Finetuning refactor

.gitignore

@@ -162,4 +162,13 @@ cython_debug/
 #.idea/
 
 # Misc
-.vscode/
+.vscode/
+
+# Project-specific
+ignore/
+*.zarr/
+.claude/
+test_corrections.zarr/
+correction_slices/
+corrections/
+output/

cellmap_flow/cli/server_cli.py

@@ -23,7 +23,6 @@
 from cellmap_flow.utils.plugin_manager import load_plugins
 
 
-logging.basicConfig()
 logger = logging.getLogger(__name__)
 
 
@@ -47,7 +46,7 @@ def cli(log_level):
         cellmap_flow_server script -s /path/to/script.py -d /path/to/data
         cellmap_flow_server cellmap-model -f /path/to/model -n mymodel -d /path/to/data
     """
-    logging.basicConfig(level=getattr(logging, log_level.upper()))
+    logging.basicConfig(level=getattr(logging, log_level.upper()), force=True)
 
 
 @cli.command(name="list-models")
@@ -82,6 +81,9 @@ def create_dynamic_server_command(cli_name: str, config_class: Type[ModelConfig]
     except:
         type_hints = {}
 
+    # Track used short names to avoid collisions with common options.
+    used_short_names = {"-d", "-p"}
+
     # Create the command function
     def command_func(**kwargs):
         # Separate model config kwargs from server kwargs
@@ -141,7 +143,9 @@ def command_func(**kwargs):
 
     # Add model-specific options based on constructor parameters
     for param_name, param_info in reversed(list(sig.parameters.items())):
-        option_config = create_click_option_from_param(param_name, param_info)
+        option_config = create_click_option_from_param(
+            param_name, param_info, used_short_names
+        )
         if option_config:
             command_func = click.option(
                 *option_config.pop("param_decls"), **option_config

cellmap_flow/cli/viewer_cli.py

@@ -0,0 +1,77 @@
+"""
+Simple CLI for viewing datasets with CellMap Flow without requiring model configs.
+"""
+
+import click
+import logging
+import neuroglancer
+from cellmap_flow.dashboard.app import create_and_run_app
+from cellmap_flow.globals import g
+from cellmap_flow.utils.scale_pyramid import get_raw_layer
+
+logging.basicConfig()
+logger = logging.getLogger(__name__)
+
+
+@click.command()
+@click.option(
+    "-d",
+    "--dataset",
+    required=True,
+    type=str,
+    help="Path to the dataset (zarr or n5)",
+)
+@click.option(
+    "--log-level",
+    type=click.Choice(
+        ["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"], case_sensitive=False
+    ),
+    default="INFO",
+    help="Set the logging level",
+)
+def main(dataset, log_level):
+    """
+    Start CellMap Flow viewer with a dataset.
+
+    Example:
+        cellmap_flow_viewer -d /path/to/dataset.zarr
+    """
+    logging.basicConfig(level=getattr(logging, log_level.upper()))
+
+    logger.info(f"Starting CellMap Flow viewer with dataset: {dataset}")
+
+    # Set up neuroglancer server
+    neuroglancer.set_server_bind_address("0.0.0.0")
+
+    # Create viewer
+    viewer = neuroglancer.Viewer()
+
+    # Set dataset path in globals
+    g.dataset_path = dataset
+    g.viewer = viewer
+
+    # Add dataset layer to viewer
+    with viewer.txn() as s:
+        # Set coordinate space
+        s.dimensions = neuroglancer.CoordinateSpace(
+            names=["z", "y", "x"],
+            units="nm",
+            scales=[8, 8, 8],
+        )
+
+        # Add data layer
+        s.layers["data"] = get_raw_layer(dataset)
+
+    # Print viewer URL
+    logger.info(f"Neuroglancer viewer URL: {viewer}")
+    print(f"\n{'='*80}")
+    print(f"Neuroglancer viewer: {viewer}")
+    print(f"Dataset: {dataset}")
+    print(f"{'='*80}\n")
+
+    # Start the dashboard app
+    create_and_run_app(neuroglancer_url=str(viewer), inference_servers=None)
+
+
+if __name__ == "__main__":
+    main()

cellmap_flow/dashboard/app.py

@@ -5,15 +5,15 @@
 from flask import Flask
 from flask_cors import CORS
 
-from cellmap_flow.dashboard import state
-from cellmap_flow.dashboard.state import LogHandler
+from cellmap_flow.globals import g, LogHandler
 from cellmap_flow.dashboard.routes.logging_routes import logging_bp
 from cellmap_flow.dashboard.routes.index_page import index_bp
 from cellmap_flow.dashboard.routes.pipeline_builder_page import pipeline_builder_bp
 from cellmap_flow.dashboard.routes.models import models_bp
 from cellmap_flow.dashboard.routes.pipeline import pipeline_bp
 from cellmap_flow.dashboard.routes.blockwise import blockwise_bp
 from cellmap_flow.dashboard.routes.bbx_generator import bbx_bp
+from cellmap_flow.dashboard.routes.finetune_routes import finetune_bp
 
 logger = logging.getLogger(__name__)
 
@@ -37,11 +37,12 @@
 app.register_blueprint(pipeline_bp)
 app.register_blueprint(blockwise_bp)
 app.register_blueprint(bbx_bp)
+app.register_blueprint(finetune_bp)
 
 
 def create_and_run_app(neuroglancer_url=None, inference_servers=None):
-    state.NEUROGLANCER_URL = neuroglancer_url
-    state.INFERENCE_SERVER = inference_servers
+    g.NEUROGLANCER_URL = neuroglancer_url
+    g.INFERENCE_SERVER = inference_servers
     hostname = socket.gethostname()
     port = 0
     logger.warning(f"Host name: {hostname}")