pre-commit

Author: JosephBrunet

docs/advanced/cardio-analysis.md

@@ -34,7 +34,7 @@ Useful options:
 
 <figure markdown="span">
 ![Cardio-analysis GUI](../assets/images/analyse_GUI_advanced.png){ width="70%" }
-<figcaption>Main GUI for profile definition and plotting. 
+<figcaption>Main GUI for profile definition and plotting.
 </figcaption>
 </figure>
 

docs/advanced/slurm-launcher.md

@@ -50,14 +50,14 @@ cardio-tensor-slurm -h
 
 ## Troubleshooting
 
-- **`sbatch` fails**  
+- **`sbatch` fails**
   Verify partition/account/time/memory policy on your cluster.
 
-- **Job fails before running `cardio-tensor`**  
+- **Job fails before running `cardio-tensor`**
   Check logs in `OUTPUT_PATH/slurm/log/`.
 
-- **No progress in monitor**  
+- **No progress in monitor**
   Confirm output folder permissions and that tasks can write outputs.
 
-- **Want to debug without submitting jobs**  
+- **Want to debug without submitting jobs**
   Use `--dry_run`.

docs/advanced/streamlines.md

@@ -16,15 +16,15 @@ Use this page to generate and inspect 3D streamlines with:
 
 !!! note
 
-    It is usefull to provide a `MASK_PATH` to avoid placing seeds and tracing streamline outside the sample, even though the FA threshold should avoid this.
+    It is useful to provide a `MASK_PATH` to avoid placing seeds and tracing streamline outside the sample, even though the FA threshold should avoid this.
 
 
 ## Generate Streamlines
 
 Basic example:
 
 ```console
-$ cardio-generate-streamlines ./parameters_example.conf 
+$ cardio-generate-streamlines ./parameters_example.conf
 ```
 
 Useful options:

pyproject.toml

@@ -50,23 +50,22 @@ version = "1.1.7"
 
 [project.optional-dependencies]
 cupy = ["cupy>=8"]
-docs = [
-    "mkdocs<2",
-    "mkdocs-material",
-    "mkdocs-autorefs",
-    "mkdocs-section-index",
-    "mkdocs-git-revision-date-localized-plugin",
-    "mkdocstrings[python]",
-    "pymdown-extensions",
-]
-
 dev = [
     "black",
     "pre-commit",
     "pytest",
     "pytest-cov",
     "ruff",
 ]
+docs = [
+    "mkdocs-autorefs",
+    "mkdocs-git-revision-date-localized-plugin",
+    "mkdocs-material",
+    "mkdocs-section-index",
+    "mkdocs<2",
+    "mkdocstrings[python]",
+    "pymdown-extensions",
+]
 git = [
     "mkdocs-git-committers-plugin-2>=1.1,<3",
     "mkdocs-git-revision-date-localized-plugin~=1.2,>=1.2.4",
@@ -116,9 +115,9 @@ testpaths = [
 ]
 
 [tool.ruff]
-target-version = "py312"
 fix = true
 force-exclude = true
+target-version = "py312"
 lint.select = ["F", "I", "UP"]
 lint.mccabe.max-complexity = 10
 lint.pep8-naming.classmethod-decorators = ["classmethod", "pydantic.validator"]

src/cardiotensor/analysis/gui_analysis_tool.py

@@ -4,8 +4,8 @@
 import cv2
 import matplotlib.pyplot as plt
 import numpy as np
-from PyQt5.QtCore import Qt
 from matplotlib.colors import Colormap
+from PyQt5.QtCore import Qt
 from PyQt5.QtGui import (
     QBrush,
     QColor,

src/cardiotensor/orientation/orientation_computation_functions.py

@@ -9,9 +9,8 @@
 from structure_tensor.multiprocessing import parallel_structure_tensor_analysis
 from tqdm import tqdm
 
-from cardiotensor.utils.utils import convert_to_8bit
-
 from cardiotensor.colormaps.helix_angle import helix_angle_cmap
+from cardiotensor.utils.utils import convert_to_8bit
 
 
 def interpolate_points(
@@ -578,9 +577,7 @@ def plot_images(
         colormap_FA = plt.cm.magma
 
     if vector_field_slice is not None and vector_field_slice.shape[1:] != img.shape:
-        raise ValueError(
-            "vector_field_slice shape must match the source image shape"
-        )
+        raise ValueError("vector_field_slice shape must match the source image shape")
     if overlay_scalar_map is not None and overlay_scalar_map.shape != img.shape:
         raise ValueError("overlay_scalar_map shape must match the source image shape")
 
@@ -635,8 +632,6 @@ def plot_images(
     plt.close(fig)
 
 
-
-
 def write_img_rgb(
     img: np.ndarray,
     out_path: str,

src/cardiotensor/scripts/compute_orientation.py

@@ -106,9 +106,7 @@ def script() -> None:
     # --- Test Mode ---
     if is_test:
         if n_slice_test is None:
-            print(
-                "❌ Test mode requires N_SLICE_TEST in the configuration file."
-            )
+            print("❌ Test mode requires N_SLICE_TEST in the configuration file.")
             sys.exit(1)
         if force_test and not params.get("TEST", False):
             print("⚙️  TEST mode forced from CLI (--test)")

src/cardiotensor/utils/DataReader.py

@@ -5,13 +5,13 @@
 from typing import Any
 
 import cv2
-from dask import compute, delayed
 import glymur
 import numpy as np
 import psutil
 import SimpleITK as sitk
 import tifffile as tiff
 from alive_progress import alive_bar
+from dask import compute, delayed
 from skimage.measure import block_reduce
 
 

src/cardiotensor/utils/downsampling.py

@@ -341,10 +341,10 @@ def downsample_volume(
     if not tasks:
         print(f"✔️ All downsampled blocks already exist for '{subfolder}'. Skipping.")
         return
-    
+
     if sys.platform.startswith("win"):
         cpu_count = min(mp.cpu_count(), 59)
-    else: 
+    else:
         cpu_count = mp.cpu_count()
 
     with mp.Pool(processes=cpu_count) as pool:

src/cardiotensor/visualization/fury_plotting_streamlines.py

@@ -169,9 +169,9 @@ def __init__(
         self.bounds = [mins[0], maxs[0], mins[1], maxs[1], mins[2], maxs[2]]
 
         self._build_pipeline()
-        
+
         # self._add_origin_marker()
-        
+
         self._add_scalar_bar()
 
     def _build_pipeline(self):
@@ -199,7 +199,6 @@ def _build_pipeline(self):
         self.scene.add(self.actor0)
         self._style_streamline_actor()
 
-
         # fast actor for interaction (cheap line rendering)
         self.actor_fast = actor.line(
             self.streamlines_xyz,
@@ -359,7 +358,6 @@ def _rebuild_unclipped_actor(self):
         self.scene.add(self.actor0)
         self._style_streamline_actor()
 
-        
         self.mapper0 = self.actor0.GetMapper()
         if clipping_on:
             self.mapper0.RemoveAllClippingPlanes()
@@ -537,12 +535,11 @@ def run(self, interactive: bool, screenshot_path: str | None):
             self.showm.iren.AddObserver("KeyPressEvent", self._on_keypress)
 
             self.scene.reset_camera()
-            
+
             self.scene.azimuth(15)
             self.scene.elevation(10)
             self.scene.zoom(1.1)
 
-            
             print(
                 "Keys: O toggle plane, H hide gizmo, I flip side, R reset plane, +/- thickness, B background, S scale bar, P save PNG"
             )
@@ -648,7 +645,7 @@ def show_streamlines(
         f"{std_points_per_streamline:.1f} "
         "(more points usually means more detail, but heavier rendering)."
     )
-    
+
     if not color_values:
         raise ValueError("No color arrays after filtering.")