👔 Make nuisance regression space non-forkable

CHANGELOG.md

@@ -44,6 +44,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Uses highest resolution available locally as reference when resampling a template to a non-packaged resolution (was always using 1mm reference before)
 - Updates config boolean validation from anything-truthy-is-True (e.g., `[True, False]`, or `[False]`, or a typo like `Offf`) to only accepting bools, ints, and YAML boolean strings like "On" and "Off" as boolean
 - When applying a filter to motion parameters, now C-PAC reports both the original and the filtered motion parameters and uses the original parameters for qc. Previous versions only reported the filtered parameters and used the filtered parameters for qc.
+- Makes nuisance regression space non-forkable. In v1.8.5, nuisance regression forking was broken, so this change should not cause backwards-compatibility issues.
 
 ### Added dependencies
 

CPAC/nuisance/nuisance.py

@@ -94,11 +94,11 @@ def choose_nuisance_blocks(cfg, rpool, generate_only=False):
             nuisance.append((nuisance_regressors_generation_EPItemplate,
                              input_interface))
 
-        if not generate_only and 'native' in cfg['nuisance_corrections',
-                                                 '2-nuisance_regression',
-                                                 'space']:
+        if not generate_only and cfg['nuisance_corrections',
+                                     '2-nuisance_regression',
+                                     'space'] == 'native':
             nuisance.append((nuisance_regression_native, input_interface))
-    
+
     return nuisance
 
 

CPAC/pipeline/cpac_pipeline.py

@@ -1356,7 +1356,7 @@ def build_workflow(subject_id, sub_dict, cfg, pipeline_name=None,
 
     pipeline_blocks += [func_despike_template]
 
-    if 'Template' in target_space_alff and 'Native' in target_space_nuis:
+    if 'Template' in target_space_alff and target_space_nuis == 'native':
         pipeline_blocks += [warp_denoiseNofilt_to_T1template]
 
     template = cfg.registration_workflows['functional_registration'][
@@ -1392,9 +1392,8 @@ def build_workflow(subject_id, sub_dict, cfg, pipeline_name=None,
                             warp_deriv_mask_to_EPItemplate]
 
     # Template-space nuisance regression
-    nuisance_template = 'template' in cfg[
-        'nuisance_corrections', '2-nuisance_regression', 'space'
-    ] and not generate_only
+    nuisance_template = (cfg['nuisance_corrections', '2-nuisance_regression',
+                             'space'] == 'template') and (not generate_only)
     if nuisance_template:
         pipeline_blocks += [nuisance_regression_template]
         # pipeline_blocks += [(nuisance_regression_template,

CPAC/pipeline/schema.py

@@ -22,11 +22,11 @@
 import numpy as np
 from pathvalidate import sanitize_filename
 from voluptuous import All, ALLOW_EXTRA, Any, BooleanInvalid, Capitalize, \
-                       Coerce, ExclusiveInvalid, In, Length, LengthInvalid, \
-                       Lower, Match, Maybe, Optional, Range, Required, \
-                       Schema, Title
+                       Coerce, CoerceInvalid, ExclusiveInvalid, In, Length, \
+                       LengthInvalid, Lower, Match, Maybe, MultipleInvalid, \
+                       Optional, Range, Required, Schema, Title
 from CPAC import docs_prefix
-from CPAC.utils.datatypes import ListFromItem
+from CPAC.utils.datatypes import ItemFromList, ListFromItem
 from CPAC.utils.utils import YAML_BOOLS
 
 # 1 or more digits, optional decimal, 'e', optional '-', 1 or more digits
@@ -134,6 +134,8 @@ def str_to_bool1_1(x):  # pylint: disable=invalid-name
     },
     'target_space': ['Native', 'Template']
 }
+valid_options['space'] = list({option.lower() for option in
+                               valid_options['target_space']})
 mutex = {  # mutually exclusive booleans
     'FSL-BET': {
         # exactly zero or one of each of the following can be True for FSL-BET
@@ -886,8 +888,8 @@ def sanitize(filename):
         },
         '2-nuisance_regression': {
             'run': forkable,
-            'space': All(Coerce(ListFromItem),
-                         [All(Lower, In({'native', 'template'}))]),
+            'space': All(Coerce(ItemFromList),
+                         Lower, In({'native', 'template'})),
             'create_regressors': bool1_1,
             'ingress_regressors': {
                 'run': bool1_1,
@@ -1096,7 +1098,17 @@ def schema(config_dict):
     dict
     '''
     from CPAC.utils.utils import _changes_1_8_0_to_1_8_1
-    partially_validated = latest_schema(_changes_1_8_0_to_1_8_1(config_dict))
+    try:
+        partially_validated = latest_schema(
+            _changes_1_8_0_to_1_8_1(config_dict))
+    except MultipleInvalid as multiple_invalid:
+        if (multiple_invalid.path == ['nuisance_corrections',
+                                      '2-nuisance_regression', 'space'] and
+                isinstance(multiple_invalid.errors[0], CoerceInvalid)):
+            raise CoerceInvalid(
+                'Nusiance regression space is not forkable. Please choose '
+                f'only one of {valid_options["space"]}',
+                path=multiple_invalid.path) from multiple_invalid
     try:
         if (partially_validated['registration_workflows'][
             'functional_registration'
@@ -1110,7 +1122,7 @@ def schema(config_dict):
             if True in partially_validated['nuisance_corrections'][
                 '2-nuisance_regression']['run'] and partially_validated[
                 'nuisance_corrections'
-            ]['2-nuisance_regression']['space'] != ['template']:
+            ]['2-nuisance_regression']['space'] != 'template':
                 raise ExclusiveInvalid(
                     '``single_step_resampling_from_stc`` requires '
                     'template-space nuisance regression. Either set '

CPAC/resources/configs/pipeline_config_default.yml

@@ -1367,13 +1367,12 @@ nuisance_corrections:
     #   run: [On, Off] - this will run both and fork the pipeline
     run: [On]
 
-    # this is a fork point
+    # this is not a fork point
     # Run nuisance regression in native or template space
-    #   - If set to [native, template], the number of outputs will be double what it would be if only one space were chosen. Nuisance regression will only be run once per fork.
     #   - If set to template, will use the brain mask configured in
     #     ``functional_preproc: func_masking: FSL_AFNI: brain_mask``
-    #   - If ``registration_workflows: functional_registration: func_registration_to_template: apply_trasnform: using: single_step_resampling_from_stc``, this must only be set to template
-    space: [native]
+    #   - If ``registration_workflows: functional_registration: func_registration_to_template: apply_trasnform: using: single_step_resampling_from_stc``, this must be set to template
+    space: native
 
     # switch to Off if nuisance regression is off and you don't want to write out the regressors
     create_regressors: On

CPAC/utils/datatypes.py

@@ -1,4 +1,32 @@
 """Custom datatypes for C-PAC"""
+class ItemFromList:  # pylint: disable=too-few-public-methods
+    """Coerce single-item lists into just the only item in the list.
+    Returns item if item is not a list, set, or tuple.
+    Raises CoerceInvalid if impossible.
+
+    Examples
+    --------
+    >>> ItemFromList(['seagull'])
+    'seagull'
+    >>> ItemFromList(['two', 'seagulls'])
+    Traceback (most recent call last):
+        ...
+    voluptuous.error.CoerceInvalid: Cannot coerce list of length 2 to item
+    >>> ItemFromList('string')
+    'string'
+    """
+    def __new__(cls, list_of_one, msg=None):
+        """Initialize item from list"""
+        from voluptuous import CoerceInvalid, Length, LengthInvalid
+        if not isinstance(list_of_one, (list, set, tuple)):
+            return list_of_one
+        try:
+            Length(max=1)(list_of_one)
+        except LengthInvalid as length_invalid:
+            raise CoerceInvalid(
+                f'Cannot coerce list of length {len(list_of_one)} to item'
+                if msg is None else msg) from length_invalid
+        return list_of_one[0]
 
 
 class ListFromItem(list):