fix all the recently broken xyz inversions

src/blik/reader.py

@@ -30,7 +30,7 @@ def _construct_positions_layer(
     )
     feat_defaults["orientation"] = np.array(Rotation.identity(), dtype=object)
     return (
-        coords,
+        invert_xyz(coords),
         {
             "name": f"{exp_id} - particle positions",
             "features": features,
@@ -55,10 +55,8 @@ def _construct_orientations_layer(coords, features, scale, exp_id, p_id, source)
         vec_data = None
         vec_color = "blue"
     else:
-        vec_data, vec_color = generate_vectors(
-            invert_xyz(coords), features["orientation"]
-        )
-        vec_data = invert_xyz(vec_data)
+        vec_data, vec_color = generate_vectors(coords, features["orientation"])
+        vec_data = invert_xyz(vec_data)  # napari works in zyx order
     return (
         vec_data,
         {
@@ -88,8 +86,7 @@ def construct_particle_layer_tuples(
     """
     Constructs particle layer tuples from particle data.
 
-    Data is assumed to already by in zyx napari format, while features is
-    the normal poseset dataframe.
+    Data should be still in xyz format (will be flipped to zyx).
     """
     # unique id so we can connect layers safely
     p_id = p_id if p_id is not None else uuid1()
@@ -128,8 +125,7 @@ def construct_particle_layer_tuples(
 
 def read_particles(particles):
     """Takes a valid poseset and converts it into napari layers."""
-    # order is zyx in napari
-    coords = invert_xyz(particles.position)
+    coords = particles.position
 
     if particles.features is not None:
         features = particles.features.copy(deep=False)
@@ -138,14 +134,13 @@ def read_particles(particles):
 
     px_size = particles.pixel_spacing
     if not px_size:
-        warnings.warn("unknown pixel spacing, setting to 1 Angstrom")
+        warnings.warn("unknown pixel spacing, setting to 1 Angstrom", stacklevel=2)
         px_size = 1
 
     if particles.shift is not None:
-        shifts = invert_xyz(particles.shift)
-        coords = coords + shifts
-        shift_cols = ["shift_z", "shift_y", "shift_x"]
-        features[shift_cols] = shifts
+        coords = coords + particles.shifts
+        shift_cols = ["shift_x", "shift_y", "shift_z"]
+        features[shift_cols] = particles.shifts
     if particles.orientation is not None:
         features["orientation"] = np.asarray(particles.orientation, dtype=object)
 
@@ -161,7 +156,7 @@ def read_particles(particles):
 def read_image(image):
     px_size = image.pixel_spacing
     if not px_size:
-        warnings.warn("unknown pixel spacing, setting to 1 Angstrom")
+        warnings.warn("unknown pixel spacing, setting to 1 Angstrom", stacklevel=2)
         px_size = 1
     return (
         image.data,

src/blik/widgets/main_widget.py

@@ -15,7 +15,7 @@
 from scipy.spatial.transform import Rotation
 
 from ..reader import construct_particle_layer_tuples
-from ..utils import generate_vectors, layer_tuples_to_layers
+from ..utils import generate_vectors, invert_xyz, layer_tuples_to_layers
 
 
 def _get_choices(wdg, condition=None):
@@ -47,8 +47,11 @@ def _update_vectors():
             obj = p.features["orientation"].astype(object)
             obj[pd.isnull(obj)] = Rotation.identity()
             p.features["orientation"] = obj
-        vec_data, vec_color = generate_vectors(p.data[...], p.features["orientation"])
-        v.data = vec_data
+        # invert xyz and zyx back and forth because calculation happens in xyz space
+        vec_data, vec_color = generate_vectors(
+            invert_xyz(p.data), p.features["orientation"]
+        )
+        v.data = invert_xyz(vec_data)
         v.edge_color = vec_color
 
     p.events.set_data.disconnect(_update_vectors)

src/blik/widgets/picking.py

@@ -13,6 +13,7 @@
 from scipy.spatial.transform import Rotation
 
 from ..reader import construct_particle_layer_tuples
+from ..utils import invert_xyz
 
 
 def _generate_surface_grids_from_shapes_layer(
@@ -29,11 +30,17 @@ def _generate_surface_grids_from_shapes_layer(
     if inside_points is None:
         inside_point = None
     else:
-        inside_point = inside_points.data[0] if len(inside_points.data) else None
+        inside_point = (
+            invert_xyz(inside_points.data[0]) if len(inside_points.data) else None
+        )
     for _, surf in surface_shapes.features.groupby("surface_id"):
         lines = data_array[surf.index]
         # sort by z so lines can be added in between at a later point
-        lines = [line.astype(float) for line in sorted(lines, key=lambda x: x[0, 0])]
+        # also invert xyz so we operate in back in xyz world and not napari inverted world
+        lines = [
+            invert_xyz(line.astype(float))
+            for line in sorted(lines, key=lambda x: x[0, 0])
+        ]
 
         try:
             surface_grids.append(
@@ -61,7 +68,7 @@ def _resample_surfaces(image_layer, surface_grids, spacing, thickness, masked):
     volumes = []
     for surf in surface_grids:
         vol = sample_volume_around_surface(
-            compute(image_layer.data)[0],
+            compute(image_layer.data)[0].T,  # transpose to go back to xyz world
             surface=surf,
             sampling_thickness=thickness,
             sampling_spacing=spacing,
@@ -74,12 +81,13 @@ def _resample_surfaces(image_layer, surface_grids, spacing, thickness, masked):
 
 def _generate_filaments_from_points_layer(filament_picks):
     """create a new filament representation from picked points."""
-    return HelicalFilament(points=filament_picks.data.astype(float))
+    # invert xyz to go back to xyz world
+    return HelicalFilament(points=invert_xyz(filament_picks.data.astype(float)))
 
 
 def _resample_filament(image_layer, filament, spacing, thickness):
     return sample_volume_along_spline(
-        compute(image_layer.data)[0],
+        compute(image_layer.data)[0].T,  # transpose to go back to xyz world
         spline=filament,
         sampling_shape=(thickness, thickness),
         sampling_spacing=spacing,
@@ -132,8 +140,9 @@ def surface(
     if colormap.shape[0] == 1:
         values += 1
 
+    # invert_xyz to go back to napari world (also invert faces order to preserve normals)
     surface_layer_tuple = (
-        (vert, faces, values),
+        (invert_xyz(vert), invert_xyz(faces), values),
         {
             "name": f"{exp_id} - surface",
             "metadata": {
@@ -240,7 +249,7 @@ def filament(
 
     exp_id = points.metadata["experiment_id"]
 
-    path = filament.sample(n_samples=len(points.data) * 50)
+    path = invert_xyz(filament.sample(n_samples=len(points.data) * 50))
     shapes_layer_tuple = (
         [path],
         {