Merge pull request #8 from lsst-ts/tickets/DM-47080

Tickets/dm 47080

.github/workflows/changelog.yaml

@@ -0,0 +1,19 @@
+name: ChangelogUpdated
+on:
+  pull_request:
+    types: [assigned, opened, synchronize, reopened, labeled, unlabeled]
+    branches:
+      - main
+jobs:
+  build:
+    name: Check Actions
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v1
+      - name: Changelog check
+        uses: Zomzog/[email protected]
+        with:
+          fileName: doc/versionHistory.rst
+          checkNotification: Simple
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

Jenkinsfile

@@ -0,0 +1,13 @@
+@Library('JenkinsShared')_
+DevelopPipeline(
+    name: "donut_viz",
+    module_name: "lsst.donut.viz",
+    idl_names: [],
+    build_all_idl: false,
+    extra_packages: ["lsst-ts/ts_wep"],
+    kickoff_jobs: [],
+    slack_build_channel: "aos-builds",
+    has_doc_site: false,
+    require_git_lfs: true,
+    require_scons: true
+)

doc/versionHistory.rst

@@ -4,6 +4,16 @@
 Version History
 ##################
 
+.. _lsst.ts.donut.viz-1.1.0:
+
+-------------
+1.1.0
+-------------
+
+* Add tests for full donut_viz pipeline.
+* Add changelog github action.
+* Add Jenkinsfile.
+
 .. _lsst.ts.donut.viz-1.0.0:
 
 -------------

pipelines/scienceDirectDetectPipeline.yaml

@@ -0,0 +1,56 @@
+# This yaml file is used to define the tasks and configuration of
+# a Gen 3 pipeline used for testing in ts_wep.
+description: wep basic processing test pipeline
+# Here we specify the corresponding instrument for the data we
+# will be using.
+instrument: lsst.obs.lsst.LsstCam
+# Then we can specify each task in our pipeline by a name
+# and then specify the class name corresponding to that task
+tasks:
+  isr:
+    class: lsst.ip.isr.IsrTaskLSST
+    config:
+      # Although we don't have to apply the amp offset corrections, we do want
+      # to compute them for analyzeAmpOffsetMetadata to report on as metrics.
+      doAmpOffset: true
+      ampOffset.doApplyAmpOffset: false
+      # Turn off slow steps in ISR
+      doBrighterFatter: false
+      doCrosstalk: false
+      # Turn off flats, biases, darks because we don't have these in test repo
+      doBias: False
+      doDark: False
+      doFlat: False
+      doBootstrap: True
+      doApplyGains: False
+      doLinearize: False
+      doDeferredCharge: False
+      doDefect: False
+  generateDonutCatalogWcsTask:
+    class: lsst.ts.wep.task.generateDonutCatalogWcsTask.GenerateDonutCatalogWcsTask
+    config:
+      donutSelector.unblendedSeparation: 1
+  cutOutDonutsScienceSensorTask:
+    class: lsst.ts.wep.task.CutOutDonutsScienceSensorTask
+  calcZernikesTask:
+    class: lsst.ts.wep.task.calcZernikesTask.CalcZernikesTask
+    config:
+      estimateZernikes.maxNollIndex: 28
+      estimateZernikes.saveHistory: False
+      estimateZernikes.maskKwargs: {'doMaskBlends': False}
+  aggregateZernikeTablesTask:
+    class: lsst.donut.viz.AggregateZernikeTablesTask
+  aggregateDonutTablesTask:
+    class: lsst.donut.viz.AggregateDonutTablesTask
+  aggregateDonutStampsTask:
+    class: lsst.donut.viz.AggregateDonutStampsTask
+  aggregateAOSVisitTableTask:
+    class: lsst.donut.viz.AggregateAOSVisitTableTask
+  plotAOSTask:
+    class: lsst.donut.viz.PlotAOSTask
+    config:
+      doRubinTVUpload: false
+  plotDonutTask:
+    class: lsst.donut.viz.PlotDonutTask
+    config:
+      doRubinTVUpload: false

python/lsst/donut/viz/aggregate_visit.py

@@ -241,11 +241,12 @@ def runQuantum(
             for ref in inputRefs.qualityTables
         }
 
-        # Find common (visit, detector) pairs
-        keys = set(donutRefDict) & set(qualityRefDict)
+        # Find common (visit, detector) extra-focal pairs
+        # DonutQualityTables only saved under extra-focal ids
+        extra_keys = set(donutRefDict) & set(qualityRefDict)
 
         # Raise error if there's no matches
-        if len(keys) == 0:
+        if len(extra_keys) == 0:
             raise RuntimeError(
                 "No (visit, detector) matches found between "
                 "the donut and quality tables"
@@ -258,51 +259,53 @@ def runQuantum(
             tables = []
 
             # Iterate over the common (visit, detector) pairs
-            for visit, detector in keys:
-                # Determine if intra or extra
-                if visit == pair.intra:
-                    intra = True
-                elif visit == pair.extra:
-                    intra = False
-                else:
-                    # This visit isn't in this pair
-                    # so we will skip for now
+            for visit, detector in extra_keys:
+                # Check if this extra-focal visit is in this pair.
+                if visit != pair.extra:
+                    # This visit isn't in this pair so we will skip for now
                     continue
 
                 # Get pixels -> field angle transform for this detector
                 det = camera[detector]
                 tform = det.getTransform(PIXELS, FIELD_ANGLE)
 
                 # Load the donut catalog table, and the donut quality table
-                donutTable = butlerQC.get(donutRefDict[(visit, detector)])
-                qualityTable = butlerQC.get(qualityRefDict[(visit, detector)])
+                intraDonutTable = butlerQC.get(donutRefDict[(pair.intra, detector)])
+                extraDonutTable = butlerQC.get(donutRefDict[(pair.extra, detector)])
+                qualityTable = butlerQC.get(qualityRefDict[(pair.extra, detector)])
 
                 # Get rows of quality table for this exposure
-                if intra:
-                    qualityTable = qualityTable[qualityTable["DEFOCAL_TYPE"] == "intra"]
-                else:
-                    qualityTable = qualityTable[qualityTable["DEFOCAL_TYPE"] == "extra"]
-
-                # Select donuts used in Zernike estimation
-                table = donutTable[qualityTable["FINAL_SELECT"]]
-
-                # Add focusZ to donut table
-                table["focusZ"] = (
-                    intraVisitInfo.focusZ if intra else extraVisitInfo.focusZ
-                )
-
-                # Add field angle in CCS to the table
-                pts = tform.applyForward(
-                    [
-                        Point2D(x, y)
-                        for x, y in zip(table["centroid_x"], table["centroid_y"])
-                    ]
-                )
-                table["thx_CCS"] = [pt.y for pt in pts]  # Transpose from DVCS to CCS
-                table["thy_CCS"] = [pt.x for pt in pts]
-                table["detector"] = det.getName()
+                intraQualityTable = qualityTable[
+                    qualityTable["DEFOCAL_TYPE"] == "intra"
+                ]
+                extraQualityTable = qualityTable[
+                    qualityTable["DEFOCAL_TYPE"] == "extra"
+                ]
+
+                for donutTable, qualityTable in zip(
+                    [intraDonutTable, extraDonutTable],
+                    [intraQualityTable, extraQualityTable],
+                ):
+                    # Select donuts used in Zernike estimation
+                    table = donutTable[qualityTable["FINAL_SELECT"]]
+
+                    # Add focusZ to donut table
+                    table["focusZ"] = table.meta["visit_info"]["focus_z"]
+
+                    # Add field angle in CCS to the table
+                    pts = tform.applyForward(
+                        [
+                            Point2D(x, y)
+                            for x, y in zip(table["centroid_x"], table["centroid_y"])
+                        ]
+                    )
+                    table["thx_CCS"] = [
+                        pt.y for pt in pts
+                    ]  # Transpose from DVCS to CCS
+                    table["thy_CCS"] = [pt.x for pt in pts]
+                    table["detector"] = det.getName()
 
-                tables.append(table)
+                    tables.append(table)
 
             # Don't attempt to stack metadata
             for table in tables: