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
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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 , |
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metadata = None , |
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* | normalize_on_init = True , |
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** | 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.
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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.
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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.
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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.
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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.
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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.
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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 |
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) |
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.
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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" |
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) |
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.
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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 |
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) |
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.
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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.
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Definition at line 138 of file calibType.py.
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Definition at line 142 of file calibType.py.
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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.
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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.
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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.
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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.
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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.
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Definition at line 86 of file calibType.py.
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Definition at line 81 of file calibType.py.