Merge pull request #1500 from AllenNeuralDynamics/develop

[production merge] 2025-04-11

Author: alexpiet

bonsai/Bonsai.config

@@ -37,7 +37,7 @@ dependencies = [
     "aind-data-schema==1.1.0",
     "aind-data-schema-models==0.5.6",
     "pydantic >=2.9.2, <3",
-    "stagewidget==1.0.4.dev5",
+    "stagewidget==1.0.4.dev11",
     "python-logging-loki >=0.3.1, <2",
     "pykeepass >=4.0.7, <5",
     "pyyaml >=6, <7",

pyproject.toml

@@ -786,7 +786,7 @@ def _CalibrateLeftOne(self, repeat=False):
                     "All measurements have been completed. Either press Repeat, or Finished"
                 )
                 return
-            next_index = np.where(self.left_measurements is False)[0][0]
+            next_index = np.where(self.left_measurements != True)[0][0]
             self.LeftOpenTime.setCurrentIndex(next_index)
         else:
             next_index = self.LeftOpenTime.currentIndex()
@@ -973,7 +973,7 @@ def _CalibrateRightOne(self, repeat=False):
                     "All measurements have been completed. Either press Repeat, or Finished"
                 )
                 return
-            next_index = np.where(self.right_measurements is False)[0][0]
+            next_index = np.where(self.right_measurements != True)[0][0]
             self.RightOpenTime.setCurrentIndex(next_index)
         else:
             next_index = self.RightOpenTime.currentIndex()
@@ -1454,7 +1454,7 @@ def _SpotCheck(self, valve: Literal["Left", "Right"]):
         if np.abs(error) > TOLERANCE:
             reply = QMessageBox.critical(
                 self,
-                f"Spot check {valve}",
+                f"Spot check {valve}".format(np.round(result, 2)),
                 "Measurement is outside expected tolerance.<br><br>"
                 "If this is a typo, please press cancel."
                 '<br><br><span style="color:purple;font-weight:bold">IMPORTANT</span>: '
@@ -1671,7 +1671,7 @@ def _StartCamera(self):
                 or self.MainWindow.logging_type == -1
             ):
                 self.MainWindow.Ot_log_folder = (
-                    self.MainWindow._restartlogging()
+                    self.MainWindow._restartlogging(start_from_camera=True)
                 )
             # set to check drop frame as true
             self.MainWindow.to_check_drop_frames = 1
@@ -2589,7 +2589,7 @@ def _Open(self):
                 if self.SleepStart == 1:  # only run once
                     self.SleepStart = 0
                     self.threadpool2.start(self.worker2)
-                if self.Open.isChecked() is False or self.SleepComplete2 == 1:
+                if self.Open.isChecked() == False or self.SleepComplete2 == 1:
                     break
             self.Open.setStyleSheet("background-color : none")
             self.Open.setChecked(False)
@@ -2619,7 +2619,7 @@ def _KeepOpen(self):
                     self.SleepComplete = 0
                     self._InitiateATrial()
                     self.threadpool1.start(self.worker1)
-                if self.KeepOpen.isChecked() is False:
+                if self.KeepOpen.isChecked() == False:
                     break
             self.KeepOpen.setStyleSheet("background-color : none")
             self.KeepOpen.setChecked(False)
@@ -2773,7 +2773,7 @@ def _update_metadata(
                 != self.RigMetadataFile.text()
                 and self.RigMetadataFile.text() != ""
             ):
-                if dont_clear is False:
+                if dont_clear == False:
                     # clear probe angles if the rig metadata file is changed
                     self.meta_data["session_metadata"]["probes"] = {}
                     self.meta_data["session_metadata"]["microscopes"] = {}

src/foraging_gui/Dialogs.py

@@ -1414,17 +1414,22 @@ def _ReconnectBonsai(self):
                 QMessageBox.Ok,
             )
 
-    def _restartlogging(self, log_folder=None):
+    def _restartlogging(self, log_folder=None,start_from_camera=False):
         """Restarting logging"""
         logging.info("Restarting logging")
         # stop the current session except it is a new session
         if self.StartANewSession == 1 and self.ANewTrial == 1:
             pass
         else:
             self._StopCurrentSession()
+        
+        # We don't need to stop the recording when the start_from_camera is True as the logging is from the camera
+        if start_from_camera == False:
+            # Turn off the camera recording if it it on
+            if self.Camera_dialog.StartRecording.isChecked():
+                self.Camera_dialog.StartRecording.setChecked(False)
+                self.Camera_dialog.StartRecording()
 
-        # Turn off the camera recording in case it is on
-        self.Camera_dialog.StartRecording.setChecked(False)
         # Turn off the preview if it is on and the autocontrol is on, which can make sure the trigger is off before starting the logging.
         if (
             self.Camera_dialog.AutoControl.currentText() == "Yes"
@@ -2660,7 +2665,7 @@ def keyPressEvent(self, event=None, allow_reset=False):
         allow_reset (bool) allows the Baseweight etc. parameters to be reset to the empty string
         """
         try:
-            if self.actionTime_distribution.isChecked() is True:
+            if self.actionTime_distribution.isChecked() == True:
                 self.PlotTime._Update(self)
         except Exception:
             logging.error(traceback.format_exc())
@@ -2889,7 +2894,7 @@ def _CheckTextChange(self):
             ):
                 if (
                     child.objectName() in ["qt_spinbox_lineedit", None, ""]
-                    or child.isEnabled() is False
+                    or child.isEnabled() == False
                 ):  # I don't understand where the qt_spinbox_lineedit comes from.
                     continue
                 if (
@@ -3447,7 +3452,7 @@ def _Optogenetics(self):
         if self.OpenOptogenetics == 0:
             self.Opto_dialog = OptogeneticsDialog(MainWindow=self)
             self.OpenOptogenetics = 1
-        if self.action_Optogenetics.isChecked() is True:
+        if self.action_Optogenetics.isChecked() == True:
             self.Opto_dialog.show()
         else:
             self.Opto_dialog.hide()
@@ -3457,7 +3462,7 @@ def _Camera(self):
         if self.OpenCamera == 0:
             self.Camera_dialog = CameraDialog(MainWindow=self)
             self.OpenCamera = 1
-        if self.action_Camera.isChecked() is True:
+        if self.action_Camera.isChecked() == True:
             self.Camera_dialog.show()
         else:
             self.Camera_dialog.hide()
@@ -3505,7 +3510,7 @@ def _Metadata(self):
         if self.OpenMetadata == 0:
             self.Metadata_dialog = MetadataDialog(MainWindow=self)
             self.OpenMetadata = 1
-        if self.actionMeta_Data.isChecked() is True:
+        if self.actionMeta_Data.isChecked() == True:
             self.Metadata_dialog.show()
         else:
             self.Metadata_dialog.hide()
@@ -3516,7 +3521,7 @@ def _WaterCalibration(self):
                 MainWindow=self
             )
             self.OpenWaterCalibration = 1
-        if self.action_Calibration.isChecked() is True:
+        if self.action_Calibration.isChecked() == True:
             self.WaterCalibration_dialog.show()
         else:
             self.WaterCalibration_dialog.hide()
@@ -3527,7 +3532,7 @@ def _LaserCalibration(self):
                 MainWindow=self
             )
             self.OpenLaserCalibration = 1
-        if self.actionLaser_Calibration.isChecked() is True:
+        if self.actionLaser_Calibration.isChecked() == True:
             self.LaserCalibration_dialog.show()
         else:
             self.LaserCalibration_dialog.hide()
@@ -3542,7 +3547,7 @@ def _TimeDistribution(self):
             self.TimeDistribution_dialog.setWindowTitle(
                 "Simulated time distribution"
             )
-        if self.actionTime_distribution.isChecked() is True:
+        if self.actionTime_distribution.isChecked() == True:
             self.TimeDistribution_dialog.show()
         else:
             self.TimeDistribution_dialog.hide()
@@ -3575,7 +3580,7 @@ def _LickSta(self):
             self.LickSta_dialog = LickStaDialog(MainWindow=self)
             self.LickSta = 1
             self.LickSta_dialog.setWindowTitle("Licks statistics")
-        if self.actionLicks_sta.isChecked() is True:
+        if self.actionLicks_sta.isChecked() == True:
             self.LickSta_dialog.show()
         else:
             self.LickSta_dialog.hide()
@@ -4000,7 +4005,6 @@ def _Save(self, ForceSave=0, SaveAs=0, SaveContinue=0, BackupSave=0):
                 ):
                     self._AddWaterLogResult(session)
 
-
         except Exception as e:
             logging.warning(
                 "Meta data is not saved!",
@@ -6166,7 +6170,7 @@ def _Start(self):
 
         self._StartTrialLoop(GeneratedTrials, worker1, worker_save)
 
-        if self.actionDrawing_after_stopping.isChecked() is True:
+        if self.actionDrawing_after_stopping.isChecked() == True:
             try:
                 self.PlotM._Update(
                     GeneratedTrials=GeneratedTrials, Channel=self.Channel2
@@ -6347,7 +6351,7 @@ def _StartTrialLoop(self, GeneratedTrials, worker1, worker_save):
                         self.Start.setStyleSheet("background-color : none")
                         break
                 # receive licks and update figures
-                if self.actionDrawing_after_stopping.isChecked() is False:
+                if self.actionDrawing_after_stopping.isChecked() == False:
                     self.PlotM._Update(
                         GeneratedTrials=GeneratedTrials, Channel=self.Channel2
                     )
@@ -6411,7 +6415,7 @@ def _StartTrialLoop(self, GeneratedTrials, worker1, worker_save):
                         )
 
                 # save the data everytrial
-                if GeneratedTrials.CurrentSimulation is True:
+                if GeneratedTrials.CurrentSimulation == True:
                     GeneratedTrials._GetAnimalResponse(
                         self.Channel, self.Channel3, self.data_lock
                     )
@@ -6429,7 +6433,7 @@ def _StartTrialLoop(self, GeneratedTrials, worker1, worker_save):
                     GeneratedTrials.B_CurrentTrialN > 0
                     and self.previous_backup_completed == 1
                     and self.save_each_trial
-                    and GeneratedTrials.CurrentSimulation is False
+                    and GeneratedTrials.CurrentSimulation == False
                 ):
                     self.previous_backup_completed = 0
                     self.threadpool6.start(worker_save)

src/foraging_gui/Foraging.py

@@ -42,6 +42,7 @@
     PowerUnit,
     SizeUnit,
     SoundIntensityUnit,
+    TimeUnit
 )
 
 import foraging_gui
@@ -905,7 +906,8 @@ def _get_photometry_detectors(self):
                     DetectorConfig(
                         name=current_detector["name"],
                         exposure_time=exposure_time,
-                        trigger_type=TriggerType.INTERNAL,
+                        exposure_time_unit=TimeUnit.US,
+                        trigger_type=TriggerType.EXTERNAL,
                     )
                 )
 
@@ -945,7 +947,7 @@ def _get_behavior_stimulus(self):
         Make the audio stimulus metadata
         """
         self.behavior_stimulus = []
-        if self.has_behavior_data is False:
+        if self.has_behavior_data == False:
             logging.info("No behavior data stream detected!")
             return
 
@@ -1376,7 +1378,7 @@ def _get_behavior_stream(self):
         Make the behavior stream metadata
         """
 
-        if self.has_behavior_data is False:
+        if self.has_behavior_data == False:
             self.behavior_streams = []
             logging.info("No behavior data detected!")
             return
@@ -1408,9 +1410,7 @@ def _get_behavior_software(self):
         self.behavior_software = []
         try:
             # Get information about task repository
-            commit_ID = (
-                self.session_model.commit_hash
-            )
+            commit_ID = self.session_model.commit_hash
             current_branch = (
                 subprocess.check_output(["git", "branch", "--show-current"])
                 .decode("ascii")

src/foraging_gui/GenerateMetadata.py

@@ -407,7 +407,7 @@ def _CheckBaitPermitted(self):
                 self.BaitPermitted = False
         else:
             self.BaitPermitted = True
-        if self.BaitPermitted is False:
+        if self.BaitPermitted == False:
             logging.warning(
                 "The active side has no reward due to consecutive \nselections("
                 + str(MaxCLen)
@@ -807,10 +807,10 @@ def _get_current_block_reward(
             self.BS_CurrentBlockTrialN[i] = length[-1]
             index[i] = indexN[-1]
         self.BS_RewardedTrialN_CurrentLeftBlock = np.sum(
-            B_RewardedHistory[0][index[0][0] : index[0][1] + 1] is True
+            B_RewardedHistory[0][index[0][0] : index[0][1] + 1] == True
         )
         self.BS_RewardedTrialN_CurrentRightBlock = np.sum(
-            B_RewardedHistory[1][index[1][0] : index[1][1] + 1] is True
+            B_RewardedHistory[1][index[1][0] : index[1][1] + 1] == True
         )
         self.AllRewardThisBlock = (
             self.BS_RewardedTrialN_CurrentLeftBlock
@@ -845,16 +845,16 @@ def _GetBasic(self):
             self.BS_RespondedRate = np.nan
         else:
             self.BS_RespondedRate = self.BS_FinisheTrialN / self.BS_AllTrialN
-        self.BS_RewardTrialN = np.sum(self.B_RewardedHistory is True)
+        self.BS_RewardTrialN = np.sum(self.B_RewardedHistory == True)
         B_RewardedHistory = self.B_RewardedHistory.copy()
         # auto reward is considered as reward
         Ind = range(len(self.B_RewardedHistory[0]))
         for i in range(len(self.B_RewardedHistory)):
             B_RewardedHistory[i] = np.logical_or(
                 self.B_RewardedHistory[i], self.B_AutoWaterTrial[i][Ind]
             )
-        self.BS_RewardN = np.sum(B_RewardedHistory[0] is True) + np.sum(
-            B_RewardedHistory[1] is True
+        self.BS_RewardN = np.sum(B_RewardedHistory[0] == True) + np.sum(
+            B_RewardedHistory[1] == True
         )
 
         (
@@ -893,8 +893,8 @@ def _GetBasic(self):
             + BS_auto_water_left
             + BS_auto_water_right
         )
-        self.BS_LeftRewardTrialN = np.sum(self.B_RewardedHistory[0] is True)
-        self.BS_RightRewardTrialN = np.sum(self.B_RewardedHistory[1] is True)
+        self.BS_LeftRewardTrialN = np.sum(self.B_RewardedHistory[0] == True)
+        self.BS_RightRewardTrialN = np.sum(self.B_RewardedHistory[1] == True)
         self.BS_LeftChoiceN = np.sum(self.B_AnimalResponseHistory == 0)
         self.BS_RightChoiceN = np.sum(self.B_AnimalResponseHistory == 1)
         self.BS_OverallRewardRate = self.BS_RewardTrialN / (
@@ -2153,9 +2153,9 @@ def _CheckAutoWater(self):
                             extra={"tags": [self.win.warning_log_tag]},
                         )
                     elif (
-                        np.all(B_RewardedHistory[0][-UnrewardedN:] is False)
+                        np.all(B_RewardedHistory[0][-UnrewardedN:] == False)
                         and np.all(
-                            B_RewardedHistory[1][-UnrewardedN:] is False
+                            B_RewardedHistory[1][-UnrewardedN:] == False
                         )
                         and np.shape(B_RewardedHistory[0])[0] >= UnrewardedN
                     ):
@@ -2497,7 +2497,7 @@ def _InitiateATrial(self, Channel1, Channel4):
         if self.TP_Task in ["Coupled Baiting", "Uncoupled Baiting"]:
             self.CurrentBait = self.CurrentBait | self.B_Baited
         # For task rewardN, if this is the "initial N trials" of the active side, no bait will be be given.
-        if self.BaitPermitted is False:
+        if self.BaitPermitted == False:
             # no reward in the active side
             max_index = np.argmax(self.B_CurrentRewardProb)
             self.CurrentBait[max_index] = False
@@ -2599,8 +2599,8 @@ def _InitiateATrial(self, Channel1, Channel4):
     def _CheckSimulationSession(self):
         """To check if this is a simulation session"""
         if (
-            self.win.actionWin_stay_lose_switch.isChecked() is True
-            or self.win.actionRandom_choice.isChecked() is True
+            self.win.actionWin_stay_lose_switch.isChecked() == True
+            or self.win.actionRandom_choice.isChecked() == True
         ):
             self.CurrentSimulation = True
             self.B_SimulationSession.append(True)
@@ -2652,7 +2652,7 @@ def _SimulateResponse(self):
             self.B_CurrentRewarded[1] = False
             self.B_CurrentRewarded[0] = True
         elif (
-            self.B_AnimalCurrentResponse == 0 and self.CurrentBait[0] is False
+            self.B_AnimalCurrentResponse == 0 and self.CurrentBait[0] == False
         ):
             self.B_Baited[0] = False
             self.B_CurrentRewarded[0] = False
@@ -2662,7 +2662,7 @@ def _SimulateResponse(self):
             self.B_CurrentRewarded[0] = False
             self.B_CurrentRewarded[1] = True
         elif (
-            self.B_AnimalCurrentResponse == 1 and self.CurrentBait[1] is False
+            self.B_AnimalCurrentResponse == 1 and self.CurrentBait[1] == False
         ):
             self.B_Baited[1] = False
             self.B_CurrentRewarded[0] = False