Merge branch 'develop'

Done

README.md

@@ -21,22 +21,7 @@ DIPLOMAT also includes a UI for performing tracking and several other tools for
 
 ## Installation
 
-To install DIPLOMAT with PIP right now, you can and install it with pip using one of the following commands below:
-```bash
-# For working with SLEAP projects:
-pip install diplomat-track[sleap]
-# For working with DeepLabCut projects:
-pip install diplomat-track[dlc]
-```
-To install DIPLOMAT with GUI elements and supervised tracking support, use one of the commands below:
-```bash
-# For using DIPLOMAT with SLEAP
-pip install diplomat-track[sleap, gui]
-# Again, replace sleap with dlc to install with DeepLabCut support.
-pip install diplomat-track[dlc, gui]
-```
-
-**NOTE:** DIPLOMAT also includes two environment configuration files for setting up DIPLOMAT with 
+DIPLOMAT also includes four environment configuration files for setting up DIPLOMAT with 
 [mamba](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html), which can
 be installed on Windows, Linux, or MacOS using the [Miniforge](https://github.com/conda-forge/miniforge) installer.
 To create an environment using mamba, run one of these four commands:
@@ -60,7 +45,8 @@ mamba activate DIPLOMAT-DEEPLABCUT
 mamba activate DIPLOMAT-SLEAP
 ```
 
-For a more thorough explanation of the installation process, see the [documentation](https://diplomat.readthedocs.io/en/latest/installation.html).
+For a more thorough explanation of the installation process and alternative installation methods, see the 
+[documentation](https://diplomat.readthedocs.io/en/latest/installation.html).
 
 ## Usage
 
@@ -69,27 +55,33 @@ For a more thorough explanation of the installation process, see the [documentat
 To run DIPLOMAT on a video once it is installed, simply use DIPLOMAT's `unsupervised` and `supervised` commands to track a video:
 ```bash
 # Run DIPLOMAT with no UI...
-diplomat unsupervised -c path/to/config -v path/to/video
+diplomat track -c path/to/config -v path/to/video
 # Run DIPLOMAT with UI...
-diplomat supervised -c path/to/config -v path/to/video
+diplomat track_and_interact -c path/to/config -v path/to/video
 ```
 
 Multiple videos can be tracked by passing them as a list:
 ```bash
-diplomat unsupervised -c path/to/config -v [path/to/video1, path/to/video2, "path/to/video3"]
+diplomat track -c path/to/config -v [path/to/video1, path/to/video2, "path/to/video3"]
 ```
 
 Once tracking is done, DIPLOMAT can create labeled videos via it's `annotate` subcommand:
 ```bash
 diplomat annotate -c path/to/config -v path/to/video
 ```
 
+If you need to reopen the UI to make further major modifications, you can do so using the interact subcommand:
+```bash
+diplomat interact -s path/to/ui_state.dipui
+```
+This displays the full UI again for making further edits. Results are saved back to the same files.
+
 If you need to make minor modifications after tracking a video, you can do so using the tweak subcommand:
 ```bash
 diplomat tweak -c path/to/config -v path/to/video
 ```
-This will display a stripped down version of the supervised editing UI, allowing for minor tweaks to be made to the tracks, and then
-saved back to the same file.
+This will display a stripped down version of the interactive editing UI, allowing for minor tweaks to be made to the 
+tracks, and then saved back to the same file.
 
 For a list of additional ways DIPLOMAT can be used, see the [documentation](https://diplomat.readthedocs.io/en/latest/basic_usage.html).
 

conda-environments/DIPLOMAT-DEEPLABCUT-CPU.yaml

@@ -17,5 +17,5 @@ dependencies:
   - tensorflow
   - keras
   - pip:
-    - deeplabcut
+    - deeplabcut==2.3.8
     - diplomat-track

conda-environments/DIPLOMAT-DEEPLABCUT.yaml

@@ -17,5 +17,5 @@ dependencies:
   - tensorflow-gpu
   - keras
   - pip:
-    - deeplabcut
+    - deeplabcut==2.3.8
     - diplomat-track

conda-environments/DIPLOMAT-SLEAP-CPU.yaml

@@ -45,5 +45,5 @@ dependencies:
   - conda-forge::cudnn=8.2.1
   - nvidia::cuda-nvcc=11.3
   - pip:
-      - sleap
+      - sleap==1.3.3
       - diplomat-track

conda-environments/DIPLOMAT-SLEAP.yaml

@@ -45,5 +45,5 @@ dependencies:
   - conda-forge::cudnn=8.2.1
   - nvidia::cuda-nvcc=11.3
   - pip:
-      - sleap
+      - sleap==1.3.3
       - diplomat-track

diplomat/__init__.py

@@ -9,7 +9,7 @@
 from diplomat.predictor_ops import list_predictor_plugins, get_predictor_settings, test_predictor_plugin
 from diplomat.frontend_ops import list_all_frontends, list_loaded_frontends
 from diplomat.utils.video_splitter import split_videos
-from diplomat.core_ops import track, supervised, unsupervised, annotate, tweak, yaml, convert, restore
+from diplomat.core_ops import track_with, track, track_and_interact, annotate, tweak, yaml, convert, interact
 
 __all__ = [
     "list_predictor_plugins",
@@ -18,14 +18,14 @@
     "list_all_frontends",
     "list_loaded_frontends",
     "split_videos",
+    "track_with",
+    "track_and_interact",
     "track",
-    "supervised",
-    "unsupervised",
     "annotate",
     "tweak",
     "yaml",
     "convert",
-    "restore"
+    "interact"
 ]
 
 

diplomat/_cli_runner.py

@@ -16,15 +16,15 @@ def get_static_cli_tree() -> dict:
             "test": diplomat.test_predictor_plugin,
             "list_settings": diplomat.get_predictor_settings
         },
+        "track_with": diplomat.track_with,
+        "track_and_interact": diplomat.track_and_interact,
         "track": diplomat.track,
-        "supervised": diplomat.supervised,
-        "unsupervised": diplomat.unsupervised,
         "annotate": diplomat.annotate,
         "split_videos": diplomat.split_videos,
         "tweak": diplomat.tweak,
         "yaml": diplomat.yaml,
         "convert": diplomat.convert,
-        "restore": diplomat.restore,
+        "interact": diplomat.interact,
         "frontends": {
             "__description": "Contains subcommands for listing available frontends and inspecting the functions "
                              "each frontend supports.",

diplomat/core_ops.py

@@ -166,7 +166,7 @@ def yaml(
 
 @allow_arbitrary_flags
 @typecaster_function
-def track(
+def track_with(
     config: Union[List[PathLike], PathLike],
     videos: Optional[Union[List[PathLike], PathLike]] = None,
     frame_stores: Optional[Union[List[PathLike], PathLike]] = None,
@@ -178,6 +178,7 @@ def track(
 ):
     """
     Run DIPLOMAT tracking on videos and/or frame stores. Automatically select a frontend based on the passed arguments.
+    Allows for selecting a specific tracker, or predictor.
 
     :param config: The path to the configuration file for the project. The format of this argument will depend on the frontend.
     :param videos: A single path or list of paths to video files to run analysis on.
@@ -243,7 +244,7 @@ def track(
 
 @allow_arbitrary_flags
 @typecaster_function
-def unsupervised(
+def track(
     config: Union[List[PathLike], PathLike],
     videos: Optional[Union[List[PathLike], PathLike]] = None,
     frame_stores: Optional[Union[List[PathLike], PathLike]] = None,
@@ -253,24 +254,28 @@ def unsupervised(
     **extra_args
 ):
     """
-    Run diplomat in unsupervised mode on the specified config and videos or frame stores. An alias for
-    DIPLOMAT track with the SegmentedFramePassEngine predictor.
+    Run diplomat in a non-interactive tracking mode on the specified config and videos or frame stores. An alias for
+    DIPLOMAT track_with with the SegmentedFramePassEngine predictor. The interactive UI can be restored later using
+    diplomat interact function or cli command.
 
-    :param config: The path to the configuration file for the project. The format of this argument will depend on the frontend.
+    :param config: The path to the configuration file for the project. The format of this argument will depend on the
+                   frontend.
     :param videos: A single path or list of paths to video files to run analysis on.
     :param frame_stores: A single path or list of paths to frame store files to run analysis on.
     :param num_outputs: An integer, the number of bodies to track in the video. Defaults to 1.
-    :param settings: An optional dictionary, listing the settings to use for the SegmentedFramePassEngine predictor plugin.
-                     If not specified, the frontend will determine the settings in a frontend specific manner. To see the settings the
-                     SegmentedFramePassEngine supports, use the "diplomat predictors list_settings -p SegmentedFramePassEngine" command
-                     or "diplomat.get_predictor_settings('SegmentedFramePassEngine')". To get more information about how a frontend gets
-                     settings if not passed, set the help_extra parameter to True to print additional settings for the selected
-                     frontend instead of running tracking.
-    :param help_extra: Boolean, if set to true print extra settings for the automatically selected frontend instead of running tracking.
-    :param extra_args: Any additional arguments (if the CLI, flags starting with '--') are passed to the automatically selected frontend.
-                       To see valid values, run track with extra_help flag set to true.
+    :param settings: An optional dictionary, listing the settings to use for the SegmentedFramePassEngine predictor
+                     plugin. If not specified, the frontend will determine the settings in a frontend specific manner.
+                     To see the settings the SegmentedFramePassEngine supports, use the
+                     "diplomat predictors list_settings -p SegmentedFramePassEngine" command
+                     or "diplomat.get_predictor_settings('SegmentedFramePassEngine')". To get more information about
+                     how a frontend gets settings if not passed, set the help_extra parameter to True to print
+                     additional settings for the selected frontend instead of running tracking.
+    :param help_extra: Boolean, if set to true print extra settings for the automatically selected frontend instead of
+                       running tracking.
+    :param extra_args: Any additional arguments (if the CLI, flags starting with '--') are passed to the automatically
+                       selected frontend. To see valid values, run track with extra_help flag set to true.
     """
-    track(
+    track_with(
         config=config,
         videos=videos,
         frame_stores=frame_stores,
@@ -284,7 +289,7 @@ def unsupervised(
 
 @allow_arbitrary_flags
 @typecaster_function
-def supervised(
+def track_and_interact(
     config: Union[List[PathLike], PathLike],
     videos: Optional[Union[List[PathLike], PathLike]] = None,
     frame_stores: Optional[Union[List[PathLike], PathLike]] = None,
@@ -294,8 +299,8 @@ def supervised(
     **extra_args
 ):
     """
-    Run diplomat in supervised mode on the specified config and videos or frame stores. An alias for
-    DIPLOMAT track with the SupervisedSegmentedFramePassEngine predictor.
+    Run diplomat in interactive tracking mode on the specified config and videos or frame stores. An alias for
+    DIPLOMAT track_with with the SupervisedSegmentedFramePassEngine predictor.
 
     :param config: The path to the configuration file for the project. The format of this argument will depend on the frontend.
     :param videos: A single path or list of paths to video files to run analysis on.
@@ -311,7 +316,7 @@ def supervised(
     :param extra_args: Any additional arguments (if the CLI, flags starting with '--') are passed to the automatically selected frontend.
                        To see valid values, run track with extra_help flag set to true.
     """
-    track(
+    track_with(
         config=config,
         videos=videos,
         frame_stores=frame_stores,
@@ -375,8 +380,9 @@ def tweak(
     **extra_args
 ):
     """
-    Make modifications to DIPLOMAT produced tracking results created for a video using a limited version supervised
-    labeling UI. Allows for touching up and fixing any minor issues that may arise after tracking and saving results.
+    Make modifications to DIPLOMAT produced tracking results created for a video using a limited version of the
+    interactive labeling UI. Allows for touching up and fixing any minor issues that may arise after tracking and
+    saving results.
 
     :param config: The path to the configuration file for the project. The format of this argument will depend on the
                    frontend.
@@ -464,12 +470,13 @@ def convert(
 
 
 @typecaster_function
-def restore(
+def interact(
     state: Union[List[PathLike], PathLike]
 ):
     """
-    Restore the state of the diplomat UI from a .dipui file. Allows for reloading the UI when diplomat crashes.
-    Settings and backend will be restored automatically based on the settings and info passed during the first run.
+    Open diplomat's interactive UI from a .dipui file. Allows for reloading the UI when diplomat crashes, or for
+    further editing. Settings and backend will be restored automatically based on the settings and info passed during
+    the first run.
 
     :param state: A path or list of paths to the ui states to restore. Files should be of ".dipui" format.
     """

diplomat/frontends/csv/tweak_results.py

@@ -19,7 +19,7 @@ def tweak_videos(
     **kwargs
 ):
     """
-    Make minor modifications and tweaks to arbitrary csv files using DIPLOMAT's supervised UI.
+    Make minor modifications and tweaks to arbitrary csv files using DIPLOMAT's light interactive UI.
 
     :param config: The path (or list of paths) to the csv file(s) to edit.
     :param videos: Paths to video file(s) corresponding to the provided csv files.

diplomat/frontends/deeplabcut/tweak_results.py

@@ -19,7 +19,8 @@ def tweak_videos(
     video_type: str = "",
 ):
     """
-    Make minor modifications and tweaks to tracked results produced by DEEPLABCUT (or DIPLOMAT) using the supervised UI.
+    Make minor modifications and tweaks to tracked results produced by DEEPLABCUT (or DIPLOMAT) using the interactive
+    UI.
 
     :param config: The path to the config.yaml file for the project.
     :param videos: A single video or list of videos to tweak, passed in order to modify.

diplomat/frontends/sleap/tweak_results_sleap.py

@@ -26,7 +26,7 @@ def tweak_videos(
     **kwargs
 ):
     """
-    Make minor modifications and tweaks to sleap results (stored in .slp files) using DIPLOMAT's supervised UI.
+    Make minor modifications and tweaks to sleap results (stored in .slp files) using DIPLOMAT's interactive UI.
 
     :param config: The path (or list of paths) to the sleap model(s) used for inference, each as either as a folder or zip file.
     :param videos: Paths to the sleap label files, or .slp files, to make minor modifications to, NOT the video files.

diplomat/predictors/supervised_sfpe/supervised_segmented_frame_pass_engine.py

@@ -114,7 +114,7 @@ def frames(self, frames):
 
 class SupervisedSegmentedFramePassEngine(SegmentedFramePassEngine):
     """
-    The supervised version of the :plugin:`~diplomat.predictors.SegmentedFramePassEngine` predictor.
+    The supervised (aka interactive) version of the :plugin:`~diplomat.predictors.SegmentedFramePassEngine` predictor.
     Provides a GUI for modifying results at the end of the tracking process.
     """
 

diplomat/utils/tweak_ui.py

@@ -1,5 +1,5 @@
 """
-Contains utilities for loading user tracks into a lighter version of the supervised UI to allow for minor modifications
+Contains utilities for loading user tracks into a lighter version of the interactive UI to allow for minor modifications
 to user saved tracking data.
 """
 
@@ -246,7 +246,7 @@ def tweak(
         make_app: bool = True
     ):
         """
-        Load a lighter version of the supervised UI to allow for minor modifications to user saved tracking data.
+        Load a lighter version of the interactive UI to allow for minor modifications to user saved tracking data.
 
         :param parent: The parent wx widget of the UI. Can be None, indicating no parent widget, or an independent window.
         :param video_path: The path to the video to display in the editor.

diplomat/wx_gui/__init__.py

@@ -3,5 +3,5 @@
 controls for video playback, pose editing, plotting, etc. Used by the
 :plugin:`~diplomat.predictors.SupervisedSegmentedFramePassEngine` predictor,
 :plugin:`~diplomat.predictors.SupervisedFramePassEngine` predictor,
-:cli:`diplomat tweak` command, :cli:`diplomat supervised` command, and :cli:`diplomat restore` command.
+:cli:`diplomat tweak` command, :cli:`diplomat track_and_interact` command, and :cli:`diplomat interact` command.
 """

diplomat/wx_gui/fpe_editor.py

@@ -1,5 +1,5 @@
 """
-Includes DIPLOMAT's main GUI editor window. Displayed when a supervised run is performed or restored.
+Includes DIPLOMAT's main GUI editor window. Displayed when an interactive run is performed or restored.
 The GUI allows for editing and rerunning tracking on the fly by the user.
 """