🥅 More specific error handling

Author: shnizzedy

CPAC/registration/exceptions.py

@@ -0,0 +1,39 @@
+# Copyright (C) 2022  C-PAC Developers
+
+# This file is part of C-PAC.
+
+# C-PAC is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+
+# C-PAC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
+# License for more details.
+
+# 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/>.
+"""Custom registration exceptions"""
+class BadRegistrationError(ValueError):
+    """Exception for when a QC measure for a registration falls below a
+    specified threshold"""
+    def __init__(self, *args, metric=None, value=None, threshold=None,
+                 **kwargs):
+        """
+        Parameters
+        ----------
+        metric : str
+            QC metric
+
+        value : float
+            calculated QC value
+
+        threshold : float
+            specified threshold
+        """
+        msg = "Registration failed quality control"
+        if all(arg is not None for arg in (metric, value, threshold)):
+            msg += f" ({metric}: {value} < {threshold})"
+        msg += "."
+        super().__init__(msg, *args, **kwargs)

CPAC/registration/guardrails.py

@@ -24,6 +24,7 @@
 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.registration.exceptions import BadRegistrationError
 from CPAC.registration.utils import hardcoded_reg
 from CPAC.utils.docs import retry_docstring
 
@@ -32,30 +33,6 @@
     Registration: {'reference': 'reference', 'registered': 'out_file'}}
 
 
-class BadRegistrationError(ValueError):
-    """Exception for when a QC measure for a registration falls below a
-    specified threshold"""
-    def __init__(self, *args, metric=None, value=None, threshold=None,
-                 **kwargs):
-        """
-        Parameters
-        ----------
-        metric : str
-            QC metric
-
-        value : float
-            calculated QC value
-
-        threshold : float
-            specified threshold
-        """
-        msg = "Registration failed quality control"
-        if all(arg is not None for arg in (metric, value, threshold)):
-            msg += f" ({metric}: {value} < {threshold})"
-        msg += "."
-        super().__init__(msg, *args, **kwargs)
-
-
 def guardrail_selection(wf: 'Workflow', node1: 'Node', node2: 'Node',
                         ) -> Node:
     """Generate requisite Nodes for choosing a path through the graph

CPAC/registration/utils.py

@@ -66,6 +66,8 @@ def hardcoded_reg(moving_brain, reference_brain, moving_skull,
                   reference_skull, ants_para, moving_mask=None,
                   reference_mask=None, fixed_image_mask=None, interp=None,
                   reg_with_skull=0):
+    import subprocess
+    from CPAC.registration.exceptions import BadRegistrationError
     # TODO: expand transforms to cover all in ANTs para
 
     regcmd = ["antsRegistration"]
@@ -444,10 +446,14 @@ def hardcoded_reg(moving_brain, reference_brain, moving_skull,
         f.write(' '.join(regcmd))
 
     try:
-        retcode = subprocess.check_output(regcmd)
+        subprocess.check_output(regcmd)
+    except BadRegistrationError as bad_registration:
+        raise bad_registration
     except Exception as e:
-        raise Exception('[!] ANTS registration did not complete successfully.'
-                        '\n\nError details:\n{0}\n{1}\n'.format(e, e.output))
+        msg = '[!] ANTS registration did not complete successfully.'
+        if hasattr(e, 'output'):
+            msg += '\n\nError details:\n{e}\n{e.output}\n'
+        raise Exception(msg)  # pylint: disable=raise-missing-from
 
     warp_list = []
     warped_image = None