Add new default ellipse estimation method for beam mask using Sobel filter

programs/decolace_pipeline/decolace_pipeline_example_config.yaml

@@ -27,9 +27,10 @@ movie_config:
 
 # --- Beam mask estimation parameters ---
 beam_mask_config:
-  threshold_method: "otsu"      # (optional, default "otsu")   Thresholding algorithm for binarising the low-pass-filtered frame sum. Only "otsu" is currently supported.
+  threshold_method: "sobel"     # (optional, default "sobel")  Ellipse fit method; only "sobel" (outermost Sobel edge along rays from the beam center; robust to dark sample at the rim) is currently supported.
   diameter_reduction: 0.0       # (optional, default 0.0)      Fractional shrink applied to both ellipse radii; 0.1 shrinks each axis by 10% to exclude fringe artifacts at the beam edge.
-  low_pass_resolution: 100.0    # (optional, default 100.0)    Low-pass filter cutoff (Angstroms) applied to the frame sum before thresholding.
+  working_pixel_size: 8.0       # (optional, default 8.0)      Approximate pixel size (Angstroms) the frame sum is binned to before edge detection.
+  edge_smoothing_sigma: 120.0   # (optional, default 120.0)    Gaussian smoothing sigma (Angstroms) applied before edge detection.
 
 # --- Output file configuration ---
 output_config:

pyproject.toml

@@ -58,7 +58,6 @@ dependencies = [
     "h5py",
     "dm4",
     "opencv-python-headless",
-    "scikit-image",
 ]
 
 # https://peps.python.org/pep-0621/#dependencies-optional-dependencies

src/ripple/config/beam_mask_config.py

@@ -3,6 +3,7 @@
 from typing import Literal
 
 import torch
+from pydantic import PositiveFloat
 from teamtomo_basemodel import BaseModelTeamTomo
 
 from ripple.config.crop_bounds_config import CropBoundsConfig
@@ -15,24 +16,30 @@ class BeamMaskConfig(BaseModelTeamTomo):
 
     Parameters
     ----------
-    threshold_method: Literal["otsu"]
-        Thresholding algorithm used to binarise the low-pass-filtered frame sum.
-        Currently only ``"otsu"`` is supported. Default is ``"otsu"``.
+    threshold_method: Literal["sobel"]
+        Method used to fit the beam ellipse to the frame sum. ``"sobel"`` fits the
+        ellipse to the outermost Sobel edge along rays cast from the beam center, and is
+        robust to dark sample lying across the beam rim. Currently only ``"sobel"`` is
+        supported. Default is ``"sobel"``.
     diameter_reduction: float
         Fractional amount by which both ellipse radii are shrunk before creating the
         final mask. ``0.0`` applies no reduction; ``0.1`` shrinks each axis by 10% to
         exclude fringe artifacts at the beam edge. Default is 0.0.
-    low_pass_resolution: float
-        Low-pass filter cutoff, in Angstroms, applied to the frame sum before
-        thresholding. Default is 100.0.
+    working_pixel_size: float
+        Approximate pixel size, in Angstroms, the frame sum is binned to before edge
+        detection. Default is 8.0.
+    edge_smoothing_sigma: float
+        Standard deviation, in Angstroms, of the Gaussian smoothing applied to the
+        binned frame sum before edge detection. Default is 120.0.
     crop_bounds_config: CropBoundsConfig
         Size policy for cropping movie frames down to the region covered by the beam
         mask. Default disables cropping (``mode="none"``).
     """
 
-    threshold_method: Literal["otsu"] = "otsu"
+    threshold_method: Literal["sobel"] = "sobel"
     diameter_reduction: float = 0.0
-    low_pass_resolution: float = 100.0
+    working_pixel_size: PositiveFloat = 8.0
+    edge_smoothing_sigma: PositiveFloat = 120.0
     crop_bounds_config: CropBoundsConfig = CropBoundsConfig()
 
 
@@ -80,9 +87,15 @@ class BeamMaskResult(BaseModelTeamTomo):
     output_crop_max_x: int
         Right column of the output crop region, inclusive.
     threshold_method: str
-        Thresholding algorithm used to binarise the filtered frame sum.
+        Method used to fit the beam ellipse (``"sobel"``).
     pixel_size: float
         Pixel size in Angstroms per pixel.
+    n_edge_points: int
+        Number of beam-edge points found (at most one per ray cast).
+    n_inliers: int
+        Number of edge points kept as beam-rim inliers.
+        ``n_inliers / ripple.core.beam_mask.DEFAULT_N_RAYS`` is the fraction of the
+        rim that was found.
     """
 
     center_y: float
@@ -103,6 +116,8 @@ class BeamMaskResult(BaseModelTeamTomo):
     output_crop_max_x: int
     threshold_method: str
     pixel_size: float
+    n_edge_points: int
+    n_inliers: int
 
     @property
     def crop_bounds(self) -> CropBounds:

src/ripple/core/__init__.py

@@ -1,6 +1,11 @@
 """Core functions for RIPPLE."""
 
-from .beam_mask import estimate_beam_mask, make_ellipse_mask, sum_movie_chunked
+from .beam_mask import (
+    estimate_beam_mask,
+    fit_beam_edge,
+    make_ellipse_mask,
+    sum_movie_chunked,
+)
 from .core_optimize_sigmas import core_optimize_sigmas
 from .core_polish_particles import core_polish_particles
 from .crop_bounds import crop_movie, determine_crop_bounds, get_crop_bounds
@@ -13,6 +18,7 @@
     "crop_movie",
     "determine_crop_bounds",
     "estimate_beam_mask",
+    "fit_beam_edge",
     "fourier_crop_movie",
     "generate_dose_weighted_image",
     "get_crop_bounds",