Coverage for python/lsst/obs/fiberspectrograph/data_manager.py: 33%
44 statements
« prev ^ index » next coverage.py v7.4.4, created at 2024-03-16 03:02 -0700
« prev ^ index » next coverage.py v7.4.4, created at 2024-03-16 03:02 -0700
1# This file is part of obs_fiberspectrograph
2#
3# Developed for the LSST Data Management System.
4# This product includes software developed by the LSST Project
5# (https://www.lsst.org).
6# See the COPYRIGHT file at the top-level directory of this distribution
7# for details of code ownership.
8#
9# This program is free software: you can redistribute it and/or modify
10# it under the terms of the GNU General Public License as published by
11# the Free Software Foundation, either version 3 of the License, or
12# (at your option) any later version.
13#
14# This program is distributed in the hope that it will be useful,
15# but WITHOUT ANY WARRANTY; without even the implied warranty of
16# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17# GNU General Public License for more details.
18#
19# You should have received a copy of the GNU General Public License
20# along with this program. If not, see <https://www.gnu.org/licenses/>.
22import astropy.io.fits
25class DataManager:
26 """A data packager for `Spectrum` objects
27 that comes from the ts_fiberspectrograph package
28 """
30 wcs_table_name = "WCS-TAB"
31 """Name of the table containing the wavelength WCS (EXTNAME)."""
32 wcs_table_ver = 1
33 """WCS table version (EXTVER)."""
34 wcs_column_name = "wavelength"
35 """Name of the table column containing the wavelength information."""
37 # The version of the FITS file format produced by this class.
38 FORMAT_VERSION = 1
40 def __init__(self, spectrum):
41 self.spectrum = spectrum
43 def make_hdulist(self):
44 """Generate a FITS hdulist built from SpectrographData.
45 Parameters
46 ----------
47 spec : `SpectrographData`
48 The data from which to build the FITS hdulist.
49 Returns
50 -------
51 hdulist : `astropy.io.fits.HDUList`
52 The FITS hdulist.
53 """
54 hdu1 = self.make_primary_hdu()
55 hdu2 = self.make_wavelength_hdu()
56 hdu3, hdu4 = self.make_maskvariance_hdu()
57 return astropy.io.fits.HDUList([hdu1, hdu2, hdu3, hdu4])
59 def make_fits_header(self):
60 """Return a FITS header built from a Spectrum"""
61 hdr = astropy.io.fits.Header()
63 hdr["FORMAT_V"] = self.FORMAT_VERSION
64 hdr.update(self.spectrum.metadata)
66 # WCS headers - Use -TAB WCS definition
67 wcs_cards = [
68 "WCSAXES = 1 / Number of WCS axes",
69 "CRPIX1 = 0.0 / Reference pixel on axis 1",
70 "CRVAL1 = 0.0 / Value at ref. pixel on axis 1",
71 "CNAME1 = 'Wavelength' / Axis name for labeling purposes",
72 "CTYPE1 = 'WAVE-TAB' / Wavelength axis by lookup table",
73 "CDELT1 = 1.0 / Pixel size on axis 1",
74 f"CUNIT1 = '{self.spectrum.wavelength.unit.name:8s}' / Units for axis 1",
75 f"PV1_1 = {self.wcs_table_ver:20d} / EXTVER of bintable extension for -TAB arrays",
76 f"PS1_0 = '{self.wcs_table_name:8s}' / EXTNAME of bintable extension for -TAB arrays",
77 f"PS1_1 = '{self.wcs_column_name:8s}' / Wavelength coordinate array",
78 ]
79 for c in wcs_cards:
80 hdr.append(astropy.io.fits.Card.fromstring(c))
82 return hdr
84 def make_primary_hdu(self):
85 """Return the primary HDU built from a Spectrum."""
87 hdu = astropy.io.fits.PrimaryHDU(
88 data=self.spectrum.flux, header=self.make_fits_header()
89 )
90 return hdu
92 def make_maskvariance_hdu(self):
93 """Return the HDU for the mask and variance plane."""
94 hdr_mask = astropy.io.fits.Header()
95 hdr_mask["EXTTYPE"] = 'MASK '
96 hdr_mask["EXTNAME"] = 'MASK '
97 hdu_mask = astropy.io.fits.ImageHDU(
98 data=self.spectrum.mask, header=hdr_mask
99 )
101 hdr_variance = astropy.io.fits.Header()
102 hdr_variance["EXTTYPE"] = 'VARIANCE'
103 hdr_variance["EXTNAME"] = 'VARIANCE'
104 hdu_variance = astropy.io.fits.ImageHDU(
105 data=self.spectrum.variance, header=hdr_variance
106 )
107 return hdu_mask, hdu_variance
109 def make_wavelength_hdu(self):
110 """Return the wavelength HDU built from a Spectrum."""
112 # The wavelength array must be 2D (N, 1) in numpy but (1, N) in FITS
113 wavelength = self.spectrum.wavelength.reshape([self.spectrum.wavelength.size, 1])
115 # Create a Table. It will be a single element table
116 table = astropy.table.Table()
118 # Create the wavelength column
119 # Create the column explicitly since it is easier to ensure the
120 # shape this way.
121 wavecol = astropy.table.Column([wavelength], unit=wavelength.unit.name)
123 # The column name must match the PS1_1 entry from the primary HDU
124 table[self.wcs_column_name] = wavecol
126 # The name MUST match the value of PS1_0 and the version MUST
127 # match the value of PV1_1
128 hdu = astropy.io.fits.BinTableHDU(table, name=self.wcs_table_name, ver=1)
129 return hdu