ForcedPhotCcdFromDataFrameTask¶
- class lsst.meas.base.ForcedPhotCcdFromDataFrameTask(butler=None, refSchema=None, initInputs=None, **kwds)¶
Bases:
ForcedPhotCcdTask
Force Photometry on a per-detector exposure with coords from a DataFrame
Uses input from a DataFrame instead of SourceCatalog like the base class ForcedPhotCcd does. Writes out a SourceCatalog so that the downstream WriteForcedSourceTableTask can be reused with output from this Task.
Attributes Summary
Methods Summary
applyOverrides
(config)A hook to allow a task to change the values of its config after the camera-specific overrides are loaded but before any command-line overrides are applied.
attachFootprints
(sources, refCat, exposure, ...)Attach footprints to blank sources prior to measurements.
df2RefCat
(dfList, exposureBBox, exposureWcs)Convert list of DataFrames to reference catalog
df2SourceCat
(df)Create minimal schema SourceCatalog from a pandas DataFrame.
Empty (clear) the metadata for this Task and all sub-Tasks.
fetchReferences
(dataRef, exposure)Get sources that overlap the exposure.
generateMeasCat
(exposureDataId, exposure, ...)Generate a measurement catalog for Gen3.
Get schema catalogs for all tasks in the hierarchy, combining the results into a single dict.
getExposure
(dataRef)Read input exposure for measurement.
getExposureId
(dataRef)Get metadata for all tasks.
Get the task name as a hierarchical name including parent task names.
getName
()Get the name of the task.
Return resource configuration for this task.
The schema catalogs that will be used by this task.
Get a dictionary of all tasks as a shallow copy.
makeField
(doc)Make a
lsst.pex.config.ConfigurableField
for this task.makeIdFactory
(dataRef)Create an object that generates globally unique source IDs.
makeSubtask
(name, **keyArgs)Create a subtask as a new instance as the
name
attribute of this task.mergeAndFilterReferences
(exposure, refCats, ...)Filter reference catalog so that all sources are within the boundaries of the exposure.
parseAndRun
([args, config, log, doReturnResults])Parse an argument list and run the command.
prepareCalibratedExposure
(exposure[, ...])Prepare a calibrated exposure and apply external calibrations and sky corrections if so configured.
run
(measCat, exposure, refCat, refWcs[, ...])Perform forced measurement on a single exposure.
runDataRef
(dataRef[, psfCache])Perform forced measurement on a single exposure.
runQuantum
(butlerQC, inputRefs, outputRefs)Method to do butler IO and or transforms to provide in memory objects for tasks run method
timer
(name[, logLevel])Context manager to log performance data for an arbitrary block of code.
writeConfig
(butler[, clobber, doBackup])Write the configuration used for processing the data, or check that an existing one is equal to the new one if present.
writeMetadata
(dataRef)Write the metadata produced from processing the data.
writeOutput
(dataRef, sources)Write forced source table
writePackageVersions
(butler[, clobber, ...])Compare and write package versions.
writeSchemas
(butler[, clobber, doBackup])Write the schemas returned by
lsst.pipe.base.Task.getAllSchemaCatalogs
.Attributes Documentation
- dataPrefix = ''¶
Methods Documentation
- classmethod applyOverrides(config)¶
A hook to allow a task to change the values of its config after the camera-specific overrides are loaded but before any command-line overrides are applied.
- Parameters:
- configinstance of task’s
ConfigClass
Task configuration.
- configinstance of task’s
Notes
This is necessary in some cases because the camera-specific overrides may retarget subtasks, wiping out changes made in ConfigClass.setDefaults. See LSST Trac ticket #2282 for more discussion.
Warning
This is called by CmdLineTask.parseAndRun; other ways of constructing a config will not apply these overrides.
- attachFootprints(sources, refCat, exposure, refWcs)¶
Attach footprints to blank sources prior to measurements.
Notes
Footprint
s for forced photometry must be in the pixel coordinate system of the image being measured, while the actual detections may start out in a different coordinate system.Subclasses of this class may implement this method to define how those
Footprint
s should be generated.This default implementation transforms depends on the
footprintSource
configuration parameter.
- df2RefCat(dfList, exposureBBox, exposureWcs)¶
Convert list of DataFrames to reference catalog
Concatenate list of DataFrames presumably from multiple patches and downselect rows that overlap the exposureBBox using the exposureWcs.
- Parameters:
- dfList
list
ofpandas.DataFrame
Each element containst diaObjects with ra/decl position in degrees Columns ‘diaObjectId’, ‘ra’, ‘decl’ are expected
- exposureBBox
lsst.geom.Box2I
Bounding box on which to select rows that overlap
- exposureWcs
lsst.afw.geom.SkyWcs
World coordinate system to convert sky coords in ref cat to pixel coords with which to compare with exposureBBox
- dfList
- Returns:
- refCat
lsst.afw.table.SourceTable
Source Catalog with minimal schema that overlaps exposureBBox
- refCat
- df2SourceCat(df)¶
Create minimal schema SourceCatalog from a pandas DataFrame.
The forced measurement subtask expects this as input.
- Parameters:
- df
pandas.DataFrame
DiaObjects with locations and ids.
- df
- Returns:
- outputCatalog
lsst.afw.table.SourceTable
Output catalog with minimal schema.
- outputCatalog
- fetchReferences(dataRef, exposure)¶
Get sources that overlap the exposure.
- Parameters:
- dataRef
lsst.daf.persistence.ButlerDataRef
Butler data reference corresponding to the image to be measured; should have
tract
,patch
, andfilter
keys.- exposure
lsst.afw.image.Exposure
The image to be measured (used only to obtain a WCS and bounding box).
- dataRef
- Returns:
- referencs
lsst.afw.table.SourceCatalog
Catalog of sources that overlap the exposure
- referencs
Notes
The returned catalog is sorted by ID and guarantees that all included children have their parent included and that all Footprints are valid.
All work is delegated to the references subtask; see
lsst.meas.base.references.CoaddSrcReferencesTask
for information about the default behavior.
- generateMeasCat(exposureDataId, exposure, refCat, refWcs, idPackerName)¶
Generate a measurement catalog for Gen3.
- Parameters:
- exposureDataId
DataId
Butler dataId for this exposure.
- exposure
lsst.afw.image.exposure.Exposure
Exposure to generate the catalog for.
- refCat
lsst.afw.table.SourceCatalog
Catalog of shapes and positions at which to force photometry.
- refWcs
lsst.afw.image.SkyWcs
Reference world coordinate system. This parameter is not currently used.
- idPackerName
str
Type of ID packer to construct from the registry.
- exposureDataId
- Returns:
- measCat
lsst.afw.table.SourceCatalog
Catalog of forced sources to measure.
- expId
int
Unique binary id associated with the input exposure
- measCat
- getAllSchemaCatalogs() Dict[str, Any] ¶
Get schema catalogs for all tasks in the hierarchy, combining the results into a single dict.
- Returns:
- schemacatalogs
dict
Keys are butler dataset type, values are a empty catalog (an instance of the appropriate
lsst.afw.table
Catalog type) for all tasks in the hierarchy, from the top-level task down through all subtasks.
- schemacatalogs
Notes
This method may be called on any task in the hierarchy; it will return the same answer, regardless.
The default implementation should always suffice. If your subtask uses schemas the override
Task.getSchemaCatalogs
, not this method.
- getExposure(dataRef)¶
Read input exposure for measurement.
- Parameters:
- dataRef
lsst.daf.persistence.ButlerDataRef
Butler data reference.
- dataRef
- getExposureId(dataRef)¶
- getFullMetadata() TaskMetadata ¶
Get metadata for all tasks.
- Returns:
- metadata
TaskMetadata
The keys are the full task name. Values are metadata for the top-level task and all subtasks, sub-subtasks, etc.
- metadata
Notes
The returned metadata includes timing information (if
@timer.timeMethod
is used) and any metadata set by the task. The name of each item consists of the full task name with.
replaced by:
, followed by.
and the name of the item, e.g.:topLevelTaskName:subtaskName:subsubtaskName.itemName
using
:
in the full task name disambiguates the rare situation that a task has a subtask and a metadata item with the same name.
- getFullName() str ¶
Get the task name as a hierarchical name including parent task names.
- Returns:
- fullName
str
The full name consists of the name of the parent task and each subtask separated by periods. For example:
The full name of top-level task “top” is simply “top”.
The full name of subtask “sub” of top-level task “top” is “top.sub”.
The full name of subtask “sub2” of subtask “sub” of top-level task “top” is “top.sub.sub2”.
- fullName
- getResourceConfig() ResourceConfig | None ¶
Return resource configuration for this task.
- Returns:
- Object of type
ResourceConfig
orNone
if resource - configuration is not defined for this task.
- Object of type
- getSchemaCatalogs()¶
The schema catalogs that will be used by this task.
- Returns:
- schemaCatalogs
dict
Dictionary mapping dataset type to schema catalog.
- schemaCatalogs
Notes
There is only one schema for each type of forced measurement. The dataset type for this measurement is defined in the mapper.
- getTaskDict() Dict[str, ReferenceType[Task]] ¶
Get a dictionary of all tasks as a shallow copy.
- Returns:
- taskDict
dict
Dictionary containing full task name: task object for the top-level task and all subtasks, sub-subtasks, etc.
- taskDict
- classmethod makeField(doc: str) ConfigurableField ¶
Make a
lsst.pex.config.ConfigurableField
for this task.- Parameters:
- doc
str
Help text for the field.
- doc
- Returns:
- configurableField
lsst.pex.config.ConfigurableField
A
ConfigurableField
for this task.
- configurableField
Examples
Provides a convenient way to specify this task is a subtask of another task.
Here is an example of use:
class OtherTaskConfig(lsst.pex.config.Config): aSubtask = ATaskClass.makeField("brief description of task")
- makeIdFactory(dataRef)¶
Create an object that generates globally unique source IDs.
Source IDs are created based on a per-CCD ID and the ID of the CCD itself.
- Parameters:
- dataRef
lsst.daf.persistence.ButlerDataRef
Butler data reference. The
ccdExposureId_bits
andccdExposureId
datasets are accessed. The data ID must have the keys that correspond toccdExposureId
, which are generally the same as those that correspond tocalexp
(visit
,raft
,sensor
for LSST data).
- dataRef
- makeSubtask(name: str, **keyArgs: Any) None ¶
Create a subtask as a new instance as the
name
attribute of this task.- Parameters:
- name
str
Brief name of the subtask.
- keyArgs
Extra keyword arguments used to construct the task. The following arguments are automatically provided and cannot be overridden:
“config”.
“parentTask”.
- name
Notes
The subtask must be defined by
Task.config.name
, an instance ofConfigurableField
orRegistryField
.
- mergeAndFilterReferences(exposure, refCats, refWcs)¶
Filter reference catalog so that all sources are within the boundaries of the exposure.
- Parameters:
- exposure
lsst.afw.image.exposure.Exposure
Exposure to generate the catalog for.
- refCatssequence of
lsst.daf.butler.DeferredDatasetHandle
Handles for catalogs of shapes and positions at which to force photometry.
- refWcs
lsst.afw.image.SkyWcs
Reference world coordinate system.
- exposure
- Returns:
- refSources
lsst.afw.table.SourceCatalog
Filtered catalog of forced sources to measure.
- refSources
Notes
Filtering the reference catalog is currently handled by Gen2 specific methods. To function for Gen3, this method copies code segments to do the filtering and transformation. The majority of this code is based on the methods of lsst.meas.algorithms.loadReferenceObjects.ReferenceObjectLoader
- classmethod parseAndRun(args=None, config=None, log=None, doReturnResults=False)¶
Parse an argument list and run the command.
- Parameters:
- args
list
, optional - config
lsst.pex.config.Config
-type, optional Config for task. If
None
useTask.ConfigClass
.- log
logging.Logger
-type, optional Log. If
None
use the default log.- doReturnResults
bool
, optional If
True
, return the results of this task. Default isFalse
. This is only intended for unit tests and similar use. It can easily exhaust memory (if the task returns enough data and you call it enough times) and it will fail when using multiprocessing if the returned data cannot be pickled.
- args
- Returns:
- struct
lsst.pipe.base.Struct
Fields are:
argumentParser
the argument parser (
lsst.pipe.base.ArgumentParser
).parsedCmd
the parsed command returned by the argument parser’s
parse_args
method (argparse.Namespace
).taskRunner
the task runner used to run the task (an instance of
Task.RunnerClass
).resultList
results returned by the task runner’s
run
method, one entry per invocation (list
). This will typically be a list ofStruct
, each containing at least anexitStatus
integer (0 or 1); seeTask.RunnerClass
(TaskRunner
by default) for more details.
- struct
Notes
Calling this method with no arguments specified is the standard way to run a command-line task from the command-line. For an example see
pipe_tasks
bin/makeSkyMap.py
or almost any other file in that directory.If one or more of the dataIds fails then this routine will exit (with a status giving the number of failed dataIds) rather than returning this struct; this behaviour can be overridden by specifying the
--noExit
command-line option.
- prepareCalibratedExposure(exposure, skyCorr=None, externalSkyWcsCatalog=None, externalPhotoCalibCatalog=None, finalizedPsfApCorrCatalog=None)¶
Prepare a calibrated exposure and apply external calibrations and sky corrections if so configured.
- Parameters:
- exposure
lsst.afw.image.exposure.Exposure
Input exposure to adjust calibrations.
- skyCorr
lsst.afw.math.backgroundList
, optional Sky correction frame to apply if doApplySkyCorr=True.
- externalSkyWcsCatalog
lsst.afw.table.ExposureCatalog
, optional Exposure catalog with external skyWcs to be applied if config.doApplyExternalSkyWcs=True. Catalog uses the detector id for the catalog id, sorted on id for fast lookup.
- externalPhotoCalibCatalog
lsst.afw.table.ExposureCatalog
, optional Exposure catalog with external photoCalib to be applied if config.doApplyExternalPhotoCalib=True. Catalog uses the detector id for the catalog id, sorted on id for fast lookup.
- finalizedPsfApCorrCatalog
lsst.afw.table.ExposureCatalog
, optional Exposure catalog with finalized psf models and aperture correction maps to be applied if config.doApplyFinalizedPsf=True. Catalog uses the detector id for the catalog id, sorted on id for fast lookup.
- exposure
- Returns:
- exposure
lsst.afw.image.exposure.Exposure
Exposure with adjusted calibrations.
- exposure
- run(measCat, exposure, refCat, refWcs, exposureId=None)¶
Perform forced measurement on a single exposure.
- Parameters:
- measCat
lsst.afw.table.SourceCatalog
The measurement catalog, based on the sources listed in the reference catalog.
- exposure
lsst.afw.image.Exposure
The measurement image upon which to perform forced detection.
- refCat
lsst.afw.table.SourceCatalog
The reference catalog of sources to measure.
- refWcs
lsst.afw.image.SkyWcs
The WCS for the references.
- exposureId
int
Optional unique exposureId used for random seed in measurement task.
- measCat
- Returns:
- result
lsst.pipe.base.Struct
Structure with fields:
measCat
Catalog of forced measurement results (
lsst.afw.table.SourceCatalog
).
- result
- runDataRef(dataRef, psfCache=None)¶
Perform forced measurement on a single exposure.
- Parameters:
- dataRef
lsst.daf.persistence.ButlerDataRef
Passed to the
references
subtask to obtain the reference WCS, thegetExposure
method (implemented by derived classes) to read the measurment image, and thefetchReferences
method to get the exposure and load the reference catalog (see :lsst-task`lsst.meas.base.references.CoaddSrcReferencesTask`). Refer to derived class documentation for details of the datasets and data ID keys which are used.- psfCache
int
, optional Size of PSF cache, or
None
. The size of the PSF cache can have a significant effect upon the runtime for complicated PSF models.
- dataRef
Notes
Sources are generated with
generateMeasCat
in themeasurement
subtask. These are passed tomeasurement
’srun
method, which fills the source catalog with the forced measurement results. The sources are then passed to thewriteOutputs
method (implemented by derived classes) which writes the outputs.
- runQuantum(butlerQC, inputRefs, outputRefs)¶
Method to do butler IO and or transforms to provide in memory objects for tasks run method
- Parameters:
- butlerQC
ButlerQuantumContext
A butler which is specialized to operate in the context of a
lsst.daf.butler.Quantum
.- inputRefs
InputQuantizedConnection
Datastructure whose attribute names are the names that identify connections defined in corresponding
PipelineTaskConnections
class. The values of these attributes are thelsst.daf.butler.DatasetRef
objects associated with the defined input/prerequisite connections.- outputRefs
OutputQuantizedConnection
Datastructure whose attribute names are the names that identify connections defined in corresponding
PipelineTaskConnections
class. The values of these attributes are thelsst.daf.butler.DatasetRef
objects associated with the defined output connections.
- butlerQC
- timer(name: str, logLevel: int = 10) Iterator[None] ¶
Context manager to log performance data for an arbitrary block of code.
- Parameters:
See also
timer.logInfo
Examples
Creating a timer context:
with self.timer("someCodeToTime"): pass # code to time
- writeConfig(butler, clobber=False, doBackup=True)¶
Write the configuration used for processing the data, or check that an existing one is equal to the new one if present.
- Parameters:
- butler
lsst.daf.persistence.Butler
Data butler used to write the config. The config is written to dataset type
CmdLineTask._getConfigName
.- clobber
bool
, optional A boolean flag that controls what happens if a config already has been saved:
- doBackup
bool
, optional Set to
True
to backup the config files if clobbering.
- butler
- writeMetadata(dataRef)¶
Write the metadata produced from processing the data.
- Parameters:
- dataRef
Butler data reference used to write the metadata. The metadata is written to dataset type
CmdLineTask._getMetadataName
.
- writeOutput(dataRef, sources)¶
Write forced source table
- Parameters:
- dataRef
lsst.daf.persistence.ButlerDataRef
Butler data reference. The forced_src dataset (with self.dataPrefix prepended) is all that will be modified.
- sources
lsst.afw.table.SourceCatalog
Catalog of sources to save.
- dataRef
- writePackageVersions(butler, clobber=False, doBackup=True, dataset='packages')¶
Compare and write package versions.
- Parameters:
- butler
lsst.daf.persistence.Butler
Data butler used to read/write the package versions.
- clobber
bool
, optional A boolean flag that controls what happens if versions already have been saved:
- doBackup
bool
, optional If
True
and clobbering, old package version files are backed up.- dataset
str
, optional Name of dataset to read/write.
- butler
- Raises:
- TaskError
Raised if there is a version mismatch with current and persisted lists of package versions.
Notes
Note that this operation is subject to a race condition.
- writeSchemas(butler, clobber=False, doBackup=True)¶
Write the schemas returned by
lsst.pipe.base.Task.getAllSchemaCatalogs
.- Parameters:
- butler
lsst.daf.persistence.Butler
Data butler used to write the schema. Each schema is written to the dataset type specified as the key in the dict returned by
getAllSchemaCatalogs
.- clobber
bool
, optional A boolean flag that controls what happens if a schema already has been saved:
- doBackup
bool
, optional Set to
True
to backup the schema files if clobbering.
- butler
Notes
If
clobber
isFalse
and an existing schema does not match a current schema, then some schemas may have been saved successfully and others may not, and there is no easy way to tell which is which.