Standardize the linearization code #25
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Use IsrTask.suspectDetection to set SUSPECT flag and use IsrTask.config.doLinearize config parameter. Add doSuspect config parameter to control setting SUSPECT flag since doLinearize is no longer appropriate.
Linearize using lsst.ip.isr.LinearizeSquared (linearization type = "Squared"), retrieving it from the camera mapper (though the coefficients come from the amp info table, as before). Remove the existing "linearize" method, since it was no longer used. Update amp info catalogs to set linearization type to "Squared" if linearization is wanted, and "None" if not (e.g. suprimecam and those HSC CCDs that had all zeros for their squared coefficient). Here is the log of conversions: hsc/camera Converting 112 files 0_00.fits: 'Squared' 0_01.fits: 'Squared' 0_02.fits: 'Squared' 0_03.fits: 'Squared' 0_04.fits: 'Squared' 0_05.fits: 'Squared' 0_06.fits: 'Squared' 0_07.fits: 'Squared' 0_08.fits: 'Squared' 0_09.fits: 'Squared' 0_10.fits: 'Squared' 0_11.fits: 'Squared' 0_12.fits: 'Squared' 0_13.fits: 'Squared' 0_14.fits: 'Squared' 0_15.fits: 'Squared' 0_16.fits: 'Squared' 0_17.fits: 'Squared' 0_18.fits: 'Squared' 0_19.fits: 'Squared' 0_20.fits: 'Squared' 0_21.fits: 'Squared' 0_22.fits: 'Squared' 0_23.fits: 'Squared' 0_24.fits: 'Squared' 0_25.fits: 'Squared' 0_26.fits: 'Squared' 0_27.fits: 'Squared' 0_28.fits: 'Squared' 0_29.fits: 'Squared' 0_30.fits: 'Squared' 0_31.fits: 'Squared' 0_32.fits: 'Squared' 0_33.fits: 'Squared' 0_34.fits: 'Squared' 0_35.fits: 'Squared' 0_36.fits: 'Squared' 0_37.fits: 'Squared' 0_38.fits: 'Squared' 0_39.fits: 'Squared' 0_40.fits: 'Squared' 0_41.fits: 'Squared' 0_42.fits: 'Squared' 0_43.fits: 'Squared' 0_44.fits: 'Squared' 0_45.fits: 'Squared' 0_46.fits: 'Squared' 0_47.fits: 'Squared' 0_48.fits: 'None' 0_51.fits: 'None' 0_52.fits: 'None' 0_53.fits: 'Squared' 0_54.fits: 'Squared' 0_55.fits: 'Squared' 0_56.fits: 'Squared' 0_57.fits: 'None' 1_00.fits: 'Squared' 1_01.fits: 'Squared' 1_02.fits: 'Squared' 1_03.fits: 'Squared' 1_04.fits: 'Squared' 1_05.fits: 'Squared' 1_06.fits: 'Squared' 1_07.fits: 'Squared' 1_08.fits: 'Squared' 1_09.fits: 'Squared' 1_10.fits: 'Squared' 1_11.fits: 'Squared' 1_12.fits: 'Squared' 1_13.fits: 'Squared' 1_14.fits: 'Squared' 1_15.fits: 'Squared' 1_16.fits: 'Squared' 1_17.fits: 'Squared' 1_18.fits: 'Squared' 1_19.fits: 'Squared' 1_20.fits: 'Squared' 1_21.fits: 'Squared' 1_22.fits: 'Squared' 1_23.fits: 'Squared' 1_24.fits: 'Squared' 1_25.fits: 'Squared' 1_26.fits: 'Squared' 1_27.fits: 'Squared' 1_28.fits: 'Squared' 1_29.fits: 'Squared' 1_30.fits: 'Squared' 1_31.fits: 'Squared' 1_32.fits: 'Squared' 1_33.fits: 'Squared' 1_34.fits: 'Squared' 1_35.fits: 'Squared' 1_36.fits: 'Squared' 1_37.fits: 'Squared' 1_38.fits: 'Squared' 1_39.fits: 'Squared' 1_40.fits: 'Squared' 1_41.fits: 'Squared' 1_42.fits: 'Squared' 1_43.fits: 'Squared' 1_44.fits: 'Squared' 1_45.fits: 'Squared' 1_46.fits: 'Squared' 1_47.fits: 'Squared' 1_48.fits: 'None' 1_51.fits: 'None' 1_52.fits: 'None' 1_53.fits: 'Squared' 1_54.fits: 'Squared' 1_55.fits: 'Squared' 1_56.fits: 'Squared' 1_57.fits: 'None' suprimecam/camera Converting 10 files Chihiro.fits: 'Squared' Clarisse.fits: 'Squared' Fio.fits: 'Squared' Kiki.fits: 'Squared' Nausicaa.fits: 'Squared' Ponyo.fits: 'Squared' San.fits: 'Squared' Satsuki.fits: 'Squared' Sheeta.fits: 'Squared' Sophie.fits: 'Squared' suprimecam/mit_camera Converting 10 files si001s.fits: 'None' si002s.fits: 'None' si005s.fits: 'None' si006s.fits: 'None' w4c5.fits: 'None' w67c1.fits: 'None' w6c1.fits: 'None' w7c3.fits: 'None' w93c2.fits: 'None' w9c2.fits: 'None'
Change self.log.log(self.log.INFO, ... to self.log.info(... and similarly for warnings.
Also fix one instance of leading tabs instead of spaces
Remove unused imports Add one or two missing imports Reorder imports to meet our standard Replace "not a in b" with "a not in b" Replace "a == None" with "a is None" Replace "raiseRuntimeError" with "raise RuntimeError" Rename a few variables in list comprehensions to avoid changing other variables (and make pyflakes happy) Break some instances of multiple imports and multiple statements into separate lines Remove trailing whitespace Remove trailing ;
ccdTesting.py used a mix of pyplot and plt; standardize on plt.
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Linearize using lsst.ip.isr.LinearizeSquared, retrieving it
from the camera mapper (though the coefficients come from
the amp info table, as before).
Remove the existing method that linearized.
Move suspect pixel masking to its standard location.
Add a config parameter to disable suspect pixel masking
(it used to be controlled by doLinearize).