Add UI/UX & 3D viewer modernization blueprint

.gitignore

@@ -1,19 +1,41 @@
+# Python
 __pycache__/
-*.pyc
+*.py[cod]
+*$py.class
+*.so
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Virtual Environment
 .venv/
-env/
 venv/
-.env
+env/
+
+# IDEs
 .idea/
 .vscode/
-*.log
-dist/
-build/
-*.egg-info/
-.DS_Store
-model_output/
+
+# Project Specific
 *.pth
-*.pt
-*.h5
-*.ckpt
-*.onnx
+model_output/
+.gemini/
+.agent/
+brain/
+scratch/
+
+# Logs
+*.log

README.md

@@ -0,0 +1,101 @@
+# NeuroSeg-Pro: MRI Segmentation & Visualization Tool
+
+NeuroSeg-Pro is a PyQt5-based application designed for visualizing and segmenting brain MRI scans using deep learning models. It provides a rich interface for comparing model outputs, ground truth, and difference maps.
+
+## 🚀 Key Features
+
+### Visualization
+- **Multi-Planar Reconstruction (MPR):** View Axial, Sagittal, and Coronal planes simultaneously.
+- **3D Viewport:** Interactive 3D visualization of segmentation masks (if enabled).
+- **Advanced Tools:** 
+  - **Grid Overlay:** Helper grid for alignment.
+  - **Crosshair:** Navigate specific coordinates across all views.
+  - **MRI Visibility Toggle:** Focus on the mask by hiding the background MRI.
+
+### AI Analysis
+- **Model Selection:** Choose between different pre-trained models (e.g., Teacher/Student variants).
+- **Comparison Modes:**
+  - **Model A vs Model B:** Side-by-side comparison.
+  - **Model A vs Ground Truth:** Validate predictions against expert annotations.
+  - **Overlay vs Raw:** Compare active segmentation with the raw scan.
+- **Metrics:** Real-time calculation of Dice Coefficient, Sensitivity, Specificity, and Hausdorff Distance.
+
+### User Interface
+- **Modern Dark Theme:** "Deep Space Medical" theme for comfortable viewing.
+- **Dynamic Legend:** Legend updates automatically based on the classes present in the current view.
+- **One-Click Export:** Save segmentation masks as `.nii.gz` files.
+
+---
+
+## 🛠️ Installation & Setup
+
+### Prerequisites
+- Python 3.8+
+- [Git](https://git-scm.com/)
+
+### 1. Clone the Repository
+```bash
+git clone https://github.com/yourusername/NeuroSeg-Pro.git
+cd NeuroSeg-Pro
+```
+
+### 2. Create a Virtual Environment (Recommended)
+```bash
+# Windows
+python -m venv .venv
+.venv\Scripts\activate
+
+# Linux/Mac
+python3 -m venv .venv
+source .venv/bin/activate
+```
+
+### 3. Install Dependencies
+```bash
+pip install -r requirements.txt
+```
+
+### 4. Setup Models
+> **Note:** Due to file size limits, pre-trained model weights (`.pth` files) are NOT included in this repository.
+> Please place your model files in the `models/` directory.
+
+Example structure:
+```
+NeuroSeg-Pro/
+├── app/
+├── models/
+│   ├── Teacher_model_50.pth
+│   └── ...
+├── assets/
+└── ...
+```
+
+---
+
+## ▶️ Running the Application
+
+To launch the main application interface:
+
+```bash
+python -m app.main
+```
+
+---
+
+## 📂 Project Structure
+
+- `app/` - Source code.
+  - `main.py` - Entry point.
+  - `ui/` - Interface widgets and themes.
+  - `core/` - Logic for inference and image processing.
+- `assets/` - Icons and resources.
+- `models/` - Directory for model weights (ignored by git).
+- `model_output/` - Saved segmentation masks.
+
+---
+
+## 🤝 Contributing
+Contributions are welcome! Please open an issue or submit a pull request for any improvements.
+
+## 📄 License
+MIT License

app/core/inference.py

@@ -7,6 +7,7 @@ class InferenceEngine:
     def __init__(self, model_path: str = None, device: str = None):
         self.device = device if device else ("cuda" if torch.cuda.is_available() else "cpu")
         self.model = None
+        self.current_model_path = None
         if model_path:
             self.load_model(model_path)
 
@@ -62,6 +63,7 @@ def load_model(self, model_path: str):
                 self.model.load_state_dict(new_state_dict, strict=False)
 
             self.model.eval()
+            self.current_model_path = model_path
             print(f"Model loaded from {model_path}")
         except Exception as e:
             print(f"Error loading model: {e}")
@@ -104,3 +106,12 @@ def predict(self, input_data: np.ndarray):
                 outputs = torch.nn.functional.interpolate(outputs, size=original_shape, mode='trilinear', align_corners=False)
 
             return torch.argmax(outputs, dim=1).detach().cpu().numpy()[0] # Remove batch dim
+
+    def run_inference(self, volume: np.ndarray, model_path: str):
+        """
+        Loads the model if necessary and runs inference.
+        """
+        if self.current_model_path != model_path:
+            self.load_model(model_path)
+
+        return self.predict(volume)

app/ui/main_window.py

@@ -14,6 +14,9 @@ class MainWindow(QMainWindow):
     def __init__(self):
         super().__init__()
         self.settings = Settings()
+        self.sidebar_expanded_width = 260
+        self.sidebar_collapsed_width = 76
+        self.sidebar_collapsed = bool(self.settings.get("sidebar_collapsed") or False)
         self.setWindowTitle("Brain Tumor Segmentation Pro")
         self.resize(1280, 850) # Slightly larger default
 
@@ -96,13 +99,30 @@ def setup_header(self):
         self.right_layout.addWidget(self.header_frame)
 
     def toggle_sidebar(self):
-        if self.sidebar.isVisible():
-            self.sidebar.hide()
+        self.sidebar_collapsed = not self.sidebar_collapsed
+        self.settings.set("sidebar_collapsed", self.sidebar_collapsed)
+        self.apply_sidebar_state()
+
+    def apply_sidebar_state(self):
+        if self.sidebar_collapsed:
+            self.sidebar.setFixedWidth(self.sidebar_collapsed_width)
+            self.title_label.setVisible(False)
+            self.btn_toggle_sidebar.setText("☷")
+            for btn in [self.btn_dashboard, self.btn_viewer, self.btn_help, self.btn_settings]:
+                btn.setText("")
+                btn.setToolTip(btn.property("full_text"))
         else:
-            self.sidebar.show()
+            self.sidebar.setFixedWidth(self.sidebar_expanded_width)
+            self.title_label.setVisible(True)
+            self.btn_toggle_sidebar.setText("☰")
+            for btn in [self.btn_dashboard, self.btn_viewer, self.btn_help, self.btn_settings]:
+                btn.setText(btn.property("full_text"))
+                btn.setToolTip("")
 
     def on_recent_file_clicked(self, file_path):
-        self.on_file_loaded(file_path, 'mri') # Default to MRI
+        import os
+        file_type = 'folder' if os.path.isdir(file_path) else 'mri'
+        self.on_file_loaded(file_path, file_type)
 
     def on_file_loaded(self, file_path, file_type):
         print(f"Loading {file_type}: {file_path}")
@@ -152,7 +172,7 @@ def refresh_theme(self):
     def setup_sidebar(self):
         self.sidebar = QFrame()
         self.sidebar.setObjectName("Sidebar")
-        self.sidebar.setFixedWidth(260)
+        self.sidebar.setFixedWidth(self.sidebar_expanded_width)
 
         self.sidebar_layout = QVBoxLayout(self.sidebar)
         self.sidebar_layout.setContentsMargins(20, 40, 20, 20)
@@ -190,13 +210,16 @@ def setup_sidebar(self):
         self.btn_settings.clicked.connect(lambda: self.switch_page(2))
         self.btn_help.clicked.connect(self.show_tutorial)
 
+        self.apply_sidebar_state()
+
     def show_tutorial(self):
         from app.ui.tutorial_dialog import TutorialDialog
         dlg = TutorialDialog(self)
         dlg.exec_()
 
     def create_nav_button(self, text, icon_name=None):
         btn = QPushButton(text)
+        btn.setProperty("full_text", text)
         btn.setCheckable(True)
         btn.setFixedHeight(50)
         btn.setCursor(Qt.PointingHandCursor)

app/ui/theme.py

@@ -119,22 +119,28 @@ def apply_theme(app: QApplication):
             border-radius: 8px;
         }}
 
-        /* GroupBox - Modern & Minimal */
+        /* GroupBox - Modern & Block-like */
+        /* GroupBox - Modern & Block-like */
         QGroupBox {{
             background-color: {c["SURFACE"]};
             border: 1px solid {c["BORDER"]};
-            border-radius: 12px;
-            margin-top: 24px;
-            padding-top: 10px;
+            border-radius: 10px;
+            margin-top: 20px; /* Leave space for title */
+            padding-top: 15px;
+            padding-bottom: 10px;
+            padding-left: 10px;
+            padding-right: 10px;
         }}
         QGroupBox::title {{
             subcontrol-origin: margin;
             subcontrol-position: top left;
             padding: 0 5px;
             left: 10px;
+            bottom: 0px; /* Overlap border */
             color: {c["ACCENT"]};
             font-weight: bold;
-            font-size: {base_font_size + 1}px;
+            font-size: {base_font_size + 2}px;
+            background-color: {c["BACKGROUND"]}; /* Mask border behind title */
         }}
 
         /* Buttons */
@@ -327,8 +333,26 @@ def apply_theme(app: QApplication):
             border: 1px solid {c["PRIMARY"]};
             image: url(assets/icons/check.svg); 
         }}
-        /* Fallback check */
-        QCheckBox::indicator:checked {{
-            background-color: {c["PRIMARY"]};
+        /* Table Widget */
+        QTableWidget {{
+            background-color: {c["SURFACE"]};
+            border: 1px solid {c["BORDER"]};
+            border-radius: 8px;
+            gridline-color: {c["BORDER"]};
+        }}
+        QHeaderView::section {{
+            background-color: {c["SURFACE_LIGHT"]};
+            padding: 4px;
+            border: none;
+            border-bottom: 2px solid {c["BORDER"]};
+            color: {c["TEXT_SECONDARY"]};
+            font-weight: bold;
+        }}
+        QTableWidget::item {{
+            padding: 5px;
+        }}
+        QTableWidget::item:selected {{
+            background-color: {c["PRIMARY"]}30;
+            color: {c["TEXT_PRIMARY"]};
         }}
     """)