Merge branch 'bf/dyn_mh_reslist' into 'master'

BF/ENH: Minor fixes post 2.0

See merge request fsl/fsl_mrs!57

CHANGELOG.rst

 This document contains the FSL-MRS release history in reverse chronological order.
 
+2.0.1 (Thursday 28th July 2022)
+-------------------------------
+- Fix results list generation from metropolis hastings dynamic optimisation
+- Fix bug in fsl_mrs_summarise that would stop data with a disabled baseline (order = -1) working.
+- Added conversion of jMRUI basis sets to basis_tools convert.
+- --mask argument no longer mandatory for fsl_mrsi.
+- Fixed bugs in mrsi_segment, auto run fsl_anat now work and qform copied to sform for MRSI in cases with small differences.
+
 2.0.0 (Wednesday 6th July 2022)
 -------------------------------
 **Major rework of basis and fitting script interaction. First release of dynamic MRS fitting.**  

fsl_mrs/dynamic/dyn_results.py

@@ -572,7 +572,7 @@ class dynRes_mcmc(dynRes):
         :return: List of FitRes objects.
         :rtype: list
         """
-        return self._dyn.form_FitRes(self.dataframe.to_numpy(), 'MH')
+        return self._dyn.form_FitRes(self.dataframe_free.to_numpy(), 'MH')
 
     @property
     def cov_free(self):

fsl_mrs/scripts/basis_tools.py

@@ -248,12 +248,18 @@ def convert(args):
 
     if args.input.is_file():
         basis_tools.convert_lcm_basis(args.input, args.output)
-    elif args.input.is_dir():
+    elif args.input.is_dir()\
+            and (len(list(args.input.glob('*.raw'))) > 0 or len(list(args.input.glob('*.RAW'))) > 0):
         basis_tools.convert_lcm_raw_basis(
             args.input,
             args.bandwidth,
             args.fieldstrength * GYRO_MAG_RATIO['1H'],
             args.output)
+    elif args.input.is_dir()\
+            and len(list(args.input.glob('*.txt'))) > 0:
+        basis_tools.convert_jmrui_basis(
+            args.input,
+            args.output)
 
     if args.remove_reference:
         # TODO sort this conjugation mess out.

fsl_mrs/scripts/fsl_mrs_proc.py

@@ -80,8 +80,9 @@ def main():
     avg_group = avgparser.add_argument_group('average arguments')
     avg_group.add_argument('--file', type=str, required=True,
                            help='MRS file(s)')
-    avg_group.add_argument('--dim', type=str,
-                           help='Select dimension to average across')
+    avg_group.add_argument('--dim', type=str, default='DIM_DYN',
+                           help='Select dimension to average across. '
+                                'Should be a NIfTI-MRS dimension tag, e.g. DIM_DYN (default)')
     avgparser.set_defaults(func=average)
     add_common_args(avgparser)
 

fsl_mrs/scripts/fsl_mrs_summarise.py

@@ -112,6 +112,8 @@ def main():
         # Generate metabolite groups
         metab_groups = misc.parse_metab_groups(mrs, orig_args['metab_groups'])
         baseline_order = orig_args['baseline_order']
+        if baseline_order < 0:
+            baseline_order = 0  # Required to make prepare_baseline_regressor run.
         ppmlim = orig_args['ppmlim']
         # Generate baseline polynomials (B)
         B = prepare_baseline_regressor(mrs, baseline_order, ppmlim)

fsl_mrs/scripts/fsl_mrsi.py

@@ -36,14 +36,14 @@ def main():
     required.add_argument('--basis',
                           required=True, type=str, metavar='<str>',
                           help='Basis file or folder')
-    required.add_argument('--mask',
-                          required=True, type=str, metavar='<str>',
-                          help='mask volume')
     required.add_argument('--output',
                           required=True, type=str, metavar='<str>',
                           help='output folder')
 
     # FITTING ARGUMENTS
+    fitting_args.add_argument('--mask',
+                              type=str, metavar='<str>',
+                              help='Optional NIfTI binary mask of voxels to fit.')
     fitting_args.add_argument('--algo', default='Newton', type=str,
                               help='algorithm [Newton (fast, default)'
                                    ' or MH (slow)]')

fsl_mrs/scripts/mrsi_segment.py

@@ -46,7 +46,7 @@ def main():
         return str(pathlib_path.resolve())
 
     # If not prevented run fsl_anat for fast segmentation
-    if (args.anat is None) and (not args.mask_only):
+    if args.anat is None:
         anat = args.output  / 'fsl_anat'
         fsl_anat(
             str_resolve_path(args.t1),
@@ -61,6 +61,10 @@ def main():
     tmp_img = np.zeros(mrsi_in.shape[0:3])
     tmp_img = Image(tmp_img, xform=mrsi_in.voxToWorldMat)
 
+    # HACK because applywarp is shite - Paul McCarthy 2022 ;-)
+    tmp_img.header.set_sform(tmp_img.header.get_qform())
+    # Can remove in FSL 6.1.0 when applywarp is fixed
+
     # Register the pvseg to the MRSI data using flirt
     def applywarp_func(i, o):
         applywarp(str_resolve_path(i),

fsl_mrs/tests/test_dynamic_dyn_results.py

@@ -155,6 +155,9 @@ def test_dynRes_mcmc(fixed_ratio_mrs):
     assert isinstance(res_obj.dataframe_mapped, pd.DataFrame)
     assert res_obj.dataframe_mapped.shape == (2, 8)
 
+    assert isinstance(res_obj.reslist, list)
+    assert len(res_obj.reslist) == 2
+
 
 def test_load_save(fixed_ratio_mrs, tmp_path):
     mrs_list = fixed_ratio_mrs

fsl_mrs/tests/test_scripts_basis_tools.py

@@ -20,6 +20,7 @@ mac = testsPath / 'testdata/basis_tools/macSeed.json'
 diff1 = testsPath / 'testdata/basis_tools/low_res_off'
 diff2 = testsPath / 'testdata/basis_tools/low_res_on'
 raw = testsPath / 'testdata/basis_tools/RawBasis_for_PRESSGE_TE_35_BW_4000_NPts_2048'
+jmrui_basis_path = testsPath / 'testdata' / 'mrs_io' / 'basisset_JMRUI'
 
 
 def test_info():
@@ -55,6 +56,17 @@ def test_convert_raw(tmp_path):
     assert (tmp_path / 'new_raw' / 'NAA.json').is_file()
 
 
+def test_convert_jmrui(tmp_path):
+    subprocess.check_call(['basis_tools', 'convert',
+                           str(jmrui_basis_path),
+                           '--bandwidth', '4000',
+                           '--fieldstrength', '3.0',
+                           str(tmp_path / 'new_jmrui')])
+
+    assert (tmp_path / 'new_jmrui').is_dir()
+    assert (tmp_path / 'new_jmrui' / 'NAA.json').is_file()
+
+
 def test_convert_with_remove(tmp_path):
     subprocess.check_call(['basis_tools', 'convert',
                            '--remove_reference',

fsl_mrs/tests/test_utils_basis_tools.py

@@ -19,6 +19,7 @@ testsPath = Path(__file__).parent
 fsl_basis_path = testsPath / 'testdata' / 'fsl_mrs' / 'steam_basis'
 lcm_basis_path = testsPath / 'testdata' / 'basis_tools' / '3T_slaser_32vespa_1250.BASIS'
 raw_basis_path = testsPath / 'testdata' / 'basis_tools' / 'RawBasis_for_PRESSGE_TE_35_BW_4000_NPts_2048'
+jmrui_basis_path = testsPath / 'testdata' / 'mrs_io' / 'basisset_JMRUI'
 extra_basis = testsPath / 'testdata' / 'basis_tools' / 'macSeed.json'
 
 
@@ -51,6 +52,17 @@ def test_convert_raw(tmp_path):
     assert new_basis.original_basis_array.shape == (2048, 3)
 
 
+def test_convert_jmrui(tmp_path):
+    out_loc = tmp_path / 'test_basis_jmrui'
+    basis_tools.convert_jmrui_basis(
+        jmrui_basis_path,
+        out_loc)
+
+    new_basis = mrs_io.read_basis(out_loc)
+
+    assert new_basis.original_basis_array.shape == (2048, 21)
+
+
 def test_add_basis():
     basis = mrs_io.read_basis(fsl_basis_path)
 

fsl_mrs/utils/basis_tools.py

@@ -86,6 +86,19 @@ def convert_lcm_raw_basis(path_to_basis, bandwidth, central_frequency, output_lo
         basis.save(output_location, info_str=sim_info)
 
 
+def convert_jmrui_basis(indir, outdir):
+    """Convert a directory of jMRUI formatted basis files (.txt) to FSL-MRS format.
+
+    :param indir: input directory
+    :type indir: pathlib.Path
+    :param outdir: output location
+    :type outdir: pathlib.Path
+    """
+    from fsl_mrs.utils import mrs_io
+    in_basis = mrs_io.read_basis(indir)
+    in_basis.save(outdir)
+
+
 def add_basis(fid, name, cf, bw, target, scale=False, width=None, conj=False, pad=False):
     """Add an additional basis spectrum to an existing FSL formatted basis set.