coralnet-toolbox 0.0.68__tar.gz → 0.0.70__tar.gz

{coralnet_toolbox-0.0.68 → coralnet_toolbox-0.0.70}/.gitignore

@@ -130,3 +130,10 @@ launch.json
 
 # Local
 data/
+
+# Faiss index files
+*.faiss
+*.db
+
+# Copilot
+.github/copilot-instructions.md

{coralnet_toolbox-0.0.68 → coralnet_toolbox-0.0.70}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: coralnet-toolbox
-Version: 0.0.68
+Version: 0.0.70
 Summary: Tools for annotating and developing ML models for benthic imagery
 Author-email: Jordan Pierce <jordan.pierce@noaa.gov>
 License: MIT License
@@ -22,6 +22,7 @@ Requires-Dist: open-clip-torch>=2.20.0
 Requires-Dist: supervision>=0.24.0
 Requires-Dist: scikit-learn
 Requires-Dist: umap-learn
+Requires-Dist: faiss-cpu
 Requires-Dist: pycocotools
 Requires-Dist: ujson
 Requires-Dist: timm==0.9.2
@@ -93,10 +94,12 @@ coralnet-toolbox
 
 ## 📚 Guides
 
-For further instructions please see the following guides:
+For further information and instructions, please see the following guides:
+- [Overview](https://jordan-pierce.github.io/CoralNet-Toolbox/overview)
 - [Installation](https://jordan-pierce.github.io/CoralNet-Toolbox/installation)
 - [Usage](https://jordan-pierce.github.io/CoralNet-Toolbox/usage)
-- [Patch-based Image Classifier](https://jordan-pierce.github.io/CoralNet-Toolbox/classify)
+- Community Provided:
+  - [Patch-based Image Classifier](https://jordan-pierce.github.io/CoralNet-Toolbox/classify)
 
 <details open>
   <summary><h2><b>🎥 Watch the Video Demos</b></h2></summary>
@@ -171,11 +174,12 @@ Enhance your CoralNet experience with these tools:
   - Uses `Grounding DINO`, `OWLViT`, `OmDetTurbo`
 - 📻 Tune: Tune hyperparameters to identify ideal training conditions
 - 🧠 Train: Build local patch-based classifiers, object detection, and instance segmentation models
-- 🔮 Deploy: Use trained models for predictions
+- 🧙‍♂️ Deploy: Use trained models for predictions
 - 📊 Evaluation: Evaluate model performance
 - 🚀 Optimize: Productionize models for faster inferencing
 - ⚙️ Batch Inference: Perform predictions on multiple images, automatically
 - 🎞️ Video Inference: Perform predictions on a video in real-time, record the output and analytics
+- 🔮 Explorer: Cluster, view, and re-label annotations using embeddings, mapped from feature-space
 - ↔️ I/O: Import and Export annotations from / to CoralNet, Viscore, and TagLab
   - Export annotations as [GeoJSONs](https://datatracker.ietf.org/doc/html/rfc7946), segmentation masks
 - 📸 YOLO: Import and Export YOLO datasets for machine learning

{coralnet_toolbox-0.0.68 → coralnet_toolbox-0.0.70}/README.md

@@ -50,10 +50,12 @@ coralnet-toolbox
 
 ## 📚 Guides
 
-For further instructions please see the following guides:
+For further information and instructions, please see the following guides:
+- [Overview](https://jordan-pierce.github.io/CoralNet-Toolbox/overview)
 - [Installation](https://jordan-pierce.github.io/CoralNet-Toolbox/installation)
 - [Usage](https://jordan-pierce.github.io/CoralNet-Toolbox/usage)
-- [Patch-based Image Classifier](https://jordan-pierce.github.io/CoralNet-Toolbox/classify)
+- Community Provided:
+  - [Patch-based Image Classifier](https://jordan-pierce.github.io/CoralNet-Toolbox/classify)
 
 <details open>
   <summary><h2><b>🎥 Watch the Video Demos</b></h2></summary>
@@ -128,11 +130,12 @@ Enhance your CoralNet experience with these tools:
   - Uses `Grounding DINO`, `OWLViT`, `OmDetTurbo`
 - 📻 Tune: Tune hyperparameters to identify ideal training conditions
 - 🧠 Train: Build local patch-based classifiers, object detection, and instance segmentation models
-- 🔮 Deploy: Use trained models for predictions
+- 🧙‍♂️ Deploy: Use trained models for predictions
 - 📊 Evaluation: Evaluate model performance
 - 🚀 Optimize: Productionize models for faster inferencing
 - ⚙️ Batch Inference: Perform predictions on multiple images, automatically
 - 🎞️ Video Inference: Perform predictions on a video in real-time, record the output and analytics
+- 🔮 Explorer: Cluster, view, and re-label annotations using embeddings, mapped from feature-space
 - ↔️ I/O: Import and Export annotations from / to CoralNet, Viscore, and TagLab
   - Export annotations as [GeoJSONs](https://datatracker.ietf.org/doc/html/rfc7946), segmentation masks
 - 📸 YOLO: Import and Export YOLO datasets for machine learning

{coralnet_toolbox-0.0.68 → coralnet_toolbox-0.0.70}/coralnet_toolbox/Annotations/QtAnnotation.py

@@ -262,7 +262,7 @@ class Annotation(QObject):
             # [1, 2] - Very small dots with small gaps
             # [2, 4] - Small dots with larger gaps
             # [1, 3] - Tiny dots with medium gaps
-            pen = QPen(pen_color, 3)  # Width for dotted line
+            pen = QPen(pen_color, 4)  # Width for dotted line
             pen.setStyle(Qt.CustomDashLine)
             pen.setDashPattern([1, 2])  # Dotted pattern: 2 pixels on, 3 pixels off
             pen.setDashOffset(self._animated_line)

{coralnet_toolbox-0.0.68 → coralnet_toolbox-0.0.70}/coralnet_toolbox/Explorer/QtDataItem.py

@@ -2,6 +2,8 @@ import warnings
 
 import os
 
+import numpy as np
+
 from PyQt5.QtCore import Qt, QTimer
 from PyQt5.QtGui import QPen, QColor, QPainter
 from PyQt5.QtWidgets import QGraphicsEllipseItem, QStyle, QVBoxLayout, QLabel, QWidget, QGraphicsItem
@@ -54,6 +56,12 @@ class EmbeddingPointItem(QGraphicsEllipseItem):
 
         # Set the position of the point based on the data item's embedding coordinates
         self.setPos(self.data_item.embedding_x, self.data_item.embedding_y)
+        # Set the tooltip with detailed information
+        self.setToolTip(self.data_item.get_tooltip_text())
+        
+    def update_tooltip(self):
+        """Updates the tooltip by fetching the latest text from the data item."""
+        self.setToolTip(self.data_item.get_tooltip_text())
 
     def paint(self, painter, option, widget):
         """
@@ -104,6 +112,10 @@ class AnnotationImageWidget(QWidget):
         self.image_label.setScaledContents(True)
         self.image_label.setStyleSheet("border: none;")
         layout.addWidget(self.image_label)
+        
+    def update_tooltip(self):
+        """Updates the tooltip by fetching the latest text from the data item."""
+        self.setToolTip(self.data_item.get_tooltip_text())
 
     def load_and_set_image(self):
         """Load image, calculate its aspect ratio, and set the widget's initial size."""
@@ -124,7 +136,10 @@ class AnnotationImageWidget(QWidget):
             self.image_label.setText("Error\nLoading Image")
             self.pixmap = None
             self.aspect_ratio = 1.0
+            
         self.update_height(self.widget_height)
+        # Set the initial tooltip
+        self.update_tooltip()
 
     def update_height(self, new_height):
         """Updates the widget's height and rescales its width and content accordingly."""
@@ -204,8 +219,12 @@ class AnnotationImageWidget(QWidget):
                 # The viewer is the controller and will decide how to change the selection state
                 self.annotation_viewer.handle_annotation_selection(self, event)
         elif event.button() == Qt.RightButton:
-            event.ignore()
-            return
+            if self.annotation_viewer and hasattr(self.annotation_viewer, 'handle_annotation_context_menu'):
+                self.annotation_viewer.handle_annotation_context_menu(self, event)
+                event.accept()
+                return
+            else:
+                event.ignore()
         super().mousePressEvent(event)
 
 
@@ -218,14 +237,20 @@ class AnnotationDataItem:
 
     def __init__(self, annotation, embedding_x=None, embedding_y=None, embedding_id=None):
         self.annotation = annotation
+        
         self.embedding_x = embedding_x if embedding_x is not None else 0.0
         self.embedding_y = embedding_y if embedding_y is not None else 0.0
         self.embedding_id = embedding_id if embedding_id is not None else 0
+        
         self._is_selected = False
         self._preview_label = None
         self._original_label = annotation.label
-        self._marked_for_deletion = False
-
+        
+        # To store pre-formatted top-k prediction details
+        self.prediction_details = None
+        # To store prediction probabilities for sorting
+        self.prediction_probabilities = None
+        
     @property
     def effective_label(self):
         """Get the current effective label (preview if it exists, otherwise original)."""
@@ -257,18 +282,6 @@ class AnnotationDataItem:
         """Check if this annotation has a temporary preview label assigned."""
         return self._preview_label is not None
 
-    def mark_for_deletion(self):
-        """Mark this annotation for deletion."""
-        self._marked_for_deletion = True
-
-    def unmark_for_deletion(self):
-        """Unmark this annotation for deletion."""
-        self._marked_for_deletion = False
-
-    def is_marked_for_deletion(self):
-        """Check if this annotation is marked for deletion."""
-        return self._marked_for_deletion
-
     def apply_preview_permanently(self):
         """Apply the preview label permanently to the underlying annotation object."""
         if self._preview_label:
@@ -290,9 +303,35 @@ class AnnotationDataItem:
             'embedding_id': self.embedding_id,
             'color': self.effective_color
         }
+    
+    def get_tooltip_text(self):
+        """
+        Generates a rich HTML-formatted tooltip with all relevant information.
+        """
+        info = self.get_display_info()
+        
+        tooltip_parts = [
+            f"<b>ID:</b> {info['id']}",
+            f"<b>Image:</b> {info['image']}",
+            f"<b>Label:</b> {info['label']}",
+            f"<b>Type:</b> {info['type']}"
+        ]
+
+        # Add prediction details if they exist
+        if self.prediction_details:
+            tooltip_parts.append(f"<hr>{self.prediction_details}")
+
+        return "<br>".join(tooltip_parts)
 
     def get_effective_confidence(self):
         """Get the effective confidence value."""
+        # First check if prediction probabilities are available from model predictions
+        if hasattr(self, 'prediction_probabilities') and self.prediction_probabilities is not None:
+            if len(self.prediction_probabilities) > 0:
+                # Use the maximum probability for confidence sorting
+                return float(np.max(self.prediction_probabilities))
+        
+        # Fallback to existing confidence values
         if self.annotation.verified and hasattr(self.annotation, 'user_confidence') and self.annotation.user_confidence:
             return list(self.annotation.user_confidence.values())[0]
         elif hasattr(self.annotation, 'machine_confidence') and self.annotation.machine_confidence: