Coverage for python/lsst/meas/algorithms/readFitsCatalogTask.py : 93%

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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 )
46## @addtogroup LSST_task_documentation
47## @{
48## @page ReadFitsCatalogTask
49## @ref ReadFitsCatalogTask_ "ReadFitsCatalogTask"
50## @copybrief ReadFitsCatalogTask
51## @}
54class ReadFitsCatalogTask(pipeBase.Task):
55 r"""!Read an object catalog from a FITS table
57 @anchor ReadFitsCatalogTask_
59 @section meas_algorithms_readFitsCatalog_Contents Contents
61 - @ref meas_algorithms_readFitsCatalog_Purpose
62 - @ref meas_algorithms_readFitsCatalog_Initialize
63 - @ref meas_algorithms_readFitsCatalog_Config
64 - @ref meas_algorithms_readFitsCatalog_Example
66 @section meas_algorithms_readFitsCatalog_Purpose Description
68 Read an object catalog from a FITS table. Designed to read foreign catalogs
69 so they can be written out in a form suitable for IngestIndexedReferenceTask.
71 @section meas_algorithms_readFitsCatalog_Initialize Task initialisation
73 @copydoc \_\_init\_\_
75 @section meas_algorithms_readFitsCatalog_Config Configuration parameters
77 See @ref ReadFitsCatalogConfig
79 @section meas_algorithms_readFitsCatalog_Example A complete example of using ReadFitsCatalogTask
81 Run the following code from the main directory of meas_algorithms:
83 from lsst.meas.algorithms.readFitsCatalogTask import ReadFitsCatalogTask
84 filePath = "tests/data/testReadFitsCatalog.fits"
85 task = ReadFitsCatalogTask()
86 catalogArray = task.run(filePath)
88 The resulting `catalogArray` is a numpy structured array containing fields such as "name", "ra" and "dec"
89 and a few rows of data. For more complicated cases config parameters allow you to rename columns
90 and choose which HDU to read.
91 """
92 _DefaultName = 'readCatalog'
93 ConfigClass = ReadFitsCatalogConfig
95 def run(self, filename):
96 """Read an object catalog from the specified FITS file
98 @param[in] filename path to FITS file
99 @return a numpy structured array containing the specified columns
100 """
102 table = Table.read(filename, hdu=self.config.hdu)
103 if table is None: 103 ↛ 104line 103 didn't jump to line 104, because the condition on line 103 was never true
104 raise RuntimeError("No data found in %s HDU %s" % (filename, self.config.hdu))
106 if not self.config.column_map:
107 # take the data as it is
108 return table.as_array()
110 missingnames = set(self.config.column_map.keys()) - set(table.columns.keys())
111 if missingnames:
112 raise RuntimeError("Columns %s in column_map were not found in %s" % (missingnames, filename))
114 for inname, outname in self.config.column_map.items():
115 table.columns[inname].name = outname
116 return table.as_array()