Add documentation to native metrics (#2144)

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Co-authored-by: Jirka Borovec <[email protected]>
Co-authored-by: Jirka <[email protected]>

Author: cuent

pytorch_lightning/metrics/functional/classification.py

@@ -9,7 +9,8 @@
 
 def to_onehot(tensor: torch.Tensor,
               n_classes: Optional[int] = None) -> torch.Tensor:
-    """ Converts a dense label tensor to one-hot format
+    """
+    Converts a dense label tensor to one-hot format
 
     Args:
         tensor: dense label tensor, with shape [N, d1, d2, ...]
@@ -29,14 +30,31 @@ def to_onehot(tensor: torch.Tensor,
 
 
 def to_categorical(tensor: torch.Tensor, argmax_dim: int = 1) -> torch.Tensor:
-    """ Converts a tensor of probabilities to a dense label tensor """
+    """
+    Converts a tensor of probabilities to a dense label tensor
+
+    Args:
+        tensor: probabilities to get the categorical label [N, d1, d2, ...]
+        argmax_dim: dimension to apply (default: 1)
+
+    Return:
+        A tensor with categorical labels [N, d2, ...]
+    """
     return torch.argmax(tensor, dim=argmax_dim)
 
 
 def get_num_classes(pred: torch.Tensor, target: torch.Tensor,
                     num_classes: Optional[int]) -> int:
-    """ Returns the number of classes for a given prediction and
-        target tensor
+    """
+    Returns the number of classes for a given prediction and target tensor.
+
+        Args:
+            pred: predicted values
+            target: true labels
+            num_classes: number of classes if known (default: None)
+
+        Return:
+            An integer that represents the number of classes.
     """
     if num_classes is None:
         if pred.ndim > target.ndim:
@@ -50,8 +68,9 @@ def stat_scores(pred: torch.Tensor, target: torch.Tensor,
                 class_index: int, argmax_dim: int = 1
                 ) -> Tuple[torch.Tensor, torch.Tensor,
                            torch.Tensor, torch.Tensor]:
-    """ Calculates the number of true postive, false postive, true negative
-    and false negative for a specfic class
+    """
+    Calculates the number of true positive, falsepositivee, true negative
+    and false negative for a specific class
 
     Args:
         pred: prediction tensor
@@ -63,6 +82,9 @@ def stat_scores(pred: torch.Tensor, target: torch.Tensor,
         argmax_dim: if pred is a tensor of probabilities, this indicates the
             axis the argmax transformation will be applied over
 
+    Return:
+        Tensors in the following order: True Positive, False Positive, True Negative, False Negative
+
     """
     if pred.ndim == target.ndim + 1:
         pred = to_categorical(pred, argmax_dim=argmax_dim)
@@ -80,20 +102,21 @@ def stat_scores_multiple_classes(pred: torch.Tensor, target: torch.Tensor,
                                  argmax_dim: int = 1
                                  ) -> Tuple[torch.Tensor, torch.Tensor,
                                             torch.Tensor, torch.Tensor]:
-    """ Calls the stat_scores function iteratively for all classes, thus
-        calculating the number of true postive, false postive, true negative
-        and false negative for each class
+    """
+    Calls the stat_scores function iteratively for all classes, thus
+    calculating the number of true postive, false postive, true negative
+    and false negative for each class
 
     Args:
         pred: prediction tensor
-
         target: target tensor
-
         class_index: class to calculate over
-
         argmax_dim: if pred is a tensor of probabilities, this indicates the
             axis the argmax transformation will be applied over
 
+    Return:
+        Returns tensors for: tp, fp, tn, fn
+
     """
     num_classes = get_num_classes(pred=pred, target=target,
                                   num_classes=num_classes)
@@ -116,6 +139,23 @@ def stat_scores_multiple_classes(pred: torch.Tensor, target: torch.Tensor,
 def accuracy(pred: torch.Tensor, target: torch.Tensor,
              num_classes: Optional[int] = None,
              reduction='elementwise_mean') -> torch.Tensor:
+    """
+    Computes the accuracy classification score
+
+    Args:
+        pred: predicted labels
+        target: ground truth labels
+        num_classes: number of classes
+        reduction: a method for reducing accuracies over labels (default: takes the mean)
+           Available reduction methods:
+
+           - elementwise_mean: takes the mean
+           - none: pass array
+           - sum: add elements
+
+    Return:
+         A Tensor with the classification score.
+    """
     tps, fps, tns, fns = stat_scores_multiple_classes(pred=pred, target=target,
                                                       num_classes=num_classes)
 
@@ -129,6 +169,18 @@ def accuracy(pred: torch.Tensor, target: torch.Tensor,
 
 def confusion_matrix(pred: torch.Tensor, target: torch.Tensor,
                      normalize: bool = False) -> torch.Tensor:
+    """
+    Computes the confusion matrix C where each entry C_{i,j} is the number of observations
+    in group i that were predicted in group j.
+
+    Args:
+        pred: estimated targets
+        target: ground truth labels
+        normalize: normalizes confusion matrix
+
+    Return:
+        Tensor, confusion matrix C [num_classes, num_classes ]
+    """
     num_classes = get_num_classes(pred, target, None)
 
     d = target.size(-1)
@@ -149,6 +201,23 @@ def precision_recall(pred: torch.Tensor, target: torch.Tensor,
                      num_classes: Optional[int] = None,
                      reduction: str = 'elementwise_mean'
                      ) -> Tuple[torch.Tensor, torch.Tensor]:
+    """
+    Computes precision and recall for different thresholds
+
+    Args:
+        pred: estimated probabilities
+        target: ground-truth labels
+        num_classes: number of classes
+        reduction: method for reducing precision-recall values (default: takes the mean)
+           Available reduction methods:
+
+           - elementwise_mean: takes the mean
+           - none: pass array
+           - sum: add elements
+
+    Return:
+        Tensor with precision and recall
+    """
     tps, fps, tns, fns = stat_scores_multiple_classes(pred=pred,
                                                       target=target,
                                                       num_classes=num_classes)
@@ -168,20 +237,77 @@ def precision_recall(pred: torch.Tensor, target: torch.Tensor,
 def precision(pred: torch.Tensor, target: torch.Tensor,
               num_classes: Optional[int] = None,
               reduction: str = 'elementwise_mean') -> torch.Tensor:
+    """
+    Computes precision score.
+
+    Args:
+        pred: estimated probabilities
+        target: ground-truth labels
+        num_classes: number of classes
+        reduction: method for reducing precision values (default: takes the mean)
+           Available reduction methods:
+
+           - elementwise_mean: takes the mean
+           - none: pass array
+           - sum: add elements
+
+    Return:
+        Tensor with precision.
+    """
     return precision_recall(pred=pred, target=target,
                             num_classes=num_classes, reduction=reduction)[0]
 
 
 def recall(pred: torch.Tensor, target: torch.Tensor,
            num_classes: Optional[int] = None,
            reduction: str = 'elementwise_mean') -> torch.Tensor:
+    """
+    Computes recall score.
+
+    Args:
+        pred: estimated probabilities
+        target: ground-truth labels
+        num_classes: number of classes
+        reduction: method for reducing recall values (default: takes the mean)
+           Available reduction methods:
+
+           - elementwise_mean: takes the mean
+           - none: pass array
+           - sum: add elements
+
+    Return:
+        Tensor with recall.
+    """
     return precision_recall(pred=pred, target=target,
                             num_classes=num_classes, reduction=reduction)[1]
 
 
 def fbeta_score(pred: torch.Tensor, target: torch.Tensor, beta: float,
                 num_classes: Optional[int] = None,
                 reduction: str = 'elementwise_mean') -> torch.Tensor:
+    """
+    Computes the F-beta score which is a weighted harmonic mean of precision and recall.
+    It ranges between 1 and 0, where 1 is perfect and the worst value is 0.
+
+    Args:
+        pred: estimated probabilities
+        target: ground-truth labels
+        beta: weights recall when combining the score.
+            beta < 1: more weight to precision.
+            beta > 1 more weight to recall
+            beta = 0: only precision
+            beta -> inf: only recall
+        num_classes: number of classes
+        reduction: method for reducing F-score (default: takes the mean)
+           Available reduction methods:
+
+           - elementwise_mean: takes the mean
+           - none: pass array
+           - sum: add elements.
+
+    Return:
+        Tensor with the value of F-score. It is a value between 0-1.
+    """
     prec, rec = precision_recall(pred=pred, target=target,
                                  num_classes=num_classes,
                                  reduction='none')
@@ -196,6 +322,23 @@ def fbeta_score(pred: torch.Tensor, target: torch.Tensor, beta: float,
 def f1_score(pred: torch.Tensor, target: torch.Tensor,
              num_classes: Optional[int] = None,
              reduction='elementwise_mean') -> torch.Tensor:
+    """
+    Computes F1-score a.k.a F-measure.
+
+    Args:
+        pred: estimated probabilities
+        target: ground-truth labels
+        num_classes: number of classes
+        reduction: method for reducing F1-score (default: takes the mean)
+           Available reduction methods:
+
+           - elementwise_mean: takes the mean
+           - none: pass array
+           - sum: add elements.
+
+    Return:
+         Tensor containing F1-score
+    """
     return fbeta_score(pred=pred, target=target, beta=1.,
                        num_classes=num_classes, reduction=reduction)
 
@@ -251,6 +394,18 @@ def roc(pred: torch.Tensor, target: torch.Tensor,
         pos_label: int = 1.) -> Tuple[torch.Tensor,
                                       torch.Tensor,
                                       torch.Tensor]:
+    """
+    Computes the Receiver Operating Characteristic (ROC). It assumes classifier is binary.
+
+    Args:
+        pred: estimated probabilities
+        target: ground-truth labels
+        sample_weight: sample weights
+        pos_label: the label for the positive class (default: 1)
+
+    Return:
+        [Tensor, Tensor, Tensor]: false-positive rate (fpr), true-positive rate (tpr), thresholds
+    """
     fps, tps, thresholds = _binary_clf_curve(pred=pred, target=target,
                                              sample_weight=sample_weight,
                                              pos_label=pos_label)
@@ -282,6 +437,19 @@ def multiclass_roc(pred: torch.Tensor, target: torch.Tensor,
                    ) -> Tuple[Tuple[torch.Tensor,
                                     torch.Tensor,
                                     torch.Tensor]]:
+    """
+    Computes the Receiver Operating Characteristic (ROC) for multiclass predictors.
+
+    Args:
+        pred: estimated probabilities
+        target: ground-truth labels
+        sample_weight: sample weights
+        num_classes: number of classes (default: None, computes automatically from data)
+
+    Return:
+        [num_classes, Tensor, Tensor, Tensor]: returns roc for each class.
+        number of classes, false-positive rate (fpr), true-positive rate (tpr), thresholds
+    """
     num_classes = get_num_classes(pred, target, num_classes)
 
     class_roc_vals = []
@@ -301,6 +469,18 @@ def precision_recall_curve(pred: torch.Tensor,
                            pos_label: int = 1.) -> Tuple[torch.Tensor,
                                                          torch.Tensor,
                                                          torch.Tensor]:
+    """
+    Computes precision-recall pairs for different thresholds.
+
+    Args:
+        pred: estimated probabilities
+        target: ground-truth labels
+        sample_weight: sample weights
+        pos_label: the label for the positive class (default: 1.)
+
+    Return:
+         [Tensor, Tensor, Tensor]: precision, recall, thresholds
+    """
     fps, tps, thresholds = _binary_clf_curve(pred=pred, target=target,
                                              sample_weight=sample_weight,
                                              pos_label=pos_label)
@@ -334,6 +514,18 @@ def multiclass_precision_recall_curve(pred: torch.Tensor, target: torch.Tensor,
                                       ) -> Tuple[Tuple[torch.Tensor,
                                                        torch.Tensor,
                                                        torch.Tensor]]:
+    """
+    Computes precision-recall pairs for different thresholds given a multiclass scores.
+
+    Args:
+        pred: estimated probabilities
+        target: ground-truth labels
+        sample_weight: sample weight
+        num_classes: number of classes
+
+    Return:
+         [num_classes, Tensor, Tensor, Tensor]: number of classes, precision, recall, thresholds
+    """
     num_classes = get_num_classes(pred, target, num_classes)
 
     class_pr_vals = []
@@ -350,6 +542,17 @@ def multiclass_precision_recall_curve(pred: torch.Tensor, target: torch.Tensor,
 
 
 def auc(x: torch.Tensor, y: torch.Tensor, reorder: bool = True):
+    """
+    Computes Area Under the Curve (AUC) using the trapezoidal rule
+
+    Args:
+        x: x-coordinates
+        y: y-coordinates
+        reorder: reorder coordinates, so they are increasing.
+
+    Return:
+        AUC score (float)
+    """
     direction = 1.
 
     if reorder:
@@ -400,6 +603,15 @@ def new_func(*args, **kwargs) -> torch.Tensor:
 def auroc(pred: torch.Tensor, target: torch.Tensor,
           sample_weight: Optional[Sequence] = None,
           pos_label: int = 1.) -> torch.Tensor:
+    """
+    Compute Area Under the Receiver Operating Characteristic Curve (ROC AUC) from prediction scores
+
+    Args:
+        pred: estimated probabilities
+        target: ground-truth labels
+        sample_weight: sample weights
+        pos_label: the label for the positive class (default: 1.)
+    """
     return roc(pred=pred, target=target, sample_weight=sample_weight,
                pos_label=pos_label)
 
@@ -410,7 +622,6 @@ def average_precision(pred: torch.Tensor, target: torch.Tensor,
     precision, recall, _ = precision_recall_curve(pred=pred, target=target,
                                                   sample_weight=sample_weight,
                                                   pos_label=pos_label)
-
     # Return the step function integral
     # The following works because the last entry of precision is
     # guaranteed to be 1, as returned by precision_recall_curve