add metric mFscore (#509)

* add mFscore and refactor the metrics return value

* fix linting

* some docstring and name fix

mmseg/core/evaluation/__init__.py

@@ -1,8 +1,8 @@
 from .class_names import get_classes, get_palette
 from .eval_hooks import DistEvalHook, EvalHook
-from .metrics import eval_metrics, mean_dice, mean_iou
+from .metrics import eval_metrics, mean_dice, mean_fscore, mean_iou
 
 __all__ = [
-    'EvalHook', 'DistEvalHook', 'mean_dice', 'mean_iou', 'eval_metrics',
-    'get_classes', 'get_palette'
+    'EvalHook', 'DistEvalHook', 'mean_dice', 'mean_iou', 'mean_fscore',
+    'eval_metrics', 'get_classes', 'get_palette'
 ]

mmseg/core/evaluation/metrics.py

@@ -1,8 +1,27 @@
+from collections import OrderedDict
+
 import mmcv
 import numpy as np
 import torch
 
 
+def f_score(precision, recall, beta=1):
+    """calcuate the f-score value.
+
+    Args:
+        precision (float | torch.Tensor): The precision value.
+        recall (float | torch.Tensor): The recall value.
+        beta (int): Determines the weight of recall in the combined score.
+            Default: False.
+
+    Returns:
+        [torch.tensor]: The f-score value.
+    """
+    score = (1 + beta**2) * (precision * recall) / (
+        (beta**2 * precision) + recall)
+    return score
+
+
 def intersect_and_union(pred_label,
                         label,
                         num_classes,
@@ -133,11 +152,12 @@ def mean_iou(results,
         reduce_zero_label (bool): Wether ignore zero label. Default: False.
 
      Returns:
-         float: Overall accuracy on all images.
-         ndarray: Per category accuracy, shape (num_classes, ).
-         ndarray: Per category IoU, shape (num_classes, ).
+        dict[str, float | ndarray]:
+            <aAcc> float: Overall accuracy on all images.
+            <Acc> ndarray: Per category accuracy, shape (num_classes, ).
+            <IoU> ndarray: Per category IoU, shape (num_classes, ).
     """
-    all_acc, acc, iou = eval_metrics(
+    iou_result = eval_metrics(
         results=results,
         gt_seg_maps=gt_seg_maps,
         num_classes=num_classes,
@@ -146,7 +166,7 @@ def mean_iou(results,
         nan_to_num=nan_to_num,
         label_map=label_map,
         reduce_zero_label=reduce_zero_label)
-    return all_acc, acc, iou
+    return iou_result
 
 
 def mean_dice(results,
@@ -171,12 +191,13 @@ def mean_dice(results,
         reduce_zero_label (bool): Wether ignore zero label. Default: False.
 
      Returns:
-         float: Overall accuracy on all images.
-         ndarray: Per category accuracy, shape (num_classes, ).
-         ndarray: Per category dice, shape (num_classes, ).
+        dict[str, float | ndarray]: Default metrics.
+            <aAcc> float: Overall accuracy on all images.
+            <Acc> ndarray: Per category accuracy, shape (num_classes, ).
+            <Dice> ndarray: Per category dice, shape (num_classes, ).
     """
 
-    all_acc, acc, dice = eval_metrics(
+    dice_result = eval_metrics(
         results=results,
         gt_seg_maps=gt_seg_maps,
         num_classes=num_classes,
@@ -185,7 +206,52 @@ def mean_dice(results,
         nan_to_num=nan_to_num,
         label_map=label_map,
         reduce_zero_label=reduce_zero_label)
-    return all_acc, acc, dice
+    return dice_result
+
+
+def mean_fscore(results,
+                gt_seg_maps,
+                num_classes,
+                ignore_index,
+                nan_to_num=None,
+                label_map=dict(),
+                reduce_zero_label=False,
+                beta=1):
+    """Calculate Mean Intersection and Union (mIoU)
+
+    Args:
+        results (list[ndarray] | list[str]): List of prediction segmentation
+            maps or list of prediction result filenames.
+        gt_seg_maps (list[ndarray] | list[str]): list of ground truth
+            segmentation maps or list of label filenames.
+        num_classes (int): Number of categories.
+        ignore_index (int): Index that will be ignored in evaluation.
+        nan_to_num (int, optional): If specified, NaN values will be replaced
+            by the numbers defined by the user. Default: None.
+        label_map (dict): Mapping old labels to new labels. Default: dict().
+        reduce_zero_label (bool): Wether ignore zero label. Default: False.
+        beta (int): Determines the weight of recall in the combined score.
+            Default: False.
+
+
+     Returns:
+        dict[str, float | ndarray]: Default metrics.
+            <aAcc> float: Overall accuracy on all images.
+            <Fscore> ndarray: Per category recall, shape (num_classes, ).
+            <Precision> ndarray: Per category precision, shape (num_classes, ).
+            <Recall> ndarray: Per category f-score, shape (num_classes, ).
+    """
+    fscore_result = eval_metrics(
+        results=results,
+        gt_seg_maps=gt_seg_maps,
+        num_classes=num_classes,
+        ignore_index=ignore_index,
+        metrics=['mFscore'],
+        nan_to_num=nan_to_num,
+        label_map=label_map,
+        reduce_zero_label=reduce_zero_label,
+        beta=beta)
+    return fscore_result
 
 
 def eval_metrics(results,
@@ -195,7 +261,8 @@ def eval_metrics(results,
                  metrics=['mIoU'],
                  nan_to_num=None,
                  label_map=dict(),
-                 reduce_zero_label=False):
+                 reduce_zero_label=False,
+                 beta=1):
     """Calculate evaluation metrics
     Args:
         results (list[ndarray] | list[str]): List of prediction segmentation
@@ -210,13 +277,13 @@ def eval_metrics(results,
         label_map (dict): Mapping old labels to new labels. Default: dict().
         reduce_zero_label (bool): Wether ignore zero label. Default: False.
      Returns:
-         float: Overall accuracy on all images.
-         ndarray: Per category accuracy, shape (num_classes, ).
-         ndarray: Per category evaluation metrics, shape (num_classes, ).
+        float: Overall accuracy on all images.
+        ndarray: Per category accuracy, shape (num_classes, ).
+        ndarray: Per category evaluation metrics, shape (num_classes, ).
     """
     if isinstance(metrics, str):
         metrics = [metrics]
-    allowed_metrics = ['mIoU', 'mDice']
+    allowed_metrics = ['mIoU', 'mDice', 'mFscore']
     if not set(metrics).issubset(set(allowed_metrics)):
         raise KeyError('metrics {} is not supported'.format(metrics))
 
@@ -225,19 +292,35 @@ def eval_metrics(results,
             results, gt_seg_maps, num_classes, ignore_index, label_map,
             reduce_zero_label)
     all_acc = total_area_intersect.sum() / total_area_label.sum()
-    acc = total_area_intersect / total_area_label
-    ret_metrics = [all_acc, acc]
+    ret_metrics = OrderedDict({'aAcc': all_acc})
     for metric in metrics:
         if metric == 'mIoU':
             iou = total_area_intersect / total_area_union
-            ret_metrics.append(iou)
+            acc = total_area_intersect / total_area_label
+            ret_metrics['IoU'] = iou
+            ret_metrics['Acc'] = acc
         elif metric == 'mDice':
             dice = 2 * total_area_intersect / (
                 total_area_pred_label + total_area_label)
-            ret_metrics.append(dice)
-    ret_metrics = [metric.numpy() for metric in ret_metrics]
+            acc = total_area_intersect / total_area_label
+            ret_metrics['Dice'] = dice
+            ret_metrics['Acc'] = acc
+        elif metric == 'mFscore':
+            precision = total_area_intersect / total_area_pred_label
+            recall = total_area_intersect / total_area_label
+            f_value = torch.tensor(
+                [f_score(x[0], x[1], beta) for x in zip(precision, recall)])
+            ret_metrics['Fscore'] = f_value
+            ret_metrics['Precision'] = precision
+            ret_metrics['Recall'] = recall
+
+    ret_metrics = {
+        metric: value.numpy()
+        for metric, value in ret_metrics.items()
+    }
     if nan_to_num is not None:
-        ret_metrics = [
-            np.nan_to_num(metric, nan=nan_to_num) for metric in ret_metrics
-        ]
+        ret_metrics = OrderedDict({
+            metric: np.nan_to_num(metric_value, nan=nan_to_num)
+            for metric, metric_value in ret_metrics.items()
+        })
     return ret_metrics

mmseg/datasets/custom.py

@@ -1,11 +1,12 @@
 import os
 import os.path as osp
+from collections import OrderedDict
 from functools import reduce
 
 import mmcv
 import numpy as np
 from mmcv.utils import print_log
-from terminaltables import AsciiTable
+from prettytable import PrettyTable
 from torch.utils.data import Dataset
 
 from mmseg.core import eval_metrics
@@ -312,8 +313,8 @@ def evaluate(self,
 
         Args:
             results (list): Testing results of the dataset.
-            metric (str | list[str]): Metrics to be evaluated. 'mIoU' and
-                'mDice' are supported.
+            metric (str | list[str]): Metrics to be evaluated. 'mIoU',
+                'mDice' and 'mFscore' are supported.
             logger (logging.Logger | None | str): Logger used for printing
                 related information during evaluation. Default: None.
 
@@ -323,7 +324,7 @@ def evaluate(self,
 
         if isinstance(metric, str):
             metric = [metric]
-        allowed_metrics = ['mIoU', 'mDice']
+        allowed_metrics = ['mIoU', 'mDice', 'mFscore']
         if not set(metric).issubset(set(allowed_metrics)):
             raise KeyError('metric {} is not supported'.format(metric))
         eval_results = {}
@@ -341,42 +342,57 @@ def evaluate(self,
             metric,
             label_map=self.label_map,
             reduce_zero_label=self.reduce_zero_label)
-        class_table_data = [['Class'] + [m[1:] for m in metric] + ['Acc']]
+
         if self.CLASSES is None:
             class_names = tuple(range(num_classes))
         else:
             class_names = self.CLASSES
-        ret_metrics_round = [
-            np.round(ret_metric * 100, 2) for ret_metric in ret_metrics
-        ]
-        for i in range(num_classes):
-            class_table_data.append([class_names[i]] +
-                                    [m[i] for m in ret_metrics_round[2:]] +
-                                    [ret_metrics_round[1][i]])
-        summary_table_data = [['Scope'] +
-                              ['m' + head
-                               for head in class_table_data[0][1:]] + ['aAcc']]
-        ret_metrics_mean = [
-            np.round(np.nanmean(ret_metric) * 100, 2)
-            for ret_metric in ret_metrics
-        ]
-        summary_table_data.append(['global'] + ret_metrics_mean[2:] +
-                                  [ret_metrics_mean[1]] +
-                                  [ret_metrics_mean[0]])
+
+        # summary table
+        ret_metrics_summary = OrderedDict({
+            ret_metric: np.round(np.nanmean(ret_metric_value) * 100, 2)
+            for ret_metric, ret_metric_value in ret_metrics.items()
+        })
+
+        # each class table
+        ret_metrics.pop('aAcc', None)
+        ret_metrics_class = OrderedDict({
+            ret_metric: np.round(ret_metric_value * 100, 2)
+            for ret_metric, ret_metric_value in ret_metrics.items()
+        })
+        ret_metrics_class.update({'Class': class_names})
+        ret_metrics_class.move_to_end('Class', last=False)
+
+        # for logger
+        class_table_data = PrettyTable()
+        for key, val in ret_metrics_class.items():
+            class_table_data.add_column(key, val)
+
+        summary_table_data = PrettyTable()
+        for key, val in ret_metrics_summary.items():
+            if key == 'aAcc':
+                summary_table_data.add_column(key, [val])
+            else:
+                summary_table_data.add_column('m' + key, [val])
+
         print_log('per class results:', logger)
-        table = AsciiTable(class_table_data)
-        print_log('\n' + table.table, logger=logger)
+        print_log('\n' + class_table_data.get_string(), logger=logger)
         print_log('Summary:', logger)
-        table = AsciiTable(summary_table_data)
-        print_log('\n' + table.table, logger=logger)
-
-        for i in range(1, len(summary_table_data[0])):
-            eval_results[summary_table_data[0]
-                         [i]] = summary_table_data[1][i] / 100.0
-        for idx, sub_metric in enumerate(class_table_data[0][1:], 1):
-            for item in class_table_data[1:]:
-                eval_results[str(sub_metric) + '.' +
-                             str(item[0])] = item[idx] / 100.0
+        print_log('\n' + summary_table_data.get_string(), logger=logger)
+
+        # each metric dict
+        for key, value in ret_metrics_summary.items():
+            if key == 'aAcc':
+                eval_results[key] = value / 100.0
+            else:
+                eval_results['m' + key] = value / 100.0
+
+        ret_metrics_class.pop('Class', None)
+        for key, value in ret_metrics_class.items():
+            eval_results.update({
+                key + '.' + str(name): value[idx] / 100.0
+                for idx, name in enumerate(class_names)
+            })
 
         if mmcv.is_list_of(results, str):
             for file_name in results:

requirements/runtime.txt

@@ -1,3 +1,3 @@
 matplotlib
 numpy
-terminaltables
+prettytable

setup.cfg

@@ -8,6 +8,6 @@ line_length = 79
 multi_line_output = 0
 known_standard_library = setuptools
 known_first_party = mmseg
-known_third_party = PIL,cityscapesscripts,cv2,detail,matplotlib,mmcv,numpy,onnxruntime,oss2,pytest,scipy,seaborn,terminaltables,torch
+known_third_party = PIL,cityscapesscripts,cv2,detail,matplotlib,mmcv,numpy,onnxruntime,oss2,prettytable,pytest,scipy,seaborn,torch
 no_lines_before = STDLIB,LOCALFOLDER
 default_section = THIRDPARTY

tests/test_data/test_dataset.py

@@ -159,7 +159,7 @@ def test_custom_dataset():
     for gt_seg_map in gt_seg_maps:
         h, w = gt_seg_map.shape
         pseudo_results.append(np.random.randint(low=0, high=7, size=(h, w)))
-    eval_results = train_dataset.evaluate(pseudo_results, metric='mIoU')
+    eval_results = train_dataset.evaluate(pseudo_results, metric=['mIoU'])
     assert isinstance(eval_results, dict)
     assert 'mIoU' in eval_results
     assert 'mAcc' in eval_results
@@ -193,13 +193,23 @@ def test_custom_dataset():
     assert 'mAcc' in eval_results
     assert 'aAcc' in eval_results
 
+    eval_results = train_dataset.evaluate(pseudo_results, metric='mFscore')
+    assert isinstance(eval_results, dict)
+    assert 'mRecall' in eval_results
+    assert 'mPrecision' in eval_results
+    assert 'mFscore' in eval_results
+    assert 'aAcc' in eval_results
+
     eval_results = train_dataset.evaluate(
-        pseudo_results, metric=['mIoU', 'mDice'])
+        pseudo_results, metric=['mIoU', 'mDice', 'mFscore'])
     assert isinstance(eval_results, dict)
     assert 'mIoU' in eval_results
     assert 'mDice' in eval_results
     assert 'mAcc' in eval_results
     assert 'aAcc' in eval_results
+    assert 'mFscore' in eval_results
+    assert 'mPrecision' in eval_results
+    assert 'mRecall' in eval_results
 
 
 @patch('mmseg.datasets.CustomDataset.load_annotations', MagicMock)