Add DICOM data for testing

fepegar · Oct 14, 2020 · 66b7a26 · 66b7a26
1 parent b9ece0e
commit 66b7a26
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Showing 19 changed files with 10 additions and 15 deletions.
diff --git a/tests/data/test_io.py b/tests/data/test_io.py
@@ -15,7 +15,9 @@ class TestIO(TorchioTestCase):
     """Tests for `io` module."""
     def setUp(self):
         super().setUp()
-        self.write_dicom()
+        self.nii_path = self.get_image_path('read_image')
+        self.dicom_dir = self.get_tests_data_dir() / 'dicom'
+        self.dicom_path = self.dicom_dir / 'IMG0001.dcm'
         string = (
             '1.5 0.18088 -0.124887 0.65072 '
             '-0.20025 0.965639 -0.165653 -11.6452 '
@@ -25,18 +27,6 @@ def setUp(self):
         tensor = torch.from_numpy(np.fromstring(string, sep=' ').reshape(4, 4))
         self.matrix = tensor
 
-    def write_dicom(self):
-        self.dicom_dir = self.dir / 'dicom'
-        self.dicom_dir.mkdir(exist_ok=True)
-        self.dicom_path = self.dicom_dir / 'dicom.dcm'
-        self.nii_path = self.get_image_path('read_image')
-        writer = sitk.ImageFileWriter()
-        writer.SetFileName(str(self.dicom_path))
-        image = sitk.ReadImage(str(self.nii_path))
-        image = sitk.Cast(image, sitk.sitkUInt16)
-        image = image[0]  # dicom reader supports 2D only
-        writer.Execute(image)
-
     def test_read_image(self):
         # I need to find something readable by nib but not sitk
         io.read_image(self.nii_path)
@@ -47,10 +37,12 @@ def test_save_rgb(self):
             im.save(self.dir / 'test.jpg')
 
     def test_read_dicom_file(self):
-        io.read_image(self.dicom_path)
+        tensor, _ = io.read_image(self.dicom_path)
+        self.assertEqual(tuple(tensor.shape), (1, 88, 128, 1))
 
     def test_read_dicom_dir(self):
-        io.read_image(self.dicom_dir)
+        tensor, _ = io.read_image(self.dicom_dir)
+        self.assertEqual(tuple(tensor.shape), (1, 88, 128, 17))
 
     def test_dicom_dir_missing(self):
         with self.assertRaises(FileNotFoundError):

diff --git a/tests/image_data/dicom/IMG0001.dcm b/tests/image_data/dicom/IMG0001.dcm
diff --git a/tests/image_data/dicom/IMG0002.dcm b/tests/image_data/dicom/IMG0002.dcm
diff --git a/tests/image_data/dicom/IMG0003.dcm b/tests/image_data/dicom/IMG0003.dcm
diff --git a/tests/image_data/dicom/IMG0004.dcm b/tests/image_data/dicom/IMG0004.dcm
diff --git a/tests/image_data/dicom/IMG0005.dcm b/tests/image_data/dicom/IMG0005.dcm
diff --git a/tests/image_data/dicom/IMG0006.dcm b/tests/image_data/dicom/IMG0006.dcm
diff --git a/tests/image_data/dicom/IMG0007.dcm b/tests/image_data/dicom/IMG0007.dcm
diff --git a/tests/image_data/dicom/IMG0008.dcm b/tests/image_data/dicom/IMG0008.dcm
diff --git a/tests/image_data/dicom/IMG0009.dcm b/tests/image_data/dicom/IMG0009.dcm
diff --git a/tests/image_data/dicom/IMG0010.dcm b/tests/image_data/dicom/IMG0010.dcm
diff --git a/tests/image_data/dicom/IMG0011.dcm b/tests/image_data/dicom/IMG0011.dcm
diff --git a/tests/image_data/dicom/IMG0012.dcm b/tests/image_data/dicom/IMG0012.dcm
diff --git a/tests/image_data/dicom/IMG0013.dcm b/tests/image_data/dicom/IMG0013.dcm
diff --git a/tests/image_data/dicom/IMG0014.dcm b/tests/image_data/dicom/IMG0014.dcm
diff --git a/tests/image_data/dicom/IMG0015.dcm b/tests/image_data/dicom/IMG0015.dcm
diff --git a/tests/image_data/dicom/IMG0016.dcm b/tests/image_data/dicom/IMG0016.dcm
diff --git a/tests/image_data/dicom/IMG0017.dcm b/tests/image_data/dicom/IMG0017.dcm
diff --git a/tests/utils.py b/tests/utils.py
@@ -158,6 +158,9 @@ def get_image_path(
         image.save(path)
         return path
 
+    def get_tests_data_dir(self):
+        return Path(__file__).parent / 'image_data'
+
     def assertTensorNotEqual(self, *args, **kwargs):  # noqa: N802
         message_kwarg = dict(msg=args[2]) if len(args) == 3 else {}
         with self.assertRaises(AssertionError, **message_kwarg):