Merge pull request #941 from shashwatsridhar/fix/#940_fix_create_group_across_segment

Fix multiples errors in BaseFromRaw.read_block()

Author: samuelgarcia

doc/source/authors.rst

@@ -53,6 +53,7 @@ and may not be the current affiliation of a contributor.
 * Hugo van Kemenade
 * Aitor Morales-Gregorio [13]
 * Peter N Steinmetz [22]
+* Shashwat Sridhar
 * Alessio Buccino [23]
 
 1. Centre de Recherche en Neuroscience de Lyon, CNRS UMR5292 - INSERM U1028 - Universite Claude Bernard Lyon 1

neo/io/basefromrawio.py

@@ -123,7 +123,7 @@ def read_block(self, block_index=0, lazy=False,
             create_group_across_segment = { k: v for k in l}
         elif isinstance(create_group_across_segment, dict):
             # put False to missing keys
-            create_group_across_segment = {create_group_across_segment.get(k, False) for k in l}
+            create_group_across_segment = {k: create_group_across_segment.get(k, False) for k in l}
         else:
             raise ValueError('create_group_across_segment must be bool or dict')
 
@@ -153,12 +153,12 @@ def read_block(self, block_index=0, lazy=False,
             unit_channels = self.header['unit_channels']
             st_groups = []
             for c in range(unit_channels.size):
-                group = Group(name='SpikeTrain group {}'.format(i))
+                group = Group(name='SpikeTrain group {}'.format(c))
                 group.annotate(unit_name=unit_channels[c]['name'])
                 group.annotate(unit_id=unit_channels[c]['id'])
                 unit_annotations = self.raw_annotations['unit_channels'][c]
                 unit_annotations = check_annotations(unit_annotations)
-                group.annotations.annotate(**unit_annotations)
+                group.annotate(**unit_annotations)
                 bl.groups.append(group)
                 st_groups.append(group)
 

neo/test/iotest/common_io_test.py

@@ -18,10 +18,12 @@
 __test__ = False
 
 import os
+import inspect
 from copy import copy
 import unittest
 
 from neo.core import Block, Segment
+from neo.io.basefromrawio import BaseFromRaw
 from neo.test.tools import (assert_same_sub_schema,
                             assert_neo_object_is_compliant,
                             assert_sub_schema_is_lazy_loaded,
@@ -154,7 +156,7 @@ def able_to_write_or_read(self, writeread=False, readwrite=False):
         # sampling_rate (RawBinaryIO...) the test is too much complex to design
         # genericaly.
         if (self.higher in self.ioclass.read_params and
-                    len(self.ioclass.read_params[self.higher]) != 0):
+                len(self.ioclass.read_params[self.higher]) != 0):
             return False
 
         # handle cases where the test should write then read
@@ -511,3 +513,48 @@ def test_readed_with_lazy_is_compliant(self):
                 # intercept exceptions and add more information
                 except BaseException as exc:
                     raise
+
+    def test_create_group_across_segment(self):
+        """
+        Read {io_name} files in 'files_to_test' with
+        create_group_across_segment test cases.
+
+        Test read_block method of BaseFromRaw with different test cases
+        for create_group_across_segment.
+
+        """.format(io_name=self.ioclass.__name__)
+
+        test_cases = [
+            {"SpikeTrain": True},
+            {"AnalogSignal": True},
+            {"Event": True},
+            {"Epoch": True},
+            {"SpikeTrain": True,
+             "AnalogSignal": True,
+             "Event": True,
+             "Epoch": True},
+            True
+        ]
+        expected_outcomes = [
+            None,
+            None,
+            NotImplementedError,
+            NotImplementedError,
+            NotImplementedError,
+            NotImplementedError,
+        ]
+
+        mock_test_case = unittest.TestCase()
+        if issubclass(self.ioclass, BaseFromRaw):
+            for obj, reader in self.iter_objects(target=Block,
+                                                 lazy=self.ioclass.support_lazy,
+                                                 return_reader=True):
+                if "create_group_across_segment" in inspect.signature(reader).parameters.keys():
+                    # Ignore testing readers for IOs where read_block is overridden to exclude
+                    # the create_group_across_segment functionality, for eg. NixIO_fr
+                    for case, outcome in zip(test_cases, expected_outcomes):
+                        if outcome is not None:
+                            with mock_test_case.assertRaises(outcome):
+                                reader(lazy=self.ioclass.support_lazy, create_group_across_segment=case)
+                        else:
+                            reader(lazy=self.ioclass.support_lazy, create_group_across_segment=case)