From a213c890501d75164264e50bad1d71ecb9965d93 Mon Sep 17 00:00:00 2001
From: Raymond <raymond.w.jang@gmail.com>
Date: Thu, 14 Aug 2025 13:21:58 -0700
Subject: [PATCH 1/3] feat: learn cell radius in detection

---
 src/cala/nodes/detect/slice_nmf.py |   9 +--
 src/cala/nodes/prep/__init__.py    |   3 +-
 src/cala/nodes/prep/r_estimate.py  |  41 +++++++++++
 tests/test_iter/test_detect.py     | 109 +++++++++++------------------
 tests/test_prep/test_r_estimate.py |  38 ++++++++++
 5 files changed, 128 insertions(+), 72 deletions(-)
 create mode 100644 src/cala/nodes/prep/r_estimate.py
 create mode 100644 tests/test_prep/test_r_estimate.py

diff --git a/src/cala/nodes/detect/slice_nmf.py b/src/cala/nodes/detect/slice_nmf.py
index d54e1346..ffda4a25 100644
--- a/src/cala/nodes/detect/slice_nmf.py
+++ b/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),
diff --git a/src/cala/nodes/prep/__init__.py b/src/cala/nodes/prep/__init__.py
index 192ff3da..361cb0cd 100644
--- a/src/cala/nodes/prep/__init__.py
+++ b/src/cala/nodes/prep/__init__.py
@@ -2,5 +2,6 @@
 from .denoise import denoise
 from .glow_removal import GlowRemover
 from .rigid_stabilization import RigidStabilizer
+from .r_estimate import SizeEst
 
-__all__ = [denoise, GlowRemover, remove_background, RigidStabilizer]
+__all__ = [denoise, GlowRemover, remove_background, RigidStabilizer, SizeEst]
diff --git a/src/cala/nodes/prep/r_estimate.py b/src/cala/nodes/prep/r_estimate.py
new file mode 100644
index 00000000..e6c4a231
--- /dev/null
+++ b/src/cala/nodes/prep/r_estimate.py
@@ -0,0 +1,41 @@
+from typing import Annotated as A, Any
+import numpy as np
+from noob import process_method, Name
+from pydantic import BaseModel, Field, ConfigDict, PrivateAttr, model_validator
+
+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)
+
+    @model_validator(mode="after")
+    def validity_check(self):
+        assert self.hardset_radius or self.n_frames
+
+    @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
diff --git a/tests/test_iter/test_detect.py b/tests/test_iter/test_detect.py
index bfcb8bc6..3dde5e43 100644
--- a/tests/test_iter/test_detect.py
+++ b/tests/test_iter/test_detect.py
@@ -28,11 +28,6 @@ def toy():
     )
 
 
-@pytest.fixture(autouse=True, scope="class")
-def single_cell_video(toy):
-    return toy.make_movie()
-
-
 @pytest.fixture(scope="class")
 def energy():
     return Energy.from_specification(
@@ -45,17 +40,16 @@ def energy():
 
 
 @pytest.fixture(scope="function")
-def energy_shape(energy, single_cell_video):
-    return energy.process(Residual.from_array(single_cell_video.array), trigger=True)
+def energy_shape(energy, toy):
+    return energy.process(Residual.from_array(toy.make_movie().array), trigger=True)
 
 
 @pytest.fixture(scope="class")
-def slice_nmf(toy):
+def slice_nmf():
     return SliceNMF.from_specification(
         spec=NodeSpecification(
             id="test_slice_nmf",
             type="cala.nodes.detect.SliceNMF",
-            params={"cell_radius": 2 * toy.cell_radii[0]},
         )
     )
 
@@ -70,29 +64,33 @@ def cataloger():
 
 
 class TestEnergy:
-    def test_estimate_gaussian_noise(self, energy, single_cell_video):
-        noise_level = energy._estimate_gaussian_noise(single_cell_video.array)
+    def test_estimate_gaussian_noise(self, energy, toy):
+        noise_level = energy._estimate_gaussian_noise(toy.make_movie().array)
         print(f"\nNoise Level: {noise_level}")
 
-    def test_center_to_median(self, energy, single_cell_video):
-        centered_video = energy._center_to_median(single_cell_video.array)
-        assert centered_video.max() < single_cell_video.array.max()
+    def test_center_to_median(self, energy, toy):
+        centered_video = energy._center_to_median(toy.make_movie().array)
+        assert centered_video.max() < toy.make_movie().array.max()
 
-    def test_process(self, energy, single_cell_video):
+    def test_process(self, energy, toy):
         energy_landscape = energy.process(
-            residuals=Residual.from_array(single_cell_video.array), trigger=True
+            residuals=Residual.from_array(toy.make_movie().array), trigger=True
         )
-        assert energy_landscape.sizes == single_cell_video.array[0].sizes
+        assert energy_landscape.sizes == toy.make_movie().array[0].sizes
         assert np.all(energy_landscape >= 0)
 
 
 class TestSliceNMF:
-    def test_get_max_energy_slice(self, slice_nmf, single_cell_video, energy_shape):
-        slice_ = slice_nmf._get_max_energy_slice(single_cell_video.array, energy_shape)
+    def test_get_max_energy_slice(self, slice_nmf, toy, energy_shape):
+        slice_ = slice_nmf._get_max_energy_slice(
+            toy.make_movie().array, energy_shape, radius=toy.cell_radii[0] * 2
+        )
         return slice_
 
-    def test_local_nmf(self, slice_nmf, single_cell_video, energy_shape, toy):
-        slice_ = slice_nmf._get_max_energy_slice(single_cell_video.array, energy_shape)
+    def test_local_nmf(self, slice_nmf, toy, energy_shape):
+        slice_ = slice_nmf._get_max_energy_slice(
+            toy.make_movie().array, energy_shape, radius=toy.cell_radii[0] * 2
+        )
         footprint, trace = slice_nmf._local_nmf(
             slice_,
             toy.frame_dims.model_dump(),
@@ -100,9 +98,11 @@ def test_local_nmf(self, slice_nmf, single_cell_video, energy_shape, toy):
 
         assert_scalar_multiple_arrays(footprint, toy.footprints.array)
 
-    def test_process(self, slice_nmf, single_cell_video, energy_shape, toy):
+    def test_process(self, slice_nmf, toy, energy_shape):
         new_component = slice_nmf.process(
-            Residual.from_array(single_cell_video.array), energy_shape
+            Residual.from_array(toy.make_movie().array),
+            energy_shape,
+            detect_radius=toy.cell_radii[0] * 2,
         )
         if new_component:
             new_fp, new_tr = new_component
@@ -112,15 +112,16 @@ def test_process(self, slice_nmf, single_cell_video, energy_shape, toy):
         for new, old in zip([new_fp[0], new_tr[0]], [toy.footprints, toy.traces]):
             assert_scalar_multiple_arrays(new.array, old.array)
 
-    def test_chunks(self, single_cell_video, energy_shape, toy):
+    def test_chunks(self, energy_shape, toy):
         nmf = SliceNMF.from_specification(
             spec=NodeSpecification(
                 id="test_slice_nmf",
                 type="cala.nodes.detect.SliceNMF",
-                params={"cell_radius": 10},
             )
         )
-        fpts, trcs = nmf.process(Residual.from_array(single_cell_video.array), energy_shape)
+        fpts, trcs = nmf.process(
+            Residual.from_array(toy.make_movie().array), energy_shape, detect_radius=10
+        )
         if not fpts or not trcs:
             raise AssertionError("Failed to detect a new component")
 
@@ -136,14 +137,10 @@ def test_chunks(self, single_cell_video, energy_shape, toy):
 
 class TestCataloger:
     @pytest.fixture(scope="function")
-    def new_component(self, single_cell_video, energy_shape):
-        return SliceNMF.from_specification(
-            spec=NodeSpecification(
-                id="test_slice_nmf",
-                type="cala.nodes.detect.slice_nmf.SliceNMF",
-                params={"cell_radius": 60},
-            )
-        ).process(Residual.from_array(single_cell_video.array), energy_shape)
+    def new_component(self, slice_nmf, toy, energy_shape):
+        return slice_nmf.process(
+            Residual.from_array(toy.make_movie().array), energy_shape, detect_radius=60
+        )
 
     def test_register(self, cataloger, new_component, toy):
         new_fp, new_tr = new_component
@@ -155,14 +152,10 @@ def test_register(self, cataloger, new_component, toy):
         assert np.array_equal(fp.array, new_fp[0].array)
         assert np.array_equal(tr.array, new_tr[0].array)
 
-    def test_merge_with(self, cataloger, toy, single_cell_video, energy_shape):
-        new_component = SliceNMF.from_specification(
-            spec=NodeSpecification(
-                id="test_slice_nmf",
-                type="cala.nodes.detect.slice_nmf.SliceNMF",
-                params={"cell_radius": 10},
-            )
-        ).process(Residual.from_array(single_cell_video.array), energy_shape)
+    def test_merge_with(self, slice_nmf, cataloger, toy, energy_shape):
+        new_component = slice_nmf.process(
+            Residual.from_array(toy.make_movie().array), energy_shape, detect_radius=10
+        )
 
         new_fp, new_tr = new_component
         fp, tr = cataloger._merge_with(
@@ -174,23 +167,17 @@ def test_merge_with(self, cataloger, toy, single_cell_video, energy_shape):
         )
 
         movie_new_comp = new_fp[0].array @ new_tr[0].array
-        movie_expected = (single_cell_video.array + movie_new_comp).transpose(*movie_result.dims)
+        movie_expected = (toy.make_movie().array + movie_new_comp).transpose(*movie_result.dims)
 
         xr.testing.assert_allclose(movie_result, movie_expected)
 
-    def test_process_ideal(self, cataloger, separate_cells, energy):
+    def test_process_ideal(self, slice_nmf, cataloger, separate_cells, energy):
         """
         test cataloging separate cells. ideal case with cell_radius=5
         """
         movie = separate_cells.make_movie().array
         ener = energy.process(Residual.from_array(movie), trigger=True)
-        fps, trs = SliceNMF.from_specification(
-            spec=NodeSpecification(
-                id="test_slice_nmf",
-                type="cala.nodes.detect.slice_nmf.SliceNMF",
-                params={"cell_radius": 5},
-            )
-        ).process(Residual.from_array(movie), ener)
+        fps, trs = slice_nmf.process(Residual.from_array(movie), ener, detect_radius=5)
 
         # NOTE: by manually putting in separate_cells, we're forcing a double-detection in this test
         new_fps, new_trs = cataloger.process(
@@ -209,19 +196,13 @@ def test_process_ideal(self, cataloger, separate_cells, energy):
         assert new_fps.array.attrs.get("replaces") == detected
         xr.testing.assert_allclose(result, expected)
 
-    def test_process_fail(self, cataloger, separate_cells, energy):
+    def test_process_fail(self, slice_nmf, cataloger, separate_cells, energy):
         """
         test cataloging separate cells. nmf supposed to fail with radius=25 (grabs too many cells)
         """
         movie = separate_cells.make_movie().array
         ener = energy.process(Residual.from_array(movie), trigger=True)
-        fps, trs = SliceNMF.from_specification(
-            spec=NodeSpecification(
-                id="test_slice_nmf",
-                type="cala.nodes.detect.slice_nmf.SliceNMF",
-                params={"cell_radius": 25},
-            )
-        ).process(Residual.from_array(movie), ener)
+        fps, trs = slice_nmf.process(Residual.from_array(movie), ener, detect_radius=25)
 
         # NOTE: by manually putting in separate_cells, we're forcing a double-detection in this test
         new_fps, new_trs = cataloger.process(
@@ -230,19 +211,13 @@ def test_process_fail(self, cataloger, separate_cells, energy):
 
         assert new_fps.array is None and new_trs.array is None
 
-    def test_process_connected(self, cataloger, connected_cells, energy):
+    def test_process_connected(self, slice_nmf, cataloger, connected_cells, energy):
         """
         trial with connected cells 🙏
         """
         movie = connected_cells.make_movie().array
         ener = energy.process(Residual.from_array(movie), trigger=True)
-        fps, trs = SliceNMF.from_specification(
-            spec=NodeSpecification(
-                id="test_slice_nmf",
-                type="cala.nodes.detect.slice_nmf.SliceNMF",
-                params={"cell_radius": 4},
-            )
-        ).process(Residual.from_array(movie), ener)
+        fps, trs = slice_nmf.process(Residual.from_array(movie), ener, detect_radius=4)
 
         # NOTE: by manually putting in connected_cells,
         # we're forcing a double-detection in this test
diff --git a/tests/test_prep/test_r_estimate.py b/tests/test_prep/test_r_estimate.py
new file mode 100644
index 00000000..b254dfd5
--- /dev/null
+++ b/tests/test_prep/test_r_estimate.py
@@ -0,0 +1,38 @@
+from cala.assets import Frame
+from cala.models import AXIS
+from cala.nodes.prep.r_estimate import SizeEst
+from cala.testing.toy import Position
+from cala.util import package_frame
+
+
+def test_size_estim(separate_cells):
+    kwargs = {
+        "min_sigma": 1,
+        "max_sigma": 10,
+        "num_sigma": 10,
+        "threshold": 0.1,
+        "overlap": 0.5,
+    }
+    node = SizeEst(n_frames=1, log_kwargs=kwargs)
+
+    max_proj = package_frame(
+        separate_cells.make_movie().array.max(dim=AXIS.frames_dim).values, index=1
+    )
+    result = node.get_median_radius(Frame.from_array(max_proj))
+
+    expected = separate_cells.cell_radii[0] - 1
+    assert result == expected
+    assert len(node.sizes_) == 3
+
+    max_proj = package_frame(
+        separate_cells.make_movie().array.max(dim=AXIS.frames_dim).values, index=3
+    )
+    result = node.get_median_radius(Frame.from_array(max_proj))
+
+    assert result == expected
+    assert len(node.sizes_) == 3
+
+    for center in node.centers_:
+        height = center[0].astype(int).item()
+        width = center[1].astype(int).item()
+        assert Position(width=width, height=height) in separate_cells.cell_positions

From 500c5444b74231a86441c9057a7ac6189af34fbc Mon Sep 17 00:00:00 2001
From: Raymond <raymond.w.jang@gmail.com>
Date: Thu, 14 Aug 2025 13:22:39 -0700
Subject: [PATCH 2/3] feat: unify test yaml files

---
 src/cala/testing/nodes.py                     |   2 +-
 .../{two_overlap_cells.yaml => odl.yaml}      |  15 +-
 tests/data/pipelines/single_cell.yaml         | 165 -----------------
 tests/data/pipelines/two_cells.yaml           | 166 ------------------
 tests/test_pipeline.py                        |  15 +-
 5 files changed, 23 insertions(+), 340 deletions(-)
 rename tests/data/pipelines/{two_overlap_cells.yaml => odl.yaml} (94%)
 delete mode 100644 tests/data/pipelines/single_cell.yaml
 delete mode 100644 tests/data/pipelines/two_cells.yaml

diff --git a/src/cala/testing/nodes.py b/src/cala/testing/nodes.py
index 182a3950..12431541 100644
--- a/src/cala/testing/nodes.py
+++ b/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:
diff --git a/tests/data/pipelines/two_overlap_cells.yaml b/tests/data/pipelines/odl.yaml
similarity index 94%
rename from tests/data/pipelines/two_overlap_cells.yaml
rename to tests/data/pipelines/odl.yaml
index 8576ceac..98419231 100644
--- a/tests/data/pipelines/two_overlap_cells.yaml
+++ b/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:
diff --git a/tests/data/pipelines/single_cell.yaml b/tests/data/pipelines/single_cell.yaml
deleted file mode 100644
index 9d6dc79f..00000000
--- a/tests/data/pipelines/single_cell.yaml
+++ /dev/null
@@ -1,165 +0,0 @@
-noob_id: cala-single-cell
-noob_model: noob.cube.CubeSpecification
-noob_version: 0.1.1.dev118+g64d81b7
-
-# Add GUI server in assets
-
-assets:
-  buffer:
-    type: cala.assets.Movie
-    scope: session
-    depends:
-      - cache.buffer
-  footprints:
-    type: cala.assets.Footprints
-    scope: session
-  traces:
-    type: cala.assets.Traces
-    scope: session
-  pix_stats:
-    type: cala.assets.PixStats
-    scope: session
-  comp_stats:
-    type: cala.assets.CompStats
-    scope: session
-  overlaps:
-    type: cala.assets.Overlaps
-    scope: session
-
-# Add refiners in nodes
-
-nodes:
-  source:
-    type: cala.testing.single_cell_source
-    params:
-      n_frames: 30
-  denoise:
-    type: cala.nodes.prep.denoise
-    params:
-      ksize:
-      - 3
-      - 3
-      sigmaX: 1.5
-    depends:
-    - frame: source.frame
-  glow:
-    type: cala.nodes.prep.GlowRemover
-    depends:
-    - frame: denoise.frame
-  motion:
-    type: cala.nodes.prep.RigidStabilizer
-    params:
-      drift_speed: 1.0
-    depends:
-    - frame: glow.frame
-  cache:
-    type: cala.nodes.buffer.fill_buffer
-    params:
-      size: 100
-    depends:
-      - buffer: assets.buffer
-      - frame: motion.frame
-
-  trace_frame:
-    type: cala.nodes.traces.FrameUpdate
-    params:
-      tolerance: 0.001
-    depends:
-      - traces: assets.traces
-      - footprints: assets.footprints
-      - frame: motion.frame
-      - overlaps: assets.overlaps
-
-  pix_frame:
-    type: cala.nodes.pixel_stats.ingest_frame
-    depends:
-      - pixel_stats: assets.pix_stats
-      - frame: motion.frame
-      - new_traces: trace_frame.latest_trace
-  comp_frame:
-    type: cala.nodes.component_stats.ingest_frame
-    depends:
-      - component_stats: assets.comp_stats
-      - frame: motion.frame
-      - new_traces: trace_frame.latest_trace
-
-  residual:
-    type: cala.nodes.residual.build
-    params:
-      clip_threshold: 0.001
-    depends:
-      - trigger: trace_frame.latest_trace
-      - frames: assets.buffer
-      - footprints: assets.footprints
-      - traces: assets.traces
-
-# DETECT BEGINS
-  energy:
-    type: cala.nodes.detect.Energy
-    params:
-      min_frames: 10
-    depends:
-      - residuals: residual.movie
-      - trigger: trace_frame.latest_trace
-  nmf:
-    type: cala.nodes.detect.SliceNMF
-    params:
-      cell_radius: 10
-    depends:
-      - residuals: residual.movie
-      - energy: energy.energy
-  catalog:
-    type: cala.nodes.detect.Cataloger
-    params:
-      merge_threshold: 0.8
-    depends:
-      - new_fps: nmf.new_fps
-      - new_trs: nmf.new_trs
-      - existing_fp: assets.footprints
-      - existing_tr: assets.traces
-
-  trace_component:
-    type: cala.nodes.traces.ingest_component
-    depends:
-      - traces: assets.traces
-      - new_traces: catalog.new_traces
-  footprint_component:
-    type: cala.nodes.footprints.ingest_component
-    depends:
-      - footprints:  assets.footprints
-      - new_footprints: catalog.new_footprints
-  pix_component:
-    type: cala.nodes.pixel_stats.ingest_component
-    depends:
-      - pixel_stats: assets.pix_stats
-      - frames: assets.buffer
-      - new_traces: catalog.new_traces
-      - traces: assets.traces
-  comp_component:
-    type: cala.nodes.component_stats.ingest_component
-    depends:
-      - component_stats: assets.comp_stats
-      - traces: assets.traces
-      - new_traces: catalog.new_traces
-#  DETECT ENDS
-
-  footprints_frame:
-    type: cala.nodes.footprints.Footprinter
-    params:
-      bep: 1
-      tol: 0.0000001
-    depends:
-      - footprints: assets.footprints
-      - pixel_stats: pix_component.value
-      - component_stats: comp_component.value
-
-  overlaps_update:
-    type: cala.nodes.overlap.ingest_frame
-    depends:
-      - overlaps: assets.overlaps
-      - footprints: footprints_frame.footprints
-
-  return:
-    type: return
-    depends:
-      - motion.frame
\ No newline at end of file
diff --git a/tests/data/pipelines/two_cells.yaml b/tests/data/pipelines/two_cells.yaml
deleted file mode 100644
index 33c5c117..00000000
--- a/tests/data/pipelines/two_cells.yaml
+++ /dev/null
@@ -1,166 +0,0 @@
-noob_id: cala-two-cells
-noob_model: noob.cube.CubeSpecification
-noob_version: 0.1.1.dev118+g64d81b7
-
-# Add GUI server in assets
-
-assets:
-  buffer:
-    type: cala.assets.Movie
-    scope: session
-    depends:
-      - cache.buffer
-  footprints:
-    type: cala.assets.Footprints
-    scope: session
-  traces:
-    type: cala.assets.Traces
-    scope: session
-  pix_stats:
-    type: cala.assets.PixStats
-    scope: session
-  comp_stats:
-    type: cala.assets.CompStats
-    scope: session
-  overlaps:
-    type: cala.assets.Overlaps
-    scope: session
-
-# Add refiners in nodes
-
-nodes:
-  source:
-    type: cala.testing.two_cells_source
-    params:
-      n_frames: 30
-
-  denoise:
-    type: cala.nodes.prep.denoise
-    params:
-      ksize:
-        - 3
-        - 3
-      sigmaX: 1.5
-    depends:
-      - frame: source.frame
-  glow:
-    type: cala.nodes.prep.GlowRemover
-    depends:
-      - frame: denoise.frame
-  motion:
-    type: cala.nodes.prep.RigidStabilizer
-    params:
-      drift_speed: 1.0
-    depends:
-      - frame: glow.frame
-  cache:
-    type: cala.nodes.buffer.fill_buffer
-    params:
-      size: 100
-    depends:
-      - buffer: assets.buffer
-      - frame: motion.frame
-
-  trace_frame:
-    type: cala.nodes.traces.FrameUpdate
-    params:
-      tolerance: 0.001
-    depends:
-      - traces: assets.traces
-      - footprints: assets.footprints
-      - frame: motion.frame
-      - overlaps: assets.overlaps
-
-  pix_frame:
-    type: cala.nodes.pixel_stats.ingest_frame
-    depends:
-      - pixel_stats: assets.pix_stats
-      - frame: motion.frame
-      - new_traces: trace_frame.latest_trace
-  comp_frame:
-    type: cala.nodes.component_stats.ingest_frame
-    depends:
-      - component_stats: assets.comp_stats
-      - frame: motion.frame
-      - new_traces: trace_frame.latest_trace
-
-  residual:
-    type: cala.nodes.residual.build
-    params:
-      clip_threshold: 0.001
-    depends:
-      - trigger: trace_frame.latest_trace
-      - frames: assets.buffer
-      - footprints: assets.footprints
-      - traces: assets.traces
-
-  # DETECT BEGINS
-  energy:
-    type: cala.nodes.detect.Energy
-    params:
-      min_frames: 10
-    depends:
-      - residuals: residual.movie
-      - trigger: trace_frame.latest_trace
-  nmf:
-    type: cala.nodes.detect.SliceNMF
-    params:
-      cell_radius: 10
-    depends:
-      - residuals: residual.movie
-      - energy: energy.energy
-  catalog:
-    type: cala.nodes.detect.Cataloger
-    params:
-      merge_threshold: 0.8
-    depends:
-      - new_fps: nmf.new_fps
-      - new_trs: nmf.new_trs
-      - existing_fp: assets.footprints
-      - existing_tr: assets.traces
-
-  trace_component:
-    type: cala.nodes.traces.ingest_component
-    depends:
-      - traces: assets.traces
-      - new_traces: catalog.new_traces
-  footprint_component:
-    type: cala.nodes.footprints.ingest_component
-    depends:
-      - footprints:  assets.footprints
-      - new_footprints: catalog.new_footprints
-  pix_component:
-    type: cala.nodes.pixel_stats.ingest_component
-    depends:
-      - pixel_stats: assets.pix_stats
-      - frames: assets.buffer
-      - new_traces: catalog.new_traces
-      - traces: assets.traces
-  comp_component:
-    type: cala.nodes.component_stats.ingest_component
-    depends:
-      - component_stats: assets.comp_stats
-      - traces: assets.traces
-      - new_traces: catalog.new_traces
-  #  DETECT ENDS
-
-  footprints_frame:
-    type: cala.nodes.footprints.Footprinter
-    params:
-      bep: 1
-      tol: 0.0000001
-    depends:
-      - footprints: assets.footprints
-      - pixel_stats: pix_component.value
-      - component_stats: comp_component.value
-
-  overlaps_update:
-    type: cala.nodes.overlap.ingest_frame
-    depends:
-      - overlaps: assets.overlaps
-      - footprints: footprints_frame.footprints
-
-  return:
-    type: return
-    depends:
-      - motion.frame
\ No newline at end of file
diff --git a/tests/test_pipeline.py b/tests/test_pipeline.py
index 2113cdaa..dfacc16f 100644
--- a/tests/test_pipeline.py
+++ b/tests/test_pipeline.py
@@ -1,18 +1,27 @@
 import pytest
 import xarray as xr
 from noob import Cube, SynchronousRunner, Tube
+from noob.node import NodeSpecification, Node
 
 from cala.models import AXIS
 
 
-@pytest.fixture(params=["cala-single-cell", "cala-two-cells", "cala-two-overlap-cells"])
+@pytest.fixture(params=["single_cell_source", "two_cells_source", "two_overlapping_source"])
 def tube(request):
-    return Tube.from_specification(request.param)
+    tube = Tube.from_specification("cala-odl")
+    source = Node.from_specification(
+        NodeSpecification(
+            id="source", type=f"cala.testing.{request.param}", params={"n_frames": 50}
+        )
+    )
+    tube.nodes["source"] = source
+
+    return tube
 
 
 @pytest.fixture
 def cube():
-    return Cube.from_specification("cala-single-cell")
+    return Cube.from_specification("cala-odl")
 
 
 @pytest.fixture

From 3b9f53985bdfb16fe54dbffb82262a72aee93cec Mon Sep 17 00:00:00 2001
From: Raymond <raymond.w.jang@gmail.com>
Date: Thu, 14 Aug 2025 13:26:30 -0700
Subject: [PATCH 3/3] format: ruff

---
 src/cala/nodes/prep/__init__.py   |  2 +-
 src/cala/nodes/prep/r_estimate.py | 14 ++++++--------
 tests/test_pipeline.py            |  2 +-
 3 files changed, 8 insertions(+), 10 deletions(-)

diff --git a/src/cala/nodes/prep/__init__.py b/src/cala/nodes/prep/__init__.py
index 361cb0cd..e100f748 100644
--- a/src/cala/nodes/prep/__init__.py
+++ b/src/cala/nodes/prep/__init__.py
@@ -1,7 +1,7 @@
 from .background_removal import remove_background
 from .denoise import denoise
 from .glow_removal import GlowRemover
-from .rigid_stabilization import RigidStabilizer
 from .r_estimate import SizeEst
+from .rigid_stabilization import RigidStabilizer
 
 __all__ = [denoise, GlowRemover, remove_background, RigidStabilizer, SizeEst]
diff --git a/src/cala/nodes/prep/r_estimate.py b/src/cala/nodes/prep/r_estimate.py
index e6c4a231..e83335ea 100644
--- a/src/cala/nodes/prep/r_estimate.py
+++ b/src/cala/nodes/prep/r_estimate.py
@@ -1,9 +1,11 @@
-from typing import Annotated as A, Any
-import numpy as np
-from noob import process_method, Name
-from pydantic import BaseModel, Field, ConfigDict, PrivateAttr, model_validator
+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
 
@@ -21,10 +23,6 @@ class SizeEst(BaseModel):
 
     model_config = ConfigDict(arbitrary_types_allowed=True)
 
-    @model_validator(mode="after")
-    def validity_check(self):
-        assert self.hardset_radius or self.n_frames
-
     @process_method
     def get_median_radius(self, frame: Frame) -> A[int, Name("radius")]:
         if self.hardset_radius:
diff --git a/tests/test_pipeline.py b/tests/test_pipeline.py
index dfacc16f..ac9cc396 100644
--- a/tests/test_pipeline.py
+++ b/tests/test_pipeline.py
@@ -1,7 +1,7 @@
 import pytest
 import xarray as xr
 from noob import Cube, SynchronousRunner, Tube
-from noob.node import NodeSpecification, Node
+from noob.node import Node, NodeSpecification
 
 from cala.models import AXIS