lsst.meas.algorithms  22.0.1-16-g996ca242+56fec35c03
readFitsCatalogTask.py
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23 
24 __all__ = ["ReadFitsCatalogConfig", "ReadFitsCatalogTask"]
25 
26 from astropy.table import Table
27 
28 import lsst.pex.config as pexConfig
29 import lsst.pipe.base as pipeBase
30 
31 
32 class 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 
47 class 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()