Independent analysis of whether a model can generalize from training data to new areas is critical for creating a robust workflow. We stress that evaluation data must be different from training data, as neural networks have millions of parameters and can easily memorize thousands of samples. Therefore, while it would be rather easy to tune the model to get extremely high scores on the training data, it would fail when exposed to new images.
To get an evaluation score, specify an annotations file in the same format as the training example above. The model will
csv_file = get_data("OSBS_029.csv") root_dir = os.path.dirname(csv_file) results = model.evaluate(csv_file, root_dir, iou_threshold = 0.4)
The returned object is a dictionary containing the three keys: results, recall, and precision. The result key in the csv-file represents the intersection-over-union score for each ground truth object.
results["results"].head() prediction_id truth_id IoU image_path match 39 39 0 0.00000 OSBS_029.tif False 19 19 1 0.50524 OSBS_029.tif True 44 44 2 0.42246 OSBS_029.tif True 67 67 3 0.41404 OSBS_029.tif True 28 28 4 0.37461 OSBS_029.tif False
This dataframe contains a numeric id for each predicted crown in each image and the matched ground truth crown in each image. The intersection-over-union score between predicted and ground truth (IoU), and whether that score is greater than the IoU threshold (’match’).
The recall is the proportion of ground truth that has a true positive match with a prediction based on the intersection-over-union threshold. The default threshold is 0.4 and can be changed in the model.evaluate(iou_threshold=<>)
The regression box precision is the proportion of predicted boxes which overlap a ground truth box.
To convert overlap among predicted and ground truth bounding boxes into measures of accuracy and precision, the most common approach is to compare the overlap using the intersection-over-union metric (IoU). IoU is the ratio between the area of the overlap between the predicted polygon box and the ground truth polygon box divided by the area of the combined bounding box region.
Let’s start by getting some sample data and predictions
from deepforest import evaluate from deepforest import main from deepforest import get_data from deepforest import visualize import os import pandas as pd m = main.deepforest() m.use_release() csv_file = get_data("OSBS_029.csv") predictions = m.predict_file(csv_file=csv_file, root_dir=os.path.dirname(csv_file)) predictions.head() xmin ymin xmax ymax label score image_path 0 330.0 342.0 373.0 391.0 Tree 0.802979 OSBS_029.tif 1 216.0 206.0 248.0 242.0 Tree 0.778803 OSBS_029.tif 2 325.0 44.0 363.0 82.0 Tree 0.751573 OSBS_029.tif 3 261.0 238.0 296.0 276.0 Tree 0.748605 OSBS_029.tif 4 173.0 0.0 229.0 33.0 Tree 0.738209 OSBS_029.tif
ground_truth = pd.read_csv(csv_file) ground_truth.head() image_path xmin ymin xmax ymax label 0 OSBS_029.tif 203 67 227 90 Tree 1 OSBS_029.tif 256 99 288 140 Tree 2 OSBS_029.tif 166 253 225 304 Tree 3 OSBS_029.tif 365 2 400 27 Tree 4 OSBS_029.tif 312 13 349 47 Tree
visualize.plot_prediction_dataframe(predictions, ground_truth, root_dir = os.path.dirname(csv_file))
The IoU metric ranges between 0 (no overlap) to 1 (perfect overlap). In the wider computer vision literature, the conventional threshold value for overlap is 0.5, but this value is arbitrary and does not ultimately relate to any particular ecological question. We considered boxes which have an IoU score of greater than 0.4 as true positive, and scores less than 0.4 as false negatives. The 0.4 value was chosen based on visual evaluation of the threshold that indicated a good visual match between the predicted and observed crown. We tested a range of overlap thresholds from 0.3 (less overlap among matching crowns) to 0.6 (more overlap among matching crowns) and found that 0.4 balanced a rigorous cutoff without spuriously removing trees that would be useful for downstream analysis.
After computing the IoU for the ground truth data, we get the resulting dataframe.
result = evaluate.evaluate_image(predictions=predictions, ground_df=ground_truth, root_dir=os.path.dirname(csv_file), savedir=None) result.head() prediction_id truth_id IoU predicted_label true_label 90 90 0 0.059406 Tree Tree 65 65 1 0.335366 Tree Tree 17 17 2 0.578551 Tree Tree 50 50 3 0.532902 Tree Tree 34 34 4 0.595862 Tree Tree
Where prediction_id is a unique ID to each predicted tree box. truth is a unique ID to each ground truth box. The predicted and true labels are tree in this, case but could generalize to multi-class problems. From here we can calculate precision and recall at a given IoU metric.
result["match"] = result.IoU > 0.4 true_positive = sum(result["match"]) recall = true_positive / result.shape precision = true_positive / predictions.shape recall 0.819672131147541 precision 0.5494505494505495
This can be stated as 81.97% of the ground truth boxes are correctly matched to a predicted box at IoU threshold of 0.4, and 54.94% of predicted boxes match a ground truth box. Optimally we want a model that is both precise and accurate.
The above logic is wrapped into the evaluate.evaluate() function
result = evaluate.evaluate(predictions=predictions, ground_df=ground_truth,root_dir=os.path.dirname(csv_file), savedir=None)
This is a dictionary with keys
result.keys() dict_keys(['results', 'box_precision', 'box_recall', 'class_recall'])
The added class_recall dataframe is mostly relevant for multi-class problems, in which the recall and precision per class is given.
result["class_recall"] label recall precision size 0 Tree 1.0 0.67033 61
One important decision was how to average precision and recall across multiple images. Two reasonable options might be to take all predictions and all ground truth and compute the statistic on the entire dataset. This strategy makes more sense for evaluation data that are relatively homogenous across images. We prefer to take the average of per-image precision and recall. This helps balanace the dataset if some images have many trees, and other have few trees, such as when you are comparing multiple habitat types. Users are welcome to calculate their own statistics directly from the results dataframe.
result["results"].head() prediction_id truth_id IoU ... true_label image_path match 90 90 0 0.059406 ... Tree OSBS_029.tif False 65 65 1 0.335366 ... Tree OSBS_029.tif False 17 17 2 0.578551 ... Tree OSBS_029.tif True 50 50 3 0.532902 ... Tree OSBS_029.tif True 34 34 4 0.595862 ... Tree OSBS_029.tif True
The evaluation method uses deepforest.predict_image for each of the paths supplied in the image_path column. This means that the entire image is passed for prediction. This will not work for large images. The deepforest.predict_tile method does a couple things under hood that need to be repeated for evaluation.
output_annotations = deepforest.preprocess.split_raster( path_to_raster = <path>, annotations_file = <original_annotation_path>, base_dir = <location to save crops> patch_size = <size of each crop> ) output_annotations.to_csv("new_annotations.csv") results = model.evaluate( csv_file="new_annotations.csv", root_dir=<base_dir from above> )