added CLAUDE.md for Claude Code guidance

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: XeniosP

CLAUDE.md

@@ -0,0 +1,146 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project Overview
+
+BioImage Suite Web (bisweb) is a web-based medical image analysis suite primarily for neuroimaging. It's a hybrid application with:
+- Web applications (browser-based)
+- Desktop applications (Electron)
+- Command-line tools (Node.js and Python)
+- WebAssembly modules compiled from C++
+
+## Build Commands
+
+### Initial Setup
+```bash
+npm install
+node ./config/createbuild.js   # Creates build directories and installs emscripten
+```
+
+### Full Build
+```bash
+cd build
+./fullbuild.sh   # Builds WASM, web app, native bindings, and runs tests
+```
+
+### Individual Build Components
+```bash
+cd build
+./wasmbuild.sh      # Build C++ to WebAssembly
+./webbuild.sh       # Build JS bundles for web
+./nativebuild.sh    # Build Python/Matlab bindings
+./testbuild.sh      # Run subset of tests
+```
+
+### Development Server
+```bash
+gulp              # Starts dev server with webpack watch on port 8080
+gulp serve        # Same as above
+gulp --portno 9000  # Use different port
+```
+
+### Build Web Application
+```bash
+gulp build -m     # Build with minification
+gulp zip          # Create distribution zip
+```
+
+### Electron Desktop App
+```bash
+gulp package      # Package as desktop application
+```
+
+### Linting
+```bash
+gulp eslint       # Run ESLint on all JS files
+gulp watch        # Watch and lint on changes
+```
+
+## Running Tests
+
+### Node.js Tests (Mocha)
+```bash
+npm test                           # Run all tests
+mocha test                         # Same as above
+mocha test/test_module.js          # Run module tests
+mocha test/test_module.js --input local  # Use local test data
+mocha test/test_module.js --first 0 --last 10  # Run tests 0-10
+mocha test/test_module.js --testname smoothImage  # Run specific module test
+```
+
+### Browser Tests
+```bash
+gulp serve
+# Navigate to http://localhost:8080/web/biswebtest.html
+```
+
+### C++ Tests (after WASM build)
+```bash
+cd build/wasm
+make test
+```
+
+## Architecture
+
+### Directory Structure
+- `js/` - JavaScript source code
+  - `core/` - Core utilities (IO, WASM interface, preferences)
+  - `dataobjects/` - Data object classes (BisWebImage, BisWebMatrix, transformations)
+  - `modules/` - Processing modules (each inherits from BaseModule)
+  - `webcomponents/` - Custom HTML elements for web UI
+  - `node/` - Node.js specific code
+  - `bin/` - Command-line entry points
+- `cpp/` - C++ source for WebAssembly modules
+- `web/` - HTML/CSS files and Electron configuration
+- `config/` - Webpack and build configuration
+- `compiletools/` - Build scripts
+- `test/` - Test files and test data
+- `biswebpython/` - Python wrapper package
+
+### Key Patterns
+
+**Module Architecture**: All processing modules extend `BaseModule` (`js/modules/basemodule.js`). Modules have:
+- `createDescription()` - Returns JSON description with inputs, outputs, parameters
+- `directInvokeAlgorithm()` - Core algorithm implementation
+- Automatic command-line and GUI generation from description
+
+**Data Objects**: Image and transform classes in `js/dataobjects/`:
+- `BisWebImage` - Medical image class (NIfTI, etc.)
+- `BisWebMatrix` - Matrix class
+- `BisWeb*Transformation` - Linear, grid, combo transformations
+
+**WASM Interface**: C++ code compiled to WebAssembly via Emscripten
+- `libbiswasm_wrapper.js` - Auto-generated JS wrapper for C++ functions
+- Memory management through serialized data transfer between JS and WASM
+
+**Web Components**: Custom elements in `js/webcomponents/` provide reusable UI
+- Viewers, controllers, dialogs built as web components
+- Entry point: `bislib.js` bundles all components
+
+### Configuration Files
+- `package.json` - NPM dependencies and scripts
+- `gulpfile.js` - Gulp task definitions
+- `config/webpack.config.js` - Webpack bundling configuration
+- `web/images/tools.json` - Tool definitions (viewers, applications)
+- `test/module_tests.json` - Test definitions for modules
+
+### Adding a New Module
+1. Create module file in `js/modules/` extending `BaseModule`
+2. Implement `createDescription()` and `directInvokeAlgorithm()`
+3. Register in `js/modules/moduleindex.js`
+4. Add tests to `test/module_tests.json`
+
+## C++ Development
+
+WASM build uses CMake with Emscripten:
+```bash
+cd build/wasm
+../cmake.sh .     # Configure (uses emscripten toolchain)
+make -j4          # Build
+```
+
+Key C++ files:
+- `cpp/bisExportedFunctions.cpp` - Functions exported to JS
+- `cpp/bisImageAlgorithms.txx` - Image processing algorithms
+- `cpp/CMakeLists.txt` - Build configuration