Coverage for python/lsst/pipe/tasks/processCcd.py: 59%
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1#
2# LSST Data Management System
3# Copyright 2008-2016 AURA/LSST.
4#
5# This product includes software developed by the
6# LSST Project (http://www.lsst.org/).
7#
8# This program is free software: you can redistribute it and/or modify
9# it under the terms of the GNU General Public License as published by
10# the Free Software Foundation, either version 3 of the License, or
11# (at your option) any later version.
12#
13# This program is distributed in the hope that it will be useful,
14# but WITHOUT ANY WARRANTY; without even the implied warranty of
15# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
16# GNU General Public License for more details.
17#
18# You should have received a copy of the LSST License Statement and
19# the GNU General Public License along with this program. If not,
20# see <https://www.lsstcorp.org/LegalNotices/>.
21#
22from lsst.ip.isr import IsrTask
23import lsst.pex.config as pexConfig
24import lsst.pipe.base as pipeBase
25from lsst.utils.timer import timeMethod
26from .calibrate import CalibrateTask
27from .characterizeImage import CharacterizeImageTask
29__all__ = ["ProcessCcdConfig", "ProcessCcdTask"]
32class ProcessCcdConfig(pexConfig.Config):
33 """Config for ProcessCcd"""
34 isr = pexConfig.ConfigurableField(
35 target=IsrTask,
36 doc="""Task to perform instrumental signature removal or load a post-ISR image; ISR consists of:
37 - assemble raw amplifier images into an exposure with image, variance and mask planes
38 - perform bias subtraction, flat fielding, etc.
39 - mask known bad pixels
40 - provide a preliminary WCS
41 """,
42 )
43 charImage = pexConfig.ConfigurableField(
44 target=CharacterizeImageTask,
45 doc="""Task to characterize a science exposure:
46 - detect sources, usually at high S/N
47 - estimate the background, which is subtracted from the image and returned as field "background"
48 - estimate a PSF model, which is added to the exposure
49 - interpolate over defects and cosmic rays, updating the image, variance and mask planes
50 """,
51 )
52 doCalibrate = pexConfig.Field(
53 dtype=bool,
54 default=True,
55 doc="Perform calibration?",
56 )
57 calibrate = pexConfig.ConfigurableField(
58 target=CalibrateTask,
59 doc="""Task to perform astrometric and photometric calibration:
60 - refine the WCS in the exposure
61 - refine the PhotoCalib object in the exposure
62 - detect sources, usually at low S/N
63 """,
64 )
66 def setDefaults(self):
67 self.isr.doWrite = False
68 self.charImage.doWriteExposure = False
70## \addtogroup LSST_task_documentation
71## \{
72## \page page_ProcessCcdTask ProcessCcdTask
73## \ref ProcessCcdTask_ "ProcessCcdTask"
74## \copybrief ProcessCcdTask
75## \}
78class ProcessCcdTask(pipeBase.CmdLineTask):
79 r"""!
80 Assemble raw data, fit the PSF, detect and measure, and fit WCS and zero-point
82 @anchor ProcessCcdTask_
84 @section pipe_tasks_processCcd_Contents Contents
86 - @ref pipe_tasks_processCcd_Purpose
87 - @ref pipe_tasks_processCcd_Initialize
88 - @ref pipe_tasks_processCcd_IO
89 - @ref pipe_tasks_processCcd_Config
90 - @ref pipe_tasks_processCcd_Debug
91 - @ref pipe_tasks_processCcd_Example
93 @section pipe_tasks_processCcd_Purpose Description
95 Perform the following operations:
96 - Call isr to unpersist raw data and assemble it into a post-ISR exposure
97 - Call charImage subtract background, fit a PSF model, repair cosmic rays,
98 detect and measure bright sources, and measure aperture correction
99 - Call calibrate to perform deep detection, deblending and single-frame measurement,
100 refine the WCS and fit the photometric zero-point
102 @section pipe_tasks_processCcd_Initialize Task initialisation
104 @copydoc \_\_init\_\_
106 @section pipe_tasks_processCcd_IO Invoking the Task
108 This task is primarily designed to be run from the command line.
110 The main method is `runDataRef`, which takes a single butler data reference for the raw input data.
112 @section pipe_tasks_processCcd_Config Configuration parameters
114 See @ref ProcessCcdConfig
116 @section pipe_tasks_processCcd_Debug Debug variables
118 ProcessCcdTask has no debug output, but its subtasks do.
120 @section pipe_tasks_processCcd_Example A complete example of using ProcessCcdTask
122 The following commands will process all raw data in obs_test's data repository.
123 Note: be sure to specify an `--output` that does not already exist:
125 setup obs_test
126 setup pipe_tasks
127 processCcd.py $OBS_TEST_DIR/data/input --output processCcdOut --id
129 The data is read from the small repository in the `obs_test` package and written `./processCcdOut`
130 (or whatever output you specified). Specifying `--id` with no values processes all data.
131 Add the option `--help` to see more options.
132 """
133 ConfigClass = ProcessCcdConfig
134 RunnerClass = pipeBase.ButlerInitializedTaskRunner
135 _DefaultName = "processCcd"
137 def __init__(self, butler=None, psfRefObjLoader=None, astromRefObjLoader=None, photoRefObjLoader=None,
138 **kwargs):
139 """!
140 @param[in] butler The butler is passed to the refObjLoader constructor in case it is
141 needed. Ignored if the refObjLoader argument provides a loader directly.
142 @param[in] psfRefObjLoader An instance of LoadReferenceObjectsTasks that supplies an
143 external reference catalog for image characterization. May be None if the desired
144 loader can be constructed from the butler argument or all steps requiring a catalog
145 are disabled.
146 @param[in] astromRefObjLoader An instance of LoadReferenceObjectsTasks that supplies an
147 external reference catalog for astrometric calibration. May be None if the desired
148 loader can be constructed from the butler argument or all steps requiring a reference
149 catalog are disabled.
150 @param[in] photoRefObjLoader An instance of LoadReferenceObjectsTasks that supplies an
151 external reference catalog for photometric calibration. May be None if the desired
152 loader can be constructed from the butler argument or all steps requiring a reference
153 catalog are disabled.
154 @param[in,out] kwargs other keyword arguments for lsst.pipe.base.CmdLineTask
155 """
156 pipeBase.CmdLineTask.__init__(self, **kwargs)
157 self.makeSubtask("isr")
158 self.makeSubtask("charImage", butler=butler, refObjLoader=psfRefObjLoader)
159 self.makeSubtask("calibrate", butler=butler, icSourceSchema=self.charImage.schema,
160 astromRefObjLoader=astromRefObjLoader, photoRefObjLoader=photoRefObjLoader)
162 @timeMethod
163 def runDataRef(self, sensorRef):
164 """Process one CCD
166 The sequence of operations is:
167 - remove instrument signature
168 - characterize image to estimate PSF and background
169 - calibrate astrometry and photometry
171 @param sensorRef: butler data reference for raw data
173 @return pipe_base Struct containing these fields:
174 - charRes: object returned by image characterization task; an lsst.pipe.base.Struct
175 that will include "background" and "sourceCat" fields
176 - calibRes: object returned by calibration task: an lsst.pipe.base.Struct
177 that will include "background" and "sourceCat" fields
178 - exposure: final exposure (an lsst.afw.image.ExposureF)
179 - background: final background model (an lsst.afw.math.BackgroundList)
180 """
181 self.log.info("Processing %s", sensorRef.dataId)
183 exposure = self.isr.runDataRef(sensorRef).exposure
185 charRes = self.charImage.runDataRef(
186 dataRef=sensorRef,
187 exposure=exposure,
188 doUnpersist=False,
189 )
190 exposure = charRes.exposure
192 if self.config.doCalibrate:
193 calibRes = self.calibrate.runDataRef(
194 dataRef=sensorRef,
195 exposure=charRes.exposure,
196 background=charRes.background,
197 doUnpersist=False,
198 icSourceCat=charRes.sourceCat,
199 )
201 return pipeBase.Struct(
202 charRes=charRes,
203 calibRes=calibRes if self.config.doCalibrate else None,
204 exposure=exposure,
205 background=calibRes.background if self.config.doCalibrate else charRes.background,
206 )
208 @classmethod
209 def _makeArgumentParser(cls):
210 """!Create and return an argument parser
212 @param[in] cls the class object
213 @return the argument parser for this task.
215 This override is used to delay making the data ref list until the dataset type is known;
216 this is done in @ref parseAndRun.
217 """
218 parser = pipeBase.ArgumentParser(name=cls._DefaultName)
219 parser.add_id_argument(name="--id",
220 datasetType=pipeBase.ConfigDatasetType(name="isr.datasetType"),
221 help="data IDs, e.g. --id visit=12345 ccd=1,2^0,3")
222 return parser