🚧 WIP 🥅 Iterate guardrail installation

Author: shnizzedy

CPAC/pipeline/nipype_pipeline_engine/utils.py

@@ -17,12 +17,11 @@
 """Custom nipype utilities"""
 
 
-def connect_from_spec(wf, spec, original_spec, exclude=None):
+def connect_from_spec(spec, original_spec, exclude=None):
     """Function to connect all original inputs to a new spec"""
     for _item, _value in original_spec.items():
         if isinstance(exclude, (list, tuple)):
             if _item not in exclude:
                 setattr(spec.inputs, _item, _value)
         elif _item != exclude:
             setattr(spec.inputs, _item, _value)
-    return wf

CPAC/pipeline/random_state/seed.py

@@ -62,7 +62,7 @@ def random_seed():
     -------
     seed : int or None
     '''
-    if _seed['seed'] == 'random':
+    if _seed['seed'] in ['random', None]:
         _seed['seed'] = random_random_seed()
     return _seed['seed']
 
@@ -153,6 +153,24 @@ def _reusable_flags():
     }
 
 
+def seed_plus_1(seed=None):
+    '''Increment seed, looping back to 1 at MAX_SEED
+
+    Parameters
+    ----------
+    seed : int, optional
+        Uses configured seed if not specified
+
+    Returns
+    -------
+    int
+    '''
+    seed = random_seed() if seed is None else int(seed)
+    if seed < MAX_SEED:  # increment random seed
+        return seed + 1
+    return 1  # loop back to 1
+
+
 def set_up_random_state(seed):
     '''Set global random seed
 

CPAC/pipeline/schema.py

@@ -18,9 +18,8 @@
 # pylint: disable=too-many-lines
 import re
 from itertools import chain, permutations
-import numpy as np
 from pathvalidate import sanitize_filename
-from voluptuous import All, ALLOW_EXTRA, Any, Capitalize, Coerce, \
+from voluptuous import All, ALLOW_EXTRA, Any, Capitalize, Coerce, Equal, \
                        ExactSequence, ExclusiveInvalid, In, Length, Lower, \
                        Match, Maybe, Optional, Range, Required, Schema
 from CPAC import docs_prefix
@@ -484,7 +483,6 @@ def sanitize(filename):
                 'interpolation': In({'trilinear', 'sinc', 'spline'}),
                 'using': str,
                 'input': str,
-                'interpolation': str,
                 'cost': str,
                 'dof': int,
                 'arguments': Maybe(str),
@@ -502,11 +500,14 @@ def sanitize(filename):
                     },
                 },
                 'boundary_based_registration': {
-                    'run': forkable,
+                    'run': All(Coerce(ListFromItem),
+                               [Any(bool, All(Lower, Equal('fallback')))],
+                               Length(max=3)),
                     'bbr_schedule': str,
-                    'bbr_wm_map': In({'probability_map', 'partial_volume_map'}),
+                    'bbr_wm_map': In(('probability_map',
+                                      'partial_volume_map')),
                     'bbr_wm_mask_args': str,
-                    'reference': In({'whole-head', 'brain'})
+                    'reference': In(('whole-head', 'brain'))
                 },
             },
             'EPI_registration': {

CPAC/registration/__init__.py

@@ -3,7 +3,6 @@
                           create_fsl_fnirt_nonlinear_reg_nhp, \
                           create_register_func_to_anat, \
                           create_register_func_to_anat_use_T2, \
-                          create_bbregister_func_to_anat, \
                           create_wf_calculate_ants_warp
 
 from .output_func_to_standard import output_func_to_standard
@@ -13,6 +12,5 @@
            'create_fsl_fnirt_nonlinear_reg_nhp',
            'create_register_func_to_anat',
            'create_register_func_to_anat_use_T2',
-           'create_bbregister_func_to_anat',
            'create_wf_calculate_ants_warp',
            'output_func_to_standard']

CPAC/registration/guardrails.py

@@ -15,6 +15,7 @@
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 """Guardrails to protect against bad registrations"""
+import logging
 from copy import deepcopy
 from nipype.interfaces.ants import Registration
 from nipype.interfaces.fsl import FLIRT
@@ -23,7 +24,7 @@
 from CPAC.pipeline.nipype_pipeline_engine.utils import connect_from_spec
 from CPAC.qc import qc_masks, REGISTRATION_GUARDRAIL_THRESHOLDS
 
-
+logger = logging.getLogger('nipype.workflow')
 _SPEC_KEYS = {
     FLIRT: {'reference': 'reference', 'registered': 'out_file'},
     Registration: {'reference': 'reference', 'registered': 'out_file'}}
@@ -54,7 +55,7 @@ def __init__(self, *args, metric=None, value=None, threshold=None,
 
 
 def registration_guardrail(registered: str, reference: str, retry: bool = False
-                           ) -> str:
+                           ):
     """Check QC metrics post-registration and throw an exception if
     metrics are below given thresholds.
 
@@ -78,23 +79,29 @@ def registration_guardrail(registered: str, reference: str, retry: bool = False
     -------
     registered_mask : str
         path to mask
+
+    failed_qc : int
+        metrics met specified thresholds?, used as index for selecting
+        outputs
     """
     qc_metrics = qc_masks(registered, reference)
+    failed_qc = 0
     for metric, threshold in REGISTRATION_GUARDRAIL_THRESHOLDS.items():
         if threshold is not None:
             value = qc_metrics.get(metric)
             if isinstance(value, list):
                 value = value[0]
             if value < threshold:
+                failed_qc = 1
                 with open(f'{registered}.failed_qc', 'w',
                           encoding='utf-8') as _f:
                     _f.write(f'{metric}: {value} < {threshold}')
                 if retry:
                     registered = f'{registered}-failed'
                 else:
-                    raise BadRegistrationError(metric=metric, value=value,
-                                               threshold=threshold)
-    return registered
+                    logger.error(str(BadRegistrationError(
+                        metric=metric, value=value, threshold=threshold)))
+    return registered, failed_qc
 
 
 def registration_guardrail_node(name=None):
@@ -112,7 +119,8 @@ def registration_guardrail_node(name=None):
         name = 'registration_guardrail'
     return Node(Function(input_names=['registered',
                                       'reference'],
-                         output_names=['registered'],
+                         output_names=['registered',
+                                       'failed_qc'],
                          imports=['from CPAC.qc import qc_masks, '
                                   'REGISTRATION_GUARDRAIL_THRESHOLDS',
                                   'from CPAC.registration.guardrails '
@@ -146,10 +154,10 @@ def registration_guardrail_workflow(registration_node, retry=True):
         (registration_node, guardrail, [(outkey, 'registered')])])
     if retry:
         wf = retry_registration(wf, registration_node,
-                                guardrail.outputs.registered)
+                                guardrail.outputs.registered)[0]
     else:
         wf.connect(guardrail, 'registered', outputspec, outkey)
-        wf = connect_from_spec(wf, outputspec, registration_node, outkey)
+        connect_from_spec(outputspec, registration_node, outkey)
     return wf
 
 
@@ -167,6 +175,8 @@ def retry_registration(wf, registration_node, registered):
     Returns
     -------
     Workflow
+
+    Node
     """
     name = f'retry_{registration_node.name}'
     retry_node = Node(Function(function=retry_registration_node,
@@ -177,14 +187,14 @@ def retry_registration(wf, registration_node, registered):
     outputspec = registration_node.outputs
     outkey = spec_key(registration_node, 'registered')
     guardrail = registration_guardrail_node(f'{name}_guardrail')
-    wf = connect_from_spec(wf, inputspec, retry_node)
+    connect_from_spec(inputspec, retry_node)
     wf.connect([
         (inputspec, guardrail, [
             (spec_key(retry_node, 'reference'), 'reference')]),
         (retry_node, guardrail, [(outkey, 'registered')]),
         (guardrail, outputspec, [('registered', outkey)])])
-    wf = connect_from_spec(wf, retry_node, outputspec, registered)
-    return wf
+    connect_from_spec(retry_node, outputspec, registered)
+    return wf, retry_node
 
 
 def retry_registration_node(registered, registration_node):
@@ -200,16 +210,12 @@ def retry_registration_node(registered, registration_node):
     -------
     Node
     """
-    from CPAC.pipeline.random_state.seed import MAX_SEED, random_seed
-    seed = random_seed()
+    from CPAC.pipeline.random_state.seed import seed_plus_1
     if registered.endswith('-failed'):
         retry_node = registration_node.clone(
             name=f'{registration_node.name}-retry')
-        if isinstance(seed, int):
-            if seed < MAX_SEED:  # increment random seed
-                retry_node.seed = seed + 1
-            else:  # loop back to minumum seed
-                retry_node.seed = 1
+        if isinstance(retry_node.seed, int):
+            retry_node.seed = seed_plus_1()
         return retry_node
     return registration_node