add warning

Author: JosephBrunet

src/cardiotensor/__init__.py

@@ -0,0 +1,93 @@
+"""
+cardiotensor — 3D cardiomyocyte orientation analysis from volumetric imaging.
+
+Core usage
+----------
+>>> from cardiotensor import compute_orientation, DataReader
+>>> reader = DataReader("path/to/images")
+>>> compute_orientation("path/to/images", output_dir="output", sigma=3.0, rho=1.0)
+
+Sub-module imports
+------------------
+For tractography::
+
+    from cardiotensor.tractography import (
+        generate_streamlines_from_vector_field,
+        generate_streamlines_from_params,
+    )
+
+For I/O utilities::
+
+    from cardiotensor.utils import (
+        read_conf_file,
+        load_npz_streamlines,
+        load_trk_streamlines,
+        write_spatialgraph_am,
+        export_vector_field_to_vtk,
+    )
+
+For analysis::
+
+    from cardiotensor.analysis import calculate_intensities, find_end_points
+
+For visualization (requires a display)::
+
+    from cardiotensor.visualization import visualize_streamlines, visualize_vector_field
+"""
+
+# --- Core ---
+from cardiotensor.orientation.orientation_computation_pipeline import compute_orientation
+from cardiotensor.utils.DataReader import DataReader
+from cardiotensor.utils.utils import convert_to_8bit, read_conf_file
+
+# --- Orientation ---
+from cardiotensor.orientation.orientation_computation_functions import (
+    calculate_structure_tensor,
+    compute_fraction_anisotropy,
+    compute_helix_and_transverse_angles,
+)
+
+# --- Tractography ---
+from cardiotensor.tractography.generate_streamlines import (
+    generate_streamlines_from_params,
+    generate_streamlines_from_vector_field,
+)
+
+# --- I/O ---
+from cardiotensor.utils.am_utils import write_spatialgraph_am
+from cardiotensor.utils.streamlines_io_utils import (
+    load_npz_streamlines,
+    load_trk_streamlines,
+)
+from cardiotensor.utils.vector_vtk_export import export_vector_field_to_vtk
+
+# --- Analysis ---
+from cardiotensor.analysis.analysis_functions import (
+    calculate_intensities,
+    find_end_points,
+    save_intensity,
+)
+
+__all__ = [
+    # Core
+    "compute_orientation",
+    "DataReader",
+    "read_conf_file",
+    "convert_to_8bit",
+    # Orientation
+    "calculate_structure_tensor",
+    "compute_fraction_anisotropy",
+    "compute_helix_and_transverse_angles",
+    # Tractography
+    "generate_streamlines_from_vector_field",
+    "generate_streamlines_from_params",
+    # I/O
+    "write_spatialgraph_am",
+    "load_npz_streamlines",
+    "load_trk_streamlines",
+    "export_vector_field_to_vtk",
+    # Analysis
+    "calculate_intensities",
+    "find_end_points",
+    "save_intensity",
+]

src/cardiotensor/utils/utils.py

@@ -121,11 +121,15 @@ def parse_coordinates(section: str, option: str, fallback: str = ""):
     }
 
 
-# Function to remove files smaller than 1KB
 def remove_corrupted_files(file_paths, size_threshold=200):
+    import warnings
     for file_path in file_paths:
         if os.path.exists(file_path) and os.path.getsize(file_path) < size_threshold:
-            print("Corrupted file removed:", file_path)
+            warnings.warn(
+                f"Removing potentially corrupted file (size < {size_threshold} bytes): {file_path}",
+                UserWarning,
+                stacklevel=2,
+            )
             os.remove(file_path)