Store lengths as strings.

xcp_d/cli/parser.py

@@ -967,9 +967,7 @@ def _validate_parameters(opts, build_log, parser):
         opts.confounds_config = (
             '36P' if (opts.confounds_config == 'auto') else opts.confounds_config
         )
-        opts.correlation_lengths = (
-            [] if opts.correlation_lengths is None else opts.correlation_lengths
-        )
+        opts.correlation_lengths = opts.correlation_lengths if opts.correlation_lengths else []
         opts.despike = True if (opts.despike == 'auto') else opts.despike
         opts.fd_thresh = 0.3 if (opts.fd_thresh == 'auto') else opts.fd_thresh
         opts.file_format = 'cifti' if (opts.file_format == 'auto') else opts.file_format
@@ -989,9 +987,7 @@ def _validate_parameters(opts, build_log, parser):
         opts.confounds_config = (
             '36P' if (opts.confounds_config == 'auto') else opts.confounds_config
         )
-        opts.correlation_lengths = (
-            [] if opts.correlation_lengths is None else opts.correlation_lengths
-        )
+        opts.correlation_lengths = opts.correlation_lengths if opts.correlation_lengths else []
         opts.despike = True if (opts.despike == 'auto') else opts.despike
         opts.fd_thresh = 0.3 if (opts.fd_thresh == 'auto') else opts.fd_thresh
         opts.file_format = 'cifti' if (opts.file_format == 'auto') else opts.file_format
@@ -1034,9 +1030,7 @@ def _validate_parameters(opts, build_log, parser):
         opts.confounds_config = (
             '36P' if (opts.confounds_config == 'auto') else opts.confounds_config
         )
-        opts.correlation_lengths = (
-            'all' if opts.correlation_lengths is None else opts.correlation_lengths
-        )
+        opts.correlation_lengths = opts.correlation_lengths if opts.correlation_lengths else 'all'
         opts.despike = True if (opts.despike == 'auto') else opts.despike
         opts.fd_thresh = 0 if (opts.fd_thresh == 'auto') else opts.fd_thresh
         opts.file_format = 'nifti' if (opts.file_format == 'auto') else opts.file_format
@@ -1056,9 +1050,7 @@ def _validate_parameters(opts, build_log, parser):
         if opts.confounds_config == 'auto':
             error_messages.append("'--nuisance-regressors' is required for 'none' mode.")
 
-        opts.correlation_lengths = (
-            [] if opts.correlation_lengths is None else opts.correlation_lengths
-        )
+        opts.correlation_lengths = opts.correlation_lengths if opts.correlation_lengths else []
 
         if opts.despike == 'auto':
             error_messages.append("'--despike' (y or n) is required for 'none' mode.")

xcp_d/cli/parser_utils.py

@@ -61,7 +61,7 @@ def _float_or_auto_or_none(string, is_parser=True):
 
     if floatarg < 0:
         raise error('Float argument must be nonnegative.')
-    return floatarg
+    return str(floatarg)
 
 
 def _restricted_float(x):

xcp_d/tests/test_cli_run.py

@@ -283,7 +283,7 @@ def test_validate_parameters_linc_mode(base_opts, base_parser, capsys):
     assert opts.correlation_lengths == ['all']
 
     # --create-matrices is not supported
-    opts.correlation_lengths = [300]
+    opts.correlation_lengths = ['300']
     with pytest.raises(SystemExit, match='2'):
         parser._validate_parameters(deepcopy(opts), build_log, parser=base_parser)
 
@@ -459,7 +459,7 @@ def test_build_parser_01(tmp_path_factory):
     opts = parser_obj.parse_args(args=test_args, namespace=None)
     assert opts.fmri_dir == data_path
     assert opts.output_dir == out_path
-    assert opts.correlation_lengths == ['all', 300, 480]
+    assert opts.correlation_lengths == ['all', '300', '480']
 
 
 def test_build_parser_02(tmp_path_factory):
@@ -496,7 +496,7 @@ def test_build_parser_02(tmp_path_factory):
     opts = parser_obj.parse_args(args=test_args, namespace=None)
     assert opts.fmri_dir == data_path
     assert opts.output_dir == out_path
-    assert opts.correlation_lengths == ['all', 300, 480]
+    assert opts.correlation_lengths == ['all', '300', '480']
 
 
 @pytest.mark.parametrize(

xcp_d/utils/doc.py

@@ -253,7 +253,7 @@
 """
 
 docdict['correlation_lengths'] = """
-correlation_lengths : :obj:`list` of :obj:`float`, optional
+correlation_lengths : :obj:`list` of :obj:`str`, optional
     If used, this parameter will produce correlation matrices limited to each requested
     amount of time.
     If there is more than the required amount of low-motion data,

xcp_d/utils/utils.py

@@ -602,3 +602,12 @@ def _create_mem_gb(bold_fname):
         mem_gbz['resampled'] = 3
 
     return mem_gbz
+
+
+def is_number(s):
+    """Check if a string is a number."""
+    try:
+        float(s)
+        return True
+    except ValueError:
+        return False

xcp_d/workflows/base.py

@@ -39,7 +39,7 @@
 )
 from xcp_d.utils.doc import fill_doc
 from xcp_d.utils.modified_data import calculate_exact_scans, flag_bad_run
-from xcp_d.utils.utils import estimate_brain_radius
+from xcp_d.utils.utils import estimate_brain_radius, is_number
 from xcp_d.workflows.anatomical.parcellation import init_parcellate_surfaces_wf
 from xcp_d.workflows.anatomical.surface import init_postprocess_surfaces_wf
 from xcp_d.workflows.anatomical.volume import init_postprocess_anat_wf
@@ -458,9 +458,7 @@ def init_single_subject_wf(subject_id: str):
 
             # Reduce exact_times to only include values greater than the post-scrubbing duration.
             exact_scans = []
-            if any(
-                isinstance(length, int | float) for length in config.workflow.correlation_lengths
-            ):
+            if any(is_number(length) for length in config.workflow.correlation_lengths):
                 exact_scans = calculate_exact_scans(
                     exact_times=config.workflow.correlation_lengths,
                     scan_length=post_scrubbing_duration,

xcp_d/workflows/bold/postprocessing.py

@@ -29,7 +29,7 @@
 )
 from xcp_d.utils.doc import fill_doc
 from xcp_d.utils.plotting import plot_design_matrix as _plot_design_matrix
-from xcp_d.utils.utils import fwhm2sigma
+from xcp_d.utils.utils import fwhm2sigma, is_number
 
 
 @fill_doc
@@ -327,7 +327,7 @@ def init_prepare_confounds_wf(
             ]),
         ])  # fmt:skip
 
-    if any(isinstance(length, int | float) for length in config.workflow.correlation_lengths):
+    if any(is_number(length) for length in config.workflow.correlation_lengths):
         random_censor = pe.Node(
             RandomCensor(exact_scans=exact_scans, random_seed=config.seeds.master),
             name='random_censor',