pre-commit

Author: JosephBrunet

.pre-commit-config.yaml

@@ -4,41 +4,41 @@ repos:
     hooks:
       - id: ruff
         args: [--fix]
-        exclude: ^examples/
+        exclude: ^(examples/|paper/)
       - id: ruff-format
-        exclude: ^examples/
+        exclude: ^(examples/|paper/)
   - repo: https://github.com/Lucas-C/pre-commit-hooks
     rev: v1.5.5
     hooks:
       - id: forbid-tabs
-        exclude: ^examples/
+        exclude: ^(examples/|paper/)
   - repo: https://github.com/pappasam/toml-sort
     rev: v0.24.2
     hooks:
       - id: toml-sort-fix
-        exclude: ^examples/
+        exclude: ^(examples/|paper/)
   # - repo: https://github.com/pre-commit/mirrors-prettier
   #   rev: v4.0.0-alpha.8
   #   hooks:
   #     - id: prettier
   #       files: ^src/cardiotensor/
-  #       exclude: ^examples/
+  #       exclude: ^(examples/|paper/)
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:
       - id: check-case-conflict
-        exclude: ^examples/
+        exclude: ^(examples/|paper/)
       - id: check-docstring-first
-        exclude: ^examples/
+        exclude: ^(examples/|paper/)
       - id: check-merge-conflict
-        exclude: ^examples/
+        exclude: ^(examples/|paper/)
       - id: check-toml
-        exclude: ^examples/
+        exclude: ^(examples/|paper/)
       - id: mixed-line-ending
         args: [--fix=lf]
-        exclude: ^examples/
+        exclude: ^(examples/|paper/)
       - id: trailing-whitespace
-        exclude: ^examples/
+        exclude: ^(examples/|paper/)
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.14.1
     hooks:
@@ -50,7 +50,7 @@ repos:
           ]
         args: [--config-file, pyproject.toml, --ignore-missing-imports]
         files: ^src/
-        exclude: ^examples/
+        exclude: ^(examples/|paper/)
   # -   repo: https://github.com/psf/black
   #     rev: 24.10.0
   #     hooks:
@@ -60,4 +60,5 @@ repos:
     hooks:
       - id: codespell
         args: [--write-changes, --skip, "*.log"]
-        exclude: ^examples/
+        exclude: ^(examples/|paper/)
+

README.md

@@ -47,14 +47,14 @@ cardiotensor's documentation is available at [josephbrunet.fr/cardiotensor/](htt
 Have a look at our [simple example](https://www.josephbrunet.fr/cardiotensor/getting-started/examples/) that runs you through all the commands of the package
 
 <p align="center">
-    <img src="https://github.com/JosephBrunet/cardiotensor/raw/main/assets/images/pipeline.png" 
-         alt="Cardiotensor pipeline for 3D cardiac orientation analysis" 
+    <img src="https://github.com/JosephBrunet/cardiotensor/raw/main/assets/images/pipeline.png"
+         alt="Cardiotensor pipeline for 3D cardiac orientation analysis"
          style="max-width: 100%; border-radius: 6px;">
     <br>
     <em>
         <strong>Overview of the <code>cardiotensor</code> pipeline for 3D cardiac orientation analysis and tractography.</strong>
         <strong>(a)</strong> Input data consist of a whole‑ or partial‑heart volume and, optionally, a binary mask to restrict analysis to myocardial tissue.
-        <strong>(b)</strong> Local cardiomyocyte orientation is derived by 3D structure tensor computation and eigenvector decomposition. 
+        <strong>(b)</strong> Local cardiomyocyte orientation is derived by 3D structure tensor computation and eigenvector decomposition.
         The third eigenvector (smallest eigenvalue) is visualized as arrows, color‑coded by helix angle (HA); inset shows a zoom of the ventricular septum highlighting transmural fiber rotation.
         <strong>(c)</strong> After transforming to a cylindrical coordinate system aligned with the left ventricle, voxel‑wise HA, transverse angle (TA), and fractional anisotropy (FA) maps are computed for quantitative analysis.
         <strong>(d)</strong> Streamline tractography generated from the eigenvector field reveals continuous cardiomyocyte bundles throughout the heart, color‑coded by HA.

docs/getting-technical/angles.md

@@ -6,9 +6,9 @@ This page explains how helix and intrusion angles are calculated from the 3D eig
 
 A transformation to a cylindrical coordinate system is defined for each voxel based on an approximation of the left ventricle (LV) centerline.
 
-- **Radial (r)**: outward from the LV center  
-- **Circumferential (θ)**: tangential around the ventricle  
-- **Longitudinal (z)**: base to apex direction 
+- **Radial (r)**: outward from the LV center
+- **Circumferential (θ)**: tangential around the ventricle
+- **Longitudinal (z)**: base to apex direction
 
 To compute local fiber angles consistently, all eigenvectors are first rotated into this cylindrical coordinate frame. This alignment is performed using Rodrigues' rotation formula, which computes the minimal-angle rotation that maps the global reference axis (here the z-axis) onto the local longitudinal axis at each point. This allows a robust comparison of orientations across the myocardium.
 

docs/getting-technical/conventions.md

@@ -2,7 +2,7 @@
 
 ## Sign conventions
 
-Cardiotensor processes full-field orientation data in 3D volumes. Consistent with NumPy matrix indexing, the position (0, 0, 0) refers to the corner at the top-left of the first slice. 
+Cardiotensor processes full-field orientation data in 3D volumes. Consistent with NumPy matrix indexing, the position (0, 0, 0) refers to the corner at the top-left of the first slice.
 
 This convention is maintained across all processing pipelines, including structure tensor calculation and streamline generation.
 

docs/getting-technical/index.md

@@ -4,12 +4,12 @@ This section provides a deeper understanding of how `cardiotensor` works, includ
 
 ## Topics Covered
 
-- [Conventions](./conventions.md)  
+- [Conventions](./conventions.md)
 
 - [Structure Tensor](./structure_tensor.md): Mathematical background on the structure tensor and eigen decomposition
 
 - [Angle Definitions](./angles.md): Detailed explanation of helix and intrusion angles
 
-- [Fractional Anisotropy](./fractional_anisotropy.md)  
+- [Fractional Anisotropy](./fractional_anisotropy.md)
 
-- [Tractography](./tractography.md)  
+- [Tractography](./tractography.md)

src/cardiotensor/analysis/gui_analysis_tool.py

@@ -1,4 +1,3 @@
-import argparse
 import sys
 from pathlib import Path
 
@@ -18,7 +17,6 @@
 )
 from PyQt5.QtWidgets import (
     QAction,
-    QApplication,
     QButtonGroup,
     QFileDialog,
     QGraphicsEllipseItem,
@@ -49,7 +47,6 @@
 from cardiotensor.utils.DataReader import DataReader
 
 
-
 def np2pixmap(np_img: np.ndarray) -> QPixmap:
     height, width, channel = np_img.shape
     bytes_per_line = 3 * width
@@ -684,4 +681,3 @@ def set_img_mode(
 
         # Close the dialog
         self.dialog.close()
-

src/cardiotensor/orientation/orientation_computation_pipeline.py

@@ -25,15 +25,14 @@
 from cardiotensor.utils.utils import remove_corrupted_files
 
 
-
 # --- small helpers ---
 def check_already_processed(
     output_dir: str,
     start_index: int,
     end_index: int,
     write_vectors: bool,
     write_angles: bool,
-    output_format: str
+    output_format: str,
 ) -> bool:
     """
     Check whether all required output files already exist.
@@ -53,11 +52,13 @@ def check_already_processed(
         expected_files = []
 
         if write_angles:
-            expected_files.extend([
-                f"{output_dir}/HA/HA_{idx:06d}.{output_format}",
-                f"{output_dir}/IA/IA_{idx:06d}.{output_format}",
-                f"{output_dir}/FA/FA_{idx:06d}.{output_format}",
-            ])
+            expected_files.extend(
+                [
+                    f"{output_dir}/HA/HA_{idx:06d}.{output_format}",
+                    f"{output_dir}/IA/IA_{idx:06d}.{output_format}",
+                    f"{output_dir}/FA/FA_{idx:06d}.{output_format}",
+                ]
+            )
 
         if write_vectors:
             expected_files.append(f"{output_dir}/eigen_vec/eigen_vec_{idx:06d}.npy")
@@ -73,7 +74,6 @@ def check_already_processed(
     return True
 
 
-
 # --- main API ---
 def compute_orientation(
     volume_path: str,
@@ -136,7 +136,6 @@ def compute_orientation(
     - Test mode:      {is_test}
     """)
 
-
     print("\n" + "-" * 40)
     print("READING VOLUME INFORMATION")
     print("-" * 40 + "\n")
@@ -149,22 +148,23 @@ def compute_orientation(
         end_index = data_reader.shape[0]
 
     print(f"Number of slices: {data_reader.shape[0]}")
-    
-        
+
     # --- Check if already processed ---
     print("Check if file is already processed...")
-    if check_already_processed(
-        output_dir,
-        start_index,
-        end_index,
-        write_vectors,
-        write_angles,
-        output_format,
-    ) and not is_test:
+    if (
+        check_already_processed(
+            output_dir,
+            start_index,
+            end_index,
+            write_vectors,
+            write_angles,
+            output_format,
+        )
+        and not is_test
+    ):
         print("\nAll images are already processed. Skipping computation.\n")
         return
-    
-    
+
     print("\n---------------------------------")
     print("CALCULATE CENTER LINE\n")
     center_line = interpolate_points(axis_points, data_reader.shape[0])
@@ -334,8 +334,6 @@ def update_bar(_):
                 )
                 bar()  # Update the progress bar for each slice
 
-
-
     print(f"\n🤖 - Finished processing slices {start_index} - {end_index}")
     print("---------------------------------\n\n")
     return

src/cardiotensor/scripts/compute_orientation.py

@@ -5,7 +5,9 @@
 from tkinter import Tk
 from tkinter.filedialog import askopenfilename
 
-from cardiotensor.orientation.orientation_computation_pipeline import compute_orientation
+from cardiotensor.orientation.orientation_computation_pipeline import (
+    compute_orientation,
+)
 from cardiotensor.utils.DataReader import DataReader
 from cardiotensor.utils.utils import read_conf_file
 
@@ -54,7 +56,10 @@ def script() -> None:
         conf_file_path: str = askopenfilename(
             initialdir=f"{os.getcwd()}/param_files",
             title="Select a configuration file",
-            filetypes=[("Config files", "*.conf *.json *.yaml *.yml"), ("All files", "*.*")]
+            filetypes=[
+                ("Config files", "*.conf *.json *.yaml *.yml"),
+                ("All files", "*.*"),
+            ],
         )
         if not conf_file_path:
             sys.exit("❌ No file selected! Exiting.")

src/cardiotensor/scripts/generate_streamlines.py

@@ -9,15 +9,20 @@
 import argparse
 import sys
 from pathlib import Path
+
+from cardiotensor.tractography.generate_streamlines import (
+    generate_streamlines_from_params,
+)
 from cardiotensor.utils.utils import read_conf_file
-from cardiotensor.tractography.generate_streamlines import generate_streamlines_from_params
 
 
 def script():
     parser = argparse.ArgumentParser(
         description="Generate streamlines from a 3D vector field and save to .npz"
     )
-    parser.add_argument("conf_file", type=Path, help="Path to configuration .conf file.")
+    parser.add_argument(
+        "conf_file", type=Path, help="Path to configuration .conf file."
+    )
     parser.add_argument("--start-z", type=int, default=0, help="Start slice index in Z")
     parser.add_argument("--end-z", type=int, default=None, help="End slice index in Z")
     parser.add_argument("--start-y", type=int, default=0, help="Start slice index in Y")
@@ -28,9 +33,15 @@ def script():
     parser.add_argument("--seeds", type=int, default=20000, help="Number of seeds")
     parser.add_argument("--fa-threshold", type=float, default=0.1, help="FA threshold")
     parser.add_argument("--step", type=float, default=0.5, help="Step length in voxels")
-    parser.add_argument("--max-steps", type=int, default=None, help="Max steps per streamline")
-    parser.add_argument("--angle", type=float, default=60.0, help="Max turning angle (deg)")
-    parser.add_argument("--min-len", type=int, default=10, help="Minimum streamline length (points)")
+    parser.add_argument(
+        "--max-steps", type=int, default=None, help="Max steps per streamline"
+    )
+    parser.add_argument(
+        "--angle", type=float, default=60.0, help="Max turning angle (deg)"
+    )
+    parser.add_argument(
+        "--min-len", type=int, default=10, help="Minimum streamline length (points)"
+    )
 
     args = parser.parse_args()
 

src/cardiotensor/scripts/gui_analysis_tool.py

@@ -1,6 +1,6 @@
 import argparse
 import sys
-from pathlib import Path
+
 from PyQt5.QtWidgets import QApplication
 
 from cardiotensor.analysis.gui_analysis_tool import Window
@@ -19,11 +19,19 @@ def parse_arguments() -> argparse.Namespace:
     parser = argparse.ArgumentParser(
         description="Open a GUI to interactively plot transmural profiles of the angles."
     )
-    parser.add_argument("conf_file_path", type=str, help="Path to the configuration file")
-    parser.add_argument("--N_slice", type=int, default=None, help="Slice number (optional)")
+    parser.add_argument(
+        "conf_file_path", type=str, help="Path to the configuration file"
+    )
+    parser.add_argument(
+        "--N_slice", type=int, default=None, help="Slice number (optional)"
+    )
     parser.add_argument("--N_line", type=int, default=5, help="Number of lines")
-    parser.add_argument("--angle_range", type=float, default=20, help="Angle range in degrees")
-    parser.add_argument("--image_mode", type=str, default="HA", help="Output mode (HA, IA, or FA)")
+    parser.add_argument(
+        "--angle_range", type=float, default=20, help="Angle range in degrees"
+    )
+    parser.add_argument(
+        "--image_mode", type=str, default="HA", help="Output mode (HA, IA, or FA)"
+    )
     return parser.parse_args()
 
 
@@ -45,7 +53,9 @@ def script() -> None:
     output_dir = params.get("OUTPUT_PATH", "./output")
 
     # Determine slice number: CLI overrides config
-    N_slice = args.N_slice if args.N_slice is not None else params.get("N_SLICE_TEST", 0)
+    N_slice = (
+        args.N_slice if args.N_slice is not None else params.get("N_SLICE_TEST", 0)
+    )
 
     # Initialize the PyQt5 application
     app = QApplication(sys.argv)