Sphere/vescicle picking (#179)

Sphere picking using the same approach as surface and filament.

src/blik/napari.yaml

@@ -40,12 +40,15 @@ contributions:
     - id: blik.main_widget
       python_name: blik.widgets.main_widget:MainBlikWidget
       title: "Open blik main widget"
-    - id: blik.filament_picking
-      python_name: blik.widgets.picking:FilamentWidget
-      title: "Open blik filament picking widget"
     - id: blik.surface_picking
       python_name: blik.widgets.picking:SurfaceWidget
       title: "Open blik surface picking widget"
+    - id: blik.sphere_picking
+      python_name: blik.widgets.picking:SphereWidget
+      title: "Open sphere picking widget"
+    - id: blik.filament_picking
+      python_name: blik.widgets.picking:FilamentWidget
+      title: "Open blik filament picking widget"
     - id: blik.file_reader_widget
       python_name: blik.widgets.file_reader:file_reader
       title: "Open blik file reader widget"
@@ -66,8 +69,8 @@ contributions:
       - command: blik.power_spectrum
     napari/layers/annotate:
       - command: blik.main_widget
-      - command: blik.filament_picking
       - command: blik.surface_picking
+      - command: blik.sphere_picking
       - command: blik.filament_picking
     napari/layers/filter:
       - command: blik.bandpass_filter
@@ -127,10 +130,12 @@ contributions:
   widgets:
     - command: blik.main_widget
       display_name: "Blik main widget"
-    - command: blik.filament_picking
-      display_name: "Filament picking"
     - command: blik.surface_picking
       display_name: "Surface picking"
+    - command: blik.sphere_picking
+      display_name: "Sphere picking"
+    - command: blik.filament_picking
+      display_name: "Filament picking"
     - command: blik.file_reader_widget
       display_name: "File reader"
     - command: blik.bandpass_filter

src/blik/widgets/main_widget.py

@@ -155,7 +155,13 @@ def add_to_exp(layer: napari.layers.Layer):
     labels=False,
     call_button="Create",
     l_type={
-        "choices": ["segmentation", "particles", "surface_picking", "filament_picking"]
+        "choices": [
+            "segmentation",
+            "particles",
+            "surface_picking",
+            "sphere_picking",
+            "filament_picking",
+        ]
     },
 )
 def new(
@@ -221,6 +227,20 @@ def new(
                     units="angstrom",
                 )
 
+                return [pts]
+    elif l_type == "sphere_picking":
+        for lay in layers:
+            if isinstance(lay, Image) and lay.metadata["experiment_id"] == exp_id:
+                pts = Points(
+                    name=f"{exp_id} - sphere picks",
+                    size=20 / lay.scale[0],
+                    scale=lay.scale,
+                    metadata={"experiment_id": exp_id},
+                    ndim=3,
+                    # axis_labels=('z', 'y', 'x'),
+                    units="angstrom",
+                )
+
                 return [pts]
 
     show_info(f"cannot create a new {l_type}")

src/blik/widgets/picking.py

@@ -5,12 +5,15 @@
 from magicgui import magicgui
 from magicgui.widgets import Container
 from morphosamplers.helical_filament import HelicalFilament
+from morphosamplers.models import Sphere
+from morphosamplers.preprocess import get_label_paths_3d
 from morphosamplers.sampler import (
     sample_volume_along_spline,
     sample_volume_around_surface,
 )
+from morphosamplers.samplers.sphere_samplers import PointSampler, PoseSampler
 from morphosamplers.surface_spline import GriddedSplineSurface
-from morphosamplers.preprocess import get_label_paths_3d
+from scipy.spatial import ConvexHull
 from scipy.spatial.transform import Rotation
 
 from ..reader import construct_particle_layer_tuples
@@ -85,7 +88,9 @@ def _generate_surface_grids_from_labels_layer(
         )
 
     # doing this "custom" because we need to flip xyz
-    surfaces_lines = get_label_paths_3d(compute(surface_label.data)[0], axis=0, slicing_step=10, sampling_step=10)
+    surfaces_lines = get_label_paths_3d(
+        compute(surface_label.data)[0], axis=0, slicing_step=10, sampling_step=10
+    )
 
     for lines in surfaces_lines:
         lines = [invert_xyz(line.astype(float)) for line in lines]
@@ -393,6 +398,99 @@ def resample_filament(
     )
 
 
+@magicgui(
+    labels=True,
+    call_button="Generate",
+)
+def sphere(
+    point_picks: napari.layers.Points,
+) -> napari.types.LayerDataTuple:
+    points = invert_xyz(point_picks.data)
+    vert_all = []
+    faces_all = []
+    spheres_all = []
+
+    exp_id = ""
+    faces_offset = 0
+    for i, (c, n) in enumerate(zip(points[::2], points[1::2])):
+        r = np.linalg.norm(n - c)
+
+        s = Sphere(center=c, radius=r)
+        ps = PointSampler(spacing=r / 10)
+        positions = ps.sample(s)
+
+        h = ConvexHull(positions)
+        tri = h.points[h.simplices]
+
+        # fix faces ordering
+        edges = tri - np.roll(tri, 1, axis=1)
+        cross = np.cross(edges[:, 0], edges[:, 1])
+        direction = np.einsum("...j,...j", cross, tri[:, 0] - (0, 0, 0))
+        faces = h.simplices.copy()
+        faces[direction < 0] = h.simplices[direction < 0][:, ::-1]
+        faces += i * faces_offset
+        faces_offset += len(positions)
+
+        exp_id = point_picks.metadata["experiment_id"]
+        vert_all.append(positions)
+        faces_all.append(faces)
+        spheres_all.append(s)
+
+    surface_layer_tuple = (
+        (invert_xyz(np.concatenate(vert_all)), np.concatenate(faces_all)),
+        {
+            "name": f"{exp_id} - surface",
+            "metadata": {
+                "experiment_id": exp_id,
+                "spheres": spheres_all,
+            },
+            "scale": point_picks.scale,
+            # smooth shading is bugged cause of some ordering issue
+            "shading": "flat",
+        },
+        "surface",
+    )
+    return [surface_layer_tuple]
+
+
+@magicgui(
+    labels=True,
+    call_button="Generate",
+    spacing_A={"widget_type": "FloatSlider", "min": 0.01, "max": 10000},
+)
+def sphere_particles(
+    sphere_surf: napari.layers.Surface,
+    spacing_A=50,
+) -> napari.types.LayerDataTuple:
+    spheres = sphere_surf.metadata.get("spheres", None)
+    if spheres is None:
+        raise ValueError("This surface layer contains no sphere objects.")
+
+    exp_id = sphere_surf.metadata["experiment_id"]
+
+    spacing_A /= sphere_surf.scale[0]
+
+    pos = []
+    ori = []
+    for s in spheres:
+        ps = PoseSampler(spacing=spacing_A)
+        poses = ps.sample(s)
+
+        features = pd.DataFrame(
+            {"orientation": np.asarray(Rotation.from_matrix(poses.orientations))}
+        )
+        pos.append(poses.positions)
+        ori.append(features)
+
+    return construct_particle_layer_tuples(
+        coords=np.concatenate(pos),
+        features=pd.concat(ori, axis=0),
+        scale=sphere_surf.scale[0],
+        exp_id=exp_id,
+        name_suffix="spheres picked",
+    )
+
+
 class FilamentWidget(Container):
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
@@ -409,3 +507,11 @@ def __init__(self, *args, **kwargs):
         self.append(surface)
         self.append(surface_particles)
         self.append(resample_surface)
+
+
+class SphereWidget(Container):
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+
+        self.append(sphere)
+        self.append(sphere_particles)