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MaimonLab · Sep 3, 2023 · 6251678 · 6251678
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diff --git a/README.md b/README.md
@@ -1,5 +1,11 @@
 # SiffRoi
 
+TODO:
+-   Rework `UsesReferenceFramesMixin` to make it opt-out: if
+there's no reference frames, it can use the `PHOTON_COUNTS`
+layer or something similar. Maybe this is a `siff-napari`
+thing to change how to pass in the data, though...
+
 Tools for `ROI` annotation, segmentation, etc.
 
 This is meant to be `napari` agnostic without being _too_

diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
@@ -0,0 +1,44 @@
+{% set pyproject = load_file_data('../pyproject.toml', from_recipe_dir=True) %}
+{% set project = pyproject.get('project',{}) %}
+
+package:
+  name: {{ project.get('name') }}
+  version: {{ project.get('version') }}
+
+source:
+  path: ../
+  git_url: ../
+  #git_url: https://github.com/maimonlab/siffpy.git
+
+build:
+  number: {{ GIT_DESCRIBE_NUMBER }}
+  script: "{{ PYTHON }} -m pip install '.'"
+
+requirements:
+  build:
+    - python >=3.9
+    - pip
+    - setuptools>=45
+    - setuptools_scm[toml]>=6.2
+    - wheel
+    - numpy >=1.15
+  host:
+    - python >=3.9
+    - numpy >=1.15
+    - scipy
+    - h5py
+  run:
+    - python >=3.9
+    - numpy >=1.15
+    - scipy
+    - h5py
+
+about:
+  home: "https://github.com/maimonlab/siffroi"
+  summary : {{ project.get('description') }}
+  license: {{ project.get('license', {}).get('text') }}
+  #license_file: ../LICENSE.md
+
+extra:
+  recipe-maintainers:
+    - StephenThornquist
diff --git a/siffroi/ellipsoid_body/protocols/use_ellipse.py b/siffroi/ellipsoid_body/protocols/use_ellipse.py
@@ -105,49 +105,6 @@ def use_ellipse(
         # and bypass the hullabaloo below
         FROM_MASK = True
 
-    # if slice_idx is None:
-    #     # Get the biggest for all planes
-    #     if FROM_MASK:
-    #         ellipses_by_slice = [
-    #             [ellipse for ellipse in ellipses if np.any(ellipse[slice_idx])]
-    #             for slice_idx in range(image_shape[0])
-    #         ]
-    #         slicewise_idx = [
-    #             np.argsort([np.sum(ellipse) for ellipse in slicewise_ellipses])
-    #             if len(slicewise_ellipses) > 0
-    #             else None
-    #             for slicewise_ellipses in ellipses_by_slice
-    #         ]
-
-    #         slicewise_biggest_ellipse = [
-    #             slicewise_ellipses[sorted_slicewise[-1]]
-    #             if sorted_slicewise is not None
-    #             else np.zeros(image_shape, dtype=bool)
-    #             for slicewise_ellipses, sorted_slicewise in zip(ellipses_by_slice, slicewise_idx)
-    #         ]
-
-    #         main_ellip = np.logical_or.reduce(slicewise_biggest_ellipse)
-
-    #     else:
-    #         raise NotImplementedError("Use ellipse only supports masks for now")
-
-    # else:
-    #     size_sorted_idx = np.argsort(
-    #         [
-    #             np.sum(ellipse)
-    #             for ellipse in ellipses
-    #             if np.round(ellipse[0][0]) == slice_idx
-    #         ]
-    #     ) if FROM_MASK else np.argsort(
-    #         [
-    #             polygon_area(ellipse)
-    #             for ellipse in ellipses
-    #             if np.round(ellipse[0][0]) == slice_idx
-    #         ]
-    #     )
-
-    #     main_ellip = ellipses[size_sorted_idx[-1]]
-
     center = None
 
     if (ExtraRois(extra_rois) == ExtraRois.CENTER):