From 4d44d74f9ad0180d4c5df974f1f2facede8a05a8 Mon Sep 17 00:00:00 2001
From: David Perl <perl_d@x06da-cons-01.psi.ch>
Date: Wed, 26 Aug 2026 15:08:17 +0200
Subject: [PATCH] WIP feat: reintegrate fluo

---
 src/aare/daq/daq.py       | 19 +++++++++++++++++--
 src/aare/daq/server.py    |  2 +-
 src/aare/daq/workflows.py |  2 +-
 3 files changed, 19 insertions(+), 4 deletions(-)

diff --git a/src/aare/daq/daq.py b/src/aare/daq/daq.py
index 57dfd103..c0613e87 100644
--- a/src/aare/daq/daq.py
+++ b/src/aare/daq/daq.py
@@ -121,6 +121,7 @@ from aare.daq.operations.rotation.service import RotationService
 from aare.daq.operations.screenshot.service import ScreenshotService
 from aare.devices.area_detector import AutoEnum
 from aare.devices.jfjoch import JFJochWrapper
+import numpy as np
 
 logger = setup_logger("aareDAQ")
 
@@ -3491,6 +3492,10 @@ class AareDAQ:
         finally:
             self._cfg.state_busy = False
 
+    @staticmethod
+    def _linear_fluo_energies(offset, slope, num = 2408):
+        return np.linspace(offset, slope*num + offset, 2048).tolist()
+    
     def fluorimeter_take_spectrum(
         self, fm: FluorescenceSpectrumParameterModel
     ) -> FluorescenceSpectrumOutputModel:
@@ -3502,11 +3507,21 @@ class AareDAQ:
             if fm.transmission is not None:
                 self._devs.transmission = fm.transmission
 
-            # TODO: Fill
+            if self._beamline != MXBeamline.X06DA:
+                raise NotImplementedError("Only enabled for PXIII right now")
+
+            fluo = self._devs.bec_worker.dev.fluorimeter
+            background = fluo.background.get().tolist()
+            spectrum = fluo.mca.get().tolist()
+            offset = fluo.calibration_offset.get()
+            slope = fluo.calibration_slope.get()
+            energies_ev = self._linear_fluo_energies(offset, slope)
+            adt = fluo.average_dead_time.get() / 100
+            out = FluorescenceSpectrumOutputModel(bkg=background, spectrum=spectrum, energy_eV=energies_ev, average_dead_time=adt)
 
             self._set_state(BeamlineStateEnum.SampleAlignment)
             self._cfg.state_busy = False
-            return None
+            return out
         except Exception:
             self._set_state(BeamlineStateEnum.SampleAlignment)
             self._cfg.state_busy = False
diff --git a/src/aare/daq/server.py b/src/aare/daq/server.py
index ce4a1c6d..434fe9c2 100644
--- a/src/aare/daq/server.py
+++ b/src/aare/daq/server.py
@@ -1435,7 +1435,7 @@ async def robot_sample_exchange(token: str = Depends(oauth2_scheme)):
 @app.post("/state/xray_fluorescence")
 async def xray_fluorescence(token: str = Depends(oauth2_scheme)):
     """
-    Transition beamline state to SampleAlignment.
+    Transition beamline state to XrayFluorescence.
 
     Args:
         token: OAuth2 access token.
diff --git a/src/aare/daq/workflows.py b/src/aare/daq/workflows.py
index 41cd0c48..8c560fb7 100644
--- a/src/aare/daq/workflows.py
+++ b/src/aare/daq/workflows.py
@@ -179,7 +179,7 @@ def dc2sa(devs: BeamlineDevices, cfg: BeamlineConfig):
 def sa2xrf(devs: BeamlineDevices, cfg: BeamlineConfig):
     """sample alignment to XrfCollection"""
     devs.samcam_auto(AutoEnum.AUTO)
-    devs.bec_worker.move_to(BeamlineState.FLUX_MEASUREMENT)
+    devs.bec_worker.move_to(BeamlineState.DC_XRF)
     devs.samcam_auto(AutoEnum.ONCE)