TEST: Test nib-roi and helpers

Author: effigies

nibabel/cmdline/tests/test_roi.py

@@ -0,0 +1,115 @@
+import os
+import numpy as np
+import nibabel as nb
+from nibabel.cmdline.roi import lossless_slice, parse_slice, main
+from nibabel.testing import data_path
+
+import unittest
+import pytest
+
+
+def test_parse_slice():
+    assert parse_slice(None) == slice(None)
+    assert parse_slice("1:5") == slice(1, 5)
+    assert parse_slice("1:") == slice(1, None)
+    assert parse_slice(":5") == slice(None, 5)
+    assert parse_slice(":-1") == slice(None, -1)
+    assert parse_slice("-5:-1") == slice(-5, -1)
+    assert parse_slice("1:5:") == slice(1, 5, None)
+    assert parse_slice("1::") == slice(1, None, None)
+    assert parse_slice(":5:") == slice(None, 5, None)
+    assert parse_slice(":-1:") == slice(None, -1, None)
+    assert parse_slice("-5:-1:") == slice(-5, -1, None)
+    assert parse_slice("1:5:1") == slice(1, 5, 1)
+    assert parse_slice("1::1") == slice(1, None, 1)
+    assert parse_slice(":5:1") == slice(None, 5, 1)
+    assert parse_slice(":-1:1") == slice(None, -1, 1)
+    assert parse_slice("-5:-1:1") == slice(-5, -1, 1)
+    assert parse_slice("5:1:-1") == slice(5, 1, -1)
+    assert parse_slice(":1:-1") == slice(None, 1, -1)
+    assert parse_slice("5::-1") == slice(5, None, -1)
+    assert parse_slice("-1::-1") == slice(-1, None, -1)
+    assert parse_slice("-1:-5:-1") == slice(-1, -5, -1)
+
+    # Max of start:stop:step
+    with pytest.raises(ValueError):
+        parse_slice("1:2:3:4")
+    # Integers only
+    with pytest.raises(ValueError):
+        parse_slice("abc:2:3")
+    with pytest.raises(ValueError):
+        parse_slice("1.2:2:3")
+    # Unit steps only
+    with pytest.raises(ValueError):
+        parse_slice("1:5:2")
+
+
+def test_parse_slice_disallow_step():
+    # Permit steps of 1
+    assert parse_slice("1:5", False) == slice(1, 5)
+    assert parse_slice("1:5:", False) == slice(1, 5)
+    assert parse_slice("1:5:1", False) == slice(1, 5, 1)
+    # Disable other steps
+    with pytest.raises(ValueError):
+        parse_slice("1:5:-1", False)
+    with pytest.raises(ValueError):
+        parse_slice("1:5:-2", False)
+
+
+def test_lossless_slice_unknown_axes():
+    img = nb.load(os.path.join(data_path, 'minc1_4d.mnc'))
+    with pytest.raises(ValueError):
+        lossless_slice(img, (slice(None), slice(None), slice(None)))
+
+
+def test_lossless_slice_scaling(tmp_path):
+    fname = tmp_path / 'image.nii'
+    img = nb.Nifti1Image(np.random.uniform(-20000, 20000, (5, 5, 5, 5)), affine=np.eye(4))
+    img.header.set_data_dtype("int16")
+    img.to_filename(fname)
+    img1 = nb.load(fname)
+    sliced_fname = tmp_path / 'sliced.nii'
+    lossless_slice(img1, (slice(None), slice(None), slice(2, 4))).to_filename(sliced_fname)
+    img2 = nb.load(sliced_fname)
+
+    assert np.array_equal(img1.get_fdata()[:, :, 2:4], img2.get_fdata())
+    assert np.array_equal(img1.dataobj.get_unscaled()[:, :, 2:4], img2.dataobj.get_unscaled())
+    assert img1.dataobj.slope == img2.dataobj.slope
+    assert img1.dataobj.inter == img2.dataobj.inter
+
+
+@pytest.mark.parametrize("inplace", (True, False))
+def test_nib_roi(tmp_path, inplace):
+    in_file = os.path.join(data_path, 'functional.nii')
+    out_file = str(tmp_path / 'sliced.nii')
+    in_img = nb.load(in_file)
+
+    if inplace:
+        in_img.to_filename(out_file)
+        in_file = out_file
+
+    retval = main([in_file, out_file, '-i', '1:-1', '-j', '-1:1:-1', '-k', '::', '-t', ':5'])
+    assert retval == 0
+
+    out_img = nb.load(out_file)
+    in_data = in_img.dataobj[:]
+    in_sliced = in_img.slicer[1:-1, -1:1:-1, :, :5]
+    assert out_img.shape == in_sliced.shape
+    assert np.array_equal(in_data[1:-1, -1:1:-1, :, :5], out_img.dataobj)
+    assert np.allclose(in_sliced.dataobj, out_img.dataobj)
+    assert np.allclose(in_sliced.affine, out_img.affine)
+
+
+@pytest.mark.parametrize("args, errmsg", (
+    (("-i", "1:1"), "Cannot take zero-length slice"),
+    (("-j", "1::2"), "Downsampling is not supported"),
+    (("-t", "5::-1"), "Step entry not permitted"),
+))
+def test_nib_roi_bad_slices(capsys, args, errmsg):
+    in_file = os.path.join(data_path, 'functional.nii')
+
+    retval = main([in_file, '/dev/null', *args])
+    assert retval != 0
+    captured = capsys.readouterr()
+    assert errmsg in captured.out
+