Width and height swapped when creating test image in data/synthetic/create_test_image_2d (#5627)

Signed-off-by: OeslleLucena <[email protected]>

Fixes #5373.

### Description
Change the `synthetic.py` script to have the (height, width, depth)
format.
Edit all the tests that uses `create_test_image_3d` to match the new
format.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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.
- [x] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [x] 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: OeslleLucena <[email protected]>

Author: OeslleLucena

monai/data/synthetic.py

@@ -19,8 +19,8 @@
 
 
 def create_test_image_2d(
-    width: int,
     height: int,
+    width: int,
     num_objs: int = 12,
     rad_max: int = 30,
     rad_min: int = 5,
@@ -37,8 +37,8 @@ def create_test_image_2d(
     an image without channel dimension, otherwise create an image with channel dimension as first dim or last dim.
 
     Args:
-        width: width of the image. The value should be larger than `2 * rad_max`.
         height: height of the image. The value should be larger than `2 * rad_max`.
+        width: width of the image. The value should be larger than `2 * rad_max`.
         num_objs: number of circles to generate. Defaults to `12`.
         rad_max: maximum circle radius. Defaults to `30`.
         rad_min: minimum circle radius. Defaults to `5`.
@@ -50,25 +50,25 @@ def create_test_image_2d(
         random_state: the random generator to use. Defaults to `np.random`.
 
     Returns:
-        Randomised Numpy array with shape (`width`, `height`)
+        Randomised Numpy array with shape (`height`, `width`)
     """
 
     if rad_max <= rad_min:
         raise ValueError("`rad_min` should be less than `rad_max`.")
     if rad_min < 1:
         raise ValueError("`rad_min` should be no less than 1.")
-    min_size = min(width, height)
+    min_size = min(height, width)
     if min_size <= 2 * rad_max:
         raise ValueError("the minimal size of the image should be larger than `2 * rad_max`.")
 
-    image = np.zeros((width, height))
+    image = np.zeros((height, width))
     rs: np.random.RandomState = np.random.random.__self__ if random_state is None else random_state  # type: ignore
 
     for _ in range(num_objs):
-        x = rs.randint(rad_max, width - rad_max)
-        y = rs.randint(rad_max, height - rad_max)
+        x = rs.randint(rad_max, height - rad_max)
+        y = rs.randint(rad_max, width - rad_max)
         rad = rs.randint(rad_min, rad_max)
-        spy, spx = np.ogrid[-x : width - x, -y : height - y]
+        spy, spx = np.ogrid[-x : height - x, -y : width - y]
         circle = (spx * spx + spy * spy) <= rad * rad
 
         if num_seg_classes > 1:
@@ -124,7 +124,7 @@ def create_test_image_3d(
         random_state: the random generator to use. Defaults to `np.random`.
 
     Returns:
-        Randomised Numpy array with shape (`width`, `height`, `depth`)
+        Randomised Numpy array with shape (`height`, `width`, `depth`)
 
     See also:
         :py:meth:`~create_test_image_2d`
@@ -134,19 +134,19 @@ def create_test_image_3d(
         raise ValueError("`rad_min` should be less than `rad_max`.")
     if rad_min < 1:
         raise ValueError("`rad_min` should be no less than 1.")
-    min_size = min(width, height, depth)
+    min_size = min(height, width, depth)
     if min_size <= 2 * rad_max:
         raise ValueError("the minimal size of the image should be larger than `2 * rad_max`.")
 
-    image = np.zeros((width, height, depth))
+    image = np.zeros((height, width, depth))
     rs: np.random.RandomState = np.random.random.__self__ if random_state is None else random_state  # type: ignore
 
     for _ in range(num_objs):
-        x = rs.randint(rad_max, width - rad_max)
-        y = rs.randint(rad_max, height - rad_max)
+        x = rs.randint(rad_max, height - rad_max)
+        y = rs.randint(rad_max, width - rad_max)
         z = rs.randint(rad_max, depth - rad_max)
         rad = rs.randint(rad_min, rad_max)
-        spy, spx, spz = np.ogrid[-x : width - x, -y : height - y, -z : depth - z]
+        spy, spx, spz = np.ogrid[-x : height - x, -y : width - y, -z : depth - z]
         circle = (spx * spx + spy * spy + spz * spz) <= rad * rad
 
         if num_seg_classes > 1:

tests/test_adn.py

@@ -46,7 +46,7 @@
     [{"norm": "INSTANCE", "norm_dim": 3, "dropout_dim": 1, "dropout": 0.8, "ordering": "AND"}],
     [
         {
-            "norm": ("layer", {"normalized_shape": (64, 80)}),
+            "norm": ("layer", {"normalized_shape": (48, 80)}),
             "norm_dim": 3,
             "dropout_dim": 1,
             "dropout": 0.8,
@@ -76,7 +76,7 @@ def test_adn_3d(self, args):
         adn = ADN(**args)
         print(adn)
         out = adn(self.imt)
-        expected_shape = (1, self.input_channels, self.im_shape[1], self.im_shape[0], self.im_shape[2])
+        expected_shape = (1, self.input_channels, self.im_shape[0], self.im_shape[1], self.im_shape[2])
         self.assertEqual(out.shape, expected_shape)
 
 

tests/test_convolutions.py

@@ -70,19 +70,19 @@ class TestConvolution3D(TorchImageTestCase3D):
     def test_conv1(self):
         conv = Convolution(3, self.input_channels, self.output_channels, dropout=0.1, adn_ordering="DAN")
         out = conv(self.imt)
-        expected_shape = (1, self.output_channels, self.im_shape[1], self.im_shape[0], self.im_shape[2])
+        expected_shape = (1, self.output_channels, self.im_shape[0], self.im_shape[1], self.im_shape[2])
         self.assertEqual(out.shape, expected_shape)
 
     def test_conv1_no_acti(self):
         conv = Convolution(3, self.input_channels, self.output_channels, act=None, adn_ordering="AND")
         out = conv(self.imt)
-        expected_shape = (1, self.output_channels, self.im_shape[1], self.im_shape[0], self.im_shape[2])
+        expected_shape = (1, self.output_channels, self.im_shape[0], self.im_shape[1], self.im_shape[2])
         self.assertEqual(out.shape, expected_shape)
 
     def test_conv_only1(self):
         conv = Convolution(3, self.input_channels, self.output_channels, conv_only=True)
         out = conv(self.imt)
-        expected_shape = (1, self.output_channels, self.im_shape[1], self.im_shape[0], self.im_shape[2])
+        expected_shape = (1, self.output_channels, self.im_shape[0], self.im_shape[1], self.im_shape[2])
         self.assertEqual(out.shape, expected_shape)
 
     def test_stride1(self):
@@ -92,34 +92,34 @@ def test_stride1(self):
             expected_shape = (
                 1,
                 self.output_channels,
-                self.im_shape[1] // 2,
                 self.im_shape[0] // 2,
+                self.im_shape[1] // 2,
                 self.im_shape[2] // 2,
             )
             self.assertEqual(out.shape, expected_shape)
 
     def test_dilation1(self):
         conv = Convolution(3, self.input_channels, self.output_channels, dilation=3)
         out = conv(self.imt)
-        expected_shape = (1, self.output_channels, self.im_shape[1], self.im_shape[0], self.im_shape[2])
+        expected_shape = (1, self.output_channels, self.im_shape[0], self.im_shape[1], self.im_shape[2])
         self.assertEqual(out.shape, expected_shape)
 
     def test_dropout1(self):
         conv = Convolution(3, self.input_channels, self.output_channels, dropout=0.15)
         out = conv(self.imt)
-        expected_shape = (1, self.output_channels, self.im_shape[1], self.im_shape[0], self.im_shape[2])
+        expected_shape = (1, self.output_channels, self.im_shape[0], self.im_shape[1], self.im_shape[2])
         self.assertEqual(out.shape, expected_shape)
 
     def test_transpose1(self):
         conv = Convolution(3, self.input_channels, self.output_channels, is_transposed=True)
         out = conv(self.imt)
-        expected_shape = (1, self.output_channels, self.im_shape[1], self.im_shape[0], self.im_shape[2])
+        expected_shape = (1, self.output_channels, self.im_shape[0], self.im_shape[1], self.im_shape[2])
         self.assertEqual(out.shape, expected_shape)
 
     def test_transpose2(self):
         conv = Convolution(3, self.input_channels, self.output_channels, strides=2, is_transposed=True)
         out = conv(self.imt)
-        expected_shape = (1, self.output_channels, self.im_shape[1] * 2, self.im_shape[0] * 2, self.im_shape[2] * 2)
+        expected_shape = (1, self.output_channels, self.im_shape[0] * 2, self.im_shape[1] * 2, self.im_shape[2] * 2)
         self.assertEqual(out.shape, expected_shape)
 
 

tests/test_denseblock.py

@@ -42,8 +42,8 @@ def test_block_conv(self):
         expected_shape = (
             1,
             self.output_channels + self.input_channels * 2,
-            self.im_shape[1],
             self.im_shape[0],
+            self.im_shape[1],
             self.im_shape[2],
         )
         self.assertEqual(out.shape, expected_shape)
@@ -87,15 +87,15 @@ def test_block1(self):
         channels = [2, 4]
         conv = ConvDenseBlock(spatial_dims=3, in_channels=self.input_channels, channels=channels)
         out = conv(self.imt)
-        expected_shape = (1, self.input_channels + sum(channels), self.im_shape[1], self.im_shape[0], self.im_shape[2])
+        expected_shape = (1, self.input_channels + sum(channels), self.im_shape[0], self.im_shape[1], self.im_shape[2])
         self.assertEqual(out.shape, expected_shape)
 
     def test_block2(self):
         channels = [2, 4]
         dilations = [1, 2]
         conv = ConvDenseBlock(spatial_dims=3, in_channels=self.input_channels, channels=channels, dilations=dilations)
         out = conv(self.imt)
-        expected_shape = (1, self.input_channels + sum(channels), self.im_shape[1], self.im_shape[0], self.im_shape[2])
+        expected_shape = (1, self.input_channels + sum(channels), self.im_shape[0], self.im_shape[1], self.im_shape[2])
         self.assertEqual(out.shape, expected_shape)
 
 

tests/test_integration_sliding_window.py

@@ -67,7 +67,7 @@ class TestIntegrationSlidingWindow(DistTestCase):
     def setUp(self):
         set_determinism(seed=0)
 
-        im, seg = create_test_image_3d(25, 28, 63, rad_max=10, noise_max=1, num_objs=4, num_seg_classes=1)
+        im, seg = create_test_image_3d(28, 25, 63, rad_max=10, noise_max=1, num_objs=4, num_seg_classes=1)
         self.img_name = make_nifti_image(im)
         self.seg_name = make_nifti_image(seg)
         self.device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu:0")

tests/test_invert.py

@@ -74,7 +74,7 @@ def test_invert(self):
                 self.assertTupleEqual(orig.shape[1:], (100, 100, 100))
                 # check the nearest interpolation mode
                 assert_allclose(i.to(torch.uint8).to(torch.float), i.to(torch.float))
-                self.assertTupleEqual(i.shape[1:], (100, 101, 107))
+                self.assertTupleEqual(i.shape[1:], (101, 100, 107))
         # check labels match
         reverted = i.detach().cpu().numpy().astype(np.int32)
         original = LoadImage(image_only=True)(data[-1])

tests/test_invertd.py

@@ -104,21 +104,21 @@ def test_invert(self):
                 # check the nearest interpolation mode
                 i = item["image_inverted"]
                 assert_allclose(i.to(torch.uint8).to(torch.float), i.to(torch.float))
-                self.assertTupleEqual(i.shape[1:], (100, 101, 107))
+                self.assertTupleEqual(i.shape[1:], (101, 100, 107))
                 i = item["label_inverted"]
                 assert_allclose(i.to(torch.uint8).to(torch.float), i.to(torch.float))
-                self.assertTupleEqual(i.shape[1:], (100, 101, 107))
+                self.assertTupleEqual(i.shape[1:], (101, 100, 107))
 
                 # check the case that different items use different interpolation mode to invert transforms
                 d = item["image_inverted1"]
                 # if the interpolation mode is nearest, accumulated diff should be smaller than 1
                 self.assertLess(torch.sum(d.to(torch.float) - d.to(torch.uint8).to(torch.float)).item(), 1.0)
-                self.assertTupleEqual(d.shape, (1, 100, 101, 107))
+                self.assertTupleEqual(d.shape, (1, 101, 100, 107))
 
                 d = item["label_inverted1"]
                 # if the interpolation mode is not nearest, accumulated diff should be greater than 10000
                 self.assertGreater(torch.sum(d.to(torch.float) - d.to(torch.uint8).to(torch.float)).item(), 10000.0)
-                self.assertTupleEqual(d.shape, (1, 100, 101, 107))
+                self.assertTupleEqual(d.shape, (1, 101, 100, 107))
 
         # check labels match
         reverted = item["label_inverted"].detach().cpu().numpy().astype(np.int32)

tests/test_rand_rotate.py

@@ -37,7 +37,7 @@
 TEST_CASES_3D: List[Tuple] = []
 for p in TEST_NDARRAYS_ALL:
     TEST_CASES_3D.append(
-        (p, np.pi / 2, -np.pi / 6, (0.0, np.pi), False, "bilinear", "border", False, (1, 87, 104, 109))
+        (p, np.pi / 2, -np.pi / 6, (0.0, np.pi), False, "bilinear", "border", False, (1, 81, 110, 112))
     )
     TEST_CASES_3D.append(
         (
@@ -49,7 +49,7 @@
             "nearest",
             "border",
             True,
-            (1, 89, 105, 104),
+            (1, 97, 100, 97),
         )
     )
     TEST_CASES_3D.append(
@@ -62,10 +62,10 @@
             "nearest",
             "zeros",
             True,
-            (1, 48, 64, 80),
+            (1, 64, 48, 80),
         )
     )
-    TEST_CASES_3D.append((p, (-np.pi / 4, 0), 0, 0, False, "nearest", "zeros", False, (1, 48, 77, 90)))
+    TEST_CASES_3D.append((p, (-np.pi / 4, 0), 0, 0, False, "nearest", "zeros", False, (1, 64, 61, 87)))
 
 
 class TestRandRotate2D(NumpyImageTestCase2D):

tests/test_rand_rotated.py

@@ -31,7 +31,7 @@
 TEST_CASES_3D: List[Tuple] = []
 for p in TEST_NDARRAYS_ALL:
     TEST_CASES_3D.append(
-        (p, np.pi / 2, -np.pi / 6, (0.0, np.pi), False, "bilinear", "border", False, (1, 87, 104, 109))
+        (p, np.pi / 2, -np.pi / 6, (0.0, np.pi), False, "bilinear", "border", False, (1, 81, 110, 112))
     )
     TEST_CASES_3D.append(
         (
@@ -43,7 +43,7 @@
             GridSampleMode.NEAREST,
             GridSamplePadMode.BORDER,
             False,
-            (1, 87, 104, 109),
+            (1, 81, 110, 112),
         )
     )
     TEST_CASES_3D.append(
@@ -56,7 +56,7 @@
             "nearest",
             "border",
             True,
-            (1, 89, 105, 104),
+            (1, 97, 100, 97),
         )
     )
     TEST_CASES_3D.append(
@@ -69,7 +69,7 @@
             GridSampleMode.NEAREST,
             GridSamplePadMode.BORDER,
             True,
-            (1, 89, 105, 104),
+            (1, 97, 100, 97),
         )
     )
     TEST_CASES_3D.append(
@@ -82,7 +82,7 @@
             "nearest",
             "zeros",
             True,
-            (1, 48, 64, 80),
+            (1, 64, 48, 80),
         )
     )
     TEST_CASES_3D.append(
@@ -95,12 +95,12 @@
             GridSampleMode.NEAREST,
             GridSamplePadMode.ZEROS,
             True,
-            (1, 48, 64, 80),
+            (1, 64, 48, 80),
         )
     )
-    TEST_CASES_3D.append((p, (-np.pi / 4, 0), 0, 0, False, "nearest", "zeros", False, (1, 48, 77, 90)))
+    TEST_CASES_3D.append((p, (-np.pi / 4, 0), 0, 0, False, "nearest", "zeros", False, (1, 64, 61, 87)))
     TEST_CASES_3D.append(
-        (p, (-np.pi / 4, 0), 0, 0, False, GridSampleMode.NEAREST, GridSamplePadMode.ZEROS, False, (1, 48, 77, 90))
+        (p, (-np.pi / 4, 0), 0, 0, False, GridSampleMode.NEAREST, GridSamplePadMode.ZEROS, False, (1, 64, 61, 87))
     )
 
 

tests/test_rand_weighted_crop.py

@@ -112,8 +112,8 @@ def get_data(ndim):
                 dict(spatial_size=(10, -1, -1), num_samples=3),
                 p(im),
                 q(weight),
-                (1, 10, 64, 80),
-                [[14, 32, 40], [41, 32, 40], [20, 32, 40]],
+                (1, 10, 48, 80),
+                [[14, 24, 40], [41, 24, 40], [20, 24, 40]],
             ]
         )
         im = SEGN_3D
@@ -126,8 +126,8 @@ def get_data(ndim):
                 dict(spatial_size=(10000, 400, 80), num_samples=3),
                 p(im),
                 q(weight),
-                (1, 48, 64, 80),
-                [[24, 32, 40], [24, 32, 40], [24, 32, 40]],
+                (1, 64, 48, 80),
+                [[32, 24, 40], [32, 24, 40], [32, 24, 40]],
             ]
         )
         im = IMT_3D
@@ -138,11 +138,11 @@ def get_data(ndim):
         TESTS.append(
             [
                 "bad w 3d",
-                dict(spatial_size=(48, 64, 80), num_samples=3),
+                dict(spatial_size=(64, 48, 80), num_samples=3),
                 p(im),
                 q(weight),
-                (1, 48, 64, 80),
-                [[24, 32, 40], [24, 32, 40], [24, 32, 40]],
+                (1, 64, 48, 80),
+                [[32, 24, 40], [32, 24, 40], [32, 24, 40]],
             ]
         )
 

tests/test_synthetic.py

@@ -21,7 +21,7 @@
     [2, {"width": 64, "height": 64, "rad_max": 10, "rad_min": 4}, 0.1479004, 0.739502, (64, 64), 5],
     [
         2,
-        {"width": 32, "height": 28, "num_objs": 3, "rad_max": 5, "rad_min": 1, "noise_max": 0.2},
+        {"width": 28, "height": 32, "num_objs": 3, "rad_max": 5, "rad_min": 1, "noise_max": 0.2},
         0.1709315,
         0.4040179,
         (32, 28),