Merge pull request #187 from chrishalcrow/add-user-settings

Add `user_setting` functionality

Author: samuelgarcia

README.md

@@ -222,7 +222,7 @@ sigui --mode=web --root-folder path-to-my-analyzers
 ![launcher_web](docs/source/images/launcher_web.png)
 
 
-## Customizing the layout
+## Customizing layout and settings
 
 You can create your own custom layout by specifying which views you'd like
 to see, and where they go. The basic window layout supports eight "zones",
@@ -248,7 +248,7 @@ E.g. suppose your layout is only non-empty in zones 1, 4, 5, 6 and 7:
 +---------------+--------------+
 ```
 
-Then zone1 will stretch right-wards to make a three-zone view. Zone4 will stretch
+Then zone1 will stretch right-wards to make a two-zone view. Zone4 will stretch
 downwards to make a long two-zone view.
 
 To specify your own layout, put the specification in a `.json` file. This should
@@ -278,6 +278,41 @@ sigui --layout_file=path/to/my_layout.json path/to/sorting_analyzer
 
 Find a list of available views [in this file](https://github.com/SpikeInterface/spikeinterface-gui/blob/main/spikeinterface_gui/viewlist.py).
 
+You can also edit the initial settings for each view. There are two ways to do this.
+First, you can open the gui, edit the settings of any or all views, then press the 
+"Save as default settings" button in the `mainsettings` view. This will save a 
+`settings.json` file in your spikeinterface-gui config (saved in `~/.config/spikeinterface_gui/`).
+The saved settings will automatically load next time you start the gui.
+
+If you want more direct control, you can pass your own setting json file
+to the `settings-file` flag (or by passing a `user_settings` dict to `run_mainwindow`). 
+The settings file should contain a settings dict for each view. The view names are the
+same as used in the layout file, and each setting name can be seen in the settings
+tab of each view. Below is an example settings file:
+
+**my_settings.json**
+
+``` json
+{
+    "probe": {
+        "show_channel_id": true
+    },
+    "waveform": {
+        "overlap": false, 
+        "plot_std": false
+    },
+    "spikeamplitude": {
+        "max_spikes_per_unit": 1000, 
+        "alpha": 0.2
+    }
+}
+```
+
+You can then use this file by running e.g.
+
+```bash
+sigui --settings_file=path/to/my_settings.json path/to/sorting_analyzer
+```
 
 ## Deploy the GUI in web mode
 

docs/source/custom_layout.rst renamed to docs/source/custom_layout_settings.rst

@@ -1,5 +1,5 @@
-Customizing the layout
-======================
+Customizing layout and settings
+===============================
 
 You can create your own custom layout by specifying which views you'd like
 to see, and where they go. The basic window layout supports eight "zones",
@@ -26,7 +26,7 @@ E.g. suppose your layout is only non-empty in zones 1, 4, 5, 6 and 7:
     +---------------+--------------+
 
 
-Then zone1 will stretch right-wards to make a three-zone view. Zone4 will stretch
+Then zone1 will stretch right-wards to make a two-zone view. Zone4 will stretch
 downwards to make a long two-zone view.
 
 To specify your own layout, put the specification in a ``.json`` file. This should
@@ -55,3 +55,40 @@ using the ``--layout_file`` flag:
    sigui --layout_file=path/to/my_layout.json path/to/sorting_analyzer
 
 Find a list of available views `in this file <https://github.com/SpikeInterface/spikeinterface-gui/blob/main/spikeinterface_gui/viewlist.py>`_.
+
+You can also edit the initial settings for each view. There are two ways to do this.
+First, you can open the gui, edit the settings of any or all views, then press the 
+"Save as default settings" button in the ``mainsettings`` view. This will save a 
+``settings.json`` file in your spikeinterface-gui config (saved in ``~/.config/spikeinterface_gui/``).
+The saved settings will automatically load next time you start the gui.
+
+If you want more direct control, you can pass your own setting json file
+to the ``settings-file`` flag (or by passing a ``user_settings`` dict to ``run_mainwindow``). 
+The settings file should contain a settings dict for each view. The view names are the
+same as used in the layout file, and each setting name can be seen in the settings
+tab of each view. Below is an example settings file:
+
+**my_settings.json**
+
+.. code-block:: json
+
+    {
+        "probe": {
+            "show_channel_id": true
+        },
+        "waveform": {
+            "overlap": false, 
+            "plot_std": false
+        },
+        "spikeamplitude": {
+            "max_spikes_per_unit": 1000, 
+            "alpha": 0.2
+        }
+    }
+
+
+You can then use this file by running e.g.
+
+.. code-block:: bash
+
+    sigui --settings_file=path/to/my_settings.json path/to/sorting_analyzer

docs/source/index.rst

@@ -50,7 +50,7 @@ This is a web app internally using Panel, useful when the data is remote
    installation
    launch
    usage
-   custom_layout
+   custom_layout_settings
    deployments
    views
    developers

spikeinterface_gui/backend_panel.py

@@ -185,13 +185,13 @@ def listen_setting_changes(view):
 
 class PanelMainWindow:
 
-    def __init__(self, controller, layout_preset=None, layout=None):
+    def __init__(self, controller, layout_preset=None, layout=None, user_settings=None):
         self.controller = controller
         self.layout_preset = layout_preset
         self.layout = layout
         self.verbose = controller.verbose
 
-        self.make_views()
+        self.make_views(user_settings)
         self.create_main_layout()
 
         # refresh all views wihtout notiying
@@ -202,7 +202,7 @@ def __init__(self, controller, layout_preset=None, layout=None):
             if view.is_view_visible():
                 view.refresh()
 
-    def make_views(self):
+    def make_views(self, user_settings):
         self.views = {}
         # this contains view layout + settings + compute
         self.view_layouts = {}
@@ -227,6 +227,13 @@ def make_views(self):
                 sizing_mode="stretch_both"
             )
 
+            if user_settings is not None and user_settings.get(view_name) is not None:
+                for setting_name, user_setting in user_settings.get(view_name).items():
+                    if setting_name not in view.settings.keys():
+                        raise KeyError(f"Setting {setting_name} is not a valid setting for View {view_name}. Check your settings file.")
+                    with param.parameterized.discard_events(view.settings._parameterized):
+                        view.settings[setting_name] = user_setting
+
             tabs = [("📊", view.layout)]
             if view_class._settings is not None:
                 settings = pn.Param(view.settings._parameterized, sizing_mode="stretch_height", 

spikeinterface_gui/backend_qt.py

@@ -134,18 +134,22 @@ def create_settings(view, parent):
 def listen_setting_changes(view):
     view.settings.sigTreeStateChanged.connect(view.on_settings_changed)
 
+def stop_listen_setting_changes(view):
+    view.settings.sigTreeStateChanged.disconnect(view.on_settings_changed)
+
 
 class QtMainWindow(QT.QMainWindow):
     main_window_closed = QT.pyqtSignal(object)
 
-    def __init__(self, controller, parent=None, layout_preset=None, layout=None):
+    def __init__(self, controller, parent=None, layout_preset=None, layout=None, user_settings=None):
         QT.QMainWindow.__init__(self, parent)
 
         self.controller = controller
         self.verbose = controller.verbose
         self.layout_preset = layout_preset
         self.layout = layout
-        self.make_views()
+        
+        self.make_views(user_settings)
         self.create_main_layout()
 
         # refresh all views wihtout notiying
@@ -159,7 +163,7 @@ def __init__(self, controller, parent=None, layout_preset=None, layout=None):
         # for view_name, dock in self.docks.items():
         #     dock.visibilityChanged.connect(self.views[view_name].refresh)
 
-    def make_views(self):
+    def make_views(self, user_settings):
         self.views = {}
         self.docks = {}
         for view_name, view_class in possible_class_views.items():
@@ -176,6 +180,16 @@ def make_views(self):
 
             widget = ViewWidget(view_class)
             view = view_class(controller=self.controller, parent=widget, backend='qt')
+
+            if user_settings is not None and user_settings.get(view_name) is not None:
+                for setting_name, user_setting in user_settings.get(view_name).items():
+                    if setting_name not in view.settings.keys().keys():
+                        raise KeyError(f"Setting {setting_name} is not a valid setting for View {view_name}. Check your settings file.")
+                    stop_listen_setting_changes(view)
+                    view.settings[setting_name] = user_setting
+                    listen_setting_changes(view)
+
+
             widget.set_view(view)
             dock = QT.QDockWidget(view_name)
             dock.setWidget(widget)

spikeinterface_gui/controller.py

@@ -34,11 +34,12 @@ class Controller():
     def __init__(self, analyzer=None, backend="qt", parent=None, verbose=False, save_on_compute=False,
                  curation=False, curation_data=None, label_definitions=None, with_traces=True,
                  displayed_unit_properties=None,
-                 extra_unit_properties=None, skip_extensions=None):
+                 extra_unit_properties=None, skip_extensions=None, disable_save_settings_button=False):
         self.views = []
         skip_extensions = skip_extensions if skip_extensions is not None else []
         self.skip_extensions = skip_extensions
         self.backend = backend
+        self.disable_save_settings_button = disable_save_settings_button
         if self.backend == "qt":
             from .backend_qt import SignalHandler
             self.signal_handler = SignalHandler(self, parent=parent)

spikeinterface_gui/main.py

@@ -7,7 +7,9 @@
 
 from spikeinterface import load_sorting_analyzer, load
 from spikeinterface.core.core_tools import is_path_remote
+from .utils_global import get_config_folder
 
+import spikeinterface_gui
 from spikeinterface_gui.controller import Controller
 
 
@@ -30,6 +32,8 @@ def run_mainwindow(
     panel_start_server_kwargs=None,
     panel_window_servable=True,
     verbose=False,
+    user_settings=None,
+    disable_save_settings_button=False,
 ):
     """
     Create the main window and start the QT app loop.
@@ -82,6 +86,10 @@ def run_mainwindow(
         the `panel_window_servable` should be set to False.
     verbose: bool, default: False
         If True, print some information in the console
+    user_settings: dict, default: None
+        A dictionary of user settings for each view, which overwrite the default settings.
+    disable_save_settings_button: bool, default: False
+        If True, disables the "save default settings" button, so that user cannot do this.
     """
 
     if mode == "desktop":
@@ -91,6 +99,21 @@ def run_mainwindow(
     else:
         raise ValueError(f"spikeinterface-gui wrong mode {mode}")
 
+    # Order of preference for settings is set here:
+    #   1) User specified settings
+    #   2) Settings in the config folder
+    #   3) Default settings of each view 
+    if user_settings is None:
+        sigui_version = spikeinterface_gui.__version__
+        config_version_folder = get_config_folder() / sigui_version
+        settings_file = config_version_folder / "settings.json"
+        if settings_file.is_file():
+            try:
+                with open(settings_file) as f:
+                    user_settings = json.load(f)
+            except json.JSONDecodeError as e:
+                print(f"Config file at {settings_file} is not decodable. Error: {e}")
+                print("Using default settings.")
 
     if recording is not None:
         analyzer.set_temporary_recording(recording)
@@ -106,6 +129,7 @@ def run_mainwindow(
         displayed_unit_properties=displayed_unit_properties,
         extra_unit_properties=extra_unit_properties,
         skip_extensions=skip_extensions,
+        disable_save_settings_button=disable_save_settings_button
     )
     if verbose:
         t1 = time.perf_counter()
@@ -122,7 +146,7 @@ def run_mainwindow(
 
         app = mkQApp()
 
-        win = QtMainWindow(controller, layout_preset=layout_preset, layout=layout)
+        win = QtMainWindow(controller, layout_preset=layout_preset, layout=layout, user_settings=user_settings)
         win.setWindowTitle('SpikeInterface GUI')
         # Set window icon
         icon_file = Path(__file__).absolute().parent / 'img' / 'si.png'
@@ -134,7 +158,7 @@ def run_mainwindow(
 
     elif backend == "panel":
         from .backend_panel import PanelMainWindow, start_server
-        win = PanelMainWindow(controller, layout_preset=layout_preset, layout=layout)
+        win = PanelMainWindow(controller, layout_preset=layout_preset, layout=layout, user_settings=user_settings)
 
         if start_app or panel_window_servable:
             win.main_layout.servable(title='SpikeInterface GUI')
@@ -261,6 +285,8 @@ def run_mainwindow_cli():
     parser.add_argument('--address', help='Address for web mode', default='localhost')
     parser.add_argument('--layout-file', help='Path to json file defining layout', default=None)
     parser.add_argument('--curation-file', help='Path to json file defining a curation', default=None)
+    parser.add_argument('--settings-file', help='Path to json file specifying the settings of each view', default=None)
+    parser.add_argument('--disable_save_settings_button', help='Disables button allowing for user to save default settings', action='store_true', default=False)
 
     args = parser.parse_args(argv)
 
@@ -302,6 +328,14 @@ def run_mainwindow_cli():
         else:
             curation_data = None
 
+        if args.settings_file is not None:
+            with open(args.settings_file, "r") as f:
+                user_settings = json.load(f)
+        else:
+            user_settings = None
+
+        disable_save_settings_button = args.disable_save_settings_button
+
         run_mainwindow(
             analyzer,
             mode=args.mode,
@@ -311,5 +345,7 @@ def run_mainwindow_cli():
             verbose=args.verbose,
             layout=args.layout_file,
             curation_dict=curation_data,
+            user_settings=user_settings,
+            disable_save_settings_button=disable_save_settings_button,
         )