コード例 #1
0
def test_predict_dti():
    with nbtmp.InTemporaryDirectory() as tmpdir:
        fbval = op.join(tmpdir, 'dti.bval')
        fbvec = op.join(tmpdir, 'dti.bvec')
        fdata = op.join(tmpdir, 'dti.nii.gz')
        make_dti_data(fbval, fbvec, fdata)
        file_dict = dti.fit_dti(fdata, fbval, fbvec, out_dir=tmpdir)
        params_file = file_dict['params']
        gtab = dpg.gradient_table(fbval, fbvec)
        predict_fname = dti.predict(params_file,
                                    gtab,
                                    S0_file=fdata,
                                    out_dir=tmpdir)
        prediction = nib.load(predict_fname).get_fdata()
        npt.assert_almost_equal(prediction, nib.load(fdata).get_fdata())

        # If you have a mask into the volume, you will predict only that
        # part of the volume:
        mask = np.zeros(prediction.shape[:3], dtype=bool)
        mask[2:4, 2:4, 2:4] = 1
        file_dict = dti.fit_dti(fdata, fbval, fbvec, mask=mask, out_dir=tmpdir)
        params_file = file_dict['params']
        predict_fname = dti.predict(params_file,
                                    gtab,
                                    S0_file=fdata,
                                    out_dir=tmpdir)
        prediction = nib.load(predict_fname).get_fdata()
        npt.assert_almost_equal(prediction[mask],
                                nib.load(fdata).get_fdata()[mask])
コード例 #2
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ファイル: test_dti.py プロジェクト: jyeatman/pyAFQ
def test_predict_dti():
    with nbtmp.InTemporaryDirectory() as tmpdir:
        fbval = op.join(tmpdir, 'dti.bval')
        fbvec = op.join(tmpdir, 'dti.bvec')
        fdata = op.join(tmpdir, 'dti.nii.gz')
        make_dti_data(fbval, fbvec, fdata)
        file_dict = dti.fit_dti(fdata, fbval, fbvec, out_dir=tmpdir)
        params_file = file_dict['params']
        gtab = dpg.gradient_table(fbval, fbvec)
        predict_fname = dti.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())

        # If you have a mask into the volume, you will predict only that
        # part of the volume:
        mask = np.zeros(prediction.shape[:3], dtype=bool)
        mask[2:4, 2:4, 2:4] = 1
        file_dict = dti.fit_dti(fdata, fbval, fbvec, mask=mask,
                                out_dir=tmpdir)
        params_file = file_dict['params']
        predict_fname = dti.predict(params_file, gtab, S0_file=fdata,
                                    out_dir=tmpdir)
        prediction = nib.load(predict_fname).get_data()
        npt.assert_almost_equal(prediction[mask],
                                nib.load(fdata).get_data()[mask])
コード例 #3
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ファイル: test_dti.py プロジェクト: Anneef/pyAFQ-1
def test_cli():
    with nbtmp.InTemporaryDirectory() as tmpdir:
        fbval = op.join(tmpdir, 'dti.bval')
        fbvec = op.join(tmpdir, 'dti.bvec')
        fdata = op.join(tmpdir, 'dti.nii.gz')
        make_dti_data(fbval, fbvec, fdata)
        cmd = " ".join([
            "pyAFQ_dti", "-d",
            op.join(tmpdir, "dti.nii.gz"), "-l",
            op.join(tmpdir, "dti.bval"), "-c",
            op.join(tmpdir, "dti.bvec")
        ])
        out = os.system(cmd)
        assert out == 0
        assert op.exists(op.join(tmpdir, 'dti', 'dti_params.nii.gz'))
コード例 #4
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ファイル: test_scripts.py プロジェクト: jyeatman/pyAFQ
def test_fit_dti():
    with nbtmp.InTemporaryDirectory() as tmpdir:
        fbval = op.join(tmpdir, 'dti.bval')
        fbvec = op.join(tmpdir, 'dti.bvec')
        fdata = op.join(tmpdir, 'dti.nii.gz')
        make_dti_data(fbval, fbvec, fdata)
        cmd = ["pyAFQ_dti", "-d", fdata, "-l", fbval, "-c", fbvec,
               "-o", tmpdir, '-b', '0']
        out = runner.run_command(cmd)
        npt.assert_equal(out[0], 0)
        # Get expected values
        names = ['FA', 'MD', 'AD', 'RD']
        for n in names:
            fname = op.join(tmpdir, "dti_%s.nii.gz" % n)
            img = nib.load(fdata)
            affine = img.get_affine()
            shape = img.shape[:-1]
            assert_image_shape_affine(fname, shape, affine)
コード例 #5
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ファイル: test_scripts.py プロジェクト: Anneef/pyAFQ-1
def test_fit_dti():
    with nbtmp.InTemporaryDirectory() as tmpdir:
        fbval = op.join(tmpdir, 'dti.bval')
        fbvec = op.join(tmpdir, 'dti.bvec')
        fdata = op.join(tmpdir, 'dti.nii.gz')
        make_dti_data(fbval, fbvec, fdata)
        cmd = ["pyAFQ_dti", "-d", fdata, "-l", fbval, "-c", fbvec,
               "-o", tmpdir, '-b', '0']
        out = runner.run_command(cmd)
        npt.assert_equal(out[0], 0)
        # Get expected values
        names = ['FA', 'MD', 'AD', 'RD']
        for n in names:
            fname = op.join(tmpdir, "dti_%s.nii.gz" % n)
            img = nib.load(fdata)
            affine = img.affine
            shape = img.shape[:-1]
            assert_image_shape_affine(fname, shape, affine)
コード例 #6
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ファイル: test_scripts.py プロジェクト: jyeatman/pyAFQ
def test_predict_dti():
    with nbtmp.InTemporaryDirectory() as tmpdir:
        fbval = op.join(tmpdir, 'dti.bval')
        fbvec = op.join(tmpdir, 'dti.bvec')
        fdata = op.join(tmpdir, 'dti.nii.gz')
        make_dti_data(fbval, fbvec, fdata)
        cmd1 = ["pyAFQ_dti", "-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, "dti_params.nii.gz")
        cmd2 = ["pyAFQ_dti_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, "dti_prediction.nii.gz")).get_data()
        data = nib.load(op.join(tmpdir, "dti.nii.gz")).get_data()
        npt.assert_array_almost_equal(pred, data)
コード例 #7
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ファイル: test_scripts.py プロジェクト: Anneef/pyAFQ-1
def test_predict_dti():
    with nbtmp.InTemporaryDirectory() as tmpdir:
        fbval = op.join(tmpdir, 'dti.bval')
        fbvec = op.join(tmpdir, 'dti.bvec')
        fdata = op.join(tmpdir, 'dti.nii.gz')
        make_dti_data(fbval, fbvec, fdata)
        cmd1 = ["pyAFQ_dti", "-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, "dti_params.nii.gz")
        cmd2 = ["pyAFQ_dti_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, "dti_prediction.nii.gz")).get_fdata()
        data = nib.load(op.join(tmpdir, "dti.nii.gz")).get_fdata()
        npt.assert_array_almost_equal(pred, data)
コード例 #8
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def test_noise_from_b0():
    out_shape = (5, 6, 7)
    with nbtmp.InTemporaryDirectory() as tmpdir:
        # make artificial dti data
        fbval = op.join(tmpdir, 'dti.bval')
        fbvec = op.join(tmpdir, 'dti.bvec')
        fdata = op.join(tmpdir, 'dti.nii.gz')
        make_dti_data(fbval, fbvec, fdata, out_shape=out_shape)

        # make artifical mask
        mask = np.ones(out_shape)
        mask[0, 0, :] = 0

        # load data and mask
        bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
        img, data, gtab, mask = ut.prepare_data(fdata,
                                                fbval,
                                                fbvec,
                                                mask=mask,
                                                b0_threshold=50)

        # test noise_from_b0
        noise = dti.noise_from_b0(data, gtab, bvals, mask=mask)
        npt.assert_almost_equal(noise, 0)