refactor: remove Optional and more generic dirs, fix redundant code line

cryoet_data_portal_neuroglancer/models/json_generator.py

@@ -131,7 +131,6 @@ def _create_shader_and_controls(self) -> dict[str, Any]:
             self.contrast_limits = self._compute_contrast_limits()
         if self.threedee_contrast_limits is None:
             self.threedee_contrast_limits = self.contrast_limits
-        self.threedee_contrast_limits = self.threedee_contrast_limits
         if self.has_volume_rendering_shader:
             shader_builder = ImageWithVolumeRenderingShaderBuilder(
                 contrast_limits=self.contrast_limits,

cryoet_data_portal_neuroglancer/precompute/contrast_limits.py

@@ -2,11 +2,12 @@
 
 import logging
 from pathlib import Path
-from typing import Literal, Optional
+from typing import Literal
 
 import dask.array as da
 import numpy as np
 from scipy.signal import find_peaks
+from scipy.spatial.distance import euclidean
 from sklearn.mixture import GaussianMixture
 
 from cryoet_data_portal_neuroglancer.utils import ParameterOptimizer
@@ -60,14 +61,10 @@ def compute_contrast_limits(
     return calculator.compute_contrast_limit()
 
 
-def _euclidean_distance(x: tuple[float, float], y: tuple[float, float]) -> float:
-    return np.sqrt(((x[0] - y[0]) ** 2) + ((x[1] - y[1]) ** 2))
-
-
 def _restrict_volume_around_central_z_slice(
     volume: "np.ndarray",
-    central_z_slice: Optional[int] = None,
-    z_radius: Optional[int] = 5,
+    central_z_slice: int | None = None,
+    z_radius: int | None = 5,
 ) -> "np.ndarray":
     """Restrict a 3D volume to a region around a central z-slice.
 
@@ -78,7 +75,7 @@ def _restrict_volume_around_central_z_slice(
         central_z_slice: int or None, optional.
             The central z-slice around which to restrict the volume.
             By default None, in which case the central z-slice is the middle slice.
-        z_radius: int, optional.
+        z_radius: int or None, optional.
             The number of z-slices to include above and below the central z-slice.
             By default 5,
             If it is None, it is auto computed - but this can be problematic for large volumes.
@@ -112,7 +109,7 @@ def _restrict_volume_around_central_z_slice(
 
 class ContrastLimitCalculator:
 
-    def __init__(self, volume: Optional["np.ndarray"] = None):
+    def __init__(self, volume: "np.ndarray" | None = None):
         """Initialize the contrast limit calculator.
 
         Parameters
@@ -125,8 +122,8 @@ def __init__(self, volume: Optional["np.ndarray"] = None):
     def set_volume_and_z_limits(
         self,
         volume: "np.ndarray",
-        central_z_slice: Optional[int] = None,
-        z_radius: Optional[int] = None,
+        central_z_slice: int | None = None,
+        z_radius: int | None = None,
     ) -> None:
         """Set the volume and z-limits for calculating contrast limits.
 
@@ -146,8 +143,8 @@ def set_volume_and_z_limits(
 
     def trim_volume_around_central_zslice(
         self,
-        central_z_slice: Optional[int] = None,
-        z_radius: Optional[int] = None,
+        central_z_slice: int | None = None,
+        z_radius: int | None = None,
     ) -> None:
         """Trim the volume around a central z-slice.
 
@@ -261,7 +258,7 @@ def _objective(params):
         return best, contrast_limits
 
     def objective_function(self, params, real_limits):
-        return _euclidean_distance(
+        return euclidean(
             self._objective_function(params),
             real_limits,
         )
@@ -412,7 +409,7 @@ def _define_parameter_space(self, parameter_optimizer):
 
 class CDFContrastLimitCalculator(ContrastLimitCalculator):
 
-    def __init__(self, volume: Optional["np.ndarray"] = None):
+    def __init__(self, volume: "np.ndarray" | None = None):
         """Initialize the contrast limit calculator.
 
         Parameters

cryoet_data_portal_neuroglancer/precompute/volume_rendering.py

@@ -1,6 +1,5 @@
 import multiprocessing as mp
 from multiprocessing import shared_memory
-from typing import Optional
 
 import numpy as np
 from tqdm import tqdm
@@ -41,7 +40,7 @@ def volume_render(
     contrast_limits: tuple[float, float],
     exponential_gain: float = 0.0,
     depth_samples: int = 64,
-    num_workers: Optional[int] = None,
+    num_workers: int | None = None,
 ):
     if num_workers is None:
         num_workers = mp.cpu_count()

manual_tests/tuning_contrast_limits_from_api.py

@@ -22,7 +22,7 @@
 # Set up logging - level is info
 # logging.basicConfig(level=logging.INFO, force=True)
 
-OUTPUT_FOLDER = "/media/starfish/LargeSSD/data/cryoET/data/FromAPI"
+OUTPUT_FOLDER = Path.cwd() / "contrast_limits_from_api"
 
 id_to_path_map = {
     1000: "1000/16.zarr",

manual_tests/volume_contrast_limits.py

@@ -16,7 +16,7 @@
 # Set up logging - level is info
 # logging.basicConfig(level=logging.INFO, force=True)
 
-OUTPUT_FOLDER = "/media/starfish/LargeSSD/data/cryoET/data/FromAPI"
+OUTPUT_FOLDER = Path.cwd() / "volume_contrast_limits"
 
 id_to_path_map = {
     773: "773/Position_513.zarr",