDict)):
return cls(data)
elif isinstance(data, (list, ndarray, tuple)):
# build table from first dict and append remaining rows
tab = cls(data[0])
for row in data[1:]:
tab.add_rows(row)
return tab
else:
raise TypeError('this function requires a dictionary or a '
'list of dictionaries')
@classmethod
def from_array(cls, data, names):
"""Create `~sbpy.data.DataClass` object from list, `~numpy.ndarray`,
or tuple.
Parameters
----------
data : list, `~numpy.ndarray`, or tuple
Data that will be ingested in `DataClass` object. A one
dimensional sequence will be interpreted as a single row. Each
element that is itself a sequence will be interpreted as a
column.
names : list
Column names, must have the same number of names as data columns.
Returns
-------
`DataClass` object
Examples
--------
>>> from sbpy.data import DataClass
>>> import astropy.units as u
>>> dat = DataClass.from_array([[1, 2, 3]*u.deg,
... [4, 5, 6]*u.km,
... ['a', 'b', 'c']],
... names=('a', 'b', 'c'))
>>> print(dat.table)
a b c
deg km
--- --- ---
1.0 4.0 a
2.0 5.0 b
3.0 6.0 c
"""
if isinstance(data, (list, ndarray, tuple)):
return cls.from_dict(OrderedDict(zip(names, data)))
else:
raise TypeError('this function requires a list, tuple or a '
'numpy array')
@classmethod
def from_table(cls, data):
"""Create `DataClass` object from `~astropy.table.Table` or
`astropy.table.QTable` object.
Parameters
----------
data : astropy `Table` object, mandatory
Data that will be ingested in `DataClass` object.
Returns
-------
`DataClass` object
Examples
--------
>>> from astropy.table import QTable
>>> import astropy.units as u
>>> from sbpy.data import DataClass
>>> tab = QTable([[1,2,3]*u.kg,
... [4,5,6]*u.m/u.s,],
... names=['mass', 'velocity'])
>>> dat = DataClass.from_table(tab)
>>> print(dat.table)
mass velocity
kg m / s
---- --------
1.0 4.0
2.0 5.0
3.0 6.0
"""
return cls({'table': data})
@classmethod
def from_file(cls, filename, **kwargs):
"""Create `DataClass` object from a file using
`~astropy.table.Table.read`.
Parameters
----------
filename : str
Name of the file that will be read and parsed.
**kwargs : additional parameters
Optional parameters that will be passed on to
`~astropy.table.Table.read`.
Returns
-------
`DataClass` object
Notes
-----
This function is merely a wrapper around
`~astropy.table.Table.read`. Please refer to the documentation of
that function for additional information on optional parameters
and data formats that are available. Furthermore, note that this
function is not able to identify units. If you want to work with
`~astropy.units` you have to assign them manually to the object
columns.
Examples
--------
>>> from sbpy.data import DataClass
>>> dat = DataClass.from_file('data.txt',
... format='ascii') # doctest: +SKIP
"""
data = QTable.read(filename, **kwargs)
return cls({'table': data})
def to_file(self, filename, format='ascii', **kwargs):
"""Write object to a file using
`~astropy.table.Table.write`.
Parameters
----------
filename : str
Name of the file that will be written.
format : str, optional
Data format in which the file should be written. Default:
``ASCII``
**kwargs : additional parameters
Optional parameters that will be passed on to
`~astropy.table.Table.write`.
Returns
-------
None
Notes
-----
This function is merely a wrapper around
`~astropy.table.Table.write`. Please refer to the
documentation of that function for additional information on
optional parameters and data formats that are
available. Furthermore, note that this function is not able to
write unit information to the file.
Examples
--------
>>> from sbpy.data import DataClass
>>> import astropy.units as u
>>> dat = DataClass.from_array([[1, 2, 3]*u.deg,
... [4, 5, 6]*u.km,
... ['a', 'b', 'c']],
... names=('a', 'b', 'c'))
>>> dat.to_file('test.txt')
"""
self._table.write(filename, format=format, **kwargs)
def __len__(self):
"""Get number of data elements in _table"""
return len(self._table)
def __getattr__(self, field):
"""Get attribute from ``self._table` (columns, rows); checks
for and may use alternative field names."""
if field in dir(self):
return self.field
else:
try:
field = self._translate_columns(field)[0]
return self._table[field]
except (KeyError, IndexError, AttributeError):
raise AttributeError('Attribute {:s} not available.'.format(
field))
def __repr__(self):
"""Return representation of the underlying data table
(``self._table.__repr__()``)"""
return self._table.__repr__()
def __getitem__(self, ident):
"""Return columns or rows from data table (``self._table``); checks
for and may use alternative field names."""
# iterable
if isinstance(ident, (list, tuple, ndarray)):
if all([isinstance(i, str) for i in ident]):
# list of column names
self = self._convert_columns(ident)
newkeylist = [self._translate_columns(i)[0] for i in ident]
ident = newkeylist
# return as new DataClass object
return self.from_table(self._table[ident])
# ignore lists of boolean (masks)
elif all([isinstance(i, bool) for i in ident]):
pass
# ignore lists of integers
elif all([isinstance(i, int) for i in ident]):
pass
# individual strings
elif isinstance(ident, str):
self = self._convert_columns(ident)
ident = self._translate_columns(ident)[0]
# return as element from self_table
return self._table[ident]
def __setitem__(self, *args):
"""Refer cls.__setitem__ to self._table"""
self._table.__setitem__(*args)
def _translate_columns(self, target_colnames):
"""Translate target_colnames to the corresponding column names
present in this object's table. Returns a list of actual column
names present in this object that corresponds to target_colnames
(order is preserved). Raises KeyError if not all columns are
present or one or more columns could not be translated.
"""
if not isinstance(target_colnames, (list, ndarray, tuple)):
target_colnames = [target_colnames]
translated_colnames = deepcopy(target_colnames)
for idx, colname in enumerate(target_colnames):
# colname is already a column name in self.table
if colname in self.column_names:
continue
# colname is an alternative column name
elif colname in sum(conf.fieldnames, []):
for alt in conf.fieldnames[conf.fieldname_idx[colname]]:
# translation available for colname
if alt in self.column_names:
translated_colnames[idx] = alt
break
# colname is unknown, raise a KeyError
else:
raise KeyError('field {:s} not available.'.format(
colname))
return translated_colnames
def _convert_columns(self, target_colnames):
"""Convert target_colnames, if necessary. Converted columns will be
added as columns to ``self`` using the field names provided in
target_colnames. No error is returned by this function if a
field could not be converted.
"""
if not isinstance(target_colnames, (list, ndarray, tuple)):
target_colnames = [target_colnames]
for colname in target_colnames:
# ignore, if colname is unknown (KeyError)
try:
# ignore if colname has already been converted
if any([alt in self.column_names for alt
in conf.fieldnames[conf.fieldname_idx[colname]]]):
continue
# consider alternative names for colname -> alt
for alt in conf.fieldnames[conf.fieldname_idx[colname]]:
if alt in list(conf.field_eq.keys()):
# conversion identified
convname = self._translate_columns(
list(conf.field_eq[alt].keys())[0])[0]
convfunc = list(conf.field_eq[alt].values())[0]
if convname in self.column_names:
# create new column for the converted field
self.add_column(convfunc(self.table[convname]),
colname)
break
except KeyError:
continue
return self
@property
def table(self):
"""Return `~astropy.table.QTable` object containing all data."""
return self._table
@property
def column_names(self):
"""Return a list of all column names in the data table."""
return self._table.columns
def add_rows(self, rows, join_type='inner'):
"""Append additional rows to the existing data table. An individual
row can be provided in list, tuple, `~numpy.ndarray`, or
dictionary form. Multiple rows can be provided in the form of
a list, tuple, or `~numpy.ndarray` of individual
rows. Multiple rows can also be provided in the form of a
`~astropy.table.QTable` or another `~sbpy.data.DataClass`
object. Parameter ``join_type`` defines which columns appear
in the final output table: ``inner`` only keeps those columns
that appear in both the original table and the rows to be
added; ``outer`` will keep all columns and populate some with
placeholders, if necessary. In case of a list, the list
elements must be in the same order as the table columns. In
either case, matching `~astropy.units` must be provided in
``rows`` if used in the data table.
Parameters
----------
rows : list, tuple, `~numpy.ndarray`, dict, or `~collections.OrderedDict`
Data to be appended to the table; required to have the same
length as the existing table, as well as the same units.
join_type : str, optional
Defines which columns are kept in the output table: ``inner``
only keeps those columns that appear in both the original
table and the rows to be added; ``outer`` will keep all
columns and populate them with placeholders, if necessary.
Default: ``inner``
Returns
-------
n : int, the total number of rows in the data table
Examples
--------
>>> from sbpy.data import DataClass
>>> import astropy.units as u
>>> dat = DataClass.from_array([[1, 2, 3]*u.Unit('m'),
... [4, 5, 6]*u.m/u.s,
... ['a', 'b', 'c']],
... names=('a', 'b', 'c'))
>>> dat.add_rows({'a': 5*u.m, 'b': 8*u.m/u.s, 'c': 'e'})
4
>>> print(dat.table)
a b c
m m / s
--- ----- ---
1.0 4.0 a
2.0 5.0 b
3.0 6.0 c
5.0 8.0 e
>>> dat.add_rows(([6*u.m, 9*u.m/u.s, 'f'],
... [7*u.m, 10*u.m/u.s, 'g']))
6
>>> dat.add_rows(dat)
12
"""
if isinstance(rows, QTable):
self._table = vstack([self._table, rows], join_type=join_type)
if isinstance(rows, DataClass):
self._table = vstack([self._table, rows.table],
join_type=join_type)
if isinstance(rows, (dict, OrderedDict)):
try:
newrow = [rows[colname] for colname in self._table.columns]
except KeyError as e:
raise ValueError('data for column {0} missing in row {1}'.
format(e, rows))
self.add_rows(newrow)
if isinstance(rows, (list, ndarray, tuple)):
if (not isinstance(rows[0], (u.quantity.Quantity, float)) and
isinstance(rows[0], (dict, OrderedDict,
list, ndarray, tuple))):
for subrow in rows:
self.add_rows(subrow)
else:
self._table.add_row(rows)
return len(self._table)
def add_column(self, data, name, **kwargs):
"""Append a single column to the current data table. The lenght of
the input list, `~numpy.ndarray`, or tuple must match the current
number of rows in the data table.
Parameters
----------
data : list, `~numpy.ndarray`, or tuple
Data to be filled into the table; required to have the same
length as the existing table's number rows.
name : str
Name of the new column; must be different from already existing
column names.
**kwargs : additional parameters
Additional optional parameters will be passed on to
`~astropy.table.Table.add_column`.
Returns
-------
n : int, the total number of columns in the data table
Examples
--------
>>> from sbpy.data import DataClass
>>> import astropy.units as u
>>> dat = DataClass.from_array([[1, 2, 3]*u.Unit('m'),
... [4, 5, 6]*u.m/u.s,
... ['a', 'b', 'c']],
... names=('a', 'b', 'c'))
>>> dat.add_column([10, 20, 30]*u.kg, name='d')
4
>>> print(dat.table)
a b c d
m m / s kg
--- ----- --- ----
1.0 4.0 a 10.0
2.0 5.0 b 20.0
3.0 6.0 c 30.0
"""
self._table.add_column(Column(data, name=name), **kwargs)
return len(self.column_names)
def _do_photometry(self, n_start=1):
"""
Helper function which performs the iterations of the photometry
process.
Parameters
----------
n_start : int
Integer representing the start index of the iteration. It
is 1 if init_guesses are None, and 2 otherwise.
Returns
-------
output_table : `~astropy.table.Table` or None
Table with the photometry results, i.e., centroids and
fluxes estimations and the initial estimates used to start
the fitting process.
"""
output_table = QTable()
self._define_fit_param_names()
for (init_parname, fit_parname) in zip(self._pars_to_set.keys(),
self._pars_to_output.keys()):
output_table.add_column(Column(name=init_parname))
output_table.add_column(Column(name=fit_parname))
sources = self.finder(self._residual_image)
n = n_start
while ((sources is not None and len(sources) > 0)
and (self.niters is None or n <= self.niters)):
positions = np.transpose(
(sources['xcentroid'], sources['ycentroid']))
apertures = CircularAperture(positions, r=self.aperture_radius)
sources['aperture_flux'] = aperture_photometry(
self._residual_image, apertures)['aperture_sum']
init_guess_tab = QTable(names=['id', 'x_0', 'y_0', 'flux_0'],
data=[
sources['id'], sources['xcentroid'],
sources['ycentroid'],
sources['aperture_flux']
])
self._get_additional_columns(sources, init_guess_tab)
for param_tab_name, param_name in self._pars_to_set.items():
if param_tab_name not in (['x_0', 'y_0', 'flux_0']):
init_guess_tab.add_column(
Column(name=param_tab_name,
data=(getattr(self.psf_model, param_name) *
np.ones(len(sources)))))
star_groups = self.group_maker(init_guess_tab)
table, self._residual_image = super().nstar(
self._residual_image, star_groups)
star_groups = star_groups.group_by('group_id')
table = hstack([star_groups, table])
table['iter_detected'] = n * np.ones(table['x_fit'].shape,
dtype=int)
output_table = vstack([output_table, table])
# do not warn if no sources are found beyond the first iteration
with warnings.catch_warnings():
warnings.simplefilter('ignore', NoDetectionsWarning)
sources = self.finder(self._residual_image)
n += 1
return output_table
def from_mpc(cls,
targetids,
epochs=None,
location='500',
ra_format=None,
dec_format=None,
**kwargs):
"""Load ephemerides from the
`Minor Planet Center <https://minorplanetcenter.net>`_.
Parameters
----------
targetids : str or iterable of str
Target identifier, resolvable by the Minor Planet
Ephemeris Service [MPES]_, e.g., 2P, C/1995 O1, P/Encke,
(1), 3200, Ceres, and packed designations, for one or more
targets.
epochs : `~astropy.time.Time` object, or dictionary, optional
Request ephemerides at these epochs. May be a single
epoch or multiple epochs as `~astropy.time.Time`
(see :ref:`epochs`)or a
dictionary describing a linearly-spaced array
of epochs. All epochs should be provided in UTC; if not,
they will be converted to UTC and a
`~sbpy.data.TimeScaleWarning` will be raised.
If ``None`` (default), the current date and
time will be used.
For the dictionary format, the keys ``start`` (start
epoch), ``step`` (step size), ``stop`` (end epoch), and/or
``number`` (number of epochs total) are used. Only one of
``stop`` and ``number`` may be specified at a time.
``step``, ``stop``, and ``number`` are optional. The values of
of ``start`` and ``stop`` must be `~astropy.time.Time` objects.
``number`` should be an integer value; ``step`` should be a
`~astropy.units.Quantity` with an integer value and units of
seconds, minutes, hours, or days.
All epochs should be provided in UTC; if not, they will be
converted to UTC and a `~sbpy.data.TimeScaleWarning` will be
raised.
location : various, optional
Location of the observer as an IAU observatory code
[OBSCODES]_ (string), a 3-element array of Earth
longitude, latitude, altitude, or an
`~astropy.coordinates.EarthLocation`. Longitude and
latitude should be parseable by
`~astropy.coordinates.Angle`, and altitude should be
parsable by `~astropy.units.Quantity` (with units of
length). If ``None``, then the geocenter (code 500) is
used.
ra_format : dict, optional
Format the RA column with
`~astropy.coordinates.Angle.to_string` using these keyword
arguments, e.g.,
``{'sep': ':', 'unit': 'hourangle', 'precision': 1}``.
dec_format : dict, optional
Format the Dec column with
`~astropy.coordinates.Angle.to_string` using these keyword
arguments, e.g., ``{'sep': ':', 'precision': 0}``.
**kwargs
Additional keyword arguments are passed to
`~astroquery.mpc.MPC.get_ephemerides`: ``eph_type``,
``proper_motion``, ``proper_motion_unit``, ``suppress_daytime``,
``suppress_set``, ``perturbed``, ``unc_links``, ``cache``.
Returns
-------
`~Ephem` object
The resulting object will be populated with columns as
defined in
`~astroquery.mpc.get_ephemerides`; refer
to that document on information on how to modify the list
of queried parameters.
Examples
--------
Query a single set of ephemerides of Ceres as observed from
Maunakea:
>>> from sbpy.data import Ephem
>>> from astropy.time import Time
>>> epoch = Time('2018-05-14', scale='utc')
>>> eph = Ephem.from_mpc('ceres', epoch, 568) # doctest: +REMOTE_DATA
Query a range of ephemerides of comet 2P/Encke as observed from
Maunakea:
>>> epochs = {'start': Time('2019-01-01'),
... 'step': 1*u.d, 'number': 365}
>>> eph = Ephem.from_mpc('2P', epochs, 568) # doctest: +REMOTE_DATA
Notes
-----
* All properties are provided in the J2000.0 reference system.
* See `astroquery.mpc.MPC.get_ephemerides` and the Minor
Planet Ephemeris Service user's guide [MPES]_ for details,
including acceptable target names.
References
----------
.. [MPES] Wiliams, G. The Minor Planet Ephemeris Service.
https://minorplanetcenter.net/iau/info/MPES.pdf
.. [OBSCODES] IAU Minor Planet Center. List of observatory
codes. https://minorplanetcenter.net/iau/lists/ObsCodesF.html
"""
# parameter check
# if targetids is a list, run separate Horizons queries and append
if not isinstance(targetids, (list, ndarray, tuple)):
targetids = [targetids]
_epochs = None # avoid modifying epochs in-place
start = None
if epochs is None:
_epochs = Time([Time.now()])
elif isinstance(epochs, Time):
if not iterable(epochs):
_epochs = Time([epochs])
else:
_epochs = epochs
if _epochs.scale != 'utc':
warn(('converting {} epochs to utc for use in '
'astroquery.mpc').format(_epochs.scale),
TimeScaleWarning)
_epochs = _epochs.utc
elif isinstance(epochs, dict):
_epochs = epochs.copy()
start = _epochs['start'] # required
if start.scale != 'utc':
warn(('converting {} start epoch to utc for use in '
'astroquery.mpc').format(start.scale), TimeScaleWarning)
start = start.utc
step = _epochs.get('step')
stop = _epochs.get('stop')
if stop is not None and stop.scale != 'utc':
warn(('converting {} stop epoch to utc for use in '
'astroquery.mpc').format(stop.scale), TimeScaleWarning)
stop = stop.utc
number = _epochs.get('number')
if step is not None and stop is None:
step = u.Quantity(step)
if step.unit not in (u.d, u.h, u.min, u.s):
raise QueryError(
'step must have units of days, hours, minutes,'
' or seconds')
if stop is not None:
if step is not None and number is None:
# start and stop both defined, estimate number of steps
dt = (Time(stop).jd - Time(start).jd) * u.d
number = int((dt / step).decompose()) + 1
elif step is None and number is not None:
step = int(
(stop - start).jd * 1440 / (number - 1)) * u.minute
else:
raise QueryError(
('epoch definition unclear; step xor number '
'must be provided with start and stop'))
else:
raise ValueError('Invalid `epochs` parameter')
# append ephemerides table for each targetid
all_eph = None
for targetid in targetids:
try:
# get ephemeris
if start is None:
eph = []
for i in range(len(_epochs)):
e = MPC.get_ephemeris(targetid,
location=location,
start=Time(_epochs[i],
scale='utc'),
number=1,
**kwargs)
e['Date'] = e['Date'].iso # for vstack to work
eph.append(e)
eph = QTable(vstack(eph))
eph['Date'] = Time(eph['Date'], scale='utc')
else:
eph = MPC.get_ephemeris(targetid,
location=location,
start=start,
step=step,
number=number,
**kwargs)
except InvalidQueryError as e:
raise QueryError('Error raised by astroquery.mpc: {:s}'.format(
str(e)))
# add targetname column
eph.add_column(Column([targetid] * len(eph), name='Targetname'),
index=0)
if all_eph is None:
all_eph = eph
else:
all_eph = vstack([all_eph, eph])
all_eph = QTable(all_eph)
# convert RA and Dec to Angle
all_eph['RA'] = Angle(all_eph['RA'], all_eph['RA'].unit)
all_eph['Dec'] = Angle(all_eph['Dec'], all_eph['Dec'].unit)
if ra_format is not None:
all_eph['RA'].info.format = lambda x: x.to_string(**ra_format)
if dec_format is not None:
all_eph['Dec'].info.format = lambda x: x.to_string(**dec_format)
return cls.from_table(all_eph)
def mk_summary(dlas, prefix, outfil, specpath=None, htmlfil=None):
""" Loops through the DLA list and generates a Table
Also pushes the 1D spectra into the folder
Parameters
----------
dlas : DLASurvey
prefix : str
outfil : str
Name of the output FITS summary file
htmlfil : str, optional
Returns
-------
"""
#
if htmlfil is None:
htmlfil = 'tmp.html'
# # Constructing
# QSO, RA/DEC
cqso = Column(dlas.qso, name='QSO')
ra = dlas.coord.ra.degree
dec = dlas.coord.dec.degree
jname = []
for abs_sys in dlas._abs_sys:
jname.append(survey_name(prefix, abs_sys))
cjname = Column(jname, name='Name')
cra = Column(ra, name='RA', unit=u.degree)
cdec = Column(dec, name='DEC', unit=u.degree)
czem = Column(dlas.zem, name='Z_QSO')
# Begin the Table
dla_table = QTable([cjname, cqso, cra, cdec, czem])
# LLS properties
czabs = Column(dlas.zabs, name='ZABS')
cNHI = Column(dlas.NHI, name='logNHI')
csigNHI = Column(dlas.sig_NHI, name='sig(logNHI)')
# Add to Table
dla_table.add_columns([czabs, cNHI, csigNHI])
# Spectra files
all_sfiles = []
for jj, ills in enumerate(dlas._abs_sys):
sub_spec = mk_1dspec(ills, name=cjname[jj], outpath=specpath)
# Pad
while len(sub_spec) < 5:
sub_spec.append(str('NULL'))
# Append
all_sfiles.append(sub_spec)
cspec = Column(np.array(all_sfiles), name='SPEC_FILES')
dla_table.add_column(cspec)
# Sort
dla_table.sort('RA')
# Write
print('Writing {:s}'.format(outfil))
xxf.table_to_fits(dla_table, outfil)
print('Writing {:s}'.format(htmlfil))
Table(dla_table).write(htmlfil)
return dla_table
def group_table(self, edges):
"""Compute bin groups table for the map axis, given coarser bin edges.
Parameters
----------
edges : `~astropy.units.Quantity`
Group bin edges.
Returns
-------
groups : `~astropy.table.Table`
Map axis group table.
"""
# TODO: try to simplify this code
if not self.node_type == "edges":
raise ValueError("Only edge based map axis can be grouped")
edges_pix = self.coord_to_pix(edges)
edges_pix = np.clip(edges_pix, -0.5, self.nbin - 0.5)
edges_idx = np.round(edges_pix + 0.5) - 0.5
edges_idx = np.unique(edges_idx)
edges_ref = self.pix_to_coord(edges_idx)
groups = QTable()
groups[f"{self.name}_min"] = edges_ref[:-1]
groups[f"{self.name}_max"] = edges_ref[1:]
groups["idx_min"] = (edges_idx[:-1] + 0.5).astype(int)
groups["idx_max"] = (edges_idx[1:] - 0.5).astype(int)
if len(groups) == 0:
raise ValueError("No overlap between reference and target edges.")
groups["bin_type"] = "normal "
edge_idx_start, edge_ref_start = edges_idx[0], edges_ref[0]
if edge_idx_start > 0:
underflow = {
"bin_type": "underflow",
"idx_min": 0,
"idx_max": edge_idx_start,
f"{self.name}_min": self.pix_to_coord(-0.5),
f"{self.name}_max": edge_ref_start,
}
groups.insert_row(0, vals=underflow)
edge_idx_end, edge_ref_end = edges_idx[-1], edges_ref[-1]
if edge_idx_end < (self.nbin - 0.5):
overflow = {
"bin_type": "overflow",
"idx_min": edge_idx_end + 1,
"idx_max": self.nbin - 1,
f"{self.name}_min": edge_ref_end,
f"{self.name}_max": self.pix_to_coord(self.nbin - 0.5),
}
groups.add_row(vals=overflow)
group_idx = Column(np.arange(len(groups)))
groups.add_column(group_idx, name="group_idx", index=0)
return groups
def initialize_galaxy(Nstep):
galaxy = QTable()
dummy = np.zeros(Nstep)
col_dummy = Column(name='age',data=dummy,unit=u.yr)
galaxy.add_column(col_dummy)
col_dummy = Column(name='Ms',data=dummy,unit=u.Msun)
galaxy.add_column(col_dummy)
col_dummy = Column(name='Mg',data=dummy,unit=u.Msun)
galaxy.add_column(col_dummy)
col_dummy = Column(name='Mh',data=dummy,unit=u.Msun)
galaxy.add_column(col_dummy)
col_dummy = Column(name='Mcgm',data=dummy,unit=u.Msun)
galaxy.add_column(col_dummy)
col_dummy = Column(name='dMrdt',data=dummy,unit=u.Msun/u.yr)
galaxy.add_column(col_dummy)
col_dummy = Column(name='sfr',data=dummy,unit=u.Msun/u.yr)
galaxy.add_column(col_dummy)
col_dummy = Column(name='tlogoh',data=dummy,unit=u.m/u.m)
galaxy.add_column(col_dummy)
col_dummy = Column(name='lookback',data=dummy,unit=u.yr)
galaxy.add_column(col_dummy)
col_dummy = Column(name='dt',data=dummy,unit=u.yr)
galaxy.add_column(col_dummy)
return galaxy
nicetable26 = np.vstack((np.round(table26, decimals=2)))
name = Table(nicetable26,
names=('Pixels', 'Speckles', 'Percent', 'Avg Intensity'))
name.pprint_all()
nicetable = np.vstack((np.round(table38, decimals=2)))
name = Table(nicetable,
names=('Pixels', 'Speckles', 'Percent', 'Avg Intensity'))
name.pprint_all()
nicetable = np.vstack((np.round(table40, decimals=2)))
name = Table(nicetable,
names=('Pixels', 'Speckles', 'Percent', 'Avg Intensity'))
name.pprint_all()
nicetable = np.vstack((np.round(table44, decimals=2)))
name = Table(nicetable,
names=('Pixels', 'Speckles', 'Percent', 'Avg Intensity'))
name.pprint_all()
bigavg = (table26 + table30 + table38 + table40 + table44) / 5
column_len = bigavg.shape[0]
print('\n\n')
"""plotting the final averages"""
t = QTable(np.round(bigavg, decimals=2),
names=('Pixels', 'Speckles', 'Percent', 'Avg Intensity'))
t.add_column(np.arange(1, 1 + column_len), name='Annulus', index=0)
#print(t)
t.pprint(align='^')
def group_table(self, edges):
"""Compute bin groups table for the map axis, given coarser bin edges.
Parameters
----------
edges : `~astropy.units.Quantity`
Group bin edges.
Returns
-------
groups : `~astropy.table.Table`
Map axis group table.
"""
# TODO: try to simplify this code
if not self.node_type == "edges":
raise ValueError("Only edge based map axis can be grouped")
edges_pix = self.coord_to_pix(edges)
edges_pix = np.clip(edges_pix, -0.5, self.nbin - 0.5)
edges_idx = np.round(edges_pix + 0.5) - 0.5
edges_idx = np.unique(edges_idx)
edges_ref = self.pix_to_coord(edges_idx) * self.unit
groups = QTable()
groups["{}_min".format(self.name)] = edges_ref[:-1]
groups["{}_max".format(self.name)] = edges_ref[1:]
groups["idx_min"] = (edges_idx[:-1] + 0.5).astype(int)
groups["idx_max"] = (edges_idx[1:] - 0.5).astype(int)
if len(groups) == 0:
raise ValueError("No overlap between reference and target edges.")
groups["bin_type"] = "normal "
edge_idx_start, edge_ref_start = edges_idx[0], edges_ref[0]
if edge_idx_start > 0:
underflow = {
"bin_type": "underflow",
"idx_min": 0,
"idx_max": edge_idx_start,
"{}_min".format(self.name): self.pix_to_coord(-0.5) * self.unit,
"{}_max".format(self.name): edge_ref_start,
}
groups.insert_row(0, vals=underflow)
edge_idx_end, edge_ref_end = edges_idx[-1], edges_ref[-1]
if edge_idx_end < (self.nbin - 0.5):
overflow = {
"bin_type": "overflow",
"idx_min": edge_idx_end + 1,
"idx_max": self.nbin - 1,
"{}_min".format(self.name): edge_ref_end,
"{}_max".format(self.name): self.pix_to_coord(self.nbin - 0.5)
* self.unit,
}
groups.add_row(vals=overflow)
group_idx = Column(np.arange(len(groups)))
groups.add_column(group_idx, name="group_idx", index=0)
return groups