Update license, add some __repr__, adjust exception logging.

src/navigate/_commit.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2022  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.
 # All rights reserved.
 
 # Redistribution and use in source and binary forms, with or without

src/navigate/config/config.py

@@ -38,13 +38,18 @@
 from pathlib import Path
 from os.path import isfile
 from multiprocessing.managers import ListProxy, DictProxy
+import logging
 
 # Third Party Imports
 import yaml
 
 # Local Imports
 from navigate.tools.common_functions import build_ref_name
 
+# Logger Setup
+p = __name__.split(".")[1]
+logger = logging.getLogger(p)
+
 
 def get_navigate_path():
     """Establish a program home directory in AppData/Local/.navigate for Windows
@@ -944,6 +949,10 @@ def verify_configuration(manager, configuration):
             continue
         parent_microscope_name = inherited_microscope_dict[microscope_name]
         if parent_microscope_name not in device_config.keys():
+            logger.error(
+                f"Microscope {parent_microscope_name} is not defined in "
+                f"configuration.yaml"
+            )
             raise Exception(
                 f"Microscope {parent_microscope_name} is not "
                 f"defined in configuration.yaml"
@@ -981,11 +990,15 @@ def verify_configuration(manager, configuration):
         for device_name in required_devices:
             if device_name not in device_config[microscope_name]:
                 print(
-                    f"*** Please make sure you have {device_name} "
+                    f"Please make sure you have {device_name} "
                     f"in the configuration for microscope {microscope_name}, or "
                     f"{microscope_name} is inherited from another valid microscope!"
                 )
-                raise Exception()
+                logger.error(
+                    f"{device_name} is not defined in configuration.yaml for "
+                    f"microscope {microscope_name}"
+                )
+                raise Exception(f"No {device_name} defined for microscope {microscope_name}")
         camera_config = device_config[microscope_name]["camera"]
         if "delay" not in camera_config.keys():
             camera_config["delay"] = camera_config.get("delay_percent", 2)

src/navigate/controller/configuration_controller.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2022  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.
 # All rights reserved.
 
 # Redistribution and use in source and binary forms, with or without

src/navigate/controller/configurator.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2022  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  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
@@ -188,7 +188,7 @@ def set_value(temp_dict, key_list, value):
                                     print(
                                         f"Notice: {hardware_name} has an empty value {ref}! Please double check if it's okay!"
                                     )
-                                    
+
                                 if k_idx in value_dict:
                                     k = value_dict[k_idx][v]
                                 v = variables[v_idx].get()
@@ -218,7 +218,7 @@ def set_value(temp_dict, key_list, value):
         if warning_info:
             messagebox.showwarning(
                 title="Configuration",
-                message=f"There are empty value(s) with {', '.join(warning_info.keys())}. Please double check!"
+                message=f"There are empty value(s) with {', '.join(warning_info.keys())}. Please double check!",
             )
 
     def write_to_yaml(self, config, filename):
@@ -305,15 +305,19 @@ def get_widgets_value(widgets, value_dict):
                     continue
                 value = get_widget_value(key, value_dict)
                 # widgets[key][3] is the value mapping dict
-                if widgets[key][1] != "Spinbox"and widgets[key][3]:
+                if widgets[key][1] != "Spinbox" and widgets[key][3]:
                     # if the value is not valid, return the last valid value
                     if type(widgets[key][3]) == list:
-                        reverse_value_dict = dict(map(lambda v: (v, v), widgets[key][3]))
+                        reverse_value_dict = dict(
+                            map(lambda v: (v, v), widgets[key][3])
+                        )
                     else:
                         reverse_value_dict = dict(
                             map(lambda v: (v[1], v[0]), widgets[key][3].items())
                         )
-                    temp[key] = reverse_value_dict.get(value, list(reverse_value_dict.values())[-1])
+                    temp[key] = reverse_value_dict.get(
+                        value, list(reverse_value_dict.values())[-1]
+                    )
                 else:
                     temp[key] = value
             return temp
@@ -358,6 +362,7 @@ def build_widgets_value(widgets, value_dict):
                 result.append(get_widgets_value(widgets, value_dict))
 
             return result
+
         # ask file name
         file_name = filedialog.askopenfilename(
             defaultextension=".yml", filetypes=[("Yaml file", "*.yml *.yaml")]
@@ -370,10 +375,10 @@ def build_widgets_value(widgets, value_dict):
         if config_dict is None or "microscopes" not in config_dict:
             messagebox.showerror(
                 title="Configuration",
-                message="It's not a valid configuration.yaml file!"
+                message="It's not a valid configuration.yaml file!",
             )
             return
-        
+
         self.delete_microscopes()
 
         for i, microscope_name in enumerate(config_dict["microscopes"].keys()):
@@ -387,7 +392,7 @@ def build_widgets_value(widgets, value_dict):
                 sticky=tk.NSEW,
             )
             self.view.microscope_window.tab_list.append(microscope_name)
-            
+
             for hardware_type, widgets in hardwares_dict.items():
                 hardware_ref_name = hardwares_config_name_dict[hardware_type]
                 # build dictionary values for widgets

src/navigate/controller/sub_controllers/adaptive_optics.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2022  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.
 # All rights reserved.
 
 # Redistribution and use in source and binary forms, with or without

src/navigate/controller/sub_controllers/autofocus.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2022  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.
 # All rights reserved.
 
 # Redistribution and use in source and binary forms, with or without

src/navigate/controller/sub_controllers/camera_map.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2022  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.
 # All rights reserved.
 
 # Redistribution and use in source and binary forms, with or without

src/navigate/controller/sub_controllers/camera_settings.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2022  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.
 # All rights reserved.
 
 # Redistribution and use in source and binary forms, with or without
@@ -256,7 +256,6 @@ def populate_experiment_values(self):
             self.camera_setting_dict["frames_to_average"]
         )
 
-
         # after initialization
         self.in_initialization = False
 

src/navigate/controller/sub_controllers/channels_settings.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2022  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.
 # All rights reserved.
 
 # Redistribution and use in source and binary forms, with or without

src/navigate/controller/sub_controllers/channels_tab.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2022  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.
 # All rights reserved.
 
 # Redistribution and use in source and binary forms, with or without

src/navigate/controller/sub_controllers/feature_advanced_setting.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2022  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.
 # All rights reserved.
 
 # Redistribution and use in source and binary forms, with or without

src/navigate/controller/sub_controllers/features_popup.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2022  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.
 # All rights reserved.
 
 # Redistribution and use in source and binary forms, with or without

src/navigate/controller/sub_controllers/gui.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2022  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.
 # All rights reserved.
 
 # Redistribution and use in source and binary forms, with or without

src/navigate/controller/sub_controllers/ilastik.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2022  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.
 # All rights reserved.
 
 # Redistribution and use in source and binary forms, with or without

src/navigate/controller/sub_controllers/keystrokes.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2022  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.
 # All rights reserved.
 
 # Redistribution and use in source and binary forms, with or without

src/navigate/controller/sub_controllers/menus.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2022  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.
 # All rights reserved.
 
 # Redistribution and use in source and binary forms, with or without

src/navigate/controller/sub_controllers/microscope_popup.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2022  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.
 # All rights reserved.
 
 # Redistribution and use in source and binary forms, with or without
@@ -237,7 +237,9 @@ def confirm_microscope_setting(self):
                 )
                 controller_name = f"{microscope_name.lower()}_camera_setting_controller"
                 if hasattr(self.parent_controller, controller_name):
-                    camera_setting_controller = getattr(self.parent_controller, controller_name)
+                    camera_setting_controller = getattr(
+                        self.parent_controller, controller_name
+                    )
                     camera_setting_controller.popup.popup.dismiss()
                     delattr(self.parent_controller, controller_name)
             else:

src/navigate/controller/sub_controllers/multiposition.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2022  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.
 # All rights reserved.
 
 # Redistribution and use in source and binary forms, with or without

src/navigate/controller/sub_controllers/stages.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2022  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.
 # All rights reserved.
 
 # Redistribution and use in source and binary forms, with or without

src/navigate/controller/sub_controllers/tiling.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2022  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.
 # All rights reserved.
 
 # Redistribution and use in source and binary forms, with or without

src/navigate/controller/sub_controllers/waveform_popup.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2022  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.
 # All rights reserved.
 
 # Redistribution and use in source and binary forms, with or without

src/navigate/controller/sub_controllers/waveform_tab.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2022  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.
 # All rights reserved.
 
 # Redistribution and use in source and binary forms, with or without

src/navigate/controller/thread_pool.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2022  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.
 # All rights reserved.
 
 # Redistribution and use in source and binary forms, with or without

src/navigate/log_files/filters.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2022  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.
 # All rights reserved.
 
 # Redistribution and use in source and binary forms, with or without

src/navigate/log_files/log_functions.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2022  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.
 # All rights reserved.
 
 # Redistribution and use in source and binary forms, with or without

src/navigate/log_files/logging.yml

@@ -46,6 +46,10 @@ loggers:
     level: DEBUG
     handlers: [console, vc_info, vc_debug, performance]
     propagate: no
+  config:
+    level: DEBUG
+    handlers: [console, vc_info, vc_debug, performance]
+    propagate: no
 
 
 # https://docs.python.org/3/library/logging.html#logrecord-objects

src/navigate/main.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2022  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.
 # All rights reserved.
 
 # Redistribution and use in source and binary forms, with or without

src/navigate/model/analysis/boundary_detect.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2023  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.
 # All rights reserved.
 
 # Redistribution and use in source and binary forms, with or without

src/navigate/model/analysis/camera.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2022  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.
 # All rights reserved.
 
 # Redistribution and use in source and binary forms, with or without

src/navigate/model/analysis/image_contrast.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2022  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.
 # All rights reserved.
 
 # Redistribution and use in source and binary forms, with or without

src/navigate/model/data_sources/__init__.py

@@ -1,9 +1,52 @@
+# Copyright (c) 2021-2024  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 Imports
+import logging
+
+# Third Party Imports
+
+# Local Imports
+
+# Logger Setup
+p = __name__.split(".")[1]
+logger = logging.getLogger(p)
+
 """ File type specific data sources. """
 
 FILE_TYPES = ["TIFF", "OME-TIFF", "H5", "N5", "OME-Zarr"]
 
 
-def get_data_source(file_type):
+def get_data_source(file_type: str):
     """Get the data source class for the given file type.
 
     Parameters
@@ -15,11 +58,6 @@ def get_data_source(file_type):
     -------
     DataSource
         Data source class for the given file type.
-
-    Examples
-    --------
-    >>> get_data_source('tif')
-    <class 'navigate.model.data_sources.tif.TifDataSource'>
     """
 
     if (file_type == "TIFF") or (file_type == "OME-TIFF"):
@@ -38,4 +76,5 @@ def get_data_source(file_type):
         return OMEZarrDataSource
 
     else:
+        logger.error(f"Unknown file type {file_type}. Cannot open.")
         raise NotImplementedError(f"Unknown file type {file_type}. Cannot open.")