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)
