chore: rename internal package to leaf_contour_efd with compatibility shims

build.spec

@@ -104,7 +104,7 @@ runtime_hooks = [
 ]
 
 a = Analysis(
-    [os.path.join("src", "leaf_shape_tool", "__main__.py")],
+    [os.path.join("src", "leaf_contour_efd", "__main__.py")],
     pathex=[],
     binaries=binaries,
     datas=datas,

pyproject.toml

@@ -30,7 +30,7 @@ dependencies = [
 ]
 
 [project.scripts]
-leaf-contour-efd = "leaf_shape_tool.main:main"
+leaf-contour-efd = "leaf_contour_efd.main:main"
 
 [tool.setuptools.packages.find]
 where = ["src"]

src/leaf_contour_efd/__init__.py

@@ -0,0 +1 @@
+"""LeafContourEFD package."""

src/leaf_contour_efd/__main__.py

@@ -0,0 +1,7 @@
+"""Command-line entry point for ``python -m leaf_contour_efd``."""
+
+from leaf_contour_efd.main import main
+
+
+if __name__ == "__main__":
+    main()

src/leaf_contour_efd/main.py

@@ -0,0 +1,190 @@
+"""
+Main entry point for the Napari-based leaf shape analysis workflow.
+
+This script initializes the Napari viewer and integrates multiple custom widgets
+for region-of-interest (ROI) extraction, landmark annotation, image rotation,
+binarization, contour extraction, scale calibration, and Elliptic Fourier Descriptor (EFD) analysis.
+
+The GUI layout and event-driven behavior are designed for interactive leaf
+image processing and morphometric analysis.
+
+Author: Maple
+License: BSD-3-Clause
+"""
+
+# For SAM2if getattr(sys, "frozen", False):
+import os
+import sys
+
+
+def _add_sam2_path():
+    if getattr(sys, "frozen", False):
+        # PyInstaller one-dir/one-file
+        base = getattr(sys, "_MEIPASS", os.path.dirname(sys.executable))
+        internal_sam2 = os.path.join(base, "_internal", "sam2")
+        if os.path.isdir(internal_sam2):
+            sys.path.insert(0, internal_sam2)
+    else:
+        # Development (run via python)
+        local_sam2 = os.path.join(os.getcwd(), "sam2")
+        if os.path.isdir(local_sam2):
+            sys.path.insert(0, local_sam2)
+
+
+_add_sam2_path()
+
+
+import torch  # noqa: E402
+
+# TODO: Add GPU support
+torch.set_default_device("cpu")  # Ensure CPU usage by default
+
+import napari  # noqa: E402
+from functools import partial  # noqa: E402
+from qtpy.QtCore import Qt, QTimer  # noqa: E402
+from qtpy.QtWidgets import QDockWidget  # noqa: E402
+
+# --- Custom widget imports ---
+from leaf_contour_efd.widgets import crop_rectangle  # noqa: E402
+from leaf_contour_efd.widgets.make_points_tool_widget import make_points_tools_widget  # noqa: E402
+from leaf_contour_efd.widgets.rotate_image import (  # noqa: E402
+    make_points_metadata_widget,
+    get_active_points_layer,
+    summarize_points_layer,
+)
+from leaf_contour_efd.widgets.binarize_image import make_binarize_image_widget  # noqa: E402
+from leaf_contour_efd.widgets.extract_contour import make_extract_contour_widget  # noqa: E402
+from leaf_contour_efd.widgets.set_scale import make_set_scale_widget  # noqa: E402
+from leaf_contour_efd.widgets.calculate_efd import calculate_efd_and_save  # noqa: E402
+from leaf_contour_efd.widgets.clear_viewer import make_clear_viewer_widget  # noqa: E402
+from leaf_contour_efd.utils.add_ROIs_layer import add_ROIs  # noqa: E402
+
+
+# ---------------------------------------------------------------------
+# Initialize Napari viewer
+# ---------------------------------------------------------------------
+
+viewer = napari.Viewer()
+# Automatically add ROI layer when a new image layer is added
+viewer.layers.events.inserted.connect(partial(add_ROIs, viewer))
+
+# ---------------------------------------------------------------------
+# Create and register widgets
+# ---------------------------------------------------------------------
+
+roi_widget = crop_rectangle.make_add_roi_widget(viewer)
+dock_00 = viewer.window.add_dock_widget(
+    roi_widget, name="ROI Extractoin Widget", area="right", tabify=False
+)
+
+
+# Callback to reset SpinBox to 1 on hard reset (check_keep_base=False)
+def _reset_roi_spinbox_to_1():
+    # Set the SpinBox value to 1 safely
+    try:
+        roi_widget.roi_index.value = 1  # Reset to 1
+    except Exception as e:
+        print("Error resetting ROI SpinBox:", e)
+
+
+# Landmark / point tools widget
+dock = make_points_tools_widget(viewer)
+viewer.window.add_dock_widget(dock, area="left", name="Point Tools")
+
+# Image rotation widget (based on landmark metadata)
+points_meta_widget = make_points_metadata_widget(
+    viewer,
+    get_active_points_layer,
+    summarize_points_layer,
+)
+dock_01 = viewer.window.add_dock_widget(
+    points_meta_widget, name="Rotation Widget", area="right", tabify=False
+)
+
+# Binarization widget (Otsu / SAM2)
+binarize_widget = make_binarize_image_widget(viewer)
+dock_02 = viewer.window.add_dock_widget(
+    binarize_widget, name="Binarization Widget", area="right", tabify=False
+)
+
+# Contour extraction widget
+contour_widget = make_extract_contour_widget(viewer)
+dock_03 = viewer.window.add_dock_widget(
+    contour_widget,
+    name="Contour Extraction Widget",
+    area="right",
+    tabify=False,
+)
+
+# Clear viewer widget
+clear_viewer_widget = make_clear_viewer_widget(
+    viewer, on_hard_reset=_reset_roi_spinbox_to_1
+)
+dock_04 = viewer.window.add_dock_widget(
+    clear_viewer_widget, name="Clear Viewer", area="right", tabify=False
+)
+
+# Scale calibration widget
+set_scale_widget = make_set_scale_widget(viewer)
+viewer.window.add_dock_widget(set_scale_widget, area="left", tabify=False)
+
+
+# ---------------------------------------------------------------------
+# Arrange dock widgets vertically (right side)
+# ---------------------------------------------------------------------
+def pack_right_docks_top():
+    """
+    Dynamically resize and align right-side dock widgets vertically.
+    Ensures consistent spacing and visibility of all widgets.
+    """
+    main_window = viewer.window._qt_window  # QMainWindow instance
+    qdocks = [
+        d
+        for d in main_window.findChildren(QDockWidget)
+        if main_window.dockWidgetArea(d) == Qt.RightDockWidgetArea
+        and not d.isFloating()
+    ]
+    if not qdocks:
+        return
+
+    # Sort by y-position (top to bottom)
+    qdocks.sort(key=lambda d: d.geometry().top())
+
+    sizes = []
+    for d in qdocks[:-1]:
+        h = d.widget().sizeHint().height()
+        d.widget().setMinimumHeight(min(h, 300))
+        sizes.append(max(h, 150))  # Ensure visibility
+
+    sizes.append(10_000)  # Let the last dock absorb remaining space
+
+    main_window.resizeDocks(qdocks, sizes, Qt.Vertical)
+
+
+# Trigger dock layout adjustment after GUI initialization
+QTimer.singleShot(0, pack_right_docks_top)
+
+# ---------------------------------------------------------------------
+# Signal connections
+# ---------------------------------------------------------------------
+# Trigger EFD calculation automatically after contour extraction
+contour_widget.called.connect(calculate_efd_and_save)  # EFD calculation
+
+
+# Add ROI shortcut (Shift + S)
+@viewer.bind_key("Shift-s")
+def _add_roi_shortcut(v):
+    roi_widget()
+
+
+# ---------------------------------------------------------------------
+# Run Napari viewer
+# ---------------------------------------------------------------------
+def main():
+    """Launch the LeafContourEFD GUI."""
+    viewer.title = "LeafContourEFD — powered by napari"  # Set window title
+    napari.run()  # Run the viewer
+
+
+if __name__ == "__main__":
+    main()

src/leaf_shape_tool/__init__.py

@@ -0,0 +1,6 @@
+"""Backward-compatible wrappers for the renamed package.
+
+This package has been renamed to ``leaf_contour_efd``.
+"""
+
+from leaf_contour_efd import *  # noqa: F401,F403

src/leaf_shape_tool/__main__.py

@@ -1,9 +1,16 @@
-# src/leaf_shape_tool/__main__.py
+"""Backward-compatible module runner for ``python -m leaf_shape_tool``."""
 
-"""
-Command-line entry point for the LeafContourEFD.
-"""
+from __future__ import annotations
 
-from leaf_shape_tool.main import main
+import warnings
 
-main()
+from leaf_contour_efd.main import main
+
+
+if __name__ == "__main__":
+    warnings.warn(
+        "`python -m leaf_shape_tool` is deprecated; use `python -m leaf_contour_efd`.",
+        DeprecationWarning,
+        stacklevel=1,
+    )
+    main()