Plot distances during FVC loop (#183)

* Add code to plot FVC distances while creating summaryF file

* Add the option to select centroid method, and log it in confSummaryF

* Allow to pass an epoch when loading a design

* Some tweaks to plotting

python/jaeger/actor/commands/configuration.py

@@ -54,6 +54,7 @@ async def _load_design(
     preload: bool = False,
     no_clone: bool = False,
     scale: float | None = None,
+    epoch: float | None = None,
     epoch_delay: float = 0.0,
     get_paths: bool = True,
 ):
@@ -173,7 +174,11 @@ async def _load_design(
         try:
             # Define the epoch for the configuration.
             command.debug(text=f"Epoch delay: {round(epoch_delay, 1)} seconds.")
-            epoch = Time.now().jd + epoch_delay / 86400.0
+
+            if epoch is None:
+                epoch = float(Time.now().jd)
+            epoch += epoch_delay / 86400.0
+
             design = await Design.create_async(design_id, epoch=epoch, scale=scale)
         except Exception as err:
             command.error(error=f"Failed retrieving design: {err}")
@@ -211,6 +216,11 @@ def configuration():
     default=True,
     help="Generates and stores the to and from destination paths.",
 )
+@click.option(
+    "--epoch",
+    type=float,
+    help="Epoch at which to create the configuration, as a Julian Day.",
+)
 @click.option(
     "--epoch-delay",
     type=float,
@@ -269,6 +279,7 @@ async def load(
     from_positions: bool = False,
     from_preloaded: bool = False,
     generate_paths: bool = False,
+    epoch: float | None = None,
     epoch_delay: float = 0.0,
     ingest: bool = False,
     write_summary: bool = False,
@@ -314,6 +325,7 @@ async def load(
             preload=False,
             no_clone=no_clone,
             scale=scale,
+            epoch=epoch,
             epoch_delay=epoch_delay,
             get_paths=False,
         )
@@ -442,6 +454,11 @@ async def clone(command: Command[JaegerActor], fps: FPS):
 
 
 @configuration.command(cancellable=True)
+@click.option(
+    "--epoch",
+    type=float,
+    help="Epoch at which to create the configuration, as a Julian Day.",
+)
 @click.option(
     "--epoch-delay",
     type=float,
@@ -474,6 +491,7 @@ async def preload(
     command: JaegerCommandType,
     fps: FPS,
     designid: int | None = None,
+    epoch: float | None = None,
     epoch_delay: float = 0.0,
     scale: float | None = None,
     no_clone: bool = False,
@@ -501,6 +519,7 @@ async def preload(
         preload=True,
         no_clone=no_clone,
         scale=scale,
+        epoch=epoch,
         epoch_delay=epoch_delay,
     )
 

python/jaeger/actor/commands/fvc.py

@@ -118,6 +118,11 @@ async def expose(
     type=float,
     help="Proportional term of the correction.",
 )
+@click.option(
+    "--centroid-method",
+    type=click.Choice(["nudge", "simple", "winpos", "sep"]),
+    help="The centroid method used to extract sources.",
+)
 @click.option(
     "--use-invkin/--no-use-invkin",
     default=True,
@@ -141,6 +146,7 @@ async def loop(
     max_correction: float | None = None,
     target_90_percentile: float | None = None,
     k: float | None = None,
+    centroid_method: str | None = None,
     use_invkin: bool = True,
     no_write_summary: bool = False,
 ):
@@ -217,6 +223,7 @@ async def loop(
                 filename,
                 positioner_coords,
                 plot=plot,
+                centroid_method=centroid_method,
                 use_new_invkin=use_invkin,
             )
 

python/jaeger/fvc.py

@@ -30,6 +30,7 @@
 from jaeger.fps import FPS
 from jaeger.ieb import IEB
 from jaeger.kaiju import get_path_pair_in_executor, get_robot_grid
+from jaeger.plotting import plot_fvc_distances
 from jaeger.target.tools import wok_to_positioner
 from jaeger.utils import run_in_executor
 
@@ -42,6 +43,7 @@
 
 
 FVC_CONFIG = config["fvc"]
+DEFAULT_CENTROID_METHOD = "nudge"
 
 
 class FVC:
@@ -57,6 +59,7 @@ class FVC:
     raw_hdu: Optional[fits.ImageHDU]
     proc_hdu: Optional[fits.ImageHDU]
 
+    centroid_method: str | None
     fitrms: float
     k: float
 
@@ -93,6 +96,7 @@ def reset(self):
         self.fitrms = -9.99
         self.perc_90 = -9.99
         self.fvc_percent_reached = -9.99
+        self.centroid_method = None
 
     def set_command(self, command: Command[JaegerActor]):
         """Sets the command."""
@@ -193,7 +197,7 @@ def process_fvc_image(
         positioner_coords: dict,
         fibre_data: Optional[pandas.DataFrame] = None,
         fibre_type: str = "Metrology",
-        use_winpos: bool = True,
+        centroid_method: str | None = None,
         use_new_invkin: bool = True,
         plot: bool | str = False,
         outdir: str | None = None,
@@ -217,8 +221,9 @@ def process_fvc_image(
         fibre_type
             The ``fibre_type`` rows in ``fibre_data`` to use. Defaults to
             ``fibre_type='Metrology'``.
-        use_winpos
-            Whether to use windowed position for centroid extraction.
+        centroid_method
+            The centroid method to use, one of ``"nudge"``, ``"sep"``, ``"winpos"``,
+            or ``"simple"``. Defaults to ``"nudge"``.
         use_new_invkin
             Use new inverse kinnematic to calculate alpha/beta.
         plot
@@ -239,6 +244,8 @@ def process_fvc_image(
         # Reset the instance
         self.reset()
 
+        centroid_method = centroid_method or DEFAULT_CENTROID_METHOD
+
         path = str(path)
         if not os.path.exists(path):
             raise FVCError(f"FVC image {path} does not exist.")
@@ -297,7 +304,8 @@ def process_fvc_image(
         )
 
         self.centroids = fvc_transform.extractCentroids()
-        fvc_transform.fit(newInvKin=use_new_invkin)
+        fvc_transform.fit(centType=centroid_method, newInvKin=use_new_invkin)
+        self.centroid_method = centroid_method
 
         assert fvc_transform.positionerTableMeas is not None
 
@@ -858,10 +866,23 @@ async def write_summary_F(self):
         await configuration_copy.write_summary(
             flavour="F",
             headers={
+                "fvc_centroid_method": self.centroid_method or "?",
                 "fvc_rms": self.fitrms,
                 "fvc_90_perc": self.perc_90,
                 "fvc_percent_reached": self.fvc_percent_reached,
                 "fvc_image_path": self.proc_image_path if self.proc_image_path else "",
             },
             overwrite=True,
         )
+
+        # Plot analysis of FVC loop.
+        if self.proc_image_path:
+            self.log("Creating FVC plots", level=logging.DEBUG)
+
+            outpath = str(self.proc_image_path).replace(".fits", "_distances.pdf")
+
+            plot_fvc_distances(
+                self.fps.configuration,
+                configuration_copy.assignment_data.fibre_table,
+                path=outpath,
+            )