lsst-ts · jbkalmbach · Oct 17, 2023 · Sep 28, 2023 · Sep 29, 2023 · Oct 9, 2023
diff --git a/README.md b/README.md
@@ -73,6 +73,12 @@ setup -k -r .
 
 To learn more about how to run the pipeline tasks associated with WEP we have a series of Jupyter Notebooks available in the AOS section of the `ts_analysis_notebooks` [repository](https://github.com/lsst-ts/ts_analysis_notebooks).
 
+## Deprecation of support for Phosim and ts_phosim
+
+Starting with v8.0 running the AOS closed loop with Phosim and `ts_phosim` will no longer work.
+We are moving to support imSim and `ts_imsim` exclusively moving forward.
+There are changes in the orientation of the DonutStamps in v8.0+ that will not work with the `ts_phosim` closed loop.
+
 ## Test Gen 3 Repository
 
 In the folder `tests/testData/` there is a test repository for tasks that run with the Gen 3 DM middleware.

diff --git a/doc/versionHistory.rst b/doc/versionHistory.rst
@@ -5,6 +5,17 @@
 ##################
 Version History
 ##################
+
+.. _lsst.ts.wep-8.0.0:
+
+-------------
+8.0.0
+-------------
+
+* Save all DonutStamps with images aligned with focal plane science sensors.
+* This version will break compatibility in the closed loop with Phosim and ts_phosim going forward.
+
+
 .. _lsst.ts.wep-7.0.1:
 
 -------------
@@ -13,7 +24,6 @@ Version History
 
 * Fix generateDonutDirectDetect when doDonutSelection is not run.
 
-
 .. _lsst.ts.wep-7.0.0:
 
 -------------
@@ -28,7 +38,7 @@ Version History
 6.4.12
 -------------
 
-* Update  ts_pre_commit_config with ruff.
+* Update ts_pre_commit_config with ruff.
 
 .. _lsst.ts.wep-6.4.11:
 

diff --git a/python/lsst/ts/wep/task/calcZernikesTask.py b/python/lsst/ts/wep/task/calcZernikesTask.py
@@ -39,7 +39,6 @@
 )
 from lsst.ts.wep.wfEstimator import WfEstimator
 from lsst.utils.timer import timeMethod
-from scipy.ndimage import rotate
 
 
 class CalcZernikesTaskConnections(
@@ -116,6 +115,7 @@ class CalcZernikesTaskConfig(
         dtype=bool,
         default=True,
         optional=True,
+        deprecated="This field is no longer used. Will be removed after the end of October 2023.",
     )
 
 
@@ -135,8 +135,6 @@ def __init__(self, **kwargs):
         # for the detector.
         self.combineZernikes = self.config.combineZernikes
         self.makeSubtask("combineZernikes")
-        # Specify whether to transpose images
-        self.transposeImages = self.config.transposeImages
         # Specify optical model
         self.opticalModel = self.config.opticalModel
         # Set up instrument configuration dict
@@ -234,38 +232,41 @@ def estimateZernikes(self, donutStampsExtra, donutStampsIntra):
             eulerZExtra = -detectorExtra.getOrientation().getYaw().asDegrees()
             eulerZIntra = -detectorIntra.getOrientation().getYaw().asDegrees()
 
-            # NOTE: TS_WEP expects these images to be transposed
-            # TODO: Look into this
             blendOffsetsExtra = self.calcBlendOffsets(donutExtra, eulerZExtra)
             blendOffsetsIntra = self.calcBlendOffsets(donutIntra, eulerZIntra)
 
-            if self.transposeImages:
-                imageExtra = rotate(
-                    donutExtra.stamp_im.getImage().getArray(), eulerZExtra
-                ).T
-                imageIntra = rotate(
-                    donutIntra.stamp_im.getImage().getArray(), eulerZIntra
-                ).T
-            else:
-                imageExtra = rotate(
-                    donutExtra.stamp_im.getImage().getArray(), eulerZExtra
-                )
-                imageIntra = rotate(
-                    donutIntra.stamp_im.getImage().getArray(), eulerZIntra
-                )
+            # Below we transform the image array and coordinates from the DVCS
+            # (Data Visualization Coordinate System) to the
+            # ZCS (Zemax Coordinate System). More information about these
+            # coordinate systems is available here: sitcomtn-003.lsst.io.
+            # This transformation below incorporates two different coordinate
+            # conversions: 1) DVCS to CCS is a transpose and 2) CCS to ZCS is
+            # an x -> -x conversion that we can apply as a left-right flip.
+            # In a future update to ts_ofc we will update the sensitivity
+            # matrix to use the CCS and we can then remove the left-right
+            # flip. That is why the current version keeps this as a
+            # two part transformation.
+            #
+            #        DVCS               CCS                 ZCS
+            #   x                   y                               y
+            #   ^                   ^                               ^
+            #   |                   |                               |
+            #   |                   |                               |
+            #   |                   |                               |
+            #   |----------> y      |----------> x     x <----------|
 
             wfEsti.setImg(
-                fieldXYExtra,
+                np.array([-fieldXYExtra[1], fieldXYExtra[0]]),
                 DefocalType.Extra,
                 filterLabel=getFilterTypeFromBandLabel(donutExtra.bandpass),
-                image=imageExtra,
+                image=np.fliplr(donutExtra.stamp_im.image.array.T),
                 blendOffsets=blendOffsetsExtra.tolist(),
             )
             wfEsti.setImg(
-                fieldXYIntra,
+                np.array([-fieldXYIntra[1], fieldXYIntra[0]]),
                 DefocalType.Intra,
                 filterLabel=getFilterTypeFromBandLabel(donutIntra.bandpass),
-                image=imageIntra,
+                image=np.fliplr(donutIntra.stamp_im.image.array.T),
                 blendOffsets=blendOffsetsIntra.tolist(),
             )
             wfEsti.reset()

diff --git a/python/lsst/ts/wep/task/cutOutDonutsBase.py b/python/lsst/ts/wep/task/cutOutDonutsBase.py
@@ -39,9 +39,10 @@
 from lsst.ts.wep.utils import (
     DonutTemplateType,
     createInstDictFromConfig,
+    getCameraFromButlerName,
     getCamTypeFromButlerName,
 )
-from scipy.ndimage import binary_dilation, shift
+from scipy.ndimage import binary_dilation, rotate, shift
 from scipy.signal import correlate
 
 
@@ -439,7 +440,7 @@ def cutOutStamps(self, exposure, donutCatalog, defocalType, cameraName):
             )
             xCornerList.append(xCorner)
             yCornerList.append(yCorner)
-            finalCutout = exposure[finalBBox]
+            finalCutout = exposure[finalBBox].clone()
 
             # Save MaskedImage to stamp
             finalStamp = finalCutout.getMaskedImage()
@@ -499,7 +500,6 @@ def cutOutStamps(self, exposure, donutCatalog, defocalType, cameraName):
             donutStamp.makeMasks(
                 inst, self.opticalModel, boundaryT, maskScalingFactorLocal
             )
-            donutStamp.stamp_im.setMask(donutStamp.mask_comp)
 
             # Create shifted mask from non-blended mask
             if (self.multiplyMask is True) and blendExists:
@@ -522,6 +522,18 @@ def cutOutStamps(self, exposure, donutCatalog, defocalType, cameraName):
                 shiftedMask -= 1
                 donutStamp.stamp_im.image.array *= shiftedMask
 
+            camera = getCameraFromButlerName(cameraName)
+            detectorInfo = camera.get(detectorName)
+
+            # Rotate sensors to line up with the science sensors in the
+            # focal plane.
+            eulerZ = -detectorInfo.getOrientation().getYaw().asDegrees()
+            donutStamp.stamp_im.image.array = rotate(
+                donutStamp.stamp_im.image.array, eulerZ
+            )
+
+            donutStamp.stamp_im.setMask(donutStamp.mask_comp)
+
             finalStamps.append(donutStamp)
 
         catalogLength = len(donutCatalog)

diff --git a/python/lsst/ts/wep/task/donutStamp.py b/python/lsst/ts/wep/task/donutStamp.py
@@ -27,12 +27,16 @@
 import lsst.afw.image as afwImage
 import lsst.afw.table as afwTable
 import lsst.geom
-import lsst.obs.lsst as obs_lsst
 import numpy as np
 from lsst.afw.cameraGeom import FIELD_ANGLE, PIXELS
 from lsst.meas.algorithms.stamps import AbstractStamp
 from lsst.ts.wep.cwfs.compensableImage import CompensableImage
-from lsst.ts.wep.utils import DefocalType, FilterType, getFilterTypeFromBandLabel
+from lsst.ts.wep.utils import (
+    DefocalType,
+    FilterType,
+    getCameraFromButlerName,
+    getFilterTypeFromBandLabel,
+)
 
 
 @dataclass
@@ -185,14 +189,7 @@ def getCamera(self):
             The camera is not supported.
         """
 
-        if self.cam_name == "LSSTCam":
-            return obs_lsst.LsstCam().getCamera()
-        elif self.cam_name == "LSSTComCam":
-            return obs_lsst.LsstComCam().getCamera()
-        elif self.cam_name == "LATISS":
-            return obs_lsst.Latiss.getCamera()
-        else:
-            raise ValueError(f"Camera {self.cam_name} is not supported.")
+        return getCameraFromButlerName(self.cam_name)
 
     def calcFieldXY(self):
         """

diff --git a/python/lsst/ts/wep/utils/taskUtils.py b/python/lsst/ts/wep/utils/taskUtils.py
@@ -23,11 +23,14 @@
     "runProgram",
     "writePipetaskCmd",
     "writeCleanUpRepoCmd",
+    "getCameraFromButlerName",
 ]
 
 import os
 import subprocess
 
+import lsst.obs.lsst as obs_lsst
+
 
 def runProgram(command, binDir=None, argstring=None):
     """Run the program w/o arguments.
@@ -131,3 +134,34 @@ def writeCleanUpRepoCmd(repoDir, runName):
     cleanUpCmd += f"{repoDir} {runName} --no-confirm"
 
     return cleanUpCmd
+
+
+def getCameraFromButlerName(camName):
+    """
+    Get the proper camera object for the donuts.
+
+    Parameters
+    ----------
+    camName : str
+        Name of instrument using butler convention. Available instruments
+        are LSSTCam, LSSTComCam, and LATISS.
+
+    Returns
+    -------
+    `lsst.afw.cameraGeom.Camera`
+        Camera object for the exposures.
+
+    Raises
+    ------
+    `ValueError`
+        The camera is not supported.
+    """
+
+    if camName == "LSSTCam":
+        return obs_lsst.LsstCam().getCamera()
+    elif camName == "LSSTComCam":
+        return obs_lsst.LsstComCam().getCamera()
+    elif camName == "LATISS":
+        return obs_lsst.Latiss.getCamera()
+    else:
+        raise ValueError(f"Camera {camName} is not supported.")
diff --git a/tests/task/test_calcZernikesTaskCwfs.py b/tests/task/test_calcZernikesTaskCwfs.py
@@ -158,25 +158,25 @@ def testEstimateCornerZernikes(self):
         ).combinedZernikes
         trueZernCoeffR04 = np.array(
             [
-                -0.71201408,
-                1.12248525,
-                0.77794367,
-                -0.04085477,
-                -0.05272933,
-                0.16054277,
-                0.081405,
-                -0.04382461,
-                -0.04830676,
-                -0.06218882,
-                0.10246469,
-                0.0197683,
-                0.007953,
-                0.00668697,
-                -0.03570788,
-                -0.03020376,
-                0.0039522,
-                0.04793133,
-                -0.00804605,
+                -0.35353452,
+                -0.07365128,
+                0.62222451,
+                -0.06206281,
+                -0.09065757,
+                0.21722746,
+                -0.20491936,
+                0.00849322,
+                -0.01150489,
+                0.02599147,
+                -0.00150702,
+                -0.14100845,
+                0.02294787,
+                0.02284791,
+                0.02116483,
+                -0.02537743,
+                0.01866772,
+                0.01653037,
+                -0.00552862,
             ]
         )
         # Make sure the total rms error is less than 0.35 microns off
@@ -198,25 +198,25 @@ def testEstimateCornerZernikes(self):
         ).combinedZernikes
         trueZernCoeffR40 = np.array(
             [
-                -0.6535694,
-                1.00838499,
-                0.55968811,
-                -0.08899825,
-                0.00173607,
-                0.04133107,
-                -0.10913093,
-                -0.04363778,
-                -0.03149601,
-                -0.04941225,
-                0.09980538,
-                0.03704486,
-                -0.00210766,
-                0.01737253,
-                0.01727539,
-                0.01278011,
-                0.01212878,
-                0.03876888,
-                -0.00559142,
+                -3.83610201e-01,
+                -2.06528254e-01,
+                5.42893431e-01,
+                7.74255848e-02,
+                3.40529812e-02,
+                5.45565149e-02,
+                8.65849308e-02,
+                1.75029212e-02,
+                -1.40149246e-04,
+                4.11223127e-02,
+                -2.42644902e-03,
+                -1.52392233e-01,
+                -1.24547354e-02,
+                -2.33075716e-02,
+                7.35477674e-04,
+                1.93518814e-02,
+                -3.65768735e-03,
+                4.12718699e-02,
+                -6.93386734e-03,
             ]
         )
         # Make sure the total rms error is less than 0.35 microns off

diff --git a/tests/task/test_cutOutDonutsBase.py b/tests/task/test_cutOutDonutsBase.py
@@ -265,7 +265,9 @@ def testCutOutStamps(self):
             lsst.geom.Extent2I(160),
         )
         expCutOut = exposure[stampBBox].image.array
-        np.testing.assert_array_equal(donutStamps[0].stamp_im.image.array, expCutOut)
+        np.testing.assert_array_almost_equal(
+            donutStamps[0].stamp_im.image.array, expCutOut
+        )
 
     def testCutOutStampsBlended(self):
         exposure = self.butler.get(

diff --git a/tests/task/test_cutOutDonutsCwfsTask.py b/tests/task/test_cutOutDonutsCwfsTask.py
@@ -20,6 +20,7 @@
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 import os
+from copy import copy
 
 import lsst.utils.tests
 from lsst.daf import butler as dafButler
@@ -172,7 +173,7 @@ def testTaskRunNormal(self):
 
         # Test normal behavior
         taskOut = self.task.run(
-            [exposureIntra, exposureExtra],
+            [copy(exposureIntra), copy(exposureExtra)],
             [donutCatalogExtra, donutCatalogIntra],
             camera,
         )