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Clarify ISR log messages, comments, and docstrings.
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Change isrFunctions.brighterFatterCorrection to return final
difference and iteration count, so an old log message can be restored.

Remove old documentation that was causing build warnings.
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@czwa
czwa committed Jun 20, 2019
1 parent fd3334c commit 95df18a
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Showing 5 changed files with 218 additions and 110 deletions.
21 changes: 0 additions & 21 deletions python/lsst/ip/isr/assembleCcdTask.py
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Expand Up @@ -105,27 +105,6 @@ class AssembleCcdTask(pipeBase.Task):
@section ip_isr_assemble_Example A complete example of using AssembleCcdTask
This code is in runAssembleTask.py in the examples directory, and can be run as @em e.g.
@code
python examples/runAssembleTask.py
@endcode
@dontinclude runAssembleTask.py
Import the task. There are other imports. Read the source file for more info.
@skipline AssembleCcdTask
@dontinclude exampleUtils.py
Create some input images with the help of some utilities in examples/exampleUtils.py
@skip makeAssemblyInput
@until inputData
The above numbers can be changed. The assumption that the readout corner is flipped on every other amp is
hardcoded in createDetector.
@dontinclude runAssembleTask.py
Run the assembler task
@skip runAssembler
@until frame += 1
<HR>
To investigate the @ref ip_isr_assemble_Debug, put something like
@code{.py}
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2 changes: 1 addition & 1 deletion python/lsst/ip/isr/crosstalk.py
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Expand Up @@ -100,7 +100,7 @@ def run(self, exposure, crosstalkSources=None, isTrimmed=False):
detector = exposure.getDetector()
if not detector.hasCrosstalk():
raise RuntimeError("Attempted to correct crosstalk without crosstalk coefficients")
self.log.info("Applying crosstalk correction")
self.log.info("Applying crosstalk correction.")
subtractCrosstalk(exposure, minPixelToMask=self.config.minPixelToMask,
crosstalkStr=self.config.crosstalkMaskPlane, isTrimmed=isTrimmed,
backgroundMethod=self.config.crosstalkBackgroundMethod)
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188 changes: 152 additions & 36 deletions python/lsst/ip/isr/fringe.py
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Original file line number Diff line number Diff line change
Expand Up @@ -74,18 +74,31 @@ class FringeTask(Task):
_DefaultName = 'isrFringe'

def readFringes(self, dataRef, assembler=None):
"""Read the fringe frame(s)
"""Read the fringe frame(s), and pack data into a Struct
The current implementation assumes only a single fringe frame and
will have to be updated to support multi-mode fringe subtraction.
This implementation could be optimised by persisting the fringe
positions and fluxes.
@param dataRef Data reference for the science exposure
@param assembler An instance of AssembleCcdTask (for assembling fringe frames)
@return Struct(fringes: fringe exposure or list of fringe exposures;
seed: 32-bit uint derived from ccdExposureId for random number generator
Parameters
----------
dataRef : `daf.butler.butlerSubset.ButlerDataRef`
Butler reference for the exposure that will have fringing
removed.
assembler : `lsst.ip.isr.AssembleCcdTask`, optional
An instance of AssembleCcdTask (for assembling fringe
frames).
Returns
-------
fringeData : `pipeBase.Struct`
Struct containing fringe data:
- ``fringes`` : `lsst.afw.image.Exposure` or `list` thereof
Calibration fringe files containing master fringe frames.
- ``seed`` : `int`, optional
Seed for random number generation.
"""
try:
fringe = dataRef.get("fringe", immediate=True)
Expand All @@ -108,14 +121,27 @@ def run(self, exposure, fringes, seed=None):
Primary method of FringeTask. Fringes are only subtracted if the
science exposure has a filter listed in the configuration.
@param exposure Science exposure from which to remove fringes
@param fringes Exposure or list of Exposures
@param seed 32-bit unsigned integer for random number generator
Parameters
----------
exposure : `lsst.afw.image.Exposure`
Science exposure from which to remove fringes.
fringes : `lsst.afw.image.Exposure` or `list` thereof
Calibration fringe files containing master fringe frames.
seed : `int`, optional
Seed for random number generation.
Returns
-------
solution : `np.array`
Fringe solution amplitudes for each input fringe frame.
rms : `float`
RMS error for the fit solution for this exposure.
"""
import lsstDebug
display = lsstDebug.Info(__name__).display

if not self.checkFilter(exposure):
self.log.info("Filter not found in FringeTaskConfig.filters. Skipping fringe correction.")
return

if seed is None:
Expand Down Expand Up @@ -148,25 +174,57 @@ def runDataRef(self, exposure, dataRef, assembler=None):
"""Remove fringes from the provided science exposure.
Retrieve fringes from butler dataRef provided and remove from
provided science exposure.
Fringes are only subtracted if the science exposure has a filter
listed in the configuration.
provided science exposure. Fringes are only subtracted if the
science exposure has a filter listed in the configuration.
@param exposure Science exposure from which to remove fringes
@param dataRef Data reference for the science exposure
@param assembler An instance of AssembleCcdTask (for assembling fringe frames)
Parameters
----------
exposure : `lsst.afw.image.Exposure`
Science exposure from which to remove fringes.
dataRef : `daf.persistence.butlerSubset.ButlerDataRef`
Butler reference to the exposure. Used to find
appropriate fringe data.
assembler : `lsst.ip.isr.AssembleCcdTask`, optional
An instance of AssembleCcdTask (for assembling fringe
frames).
Returns
-------
solution : `np.array`
Fringe solution amplitudes for each input fringe frame.
rms : `float`
RMS error for the fit solution for this exposure.
"""
if not self.checkFilter(exposure):
self.log.info("Filter not found in FringeTaskConfig.filters. Skipping fringe correction.")
return
fringeStruct = self.readFringes(dataRef, assembler=assembler)
return self.run(exposure, **fringeStruct.getDict())

def checkFilter(self, exposure):
"""Check whether we should fringe-subtract the science exposure"""
"""Check whether we should fringe-subtract the science exposure.
Parameters
----------
exposure : `lsst.afw.image.Exposure`
Exposure to check the filter of.
Returns
-------
needsFringe : `bool`
If True, then the exposure has a filter listed in the
configuration, and should have the fringe applied.
"""
return exposure.getFilter().getName() in self.config.filters

def removePedestal(self, fringe):
"""Remove pedestal from fringe exposure"""
"""Remove pedestal from fringe exposure.
Parameters
----------
fringe : `lsst.afw.image.Exposure`
Fringe data to subtract the pedestal value from.
"""
stats = afwMath.StatisticsControl()
stats.setNumSigmaClip(self.config.stats.clip)
stats.setNumIter(self.config.stats.iterations)
Expand All @@ -176,7 +234,21 @@ def removePedestal(self, fringe):
mi -= pedestal

def generatePositions(self, exposure, rng):
"""Generate a random distribution of positions for measuring fringe amplitudes"""
"""Generate a random distribution of positions for measuring fringe amplitudes.
Parameters
----------
exposure : `lsst.afw.image.Exposure`
Exposure to measure the positions on.
rng : `numpy.random.RandomState`
Random number generator to use.
Returns
-------
positions : `numpy.array`
Two-dimensional array containing the positions to sample
for fringe amplitudes.
"""
start = self.config.large
num = self.config.num
width = exposure.getWidth() - self.config.large
Expand All @@ -192,10 +264,21 @@ def measureExposure(self, exposure, positions, title="Fringe"):
aperture. The statistic within a larger aperture are subtracted so
as to remove the background.
@param exposure Exposure to measure
@param positions Array of (x,y) for fringe measurement
@param title Title for display
@return Array of fringe measurements
Parameters
----------
exposure : `lsst.afw.image.Exposure`
Exposure to measure the positions on.
positions : `numpy.array`
Two-dimensional array containing the positions to sample
for fringe amplitudes.
title : `str`, optional
Title used for debug out plots.
Returns
-------
fringes : `numpy.array`
Array of measured exposure values at each of the positions
supplied.
"""
stats = afwMath.StatisticsControl()
stats.setNumSigmaClip(self.config.stats.clip)
Expand Down Expand Up @@ -227,11 +310,23 @@ def measureExposure(self, exposure, positions, title="Fringe"):

@timeMethod
def solve(self, science, fringes):
"""Solve (with iterative clipping) for the scale factors
@param science Array of science exposure fringe amplitudes
@param fringes Array of arrays of fringe frame fringe amplitudes
@return Array of scale factors for the fringe frames
"""Solve for the scale factors with iterative clipping.
Parameters
----------
science : `numpy.array`
Array of measured science image values at each of the
positions supplied.
fringes : `numpy.array`
Array of measured fringe values at each of the positions
supplied.
Returns
-------
solution : `np.array`
Fringe solution amplitudes for each input fringe frame.
rms : `float`
RMS error for the fit solution for this exposure.
"""
import lsstDebug
doPlot = lsstDebug.Info(__name__).plot
Expand Down Expand Up @@ -330,21 +425,42 @@ def emptyResult(msg=""):
return solution, rms

def _solve(self, science, fringes):
"""Solve for the scale factors
@param science Array of science exposure fringe amplitudes
@param fringes Array of arrays of fringe frame fringe amplitudes
@return Array of scale factors for the fringe frames
"""Solve for the scale factors.
Parameters
----------
science : `numpy.array`
Array of measured science image values at each of the
positions supplied.
fringes : `numpy.array`
Array of measured fringe values at each of the positions
supplied.
Returns
-------
solution : `np.array`
Fringe solution amplitudes for each input fringe frame.
"""
return afwMath.LeastSquares.fromDesignMatrix(fringes, science,
afwMath.LeastSquares.DIRECT_SVD).getSolution()

def subtract(self, science, fringes, solution):
"""Subtract the fringes
@param science Science exposure
@param fringes List of fringe frames
@param solution Array of scale factors for the fringe frames
"""Subtract the fringes.
Parameters
----------
science : `lsst.afw.image.Exposure`
Science exposure from which to remove fringes.
fringes : `lsst.afw.image.Exposure` or `list` thereof
Calibration fringe files containing master fringe frames.
solution : `np.array`
Fringe solution amplitudes for each input fringe frame.
Raises
------
RuntimeError :
Raised if the number of fringe frames does not match the
number of measured amplitudes.
"""
if len(solution) != len(fringes):
raise RuntimeError("Number of fringe frames (%s) != number of scale factors (%s)" %
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14 changes: 9 additions & 5 deletions python/lsst/ip/isr/isrFunctions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -740,6 +740,13 @@ def brighterFatterCorrection(exposure, kernel, maxIter, threshold, applyGain):
If True, then the exposure values are scaled by the gain prior
to correction.
Returns
-------
diff : `float`
Final difference between iterations achieved in correction.
iteration : `int`
Number of iterations used to calculate correction.
Notes
-----
This correction takes a kernel that has been derived from flat
Expand Down Expand Up @@ -827,14 +834,11 @@ def brighterFatterCorrection(exposure, kernel, maxIter, threshold, applyGain):
break
prev_image[:, :] = tmpArray[:, :]

# if iteration == maxIter - 1:
# self.log.warn("Brighter fatter correction did not converge,
# final difference %f" % diff)

# self.log.info("Finished brighter fatter in %d iterations" % (iteration + 1))
image.getArray()[startY + 1:endY - 1, startX + 1:endX - 1] += \
corr[startY + 1:endY - 1, startX + 1:endX - 1]

return diff, iteration


@contextmanager
def gainContext(exp, image, apply):
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