Public Member Functions |
Public Attributes |
Protected Attributes |
Static Protected Attributes |
List of all members
lsst.ip.isr.linearize.Linearizer Class Reference
Inheritance diagram for lsst.ip.isr.linearize.Linearizer:
Public Member Functions | |
| __init__ (self, table=None, **kwargs) | |
| updateMetadata (self, setDate=False, **kwargs) | |
| fromDetector (self, detector) | |
| fromDict (cls, dictionary) | |
| toDict (self) | |
| fromTable (cls, tableList) | |
| toTable (self) | |
| getLinearityTypeByName (self, linearityTypeName) | |
| validate (self, detector=None, amplifier=None) | |
| applyLinearity (self, image, detector=None, log=None, gains=None) | |
| requiredAttributes (self) | |
| requiredAttributes (self, value) | |
| __str__ (self) | |
| __eq__ (self, other) | |
| metadata (self) | |
| getMetadata (self) | |
| setMetadata (self, metadata) | |
| 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) | |
| apply (self, target) | |
Public Attributes | |
| bool | hasLinearity = False |
| bool | override = False |
| ampNames = list() | |
| linearityCoeffs = dict() | |
| linearityType = dict() | |
| linearityBBox = dict() | |
| inputAbscissa = dict() | |
| inputOrdinate = dict() | |
| inputMask = dict() | |
| inputGroupingIndex = dict() | |
| inputNormalization = dict() | |
| fitParams = dict() | |
| fitParamsErr = dict() | |
| fitChiSq = dict() | |
| fitResiduals = dict() | |
| fitResidualsSigmaMad = dict() | |
| fitResidualsUnmasked = dict() | |
| fitResidualsModel = dict() | |
| linearFit = dict() | |
| linearityTurnoff = dict() | |
| linearityMaxSignal = dict() | |
| str | absoluteReferenceAmplifier = "" |
| tableData = None | |
| str | linearityUnits = 'adu' |
| requiredAttributes = set(["_OBSTYPE", "_SCHEMA", "_VERSION"]) | |
| log = log if log else logging.getLogger(__name__) | |
Protected Attributes | |
| _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
Parameter set for linearization.
These parameters are included in `lsst.afw.cameraGeom.Amplifier`, but
should be accessible externally to allow for testing.
Parameters
----------
table : `numpy.array`, optional
Lookup table; a 2-dimensional array of floats:
- one row for each row index (value of coef[0] in the amplifier)
- one column for each image value
To avoid copying the table the last index should vary fastest
(numpy default "C" order)
detector : `lsst.afw.cameraGeom.Detector`, optional
Detector object. Passed to self.fromDetector() on init.
log : `logging.Logger`, optional
Logger to handle messages.
kwargs : `dict`, optional
Other keyword arguments to pass to the parent init.
Raises
------
RuntimeError
Raised if the supplied table is not 2D, or if the table has fewer
columns than rows (indicating that the indices are swapped).
Notes
-----
The linearizer attributes stored are:
hasLinearity : `bool`
Whether a linearity correction is defined for this detector.
override : `bool`
Whether the detector parameters should be overridden.
ampNames : `list` [`str`]
List of amplifier names to correct.
linearityCoeffs : `dict` [`str`, `np.ndarray`]
Coefficients to use in correction. Indexed by amplifier
names. The format of the array depends on the type of
correction to apply.
linearityType : `dict` [`str`, `str`]
Type of correction to use, indexed by amplifier names.
linearityBBox : `dict` [`str`, `lsst.geom.Box2I`]
Bounding box the correction is valid over, indexed by
amplifier names.
fitParams : `dict` [`str`, `np.ndarray`], optional
Linearity fit parameters used to construct the correction
coefficients, indexed as above.
fitParamsErr : `dict` [`str`, `np.ndarray`], optional
Uncertainty values of the linearity fit parameters used to
construct the correction coefficients, indexed as above.
fitChiSq : `dict` [`str`, `float`], optional
Chi-squared value of the linearity fit, indexed as above.
fitResiduals : `dict` [`str`, `np.ndarray`], optional
Residuals of the fit, indexed as above. Used for
calculating photodiode corrections
fitResidualsSigmaMad : `dict` [`str`, `float`], optional
Robust median-absolute-deviation of fit residuals, scaled
by the signal level.
fitResidualsUnmasked : `dict` [`str`, `np.ndarray`], optional
Same as fitResiduals, but all outliers are included and
not masked as nans.
fitResidualsModel : `dict` [`str`, `np.ndarray`], optional
The model count level for each of the fitResiduals.
linearFit : The linear fit to the low flux region of the curve.
[intercept, slope].
tableData : `np.ndarray`, optional
Lookup table data for the linearity correction.
inputAbscissa : `dict` [`str`, `np.ndarray`], optional
Input abscissa used to construct linearizer (usually photodiode
or exposure time).
inputOrdinate : `dict` [`str`, `np.ndarray`], optional
Input ordinate used to construct linearizer (raw mean counts).
inputMask : `dict` [`str`, `np.ndarray`], optional
Input mask used for the fitting.
inputGroupingIndex : `dict` [`str`, `np.ndarray`], optional
Input grouping index used for fitting.
inputNormalization : `dict` [`str`, `np.ndarray`], optional
Input normalization that was applied to the abscissa for
each pair from the PTC used for the linearization fit.
absoluteReferenceAmplifier : `str`, optional
Amplifier used for the reference for absolute linearization
(DoubleSpline) mode.
Version 1.4 adds ``linearityTurnoff`` and ``linearityMaxSignal``.
Version 1.5 adds ``fitResidualsUnmasked``, ``inputAbscissa``,
``inputOrdinate``, ``inputMask``, ``inputGroupingIndex``,
``fitResidualsModel``, and ``inputNormalization``.
Version 1.6 adds ``absoluteReferenceAmplifier``.
Definition at line 48 of file linearize.py.
Constructor & Destructor Documentation
◆ __init__()
| lsst.ip.isr.linearize.Linearizer.__init__ | ( | self, | |
| table = None, | |||
| ** | kwargs ) |
Definition at line 145 of file linearize.py.
145 def __init__(self, table=None, **kwargs):
146 self.hasLinearity = False
147 self.override = False
148
149 self.ampNames = list()
150 self.linearityCoeffs = dict()
151 self.linearityType = dict()
152 self.linearityBBox = dict()
153 self.inputAbscissa = dict()
154 self.inputOrdinate = dict()
155 self.inputMask = dict()
156 self.inputGroupingIndex = dict()
157 self.inputNormalization = dict()
158 self.fitParams = dict()
159 self.fitParamsErr = dict()
160 self.fitChiSq = dict()
161 self.fitResiduals = dict()
162 self.fitResidualsSigmaMad = dict()
163 self.fitResidualsUnmasked = dict()
164 self.fitResidualsModel = dict()
165 self.linearFit = dict()
166 self.linearityTurnoff = dict()
167 self.linearityMaxSignal = dict()
168 self.absoluteReferenceAmplifier = ""
169 self.tableData = None
170 if table is not None:
171 if len(table.shape) != 2:
172 raise RuntimeError("table shape = %s; must have two dimensions" % (table.shape,))
173 if table.shape[1] < table.shape[0]:
174 raise RuntimeError("table shape = %s; indices are switched" % (table.shape,))
175 self.tableData = np.array(table, order="C")
176
177 # The linearizer is always natively in adu because it
178 # is computed prior to computing gains.
179 self.linearityUnits = 'adu'
180
181 super().__init__(**kwargs)
182 self.requiredAttributes.update(['hasLinearity', 'override',
183 'ampNames',
184 'linearityCoeffs', 'linearityType', 'linearityBBox',
185 'fitParams', 'fitParamsErr', 'fitChiSq',
186 'fitResiduals', 'fitResidualsSigmaMad', 'linearFit', 'tableData',
187 'units', 'linearityTurnoff', 'linearityMaxSignal',
188 'fitResidualsUnmasked', 'inputAbscissa', 'inputOrdinate',
189 'inputMask', 'inputGroupingIndex', 'fitResidualsModel',
190 'inputNormalization', 'absoluteReferenceAmplifier'])
191
Member Function Documentation
◆ __eq__()
|
inherited |
Calibration equivalence. Running ``calib.log.setLevel(0)`` enables debug statements to identify problematic fields.
Definition at line 105 of file calibType.py.
105 def __eq__(self, other):
106 """Calibration equivalence.
107
108 Running ``calib.log.setLevel(0)`` enables debug statements to
109 identify problematic fields.
110 """
111 if not isinstance(other, self.__class__):
112 self.log.debug("Incorrect class type: %s %s", self.__class__, other.__class__)
113 return False
114
115 for attr in self._requiredAttributes:
116 attrSelf = getattr(self, attr)
117 attrOther = getattr(other, attr)
118
119 if isinstance(attrSelf, dict):
120 # Dictionary of arrays.
121 if attrSelf.keys() != attrOther.keys():
122 self.log.debug("Dict Key Failure: %s %s %s", attr, attrSelf.keys(), attrOther.keys())
123 return False
124 for key in attrSelf:
125 try:
126 if not np.allclose(attrSelf[key], attrOther[key], equal_nan=True):
127 self.log.debug("Array Failure: %s %s %s", key, attrSelf[key], attrOther[key])
128 return False
129 except TypeError:
130 # If it is not something numpy can handle
131 # (it's not a number or array of numbers),
132 # then it needs to have its own equivalence
133 # operator.
134 if np.all(attrSelf[key] != attrOther[key]):
135 return False
136 elif (isinstance(attrSelf, np.ndarray) or isinstance(attrSelf, Column)
137 or isinstance(attrOther, np.ndarray) or isinstance(attrOther, Column)):
138 # Bare array.
139 if isinstance(attrSelf[0], (str, np.str_, np.bytes_)):
140 if not np.all(attrSelf == attrOther):
141 self.log.debug("Array Failure: %s %s %s", attr, attrSelf, attrOther)
142 return False
143 else:
144 if not np.allclose(attrSelf, attrOther, equal_nan=True):
145 self.log.debug("Array Failure: %s %s %s", attr, attrSelf, attrOther)
146 return False
147 elif type(attrSelf) is not type(attrOther):
148 if set([attrSelf, attrOther]) == set([None, ""]):
149 # Fits converts None to "", but None is not "".
150 continue
151 self.log.debug("Type Failure: %s %s %s %s %s", attr, type(attrSelf), type(attrOther),
152 attrSelf, attrOther)
153 return False
154 else:
155 if attrSelf != attrOther:
156 self.log.debug("Value Failure: %s %s %s", attr, attrSelf, attrOther)
157 return False
158
159 return True
160
◆ __str__()
|
inherited |
Definition at line 102 of file calibType.py.
102 def __str__(self):
103 return f"{self.__class__.__name__}(obstype={self._OBSTYPE}, detector={self._detectorName}, )"
104
◆ 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 704 of file calibType.py.
704 def apply(self, target):
705 """Method to apply the calibration to the target object.
706
707 Parameters
708 ----------
709 target : `object`
710 Thing to validate against.
711
712 Returns
713 -------
714 valid : `bool`
715 Returns true if the calibration was applied correctly.
716
717 Raises
718 ------
719 NotImplementedError
720 Raised if not implemented.
721 """
722 raise NotImplementedError("Must be implemented by subclass.")
723
724
◆ applyLinearity()
| lsst.ip.isr.linearize.Linearizer.applyLinearity | ( | self, | |
| image, | |||
| detector = None, | |||
| log = None, | |||
| gains = None ) |
Apply the linearity to an image.
If the linearity parameters are populated, use those,
otherwise use the values from the detector.
Parameters
----------
image : `~lsst.afw.image.image`
Image to correct.
detector : `~lsst.afw.cameraGeom.detector`, optional
Detector to use to determine exposure trimmed state. If
supplied, but no other linearity information is provided
by the calibration, then the static solution stored in the
detector will be used.
log : `~logging.Logger`, optional
Log object to use for logging.
gains : `dict` [`str`, `float`], optional
Dictionary of amp name to gain. If this is provided then
linearity terms will be converted from adu to electrons.
Only used for Spline linearity corrections.
Definition at line 593 of file linearize.py.
593 def applyLinearity(self, image, detector=None, log=None, gains=None):
594 """Apply the linearity to an image.
595
596 If the linearity parameters are populated, use those,
597 otherwise use the values from the detector.
598
599 Parameters
600 ----------
601 image : `~lsst.afw.image.image`
602 Image to correct.
603 detector : `~lsst.afw.cameraGeom.detector`, optional
604 Detector to use to determine exposure trimmed state. If
605 supplied, but no other linearity information is provided
606 by the calibration, then the static solution stored in the
607 detector will be used.
608 log : `~logging.Logger`, optional
609 Log object to use for logging.
610 gains : `dict` [`str`, `float`], optional
611 Dictionary of amp name to gain. If this is provided then
612 linearity terms will be converted from adu to electrons.
613 Only used for Spline linearity corrections.
614 """
615 if log is None:
616 log = self.log
617 if detector and not self.hasLinearity:
618 self.fromDetector(detector)
619
620 self.validate(detector)
621
622 # Check if the image is trimmed.
623 isTrimmed = None
624 if detector:
625 isTrimmed = isTrimmedImage(image, detector)
626
627 numAmps = 0
628 numLinearized = 0
629 numOutOfRange = 0
630 for ampName in self.linearityType.keys():
631 linearizer = self.getLinearityTypeByName(self.linearityType[ampName])
632 numAmps += 1
633
634 if gains and self.linearityUnits == 'adu':
635 gainValue = gains[ampName]
636 else:
637 gainValue = 1.0
638
639 if linearizer is not None:
640 match isTrimmed:
641 case True:
642 bbox = detector[ampName].getBBox()
643 case False:
644 bbox = detector[ampName].getRawBBox()
645 case None:
646 bbox = self.linearityBBox[ampName]
647
648 ampView = image.Factory(image, bbox)
649 success, outOfRange = linearizer()(ampView, **{'coeffs': self.linearityCoeffs[ampName],
650 'table': self.tableData,
651 'log': self.log,
652 'gain': gainValue})
653 numOutOfRange += outOfRange
654 if success:
655 numLinearized += 1
656 elif log is not None:
657 log.warning("Amplifier %s did not linearize.",
658 ampName)
659 return Struct(
660 numAmps=numAmps,
661 numLinearized=numLinearized,
662 numOutOfRange=numOutOfRange
663 )
664
665
◆ 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 325 of file calibType.py.
325 def calibInfoFromDict(self, dictionary):
326 """Handle common keywords.
327
328 This isn't an ideal solution, but until all calibrations
329 expect to find everything in the metadata, they still need to
330 search through dictionaries.
331
332 Parameters
333 ----------
334 dictionary : `dict` or `lsst.daf.base.PropertyList`
335 Source for the common keywords.
336
337 Raises
338 ------
339 RuntimeError
340 Raised if the dictionary does not match the expected OBSTYPE.
341 """
342
343 def search(haystack, needles):
344 """Search dictionary 'haystack' for an entry in 'needles'
345 """
346 test = [haystack.get(x) for x in needles]
347 test = set([x for x in test if x is not None])
348 if len(test) == 0:
349 if "metadata" in haystack:
350 return search(haystack["metadata"], needles)
351 else:
352 return None
353 elif len(test) == 1:
354 value = list(test)[0]
355 if value == "":
356 return None
357 else:
358 return value
359 else:
360 raise ValueError(f"Too many values found: {len(test)} {test} {needles}")
361
362 if "metadata" in dictionary:
363 metadata = dictionary["metadata"]
364
365 if self._OBSTYPE != metadata["OBSTYPE"]:
366 raise RuntimeError(f"Incorrect calibration supplied. Expected {self._OBSTYPE}, "
367 f"found {metadata['OBSTYPE']}")
368
369 if (value := search(dictionary, ["INSTRUME", "instrument"])) is not None:
370 self._instrument = value
371 if (value := search(dictionary, ["RAFTNAME"])) is not None:
372 self._slotName = value
373 if (value := search(dictionary, ["DETECTOR", "detectorId"])) is not None:
374 self._detectorId = value
375 if (value := search(dictionary, ["DET_NAME", "DETECTOR_NAME", "detectorName"])) is not None:
376 self._detectorName = value
377 if (value := search(dictionary, ["DET_SER", "DETECTOR_SERIAL", "detectorSerial"])) is not None:
378 self._detectorSerial = value
379 if (value := search(dictionary, ["FILTER", "filterName"])) is not None:
380 self._filter = value
381 if (value := search(dictionary, ["CALIB_ID"])) is not None:
382 self._calibId = value
383 if (value := search(dictionary, ["SEQFILE"])) is not None:
384 self._seqfile = value
385 if (value := search(dictionary, ["SEQNAME"])) is not None:
386 self._seqname = value
387 if (value := search(dictionary, ["SEQCKSUM"])) is not None:
388 self._seqcksum = value
389
◆ 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 391 of file calibType.py.
391 def determineCalibClass(cls, metadata, message):
392 """Attempt to find calibration class in metadata.
393
394 Parameters
395 ----------
396 metadata : `dict` or `lsst.daf.base.PropertyList`
397 Metadata possibly containing a calibration class entry.
398 message : `str`
399 Message to include in any errors.
400
401 Returns
402 -------
403 calibClass : `object`
404 The class to use to read the file contents. Should be an
405 `lsst.ip.isr.IsrCalib` subclass.
406
407 Raises
408 ------
409 ValueError
410 Raised if the resulting calibClass is the base
411 `lsst.ip.isr.IsrClass` (which does not implement the
412 content methods).
413 """
414 calibClassName = metadata.get("CALIBCLS")
415 if calibClassName is None:
416 calibClassName = metadata.get("fileType")
417 if calibClassName == "shutterMotionProfile":
418 calibClassName = "lsst.ip.isr.ShutterMotionProfile"
419 calibClass = doImport(calibClassName) if calibClassName is not None else cls
420 if calibClass is IsrCalib:
421 raise ValueError(f"Cannot use base class to read calibration data: {message}")
422 return calibClass
423
◆ fromDetector()
| lsst.ip.isr.linearize.Linearizer.fromDetector | ( | self, | |
| detector ) |
Read linearity parameters from a detector.
Parameters
----------
detector : `lsst.afw.cameraGeom.detector`
Input detector with parameters to use.
Returns
-------
calib : `lsst.ip.isr.Linearizer`
The calibration constructed from the detector.
Reimplemented from lsst.ip.isr.calibType.IsrCalib.
Definition at line 213 of file linearize.py.
213 def fromDetector(self, detector):
214 """Read linearity parameters from a detector.
215
216 Parameters
217 ----------
218 detector : `lsst.afw.cameraGeom.detector`
219 Input detector with parameters to use.
220
221 Returns
222 -------
223 calib : `lsst.ip.isr.Linearizer`
224 The calibration constructed from the detector.
225 """
226 self._detectorName = detector.getName()
227 self._detectorSerial = detector.getSerial()
228 self._detectorId = detector.getId()
229 self.hasLinearity = True
230
231 # Do not translate Threshold, Maximum, Units.
232 for amp in detector.getAmplifiers():
233 ampName = amp.getName()
234 self.ampNames.append(ampName)
235 self.linearityType[ampName] = amp.getLinearityType()
236 self.linearityCoeffs[ampName] = amp.getLinearityCoeffs()
237 self.linearityBBox[ampName] = amp.getBBox()
238
239 # Detector linearizers (legacy) are assumed to be adu units.
240 self.linearityUnits = 'adu'
241
242 return self
243
◆ fromDict()
| lsst.ip.isr.linearize.Linearizer.fromDict | ( | cls, | |
| dictionary ) |
Construct a calibration from a dictionary of properties
Parameters
----------
dictionary : `dict`
Dictionary of properties
Returns
-------
calib : `lsst.ip.isr.Linearity`
Constructed calibration.
Raises
------
RuntimeError
Raised if the supplied dictionary is for a different
calibration.
Reimplemented from lsst.ip.isr.calibType.IsrCalib.
Definition at line 245 of file linearize.py.
245 def fromDict(cls, dictionary):
246 """Construct a calibration from a dictionary of properties
247
248 Parameters
249 ----------
250 dictionary : `dict`
251 Dictionary of properties
252
253 Returns
254 -------
255 calib : `lsst.ip.isr.Linearity`
256 Constructed calibration.
257
258 Raises
259 ------
260 RuntimeError
261 Raised if the supplied dictionary is for a different
262 calibration.
263 """
264
265 calib = cls()
266
267 if calib._OBSTYPE != dictionary['metadata']['OBSTYPE']:
268 raise RuntimeError(f"Incorrect linearity supplied. Expected {calib._OBSTYPE}, "
269 f"found {dictionary['metadata']['OBSTYPE']}")
270
271 calib.setMetadata(dictionary['metadata'])
272
273 calib.hasLinearity = dictionary.get('hasLinearity',
274 dictionary['metadata'].get('HAS_LINEARITY', False))
275 calib.override = dictionary.get('override', True)
276
277 # Old linearizers which do not have linearityUnits are
278 # assumed to be adu because that's all that has been
279 # supported.
280 calib.linearityUnits = dictionary.get('linearityUnits', 'adu')
281
282 if calib.hasLinearity:
283 for ampName in dictionary['amplifiers']:
284 amp = dictionary['amplifiers'][ampName]
285 calib.ampNames.append(ampName)
286 calib.linearityCoeffs[ampName] = np.array(amp.get('linearityCoeffs', [0.0]))
287 calib.linearityType[ampName] = amp.get('linearityType', 'None')
288 calib.linearityBBox[ampName] = amp.get('linearityBBox', None)
289
290 calib.inputAbscissa[ampName] = np.array(amp.get('inputAbscissa', [0.0]))
291 calib.inputOrdinate[ampName] = np.array(amp.get('inputOrdinate', [0.0]))
292 calib.inputMask[ampName] = np.array(amp.get('inputMask', [False]))
293 calib.inputGroupingIndex[ampName] = np.array(amp.get('inputGroupingIndex', [0.0]))
294 calib.inputNormalization[ampName] = np.array(amp.get('inputNormalization', [1.0]))
295
296 calib.fitParams[ampName] = np.array(amp.get('fitParams', [0.0]))
297 calib.fitParamsErr[ampName] = np.array(amp.get('fitParamsErr', [0.0]))
298 calib.fitChiSq[ampName] = amp.get('fitChiSq', np.nan)
299 calib.fitResiduals[ampName] = np.array(amp.get('fitResiduals', [0.0]))
300 calib.fitResidualsSigmaMad[ampName] = np.array(amp.get('fitResidualsSigmaMad', np.nan))
301 calib.fitResidualsUnmasked[ampName] = np.array(amp.get('fitResidualsUnmasked', [0.0]))
302 calib.fitResidualsModel[ampName] = np.array(amp.get('fitResidualsModel', [0.0]))
303 calib.linearFit[ampName] = np.array(amp.get('linearFit', [0.0]))
304
305 calib.linearityTurnoff[ampName] = np.array(amp.get('linearityTurnoff', np.nan))
306 calib.linearityMaxSignal[ampName] = np.array(amp.get('linearityMaxSignal', np.nan))
307
308 calib.tableData = dictionary.get('tableData', None)
309 if calib.tableData:
310 calib.tableData = np.array(calib.tableData)
311
312 calib.absoluteReferenceAmplifier = dictionary.get(
313 'absoluteReferenceAmplifier', calib.absoluteReferenceAmplifier,
314 )
315
316 return calib
317
◆ fromTable()
| lsst.ip.isr.linearize.Linearizer.fromTable | ( | cls, | |
| tableList ) |
Read linearity from a FITS file.
This method uses the `fromDict` method to create the
calibration, after constructing an appropriate dictionary from
the input tables.
Parameters
----------
tableList : `list` [`astropy.table.Table`]
afwTable read from input file name.
Returns
-------
linearity : `~lsst.ip.isr.linearize.Linearizer``
Linearity parameters.
Notes
-----
The method reads a FITS file with 1 or 2 extensions. The metadata is
read from the header of extension 1, which must exist. Then the table
is loaded, and the ['AMPLIFIER_NAME', 'TYPE', 'COEFFS', 'BBOX_X0',
'BBOX_Y0', 'BBOX_DX', 'BBOX_DY'] columns are read and used to set each
dictionary by looping over rows.
Extension 2 is then attempted to read in the try block (which only
exists for lookup tables). It has a column named 'LOOKUP_VALUES' that
contains a vector of the lookup entries in each row.
Reimplemented from lsst.ip.isr.calibType.IsrCalib.
Definition at line 364 of file linearize.py.
364 def fromTable(cls, tableList):
365 """Read linearity from a FITS file.
366
367 This method uses the `fromDict` method to create the
368 calibration, after constructing an appropriate dictionary from
369 the input tables.
370
371 Parameters
372 ----------
373 tableList : `list` [`astropy.table.Table`]
374 afwTable read from input file name.
375
376 Returns
377 -------
378 linearity : `~lsst.ip.isr.linearize.Linearizer``
379 Linearity parameters.
380
381 Notes
382 -----
383 The method reads a FITS file with 1 or 2 extensions. The metadata is
384 read from the header of extension 1, which must exist. Then the table
385 is loaded, and the ['AMPLIFIER_NAME', 'TYPE', 'COEFFS', 'BBOX_X0',
386 'BBOX_Y0', 'BBOX_DX', 'BBOX_DY'] columns are read and used to set each
387 dictionary by looping over rows.
388 Extension 2 is then attempted to read in the try block (which only
389 exists for lookup tables). It has a column named 'LOOKUP_VALUES' that
390 contains a vector of the lookup entries in each row.
391 """
392 coeffTable = tableList[0]
393
394 metadata = coeffTable.meta
395 inDict = dict()
396 inDict['metadata'] = metadata
397 inDict['hasLinearity'] = metadata.get('HAS_LINEARITY', False)
398 inDict['amplifiers'] = dict()
399 inDict['linearityUnits'] = metadata.get('LINEARITY_UNITS', 'adu')
400
401 for record in coeffTable:
402 ampName = record['AMPLIFIER_NAME']
403
404 inputAbscissa = record['INP_ABSCISSA'] if 'INP_ABSCISSA' in record.columns else np.array([0.0])
405 inputOrdinate = record['INP_ORDINATE'] if 'INP_ORDINATE' in record.columns else np.array([0.0])
406 inputMask = record['INP_MASK'] if 'INP_MASK' in record.columns else np.array([False])
407 inputGroupingIndex = record['INP_GROUPING_INDEX'] if 'INP_GROUPING_INDEX' in record.columns \
408 else np.array([0])
409 inputNormalization = record['INP_NORMALIZATION'] if 'INP_NORMALIZATION' in record.columns \
410 else np.array([1.0])
411 fitParams = record['FIT_PARAMS'] if 'FIT_PARAMS' in record.columns else np.array([0.0])
412 fitParamsErr = record['FIT_PARAMS_ERR'] if 'FIT_PARAMS_ERR' in record.columns else np.array([0.0])
413 fitChiSq = record['RED_CHI_SQ'] if 'RED_CHI_SQ' in record.columns else np.nan
414 fitResiduals = record['FIT_RES'] if 'FIT_RES' in record.columns else np.array([0.0])
415 fitResidualsSigmaMad = record['FIT_RES_SIGMAD'] if 'FIT_RES_SIGMAD' in record.columns else np.nan
416 fitResidualsUnmasked = record['FIT_RES_UNMASKED'] \
417 if 'FIT_RES_UNMASKED' in record.columns else np.array([0.0])
418 fitResidualsModel = record['FIT_RES_MODEL'] \
419 if 'FIT_RES_MODEL' in record.columns else np.array([0.0])
420 linearFit = record['LIN_FIT'] if 'LIN_FIT' in record.columns else np.array([0.0])
421
422 linearityTurnoff = record['LINEARITY_TURNOFF'] if 'LINEARITY_TURNOFF' in record.columns \
423 else np.nan
424 linearityMaxSignal = record['LINEARITY_MAX_SIGNAL'] if 'LINEARITY_MAX_SIGNAL' in record.columns \
425 else np.nan
426
427 inDict['amplifiers'][ampName] = {
428 'linearityType': record['TYPE'],
429 'linearityCoeffs': record['COEFFS'],
430 'linearityBBox': Box2I(Point2I(record['BBOX_X0'], record['BBOX_Y0']),
431 Extent2I(record['BBOX_DX'], record['BBOX_DY'])),
432 'inputAbscissa': inputAbscissa,
433 'inputOrdinate': inputOrdinate,
434 'inputMask': inputMask,
435 'inputGroupingIndex': inputGroupingIndex,
436 'inputNormalization': inputNormalization,
437 'fitParams': fitParams,
438 'fitParamsErr': fitParamsErr,
439 'fitChiSq': fitChiSq,
440 'fitResiduals': fitResiduals,
441 'fitResidualsSigmaMad': fitResidualsSigmaMad,
442 'fitResidualsUnmasked': fitResidualsUnmasked,
443 'fitResidualsModel': fitResidualsModel,
444 'linearFit': linearFit,
445 'linearityTurnoff': linearityTurnoff,
446 'linearityMaxSignal': linearityMaxSignal,
447 }
448
449 if len(tableList) > 1:
450 tableData = tableList[1]
451 inDict['tableData'] = [record['LOOKUP_VALUES'] for record in tableData]
452
453 if 'ABS_REF_AMP' in coeffTable.columns:
454 inDict['absoluteReferenceAmplifier'] = str(coeffTable['ABS_REF_AMP'][0])
455 else:
456 inDict['absoluteReferenceAmplifier'] = ''
457
458 return cls().fromDict(inDict)
459
◆ getLinearityTypeByName()
| lsst.ip.isr.linearize.Linearizer.getLinearityTypeByName | ( | self, | |
| linearityTypeName ) |
Determine the linearity class to use from the type name.
Parameters
----------
linearityTypeName : str
String name of the linearity type that is needed.
Returns
-------
linearityType : `~lsst.ip.isr.linearize.LinearizeBase`
The appropriate linearity class to use. If no matching class
is found, `None` is returned.
Definition at line 508 of file linearize.py.
508 def getLinearityTypeByName(self, linearityTypeName):
509 """Determine the linearity class to use from the type name.
510
511 Parameters
512 ----------
513 linearityTypeName : str
514 String name of the linearity type that is needed.
515
516 Returns
517 -------
518 linearityType : `~lsst.ip.isr.linearize.LinearizeBase`
519 The appropriate linearity class to use. If no matching class
520 is found, `None` is returned.
521 """
522 for t in [LinearizeLookupTable,
523 LinearizeSquared,
524 LinearizePolynomial,
525 LinearizeProportional,
526 LinearizeSpline,
527 LinearizeDoubleSpline,
528 LinearizeNone]:
529 if t.LinearityType == linearityTypeName:
530 return t
531 return None
532
◆ 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 174 of file calibType.py.
174 def getMetadata(self):
175 """Retrieve metadata associated with this calibration.
176
177 Returns
178 -------
179 meta : `lsst.daf.base.PropertyList`
180 Metadata. The returned `~lsst.daf.base.PropertyList` can be
181 modified by the caller and the changes will be written to
182 external files.
183 """
184 return self._metadata
185
◆ metadata()
|
inherited |
Definition at line 171 of file calibType.py.
171 def metadata(self):
172 return self._metadata
173
◆ 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 517 of file calibType.py.
517 def readFits(cls, filename, **kwargs):
518 """Read calibration data from a FITS file.
519
520 Parameters
521 ----------
522 filename : `str`
523 Filename to read data from.
524 kwargs : `dict` or collections.abc.Mapping`, optional
525 Set of key=value pairs to pass to the ``fromTable``
526 method.
527
528 Returns
529 -------
530 calib : `lsst.ip.isr.IsrCalib`
531 Calibration contained within the file.
532 """
533 tableList = []
534 tableList.append(Table.read(filename, hdu=1, mask_invalid=False))
535 extNum = 2 # Fits indices start at 1, we've read one already.
536 keepTrying = True
537
538 while keepTrying:
539 with warnings.catch_warnings():
540 warnings.simplefilter("error")
541 try:
542 newTable = Table.read(filename, hdu=extNum, mask_invalid=False)
543 tableList.append(newTable)
544 extNum += 1
545 except Exception:
546 keepTrying = False
547
548 for table in tableList:
549 for k, v in table.meta.items():
550 if isinstance(v, fits.card.Undefined):
551 table.meta[k] = None
552
553 calibClass = cls.determineCalibClass(tableList[0].meta, "readFits")
554 if calibClass._OBSTYPE in ("PHOTODIODE", ):
555 # Merge primary header, as these types store information
556 # there.
557 with fits.open(filename) as hdul:
558 primaryHeader = hdul[0].header
559 tableList[0].meta = merge_headers([tableList[0].meta, primaryHeader], mode="first")
560
561 return calibClass.fromTable(tableList, **kwargs)
562
◆ 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 425 of file calibType.py.
425 def readText(cls, filename, **kwargs):
426 """Read calibration representation from a yaml/ecsv file.
427
428 Parameters
429 ----------
430 filename : `str`
431 Name of the file containing the calibration definition.
432 kwargs : `dict` or collections.abc.Mapping`, optional
433 Set of key=value pairs to pass to the ``fromDict`` or
434 ``fromTable`` methods.
435
436 Returns
437 -------
438 calib : `~lsst.ip.isr.IsrCalibType`
439 Calibration class.
440
441 Raises
442 ------
443 RuntimeError
444 Raised if the filename does not end in ".ecsv" or ".yaml".
445 """
446 if filename.endswith((".ecsv", ".ECSV")):
447 data = Table.read(filename, format="ascii.ecsv")
448 calibClass = cls.determineCalibClass(data.meta, "readText/ECSV")
449 return calibClass.fromTable([data], **kwargs)
450 elif filename.endswith((".yaml", ".YAML")):
451 with open(filename, "r") as f:
452 data = yaml.load(f, Loader=yaml.CLoader)
453 calibClass = cls.determineCalibClass(data["metadata"], "readText/YAML")
454 return calibClass.fromDict(data, **kwargs)
455 elif filename.endswith((".json", ".JSON")):
456 with open(filename, "r") as f:
457 data = json.load(f)
458 calibClass = cls.determineCalibClass(data, "readText/JSON")
459 return calibClass.fromDict(data, **kwargs)
460 else:
461 raise RuntimeError(f"Unknown filename extension: {filename}")
462
◆ requiredAttributes() [1/2]
|
inherited |
Definition at line 162 of file calibType.py.
162 def requiredAttributes(self):
163 return self._requiredAttributes
164
◆ requiredAttributes() [2/2]
|
inherited |
Definition at line 166 of file calibType.py.
166 def requiredAttributes(self, value):
167 self._requiredAttributes = value
168
◆ 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 186 of file calibType.py.
186 def setMetadata(self, metadata):
187 """Store a copy of the supplied metadata with this calibration.
188
189 Parameters
190 ----------
191 metadata : `lsst.daf.base.PropertyList`
192 Metadata to associate with the calibration. Will be copied and
193 overwrite existing metadata.
194 """
195 if metadata is not None:
196 self._metadata.update(metadata)
197
198 # Ensure that we have the obs type required by calibration ingest
199 self._metadata["OBSTYPE"] = self._OBSTYPE
200 self._metadata[self._OBSTYPE + "_SCHEMA"] = self._SCHEMA
201 self._metadata[self._OBSTYPE + "_VERSION"] = self._VERSION
202
203 if isinstance(metadata, dict):
204 self.calibInfoFromDict(metadata)
205 elif isinstance(metadata, PropertyList):
206 self.calibInfoFromDict(metadata.toDict())
207
◆ toDict()
| lsst.ip.isr.linearize.Linearizer.toDict | ( | self | ) |
Return linearity parameters as a dict. Returns ------- outDict : `dict`:
Reimplemented from lsst.ip.isr.calibType.IsrCalib.
Definition at line 318 of file linearize.py.
318 def toDict(self):
319 """Return linearity parameters as a dict.
320
321 Returns
322 -------
323 outDict : `dict`:
324 """
325 self.updateMetadata()
326
327 outDict = {'metadata': self.getMetadata(),
328 'detectorName': self._detectorName,
329 'detectorSerial': self._detectorSerial,
330 'detectorId': self._detectorId,
331 'hasTable': self.tableData is not None,
332 'amplifiers': dict(),
333 'linearityUnits': self.linearityUnits,
334 }
335 for ampName in self.linearityType:
336 outDict['amplifiers'][ampName] = {
337 'linearityType': self.linearityType[ampName],
338 'linearityCoeffs': self.linearityCoeffs[ampName].tolist(),
339 'linearityBBox': self.linearityBBox[ampName],
340 'inputAbscissa': self.inputAbscissa[ampName].tolist(),
341 'inputOrdinate': self.inputOrdinate[ampName].tolist(),
342 'inputMask': self.inputMask[ampName].tolist(),
343 'inputGroupingIndex': self.inputGroupingIndex[ampName].tolist(),
344 'inputNormalization': self.inputNormalization[ampName].tolist(),
345 'fitParams': self.fitParams[ampName].tolist(),
346 'fitParamsErr': self.fitParamsErr[ampName].tolist(),
347 'fitChiSq': self.fitChiSq[ampName],
348 'fitResiduals': self.fitResiduals[ampName].tolist(),
349 'fitResidualsSigmaMad': self.fitResidualsSigmaMad[ampName],
350 'fitResidualsUnmasked': self.fitResidualsUnmasked[ampName].tolist(),
351 'fitResidualsModel': self.fitResidualsModel[ampName].tolist(),
352 'linearFit': self.linearFit[ampName].tolist(),
353 'linearityTurnoff': self.linearityTurnoff[ampName],
354 'linearityMaxSignal': self.linearityMaxSignal[ampName],
355 }
356 if self.tableData is not None:
357 outDict['tableData'] = self.tableData.tolist()
358
359 outDict['absoluteReferenceAmplifier'] = self.absoluteReferenceAmplifier
360
361 return outDict
362
◆ toTable()
| lsst.ip.isr.linearize.Linearizer.toTable | ( | self | ) |
Construct a list of tables containing the information in this
calibration.
The list of tables should create an identical calibration
after being passed to this class's fromTable method.
Returns
-------
tableList : `list` [`astropy.table.Table`]
List of tables containing the linearity calibration
information.
Reimplemented from lsst.ip.isr.calibType.IsrCalib.
Definition at line 460 of file linearize.py.
460 def toTable(self):
461 """Construct a list of tables containing the information in this
462 calibration.
463
464 The list of tables should create an identical calibration
465 after being passed to this class's fromTable method.
466
467 Returns
468 -------
469 tableList : `list` [`astropy.table.Table`]
470 List of tables containing the linearity calibration
471 information.
472 """
473
474 tableList = []
475 self.updateMetadata()
476 catalog = Table([{'AMPLIFIER_NAME': ampName,
477 'TYPE': self.linearityType[ampName],
478 'COEFFS': self.linearityCoeffs[ampName],
479 'BBOX_X0': self.linearityBBox[ampName].getMinX(),
480 'BBOX_Y0': self.linearityBBox[ampName].getMinY(),
481 'BBOX_DX': self.linearityBBox[ampName].getWidth(),
482 'BBOX_DY': self.linearityBBox[ampName].getHeight(),
483 'INP_ABSCISSA': self.inputAbscissa[ampName],
484 'INP_ORDINATE': self.inputOrdinate[ampName],
485 'INP_MASK': self.inputMask[ampName],
486 'INP_GROUPING_INDEX': self.inputGroupingIndex[ampName],
487 'INP_NORMALIZATION': self.inputNormalization[ampName],
488 'FIT_PARAMS': self.fitParams[ampName],
489 'FIT_PARAMS_ERR': self.fitParamsErr[ampName],
490 'RED_CHI_SQ': self.fitChiSq[ampName],
491 'FIT_RES': self.fitResiduals[ampName],
492 'FIT_RES_SIGMAD': self.fitResidualsSigmaMad[ampName],
493 'FIT_RES_UNMASKED': self.fitResidualsUnmasked[ampName],
494 'FIT_RES_MODEL': self.fitResidualsModel[ampName],
495 'LIN_FIT': self.linearFit[ampName],
496 'LINEARITY_TURNOFF': self.linearityTurnoff[ampName],
497 'LINEARITY_MAX_SIGNAL': self.linearityMaxSignal[ampName],
498 'ABS_REF_AMP': self.absoluteReferenceAmplifier,
499 } for ampName in self.ampNames])
500 catalog.meta = self.getMetadata().toDict()
501 tableList.append(catalog)
502
503 if self.tableData is not None:
504 catalog = Table([{'LOOKUP_VALUES': value} for value in self.tableData])
505 tableList.append(catalog)
506 return tableList
507
◆ updateMetadata()
| lsst.ip.isr.linearize.Linearizer.updateMetadata | ( | self, | |
| setDate = False, | |||
| ** | kwargs ) |
Update metadata keywords with new values.
This calls the base class's method after ensuring the required
calibration keywords will be saved.
Parameters
----------
setDate : `bool`, optional
Update the CALIBDATE fields in the metadata to the current
time. Defaults to False.
kwargs :
Other keyword parameters to set in the metadata.
Reimplemented from lsst.ip.isr.calibType.IsrCalib.
Definition at line 192 of file linearize.py.
192 def updateMetadata(self, setDate=False, **kwargs):
193 """Update metadata keywords with new values.
194
195 This calls the base class's method after ensuring the required
196 calibration keywords will be saved.
197
198 Parameters
199 ----------
200 setDate : `bool`, optional
201 Update the CALIBDATE fields in the metadata to the current
202 time. Defaults to False.
203 kwargs :
204 Other keyword parameters to set in the metadata.
205 """
206 kwargs['HAS_LINEARITY'] = self.hasLinearity
207 kwargs['OVERRIDE'] = self.override
208 kwargs['HAS_TABLE'] = self.tableData is not None
209 kwargs['LINEARITY_UNITS'] = self.linearityUnits
210
211 super().updateMetadata(setDate=setDate, **kwargs)
212
◆ updateMetadataFromExposures()
|
inherited |
Extract and unify metadata information.
Parameters
----------
exposures : `list`
Exposures or other calibrations to scan.
Definition at line 294 of file calibType.py.
294 def updateMetadataFromExposures(self, exposures):
295 """Extract and unify metadata information.
296
297 Parameters
298 ----------
299 exposures : `list`
300 Exposures or other calibrations to scan.
301 """
302 # This list of keywords is the set of header entries that
303 # should be checked and propagated. Not having an entry is
304 # not a failure, as they may not be defined for the exposures
305 # being used.
306 keywords = ["SEQNAME", "SEQFILE", "SEQCKSUM", "ODP", "AP0_RC"]
307 metadata = {}
308
309 for exp in exposures:
310 try:
311 expMeta = exp.getMetadata()
312 except AttributeError:
313 continue
314 for key in keywords:
315 if key in expMeta:
316 if key in metadata:
317 if metadata[key] != expMeta[key]:
318 self.log.warning("Metadata mismatch! Have: %s Found %s",
319 metadata[key], expMeta[key])
320 else:
321 metadata[key] = expMeta[key]
322
323 self.updateMetadata(**metadata, setCalibInfo=True)
324
◆ validate()
| lsst.ip.isr.linearize.Linearizer.validate | ( | self, | |
| detector = None, | |||
| amplifier = None ) |
Validate linearity for a detector/amplifier.
Parameters
----------
detector : `lsst.afw.cameraGeom.Detector`, optional
Detector to validate, along with its amplifiers.
amplifier : `lsst.afw.cameraGeom.Amplifier`, optional
Single amplifier to validate.
Raises
------
RuntimeError
Raised if there is a mismatch in linearity parameters, and
the cameraGeom parameters are not being overridden.
Reimplemented from lsst.ip.isr.calibType.IsrCalib.
Definition at line 533 of file linearize.py.
533 def validate(self, detector=None, amplifier=None):
534 """Validate linearity for a detector/amplifier.
535
536 Parameters
537 ----------
538 detector : `lsst.afw.cameraGeom.Detector`, optional
539 Detector to validate, along with its amplifiers.
540 amplifier : `lsst.afw.cameraGeom.Amplifier`, optional
541 Single amplifier to validate.
542
543 Raises
544 ------
545 RuntimeError
546 Raised if there is a mismatch in linearity parameters, and
547 the cameraGeom parameters are not being overridden.
548 """
549 amplifiersToCheck = []
550 if detector:
551 if self._detectorName != detector.getName():
552 raise RuntimeError("Detector names don't match: %s != %s" %
553 (self._detectorName, detector.getName()))
554 if int(self._detectorId) != int(detector.getId()):
555 raise RuntimeError("Detector IDs don't match: %s != %s" %
556 (int(self._detectorId), int(detector.getId())))
557 # TODO: DM-38778: This check fails on LATISS due to an
558 # error in the camera configuration.
559 # if self._detectorSerial != detector.getSerial():
560 # raise RuntimeError(
561 # "Detector serial numbers don't match: %s != %s" %
562 # (self._detectorSerial, detector.getSerial()))
563 if len(detector.getAmplifiers()) != len(self.linearityCoeffs.keys()):
564 raise RuntimeError("Detector number of amps = %s does not match saved value %s" %
565 (len(detector.getAmplifiers()),
566 len(self.linearityCoeffs.keys())))
567 amplifiersToCheck.extend(detector.getAmplifiers())
568
569 if amplifier:
570 amplifiersToCheck.extend(amplifier)
571
572 for amp in amplifiersToCheck:
573 ampName = amp.getName()
574 if ampName not in self.linearityCoeffs.keys():
575 raise RuntimeError("Amplifier %s is not in linearity data" %
576 (ampName, ))
577 if amp.getLinearityType() != self.linearityType[ampName]:
578 if self.override:
579 self.log.debug("Overriding amplifier defined linearityType (%s) for %s",
580 self.linearityType[ampName], ampName)
581 else:
582 raise RuntimeError("Amplifier %s type %s does not match saved value %s" %
583 (ampName, amp.getLinearityType(), self.linearityType[ampName]))
584 if (amp.getLinearityCoeffs().shape != self.linearityCoeffs[ampName].shape or not
585 np.allclose(amp.getLinearityCoeffs(), self.linearityCoeffs[ampName], equal_nan=True)):
586 if self.override:
587 self.log.debug("Overriding amplifier defined linearityCoeffs (%s) for %s",
588 self.linearityCoeffs[ampName], ampName)
589 else:
590 raise RuntimeError("Amplifier %s coeffs %s does not match saved value %s" %
591 (ampName, amp.getLinearityCoeffs(), self.linearityCoeffs[ampName]))
592
◆ 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 563 of file calibType.py.
563 def writeFits(self, filename):
564 """Write calibration data to a FITS file.
565
566 Parameters
567 ----------
568 filename : `str`
569 Filename to write data to.
570
571 Returns
572 -------
573 used : `str`
574 The name of the file used to write the data.
575 """
576 tableList = self.toTable()
577 with warnings.catch_warnings():
578 warnings.filterwarnings("ignore", category=Warning, module="astropy.io")
579 astropyList = [fits.table_to_hdu(table) for table in tableList]
580 astropyList.insert(0, fits.PrimaryHDU())
581
582 writer = fits.HDUList(astropyList)
583 writer.writeto(filename, overwrite=True)
584 return filename
585
◆ 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 463 of file calibType.py.
463 def writeText(self, filename, format="auto"):
464 """Write the calibration data to a text file.
465
466 Parameters
467 ----------
468 filename : `str`
469 Name of the file to write.
470 format : `str`
471 Format to write the file as. Supported values are:
472 ``"auto"`` : Determine filetype from filename.
473 ``"yaml"`` : Write as yaml.
474 ``"ecsv"`` : Write as ecsv.
475
476 Returns
477 -------
478 used : `str`
479 The name of the file used to write the data. This may
480 differ from the input if the format is explicitly chosen.
481
482 Raises
483 ------
484 RuntimeError
485 Raised if filename does not end in a known extension, or
486 if all information cannot be written.
487
488 Notes
489 -----
490 The file is written to YAML/ECSV format and will include any
491 associated metadata.
492 """
493 if format == "yaml" or (format == "auto" and filename.lower().endswith((".yaml", ".YAML"))):
494 outDict = self.toDict()
495 path, ext = os.path.splitext(filename)
496 filename = path + ".yaml"
497 with open(filename, "w") as f:
498 yaml.dump(outDict, f)
499 elif format == "ecsv" or (format == "auto" and filename.lower().endswith((".ecsv", ".ECSV"))):
500 tableList = self.toTable()
501 if len(tableList) > 1:
502 # ECSV doesn't support multiple tables per file, so we
503 # can only write the first table.
504 raise RuntimeError(f"Unable to persist {len(tableList)}tables in ECSV format.")
505
506 table = tableList[0]
507 path, ext = os.path.splitext(filename)
508 filename = path + ".ecsv"
509 table.write(filename, format="ascii.ecsv")
510 else:
511 raise RuntimeError(f"Attempt to write to a file {filename} "
512 "that does not end in '.yaml' or '.ecsv'")
513
514 return filename
515
Member Data Documentation
◆ _calibId
|
protectedinherited |
Definition at line 76 of file calibType.py.
◆ _detectorId
|
protectedinherited |
Definition at line 74 of file calibType.py.
◆ _detectorName
|
protectedinherited |
Definition at line 72 of file calibType.py.
◆ _detectorSerial
|
protectedinherited |
Definition at line 73 of file calibType.py.
◆ _filter
|
protectedinherited |
Definition at line 75 of file calibType.py.
◆ _instrument
|
protectedinherited |
Definition at line 69 of file calibType.py.
◆ _metadata
|
protectedinherited |
Definition at line 80 of file calibType.py.
◆ _OBSTYPE
|
staticprotectedinherited |
Definition at line 64 of file calibType.py.
◆ _raftName
|
protectedinherited |
Definition at line 70 of file calibType.py.
◆ _requiredAttributes
|
protectedinherited |
Definition at line 115 of file calibType.py.
◆ _SCHEMA
|
staticprotectedinherited |
Definition at line 65 of file calibType.py.
◆ _seqcksum
|
protectedinherited |
Definition at line 79 of file calibType.py.
◆ _seqfile
|
protectedinherited |
Definition at line 77 of file calibType.py.
◆ _seqname
|
protectedinherited |
Definition at line 78 of file calibType.py.
◆ _slotName
|
protectedinherited |
Definition at line 71 of file calibType.py.
◆ _VERSION
|
staticprotectedinherited |
Definition at line 66 of file calibType.py.
◆ absoluteReferenceAmplifier
| str lsst.ip.isr.linearize.Linearizer.absoluteReferenceAmplifier = "" |
Definition at line 168 of file linearize.py.
◆ ampNames
| lsst.ip.isr.linearize.Linearizer.ampNames = list() |
Definition at line 149 of file linearize.py.
◆ fitChiSq
| lsst.ip.isr.linearize.Linearizer.fitChiSq = dict() |
Definition at line 160 of file linearize.py.
◆ fitParams
| lsst.ip.isr.linearize.Linearizer.fitParams = dict() |
Definition at line 158 of file linearize.py.
◆ fitParamsErr
| lsst.ip.isr.linearize.Linearizer.fitParamsErr = dict() |
Definition at line 159 of file linearize.py.
◆ fitResiduals
| lsst.ip.isr.linearize.Linearizer.fitResiduals = dict() |
Definition at line 161 of file linearize.py.
◆ fitResidualsModel
| lsst.ip.isr.linearize.Linearizer.fitResidualsModel = dict() |
Definition at line 164 of file linearize.py.
◆ fitResidualsSigmaMad
| lsst.ip.isr.linearize.Linearizer.fitResidualsSigmaMad = dict() |
Definition at line 162 of file linearize.py.
◆ fitResidualsUnmasked
| lsst.ip.isr.linearize.Linearizer.fitResidualsUnmasked = dict() |
Definition at line 163 of file linearize.py.
◆ hasLinearity
| bool lsst.ip.isr.linearize.Linearizer.hasLinearity = False |
Definition at line 146 of file linearize.py.
◆ inputAbscissa
| lsst.ip.isr.linearize.Linearizer.inputAbscissa = dict() |
Definition at line 153 of file linearize.py.
◆ inputGroupingIndex
| lsst.ip.isr.linearize.Linearizer.inputGroupingIndex = dict() |
Definition at line 156 of file linearize.py.
◆ inputMask
| lsst.ip.isr.linearize.Linearizer.inputMask = dict() |
Definition at line 155 of file linearize.py.
◆ inputNormalization
| lsst.ip.isr.linearize.Linearizer.inputNormalization = dict() |
Definition at line 157 of file linearize.py.
◆ inputOrdinate
| lsst.ip.isr.linearize.Linearizer.inputOrdinate = dict() |
Definition at line 154 of file linearize.py.
◆ linearFit
| lsst.ip.isr.linearize.Linearizer.linearFit = dict() |
Definition at line 165 of file linearize.py.
◆ linearityBBox
| lsst.ip.isr.linearize.Linearizer.linearityBBox = dict() |
Definition at line 152 of file linearize.py.
◆ linearityCoeffs
| lsst.ip.isr.linearize.Linearizer.linearityCoeffs = dict() |
Definition at line 150 of file linearize.py.
◆ linearityMaxSignal
| lsst.ip.isr.linearize.Linearizer.linearityMaxSignal = dict() |
Definition at line 167 of file linearize.py.
◆ linearityTurnoff
| lsst.ip.isr.linearize.Linearizer.linearityTurnoff = dict() |
Definition at line 166 of file linearize.py.
◆ linearityType
| lsst.ip.isr.linearize.Linearizer.linearityType = dict() |
Definition at line 151 of file linearize.py.
◆ linearityUnits
| str lsst.ip.isr.linearize.Linearizer.linearityUnits = 'adu' |
Definition at line 179 of file linearize.py.
◆ log
|
inherited |
Definition at line 96 of file calibType.py.
◆ override
| bool lsst.ip.isr.linearize.Linearizer.override = False |
Definition at line 147 of file linearize.py.
◆ requiredAttributes
|
inherited |
Definition at line 90 of file calibType.py.
◆ tableData
| lsst.ip.isr.linearize.Linearizer.tableData = None |
Definition at line 169 of file linearize.py.
The documentation for this class was generated from the following file:
- /j/snowflake/release/lsstsw/stack/lsst-scipipe-12.0.0/Linux/ip_isr/gc2a301910b+c4742f2e9e/python/lsst/ip/isr/linearize.py
Generated on Mon Nov 3 2025 08:01:48 for LSST Applications by
1.13.2