Dev

coralnet_toolbox/AutoDistill/QtDeployModel.py

@@ -382,18 +382,6 @@ def get_ontology_mapping(self):
                 ontology_mapping[text_input.text()] = label_dropdown.currentText()
         return ontology_mapping
 
-    def get_uncertainty_threshold(self):
-        """
-        Get the uncertainty threshold, limiting it to a maximum of 0.10.
-
-        Returns:
-            Adjusted uncertainty threshold value.
-        """
-        if self.main_window.get_uncertainty_thresh() < 0.10:
-            return self.main_window.get_uncertainty_thresh()
-        else:
-            return 0.10  # Arbitrary value to prevent too many detections
-
     def load_new_model(self, model_name, uncertainty_thresh):
         """
         Load a new model based on the selected model name.
@@ -406,8 +394,8 @@ def load_new_model(self, model_name, uncertainty_thresh):
             from autodistill_grounding_dino import GroundingDINO
             self.model_name = model_name
             self.loaded_model = GroundingDINO(ontology=self.ontology,
-                                              box_threshold=uncertainty_thresh,
-                                              text_threshold=uncertainty_thresh)
+                                              box_threshold=0.025,
+                                              text_threshold=0.025)
 
     def predict(self, image_paths=None):
         """
@@ -417,7 +405,6 @@ def predict(self, image_paths=None):
             image_paths: List of image paths to process. If None, uses the current image.
         """
         if not self.loaded_model:
-            QMessageBox.critical(self, "Error", "No model loaded")
             return
 
         if not image_paths:
@@ -440,7 +427,7 @@ def predict(self, image_paths=None):
             # Create a results processor
             results_processor = ResultsProcessor(self.main_window, 
                                                  self.class_mapping,
-                                                 uncertainty_thresh=self.get_uncertainty_threshold(),
+                                                 uncertainty_thresh=self.uncertainty_thresh,
                                                  iou_thresh=self.iou_thresh,
                                                  min_area_thresh=self.area_thresh_min,
                                                  max_area_thresh=self.area_thresh_max)

coralnet_toolbox/MachineLearning/BatchInference/QtClassify.py

@@ -101,27 +101,21 @@ def preprocess_patch_annotations(self):
         progress_bar.show()
         progress_bar.start_progress(len(self.image_paths))
 
-        def crop(image_path, image_annotations):
-            # Crop the image based on the annotations
-            return self.annotation_window.crop_these_image_annotations(image_path, image_annotations)
-
         # Group annotations by image path
-        groups = groupby(sorted(self.annotations, key=attrgetter('image_path')), key=attrgetter('image_path'))
-
-        with ThreadPoolExecutor() as executor:
-            future_to_image = {}
-            for path, group in groups:
-                future = executor.submit(crop, path, list(group))
-                future_to_image[future] = path
-
-            for future in as_completed(future_to_image):
-                image_path = future_to_image[future]
-                try:
-                    self.prepared_patches.extend(future.result())
-                except Exception as exc:
-                    print(f'{image_path} generated an exception: {exc}')
-                finally:
-                    progress_bar.update_progress()
+        grouped_annotations = groupby(sorted(self.annotations, key=attrgetter('image_path')), 
+                                   key=attrgetter('image_path'))
+
+        for image_path, group in grouped_annotations:
+            try:
+                # Process image annotations
+                image_annotations = list(group)
+                image_annotations = self.annotation_window.crop_these_image_annotations(image_path, image_annotations)
+                self.prepared_patches.extend(image_annotations)
+
+            except Exception as exc:
+                print(f'{image_path} generated an exception: {exc}')
+            finally:
+                progress_bar.update_progress()
 
         progress_bar.stop_progress()
         progress_bar.close()
@@ -147,4 +141,8 @@ def batch_inference(self):
                 progress_bar.update_progress()
 
         progress_bar.stop_progress()
-        progress_bar.close()
+        progress_bar.close()
+
+        # Clear the list of annotations
+        self.annotations = []
+        self.prepared_patches = []

coralnet_toolbox/MachineLearning/DeployModel/QtBase.py

@@ -339,10 +339,10 @@ def create_generic_labels(self):
 
     def get_uncertainty_threshold(self):
         """
-        Get the confidence threshold for predictions
+        Get the confidence threshold for classification predictions
         """
         threshold = self.main_window.get_uncertainty_thresh()
-        return threshold if threshold < 0.10 else 0.10
+        return threshold if threshold > 0.10 else 0.10
 
     def predict(self, inputs):
         """

coralnet_toolbox/MachineLearning/DeployModel/QtClassify.py

@@ -110,19 +110,23 @@ def predict(self, inputs=None):
         if not inputs:
             # If no annotations are selected, predict all annotations in the image
             inputs = self.annotation_window.get_image_review_annotations()
+        if not inputs:
+            # If no annotations are available, return
+            return
 
         images_np = []
         for annotation in inputs:
             images_np.append(pixmap_to_numpy(annotation.cropped_image))
 
         # Predict the classification results
         results = self.loaded_model(images_np,
+                                    conf=self.uncertainty_thresh,
                                     device=self.main_window.device,
                                     stream=True)
         # Create a result processor
         results_processor = ResultsProcessor(self.main_window,
                                              self.class_mapping,
-                                             uncertainty_thresh=self.get_uncertainty_threshold())
+                                             uncertainty_thresh=self.uncertainty_thresh)
 
         # Process the classification results
         results_processor.process_classification_results(results, inputs)

coralnet_toolbox/MachineLearning/DeployModel/QtDetect.py

@@ -143,15 +143,15 @@ def predict(self, inputs=None):
         # Predict the detection results
         results = self.loaded_model(inputs,
                                     agnostic_nms=True,
-                                    conf=self.get_uncertainty_threshold(),
+                                    conf=self.uncertainty_thresh,
                                     iou=self.iou_thresh,
                                     device=self.main_window.device,
                                     stream=True)
 
         # Create a result processor
         results_processor = ResultsProcessor(self.main_window,
                                              self.class_mapping,
-                                             uncertainty_thresh=self.get_uncertainty_threshold(),
+                                             uncertainty_thresh=self.uncertainty_thresh,
                                              iou_thresh=self.iou_thresh,
                                              min_area_thresh=self.area_thresh_min,
                                              max_area_thresh=self.area_thresh_max)

coralnet_toolbox/MachineLearning/DeployModel/QtSegment.py

@@ -143,15 +143,15 @@ def predict(self, inputs=None):
         # Predict the segmentation results
         results = self.loaded_model(inputs,
                                     agnostic_nms=True,
-                                    conf=self.get_uncertainty_threshold(),
+                                    conf=self.uncertainty_thresh,
                                     iou=self.iou_thresh,
                                     device=self.main_window.device,
                                     stream=True)
 
         # Create a result processor
         results_processor = ResultsProcessor(self.main_window,
                                              self.class_mapping,
-                                             uncertainty_thresh=self.get_uncertainty_threshold(),
+                                             uncertainty_thresh=self.uncertainty_thresh,
                                              iou_thresh=self.iou_thresh,
                                              min_area_thresh=self.area_thresh_min,
                                              max_area_thresh=self.area_thresh_max)

coralnet_toolbox/QtMainWindow.py

@@ -1145,25 +1145,6 @@ def open_segment_deploy_model_dialog(self):
             self.segment_deploy_model_dialog.exec_()
         except Exception as e:
             QMessageBox.critical(self, "Critical Error", f"{e}")
-
-    def open_batch_inference_dialog(self):
-        if not self.image_window.image_paths:
-            QMessageBox.warning(self,
-                                "Batch Inference",
-                                "No images are present in the project.")
-            return
-
-        if not any(list(self.deploy_model_dialog.loaded_models.values())):
-            QMessageBox.warning(self,
-                                "Batch Inference",
-                                "Please deploy a model before running batch inference.")
-            return
-
-        try:
-            self.untoggle_all_tools()
-            self.batch_inference_dialog.exec_()
-        except Exception as e:
-            QMessageBox.critical(self, "Critical Error", f"{e}")
 
     def open_classify_batch_inference_dialog(self):
         if not self.image_window.image_paths:
@@ -1177,6 +1158,12 @@ def open_classify_batch_inference_dialog(self):
                                 "Batch Inference",
                                 "Please deploy a model before running batch inference.")
             return
+
+        if not self.annotation_window.annotations_dict:
+            QMessageBox.warning(self,
+                                "Batch Inference",
+                                "No annotations are present in the project.")
+            return
 
         try:
             self.untoggle_all_tools()

coralnet_toolbox/ResultsProcessor.py

@@ -3,6 +3,7 @@
 
 from PyQt5.QtCore import QPointF
 
+from torchvision.ops import nms
 from ultralytics.engine.results import Results
 from ultralytics.models.sam.amg import batched_mask_to_box
 from ultralytics.utils import ops
@@ -23,9 +24,9 @@ def __init__(self,
                  main_window, 
                  class_mapping, 
                  uncertainty_thresh=0.3, 
-                 iou_thresh=0.7, 
-                 min_area_thresh=0.01, 
-                 max_area_thresh=0.5):
+                 iou_thresh=0.2, 
+                 min_area_thresh=0.00, 
+                 max_area_thresh=0.40):
         self.main_window = main_window
         self.label_window = main_window.label_window
         self.annotation_window = main_window.annotation_window
@@ -37,39 +38,30 @@ def __init__(self,
         self.min_area_thresh = min_area_thresh
         self.max_area_thresh = max_area_thresh
 
-    def filter_by_uncertainty(self, result):
+    def filter_by_uncertainty(self, results):
         """
         Filter the results based on the uncertainty threshold.
         """
-        # Get the confidence score
-        conf = float(result.boxes.conf.cpu().numpy()[0])
-        # Check if the confidence is within the threshold
-        if conf < self.uncertainty_thresh:
-            return False
-        return True
+        return results[results.boxes.conf > self.uncertainty_thresh]
 
-    def filter_by_area(self, result):
+    def filter_by_iou(self, results):
+        """Filter the results based on the IoU threshold."""
+        return results[nms(results.boxes.xyxy, results.boxes.conf, self.iou_thresh)]
+
+    def filter_by_area(self, results):
         """
         Filter the results based on the area threshold.
         """
-        # Get the normalized bounding box coordinates
-        x_norm, y_norm, w_norm, h_norm = map(float, result.boxes.xywhn.cpu().numpy()[0])
-        # Calculate the normalized area
+        x_norm, y_norm, w_norm, h_norm = results.boxes.xywhn.T
         area_norm = w_norm * h_norm
-        # Check if the area is within the threshold
-        if area_norm < self.min_area_thresh:
-            return False
-        if area_norm > self.max_area_thresh:
-            return False
-        return True
+        return results[(area_norm > self.min_area_thresh) & (area_norm < self.max_area_thresh)]
 
-    def passed_filters(self, result):
+    def apply_filters(self, results):
         """Check if the results passed all filters."""
-        if not self.filter_by_uncertainty(result):
-            return False
-        if not self.filter_by_area(result):
-            return False
-        return True
+        results = self.filter_by_uncertainty(results)
+        results = self.filter_by_iou(results)
+        results = self.filter_by_area(results)
+        return results
 
     def extract_classification_result(self, result):
         """
@@ -141,10 +133,7 @@ def extract_detection_result(self, result):
     def process_single_detection_result(self, result):
         """
         Process a single detection result.
-        """
-        if not self.passed_filters(result):
-            return
-
+        """       
         # Get image path, class, class name, confidence, and bounding box coordinates
         image_path, cls, cls_name, conf, x_min, y_min, x_max, y_max = self.extract_detection_result(result)
         # Get the short label given the class name and confidence
@@ -166,6 +155,8 @@ def process_detection_results(self, results_generator):
         progress_bar.show()
 
         for results in results_generator:
+            # Apply filtering to the results
+            results = self.apply_filters(results)
             for result in results:
                 if result:
                     self.process_single_detection_result(result)
@@ -193,9 +184,6 @@ def process_single_segmentation_result(self, result):
         """
         Process a single segmentation result.
         """
-        if not self.passed_filters(result):
-            return
-
         # Get image path, class, class name, confidence, and polygon points
         image_path, cls, cls_name, conf, points = self.extract_segmentation_result(result)
         # Get the short label given the class name and confidence
@@ -217,6 +205,8 @@ def process_segmentation_results(self, results_generator):
         progress_bar.show()
 
         for results in results_generator:
+            # Apply filtering to the results
+            results = self.apply_filters(results)
             for result in results:
                 if result:
                     self.process_single_segmentation_result(result)

coralnet_toolbox/SAM/QtDeployGenerator.py

@@ -318,11 +318,12 @@ def load_model(self):
                              task=self.task, 
                              mode='predict', 
                              save=False, 
-                             max_det=1000,
+                             max_det=500,
                              imgsz=self.get_imgsz(),
-                             conf=self.get_uncertainty_threshold(), 
-                             iou=self.iou_thresh, 
+                             conf=0.05, 
+                             iou=1.0, 
                              device=self.main_window.device)
+
             # Load the model
             self.loaded_model = FastSAMPredictor(overrides=overrides)
 
@@ -349,18 +350,6 @@ def get_imgsz(self):
         self.imgsz = self.imgsz_spinbox.value()
         return self.imgsz
 
-    def get_uncertainty_threshold(self):
-        """
-        Get the uncertainty threshold, limiting it to a maximum of 0.10.
-
-        Returns:
-            Adjusted uncertainty threshold value.
-        """
-        if self.main_window.get_uncertainty_thresh() < 0.10:
-            return self.main_window.get_uncertainty_thresh()
-        else:
-            return 0.10  # Arbitrary value to prevent too many detections
-
     def predict(self, image_paths=None):
         """
         Make predictions on the given image paths using the loaded model.
@@ -402,15 +391,15 @@ def predict(self, image_paths=None):
             # Create a results processor
             results_processor = ResultsProcessor(self.main_window, 
                                                  self.class_mapping,
-                                                 uncertainty_thresh=self.get_uncertainty_threshold(),
+                                                 uncertainty_thresh=self.uncertainty_thresh,
                                                  iou_thresh=self.iou_thresh,
                                                  min_area_thresh=self.area_thresh_min,
                                                  max_area_thresh=self.area_thresh_max)
 
             # Update the progress bar
             progress_bar.update_progress()
 
-            if self.task == 'segment' or self.use_sam_dropdown.currentText() == "True":
+            if self.task.lower() == 'segment' or self.use_sam_dropdown.currentText() == "True":
                 results_processor.process_segmentation_results(results)
             else:
                 results_processor.process_detection_results(results)

coralnet_toolbox/__init__.py

@@ -2,7 +2,7 @@
 
 from coralnet_toolbox.main import run
 
-__version__ = "0.0.3"
+__version__ = "0.0.4"
 __author__ = "Jordan Pierce"
 __email__ = "[email protected]"
 __credits__ = "National Center for Coastal and Ocean Sciences (NCCOS)"