23 """Base classes for single-frame measurement plugins and the driver task for these. 25 In single-frame measurement, we assume that detection and probably deblending have already been run on 26 the same frame, so a SourceCatalog has already been created with Footprints (which may be HeavyFootprints). 27 Measurements are generally recorded in the coordinate system of the image being measured (and all 28 slot-eligible fields must be), but non-slot fields may be recorded in other coordinate systems if necessary 29 to avoid information loss (this should, of course, be indicated in the field documentation). 32 from .pluginRegistry
import PluginRegistry
33 from .baseMeasurement
import (BaseMeasurementPluginConfig, BaseMeasurementPlugin,
34 BaseMeasurementConfig, BaseMeasurementTask)
35 from .noiseReplacer
import NoiseReplacer, DummyNoiseReplacer
37 __all__ = (
"SingleFramePluginConfig",
"SingleFramePlugin",
38 "SingleFrameMeasurementConfig",
"SingleFrameMeasurementTask")
43 Base class for configs of single-frame plugin algorithms. 50 Base class for single-frame plugin algorithms. 52 New Plugins can be created in Python by inheriting directly from this class 53 and implementing measure(), fail() (from BasePlugin), and optionally __init__ 54 and measureN(). Plugins can also be defined in C++ via the WrappedSingleFramePlugin 60 ConfigClass = SingleFramePluginConfig
62 def __init__(self, config, name, schema, metadata, logName=None, **kwds):
64 Initialize the measurement object. 66 @param[in] config An instance of this class's ConfigClass. 67 @param[in] name The string the plugin was registered with. 68 @param[in,out] schema The Source schema. New fields should be added here to 69 hold measurements produced by this plugin. 70 @param[in] metadata Plugin metadata that will be attached to the output catalog 71 @param[in] logName May include logName to use for this plugin 73 BaseMeasurementPlugin.__init__(self, config, name, logName=logName)
77 Measure the properties of a source on a single image (single-epoch image or coadd). 79 @param[in,out] measRecord lsst.afw.table.SourceRecord to be filled with outputs, 80 and from which previously-measured quantities can be 83 @param[in] exposure lsst.afw.image.ExposureF, containing the pixel data to 84 be measured and the associated Psf, Wcs, etc. All 85 other sources in the image will have been replaced by 86 noise according to deblender outputs. 89 raise NotImplementedError()
93 Measure the properties of a group of blended sources on a single image 94 (single-epoch image or coadd). 96 @param[in,out] measCat lsst.afw.table.SourceCatalog to be filled with outputs, 97 and from which previously-measured quantities can be 98 retrieved, containing only the sources that should be 99 measured together in this call. 101 @param[in] exposure lsst.afw.image.ExposureF, containing the pixel data to 102 be measured and the associated Psf, Wcs, etc. Sources 103 not in the blended hierarchy to be measured will have 104 been replaced with noise using deblender outputs. 106 Derived classes that do not implement measureN() should just inherit this 107 disabled version. Derived classes that do implement measureN() should additionally 108 add a bool doMeasureN config field to their config class to signal that measureN-mode 111 raise NotImplementedError()
116 Config class for single frame measurement driver task. 119 plugins = SingleFramePlugin.registry.makeField(
121 default=[
"base_PixelFlags",
123 "base_GaussianCentroid",
124 "base_NaiveCentroid",
128 "base_CircularApertureFlux",
133 doc=
"Plugins to be run and their configuration" 135 algorithms = property(
lambda self: self.
plugins, doc=
"backwards-compatibility alias for plugins")
136 undeblended = SingleFramePlugin.registry.makeField(
139 doc=
"Plugins to run on undeblended image" 152 \anchor SingleFrameMeasurementTask_ 154 \brief A subtask for measuring the properties of sources on a single exposure. 156 The task is configured with a list of "plugins": each plugin defines the values it 157 measures (i.e. the columns in a table it will fill) and conducts that measurement 158 on each detected source (see SingleFramePlugin). The job of the 159 measurement task is to initialize the set of plugins (which includes setting up the 160 catalog schema) from their configuration, and then invoke each plugin on each 163 When run after the deblender (see lsst.meas.deblender.SourceDeblendTask), 164 SingleFrameMeasurementTask also replaces each source's neighbors with noise before 165 measuring each source, utilizing the HeavyFootprints created by the deblender (see 168 SingleFrameMeasurementTask has only two methods: __init__() and run(). For configuration 169 options, see SingleFrameMeasurementConfig. 171 @section meas_base_sfm_Example A complete example of using SingleFrameMeasurementTask 173 The code below is in examples/runSingleFrameTask.py 175 @dontinclude runSingleFrameTask.py 177 See meas_algorithms_detection_Example for more information on SourceDetectionTask. 179 First, import the required tasks (there are some other standard imports; 180 read the file if you're confused): 182 @skip SourceDetectionTask 183 @until SingleFrameMeasurementTask 185 We need to create our tasks before processing any data as the task constructors 186 can add extra columns to the schema. The most important argument we pass these to these 187 is an lsst.afw.table.Schema object, which contains information about the fields (i.e. columns) of the 188 measurement catalog we'll create, including names, types, and additional documentation. 189 Tasks that operate on a catalog are typically passed a Schema upon construction, to which 190 they add the fields they'll fill later when run. We construct a mostly empty Schema that 191 contains just the fields required for a SourceCatalog like this: 195 Now we can configure and create the SourceDetectionTask: 199 We then move on to configuring the measurement task: 203 While a reasonable set of plugins is configured by default, we'll customize the list. 204 We also need to unset one of the slots at the same time, because we're 205 not running the algorithm that it's set to by default, and that would cause problems later: 209 Now, finally, we can construct the measurement task: 211 @skipline measureTask 213 After constructing all the tasks, we can inspect the Schema we've created: 215 @skipline print schema 217 All of the fields in the 218 schema can be accessed via the get() method on a record object. See afwTable for more 221 We're now ready to process the data (we could loop over multiple exposures/catalogs using the same 222 task objects). First create the output table and process the image to find sources: 232 We then might plot the results (@em e.g. if you set `--ds9` on the command line) 237 and end up with something like 239 @image html runSingleFrameTask-ds9.png 242 ConfigClass = SingleFrameMeasurementConfig
244 NOISE_SEED_MULTIPLIER =
"NOISE_SEED_MULTIPLIER" 245 NOISE_SOURCE =
"NOISE_SOURCE" 246 NOISE_OFFSET =
"NOISE_OFFSET" 247 NOISE_EXPOSURE_ID =
"NOISE_EXPOSURE_ID" 249 def __init__(self, schema, algMetadata=None, **kwds):
251 Initialize the task. Set up the execution order of the plugins and initialize 252 the plugins, giving each plugin an opportunity to add its measurement fields to 253 the output schema and to record information in the task metadata. 255 @param[in,out] schema lsst.afw.table.Schema, to be initialized to include the 256 measurement fields from the plugins already 257 @param[in,out] algMetadata lsst.daf.base.PropertyList used to record information about 258 each algorithm. An empty PropertyList will be created if None. 259 @param[in] **kwds Keyword arguments forwarded to lsst.pipe.base.Task.__init__ 262 super(SingleFrameMeasurementTask, self).
__init__(algMetadata=algMetadata, **kwds)
264 self.config.slots.setupSchema(self.
schema)
268 if 'base_Blendedness' in self.
plugins:
274 def run(self, measCat, exposure, noiseImage=None, exposureId=None, beginOrder=None, endOrder=None):
276 Run single frame measurement over an exposure and source catalog 278 @param[in,out] measCat lsst.afw.table.SourceCatalog to be filled with outputs. Must 279 contain all the SourceRecords to be measured (with Footprints 280 attached), and have a schema that is a superset of self.schema. 282 @param[in] exposure lsst.afw.image.ExposureF, containing the pixel data to 283 be measured and the associated Psf, Wcs, etc. 284 @param[in] noiseImage optional lsst.afw.image.ImageF for test which need to control 286 @param[in] exposureId optional unique exposureId used to calculate random number 287 generator seed in the NoiseReplacer. 288 @param[in] beginOrder beginning execution order (inclusive): measurements with 289 executionOrder < beginOrder are not executed. None for no limit. 290 @param[in] endOrder ending execution order (exclusive): measurements with 291 executionOrder >= endOrder are not executed. None for no limit. 293 assert measCat.getSchema().contains(self.
schema)
294 footprints = {measRecord.getId(): (measRecord.getParent(), measRecord.getFootprint())
295 for measRecord
in measCat}
301 if self.config.doReplaceWithNoise:
302 noiseReplacer =
NoiseReplacer(self.config.noiseReplacer, exposure, footprints,
303 noiseImage=noiseImage, log=self.log, exposureId=exposureId)
304 algMetadata = measCat.getMetadata()
305 if algMetadata
is not None:
307 algMetadata.addString(self.
NOISE_SOURCE, self.config.noiseReplacer.noiseSource)
308 algMetadata.addDouble(self.
NOISE_OFFSET, self.config.noiseReplacer.noiseOffset)
309 if exposureId
is not None:
314 self.
runPlugins(noiseReplacer, measCat, exposure, beginOrder, endOrder)
316 def runPlugins(self, noiseReplacer, measCat, exposure, beginOrder=None, endOrder=None):
317 """Function which calls the defined measument plugins on an exposure 321 noiseReplacer : lsst.meas.base.NoiseReplacer 322 noiseReplacer to fill sources not being measured with noise. 324 measCat : lsst.afw.table.SourceCatalog 325 SourceCatalog to be filled with outputs. Must contain all the SourceRecords to be measured (with 326 Footprints attached), and have a schema that is a superset of self.schema. 328 exposure : lsst.afw.image.ExposureF 329 Exposure contaning the pixel data to be measured and the associated PSF, WCS, etc. 332 beginning execution order (inclusive): measurements with executionOrder < beginOrder are not 333 executed. None for no limit. 336 ending execution order (exclusive): measurements with executionOrder >= endOrder are not 337 executed. None for no limit. 341 measParentCat = measCat.getChildren(0)
343 self.log.info(
"Measuring %d sources (%d parents, %d children) " 344 % (len(measCat), len(measParentCat), len(measCat) - len(measParentCat)))
346 for parentIdx, measParentRecord
in enumerate(measParentCat):
348 measChildCat = measCat.getChildren(measParentRecord.getId())
350 for measChildRecord
in measChildCat:
351 noiseReplacer.insertSource(measChildRecord.getId())
352 self.
callMeasure(measChildRecord, exposure, beginOrder=beginOrder, endOrder=endOrder)
355 self.
blendPlugin.cpp.measureChildPixels(exposure.getMaskedImage(), measChildRecord)
357 noiseReplacer.removeSource(measChildRecord.getId())
360 noiseReplacer.insertSource(measParentRecord.getId())
361 self.
callMeasure(measParentRecord, exposure, beginOrder=beginOrder, endOrder=endOrder)
364 self.
blendPlugin.cpp.measureChildPixels(exposure.getMaskedImage(), measParentRecord)
367 self.
callMeasureN(measParentCat[parentIdx:parentIdx+1], exposure,
368 beginOrder=beginOrder, endOrder=endOrder)
369 self.
callMeasureN(measChildCat, exposure, beginOrder=beginOrder, endOrder=endOrder)
370 noiseReplacer.removeSource(measParentRecord.getId())
376 for source
in measCat:
382 for source
in measCat:
383 self.
blendPlugin.cpp.measureParentPixels(exposure.getMaskedImage(), source)
387 Backwards-compatibility alias for run() 389 self.
run(measCat, exposure)
Base config class for all measurement plugins.
def callMeasure(self, measRecord, args, kwds)
Call the measure() method on all plugins, handling exceptions in a consistent way.
def measure(self, measRecord, exposure)
Measure the properties of a source on a single image (single-epoch image or coadd).
A subtask for measuring the properties of sources on a single exposure.
def measureN(self, measCat, exposure)
Measure the properties of a group of blended sources on a single image (single-epoch image or coadd)...
def measure(self, measCat, exposure)
Backwards-compatibility alias for run()
def runPlugins(self, noiseReplacer, measCat, exposure, beginOrder=None, endOrder=None)
string NOISE_SEED_MULTIPLIER
def callMeasureN(self, measCat, args, kwds)
Call the measureN() method on all plugins, handling exceptions in a consistent way.
Base class for configs of single-frame plugin algorithms.
Base class for single-frame plugin algorithms.
def __init__(self, config, name, schema, metadata, logName=None, kwds)
Initialize the measurement object.
def run(self, measCat, exposure, noiseImage=None, exposureId=None, beginOrder=None, endOrder=None)
Run single frame measurement over an exposure and source catalog.
Config class for single frame measurement driver task.
Base class for plugin registries.
A do-nothing standin for NoiseReplacer, used when we want to disable NoiseReplacer.
def __init__(self, schema, algMetadata=None, kwds)
Initialize the task.
Class that handles replacing sources with noise during measurement.
Ultimate base class for all measurement tasks.
Base config class for all measurement driver tasks.
def initializePlugins(self, kwds)
def doMeasurement(self, plugin, measRecord, args, kwds)
Call the measure() method on the nominated plugin, handling exceptions in a consistent way...