lsst.meas.algorithms gf36ae6ace1+09a7694010
readFitsCatalogTask.py
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2# LSST Data Management System
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23
24__all__ = ["ReadFitsCatalogConfig", "ReadFitsCatalogTask"]
25
26from astropy.table import Table
27
28import lsst.pex.config as pexConfig
29import lsst.pipe.base as pipeBase
30
31
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 )
45
46
47class ReadFitsCatalogTask(pipeBase.Task):
48 """Read an object catalog from a FITS table
49
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
56
57 def run(self, filename):
58 """Read an object catalog from the specified FITS file
59
60 Parameters
61 ----------
62 filename : `str`
63 Path to specified FITS file
64
65 Returns
66 -------
67 table : `np.array`
68 a numpy structured array containing the specified columns
69 """
70
71 table = Table.read(filename, hdu=self.config.hdu)
72 if table is None:
73 raise RuntimeError("No data found in %s HDU %s" % (filename, self.config.hdu))
74
75 if not self.config.column_map:
76 # take the data as it is
77 return table.as_array()
78
79 missingnames = set(self.config.column_map.keys()) - set(table.columns.keys())
80 if missingnames:
81 raise RuntimeError("Columns %s in column_map were not found in %s" % (missingnames, filename))
82
83 for inname, outname in self.config.column_map.items():
84 table.columns[inname].name = outname
85 return table.as_array()