"""Testing loadsave module""" import pathlib import shutil from os.path import dirname from os.path import join as pjoin from tempfile import TemporaryDirectory import numpy as np from .. import ( Nifti1Image, Nifti1Pair, Nifti2Image, Nifti2Pair, Spm2AnalyzeImage, Spm99AnalyzeImage, ) from .._compression import HAVE_ZSTD from ..filebasedimages import ImageFileError from ..loadsave import _signature_matches_extension, load, read_img_data from ..openers import Opener from ..optpkg import optional_package from ..testing import deprecated_to, expires from ..tmpdirs import InTemporaryDirectory _, have_scipy, _ = optional_package('scipy') import pytest from numpy.testing import assert_almost_equal, assert_array_equal data_path = pjoin(dirname(__file__), 'data') @expires('5.0.0') def test_read_img_data(): fnames_test = [ 'example4d.nii.gz', 'example_nifti2.nii.gz', 'minc1_1_scale.mnc', 'minc1_4d.mnc', 'test.mgz', 'tiny.mnc', ] fnames_test += [pathlib.Path(p) for p in fnames_test] for fname in fnames_test: fpath = pjoin(data_path, fname) if isinstance(fname, pathlib.Path): fpath = pathlib.Path(fpath) img = load(fpath) data = img.get_fdata() with deprecated_to('5.0.0'): data2 = read_img_data(img) assert_array_equal(data, data2) # These examples have null scaling - assert prefer=unscaled is the same dao = img.dataobj if hasattr(dao, 'slope') and hasattr(img.header, 'raw_data_from_fileobj'): assert (dao.slope, dao.inter) == (1, 0) with deprecated_to('5.0.0'): assert_array_equal(read_img_data(img, prefer='unscaled'), data) # Assert all caps filename works as well with TemporaryDirectory() as tmpdir: up_fpath = pjoin(tmpdir, str(fname).upper()) if isinstance(fname, pathlib.Path): up_fpath = pathlib.Path(up_fpath) shutil.copyfile(fpath, up_fpath) img = load(up_fpath) assert_array_equal(img.dataobj, data) del img def test_file_not_found(): with pytest.raises(FileNotFoundError): load('does_not_exist.nii.gz') def test_load_empty_image(): with InTemporaryDirectory(): open('empty.nii', 'w').close() with pytest.raises(ImageFileError) as err: load('empty.nii') assert str(err.value).startswith('Empty file: ') @pytest.mark.parametrize('extension', ['.gz', '.bz2', '.zst']) def test_load_bad_compressed_extension(tmp_path, extension): if extension == '.zst' and not HAVE_ZSTD: pytest.skip() file_path = tmp_path / f'img.nii{extension}' file_path.write_bytes(b'bad') with pytest.raises(ImageFileError, match=r'.*is not a .* file'): load(file_path) @pytest.mark.parametrize('extension', ['.gz', '.bz2', '.zst']) def test_load_good_extension_with_bad_data(tmp_path, extension): if extension == '.zst' and not HAVE_ZSTD: pytest.skip() file_path = tmp_path / f'img.nii{extension}' with Opener(file_path, 'wb') as fobj: fobj.write(b'bad') with pytest.raises(ImageFileError, match=r'Cannot work out file type of .*'): load(file_path) def test_signature_matches_extension(tmp_path): gz_signature = b'\x1f\x8b' good_file = tmp_path / 'good.gz' good_file.write_bytes(gz_signature) bad_file = tmp_path / 'bad.gz' bad_file.write_bytes(b'bad') matches, msg = _signature_matches_extension(tmp_path / 'uncompressed.nii') assert matches assert msg == '' matches, msg = _signature_matches_extension(tmp_path / 'missing.gz') assert not matches assert msg.startswith('Could not read') matches, msg = _signature_matches_extension(bad_file) assert not matches assert 'is not a' in msg matches, msg = _signature_matches_extension(good_file) assert matches assert msg == '' matches, msg = _signature_matches_extension(tmp_path / 'missing.nii') assert matches assert msg == '' @expires('5.0.0') def test_read_img_data_nifti(): shape = (2, 3, 4) data = np.random.normal(size=shape) out_dtype = np.dtype(np.int16) classes = (Nifti1Pair, Nifti1Image, Nifti2Pair, Nifti2Image) if have_scipy: classes += (Spm99AnalyzeImage, Spm2AnalyzeImage) with InTemporaryDirectory(): for i, img_class in enumerate(classes): img = img_class(data, np.eye(4)) img.set_data_dtype(out_dtype) # No filemap => error with deprecated_to('5.0.0'), pytest.raises(ImageFileError): read_img_data(img) # Make a filemap froot = f'an_image_{i}' img.file_map = img.filespec_to_file_map(froot) # Trying to read from this filemap will generate an error because # we are going to read from files that do not exist with deprecated_to('5.0.0'), pytest.raises(OSError): read_img_data(img) img.to_file_map() # Load - now the scaling and offset correctly applied img_fname = img.file_map['image'].filename img_back = load(img_fname) data_back = img_back.get_fdata() with deprecated_to('5.0.0'): assert_array_equal(data_back, read_img_data(img_back)) # This is the same as if we loaded the image and header separately hdr_fname = img.file_map['header'].filename if 'header' in img.file_map else img_fname with open(hdr_fname, 'rb') as fobj: hdr_back = img_back.header_class.from_fileobj(fobj) with open(img_fname, 'rb') as fobj: scaled_back = hdr_back.data_from_fileobj(fobj) assert_array_equal(data_back, scaled_back) # Unscaled is the same as returned from raw_data_from_fileobj with open(img_fname, 'rb') as fobj: unscaled_back = hdr_back.raw_data_from_fileobj(fobj) with deprecated_to('5.0.0'): assert_array_equal(unscaled_back, read_img_data(img_back, prefer='unscaled')) # If we futz with the scaling in the header, the result changes with deprecated_to('5.0.0'): assert_array_equal(data_back, read_img_data(img_back)) has_inter = hdr_back.has_data_intercept old_slope = hdr_back['scl_slope'] old_inter = hdr_back['scl_inter'] if has_inter else 0 est_unscaled = (data_back - old_inter) / old_slope with deprecated_to('5.0.0'): actual_unscaled = read_img_data(img_back, prefer='unscaled') assert_almost_equal(est_unscaled, actual_unscaled) img_back.header['scl_slope'] = 2.1 if has_inter: new_inter = 3.14 img_back.header['scl_inter'] = 3.14 else: new_inter = 0 # scaled scaling comes from new parameters in header with deprecated_to('5.0.0'): assert np.allclose(actual_unscaled * 2.1 + new_inter, read_img_data(img_back)) # Unscaled array didn't change with deprecated_to('5.0.0'): assert_array_equal(actual_unscaled, read_img_data(img_back, prefer='unscaled')) # Check the offset too img.header.set_data_offset(1024) # Delete arrays still pointing to file, so Windows can reuse del actual_unscaled, unscaled_back img.to_file_map() # Write an integer of zeros after with open(img_fname, 'ab') as fobj: fobj.write(b'\x00\x00') img_back = load(img_fname) data_back = img_back.get_fdata() with deprecated_to('5.0.0'): assert_array_equal(data_back, read_img_data(img_back)) img_back.header.set_data_offset(1026) # Check we pick up new offset exp_offset = np.zeros((data.size,), data.dtype) + old_inter exp_offset[:-1] = np.ravel(data_back, order='F')[1:] exp_offset = np.reshape(exp_offset, shape, order='F') with deprecated_to('5.0.0'): assert_array_equal(exp_offset, read_img_data(img_back)) # Delete stuff that might hold onto file references del img, img_back, data_back