Update the segmentation settings (#84)

* Update SGN model

* Update segmentation setting logic

Author: constantinpape

flamingo_tools/model_utils.py

@@ -117,6 +117,51 @@ def get_model(model_type: str, device: Optional[Union[str, torch.device]] = None
     return model
 
 
+def get_default_segmentation_settings(model_type: str) -> Dict[str, Union[str, float]]:
+    """Get the default settings for instance segmentation post-processing for a given model.
+
+    Args:
+        model_type: The model. One of 'SGN', 'SGN-lowres', 'IHC', 'IHC-lowres'.
+
+    Returns:
+        Dictionary with the default segmentation settings.
+    """
+    all_default_kwargs = {
+        "SGN": {
+            "center_distance_threshold": 0.4,
+            "boundary_distance_threshold": 0.5,
+            "fg_threshold": 0.5,
+            "distance_smoothing": 0.0,
+            "seg_class": "sgn",
+        },
+        "SGN-lowres": {
+            "center_distance_threshold": None,
+            "boundary_distance_threshold": 0.5,
+            "fg_threshold": 0.5,
+            "distance_smoothing": 0.0,
+            "seg_class": "sgn_low",
+        },
+        "IHC": {
+            "center_distance_threshold": 0.5,
+            "boundary_distance_threshold": 0.6,
+            "fg_threshold": 0.5,
+            "distance_smoothing": 0.6,
+            "seg_class": "ihc",
+        },
+        "IHC-lowres": {
+            "center_distance_threshold": 0.5,
+            "boundary_distance_threshold": 0.6,
+            "fg_threshold": 0.5,
+            "distance_smoothing": 0.6,
+            "seg_class": "ihc",
+        },
+    }
+    if model_type not in all_default_kwargs:
+        raise ValueError(f"Invalid model: {model_type}. Choose one of {list(all_default_kwargs.keys())}.")
+    default_kwargs = all_default_kwargs[model_type]
+    return default_kwargs
+
+
 def get_default_tiling() -> Dict[str, Dict[str, int]]:
     """Determine the tile shape and halo depending on the available VRAM.
 

flamingo_tools/plugin/segmentation_widget.py

@@ -9,25 +9,27 @@
 
 from .base_widget import BaseWidget
 from .util import _load_custom_model, _available_devices, _get_current_tiling
-from ..model_utils import get_model, get_model_registry, get_device, get_default_tiling
+from ..model_utils import (
+    get_model, get_model_registry, get_device, get_default_tiling, get_default_segmentation_settings
+)
 
 
-# TODO Expose segmentation kwargs.
-def _run_segmentation(image, model, model_type, tiling, device):
+def _run_segmentation(image, model, model_type, tiling, device, min_size):
     block_shape = [tiling["tile"][ax] for ax in "zyx"]
     halo = [tiling["halo"][ax] for ax in "zyx"]
     prediction = predict_with_halo(
         image, model, gpu_ids=[device], block_shape=block_shape, halo=halo,
         tqdm_desc="Run prediction"
     )
+    settings = get_default_segmentation_settings(model_type)
+    foreground_threshold = settings.pop("fg_threshold", 0.5)
+    settings.pop("seg_class", None)
+    settings = {name: 1.0 if val is None else val for name, val in settings.items()}
     foreground_map, center_distances, boundary_distances = prediction
     segmentation = watershed_from_center_and_boundary_distances(
         center_distances, boundary_distances, foreground_map,
-        center_distance_threshold=0.5,
-        boundary_distance_threshold=0.5,
-        foreground_threshold=0.5,
-        distance_smoothing=1.6,
-        min_size=100,
+        min_size=min_size, foreground_threshold=foreground_threshold,
+        **settings,
     )
     return segmentation
 
@@ -110,7 +112,9 @@ def on_predict(self):
 
         # Get the current tiling.
         self.tiling = _get_current_tiling(self.tiling, self.default_tiling, model_type)
-        segmentation = _run_segmentation(image, model=model, model_type=model_type, tiling=self.tiling, device=device)
+        segmentation = _run_segmentation(
+            image, model=model, model_type=model_type, tiling=self.tiling, device=device, min_size=self.min_size
+        )
 
         self.viewer.add_labels(segmentation, name=model_type)
         show_info(f"INFO: Segmentation of {model_type} added to layers.")
@@ -120,6 +124,11 @@ def _create_settings_widget(self):
         # setting_values.setToolTip(get_tooltip("embedding", "settings"))
         setting_values.setLayout(QVBoxLayout())
 
+        # Create UI for the min-size parameter.
+        self.min_size = 100
+        self.min_size_menu, layout = self._add_int_param("min_size", self.min_size, 0, 10000)
+        setting_values.layout().addLayout(layout)
+
         # Create UI for the device.
         device = "auto"
         device_options = ["auto"] + _available_devices()

flamingo_tools/segmentation/cli.py

@@ -4,7 +4,7 @@
 
 from .unet_prediction import run_unet_prediction
 from .synapse_detection import marker_detection
-from ..model_utils import get_model_path
+from ..model_utils import get_model_path, get_default_segmentation_settings
 
 
 def _get_model_path(model_type, checkpoint_path=None):
@@ -49,32 +49,7 @@ def _convert_argval(value):
 
 
 def _parse_segmentation_kwargs(extra_kwargs, model_type):
-    if model_type == "SGN":
-        default_kwargs = {
-            "center_distance_threshold": 0.4,
-            "boundary_distance_threshold": 0.5,
-            "fg_threshold": 0.5,
-            "distance_smoothing": 0.0,
-            "seg_class": "sgn",
-        }
-    elif model_type == "SGN-lowres":
-        default_kwargs = {
-            "center_distance_threshold": None,
-            "boundary_distance_threshold": 0.5,
-            "fg_threshold": 0.5,
-            "distance_smoothing": 0.0,
-            "seg_class": "sgn_low",
-        }
-    else:
-        assert model_type.startswith("IHC")
-        default_kwargs = {
-            "center_distance_threshold": 0.5,
-            "boundary_distance_threshold": 0.6,
-            "fg_threshold": 0.5,
-            "distance_smoothing": 0.6,
-            "seg_class": "ihc",
-        }
-
+    default_kwargs = get_default_segmentation_settings(model_type)
     kwargs = _parse_kwargs(extra_kwargs, **default_kwargs)
     return kwargs