Merge branch 'enh/improved_preproc_edit' into 'master'

Enh: Improved preproc edit

See merge request !40

CHANGELOG.rst

 This document contains the FSL-MRS release history in reverse chronological order.
 
+1.1.10 (WIP)
+----------------------------------
+- Updates to fsl_mrs_preproc_edit
+- Updated install documentation.
+
 1.1.9 (Tuesday 30th November 2021)
 ----------------------------------
 - Fixed typos in fsl_mrs_proc help.

docs/user_docs/install.rst

@@ -27,6 +27,14 @@ The primary installation method is via *conda*. After installing conda and creat
                   -c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/ \
                   fsl_mrs
 
+To check the version installed run :code:`fsl_mrs --version`. FSL-MRS can be updated by running :code:`conda update`:
+
+::
+
+    conda update -c conda-forge -c defaults \
+                  -c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/ \
+                  fsl_mrs
+
 Example data with conda
 -----------------------
 Installation with conda is easy, but you won't get the packaged example data and notebooks. This can be downloaded separately here: |fslmrs_pkg_data|_.

fsl_mrs/scripts/fsl_mrs_preproc_edit

@@ -55,15 +55,17 @@ def main():
                           help='Apply HLSVD for residual water removal.')
     optional.add_argument('--dynamic_align', action="store_true",
                           help='Align spectra based on dynamic fitting. Must specify dynamic basis sets.')
+    optional.add_argument('--dynamic_align_edit', action="store_true",
+                          help='Align conditions based on dynamic fitting. Must specify dynamic basis sets.')
     optional.add_argument('--dynamic_basis', type=str, nargs=2,
                           help='Paths to the two editing condition basis sets. '
                           'Only needed if --dynamic_align is specified.')
     optional.add_argument('--leftshift', type=int, metavar='POINTS',
                           help='Remove points at the start of the fid.')
-    optional.add_argument('--dynamic_align_ppm', type=float, nargs=2, default=(1.9, 4.2),
+    optional.add_argument('--align_ppm_dynamic', type=float, nargs=2, default=(1.9, 4.2),
                           help='PPM limit for dynamics dimension alignment. Default=(0.0, 4.2).')
-    optional.add_argument('--edit_align_ppm', type=float, nargs=2, default=(2.5, 4.2),
-                          help='PPM limit for edit dimension alignment. Default=(2.5, 4.2).')
+    optional.add_argument('--align_ppm_edit', type=float, nargs=2, default=None,
+                          help='PPM limit for edit dimension alignment. Default=full spectrum.')
     optional.add_argument('--t1', type=str, default=None, metavar='IMAGE',
                           help='structural image (for report)')
     optional.add_argument('--verbose', action="store_true",
@@ -212,7 +214,7 @@ def main():
     supp_data = nifti_mrs_proc.align(
         supp_data,
         'DIM_DYN',
-        ppmlim=args.dynamic_align_ppm,
+        ppmlim=args.align_ppm_dynamic,
         niter=4,
         apodize=0.0,
         report=report_dir,
@@ -319,12 +321,12 @@ def main():
         final_wref = nifti_mrs_proc.phase_correct(ref_data, (4.55, 4.7), hlsvd=False, report=report_dir)
 
     # Align between edit dimension
-    if args.dynamic_align and args.average:
+    if args.dynamic_align_edit and args.average:
         metab_edit_align, eps, phi = dproc.align_by_dynamic_fit(supp_data, [basis_0, basis_1], fitargs_1)
         if report_dir is not None:
             dproc.align_by_dynamic_fit_report(supp_data, metab_edit_align, eps, phi, html=report_dir)
 
-    elif args.dynamic_align:
+    elif args.dynamic_align_edit:
         # Do not average and dynamic alignment
         # Work out alignement on averaged data
         supp_data_avg = nifti_mrs_proc.average(supp_data, 'DIM_DYN')
@@ -345,9 +347,9 @@ def main():
         metab_edit_align = nifti_mrs_proc.align(
             supp_data,
             'DIM_EDIT',
-            ppmlim=args.edit_align_ppm,
+            ppmlim=args.align_ppm_edit,
             niter=4,
-            apodize=0.0,
+            apodize=10.0,
             report=report_dir)
 
     # Differencing

fsl_mrs/tests/test_scripts_preproc_edit.py

@@ -14,6 +14,37 @@ data = testsPath / 'testdata/fsl_mrs_preproc_edit'
 t1 = str(testsPath / 'testdata/svs_segment/T1.anat/T1_biascorr.nii.gz')
 
 
+def test_preproc_defaults(tmp_path):
+
+    metab = str(data / 'metab_raw.nii.gz')
+    wrefc = str(data / 'wref_internal.nii.gz')
+    wrefq = str(data / 'wref_quant.nii.gz')
+    ecc = str(data / 'wref_internal.nii.gz')
+
+    retcode = subprocess.check_call(
+        ['fsl_mrs_preproc_edit',
+         '--output', str(tmp_path),
+         '--data', metab,
+         '--reference', wrefc,
+         '--quant', wrefq,
+         '--ecc', ecc,
+         '--t1', t1,
+         '--hlsvd',
+         '--leftshift', '2',
+         '--overwrite',
+         '--report',
+         '--verbose'])
+
+    assert retcode == 0
+    assert (tmp_path / 'diff.nii.gz').exists()
+    assert (tmp_path / 'edit_0.nii.gz').exists()
+    assert (tmp_path / 'edit_1.nii.gz').exists()
+    assert (tmp_path / 'wref.nii.gz').exists()
+    assert (tmp_path / 'options.txt').exists()
+    assert (tmp_path / 'mergedReports.html').exists()
+    assert (tmp_path / 'voxel_location.png').exists()
+
+
 def test_preproc(tmp_path):
 
     metab = str(data / 'metab_raw.nii.gz')
@@ -29,8 +60,8 @@ def test_preproc(tmp_path):
          '--quant', wrefq,
          '--ecc', ecc,
          '--t1', t1,
-         '--dynamic_align_ppm', '1.8', '4.2',
-         '--edit_align_ppm', '2.5', '4.2',
+         '--align_ppm_dynamic', '1.8', '4.2',
+         '--align_ppm_edit', '2.5', '4.2',
          '--hlsvd',
          '--leftshift', '2',
          '--overwrite',
@@ -62,8 +93,8 @@ def test_preproc_noavg(tmp_path):
          '--quant', wrefq,
          '--ecc', ecc,
          '--t1', t1,
-         '--dynamic_align_ppm', '1.8', '4.2',
-         '--edit_align_ppm', '2.5', '4.2',
+         '--align_ppm_dynamic', '1.8', '4.2',
+         '--align_ppm_edit', '2.5', '4.2',
          '--leftshift', '2',
          '--overwrite',
          '--report',