♻️ Better handling of global thresholds

Author: shnizzedy

CPAC/qc/__init__.py

@@ -15,6 +15,8 @@
 # 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/>.
 """Quality control utilities for C-PAC"""
-from CPAC.qc.globals import REGISTRATION_GUARDRAIL_THRESHOLDS
+from CPAC.qc.globals import registration_guardrail_thresholds, \
+                            update_thresholds
 from CPAC.qc.qcmetrics import qc_masks
-__all__ = ['qc_masks', 'REGISTRATION_GUARDRAIL_THRESHOLDS']
+__all__ = ['qc_masks', 'registration_guardrail_thresholds',
+           'update_thresholds']

CPAC/qc/globals.py

@@ -15,4 +15,28 @@
 # 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/>.
 """Global QC values"""
-REGISTRATION_GUARDRAIL_THRESHOLDS = {}
+_REGISTRATION_GUARDRAIL_THRESHOLDS = {'thresholds': {}}
+
+
+def registration_guardrail_thresholds() -> dict:
+    """Get registration guardrail thresholds
+
+    Returns
+    -------
+    dict
+    """
+    return _REGISTRATION_GUARDRAIL_THRESHOLDS['thresholds']
+
+
+def update_thresholds(thresholds) -> None:
+    """Set a registration guardrail threshold
+
+    Parameters
+    ----------
+    thresholds : dict of {str: float or int}
+
+    Returns
+    -------
+    None
+    """
+    _REGISTRATION_GUARDRAIL_THRESHOLDS['thresholds'].update(thresholds)

CPAC/registration/guardrails.py

@@ -15,13 +15,14 @@
 # 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
 from nipype.interfaces.utility import Function
 from CPAC.pipeline.nipype_pipeline_engine import Node, Workflow
 from CPAC.pipeline.nipype_pipeline_engine.utils import connect_from_spec
-from CPAC.qc import qc_masks, REGISTRATION_GUARDRAIL_THRESHOLDS
+from CPAC.qc import qc_masks, registration_guardrail_thresholds
 
 _SPEC_KEYS = {
     FLIRT: {'reference': 'reference', 'registered': 'out_file'},
@@ -82,11 +83,10 @@ def registration_guardrail(registered: str, reference: str, retry: bool = False
         metrics met specified thresholds?, used as index for selecting
         outputs
     """
-    import logging
     logger = logging.getLogger('nipype.workflow')
     qc_metrics = qc_masks(registered, reference)
     failed_qc = 0
-    for metric, threshold in REGISTRATION_GUARDRAIL_THRESHOLDS.items():
+    for metric, threshold in registration_guardrail_thresholds().items():
         if threshold is not None:
             value = qc_metrics.get(metric)
             if isinstance(value, list):
@@ -121,8 +121,9 @@ def registration_guardrail_node(name=None):
                                       'reference'],
                          output_names=['registered',
                                        'failed_qc'],
-                         imports=['from CPAC.qc import qc_masks, '
-                                  'REGISTRATION_GUARDRAIL_THRESHOLDS',
+                         imports=['import logging',
+                                  'from CPAC.qc import qc_masks, '
+                                  'registration_guardrail_thresholds',
                                   'from CPAC.registration.guardrails '
                                   'import BadRegistrationError'],
                          function=registration_guardrail), name=name)

CPAC/utils/configuration/configuration.py

@@ -23,7 +23,7 @@
 from typing import Optional, Tuple
 from warnings import warn
 import yaml
-from CPAC.qc import REGISTRATION_GUARDRAIL_THRESHOLDS
+from CPAC.qc import update_thresholds
 from CPAC.utils.utils import load_preconfig
 from .diff import dct_diff
 
@@ -152,8 +152,7 @@ def __init__(self, config_map=None):
             setattr(self, key, set_from_ENV(config_map[key]))
 
         # set global QC thresholds
-        REGISTRATION_GUARDRAIL_THRESHOLDS.update(self[
-            'registration_workflows', 'quality_thresholds'])
+        update_thresholds(self['registration_workflows', 'quality_thresholds'])
 
         self.__update_attr()