Merge pull request #1516 from AllenNeuralDynamics/revert-1515-production_testing

Revert "[update main] 2025-04-29"

Author: alexpiet

src/foraging_gui/Foraging.py

@@ -243,10 +243,6 @@ def __init__(self, parent=None, box_number=1, start_bonsai_ide=True):
         # initialize thread lock
         self.data_lock = threading.Lock()
 
-        # intialize behavior baseline time flag
-        self.behavior_baseline_period = threading.Event()
-        self.baseline_min_elapsed = 0
-
         # create bias indicator
         self.bias_n_size = 200
         self.bias_indicator = BiasIndicator(
@@ -2765,7 +2761,6 @@ def keyPressEvent(self, event=None, allow_reset=False):
                         "laser_2_calibration_power",
                         "laser_1_calibration_voltage",
                         "laser_2_calibration_voltage",
-                        "hab_time_box"
                     }:
                         continue
                     if child.objectName() == "UncoupledReward":
@@ -4011,11 +4006,11 @@ def _Save(self, ForceSave=0, SaveAs=0, SaveContinue=0, BackupSave=0):
                 ):
                     self._AddWaterLogResult(session)
                 elif self.BaseWeight.text() == "" or self.WeightAfter.text() == "":
-                    logging.warning(f"Waterlog for mouse {self.behavior_session_model.subject} cannot be added to slims"
-                                   f" due do unrecorded weight information.")
+                    logging.error(f"Waterlog for mouse {self.behavior_session_model.subject} cannot be added to slims "
+                                  f"due do unrecorded weight information.")
                 elif session is None:
-                    logging.warning(f"Waterlog for mouse {self.behavior_session_model.subject} cannot be added to slims"
-                                  f" due do metadata generation failure.")
+                    logging.error(f"Waterlog for mouse {self.behavior_session_model.subject} cannot be added to slims "
+                                 f"due do metadata generation failure.")
         except Exception as e:
             logging.warning(
                 "Meta data is not saved!",
@@ -5461,7 +5456,6 @@ def _NewSession(self):
 
         self.unsaved_data = False
         self.ManualWaterVolume = [0, 0]
-        self.baseline_min_elapsed = 0   # variable to track baseline time elapsed before session for start/stop
 
         # Clear Plots
         if hasattr(self, "PlotM") and self.clear_figure_after_save:
@@ -5898,6 +5892,57 @@ def _Start(self):
             elif self.behavior_session_model.allow_dirty_repo is None:
                 logging.error("Could not check for untracked local changes")
 
+            if self.PhotometryB.currentText() == "on" and (
+                not self.FIP_started
+            ):
+                reply = QMessageBox.critical(
+                    self,
+                    "Box {}, Start".format(self.box_letter),
+                    'Photometry is set to "on", but the FIP workflow has not been started',
+                    QMessageBox.Ok,
+                )
+                self.Start.setChecked(False)
+                logging.info(
+                    "Cannot start session without starting FIP workflow"
+                )
+                return
+
+            # Check if photometry excitation is running or not
+            if self.PhotometryB.currentText() == "on" and (
+                not self.StartExcitation.isChecked()
+            ):
+                logging.warning(
+                    'photometry is set to "on", but excitation is not running'
+                )
+
+                reply = QMessageBox.question(
+                    self,
+                    "Box {}, Start".format(self.box_letter),
+                    'Photometry is set to "on", but excitation is not running. Start excitation now?',
+                    QMessageBox.Yes | QMessageBox.No,
+                    QMessageBox.Yes,
+                )
+                if reply == QMessageBox.Yes:
+                    self.StartExcitation.setChecked(True)
+                    logging.info("User selected to start excitation")
+                    started = self._StartExcitation()
+                    if started == 0:
+                        reply = QMessageBox.critical(
+                            self,
+                            "Box {}, Start".format(self.box_letter),
+                            "Could not start excitation, therefore cannot start the session",
+                            QMessageBox.Ok,
+                        )
+                        logging.info(
+                            "could not start session, due to failure to start excitation"
+                        )
+                        self.Start.setChecked(False)
+                        return
+                else:
+                    logging.info("User selected not to start excitation")
+                    self.Start.setChecked(False)
+                    return
+
             # disable sound button
             self.sound_button.setEnabled(False)
 
@@ -5914,9 +5959,6 @@ def _Start(self):
             self.session_run = True  # session has been started
             self.keyPressEvent(allow_reset=True)
 
-            # set flag to perform habituation period
-            self.behavior_baseline_period.set()
-
         else:
             # Prompt user to confirm stopping trials
             reply = QMessageBox.question(
@@ -5948,7 +5990,6 @@ def _Start(self):
 
             self.session_end_tasks()
             self.sound_button.setEnabled(True)
-            self.behavior_baseline_period.clear()   # set flag to break out of habituation period
 
         if (self.StartANewSession == 1) and (self.ANewTrial == 0):
             # If we are starting a new session, we should wait for the last trial to finish
@@ -6095,21 +6136,12 @@ def _Start(self):
             workerStartTrialLoop1 = self.workerStartTrialLoop1
             worker_save = self.worker_save
 
-        # pause for specified habituation time
-        if self.baseline_min_elapsed <= self.hab_time_box.value():
-            self.wait_for_baseline()
-
         # collecting the base signal for photometry. Only run once
         if (
-                self.Start.isChecked()
-                and self.PhotometryB.currentText() == "on"
-                and self.PhotometryRun == 0
+            self.Start.isChecked()
+            and self.PhotometryB.currentText() == "on"
+            and self.PhotometryRun == 0
         ):
-            # check if workflow is running and start photometry timer
-            if not self.photometry_workflow_running():
-                self.Start.setChecked(False)
-                return
-
             logging.info("Starting photometry baseline timer")
             self.finish_Timer = 0
             self.PhotometryRun = 1
@@ -6152,62 +6184,6 @@ def _Start(self):
             except Exception:
                 logging.error(traceback.format_exc())
 
-    def photometry_workflow_running(self) -> bool or None:
-        """
-        If fiber photometery is configured for session, check if work flow is running
-
-        :returns: boolean indicating if workflow is running or not. If None, fip is not configured
-        """
-
-        if self.PhotometryB.currentText() == "on" and (
-                not self.FIP_started
-        ):
-            reply = QMessageBox.critical(
-                self,
-                "Box {}, Start".format(self.box_letter),
-                'Photometry is set to "on", but the FIP workflow has not been started',
-                QMessageBox.Ok,
-            )
-
-            logging.info(
-                "Cannot start session without starting FIP workflow"
-            )
-            return False
-
-        # Check if photometry excitation is running or not
-        if self.PhotometryB.currentText() == "on" and not self.StartExcitation.isChecked():
-            logging.warning('photometry is set to "on", but excitation is not running')
-
-            reply = QMessageBox.question(
-                self,
-                "Box {}, Start".format(self.box_letter),
-                'Photometry is set to "on", but excitation is not running. Start excitation now?',
-                QMessageBox.Yes | QMessageBox.No,
-                QMessageBox.Yes,
-            )
-            if reply == QMessageBox.Yes:
-                self.StartExcitation.setChecked(True)
-                logging.info("User selected to start excitation")
-                started = self._StartExcitation()
-                if started == 0:
-                    reply = QMessageBox.critical(
-                        self,
-                        "Box {}, Start".format(self.box_letter),
-                        "Could not start excitation, therefore cannot start the session",
-                        QMessageBox.Ok,
-                    )
-                    logging.info(
-                        "could not start session, due to failure to start excitation"
-                    )
-                    self.Start.setChecked(False)
-                    return False
-            else:
-                logging.info("User selected not to start excitation")
-                self.Start.setChecked(False)
-                return False
-
-            return True
-
     def session_end_tasks(self):
         """
         Data cleanup and saving that needs to be done at end of session.
@@ -6289,53 +6265,17 @@ def end_session_log(self) -> None:
         else:
             logging.info("No active session logger")
 
-    def wait_for_baseline(self) -> None:
-        """
-            Function to wait for a baseline time before behavior
-        """
-
-        # pause for specified habituation time
-        start_time = time.time()
-
-        # create habituation timer label and update every minute
-        hab_lab = QLabel()
-        hab_lab.setStyleSheet(f"color: {self.default_warning_color};")
-        self.warning_widget.layout().insertWidget(0, hab_lab)
-        update_hab_timer = QtCore.QTimer(
-            timeout=lambda: hab_lab.setText(f"Time elapsed: "
-                                            f"{round((self.baseline_min_elapsed * 60) // 60)} minutes"
-                                            f" {round((self.baseline_min_elapsed * 60) % 60)} seconds"),
-            interval=1000)
-        update_hab_timer.start()
-
-        logging.info(f"Waiting {round(self.hab_time_box.value() - self.baseline_min_elapsed)} min before starting "
-                     f"session.")
-
-        elapsed = self.baseline_min_elapsed
-        while self.baseline_min_elapsed < self.hab_time_box.value() and self.behavior_baseline_period.is_set():
-            QApplication.processEvents()
-            # update baseline time elapsed before session for start/stop logic
-            self.baseline_min_elapsed = ((time.time() - start_time) / 60) + elapsed
-
-        update_hab_timer.stop()
-        self.behavior_baseline_period.clear()
-
-
     def _StartTrialLoop(self, GeneratedTrials, worker1, worker_save):
-
-        if not self.Start.isChecked():
+        if self.Start.isChecked():
+            logging.info("starting trial loop")
+        else:
             logging.info("ending trial loop")
-            return
-        
-        logging.info("starting trial loop")
 
         # Track elapsed time in case Bonsai Stalls
         last_trial_start = time.time()
         stall_iteration = 1
         stall_duration = 5 * 60
 
-        logging.info(f"Starting session.")
-
         while self.Start.isChecked():
             QApplication.processEvents()
             if (

src/foraging_gui/ForagingGUI.ui

@@ -262,28 +262,6 @@
           </property>
          </widget>
         </item>
-        <item row="2" column="3">
-         <widget class="QSpinBox" name="hab_time_box">
-          <property name="sizePolicy">
-           <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
-            <horstretch>0</horstretch>
-            <verstretch>0</verstretch>
-           </sizepolicy>
-          </property>
-          <property name="minimum">
-            <number>0</number>
-           </property>
-           <property name="maximum">
-            <number>90</number>
-           </property>
-           <property name="suffix">
-           <string> min</string>
-          </property>
-          <property name="prefix">
-           <string> Baseline: </string>
-          </property>
-         </widget>
-        </item>
         <item row="2" column="1">
          <widget class="QPushButton" name="Save">
           <property name="sizePolicy">

src/foraging_gui/ForagingGUI_Ephys.ui

@@ -69,7 +69,7 @@
    <widget class="QComboBox" name="Task">
     <property name="geometry">
      <rect>
-      <x>650</x>
+      <x>620</x>
       <y>20</y>
       <width>152</width>
       <height>20</height>
@@ -2763,40 +2763,6 @@
      <bool>false</bool>
     </property>
    </widget>
-   <widget class="QSpinBox" name="hab_time_box">
-    <property name="enabled">
-     <bool>true</bool>
-    </property>
-    <property name="geometry">
-     <rect>
-      <x>240</x>
-      <y>20</y>
-      <width>110</width>
-      <height>23</height>
-     </rect>
-    </property>
-    <property name="sizePolicy">
-     <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
-      <horstretch>0</horstretch>
-      <verstretch>0</verstretch>
-     </sizepolicy>
-    </property>
-    <property name="styleSheet">
-     <string notr="true"/>
-    </property>
-    <property name="minimum">
-      <number>0</number>
-     </property>
-     <property name="maximum">
-      <number>90</number>
-     </property>
-     <property name="suffix">
-     <string> min</string>
-      </property>
-     <property name="prefix">
-     <string> Baseline: </string>
-    </property>
-   </widget>
    <widget class="QPushButton" name="NewSession">
     <property name="enabled">
      <bool>true</bool>
@@ -3297,7 +3263,7 @@
    <widget class="QLineEdit" name="ID">
     <property name="geometry">
      <rect>
-      <x>380</x>
+      <x>324</x>
       <y>20</y>
       <width>71</width>
       <height>20</height>
@@ -3316,7 +3282,7 @@
    <widget class="QLabel" name="label_72">
     <property name="geometry">
      <rect>
-      <x>350</x>
+      <x>300</x>
       <y>20</y>
       <width>21</width>
       <height>20</height>
@@ -3692,7 +3658,7 @@
    <widget class="QLabel" name="label_74">
     <property name="geometry">
      <rect>
-      <x>450</x>
+      <x>400</x>
       <y>20</y>
       <width>71</width>
       <height>20</height>
@@ -3717,7 +3683,7 @@
    <widget class="QLineEdit" name="Experimenter">
     <property name="geometry">
      <rect>
-      <x>524</x>
+      <x>474</x>
       <y>20</y>
       <width>121</width>
       <height>20</height>