TEST: Test nib-convert functionality

Author: effigies

nibabel/cmdline/tests/test_convert.py

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+#!python
+# emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+#
+#   See COPYING file distributed along with the NiBabel package for the
+#   copyright and license terms.
+#
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+
+import pytest
+
+import numpy as np
+
+import nibabel as nib
+from nibabel.testing import test_data
+from nibabel.cmdline import convert
+
+
+def test_convert_noop(tmp_path):
+    infile = test_data(fname='anatomical.nii')
+    outfile = tmp_path / 'output.nii.gz'
+
+    orig = nib.load(infile)
+    assert not outfile.exists()
+
+    convert.main([str(infile), str(outfile)])
+    assert outfile.is_file()
+
+    converted = nib.load(outfile)
+    assert np.allclose(converted.affine, orig.affine)
+    assert converted.shape == orig.shape
+    assert converted.get_data_dtype() == orig.get_data_dtype()
+
+    with pytest.raises(FileExistsError):
+        convert.main([str(infile), str(outfile)])
+
+    convert.main([str(infile), str(outfile), '--force'])
+    assert outfile.is_file()
+
+
+@pytest.mark.parametrize('data_dtype', ('u1', 'i2', 'float32', 'float', 'int64'))
+def test_convert_dtype(tmp_path, data_dtype):
+    infile = test_data(fname='anatomical.nii')
+    outfile = tmp_path / 'output.nii.gz'
+
+    orig = nib.load(infile)
+    assert not outfile.exists()
+
+    # np.dtype() will give us the dtype for the system endianness if that
+    # mismatches the data file, we will fail equality, so get the dtype that
+    # matches the requested precision but in the endianness of the file
+    expected_dtype = np.dtype(data_dtype).newbyteorder(orig.header.endianness)
+
+    convert.main([str(infile), str(outfile), '--out-dtype', data_dtype])
+    assert outfile.is_file()
+
+    converted = nib.load(outfile)
+    assert np.allclose(converted.affine, orig.affine)
+    assert converted.shape == orig.shape
+    assert converted.get_data_dtype() == expected_dtype
+
+
+@pytest.mark.parametrize('ext,img_class', [
+    ('mgh', nib.MGHImage),
+    ('img', nib.Nifti1Pair),
+])
+def test_convert_by_extension(tmp_path, ext, img_class):
+    infile = test_data(fname='anatomical.nii')
+    outfile = tmp_path / f'output.{ext}'
+
+    orig = nib.load(infile)
+    assert not outfile.exists()
+
+    convert.main([str(infile), str(outfile)])
+    assert outfile.is_file()
+
+    converted = nib.load(outfile)
+    assert np.allclose(converted.affine, orig.affine)
+    assert converted.shape == orig.shape
+    assert converted.__class__ == img_class
+
+
+@pytest.mark.parametrize('ext,img_class', [
+    ('mgh', nib.MGHImage),
+    ('img', nib.Nifti1Pair),
+    ('nii', nib.Nifti2Image),
+])
+def test_convert_imgtype(tmp_path, ext, img_class):
+    infile = test_data(fname='anatomical.nii')
+    outfile = tmp_path / f'output.{ext}'
+
+    orig = nib.load(infile)
+    assert not outfile.exists()
+
+    convert.main([str(infile), str(outfile), '--image-type', img_class.__name__])
+    assert outfile.is_file()
+
+    converted = nib.load(outfile)
+    assert np.allclose(converted.affine, orig.affine)
+    assert converted.shape == orig.shape
+    assert converted.__class__ == img_class
+
+
+def test_convert_nifti_int_fail(tmp_path):
+    infile = test_data(fname='anatomical.nii')
+    outfile = tmp_path / f'output.nii'
+
+    orig = nib.load(infile)
+    assert not outfile.exists()
+
+    with pytest.raises(ValueError):
+        convert.main([str(infile), str(outfile), '--out-dtype', 'int'])
+    assert not outfile.exists()
+    
+    with pytest.warns(UserWarning):
+        convert.main([str(infile), str(outfile), '--out-dtype', 'int', '--force'])
+    assert outfile.is_file()
+
+    converted = nib.load(outfile)
+    assert np.allclose(converted.affine, orig.affine)
+    assert converted.shape == orig.shape
+    # Note: '--force' ignores the error, but can't interpret it enough to do
+    # the cast anyway
+    assert converted.get_data_dtype() == orig.get_data_dtype()
+
+
+@pytest.mark.parametrize('orig_dtype,alias,expected_dtype', [
+    ('int64', 'mask', 'uint8'),
+    ('int64', 'compat', 'int32'),
+    ('int64', 'smallest', 'uint8'),
+    ('float64', 'mask', 'uint8'),
+    ('float64', 'compat', 'float32'),
+])
+def test_convert_aliases(tmp_path, orig_dtype, alias, expected_dtype):
+    orig_fname = tmp_path / 'orig.nii'
+    out_fname = tmp_path / 'out.nii'
+
+    arr = np.arange(24).reshape((2, 3, 4))
+    img = nib.Nifti1Image(arr, np.eye(4), dtype=orig_dtype)
+    img.to_filename(orig_fname)
+
+    assert orig_fname.exists()
+    assert not out_fname.exists()
+
+    convert.main([str(orig_fname), str(out_fname), '--out-dtype', alias])
+    assert out_fname.is_file()
+
+    expected_dtype = np.dtype(expected_dtype).newbyteorder(img.header.endianness)
+
+    converted = nib.load(out_fname)
+    assert converted.get_data_dtype() == expected_dtype