def test_predict_dki(): with nbtmp.InTemporaryDirectory() as tmpdir: fbval = op.join(tmpdir, 'dki.bval') fbvec = op.join(tmpdir, 'dki.bvec') fdata = op.join(tmpdir, 'dki.nii.gz') make_dki_data(fbval, fbvec, fdata) file_dict = dki.fit_dki(fdata, fbval, fbvec, out_dir=tmpdir) params_file = file_dict['params'] gtab = dpg.gradient_table(fbval, fbvec) predict_fname = dki.predict(params_file, gtab, S0_file=fdata, out_dir=tmpdir) prediction = nib.load(predict_fname).get_data() npt.assert_almost_equal(prediction, nib.load(fdata).get_data())
def test_cli_dkimicro(): with nbtmp.InTemporaryDirectory() as tmpdir: fbval = op.join(tmpdir, 'dki.bval') fbvec = op.join(tmpdir, 'dki.bvec') fdata = op.join(tmpdir, 'dki.nii.gz') make_dki_data(fbval, fbvec, fdata) cmd = " ".join( ["pyAFQ_dkimicro", "-d", op.join(tmpdir, "dki.nii.gz"), "-l", op.join(tmpdir, "dki.bval"), "-c", op.join(tmpdir, "dki.bvec")]) out = os.system(cmd) assert out == 0
def test_fit_dki(): with nbtmp.InTemporaryDirectory() as tmpdir: fbval = op.join(tmpdir, 'dki.bval') fbvec = op.join(tmpdir, 'dki.bvec') fdata = op.join(tmpdir, 'dki.nii.gz') make_dki_data(fbval, fbvec, fdata) cmd = ["pyAFQ_dki", "-d", fdata, "-l", fbval, "-c", fbvec, "-o", tmpdir] out = runner.run_command(cmd) npt.assert_equal(out[0], 0) # Get expected values names = ['FA', 'MD', 'AD', 'RD', 'MK', 'AK', 'RK'] for n in names: fname = op.join(tmpdir, "dki_%s.nii.gz" % n) img = nib.load(fdata) affine = img.get_affine() shape = img.shape[:-1] assert_image_shape_affine(fname, shape, affine)
def test_fit_dki(): with nbtmp.InTemporaryDirectory() as tmpdir: fbval = op.join(tmpdir, 'dki.bval') fbvec = op.join(tmpdir, 'dki.bvec') fdata = op.join(tmpdir, 'dki.nii.gz') make_dki_data(fbval, fbvec, fdata) cmd = ["pyAFQ_dki", "-d", fdata, "-l", fbval, "-c", fbvec, "-o", tmpdir] out = runner.run_command(cmd) npt.assert_equal(out[0], 0) # Get expected values names = ['FA', 'MD', 'AD', 'RD', 'MK', 'AK', 'RK'] for n in names: fname = op.join(tmpdir, "dki_%s.nii.gz" % n) img = nib.load(fdata) affine = img.affine shape = img.shape[:-1] assert_image_shape_affine(fname, shape, affine)
def test_predict_dki(): with nbtmp.InTemporaryDirectory() as tmpdir: fbval = op.join(tmpdir, 'dki.bval') fbvec = op.join(tmpdir, 'dki.bvec') fdata = op.join(tmpdir, 'dki.nii.gz') make_dki_data(fbval, fbvec, fdata) cmd1 = ["pyAFQ_dki", "-d", fdata, "-l", fbval, "-c", fbvec, "-o", tmpdir] out = runner.run_command(cmd1) npt.assert_equal(out[0], 0) # Get expected values fparams = op.join(tmpdir, "dki_params.nii.gz") cmd2 = ["pyAFQ_dki_predict", "-p", fparams, "-l", fbval, "-c", fbvec, "-o", tmpdir, '-b', '0'] out = runner.run_command(cmd2) npt.assert_equal(out[0], 0) pred = nib.load(op.join(tmpdir, "dki_prediction.nii.gz")).get_data() data = nib.load(op.join(tmpdir, "dki.nii.gz")).get_data() npt.assert_array_almost_equal(pred, data)
def test_predict_dki(): with nbtmp.InTemporaryDirectory() as tmpdir: fbval = op.join(tmpdir, 'dki.bval') fbvec = op.join(tmpdir, 'dki.bvec') fdata = op.join(tmpdir, 'dki.nii.gz') make_dki_data(fbval, fbvec, fdata) cmd1 = ["pyAFQ_dki", "-d", fdata, "-l", fbval, "-c", fbvec, "-o", tmpdir] out = runner.run_command(cmd1) npt.assert_equal(out[0], 0) # Get expected values fparams = op.join(tmpdir, "dki_params.nii.gz") cmd2 = ["pyAFQ_dki_predict", "-p", fparams, "-l", fbval, "-c", fbvec, "-o", tmpdir, '-b', '0'] out = runner.run_command(cmd2) npt.assert_equal(out[0], 0) pred = nib.load(op.join(tmpdir, "dki_prediction.nii.gz")).get_fdata() data = nib.load(op.join(tmpdir, "dki.nii.gz")).get_fdata() npt.assert_array_almost_equal(pred, data)