lsst.ip.isr g5e83b0b6c4+a14874d2d8
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Public Member Functions | Protected Member Functions | Static Protected Member Functions | Protected Attributes | Static Protected Attributes | List of all members
lsst.ip.isr.defects.Defects Class Reference
Inheritance diagram for lsst.ip.isr.defects.Defects:
lsst.ip.isr.calibType.IsrCalib

Public Member Functions

 __init__ (self, defectList=None, metadata=None, *normalize_on_init=True, **kwargs)
 
 __len__ (self)
 
 __getitem__ (self, index)
 
 __setitem__ (self, index, value)
 
 __iter__ (self)
 
 __delitem__ (self, index)
 
 __eq__ (self, other)
 
 __str__ (self)
 
 bulk_update (self)
 
 append (self, value)
 
 insert (self, index, value)
 
 copy (self)
 
 transpose (self)
 
 maskPixels (self, mask, maskName="BAD")
 
 toFitsRegionTable (self)
 
 fromDict (cls, dictionary)
 
 toDict (self)
 
 toTable (self)
 
 fromTable (cls, tableList, normalize_on_init=True)
 
 readLsstDefectsFile (cls, filename, normalize_on_init=False)
 
 fromFootprintList (cls, fpList)
 
 fromMask (cls, mask, maskName)
 

Protected Member Functions

 _check_value (self, value)
 
 _normalize (self)
 

Static Protected Member Functions

 _get_values (values, n=1)
 

Protected Attributes

 _defects
 
 _bulk_update
 

Static Protected Attributes

str _OBSTYPE = "defects"
 
str _SCHEMA = ''
 
float _VERSION = 2.0
 

Detailed Description

Calibration handler for collections of `lsst.meas.algorithms.Defect`.

Parameters
----------
defectList : iterable, optional
    Collections of defects to apply to the image. Can be an iterable of
    `lsst.meas.algorithms.Defect` or `lsst.geom.BoxI`.
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.

Constructor & Destructor Documentation

◆ __init__()

lsst.ip.isr.defects.Defects.__init__ (   self,
  defectList = None,
  metadata = None,
normalize_on_init = True,
**  kwargs 
)

Reimplemented from lsst.ip.isr.calibType.IsrCalib.

Definition at line 83 of file defects.py.

Member Function Documentation

◆ __delitem__()

lsst.ip.isr.defects.Defects.__delitem__ (   self,
  index 
)

Definition at line 145 of file defects.py.

◆ __eq__()

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.

◆ __getitem__()

lsst.ip.isr.defects.Defects.__getitem__ (   self,
  index 
)

Definition at line 133 of file defects.py.

◆ __iter__()

lsst.ip.isr.defects.Defects.__iter__ (   self)

Definition at line 142 of file defects.py.

◆ __len__()

lsst.ip.isr.defects.Defects.__len__ (   self)

Definition at line 130 of file defects.py.

◆ __setitem__()

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.

◆ __str__()

lsst.ip.isr.defects.Defects.__str__ (   self)

Reimplemented from lsst.ip.isr.calibType.IsrCalib.

Definition at line 170 of file defects.py.

◆ _check_value()

lsst.ip.isr.defects.Defects._check_value (   self,
  value 
)
protected
Check that the supplied value is a `~lsst.meas.algorithms.Defect`
or can be converted to one.

Parameters
----------
value : `object`
    Value to check.

Returns
-------
new : `~lsst.meas.algorithms.Defect`
    Either the supplied value or a new object derived from it.

Raises
------
ValueError
    Raised if the supplied value can not be converted to
    `~lsst.meas.algorithms.Defect`

Definition at line 98 of file defects.py.

◆ _get_values()

lsst.ip.isr.defects.Defects._get_values (   values,
  n = 1 
)
staticprotected
Retrieve N values from the supplied values.

Parameters
----------
values : `numbers.Number` or `list` or `np.array`
    Input values.
n : `int`
    Number of values to retrieve.

Returns
-------
vals : `list` or `np.array` or `numbers.Number`
    Single value from supplied list if ``n`` is 1, or `list`
    containing first ``n`` values from supplied values.

Notes
-----
Some supplied tables have vectors in some columns that can also
be scalars.  This method can be used to get the first number as
a scalar or the first N items from a vector as a vector.

Definition at line 463 of file defects.py.

◆ _normalize()

lsst.ip.isr.defects.Defects._normalize (   self)
protected
Recalculate defect bounding boxes for efficiency.

Notes
-----
Ideally, this would generate the provably-minimal set of bounding
boxes necessary to represent the defects. At present, however, that
doesn't happen: see DM-24781. In the cases of substantial overlaps or
duplication, though, this will produce a much reduced set.

Definition at line 174 of file defects.py.

◆ append()

lsst.ip.isr.defects.Defects.append (   self,
  value 
)

Definition at line 219 of file defects.py.

◆ bulk_update()

lsst.ip.isr.defects.Defects.bulk_update (   self)
Temporarily suspend normalization of the defect list.

Definition at line 209 of file defects.py.

◆ copy()

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.

◆ fromDict()

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.

Reimplemented from lsst.ip.isr.calibType.IsrCalib.

Definition at line 334 of file defects.py.

◆ fromFootprintList()

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 643 of file defects.py.

◆ fromMask()

lsst.ip.isr.defects.Defects.fromMask (   cls,
  mask,
  maskName 
)
Compute a defect list from a specified mask plane.

Parameters
----------
mask : `lsst.afw.image.Mask` or `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 663 of file defects.py.

◆ fromTable()

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.

Reimplemented from lsst.ip.isr.calibType.IsrCalib.

Definition at line 494 of file defects.py.

◆ insert()

lsst.ip.isr.defects.Defects.insert (   self,
  index,
  value 
)

Definition at line 223 of file defects.py.

◆ maskPixels()

lsst.ip.isr.defects.Defects.maskPixels (   self,
  mask,
  maskName = "BAD" 
)
Set mask plane based on these defects.

Parameters
----------
maskedImage : `lsst.afw.image.MaskedImage` or `lsst.afw.image.Mask`
    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.

◆ readLsstDefectsFile()

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 592 of file defects.py.

◆ toDict()

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 375 of file defects.py.

◆ toFitsRegionTable()

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 279 of file defects.py.

◆ toTable()

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 413 of file defects.py.

◆ transpose()

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.

Member Data Documentation

◆ _bulk_update

lsst.ip.isr.defects.Defects._bulk_update
protected

Definition at line 87 of file defects.py.

◆ _defects

lsst.ip.isr.defects.Defects._defects
protected

Definition at line 84 of file defects.py.

◆ _OBSTYPE

str lsst.ip.isr.defects.Defects._OBSTYPE = "defects"
staticprotected

Definition at line 79 of file defects.py.

◆ _SCHEMA

str lsst.ip.isr.defects.Defects._SCHEMA = ''
staticprotected

Definition at line 80 of file defects.py.

◆ _VERSION

float lsst.ip.isr.defects.Defects._VERSION = 2.0
staticprotected

Definition at line 81 of file defects.py.


The documentation for this class was generated from the following file: