SourceDetectionConfig¶

class lsst.meas.algorithms.SourceDetectionConfig(*args, **kw)¶

Bases: Config

Configuration parameters for the SourceDetectionTask

Attributes Summary

`adjustBackground`	Fiddle factor to add to the background; debugging only (`float`, default `0.0`)
`background`	Background re-estimation; ignored if reEstimateBackground false (`ConfigurableInstance`, default `<class 'lsst.meas.algorithms.subtractBackground.SubtractBackgroundConfig'>`)
`combinedGrow`	Grow all footprints at the same time? This allows disconnected footprints to merge.
`doTempLocalBackground`	Enable temporary local background subtraction? (see tempLocalBackground) (`bool`, default `True`)
`doTempWideBackground`	Do temporary wide (large-scale) background subtraction before footprint detection? (`bool`, default `False`)
`excludeMaskPlanes`	Mask planes to exclude when detecting sources.
`history`
`includeThresholdMultiplier`	Include threshold relative to thresholdValue.
`isotropicGrow`	Grow pixels as isotropically as possible? If False, use a Manhattan metric instead.
`minPixels`	detected sources with fewer than the specified number of pixels will be ignored (`int`, default `1`)
`nPeaksMaxSimple`	The maximum number of peaks in a Footprint before trying to replace its peaks using the temporary local background (`int`, default `1`)
`nSigmaForKernel`	Multiple of PSF RMS size to use for convolution kernel bounding box size; note that this is not a half-size.
`nSigmaToGrow`	Grow detections by nSigmaToGrow * [PSF RMS width]; if 0 then do not grow (`float`, default `2.4`)
`reEstimateBackground`	Estimate the background again after final source detection? (`bool`, default `True`)
`returnOriginalFootprints`	Grow detections to set the image mask bits, but return the original (not-grown) footprints (`bool`, default `False`)
`statsMask`	Mask planes to ignore when calculating statistics of image (for thresholdType=stdev) (`List`, default `['BAD', 'SAT', 'EDGE', 'NO_DATA']`)
`tempLocalBackground`	A local (small-scale), temporary background estimation step run between detecting above-threshold regions and detecting the peaks within them; used to avoid detecting spuerious peaks in the wings.
`tempWideBackground`	A wide (large-scale) background estimation and removal before footprint and peak detection.
`thresholdPolarity`	Specifies whether to detect positive, or negative sources, or both.
`thresholdType`	Specifies the meaning of thresholdValue.
`thresholdValue`	Threshold for footprints; exact meaning and units depend on thresholdType.

Methods Summary

`compare`(other[, shortcut, rtol, atol, output])	Compare this configuration to another `Config` for equality.
`formatHistory`(name, **kwargs)	Format a configuration field's history to a human-readable format.
`freeze`()	Make this config, and all subconfigs, read-only.
`items`()	Get configurations as `(field name, field value)` pairs.
`keys`()	Get field names.
`load`(filename[, root])	Modify this config in place by executing the Python code in a configuration file.
`loadFromStream`(stream[, root, filename, ...])	Modify this Config in place by executing the Python code in the provided stream.
`loadFromString`(code[, root, filename, ...])	Modify this Config in place by executing the Python code in the provided string.
`names`()	Get all the field names in the config, recursively.
`save`(filename[, root])	Save a Python script to the named file, which, when loaded, reproduces this config.
`saveToStream`(outfile[, root, skipImports])	Save a configuration file to a stream, which, when loaded, reproduces this config.
`saveToString`([skipImports])	Return the Python script form of this configuration as an executable string.
`setDefaults`()	Subclass hook for computing defaults.
`toDict`()	Make a dictionary of field names and their values.
`update`(**kw)	Update values of fields specified by the keyword arguments.
`validate`()	Validate the Config, raising an exception if invalid.
`values`()	Get field values.

Attributes Documentation

adjustBackground¶: Fiddle factor to add to the background; debugging only (float, default 0.0)

background¶: Background re-estimation; ignored if reEstimateBackground false (ConfigurableInstance, default <class 'lsst.meas.algorithms.subtractBackground.SubtractBackgroundConfig'>)

combinedGrow¶: Grow all footprints at the same time? This allows disconnected footprints to merge. (bool, default True)

doTempLocalBackground¶: Enable temporary local background subtraction? (see tempLocalBackground) (bool, default True)

doTempWideBackground¶: Do temporary wide (large-scale) background subtraction before footprint detection? (bool, default False)

excludeMaskPlanes¶: Mask planes to exclude when detecting sources. (List, default [])

history¶: Read-only history.

includeThresholdMultiplier¶

Include threshold relative to thresholdValue. (float, default 1.0)

Valid Range = [0.0,inf)

isotropicGrow¶: Grow pixels as isotropically as possible? If False, use a Manhattan metric instead. (bool, default True)

minPixels¶

detected sources with fewer than the specified number of pixels will be ignored (int, default 1)

Valid Range = [0,inf)

nPeaksMaxSimple¶: The maximum number of peaks in a Footprint before trying to replace its peaks using the temporary local background (int, default 1)

nSigmaForKernel¶: Multiple of PSF RMS size to use for convolution kernel bounding box size; note that this is not a half-size. The size will be rounded up to the nearest odd integer (float, default 7.0)

nSigmaToGrow¶: Grow detections by nSigmaToGrow * [PSF RMS width]; if 0 then do not grow (float, default 2.4)

reEstimateBackground¶: Estimate the background again after final source detection? (bool, default True)

returnOriginalFootprints¶: Grow detections to set the image mask bits, but return the original (not-grown) footprints (bool, default False)

statsMask¶: Mask planes to ignore when calculating statistics of image (for thresholdType=stdev) (List, default ['BAD', 'SAT', 'EDGE', 'NO_DATA'])

tempLocalBackground¶: A local (small-scale), temporary background estimation step run between detecting above-threshold regions and detecting the peaks within them; used to avoid detecting spuerious peaks in the wings. (ConfigurableInstance, default <class 'lsst.meas.algorithms.subtractBackground.SubtractBackgroundConfig'>)

tempWideBackground¶: A wide (large-scale) background estimation and removal before footprint and peak detection. It is added back into the image after detection. The purpose is to suppress very large footprints (e.g., from large artifacts) that the deblender may choke on. (ConfigurableInstance, default <class 'lsst.meas.algorithms.subtractBackground.SubtractBackgroundConfig'>)

thresholdPolarity¶

Specifies whether to detect positive, or negative sources, or both. (str, default 'positive')

Allowed values:

'positive': detect only positive sources
'negative': detect only negative sources
'both': detect both positive and negative sources

thresholdType¶

Specifies the meaning of thresholdValue. (str, default 'pixel_stdev')

Allowed values:

'variance': threshold applied to image variance
'stdev': threshold applied to image std deviation
'value': threshold applied to image value
'pixel_stdev': threshold applied to per-pixel std deviation

thresholdValue¶

Threshold for footprints; exact meaning and units depend on thresholdType. (float, default 5.0)

Valid Range = [0.0,inf)

Methods Documentation

compare(other, shortcut=True, rtol=1e-08, atol=1e-08, output=None)¶

Compare this configuration to another Config for equality.

Parameters:

otherlsst.pex.config.Config: Other Config object to compare against this config.
shortcutbool, optional: If True, return as soon as an inequality is found. Default is True.
rtolfloat, optional: Relative tolerance for floating point comparisons.
atolfloat, optional: Absolute tolerance for floating point comparisons.
outputcallable, optional: A callable that takes a string, used (possibly repeatedly) to report inequalities.

Returns:

isEqualbool: True when the two lsst.pex.config.Config instances are equal. False if there is an inequality.

See also

lsst.pex.config.compareConfigs

Notes

Unselected targets of RegistryField fields and unselected choices of ConfigChoiceField fields are not considered by this method.

Floating point comparisons are performed by numpy.allclose.

formatHistory(name, **kwargs)¶

Format a configuration field’s history to a human-readable format.

Parameters:

namestr: Name of a Field in this config.
kwargs: Keyword arguments passed to lsst.pex.config.history.format.

Returns:

historystr: A string containing the formatted history.

See also

lsst.pex.config.history.format

freeze()¶: Make this config, and all subconfigs, read-only.

items()¶

Get configurations as (field name, field value) pairs.

Returns:

itemsItemsView

Iterator of tuples for each configuration. Tuple items are:

Field name.
Field value.

keys()¶

Get field names.

Returns:

namesKeysView: List of lsst.pex.config.Field names.

load(filename, root='config')¶

Modify this config in place by executing the Python code in a configuration file.

Parameters:

filenamestr

Name of the configuration file. A configuration file is Python module.

rootstr, optional

Name of the variable in file that refers to the config being overridden.

For example, the value of root is "config" and the file contains:

config.myField = 5

Then this config’s field myField is set to 5.

See also

lsst.pex.config.Config.loadFromStream
lsst.pex.config.Config.loadFromString
lsst.pex.config.Config.save
lsst.pex.config.Config.saveToStream
lsst.pex.config.Config.saveToString

loadFromStream(stream, root='config', filename=None, extraLocals=None)¶

Modify this Config in place by executing the Python code in the provided stream.

Parameters:

streamfile-like object, str, bytes, or compiled string

Stream containing configuration override code. If this is a code object, it should be compiled with mode="exec".

rootstr, optional

Name of the variable in file that refers to the config being overridden.

For example, the value of root is "config" and the file contains:

config.myField = 5

Then this config’s field myField is set to 5.

filenamestr, optional

Name of the configuration file, or None if unknown or contained in the stream. Used for error reporting.

extraLocalsdict of str to object, optional

Any extra variables to include in local scope when loading.

See also

lsst.pex.config.Config.load
lsst.pex.config.Config.loadFromString
lsst.pex.config.Config.save
lsst.pex.config.Config.saveToStream
lsst.pex.config.Config.saveToString

Notes

For backwards compatibility reasons, this method accepts strings, bytes and code objects as well as file-like objects. New code should use loadFromString instead for most of these types.

loadFromString(code, root='config', filename=None, extraLocals=None)¶

Modify this Config in place by executing the Python code in the provided string.

Parameters:

codestr, bytes, or compiled string

Stream containing configuration override code.

rootstr, optional

Name of the variable in file that refers to the config being overridden.

For example, the value of root is "config" and the file contains:

config.myField = 5

Then this config’s field myField is set to 5.

filenamestr, optional

Name of the configuration file, or None if unknown or contained in the stream. Used for error reporting.

extraLocalsdict of str to object, optional

Any extra variables to include in local scope when loading.

Raises:

ValueError: Raised if a key in extraLocals is the same value as the value of the root argument.

See also

lsst.pex.config.Config.load
lsst.pex.config.Config.loadFromStream
lsst.pex.config.Config.save
lsst.pex.config.Config.saveToStream
lsst.pex.config.Config.saveToString

names()¶

Get all the field names in the config, recursively.

Returns:

nameslist of str: Field names.

save(filename, root='config')¶

Save a Python script to the named file, which, when loaded, reproduces this config.

Parameters:

filenamestr: Desination filename of this configuration.
rootstr, optional: Name to use for the root config variable. The same value must be used when loading (see lsst.pex.config.Config.load).

See also

lsst.pex.config.Config.saveToStream
lsst.pex.config.Config.saveToString
lsst.pex.config.Config.load
lsst.pex.config.Config.loadFromStream
lsst.pex.config.Config.loadFromString

saveToStream(outfile, root='config', skipImports=False)¶

Save a configuration file to a stream, which, when loaded, reproduces this config.

Parameters:

outfilefile-like object: Destination file object write the config into. Accepts strings not bytes.
root: Name to use for the root config variable. The same value must be used when loading (see lsst.pex.config.Config.load).
skipImportsbool, optional: If True then do not include import statements in output, this is to support human-oriented output from pipetask where additional clutter is not useful.

See also

lsst.pex.config.Config.save
lsst.pex.config.Config.saveToString
lsst.pex.config.Config.load
lsst.pex.config.Config.loadFromStream
lsst.pex.config.Config.loadFromString

saveToString(skipImports=False)¶

Return the Python script form of this configuration as an executable string.

Parameters:

skipImportsbool, optional: If True then do not include import statements in output, this is to support human-oriented output from pipetask where additional clutter is not useful.

Returns:

codestr: A code string readable by loadFromString.

See also

lsst.pex.config.Config.save
lsst.pex.config.Config.saveToStream
lsst.pex.config.Config.load
lsst.pex.config.Config.loadFromStream
lsst.pex.config.Config.loadFromString

setDefaults()¶

Subclass hook for computing defaults.

Notes

Derived Config classes that must compute defaults rather than using the Field instances’s defaults should do so here. To correctly use inherited defaults, implementations of setDefaults must call their base class’s setDefaults.

toDict()¶

Make a dictionary of field names and their values.

Returns:

dict_dict: Dictionary with keys that are Field names. Values are Field values.

See also

lsst.pex.config.Field.toDict

Notes

This method uses the toDict method of individual fields. Subclasses of Field may need to implement a toDict method for this method to work.

update(**kw)¶

Update values of fields specified by the keyword arguments.

Parameters:

kw: Keywords are configuration field names. Values are configuration field values.

Notes

The __at and __label keyword arguments are special internal keywords. They are used to strip out any internal steps from the history tracebacks of the config. Do not modify these keywords to subvert a Config instance’s history.

Examples

This is a config with three fields:

>>> from lsst.pex.config import Config, Field
>>> class DemoConfig(Config):
...     fieldA = Field(doc='Field A', dtype=int, default=42)
...     fieldB = Field(doc='Field B', dtype=bool, default=True)
...     fieldC = Field(doc='Field C', dtype=str, default='Hello world')
...
>>> config = DemoConfig()

These are the default values of each field:

>>> for name, value in config.iteritems():
...     print(f"{name}: {value}")
...
fieldA: 42
fieldB: True
fieldC: 'Hello world'

Using this method to update fieldA and fieldC:

>>> config.update(fieldA=13, fieldC='Updated!')

Now the values of each field are:

>>> for name, value in config.iteritems():
...     print(f"{name}: {value}")
...
fieldA: 13
fieldB: True
fieldC: 'Updated!'

validate()¶

Validate the Config, raising an exception if invalid.

Raises:

lsst.pex.config.FieldValidationError: Raised if verification fails.

Notes

The base class implementation performs type checks on all fields by calling their validate methods.

Complex single-field validation can be defined by deriving new Field types. For convenience, some derived lsst.pex.config.Field-types (ConfigField and ConfigChoiceField) are defined in lsst.pex.config that handle recursing into subconfigs.

Inter-field relationships should only be checked in derived Config classes after calling this method, and base validation is complete.

values()¶

Get field values.

Returns:

valuesValuesView: Iterator of field values.

Navigation

SourceDetectionConfig¶