coralnet-toolbox 0.0.75__tar.gz → 0.0.76__tar.gz

{coralnet_toolbox-0.0.75 → coralnet_toolbox-0.0.76}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: coralnet-toolbox
-Version: 0.0.75
+Version: 0.0.76
 Summary: Tools for annotating and developing ML models for benthic imagery
 Author-email: Jordan Pierce <jordan.pierce@noaa.gov>
 License: MIT License
@@ -16,7 +16,7 @@ License-File: LICENSE.txt
 Requires-Dist: PyQt5>=5.15.11
 Requires-Dist: pyqtdarktheme
 Requires-Dist: pyqtgraph
-Requires-Dist: ultralytics>=8.3.152
+Requires-Dist: ultralytics>=8.3.191
 Requires-Dist: lap>=0.5.12
 Requires-Dist: open-clip-torch>=2.20.0
 Requires-Dist: supervision>=0.24.0
@@ -27,7 +27,7 @@ Requires-Dist: pycocotools
 Requires-Dist: ujson
 Requires-Dist: timm==0.9.2
 Requires-Dist: autodistill
-Requires-Dist: transformers>=4.55.4
+Requires-Dist: transformers>=4.56.0
 Requires-Dist: hf_xet
 Requires-Dist: x-segment-anything>=0.0.8
 Requires-Dist: yolo-tiling>=0.0.19
@@ -39,6 +39,8 @@ Requires-Dist: beautifulsoup4>=4.12.2
 Requires-Dist: webdriver_manager
 Requires-Dist: dill
 Requires-Dist: seaborn
+Requires-Dist: GPUtil
+Requires-Dist: psutil
 Provides-Extra: all
 Requires-Dist: coralnet-toolbox[extra]; extra == "all"
 Dynamic: license-file
@@ -114,6 +116,7 @@ For a complete installation guide (including CUDA setup), see the [Installation
 | **Overview** | Get the big picture | [📋 Read More](https://jordan-pierce.github.io/CoralNet-Toolbox/overview) |
 | **Installation** | Detailed setup instructions | [⚙️ Setup Guide](https://jordan-pierce.github.io/CoralNet-Toolbox/installation) |
 | **Usage** | Learn the tools | [🛠️ User Manual](https://jordan-pierce.github.io/CoralNet-Toolbox/usage) |
+| **Hot Keys** | Keyboard shortcuts | [⌨️ Shortcuts](https://jordan-pierce.github.io/CoralNet-Toolbox/hot-keys) |
 | **Classification** | Community tutorial | [🧠 AI Tutorial](https://jordan-pierce.github.io/CoralNet-Toolbox/classify) |
 
 </div>
@@ -179,7 +182,7 @@ The toolbox integrates state-of-the-art models for efficient annotation workflow
 | **Framework** | **Models** | **Capability** |
 |:---:|:---:|:---:|
 | **YOLOE** | See Anything | Visual prompt detection |
-| **AutoDistill** | Grounding DINO • OWLViT • OmDetTurbo | Zero-shot detection |
+| **Transformers** | Grounding DINO • OWLViT • OmDetTurbo | Zero-shot detection |
 
 </div>
 
@@ -277,12 +280,9 @@ uv pip install coralnet-toolbox
 ### 🚀 **Step 3: GPU Acceleration (Optional)**
 For CUDA-enabled systems:
 ```bash
-# Example for CUDA 11.8
-conda install nvidia/label/cuda-11.8.0::cuda-nvcc -y
-conda install nvidia/label/cuda-11.8.0::cuda-toolkit -y
-
+# Example for CUDA 12.9
 # Install PyTorch with CUDA support
-uv pip install torch torchvision --index-url https://download.pytorch.org/whl/cu118 --upgrade
+uv pip install torch torchvision --index-url https://download.pytorch.org/whl/cu129 --upgrade
 ```
 
 ### 🏃‍♂️ **Step 4: Launch**

{coralnet_toolbox-0.0.75 → coralnet_toolbox-0.0.76}/README.md

@@ -69,6 +69,7 @@ For a complete installation guide (including CUDA setup), see the [Installation
 | **Overview** | Get the big picture | [📋 Read More](https://jordan-pierce.github.io/CoralNet-Toolbox/overview) |
 | **Installation** | Detailed setup instructions | [⚙️ Setup Guide](https://jordan-pierce.github.io/CoralNet-Toolbox/installation) |
 | **Usage** | Learn the tools | [🛠️ User Manual](https://jordan-pierce.github.io/CoralNet-Toolbox/usage) |
+| **Hot Keys** | Keyboard shortcuts | [⌨️ Shortcuts](https://jordan-pierce.github.io/CoralNet-Toolbox/hot-keys) |
 | **Classification** | Community tutorial | [🧠 AI Tutorial](https://jordan-pierce.github.io/CoralNet-Toolbox/classify) |
 
 </div>
@@ -134,7 +135,7 @@ The toolbox integrates state-of-the-art models for efficient annotation workflow
 | **Framework** | **Models** | **Capability** |
 |:---:|:---:|:---:|
 | **YOLOE** | See Anything | Visual prompt detection |
-| **AutoDistill** | Grounding DINO • OWLViT • OmDetTurbo | Zero-shot detection |
+| **Transformers** | Grounding DINO • OWLViT • OmDetTurbo | Zero-shot detection |
 
 </div>
 
@@ -232,12 +233,9 @@ uv pip install coralnet-toolbox
 ### 🚀 **Step 3: GPU Acceleration (Optional)**
 For CUDA-enabled systems:
 ```bash
-# Example for CUDA 11.8
-conda install nvidia/label/cuda-11.8.0::cuda-nvcc -y
-conda install nvidia/label/cuda-11.8.0::cuda-toolkit -y
-
+# Example for CUDA 12.9
 # Install PyTorch with CUDA support
-uv pip install torch torchvision --index-url https://download.pytorch.org/whl/cu118 --upgrade
+uv pip install torch torchvision --index-url https://download.pytorch.org/whl/cu129 --upgrade
 ```
 
 ### 🏃‍♂️ **Step 4: Launch**

{coralnet_toolbox-0.0.75 → coralnet_toolbox-0.0.76}/coralnet_toolbox/Annotations/QtPolygonAnnotation.py

@@ -306,20 +306,30 @@ class PolygonAnnotation(Annotation):
         self.set_cropped_bbox()
         # Get the bounding box of the polygon
         min_x, min_y, max_x, max_y = self.cropped_bbox
-
+        
+        # Ensure min/max values are correctly ordered
+        min_x, max_x = min(min_x, max_x), max(min_x, max_x)
+        min_y, max_y = min(min_y, max_y), max(min_y, max_y)
+        
+        # Clamp values to image bounds
+        min_x = max(0, min(rasterio_src.width - 1, min_x))
+        min_y = max(0, min(rasterio_src.height - 1, min_y))
+        max_x = max(min_x + 1, min(rasterio_src.width, max_x))
+        max_y = max(min_y + 1, min(rasterio_src.height, max_y))
+    
         # Calculate the window for rasterio
         window = Window(
-            col_off=max(0, int(min_x)),
-            row_off=max(0, int(min_y)),
-            width=min(rasterio_src.width - int(min_x), int(max_x - min_x)),
-            height=min(rasterio_src.height - int(min_y), int(max_y - min_y))
+            col_off=int(min_x),
+            row_off=int(min_y),
+            width=int(max_x - min_x),
+            height=int(max_y - min_y)
         )
-
+    
         # Convert rasterio to QImage
         q_image = rasterio_to_cropped_image(self.rasterio_src, window)
         # Convert QImage to QPixmap
         self.cropped_image = QPixmap.fromImage(q_image)
-
+    
         self.annotationUpdated.emit(self)  # Notify update
 
     def create_graphics_item(self, scene: QGraphicsScene):
@@ -423,7 +433,7 @@ class PolygonAnnotation(Annotation):
         self.update_graphics_item()
         self.annotationUpdated.emit(self)  # Notify update
 
-    def update_annotation_size(self, delta: float):
+    def update_annotation_size(self, scale_factor: float):
         """
         Grow/shrink the polygon and its holes by scaling vertices radially from the centroid.
         """
@@ -433,18 +443,53 @@ class PolygonAnnotation(Annotation):
             return
 
         # 1. Use the true geometric centroid as the pivot for scaling.
-        # This is correctly calculated by the new set_centroid() method.
         centroid_x = self.center_xy.x()
         centroid_y = self.center_xy.y()
 
-        # 2. Determine the scale factor (this logic remains the same).
+        # 2. Determine the scale factor.
         step = 0.01  # Adjust for finer or coarser changes
-        if delta > 1.0:
+        if scale_factor > 1.0:
             scale = 1.0 + step
-        elif delta < 1.0:
+        elif scale_factor < 1.0:
             scale = 1.0 - step
         else:
             scale = 1.0
+        
+        # Check for image boundaries before scaling
+        if hasattr(self, 'rasterio_src'):
+            # Before scaling, check if any point would go beyond image boundaries
+            img_width = self.rasterio_src.width
+            img_height = self.rasterio_src.height
+            padding = 10  # pixels of padding
+            
+            # Check outer boundary points
+            for p in self.points:
+                dx = p.x() - centroid_x
+                dy = p.y() - centroid_y
+                new_x = centroid_x + dx * scale
+                new_y = centroid_y + dy * scale
+                
+                if new_x < -padding or \
+                   new_y < -padding or \
+                   new_x > img_width + padding or \
+                   new_y > img_height + padding:
+                    # Point would be out of bounds, don't scale
+                    return
+            
+            # Check holes points too
+            for hole in self.holes:
+                for p in hole:
+                    dx = p.x() - centroid_x
+                    dy = p.y() - centroid_y
+                    new_x = centroid_x + dx * scale
+                    new_y = centroid_y + dy * scale
+                    
+                    if new_x < -padding or \
+                       new_y < -padding or \
+                       new_x > img_width + padding or \
+                       new_y > img_height + padding:
+                        # Point would be out of bounds, don't scale
+                        return
 
         # 3. Scale the outer boundary points.
         new_points = []

{coralnet_toolbox-0.0.75 → coralnet_toolbox-0.0.76}/coralnet_toolbox/Annotations/QtRectangleAnnotation.py

@@ -213,23 +213,29 @@ class RectangleAnnotation(Annotation):
         # Get the bounding box of the rectangle
         min_x, min_y, max_x, max_y = self.cropped_bbox
         
-        # Ensure min/max values are correctly ordered to avoid negative width/height
+        # Ensure min/max values are correctly ordered
         min_x, max_x = min(min_x, max_x), max(min_x, max_x)
         min_y, max_y = min(min_y, max_y), max(min_y, max_y)
-
+        
+        # Clamp values to image bounds
+        min_x = max(0, min(rasterio_src.width - 1, min_x))
+        min_y = max(0, min(rasterio_src.height - 1, min_y))
+        max_x = max(min_x + 1, min(rasterio_src.width, max_x))
+        max_y = max(min_y + 1, min(rasterio_src.height, max_y))
+        
         # Calculate the window for rasterio
         window = Window(
-            col_off=max(0, int(min_x)),
-            row_off=max(0, int(min_y)),
-            width=min(rasterio_src.width - int(min_x), int(max_x - min_x)),
-            height=min(rasterio_src.height - int(min_y), int(max_y - min_y))
+            col_off=int(min_x),
+            row_off=int(min_y),
+            width=int(max_x - min_x),
+            height=int(max_y - min_y)
         )
-
+        
         # Convert rasterio to QImage
         q_image = rasterio_to_cropped_image(self.rasterio_src, window)
         # Convert QImage to QPixmap
         self.cropped_image = QPixmap.fromImage(q_image)
-
+        
         self.annotationUpdated.emit(self)  # Notify update
 
     def create_graphics_item(self, scene: QGraphicsScene):
@@ -282,13 +288,37 @@ class RectangleAnnotation(Annotation):
         # Clear the machine confidence
         self.update_user_confidence(self.label)
 
-        # Update the size, graphic
-        width = (self.bottom_right.x() - self.top_left.x()) * scale_factor
-        height = (self.bottom_right.y() - self.top_left.y()) * scale_factor
-        self.top_left = QPointF(self.center_xy.x() - width / 2, self.center_xy.y() - height / 2)
-        self.bottom_right = QPointF(self.center_xy.x() + width / 2, self.center_xy.y() + height / 2)
+        # Calculate new dimensions
+        current_width = self.bottom_right.x() - self.top_left.x()
+        current_height = self.bottom_right.y() - self.top_left.y()
+        new_width = current_width * scale_factor
+        new_height = current_height * scale_factor
+        
+        # Calculate tentative new corners
+        new_left = self.center_xy.x() - new_width / 2
+        new_top = self.center_xy.y() - new_height / 2
+        new_right = self.center_xy.x() + new_width / 2
+        new_bottom = self.center_xy.y() + new_height / 2
+        
+        # Check if we're within valid image bounds (or use a reasonable padding)
+        # Assuming we have access to the image dimensions
+        if hasattr(self, 'rasterio_src'):
+            img_width = self.rasterio_src.width
+            img_height = self.rasterio_src.height
+            
+            # Apply reasonable bounds with some margin
+            padding = 10  # pixels
+            if new_left < -padding or new_top < -padding or new_right > img_width + padding or new_bottom > img_height + padding:
+                # Don't resize beyond these limits
+                return
+        
+        # Update the rectangle coordinates
+        self.top_left = QPointF(new_left, new_top)
+        self.bottom_right = QPointF(new_right, new_bottom)
+        
+        # Update graphics and notify
         self.update_graphics_item()
-        self.annotationUpdated.emit(self)  # Notify update
+        self.annotationUpdated.emit(self)
 
     def resize(self, handle: str, new_pos: QPointF):
         """Resize the annotation based on the handle and new position."""

{coralnet_toolbox-0.0.75 → coralnet_toolbox-0.0.76}/coralnet_toolbox/Explorer/transformer_models.py

@@ -7,12 +7,23 @@ Qt dependencies.
 """
 
 TRANSFORMER_MODELS = {
+    'ResNet-50': 'microsoft/resnet-50',
+    'ResNet-101': 'microsoft/resnet-101',
     'DINOv2 (Small)': 'facebook/dinov2-small',
     'DINOv2 (Base)': 'facebook/dinov2-base',
     'DINOv2 (Large)': 'facebook/dinov2-large',
+    'DINOv2 (Giant)': 'facebook/dinov2-giant',
+    'DINOv2 (Giant ImageNet1k)': 'facebook/dinov2-giant-imagenet1k-1-layer',
     'DINOv3 ConvNext (Tiny)': 'facebook/dinov3-convnext-tiny-pretrain-lvd1689m',
-    'ResNet-50': 'microsoft/resnet-50',
-    'ResNet-101': 'microsoft/resnet-101',
+    'DINOv3 ConvNext (Small)': 'facebook/dinov3-convnext-small-pretrain-lvd1689m',
+    'DINOv3 ConvNext (Base)': 'facebook/dinov3-convnext-base-pretrain-lvd1689m',
+    'DINOv3 ConvNext (Large)': 'facebook/dinov3-convnext-large-pretrain-lvd1689m',
+    'DINOv3 ViT (Small/16)': 'facebook/dinov3-vits16-pretrain-lvd1689m',
+    'DINOv3 ViT (Small/16+)': 'facebook/dinov3-vits16plus-pretrain-lvd1689m',
+    'DINOv3 ViT (Base/16)': 'facebook/dinov3-vitb16-pretrain-lvd1689m',
+    'DINOv3 ViT (Large/16)': 'facebook/dinov3-vitl16-pretrain-lvd1689m',
+    'DINOv3 ViT (Huge/16+)': 'facebook/dinov3-vith16plus-pretrain-lvd1689m',
+    'DINOv3 ViT (7B/16)': 'facebook/dinov3-vit7b16-pretrain-lvd1689m',
     'Swin Transformer (Tiny)': 'microsoft/swin-tiny-patch4-window7-224',
     'Swin Transformer (Base)': 'microsoft/swin-base-patch4-window7-224',
     'ViT (Base)': 'google/vit-base-patch16-224',