Write out correlations when --create-matrices doesn't include "all" (…

…#1326)

xcp_d/cli/parser.py

@@ -546,7 +546,7 @@ def _build_parser():
     g_dcan.add_argument(
         '--create-matrices',
         '--create_matrices',
-        dest='dcan_correlation_lengths',
+        dest='correlation_lengths',
         required=False,
         default=None,
         nargs='+',
@@ -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.dcan_correlation_lengths = (
-            [] if opts.dcan_correlation_lengths is None else opts.dcan_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
@@ -978,23 +976,18 @@ def _validate_parameters(opts, build_log, parser):
         opts.min_coverage = 0.5 if opts.min_coverage == 'auto' else opts.min_coverage
         if opts.motion_filter_type is None:
             error_messages.append(f"'--motion-filter-type' is required for '{opts.mode}' mode.")
-        opts.output_correlations = True if 'all' in opts.dcan_correlation_lengths else False
         if opts.output_type == 'censored':
             error_messages.append(f"'--output-type' cannot be 'censored' for '{opts.mode}' mode.")
         opts.output_type = 'interpolated'
         opts.process_surfaces = True if opts.process_surfaces == 'auto' else opts.process_surfaces
         opts.smoothing = 6 if opts.smoothing == 'auto' else opts.smoothing
-        # Remove "all" from the list of correlation lengths
-        opts.dcan_correlation_lengths = [c for c in opts.dcan_correlation_lengths if c != 'all']
     elif opts.mode == 'hbcd':
         opts.abcc_qc = True if (opts.abcc_qc == 'auto') else opts.abcc_qc
         opts.combine_runs = True if (opts.combine_runs == 'auto') else opts.combine_runs
         opts.confounds_config = (
             '36P' if (opts.confounds_config == 'auto') else opts.confounds_config
         )
-        opts.dcan_correlation_lengths = (
-            [] if opts.dcan_correlation_lengths is None else opts.dcan_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
@@ -1003,14 +996,11 @@ def _validate_parameters(opts, build_log, parser):
         opts.min_coverage = 0.5 if opts.min_coverage == 'auto' else opts.min_coverage
         if opts.motion_filter_type is None:
             error_messages.append(f"'--motion-filter-type' is required for '{opts.mode}' mode.")
-        opts.output_correlations = True if 'all' in opts.dcan_correlation_lengths else False
         if opts.output_type == 'censored':
             error_messages.append(f"'--output-type' cannot be 'censored' for '{opts.mode}' mode.")
         opts.output_type = 'interpolated'
         opts.process_surfaces = True if opts.process_surfaces == 'auto' else opts.process_surfaces
         opts.smoothing = 6 if opts.smoothing == 'auto' else opts.smoothing
-        # Remove "all" from the list of correlation lengths
-        opts.dcan_correlation_lengths = [c for c in opts.dcan_correlation_lengths if c != 'all']
     elif opts.mode == 'linc':
         opts.abcc_qc = False if (opts.abcc_qc == 'auto') else opts.abcc_qc
         opts.combine_runs = False if opts.combine_runs == 'auto' else opts.combine_runs
@@ -1023,37 +1013,33 @@ def _validate_parameters(opts, build_log, parser):
         opts.input_type = 'fmriprep' if opts.input_type == 'auto' else opts.input_type
         opts.linc_qc = True if (opts.linc_qc == 'auto') else opts.linc_qc
         opts.min_coverage = 0.5 if opts.min_coverage == 'auto' else opts.min_coverage
-        opts.output_correlations = True
         if opts.output_type == 'interpolated':
             error_messages.append(
                 f"'--output-type' cannot be 'interpolated' for '{opts.mode}' mode."
             )
         opts.output_type = 'censored'
         opts.process_surfaces = False if opts.process_surfaces == 'auto' else opts.process_surfaces
         opts.smoothing = 6 if opts.smoothing == 'auto' else opts.smoothing
-        if opts.dcan_correlation_lengths is not None:
+        if opts.correlation_lengths is not None:
             error_messages.append(f"'--create-matrices' is not supported for '{opts.mode}' mode.")
+        # Patch 'all' into the list of correlation lengths
+        opts.correlation_lengths = ['all']
     elif opts.mode == 'nichart':
         opts.abcc_qc = False if (opts.abcc_qc == 'auto') else opts.abcc_qc
         opts.combine_runs = False if opts.combine_runs == 'auto' else opts.combine_runs
         opts.confounds_config = (
             '36P' if (opts.confounds_config == 'auto') else opts.confounds_config
         )
-        opts.dcan_correlation_lengths = (
-            'all' if opts.dcan_correlation_lengths is None else opts.dcan_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
         opts.input_type = 'fmriprep' if opts.input_type == 'auto' else opts.input_type
         opts.linc_qc = True if (opts.linc_qc == 'auto') else opts.linc_qc
         opts.min_coverage = 0.4 if opts.min_coverage == 'auto' else opts.min_coverage
-        opts.output_correlations = True if 'all' in opts.dcan_correlation_lengths else False
         opts.output_type = 'censored' if opts.output_type == 'auto' else opts.output_type
         opts.process_surfaces = False if opts.process_surfaces == 'auto' else opts.process_surfaces
         opts.smoothing = 0 if opts.smoothing == 'auto' else opts.smoothing
-        # Remove "all" from the list of correlation lengths
-        opts.dcan_correlation_lengths = [c for c in opts.dcan_correlation_lengths if c != 'all']
     elif opts.mode == 'none':
         if opts.abcc_qc == 'auto':
             error_messages.append("'--abcc-qc' (y or n) is required for 'none' mode.")
@@ -1064,9 +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.dcan_correlation_lengths = (
-            [] if opts.dcan_correlation_lengths is None else opts.dcan_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.")
@@ -1090,8 +1074,6 @@ def _validate_parameters(opts, build_log, parser):
         if opts.motion_filter_type is None:
             error_messages.append("'--motion-filter-type' is required for 'none' mode.")
 
-        opts.output_correlations = True if 'all' in opts.dcan_correlation_lengths else False
-
         if opts.output_type == 'auto':
             error_messages.append("'--output-type' is required for 'none' mode.")
 
@@ -1103,9 +1085,6 @@ def _validate_parameters(opts, build_log, parser):
         if opts.smoothing == 'auto':
             error_messages.append("'--smoothing' is required for 'none' mode.")
 
-        # Remove "all" from the list of correlation lengths
-        opts.dcan_correlation_lengths = [c for c in opts.dcan_correlation_lengths if c != 'all']
-
     # Load the confound configuration file
     if opts.confounds_config == 'none':
         opts.confounds_config = None

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/config.py

@@ -562,8 +562,6 @@ class workflow(_Config):
     """Full-width at half-maximum (FWHM) of the smoothing kernel."""
     output_interpolated = None
     """Output interpolated data, not censored data."""
-    output_correlations = None
-    """Output correlations from censored data. This doesn't affect exact_scans."""
     combine_runs = None
     """Combine runs of the same task."""
     motion_filter_type = None
@@ -590,8 +588,10 @@ class workflow(_Config):
     """Order of the band-pass filter."""
     min_coverage = None
     """Coverage threshold to apply to parcels in each atlas."""
-    dcan_correlation_lengths = None
-    """Produce correlation matrices limited to each requested amount of time."""
+    correlation_lengths = None
+    """Produce correlation matrices limited to each requested amount of time.
+    If this list includes 'all' then correlations from the full (censored) time series will
+    be produced."""
     process_surfaces = None
     """Warp fsnative-space surfaces to the MNI space."""
     abcc_qc = None

xcp_d/data/tests/config.toml

@@ -47,7 +47,7 @@ low_pass = 0.1
 bpf_order = 2
 atlases = []
 min_coverage = 0.5
-dcan_correlation_lengths = []
+correlation_lengths = []
 process_surfaces = false
 abcc_qc = false