GUI: Fluorescence improvements

common/src/aaredaqlib/models.py

@@ -430,6 +430,7 @@ class BeamMarkCoeffModel(BaseModel):
         )
 
 class FluorescenceSpectrumParameterModel(BaseModel):
+    erase: bool = True
     acq_time_s: float
     transmission: Annotated[float, Field(ge=0,le=1)] | None = None
 

daq/src/aaredaq/daq.py

@@ -1,21 +1,16 @@
 import copy
 import json
-import math
-import statistics
+import secrets
 import time
-from asyncio import sleep
 from datetime import datetime
 from math import ceil
-from typing import List, Tuple, Optional, Callable, Dict
-import secrets
-import os
+from typing import List, Tuple, Optional
 
 import cv2
 import numpy as np
 import redis
-from scipy import ndimage
-from scipy.optimize import curve_fit
 
+import aaredaqlib.face_detection as fd
 from aaredaq import workflows
 from aaredaq.aaredb import AareWrapper
 from aaredaq.autofocus import calculate_focus_measure
@@ -26,16 +21,15 @@ from aaredaq.mlbox import MlBox
 from aaredaqlib.beamline import MXBeamline
 from aaredaqlib.coordinate import Coordinate, SmargonCoordinate
 from aaredaqlib.diffraction_geometry import DiffractionGeometry
-import aaredaqlib.face_detection as fd
-from aaredaqlib.logger_config import setup_logger
 from aaredaqlib.find_xtal import raster_centre_of_mass, create_quality_filtered_array, identify_crystal_raster, \
     get_result_list_from_com, get_best_b_factor, get_best_res, get_xtal_size
+from aaredaqlib.logger_config import setup_logger
 from aaredaqlib.models import (
     SampleShortInfo,
     PuckLoadedInfo,
     SampleShortInfoList,
-    DAQStatusModel, BeamlineStatus, SessionStatus, SampleCameraSettings, AutofocusSettings, BoundingBoxModel,
-    ZoomModeEnum, CrystalSize, SimpleScanParameters, MLBoxModel, FluorescenceSpectrumParameterModel,
+    DAQStatusModel, BeamlineStatus, SessionStatus, SampleCameraSettings, AutofocusSettings, ZoomModeEnum, CrystalSize,
+    SimpleScanParameters, MLBoxModel, FluorescenceSpectrumParameterModel,
     FluorescenceSpectrumOutputModel)
 from aaredaqlib.raster_grid import RasterGridRequest, CompletedRasterGrid, CompletedRasterGridElem
 from aaredaqlib.rotation_scan import RotationScanRequest, CompletedRotationScan
@@ -1533,11 +1527,12 @@ class AareDAQ:
             if fm.transmission is not None:
                 self.__devs.transmission.set(fm.transmission, wait=True)
 
-            self.__devs.fluorimeter.start_acquisition(erase=True)
+            self.__devs.fluorimeter.start_acquisition(erase=fm.erase)
             self.__devs.aerotech.set_shutter(1)
-            sleep(fm.acq_time_s)
+            time.sleep(fm.acq_time_s)
             self.__devs.aerotech.set_shutter(0)
             self.__devs.fluorimeter.stop_acquisition()
+            time.sleep(0.2)
             spectrum = self.__devs.fluorimeter.get_current_data()
 
             offset = self.__devs.fluorimeter.offset

gui/src/aaregui/main_window.py

@@ -36,7 +36,7 @@ from aaregui.widgets.camera_image import SampleCameraImageLabel
 from aaregui.widgets.no_wheel_scroll_area import NoWheelScrollArea
 from aaregui.widgets.status_bar import StatusBar
 from aaregui.widgets.video_image import VideoGraphicsView
-from aaregui.panels.fluoresence_panel import FluorescencePanel
+from aaregui.panels.fluorescence_panel import FluorescencePanel
 
 logger = setup_logger("aareGUI")
 
@@ -358,6 +358,7 @@ class MainWindow(QMainWindow):
 
         self.data_collection.fluo.fluo_scan.connect(self.daq.fluorimeter_spectrum)
         self.daq.fluorimeter_spectrum_update.connect(self.fluor_panel.update_plot)
+        self.daq.fluorimeter_spectrum_update.connect(lambda: self.fluor_panel_dock.setVisible(True))
 
     def create_menu_bar(self):
         """Create a menu bar with File->Quit and Help->About."""

gui/src/aaregui/panels/fluorescence_data_collection.py

@@ -1,5 +1,5 @@
 from PySide6.QtCore import Signal, Slot
-from PySide6.QtWidgets import QWidget, QGridLayout, QLabel, QPushButton
+from PySide6.QtWidgets import QWidget, QGridLayout, QLabel, QPushButton, QCheckBox
 
 from aaredaqlib.models import FluorescenceSpectrumParameterModel
 from aaregui.widgets.number_line_edit import NumberLineEdit
@@ -24,13 +24,18 @@ class FluorescenceDataCollectionPanel(QWidget):
         lay.addWidget(self.exposure, 1, 1)
         lay.addWidget(QLabel("s", self), 1, 2)
 
+        # Accumulate checkbox (reverse of erase)
+        self.accumulate_cb = QCheckBox("Accumulate", self)  # accumulate=True => erase=False
+        self.accumulate_cb.setChecked(False)
+        lay.addWidget(self.accumulate_cb, 2, 0, 1, 3)
+
         # Add vertical stretch
-        lay.setRowStretch(2, 1)
+        lay.setRowStretch(3, 1)
 
         # Run button
         self.run_btn = QPushButton("Run fluorescence", self)
         self.run_btn.setStyleSheet("color: rgb(78, 154, 6);")
-        lay.addWidget(self.run_btn, 3, 0, 1, 3)
+        lay.addWidget(self.run_btn, 4, 0, 1, 3)
 
         self.run_btn.clicked.connect(self._emit_params)
 
@@ -38,4 +43,5 @@ class FluorescenceDataCollectionPanel(QWidget):
     def _emit_params(self):
         t = float(self.transmission.value)
         exp = float(self.exposure.value)
-        self.fluo_scan.emit(FluorescenceSpectrumParameterModel(acq_time_s=exp, transmission=t))
+        erase = not self.accumulate_cb.isChecked()
+        self.fluo_scan.emit(FluorescenceSpectrumParameterModel(acq_time_s=exp, transmission=t, erase=erase))

gui/src/aaregui/panels/fluorescence_panel.py

@@ -13,6 +13,7 @@ class FluorescencePanel(QWidget):
     def __init__(self, parent=None):
         super().__init__(parent)
 
+        self.setMinimumWidth(300)
         grid = QGridLayout(self)
 
         # Replace Matplotlib with Qt Charts