rename

Author: annie-xd-wang

.gitignore

@@ -288,7 +288,7 @@ temp-BICF-JG-LE4350.txt
 # Custom Ignore
 *.log
 *.icloud
-src/aslm/log_files/LOGS
+src/navigate/log_files/LOGS
 *.tiff
 *.ipynb
 *.tif

README.md

@@ -1,5 +1,5 @@
 <h1 align="center">
-<img src="./src/aslm/view/icon/mic.ico?raw=true" />
+<img src="./src/navigate/view/icon/mic.ico?raw=true" />
 
 ASLM - Autonomous Software for Light Microscopy
 </h1>
@@ -14,11 +14,11 @@ ASLM is an open source Python package for control of light-sheet microscopes. It
 Download and install [Miniconda](https://docs.conda.io/en/latest/miniconda.html#latest-miniconda-installer-links).
 
 ```
-conda create -n aslm python=3.9.7
+conda create -n navigate python=3.9.7
 pip install git+https://github.com/TheDeanLab/ASLM.git
 ```
 
-To test, run `conda activate aslm` and launch in synthetic hardware mode with `aslm
+To test, run `conda activate navigate` and launch in synthetic hardware mode with `navigate
 -sh`. Developers will have to install additional dependencies with
 `pip install -e '.[dev]'`.
 ### Documentation

docs/source/api.rst

@@ -6,9 +6,9 @@ API Reference
    :template: custom_module.rst
    :recursive:
 
-   aslm.config
-   aslm.controller
-   aslm.log_files
-   aslm.model
-   aslm.tools
-   aslm.view
+   navigate.config
+   navigate.controller
+   navigate.log_files
+   navigate.model
+   navigate.tools
+   navigate.view

docs/source/conf.py

@@ -99,4 +99,4 @@
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ["_static"]
 
-html_logo = "../../src/aslm/view/icon/mic.png"
+html_logo = "../../src/navigate/view/icon/mic.png"

docs/source/contributing/contributing_guidelines.rst

@@ -54,13 +54,13 @@ We leverage pre-commit workflows to enforce consistent code formatting. In some
 cases, Ruff may complain about a line of code that is actually fine. For example, in the example code below,
 Ruff complains that the start_stage class is imported but not used. However, it is actually used in as part of an `exec` statement::
 
-        from aslm.model.device_startup_functions import start_stage
+        from navigate.model.device_startup_functions import start_stage
         device_name = stage
         exec(f"self.{device_name} = start_{device_name}(name, device_connection, configuration, i, is_synthetic)")
 
 To avoid this error, you can add a `# noqa` comment to the end of the line to tell Ruff to ignore the error::
 
-        from aslm.model.device_startup_functions import start_stage  # noqa
+        from navigate.model.device_startup_functions import start_stage  # noqa
 
 Dictionary Parsing
 ------------------

docs/source/feature_container/feature_container_home.rst

@@ -17,8 +17,8 @@ will execute (for example, move the stage, then snap a picture). Following
 this, the next set of features in sequence will be executed.
 
 Examples of some existing features include
-``aslm.model.features.common_features.ZStackAcquisition``, which acquires a
-z-stack, and ``aslm.model.features.autofocus.Autofocus``, which finds the
+``navigate.model.features.common_features.ZStackAcquisition``, which acquires a
+z-stack, and ``navigate.model.features.autofocus.Autofocus``, which finds the
 ideal plane of focus of a sample using a Discrete Cosine Transform.
 
 Currently Implemented Features
@@ -45,7 +45,7 @@ Currently Implemented Features
 The Feature Object
 ------------------
 
-Each feature is an object that accepts a pointer to ``aslm.model.model`` in its
+Each feature is an object that accepts a pointer to ``navigate.model.model`` in its
 ``__init__()``  arguments and contains a configuration dictionary that dictates
 feature behavior in its ``__init__()`` function. A complete configuration
 dictionary is shown below. As few or as many of these options can be specified
@@ -106,8 +106,8 @@ To create a customized feature, follow these steps:
 
 .. code-block:: python
 
-   from aslm.tools.decorators import FeatureList
-   from aslm.model.features.feature_related_functions import *
+   from navigate.tools.decorators import FeatureList
+   from navigate.model.features.feature_related_functions import *
 
    @FeatureList
    def feature_example():

docs/source/index.rst

@@ -1,5 +1,5 @@
 
-.. _aslm-home:
+.. _navigate-home:
 
 ############################################
 **Autonomous Software for Light Microscopy**

docs/source/software_configuration.rst

@@ -18,7 +18,7 @@ Mac/Linux.
 
 To avoid confusion, we recommend launching the software in the synthetic hardware
 mode initially. Within your Terminal, or Anaconda Prompt, activate your ASLM Python
-environment and launch the software by typing: ``aslm -sh``. Thereafter, you should
+environment and launch the software by typing: ``navigate -sh``. Thereafter, you should
 only modify the ``configuration.yaml`` file in your local ``/.ASLM`` directory. The
 local copy avoids conflicts between different microscopes after pulling new
 changes on GitHub.

docs/source/software_installation.rst

@@ -70,25 +70,25 @@ The last step requires you to change into the ASLM directory and the install the
 
 
 **Run the ASLM software**::
-    (ASLM) MyComputer ASLM $ aslm
+    (ASLM) MyComputer ASLM $ navigate
 
 .. note::
 
-    If you are running the software on a computer that does not have the appropriate hardware you will need to add the flag -sh after aslm:
+    If you are running the software on a computer that does not have the appropriate hardware you will need to add the flag -sh after navigate:
 
-        aslm -sh
+        navigate -sh
 
 
 After completeting these steps you will only need to do the below to start the software upon opening the prompt:
 
 .. code-block::
 
     (base) MyComputer ~ $ conda activate ASLM
-    (ASLM) MyComputer ~ $ aslm
+    (ASLM) MyComputer ~ $ navigate
 
 .. note::
 
-    If you are running Windows, you can create a desktop shortcut to ASLM by right-clicking the Desktop, navigating to New and then Shortcut and entering ``%windir%\system32\cmd.exe "/c" C:\path\to\miniconda\Scripts\activate.bat aslm && aslm`` into the location text box.
+    If you are running Windows, you can create a desktop shortcut to ASLM by right-clicking the Desktop, navigating to New and then Shortcut and entering ``%windir%\system32\cmd.exe "/c" C:\path\to\miniconda\Scripts\activate.bat navigate && navigate`` into the location text box.
 
 Troubleshooting
 ---------------

pyproject.toml

@@ -44,7 +44,7 @@ dependencies = [
     ]
 
 [project.scripts]
-aslm = "aslm.main:main"
+navigate = "navigate.main:main"
 
 [project.optional-dependencies]
 dev = [

src/aslm/aslm_startup_windows.bat

@@ -6,7 +6,7 @@ set root=C:\Users\Dax\AppData\Local\Continuum\anaconda3
 
 call %root%\Scripts\activate.bat %root%
 
-call conda activate aslm
+call conda activate navigate
 
 call python main.py --synthetic_hardware
 

src/aslm/config/config.py

@@ -46,7 +46,7 @@
 # Local Imports
 
 
-def get_aslm_path():
+def get_navigate_path():
     """Establish a program home directory in AppData/Local/.ASLM for Windows
     or ~/.ASLM for Mac and Linux.
 
@@ -57,19 +57,19 @@ def get_aslm_path():
 
     Examples
     --------
-    >>> get_aslm_path()
+    >>> get_navigate_path()
     'C:\\Users\\username\\AppData\\Local\\.ASLM'
     """
     if platform.system() == "Windows":
         base_directory = os.getenv("LOCALAPPDATA")
     else:
         base_directory = os.getenv("HOME")
-    aslm_path = os.path.join(base_directory, ".ASLM")
+    navigate_path = os.path.join(base_directory, ".ASLM")
 
-    if not os.path.exists(aslm_path):
-        os.mkdir(aslm_path)
+    if not os.path.exists(navigate_path):
+        os.mkdir(navigate_path)
 
-    return aslm_path
+    return navigate_path
 
 
 def get_configuration_paths():
@@ -89,10 +89,10 @@ def get_configuration_paths():
     waveform_templates_path : str
         Path to file containing waveform templates
     """
-    aslm_directory = get_aslm_path()
-    if not os.path.exists(aslm_directory):
-        os.mkdir(aslm_directory)
-    configuration_directory = Path(os.path.join(aslm_directory, "config"))
+    navigate_directory = get_navigate_path()
+    if not os.path.exists(navigate_directory):
+        os.mkdir(navigate_directory)
+    configuration_directory = Path(os.path.join(navigate_directory, "config"))
     if not os.path.exists(configuration_directory):
         os.mkdir(configuration_directory)
 
@@ -360,8 +360,8 @@ def verify_experiment_config(manager, configuration):
 
     # saving info
     saving_dict_sample = {
-        "root_directory": get_aslm_path(),
-        "save_directory": get_aslm_path(),
+        "root_directory": get_navigate_path(),
+        "save_directory": get_navigate_path(),
         "user": "Kevin",
         "tissue": "Lung",
         "celltype": "MV3",

src/aslm/controller/controller.py

@@ -44,13 +44,13 @@
 # Third Party Imports
 
 # Local View Imports
-from aslm.view.main_application_window import MainApp as view
-from aslm.view.popups.camera_view_popup_window import CameraViewPopupWindow
-from aslm.view.popups.feature_list_popup import FeatureListPopup
+from navigate.view.main_application_window import MainApp as view
+from navigate.view.popups.camera_view_popup_window import CameraViewPopupWindow
+from navigate.view.popups.feature_list_popup import FeatureListPopup
 
 # Local Sub-Controller Imports
-from aslm.controller.configuration_controller import ConfigurationController
-from aslm.controller.sub_controllers import (
+from navigate.controller.configuration_controller import ConfigurationController
+from navigate.controller.sub_controllers import (
     KeystrokeController,
     WaveformTabController,
     StageController,
@@ -65,24 +65,24 @@
     # AdaptiveOpticsPopupController,
 )
 
-from aslm.controller.thread_pool import SynchronizedThreadPool
+from navigate.controller.thread_pool import SynchronizedThreadPool
 
 # Local Model Imports
-from aslm.model.model import Model
-from aslm.model.concurrency.concurrency_tools import ObjectInSubprocess
+from navigate.model.model import Model
+from navigate.model.concurrency.concurrency_tools import ObjectInSubprocess
 
 # Misc. Local Imports
-from aslm.config.config import (
+from navigate.config.config import (
     load_configs,
     update_config_dict,
     verify_experiment_config,
     verify_waveform_constants,
-    get_aslm_path,
+    get_navigate_path,
 )
-from aslm.tools.file_functions import create_save_path, save_yaml_file
-from aslm.tools.common_dict_tools import update_stage_dict
-from aslm.tools.multipos_table_tools import update_table
-from aslm.tools.common_functions import combine_funcs
+from navigate.tools.file_functions import create_save_path, save_yaml_file
+from navigate.tools.common_dict_tools import update_stage_dict
+from navigate.tools.multipos_table_tools import update_table
+from navigate.tools.common_functions import combine_funcs
 
 # Logger Setup
 import logging
@@ -809,7 +809,7 @@ def execute(self, command, *args):
             # self.menu_controller.feature_id_val.set(0)
 
             self.update_experiment_setting()
-            file_directory = os.path.join(get_aslm_path(), "config")
+            file_directory = os.path.join(get_navigate_path(), "config")
             save_yaml_file(
                 file_directory=file_directory,
                 content_dict=self.configuration["experiment"],

src/aslm/controller/sub_controllers/acquire_bar_controller.py

@@ -37,8 +37,8 @@
 # Third Party Imports
 
 # Local Imports
-from aslm.controller.sub_controllers.gui_controller import GUIController
-from aslm.view.popups.acquire_popup import AcquirePopUp
+from navigate.controller.sub_controllers.gui_controller import GUIController
+from navigate.view.popups.acquire_popup import AcquirePopUp
 
 # Logger Setup
 p = __name__.split(".")[1]

src/aslm/controller/sub_controllers/adaptiveoptics_popup_controller.py

@@ -40,7 +40,7 @@
 # from matplotlib.axes import Axes
 
 # Local application imports
-from aslm.controller.sub_controllers.gui_controller import GUIController
+from navigate.controller.sub_controllers.gui_controller import GUIController
 
 # Logger Setup
 p = __name__.split(".")[1]

src/aslm/controller/sub_controllers/autofocus_popup_controller.py

@@ -37,8 +37,8 @@
 import matplotlib.ticker as tck
 
 # Local Imports
-from aslm.controller.sub_controllers.gui_controller import GUIController
-from aslm.tools.common_functions import combine_funcs
+from navigate.controller.sub_controllers.gui_controller import GUIController
+from navigate.tools.common_functions import combine_funcs
 
 
 import logging
@@ -55,9 +55,9 @@ def __init__(self, view, parent_controller):
         """
         Parameters
         ----------
-        view : aslm.view.popups.autofocus_setting_popup.AutofocusPopup
+        view : navigate.view.popups.autofocus_setting_popup.AutofocusPopup
             The view of the autofocus popup.
-        parent_controller : aslm.controller.main_controller.MainController
+        parent_controller : navigate.controller.main_controller.MainController
             The parent controller of the autofocus popup.
         """
         super().__init__(view, parent_controller)

src/aslm/controller/sub_controllers/camera_map_setting_popup_controller.py

@@ -39,9 +39,9 @@
 import tifffile
 
 # Local application imports
-from aslm.controller.sub_controllers.gui_controller import GUIController
-from aslm.config import get_aslm_path
-from aslm.model.analysis.camera import compute_scmos_offset_and_variance_map
+from navigate.controller.sub_controllers.gui_controller import GUIController
+from navigate.config import get_navigate_path
+from navigate.model.analysis.camera import compute_scmos_offset_and_variance_map
 
 
 class CameraMapSettingPopupController(GUIController):
@@ -56,14 +56,14 @@ def __init__(self, view, parent_controller=None):
 
         Parameters
         ----------
-        view : aslm.view.sub_views.camera_map_setting_popup.CameraMapSettingPopup
+        view : navigate.view.sub_views.camera_map_setting_popup.CameraMapSettingPopup
             View for the camera map setting popup.
-        parent_controller : aslm.controller.main_controller.MainController
+        parent_controller : navigate.controller.main_controller.MainController
             Parent controller of this controller.
         """
         super().__init__(view, parent_controller)
         #: str: Path to the camera maps directory.
-        self.map_path = os.path.join(get_aslm_path(), "camera_maps")
+        self.map_path = os.path.join(get_navigate_path(), "camera_maps")
         #: np.ndarray: Offset map.
         self.off = None
         #: np.ndarray: Variance map.

src/aslm/controller/sub_controllers/camera_setting_controller.py

@@ -36,7 +36,7 @@
 # Third Party Imports
 
 # Local Imports
-from aslm.controller.sub_controllers.gui_controller import GUIController
+from navigate.controller.sub_controllers.gui_controller import GUIController
 
 # Logger Setup
 p = __name__.split(".")[1]
@@ -53,7 +53,7 @@ def __init__(self, view, parent_controller=None):
         ----------
         view : tkinter.Frame
             The view for the camera settings.
-        parent_controller : aslm.controller.main_controller.MainController
+        parent_controller : navigate.controller.main_controller.MainController
             The parent controller.
         """
         super().__init__(view, parent_controller)

src/aslm/controller/sub_controllers/camera_view_controller.py

@@ -44,9 +44,9 @@
 import copy
 
 # Local Imports
-from aslm.controller.sub_controllers.gui_controller import GUIController
-from aslm.model.analysis.camera import compute_signal_to_noise
-from aslm.tools.common_functions import VariableWithLock
+from navigate.controller.sub_controllers.gui_controller import GUIController
+from navigate.model.analysis.camera import compute_signal_to_noise
+from navigate.tools.common_functions import VariableWithLock
 
 # Logger Setup
 p = __name__.split(".")[1]