Merge pull request #2560 from effigies/enh/rci

ENH: ReportCapableInterface mix-in/base interface

Author: effigies

nipype/interfaces/base/core.py

@@ -517,7 +517,9 @@ def run(self, cwd=None, ignore_exception=None, **inputs):
         outputs = None
 
         try:
+            runtime = self._pre_run_hook(runtime)
             runtime = self._run_interface(runtime)
+            runtime = self._post_run_hook(runtime)
             outputs = self.aggregate_outputs(runtime)
         except Exception as e:
             import traceback
@@ -653,6 +655,28 @@ def save_inputs_to_json(self, json_file):
         with open(json_file, 'w' if PY3 else 'wb') as fhandle:
             json.dump(inputs, fhandle, indent=4, ensure_ascii=False)
 
+    def _pre_run_hook(self, runtime):
+        """
+        Perform any pre-_run_interface() processing
+
+        Subclasses may override this function to modify ``runtime`` object or
+        interface state
+
+        MUST return runtime object
+        """
+        return runtime
+
+    def _post_run_hook(self, runtime):
+        """
+        Perform any post-_run_interface() processing
+
+        Subclasses may override this function to modify ``runtime`` object or
+        interface state
+
+        MUST return runtime object
+        """
+        return runtime
+
 
 class SimpleInterface(BaseInterface):
     """ An interface pattern that allows outputs to be set in a dictionary

nipype/interfaces/mixins/__init__.py

@@ -0,0 +1,2 @@
+from .reporting import (
+    ReportCapableInterface, ReportCapableInputSpec, ReportCapableOutputSpec)

nipype/interfaces/mixins/reporting.py

@@ -0,0 +1,65 @@
+# -*- coding: utf-8 -*-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+""" class mixin and utilities for enabling reports for nipype interfaces """
+from __future__ import (print_function, division, unicode_literals,
+                        absolute_import)
+
+import os
+from abc import abstractmethod
+
+from ... import logging
+from ..base import (
+    File, BaseInterface, BaseInterfaceInputSpec, TraitedSpec)
+
+iflogger = logging.getLogger('interface')
+
+
+class ReportCapableInputSpec(BaseInterfaceInputSpec):
+    out_report = File('report', usedefault=True, hash_files=False,
+                      desc='filename for the visual report')
+
+
+class ReportCapableOutputSpec(TraitedSpec):
+    out_report = File(desc='filename for the visual report')
+
+
+class ReportCapableInterface(BaseInterface):
+    """Mixin to enable reporting for Nipype interfaces"""
+    _out_report = None
+
+    def __init__(self, generate_report=False, **kwargs):
+        super(ReportCapableInterface, self).__init__(**kwargs)
+        self.generate_report = generate_report
+
+    def _post_run_hook(self, runtime):
+        runtime = super(ReportCapableInterface, self)._post_run_hook(runtime)
+
+        # leave early if there's nothing to do
+        if not self.generate_report:
+            return runtime
+
+        self._out_report = self.inputs.out_report
+        if not os.path.isabs(self._out_report):
+            self._out_report = os.path.abspath(os.path.join(runtime.cwd,
+                                                            self._out_report))
+
+        self._generate_report()
+
+        return runtime
+
+    def _list_outputs(self):
+        try:
+            outputs = super(ReportCapableInterface, self)._list_outputs()
+        except NotImplementedError:
+            outputs = {}
+        if self._out_report is not None:
+            outputs['out_report'] = self._out_report
+        return outputs
+
+    @abstractmethod
+    def _generate_report(self):
+        """
+        Saves report to file identified by _out_report instance variable
+        """
+        raise NotImplementedError