def save(self):
""" modified from suvi code by vhsu """
pri_hdu = fits.PrimaryHDU(data=self.thmap)
# Temporal Information
date_fmt = '%Y-%m-%dT%H:%M:%S.%f'
date_beg = self.start_time.strftime(date_fmt)
date_end = self.end_time.strftime(date_fmt)
date_now = datetime.utcnow().strftime(date_fmt)
self.set_fits_header("TIMESYS", self.ref_hdr, pri_hdu)
pri_hdu.header.append(
("DATE-BEG", date_beg, "sun observation start time on sat"))
pri_hdu.header.append(
("DATE-END", date_end, "sun observation end time on sat"))
pri_hdu.header.append(("DATE", date_now, "file generation time"))
pri_hdu.header.append(
("EXPERT", self.config.expert, "person who labeled image"))
pri_hdu.header.append(
("DATE-LAB", date_now, "date of labeling for the image"))
# Instrument & Spacecraft State during Observation
pri_hdu.header.append(
("EXPTIME", 1., "[s] effective imaging exposure time"))
self.set_fits_header("YAW_FLIP", self.ref_hdr, pri_hdu)
self.set_fits_header("ECLIPSE", self.ref_hdr, pri_hdu)
# Pointing & Projection
self.set_fits_header("WCSNAME", self.ref_hdr, pri_hdu)
self.set_fits_header("CTYPE1", self.ref_hdr, pri_hdu)
self.set_fits_header("CTYPE2", self.ref_hdr, pri_hdu)
self.set_fits_header("CUNIT1", self.ref_hdr, pri_hdu)
self.set_fits_header("CUNIT2", self.ref_hdr, pri_hdu)
self.set_fits_header("PC1_1", self.ref_hdr, pri_hdu)
self.set_fits_header("PC1_2", self.ref_hdr, pri_hdu)
self.set_fits_header("PC2_1", self.ref_hdr, pri_hdu)
self.set_fits_header("PC2_2", self.ref_hdr, pri_hdu)
self.set_fits_header("CDELT1", self.ref_hdr, pri_hdu)
self.set_fits_header("CDELT2", self.ref_hdr, pri_hdu)
self.set_fits_header("CRVAL1", self.ref_hdr, pri_hdu)
self.set_fits_header("CRVAL2", self.ref_hdr, pri_hdu)
self.set_fits_header("CRPIX1", self.ref_hdr, pri_hdu)
self.set_fits_header("CRPIX2", self.ref_hdr, pri_hdu)
self.set_fits_header("DIAM_SUN", self.ref_hdr, pri_hdu)
self.set_fits_header("LONPOLE", self.ref_hdr, pri_hdu)
self.set_fits_header("CROTA", self.ref_hdr, pri_hdu)
self.set_fits_header("SOLAR_B0", self.ref_hdr, pri_hdu)
# File Provenance
pri_hdu.header.append(
("TITLE", "Expert Labeled Thematic Map Image", "image title"))
pri_hdu.header.append(
("MAP_MTHD", "human", "thematic map classifier method"))
try:
# Add COMMENT cards
pri_hdu.header.insert(
pri_hdu.header.index("TITLE") + 1,
("COMMENT",
'------------------------------------------------------------------------'
))
pri_hdu.header.insert(
pri_hdu.header.index("TITLE") + 2,
("COMMENT", 'USING SUVI THEMATIC MAP FILES'))
pri_hdu.header.insert(
pri_hdu.header.index("TITLE") + 3,
("COMMENT",
'------------------------------------------------------------------------'
))
pri_hdu.header.insert(
pri_hdu.header.index("TITLE") + 4,
("COMMENT", 'Map labels are described in the FITS extension.'))
pri_hdu.header.insert(
pri_hdu.header.index("TITLE") + 5, ("COMMENT", 'Example:'))
pri_hdu.header.insert(
pri_hdu.header.index("TITLE") + 6,
("COMMENT", 'from astropy.io import fits as pyfits'))
pri_hdu.header.insert(
pri_hdu.header.index("TITLE") + 7,
("COMMENT", 'img = pyfits.open(<filename>)'))
pri_hdu.header.insert(
pri_hdu.header.index("TITLE") + 8,
("COMMENT", 'map_labels = img[1].data'))
pri_hdu.header.insert(
pri_hdu.header.index("TITLE") + 9,
("COMMENT",
'------------------------------------------------------------------------'
))
pri_hdu.header.insert(
pri_hdu.header.index("TITLE") + 10,
("COMMENT", 'TEMPORAL INFORMATION'))
pri_hdu.header.insert(
pri_hdu.header.index("TITLE") + 11,
("COMMENT",
'------------------------------------------------------------------------'
))
pri_hdu.header.insert(
pri_hdu.header.index("DATE") + 1,
("COMMENT",
'------------------------------------------------------------------------'
))
pri_hdu.header.insert(
pri_hdu.header.index("DATE") + 2,
("COMMENT",
'INSTRUMENT & SPACECRAFT STATE DURING OBSERVATION'))
pri_hdu.header.insert(
pri_hdu.header.index("DATE") + 3,
("COMMENT",
'------------------------------------------------------------------------'
))
pri_hdu.header.insert(
pri_hdu.header.index("ECLIPSE") + 1,
("COMMENT",
'------------------------------------------------------------------------'
))
pri_hdu.header.insert(
pri_hdu.header.index("ECLIPSE") + 2,
("COMMENT", 'POINTING & PROJECTION'))
pri_hdu.header.insert(
pri_hdu.header.index("ECLIPSE") + 3,
("COMMENT",
'------------------------------------------------------------------------'
))
pri_hdu.header.insert(
pri_hdu.header.index("SOLAR_B0") + 1,
("COMMENT",
'------------------------------------------------------------------------'
))
pri_hdu.header.insert(
pri_hdu.header.index("SOLAR_B0") + 2,
("COMMENT", 'FILE PROVENANCE'))
pri_hdu.header.insert(
pri_hdu.header.index("SOLAR_B0") + 3,
("COMMENT",
'------------------------------------------------------------------------'
))
except:
print(
"This thematic map may be degraded and missing many keywords.")
# Thematic map feature list (Secondary HDU extension)
map_val = []
map_label = []
for key, value in self.config.solar_class_index.items(
): #sorted(SOLAR_CLASS_INDEX.items(), key=lambda p: (lambda k, v: (v, k))):
map_label.append(key)
map_val.append(value)
c1 = fits.Column(name="Thematic Map Value",
format="B",
array=np.array(map_val))
c2 = fits.Column(name="Feature Name",
format="22A",
array=np.array(map_label))
bintbl_hdr = fits.Header([("XTENSION", "BINTABLE")])
sec_hdu = fits.BinTableHDU.from_columns([c1, c2], header=bintbl_hdr)
# Output thematic map as the primary HDU and the list of map features as an extension BinTable HDU
hdu = fits.HDUList([pri_hdu, sec_hdu])
hdu.writeto(self.filename, overwrite=True, checksum=True)
def _from_data(cls, *, version=None, fits_keywords={}, **columns):
if not hasattr(cls, '_OI_VER'):
if version is None:
version = getattr(cls, '_OI_VER', 2)
cls = cls.get_class(version=version)
# FITS keywords and column names are upper case
if isinstance(fits_keywords, fits.Header):
fits_keywords = {c[0]: c[1:] for c in fits_keywords.cards}
fits_keywords = {
k.upper(): v
for k, v in fits_keywords.items() if v is not None
}
columns = {k.upper(): v for k, v in columns.items()}
# prefix non-standard columns
oi_colnames = cls._get_oi_columns(required=False)['name']
columns = {
n if n in oi_colnames else f"NS_{n}": v
for n, v in columns.items()
}
# Header
header = fits.Header()
for card in cls._CARDS:
name = card['name']
comment = card['comment']
if name in fits_keywords:
value = fits_keywords[name]
if isinstance(value, (list, tuple)):
value = value[0]
header.set(name, value, comment)
del fits_keywords[name]
elif card['required']:
if card['default'] is not None:
header.set(name, card['default'], comment)
for name, value in fits_keywords.items():
if not isinstance(value, (tuple, list)):
value = [value]
header.set(name, *value)
# Guess shape
shape = cls._guess_shape(columns)
nrows = shape[0]
def full(s, x):
if np.ndim(x) > len(s):
return np.asarray(x)
return np.full(s, x)
# Guess errors from data
obs_names = cls.get_observable_names()
err_names = cls.get_error_names()
for obs, err in zip(obs_names, err_names):
if obs in columns:
if err not in columns:
columns[err] = 0.
fcols = []
# official OIFITS columns
for col in cls._get_oi_columns(required=False):
name = col['name']
if name not in columns:
if col['required']:
columns[name] = col['default']
else:
continue
if name in [*obs_names, *err_names, 'FLAG']:
new_shape = shape
else:
new_shape = (nrows, )
array = full(new_shape, columns[name])
del columns[name]
fcol = fu.ascolumn(array,
format=col['format'],
unit=col['unit'],
name=name)
fcols.append(fcol)
# additional columns
for name, array in columns.items():
fcol = fu.ascolumn(array, name=name)
fcols.append(fcol)
tab = super().from_columns(fcols, header=header)
return tab
}
"""
Goal:
For each core in the core photometry catalog, determine the corresponding
brightness in the above images, then put the core CDF on top of the
brightness ("column") PDF.
"""
alma_hdr = fits.Header(
dict(
NAXIS=2,
NAXIS1=450,
NAXIS2=450,
CTYPE1='RA---SIN',
CRVAL1=2.668301750000E+02,
CDELT1=-0.0002777777777777778,
CRPIX1=225.0,
CUNIT1='deg ',
CTYPE2='DEC--SIN',
CRVAL2=-2.839256111111E+01,
CDELT2=0.0002777777777777778,
CRPIX2=225.0,
CUNIT2='deg ',
))
tbl = table.Table.read(
paths.tpath("continuum_photometry_withSIMBAD.ipac"),
format='ascii.ipac',
)
regfile = pyregion.open(paths.rpath('coverage.reg'))
def resamp_func(
d_file,
z_set,
ra_set,
dec_set,
img_x,
img_y,
band,
out_file,
z_ref,
stack_info=None,
pixel=0.396,
id_dimm=False,
):
"""
d_file : path where save the masked data (include file-name structure:'/xxx/xxx/xxx.xxx')
z_set, ra_set, dec_set : ra, dec, z of will be resampled imgs
band : the band of imgs, 'str' type
out_file : path where to save the resampling img
pixel : pixel scale, in unit 'arcsec' (default is 0.396)
z_ref : reference redshift, the redshift to which all clusters will be scaled
id_dimm : if do cosmic dimming correction or not
img_x, img_y : BCG location on image frame before pixel resampling
"""
zn = len(z_set)
bcg_x, bcg_y = [], []
for k in range(zn):
ra_g = ra_set[k]
dec_g = dec_set[k]
z_g = z_set[k]
file = d_file % (band, ra_g, dec_g, z_g)
data = fits.getdata(file, header=True)
img = data[0]
cx0 = data[1]['CRPIX1']
cy0 = data[1]['CRPIX2']
RA0 = data[1]['CRVAL1']
DEC0 = data[1]['CRVAL2']
#. convert (ra, dec) to location in image frame
#wcs = awc.WCS(data[1])
#cx, cy = wcs.all_world2pix(ra_g * U.deg, dec_g * U.deg, 1)
#. read BCG position from catalog
cx, cy = img_x[k], img_y[k]
Da_g = Test_model.angular_diameter_distance(z_g).value
Da_ref = Test_model.angular_diameter_distance(z_ref).value
Dl_g = Test_model.luminosity_distance(z_g).value
Dl_ref = Test_model.luminosity_distance(z_ref).value
#. observation angle and flux factor at z_ref
pixel_ref = pixel * (Da_g / Da_ref)
eta_flux = Dl_g**2 / Dl_ref**2 #... flux change due to distance
eta_pix = pixel / pixel_ref
if id_dimm == True:
dimm_flux = flux_recal(img, z_g, z_ref)
pre_img = dimm_flux * eta_flux
else:
pre_img = img * 1.
ix0 = np.int(cx0 / eta_pix)
iy0 = np.int(cy0 / eta_pix)
if eta_pix > 1:
resam, xn, yn = sum_samp(eta_pix, eta_pix, pre_img, cx, cy)
else:
resam, xn, yn = down_samp(eta_pix, eta_pix, pre_img, cx, cy)
# cheng the data type
out_data = resam.astype('float32')
bcg_x.append(xn)
bcg_y.append(yn)
x0 = resam.shape[1]
y0 = resam.shape[0]
keys = [
'SIMPLE', 'BITPIX', 'NAXIS', 'NAXIS1', 'NAXIS2', 'CRPIX1',
'CRPIX2', 'CENTER_X', 'CENTER_Y', 'CRVAL1', 'CRVAL2', 'BCG_RA',
'BCG_DEC', 'ORIGN_Z', 'P_SCALE'
]
value = [
'T', 32, 2, x0, y0, ix0, iy0, xn, yn, RA0, DEC0, ra_g, dec_g, z_g,
pixel
]
ff = dict(zip(keys, value))
fil = fits.Header(ff)
fits.writeto(out_file % (band, ra_g, dec_g, z_g),
out_data,
header=fil,
overwrite=True)
bcg_x = np.array(bcg_x)
bcg_y = np.array(bcg_y)
if stack_info != None:
keys = ['ra', 'dec', 'z', 'bcg_x', 'bcg_y']
values = [ra_set, dec_set, z_set, bcg_x, bcg_y]
fill = dict(zip(keys, values))
data = pds.DataFrame(fill)
data.to_csv(stack_info)
return
def dict_to_hdu(d, name=None, hdr=None, force_to_bintbl=False):
"""
Write a dictionary to a fits HDU.
Elements in the dictionary that are integers, floats, or strings
(specific numpy types or otherwise) are written to the HDU
header. The header keywords are identical to the dictionary keys.
If any of the elements in the dictionary are an
`astropy.table.Table`_, that dictionary can *only* contain that
table and single values that will be written to the extension
header. That is, there can be only one `astropy.table.Table`_
element, and none of the elements can be a :obj:`list` or
`numpy.ndarray`_. By default the extension name is the dictionary
key for the `astropy.table.Table`_ item; this can be overridden
using the ``name`` argument.
Elements in the dictionary that are a list or a `numpy.ndarray`_
are written as either an image (if there is only one array and a
binary table is not specifically requested using
``force_to_bintbl``) or a series of table columns. The lists are
assumed to be interpretable as the ``array`` argument of
`astropy.io.fits.Column`_ (for a table) or the ``data`` argument
of `astropy.io.fits.ImageHDU`_ (for an image).
- If an image is to be written, the extension name, by
default, is the dictionary key for the array item; this can
be overridden using the ``name`` argument.
- If a table is to be written, the method checks that the
relevant arrays have a consistent number of rows. If they
do not, the format and dimensions of the table written are
set so that the arrays are contained in a single row. The
column names in the table are identical to the dictionary
keywords. In this case, ``name`` must be provided if you
want the extension to have a name; there is no default
name.
Args:
d (:obj:`dict`):
Dictionary with data to write to the
`astropy.io.fits.BinTableHDU`_.
name (:obj:`str`, optional):
Name to give the HDU extension. If None and the input is
a dictionary with a single array or
`astropy.table.Table`_ to write, the name of the
extension is the relevant dictionary keyword. Any
provided value for ``name`` will override this behavior.
If the provided dictionary is used to construct a table,
where the dictionary keys are used for the table column
names, there is no default name for the extension (i.e.,
no extension name is used if ``name is None``).
hdr (`astropy.io.fits.Header`_, optional):
Base-level header to include in the HDU. If None, an
empty header is used and then added to.
force_to_bintbl (:obj:`bool`, optional):
Force a BinTableHDU to be constructed instead of an
ImageHDU when either there are no arrays or tables to
write or only a single array is provided.
Returns:
`astropy.io.fits.ImageHDU`_, `astropy.io.fits.BinTableHDU`_:
HDU with the data. An `astropy.io.fits.ImageHDU`_ object is
returned if there is 1 (or fewer) array-like objects in the
dictionary. Otherwise, an `astropy.io.fits.BinTableHDU`_
object is returned with the data.
Raises:
TypeError:
Raised if the input object is not a dictionary or the
method cannot interpret how to use an element of the
dictionary.
ValueError:
Raised if dictionary contains another dictionary, more
than one `astropy.table.Table`_ object, or both an
`astropy.table.Table`_ and an array-like object
(:obj:`list` or `numpy.ndarray`_).
"""
# Check the input is a dictionary (not very pythonic...)
if not isinstance(d, dict):
raise TypeError('Input must be a dictionary.')
# Check the dictionary contents
ndict = numpy.sum([isinstance(d[key], dict) for key in d.keys()])
if ndict > 0:
raise ValueError('Cannot write nested dictionaries.')
ntab = numpy.sum([isinstance(d[key], Table) for key in d.keys()])
if ntab > 1:
raise ValueError(
'Cannot write dictionaries with more than one astropy.table.Table.'
)
narr = numpy.sum(
[isinstance(d[key], (list, numpy.ndarray)) for key in d.keys()])
if ntab > 0 and narr > 0:
raise ValueError(
'Cannot write dictionaries with both arrays and Tables.')
# Write any header data and find arrays and Tables
_hdr = fits.Header() if hdr is None else hdr.copy()
array_keys = []
table_keys = []
for key in d.keys():
if d[key] is None:
continue
# TODO: may be better to do this
# isinstance(d[key], (collections.Sequence, numpy.ndarray)):
# This ignores the defined otype...
if isinstance(d[key], (list, numpy.ndarray)):
array_keys += [key]
elif isinstance(d[key], Table):
table_keys += [key]
elif isinstance(d[key],
(int, numpy.integer, float, numpy.floating, str)):
_hdr[key.upper()] = d[key]
else:
raise TypeError(
'Do not know how to write object with type {0}'.format(
type(d[key])))
# If there aren't any arrays or tables, return an empty ImageHDU or
# BinTableHDU with just the header data.
if len(array_keys) < 1 and len(table_keys) < 1:
return fits.BinTableHDU(header=_hdr, name=name) if force_to_bintbl \
else fits.ImageHDU(header=_hdr, name=name)
# If there's only a single array, return it in an ImageHDU or, if
# requested, a BinTableHDU
if len(array_keys) == 1 and not force_to_bintbl:
return fits.ImageHDU(data=d[array_keys[0]],
header=_hdr,
name=array_keys[0] if name is None else name)
# If there's only a single Table, return it in a BinTableHDU
if len(table_keys) == 1:
# TODO: If we pass hdr directly, does this call include any
# table meta?
return fits.BinTableHDU(data=d[table_keys[0]],
header=_hdr,
name=table_keys[0] if name is None else name)
# Only remaining option is to build a BinTableHDU based on the
# dictionary contents.
# Do all arrays have the same number of rows?
single_row = len(
numpy.unique([numpy.asarray(d[key]).shape[0]
for key in array_keys])) > 1
# If the number of rows is inconsistent, save the data in a single
# row. Otherwise, save the data as a multi-row table.
cols = []
for key in array_keys:
cols += [
fits.Column(name=key,
format=rec_to_fits_type(numpy.asarray(d[key]),
single_row=single_row),
dim=rec_to_fits_col_dim(d[key], single_row=single_row),
array=numpy.expand_dims(d[key], 0)
if single_row else numpy.asarray(d[key]))
]
return fits.BinTableHDU.from_columns(cols, header=_hdr, name=name)
def _ffi_todo(input_folder, sector, camera, ccd):
logger = logging.getLogger(__name__)
cat_tmp = []
# See if there are any FFIs for this camera and ccd.
# We just check if an HDF5 file exist.
hdf5_file = find_hdf5_files(input_folder,
sector=sector,
camera=camera,
ccd=ccd)
if len(hdf5_file) != 1:
raise FileNotFoundError("Could not find HDF5 file")
# Load the relevant information from the HDF5 file for this camera and ccd:
with h5py.File(hdf5_file[0], 'r') as hdf:
if isinstance(hdf['wcs'], h5py.Group):
refindx = hdf['wcs'].attrs['ref_frame']
hdr_string = hdf['wcs']['%04d' % refindx][0]
else:
hdr_string = hdf['wcs'][0]
if not isinstance(hdr_string, str):
hdr_string = hdr_string.decode("utf-8") # For Python 3
wcs = WCS(header=fits.Header().fromstring(hdr_string))
offset_rows = hdf['images'].attrs.get('PIXEL_OFFSET_ROW', 0)
offset_cols = hdf['images'].attrs.get('PIXEL_OFFSET_COLUMN', 0)
image_shape = hdf['images']['0000'].shape
# Load the corresponding catalog:
catalog_file = find_catalog_files(input_folder,
sector=sector,
camera=camera,
ccd=ccd)
if len(catalog_file) != 1:
raise FileNotFoundError(
"Catalog file not found: SECTOR=%s, CAMERA=%s, CCD=%s" %
(sector, camera, ccd))
with contextlib.closing(sqlite3.connect(catalog_file[0])) as conn:
conn.row_factory = sqlite3.Row
cursor = conn.cursor()
# Load the settings:
cursor.execute(
"SELECT * FROM settings WHERE camera=? AND ccd=? LIMIT 1;",
(camera, ccd))
settings = cursor.fetchone()
# Find all the stars in the catalog brigher than a certain limit:
cursor.execute(
"SELECT starid,tmag,ra,decl FROM catalog WHERE tmag < 15 ORDER BY tmag;"
)
for row in cursor.fetchall():
logger.debug("%011d - %.3f", row['starid'], row['tmag'])
# Calculate the position of this star on the CCD using the WCS:
ra_dec = np.atleast_2d([row['ra'], row['decl']])
x, y = wcs.all_world2pix(ra_dec, 0)[0]
# Subtract the pixel offset if there is one:
x -= offset_cols
y -= offset_rows
# If the target falls outside silicon, do not add it to the todo list:
# The reason for the strange 0.5's is that pixel centers are at integers.
if x < -0.5 or y < -0.5 or x > image_shape[
1] - 0.5 or y > image_shape[0] - 0.5:
continue
# Calculate distance from target to edge of image:
EdgeDist = edge_distance(y, x, image_shape=image_shape)
# Calculate the Cotrending Basis Vector area the star falls in:
cbv_area = calc_cbv_area(row, settings)
# The targets is on silicon, so add it to the todo list:
cat_tmp.append({
'starid': row['starid'],
'sector': sector,
'camera': camera,
'ccd': ccd,
'datasource': 'ffi',
'tmag': row['tmag'],
'cbv_area': cbv_area,
'edge_dist': EdgeDist
})
cursor.close()
# Create the TODO list as a table which we will fill with targets:
return Table(rows=cat_tmp,
names=('starid', 'sector', 'camera', 'ccd', 'datasource',
'tmag', 'cbv_area', 'edge_dist'),
dtype=('int64', 'int32', 'int32', 'int32', 'S256', 'float32',
'int32', 'float32'))
def save(self,
outfile=None,
overwrite=True,
traceImage=None,
tslits_dict=None):
"""
Save the main TraceSlits data as a MasterFrame.
TODO: Change the format of this...
Args:
outfile (:obj:`str`, optional):
Name for the output file. Defaults to
:attr:`file_path`.
overwrite (:obj:`bool`, optional):
Overwrite any existing file.
traceImage (`numpy.ndarray`_, :class:`pypeit.traceimage.TraceImage`, optional):
An array with only the image data or the full
:class:`pypeit.traceimage.TraceImage` instance with the
data used to construct the slit traces.
"""
_outfile = self.file_path if outfile is None else outfile
# Check if it exists
if os.path.exists(_outfile) and not overwrite:
msgs.warn('Master file exists: {0}'.format(_outfile) +
msgs.newline() + 'Set overwrite=True to overwrite it.')
return
_tslits_dict = self.tslits_dict if tslits_dict is None else tslits_dict
# Log
msgs.info('Saving master frame to {0}'.format(_outfile))
# Build the header
hdr = fits.Header()
# - Set the master frame type
hdr['FRAMETYP'] = (self.master_type,
'PypeIt: Master calibration frame type')
# - List the completed steps
hdr['STEPS'] = (','.join(self.steps), 'Completed reduction steps')
# - Provide the file names
if traceImage is not None:
try:
nfiles = len(traceImage.files)
ndig = int(np.log10(nfiles)) + 1
for i in range(nfiles):
hdr['F{0}'.format(i+1).zfill(ndig)] \
= (traceImage.files[i], 'PypeIt: Processed raw file')
except:
msgs.warn(
'Master trace frame does not include list of source files.'
)
# - Slit metadata
# TODO: Provide header comments
hdr['DET'] = self.det
hdr['NSPEC'] = _tslits_dict['nspec']
hdr['NSPAT'] = _tslits_dict['nspat']
hdr['NSLITS'] = _tslits_dict['nslits']
hdr['PAD'] = _tslits_dict['pad']
hdr['BINSPEC'] = _tslits_dict['binspectral']
hdr['BINSPAT'] = _tslits_dict['binspatial']
hdr['SPECTROG'] = _tslits_dict['spectrograph']
# Collect data that may be None. If they are None, no data will
# be in the relevant extensions.
mstrace = self.mstrace
if traceImage is not None:
try:
mstrace = traceImage.stack
except:
# Assume it failed because it's not a TraceImage object
# and it's a numpy.ndarray to write.
mstrace = traceImage
left_orig = None if 'slit_left_orig' not in _tslits_dict.keys() \
else _tslits_dict['slit_left_orig']
righ_orig = None if 'slit_righ_orig' not in _tslits_dict.keys() \
else _tslits_dict['slit_righ_orig']
# Write the file
fits.HDUList([
fits.PrimaryHDU(header=hdr),
fits.ImageHDU(data=mstrace, name='TRACEIMG'),
# TODO: These should be written to a BinaryTable
fits.ImageHDU(data=_tslits_dict['slit_left'], name='SLIT_LEFT'),
fits.ImageHDU(data=_tslits_dict['slit_righ'], name='SLIT_RIGH'),
fits.ImageHDU(data=_tslits_dict['slitcen'], name='SLITCEN'),
fits.ImageHDU(data=_tslits_dict['spec_min'], name='SPEC_MIN'),
fits.ImageHDU(data=_tslits_dict['spec_max'], name='SPEC_MAX'),
fits.ImageHDU(data=left_orig, name='SLIT_LEFT_ORIG'),
fits.ImageHDU(data=righ_orig, name='SLIT_RIGH_ORIG'),
fits.ImageHDU(data=_tslits_dict['maskslits'].astype(int),
name='MASK'), # int deals with bool
]).writeto(_outfile, overwrite=True)
# Load map
DL07_paras, hp_header = hp.read_map(
map_name,
# field indicates which column you choose to load, starting from 0.
field = 0,
h = True,
nest=None,
)
e_DL07_paras, e_hp_header = hp.read_map(
map_name,
# field indicates which column you choose to load, starting from 0.
field = 1,
h = True,
nest=None,
)
hp_hdu = fits.ImageHDU(DL07_paras, fits.Header(hp_header))
hp_hdu.header['UNIT'] = r"$M_{sun}/kpc^2$"
e_hp_hdu = fits.ImageHDU(e_DL07_paras, fits.Header(e_hp_header))
e_hp_hdu.header['UNIT'] = r"$M_{sun}/kpc^2$"
# Show the header of this map.
hdul = fits.open(map_name)
hdul.info()
hdr = hdul[1].header
print("### HEADER for this map ###")
print(repr(hdr))
print("### END of HEADER ###")
#--------------------------------------------------
# Initialize the target coordinate
cloud_skycoord_list = []
cloud_ra_list = []
cloud_dec_list = []
'psi': psi,
'r': r,
'x': x,
'y': y,
'intensity': intensity,
'mcAlttel': mcAlttel,
'mcAztel': mcAztel
}
ntuple = Table(output)
#If destination fitsfile doesn't exist, will create a new one with proper headers
if os.path.isfile(outfile) == False:
if filetype == 'fits':
#Convert Tables of data into HDUBinTables to write them into fits files
pardata = ntuple.as_array()
parheader = fits.Header()
parheader.update(ntuple.meta)
if storeimg == True:
pixels = fits.ImageHDU(fitsdata) #Image with pixel content
#Write the data in an HDUList for storing in a fitsfile
hdr = fits.Header(
) #Example header, we can add more things to this header
hdr['TEL'] = 'LST1'
primary_hdu = fits.PrimaryHDU(header=hdr)
hdul = fits.HDUList([primary_hdu])
hdul.append(fits.BinTableHDU(data=pardata, header=parheader))
if storeimg == True:
hdul.append(pixels)
hdul.writeto(outfile)
def resamp_sky(band_id, sub_z, sub_ra, sub_dec):
ii = np.int(band_id)
zn = len(sub_z)
for k in range(zn):
ra_g = sub_ra[k]
dec_g = sub_dec[k]
z_g = sub_z[k]
Da_g = Test_model.angular_diameter_distance(z_g).value
try:
data = fits.open(
load +
'random_cat/sky_img/rand_sky-ra%.3f-dec%.3f-z%.3f-%s-band.fits'
% (ra_g, dec_g, z_g, band[ii]))
img = data[0].data
head = data[0].header
cx0 = data[0].header['CRPIX1']
cy0 = data[0].header['CRPIX2']
RA0 = data[0].header['CRVAL1']
DEC0 = data[0].header['CRVAL2']
wcs = awc.WCS(head)
cx, cy = wcs.all_world2pix(ra_g * U.deg, dec_g * U.deg, 1)
Angur = rad2asec / Da_g
Rp = Angur / pixel
L_ref = Da_ref * pixel / rad2asec
L_z0 = Da_g * pixel / rad2asec
b = L_ref / L_z0
ix0 = np.int(cx0 / b)
iy0 = np.int(cy0 / b)
if b > 1:
resam, xn, yn = sum_samp(b, b, img, cx, cy)
else:
resam, xn, yn = down_samp(b, b, img, cx, cy)
xn = np.int(xn)
yn = np.int(yn)
x0 = resam.shape[1]
y0 = resam.shape[0]
keys = [
'SIMPLE', 'BITPIX', 'NAXIS', 'NAXIS1', 'NAXIS2', 'CRPIX1',
'CRPIX2', 'CENTER_X', 'CENTER_Y', 'CRVAL1', 'CRVAL2',
'CENTER_RA', 'CENTER_DEC', 'ORIGN_Z', 'P_SCALE'
]
value = [
'T', 32, 2, x0, y0, ix0, iy0, xn, yn, RA0, DEC0, ra_g, dec_g,
z_g, pixel
]
ff = dict(zip(keys, value))
fil = fits.Header(ff)
fits.writeto(
load +
'random_cat/sky_resamp_img/rand_resamp-sky-%s-ra%.3f-dec%.3f-redshift%.3f.fits'
% (band[ii], ra_g, dec_g, z_g),
resam,
header=fil,
overwrite=True)
except FileNotFoundError:
continue
return
def fits_header():
hdr = fits.Header()
hdr[KEY] = (VALUE, COMMENT)
hdr[ADDITIVE_KEY] = ADDITIVE_ENTRY
return hdr
def createNpolHdr(cls, sciheader, npolfile, wdvarr_ver, npl_extname, ccdchip):
"""
Creates a header for the WCSDVARR extension based on the NPOL reference file
and sci extension header. The goal is to always work in image coordinates
(also for subarrays and binned images. The WCS for the WCSDVARR extension
i ssuch that a full size npol table is created and then shifted or scaled
if the science image is a subarray or binned image.
"""
npl = fits.open(npolfile)
npol_phdr = npl[0].header
for ext in npl:
try:
nplextname = ext.header['EXTNAME']
nplextver = ext.header['EXTVER']
except KeyError:
continue
nplccdchip = cls.get_ccdchip(npl, extname=nplextname, extver=nplextver)
if nplextname == npl_extname and nplccdchip == ccdchip:
npol_header = ext.header
break
npl.close()
naxis = npl[1].header['NAXIS']
ccdchip = nplextname # npol_header['CCDCHIP']
cdl = [
('XTENSION', 'IMAGE', 'Image extension'),
('BITPIX', -32, 'number of bits per data pixel'),
('NAXIS', naxis, 'Number of data axes'),
('EXTNAME', 'WCSDVARR', 'WCS distortion array'),
('EXTVER', wdvarr_ver, 'Distortion array version number'),
('PCOUNT', 0, 'number of parameters'),
('GCOUNT', 1, 'number of groups'),
('CCDCHIP', ccdchip),
]
for i in range(1, naxis + 1):
cdl.append((f'NAXIS{i:d}', npol_header.get(f'NAXIS{i:d}'),
f"length of data axis {i:d}"))
cdl.append((f'CDELT{i:d}', npol_header.get(f'CDELT{i:d}', 1.0) *
sciheader.get(f'LTM{i:d}_{i:d}', 1),
"Coordinate increment at reference point"))
cdl.append((f'CRPIX{i:d}', npol_header.get(f'CRPIX{i:d}', 0.0),
"Pixel coordinate of reference point"))
cdl.append((f'CRVAL{i:d}', npol_header.get(f'CRVAL{i:d}', 0.0) -
sciheader.get(f'LTV{i:d}', 0),
"Coordinate value at reference point"))
# Now add keywords from NPOLFILE header to document source of calibration
# include all keywords after and including 'FILENAME' from header
start_indx = -1
end_indx = 0
for i, c in enumerate(npol_phdr):
if c == 'FILENAME':
start_indx = i
if c == '': # remove blanks from end of header
end_indx = i + 1
break
if start_indx >= 0:
for card in npol_phdr.cards[start_indx: end_indx]:
cdl.append(card)
hdr = fits.Header(cards=cdl)
return hdr
def combine_bias(config, logtable):
"""Combine the bias images.
Args:
config (:class:`configparser.ConfigParser`): Config object.
logtable (:class:`astropy.table.Table`): Table of Observing log.
Returns:
tuple: A tuple containing:
* **bias** (:class:`numpy.ndarray`) – Output bias image.
* **bias_card_lst** (list) – List of FITS header cards related to
the bias correction.
"""
rawpath = config['data']['rawpath']
readout_mode = config['data']['readout_mode']
# determine number of cores to be used
ncores = config['reduce'].get('ncores')
if ncores == 'max':
ncores = os.cpu_count()
else:
ncores = min(os.cpu_count(), int(ncores))
section = config['reduce.bias']
bias_file = section['bias_file']
bias_data_lst = []
bias_card_lst = []
bias_items = list(filter(lambda item: item['object'].lower()=='bias',
logtable))
# get the number of bias images
n_bias = len(bias_items)
if n_bias == 0:
# there is no bias frames
return None, []
fmt_str = ' - {:>7s} {:^11} {:^8s} {:^7} {:^19s}'
head_str = fmt_str.format('frameid', 'FileID', 'Object', 'exptime',
'obsdate')
for iframe, logitem in enumerate(bias_items):
# now filter the bias frames
fname = '{}.fits'.format(logitem['fileid'])
filename = os.path.join(rawpath, fname)
data, head = fits.getdata(filename, header=True)
mask = get_mask(data, head)
data, card_lst = correct_overscan(data, head, readout_mode)
# pack the data and fileid list
bias_data_lst.append(data)
# append the file information
prefix = 'HIERARCH GAMSE BIAS FILE {:03d}'.format(iframe+1)
card = (prefix+' FILEID', logitem['fileid'])
bias_card_lst.append(card)
# append the overscan information of each bias frame to
# bias_card_lst
for keyword, value in card_lst:
mobj = re.match('^HIERARCH GAMSE (OVERSCAN[\s\S]*)', keyword)
if mobj:
newkey = prefix + ' ' + mobj.group(1)
bias_card_lst.append((newkey, value))
# print info
if iframe == 0:
print('* Combine Bias Images: "{}"'.format(bias_file))
print(head_str)
message = fmt_str.format(
'[{:d}]'.format(logitem['frameid']),
logitem['fileid'], logitem['object'],
logitem['exptime'], logitem['obsdate'],
)
print(message)
prefix = 'HIERARCH GAMSE BIAS '
bias_card_lst.append((prefix + 'NFILE', n_bias))
# combine bias images
bias_data_lst = np.array(bias_data_lst)
combine_mode = 'mean'
cosmic_clip = section.getfloat('cosmic_clip')
maxiter = section.getint('maxiter')
maskmode = (None, 'max')[n_bias>=3]
bias_combine = combine_images(bias_data_lst,
mode = combine_mode,
upper_clip = cosmic_clip,
maxiter = maxiter,
maskmode = maskmode,
ncores = ncores,
)
bias_card_lst.append((prefix+'COMBINE_MODE', combine_mode))
bias_card_lst.append((prefix+'COSMIC_CLIP', cosmic_clip))
bias_card_lst.append((prefix+'MAXITER', maxiter))
bias_card_lst.append((prefix+'MASK_MODE', str(maskmode)))
# create the hdu list to be saved
hdu_lst = fits.HDUList()
# create new FITS Header for bias
head = fits.Header()
for card in bias_card_lst:
head.append(card)
head['HIERARCH GAMSE FILECONTENT 0'] = 'BIAS COMBINED'
hdu_lst.append(fits.PrimaryHDU(data=bias_combine, header=head))
############## bias smooth ##################
if section.getboolean('smooth'):
# bias needs to be smoothed
smooth_method = section.get('smooth_method')
ny, nx = bias_combine.shape
newcard_lst = []
if smooth_method in ['gauss', 'gaussian']:
# perform 2D gaussian smoothing
smooth_sigma = section.getint('smooth_sigma')
smooth_mode = section.get('smooth_mode')
bias_smooth = np.zeros_like(bias_combine, dtype=np.float64)
bias_smooth[0:ny//2, :] = gaussian_filter(
bias_combine[0:ny//2, :],
sigma = smooth_sigma,
mode = smooth_mode)
bias_smooth[ny//2:ny, :] = gaussian_filter(
bias_combine[ny//2:ny, :],
sigma = smooth_sigma,
mode = smooth_mode)
# write information to FITS header
newcard_lst.append((prefix+'SMOOTH CORRECTED', True))
newcard_lst.append((prefix+'SMOOTH METHOD', 'GAUSSIAN'))
newcard_lst.append((prefix+'SMOOTH SIGMA', smooth_sigma))
newcard_lst.append((prefix+'SMOOTH MODE', smooth_mode))
else:
print('Unknown smooth method: ', smooth_method)
pass
# pack the cards to bias_card_lst and also hdu_lst
for card in newcard_lst:
hdu_lst[0].header.append(card)
bias_card_lst.append(card)
hdu_lst.append(fits.ImageHDU(data=bias_smooth))
card = ('HIERARCH GAMSE FILECONTENT 1', 'BIAS SMOOTHED')
hdu_lst[0].header.append(card)
# bias is the result array to return
bias = bias_smooth
else:
# bias not smoothed
card = (prefix+'SMOOTH CORRECTED', False)
bias_card_lst.append(card)
hdu_lst[0].header.append(card)
# bias is the result array to return
bias = bias_combine
hdu_lst.writeto(bias_file, overwrite=True)
message = 'Bias image written to "{}"'.format(bias_file)
logger.info(message)
print(message)
return bias, bias_card_lst
def convert(input):
"""Input GEIS files "input" will be read and a HDUList object will
be returned that matches the waiver-FITS format written out by 'stwfits' in IRAF.
The user can use the writeto method to write the HDUList object to
a FITS file.
"""
global dat
cardLen = fits.Card.length
# input file(s) must be of the form *.??h and *.??d
if input[-1] != 'h' or input[-4] != '.':
raise "Illegal input GEIS file name %s" % input
data_file = input[:-1]+'d'
_os = sys.platform
if _os[:5] == 'linux' or _os[:5] == 'win32' or _os[:5] == 'sunos' or _os[:3] == 'osf' or _os[:6] == 'darwin':
bytes_per_line = cardLen+1
else:
raise "Platform %s is not supported (yet)." % _os
end_card = 'END'+' '* (cardLen-3)
# open input file
im = open(input)
# Generate the primary HDU
cards = []
while 1:
line = im.read(bytes_per_line)[:cardLen]
line = line[:8].upper() + line[8:]
if line == end_card:
break
cards.append(fits.Card.fromstring(line))
phdr = fits.Header(cards)
im.close()
# Determine starting point for adding Group Parameter Block keywords to Primary header
phdr_indx = phdr.index('PSIZE')
_naxis0 = phdr.get('NAXIS', 0)
_naxis = [phdr['NAXIS'+str(j)] for j in range(1, _naxis0+1)]
_naxis.insert(0, _naxis0)
_bitpix = phdr['BITPIX']
_psize = phdr['PSIZE']
if phdr['DATATYPE'][:4] == 'REAL':
_bitpix = -_bitpix
if _naxis0 > 0:
size = reduce(lambda x,y:x*y, _naxis[1:])
data_size = abs(_bitpix) * size // 8
else:
data_size = 0
group_size = data_size + _psize // 8
# decode the group parameter definitions,
# group parameters will become extension table
groups = phdr['GROUPS']
gcount = phdr['GCOUNT']
pcount = phdr['PCOUNT']
formats = []
bools = []
floats = []
cols = [] # column definitions used for extension table
cols_dict = {} # provides name access to Column defs
_range = range(1, pcount+1)
key = [phdr['PTYPE'+str(j)] for j in _range]
comm = [phdr.cards['PTYPE'+str(j)].comment for j in _range]
# delete group parameter definition header keywords
_list = ['PTYPE'+str(j) for j in _range] + \
['PDTYPE'+str(j) for j in _range] + \
['PSIZE'+str(j) for j in _range] + \
['DATATYPE', 'PSIZE', 'GCOUNT', 'PCOUNT', 'BSCALE', 'BZERO']
# Construct record array formats for the group parameters
# as interpreted from the Primary header file
for i in range(1, pcount+1):
ptype = key[i-1]
pdtype = phdr['PDTYPE'+str(i)]
star = pdtype.find('*')
_type = pdtype[:star]
_bytes = pdtype[star+1:]
# collect boolean keywords since they need special attention later
if _type == 'LOGICAL':
bools.append(i)
if pdtype == 'REAL*4':
floats.append(i)
# identify keywords which require conversion to special units
if ptype in kw_DOUBLE:
_type = 'DOUBLE'
fmt = geis_fmt[_type] + _bytes
formats.append((ptype,fmt))
# Set up definitions for use in creating the group-parameter block table
nrpt = ''
nbits = str(int(_bytes)*8)
if 'CHAR' in _type:
nrpt = _bytes
nbits = _bytes
afmt = cols_fmt[_type]+ nbits
if 'LOGICAL' in _type:
afmt = cols_fmt[_type]
cfmt = cols_pfmt[_type]+nrpt
#print 'Column format for ',ptype,': ',cfmt,' with dtype of ',afmt
cols_dict[ptype] = fits.Column(name=ptype,format=cfmt,array=numpy.zeros(gcount,dtype=afmt))
cols.append(cols_dict[ptype]) # This keeps the columns in order
_shape = _naxis[1:]
_shape.reverse()
_code = fits.hdu.ImageHDU.NumCode[_bitpix]
_bscale = phdr.get('BSCALE', 1)
_bzero = phdr.get('BZERO', 0)
if phdr['DATATYPE'][:10] == 'UNSIGNED*2':
_uint16 = 1
_bzero = 32768
else:
_uint16 = 0
# delete from the end, so it will not conflict with previous delete
for i in range(len(phdr)-1, -1, -1):
if phdr.cards[i].keyword in _list:
del phdr[i]
# clean up other primary header keywords
phdr['SIMPLE'] = True
phdr['GROUPS'] = False
_after = 'NAXIS'
if _naxis0 > 0:
_after += str(_naxis0)
phdr.set('EXTEND', value=True, comment="FITS dataset may contain extensions", after=_after)
# Use copy-on-write for all data types since byteswap may be needed
# in some platforms.
f1 = open(data_file, mode='rb')
dat = f1.read()
errormsg = ""
# Define data array for all groups
arr_shape = _naxis[:]
arr_shape[0] = gcount
arr_stack = numpy.zeros(arr_shape,dtype=_code)
loc = 0
for k in range(gcount):
ext_dat = numpy.fromstring(dat[loc:loc+data_size], dtype=_code)
ext_dat = ext_dat.reshape(_shape)
if _uint16:
ext_dat += _bzero
# Check to see whether there are any NaN's or infs which might indicate
# a byte-swapping problem, such as being written out on little-endian
# and being read in on big-endian or vice-versa.
if _code.find('float') >= 0 and \
(numpy.any(numpy.isnan(ext_dat)) or numpy.any(numpy.isinf(ext_dat))):
errormsg += "===================================\n"
errormsg += "= WARNING: =\n"
errormsg += "= Input image: =\n"
errormsg += input+"[%d]\n"%(k+1)
errormsg += "= had floating point data values =\n"
errormsg += "= of NaN and/or Inf. =\n"
errormsg += "===================================\n"
elif _code.find('int') >= 0:
# Check INT data for max values
ext_dat_frac,ext_dat_exp = numpy.frexp(ext_dat)
if ext_dat_exp.max() == int(_bitpix) - 1:
# Potential problems with byteswapping
errormsg += "===================================\n"
errormsg += "= WARNING: =\n"
errormsg += "= Input image: =\n"
errormsg += input+"[%d]\n"%(k+1)
errormsg += "= had integer data values =\n"
errormsg += "= with maximum bitvalues. =\n"
errormsg += "===================================\n"
arr_stack[k] = ext_dat
#ext_hdu = fits.hdu.ImageHDU(data=ext_dat)
rec = numpy.fromstring(dat[loc+data_size:loc+group_size], dtype=formats)
loc += group_size
# Add data from this GPB to table
for i in range(1, pcount+1):
val = rec[0][i-1]
if i in bools:
if val:
val = 'T'
else:
val = 'F'
cols[i-1].array[k] = val
# Based on the first group, add GPB keywords to PRIMARY header
if k == 0:
# Create separate PyFITS Card objects for each entry in 'rec'
# and update Primary HDU with these keywords after PSIZE
for i in range(1, pcount+1):
#val = rec.field(i-1)[0]
val = rec[0][i-1]
if val.dtype.kind == 'S':
val = val.decode('ascii')
if i in bools:
if val:
val = True
else:
val = False
elif i in floats:
# use fromstring, format in Card is deprecated in pyfits 0.9
_str = '%-8s= %20.13G / %s' % (key[i-1], val, comm[i-1])
_card = fits.Card.fromstring(_str)
else:
_card = fits.Card(key=key[i-1], value=val, comment=comm[i-1])
phdr.insert(phdr_indx+i, _card)
# deal with bscale/bzero
if (_bscale != 1 or _bzero != 0):
phdr['BSCALE'] = _bscale
phdr['BZERO'] = _bzero
#hdulist.append(ext_hdu)
# Define new table based on Column definitions
ext_table = fits.new_table(cols,tbtype='TableHDU')
ext_table.header.set('EXTNAME', value=input+'.tab', after='TFIELDS')
# Add column descriptions to header of table extension to match stwfits output
for i in range(len(key)):
ext_table.header.append(fits.Card(keyword=key[i], value=comm[i]))
if errormsg != "":
errormsg += "===================================\n"
errormsg += "= This file may have been =\n"
errormsg += "= written out on a platform =\n"
errormsg += "= with a different byte-order. =\n"
errormsg += "= =\n"
errormsg += "= Please verify that the values =\n"
errormsg += "= are correct or apply the =\n"
errormsg += "= '.byteswap()' method. =\n"
errormsg += "===================================\n"
print(errormsg)
f1.close()
hdulist = fits.HDUList([fits.PrimaryHDU(header=phdr, data=arr_stack)])
hdulist.append(ext_table)
stsci2(hdulist,input)
return hdulist
def create_catalogs_out(fileList, z, snap_name):
"""
Adds Xray emission mass using the Bongiorno et al. 2016 model to the rockstar outputs.
"""
def f_lambda_sar(DATA):
logM, log_lambda_SAR = DATA
log_lambda_SAR_var = 10**(log_lambda_SAR - 33.8 + 0.48 * (logM - 11.))
return 1. / (log_lambda_SAR_var**(1.01 - 0.58 * (z - 1.1)) +
log_lambda_SAR_var**(3.72))
dl = 0.01
log_lambda_SAR_values = n.arange(32 - dl, 36 + 2 * dl, dl)
# loops over files
for fileName in fileList:
t0 = time.time()
outFile = fileName[:-5] + "_LSAR.fits"
# opens all relevant files
msFile = fileName[:-5] + "_Ms.fits"
hd = fits.open(fileName)
hm = fits.open(msFile)
logM = hm[1].data['stellar_mass_Mo13_mvir']
agn_random_number = n.random.random(len(logM))
log_lSAR = n.zeros(len(logM))
t0 = time.time()
ii0 = 0
ii_step = 10000
for ii0 in n.arange(0, len(logM), ii_step):
ii1 = ii0 + ii_step
X, Y = n.meshgrid(logM[ii0:ii1], log_lambda_SAR_values)
#Z = n.ones_like(X)*z
probas_un = f_lambda_sar([X, Y]) #, Z ])
norm = n.sum(probas_un, axis=0)
probas = probas_un / norm
cmat = n.array([
agn_random_number[ii0:ii1] > n.sum(probas.T[:, jj:], axis=1)
for jj in n.arange(len(log_lambda_SAR_values))
])
#print(cmat.shape, cmat[0])
#print(cmat.T[1])
values = log_lambda_SAR_values[n.array([
n.min(n.where(cmat.T[jj] == True))
for jj in n.arange(len(cmat.T))
])]
#print(values.shape, values[:10])
log_lSAR[ii0:ii1] = values
print(ii0, len(logM), time.time() - t0)
# columns related to Xray AGN
col1 = fits.Column(name='lambda_sar_Bo16', format='D', array=log_lSAR)
col1b = fits.Column(name='agn_random_number',
format='D',
array=agn_random_number)
#define the table hdu
colArray = [col1]
colArray.append(col1b)
#for col in hd[1].columns :
#colArray.append(col)
hdu_cols = fits.ColDefs(colArray)
tb_hdu = fits.BinTableHDU.from_columns(hdu_cols)
#define the header
prihdr = fits.Header()
prihdr['author'] = 'JC'
prihdu = fits.PrimaryHDU(header=prihdr)
#writes the file
thdulist = fits.HDUList([prihdu, tb_hdu])
if os.path.isfile(outFile):
os.system("rm " + outFile)
thdulist.writeto(outFile)
print time.time() - t0
def api_search(request, query):
import numpy as np
from astropy.io import fits
from astropy.io.fits import Column
result = unsqurl(query)
if result['returncode'] != '200':
#return error
return HttpResponse(result['error'])
print('UNSqurl:', result)
#run the query
cursor = connections['cosmo'].cursor()
cursor.execute(result['sql'])
rows = cursor.fetchall()
#return FITS file
priheader = fits.Header()
priheader['COMMENT'] = "This file was generated by the Cosmo web portal."
prihdu = fits.PrimaryHDU(header=priheader)
# this works if the fields all map directly with no arrays
# for i in range (0, nrows):
# for j in range (0, len(dtypes)):
# data[i][dtypes[j][0]] = rows[i][j]
nrows = len(rows)
if result['table'] == "DEFAULT":
# try building from columns
data = {
'cand_id': [],
'brickid': [],
'objid': [],
'type': [],
'ra': [],
'ra_ivar': [],
'dec': [],
'dec_ivar': [],
'bx': [],
'by': [],
'bx0': [],
'by0': [],
'ebv': [],
'dchisq': [],
'fracDev': [],
'fracDev_ivar': [],
'shapeExp_r': [],
'shapeExp_r_ivar': [],
'shapeExp_e1': [],
'shapeExp_e1_ivar': [],
'shapeExp_e2': [],
'shapeExp_e2_ivar': [],
'shapeDev_r': [],
'shapeDev_r_ivar': [],
'shapeDev_e1': [],
'shapeDev_e1_ivar': [],
'shapeDev_e2': [],
'shapeDev_e2_ivar': [],
'decam_flux': [],
'decam_flux_ivar': [],
'decam_fracflux': [],
'decam_fracmasked': [],
'decam_fracin': [],
'decam_rchi2': [],
'decam_nobs': [],
'decam_anymask': [],
'decam_allmask': [],
'decam_mw_transmission': [],
'wise_flux': [],
'wise_flux_ivar': [],
'wise_fracflux': [],
'wise_rchi2': [],
'wise_nobs': [],
'wise_mw_transmission': [],
'decam_apflux': [],
'decam_apflux_resid': [],
'decam_apflux_ivar': [],
}
for i in range(0, nrows):
data['cand_id'].append(rows[i][0])
data['brickid'].append(rows[i][3])
data['objid'].append(rows[i][4])
data['type'].append(rows[i][5])
data['ra'].append(rows[i][6])
data['ra_ivar'].append(rows[i][7])
data['dec'].append(rows[i][8])
data['dec_ivar'].append(rows[i][9])
data['bx'].append(rows[i][10])
data['by'].append(rows[i][11])
data['bx0'].append(rows[i][12])
data['by0'].append(rows[i][13])
data['ebv'].append(rows[i][14])
data['dchisq'].append(
[rows[i][15], rows[i][16], rows[i][17], rows[i][18]])
data['fracDev'].append(rows[i][19])
data['fracDev_ivar'].append(rows[i][20])
data['shapeExp_r'].append(rows[i][21])
data['shapeExp_r_ivar'].append(rows[i][22])
data['shapeExp_e1'].append(rows[i][23])
data['shapeExp_e1_ivar'].append(rows[i][24])
data['shapeExp_e2'].append(rows[i][25])
data['shapeExp_e2_ivar'].append(rows[i][26])
data['shapeDev_r'].append(rows[i][27])
data['shapeDev_r_ivar'].append(rows[i][28])
data['shapeDev_e1'].append(rows[i][29])
data['shapeDev_e1_ivar'].append(rows[i][30])
data['shapeDev_e2'].append(rows[i][31])
data['shapeDev_e2_ivar'].append(rows[i][32])
data['decam_flux'].append([
rows[i][33], rows[i][34], rows[i][35], rows[i][36],
rows[i][37], rows[i][38]
])
data['decam_flux_ivar'].append([
rows[i][39], rows[i][40], rows[i][41], rows[i][42],
rows[i][43], rows[i][44]
])
data['decam_fracflux'].append([
rows[i][45], rows[i][46], rows[i][47], rows[i][48],
rows[i][49], rows[i][50]
])
data['decam_fracmasked'].append([
rows[i][51], rows[i][52], rows[i][53], rows[i][54],
rows[i][55], rows[i][56]
])
data['decam_fracin'].append([
rows[i][57], rows[i][58], rows[i][59], rows[i][60],
rows[i][61], rows[i][62]
])
data['decam_rchi2'].append([
rows[i][63], rows[i][64], rows[i][65], rows[i][66],
rows[i][67], rows[i][68]
])
data['decam_nobs'].append([
rows[i][69], rows[i][70], rows[i][71], rows[i][72],
rows[i][73], rows[i][74]
])
data['decam_anymask'].append([
rows[i][75], rows[i][76], rows[i][77], rows[i][78],
rows[i][79], rows[i][80]
])
data['decam_allmask'].append([
rows[i][81], rows[i][82], rows[i][83], rows[i][84],
rows[i][85], rows[i][86]
])
data['decam_mw_transmission'].append([
rows[i][87], rows[i][88], rows[i][89], rows[i][90],
rows[i][91], rows[i][92]
])
data['wise_flux'].append(
[rows[i][93], rows[i][99], rows[i][105], rows[i][111]])
data['wise_flux_ivar'].append(
[rows[i][94], rows[i][100], rows[i][106], rows[i][112]])
data['wise_fracflux'].append(
[rows[i][95], rows[i][101], rows[i][107], rows[i][113]])
data['wise_rchi2'].append(
[rows[i][96], rows[i][102], rows[i][108], rows[i][114]])
data['wise_nobs'].append(
[rows[i][97], rows[i][103], rows[i][109], rows[i][115]])
data['wise_mw_transmission'].append(
[rows[i][98], rows[i][104], rows[i][110], rows[i][116]])
data['decam_apflux'].append([
rows[i][118], rows[i][119], rows[i][120], rows[i][121],
rows[i][122], rows[i][123], rows[i][124], rows[i][125],
rows[i][142], rows[i][143], rows[i][144], rows[i][145],
rows[i][146], rows[i][147], rows[i][148], rows[i][149],
rows[i][166], rows[i][167], rows[i][168], rows[i][169],
rows[i][170], rows[i][171], rows[i][172], rows[i][173],
rows[i][190], rows[i][191], rows[i][192], rows[i][193],
rows[i][194], rows[i][195], rows[i][196], rows[i][197],
rows[i][214], rows[i][215], rows[i][216], rows[i][217],
rows[i][218], rows[i][219], rows[i][220], rows[i][221],
rows[i][238], rows[i][239], rows[i][240], rows[i][241],
rows[i][242], rows[i][243], rows[i][244], rows[i][245]
])
data['decam_apflux_resid'].append([
rows[i][126], rows[i][127], rows[i][128], rows[i][129],
rows[i][130], rows[i][131], rows[i][132], rows[i][133],
rows[i][150], rows[i][151], rows[i][152], rows[i][153],
rows[i][154], rows[i][155], rows[i][156], rows[i][157],
rows[i][174], rows[i][175], rows[i][176], rows[i][177],
rows[i][178], rows[i][179], rows[i][180], rows[i][181],
rows[i][198], rows[i][199], rows[i][200], rows[i][201],
rows[i][202], rows[i][203], rows[i][204], rows[i][205],
rows[i][222], rows[i][223], rows[i][224], rows[i][225],
rows[i][226], rows[i][227], rows[i][228], rows[i][229],
rows[i][246], rows[i][247], rows[i][248], rows[i][249],
rows[i][250], rows[i][251], rows[i][252], rows[i][253]
])
data['decam_apflux_ivar'].append([
rows[i][134], rows[i][135], rows[i][136], rows[i][137],
rows[i][138], rows[i][139], rows[i][140], rows[i][141],
rows[i][158], rows[i][159], rows[i][160], rows[i][161],
rows[i][162], rows[i][163], rows[i][164], rows[i][165],
rows[i][182], rows[i][183], rows[i][184], rows[i][185],
rows[i][186], rows[i][187], rows[i][188], rows[i][189],
rows[i][206], rows[i][207], rows[i][208], rows[i][209],
rows[i][210], rows[i][211], rows[i][212], rows[i][213],
rows[i][230], rows[i][231], rows[i][232], rows[i][233],
rows[i][234], rows[i][235], rows[i][236], rows[i][237],
rows[i][254], rows[i][255], rows[i][256], rows[i][257],
rows[i][258], rows[i][259], rows[i][260], rows[i][261]
])
c0 = Column(name='cand_id', format='J', array=data['cand_id'])
c1 = Column(name='brickid', format='J', array=data['brickid'])
c2 = Column(name='objid', format='J', array=data['objid'])
c3 = Column(name='type', format='10A', array=data['type'])
c4 = Column(name='ra', format='D', array=data['ra'])
c5 = Column(name='ra_ivar', format='E', array=data['ra_ivar'])
c6 = Column(name='dec', format='D', array=data['dec'])
c7 = Column(name='dec_ivar', format='E', array=data['dec_ivar'])
c8 = Column(name='bx', format='D', array=data['bx'])
c9 = Column(name='by', format='D', array=data['by'])
c10 = Column(name='bx0', format='E', array=data['bx0'])
c11 = Column(name='by0', format='E', array=data['by0'])
c12 = Column(name='ebv', format='E', array=data['ebv'])
c13 = Column(name='dchisq', format='4D', array=data['dchisq'])
c14 = Column(name='fracDev', format='E', array=data['fracDev'])
c15 = Column(name='fracDev_ivar',
format='E',
array=data['fracDev_ivar'])
c16 = Column(name='shapeExp_r', format='E', array=data['shapeExp_r'])
c17 = Column(name='shapeExp_r_ivar',
format='E',
array=data['shapeExp_r_ivar'])
c18 = Column(name='shapeExp_e1', format='E', array=data['shapeExp_e1'])
c19 = Column(name='shapeExp_e1_ivar',
format='E',
array=data['shapeExp_e1_ivar'])
c20 = Column(name='shapeExp_e2', format='E', array=data['shapeExp_e2'])
c21 = Column(name='shapeExp_e2_ivar',
format='E',
array=data['shapeExp_e2_ivar'])
c22 = Column(name='shapeDev_r', format='E', array=data['shapeDev_r'])
c23 = Column(name='shapeDev_r_ivar',
format='E',
array=data['shapeDev_r_ivar'])
c24 = Column(name='shapeDev_e1', format='E', array=data['shapeDev_e1'])
c25 = Column(name='shapeDev_e1_ivar',
format='E',
array=data['shapeDev_e1_ivar'])
c26 = Column(name='shapeDev_e2', format='E', array=data['shapeDev_e2'])
c27 = Column(name='shapeDev_e2_ivar',
format='E',
array=data['shapeDev_e2_ivar'])
c28 = Column(name='decam_flux', format='6E', array=data['decam_flux'])
c29 = Column(name='decam_flux_ivar',
format='6E',
array=data['decam_flux_ivar'])
c30 = Column(name='decam_fracflux',
format='6E',
array=data['decam_fracflux'])
c31 = Column(name='decam_fracmasked',
format='6E',
array=data['decam_fracmasked'])
c32 = Column(name='decam_fracin',
format='6E',
array=data['decam_fracin'])
c33 = Column(name='decam_rchi2',
format='6E',
array=data['decam_rchi2'])
c34 = Column(name='decam_nobs', format='6I', array=data['decam_nobs'])
c35 = Column(name='decam_anymask',
format='6I',
array=data['decam_anymask'])
c36 = Column(name='decam_allmask',
format='6I',
array=data['decam_allmask'])
c37 = Column(name='decam_mw_transmission',
format='6E',
array=data['decam_mw_transmission'])
c38 = Column(name='wise_flux', format='4E', array=data['wise_flux'])
c39 = Column(name='wise_flux_ivar',
format='4E',
array=data['wise_flux_ivar'])
c40 = Column(name='wise_fracflux',
format='4E',
array=data['wise_fracflux'])
c41 = Column(name='wise_rchi2', format='4E', array=data['wise_rchi2'])
c42 = Column(name='wise_nobs', format='4I', array=data['wise_nobs'])
c43 = Column(name='wise_mw_transmission',
format='4E',
array=data['wise_mw_transmission'])
c44 = Column(name='decam_apflux',
format='48E',
array=data['decam_apflux'])
c45 = Column(name='decam_apflux_resid',
format='48E',
array=data['decam_apflux_resid'])
c46 = Column(name='decam_apflux_ivar',
format='48E',
array=data['decam_apflux_ivar'])
hdu = fits.BinTableHDU.from_columns([
c0, c1, c2, c3, c4, c5, c6, c7, c8, c9, c10, c11, c12, c13, c14,
c15, c16, c17, c18, c19, c20, c21, c22, c23, c24, c25, c26, c27,
c28, c29, c30, c31, c32, c33, c34, c35, c36, c37, c38, c39, c40,
c41, c42, c43, c44, c45, c46
])
elif result['table'] == 'CANDIDATE':
dtypes = [('brickid', 'i4'), ('objid', 'i4'), ('blob', 'i8'),
('type', 'S10'), ('ra', 'float64'), ('ra_ivar', 'float64'),
('dec', 'float64'), ('dec_ivar', 'float64'),
('bx', 'float64'), ('by', 'float64'), ('bx0', 'float64'),
('by0', 'float64'), ('ebv', 'float64'),
('dchisq1', 'float64'), ('dchisq2', 'float64'),
('dchisq3', 'float64'), ('dchisq4', 'float64'),
('fracdev', 'float64'), ('fracdev_ivar', 'float64'),
('shapeexp_r', 'float64'), ('shapeexp_r_ivar', 'float64'),
('shapeexp_e1', 'float64'), ('shapeexp_e1_ivar', 'float64'),
('shapeexp_e2', 'float64'), ('shapeexp_e2_ivar', 'float64'),
('shapedev_r', 'float64'), ('shapedev_r_ivar', 'float64'),
('shapedev_e1', 'float64'), ('shapedev_e1_ivar', 'float64'),
('shapedev_e2', 'float64'), ('shapedev_e2_ivar', 'float64')]
data = np.zeros(nrows, dtype=dtypes)
for i in range(0, nrows):
data[i]['brickid'] = rows[i][0]
data[i]['objid'] = rows[i][1]
data[i]['blob'] = rows[i][2]
data[i]['type'] = str(rows[i][3])
data[i]['ra'] = rows[i][4]
data[i]['ra_ivar'] = rows[i][5]
data[i]['dec'] = rows[i][6]
data[i]['dec_ivar'] = rows[i][7]
data[i]['bx'] = rows[i][8]
data[i]['by'] = rows[i][9]
data[i]['bx0'] = rows[i][10]
data[i]['by0'] = rows[i][11]
data[i]['ebv'] = rows[i][12]
data[i]['dchisq1'] = rows[i][13]
data[i]['dchisq2'] = rows[i][14]
data[i]['dchisq3'] = rows[i][15]
data[i]['dchisq4'] = rows[i][16]
data[i]['fracdev'] = rows[i][17]
data[i]['fracdev_ivar'] = rows[i][18]
data[i]['shapeexp_r'] = rows[i][19]
data[i]['shapeexp_r_ivar'] = rows[i][20]
data[i]['shapeexp_e1'] = rows[i][21]
data[i]['shapeexp_e1_ivar'] = rows[i][22]
data[i]['shapeexp_e2'] = rows[i][23]
data[i]['shapeexp_e2_ivar'] = rows[i][24]
data[i]['shapedev_r'] = rows[i][25]
data[i]['shapedev_r_ivar'] = rows[i][26]
data[i]['shapedev_e1'] = rows[i][27]
data[i]['shapedev_e1_ivar'] = rows[i][28]
data[i]['shapedev_e2'] = rows[i][29]
data[i]['shapedev_e2_ivar'] = rows[i][30]
hdu = fits.BinTableHDU(data, header=priheader)
elif result['table'] == 'DECAM':
# try building from columns
data = {
'cand_id': [],
'decam_flux': [],
'decam_flux_ivar': [],
'decam_fracflux': [],
'decam_fracmasked': [],
'decam_fracin': [],
'decam_rchi2': [],
'decam_nobs': [],
'decam_anymask': [],
'decam_allmask': [],
'decam_ext': []
}
for i in range(0, nrows):
data['cand_id'].append(rows[i][0])
data['decam_flux'].append([
rows[i][1], rows[i][11], rows[i][21], rows[i][31], rows[i][41],
rows[i][51]
])
data['decam_flux_ivar'].append([
rows[i][2], rows[i][12], rows[i][22], rows[i][32], rows[i][42],
rows[i][52]
])
data['decam_fracflux'].append([
rows[i][3], rows[i][13], rows[i][23], rows[i][33], rows[i][43],
rows[i][53]
])
data['decam_fracmasked'].append([
rows[i][4], rows[i][14], rows[i][24], rows[i][34], rows[i][44],
rows[i][54]
])
data['decam_fracin'].append([
rows[i][5], rows[i][15], rows[i][25], rows[i][35], rows[i][45],
rows[i][55]
])
data['decam_rchi2'].append([
rows[i][6], rows[i][16], rows[i][26], rows[i][36], rows[i][46],
rows[i][56]
])
data['decam_nobs'].append([
rows[i][7], rows[i][17], rows[i][27], rows[i][37], rows[i][47],
rows[i][57]
])
data['decam_anymask'].append([
rows[i][8], rows[i][18], rows[i][28], rows[i][38], rows[i][48],
rows[i][58]
])
data['decam_allmask'].append([
rows[i][9], rows[i][19], rows[i][29], rows[i][39], rows[i][49],
rows[i][59]
])
data['decam_ext'].append([
rows[i][10], rows[i][20], rows[i][30], rows[i][40],
rows[i][50], rows[i][60]
])
c1 = Column(name='cand_id', format='J', array=data['cand_id'])
c2 = Column(name='decam_flux', format='6D', array=data['decam_flux'])
c3 = Column(name='decam_flux_ivar',
format='6D',
array=data['decam_flux_ivar'])
c4 = Column(name='decam_fracflux',
format='6D',
array=data['decam_fracflux'])
c5 = Column(name='decam_fracmasked',
format='6D',
array=data['decam_fracmasked'])
c6 = Column(name='decam_fracin',
format='6D',
array=data['decam_fracin'])
c7 = Column(name='decam_rchi2', format='6D', array=data['decam_rchi2'])
c8 = Column(name='decam_nobs', format='6D', array=data['decam_nobs'])
c9 = Column(name='decam_anymask',
format='6D',
array=data['decam_anymask'])
c10 = Column(name='decam_allmask',
format='6D',
array=data['decam_allmask'])
c11 = Column(name='decam_ext', format='6D', array=data['decam_ext'])
hdu = fits.BinTableHDU.from_columns(
[c1, c2, c3, c4, c5, c6, c7, c8, c9, c10, c11])
# dtypes = [('cand_id', 'i4'),('decam_flux',np.float64(6,)),
# ('decam_flux_ivar',np.float64(6,)),('decam_fracflux',np.float64(6,)),('decam_fracmasked',np.float64(6,)),('decam_fracin',np.float64(6,)),
# ('decam_rchi2',np.float64(6,)),('decam_nobs',np.float64(6,)),('decam_anymask',np.float64(6,)),('decam_allmask',np.float64(6,)),('decam_ext',np.float64(6,))]
# data = np.zeros((nrows,6), dtype=dtypes)
elif result['table'] == 'WISE':
dtypes = [()]
#line_cand = [ tbdata['brickid'][i], tbdata['objid'][i], tbdata['blob'][i], tbdata['type'][i], tbdata['ra'][i], tbdata['ra_ivar'][i], tbdata['dec'][i], tbdata['dec_ivar'][i], tbdata['bx'][i], tbdata['by'][i], tbdata['bx0'][i], tbdata['by0'][i], bool(lb), bool(oob), tbdata['ebv'][i], tbdata['dchisq'][i][0], tbdata['dchisq'][i][1], tbdata['dchisq'][i][2], tbdata['dchisq'][i][3], tbdata['fracDev'][i], tbdata['fracDev_ivar'][i], tbdata['shapeExp_r'][i], tbdata['shapeExp_r_ivar'][i], tbdata['shapeExp_e1'][i], tbdata['shapeExp_e1_ivar'][i], tbdata['shapeExp_e2'][i], tbdata['shapeExp_e2_ivar'][i], tbdata['shapeDev_r'][i], tbdata['shapeDev_r_ivar'][i], tbdata['shapeDev_e1'][i], tbdata['shapeDev_e1_ivar'][i], tbdata['shapeDev_e2'][i], tbdata['shapeDev_e2_ivar'][i] ]
# for later
# ('decam_flux','f8',(3,4)),('decam_flux_ivar','f8',(3,4)),('decam_apflux','f8',(3,4)),
# ('decam_apflux_resid','f8',(3,4)),('decam_apflux_ivar','f8',(3,4)),('decam_mw_transmission','f8',(3,4)),
# ('decam_nobs','f8',(3,4)),('decam_rchi2','f8',(3,4)),('decam_fracflux','f8',(3,4)),('decam_fracmasked','f8',(3,4)),
# ('decam_fracin','f8',(3,4)),('decam_saturated','f8',(3,4)),('out_of_bounds','f8',(3,4)),('decam_anymask','f8',(3,4)),
# ('decam_allmask','f8',(3,4))
outfile = 'data.fits'
fits.writeto(outfile, hdu.data, hdu.header, clobber=True)
fsock = open(outfile, "rb")
response = StreamingHttpResponse(fsock, content_type='application/fits')
response['Content-Disposition'] = 'attachment; filename="' + outfile + '"'
return response
return_S2=True,
ncores=ncores)
table = [
fits.Column(name='rmpc', format='E', array=r),
fits.Column(name='xmpc', format='E', array=x),
fits.Column(name='ympc', format='E', array=y),
fits.Column(name='S0', format='E', array=S0),
fits.Column(name='DS0', format='E', array=DS0),
fits.Column(name='S', format='E', array=S),
fits.Column(name='DS', format='E', array=DS),
fits.Column(name='Gt', format='E', array=gt),
fits.Column(name='S2', format='E', array=s2),
fits.Column(name='Gx', format='E', array=gx)
]
tbhdu = fits.BinTableHDU.from_columns(fits.ColDefs(table))
h = fits.Header()
h.append(('lM200', np.round(lM200_miss, 4)))
h.append(('soff', np.round(c200_miss, 4)))
h.append(('c200', np.round(soff, 4)))
h.append(('q', np.round(q, 4)))
primary_hdu = fits.PrimaryHDU(header=h)
hdul = fits.HDUList([primary_hdu, tbhdu])
hdul.writeto(folder + 'mapas/mapa_bin_' + sampname + '_miss.fits',
overwrite=True)
def createLCproperties(self, z, appmag, sig, fname, lag_frac, fdir=None):
'''
Generates a few parameters necessary for AGN simulation.
Parameters are saved to zeroeth extension header of .fits-file
saved with name and directory specified by input parameters.
If an identical file already exists, the file will be overwritten.
---
INPUT:
z: float
Redshift of the AGN we wish to create.
appmag: float
Apparent magnitude (in r-band) of the AGN we wish to create.
fdir: string
Directory where we wish to save the .fits-file containing the
light-curves representing the AGN we are about to create.
fname: string
Name of .fits-file containing the light-curve representing the
AGN we are about to create. Do not include ".fits".
---
'''
# Define AGN parameters directly dependent on z and rmag
waveZ, lum, Lbol = self.getLbol(z, appmag, self.gFilter)
absMag = self.getAbsMag(z, appmag, Lbol, self.iFilter)
lL5100, lL3000, lL1350, Hbeta, MgII, CIV = self.getLag(z, waveZ, lum)
Hbeta *= lag_frac
MgII *= lag_frac
CIV *= lag_frac
if z <= 0.62: # H beta
logmBH = np.random.normal(8.23,0.37)-9.
elif z <= 1.8 and z >0.62: # MgII
logmBH = np.random.normal(9.65,0.39)-9.
else: # CIV
logmBH = np.random.normal(9.55,0.27)-9.
'''
if z <= 0.62: # H beta
lag = Hbeta/(1+z)
elif z <= 1.8 and z >0.62: # MgII
lag = MgII/(1+z)
else: # CIV
lag = CIV/(1+z)
G = 6.67*10**-11
c = 2.998*10**8
f = 4.47
Msun = 1.989*10**30
lag = lag*86400
velocity = velocity*1000
logmBH = np.log10(f*(pow(velocity, 2)*c*lag/G)/Msun)-9
'''
# Define SFinfty and tau parameters based on MacLeod+10
Asf = -0.51
Bsf = -0.479
Csf = 0.131
Dsf = 0.18
Atau = 2.4
Btau = 0.17
Ctau = 0.03
Dtau = 0.21
# Define wavelengths for specific emission lines
LamH = 5100.
LamMg = 3000.
LamC = 1350.
# Define SFinfty and tau for each emission line
# use 2*std of cont data
sfH = 2.*sig
sfMg = 2.*sig
sfC = 2.*sig
#sfH = 10**( Asf + Bsf*np.log10(LamH/4000) + Csf*(absMag+23) + Dsf*logmBH )
#sfMg = 10**( Asf + Bsf*np.log10(LamMg/4000) + Csf*(absMag+23) + Dsf*logmBH )
#sfC = 10**( Asf + Bsf*np.log10(LamC/4000) + Csf*(absMag+23) + Dsf*logmBH )
tauH = 10**( Atau + Btau*np.log10(LamH/4000) + Ctau*(absMag+23) + Dtau*logmBH ) * (1.+z)
tauMg = 10**( Atau + Btau*np.log10(LamMg/4000) + Ctau*(absMag+23) + Dtau*logmBH ) * (1.+z)
tauC = 10**( Atau + Btau*np.log10(LamC/4000) + Ctau*(absMag+23) + Dtau*logmBH ) * (1.+z)
# Create .fits-header
hdr = fits.Header()
hdr['Z'] = z # Redshift
hdr['L'] = Lbol # Bolometric luminosity
hdr['MBH'] = 10**(logmBH+9) # Black hole mass
hdr['SFH'] = sfH # SFinfty for Hbeta
hdr['SFM'] = sfMg # SFinfty for MgII
hdr['SFC'] = sfC # SFinfty for CIV
hdr['TAUDH'] = tauH # tau for Hbeta
hdr['TAUDM'] = tauMg # tau for MgII
hdr['TAUDC'] = tauC # tau for CIV
hdr['LAMBDAH'] = LamH # Wavelength of Hbeta
hdr['LAMBDAM'] = LamMg # Wavelength of MgII
hdr['LAMBDAC'] = LamC # Wavelength of CIV
hdr['LAMLUMH'] = lL5100 # Wavelength * spectral luminosity for Hbeta
hdr['LAMLUMM'] = lL3000 # Wavelength * spectral luminosity for MgII
hdr['LAMLUMC'] = lL1350 # Wavelength * spectral luminosity for CIV
hdr['AGNLAGH'] = Hbeta # AGN Hbeta lag
hdr['AGNLAGM'] = MgII # AGN MgII lag
hdr['AGNLAGC'] = CIV # AGN CIV lag
hdr['RAPPMAG'] = appmag # Apparent magnitude through r-band filter
hdr['IABSMAG'] = absMag # Absolute magnitude through i-band filter
hdu = fits.PrimaryHDU(header=hdr)
# Check whether directory is specified, name .fits-file accordingly
if fdir:
if not os.path.exists(fdir): os.makedirs(fdir)
ffile = fdir+fname+'_sim.fits'
else:
ffile = fname+'_sim.fits'
# End if-statement
# Save .fits-file
if os.path.isfile(ffile): os.remove(ffile)
hdu.writeto(ffile)
os.path.join(
rootdir,
'sector001_camera{camera:d}_ccd{ccd:d}.hdf5'.format(
camera=camera, ccd=ccd)), 'r') as hdf:
N = len(hdf['images'])
a = np.full(N, np.NaN)
b = np.full(N, np.NaN)
cno = np.arange(0, N, 1)
for k in trange(N):
if hdf['quality'][k] == 0:
hdr_string = hdf['wcs']['%04d' % k][0]
if not isinstance(hdr_string, str):
hdr_string = hdr_string.decode("utf-8") # For Python 3
wcs = WCS(header=fits.Header().fromstring(hdr_string),
relax=True)
xycen = wcs.all_world2pix(np.atleast_2d(camera_centre),
0,
ra_dec_order=True)
a[k] = xycen[0][0]
b[k] = xycen[0][1]
am = np.nanmedian(a)
bm = np.nanmedian(b)
plt.figure()
plt.scatter(cno, a)
plt.axhline(am)
def create_catalog(snap_name, z):
"""
Creates summary catalog for AGN only"""
#
fileList_snap = n.array(
glob.glob(
os.path.join(os.environ["MD10"], 'work_agn',
'out_' + snap_name + '_SAM_Nb_?.fits')))
fileList_ms = n.array(
glob.glob(
os.path.join(os.environ["MD10"], 'work_agn',
'out_' + snap_name + '_SAM_Nb_?_Ms.fits')))
fileList_Xray = n.array(
glob.glob(
os.path.join(os.environ["MD10"], 'work_agn',
'out_' + snap_name + '_SAM_Nb_?_Xray.fits')))
fileList_snap.sort()
fileList_ms.sort()
fileList_Xray.sort()
out_snap = os.path.join(os.environ['MD10'], "catalogs",
'out_' + snap_name + "_AGN_snapshot.fits")
out_ms = os.path.join(os.environ['MD10'], "catalogs",
'out_' + snap_name + "_AGN_Ms.fits")
out_xray = os.path.join(os.environ['MD10'], "catalogs",
'out_' + snap_name + "_AGN_Xray.fits")
# loops over files
dat_snap = []
dat_ms = []
dat_xray = []
LX = []
index = n.searchsorted(z_vals, z)
for fileSnap, fileMs, fileXray in zip(fileList_snap, fileList_ms,
fileList_Xray):
print fileSnap
print fileMs
print fileXray
hd = fits.open(fileSnap)
hm = fits.open(fileMs)
hx = fits.open(fileXray)
MS = hm[1].data['stellar_mass_Mo13_mvir']
SAR = hx[1].data['lambda_sar_Bo16']
agn = (hx[1].data['activity']) & (MS > 0)
lognh = hx[1].data['log_NH_Buchner2017']
dat_snap.append(hd[1].data[agn])
dat_ms.append(hm[1].data[agn])
dat_xray.append(hx[1].data[agn])
percent_observed = obscuration_interpolation_grid[index](lognh)
LX.append(n.log10(10**(MS[agn] + SAR[agn]) * percent_observed[agn]))
hdu_cols = fits.ColDefs(n.hstack((dat_snap)))
print "snap", n.hstack((dat_snap)).shape
tb_hdu = fits.BinTableHDU.from_columns(hdu_cols)
#define the header
prihdr = fits.Header()
prihdr['author'] = 'JC'
prihdr['info'] = 'snapshot'
prihdu = fits.PrimaryHDU(header=prihdr)
#writes the file
thdulist = fits.HDUList([prihdu, tb_hdu])
if os.path.isfile(out_snap):
os.system("rm " + out_snap)
thdulist.writeto(out_snap)
hdu_cols = fits.ColDefs(n.hstack((dat_ms)))
print "ms", n.hstack((dat_ms)).shape
tb_hdu = fits.BinTableHDU.from_columns(hdu_cols)
#define the header
prihdr = fits.Header()
prihdr['author'] = 'JC'
prihdr['info'] = 'ms'
prihdu = fits.PrimaryHDU(header=prihdr)
#writes the file
thdulist = fits.HDUList([prihdu, tb_hdu])
if os.path.isfile(out_ms):
os.system("rm " + out_ms)
thdulist.writeto(out_ms)
hdu_cols = fits.ColDefs(n.hstack((dat_xray)))
hdu_cols.add_col(
fits.Column(name='LX_05_2_keV', format='D', array=n.hstack((LX))))
print "xray", n.hstack((dat_xray)).shape
tb_hdu = fits.BinTableHDU.from_columns(hdu_cols)
#define the header
prihdr = fits.Header()
prihdr['author'] = 'JC'
prihdr['info'] = 'xray'
prihdu = fits.PrimaryHDU(header=prihdr)
#writes the file
thdulist = fits.HDUList([prihdu, tb_hdu])
if os.path.isfile(out_xray):
os.system("rm " + out_xray)
thdulist.writeto(out_xray)
theta = float(hdulist[0].header['BPA']) # degree, from +Y, https://github.com/astropy/astropy/issues/3550
print('psf major minor theta %.4f %.4f %.2f'%(stddev_major, stddev_minor, theta))
#theta = 0.0 # theta = 0.0 is +X direction! checked by dzliu 20170305.
#theta = 90.0/180.0*numpy.pi # theta = 90.0 is +Y direction! checked by dzliu 20170305.
PsfModel = Gaussian2D(1.0000, 0.0, 0.0, stddev_major/pixscale, stddev_minor/pixscale, (theta+90.0)/180.0*numpy.pi) # amplitude, x_mean, y_mean, x_stddev, y_stddev, theta
PsfNAXIS = numpy.max([stddev_major, stddev_minor]) / pixscale * 15.0
PsfNAXIS = numpy.round((PsfNAXIS-1.0)/2.0)*2+1 # make it odd number
PsfNAXIS = numpy.array([PsfNAXIS, PsfNAXIS])
print('psf model model naxis %d %d'%(PsfNAXIS[0], PsfNAXIS[1]))
PsfModel.bounding_box = ((-(PsfNAXIS[0]-1)/2, (PsfNAXIS[0]-1)/2), (-(PsfNAXIS[1]-1)/2, (PsfNAXIS[1]-1)/2))
PsfImage = PsfModel.render()
#print(PsfModel.render())
hdr = fits.Header()
hdr['BMAJ'] = hdulist[0].header['BMAJ']
hdr['BMIN'] = hdulist[0].header['BMIN']
hdr['BPA'] = hdulist[0].header['BPA']
hdr['PIXSCALE'] = pixscale
hdu = fits.PrimaryHDU(PsfImage, header=hdr)
hduli = fits.HDUList([hdu])
# output to outfile
if os.path.isfile(outfile):
os.system('mv \"%s\" \"%s\"'%(outfile, outfile.replace('.fits','.backup.fits')))
print('Backed up existing \"%s\" as \"%s\"!'%(outfile, outfile.replace('.fits','.backup.fits')))
hduli.writeto(outfile)
print('Output to \"%s\"!'%(outfile))
def head(self):
"""Returns the first Window or an empty fits.Header if there is
no first Window. The header of the first Window is where general
header items of the CCD are stored."""
return next(iter(self.values()), fits.Header())
def cube2spec(cube,x,y,s,write=None,shape='box',helio=0,mask=None,twod=True,tovac=False,idsource=None):
"""
Extract a 1D spectrum from a cube at position x,y in box or circle of radius s
If shape = 'mask', then mask is a boolean mask and pixels within it will be extracted form
argument mask. Mask is a datacube [e.g. from cubex]
idsource -> if > 0, then only pixels in mask with that ID will be extracted
helio passes an heliocentric correction in km/s [should be 0 with pipeline v1.2.1]
twod -> also reconstruct a 2D spec
tovac -> if true, return wavelengths in vacuum
write -> output file
"""
import matplotlib.pyplot as plt
import numpy as np
from astropy.io import fits
#read the cube
cubdata,vardata,wcsc,wavec,regi=readcube(cube,helio=helio)
cubdata=np.nan_to_num(cubdata)
#if mask extract all True pixels
if('mask' in shape):
if(idsource):
goodpix=np.nonzero(mask == idsource)
else:
goodpix=np.nonzero(mask)
xpix=goodpix[1]
ypix=goodpix[2]
else:
#If user defined region, grab inner pixels
#cut region of interest according to shape
xpix=[]
ypix=[]
xside=np.arange(x-s-1,x+s+1,1)
yside=np.arange(y-s-1,y+s+1,1)
for xx in xside:
for yy in yside:
if('box' in shape):
if((abs(xx-x) <= s) & (abs(yy-y) <= s)):
xpix.append(xx)
ypix.append(yy)
if('circ' in shape):
dist=np.sqrt((xx-x)**2+(yy-y)**2)
if(dist <= s):
xpix.append(xx)
ypix.append(yy)
#Some checks...
#cbmed=np.median(cubdata,axis=0)
#cbmed[xpix,ypix]=100000
#imgplot=plt.imshow(cbmed,origin='lower')
#imgplot.set_clim(-5,5)
#plt.show()
#now make space for the 1d spectrum
spec_flx=np.zeros(len(wavec))
spec_var=np.zeros(len(wavec))
spec_med=np.zeros(len(wavec))
#if want 2d, prepapre space for it
#This simulates a slit in the x direction
#adding up all the flux on the y
if(twod):
#find unique pixels (not all x,y) - need to sort for later
uxpix=np.sort(list(set(xpix)))
uypix=np.sort(list(set(ypix)))
npix=len(uxpix)
nwv=len(wavec)
twodspec=np.zeros((nwv,npix))
twoderr=np.zeros((nwv,npix))
#loop over all wavelength to fill in spectrum
for ii,ww in enumerate(wavec):
#get the total spec in the aperture,
#summing over all the pixels
spec_flx[ii]=np.sum(cubdata[ii,xpix,ypix])
spec_var[ii]=np.sum(vardata[ii,xpix,ypix])
spec_med[ii]=np.median(cubdata[ii,xpix,ypix])
#fill in 2D spectrum in a box
if(twod):
#sum only on the full x-extent
for jj in range(npix):
#add all the pixels in y
twodspec[ii,jj]=np.sum(cubdata[ii,uxpix[jj],uypix])
twoderr[ii,jj]=np.sum(vardata[ii,uxpix[jj],uypix])
#extract the 2D image with a small buffer around
if(twod):
twodimg=np.median(cubdata[:,uxpix[0]-5:uxpix[-1]+6,uypix[0]-5:uypix[-1]+6],axis=0)
#from variance to error
twoderr=np.sqrt(twoderr)
#mean in aperture
#totpix=len(xpix)
#spec_flx=spec_flx/totpix
#spec_err=np.sqrt(spec_var/totpix)
#keep total spectrum and not mean
totpix=len(xpix)
spec_err=np.sqrt(spec_var)
#if set, convert to vacuum using airtovac.pro conversion
if(tovac):
#save current wave
wavec=np.array(wavec,dtype=np.float64)
wave_air=wavec
sigma2 = (1e4/wavec)**2.
fact = 1.+5.792105e-2/(238.0185-sigma2)+1.67917e-3/(57.362-sigma2)
wavec = wavec*fact
#tested and working
#fl=open('test.txt','w')
#for rr in range(len(wavec)):
# fl.write("{} {}\n".format(wave_air[rr],wavec[rr]))
#fl.close()
#if write, write
if(write):
prihdr = fits.Header()
prihdr['NPIX'] = totpix
hduflx = fits.PrimaryHDU(spec_flx,header=prihdr) #total in region
hduerr = fits.ImageHDU(spec_err) #associated errors
hduwav = fits.ImageHDU(wavec) #wave
hdumed = fits.ImageHDU(spec_med) #median spectrum
if(twod): #twod
hdu2flx = fits.ImageHDU(twodspec)
hdu2err = fits.ImageHDU(twoderr)
hduimg = fits.ImageHDU(twodimg)
hdulist = fits.HDUList([hduflx,hduerr,hduwav,hdumed,hdu2flx,hdu2err,hduimg])
else:
hdulist = fits.HDUList([hduflx,hduerr,hduwav,hdumed])
hdulist.writeto(write,clobber=True)
return wavec, spec_flx, spec_err, spec_med
def write(self, fname, overwrite=False, xgap=200, ygap=200):
"""Writes out the MCCD to a FITS file.
Arguments::
fname : string or file-like object
Name of file to write to. Can also be a file, opened in
writeable binary mode.
overwrite : bool
True to overwrite pre-existing files
xgap : int
X-gap used to space CCDs for ds9 mosaicing (unbinned pixels)
ygap : int
Y-gap used to space CCDs for ds9 mosaicing (unbinned pixels)
"""
phead = self.head.copy()
phead["NUMCCD"] = (len(self), "Number of CCDs")
phead["HIPERCAM"] = ("MCCD", "Type of HiPERCAM data (CCD | MCCD)")
# Add comments if not already present.
comm1 = "Data representing multiple CCDs written by hipercam.MCCD.write."
if "COMMENT" not in phead or str(phead["COMMENT"]).find(comm1) == -1:
phead.add_comment(comm1)
phead.add_comment(
"Each window of each CCD is written in a series of HDUs following an"
)
phead.add_comment(
"HDU containing only the header. These follow an overall header for the"
)
phead.add_comment(
"MCCD containing top-level information. The headers of the data window"
)
phead.add_comment(
"HDUs have keywords LLX, LLY giving the pixel location in unbinned"
)
phead.add_comment(
"pixels and XBIN and YBIN for their binning factors. The total unbinned"
)
phead.add_comment(
"dimensions of each CCD are stored under keywords NXTOT and NYTOT for"
)
phead.add_comment(
"each CCD. Each HDU associated with a given CCD is labelled with a"
)
phead.add_comment("header keyword CCD.")
# make the first HDU
hdul = fits.HDUList()
hdul.append(fits.PrimaryHDU(header=fits.Header(phead.cards)))
# add in the HDUs of all the CCDs NX = 3 specific to HiPERCAM but
# should do reasonably generally I think.
xoff, yoff, noff = 0, 0, 0
NX = 3
for cnam, ccd in self.items():
ccd.whdul(hdul, cnam, xoff, yoff)
noff += 1
if noff % NX == 0:
xoff = 0
yoff -= (ccd.nytot + 2 * ccd.nypad) + ygap
else:
xoff += (ccd.nxtot + 2 * ccd.nxpad) + xgap
hdul.writeto(fname, overwrite=overwrite)
def writeSingleFITS(data, wcs, output, template, clobber=True, verbose=True):
""" Write out a simple FITS file given a numpy array and the name of another
FITS file to use as a template for the output image header.
"""
outname, outextn = fileutil.parseFilename(output)
outextname, outextver = fileutil.parseExtn(outextn)
if fileutil.findFile(outname):
if clobber:
log.info('Deleting previous output product: %s' % outname)
fileutil.removeFile(outname)
else:
log.warning('Output file %s already exists and overwrite not '
'specified!' % outname)
log.error('Quitting... Please remove before resuming operations.')
raise IOError
# Now update WCS keywords with values from provided WCS
if hasattr(wcs.sip, 'a_order'):
siphdr = True
else:
siphdr = False
wcshdr = wcs.wcs2header(sip2hdr=siphdr)
if template is not None:
# Get default headers from multi-extension FITS file
# If input data is not in MEF FITS format, it will return 'None'
# NOTE: These are HEADER objects, not HDUs
(prihdr, scihdr, errhdr,
dqhdr), newtab = getTemplates(template, EXTLIST)
if scihdr is None:
scihdr = fits.Header()
indx = 0
for c in prihdr.cards:
if c.keyword not in ['INHERIT', 'EXPNAME']: indx += 1
else: break
for i in range(indx, len(prihdr)):
scihdr.append(prihdr.cards[i])
for i in range(indx, len(prihdr)):
del prihdr[indx]
else:
scihdr = fits.Header()
prihdr = fits.Header()
# Start by updating PRIMARY header keywords...
prihdr.set('EXTEND', value=True, after='NAXIS')
prihdr['FILENAME'] = outname
if outextname == '':
outextname = 'sci'
if outextver == 0: outextver = 1
scihdr['EXTNAME'] = outextname.upper()
scihdr['EXTVER'] = outextver
for card in wcshdr.cards:
scihdr[card.keyword] = (card.value, card.comment)
# Create PyFITS HDUList for all extensions
outhdu = fits.HDUList()
# Setup primary header as an HDU ready for appending to output FITS file
prihdu = fits.PrimaryHDU(header=prihdr)
scihdu = fits.ImageHDU(header=scihdr, data=data)
outhdu.append(prihdu)
outhdu.append(scihdu)
outhdu.writeto(outname)
if verbose:
print('Created output image: %s' % outname)
def parse(file, psfTable, outFolder, pixelPlane):
'''
a parser for G4output.
It's easier to parallelize if written as a separate function.
'''
# initialization
lineNum = 0
nTrk = 0 # count number of tracks
# prepare files
print 'parsing # ', file
f = open(file, 'r')
lines = f.readlines()
fileIdx = re.split('\.', file)[0]
x_tmp = []
y_tmp = []
z_tmp = []
dE_tmp = []
xDir = -1
yDir = -1
if os.path.isfile('%s/%s.fits' % (outFolder, fileIdx)):
return
for line in lines:
if line[0] == '*' and x_tmp:
print 'see * in ', file
elif 'physiTracker' not in line:
continue
elif 'physiTracker' in line:
lineSplit = re.split(r'\s*[(), \s]\s*', line)
if lineSplit[0] == '':
lineSplit = lineSplit[1:]
if not x_tmp:
xDir = float(lineSplit[7])
yDir = float(lineSplit[8])
xInit = float(lineSplit[0])
yInit = float(lineSplit[1])
eInit = float(lineSplit[5])
x_tmp.append(float(lineSplit[0]))
y_tmp.append(float(lineSplit[1]))
z_tmp.append(float(lineSplit[2]))
dE_tmp.append(float(lineSplit[6]))
else:
# executed after 'for' terminates normally
# when 'for' terminates normally, it reaches the end of file
if x_tmp:
x = []
y = []
z = []
dE = []
x = np.array(x_tmp)
y = np.array(y_tmp) - 2000.
z = np.array(z_tmp)
dE = np.array(dE_tmp)
alpha_true = rad2deg(arctan(xDir / yDir))
if alpha_true < 0:
alpha_true += 360.
del x_tmp, y_tmp, z_tmp, dE_tmp
track, row0_pos_um, col0_pos_um = XYZdE2track(
x, y, z, dE, psfTable, pixelPlane)
h = fits.Header()
h['row0_um'] = row0_pos_um
h['col0_um'] = col0_pos_um
h['alphaT'] = alpha_true
h['xInit'] = xInit
h['yInit'] = yInit
h['eInit'] = eInit
prihdu = fits.PrimaryHDU(track, header=h)
row_pix = (y - row0_pos_um) / 10.5
col_pix = (x - col0_pos_um) / 10.5
row = fits.Column(name='row', format='F', array=row_pix)
col = fits.Column(name='col', format='F', array=col_pix)
tbhdu = fits.BinTableHDU.from_columns(fits.ColDefs([row, col]))
hdulist = fits.HDUList([prihdu, tbhdu])
hdulist.writeto('%s/%s.fits' % (outFolder, fileIdx))
f.close()
unpack=True,
dtype='float',
skiprows=1)
# Rebinando de modo a ter um passo constante, pequeno o suficiente para nao perder informacoes
rebin = interpolate.interp1d(l, f)
# calculando o tamanho do passo no inicio do espectro e pegando soh 10%
binsize = 0.1 * (l[1] - l[0])
# criando um array com os novos comprimentos de onda (rebinados)
n_l = np.arange(l[0], l[-1], binsize)
# Interpolando os antigos para poder calcular os novos valores
n_f = rebin(n_l) * NormalizationFactor
# criando a lista de HDU (para fazer o fits)
savefile = pf.HDUList()
# criando a lista de header (para fazer o fits)
hdr = pf.Header()
# Adicionando keywords aos header
hdr.append(('OBJECT', sourceName.split('.')[0]))
hdr.append(('CTYPE1', 'LINEAR'))
# hdr.append(('CRPIX1',float(n_l[0])))
hdr.append(('CRVAL1', float(n_l[0])))
hdr.append(('CD1_1', float(binsize)))
#hdr.append(('WAT1_001', 'wtype=linear axtype=wave' ))
# Salvando os valores de fluxo no HDU
savefile.append(pf.ImageHDU(data=n_f, header=hdr))
# grando o HDU em fits
savefile.writeto(sourceName.split('.')[0] + '.fits', overwrite=True)
if savetxt:
save = np.column_stack((n_l, n_f))
np.savetxt(sourceName.split('.')[0] + '.txt',
for i in range(5, 10):
h = fits.open('trnslos_20180414_%i.fits' % i)
trnslos[(i - 5) * 1000:(i - 4) * 1000] = h[0].data
h.close()
'''open training slopes'''
h = fits.open('trnslos_20180405.fits')
trnslos_all = h[0].data
h.close()
'''remove mean from raw x and y slopes'''
trnslos = trnslos.reshape((5000 * 100 * 2, 36))
nor_trnslos = np.empty((1000000, 36))
for i in range(1000000):
tmp = trnslos[i].copy()
nor_trnslos[i] = tmp - tmp.mean()
nor_trnslos = nor_trnslos.reshape((5000, 7200))
header = fits.Header()
header["r_0"] = str([0.16])
header["WINDSPD"] = str([5, 6, 7, 8, 9])
header["WINDDIR"] = str([0])
header["SAVETIME"] = datetime.datetime.now().strftime("%Y-%m-%d-%H-%M-%S")
header["ITERS"] = str([1000])
header['ITERTIME'] = str([0.012])
fits.writeto('trnslos_20180416.fits', nor_trnslos)
'''multi sets augmentation'''
n_frame = 100
trnslos = np.zeros((15000, 72 * n_frame))
h = fits.open('trnslos_20180414.fits')
tmp = h[0].data
h.close()
for i in range(0, 15, 3):
j = i / 3
def _make_image_header(
nxpix=100,
nypix=100,
binsz=0.1,
xref=0,
yref=0,
proj="CAR",
coordsys="GAL",
xrefpix=None,
yrefpix=None,
):
"""Generate a FITS header from scratch.
Uses the same parameter names as the Fermi tool gtbin.
If no reference pixel position is given it is assumed ot be
at the center of the image.
Parameters
----------
nxpix : int, optional
Number of pixels in x axis. Default is 100.
nypix : int, optional
Number of pixels in y axis. Default is 100.
binsz : float, optional
Bin size for x and y axes in units of degrees. Default is 0.1.
xref : float, optional
Coordinate system value at reference pixel for x axis. Default is 0.
yref : float, optional
Coordinate system value at reference pixel for y axis. Default is 0.
proj : string, optional
Projection type. Default is 'CAR' (cartesian).
coordsys : {'CEL', 'GAL'}, optional
Coordinate system. Default is 'GAL' (Galactic).
xrefpix : float, optional
Coordinate system reference pixel for x axis. Default is None.
yrefpix: float, optional
Coordinate system reference pixel for y axis. Default is None.
Returns
-------
header : `~astropy.io.fits.Header`
Header
"""
nxpix = int(nxpix)
nypix = int(nypix)
if not xrefpix:
xrefpix = (nxpix + 1) / 2.
if not yrefpix:
yrefpix = (nypix + 1) / 2.
if coordsys == "CEL":
ctype1, ctype2 = "RA---", "DEC--"
elif coordsys == "GAL":
ctype1, ctype2 = "GLON-", "GLAT-"
else:
raise ValueError("Unsupported coordsys: {!r}".format(coordsys))
pars = {
"NAXIS": 2,
"NAXIS1": nxpix,
"NAXIS2": nypix,
"CTYPE1": ctype1 + proj,
"CRVAL1": xref,
"CRPIX1": xrefpix,
"CUNIT1": "deg",
"CDELT1": -binsz,
"CTYPE2": ctype2 + proj,
"CRVAL2": yref,
"CRPIX2": yrefpix,
"CUNIT2": "deg",
"CDELT2": binsz,
}
header = fits.Header()
header.update(pars)
return header
def split_file(N_side, original_filename, file_number, save_location,
output_format):
#Open the original .fits file, and extract the data we need.
print('Opening ', original_filename, ' ...')
initial = fits.open(original_filename)
#NORMALISE THE DELTA FIELD SO THAT ITS MEAN IS 0.
#THIS IS AN ONGOING ISSUE IN COLORE, AND IS LISTED TO BE FIXED SO THAT THE DELTA MEAN IS 0 AUTOMATICALLY.
#initial = stats.normalise_delta(initial)
RA = initial[1].data['RA']
DEC = initial[1].data['DEC']
z_qso = initial[1].data['Z_COSMO']
z = initial[4].data['Z']
DELTA = initial[2].data[:]
initial.close()
N_cells = z.shape[0]
N_qso = z_qso.shape[0]
N_pix = 12 * N_side**2
iv = np.ones((N_qso, N_cells))
PLATE = np.zeros(N_qso, dtype=np.int)
MJD = np.zeros(N_qso, dtype=np.int)
FIBER = np.zeros(N_qso, dtype=np.int)
#Set THING_ID as a 10 digit string, of which the first 3 digits correspond to the node number, and the last 7 correspond to the row number in the original file.
THING_ID = [''] * N_qso
node = str(file_number)
if len(node) <= 3:
node = '0' * (3 - len(node)) + node
else:
exit(
'The node number is too great to construct a unique THING_ID (more than 3 digits).'
)
row_numbers = list(range(N_qso))
for i in range(len(row_numbers)):
row_numbers[i] = str(row_numbers[i])
if len(row_numbers[i]) <= 7:
row_numbers[i] = '0' * (7 - len(row_numbers[i])) + row_numbers[i]
else:
exit(
'The row number is too great to construct a unique THING_ID (more than 7 digits).'
)
THING_ID[i] = node + row_numbers[i]
#Set up the LOGLAM_MAP
lya = 1215.67
LOGLAM_MAP = np.log10(lya * (1 + z))
#Convert the coordinates into new pixel identifier numbers, according to the N_side specified.
pixel_ID = np.zeros([1, len(RA)])
#Convert DEC and RA in degrees to theta and phi in radians.
theta = (np.pi / 180.0) * (90.0 - DEC)
phi = (np.pi / 180.0) * RA
#Make a list of the HEALPix pixel coordinate of each quasar.
for i in range(len(RA)):
#Can we just import healpy on cori? May need to install
#Check that the angular coordinates are valid. Put all objects with invalid coordinates into a non-realistic ID number (-1).
if 0 <= theta[i] <= np.pi and 0 <= phi[i] <= 2 * np.pi:
pixel_ID[0, i] = hp.pixelfunc.ang2pix(N_side, theta[i], phi[i])
else:
pixel_ID[0, i] = int(node) - 12 * N_side**2
#print('There are %d objects with invalid angular coordinates.' % (sum(pixel_ID[i] == -1 for i in range(len(pixel_ID)))))
print(
'Details of these objects are stored in a file corresponding to a pixel number of -(node number).'
)
#Set up a pixel_ID list to map between objects and their pixel.
pixel_ID = pixel_ID.reshape(-1)
#Set up a list of pixels represented in the original .fits file.
pixel_list = list(np.sort(list(set(pixel_ID))))
#For each pixel represented in the original .fits file, make a new file.
for n in pixel_list:
#Progress check aide.
if n + 1 > 0:
print('Working on pixel %d (N_pix = %d)' % (n, N_pix))
else:
print(
'Working on set of objects with invalid angular coordinates.')
pixel_indices = [i for i in range(len(pixel_ID)) if pixel_ID[i] == n]
pixel_DELTA = np.array([DELTA[i, :] for i in pixel_indices])
pixel_iv = np.array([iv[i, :] for i in pixel_indices])
pixel_RA = [RA[i] for i in pixel_indices]
pixel_DEC = [DEC[i] for i in pixel_indices]
pixel_z_qso = [z_qso[i] for i in pixel_indices]
pixel_PLATE = [PLATE[i] for i in pixel_indices]
pixel_MJD = [MJD[i] for i in pixel_indices]
pixel_FIBER = [FIBER[i] for i in pixel_indices]
pixel_THING_ID = [THING_ID[i] for i in pixel_indices]
#Transpose pixel_DELTA and pixel_iv to match picca input.
pixel_DELTA = np.transpose(pixel_DELTA)
pixel_iv = np.transpose(pixel_iv)
if n >= 0:
print('There are %d quasars in pixel %d.' %
(len(pixel_THING_ID), n))
else:
print('There are %d quasars with invalid angular coordinates.' %
(len(pixel_THING_ID)))
if len(pixel_THING_ID) != 0:
if output_format == 0:
#Make output for from fitsio
print('Not written yet!')
elif output_format == 1:
#Construct a table for the final hdu.
col_RA = fits.Column(name='RA', array=pixel_RA, format='E')
col_DEC = fits.Column(name='DEC', array=pixel_DEC, format='E')
col_z_qso = fits.Column(name='Z',
array=pixel_z_qso,
format='E')
col_PLATE = fits.Column(name='PLATE',
array=pixel_PLATE,
format='E')
col_MJD = fits.Column(name='MJD', array=pixel_MJD, format='E')
col_FIBER = fits.Column(name='FIBER',
array=pixel_FIBER,
format='E')
col_THING_ID = fits.Column(name='THING_ID',
array=pixel_THING_ID,
format='10A')
cols = fits.ColDefs([
col_RA, col_DEC, col_z_qso, col_PLATE, col_MJD, col_FIBER,
col_THING_ID
])
#Add a couple of headers to the file.
header = fits.Header()
header['NSIDE'] = N_side
header['NQSO'] = len(pixel_THING_ID)
header['PIX'] = int(n)
header['LYA'] = lya
#Create hdus from the data arrays
hdu_DELTA = fits.PrimaryHDU(data=pixel_DELTA, header=header)
hdu_iv = fits.ImageHDU(data=pixel_iv, header=header, name='IV')
hdu_LOGLAM_MAP = fits.ImageHDU(data=LOGLAM_MAP,
header=header,
name='LOGLAM_MAP')
tbhdu = fits.BinTableHDU.from_columns(cols, header=header)
hdulist = fits.HDUList(
[hdu_DELTA, hdu_iv, hdu_LOGLAM_MAP, tbhdu])
if n >= 0:
new_filename = save_location + '/' + 'node_%s_nside_%d_pix_%d.fits' % (
node, N_side, n)
else:
new_filename = save_location + '/' + 'invalid_coords_node_%s_nside_%d.fits' % (
node, N_side)
hdulist.writeto(new_filename)
else:
#Some kind of error and option to put in a new format code?
print('Try another format!')
else:
print('No objects in pixel %d.' % n)
return THING_ID, pixel_ID