diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 18a8bb6b79984407701c08b18b2c9c2a83dfbb96..6ee756a17c0c7a0d9f1288ba79937d92ee462bc0 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -1,13 +1,14 @@
This document contains the FSL-MRS release history in reverse chronological order.
-2.4.2 (WIP)
--------------------------------
+2.4.2 (Monday 17th March 2025)
+------------------------------
- Added a `freeshift_lorentzian` model with inter-metabolite shifts (freeshift) and lorentzian lineshape.
- Added `freeshift` option to mrsi `fsl_mrsi` and dynamic `fsl_dynmrs` fitting scripts.
- Added option to show phase corrected spectum in the `fsl_mrs` HTML fitting report.
- Added option to suppress alignment step in `fsl_mrs_preproc{_edit}`.
- Changed syntax for water removal in `fsl_mrs_preproc{_edit}` from `--hlsvd` to `--remove-water`
- Changed syntax for truncation in `fsl_mrs_preproc{_edit}` from `--leftshift {N}` to `--truncate-fid {N}`
+- Basis sets are automatically conjugated when using `basis_tools shift_all`.
2.4.1 (Saturday 1st March 2025)
-------------------------------
diff --git a/fsl_mrs/core/mrs.py b/fsl_mrs/core/mrs.py
index 0904c529e913907b4a7dd48f702e98bb6ff1f176..4f692b2f0c2d686a15cf98389d60edcc75d8bbe5 100644
--- a/fsl_mrs/core/mrs.py
+++ b/fsl_mrs/core/mrs.py
@@ -587,12 +587,10 @@ class MRS(object):
if ppmlim is None:
ppmlim = self.default_ppm_range
- first, last = self.ppmlim_to_range(ppmlim)
- Spec1 = np.real(misc.FIDToSpec(self.FID))[first:last]
- Spec2 = np.real(misc.FIDToSpec(np.conj(self.FID)))[first:last]
-
- if np.linalg.norm(misc.detrend(Spec1, deg=4)) < \
- np.linalg.norm(misc.detrend(Spec2, deg=4)):
+ if misc.detect_conjugation(
+ self.FID,
+ self.ppmAxisShift,
+ ppmlim):
if repair is False:
warnings.warn('YOU MAY NEED TO CONJUGATE YOUR FID!!!')
return -1
@@ -620,27 +618,16 @@ class MRS(object):
if ppmlim is None:
ppmlim = self.default_ppm_range
- first, last = self.ppmlim_to_range(ppmlim)
-
- conjOrNot = []
- basis = self.basis
- for b in basis.T:
- Spec1 = np.real(misc.FIDToSpec(b))[first:last]
- Spec2 = np.real(misc.FIDToSpec(np.conj(b)))[first:last]
- if np.linalg.norm(misc.detrend(Spec1, deg=4)) < \
- np.linalg.norm(misc.detrend(Spec2, deg=4)):
- conjOrNot.append(1.0)
- else:
- conjOrNot.append(0.0)
-
- if (sum(conjOrNot) / len(conjOrNot)) > 0.5:
+ if misc.detect_conjugation(
+ self.basis.T,
+ self.ppmAxisShift,
+ ppmlim):
if repair is False:
warnings.warn('YOU MAY NEED TO CONJUGATE YOUR BASIS!!!')
return -1
else:
self.conj_Basis = True
return 1
-
return 0
# Plotting functions
diff --git a/fsl_mrs/scripts/basis_tools.py b/fsl_mrs/scripts/basis_tools.py
index 76e436dc4f80ab790929a994550f2f08700f0d3b..5e73c101581ebc9507e6dc97c4754c36a5546d96 100644
--- a/fsl_mrs/scripts/basis_tools.py
+++ b/fsl_mrs/scripts/basis_tools.py
@@ -345,14 +345,42 @@ def shift(args):
def all_shift(args):
from fsl_mrs.utils import basis_tools
from fsl_mrs.utils.mrs_io import read_basis
+ from fsl_mrs.utils.misc import detect_conjugation
import pandas as pd
import numpy as np
+ import json
+ from fsl_mrs.utils.constants import PPM_RANGE
basis = read_basis(args.file)
+
+ # Extract settings from the saved fitting arguments
+ with open(args.results_dir / 'options.txt', "r") as f:
+ fit_args = json.loads(f.readline())
+ ppmlims = fit_args['ppmlim'] if fit_args['ppmlim'] else PPM_RANGE['1H']
+
+ # Load fitting results
all_results = pd.read_csv(args.results_dir / 'all_parameters.csv', index_col=0)
shift_res = all_results.filter(regex='eps', axis=0)['mean'] / (2 * np.pi * basis.cf)
- for name, shift in zip(basis.names, shift_res.to_list()):
- basis = basis_tools.shift_basis(basis, name, shift)
+
+ # Apply shifts to each basis
+ # Currently this assumes that all basis spectra are used.
+ assert len(basis.names) == len(shift_res.to_list())
+
+ def apply_shifts(x):
+ for name, shift in zip(x.names, shift_res.to_list()):
+ x = basis_tools.shift_basis(x, name, shift)
+ return x
+
+ if detect_conjugation(
+ basis.original_basis_array.T,
+ basis.original_ppm_shift_axis,
+ ppmlims):
+ from fsl_mrs.utils.basis_tools import conjugate_basis
+ basis = conjugate_basis(basis)
+ basis = apply_shifts(basis)
+ basis = conjugate_basis(basis)
+ else:
+ basis = apply_shifts(basis)
basis.save(args.output, overwrite=True)
diff --git a/fsl_mrs/tests/test_utils_misc.py b/fsl_mrs/tests/test_utils_misc.py
index 374c7cb4e05ceb0d1e2c88a4aeb70dd14c3447d3..61395388ccfe60160eb1fab5a6dcd12c117a14f4 100644
--- a/fsl_mrs/tests/test_utils_misc.py
+++ b/fsl_mrs/tests/test_utils_misc.py
@@ -222,3 +222,31 @@ def test_create_peak():
gamma=10)
assert np.allclose(one_ppm + zero_ppm, both_peaks)
+
+
+def test_detect_conjugation():
+ FIDs, headers = synth.syntheticFID(
+ chemicalshift=[-2, -3])
+ FID = FIDs[0]
+ FIDs = np.stack((FIDs[0], FIDs[0], FIDs[0].conj()))
+
+ assert not misc.detect_conjugation(
+ FID,
+ headers['ppmaxis'],
+ (0, -4))
+ assert misc.detect_conjugation(
+ FID.conj(),
+ headers['ppmaxis'],
+ (0, -4))
+
+ assert misc.detect_conjugation(
+ FIDs.conj(),
+ headers['ppmaxis'],
+ (0, -4))
+
+ # Test wrong orientation of data raises error
+ with pytest.raises(ValueError):
+ misc.detect_conjugation(
+ FIDs.T,
+ headers['ppmaxis'],
+ (0, -4))
diff --git a/fsl_mrs/utils/misc.py b/fsl_mrs/utils/misc.py
index 2e1f03bf151ddc20568ce9f8392555a31a0fb5e1..448d876037f01663c7dcca5aac6ad606d6106df3 100644
--- a/fsl_mrs/utils/misc.py
+++ b/fsl_mrs/utils/misc.py
@@ -792,6 +792,44 @@ def parse_metab_groups(mrs, metab_groups):
return out
+def detect_conjugation(
+ data: np.ndarray,
+ ppmaxis: np.ndarray,
+ ppmlim: tuple) -> bool:
+ """Detect whether data should be conjugated based on
+ the amount of information content in ppm range.
+
+ :param data: FID or stack of FIDS (last dimension is time).
+ :type data: np.ndarray
+ :param ppmaxis: ppmaxis to match FFT of FID
+ :type ppmaxis: np.ndarray
+ :param ppmlim: Limits that define region of expected signal
+ :type ppmlim: tuple
+ :return: True if FIDs should be conjugated to maximise signal in limits.
+ :rtype: bool
+ """
+ if data.shape[-1] != ppmaxis.size:
+ raise ValueError("data's last dimension must matcht he size of ppmaxis.")
+
+ first, last = limit_to_range(ppmaxis, ppmlim)
+
+ def conj_or_not(x):
+ Spec1 = np.real(FIDToSpec(x))[first:last]
+ Spec2 = np.real(FIDToSpec(np.conj(x)))[first:last]
+ if np.linalg.norm(detrend(Spec1, deg=4)) < \
+ np.linalg.norm(detrend(Spec2, deg=4)):
+ return 1
+ else:
+ return 0
+
+ if data.ndim == 2:
+ return sum([conj_or_not(fid) for fid in data]) >= 0.5
+ elif data.ndim == 1:
+ return bool(conj_or_not(data))
+ else:
+ raise ValueError(f'data must have one or two dimensions, not {data.ndim}.')
+
+
# ----- MRSI stuff ---- #
def volume_to_list(data, mask):
"""