Error propagation

src/navigate/model/features/feature_container.py

@@ -38,6 +38,7 @@
 # Third Party Imports
 
 # Local Imports
+from navigate.model.utils.exceptions import UserVisibleException
 
 p = __name__.split(".")[1]
 
@@ -488,7 +489,7 @@ class SignalContainer(Container):
       track of the remaining executions.
     """
 
-    def __init__(self, root=None, cleanup_list=[], number_of_execution=1):
+    def __init__(self, root=None, cleanup_list=[], warning_queue=None, number_of_execution=1):
         """Initialize the SignalContainer object.
 
         Parameters:
@@ -498,6 +499,8 @@ def __init__(self, root=None, cleanup_list=[], number_of_execution=1):
         cleanup_list : list of TreeNode, optional
             A list of nodes containing 'cleanup' functions to be executed when the
             container is closed. Default is an empty list.
+        warning_queue : Queue, optional
+            A queue for warning messages. Default is None.
         number_of_execution : int, optional
             The number of times the control sequence should be executed. Default is 1.
         """
@@ -509,6 +512,9 @@ def __init__(self, root=None, cleanup_list=[], number_of_execution=1):
         #: int: The remaining number of executions of the control sequence.
         self.remaining_number_of_execution = number_of_execution
 
+        #: Queue: A queue for warning messages related to the control sequence.
+        self.warning_queue = warning_queue
+
     def reset(self):
         """Reset the container's state, including the current node and end flag.
 
@@ -556,8 +562,12 @@ def run(self, *args, wait_response=False):
         while self.curr_node:
             try:
                 result, is_end = self.curr_node.run(*args, wait_response=wait_response)
-            except Exception:
+            except Exception as e:
                 logger.debug(f"SignalContainer - {traceback.format_exc()}")
+                if self.warning_queue and isinstance(e, UserVisibleException):
+                    self.warning_queue.put(
+                        ("warning", f"Warning: review details below.\n{str(e)}")
+                    )
                 self.end_flag = True
                 self.cleanup()
                 return
@@ -1031,7 +1041,7 @@ def build_feature_tree(feature_list, continue_list, break_list):
     for node in break_list:
         if node[0] == "child":
             node[1].child, node[2].child = create_node({"name": DummyFeature})
-    return SignalContainer(signal_root, signal_cleanup_list), DataContainer(
+    return SignalContainer(signal_root, signal_cleanup_list, getattr(model, "event_queue", None)), DataContainer(
         data_root, data_cleanup_list
     )
 

src/navigate/model/model.py

@@ -70,6 +70,7 @@
     SharedList,
     load_dynamic_parameter_functions,
 )
+from navigate.model.utils.threads import ThreadWithWarning
 from navigate.log_files.log_functions import log_setup
 from navigate.tools.common_dict_tools import update_stage_dict
 from navigate.tools.common_functions import load_module_from_file, VariableWithLock
@@ -587,9 +588,13 @@ def run_command(
                 self.data_buffer_saving_flags = None
 
             if self.imaging_mode == "live":
-                self.signal_thread = threading.Thread(target=self.run_live_acquisition)
+                self.signal_thread = ThreadWithWarning(target=self.run_live_acquisition,
+                                                       warning_queue=self.event_queue,
+                                                       logger=self.logger)
             else:
-                self.signal_thread = threading.Thread(target=self.run_acquisition)
+                self.signal_thread = ThreadWithWarning(target=self.run_acquisition,
+                                                       warning_queue=self.event_queue,
+                                                       logger=self.logger)
 
             self.signal_thread.name = f"{self.imaging_mode} signal"
 
@@ -685,7 +690,9 @@ def run_command(
                     self, self.acquisition_modes_feature_setting[self.imaging_mode]
                 )
                 self.stop_send_signal = False
-                self.signal_thread = threading.Thread(target=self.run_live_acquisition)
+                self.signal_thread = ThreadWithWarning(target=self.run_live_acquisition, 
+                                                       warning_queue=self.event_queue,
+                                                       logger=self.logger)
                 self.signal_thread.name = "Waveform Popup Signal"
                 self.signal_thread.start()
 

src/navigate/model/utils/exceptions.py

@@ -0,0 +1,41 @@
+# Copyright (c) 2021-2025  The University of Texas Southwestern Medical Center.
+# All rights reserved.
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted for academic and research use only (subject to the
+# limitations in the disclaimer below) provided that the following conditions are met:
+
+#      * Redistributions of source code must retain the above copyright notice,
+#      this list of conditions and the following disclaimer.
+
+#      * Redistributions in binary form must reproduce the above copyright
+#      notice, this list of conditions and the following disclaimer in the
+#      documentation and/or other materials provided with the distribution.
+
+#      * Neither the name of the copyright holders nor the names of its
+#      contributors may be used to endorse or promote products derived from this
+#      software without specific prior written permission.
+
+# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+# BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
+# IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+#
+
+class UserVisibleException(Exception):
+    """Base class for exceptions that should be visible to the user."""
+    def __init__(self, message: str):
+        """Initialize the exception with a user-friendly message.
+        Parameters
+        ----------
+        message : str
+            A message that describes the exception in a user-friendly way.
+        """
+        super().__init__(message)

src/navigate/model/utils/threads.py

@@ -0,0 +1,65 @@
+# Copyright (c) 2021-2025  The University of Texas Southwestern Medical Center.
+# All rights reserved.
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted for academic and research use only (subject to the
+# limitations in the disclaimer below) provided that the following conditions are met:
+
+#      * Redistributions of source code must retain the above copyright notice,
+#      this list of conditions and the following disclaimer.
+
+#      * Redistributions in binary form must reproduce the above copyright
+#      notice, this list of conditions and the following disclaimer in the
+#      documentation and/or other materials provided with the distribution.
+
+#      * Neither the name of the copyright holders nor the names of its
+#      contributors may be used to endorse or promote products derived from this
+#      software without specific prior written permission.
+
+# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+# BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
+# IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+#
+
+# Standard Library Imports
+import threading
+import logging
+# Local Imports
+from navigate.model.utils.exceptions import UserVisibleException
+
+# Logger Setup
+p = __name__.split(".")[1]
+logger = logging.getLogger(p)
+
+class ThreadWithWarning(threading.Thread):
+    """A custom thread class that raises a warning to the user if any error is raised."""
+
+    def __init__(self, *args, **kwargs):
+        """Initialize the ThreadWithWarning."""
+        if "warning_queue" in kwargs:
+            self._warning_queue = kwargs["warning_queue"]
+            del kwargs["warning_queue"]
+        self._logger = logger
+        if "logger" in kwargs:
+            self._logger = kwargs["logger"]
+            del kwargs["logger"]
+        super().__init__(*args, **kwargs)
+
+    def run(self):
+        """Run the thread and handle warnings."""
+        try:
+            super().run()
+        except Exception as e:
+            self._logger.error(f"Error in thread {self.name}: {e}")
+            if hasattr(self, "_warning_queue") and isinstance(e, UserVisibleException):
+                self._warning_queue.put(("warning", str(e)))
+            raise e
+