save voxelsize as explictit parameters rather than np array

.pre-commit-config.yaml

@@ -1,22 +1,27 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v4.5.0
     hooks:
       - id: check-docstring-first
       - id: end-of-file-fixer
       - id: trailing-whitespace
         exclude: ^\.napari-hub/.*
       - id: check-yaml # checks for correct yaml syntax for github actions ex.
-        exclude: ^docs/04_FAQ/settings_reconstruction_(bulk|surface).yaml$
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.7
+    rev: v0.3.4
     hooks:
       - id: ruff
   - repo: https://github.com/psf/black
-    rev: 24.4.0
+    rev: 24.3.0
     hooks:
       - id: black
   - repo: https://github.com/tlambert03/napari-plugin-checks
     rev: v0.3.0
     hooks:
       - id: napari-plugin-checks
+  # https://mypy.readthedocs.io/en/stable/
+  # you may wish to add this as well!
+  # - repo: https://github.com/pre-commit/mirrors-mypy
+  #   rev: v1.9.0
+  #   hooks:
+  #     - id: mypy

docs/01_code_usage/reconstruction_settings.yaml

@@ -11,7 +11,6 @@ sampling_distance: 2.0
 smoothing_sigma: 2.0
 target_voxelsize: 0.23
 trace_length: 80.0
-voxelsize: !!ndarray
-- 0.37
-- 0.0901
-- 0.0901
+voxelsize_z: 0.37
+voxelsize_y: 0.0901
+voxelsize_x: 0.0901

docs/04_FAQ/settings_reconstruction_bulk.yaml

@@ -12,7 +12,6 @@ smoothing_sigma: 1.0
 target_voxelsize: 0.2868
 trace_length: 30.0
 return_intermediate_results: true
-voxelsize: !!ndarray
-- 0.47
-- 0.1036
-- 0.1036
+voxelsize_z: 0.47
+voxelsize_y: 0.1036
+voxelsize_x: 0.1036

docs/04_FAQ/settings_reconstruction_surface.yaml

@@ -12,7 +12,6 @@ smoothing_sigma: 1.0
 target_voxelsize: 0.2868
 trace_length: 30.0
 return_intermediate_results: true
-voxelsize: !!ndarray
-- 0.47
-- 0.1036
-- 0.1036
+voxelsize_z: 0.47
+voxelsize_y: 0.1036
+voxelsize_x: 0.1036

src/napari_stress/_approximation/expansion.py

@@ -1,4 +1,8 @@
 import numpy as np
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    import napari
 
 from .expansion_base import Expander
 

src/napari_stress/_approximation/expansion_base.py

@@ -1,4 +1,7 @@
 from abc import ABC, abstractmethod
+from typing import TYPE_CHECKING
+if TYPE_CHECKING:
+    import napari
 
 
 class Expander(ABC):

src/napari_stress/_approximation/expansion_napari.py

@@ -1,4 +1,7 @@
 from napari_tools_menu import register_function
+from typing import TYPE_CHECKING
+if TYPE_CHECKING:
+    import napari
 
 from .._utils import frame_by_frame
 from .expansion import EllipsoidExpander, SphericalHarmonicsExpander

src/napari_stress/_approximation/fit_ellipsoid.py

@@ -2,6 +2,9 @@
 import numpy as np
 from napari.types import PointsData, VectorsData
 from napari_tools_menu import register_function
+from typing import TYPE_CHECKING
+if TYPE_CHECKING:
+    import napari
 
 from .. import __version__
 from .._utils.frame_by_frame import frame_by_frame

src/napari_stress/_measurements/curvature.py

@@ -25,6 +25,10 @@
     manifold,
 )
 
+from typing import TYPE_CHECKING
+if TYPE_CHECKING:
+    import napari
+
 
 @register_function(
     menu="Measurement > Measure mean curvature on ellipsoid (n-STRESS)"

src/napari_stress/_measurements/geodesics.py

@@ -6,6 +6,10 @@
 
 from .._utils.frame_by_frame import frame_by_frame
 
+from typing import TYPE_CHECKING
+if TYPE_CHECKING:
+    import napari
+
 
 def geodesic_distance_matrix(surface: SurfaceData) -> np.ndarray:
     """

src/napari_stress/_measurements/intensity.py

@@ -4,7 +4,9 @@
 from napari_tools_menu import register_function
 
 from .._utils.frame_by_frame import frame_by_frame
-
+from typing import TYPE_CHECKING
+if TYPE_CHECKING:
+    import napari
 
 @register_function(
     menu="Measurement > Measure intensities on surface (n-STRESS)"

src/napari_stress/_measurements/stresses.py

@@ -1,4 +1,6 @@
-from typing import Tuple
+from typing import Tuple, TYPE_CHECKING
+if TYPE_CHECKING:
+    import napari
 
 import numpy as np
 import pandas as pd

src/napari_stress/_measurements/toolbox.py

@@ -1,6 +1,9 @@
 import os
 from pathlib import Path
-from typing import List
+from typing import List, TYPE_CHECKING
+
+if TYPE_CHECKING:
+    import napari
 
 import numpy as np
 from magicgui.widgets import create_widget
@@ -41,7 +44,7 @@ def __init__(self, napari_viewer):
         # populate quadrature dropdown: Only specific n_quadrature points
         # are allowed
         points_lookup = lebedev_info_SPB.quad_deg_lookUp
-        for n_points in points_lookup.keys():
+        for n_points in points_lookup:
             self.comboBox_quadpoints.addItem(str(n_points), n_points)
 
         # select default value corresponding to current max_degree
@@ -128,7 +131,7 @@ def _check_minimal_point_number(self) -> None:
         max_degree = self.spinBox_max_degree.value()
         lookup = lebedev_info_SPB.pts_of_lbdv_lookup
         for degree in range(max_degree, list(lookup.keys())[-1] + 1):
-            if degree in lookup.keys():
+            if degree in lookup:
                 minimal_point_number = lookup.get(degree)
                 break
 
@@ -249,15 +252,15 @@ def _export(self, results_stress_analysis):
             n_frames=self.n_frames,
         )
 
-        for fig in figures_dict.keys():
+        for fig in figures_dict:
             figure = figures_dict[fig]
             figure["figure"].tight_layout()
             figure["figure"].savefig(
                 os.path.join(figure_directory, figure["path"])
             )
 
         # Export pointclouds
-        for i, layer in enumerate(results_stress_analysis):
+        for layer in results_stress_analysis:
             if layer[2] == "points":
                 export_layer = napari.layers.Layer.create(*layer)
                 napari.save_layers(

src/napari_stress/_reconstruction/fit_utils.py

@@ -1,6 +1,8 @@
 import inspect
 from enum import Enum
-from typing import List
+from typing import List, TYPE_CHECKING
+if TYPE_CHECKING:
+    import napari
 
 import numpy as np
 import pandas as pd
@@ -221,7 +223,7 @@ def _fancy_edge_fit(
         parameter_error = np.sqrt(np.diag(_covariance))
 
     # If fit fails, replace bad values with NaN
-    except Exception:
+    except (RuntimeError, ValueError):
         optimal_fit_parameters = np.repeat(np.nan, len(params))
         parameter_error = np.repeat(np.nan, len(params))
 

src/napari_stress/_reconstruction/patches.py

@@ -1,4 +1,6 @@
-from typing import Tuple
+from typing import Tuple, TYPE_CHECKING
+if TYPE_CHECKING:
+    import napari
 
 import numpy as np
 
@@ -472,7 +474,7 @@ def iterative_curvature_adaptive_patch_fitting(
         point_cloud, minimum_permitted_range=minimum_search_radius
     )
 
-    for it in range(n_iterations):
+    for _ in range(n_iterations):
         neighbor_indices = _find_neighbor_indices(point_cloud, search_radii)
         mean_curvatures = [np.nan] * len(point_cloud)
         principal_curvatures = [np.nan] * len(point_cloud)

src/napari_stress/_reconstruction/reconstruct_surface.py

@@ -3,6 +3,11 @@
 
 from .._utils.frame_by_frame import frame_by_frame
 
+from typing import TYPE_CHECKING
+if TYPE_CHECKING:
+    import napari
+
+
 
 @register_function(
     menu="Surfaces > Create surface from lebedev points (n-STRESS)"

src/napari_stress/_reconstruction/refine_surfaces.py

@@ -1,5 +1,7 @@
 import warnings
-from typing import List
+from typing import List, TYPE_CHECKING
+if TYPE_CHECKING:
+    import napari
 
 import numpy as np
 import pandas as pd

src/napari_stress/_reconstruction/toolbox.py

@@ -1,6 +1,8 @@
 import os
 from pathlib import Path
-from typing import List
+from typing import List, TYPE_CHECKING
+if TYPE_CHECKING:
+    import napari
 
 import numpy as np
 from magicgui.widgets import create_widget
@@ -68,7 +70,7 @@ def _set_scales(self):
             # set target voxel size to mean of scales as default
             mean_scale = np.mean([scales[0], scales[2]])
             self.doubleSpinBox_target_voxelsize.setValue(mean_scale)
-        except Exception:
+        except Exception as e:
             pass
 
     def _export_settings(self, file_name: str = None):
@@ -78,13 +80,9 @@ def _export_settings(self, file_name: str = None):
         from .._utils.import_export_settings import export_settings
 
         reconstruction_parameters = {
-            "voxelsize": np.asarray(
-                [
-                    self.doubleSpinBox_voxelsize_z.value(),
-                    self.doubleSpinBox_voxelsize_y.value(),
-                    self.doubleSpinBox_voxelsize_x.value(),
-                ]
-            ),
+            "voxelsize_z": self.doubleSpinBox_voxelsize_z.value(),
+            "voxelsize_y": self.doubleSpinBox_voxelsize_y.value(),
+            "voxelsize_x": self.doubleSpinBox_voxelsize_x.value(),
             "target_voxelsize": self.doubleSpinBox_target_voxelsize.value(),
             "smoothing_sigma": self.doubleSpinBox_gaussian_blur.value(),
             "n_smoothing_iterations": self.spinBox_n_smoothing.value(),
@@ -111,13 +109,13 @@ def _import_settings(self, file_name: str = None):
         reconstruction_parameters = import_settings(self, file_name=file_name)
 
         self.doubleSpinBox_voxelsize_z.setValue(
-            reconstruction_parameters["voxelsize"][0]
+            reconstruction_parameters["voxelsize_z"]
         )
         self.doubleSpinBox_voxelsize_y.setValue(
-            reconstruction_parameters["voxelsize"][1]
+            reconstruction_parameters["voxelsize_y"]
         )
         self.doubleSpinBox_voxelsize_x.setValue(
-            reconstruction_parameters["voxelsize"][2]
+            reconstruction_parameters["voxelsize_x"]
         )
         self.doubleSpinBox_target_voxelsize.setValue(
             reconstruction_parameters["target_voxelsize"]
@@ -324,7 +322,7 @@ def reconstruct_droplet(
     points = copy.deepcopy(points_first_guess)
 
     # repeat tracing `n_tracing_iterations` times
-    for i in range(n_tracing_iterations):
+    for _ in range(n_tracing_iterations):
         resampled_points = resample_pointcloud(
             points, sampling_length=resampling_length
         )

src/napari_stress/_spherical_harmonics/spherical_harmonics_napari.py

@@ -107,10 +107,10 @@ def perform_lebedev_quadrature(
     """
     metadata = points.metadata
 
-    if "spherical_harmonics_coefficients" not in metadata.keys():
+    if "spherical_harmonics_coefficients" not in metadata:
         raise ValueError(
             "Missing spherical harmonics coefficients. "
-            + "Use spherical harmonics expansion first"
+            "Use spherical harmonics expansion first"
         )
 
     max_degree = metadata["spherical_harmonics_coefficients"].shape[-1] - 1

src/napari_stress/_stress/euclidian_k_form_SPB.py

@@ -2042,14 +2042,12 @@ def Divergence_1_Form(self, lbdv, debug_mode=False):
 
             if debug_mode is True:
                 print(
-                    "\n"
-                    + "All_A_inv_successful = "
+                    "\nAll_A_inv_successful = "
                     + str(All_A_inv_successful)
                 )
                 print(
                     "All_B_inv_successful = "
-                    + str(All_B_inv_successful)
-                    + "\n"
+                    + str(All_B_inv_successful) + "\n"
                 )
                 return Debug_Dict
             else:

src/napari_stress/_stress/lebedev_info_SPB.py

@@ -638,18 +638,16 @@ def __init__(
                         -1 * np.cos(theta_bar_pt_rot) * np.sin(phi_bar_pt_rot)
                     )
 
-                    if abs(x_pt - x_pt_rot) < 1e-7:
-                        if abs(y_pt - y_pt_rot) < 1e-7:
-                            if abs(z_pt - z_pt_rot) < 1e-7:
-                                if rot_pt_found is False:
-                                    rot_pt_found = True
-
-                                    self.Rot_Lbdv_Quad_vals[quad_pt] = (
-                                        quad_pt_rot
-                                    )
-                                    self.Inv_Rot_Lbdv_Quad_vals[
-                                        quad_pt_rot
-                                    ] = quad_pt
+                    if all(abs(pt - pt_rot) < 1e-7 for pt, pt_rot in zip((x_pt, y_pt, z_pt), (x_pt_rot, y_pt_rot, z_pt_rot))):
+                        if rot_pt_found is False:
+                            rot_pt_found = True
+
+                            self.Rot_Lbdv_Quad_vals[quad_pt] = (
+                                quad_pt_rot
+                            )
+                            self.Inv_Rot_Lbdv_Quad_vals[
+                                quad_pt_rot
+                            ] = quad_pt
 
                 if rot_pt_found is False:
                     print("!!ROTATED QUAD PT NOT FOUND!!")