fixes for offline_analysis

TODO something is wrong between matplotlib and pyqt6

bcipy/gui/alert.py

@@ -15,7 +15,9 @@ def confirm(message: str) -> bool:
     -------
         users selection : True for selecting Ok, False for Cancel.
     """
-    app = QApplication(sys.argv)
+    app = QApplication(sys.argv).instance()
+    if not app:
+        app = QApplication(sys.argv)
     dialog = alert_message(message,
                            message_type=AlertMessageType.INFO,
                            message_response=AlertMessageResponse.OCE)

bcipy/gui/intertask_gui.py

@@ -24,12 +24,13 @@ def __init__(
         tasks: List[str],
         exit_callback: Callable,
     ):
-        # check if IntertaskGUI in tasks, if so, remove it
         self.tasks = tasks
-        tasks = [task for task in tasks if task != self.action_name]
-        self.total_tasks = len(tasks)
         self.current_task_index = next_task_index
         self.next_task_name = tasks[self.current_task_index]
+        self.task_progress = next_task_index - 1 
+        tasks = [task for task in tasks if task != self.action_name]
+        self.total_tasks = len(tasks)
+
         self.callback = exit_callback
         super().__init__("Progress", 800, 150)
 
@@ -38,10 +39,10 @@ def app(self):
 
         progress_container = QHBoxLayout()
         progress_container.addWidget(
-            QLabel(f"({self.current_task_index}/{self.total_tasks})")
+            QLabel(f"({self.task_progress}/{self.total_tasks})")
         )
         self.progress = QProgressBar()
-        self.progress.setValue(int(self.current_task_index / self.total_tasks * 100))
+        self.progress.setValue(int(self.task_progress / self.total_tasks * 100))
         self.progress.setTextVisible(False)
         progress_container.addWidget(self.progress)
         self.contents.addLayout(progress_container)

bcipy/signal/evaluate/artifact.py

@@ -40,7 +40,7 @@ class DefaultArtifactParameters(Enum):
     """
 
     # Voltage
-    PEAK_THRESHOLD = 100e-7
+    PEAK_THRESHOLD = 75e-7
     PEAK_MIN_DURATION = 0.005
     FLAT_THRESHOLD = 0.5e-6
     FLAT_MIN_DURATION = 0.1

bcipy/signal/model/offline_analysis.py

@@ -547,7 +547,7 @@ def offline_analysis(
             figure_handles.extend(et_figure_handles)
 
     if alert_finished:
-        results = [f"\n {model.name}: {model.auc} \n" for model in models]
+        results = [f"{model.name}: {model.auc}" for model in models]
         confirm(f"Offline analysis complete! \n Results={results}")
     log.info("Offline analysis complete")
     return models, figure_handles

bcipy/task/actions.py

@@ -96,7 +96,7 @@ def execute(self) -> TaskData:
         """
         logger.info("Running offline analysis action")
         try:
-            cmd = f"bcipy-train --parameters {self.parameters_path} -v"
+            cmd = f"bcipy-train --parameters {self.parameters_path}"
             if self.alert_finished:
                 cmd += " --alert"
             response = subprocess.run(
@@ -132,7 +132,7 @@ def __init__(
         self.save_folder = save_path
         self.parameters = parameters
         assert progress is not None and tasks is not None, "Either progress or tasks must be provided"
-        self.next_task_index = progress - 1  # progress is 1-indexed, tasks is 0-indexed so we can use the same index
+        self.next_task_index = progress  # progress is 1-indexed, tasks is 0-indexed so we can use the same index
         assert self.next_task_index >= 0, "Progress must be greater than 1 "
         self.tasks = tasks
         self.task_name = self.tasks[self.next_task_index].name

bcipy/task/orchestrator/orchestrator.py

@@ -183,10 +183,11 @@ def execute(self) -> None:
                     # Visualize session data and fail silently if it errors
                     try:
                         visualize_session_data(data_save_location, self.parameters)
-                        pass
                     except Exception as e:
                         self.logger.info(f'Error visualizing session data: {e}')
 
+                initialized_task = None
+
             except Exception as e:
                 self.logger.error(f"Task {task.name} failed to execute")
                 self.logger.exception(e)

requirements.txt

@@ -13,9 +13,9 @@ SoundFile==0.12.1
 scipy==1.10.1
 scikit-learn==1.2.2
 seaborn==0.9.0
-matplotlib==3.7.2
+matplotlib==3.7.5
 pylsl==1.16.2
-pandas==2.2.3
+pandas==2.0.3
 psutil==5.7.2
 Pillow==9.4.0
 py-cpuinfo==9.0.0