Add function in monai.transforms.utils.py (#7712)

Fixes #6704

### Description
Combined `map_classes_to_indices` and
`generate_label_classes_crop_centers` to a single function
`map_and_generate_sampling_centers` in monai.transforms.utils.py.

### Types of changes
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

---------

Signed-off-by: ytl0623 <david89062388@gmail.com>
Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Yu <146002968+Yu0610@users.noreply.github.com>
Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>

Author: 5 people

monai/transforms/__init__.py

@@ -671,6 +671,7 @@
     in_bounds,
     is_empty,
     is_positive,
+    map_and_generate_sampling_centers,
     map_binary_to_indices,
     map_classes_to_indices,
     map_spatial_axes,

monai/transforms/utils.py

@@ -108,6 +108,7 @@
     "in_bounds",
     "is_empty",
     "is_positive",
+    "map_and_generate_sampling_centers",
     "map_binary_to_indices",
     "map_classes_to_indices",
     "map_spatial_axes",
@@ -368,6 +369,70 @@ def check_non_lazy_pending_ops(
         warnings.warn(msg)
 
 
+def map_and_generate_sampling_centers(
+    label: NdarrayOrTensor,
+    spatial_size: Sequence[int] | int,
+    num_samples: int,
+    label_spatial_shape: Sequence[int] | None = None,
+    num_classes: int | None = None,
+    image: NdarrayOrTensor | None = None,
+    image_threshold: float = 0.0,
+    max_samples_per_class: int | None = None,
+    ratios: list[float | int] | None = None,
+    rand_state: np.random.RandomState | None = None,
+    allow_smaller: bool = False,
+    warn: bool = True,
+) -> tuple[tuple]:
+    """
+    Combine "map_classes_to_indices" and "generate_label_classes_crop_centers" functions, return crop center coordinates.
+    This calls `map_classes_to_indices` to get indices from `label`, gets the shape from `label_spatial_shape`
+    is given otherwise from the labels, calls `generate_label_classes_crop_centers`, and returns its results.
+
+    Args:
+        label: use the label data to get the indices of every class.
+        spatial_size: spatial size of the ROIs to be sampled.
+        num_samples: total sample centers to be generated.
+        label_spatial_shape: spatial shape of the original label data to unravel selected centers.
+        indices: sequence of pre-computed foreground indices of every class in 1 dimension.
+        num_classes: number of classes for argmax label, not necessary for One-Hot label.
+        image: if image is not None, only return the indices of every class that are within the valid
+            region of the image (``image > image_threshold``).
+        image_threshold: if enabled `image`, use ``image > image_threshold`` to
+            determine the valid image content area and select class indices only in this area.
+        max_samples_per_class: maximum length of indices in each class to reduce memory consumption.
+            Default is None, no subsampling.
+        ratios: ratios of every class in the label to generate crop centers, including background class.
+            if None, every class will have the same ratio to generate crop centers.
+        rand_state: numpy randomState object to align with other modules.
+        allow_smaller: if `False`, an exception will be raised if the image is smaller than
+            the requested ROI in any dimension. If `True`, any smaller dimensions will be set to
+            match the cropped size (i.e., no cropping in that dimension).
+        warn: if `True` prints a warning if a class is not present in the label.
+    Returns:
+        Tuple of crop centres
+    """
+    if label is None:
+        raise ValueError("label must not be None.")
+    indices = map_classes_to_indices(label, num_classes, image, image_threshold, max_samples_per_class)
+
+    if label_spatial_shape is not None:
+        _shape = label_spatial_shape
+    elif isinstance(label, monai.data.MetaTensor):
+        _shape = label.peek_pending_shape()
+    else:
+        _shape = label.shape[1:]
+
+    if _shape is None:
+        raise ValueError(
+            "label_spatial_shape or label with a known shape must be provided to infer the output spatial shape."
+        )
+    centers = generate_label_classes_crop_centers(
+        spatial_size, num_samples, _shape, indices, ratios, rand_state, allow_smaller, warn
+    )
+
+    return ensure_tuple(centers)
+
+
 def map_binary_to_indices(
     label: NdarrayOrTensor, image: NdarrayOrTensor | None = None, image_threshold: float = 0.0
 ) -> tuple[NdarrayOrTensor, NdarrayOrTensor]:

tests/test_map_and_generate_sampling_centers.py

@@ -0,0 +1,87 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import annotations
+
+import unittest
+from copy import deepcopy
+
+import numpy as np
+from parameterized import parameterized
+
+from monai.transforms import map_and_generate_sampling_centers
+from monai.utils.misc import set_determinism
+from tests.utils import TEST_NDARRAYS, assert_allclose
+
+TEST_CASE_1 = [
+    # test Argmax data
+    {
+        "label": (np.array([[[0, 1, 2], [2, 0, 1], [1, 2, 0]]])),
+        "spatial_size": [2, 2, 2],
+        "num_samples": 2,
+        "label_spatial_shape": [3, 3, 3],
+        "num_classes": 3,
+        "image": None,
+        "ratios": [0, 1, 2],
+        "image_threshold": 0.0,
+    },
+    tuple,
+    2,
+    3,
+]
+
+TEST_CASE_2 = [
+    {
+        "label": (
+            np.array(
+                [
+                    [[1, 0, 0], [0, 1, 0], [0, 0, 1]],
+                    [[0, 1, 0], [0, 0, 1], [1, 0, 0]],
+                    [[0, 0, 1], [1, 0, 0], [0, 1, 0]],
+                ]
+            )
+        ),
+        "spatial_size": [2, 2, 2],
+        "num_samples": 1,
+        "ratios": None,
+        "label_spatial_shape": [3, 3, 3],
+        "image": None,
+        "image_threshold": 0.0,
+    },
+    tuple,
+    1,
+    3,
+]
+
+
+class TestMapAndGenerateSamplingCenters(unittest.TestCase):
+
+    @parameterized.expand([TEST_CASE_1, TEST_CASE_2])
+    def test_map_and_generate_sampling_centers(self, input_data, expected_type, expected_count, expected_shape):
+        results = []
+        for p in TEST_NDARRAYS + (None,):
+            input_data = deepcopy(input_data)
+            if p is not None:
+                input_data["label"] = p(input_data["label"])
+            set_determinism(0)
+            result = map_and_generate_sampling_centers(**input_data)
+            self.assertIsInstance(result, expected_type)
+            self.assertEqual(len(result), expected_count)
+            self.assertEqual(len(result[0]), expected_shape)
+            # check for consistency between numpy, torch and torch.cuda
+            results.append(result)
+            if len(results) > 1:
+                for x, y in zip(result[0], result[-1]):
+                    assert_allclose(x, y, type_test=False)
+
+
+if __name__ == "__main__":
+    unittest.main()