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LSST Applications
21.0.0-172-gfb10e10a+18fedfabac,22.0.0+297cba6710,22.0.0+80564b0ff1,22.0.0+8d77f4f51a,22.0.0+a28f4c53b1,22.0.0+dcf3732eb2,22.0.1-1-g7d6de66+2a20fdde0d,22.0.1-1-g8e32f31+297cba6710,22.0.1-1-geca5380+7fa3b7d9b6,22.0.1-12-g44dc1dc+2a20fdde0d,22.0.1-15-g6a90155+515f58c32b,22.0.1-16-g9282f48+790f5f2caa,22.0.1-2-g92698f7+dcf3732eb2,22.0.1-2-ga9b0f51+7fa3b7d9b6,22.0.1-2-gd1925c9+bf4f0e694f,22.0.1-24-g1ad7a390+a9625a72a8,22.0.1-25-g5bf6245+3ad8ecd50b,22.0.1-25-gb120d7b+8b5510f75f,22.0.1-27-g97737f7+2a20fdde0d,22.0.1-32-gf62ce7b1+aa4237961e,22.0.1-4-g0b3f228+2a20fdde0d,22.0.1-4-g243d05b+871c1b8305,22.0.1-4-g3a563be+32dcf1063f,22.0.1-4-g44f2e3d+9e4ab0f4fa,22.0.1-42-gca6935d93+ba5e5ca3eb,22.0.1-5-g15c806e+85460ae5f3,22.0.1-5-g58711c4+611d128589,22.0.1-5-g75bb458+99c117b92f,22.0.1-6-g1c63a23+7fa3b7d9b6,22.0.1-6-g50866e6+84ff5a128b,22.0.1-6-g8d3140d+720564cf76,22.0.1-6-gd805d02+cc5644f571,22.0.1-8-ge5750ce+85460ae5f3,master-g6e05de7fdc+babf819c66,master-g99da0e417a+8d77f4f51a,w.2021.48
LSST Data Management Base Package
|
Public Member Functions | |
| def | __init__ (self, defectList=None, metadata=None, *normalize_on_init=True, **kwargs) |
| def | __len__ (self) |
| def | __getitem__ (self, index) |
| def | __setitem__ (self, index, value) |
| def | __iter__ (self) |
| def | __delitem__ (self, index) |
| def | __eq__ (self, other) |
| def | __str__ (self) |
| def | bulk_update (self) |
| def | append (self, value) |
| def | insert (self, index, value) |
| def | copy (self) |
| def | transpose (self) |
| def | maskPixels (self, maskedImage, maskName="BAD") |
| def | toFitsRegionTable (self) |
| def | fromDict (cls, dictionary) |
| def | toDict (self) |
| def | toTable (self) |
| def | fromTable (cls, tableList, normalize_on_init=True) |
| def | readLsstDefectsFile (cls, filename, normalize_on_init=False) |
| def | fromFootprintList (cls, fpList) |
| def | fromMask (cls, maskedImage, maskName) |
| def | requiredAttributes (self) |
| def | requiredAttributes (self, value) |
| def | getMetadata (self) |
| def | setMetadata (self, metadata) |
| def | updateMetadata (self, camera=None, detector=None, filterName=None, setCalibId=False, setCalibInfo=False, setDate=False, **kwargs) |
| def | calibInfoFromDict (self, dictionary) |
| def | determineCalibClass (cls, metadata, message) |
| def | readText (cls, filename, **kwargs) |
| def | writeText (self, filename, format="auto") |
| def | readFits (cls, filename, **kwargs) |
| def | writeFits (self, filename) |
| def | fromDetector (self, detector) |
| def | fromDict (cls, dictionary, **kwargs) |
| def | fromTable (cls, tableList, **kwargs) |
| def | validate (self, other=None) |
| def | apply (self, target) |
Public Attributes | |
| requiredAttributes | |
| log | |
Calibration handler for collections of `lsst.meas.algorithms.Defect`.
Parameters
----------
defectList : iterable of `lsst.meas.algorithms.Defect`
or `lsst.geom.BoxI`, optional
Collections of defects to apply to the image.
metadata : `lsst.daf.base.PropertyList`, optional
Metadata to associate with the defects. Will be copied and
overwrite existing metadata, if any. If not supplied the existing
metadata will be reset.
normalize_on_init : `bool`
If True, normalization is applied to the defects in ``defectList`` to
remove duplicates, eliminate overlaps, etc.
Notes
-----
Defects are stored within this collection in a "reduced" or "normalized"
form: rather than simply storing the bounding boxes which are added to the
collection, we eliminate overlaps and duplicates. This normalization
procedure may introduce overhead when adding many new defects; it may be
temporarily disabled using the `Defects.bulk_update` context manager if
necessary.
The attributes stored in this calibration are:
_defects : `list` [`lsst.meas.algorithms.Defect`]
The collection of Defect objects.
The calibration type used for ingest.
Definition at line 47 of file defects.py.
| def lsst.ip.isr.defects.Defects.__init__ | ( | self, | |
defectList = None, |
|||
metadata = None, |
|||
| * | normalize_on_init = True, |
||
| ** | kwargs | ||
| ) |
Definition at line 83 of file defects.py.
| def lsst.ip.isr.defects.Defects.__delitem__ | ( | self, | |
| index | |||
| ) |
Definition at line 145 of file defects.py.
| def lsst.ip.isr.defects.Defects.__eq__ | ( | self, | |
| other | |||
| ) |
Compare if two `Defects` are equal. Two `Defects` are equal if their bounding boxes are equal and in the same order. Metadata content is ignored.
Reimplemented from lsst.ip.isr.calibType.IsrCalib.
Definition at line 148 of file defects.py.
| def lsst.ip.isr.defects.Defects.__getitem__ | ( | self, | |
| index | |||
| ) |
Definition at line 133 of file defects.py.
| def lsst.ip.isr.defects.Defects.__iter__ | ( | self | ) |
Definition at line 142 of file defects.py.
| def lsst.ip.isr.defects.Defects.__len__ | ( | self | ) |
Definition at line 130 of file defects.py.
| def lsst.ip.isr.defects.Defects.__setitem__ | ( | self, | |
| index, | |||
| value | |||
| ) |
Can be given a `~lsst.meas.algorithms.Defect` or a `lsst.geom.BoxI`
Definition at line 136 of file defects.py.
| def lsst.ip.isr.defects.Defects.__str__ | ( | self | ) |
Reimplemented from lsst.ip.isr.calibType.IsrCalib.
Definition at line 170 of file defects.py.
| def lsst.ip.isr.defects.Defects.append | ( | self, | |
| value | |||
| ) |
Definition at line 219 of file defects.py.
|
inherited |
Method to apply the calibration to the target object.
Parameters
----------
target : `object`
Thing to validate against.
Returns
-------
valid : `bool`
Returns true if the calibration was applied correctly.
Raises
------
NotImplementedError :
Raised if not implemented.
Definition at line 612 of file calibType.py.
| def lsst.ip.isr.defects.Defects.bulk_update | ( | self | ) |
Temporarily suspend normalization of the defect list.
Definition at line 209 of file defects.py.
|
inherited |
Handle common keywords.
This isn't an ideal solution, but until all calibrations
expect to find everything in the metadata, they still need to
search through dictionaries.
Parameters
----------
dictionary : `dict` or `lsst.daf.base.PropertyList`
Source for the common keywords.
Raises
------
RuntimeError :
Raised if the dictionary does not match the expected OBSTYPE.
Definition at line 261 of file calibType.py.
| def lsst.ip.isr.defects.Defects.copy | ( | self | ) |
Copy the defects to a new list, creating new defects from the
bounding boxes.
Returns
-------
new : `Defects`
New list with new `Defect` entries.
Notes
-----
This is not a shallow copy in that new `Defect` instances are
created from the original bounding boxes. It's also not a deep
copy since the bounding boxes are not recreated.
Definition at line 227 of file defects.py.
|
inherited |
Attempt to find calibration class in metadata.
Parameters
----------
metadata : `dict` or `lsst.daf.base.PropertyList`
Metadata possibly containing a calibration class entry.
message : `str`
Message to include in any errors.
Returns
-------
calibClass : `object`
The class to use to read the file contents. Should be an
`lsst.ip.isr.IsrCalib` subclass.
Raises
------
ValueError :
Raised if the resulting calibClass is the base
`lsst.ip.isr.IsrClass` (which does not implement the
content methods).
Definition at line 316 of file calibType.py.
|
inherited |
Modify the calibration parameters to match the supplied detector.
Parameters
----------
detector : `lsst.afw.cameraGeom.Detector`
Detector to use to set parameters from.
Raises
------
NotImplementedError
This needs to be implemented by subclasses for each
calibration type.
Reimplemented in lsst.ip.isr.linearize.Linearizer.
Definition at line 495 of file calibType.py.
| def lsst.ip.isr.defects.Defects.fromDict | ( | cls, | |
| dictionary | |||
| ) |
Construct a calibration from a dictionary of properties.
Must be implemented by the specific calibration subclasses.
Parameters
----------
dictionary : `dict`
Dictionary of properties.
Returns
-------
calib : `lsst.ip.isr.CalibType`
Constructed calibration.
Raises
------
RuntimeError :
Raised if the supplied dictionary is for a different
calibration.
Definition at line 333 of file defects.py.
|
inherited |
Construct a calibration from a dictionary of properties.
Must be implemented by the specific calibration subclasses.
Parameters
----------
dictionary : `dict`
Dictionary of properties.
kwargs : `dict` or collections.abc.Mapping`, optional
Set of key=value options.
Returns
------
calib : `lsst.ip.isr.CalibType`
Constructed calibration.
Raises
------
NotImplementedError :
Raised if not implemented.
Definition at line 512 of file calibType.py.
| def lsst.ip.isr.defects.Defects.fromFootprintList | ( | cls, | |
| fpList | |||
| ) |
Compute a defect list from a footprint list, optionally growing
the footprints.
Parameters
----------
fpList : `list` of `lsst.afw.detection.Footprint`
Footprint list to process.
Returns
-------
defects : `Defects`
List of defects.
Definition at line 642 of file defects.py.
| def lsst.ip.isr.defects.Defects.fromMask | ( | cls, | |
| maskedImage, | |||
| maskName | |||
| ) |
Compute a defect list from a specified mask plane.
Parameters
----------
maskedImage : `lsst.afw.image.MaskedImage`
Image to process.
maskName : `str` or `list`
Mask plane name, or list of names to convert.
Returns
-------
defects : `Defects`
Defect list constructed from masked pixels.
Definition at line 662 of file defects.py.
|
inherited |
Construct a calibration from a dictionary of properties.
Must be implemented by the specific calibration subclasses.
Parameters
----------
tableList : `list` [`lsst.afw.table.Table`]
List of tables of properties.
kwargs : `dict` or collections.abc.Mapping`, optional
Set of key=value options.
Returns
------
calib : `lsst.ip.isr.CalibType`
Constructed calibration.
Raises
------
NotImplementedError :
Raised if not implemented.
Definition at line 555 of file calibType.py.
| def lsst.ip.isr.defects.Defects.fromTable | ( | cls, | |
| tableList, | |||
normalize_on_init = True |
|||
| ) |
Construct a `Defects` from the contents of a
`~lsst.afw.table.BaseCatalog`.
Parameters
----------
table : `lsst.afw.table.BaseCatalog`
Table with one row per defect.
normalize_on_init : `bool`, optional
If `True`, normalization is applied to the defects listed in the
table to remove duplicates, eliminate overlaps, etc. Otherwise
the defects in the returned object exactly match those in the
table.
Returns
-------
defects : `Defects`
A `Defects` list.
Notes
-----
Two table formats are recognized. The first is the
`FITS regions <https://fits.gsfc.nasa.gov/registry/region.html>`_
definition tabular format written by `toFitsRegionTable` where the
pixel origin is corrected from FITS 1-based to a 0-based origin.
The second is the legacy defects format using columns ``x0``, ``y0``
(bottom left hand pixel of box in 0-based coordinates), ``width``
and ``height``.
The FITS standard regions can only read BOX, POINT, or ROTBOX with
a zero degree rotation.
Definition at line 493 of file defects.py.
|
inherited |
Retrieve metadata associated with this calibration.
Returns
-------
meta : `lsst.daf.base.PropertyList`
Metadata. The returned `~lsst.daf.base.PropertyList` can be
modified by the caller and the changes will be written to
external files.
Definition at line 145 of file calibType.py.
| def lsst.ip.isr.defects.Defects.insert | ( | self, | |
| index, | |||
| value | |||
| ) |
Definition at line 223 of file defects.py.
| def lsst.ip.isr.defects.Defects.maskPixels | ( | self, | |
| maskedImage, | |||
maskName = "BAD" |
|||
| ) |
Set mask plane based on these defects.
Parameters
----------
maskedImage : `lsst.afw.image.MaskedImage`
Image to process. Only the mask plane is updated.
maskName : str, optional
Mask plane name to use.
Definition at line 261 of file defects.py.
|
inherited |
Read calibration data from a FITS file.
Parameters
----------
filename : `str`
Filename to read data from.
kwargs : `dict` or collections.abc.Mapping`, optional
Set of key=value pairs to pass to the ``fromTable``
method.
Returns
-------
calib : `lsst.ip.isr.IsrCalib`
Calibration contained within the file.
Definition at line 432 of file calibType.py.
| def lsst.ip.isr.defects.Defects.readLsstDefectsFile | ( | cls, | |
| filename, | |||
normalize_on_init = False |
|||
| ) |
Read defects information from a legacy LSST format text file.
Parameters
----------
filename : `str`
Name of text file containing the defect information.
normalize_on_init : `bool`, optional
If `True`, normalization is applied to the defects listed in the
table to remove duplicates, eliminate overlaps, etc. Otherwise
the defects in the returned object exactly match those in the
table.
Returns
-------
defects : `Defects`
The defects.
Notes
-----
These defect text files are used as the human readable definitions
of defects in calibration data definition repositories. The format
is to use four columns defined as follows:
x0 : `int`
X coordinate of bottom left corner of box.
y0 : `int`
Y coordinate of bottom left corner of box.
width : `int`
X extent of the box.
height : `int`
Y extent of the box.
Files of this format were used historically to represent defects
in simple text form. Use `Defects.readText` and `Defects.writeText`
to use the more modern format.
Definition at line 591 of file defects.py.
|
inherited |
Read calibration representation from a yaml/ecsv file.
Parameters
----------
filename : `str`
Name of the file containing the calibration definition.
kwargs : `dict` or collections.abc.Mapping`, optional
Set of key=value pairs to pass to the ``fromDict`` or
``fromTable`` methods.
Returns
-------
calib : `~lsst.ip.isr.IsrCalibType`
Calibration class.
Raises
------
RuntimeError :
Raised if the filename does not end in ".ecsv" or ".yaml".
Definition at line 346 of file calibType.py.
|
inherited |
Definition at line 138 of file calibType.py.
|
inherited |
Definition at line 142 of file calibType.py.
|
inherited |
Store a copy of the supplied metadata with this calibration.
Parameters
----------
metadata : `lsst.daf.base.PropertyList`
Metadata to associate with the calibration. Will be copied and
overwrite existing metadata.
Definition at line 157 of file calibType.py.
| def lsst.ip.isr.defects.Defects.toDict | ( | self | ) |
Return a dictionary containing the calibration properties.
The dictionary should be able to be round-tripped through
`fromDict`.
Returns
-------
dictionary : `dict`
Dictionary of properties.
Reimplemented from lsst.ip.isr.calibType.IsrCalib.
Definition at line 374 of file defects.py.
| def lsst.ip.isr.defects.Defects.toFitsRegionTable | ( | self | ) |
Convert defect list to `~lsst.afw.table.BaseCatalog` using the
FITS region standard.
Returns
-------
table : `lsst.afw.table.BaseCatalog`
Defects in tabular form.
Notes
-----
The table created uses the
`FITS regions <https://fits.gsfc.nasa.gov/registry/region.html>`_
definition tabular format. The ``X`` and ``Y`` coordinates are
converted to FITS Physical coordinates that have origin pixel (1, 1)
rather than the (0, 0) used in LSST software.
Definition at line 278 of file defects.py.
| def lsst.ip.isr.defects.Defects.toTable | ( | self | ) |
Convert defects to a simple table form that we use to write
to text files.
Returns
-------
table : `lsst.afw.table.BaseCatalog`
Defects in simple tabular form.
Notes
-----
These defect tables are used as the human readable definitions
of defects in calibration data definition repositories. The format
is to use four columns defined as follows:
x0 : `int`
X coordinate of bottom left corner of box.
y0 : `int`
Y coordinate of bottom left corner of box.
width : `int`
X extent of the box.
height : `int`
Y extent of the box.
Reimplemented from lsst.ip.isr.calibType.IsrCalib.
Definition at line 412 of file defects.py.
| def lsst.ip.isr.defects.Defects.transpose | ( | self | ) |
Make a transposed copy of this defect list.
Returns
-------
retDefectList : `Defects`
Transposed list of defects.
Definition at line 244 of file defects.py.
|
inherited |
Update metadata keywords with new values.
Parameters
----------
camera : `lsst.afw.cameraGeom.Camera`, optional
Reference camera to use to set _instrument field.
detector : `lsst.afw.cameraGeom.Detector`, optional
Reference detector to use to set _detector* fields.
filterName : `str`, optional
Filter name to assign to this calibration.
setCalibId : `bool`, optional
Construct the _calibId field from other fields.
setCalibInfo : `bool`, optional
Set calibration parameters from metadata.
setDate : `bool`, optional
Ensure the metadata CALIBDATE fields are set to the current datetime.
kwargs : `dict` or `collections.abc.Mapping`, optional
Set of key=value pairs to assign to the metadata.
Definition at line 179 of file calibType.py.
|
inherited |
Validate that this calibration is defined and can be used.
Parameters
----------
other : `object`, optional
Thing to validate against.
Returns
-------
valid : `bool`
Returns true if the calibration is valid and appropriate.
Definition at line 597 of file calibType.py.
|
inherited |
Write calibration data to a FITS file.
Parameters
----------
filename : `str`
Filename to write data to.
Returns
-------
used : `str`
The name of the file used to write the data.
Definition at line 471 of file calibType.py.
|
inherited |
Write the calibration data to a text file.
Parameters
----------
filename : `str`
Name of the file to write.
format : `str`
Format to write the file as. Supported values are:
``"auto"`` : Determine filetype from filename.
``"yaml"`` : Write as yaml.
``"ecsv"`` : Write as ecsv.
Returns
-------
used : `str`
The name of the file used to write the data. This may
differ from the input if the format is explicitly chosen.
Raises
------
RuntimeError :
Raised if filename does not end in a known extension, or
if all information cannot be written.
Notes
-----
The file is written to YAML/ECSV format and will include any
associated metadata.
Definition at line 379 of file calibType.py.
|
inherited |
Definition at line 86 of file calibType.py.
|
inherited |
Definition at line 81 of file calibType.py.