Resolve "ilastik models do not validate dimensionality of input data"

Closes #1 (closed)

tests/test_accessors.py

@@ -7,6 +7,9 @@ from model_server.base.accessors import PatchStack, make_patch_stack_from_file,
 from model_server.conf.testing import czifile, output_path, monopngfile, rgbpngfile, tifffile, monozstackmask
 from model_server.base.accessors import CziImageFileAccessor, DataShapeError, generate_file_accessor, InMemoryDataAccessor, PngFileAccessor, write_accessor_data_to_file, TifSingleSeriesFileAccessor
 
+def _random_int(*args):
+    return np.random.randint(0, 2 ** 8, size=args, dtype='uint8')
+
 class TestCziImageFileAccess(unittest.TestCase):
 
     def setUp(self) -> None:
@@ -40,7 +43,7 @@ class TestCziImageFileAccess(unittest.TestCase):
         nc = 4
         nz = 11
         c = 3
-        cf = InMemoryDataAccessor(np.random.rand(h, w, nc, nz))
+        cf = InMemoryDataAccessor(_random_int(h, w, nc, nz))
         sc = cf.get_one_channel_data(c)
         self.assertEqual(sc.shape, (h, w, 1, nz))
 
@@ -70,7 +73,7 @@ class TestCziImageFileAccess(unittest.TestCase):
     def test_conform_data_shorter_than_xycz(self):
         h = 256
         w = 512
-        data = np.random.rand(h, w, 1)
+        data = _random_int(h, w, 1)
         acc = InMemoryDataAccessor(data)
         self.assertEqual(
             InMemoryDataAccessor.conform_data(data).shape,
@@ -82,7 +85,7 @@ class TestCziImageFileAccess(unittest.TestCase):
         )
 
     def test_conform_data_longer_than_xycz(self):
-        data = np.random.rand(256, 512, 12, 8, 3)
+        data = _random_int(256, 512, 12, 8, 3)
         with self.assertRaises(DataShapeError):
             acc = InMemoryDataAccessor(data)
 
@@ -93,7 +96,7 @@ class TestCziImageFileAccess(unittest.TestCase):
         c = 3
         nz = 10
 
-        yxcz = (2**8 * np.random.rand(h, w, c, nz)).astype('uint8')
+        yxcz = _random_int(h, w, c, nz)
         acc = InMemoryDataAccessor(yxcz)
         fp = output_path / f'rand3d.tif'
         self.assertTrue(
@@ -138,7 +141,7 @@ class TestPatchStackAccessor(unittest.TestCase):
         w = 256
         h = 512
         n = 4
-        acc = PatchStack(np.random.rand(n, h, w, 1, 1))
+        acc = PatchStack(_random_int(n, h, w, 1, 1))
         self.assertEqual(acc.count, n)
         self.assertEqual(acc.hw, (h, w))
         self.assertEqual(acc.pyxcz.shape, (n, h, w, 1, 1))
@@ -147,7 +150,7 @@ class TestPatchStackAccessor(unittest.TestCase):
         w = 256
         h = 512
         n = 4
-        acc = PatchStack([np.random.rand(h, w, 1, 1) for _ in range(0, n)])
+        acc = PatchStack([_random_int(h, w, 1, 1) for _ in range(0, n)])
         self.assertEqual(acc.count, n)
         self.assertEqual(acc.hw, (h, w))
         self.assertEqual(acc.pyxcz.shape, (n, h, w, 1, 1))
@@ -176,8 +179,8 @@ class TestPatchStackAccessor(unittest.TestCase):
         nz = 5
         n = 4
 
-        patches = [np.random.rand(h, w, c, nz) for _ in range(0, n)]
-        patches.append(np.random.rand(h, 2 * w, c, nz))
+        patches = [_random_int(h, w, c, nz) for _ in range(0, n)]
+        patches.append(_random_int(h, 2 * w, c, nz))
         acc = PatchStack(patches)
         self.assertEqual(acc.count, n + 1)
         self.assertEqual(acc.hw, (h, 2 * w))
@@ -191,7 +194,8 @@ class TestPatchStackAccessor(unittest.TestCase):
         n = 4
         nz = 15
         nc = 2
-        acc = PatchStack(np.random.rand(n, h, w, nc, nz))
+        acc = PatchStack(_random_int(n, h, w, nc, nz))
         self.assertEqual(acc.count, n)
         self.assertEqual(acc.pczyx.shape, (n, nc, nz, h, w))
         self.assertEqual(acc.hw, (h, w))
+        return acc
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