mrid-python 0.1.3__py3-none-any.whl

tests/test_preprocessing.py

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+"""sanity tests"""
+import numpy as np
+import SimpleITK as sitk
+
+from mrid.preprocessing import bias_field_correction
+
+
+def test_resize():
+    from mrid import Study
+    study = Study(t1=np.random.rand(10, 20, 30).astype(np.float32))
+    resized = study.resize([5, 10, 15])
+    assert 't1' in resized
+    assert study.numpy("t1").shape == (10, 20, 30)
+    assert resized.numpy("t1").shape == (5, 10, 15)
+
+
+def test_downsample():
+    from mrid import Study
+    study = Study(t1=np.random.rand(10, 20, 30).astype(np.float32))
+    downsampled = study.downsample(factor=2.0)  # 2x downsampling
+    assert 't1' in downsampled
+    assert study.numpy("t1").shape == (10, 20, 30)
+    assert downsampled.numpy("t1").shape == (5, 10, 15)
+
+
+def test_bias_field_correction():
+    img = sitk.Image(10, 10, 10, sitk.sitkFloat32)
+    corrected = bias_field_correction.n4_bias_field_correction(img, shrink=4)
+    assert isinstance(corrected, sitk.Image)
+
+
+def test_crop_bg():
+    from mrid import Study
+    data = {
+        't1': np.random.rand(20, 20, 20).astype(np.float32),
+        't2': np.random.rand(20, 20, 20).astype(np.float32)
+    }
+    study = Study(data)
+    cropped = study.crop_bg('t1')
+    assert 't1' in cropped
+    assert 't2' in cropped
+
+    assert study.numpy("t1").shape == study.numpy("t2").shape

tests/test_study.py

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+import os
+import tempfile
+import numpy as np
+import pytest
+import SimpleITK as sitk
+
+from mrid import Study
+
+
+def test_study_init():
+    # numpy
+    study1 = Study(
+        t1=np.random.rand(10, 20, 30).astype(np.float32),
+        t2=np.random.rand(10, 20, 30).astype(np.float32)
+    )
+    assert len(study1) == 2
+
+    # sitk
+    sitk_img1 = sitk.Image(10, 20, 30, sitk.sitkFloat32)
+    sitk_img2 = sitk.Image(15, 25, 35, sitk.sitkFloat32)
+    study2 = Study(t1=sitk_img1, t2=sitk_img2)
+    assert len(study2) == 2
+
+
+def test_study_get():
+    study = Study(
+        t1=np.random.rand(10, 20, 30),
+        t2=np.random.rand(10, 20, 30),
+        seg_brain=np.random.randint(0, 2, (10, 20, 30)),
+        info_patient={'age': 25, 'gender': 'M'}
+    )
+
+    assert 't1' in study
+    assert 't2' in study
+    assert 'seg_brain' in study
+    assert 'info_patient' in study
+
+    # test get_images
+    images = study.get_images()
+    assert tuple(images.keys()) == ("t1", "t2", "seg_brain")
+
+    # test get_scans method (excludes segmentations and info)
+    scans = study.get_scans()
+    assert tuple(scans.keys()) == ("t1", "t2",)
+
+    # test get_segmentations
+    segmentations = study.get_segmentations()
+    assert tuple(segmentations.keys()) == ("seg_brain", )
+
+    #test get_info
+    info = study.get_info()
+    assert tuple(info.keys()) == ("info_patient", )
+
+
+def test_apply():
+    study = Study(t1=np.random.rand(10, 20, 30))
+    result = study.apply(lambda x: x, lambda x: x)
+    assert 't1' in result
+
+    result2 = study.apply(None, None)
+    assert 't1' in result2
+
+
+@pytest.mark.parametrize("dtype", [np.float32, np.float64])
+def test_cast(dtype):
+    data = np.random.rand(5, 10, 15).astype(np.float32)
+    study = Study(t1=data)
+
+    if dtype == np.float32:
+        casted = study.cast_float32()
+    else:
+        casted = study.cast_float64()
+
+    assert 't1' in casted
+
+
+def test_normalize():
+    study = Study(t1=np.random.rand(10, 20, 30).astype(np.float32))
+    normalized = study.normalize()
+    assert 't1' in normalized
+
+
+def test_rescale_intensity():
+    study = Study(t1=np.random.rand(10, 20, 30).astype(np.float32))
+    rescaled = study.rescale_intensity(0.0, 1.0)
+    assert 't1' in rescaled
+
+
+def test_numpy_method():
+    data = np.random.rand(10, 20, 30).astype(np.float32)
+    study = Study(t1=data)
+
+    numpy_array = study.numpy('t1')
+    assert isinstance(numpy_array, np.ndarray)
+    assert numpy_array.shape == (10, 20, 30)
+
+
+def test_stack_numpy():
+    data = {
+        't1': np.random.rand(10, 20, 30),
+        't2': np.random.rand(10, 20, 30)
+    }
+    study = Study(data)
+
+    stacked = study.stack_numpy(scans=True, seg=False)
+    assert stacked.shape == (2, 10, 20, 30)  # 2 images, each 10x20x30
+
+@pytest.mark.parametrize("prefix", ("", "prefix"))
+@pytest.mark.parametrize("suffix", ("", "suffix"))
+def test_serialization(prefix,suffix):
+    data = dict(
+        t1=np.random.rand(10,20,30),
+        t2=np.random.rand(40,50,60),
+        seg_brain=np.random.randint(0,2, (10,20,30)),
+        seg_tumor=np.random.randint(0,5, (40,50,60)),
+        info_id=10,
+        info_name="Name"
+    )
+
+    study = Study(data)
+    assert sorted(study.keys()) == sorted(["t1", "t2", "seg_brain", "seg_tumor", "info_id", "info_name"])
+
+    with tempfile.TemporaryDirectory() as tmpdir:
+        out_dir = os.path.join(tmpdir, "study")
+        study.save(out_dir, prefix=prefix, suffix=suffix)
+        loaded = Study.from_dir(out_dir, prefix=prefix, suffix=suffix)
+
+    assert sorted(loaded.keys()) == sorted(["t1", "t2", "seg_brain", "seg_tumor", "info_id", "info_name"])
+
+    for k, v in study.items():
+        if isinstance(v, sitk.Image):
+            assert sitk.GetArrayFromImage(v).shape == sitk.GetArrayFromImage(loaded[k]).shape
+            assert sitk.GetArrayFromImage(v).dtype == sitk.GetArrayFromImage(loaded[k]).dtype
+            assert np.all(sitk.GetArrayFromImage(v) == sitk.GetArrayFromImage(loaded[k]))
+        else:
+            assert v == loaded[k]

tests/test_utils.py

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+import pytest
+from mrid.utils.python_utils import LazyLoader
+
+
+def test_lazy_loader():
+    loader = LazyLoader("os")
+    assert loader is not None
+
+    assert hasattr(loader, 'path')
+
+
+def test_lazy_loader_nonexistent_module():
+    loader = LazyLoader("this_module_does_not_exist_12345")
+
+    with pytest.raises(ImportError):
+        _ = loader.some_attribute