From bed4f6a51b31d004d05946bc4b08bfaa36448117 Mon Sep 17 00:00:00 2001
From: Wilfred Tyler Gee <wtylergee@gmail.com>
Date: Mon, 15 Jul 2024 14:03:21 -1000
Subject: [PATCH] fiberNorms QA Plot

* Adding the basic plotting for the fiberNorms.
* Adding the cli bin.
---
 bin.src/plotFiberNorms.py         |   4 +
 python/pfs/drp/qa/fiberNormsQa.py | 121 ++++++++++++++++++++++++++++++
 2 files changed, 125 insertions(+)
 create mode 100644 bin.src/plotFiberNorms.py
 create mode 100644 python/pfs/drp/qa/fiberNormsQa.py

diff --git a/bin.src/plotFiberNorms.py b/bin.src/plotFiberNorms.py
new file mode 100644
index 00000000..afbcb868
--- /dev/null
+++ b/bin.src/plotFiberNorms.py
@@ -0,0 +1,4 @@
+#!/usr/bin/env python
+from pfs.drp.qa.fiberNormsQa import FiberNormQaTask
+
+FiberNormQaTask.parseAndRun()
diff --git a/python/pfs/drp/qa/fiberNormsQa.py b/python/pfs/drp/qa/fiberNormsQa.py
new file mode 100644
index 00000000..e6b64478
--- /dev/null
+++ b/python/pfs/drp/qa/fiberNormsQa.py
@@ -0,0 +1,121 @@
+from collections import defaultdict
+from typing import Dict, List
+
+import lsstDebug
+from lsst.daf.persistence import ButlerDataRef
+from lsst.pex.config import Field
+from lsst.pipe.base import (
+    CmdLineTask,
+    PipelineTask,
+    PipelineTaskConfig,
+    PipelineTaskConnections,
+    Struct,
+    TaskRunner,
+)
+from lsst.pipe.base.connectionTypes import Input as InputConnection
+from pfs.drp.stella import PfsConfig, PfsFiberNorms
+
+
+class FiberNormQaConnections(
+    PipelineTaskConnections,
+    dimensions=("instrument", "arm"),
+):
+    """Connections for fiberNormQaTask"""
+
+    fiberNorms = InputConnection(
+        name="fiberNorms_meas",
+        doc="Measured fiber normalisations",
+        storageClass="PfsFiberNorms",
+        dimensions=("instrument", "arm"),
+    )
+    pfsConfig = InputConnection(
+        name="pfsConfig",
+        doc="Top-end configuration",
+        storageClass="PfsConfig",
+        dimensions=("instrument", "exposure"),
+    )
+
+
+class FiberNormsQaRunner(TaskRunner):
+    """Runner for fiberNormQaTask"""
+
+    @staticmethod
+    def getTargetList(parsedCmd, **kwargs):
+        """We operate on sets of arms."""
+        groups = dict()
+        for ref in parsedCmd.id.refList:
+            arm = ref.dataId["arm"]
+            groups[arm] = ref
+
+        return [(groups[arm], kwargs) for arm in groups.keys()]
+
+
+class FiberNormQaConfig(PipelineTaskConfig, pipelineConnections=FiberNormQaConnections):
+    """Configuration for fiberNormQaTask"""
+
+    plotLower = Field(dtype=float, default=2.5, doc="Lower bound for plot (standard deviations from median)")
+    plotUpper = Field(dtype=float, default=2.5, doc="Upper bound for plot (standard deviations from median)")
+
+
+class FiberNormQaTask(CmdLineTask, PipelineTask):
+    """Task for QA of fiberNorms"""
+
+    ConfigClass = FiberNormQaConfig
+    _DefaultName = "fiberNormsQa"
+    RunnerClass = FiberNormsQaRunner
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.debugInfo = lsstDebug.Info(__name__)
+
+    def runDataRef(self, dataRef: ButlerDataRef) -> None:
+        """Calls ``self.run()``
+
+        Parameters
+        ----------
+        dataRef : `ButlerDataRef`
+            Data reference for merged spectrum.
+        """
+        self.log.info(f"Running fiberNormsQaTask on {dataRef.dataId}")
+        fiberNorms = dataRef.get("fiberNorms_meas")
+        pfsConfig = dataRef.get("pfsConfig")
+
+        outputs = self.run(fiberNorms, pfsConfig)
+        for datasetType, data in outputs.getDict().items():
+            if data is not None:
+                dataRef.put(data, datasetType=datasetType)
+
+    def run(self, fiberNorms: PfsFiberNorms, pfsConfig: PfsConfig) -> Struct:
+        """QA of fiberNorms.
+
+        Parameters
+        ----------
+        fiberNorms : `PfsFiberNorms`
+            Measured fiber normalisations.
+        pfsConfig : `PfsConfig`
+            Top-end configuration.
+
+        Returns
+        -------
+        outputs : `Struct`
+            QA outputs.
+        """
+        self.log.info(f"Plotting fiber norms QA for {fiberNorms.identity}")
+
+        fig, axes = fiberNorms.plot(pfsConfig, lower=self.config.plotLower, upper=self.config.plotUpper)
+        visitList = fiberNorms.identity.visit0
+        arm = fiberNorms.identity.arm
+        axes.set_title(f"Fiber normalization for {arm=}\nvisits: {visitList}")
+
+        return Struct(fiberNorms_plot=fig)
+
+    def _getMetadataName(self):
+        """Get the name of the metadata dataset type, or `None` if metadata is
+        not to be persisted.
+
+        Notes
+        -----
+        The name may depend on the config; that is why this is not a class
+        method.
+        """
+        return None