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Commit 353dbaae authored by William Clarke's avatar William Clarke
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Fix central frequency for synthetically made spectra and in proc tests.

parent e44e1f88
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fsl_mrs/tests/test_scripts_proc.py
View file @ 353dbaae
......@@ -17,7 +17,7 @@ import subprocess
@pytest.fixture
def svs_data(tmp_path):
reps = 3
noiseconv = 0.1*np.eye(reps)
noiseconv = 0.1 * np.eye(reps)
coilamps = np.ones(reps)
coilphs = np.zeros(reps)
FID, hdr = syntheticFID(noisecovariance=noiseconv,
......@@ -40,7 +40,7 @@ def svs_data(tmp_path):
@pytest.fixture
def mrsi_data(tmp_path):
reps = 3
noiseconv = 0.1*np.eye(reps)
noiseconv = 0.1 * np.eye(reps)
coilamps = np.ones(reps)
coilphs = np.zeros(reps)
FID, hdr = syntheticFID(noisecovariance=noiseconv,
......@@ -63,9 +63,9 @@ def mrsi_data(tmp_path):
@pytest.fixture
def svs_data_uncomb(tmp_path):
coils = 4
noiseconv = 0.1*np.eye(coils)
noiseconv = 0.1 * np.eye(coils)
coilamps = np.random.randn(coils)
coilphs = np.random.random(coils)*2*np.pi
coilphs = np.random.random(coils) * 2 * np.pi
FID, hdr = syntheticFID(noisecovariance=noiseconv,
coilamps=coilamps,
coilphase=coilphs)
......@@ -83,9 +83,9 @@ def svs_data_uncomb(tmp_path):
@pytest.fixture
def mrsi_data_uncomb(tmp_path):
coils = 4
noiseconv = 0.1*np.eye(coils)
noiseconv = 0.1 * np.eye(coils)
coilamps = np.random.randn(coils)
coilphs = np.random.random(coils)*2*np.pi
coilphs = np.random.random(coils) * 2 * np.pi
FID, hdr = syntheticFID(noisecovariance=noiseconv,
coilamps=coilamps,
coilphase=coilphs)
......@@ -103,7 +103,7 @@ def mrsi_data_uncomb(tmp_path):
@pytest.fixture
def svs_data_diff(tmp_path):
reps = 2
noiseconv = 0.1*np.eye(reps)
noiseconv = 0.1 * np.eye(reps)
coilamps = np.ones(reps)
coilphs = np.zeros(reps)
FID, hdr = syntheticFID(noisecovariance=noiseconv,
......@@ -140,7 +140,7 @@ def svs_data_diff(tmp_path):
@pytest.fixture
def mrsi_data_diff(tmp_path):
reps = 2
noiseconv = 0.1*np.eye(reps)
noiseconv = 0.1 * np.eye(reps)
coilamps = np.ones(reps)
coilphs = np.zeros(reps)
FID, hdr = syntheticFID(noisecovariance=noiseconv,
......@@ -300,7 +300,7 @@ def test_align(svs_data, mrsi_data, tmp_path):
allFileData = [d for d in svsdata]
directRun, _, _ = preproc.phase_freq_align(allFileData,
4000,
123E6,
123.2E6,
niter=2,
ppmlim=[-10.0, 10.0],
verbose=False,
......@@ -325,7 +325,7 @@ def test_align(svs_data, mrsi_data, tmp_path):
allFileData = [d[2, 2, 2, ...] for d in mrsidata[0:3]]
directRun, _, _ = preproc.phase_freq_align(allFileData,
4000,
123E6,
123.2E6,
niter=2,
ppmlim=[-10.0, 10.0],
verbose=False,
......@@ -393,8 +393,8 @@ def test_remove(svs_data, mrsi_data, tmp_path):
# Run using preproc.py directly
limits = (-10, 10)
directRun = preproc.hlsvd(svsdata[0],
1/4000,
123.0,
1 / 4000,
123.2,
limits,
limitUnits='ppm+shift')
......@@ -415,8 +415,8 @@ def test_remove(svs_data, mrsi_data, tmp_path):
# Run using preproc.py directly
limits = (-10, 10)
directRun = preproc.hlsvd(mrsidata[0][2, 2, 2, ...],
1/4000.0,
123.0,
1 / 4000.0,
123.2,
limits,
limitUnits='ppm+shift')
......@@ -425,9 +425,9 @@ def test_remove(svs_data, mrsi_data, tmp_path):
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]
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], \
......@@ -450,7 +450,7 @@ def test_align_diff(svs_data_diff, mrsi_data_diff, tmp_path):
directRun, _, _, _ = preproc.phase_freq_align_diff(svsdata1,
svsdata2,
4000,
123E6,
123.2E6,
ppmlim=[-10.0, 10.0])
assert np.isclose(data, directRun[0]).all()
......@@ -472,7 +472,7 @@ def test_fshift(svs_data, mrsi_data, tmp_path):
squeezeSVS=True)
# Run using preproc.py directly
directRun = preproc.freqshift(svsdata[0], 1/4000, 1.0*123)
directRun = preproc.freqshift(svsdata[0], 1 / 4000, 1.0 * 123.2)
assert np.allclose(data, directRun)
......@@ -493,7 +493,7 @@ def test_fshift(svs_data, mrsi_data, tmp_path):
directRun, _ = preproc.shiftToRef(svsdata[0],
4.0,
4000.0,
123E6,
123.2E6,
ppmlim=(-5.0, 5.0))
assert np.allclose(data, directRun)
......@@ -556,14 +556,14 @@ def test_fixed_phase(svs_data, mrsi_data, tmp_path):
# Run using numpy directly
directRun = preproc.applyPhase(svsdata[0],
(np.pi/180.0)*90)
(np.pi / 180.0) * 90)
directRun, newDT = preproc.timeshift(
directRun,
1/4000,
0.001,
0.001,
samples=directRun.size)
directRun,
1 / 4000,
0.001,
0.001,
samples=directRun.size)
assert np.allclose(data, directRun)
......@@ -582,13 +582,13 @@ def test_fixed_phase(svs_data, mrsi_data, tmp_path):
# Run using preproc.py directly
directRun = preproc.applyPhase(mrsidata[0][2, 2, 2, ...],
(np.pi/180.0)*90)
(np.pi / 180.0) * 90)
directRun, newDT = preproc.timeshift(
directRun,
1/4000,
0.001,
0.001,
samples=directRun.size)
directRun,
1 / 4000,
0.001,
0.001,
samples=directRun.size)
assert np.allclose(data[2, 2, 2, ...], directRun)
\ No newline at end of file
assert np.allclose(data[2, 2, 2, ...], directRun)
fsl_mrs/utils/synthetic/synthetic.py
View file @ 353dbaae
......@@ -14,7 +14,7 @@ def syntheticFID(coilamps=[1.0],
noisecovariance=[[0.1]],
bandwidth=4000,
points=2048,
centralfrequency=123.0,
centralfrequency=123.2,
chemicalshift=[-2, 3],
amplitude=[1.0, 1.0],
phase=[0, 0],
......
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