lsst.meas.algorithms  20.0.0-2-g92e20685
Public Member Functions | List of all members
lsst.meas.algorithms.defects.Defects Class Reference
Inheritance diagram for lsst.meas.algorithms.defects.Defects:

Public Member Functions

def __init__ (self, defectList=None, metadata=None, *normalize_on_init=True)
 
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 insert (self, index, value)
 
def getMetadata (self)
 
def setMetadata (self, metadata=None)
 
def copy (self)
 
def transpose (self)
 
def maskPixels (self, maskedImage, maskName="BAD")
 
def toFitsRegionTable (self)
 
def writeFits (self, *args)
 
def toSimpleTable (self)
 
def writeText (self, filename)
 
def fromTable (cls, table)
 
def readFits (cls, *args)
 
def readText (cls, filename)
 
def readLsstDefectsFile (cls, filename)
 
def fromFootprintList (cls, fpList)
 
def fromMask (cls, maskedImage, maskName)
 

Detailed Description

Collection 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.

Definition at line 55 of file defects.py.

Constructor & Destructor Documentation

◆ __init__()

def lsst.meas.algorithms.defects.Defects.__init__ (   self,
  defectList = None,
  metadata = None,
normalize_on_init = True 
)

Definition at line 84 of file defects.py.

Member Function Documentation

◆ __delitem__()

def lsst.meas.algorithms.defects.Defects.__delitem__ (   self,
  index 
)

Definition at line 148 of file defects.py.

◆ __eq__()

def lsst.meas.algorithms.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.

Definition at line 151 of file defects.py.

◆ __getitem__()

def lsst.meas.algorithms.defects.Defects.__getitem__ (   self,
  index 
)

Definition at line 136 of file defects.py.

◆ __iter__()

def lsst.meas.algorithms.defects.Defects.__iter__ (   self)

Definition at line 145 of file defects.py.

◆ __len__()

def lsst.meas.algorithms.defects.Defects.__len__ (   self)

Definition at line 133 of file defects.py.

◆ __setitem__()

def lsst.meas.algorithms.defects.Defects.__setitem__ (   self,
  index,
  value 
)
Can be given a `~lsst.meas.algorithms.Defect` or a `lsst.geom.BoxI`

Definition at line 139 of file defects.py.

◆ __str__()

def lsst.meas.algorithms.defects.Defects.__str__ (   self)

Definition at line 171 of file defects.py.

◆ bulk_update()

def lsst.meas.algorithms.defects.Defects.bulk_update (   self)
Temporarily suspend normalization of the defect list.

Definition at line 205 of file defects.py.

◆ copy()

def lsst.meas.algorithms.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 249 of file defects.py.

◆ fromFootprintList()

def lsst.meas.algorithms.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 753 of file defects.py.

◆ fromMask()

def lsst.meas.algorithms.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 773 of file defects.py.

◆ fromTable()

def lsst.meas.algorithms.defects.Defects.fromTable (   cls,
  table 
)
Construct a `Defects` from the contents of a
`~lsst.afw.table.BaseCatalog`.

Parameters
----------
table : `lsst.afw.table.BaseCatalog`
    Table with one row per defect.

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 533 of file defects.py.

◆ getMetadata()

def lsst.meas.algorithms.defects.Defects.getMetadata (   self)
Retrieve metadata associated with these `Defects`.

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 219 of file defects.py.

◆ insert()

def lsst.meas.algorithms.defects.Defects.insert (   self,
  index,
  value 
)

Definition at line 215 of file defects.py.

◆ maskPixels()

def lsst.meas.algorithms.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 283 of file defects.py.

◆ readFits()

def lsst.meas.algorithms.defects.Defects.readFits (   cls,
args 
)
Read defect list from FITS table.

Parameters
----------
*args
    Arguments to be forwarded to
    `lsst.afw.table.BaseCatalog.writeFits`.

Returns
-------
defects : `Defects`
    Defects read from a FITS table.

Definition at line 648 of file defects.py.

◆ readLsstDefectsFile()

def lsst.meas.algorithms.defects.Defects.readLsstDefectsFile (   cls,
  filename 
)
Read defects information from a legacy LSST format text file.

Parameters
----------
filename : `str`
    Name of text file containing the defect information.

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 710 of file defects.py.

◆ readText()

def lsst.meas.algorithms.defects.Defects.readText (   cls,
  filename 
)
Read defect list from standard format text table file.

Parameters
----------
filename : `str`
    Name of the file containing the defects definitions.

Returns
-------
defects : `Defects`
    Defects read from a FITS table.

Definition at line 666 of file defects.py.

◆ setMetadata()

def lsst.meas.algorithms.defects.Defects.setMetadata (   self,
  metadata = None 
)
Store a copy of the supplied metadata with the defects.

Parameters
----------
metadata : `lsst.daf.base.PropertyList`, optional
    Metadata to associate with the defects.  Will be copied and
    overwrite existing metadata.  If not supplied the existing
    metadata will be reset.

Definition at line 231 of file defects.py.

◆ toFitsRegionTable()

def lsst.meas.algorithms.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 300 of file defects.py.

◆ toSimpleTable()

def lsst.meas.algorithms.defects.Defects.toSimpleTable (   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.

Definition at line 395 of file defects.py.

◆ transpose()

def lsst.meas.algorithms.defects.Defects.transpose (   self)
Make a transposed copy of this defect list.

Returns
-------
retDefectList : `Defects`
    Transposed list of defects.

Definition at line 266 of file defects.py.

◆ writeFits()

def lsst.meas.algorithms.defects.Defects.writeFits (   self,
args 
)
Write defect list to FITS.

Parameters
----------
*args
    Arguments to be forwarded to
    `lsst.afw.table.BaseCatalog.writeFits`.

Definition at line 375 of file defects.py.

◆ writeText()

def lsst.meas.algorithms.defects.Defects.writeText (   self,
  filename 
)
Write the defects out to a text file with the specified name.

Parameters
----------
filename : `str`
    Name of the file to write.  The file extension ".ecsv" will
    always be used.

Returns
-------
used : `str`
    The name of the file used to write the data (which may be
    different from the supplied name given the change to file
    extension).

Notes
-----
The file is written to ECSV format and will include any metadata
associated with the `Defects`.

Definition at line 461 of file defects.py.


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