Merge pull request #143 from samuelgarcia/some_fix

More explicite root_folder in launcher

Author: samuelgarcia

spikeinterface_gui/launcher.py

@@ -15,36 +15,32 @@ class Launcher:
     analyzers_folder : str, list or None
         Path to the folder containing analyzer folders or a list/dict of analyzer paths.
         If None, the user will be prompted to select an analyzer folder.
+    root_folder: str|Path| None
+        A folder that is explore to construct the list of analyzers.
+        When not None analyzer_folders must be None.
     backend : str
         The backend to use for the GUI. Options are "qt" or "panel".
     verbose : bool
         If True, enables verbose logging in the GUI.
     """
 
-    def __init__(self, analyzer_folders=None, backend="qt", verbose=False):
+    def __init__(self, analyzer_folders=None, root_folder=None, backend="qt", verbose=False):
         from spikeinterface_gui.main import check_folder_is_analyzer
 
-        if analyzer_folders is not None:
-            if isinstance(analyzer_folders, (str, Path)):
-                # self.analyzer_folders = [
-                #     p for p in Path(analyzer_folders).iterdir() if p.is_dir() and check_folder_is_analyzer(p)
-                # ]
-                # @alessio I prefer this which explore also sub folders
-                self.analyzer_folders = [
-                    f.parent for f in Path(analyzer_folders).glob('**/spikeinterface_info.json') if f.parent.is_dir() and check_folder_is_analyzer(f.parent)
-                ]
-            elif isinstance(analyzer_folders, (list, tuple)):
-                self.analyzer_folders = [
-                    p for p in analyzer_folders if isinstance(p, (str, Path)) and check_folder_is_analyzer(p)
-                ]
+        self.analyzer_folders = None
+        if root_folder is not None:
+            assert analyzer_folders is None, "When using root_folder, analyzer_folders must be None"
+            root_folder = Path(root_folder)
+            self.analyzer_folders = [
+                f.parent for f in root_folder.glob('**/spikeinterface_info.json') if check_folder_is_analyzer(f.parent)
+            ] + [
+                f.parent for f in root_folder.glob('**/.zmetadata') if check_folder_is_analyzer(f.parent)
+            ]
+        elif analyzer_folders is not None:
+            if isinstance(analyzer_folders, (list, tuple)):
+                self.analyzer_folders = [ p for p in analyzer_folders if check_folder_is_analyzer(p) ]
             elif isinstance(analyzer_folders, dict):
-                self.analyzer_folders = {
-                    k: p for k, p in analyzer_folders.items() if isinstance(p, (str, Path)) and check_folder_is_analyzer(p)
-                }
-            else:
-                self.analyzer_folders = None
-        else:
-            self.analyzer_folders = None
+                self.analyzer_folders = { k: p for k, p in analyzer_folders.items() if check_folder_is_analyzer(p)}
 
 
         self.verbose = verbose
@@ -231,8 +227,12 @@ def _qt_on_launch_clicked(self):
             analyzer_path = self.analyzer_path_input.text()
         else:
             ind = self.analyzer_path_input.currentIndex()
-            k = list(self.analyzer_folders.keys())[ind]
-            analyzer_path = str(self.analyzer_folders[k])
+            if isinstance(self.analyzer_folders, dict):
+                k = list(self.analyzer_folders.keys())[ind]
+                analyzer_path = str(self.analyzer_folders[k])
+            else:
+                analyzer_path = self.analyzer_folders[ind]
+
 
         if self.select_recording_checkbox.isChecked():
             recording_path = self.recording_path_input.text()

spikeinterface_gui/main.py

@@ -138,16 +138,20 @@ def run_mainwindow(
     return win
 
 
-def run_launcher(mode="desktop", analyzer_folders=None, address="localhost", port=0, verbose=False):
+
+def run_launcher(mode="desktop", analyzer_folders=None, root_folder=None, address="localhost", port=0, verbose=False):
     """
     Run the launcher for the SpikeInterface GUI.
 
     Parameters
     ----------
     mode: 'desktop' | 'app', default: 'desktop'
         The backend to use for the GUI.
-    analyzer_folders: list of str | None, default: None
-        List of analyzer folders to load. If str, it is a single folder and subfolders are searched.
+    analyzer_folders: list of str | dict | None, default: None
+        List of analyzer folders to load.
+    root_folder: str|Path| None
+        A folder that is explore to construct the list of analyzers.
+        When not None analyzer_folders must be None.
     address: str, default: "localhost"
         The address to use for the web mode. Default is "localhost".
         Use "auto-ip" to use the real IP address of the machine.
@@ -161,7 +165,7 @@ def run_launcher(mode="desktop", analyzer_folders=None, address="localhost", por
     if mode == "desktop":
         from .myqt import QT, mkQApp
         app = mkQApp()
-        launcher = Launcher(analyzer_folders=analyzer_folders, backend="qt", verbose=verbose)
+        launcher = Launcher(analyzer_folders=analyzer_folders, root_folder=root_folder, backend="qt", verbose=verbose)
         app.exec()
 
     elif mode == "web":
@@ -171,7 +175,7 @@ def run_launcher(mode="desktop", analyzer_folders=None, address="localhost", por
         from spikeinterface_gui.launcher import panel_gui_view
         from spikeinterface_gui.backend_panel import start_server
 
-        launcher = Launcher(analyzer_folders=analyzer_folders, backend="panel", verbose=verbose)
+        launcher = Launcher(analyzer_folders=analyzer_folders, root_folder=root_folder, backend="panel", verbose=verbose)
 
         server, address, port, _ = start_server(
             {"/launcher": launcher.layout, "/gui": panel_gui_view},
@@ -202,7 +206,13 @@ def check_folder_is_analyzer(folder):
     bool
         True if the folder is a valid SortingAnalyzer folder, False otherwise.
     """
+    if not isinstance(folder, (str, Path)):
+        return False
+
     folder = Path(folder)
+    if not folder.is_dir():
+        return False
+
     if not str(folder).endswith(".zarr"):
         spikeinterface_info_file = folder / 'spikeinterface_info.json'
         if not spikeinterface_info_file.exists():
@@ -217,10 +227,8 @@ def check_folder_is_analyzer(folder):
     else:  #zarr folder
         import zarr
         # Check if the folder contains the necessary files for a SortingAnalyzer
-        if not folder.exists():
-            return False
         zarr_root = zarr.open(folder, mode='r')
-        spikeinterface_info = zarr_root.get('spikeinterface_info')
+        spikeinterface_info = zarr_root.attrs.get('spikeinterface_info')
         if spikeinterface_info is None:
             return False
         if spikeinterface_info.get("object") != "SortingAnalyzer":
@@ -234,7 +242,7 @@ def run_mainwindow_cli():
 
     parser = argparse.ArgumentParser(description='spikeinterface-gui')
     parser.add_argument('analyzer_folder', help='SortingAnalyzer folder path', default=None, nargs='?')
-    parser.add_argument('--analyzer-folders', help='Base folder for launcher mode with multiple analyzer folders', default=None)
+    parser.add_argument('--root-folder', help='Base folder for launcher mode with multiple analyzer folders', default=None)
     parser.add_argument('--mode', help='Mode desktop or web', default='desktop')
     parser.add_argument('--no-traces', help='Do not show traces', action='store_true', default=False)
     parser.add_argument('--curation', help='Enable curation panel', action='store_true', default=False)
@@ -248,9 +256,9 @@ def run_mainwindow_cli():
 
     analyzer_folder = args.analyzer_folder
     if analyzer_folder is None:
-        print('Running launcher...')
-        analyzer_folders = args.analyzer_folders
-        run_launcher(analyzer_folders=analyzer_folders, mode=args.mode, address=args.address, port=args.port, verbose=args.verbose)
+        if args.verbose:
+            print('Running launcher...')
+        run_launcher(root_folder=args.root_folder, mode=args.mode, address=args.address, port=args.port, verbose=args.verbose)
     else:
         if args.verbose:
             print('Loading analyzer...')

spikeinterface_gui/tests/test_mainwindow_qt.py

@@ -83,21 +83,28 @@ def test_mainwindow(start_app=False, verbose=True, curation=False, only_some_ext
 def test_launcher(verbose=True):
 
     # case 1
-    # analyzer_folders = None
+    analyzer_folders = None
+    root_folder = None
+    
     # case 2 : explore parent
-    analyzer_folders = Path(__file__).parent 
+    analyzer_folders = None
+    root_folder = Path(__file__).parent 
+    
     # case 3 : list
-    analyzer_folders = [
-        Path(__file__).parent / 'my_dataset_small/sorting_analyzer',
-        Path(__file__).parent / 'my_dataset_big/sorting_analyzer',
-    ]
+    # analyzer_folders = [
+    #     Path(__file__).parent / 'my_dataset_small/sorting_analyzer',
+    #     Path(__file__).parent / 'my_dataset_big/sorting_analyzer',
+    # ]
+    # root_folder = None
+
     # case 4 : dict
-    analyzer_folders = {
-        'small' : Path(__file__).parent / 'my_dataset_small/sorting_analyzer',
-        'big' : Path(__file__).parent / 'my_dataset_big/sorting_analyzer',
-    }
+    # analyzer_folders = {
+    #     'small' : Path(__file__).parent / 'my_dataset_small/sorting_analyzer',
+    #     'big' : Path(__file__).parent / 'my_dataset_big/sorting_analyzer',
+    # }
+    # root_folder = None
 
-    win = run_launcher(mode="desktop", analyzer_folders=analyzer_folders, verbose=verbose)
+    win = run_launcher(mode="desktop", analyzer_folders=analyzer_folders, root_folder=root_folder,  verbose=verbose)
 
 
 if __name__ == '__main__':