Merge pull request #15 from maple60/codex/rename-app-and-repository-to-leafcontourefd

Rename/rebrand project and artifacts to LeafContourEFD

Author: maple60

.github/workflows/release-standalone.yml

@@ -19,16 +19,16 @@ jobs:
         include:
           - name: windows-x64
             os: windows-latest
-            archive_name: LeafShapeTool-windows-x64.zip
+            archive_name: LeafContourEFD-windows-x64.zip
           - name: macos-arm64
             os: macos-15
-            archive_name: LeafShapeTool-macos-arm64.tar.gz
+            archive_name: LeafContourEFD-macos-arm64.tar.gz
           - name: macos-x64
             os: macos-15-intel
-            archive_name: LeafShapeTool-macos-x64.tar.gz
+            archive_name: LeafContourEFD-macos-x64.tar.gz
           - name: ubuntu-x64
             os: ubuntu-latest
-            archive_name: LeafShapeTool-ubuntu-x64.tar.gz
+            archive_name: LeafContourEFD-ubuntu-x64.tar.gz
 
     steps:
       - name: Checkout
@@ -58,17 +58,17 @@ jobs:
         if: startsWith(matrix.os, 'windows')
         shell: pwsh
         run: |
-          Compress-Archive -Path dist/LeafShapeTool/* -DestinationPath ${{ matrix.archive_name }}
+          Compress-Archive -Path dist/LeafContourEFD/* -DestinationPath ${{ matrix.archive_name }}
 
       - name: Archive build output (macOS/Linux)
         if: ${{ !startsWith(matrix.os, 'windows') }}
         run: |
-          tar -C dist -czf "${{ matrix.archive_name }}" LeafShapeTool
+          tar -C dist -czf "${{ matrix.archive_name }}" LeafContourEFD
 
       - name: Upload build artifact
         uses: actions/upload-artifact@v4
         with:
-          name: LeafShapeTool-${{ matrix.name }}
+          name: LeafContourEFD-${{ matrix.name }}
           path: ${{ matrix.archive_name }}
 
   release:
@@ -92,7 +92,7 @@ jobs:
           mkdir -p release-assets
 
           shopt -s globstar nullglob
-          for file in artifacts/**/LeafShapeTool-*.zip artifacts/**/LeafShapeTool-*.tar.gz; do
+          for file in artifacts/**/LeafContourEFD-*.zip artifacts/**/LeafContourEFD-*.tar.gz; do
             [ -f "$file" ] || continue
             base="$(basename "$file")"
             size_bytes="$(stat -c%s "$file")"
@@ -124,7 +124,7 @@ jobs:
           } > "$notes_file"
 
           shopt -s nullglob
-          for asset in release-assets/LeafShapeTool-*.zip release-assets/LeafShapeTool-*.tar.gz; do
+          for asset in release-assets/LeafContourEFD-*.zip release-assets/LeafContourEFD-*.tar.gz; do
             [ -f "$asset" ] || continue
             base="$(basename "$asset")"
 
@@ -134,10 +134,10 @@ jobs:
 
             if [[ "$asset" == *.zip ]]; then
               unzip -q "$asset" -d "$workdir"
-              exe_path="$(find "$workdir" -type f -name 'LeafShapeTool.exe' | head -n 1 || true)"
+              exe_path="$(find "$workdir" -type f -name 'LeafContourEFD.exe' | head -n 1 || true)"
             else
               tar -xzf "$asset" -C "$workdir"
-              exe_path="$(find "$workdir" -type f -name 'LeafShapeTool' | head -n 1 || true)"
+              exe_path="$(find "$workdir" -type f -name 'LeafContourEFD' | head -n 1 || true)"
             fi
 
             if [ -n "$exe_path" ] && [ -f "$exe_path" ]; then

README.md

@@ -1,8 +1,8 @@
-# Leaf Shape Analysis Tool
+# LeafContourEFD
 
 [**日本語のREADMEはこちら (Japanese README is here)**](README_ja.md)
 
-**Full documentation:** [https://maple60.github.io/morphometrics-tool/](https://maple60.github.io/morphometrics-tool/)
+**Full documentation:** [https://maple60.github.io/leaf-contour-efd/](https://maple60.github.io/leaf-contour-efd/)
 
 A **[**napari**](https://napari.org/stable/)-based graphical user interface (GUI)** for fully reproducible extraction, orientation, and morphometric analysis of leaf outlines.  
 This tool allows researchers to perform every processing step interactively — from setting image scale to exporting normalized Elliptic Fourier Descriptors (EFDs) — all within a single, unified environment.
@@ -29,7 +29,7 @@ This tool allows researchers to perform every processing step interactively —
 
 ## Installation
 
-There are three ways to install and run the Leaf Shape Analysis Tool.
+There are three ways to install and run the LeafContourEFD.
 Choose the method that best fits your environment.
 
 | Method             | Description                                                                          | Recommended for        |
@@ -40,12 +40,12 @@ Choose the method that best fits your environment.
 
 ### 1. Standalone App (Recommended) 
 
-Download the latest release from the [Releases page](https://github.com/maple60/morphometrics-tool/releases)
+Download the latest release from the [Releases page](https://github.com/maple60/leaf-contour-efd/releases)
 No Python installation is required.
 
-- On **Windows**: run `LeafShapeTool.exe`
+- On **Windows**: run `LeafContourEFD.exe`
 - On **macOS**: run the app bundle or binary from the downloaded archive
-- On **Linux**: extract the release archive and run `LeafShapeTool` from the `LeafShapeTool/` folder
+- On **Linux**: extract the release archive and run `LeafContourEFD` from the `LeafContourEFD/` folder
 
 ::: {.callout-warning}
 ## If the app does not open on macOS
@@ -55,10 +55,10 @@ On macOS, a warning dialog may appear the first time you launch the app, and the
 If this happens, run the following command in Terminal:
 
 ```bash
-/usr/bin/xattr -dr com.apple.quarantine ~/path/to/LeafShapeTool
+/usr/bin/xattr -dr com.apple.quarantine ~/path/to/LeafContourEFD
 ```
 
-Replace `~/path/to/LeafShapeTool` with the path to the downloaded app.
+Replace `~/path/to/LeafContourEFD` with the path to the downloaded app.
 
 After running the command, try launching the app again.
 :::
@@ -68,8 +68,8 @@ After running the command, try launching the app again.
 Clone the repository and launch the tool using the provided script.
 
 ```bash
-git clone https://github.com/maple60/morphometrics-tool.git
-cd morphometrics-tool
+git clone https://github.com/maple60/leaf-contour-efd.git
+cd leaf-contour-efd
 ```
 - Windows
 
@@ -113,11 +113,11 @@ For details about each model, refer to the following page:
 After installation, launch the tool with:
 
 ```bash
-leaf-shape-tool
+leaf-contour-efd
 ```
 
 > [!NOTE]
-> For full setup instructions (including uv, git, and checkpoint downloads), see the [Installation Guide](https://maple60.github.io/morphometrics-tool/installation.html).
+> For full setup instructions (including uv, git, and checkpoint downloads), see the [Installation Guide](https://maple60.github.io/leaf-contour-efd/installation.html).
 
 ## Workflow & Usage
 
@@ -150,7 +150,7 @@ flowchart LR
 Each processing step corresponds to a dedicated GUI widget,  
 and all results (images, contours, metadata, EFDs) are automatically exported to the `output/` directory.
 
-For a detailed step-by-step guide, please refer to the [Usage page](https://maple60.github.io/morphometrics-tool/usage.html).
+For a detailed step-by-step guide, please refer to the [Usage page](https://maple60.github.io/leaf-contour-efd/usage.html).
 
 ## Citation
 
@@ -170,14 +170,14 @@ The design and implementation of this tool were inspired by the methodology and
 
 We also acknowledge the contributions of many other open-source tools and studies  
 that have advanced automated leaf image analysis.  
-A summary of related software can be found on the [Related Tools page](https://maple60.github.io/morphometrics-tool/related_tools.html).
+A summary of related software can be found on the [Related Tools page](https://maple60.github.io/leaf-contour-efd/related_tools.html).
 
 We express our sincere gratitude to the open-source community and all contributors  
 whose work made this tool possible.
 
 ## License 
 
-Distributed under the BSD 3-Clause License. See [LICENSE](https://github.com/maple60/morphometrics-tool/blob/main/LICENSE) for more information.
+Distributed under the BSD 3-Clause License. See [LICENSE](https://github.com/maple60/leaf-contour-efd/blob/main/LICENSE) for more information.
 
 ## AI Assistant
 

README_ja.md

@@ -1,8 +1,8 @@
-# Leaf Shape Analysis Tool
+# LeafContourEFD
 
-[English README is here (README.md)](https://github.com/maple60/morphometrics-tool/tree/main)
+[English README is here (README.md)](https://github.com/maple60/leaf-contour-efd/tree/main)
 
-**ドキュメントサイト:** [https://maple60.github.io/morphometrics-tool/](https://maple60.github.io/morphometrics-tool/)
+**ドキュメントサイト:** [https://maple60.github.io/leaf-contour-efd/](https://maple60.github.io/leaf-contour-efd/)
 
 [**napari**](https://napari.org/stable/) を基盤としたグラフィカルユーザーインターフェース（GUI）で、葉の輪郭抽出・方向補正・楕円フーリエ記述子(elliptic Fourier descriptor) の算出を再現可能な形で実行できます。
 
@@ -40,12 +40,12 @@
 
 ### 1. スタンドアロンアプリ（推奨）
 
-最新のリリースは [Releasesページ](https://github.com/maple60/morphometrics-tool/releases) からダウンロードいただけます。
+最新のリリースは [Releasesページ](https://github.com/maple60/leaf-contour-efd/releases) からダウンロードいただけます。
 Python のインストールは不要です。
 
-- **Windows**：`LeafShapeTool.exe` を実行
+- **Windows**：`LeafContourEFD.exe` を実行
 - **macOS**：ダウンロードしたアーカイブ内のアプリバンドルまたは実行ファイルを起動
-- **Linux**: リリースアーカイブを展開し、`LeafShapeTool/` フォルダ内の `LeafShapeTool` を起動
+- **Linux**: リリースアーカイブを展開し、`LeafContourEFD/` フォルダ内の `LeafContourEFD` を起動
 
 ::: {.callout-warning}
 ## macOSでアプリが開けない場合
@@ -54,10 +54,10 @@ macOSでは、アプリの初回起動時に警告ダイアログが表示され
 その場合は、ターミナルで以下のコマンドを実行してください。
 
 ```bash
-/usr/bin/xattr -dr com.apple.quarantine ~/path/to/LeafShapeTool
+/usr/bin/xattr -dr com.apple.quarantine ~/path/to/LeafContourEFD
 ```
 
-`~/path/to/LeafShapeTool`は、ダウンロードしたアプリのパスに置き換えてください。
+`~/path/to/LeafContourEFD`は、ダウンロードしたアプリのパスに置き換えてください。
 コマンド実行後、再度アプリを起動してください。
 :::
 
@@ -66,8 +66,8 @@ macOSでは、アプリの初回起動時に警告ダイアログが表示され
 リポジトリをクローンし、提供されているスクリプトでツールを起動します。
 
 ```bash
-git clone https://github.com/maple60/morphometrics-tool.git
-cd morphometrics-tool
+git clone https://github.com/maple60/leaf-contour-efd.git
+cd leaf-contour-efd
 ```
 
 - Windows
@@ -111,11 +111,11 @@ SAM2 を利用する場合は、チェックポイントを sam2/checkpoints/ 
 インストールが完了したら、以下の方法で起動します：
 
 ```bash
-leaf-shape-tool
+leaf-contour-efd
 ```
 
 > [!NOTE]
-> `uv`・`git`・チェックポイントのダウンロードなど、より詳細な手順は [Installation ページ](https://maple60.github.io/morphometrics-tool/installation.html) を参照してください。
+> `uv`・`git`・チェックポイントのダウンロードなど、より詳細な手順は [Installation ページ](https://maple60.github.io/leaf-contour-efd/installation.html) を参照してください。
 
 ### ワークフローと使い方
 
@@ -148,7 +148,7 @@ flowchart LR
 各処理ステップは専用のGUIウィジェットに対応しており、  
 解析結果（画像・輪郭・メタデータ・EFD）は自動的に `output/` ディレクトリに保存されます。
 
-詳しい操作手順については、[Usage ページ](https://maple60.github.io/morphometrics-tool/usage.html) を参照してください。
+詳しい操作手順については、[Usage ページ](https://maple60.github.io/leaf-contour-efd/usage.html) を参照してください。
 
 ## 引用情報（Citation）
 
@@ -169,12 +169,12 @@ flowchart LR
 さらに、本研究を支える数多くのオープンソースプロジェクトの開発者・貢献者の皆様に深く感謝申し上げます。
 
 また、葉画像解析の自動化分野を発展させてきた多くのオープンソースツールや研究に感謝いたします。  
-関連するソフトウェアの概要は、[Related Tools ページ](https://maple60.github.io/morphometrics-tool/related_tools.html) にまとめています。
+関連するソフトウェアの概要は、[Related Tools ページ](https://maple60.github.io/leaf-contour-efd/related_tools.html) にまとめています。
 
 ## ライセンス
 
 本ソフトウェアは **BSD 3-Clause License** の下で配布されています。
-詳細は [LICENSE](https://github.com/maple60/morphometrics-tool/blob/main/LICENSE) をご覧ください。
+詳細は [LICENSE](https://github.com/maple60/leaf-contour-efd/blob/main/LICENSE) をご覧ください。
 
 ## AI利用について
 

build.spec

@@ -129,7 +129,7 @@ exe = EXE(
     a.scripts,
     [],
     exclude_binaries=True,
-    name="LeafShapeTool",
+    name="LeafContourEFD",
     debug=False,
     bootloader_ignore_signals=False,
     strip=False,
@@ -144,5 +144,5 @@ coll = COLLECT(
     a.datas,
     strip=False,
     upx=True,
-    name="LeafShapeTool",
+    name="LeafContourEFD",
 )

pyproject.toml

@@ -1,5 +1,5 @@
 [project]
-name = "leaf-shape-tool"
+name = "leaf-contour-efd"
 version = "1.0.0"
 
 requires-python = ">=3.11, <3.13"
@@ -30,7 +30,7 @@ dependencies = [
 ]
 
 [project.scripts]
-leaf-shape-tool = "leaf_shape_tool.main:main"
+leaf-contour-efd = "leaf_shape_tool.main:main"
 
 [tool.setuptools.packages.find]
 where = ["src"]
@@ -54,4 +54,4 @@ members = [
 ]
 
 [tool.uv.sources]
-leaf-shape-tool = { workspace = true }
+leaf-contour-efd = { workspace = true }

setup/setup_unix.sh

@@ -47,9 +47,9 @@ else
     echo "[Info] sam2/checkpoints directory not found."
 fi
 
-# === Step 6: Run the Leaf Shape Tool ===
-echo "Launching Leaf Shape Tool..."
-leaf-shape-tool
+# === Step 6: Run the LeafContourEFD ===
+echo "Launching LeafContourEFD..."
+leaf-contour-efd
 
 # =========================
 # Functions

setup/setup_windows.bat

@@ -42,9 +42,9 @@ if exist "sam2\checkpoints" (
     echo [Info] sam2\checkpoints directory not found. Skipping checkpoint download.
 )
 
-REM === Step 6: Run the Leaf Shape Tool ===
-echo Launching Leaf Shape Tool...
-leaf-shape-tool
+REM === Step 6: Run the LeafContourEFD ===
+echo Launching LeafContourEFD...
+leaf-contour-efd
 
 pause
 exit /b 0

src/leaf_shape_tool/__main__.py

@@ -1,7 +1,7 @@
 # src/leaf_shape_tool/__main__.py
 
 """
-Command-line entry point for the Leaf Shape Analysis Tool.
+Command-line entry point for the LeafContourEFD.
 """
 
 from leaf_shape_tool.main import main

src/leaf_shape_tool/main.py

@@ -181,8 +181,8 @@ def _add_roi_shortcut(v):
 # Run Napari viewer
 # ---------------------------------------------------------------------
 def main():
-    """Launch the Leaf Shape Analysis Tool GUI."""
-    viewer.title = "Leaf Shape Analysis Tool — powered by napari"  # Set window title
+    """Launch the LeafContourEFD GUI."""
+    viewer.title = "LeafContourEFD — powered by napari"  # Set window title
     napari.run()  # Run the viewer
 
 

src/leaf_shape_tool/widgets/binarize_image.py

@@ -2,7 +2,7 @@
 binarize_image.py
 -----------------
 A napari widget for image binarization using Otsu thresholding or SAM2 segmentation.
-This module is part of the Leaf Shape Analysis Tool.
+This module is part of the LeafContourEFD.
 """
 
 # --- Fix PyTorch DLL loading in PyInstaller ---