Cell size est

src/cala/nodes/detect/slice_nmf.py

@@ -14,7 +14,6 @@
 
 
 class SliceNMF(Node):
-    cell_radius: int
     nmf_kwargs: dict[str, Any] = Field(default_factory=dict)
 
     errors_: list[float] = Field(default_factory=list)
@@ -28,7 +27,7 @@ def model_post_init(self, context: Any, /) -> None:
         self._model = NMF(**self.nmf_kwargs)
 
     def process(
-        self, residuals: Residual, energy: xr.DataArray
+        self, residuals: Residual, energy: xr.DataArray, detect_radius: int
     ) -> tuple[A[list[Footprint], Name("new_fps")], A[list[Trace], Name("new_trs")]]:
         residuals = residuals.array.copy()
 
@@ -38,7 +37,9 @@ def process(
         if energy.size > 1:
             while np.sqrt(energy.max()).item() > self.nmf_kwargs["tol"]:
                 # Find and analyze neighborhood of maximum variance
-                slice_ = self._get_max_energy_slice(arr=residuals, energy_landscape=energy)
+                slice_ = self._get_max_energy_slice(
+                    arr=residuals, energy_landscape=energy, radius=detect_radius
+                )
 
                 a_new, c_new = self._local_nmf(
                     slice_=slice_,
@@ -66,13 +67,13 @@ def _get_max_energy_slice(
         self,
         arr: xr.DataArray,
         energy_landscape: xr.DataArray,
+        radius: int,
     ) -> xr.DataArray:
         """Find neighborhood around point of maximum variance."""
         # Find maximum point
         max_coords = energy_landscape.argmax(dim=AXIS.spatial_dims)
 
         # Define neighborhood
-        radius = int(np.round(self.cell_radius))
         window = {
             ax: slice(
                 max(0, pos.values - radius),

src/cala/nodes/prep/__init__.py

@@ -1,6 +1,7 @@
 from .background_removal import remove_background
 from .denoise import denoise
 from .glow_removal import GlowRemover
+from .r_estimate import SizeEst
 from .rigid_stabilization import RigidStabilizer
 
-__all__ = [denoise, GlowRemover, remove_background, RigidStabilizer]
+__all__ = [denoise, GlowRemover, remove_background, RigidStabilizer, SizeEst]

src/cala/nodes/prep/r_estimate.py

@@ -0,0 +1,39 @@
+from typing import Annotated as A
+from typing import Any
+
+import numpy as np
+from noob import Name, process_method
+from pydantic import BaseModel, ConfigDict, Field, PrivateAttr
+from skimage.feature import blob_log
+
+from cala.assets import Frame
+from cala.models import AXIS
+
+
+class SizeEst(BaseModel):
+    hardset_radius: int | None = None
+    """if this is set, no learning occurs."""
+    n_frames: int | None = None
+    """how many first n frames to learn from. if none, keep learning forever"""
+    log_kwargs: dict[str, Any] = Field(default_factory=dict)
+
+    sizes_: list[float] = Field(default_factory=list)
+    centers_: list[np.ndarray] = Field(default_factory=list)
+    _est_radius: int = PrivateAttr(None)
+
+    model_config = ConfigDict(arbitrary_types_allowed=True)
+
+    @process_method
+    def get_median_radius(self, frame: Frame) -> A[int, Name("radius")]:
+        if self.hardset_radius:
+            return self.hardset_radius
+
+        if self.n_frames and self.n_frames < frame.array[AXIS.frame_coord]:
+            return self._est_radius
+
+        blobs = blob_log(frame.array, **self.log_kwargs)
+        self.centers_ = [blobs[:-1] for blobs in blobs]
+        self.sizes_ += [blob[-1].item() for blob in blobs]
+        self._est_radius = int(np.round(np.median(self.sizes_)).item())
+
+        return self._est_radius

src/cala/testing/nodes.py

@@ -38,7 +38,7 @@ def two_cells_source(
     positions: list[dict] = None,
 ) -> Generator[A[Frame, Name("frame")]]:
     frame_dims = FrameDims(width=512, height=512) if frame_dims is None else FrameDims(**frame_dims)
-    traces = [np.array(range(0, n_frames)), np.array([0, *range(30 - 1, 0, -1)])]
+    traces = [np.array(range(0, n_frames)), np.array([0, *range(n_frames - 1, 0, -1)])]
     if positions is None:
         positions = [Position(width=206, height=206), Position(width=306, height=306)]
     else:

tests/data/pipelines/two_overlap_cells.yaml → tests/data/pipelines/odl.yaml

@@ -1,4 +1,4 @@
-noob_id: cala-two-overlap-cells
+noob_id: cala-odl
 noob_model: noob.cube.CubeSpecification
 noob_version: 0.1.1.dev118+g64d81b7
 
@@ -30,9 +30,9 @@ assets:
 
 nodes:
   source:
-    type: cala.testing.two_overlapping_source
+    type: cala.testing.single_cell_source
     params:
-      n_frames: 50
+      n_frames: 30
   denoise:
     type: cala.nodes.prep.denoise
     params:
@@ -52,6 +52,12 @@ nodes:
       drift_speed: 1.0
     depends:
       - frame: glow.frame
+  size_est:
+    type: cala.nodes.prep.SizeEst
+    params:
+      hardset_radius: 10
+    depends:
+      - frame: motion.frame
   cache:
     type: cala.nodes.buffer.fill_buffer
     params:
@@ -121,11 +127,10 @@ nodes:
       - trigger: trace_frame.latest_trace
   nmf:
     type: cala.nodes.detect.SliceNMF
-    params:
-      cell_radius: 10
     depends:
       - residuals: residual.movie
       - energy: energy.energy
+      - detect_radius: size_est.radius
   catalog:
     type: cala.nodes.detect.Cataloger
     params: