def test_conj(svs_data, mrsi_data, tmp_path):
""" Test fsl_mrs_proc conj"""
svsfile, mrsifile, svsdata, mrsidata = splitdata(svs_data, mrsi_data)
# Run remove on both sets of data using the command line
subprocess.check_call(['fsl_mrs_proc',
'conj',
'--file', svsfile[0],
'--output', tmp_path,
'--filename', 'tmp'])
# Load result for comparison
data, hdr = fsl_io.readNIFTI(op.join(tmp_path, 'tmp.nii.gz'),
squeezeSVS=True)
# Run using numpy directly
directRun = np.conj(svsdata[0])
assert np.allclose(data, directRun)
# Run coil combination on both sets of data using the command line
subprocess.check_call(['fsl_mrs_proc',
'conj',
'--file', mrsifile[0],
'--output', tmp_path,
'--filename', 'tmp'])
# Load result for comparison
data, hdr = fsl_io.readNIFTI(op.join(tmp_path, 'tmp.nii.gz'),
squeezeSVS=True)
# Run using preproc.py directly
directRun = np.conj(mrsidata[0][2, 2, 2, ...])
assert np.allclose(data[2, 2, 2, ...], directRun)
def test_fixed_phase(svs_data, mrsi_data, tmp_path):
""" Test fsl_mrs_proc fixed_phase"""
svsfile, mrsifile, svsdata, mrsidata = splitdata(svs_data, mrsi_data)
# Run remove on both sets of data using the command line
subprocess.check_call(['fsl_mrs_proc',
'fixed_phase',
'--file', svsfile[0],
'--p0', '90',
'--p1', '0.001',
'--output', tmp_path,
'--filename', 'tmp'])
# Load result for comparison
data, hdr = fsl_io.readNIFTI(op.join(tmp_path, 'tmp.nii.gz'),
squeezeSVS=True)
# Run using numpy directly
directRun = preproc.applyPhase(svsdata[0],
(np.pi/180.0)*90)
directRun, newDT = preproc.timeshift(
directRun,
1/4000,
0.001,
0.001,
samples=directRun.size)
assert np.allclose(data, directRun)
# Run coil combination on both sets of data using the command line
subprocess.check_call(['fsl_mrs_proc',
'fixed_phase',
'--file', mrsifile[0],
'--p0', '90',
'--p1', '0.001',
'--output', tmp_path,
'--filename', 'tmp'])
# Load result for comparison
data, hdr = fsl_io.readNIFTI(op.join(tmp_path, 'tmp.nii.gz'),
squeezeSVS=True)
# Run using preproc.py directly
directRun = preproc.applyPhase(mrsidata[0][2, 2, 2, ...],
(np.pi/180.0)*90)
directRun, newDT = preproc.timeshift(
directRun,
1/4000,
0.001,
0.001,
samples=directRun.size)
assert np.allclose(data[2, 2, 2, ...], directRun)
def test_align(svs_data, mrsi_data, tmp_path):
svsfile, mrsifile, svsdata, mrsidata = splitdata(svs_data, mrsi_data)
# Run align on both sets of data using the command line
subprocess.check_call(['fsl_mrs_proc',
'align',
'--file', svsfile[0], svsfile[1], svsfile[2],
'--ppm', '-10', '10',
'--output', tmp_path,
'--filename', 'tmp'])
# Load result for comparison
data, hdr = fsl_io.readNIFTI(op.join(tmp_path, 'tmp_000.nii.gz'),
squeezeSVS=True)
# Run using preproc.py directly
allFileData = [d for d in svsdata]
directRun, _, _ = preproc.phase_freq_align(allFileData,
4000,
123E6,
niter=2,
ppmlim=[-10.0, 10.0],
verbose=False,
target=None,
apodize=10)
assert np.allclose(data, directRun[0])
# Run coil combination on both sets of data using the command line
subprocess.check_call(['fsl_mrs_proc',
'align',
'--file', mrsifile[0], mrsifile[1], mrsifile[2],
'--ppm', '-10', '10',
'--output', tmp_path,
'--filename', 'tmp'])
# Load result for comparison
data, hdr = fsl_io.readNIFTI(op.join(tmp_path, 'tmp_000.nii.gz'),
squeezeSVS=True)
# Run using preproc.py directly
allFileData = [d[2, 2, 2, ...] for d in mrsidata[0:3]]
directRun, _, _ = preproc.phase_freq_align(allFileData,
4000,
123E6,
niter=2,
ppmlim=[-10.0, 10.0],
verbose=False,
target=None,
apodize=10)
assert np.allclose(data[2, 2, 2, ...], directRun[0],
atol=1E-1, rtol=1E-1)
def test_align_diff(svs_data_diff, mrsi_data_diff, tmp_path):
svsfile1, svsfile2, svsdata1, svsdata2 = svs_data_diff[0], \
svs_data_diff[1], \
svs_data_diff[2], \
svs_data_diff[3]
# mrsifile1, mrsifile2, mrsidata1, mrsidata2 = mrsi_data_diff[0], \
# mrsi_data_diff[1], \
# mrsi_data_diff[2], \
# mrsi_data_diff[3]
# Run alignment via commandline
subprocess.check_call(['fsl_mrs_proc',
'align-diff',
'--file', svsfile1[0], svsfile1[1],
'--reference', svsfile2[0], svsfile2[1],
'--ppm', '-10', '10',
'--output', tmp_path,
'--filename', 'tmp'])
# Load result for comparison
data, hdr = fsl_io.readNIFTI(op.join(tmp_path, 'tmp_000.nii.gz'),
squeezeSVS=True)
# Run using preproc.py directly
directRun, _, _, _ = preproc.phase_freq_align_diff(svsdata1,
svsdata2,
4000,
123E6,
ppmlim=[-10.0, 10.0])
assert np.isclose(data, directRun[0]).all()
def read_FID(filename, squeezeSVS=True):
"""
Read FID file. Tries to detect type automatically
Parameters
----------
filename : str
squeezeSVS : optional , bool Remove signleton dimensions in nifti load of svs
Returns:
--------
array-like (complex)
dict (header info)
"""
data_type = check_datatype(filename)
if data_type == 'RAW':
data, header = lcm.readLCModelRaw(filename)
elif data_type == 'NIFTI':
data, header = fsl.readNIFTI(filename, squeezeSVS=squeezeSVS)
elif data_type == 'TXT':
data, header = jmrui.readjMRUItxt(filename)
else:
raise ValueError(
f'Cannot read data format {data_type} for file {filename}.')
return data, header
def test_remove(svs_data, mrsi_data, tmp_path):
svsfile, mrsifile, svsdata, mrsidata = splitdata(svs_data, mrsi_data)
# Run remove on both sets of data using the command line
subprocess.check_call(['fsl_mrs_proc',
'remove',
'--file', svsfile[0],
'--ppm', '-10', '10',
'--output', tmp_path,
'--filename', 'tmp'])
# Load result for comparison
data, hdr = fsl_io.readNIFTI(op.join(tmp_path, 'tmp.nii.gz'),
squeezeSVS=True)
# Run using preproc.py directly
limits = (-10, 10)
directRun = preproc.hlsvd(svsdata[0],
1/4000,
123.0,
limits,
limitUnits='ppm+shift')
assert np.isclose(data, directRun).all()
# Run coil combination on both sets of data using the command line
subprocess.check_call(['fsl_mrs_proc',
'remove', '--file',
mrsifile[0],
'--ppm', '-10', '10',
'--output', tmp_path,
'--filename', 'tmp'])
# Load result for comparison
data, hdr = fsl_io.readNIFTI(op.join(tmp_path, 'tmp.nii.gz'),
squeezeSVS=True)
# Run using preproc.py directly
limits = (-10, 10)
directRun = preproc.hlsvd(mrsidata[0][2, 2, 2, ...],
1/4000.0,
123.0,
limits,
limitUnits='ppm+shift')
assert np.isclose(data[2, 2, 2, ...], directRun).all()
def test_filecreation(svs_data, mrsi_data, svs_data_uncomb, mrsi_data_uncomb):
svsfile, mrsifile, svsdata, mrsidata = splitdata(svs_data, mrsi_data)
data, hdr = fsl_io.readNIFTI(svsfile[0], squeezeSVS=False)
assert data.shape == (1, 1, 1, 2048)
assert np.isclose(data, svsdata[0]).all()
data, hdr = fsl_io.readNIFTI(mrsifile[0], squeezeSVS=False)
assert data.shape == (3, 3, 3, 2048)
assert np.isclose(data, mrsidata[0]).all()
svsfile, mrsifile, svsdata, mrsidata = splitdata(svs_data_uncomb,
mrsi_data_uncomb)
data, hdr = fsl_io.readNIFTI(svsfile, squeezeSVS=False)
assert data.shape == (1, 1, 1, 2048, 4)
assert np.isclose(data, svsdata).all()
data, hdr = fsl_io.readNIFTI(mrsifile, squeezeSVS=False)
assert data.shape == (3, 3, 3, 2048, 4)
assert np.isclose(data, mrsidata).all()
def test_fshift(svs_data, mrsi_data, tmp_path):
svsfile, mrsifile, svsdata, mrsidata = splitdata(svs_data, mrsi_data)
subprocess.check_call(['fsl_mrs_proc',
'fshift',
'--file', svsfile[0],
'--shiftppm', '1.0',
'--output', tmp_path,
'--filename', 'tmp'])
# Load result for comparison
data, hdr = fsl_io.readNIFTI(op.join(tmp_path, 'tmp.nii.gz'),
squeezeSVS=True)
# Run using preproc.py directly
directRun = preproc.freqshift(svsdata[0], 1/4000, 1.0*123)
assert np.allclose(data, directRun)
subprocess.check_call(['fsl_mrs_proc',
'fshift',
'--file', svsfile[0],
'--shiftRef',
'--ppm', '-5.0', '5.0',
'--target', '4.0',
'--output', tmp_path,
'--filename', 'tmp'])
# Load result for comparison
data, hdr = fsl_io.readNIFTI(op.join(tmp_path, 'tmp.nii.gz'),
squeezeSVS=True)
# Run using preproc.py directly
directRun, _ = preproc.shiftToRef(svsdata[0],
4.0,
4000.0,
123E6,
ppmlim=(-5.0, 5.0))
assert np.allclose(data, directRun)
def test_average(svs_data, mrsi_data, tmp_path):
svsfile, mrsifile, svsdata, mrsidata = splitdata(svs_data, mrsi_data)
# Run coil combination on both sets of data using the command line
subprocess.check_call(['fsl_mrs_proc',
'average',
'--file', svsfile[0], svsfile[1], svsfile[2],
'--avgfiles',
'--output', tmp_path,
'--filename', 'tmp'])
# Load result for comparison
data, hdr = fsl_io.readNIFTI(op.join(tmp_path, 'tmp.nii.gz'),
squeezeSVS=True)
# Run using preproc.py directly
allFileData = np.array([d for d in svsdata])
directRun = preproc.combine_FIDs(allFileData.T, 'mean')
assert np.isclose(data, directRun).all()
# Run coil combination on both sets of data using the command line
subprocess.check_call(['fsl_mrs_proc',
'average',
'--file', mrsifile[0], mrsifile[1], mrsifile[2],
'--avgfiles',
'--output', tmp_path,
'--filename', 'tmp'])
# Load result for comparison
data, hdr = fsl_io.readNIFTI(op.join(tmp_path, 'tmp.nii.gz'),
squeezeSVS=True)
# Run using preproc.py directly
allFileData = np.array([d for d in mrsidata])
directRun = preproc.combine_FIDs(allFileData.T, 'mean')
assert np.isclose(data, directRun).all()
def test_coilcombine(svs_data_uncomb, mrsi_data_uncomb, tmp_path):
svsfile, mrsifile, svsdata, mrsidata = splitdata(svs_data_uncomb,
mrsi_data_uncomb)
# Run coil combination on both sets of data using the command line
subprocess.check_call(['fsl_mrs_proc',
'coilcombine',
'--file', svsfile,
'--output', tmp_path,
'--filename', 'tmp'])
# Load result for comparison
data, hdr = fsl_io.readNIFTI(op.join(tmp_path, 'tmp.nii.gz'),
squeezeSVS=True)
# Run using preproc.py directly
directRun = preproc.combine_FIDs(svsdata[0, 0, 0, ...],
'svd',
do_prewhiten=True)
assert np.isclose(data, directRun).all()
# Run coil combination on both sets of data using the command line
subprocess.check_call(['fsl_mrs_proc',
'coilcombine',
'--file', mrsifile,
'--output', tmp_path,
'--filename', 'tmp'])
# Load result for comparison
data, hdr = fsl_io.readNIFTI(op.join(tmp_path, 'tmp.nii.gz'),
squeezeSVS=True)
# Run using preproc.py directly
directRun = preproc.combine_FIDs(mrsidata[2, 2, 2, ...], 'svd',
do_prewhiten=True)
assert np.isclose(data[2, 2, 2, ...], directRun).all()
def test_ecc(svs_data, mrsi_data, tmp_path):
svsfile, mrsifile, svsdata, mrsidata = splitdata(svs_data, mrsi_data)
# Run coil combination on both sets of data using the command line
subprocess.check_call(['fsl_mrs_proc',
'ecc',
'--file', svsfile[0],
'--reference', svsfile[1],
'--output', tmp_path,
'--filename', 'tmp'])
# Load result for comparison
data, hdr = fsl_io.readNIFTI(op.join(tmp_path, 'tmp.nii.gz'),
squeezeSVS=True)
# Run using preproc.py directly
directRun = preproc.eddy_correct(svsdata[0], svsdata[1])
assert np.isclose(data, directRun).all()
# Run coil combination on both sets of data using the command line
subprocess.check_call(['fsl_mrs_proc',
'ecc',
'--file', mrsifile[0],
'--reference', mrsifile[1],
'--output', tmp_path,
'--filename', 'tmp'])
# Load result for comparison
data, hdr = fsl_io.readNIFTI(op.join(tmp_path, 'tmp.nii.gz'),
squeezeSVS=True)
# Run using preproc.py directly
directRun = preproc.eddy_correct(mrsidata[0][2, 2, 2, ...],
mrsidata[1][2, 2, 2, ...])
assert np.isclose(data[2, 2, 2, ...], directRun).all()
