lsst.meas.algorithms  16.0-29-g31fb3001+2
readFitsCatalogTask.py
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23 
24 __all__ = ["ReadFitsCatalogConfig", "ReadFitsCatalogTask"]
25 
26 from astropy.io import fits
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 
52 
53 
54 class ReadFitsCatalogTask(pipeBase.Task):
55  r"""!Read an object catalog from a FITS table
56 
57  @anchor ReadFitsCatalogTask_
58 
59  @section meas_algorithms_readFitsCatalog_Contents Contents
60 
61  - @ref meas_algorithms_readFitsCatalog_Purpose
62  - @ref meas_algorithms_readFitsCatalog_Initialize
63  - @ref meas_algorithms_readFitsCatalog_Config
64  - @ref meas_algorithms_readFitsCatalog_Example
65 
66  @section meas_algorithms_readFitsCatalog_Purpose Description
67 
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.
70 
71  @section meas_algorithms_readFitsCatalog_Initialize Task initialisation
72 
73  @copydoc \_\_init\_\_
74 
75  @section meas_algorithms_readFitsCatalog_Config Configuration parameters
76 
77  See @ref ReadFitsCatalogConfig
78 
79  @section meas_algorithms_readFitsCatalog_Example A complete example of using ReadFitsCatalogTask
80 
81  Run the following code from the main directory of meas_algorithms:
82 
83  from lsst.meas.algorithms.readFitsCatalogTask import ReadFitsCatalogTask
84  filePath = "tests/data/testReadFitsCatalog.fits"
85  task = ReadFitsCatalogTask()
86  catalogArray = task.run(filePath)
87 
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
94 
95  def run(self, filename):
96  """Read an object catalog from the specified FITS file
97 
98  @param[in] filename path to FITS file
99  @return a numpy structured array containing the specified columns
100  """
101  with fits.open(filename) as f:
102  hdu = f[self.config.hdu]
103  if hdu.data is None:
104  raise RuntimeError("No data found in %s HDU %s" % (filename, self.config.hdu))
105  if hdu.is_image:
106  raise RuntimeError("%s HDU %s is an image" % (filename, self.config.hdu))
107 
108  if not self.config.column_map:
109  # take the data as it is
110  return hdu.data
111 
112  missingnames = set(self.config.column_map.keys()) - set(hdu.columns.names)
113  if missingnames:
114  raise RuntimeError("Columns %s in column_map were not found in %s" % (missingnames, filename))
115 
116  for inname, outname in self.config.column_map.items():
117  hdu.columns[inname].name = outname
118  return hdu.data