Coverage for python/lsst/meas/algorithms/readFitsCatalogTask.py: 37%
22 statements
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1#
2# LSST Data Management System
3#
4# Copyright 2008-2017 AURA/LSST.
5#
6# This product includes software developed by the
7# LSST Project (http://www.lsst.org/).
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 LSST License Statement and
20# the GNU General Public License along with this program. If not,
21# see <https://www.lsstcorp.org/LegalNotices/>.
22#
24__all__ = ["ReadFitsCatalogConfig", "ReadFitsCatalogTask"]
26from astropy.table import Table
28import lsst.pex.config as pexConfig
29import lsst.pipe.base as pipeBase
32class ReadFitsCatalogConfig(pexConfig.Config):
33 hdu = pexConfig.Field(
34 dtype=int,
35 default=1,
36 doc="HDU containing the desired binary table, 0-based but a binary table never occurs in HDU 0",
37 )
38 column_map = pexConfig.DictField(
39 doc="Mapping of input column name: output column name; each specified column must exist, "
40 "but additional columns in the input data are written using their original name. ",
41 keytype=str,
42 itemtype=str,
43 default={},
44 )
47class ReadFitsCatalogTask(pipeBase.Task):
48 """Read an object catalog from a FITS table
50 The resulting `catalogArray` is a numpy structured array containing fields such as "name", "ra" and "dec"
51 and a few rows of data. For more complicated cases config parameters allow you to rename columns
52 and choose which HDU to read.
53 """
54 _DefaultName = 'readCatalog'
55 ConfigClass = ReadFitsCatalogConfig
57 def run(self, filename):
58 """Read an object catalog from the specified FITS file
60 Parameters
61 ----------
62 filename : `str`
63 Path to specified FITS file
65 Returns
66 -------
67 table : `np.array`
68 a numpy structured array containing the specified columns
69 """
71 # Set character_as_bytes=False to ensure that all string columns are
72 # set to python string types rather than byte arrays.
73 table = Table.read(filename, hdu=self.config.hdu, character_as_bytes=False)
74 if table is None:
75 raise RuntimeError("No data found in %s HDU %s" % (filename, self.config.hdu))
77 if not self.config.column_map:
78 # take the data as it is
79 return table.as_array()
81 missingnames = set(self.config.column_map.keys()) - set(table.columns.keys())
82 if missingnames:
83 raise RuntimeError("Columns %s in column_map were not found in %s" % (missingnames, filename))
85 for inname, outname in self.config.column_map.items():
86 table.columns[inname].name = outname
87 return table.as_array()