Rename Display Pyramid to Pyramidal Downsampling and align pyramid outputs

docs/source/conf.py

@@ -9,7 +9,6 @@
 import sys
 import types
 
-
 sys.path.insert(0, os.path.abspath("../../src"))
 
 

examples/scripts/registration/image_registration_class.py

@@ -105,4 +105,3 @@ def main_class_based():
 
 if __name__ == "__main__":
     main_class_based()
-

examples/scripts/registration/register_round_function.py

@@ -73,4 +73,3 @@ def main_functional():
 
 if __name__ == "__main__":
     main_functional()
-

setup.py

@@ -4,7 +4,6 @@
 
 from setuptools import setup
 
-
 if sys.version_info[:2] != (3, 12):
     detected = ".".join(str(part) for part in sys.version_info[:3])
     raise RuntimeError(

src/clearex/context/__init__.py

@@ -23,4 +23,3 @@
 #  IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
 #  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 #  POSSIBILITY OF SUCH DAMAGE.
-

src/clearex/detect/pipeline.py

@@ -54,7 +54,14 @@
 
 
 DetectionsArray = np.ndarray
-RegionBounds = tuple[tuple[int, int], tuple[int, int], tuple[int, int], tuple[int, int], tuple[int, int], tuple[int, int]]
+RegionBounds = tuple[
+    tuple[int, int],
+    tuple[int, int],
+    tuple[int, int],
+    tuple[int, int],
+    tuple[int, int],
+    tuple[int, int],
+]
 ProgressCallback = Callable[[int, str], None]
 
 _PARTICLE_COLUMNS = (
@@ -134,9 +141,7 @@ def _normalize_particle_parameters(
     normalized["remove_close_particles"] = bool(
         normalized.get("remove_close_particles", False)
     )
-    normalized["min_distance_sigma"] = float(
-        normalized.get("min_distance_sigma", 10.0)
-    )
+    normalized["min_distance_sigma"] = float(normalized.get("min_distance_sigma", 10.0))
     overlap_zyx = normalized.get("overlap_zyx", [0, 0, 0])
     if not isinstance(overlap_zyx, (tuple, list)) or len(overlap_zyx) != 3:
         raise ValueError(
@@ -162,12 +167,13 @@ def _axis_chunk_bounds(size: int, chunk_size: int) -> list[tuple[int, int]]:
         Ordered ``(start, stop)`` bounds covering the full axis.
     """
     return [
-        (start, min(start + chunk_size, size))
-        for start in range(0, size, chunk_size)
+        (start, min(start + chunk_size, size)) for start in range(0, size, chunk_size)
     ]
 
 
-def _region_to_slices(region: RegionBounds) -> tuple[slice, slice, slice, slice, slice, slice]:
+def _region_to_slices(
+    region: RegionBounds,
+) -> tuple[slice, slice, slice, slice, slice, slice]:
     """Convert six-axis integer bounds into Python slices.
 
     Parameters
@@ -635,6 +641,7 @@ def run_particle_detection_analysis(
     ValueError
         If required source data are missing or channel index is out of bounds.
     """
+
     def _emit(percent: int, message: str) -> None:
         if progress_callback is None:
             return

src/clearex/file_operations/__init__.py

@@ -23,4 +23,3 @@
 #  IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
 #  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 #  POSSIBILITY OF SUCH DAMAGE.
-

src/clearex/filter/__init__.py

@@ -23,4 +23,3 @@
 #  IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
 #  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 #  POSSIBILITY OF SUCH DAMAGE.
-

src/clearex/filter/filters.py

@@ -32,11 +32,11 @@
 import numpy as np
 from skimage import filters as skfilters
 
-
 # Local Imports
 
+
 def fwhm_to_sigma(fwhm_px: float) -> float:
-    """ Convert from FWHM to sigma.
+    """Convert from FWHM to sigma.
 
     FWHM = 2*sqrt(2*ln2)*sigma ≈ 2.35482*sigma
 

src/clearex/filter/kernels.py

@@ -50,7 +50,7 @@ def make_3d_structured_element(radius: int, shape: str = "sphere") -> np.ndarray
 
     radius = int(radius)
     structured_element = np.zeros((radius, radius, radius))
-    (z_len, y_len, x_len) = structured_element.shape
+    z_len, y_len, x_len = structured_element.shape
 
     if shape == "sphere":
         for i in range(int(z_len)):