WIP - Large db

scripts/demo_neuromast.py

@@ -13,17 +13,30 @@
 
 # **********INPUTS*********
 # path to the working directory that contains the database file AND metadata.toml:
+
 working_directory = Path(
     "/home/teun.huijben/Documents/data/Akila/20241003/neuromast4_t851/adjusted/"
 )
+
+# working_directory = Path(
+#     "/mnt/md0/Teun/data/Chromatrace/2024_08_14/adjusted/"
+# )
+
 # name of the database file to start from, or "latest" to start from the latest version, defaults to "data.db"
-db_filename_start = "latest"
+db_filename_start = "data_updated.db"
 # maximum number of frames display, defaults to None (use all frames)
 tmax = 600
 # (Z),Y,X, defaults to (1, 1, 1)
-scale = (2.31, 1, 1)
+scale = (4, 1, 1)
 # overwrite existing database/changelog, defaults to False (not used when db_filename_start is "latest")
 allow_overwrite = False
+# NEW:
+work_in_existing_db = True
+flag_show_hierarchy = True
+# focus_id = 7000031
+focus_id = 3000020
+# focus_id = None
+margin = 150
 
 # OPTIONAL: imaging data
 # imaging_zarr_file = (
@@ -44,6 +57,10 @@
         tmax=tmax,
         scale=scale,
         allow_overwrite=allow_overwrite,
+        work_in_existing_db=work_in_existing_db,
         imaging_zarr_file=imaging_zarr_file,
         imaging_channel=imaging_channel,
+        flag_show_hierarchy=flag_show_hierarchy,
+        focus_id=focus_id,
+        margin=margin,
     )

scripts/test_large_db.py

@@ -0,0 +1,85 @@
+from pathlib import Path
+
+import napari
+from ultrack.config import MainConfig
+
+from trackedit.widgets.HierarchyWidget import HierarchyVizWidget
+
+# def check_database(db_path: Path):
+#     """Check if database exists and print its structure"""
+#     if not db_path.exists():
+#         print(f"Database file does not exist at: {db_path}")
+#         return False
+
+#     print(f"Database file found at: {db_path}")
+#     print(f"File size: {db_path.stat().st_size / (1024*1024):.2f} MB")
+
+#     # Try to connect and list tables
+#     engine = sqla.create_engine(f"sqlite:///{db_path}")
+#     inspector = inspect(engine)
+#     tables = inspector.get_table_names()
+#     print(f"Tables in database: {tables}")
+
+#     # Print column information for each table
+#     for table_name in tables:
+#         columns = inspector.get_columns(table_name)
+#         print(f"\nColumns in {table_name} table:")
+#         for column in columns:
+#             print(f"  - {column['name']}: {column['type']}")
+
+#     # Get a sample row from each table
+#     with engine.connect() as conn:
+#         for table_name in tables:
+#             result = conn.execute(
+#                 text(f"SELECT * FROM {table_name} LIMIT 1")
+#             ).fetchone()
+#             if result:
+#                 print(f"\nSample row from {table_name}:")
+#                 print(result)
+
+#     return True
+
+
+def initialize_config():
+    working_directory = Path("/mnt/md0/Teun/data/Chromatrace/2024_08_14/")
+    db_filename = "data.db"
+    # db_path = working_directory / db_filename
+
+    # if not check_database(db_path):
+    #     raise FileNotFoundError(f"Database not found or invalid at {db_path}")
+
+    # import db filename properly into an Ultrack config
+    config_adjusted = MainConfig()
+    config_adjusted.data_config.working_dir = working_directory
+    config_adjusted.data_config.database_file_name = db_filename
+    return config_adjusted
+
+
+# def main():
+#     config = initialize_config()
+#     ultrack_array = HierarchyArray(config)
+
+#     labels_layer = HierarchyLabels(
+#         data=ultrack_array, scale=(4,1,1), name="hierarchy"
+#     )
+#     viewer = napari.Viewer()
+#     viewer.add_layer(labels_layer)
+#     labels_layer.refresh()
+#     labels_layer.mode = "pan_zoom"
+#     napari.run()
+
+
+def main2():
+    config = initialize_config()
+    viewer = napari.Viewer()
+    hier_widget = HierarchyVizWidget(
+        viewer=viewer,
+        scale=(4, 1, 1),
+        config=config,
+    )
+    viewer.window.add_dock_widget(hier_widget, area="bottom")
+    napari.run()
+
+
+if __name__ == "__main__":
+    main2()