Public Member Functions |
Public Attributes |
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:
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") | |
| updateCounters (self, columns=None, hot=None, cold=None) | |
| 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) | |
| requiredAttributes (self) | |
| requiredAttributes (self, value) | |
| metadata (self) | |
| getMetadata (self) | |
| setMetadata (self, metadata) | |
| updateMetadata (self, camera=None, detector=None, filterName=None, setCalibId=False, setCalibInfo=False, setDate=False, **kwargs) | |
| updateMetadataFromExposures (self, exposures) | |
| calibInfoFromDict (self, dictionary) | |
| determineCalibClass (cls, metadata, message) | |
| readText (cls, filename, **kwargs) | |
| writeText (self, filename, format="auto") | |
| readFits (cls, filename, **kwargs) | |
| writeFits (self, filename) | |
| fromDetector (self, detector) | |
| validate (self, other=None) | |
| apply (self, target) | |
Public Attributes | |
| requiredAttributes = set(["_OBSTYPE", "_SCHEMA", "_VERSION"]) | |
| log = log if log else logging.getLogger(__name__) | |
Protected Member Functions | |
| _check_value (self, value) | |
| _normalize (self) | |
Static Protected Member Functions | |
| _get_values (values, n=1) | |
Protected Attributes | |
| list | _defects = [] |
| bool | _bulk_update = True |
| _instrument = None | |
| _raftName = None | |
| _slotName = None | |
| _detectorName = None | |
| _detectorSerial = None | |
| _detectorId = None | |
| _filter = None | |
| str | _calibId = None |
| _seqfile = None | |
| _seqname = None | |
| _seqcksum = None | |
| _metadata = PropertyList() | |
| _requiredAttributes | |
Static Protected Attributes | |
| str | _OBSTYPE = "generic" |
| str | _SCHEMA = "NO SCHEMA" |
| int | _VERSION = 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 ) |
Definition at line 83 of file defects.py.
83 def __init__(self, defectList=None, metadata=None, *, normalize_on_init=True, **kwargs):
84 self._defects = []
85
86 if defectList is not None:
87 self._bulk_update = True
88 for d in defectList:
89 self.append(d)
90 self._bulk_update = False
91
92 if normalize_on_init:
93 self._normalize()
94
95 super().__init__(**kwargs)
96 self.requiredAttributes.update(['_defects'])
97
Member Function Documentation
◆ __delitem__()
| lsst.ip.isr.defects.Defects.__delitem__ | ( | self, | |
| index ) |
Definition at line 145 of file defects.py.
145 def __delitem__(self, index):
146 del self._defects[index]
147
◆ __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.
Definition at line 148 of file defects.py.
148 def __eq__(self, other):
149 """Compare if two `Defects` are equal.
150
151 Two `Defects` are equal if their bounding boxes are equal and in
152 the same order. Metadata content is ignored.
153 """
154 super().__eq__(other)
155
156 if not isinstance(other, self.__class__):
157 return False
158
159 # checking the bboxes with zip() only works if same length
160 if len(self) != len(other):
161 return False
162
163 # Assume equal if bounding boxes are equal
164 for d1, d2 in zip(self, other):
165 if d1.getBBox() != d2.getBBox():
166 return False
167
168 return True
169
◆ __getitem__()
| lsst.ip.isr.defects.Defects.__getitem__ | ( | self, | |
| index ) |
Definition at line 133 of file defects.py.
133 def __getitem__(self, index):
134 return self._defects[index]
135
◆ __iter__()
| lsst.ip.isr.defects.Defects.__iter__ | ( | self | ) |
Definition at line 142 of file defects.py.
142 def __iter__(self):
143 return iter(self._defects)
144
◆ __len__()
| lsst.ip.isr.defects.Defects.__len__ | ( | self | ) |
Definition at line 130 of file defects.py.
130 def __len__(self):
131 return len(self._defects)
132
◆ __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.
136 def __setitem__(self, index, value):
137 """Can be given a `~lsst.meas.algorithms.Defect` or a `lsst.geom.BoxI`
138 """
139 self._defects[index] = self._check_value(value)
140 self._normalize()
141
◆ __str__()
| lsst.ip.isr.defects.Defects.__str__ | ( | self | ) |
Definition at line 170 of file defects.py.
170 def __str__(self):
171 baseStr = super().__str__()
172 return baseStr + ",".join(str(d.getBBox()) for d in self) + ")"
173
◆ _check_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.
98 def _check_value(self, value):
99 """Check that the supplied value is a `~lsst.meas.algorithms.Defect`
100 or can be converted to one.
101
102 Parameters
103 ----------
104 value : `object`
105 Value to check.
106
107 Returns
108 -------
109 new : `~lsst.meas.algorithms.Defect`
110 Either the supplied value or a new object derived from it.
111
112 Raises
113 ------
114 ValueError
115 Raised if the supplied value can not be converted to
116 `~lsst.meas.algorithms.Defect`
117 """
118 if isinstance(value, Defect):
119 pass
121 value = Defect(value)
125 value = Defect(value.getBBox())
126 else:
127 raise ValueError(f"Defects must be of type Defect, BoxI, or PointI, not '{value!r}'")
128 return value
129
Encapsulate information about a bad portion of a detector.
Definition Defect.h:39
◆ _get_values()
|
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 486 of file defects.py.
486 def _get_values(values, n=1):
487 """Retrieve N values from the supplied values.
488
489 Parameters
490 ----------
491 values : `numbers.Number` or `list` or `np.array`
492 Input values.
493 n : `int`
494 Number of values to retrieve.
495
496 Returns
497 -------
498 vals : `list` or `np.array` or `numbers.Number`
499 Single value from supplied list if ``n`` is 1, or `list`
500 containing first ``n`` values from supplied values.
501
502 Notes
503 -----
504 Some supplied tables have vectors in some columns that can also
505 be scalars. This method can be used to get the first number as
506 a scalar or the first N items from a vector as a vector.
507 """
508 if n == 1:
509 if isinstance(values, numbers.Number):
510 return values
511 else:
512 return values[0]
513
514 return values[:n]
515
◆ _normalize()
|
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.
174 def _normalize(self):
175 """Recalculate defect bounding boxes for efficiency.
176
177 Notes
178 -----
179 Ideally, this would generate the provably-minimal set of bounding
180 boxes necessary to represent the defects. At present, however, that
181 doesn't happen: see DM-24781. In the cases of substantial overlaps or
182 duplication, though, this will produce a much reduced set.
183 """
184 # In bulk-update mode, normalization is a no-op.
185 if self._bulk_update:
186 return
187
188 # If we have no defects, there is nothing to normalize.
189 if len(self) == 0:
190 return
191
192 # work out the minimum and maximum bounds from all defect regions.
193 minX, minY, maxX, maxY = float('inf'), float('inf'), float('-inf'), float('-inf')
194 for defect in self:
195 bbox = defect.getBBox()
196 minX = min(minX, bbox.getMinX())
197 minY = min(minY, bbox.getMinY())
198 maxX = max(maxX, bbox.getMaxX())
199 maxY = max(maxY, bbox.getMaxY())
200
202 lsst.geom.Point2I(maxX, maxY))
203
204 mask = lsst.afw.image.Mask(region)
205 self.maskPixels(mask, maskName="BAD")
206 self._defects = Defects.fromMask(mask, "BAD")._defects
207
◆ append()
| lsst.ip.isr.defects.Defects.append | ( | self, | |
| value ) |
Definition at line 219 of file defects.py.
219 def append(self, value):
220 self._defects.append(self._check_value(value))
221 self._normalize()
222
◆ apply()
|
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 685 of file calibType.py.
685 def apply(self, target):
686 """Method to apply the calibration to the target object.
687
688 Parameters
689 ----------
690 target : `object`
691 Thing to validate against.
692
693 Returns
694 -------
695 valid : `bool`
696 Returns true if the calibration was applied correctly.
697
698 Raises
699 ------
700 NotImplementedError
701 Raised if not implemented.
702 """
703 raise NotImplementedError("Must be implemented by subclass.")
704
705
◆ 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.
209 def bulk_update(self):
210 """Temporarily suspend normalization of the defect list.
211 """
212 self._bulk_update = True
213 try:
214 yield
215 finally:
216 self._bulk_update = False
217 self._normalize()
218
◆ calibInfoFromDict()
|
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 322 of file calibType.py.
322 def calibInfoFromDict(self, dictionary):
323 """Handle common keywords.
324
325 This isn't an ideal solution, but until all calibrations
326 expect to find everything in the metadata, they still need to
327 search through dictionaries.
328
329 Parameters
330 ----------
331 dictionary : `dict` or `lsst.daf.base.PropertyList`
332 Source for the common keywords.
333
334 Raises
335 ------
336 RuntimeError
337 Raised if the dictionary does not match the expected OBSTYPE.
338 """
339
340 def search(haystack, needles):
341 """Search dictionary 'haystack' for an entry in 'needles'
342 """
343 test = [haystack.get(x) for x in needles]
344 test = set([x for x in test if x is not None])
345 if len(test) == 0:
346 if "metadata" in haystack:
347 return search(haystack["metadata"], needles)
348 else:
349 return None
350 elif len(test) == 1:
351 value = list(test)[0]
352 if value == "":
353 return None
354 else:
355 return value
356 else:
357 raise ValueError(f"Too many values found: {len(test)} {test} {needles}")
358
359 if "metadata" in dictionary:
360 metadata = dictionary["metadata"]
361
362 if self._OBSTYPE != metadata["OBSTYPE"]:
363 raise RuntimeError(f"Incorrect calibration supplied. Expected {self._OBSTYPE}, "
364 f"found {metadata['OBSTYPE']}")
365
366 if (value := search(dictionary, ["INSTRUME", "instrument"])) is not None:
367 self._instrument = value
368 if (value := search(dictionary, ["RAFTNAME"])) is not None:
369 self._slotName = value
370 if (value := search(dictionary, ["DETECTOR", "detectorId"])) is not None:
371 self._detectorId = value
372 if (value := search(dictionary, ["DET_NAME", "DETECTOR_NAME", "detectorName"])) is not None:
373 self._detectorName = value
374 if (value := search(dictionary, ["DET_SER", "DETECTOR_SERIAL", "detectorSerial"])) is not None:
375 self._detectorSerial = value
376 if (value := search(dictionary, ["FILTER", "filterName"])) is not None:
377 self._filter = value
378 if (value := search(dictionary, ["CALIB_ID"])) is not None:
379 self._calibId = value
380 if (value := search(dictionary, ["SEQFILE"])) is not None:
381 self._seqfile = value
382 if (value := search(dictionary, ["SEQNAME"])) is not None:
383 self._seqname = value
384 if (value := search(dictionary, ["SEQCKSUM"])) is not None:
385 self._seqcksum = value
386
◆ 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.
227 def copy(self):
228 """Copy the defects to a new list, creating new defects from the
229 bounding boxes.
230
231 Returns
232 -------
233 new : `Defects`
234 New list with new `Defect` entries.
235
236 Notes
237 -----
238 This is not a shallow copy in that new `Defect` instances are
239 created from the original bounding boxes. It's also not a deep
240 copy since the bounding boxes are not recreated.
241 """
242 return self.__class__(d.getBBox() for d in self)
243
◆ determineCalibClass()
|
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 388 of file calibType.py.
388 def determineCalibClass(cls, metadata, message):
389 """Attempt to find calibration class in metadata.
390
391 Parameters
392 ----------
393 metadata : `dict` or `lsst.daf.base.PropertyList`
394 Metadata possibly containing a calibration class entry.
395 message : `str`
396 Message to include in any errors.
397
398 Returns
399 -------
400 calibClass : `object`
401 The class to use to read the file contents. Should be an
402 `lsst.ip.isr.IsrCalib` subclass.
403
404 Raises
405 ------
406 ValueError
407 Raised if the resulting calibClass is the base
408 `lsst.ip.isr.IsrClass` (which does not implement the
409 content methods).
410 """
411 calibClassName = metadata.get("CALIBCLS")
412 calibClass = doImport(calibClassName) if calibClassName is not None else cls
413 if calibClass is IsrCalib:
414 raise ValueError(f"Cannot use base class to read calibration data: {message}")
415 return calibClass
416
◆ fromDetector()
|
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
Raised if not implemented by a subclass.
This needs to be implemented by subclasses for each
calibration type.
Reimplemented in lsst.ip.isr.crosstalk.CrosstalkCalib, lsst.ip.isr.deferredCharge.DeferredChargeCalib, lsst.ip.isr.linearize.Linearizer, and lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.
Definition at line 567 of file calibType.py.
567 def fromDetector(self, detector):
568 """Modify the calibration parameters to match the supplied detector.
569
570 Parameters
571 ----------
572 detector : `lsst.afw.cameraGeom.Detector`
573 Detector to use to set parameters from.
574
575 Raises
576 ------
577 NotImplementedError
578 Raised if not implemented by a subclass.
579 This needs to be implemented by subclasses for each
580 calibration type.
581 """
582 raise NotImplementedError("Must be implemented by subclass.")
583
◆ 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 357 of file defects.py.
357 def fromDict(cls, dictionary):
358 """Construct a calibration from a dictionary of properties.
359
360 Must be implemented by the specific calibration subclasses.
361
362 Parameters
363 ----------
364 dictionary : `dict`
365 Dictionary of properties.
366
367 Returns
368 -------
369 calib : `lsst.ip.isr.CalibType`
370 Constructed calibration.
371
372 Raises
373 ------
374 RuntimeError
375 Raised if the supplied dictionary is for a different
376 calibration.
377 """
378 calib = cls()
379
380 if calib._OBSTYPE != dictionary['metadata']['OBSTYPE']:
381 raise RuntimeError(f"Incorrect crosstalk supplied. Expected {calib._OBSTYPE}, "
382 f"found {dictionary['metadata']['OBSTYPE']}")
383
384 calib.setMetadata(dictionary['metadata'])
385 calib.calibInfoFromDict(dictionary)
386
387 xCol = dictionary['x0']
388 yCol = dictionary['y0']
389 widthCol = dictionary['width']
390 heightCol = dictionary['height']
391
392 with calib.bulk_update:
393 for x0, y0, width, height in zip(xCol, yCol, widthCol, heightCol):
395 lsst.geom.Extent2I(width, height)))
396 return calib
397
◆ 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 666 of file defects.py.
666 def fromFootprintList(cls, fpList):
667 """Compute a defect list from a footprint list, optionally growing
668 the footprints.
669
670 Parameters
671 ----------
672 fpList : `list` of `lsst.afw.detection.Footprint`
673 Footprint list to process.
674
675 Returns
676 -------
677 defects : `Defects`
678 List of defects.
679 """
680 # normalize_on_init is set to False to avoid recursively calling
681 # fromMask/fromFootprintList in Defects.__init__.
683 for fp in fpList), normalize_on_init=False)
684
std::vector< lsst::geom::Box2I > footprintToBBoxList(Footprint const &footprint)
Return a list of BBoxs, whose union contains exactly the pixels in the footprint, neither more nor le...
Definition Footprint.cc:366
◆ 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 686 of file defects.py.
686 def fromMask(cls, mask, maskName):
687 """Compute a defect list from a specified mask plane.
688
689 Parameters
690 ----------
691 mask : `lsst.afw.image.Mask` or `lsst.afw.image.MaskedImage`
692 Image to process.
693 maskName : `str` or `list`
694 Mask plane name, or list of names to convert.
695
696 Returns
697 -------
698 defects : `Defects`
699 Defect list constructed from masked pixels.
700 """
701 if hasattr(mask, "getMask"):
702 mask = mask.getMask()
703 thresh = lsst.afw.detection.Threshold(mask.getPlaneBitMask(maskName),
704 lsst.afw.detection.Threshold.BITMASK)
705 fpList = lsst.afw.detection.FootprintSet(mask, thresh).getFootprints()
706 return cls.fromFootprintList(fpList)
A set of Footprints, associated with a MaskedImage.
Definition FootprintSet.h:55
A Threshold is used to pass a threshold value to detection algorithms.
Definition Threshold.h:43
◆ 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 517 of file defects.py.
517 def fromTable(cls, tableList, normalize_on_init=True):
518 """Construct a `Defects` from the contents of a
519 `~lsst.afw.table.BaseCatalog`.
520
521 Parameters
522 ----------
523 table : `lsst.afw.table.BaseCatalog`
524 Table with one row per defect.
525 normalize_on_init : `bool`, optional
526 If `True`, normalization is applied to the defects listed in the
527 table to remove duplicates, eliminate overlaps, etc. Otherwise
528 the defects in the returned object exactly match those in the
529 table.
530
531 Returns
532 -------
533 defects : `Defects`
534 A `Defects` list.
535
536 Notes
537 -----
538 Two table formats are recognized. The first is the
539 `FITS regions <https://fits.gsfc.nasa.gov/registry/region.html>`_
540 definition tabular format written by `toFitsRegionTable` where the
541 pixel origin is corrected from FITS 1-based to a 0-based origin.
542 The second is the legacy defects format using columns ``x0``, ``y0``
543 (bottom left hand pixel of box in 0-based coordinates), ``width``
544 and ``height``.
545
546 The FITS standard regions can only read BOX, POINT, or ROTBOX with
547 a zero degree rotation.
548 """
549 table = tableList[0]
550 defectList = []
551
552 schema = table.columns
553 # Check schema to see which definitions we have
554 if "X" in schema and "Y" in schema and "R" in schema and "SHAPE" in schema:
555 # This is a FITS region style table
556 isFitsRegion = True
557 elif "x0" in schema and "y0" in schema and "width" in schema and "height" in schema:
558 # This is a classic LSST-style defect table
559 isFitsRegion = False
560 else:
561 raise ValueError("Unsupported schema for defects extraction")
562
563 for record in table:
564 if isFitsRegion:
565 # Coordinates can be arrays (some shapes in the standard
566 # require this)
567 # Correct for FITS 1-based origin
568 xcen = cls._get_values(record['X']) - 1.0
569 ycen = cls._get_values(record['Y']) - 1.0
570 shape = record['SHAPE'].upper().rstrip()
571 if shape == "BOX":
574 n=2)))
575 elif shape == "POINT":
576 # Handle the case where we have an externally created
577 # FITS file.
578 box = lsst.geom.Point2I(xcen, ycen)
579 elif shape == "ROTBOX":
580 # Astropy regions always writes ROTBOX
581 rotang = cls._get_values(record['ROTANG'])
582 # We can support 0 or 90 deg
583 if math.isclose(rotang % 90.0, 0.0):
584 # Two values required
585 r = cls._get_values(record['R'], n=2)
586 if math.isclose(rotang % 180.0, 0.0):
587 width = r[0]
588 height = r[1]
589 else:
590 width = r[1]
591 height = r[0]
593 lsst.geom.Extent2I(width, height))
594 else:
595 log.warning("Defect can not be defined using ROTBOX with non-aligned rotation angle")
596 continue
597 else:
598 log.warning("Defect lists can only be defined using BOX or POINT not %s", shape)
599 continue
600
601 else:
602 # This is a classic LSST-style defect table
605
606 defectList.append(box)
607
608 defects = cls(defectList, normalize_on_init=normalize_on_init)
609 newMeta = dict(table.meta)
610 defects.updateMetadata(setCalibInfo=True, **newMeta)
611
612 return defects
613
static Box2I makeCenteredBox(Point2D const ¢er, Extent const &size)
Create a box centered as closely as possible on a particular point.
Definition Box.cc:97
◆ getMetadata()
|
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 171 of file calibType.py.
171 def getMetadata(self):
172 """Retrieve metadata associated with this calibration.
173
174 Returns
175 -------
176 meta : `lsst.daf.base.PropertyList`
177 Metadata. The returned `~lsst.daf.base.PropertyList` can be
178 modified by the caller and the changes will be written to
179 external files.
180 """
181 return self._metadata
182
◆ insert()
| lsst.ip.isr.defects.Defects.insert | ( | self, | |
| index, | |||
| value ) |
Definition at line 223 of file defects.py.
223 def insert(self, index, value):
224 self._defects.insert(index, self._check_value(value))
225 self._normalize()
226
◆ 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.
261 def maskPixels(self, mask, maskName="BAD"):
262 """Set mask plane based on these defects.
263
264 Parameters
265 ----------
266 maskedImage : `lsst.afw.image.MaskedImage` or `lsst.afw.image.Mask`
267 Image to process. Only the mask plane is updated.
268 maskName : str, optional
269 Mask plane name to use.
270 """
271 # mask bad pixels
272 if hasattr(mask, "getMask"):
273 mask = mask.getMask()
274 bitmask = mask.getPlaneBitMask(maskName)
275 for defect in self:
276 bbox = defect.getBBox()
277 lsst.afw.geom.SpanSet(bbox).clippedTo(mask.getBBox()).setMask(mask, bitmask)
278
◆ metadata()
|
inherited |
Definition at line 168 of file calibType.py.
168 def metadata(self):
169 return self._metadata
170
◆ readFits()
|
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 505 of file calibType.py.
505 def readFits(cls, filename, **kwargs):
506 """Read calibration data from a FITS file.
507
508 Parameters
509 ----------
510 filename : `str`
511 Filename to read data from.
512 kwargs : `dict` or collections.abc.Mapping`, optional
513 Set of key=value pairs to pass to the ``fromTable``
514 method.
515
516 Returns
517 -------
518 calib : `lsst.ip.isr.IsrCalib`
519 Calibration contained within the file.
520 """
521 tableList = []
522 tableList.append(Table.read(filename, hdu=1, mask_invalid=False))
523 extNum = 2 # Fits indices start at 1, we've read one already.
524 keepTrying = True
525
526 while keepTrying:
527 with warnings.catch_warnings():
528 warnings.simplefilter("error")
529 try:
530 newTable = Table.read(filename, hdu=extNum, mask_invalid=False)
531 tableList.append(newTable)
532 extNum += 1
533 except Exception:
534 keepTrying = False
535
536 for table in tableList:
537 for k, v in table.meta.items():
538 if isinstance(v, fits.card.Undefined):
539 table.meta[k] = None
540
541 calibClass = cls.determineCalibClass(tableList[0].meta, "readFits")
542 return calibClass.fromTable(tableList, **kwargs)
543
◆ 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 615 of file defects.py.
615 def readLsstDefectsFile(cls, filename, normalize_on_init=False):
616 """Read defects information from a legacy LSST format text file.
617
618 Parameters
619 ----------
620 filename : `str`
621 Name of text file containing the defect information.
622
623 normalize_on_init : `bool`, optional
624 If `True`, normalization is applied to the defects listed in the
625 table to remove duplicates, eliminate overlaps, etc. Otherwise
626 the defects in the returned object exactly match those in the
627 table.
628
629 Returns
630 -------
631 defects : `Defects`
632 The defects.
633
634 Notes
635 -----
636 These defect text files are used as the human readable definitions
637 of defects in calibration data definition repositories. The format
638 is to use four columns defined as follows:
639
640 x0 : `int`
641 X coordinate of bottom left corner of box.
642 y0 : `int`
643 Y coordinate of bottom left corner of box.
644 width : `int`
645 X extent of the box.
646 height : `int`
647 Y extent of the box.
648
649 Files of this format were used historically to represent defects
650 in simple text form. Use `Defects.readText` and `Defects.writeText`
651 to use the more modern format.
652 """
653 # Use loadtxt so that ValueError is thrown if the file contains a
654 # non-integer value. genfromtxt converts bad values to -1.
655 defect_array = np.loadtxt(filename,
656 dtype=[("x0", "int"), ("y0", "int"),
657 ("x_extent", "int"), ("y_extent", "int")])
658
661 for row in defect_array)
662
663 return cls(defects, normalize_on_init=normalize_on_init)
664
◆ readText()
|
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 418 of file calibType.py.
418 def readText(cls, filename, **kwargs):
419 """Read calibration representation from a yaml/ecsv file.
420
421 Parameters
422 ----------
423 filename : `str`
424 Name of the file containing the calibration definition.
425 kwargs : `dict` or collections.abc.Mapping`, optional
426 Set of key=value pairs to pass to the ``fromDict`` or
427 ``fromTable`` methods.
428
429 Returns
430 -------
431 calib : `~lsst.ip.isr.IsrCalibType`
432 Calibration class.
433
434 Raises
435 ------
436 RuntimeError
437 Raised if the filename does not end in ".ecsv" or ".yaml".
438 """
439 if filename.endswith((".ecsv", ".ECSV")):
440 data = Table.read(filename, format="ascii.ecsv")
441 calibClass = cls.determineCalibClass(data.meta, "readText/ECSV")
442 return calibClass.fromTable([data], **kwargs)
443 elif filename.endswith((".yaml", ".YAML")):
444 with open(filename, "r") as f:
445 data = yaml.load(f, Loader=yaml.CLoader)
446 calibClass = cls.determineCalibClass(data["metadata"], "readText/YAML")
447 return calibClass.fromDict(data, **kwargs)
448 else:
449 raise RuntimeError(f"Unknown filename extension: {filename}")
450
◆ requiredAttributes() [1/2]
|
inherited |
Definition at line 159 of file calibType.py.
159 def requiredAttributes(self):
160 return self._requiredAttributes
161
◆ requiredAttributes() [2/2]
|
inherited |
Definition at line 163 of file calibType.py.
163 def requiredAttributes(self, value):
164 self._requiredAttributes = value
165
◆ setMetadata()
|
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.
Reimplemented in lsst.ip.isr.transmissionCurve.IntermediateTransmissionCurve.
Definition at line 183 of file calibType.py.
183 def setMetadata(self, metadata):
184 """Store a copy of the supplied metadata with this calibration.
185
186 Parameters
187 ----------
188 metadata : `lsst.daf.base.PropertyList`
189 Metadata to associate with the calibration. Will be copied and
190 overwrite existing metadata.
191 """
192 if metadata is not None:
193 self._metadata.update(metadata)
194
195 # Ensure that we have the obs type required by calibration ingest
196 self._metadata["OBSTYPE"] = self._OBSTYPE
197 self._metadata[self._OBSTYPE + "_SCHEMA"] = self._SCHEMA
198 self._metadata[self._OBSTYPE + "_VERSION"] = self._VERSION
199
200 if isinstance(metadata, dict):
201 self.calibInfoFromDict(metadata)
202 elif isinstance(metadata, PropertyList):
203 self.calibInfoFromDict(metadata.toDict())
204
◆ 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 398 of file defects.py.
398 def toDict(self):
399 """Return a dictionary containing the calibration properties.
400
401 The dictionary should be able to be round-tripped through
402 `fromDict`.
403
404 Returns
405 -------
406 dictionary : `dict`
407 Dictionary of properties.
408 """
409 self.updateMetadata()
410
411 outDict = {}
412 metadata = self.getMetadata()
413 outDict['metadata'] = metadata
414
415 xCol = []
416 yCol = []
417 widthCol = []
418 heightCol = []
419
420 nrows = len(self._defects)
421 if nrows:
422 for defect in self._defects:
423 box = defect.getBBox()
424 xCol.append(box.getBeginX())
425 yCol.append(box.getBeginY())
426 widthCol.append(box.getWidth())
427 heightCol.append(box.getHeight())
428
429 outDict['x0'] = xCol
430 outDict['y0'] = yCol
431 outDict['width'] = widthCol
432 outDict['height'] = heightCol
433
434 return outDict
435
◆ 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 302 of file defects.py.
302 def toFitsRegionTable(self):
303 """Convert defect list to `~lsst.afw.table.BaseCatalog` using the
304 FITS region standard.
305
306 Returns
307 -------
308 table : `lsst.afw.table.BaseCatalog`
309 Defects in tabular form.
310
311 Notes
312 -----
313 The table created uses the
314 `FITS regions <https://fits.gsfc.nasa.gov/registry/region.html>`_
315 definition tabular format. The ``X`` and ``Y`` coordinates are
316 converted to FITS Physical coordinates that have origin pixel (1, 1)
317 rather than the (0, 0) used in LSST software.
318 """
319 self.updateMetadata()
320 nrows = len(self._defects)
321
322 if nrows:
323 # Adding entire columns is more efficient than adding
324 # each element separately
325 xCol = []
326 yCol = []
327 rCol = []
328 shapes = []
329 for i, defect in enumerate(self._defects):
330 box = defect.getBBox()
331 center = box.getCenter()
332 # Correct for the FITS 1-based offset
333 xCol.append(center.getX() + 1.0)
334 yCol.append(center.getY() + 1.0)
335
336 width = box.width
337 height = box.height
338
339 if width == 1 and height == 1:
340 # Call this a point
341 shapeType = "POINT"
342 else:
343 shapeType = "BOX"
344
345 # Strings have to be added per row
346 shapes.append(shapeType)
347
348 rCol.append(np.array([width, height], dtype=np.float64))
349
350 table = astropy.table.Table({'X': xCol, 'Y': yCol, 'SHAPE': shapes,
351 'R': rCol, 'ROTANG': np.zeros(nrows),
352 'COMPONENT': np.arange(nrows)})
353 table.meta = self.getMetadata().toDict()
354 return table
355
◆ 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 436 of file defects.py.
436 def toTable(self):
437 """Convert defects to a simple table form that we use to write
438 to text files.
439
440 Returns
441 -------
442 table : `lsst.afw.table.BaseCatalog`
443 Defects in simple tabular form.
444
445 Notes
446 -----
447 These defect tables are used as the human readable definitions
448 of defects in calibration data definition repositories. The format
449 is to use four columns defined as follows:
450
451 x0 : `int`
452 X coordinate of bottom left corner of box.
453 y0 : `int`
454 Y coordinate of bottom left corner of box.
455 width : `int`
456 X extent of the box.
457 height : `int`
458 Y extent of the box.
459 """
460 tableList = []
461 self.updateMetadata()
462
463 xCol = []
464 yCol = []
465 widthCol = []
466 heightCol = []
467
468 nrows = len(self._defects)
469 if nrows:
470 for defect in self._defects:
471 box = defect.getBBox()
472 xCol.append(box.getBeginX())
473 yCol.append(box.getBeginY())
474 widthCol.append(box.getWidth())
475 heightCol.append(box.getHeight())
476
477 catalog = astropy.table.Table({'x0': xCol, 'y0': yCol, 'width': widthCol, 'height': heightCol})
478 inMeta = self.getMetadata().toDict()
479 outMeta = {k: v for k, v in inMeta.items() if v is not None}
480 catalog.meta = outMeta
481 tableList.append(catalog)
482
483 return tableList
484
◆ 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.
244 def transpose(self):
245 """Make a transposed copy of this defect list.
246
247 Returns
248 -------
249 retDefectList : `Defects`
250 Transposed list of defects.
251 """
252 retDefectList = self.__class__()
253 for defect in self:
254 bbox = defect.getBBox()
255 dimensions = bbox.getDimensions()
257 lsst.geom.Extent2I(dimensions[1], dimensions[0]))
258 retDefectList.append(nbbox)
259 return retDefectList
260
◆ updateCounters()
| lsst.ip.isr.defects.Defects.updateCounters | ( | self, | |
| columns = None, | |||
| hot = None, | |||
| cold = None ) |
Update metadata with pixel and column counts.
Parameters
----------
columns : `int`, optional
Number of full columns masked.
hot : `dict` [`str`, `int`], optional
Dictionary with the count of hot pixels, indexed by amplifier name.
cold : `dict` [`str`, `int`], optional
Dictionary with the count of hot pixels, indexed by amplifier name.
Definition at line 279 of file defects.py.
279 def updateCounters(self, columns=None, hot=None, cold=None):
280 """Update metadata with pixel and column counts.
281
282 Parameters
283 ----------
284 columns : `int`, optional
285 Number of full columns masked.
286 hot : `dict` [`str`, `int`], optional
287 Dictionary with the count of hot pixels, indexed by amplifier name.
288 cold : `dict` [`str`, `int`], optional
289 Dictionary with the count of hot pixels, indexed by amplifier name.
290 """
291 mdSupplemental = dict()
292 if columns:
293 mdSupplemental["LSST CALIB DEFECTS N_BAD_COLUMNS"] = columns
294 if hot:
295 for amp, count in hot.items():
296 mdSupplemental[f"LSST CALIB DEFECTS {amp} N_HOT"] = count
297 if cold:
298 for amp, count in cold.items():
299 mdSupplemental[f"LSST CALIB DEFECTS {amp} N_COLD"] = count
300 self.getMetadata().update(mdSupplemental)
301
◆ updateMetadata()
|
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.
Reimplemented in lsst.ip.isr.brighterFatterKernel.BrighterFatterKernel, lsst.ip.isr.calibType.IsrProvenance, lsst.ip.isr.crosstalk.CrosstalkCalib, lsst.ip.isr.linearize.Linearizer, lsst.ip.isr.photodiodeCorrection.PhotodiodeCorrection, and lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.
Definition at line 205 of file calibType.py.
207 **kwargs):
208 """Update metadata keywords with new values.
209
210 Parameters
211 ----------
212 camera : `lsst.afw.cameraGeom.Camera`, optional
213 Reference camera to use to set ``_instrument`` field.
214 detector : `lsst.afw.cameraGeom.Detector`, optional
215 Reference detector to use to set ``_detector*`` fields.
216 filterName : `str`, optional
217 Filter name to assign to this calibration.
218 setCalibId : `bool`, optional
219 Construct the ``_calibId`` field from other fields.
220 setCalibInfo : `bool`, optional
221 Set calibration parameters from metadata.
222 setDate : `bool`, optional
223 Ensure the metadata ``CALIBDATE`` fields are set to the current
224 datetime.
225 kwargs : `dict` or `collections.abc.Mapping`, optional
226 Set of ``key=value`` pairs to assign to the metadata.
227 """
228 mdOriginal = self.getMetadata()
229 mdSupplemental = dict()
230
231 for k, v in kwargs.items():
232 if isinstance(v, fits.card.Undefined):
233 kwargs[k] = None
234
235 if setCalibInfo:
236 self.calibInfoFromDict(kwargs)
237
238 if camera:
239 self._instrument = camera.getName()
240
241 if detector:
242 self._detectorName = detector.getName()
243 self._detectorSerial = detector.getSerial()
244 self._detectorId = detector.getId()
245 if "_" in self._detectorName:
246 (self._raftName, self._slotName) = self._detectorName.split("_")
247
248 if filterName:
249 # TOD0 DM-28093: I think this whole comment can go away, if we
250 # always use physicalLabel everywhere in ip_isr.
251 # If set via:
252 # exposure.getInfo().getFilter().getName()
253 # then this will hold the abstract filter.
254 self._filter = filterName
255
256 if setDate:
257 date = datetime.datetime.now()
258 mdSupplemental["CALIBDATE"] = date.isoformat()
259 mdSupplemental["CALIB_CREATION_DATE"] = date.date().isoformat()
260 mdSupplemental["CALIB_CREATION_TIME"] = date.time().isoformat()
261
262 if setCalibId:
263 values = []
264 values.append(f"instrument={self._instrument}") if self._instrument else None
265 values.append(f"raftName={self._raftName}") if self._raftName else None
266 values.append(f"detectorName={self._detectorName}") if self._detectorName else None
267 values.append(f"detector={self._detectorId}") if self._detectorId else None
268 values.append(f"filter={self._filter}") if self._filter else None
269
270 calibDate = mdOriginal.get("CALIBDATE", mdSupplemental.get("CALIBDATE", None))
271 values.append(f"calibDate={calibDate}") if calibDate else None
272
273 self._calibId = " ".join(values)
274
275 self._metadata["INSTRUME"] = self._instrument if self._instrument else None
276 self._metadata["RAFTNAME"] = self._raftName if self._raftName else None
277 self._metadata["SLOTNAME"] = self._slotName if self._slotName else None
278 self._metadata["DETECTOR"] = self._detectorId
279 self._metadata["DET_NAME"] = self._detectorName if self._detectorName else None
280 self._metadata["DET_SER"] = self._detectorSerial if self._detectorSerial else None
281 self._metadata["FILTER"] = self._filter if self._filter else None
282 self._metadata["CALIB_ID"] = self._calibId if self._calibId else None
283 self._metadata["SEQFILE"] = self._seqfile if self._seqfile else None
284 self._metadata["SEQNAME"] = self._seqname if self._seqname else None
285 self._metadata["SEQCKSUM"] = self._seqcksum if self._seqcksum else None
286 self._metadata["CALIBCLS"] = get_full_type_name(self)
287
288 mdSupplemental.update(kwargs)
289 mdOriginal.update(mdSupplemental)
290
◆ updateMetadataFromExposures()
|
inherited |
Extract and unify metadata information.
Parameters
----------
exposures : `list`
Exposures or other calibrations to scan.
Definition at line 291 of file calibType.py.
291 def updateMetadataFromExposures(self, exposures):
292 """Extract and unify metadata information.
293
294 Parameters
295 ----------
296 exposures : `list`
297 Exposures or other calibrations to scan.
298 """
299 # This list of keywords is the set of header entries that
300 # should be checked and propagated. Not having an entry is
301 # not a failure, as they may not be defined for the exposures
302 # being used.
303 keywords = ["SEQNAME", "SEQFILE", "SEQCKSUM", "ODP", "AP0_RC"]
304 metadata = {}
305
306 for exp in exposures:
307 try:
308 expMeta = exp.getMetadata()
309 except AttributeError:
310 continue
311 for key in keywords:
312 if key in expMeta:
313 if key in metadata:
314 if metadata[key] != expMeta[key]:
315 self.log.warning("Metadata mismatch! Have: %s Found %s",
316 metadata[key], expMeta[key])
317 else:
318 metadata[key] = expMeta[key]
319
320 self.updateMetadata(**metadata, setCalibInfo=True)
321
◆ validate()
|
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.
Reimplemented in lsst.ip.isr.linearize.Linearizer, and lsst.ip.isr.photodiodeCorrection.PhotodiodeCorrection.
Definition at line 670 of file calibType.py.
670 def validate(self, other=None):
671 """Validate that this calibration is defined and can be used.
672
673 Parameters
674 ----------
675 other : `object`, optional
676 Thing to validate against.
677
678 Returns
679 -------
680 valid : `bool`
681 Returns true if the calibration is valid and appropriate.
682 """
683 return False
684
◆ writeFits()
|
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.
Reimplemented in lsst.ip.isr.transmissionCurve.IntermediateTransmissionCurve.
Definition at line 544 of file calibType.py.
544 def writeFits(self, filename):
545 """Write calibration data to a FITS file.
546
547 Parameters
548 ----------
549 filename : `str`
550 Filename to write data to.
551
552 Returns
553 -------
554 used : `str`
555 The name of the file used to write the data.
556 """
557 tableList = self.toTable()
558 with warnings.catch_warnings():
559 warnings.filterwarnings("ignore", category=Warning, module="astropy.io")
560 astropyList = [fits.table_to_hdu(table) for table in tableList]
561 astropyList.insert(0, fits.PrimaryHDU())
562
563 writer = fits.HDUList(astropyList)
564 writer.writeto(filename, overwrite=True)
565 return filename
566
◆ writeText()
|
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 451 of file calibType.py.
451 def writeText(self, filename, format="auto"):
452 """Write the calibration data to a text file.
453
454 Parameters
455 ----------
456 filename : `str`
457 Name of the file to write.
458 format : `str`
459 Format to write the file as. Supported values are:
460 ``"auto"`` : Determine filetype from filename.
461 ``"yaml"`` : Write as yaml.
462 ``"ecsv"`` : Write as ecsv.
463
464 Returns
465 -------
466 used : `str`
467 The name of the file used to write the data. This may
468 differ from the input if the format is explicitly chosen.
469
470 Raises
471 ------
472 RuntimeError
473 Raised if filename does not end in a known extension, or
474 if all information cannot be written.
475
476 Notes
477 -----
478 The file is written to YAML/ECSV format and will include any
479 associated metadata.
480 """
481 if format == "yaml" or (format == "auto" and filename.lower().endswith((".yaml", ".YAML"))):
482 outDict = self.toDict()
483 path, ext = os.path.splitext(filename)
484 filename = path + ".yaml"
485 with open(filename, "w") as f:
486 yaml.dump(outDict, f)
487 elif format == "ecsv" or (format == "auto" and filename.lower().endswith((".ecsv", ".ECSV"))):
488 tableList = self.toTable()
489 if len(tableList) > 1:
490 # ECSV doesn't support multiple tables per file, so we
491 # can only write the first table.
492 raise RuntimeError(f"Unable to persist {len(tableList)}tables in ECSV format.")
493
494 table = tableList[0]
495 path, ext = os.path.splitext(filename)
496 filename = path + ".ecsv"
497 table.write(filename, format="ascii.ecsv")
498 else:
499 raise RuntimeError(f"Attempt to write to a file {filename} "
500 "that does not end in '.yaml' or '.ecsv'")
501
502 return filename
503
Member Data Documentation
◆ _bulk_update
|
protected |
Definition at line 87 of file defects.py.
◆ _calibId
|
protectedinherited |
Definition at line 74 of file calibType.py.
◆ _defects
|
protected |
Definition at line 84 of file defects.py.
◆ _detectorId
|
protectedinherited |
Definition at line 72 of file calibType.py.
◆ _detectorName
|
protectedinherited |
Definition at line 70 of file calibType.py.
◆ _detectorSerial
|
protectedinherited |
Definition at line 71 of file calibType.py.
◆ _filter
|
protectedinherited |
Definition at line 73 of file calibType.py.
◆ _instrument
|
protectedinherited |
Definition at line 67 of file calibType.py.
◆ _metadata
|
protectedinherited |
Definition at line 78 of file calibType.py.
◆ _OBSTYPE
|
staticprotectedinherited |
Definition at line 62 of file calibType.py.
◆ _raftName
|
protectedinherited |
Definition at line 68 of file calibType.py.
◆ _requiredAttributes
|
protectedinherited |
Definition at line 113 of file calibType.py.
◆ _SCHEMA
|
staticprotectedinherited |
Definition at line 63 of file calibType.py.
◆ _seqcksum
|
protectedinherited |
Definition at line 77 of file calibType.py.
◆ _seqfile
|
protectedinherited |
Definition at line 75 of file calibType.py.
◆ _seqname
|
protectedinherited |
Definition at line 76 of file calibType.py.
◆ _slotName
|
protectedinherited |
Definition at line 69 of file calibType.py.
◆ _VERSION
|
staticprotectedinherited |
Definition at line 64 of file calibType.py.
◆ log
|
inherited |
Definition at line 94 of file calibType.py.
◆ requiredAttributes
|
inherited |
Definition at line 88 of file calibType.py.
The documentation for this class was generated from the following file:
- /j/snowflake/release/lsstsw/stack/lsst-scipipe-10.0.0/Linux64/ip_isr/g55585698de+c657de43f9/python/lsst/ip/isr/defects.py
Generated on Sun May 11 2025 07:54:33 for LSST Applications by
1.13.2