.gitignore

@@ -13,6 +13,7 @@ build/
 .idea/
 .cache/
 .pytest_cache/
+.ruff_cache/
 *.swp
 *.swo
 *.pyc

.pre-commit-config.yaml

+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    -   id: detect-private-key
+    -   id: check-added-large-files
+    -   id: check-docstring-first
+    -   id: debug-statements
+    -   id: double-quote-string-fixer
+    -   id: name-tests-test
+
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.7
+    hooks:
+      # Run the formatter and fix code styling
+    - id: ruff-format
+
+    # Run the linter and fix what is possible
+    - id: ruff
+      args: ['--fix']
\ No newline at end of file

docs/doc/cli/cli.md

@@ -44,7 +44,7 @@ The command line interface allows you to run graphical user interfaces directly
 
 !!! Example
 
-    Here's an example of how to open the [Data Explorer](gui.md#qim3d.gui.data_explorer)
+    Here's an example of how to open the [Data Explorer](../gui/gui.md#qim3d.gui.data_explorer)
 
     ``` title="Command"
     qim3d gui --data-explorer

docs/doc/data_handling/io.md

@@ -8,5 +8,5 @@
             - Downloader
             - export_ome_zarr
             - import_ome_zarr
-            - save_mesh
-            - load_mesh
\ No newline at end of file
+            - load_mesh
+            - save_mesh
\ No newline at end of file

docs/doc/gui/gui.md

@@ -21,7 +21,7 @@ The `qim3d` library provides a set of custom made GUIs that ease the interaction
     ```
 
 In general, the GUIs can be launched directly from the command line. 
-For details see [here](cli.md#qim3d-gui).
+For details see [here](../cli/cli.md#qim3d-gui).
 
 ::: qim3d.gui.data_explorer
     options:

docs/doc/releases/releases.md

@@ -11,7 +11,7 @@ hide:
 
 Below, you'll find details about the version history of `qim3d`.
 
-Remember to keep your pip installation [up to date](index.md/#get-the-latest-version) so that you have the latest features!
+Remember to keep your pip installation [up to date](../../index.md/#get-the-latest-version) so that you have the latest features!
 
 ### v1.0.0 (21/01/2025)
 

docs/doc/visualization/viz.md

@@ -23,6 +23,8 @@ The `qim3d` library aims to provide easy ways to explore and get insights from v
             - plot_cc
             - colormaps
             - fade_mask
+            - line_profile
+            - threshold
             
 ::: qim3d.viz.colormaps
     options:

pyproject.toml

+# See list of rules here: https://docs.astral.sh/ruff/rules/
+
+[tool.ruff]
+line-length = 88
+indent-width = 4
+
+[tool.ruff.lint]
+# Allow fix for all enabled rules (when `--fix`) is provided.
+fixable = ["ALL"]
+unfixable = []
+
+# Allow unused variables when underscore-prefixed
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+
+select = [
+    "F",
+    "E",        # Errors
+    "W",        # Warnings
+    "I",        # Imports
+    "N",        # Naming
+    "D",        # Documentation
+    "UP",       # Upgrades
+    "YTT",
+    "ANN",
+    "ASYNC",
+    "S",
+    "BLE",
+    "B",
+    "A",
+    "COM",
+    "C4",
+    "T10",
+    "DJ",
+    "EM",
+    "EXE",
+    "ISC",
+    "LOG",
+    "PIE",
+    "PYI",
+    "PT",
+    "RSE",
+    "SLF",
+    "SLOT",
+    "SIM",
+    "TID",
+    "TCH",
+    "INT",
+    "ERA",
+    "PGH",
+]
+
+ignore = [
+    "F821",
+    "F841",
+    "E501",
+    "E731",
+    "D100",
+    "D101",
+    "D107",
+    "D201", 
+    "D202",
+    "D205",
+    "D211",
+    "D212",
+    "D401", 
+    "D407", 
+    "ANN002",
+    "ANN003",
+    "ANN101",
+    "ANN201",
+    "ANN204",
+    "S101",
+    "S301",
+    "S311",
+    "S507",
+    "S603",
+    "S605",
+    "S607",
+    "B008",
+    "B026",
+    "B028",
+    "B905",
+    "W291",
+    "W293",
+    "COM812",
+    "ISC001",
+    "SIM113",
+]
+
+[tool.ruff.format]
+# Use single quotes for strings
+quote-style = "single"
\ No newline at end of file

qim3d/__init__.py

-"""qim3d: A Python package for 3D image processing and visualization.
+"""
+qim3d: A Python package for 3D image processing and visualization.
 
-The qim3d library is designed to make it easier to work with 3D imaging data in Python. 
+The qim3d library is designed to make it easier to work with 3D imaging data in Python.
 It offers a range of features, including data loading and manipulation,
 image processing and filtering, visualization of 3D data, and analysis of imaging results.
 
@@ -8,13 +9,14 @@ Documentation available at https://platform.qim.dk/qim3d/
 
 """
 
-__version__ = "1.0.0"
+__version__ = '1.1.0'
 
 
 import importlib as _importlib
 
 
 class _LazyLoader:
+
     """Lazy loader to load submodules only when they are accessed"""
 
     def __init__(self, module_name):
@@ -48,7 +50,7 @@ _submodules = [
     'mesh',
     'features',
     'operations',
-    'detection'
+    'detection',
 ]
 
 # Creating lazy loaders for each submodule

qim3d/cli/__init__.py

 import argparse
-import webbrowser
+import os
 import platform
+import webbrowser
+
 import outputformat as ouf
+
 import qim3d
-import os
 
 QIM_TITLE = ouf.rainbow(
     rf"""
@@ -16,126 +18,123 @@ QIM_TITLE = ouf.rainbow(
 
     """,
     return_str=True,
-    cmap="hot",
+    cmap='hot',
 )
 
 
 def parse_tuple(arg):
     # Remove parentheses if they are included and split by comma
-    return tuple(map(int, arg.strip("()").split(",")))
+    return tuple(map(int, arg.strip('()').split(',')))
 
 
 def main():
-    parser = argparse.ArgumentParser(description="qim3d command-line interface.")
-    subparsers = parser.add_subparsers(title="Subcommands", dest="subcommand")
+    parser = argparse.ArgumentParser(description='qim3d command-line interface.')
+    subparsers = parser.add_subparsers(title='Subcommands', dest='subcommand')
 
     # GUIs
-    gui_parser = subparsers.add_parser("gui", help="Graphical User Interfaces.")
+    gui_parser = subparsers.add_parser('gui', help='Graphical User Interfaces.')
 
     gui_parser.add_argument(
-        "--data-explorer", action="store_true", help="Run data explorer."
-    )
-    gui_parser.add_argument("--iso3d", action="store_true", help="Run iso3d.")
-    gui_parser.add_argument(
-        "--annotation-tool", action="store_true", help="Run annotation tool."
+        '--data-explorer', action='store_true', help='Run data explorer.'
     )
+    gui_parser.add_argument('--iso3d', action='store_true', help='Run iso3d.')
     gui_parser.add_argument(
-        "--local-thickness", action="store_true", help="Run local thickness tool."
+        '--annotation-tool', action='store_true', help='Run annotation tool.'
     )
     gui_parser.add_argument(
-        "--layers", action="store_true", help="Run Layers."
+        '--local-thickness', action='store_true', help='Run local thickness tool.'
     )
-    gui_parser.add_argument("--host", default="0.0.0.0", help="Desired host.")
+    gui_parser.add_argument('--layers', action='store_true', help='Run Layers.')
+    gui_parser.add_argument('--host', default='0.0.0.0', help='Desired host.')
     gui_parser.add_argument(
-        "--platform", action="store_true", help="Use QIM platform address"
+        '--platform', action='store_true', help='Use QIM platform address'
     )
     gui_parser.add_argument(
-        "--no-browser", action="store_true", help="Do not launch browser."
+        '--no-browser', action='store_true', help='Do not launch browser.'
     )
 
     # Viz
-    viz_parser = subparsers.add_parser("viz", help="Volumetric visualization.")
-    viz_parser.add_argument("source", help="Path to the image file")
+    viz_parser = subparsers.add_parser('viz', help='Volumetric visualization.')
+    viz_parser.add_argument('source', help='Path to the image file')
     viz_parser.add_argument(
-        "-m",
-        "--method",
+        '-m',
+        '--method',
         type=str,
-        metavar="METHOD",
-        default="itk-vtk",
-        help="Which method is used to display file.",
+        metavar='METHOD',
+        default='itk-vtk',
+        help='Which method is used to display file.',
     )
     viz_parser.add_argument(
-        "--destination", default="k3d.html", help="Path to save html file."
+        '--destination', default='k3d.html', help='Path to save html file.'
     )
     viz_parser.add_argument(
-        "--no-browser", action="store_true", help="Do not launch browser."
+        '--no-browser', action='store_true', help='Do not launch browser.'
     )
 
     # Preview
     preview_parser = subparsers.add_parser(
-        "preview", help="Preview of the image in CLI"
+        'preview', help='Preview of the image in CLI'
     )
     preview_parser.add_argument(
-        "filename",
+        'filename',
         type=str,
-        metavar="FILENAME",
-        help="Path to image that will be displayed",
+        metavar='FILENAME',
+        help='Path to image that will be displayed',
     )
     preview_parser.add_argument(
-        "--slice",
+        '--slice',
         type=int,
-        metavar="S",
+        metavar='S',
         default=None,
-        help="Specifies which slice of the image will be displayed.\nDefaults to middle slice. If number exceeds number of slices, last slice will be displayed.",
+        help='Specifies which slice of the image will be displayed.\nDefaults to middle slice. If number exceeds number of slices, last slice will be displayed.',
     )
     preview_parser.add_argument(
-        "--axis",
+        '--axis',
         type=int,
-        metavar="AX",
+        metavar='AX',
         default=0,
-        help="Specifies from which axis will be the slice taken. Defaults to 0.",
+        help='Specifies from which axis will be the slice taken. Defaults to 0.',
     )
     preview_parser.add_argument(
-        "--resolution",
+        '--resolution',
         type=int,
-        metavar="RES",
+        metavar='RES',
         default=80,
-        help="Resolution of displayed image. Defaults to 80.",
+        help='Resolution of displayed image. Defaults to 80.',
     )
     preview_parser.add_argument(
-        "--absolute_values",
-        action="store_false",
-        help="By default set the maximum value to be 255 so the contrast is strong. This turns it off.",
+        '--absolute_values',
+        action='store_false',
+        help='By default set the maximum value to be 255 so the contrast is strong. This turns it off.',
     )
 
     # File Convert
     convert_parser = subparsers.add_parser(
-        "convert",
-        help="Convert files to different formats without loading the entire file into memory",
+        'convert',
+        help='Convert files to different formats without loading the entire file into memory',
     )
     convert_parser.add_argument(
-        "input_path",
+        'input_path',
         type=str,
-        metavar="Input path",
-        help="Path to image that will be converted",
+        metavar='Input path',
+        help='Path to image that will be converted',
     )
     convert_parser.add_argument(
-        "output_path",
+        'output_path',
         type=str,
-        metavar="Output path",
-        help="Path to save converted image",
+        metavar='Output path',
+        help='Path to save converted image',
     )
     convert_parser.add_argument(
-        "--chunks",
+        '--chunks',
         type=parse_tuple,
-        metavar="Chunk shape",
+        metavar='Chunk shape',
         default=(64, 64, 64),
-        help="Chunk size for the zarr file. Defaults to (64, 64, 64).",
+        help='Chunk size for the zarr file. Defaults to (64, 64, 64).',
     )
     args = parser.parse_args()
 
-    if args.subcommand == "gui":
-
+    if args.subcommand == 'gui':
         arghost = args.host
         inbrowser = not args.no_browser  # Should automatically open in browser
 
@@ -152,7 +151,7 @@ def main():
             interface_class = qim3d.gui.layers2d.Interface
         else:
             print(
-                "Please select a tool by choosing one of the following flags:\n\t--data-explorer\n\t--iso3d\n\t--annotation-tool\n\t--local-thickness"
+                'Please select a tool by choosing one of the following flags:\n\t--data-explorer\n\t--iso3d\n\t--annotation-tool\n\t--local-thickness'
             )
             return
         interface = (
@@ -164,31 +163,27 @@ def main():
         else:
             interface.launch(inbrowser=inbrowser, force_light_mode=False)
 
-    elif args.subcommand == "viz":
-
-        if args.method == "itk-vtk":
-
+    elif args.subcommand == 'viz':
+        if args.method == 'itk-vtk':
             # We need the full path to the file for the viewer
             current_dir = os.getcwd()
             full_path = os.path.normpath(os.path.join(current_dir, args.source))
-            qim3d.viz.itk_vtk(full_path, open_browser = not args.no_browser)
+            qim3d.viz.itk_vtk(full_path, open_browser=not args.no_browser)
 
-
-        elif args.method == "k3d":
+        elif args.method == 'k3d':
             volume = qim3d.io.load(str(args.source))
-            print("\nGenerating k3d plot...")
+            print('\nGenerating k3d plot...')
             qim3d.viz.volumetric(volume, show=False, save=str(args.destination))
-            print(f"Done, plot available at <{args.destination}>")
+            print(f'Done, plot available at <{args.destination}>')
             if not args.no_browser:
-                print("Opening in default browser...")
+                print('Opening in default browser...')
                 webbrowser.open_new_tab(args.destination)
         else:
             raise NotImplementedError(
                 f"Method '{args.method}' is not valid. Try 'k3d' or default 'itk-vtk-viewer'"
             )
 
-    elif args.subcommand == "preview":
-
+    elif args.subcommand == 'preview':
         image = qim3d.io.load(args.filename)
 
         qim3d.viz.image_preview(
@@ -199,22 +194,21 @@ def main():
             relative_intensity=args.absolute_values,
         )
 
-    elif args.subcommand == "convert":
-
+    elif args.subcommand == 'convert':
         qim3d.io.convert(args.input_path, args.output_path, chunk_shape=args.chunks)
 
     elif args.subcommand is None:
         print(QIM_TITLE)
         welcome_text = (
-            "\nqim3d is a Python package for 3D image processing and visualization.\n"
+            '\nqim3d is a Python package for 3D image processing and visualization.\n'
             f"For more information, please visit {ouf.c('https://platform.qim.dk/qim3d/', color='orange', return_str=True)}\n"
-            " \n"
+            ' \n'
             "For more information on each subcommand, type 'qim3d <subcommand> --help'.\n"
         )
         print(welcome_text)
         parser.print_help()
-        print("\n")
+        print('\n')
 
 
-if __name__ == "__main__":
+if __name__ == '__main__':
     main()

qim3d/detection/__init__.py

-from qim3d.detection._common_detection_methods import *
\ No newline at end of file
+from qim3d.detection._common_detection_methods import *

qim3d/detection/_common_detection_methods.py

-""" Blob detection using Difference of Gaussian (DoG) method """
+"""Blob detection using Difference of Gaussian (DoG) method"""
 
 import numpy as np
+
 from qim3d.utils._logger import log
 
-__all__ = ["blobs"]
+__all__ = ['blobs']
+
 
 def blobs(
     vol: np.ndarray,
-    background: str = "dark",
+    background: str = 'dark',
     min_sigma: float = 1,
     max_sigma: float = 50,
     sigma_ratio: float = 1.6,
@@ -56,18 +58,19 @@ def blobs(
             # Visualize detected blobs
             qim3d.viz.circles(blobs, vol, alpha=0.8, color='blue')
             ```
-            ![blob detection](../../assets/screenshots/blob_detection.gif)    
+            ![blob detection](../../assets/screenshots/blob_detection.gif)
 
             ```python
             # Visualize binary binary_volume
             qim3d.viz.slicer(binary_volume)
             ```
             ![blob detection](../../assets/screenshots/blob_get_mask.gif)
+
     """
     from skimage.feature import blob_dog
 
-    if background == "bright":
-        log.info("Bright background selected, volume will be inverted.")
+    if background == 'bright':
+        log.info('Bright background selected, volume will be inverted.')
         vol = np.invert(vol)
 
     blobs = blob_dog(
@@ -109,8 +112,8 @@ def blobs(
             (x_indices - x) ** 2 + (y_indices - y) ** 2 + (z_indices - z) ** 2
         )
 
-        binary_volume[z_start:z_end, y_start:y_end, x_start:x_end][
-            dist <= radius
-        ] = True
+        binary_volume[z_start:z_end, y_start:y_end, x_start:x_end][dist <= radius] = (
+            True
+        )
 
     return blobs, binary_volume

qim3d/examples/__init__.py

-""" Example images for testing and demonstration purposes. """
+"""Example images for testing and demonstration purposes."""
 
 from pathlib import Path as _Path
-from qim3d.utils._logger import log as _log
+
 from qim3d.io import load as _load
+from qim3d.utils._logger import log as _log
 
 # Save the original log level and set to ERROR
 # to suppress the log messages during loading
 _original_log_level = _log.level
-_log.setLevel("ERROR")
+_log.setLevel('ERROR')
 
 # Load image examples
-for _file_path in _Path(__file__).resolve().parent.glob("*.tif"):
+for _file_path in _Path(__file__).resolve().parent.glob('*.tif'):
     globals().update({_file_path.stem: _load(_file_path, progress_bar=False)})
 
 # Restore the original log level

qim3d/features/__init__.py

-from ._common_features_methods import volume, area, sphericity
+from ._common_features_methods import area, sphericity, volume

qim3d/features/_common_features_methods.py

 import numpy as np
-import qim3d.processing
+import qim3d
 from qim3d.utils._logger import log
-import trimesh
 import qim3d
+from pygel3d import hmesh
 
-
-def volume(obj: np.ndarray|trimesh.Trimesh, 
-           **mesh_kwargs
-           ) -> float:
+def volume(obj: np.ndarray|hmesh.Manifold) -> float:
     """
-    Compute the volume of a 3D volume or mesh.
+    Compute the volume of a 3D mesh using the Pygel3D library.
 
     Args:
-        obj (np.ndarray or trimesh.Trimesh): Either a np.ndarray volume or a mesh object of type trimesh.Trimesh.
-        **mesh_kwargs (Any): Additional arguments for mesh creation if the input is a volume.
+        obj (numpy.ndarray or pygel3d.hmesh.Manifold): Either a np.ndarray volume or a mesh object of type pygel3d.hmesh.Manifold.
 
     Returns:
         volume (float): The volume of the object.
-
+    
     Example:
         Compute volume from a mesh:
         ```python
@@ -27,8 +23,8 @@ def volume(obj: np.ndarray|trimesh.Trimesh,
         mesh = qim3d.io.load_mesh('path/to/mesh.obj')
 
         # Compute the volume of the mesh
-        vol = qim3d.features.volume(mesh)
-        print('Volume:', vol)
+        volume = qim3d.features.volume(mesh)
+        print(f'Volume: {volume}')
         ```
 
         Compute volume from a np.ndarray:
@@ -37,35 +33,30 @@ def volume(obj: np.ndarray|trimesh.Trimesh,
 
         # Generate a 3D blob
         synthetic_blob = qim3d.generate.noise_object(noise_scale = 0.015)
-        synthetic_blob = qim3d.generate.noise_object(noise_scale = 0.015)
 
         # Compute the volume of the blob
-        volume = qim3d.features.volume(synthetic_blob, level=0.5)
-        volume = qim3d.features.volume(synthetic_blob, level=0.5)
-        print('Volume:', volume)
+        volume = qim3d.features.volume(synthetic_blob)
+        print(f'Volume: {volume}')
         ```
 
     """
+
     if isinstance(obj, np.ndarray):
         log.info("Converting volume to mesh.")
-        obj = qim3d.mesh.from_volume(obj, **mesh_kwargs)
+        obj = qim3d.mesh.from_volume(obj)
 
-    return obj.volume
+    return hmesh.volume(obj)
 
-
-def area(obj: np.ndarray|trimesh.Trimesh, 
-         **mesh_kwargs
-         ) -> float:
+def area(obj: np.ndarray|hmesh.Manifold) -> float:
     """
-    Compute the surface area of a 3D volume or mesh.
+    Compute the surface area of a 3D mesh using the Pygel3D library.
 
     Args:
-        obj (np.ndarray or trimesh.Trimesh): Either a np.ndarray volume or a mesh object of type trimesh.Trimesh.
-        **mesh_kwargs (Any): Additional arguments for mesh creation if the input is a volume.
+        obj (numpy.ndarray or pygel3d.hmesh.Manifold): Either a np.ndarray volume or a mesh object of type pygel3d.hmesh.Manifold.
 
     Returns:
-        area (float): The surface area of the object.
-
+        area (float): The surface area of the object. 
+    
     Example:
         Compute area from a mesh:
         ```python
@@ -76,8 +67,7 @@ def area(obj: np.ndarray|trimesh.Trimesh,
 
         # Compute the surface area of the mesh
         area = qim3d.features.area(mesh)
-        area = qim3d.features.area(mesh)
-        print(f"Area: {area}")
+        print(f'Area: {area}')
         ```
 
         Compute area from a np.ndarray:
@@ -86,39 +76,30 @@ def area(obj: np.ndarray|trimesh.Trimesh,
 
         # Generate a 3D blob
         synthetic_blob = qim3d.generate.noise_object(noise_scale = 0.015)
-        synthetic_blob = qim3d.generate.noise_object(noise_scale = 0.015)
 
         # Compute the surface area of the blob
-        volume = qim3d.features.area(synthetic_blob, level=0.5)
-        volume = qim3d.features.area(synthetic_blob, level=0.5)
-        print('Area:', volume)
+        area = qim3d.features.area(synthetic_blob)
+        print(f'Area: {area}')
         ```
+    
     """
+
     if isinstance(obj, np.ndarray):
         log.info("Converting volume to mesh.")
-        obj = qim3d.mesh.from_volume(obj, **mesh_kwargs)
-        obj = qim3d.mesh.from_volume(obj, **mesh_kwargs)
-
-    return obj.area
+        obj = qim3d.mesh.from_volume(obj)
 
+    return hmesh.area(obj)
 
-def sphericity(obj: np.ndarray|trimesh.Trimesh, 
-               **mesh_kwargs
-               ) -> float:
+def sphericity(obj: np.ndarray|hmesh.Manifold) -> float:
     """
-    Compute the sphericity of a 3D volume or mesh.
-
-    Sphericity is a measure of how spherical an object is. It is defined as the ratio
-    of the surface area of a sphere with the same volume as the object to the object's
-    actual surface area.
+    Compute the sphericity of a 3D mesh using the Pygel3D library.
 
     Args:
-        obj (np.ndarray or trimesh.Trimesh): Either a np.ndarray volume or a mesh object of type trimesh.Trimesh.
-        **mesh_kwargs (Any): Additional arguments for mesh creation if the input is a volume.
+        obj (numpy.ndarray or pygel3d.hmesh.Manifold): Either a np.ndarray volume or a mesh object of type pygel3d.hmesh.Manifold.
 
     Returns:
-        sphericity (float): A float value representing the sphericity of the object.
-
+        sphericity (float): The sphericity of the object. 
+    
     Example:
         Compute sphericity from a mesh:
         ```python
@@ -129,7 +110,7 @@ def sphericity(obj: np.ndarray|trimesh.Trimesh,
 
         # Compute the sphericity of the mesh
         sphericity = qim3d.features.sphericity(mesh)
-        sphericity = qim3d.features.sphericity(mesh)
+        print(f'Sphericity: {sphericity}')
         ```
 
         Compute sphericity from a np.ndarray:
@@ -138,32 +119,25 @@ def sphericity(obj: np.ndarray|trimesh.Trimesh,
 
         # Generate a 3D blob
         synthetic_blob = qim3d.generate.noise_object(noise_scale = 0.015)
-        synthetic_blob = qim3d.generate.noise_object(noise_scale = 0.015)
 
         # Compute the sphericity of the blob
-        sphericity = qim3d.features.sphericity(synthetic_blob, level=0.5)
-        sphericity = qim3d.features.sphericity(synthetic_blob, level=0.5)
+        sphericity = qim3d.features.sphericity(synthetic_blob)
+        print(f'Sphericity: {sphericity}')
         ```
 
-    !!! info "Limitations due to pixelation"
-        Sphericity is particularly sensitive to the resolution of the mesh, as it directly impacts the accuracy of surface area and volume calculations.
-        Since the mesh is generated from voxel-based 3D volume data, the discrete nature of the voxels leads to pixelation effects that reduce the precision of sphericity measurements.
-        Higher resolution meshes may mitigate these errors but often at the cost of increased computational demands.
     """
+
     if isinstance(obj, np.ndarray):
         log.info("Converting volume to mesh.")
-        obj = qim3d.mesh.from_volume(obj, **mesh_kwargs)
-        obj = qim3d.mesh.from_volume(obj, **mesh_kwargs)
+        obj = qim3d.mesh.from_volume(obj)
 
     volume = qim3d.features.volume(obj)
     area = qim3d.features.area(obj)
-    volume = qim3d.features.volume(obj)
-    area = qim3d.features.area(obj)
 
     if area == 0:
-        log.warning("Surface area is zero, sphericity is undefined.")
+        log.warning('Surface area is zero, sphericity is undefined.')
         return np.nan
 
     sphericity = (np.pi ** (1 / 3) * (6 * volume) ** (2 / 3)) / area
-    log.info(f"Sphericity: {sphericity}")
-    return sphericity
+    # log.info(f"Sphericity: {sphericity}")
+    return sphericity
\ No newline at end of file

qim3d/filters/__init__.py

-from ._common_filter_methods import *
\ No newline at end of file
+from ._common_filter_methods import *

qim3d/filters/_common_filter_methods.py

 """Provides filter functions and classes for image processing"""
 
-from typing import Type, Union
+from typing import Type
 
+import dask.array as da
+import dask_image.ndfilters as dask_ndfilters
 import numpy as np
 from scipy import ndimage
 from skimage import morphology
-import dask.array as da
-import dask_image.ndfilters as dask_ndfilters
 
 from qim3d.utils import log
 
 __all__ = [
-    "FilterBase",
-    "Gaussian",
-    "Median",
-    "Maximum",
-    "Minimum",
-    "Pipeline",
-    "Tophat",
-    "gaussian",
-    "median",
-    "maximum",
-    "minimum",
-    "tophat",
+    'FilterBase',
+    'Gaussian',
+    'Median',
+    'Maximum',
+    'Minimum',
+    'Pipeline',
+    'Tophat',
+    'gaussian',
+    'median',
+    'maximum',
+    'minimum',
+    'tophat',
 ]
 
 
 class FilterBase:
-    def __init__(self, 
-                 *args, 
-                 dask: bool = False, 
-                 chunks: str = "auto", 
-                 **kwargs):
+    def __init__(self, *args, dask: bool = False, chunks: str = 'auto', **kwargs):
         """
         Base class for image filters.
 
         Args:
             *args: Additional positional arguments for filter initialization.
             **kwargs: Additional keyword arguments for filter initialization.
+
         """
         self.args = args
         self.dask = dask
@@ -54,6 +51,7 @@ class Gaussian(FilterBase):
             sigma (float): Standard deviation for Gaussian kernel.
             *args: Additional arguments.
             **kwargs: Additional keyword arguments.
+
         """
         super().__init__(*args, **kwargs)
         self.sigma = sigma
@@ -67,14 +65,22 @@ class Gaussian(FilterBase):
 
         Returns:
             The filtered image or volume.
+
         """
         return gaussian(
-            input, sigma=self.sigma, dask=self.dask, chunks=self.chunks, *self.args, **self.kwargs
+            input,
+            sigma=self.sigma,
+            dask=self.dask,
+            chunks=self.chunks,
+            *self.args,
+            **self.kwargs,
         )
 
 
 class Median(FilterBase):
-    def __init__(self, size: float = None, footprint: np.ndarray = None, *args, **kwargs):
+    def __init__(
+        self, size: float = None, footprint: np.ndarray = None, *args, **kwargs
+    ):
         """
         Median filter initialization.
 
@@ -83,6 +89,7 @@ class Median(FilterBase):
             footprint (np.ndarray, optional): The structuring element for filtering.
             *args: Additional arguments.
             **kwargs: Additional keyword arguments.
+
         """
         if size is None and footprint is None:
             raise ValueError("Either 'size' or 'footprint' must be provided.")
@@ -99,12 +106,22 @@ class Median(FilterBase):
 
         Returns:
             The filtered image or volume.
+
         """
-        return median(vol=input, size=self.size, footprint=self.footprint, dask=self.dask, chunks=self.chunks, **self.kwargs)
+        return median(
+            vol=input,
+            size=self.size,
+            footprint=self.footprint,
+            dask=self.dask,
+            chunks=self.chunks,
+            **self.kwargs,
+        )
 
 
 class Maximum(FilterBase):
-    def __init__(self, size: float = None, footprint: np.ndarray = None, *args, **kwargs):
+    def __init__(
+        self, size: float = None, footprint: np.ndarray = None, *args, **kwargs
+    ):
         """
         Maximum filter initialization.
 
@@ -113,6 +130,7 @@ class Maximum(FilterBase):
             footprint (np.ndarray, optional): The structuring element for filtering.
             *args: Additional arguments.
             **kwargs: Additional keyword arguments.
+
         """
         if size is None and footprint is None:
             raise ValueError("Either 'size' or 'footprint' must be provided.")
@@ -129,12 +147,22 @@ class Maximum(FilterBase):
 
         Returns:
             The filtered image or volume.
+
         """
-        return maximum(vol=input, size=self.size, footprint=self.footprint, dask=self.dask, chunks=self.chunks, **self.kwargs)
+        return maximum(
+            vol=input,
+            size=self.size,
+            footprint=self.footprint,
+            dask=self.dask,
+            chunks=self.chunks,
+            **self.kwargs,
+        )
 
 
 class Minimum(FilterBase):
-    def __init__(self, size: float = None, footprint: np.ndarray = None, *args, **kwargs):
+    def __init__(
+        self, size: float = None, footprint: np.ndarray = None, *args, **kwargs
+    ):
         """
         Minimum filter initialization.
 
@@ -143,6 +171,7 @@ class Minimum(FilterBase):
             footprint (np.ndarray, optional): The structuring element for filtering.
             *args: Additional arguments.
             **kwargs: Additional keyword arguments.
+
         """
         if size is None and footprint is None:
             raise ValueError("Either 'size' or 'footprint' must be provided.")
@@ -159,8 +188,16 @@ class Minimum(FilterBase):
 
         Returns:
             The filtered image or volume.
+
         """
-        return minimum(vol=input, size=self.size, footprint=self.footprint, dask=self.dask, chunks=self.chunks, **self.kwargs)
+        return minimum(
+            vol=input,
+            size=self.size,
+            footprint=self.footprint,
+            dask=self.dask,
+            chunks=self.chunks,
+            **self.kwargs,
+        )
 
 
 class Tophat(FilterBase):
@@ -173,11 +210,13 @@ class Tophat(FilterBase):
 
         Returns:
             The filtered image or volume.
+
         """
         return tophat(input, dask=self.dask, **self.kwargs)
 
 
 class Pipeline:
+
     """
     Example:
         ```python
@@ -216,6 +255,7 @@ class Pipeline:
 
         Args:
             *args: Variable number of filter instances to be applied sequentially.
+
         """
         self.filters = {}
 
@@ -232,13 +272,14 @@ class Pipeline:
 
         Raises:
             AssertionError: If `fn` is not an instance of the FilterBase class.
+
         """
         if not isinstance(fn, FilterBase):
             filter_names = [
                 subclass.__name__ for subclass in FilterBase.__subclasses__()
             ]
             raise AssertionError(
-                f"filters should be instances of one of the following classes: {filter_names}"
+                f'filters should be instances of one of the following classes: {filter_names}'
             )
         self.filters[name] = fn
 
@@ -248,7 +289,7 @@ class Pipeline:
 
         Args:
             fn (FilterBase): An instance of a FilterBase subclass to be appended.
-        
+
         Example:
             ```python
             import qim3d
@@ -262,6 +303,7 @@ class Pipeline:
             # Append a second filter to the pipeline
             pipeline.append(Median(size=5))
             ```
+
         """
         self._add_filter(str(len(self.filters)), fn)
 
@@ -274,6 +316,7 @@ class Pipeline:
 
         Returns:
             The filtered image or volume after applying all sequential filters.
+
         """
         for fn in self.filters.values():
             input = fn(input)
@@ -281,12 +324,8 @@ class Pipeline:
 
 
 def gaussian(
-    vol: np.ndarray, 
-    sigma: float, 
-    dask: bool = False, 
-    chunks: str = "auto", 
-    **kwargs
-    ) -> np.ndarray:
+    vol: np.ndarray, sigma: float, dask: bool = False, chunks: str = 'auto', **kwargs
+) -> np.ndarray:
     """
     Applies a Gaussian filter to the input volume using scipy.ndimage.gaussian_filter or dask_image.ndfilters.gaussian_filter.
 
@@ -295,11 +334,11 @@ def gaussian(
         sigma (float or sequence of floats): The standard deviations of the Gaussian filter are given for each axis as a sequence, or as a single number, in which case it is equal for all axes.
         dask (bool, optional): Whether to use Dask for the Gaussian filter.
         chunks (int or tuple or "'auto'", optional): Defines how to divide the array into blocks when using Dask. Can be an integer, tuple, size in bytes, or "auto" for automatic sizing.
-        *args (Any): Additional positional arguments for the Gaussian filter.
         **kwargs (Any): Additional keyword arguments for the Gaussian filter.
 
     Returns:
         filtered_vol (np.ndarray): The filtered image or volume.
+
     """
 
     if dask:
@@ -314,12 +353,12 @@ def gaussian(
 
 
 def median(
-    vol: np.ndarray, 
+    vol: np.ndarray,
     size: float = None,
     footprint: np.ndarray = None,
-    dask: bool = False, 
-    chunks: str = "auto", 
-    **kwargs
+    dask: bool = False,
+    chunks: str = 'auto',
+    **kwargs,
 ) -> np.ndarray:
     """
     Applies a median filter to the input volume using scipy.ndimage.median_filter or dask_image.ndfilters.median_filter.
@@ -337,11 +376,12 @@ def median(
 
     Raises:
         RuntimeError: If neither size nor footprint is defined
+
     """
     if size is None:
         if footprint is None:
-            raise RuntimeError("no footprint or filter size provided")
-    
+            raise RuntimeError('no footprint or filter size provided')
+
     if dask:
         if not isinstance(vol, da.Array):
             vol = da.from_array(vol, chunks=chunks)
@@ -357,9 +397,9 @@ def maximum(
     vol: np.ndarray,
     size: float = None,
     footprint: np.ndarray = None,
-    dask: bool = False, 
-    chunks: str = "auto", 
-    **kwargs
+    dask: bool = False,
+    chunks: str = 'auto',
+    **kwargs,
 ) -> np.ndarray:
     """
     Applies a maximum filter to the input volume using scipy.ndimage.maximum_filter or dask_image.ndfilters.maximum_filter.
@@ -374,14 +414,15 @@ def maximum(
 
     Returns:
         filtered_vol (np.ndarray): The filtered image or volume.
-    
+
     Raises:
         RuntimeError: If neither size nor footprint is defined
+
     """
     if size is None:
         if footprint is None:
-            raise RuntimeError("no footprint or filter size provided")
-    
+            raise RuntimeError('no footprint or filter size provided')
+
     if dask:
         if not isinstance(vol, da.Array):
             vol = da.from_array(vol, chunks=chunks)
@@ -394,12 +435,12 @@ def maximum(
 
 
 def minimum(
-    vol: np.ndarray, 
+    vol: np.ndarray,
     size: float = None,
     footprint: np.ndarray = None,
-    dask: bool = False, 
-    chunks: str = "auto", 
-    **kwargs
+    dask: bool = False,
+    chunks: str = 'auto',
+    **kwargs,
 ) -> np.ndarray:
     """
     Applies a minimum filter to the input volume using scipy.ndimage.minimum_filter or dask_image.ndfilters.minimum_filter.
@@ -417,11 +458,12 @@ def minimum(
 
     Raises:
         RuntimeError: If neither size nor footprint is defined
+
     """
     if size is None:
         if footprint is None:
-            raise RuntimeError("no footprint or filter size provided")
-    
+            raise RuntimeError('no footprint or filter size provided')
+
     if dask:
         if not isinstance(vol, da.Array):
             vol = da.from_array(vol, chunks=chunks)
@@ -432,10 +474,8 @@ def minimum(
         res = ndimage.minimum_filter(vol, size, footprint, **kwargs)
         return res
 
-def tophat(vol: np.ndarray, 
-           dask: bool = False, 
-           **kwargs
-           ):
+
+def tophat(vol: np.ndarray, dask: bool = False, **kwargs):
     """
     Remove background from the volume.
 
@@ -448,24 +488,25 @@ def tophat(vol: np.ndarray,
 
     Returns:
         filtered_vol (np.ndarray): The volume with background removed.
+
     """
 
-    radius = kwargs["radius"] if "radius" in kwargs else 3
-    background = kwargs["background"] if "background" in kwargs else "dark"
+    radius = kwargs['radius'] if 'radius' in kwargs else 3
+    background = kwargs['background'] if 'background' in kwargs else 'dark'
 
     if dask:
-        log.info("Dask not supported for tophat filter, switching to scipy.")
+        log.info('Dask not supported for tophat filter, switching to scipy.')
 
-    if background == "bright":
+    if background == 'bright':
         log.info(
-            "Bright background selected, volume will be temporarily inverted when applying white_tophat"
+            'Bright background selected, volume will be temporarily inverted when applying white_tophat'
         )
         vol = np.invert(vol)
 
     selem = morphology.ball(radius)
     vol = vol - morphology.white_tophat(vol, selem)
 
-    if background == "bright":
+    if background == 'bright':
         vol = np.invert(vol)
 
-    return vol
\ No newline at end of file
+    return vol