task: metadata: install: pip install -e .
patch: diff --git a/ignite/metrics/confusion_matrix.py b/ignite/metrics/confusion_matrix.py
index 3546796a..91fa1df4 100644
--- a/ignite/metrics/confusion_matrix.py
+++ b/ignite/metrics/confusion_matrix.py
@@ -4,7 +4,6 @@ import torch
 
 from ignite.metrics import Metric, MetricsLambda
 from ignite.exceptions import NotComputableError
-from ignite.utils import to_onehot
 
 
 class ConfusionMatrix(Metric):
@@ -12,12 +11,12 @@ class ConfusionMatrix(Metric):
 
     - `update` must receive output of the form `(y_pred, y)`.
     - `y_pred` must contain logits and has the following shape (batch_size, num_categories, ...)
-    - `y` can be of two types:
-        - shape (batch_size, num_categories, ...)
-        - shape (batch_size, ...) and contains ground-truth class indices
+    - `y` should have the following shape (batch_size, ...) and contains ground-truth class indices
+        with or without the background class. During the computation, argmax of `y_pred` is taken to determine
+        predicted classes.
 
     Args:
-        num_classes (int): number of classes. In case of images, num_classes should also count the background index 0.
+        num_classes (int): number of classes. See notes for more details.
         average (str, optional): confusion matrix values averaging schema: None, "samples", "recall", "precision".
             Default is None. If `average="samples"` then confusion matrix values are normalized by the number of seen
             samples. If `average="recall"` then confusion matrix values are normalized such that diagonal values
@@ -27,6 +26,12 @@ class ConfusionMatrix(Metric):
             :class:`~ignite.engine.Engine`'s `process_function`'s output into the
             form expected by the metric. This can be useful if, for example, you have a multi-output model and
             you want to compute the metric with respect to one of the outputs.
+
+    Note:
+        In case of the targets `y` in `(batch_size, ...)` format, target indices between 0 and `num_classes` only
+        contribute to the confusion matrix and others are neglected. For example, if `num_classes=20` and target index
+        equal 255 is encountered, then it is filtered out.
+
     """
 
     def __init__(self, num_classes, average=None, output_transform=lambda x: x):
@@ -40,7 +45,8 @@ class ConfusionMatrix(Metric):
         super(ConfusionMatrix, self).__init__(output_transform=output_transform)
 
     def reset(self):
-        self.confusion_matrix = torch.zeros(self.num_classes, self.num_classes, dtype=torch.float)
+        self.confusion_matrix = torch.zeros(self.num_classes, self.num_classes,
+                                            dtype=torch.int64, device='cpu')
         self._num_examples = 0
 
     def _check_shape(self, output):
@@ -54,9 +60,9 @@ class ConfusionMatrix(Metric):
             raise ValueError("y_pred does not have correct number of categories: {} vs {}"
                              .format(y_pred.shape[1], self.num_classes))
 
-        if not (y.ndimension() == y_pred.ndimension() or y.ndimension() + 1 == y_pred.ndimension()):
+        if not (y.ndimension() + 1 == y_pred.ndimension()):
             raise ValueError("y_pred must have shape (batch_size, num_categories, ...) and y must have "
-                             "shape of (batch_size, num_categories, ...) or (batch_size, ...), "
+                             "shape of (batch_size, ...), "
                              "but given {} vs {}.".format(y.shape, y_pred.shape))
 
         y_shape = y.shape
@@ -68,38 +74,36 @@ class ConfusionMatrix(Metric):
         if y_shape != y_pred_shape:
             raise ValueError("y and y_pred must have compatible shapes.")
 
-        return y_pred, y
-
     def update(self, output):
-        y_pred, y = self._check_shape(output)
+        self._check_shape(output)
+        y_pred, y = output
 
-        if y_pred.shape != y.shape:
-            y_ohe = to_onehot(y.reshape(-1), self.num_classes)
-            y_ohe_t = y_ohe.transpose(0, 1).float()
-        else:
-            y_ohe_t = y.transpose(0, 1).reshape(y.shape[1], -1).float()
+        self._num_examples += y_pred.shape[0]
 
-        indices = torch.argmax(y_pred, dim=1)
-        y_pred_ohe = to_onehot(indices.reshape(-1), self.num_classes)
-        y_pred_ohe = y_pred_ohe.float()
+        # target is (batch_size, ...)
+        y_pred = torch.argmax(y_pred, dim=1).flatten()
+        y = y.flatten()
 
-        if self.confusion_matrix.type() != y_ohe_t.type():
-            self.confusion_matrix = self.confusion_matrix.type_as(y_ohe_t)
+        target_mask = (y >= 0) & (y < self.num_classes)
+        y = y[target_mask]
+        y_pred = y_pred[target_mask]
 
-        self.confusion_matrix += torch.matmul(y_ohe_t, y_pred_ohe).float()
-        self._num_examples += y_pred.shape[0]
+        indices = self.num_classes * y + y_pred
+        m = torch.bincount(indices, minlength=self.num_classes ** 2).reshape(self.num_classes, self.num_classes)
+        self.confusion_matrix += m.to(self.confusion_matrix)
 
     def compute(self):
         if self._num_examples == 0:
             raise NotComputableError('Confusion matrix must have at least one example before it can be computed.')
         if self.average:
+            self.confusion_matrix = self.confusion_matrix.float()
             if self.average == "samples":
                 return self.confusion_matrix / self._num_examples
             elif self.average == "recall":
                 return self.confusion_matrix / (self.confusion_matrix.sum(dim=1) + 1e-15)
             elif self.average == "precision":
                 return self.confusion_matrix / (self.confusion_matrix.sum(dim=0) + 1e-15)
-        return self.confusion_matrix.cpu()
+        return self.confusion_matrix
 
 
 def IoU(cm, ignore_index=None):

problem_statement: Problem with IoU
I'm training a FCN on the Cityscapes dataset. All ignored classes are mapped to 255. This works perfectly fine for the loss function using ignore_index.

Using the Ignite IoU metric however results in this error:

```/pytorch/aten/src/THC/THCTensorScatterGather.cu:188: void THCudaTensor_scatterFillKernel(TensorInfo<Real, IndexType>, TensorInfo<long, IndexType>, Real, int, IndexType) [with IndexType = unsigned int, Real = float, Dims = 2]: block: [36,0,0], thread: [0,0,0] Assertion `indexValue >= 0 && indexValue < tensor.sizes[dim]` failed.```

triggered here:
```
y_pred_ohe = to_onehot(indices.reshape(-1), self.num_classes)
  File "/usr/local/lib/python3.6/dist-packages/ignite/utils.py", line 48, in to_onehot
    onehot = torch.zeros(indices.shape[0], num_classes, *indices.shape[1:], device=indices.device)
RuntimeError: cuda runtime error (59) : device-side assert triggered at /pytorch/aten/src/THC/generic/THCTensorMath.cu:26
```

It's probably because there are only 19 classes and some values are 255.

repo: pytorch/ignite
test_cmd: pytest --no-header -rA --tb=line --color=no -p no:cacheprovider -W ignore::DeprecationWarning
test_patch: diff --git a/tests/ignite/metrics/test_confusion_matrix.py b/tests/ignite/metrics/test_confusion_matrix.py
index e0d84b19..f91f4b14 100644
--- a/tests/ignite/metrics/test_confusion_matrix.py
+++ b/tests/ignite/metrics/test_confusion_matrix.py
@@ -7,7 +7,6 @@ from sklearn.metrics import confusion_matrix, accuracy_score, precision_score, r
 from ignite.exceptions import NotComputableError
 from ignite.metrics import ConfusionMatrix, IoU, mIoU
 from ignite.metrics.confusion_matrix import cmAccuracy, cmPrecision, cmRecall
-from ignite.utils import to_onehot
 
 import pytest
 
@@ -25,37 +24,33 @@ def test_multiclass_wrong_inputs():
     cm = ConfusionMatrix(10)
 
     with pytest.raises(ValueError, match=r"y_pred must have shape \(batch_size, num_categories, ...\)"):
-        # incompatible shapes
         cm.update((torch.rand(10),
-                   torch.randint(0, 2, size=(10,)).type(torch.LongTensor)))
+                   torch.randint(0, 2, size=(10,)).long()))
 
     with pytest.raises(ValueError, match=r"y_pred does not have correct number of categories:"):
-        # incompatible shapes
         cm.update((torch.rand(10, 5, 4),
-                   torch.randint(0, 2, size=(10,)).type(torch.LongTensor)))
+                   torch.randint(0, 2, size=(10,)).long()))
 
     with pytest.raises(ValueError, match=r"y_pred must have shape \(batch_size, num_categories, ...\) "
                                          r"and y must have "):
-        # incompatible shapes
         cm.update((torch.rand(4, 10, 12, 12),
-                   torch.randint(0, 10, size=(10, )).type(torch.LongTensor)))
+                   torch.randint(0, 10, size=(10, )).long()))
 
     with pytest.raises(ValueError, match=r"y and y_pred must have compatible shapes."):
-        # incompatible shapes
         cm.update((torch.rand(4, 10, 12, 14),
-                   torch.randint(0, 10, size=(4, 5, 6)).type(torch.LongTensor)))
+                   torch.randint(0, 10, size=(4, 5, 6)).long()))
 
     with pytest.raises(ValueError, match=r"Argument average can None or one of"):
         ConfusionMatrix(num_classes=10, average="abc")
 
 
 def test_multiclass_input_N():
-    # Multiclass input data of shape (N, ) and (N, C)
+    # Multiclass input data of shape (N, )
     def _test_N():
         num_classes = 4
         cm = ConfusionMatrix(num_classes=num_classes)
         y_pred = torch.rand(10, num_classes)
-        y = torch.randint(0, num_classes, size=(10,)).type(torch.LongTensor)
+        y = torch.randint(0, num_classes, size=(10,)).long()
         cm.update((y_pred, y))
         np_y_pred = y_pred.numpy().argmax(axis=1).ravel()
         np_y = y.numpy().ravel()
@@ -64,7 +59,7 @@ def test_multiclass_input_N():
         num_classes = 10
         cm = ConfusionMatrix(num_classes=num_classes)
         y_pred = torch.rand(4, num_classes)
-        y = torch.randint(0, num_classes, size=(4, )).type(torch.LongTensor)
+        y = torch.randint(0, num_classes, size=(4, )).long()
         cm.update((y_pred, y))
         np_y_pred = y_pred.numpy().argmax(axis=1).ravel()
         np_y = y.numpy().ravel()
@@ -74,7 +69,7 @@ def test_multiclass_input_N():
         num_classes = 2
         cm = ConfusionMatrix(num_classes=num_classes)
         y_pred = torch.rand(4, num_classes)
-        y = torch.randint(0, num_classes, size=(4,)).type(torch.LongTensor)
+        y = torch.randint(0, num_classes, size=(4,)).long()
         cm.update((y_pred, y))
         np_y_pred = y_pred.numpy().argmax(axis=1).ravel()
         np_y = y.numpy().ravel()
@@ -85,7 +80,7 @@ def test_multiclass_input_N():
         cm = ConfusionMatrix(num_classes=num_classes)
 
         y_pred = torch.rand(100, num_classes)
-        y = torch.randint(0, num_classes, size=(100,)).type(torch.LongTensor)
+        y = torch.randint(0, num_classes, size=(100,)).long()
 
         batch_size = 16
         n_iters = y.shape[0] // batch_size + 1
@@ -98,71 +93,19 @@ def test_multiclass_input_N():
         np_y_pred = y_pred.numpy().argmax(axis=1).ravel()
         assert np.all(confusion_matrix(np_y, np_y_pred, labels=list(range(num_classes))) == cm.compute().numpy())
 
-    def _test_NC():
-        num_classes = 4
-        cm = ConfusionMatrix(num_classes=num_classes)
-        y_pred = torch.rand(10, num_classes)
-        y_labels = torch.randint(0, num_classes, size=(10,)).type(torch.LongTensor)
-        y = to_onehot(y_labels, num_classes=num_classes)
-        cm.update((y_pred, y))
-        np_y_pred = y_pred.numpy().argmax(axis=1).ravel()
-        np_y = y_labels.numpy().ravel()
-        assert np.all(confusion_matrix(np_y, np_y_pred, labels=list(range(num_classes))) == cm.compute().numpy())
-
-        num_classes = 10
-        cm = ConfusionMatrix(num_classes=num_classes)
-        y_pred = torch.rand(4, num_classes)
-        y_labels = torch.randint(0, num_classes, size=(4, )).type(torch.LongTensor)
-        y = to_onehot(y_labels, num_classes=num_classes)
-        cm.update((y_pred, y))
-        np_y_pred = y_pred.numpy().argmax(axis=1).ravel()
-        np_y = y_labels.numpy().ravel()
-        assert np.all(confusion_matrix(np_y, np_y_pred, labels=list(range(num_classes))) == cm.compute().numpy())
-
-        # 2-classes
-        num_classes = 2
-        cm = ConfusionMatrix(num_classes=num_classes)
-        y_pred = torch.rand(4, num_classes)
-        y_labels = torch.randint(0, num_classes, size=(4,)).type(torch.LongTensor)
-        y = to_onehot(y_labels, num_classes=num_classes)
-        cm.update((y_pred, y))
-        np_y_pred = y_pred.numpy().argmax(axis=1).ravel()
-        np_y = y_labels.numpy().ravel()
-        assert np.all(confusion_matrix(np_y, np_y_pred, labels=list(range(num_classes))) == cm.compute().numpy())
-
-        # Batched Updates
-        num_classes = 5
-        cm = ConfusionMatrix(num_classes=num_classes)
-
-        y_pred = torch.rand(100, num_classes)
-        y_labels = torch.randint(0, num_classes, size=(100,)).type(torch.LongTensor)
-        y = to_onehot(y_labels, num_classes=num_classes)
-
-        batch_size = 16
-        n_iters = y.shape[0] // batch_size + 1
-
-        for i in range(n_iters):
-            idx = i * batch_size
-            cm.update((y_pred[idx: idx + batch_size], y[idx: idx + batch_size]))
-
-        np_y = y_labels.numpy().ravel()
-        np_y_pred = y_pred.numpy().argmax(axis=1).ravel()
-        assert np.all(confusion_matrix(np_y, np_y_pred, labels=list(range(num_classes))) == cm.compute().numpy())
-
     # check multiple random inputs as random exact occurencies are rare
     for _ in range(10):
         _test_N()
-        _test_NC()
 
 
 def test_multiclass_input_NL():
-    # Multiclass input data of shape (N, L) and (N, C, L)
+    # Multiclass input data of shape (N, L)
     def _test_NL():
         num_classes = 4
         cm = ConfusionMatrix(num_classes=num_classes)
 
         y_pred = torch.rand(10, num_classes, 5)
-        y = torch.randint(0, num_classes, size=(10, 5)).type(torch.LongTensor)
+        y = torch.randint(0, num_classes, size=(10, 5)).long()
         cm.update((y_pred, y))
         np_y_pred = y_pred.numpy().argmax(axis=1).ravel()
         np_y = y.numpy().ravel()
@@ -171,7 +114,7 @@ def test_multiclass_input_NL():
         num_classes = 10
         cm = ConfusionMatrix(num_classes=num_classes)
         y_pred = torch.rand(4, num_classes, 5)
-        y = torch.randint(0, num_classes, size=(4, 5)).type(torch.LongTensor)
+        y = torch.randint(0, num_classes, size=(4, 5)).long()
         cm.update((y_pred, y))
         np_y_pred = y_pred.numpy().argmax(axis=1).ravel()
         np_y = y.numpy().ravel()
@@ -182,7 +125,7 @@ def test_multiclass_input_NL():
         cm = ConfusionMatrix(num_classes=num_classes)
 
         y_pred = torch.rand(100, num_classes, 7)
-        y = torch.randint(0, num_classes, size=(100, 7)).type(torch.LongTensor)
+        y = torch.randint(0, num_classes, size=(100, 7)).long()
 
         batch_size = 16
         n_iters = y.shape[0] // batch_size + 1
@@ -195,61 +138,19 @@ def test_multiclass_input_NL():
         np_y_pred = y_pred.numpy().argmax(axis=1).ravel()
         assert np.all(confusion_matrix(np_y, np_y_pred, labels=list(range(num_classes))) == cm.compute().numpy())
 
-    def _test_NCL():
-        num_classes = 4
-        cm = ConfusionMatrix(num_classes=num_classes)
-
-        y_pred = torch.rand(10, num_classes, 5)
-        y_labels = torch.randint(0, num_classes, size=(10, 5)).type(torch.LongTensor)
-        y = to_onehot(y_labels, num_classes=num_classes)
-        cm.update((y_pred, y))
-        np_y_pred = y_pred.numpy().argmax(axis=1).ravel()
-        np_y = y_labels.numpy().ravel()
-        assert np.all(confusion_matrix(np_y, np_y_pred, labels=list(range(num_classes))) == cm.compute().numpy())
-
-        num_classes = 10
-        cm = ConfusionMatrix(num_classes=num_classes)
-        y_pred = torch.rand(4, num_classes, 5)
-        y_labels = torch.randint(0, num_classes, size=(4, 5)).type(torch.LongTensor)
-        y = to_onehot(y_labels, num_classes=num_classes)
-        cm.update((y_pred, y))
-        np_y_pred = y_pred.numpy().argmax(axis=1).ravel()
-        np_y = y_labels.numpy().ravel()
-        assert np.all(confusion_matrix(np_y, np_y_pred, labels=list(range(num_classes))) == cm.compute().numpy())
-
-        # Batched Updates
-        num_classes = 9
-        cm = ConfusionMatrix(num_classes=num_classes)
-
-        y_pred = torch.rand(100, num_classes, 7)
-        y_labels = torch.randint(0, num_classes, size=(100, 7)).type(torch.LongTensor)
-        y = to_onehot(y_labels, num_classes=num_classes)
-
-        batch_size = 16
-        n_iters = y.shape[0] // batch_size + 1
-
-        for i in range(n_iters):
-            idx = i * batch_size
-            cm.update((y_pred[idx: idx + batch_size], y[idx: idx + batch_size]))
-
-        np_y = y_labels.numpy().ravel()
-        np_y_pred = y_pred.numpy().argmax(axis=1).ravel()
-        assert np.all(confusion_matrix(np_y, np_y_pred, labels=list(range(num_classes))) == cm.compute().numpy())
-
     # check multiple random inputs as random exact occurencies are rare
     for _ in range(10):
         _test_NL()
-        _test_NCL()
 
 
 def test_multiclass_input_NHW():
-    # Multiclass input data of shape (N, H, W, ...) and (N, C, H, W, ...)
+    # Multiclass input data of shape (N, H, W, ...)
     def _test_NHW():
         num_classes = 5
         cm = ConfusionMatrix(num_classes=num_classes)
 
         y_pred = torch.rand(4, num_classes, 12, 10)
-        y = torch.randint(0, num_classes, size=(4, 12, 10)).type(torch.LongTensor)
+        y = torch.randint(0, num_classes, size=(4, 12, 10)).long()
         cm.update((y_pred, y))
         np_y_pred = y_pred.numpy().argmax(axis=1).ravel()
         np_y = y.numpy().ravel()
@@ -258,7 +159,7 @@ def test_multiclass_input_NHW():
         num_classes = 5
         cm = ConfusionMatrix(num_classes=num_classes)
         y_pred = torch.rand(4, num_classes, 10, 12, 8)
-        y = torch.randint(0, num_classes, size=(4, 10, 12, 8)).type(torch.LongTensor)
+        y = torch.randint(0, num_classes, size=(4, 10, 12, 8)).long()
         cm.update((y_pred, y))
         np_y_pred = y_pred.numpy().argmax(axis=1).ravel()
         np_y = y.numpy().ravel()
@@ -268,7 +169,7 @@ def test_multiclass_input_NHW():
         num_classes = 3
         cm = ConfusionMatrix(num_classes=num_classes)
         y_pred = torch.rand(100, num_classes, 8, 8)
-        y = torch.randint(0, num_classes, size=(100, 8, 8)).type(torch.LongTensor)
+        y = torch.randint(0, num_classes, size=(100, 8, 8)).long()
 
         batch_size = 16
         n_iters = y.shape[0] // batch_size + 1
@@ -281,50 +182,21 @@ def test_multiclass_input_NHW():
         np_y_pred = y_pred.numpy().argmax(axis=1).ravel()
         assert np.all(confusion_matrix(np_y, np_y_pred, labels=list(range(num_classes))) == cm.compute().numpy())
 
-    def _test_NCHW():
-        num_classes = 5
-        cm = ConfusionMatrix(num_classes=num_classes)
-
-        y_pred = torch.rand(4, num_classes, 12, 10)
-        y_labels = torch.randint(0, num_classes, size=(4, 12, 10)).type(torch.LongTensor)
-        y = to_onehot(y_labels, num_classes=num_classes)
-        cm.update((y_pred, y))
-        np_y_pred = y_pred.numpy().argmax(axis=1).ravel()
-        np_y = y_labels.numpy().ravel()
-        assert np.all(confusion_matrix(np_y, np_y_pred, labels=list(range(num_classes))) == cm.compute().numpy())
-
-        num_classes = 5
-        cm = ConfusionMatrix(num_classes=num_classes)
-        y_pred = torch.rand(4, num_classes, 10, 12, 8)
-        y_labels = torch.randint(0, num_classes, size=(4, 10, 12, 8)).type(torch.LongTensor)
-        y = to_onehot(y_labels, num_classes=num_classes)
-        cm.update((y_pred, y))
-        np_y_pred = y_pred.numpy().argmax(axis=1).ravel()
-        np_y = y_labels.numpy().ravel()
-        assert np.all(confusion_matrix(np_y, np_y_pred, labels=list(range(num_classes))) == cm.compute().numpy())
-
-        # Batched Updates
-        num_classes = 3
-        cm = ConfusionMatrix(num_classes=num_classes)
-        y_pred = torch.rand(100, num_classes, 8, 8)
-        y_labels = torch.randint(0, num_classes, size=(100, 8, 8)).type(torch.LongTensor)
-        y = to_onehot(y_labels, num_classes=num_classes)
-
-        batch_size = 16
-        n_iters = y.shape[0] // batch_size + 1
-
-        for i in range(n_iters):
-            idx = i * batch_size
-            cm.update((y_pred[idx: idx + batch_size], y[idx: idx + batch_size]))
-
-        np_y = y_labels.numpy().ravel()
-        np_y_pred = y_pred.numpy().argmax(axis=1).ravel()
-        assert np.all(confusion_matrix(np_y, np_y_pred, labels=list(range(num_classes))) == cm.compute().numpy())
-
     # check multiple random inputs as random exact occurencies are rare
     for _ in range(10):
         _test_NHW()
-        _test_NCHW()
+
+
+def test_ignored_out_of_num_classes_indices():
+    num_classes = 21
+    cm = ConfusionMatrix(num_classes=num_classes)
+
+    y_pred = torch.rand(4, num_classes, 12, 10)
+    y = torch.randint(0, 255, size=(4, 12, 10)).long()
+    cm.update((y_pred, y))
+    np_y_pred = y_pred.numpy().argmax(axis=1).ravel()
+    np_y = y.numpy().ravel()
+    assert np.all(confusion_matrix(np_y, np_y_pred, labels=list(range(num_classes))) == cm.compute().numpy())
 
 
 def get_y_true_y_pred():
@@ -581,7 +453,7 @@ def test_cm_recall():
 def test_cm_with_average():
     num_classes = 5
     y_pred = torch.rand(20, num_classes)
-    y = torch.randint(0, num_classes, size=(20,)).type(torch.LongTensor)
+    y = torch.randint(0, num_classes, size=(20,)).long()
     np_y_pred = y_pred.numpy().argmax(axis=1).ravel()
     np_y = y.numpy().ravel()