lsst.pipe.tasks  13.0-66-gfbf2f2ce+5
exampleCmdLineTask.py
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22 from __future__ import absolute_import, division, print_function
23 from lsst.afw.display.ds9 import mtv
24 import lsst.pex.config as pexConfig
25 import lsst.pipe.base as pipeBase
26 from .exampleStatsTasks import ExampleSigmaClippedStatsTask
27 
28 __all__ = ["ExampleCmdLineConfig", "ExampleCmdLineTask"]
29 
30 # The following block adds links to this task from the Task Documentation page.
31 # This works even for task(s) that are not in lsst.pipe.tasks.
32 
38 
39 
40 class ExampleCmdLineConfig(pexConfig.Config):
41  """!Configuration for ExampleCmdLineTask
42  """
43  stats = pexConfig.ConfigurableField(
44  doc="Subtask to compute statistics of an image",
45  target=ExampleSigmaClippedStatsTask,
46  )
47  doFail = pexConfig.Field(
48  doc="Raise an lsst.base.TaskError exception when processing each image? "
49  + "This allows one to see the effects of the --doraise command line flag",
50  dtype=bool,
51  default=False,
52  )
53 
54 
55 class ExampleCmdLineTask(pipeBase.CmdLineTask):
56  """!Example command-line task that computes simple statistics on an image
57 
58  \section pipeTasks_ExampleCmdLineTask_Contents Contents
59 
60  - \ref pipeTasks_ExampleCmdLineTask_Purpose
61  - \ref pipeTasks_ExampleCmdLineTask_Config
62  - \ref pipeTasks_ExampleCmdLineTask_Debug
63  - \ref pipeTasks_ExampleCmdLineTask_Example
64 
65  \section pipeTasks_ExampleCmdLineTask_Purpose Description
66 
67  \copybrief ExampleCmdLineTask
68 
69  This task was written as an example for the documents \ref pipeTasks_writeTask
70  and \ref pipeTasks_writeCmdLineTask.
71  The task reads in a "calexp" (a calibrated science \ref lsst::afw::image::Exposure "exposure"),
72  computes statistics on the image plane, and logs and returns the statistics.
73  In addition, if debugging is enabled, it displays the image in ds9.
74 
75  The image statistics are computed using a subtask, in order to show how to call subtasks and how to
76  \ref pipeBase_argumentParser_retargetSubtasks "retarget" (replace) them with variant subtasks.
77 
78  The main method is \ref ExampleCmdLineTask.run "run".
79 
80  \section pipeTasks_ExampleCmdLineTask_Config Configuration parameters
81 
82  See \ref ExampleCmdLineConfig
83 
84  \section pipeTasks_ExampleCmdLineTask_Debug Debug variables
85 
86  This task supports the following debug variables:
87  <dl>
88  <dt>`display`
89  <dd>If True then display the exposure in ds9
90  </dl>
91 
92  To enable debugging, see \ref baseDebug.
93 
94  \section pipeTasks_ExampleCmdLineTask_Example A complete example of using ExampleCmdLineTask
95 
96  This code is in examples/exampleCmdLineTask.py, and can be run as follows:
97  \code
98  examples/exampleCmdLineTask.py $OBS_TEST_DIR/data/input --id
99  # that will process all data; you can also try any combination of these flags:
100  --id filter=g
101  --config doFail=True --doraise
102  --show config data
103  \endcode
104  """
105  ConfigClass = ExampleCmdLineConfig
106  _DefaultName = "exampleTask"
107 
108  def __init__(self, *args, **kwargs):
109  """Construct an ExampleCmdLineTask
110 
111  Call the parent class constructor and make the "stats" subtask from the config field of the same name.
112  """
113  pipeBase.CmdLineTask.__init__(self, *args, **kwargs)
114  self.makeSubtask("stats")
115 
116  @pipeBase.timeMethod
117  def run(self, dataRef):
118  """!Compute a few statistics on the image plane of an exposure
119 
120  @param dataRef: data reference for a calibrated science exposure ("calexp")
121  @return a pipeBase Struct containing:
122  - mean: mean of image plane
123  - meanErr: uncertainty in mean
124  - stdDev: standard deviation of image plane
125  - stdDevErr: uncertainty in standard deviation
126  """
127  self.log.info("Processing data ID %s" % (dataRef.dataId,))
128  if self.config.doFail:
129  raise pipeBase.TaskError("Raising TaskError by request (config.doFail=True)")
130 
131  # Unpersist the raw exposure pointed to by the data reference
132  rawExp = dataRef.get("raw")
133  maskedImage = rawExp.getMaskedImage()
134 
135  # Support extra debug output.
136  # -
137  import lsstDebug
138  display = lsstDebug.Info(__name__).display
139  if display:
140  frame = 1
141  mtv(rawExp, frame=frame, title="exposure")
142 
143  # return the pipe_base Struct that is returned by self.stats.run
144  return self.stats.run(maskedImage)
145 
146  def _getConfigName(self):
147  """!Get the name prefix for the task config's dataset type, or None to prevent persisting the config
148 
149  This override returns None to avoid persisting metadata for this trivial task.
150 
151  However, if the method returns a name, then the full name of the dataset type will be <name>_config.
152  The default CmdLineTask._getConfigName returns _DefaultName,
153  which for this task would result in a dataset name of "exampleTask_config".
154 
155  Normally you can use the default CmdLineTask._getConfigName, but here are two reasons
156  why you might want to override it:
157  - If you do not want your task to write its config, then have the override return None.
158  That is done for this example task, because I didn't want to clutter up the
159  repository with config information for a trivial task.
160  - If the default name would not be unique. An example is
161  \ref lsst.pipe.tasks.makeSkyMap.MakeSkyMapTask "MakeSkyMapTask": it makes a
162  \ref lsst.skymap.SkyMap "sky map" (sky pixelization for a coadd)
163  for any of several different types of coadd, such as deep or goodSeeing.
164  As such, the name of the persisted config must include the coadd type in order to be unique.
165 
166  Normally if you override _getConfigName then you override _getMetadataName to match.
167  """
168  return None
169 
170  def _getMetadataName(self):
171  """!Get the name prefix for the task metadata's dataset type, or None to prevent persisting metadata
172 
173  This override returns None to avoid persisting metadata for this trivial task.
174 
175  However, if the method returns a name, then the full name of the dataset type will be <name>_metadata.
176  The default CmdLineTask._getConfigName returns _DefaultName,
177  which for this task would result in a dataset name of "exampleTask_metadata".
178 
179  See the description of _getConfigName for reasons to override this method.
180  """
181  return None
def run(self, dataRef)
Compute a few statistics on the image plane of an exposure.
Example command-line task that computes simple statistics on an image.