Merge pull request #837 from samuelgarcia/group_mode

apdavison · web-flow · commit 79df3c88a78d · 2020-09-24T10:01:45.000+02:00
Default group mode to 'group-by-same-units'
diff --git a/neo/io/axographio.py b/neo/io/axographio.py
@@ -48,7 +48,8 @@ class AxographIO(AxographRawIO, BaseFromRaw):
     name = 'AxographIO'
     description = 'This IO reads .axgd/.axgx files created with AxoGraph'
 
-    _prefered_signal_group_mode = 'split-all'
+    _prefered_signal_group_mode = 'group-by-same-units'
+    _default_group_mode_have_change_in_0_9 = True
 
     def __init__(self, filename='', force_single_segment=False):
         AxographRawIO.__init__(self, filename, force_single_segment)
diff --git a/neo/io/axonio.py b/neo/io/axonio.py
@@ -36,7 +36,8 @@ class AxonIO(AxonRawIO, BaseFromRaw):
     set of data. The `AxonIO._axon_info['EpochInfo']` section doesn't currently exist.
 
     """
-    _prefered_signal_group_mode = 'split-all'
+    _prefered_signal_group_mode = 'group-by-same-units'
+    _default_group_mode_have_change_in_0_9 = True
 
     def __init__(self, filename):
         AxonRawIO.__init__(self, filename=filename)
diff --git a/neo/io/basefromrawio.py b/neo/io/basefromrawio.py
@@ -14,6 +14,7 @@
 
 """
 import collections
+import warnings
 import numpy as np
 
 from neo import logging_handler
@@ -66,8 +67,9 @@ class BaseFromRaw(BaseIO):
 
     mode = 'file'
 
-    _prefered_signal_group_mode = 'split-all'  # 'group-by-same-units'
-    _prefered_units_group_mode = 'split-all'  # 'all-in-one'
+    _prefered_signal_group_mode = 'group-by-same-units'  # 'split-all'
+    _prefered_units_group_mode = 'all-in-one'  # 'split-all'
+    _default_group_mode_have_change_in_0_9 = False
 
     def __init__(self, *args, **kargs):
         BaseIO.__init__(self, *args, **kargs)
@@ -100,9 +102,9 @@ def read_block(self, block_index=0, lazy=False, signal_group_mode=None,
 
         if signal_group_mode is None:
             signal_group_mode = self._prefered_signal_group_mode
-            if self._prefered_signal_group_mode == 'split-all':
-                self.logger.warning("the default signal_group_mode will change from "\
-                                "'split-all' to 'group-by-same-units' in next release")
+            if self._default_group_mode_have_change_in_0_9:
+                warnings.warn('default "signal_group_mode" have change in version 0.9:'
+                        'now all channels are group together in AnalogSignal')
 
         if units_group_mode is None:
             units_group_mode = self._prefered_units_group_mode
diff --git a/neo/io/bci2000io.py b/neo/io/bci2000io.py
@@ -4,7 +4,8 @@
 
 class BCI2000IO(BCI2000RawIO, BaseFromRaw):
     """Class for reading data from a BCI2000 .dat file, either version 1.0 or 1.1"""
-    _prefered_signal_group_mode = 'split-all'
+    _prefered_signal_group_mode = 'group-by-same-units'
+    _default_group_mode_have_change_in_0_9 = True
 
     def __init__(self, filename):
         BCI2000RawIO.__init__(self, filename=filename)
diff --git a/neo/io/brainvisionio.py b/neo/io/brainvisionio.py
@@ -4,7 +4,8 @@
 
 class BrainVisionIO(BrainVisionRawIO, BaseFromRaw):
     """Class for reading data from the BrainVision product."""
-    _prefered_signal_group_mode = 'split-all'
+    _prefered_signal_group_mode = 'group-by-same-units'
+    _default_group_mode_have_change_in_0_9 = True
 
     def __init__(self, filename):
         BrainVisionRawIO.__init__(self, filename=filename)
diff --git a/neo/io/elanio.py b/neo/io/elanio.py
@@ -12,8 +12,8 @@ class ElanIO(ElanRawIO, BaseFromRaw):
 
     https://elan.lyon.inserm.fr
     """
-    _prefered_signal_group_mode = 'split-all'
-    # _prefered_signal_group_mode = 'group-by-same-units'
+    _prefered_signal_group_mode = 'group-by-same-units'
+    _default_group_mode_have_change_in_0_9 = True
 
     def __init__(self, filename):
         ElanRawIO.__init__(self, filename=filename)
diff --git a/neo/io/neuroexplorerio.py b/neo/io/neuroexplorerio.py
@@ -4,7 +4,8 @@
 
 class NeuroExplorerIO(NeuroExplorerRawIO, BaseFromRaw):
     """Class for reading data from NeuroExplorer (.nex)"""
-    _prefered_signal_group_mode = 'split-all'
+    _prefered_signal_group_mode = 'group-by-same-units'
+    _default_group_mode_have_change_in_0_9 = True
 
     def __init__(self, filename):
         NeuroExplorerRawIO.__init__(self, filename=filename)
diff --git a/neo/io/nixio_fr.py b/neo/io/nixio_fr.py
@@ -9,7 +9,7 @@ class NixIO(NIXRawIO, BaseFromRaw):
     name = 'NIX IO'
 
     _prefered_signal_group_mode = 'group-by-same-units'
-    _prefered_units_group_mode = 'split-all'
+    _prefered_units_group_mode = 'all-in-one'
 
     def __init__(self, filename):
         NIXRawIO.__init__(self, filename)
diff --git a/neo/io/plexonio.py b/neo/io/plexonio.py
@@ -13,7 +13,8 @@ class PlexonIO(PlexonRawIO, BaseFromRaw):
     Compatible with versions 100 to 106.
     Other versions have not been tested.
     """
-    _prefered_signal_group_mode = 'split-all'
+    _prefered_signal_group_mode = 'group-by-same-units'
+    _default_group_mode_have_change_in_0_9 = True
 
     def __init__(self, filename):
         PlexonRawIO.__init__(self, filename=filename)
diff --git a/neo/io/rawbinarysignalio.py b/neo/io/rawbinarysignalio.py
@@ -40,7 +40,8 @@ class RawBinarySignalIO(RawBinarySignalRawIO, BaseFromRaw):
 
     """
 
-    _prefered_signal_group_mode = 'split-all'
+    _prefered_signal_group_mode = 'group-by-same-units'
+    _default_group_mode_have_change_in_0_9 = True
 
     is_readable = True
     is_writable = True
diff --git a/neo/io/tdtio.py b/neo/io/tdtio.py
@@ -11,7 +11,8 @@ class TdtIO(TdtRawIO, BaseFromRaw):
     (sub directories).
     Tanks correspond to Neo Blocks and TDT blocks correspond to Neo Segments.
     """
-    _prefered_signal_group_mode = 'split-all'
+    _prefered_signal_group_mode = 'group-by-same-units'
+    _default_group_mode_have_change_in_0_9 = True
     mode = 'dir'
 
     def __init__(self, dirname):
diff --git a/neo/io/winedrio.py b/neo/io/winedrio.py
@@ -10,7 +10,8 @@ class WinEdrIO(WinEdrRawIO, BaseFromRaw):
     WinEdr is free:
     http://spider.science.strath.ac.uk/sipbs/software.htm
     """
-    _prefered_signal_group_mode = 'split-all'
+    _prefered_signal_group_mode = 'group-by-same-units'
+    _default_group_mode_have_change_in_0_9 = True
 
     def __init__(self, filename):
         WinEdrRawIO.__init__(self, filename=filename)
diff --git a/neo/io/winwcpio.py b/neo/io/winwcpio.py
@@ -10,7 +10,8 @@ class WinWcpIO(WinWcpRawIO, BaseFromRaw):
     WinWCP is free:
     http://spider.science.strath.ac.uk/sipbs/software.htm
     """
-    _prefered_signal_group_mode = 'split-all'
+    _prefered_signal_group_mode = 'group-by-same-units'
+    _default_group_mode_have_change_in_0_9 = True
 
     def __init__(self, filename):
         WinWcpRawIO.__init__(self, filename=filename)
diff --git a/neo/test/iotest/test_axographio.py b/neo/test/iotest/test_axographio.py
@@ -33,7 +33,7 @@ def test_version_1(self):
 
         filename = self.get_filename_path('AxoGraph_Graph_File')
         reader = AxographIO(filename=filename)
-        blk = reader.read_block()
+        blk = reader.read_block(signal_group_mode='split-all')
         assert_equal(blk.annotations['format_ver'], 1)
 
         names = [sig.name for sig in blk.segments[0].analogsignals]
@@ -57,7 +57,7 @@ def test_version_2(self):
 
         filename = self.get_filename_path('AxoGraph_Digitized_File')
         reader = AxographIO(filename=filename)
-        blk = reader.read_block()
+        blk = reader.read_block(signal_group_mode='split-all')
         assert_equal(blk.annotations['format_ver'], 2)
 
         names = [sig.name for sig in blk.segments[0].analogsignals]
@@ -87,7 +87,7 @@ def test_version_5(self):
 
         filename = self.get_filename_path('AxoGraph_X_File.axgx')
         reader = AxographIO(filename=filename)
-        blk = reader.read_block()
+        blk = reader.read_block(signal_group_mode='split-all')
         assert_equal(blk.annotations['format_ver'], 5)
 
         names = [sig.name for sig in blk.segments[0].analogsignals]
@@ -135,7 +135,7 @@ def test_file_written_by_axographio_package_with_linearsequence(self):
 
         filename = self.get_filename_path('written-by-axographio-with-linearsequence.axgx')
         reader = AxographIO(filename=filename)
-        blk = reader.read_block()
+        blk = reader.read_block(signal_group_mode='split-all')
         assert_equal(blk.annotations['format_ver'], 6)
 
         names = [sig.name for sig in blk.segments[0].analogsignals]
@@ -159,7 +159,7 @@ def test_file_written_by_axographio_package_without_linearsequence(self):
 
         filename = self.get_filename_path('written-by-axographio-without-linearsequence.axgx')
         reader = AxographIO(filename=filename)
-        blk = reader.read_block()
+        blk = reader.read_block(signal_group_mode='split-all')
         assert_equal(blk.annotations['format_ver'], 6)
 
         names = [sig.name for sig in blk.segments[0].analogsignals]
@@ -183,7 +183,7 @@ def test_file_with_corrupt_comment(self):
 
         filename = self.get_filename_path('corrupt-comment.axgx')
         reader = AxographIO(filename=filename)
-        blk = reader.read_block()
+        blk = reader.read_block(signal_group_mode='split-all')
         assert_equal(blk.annotations['format_ver'], 6)
 
         names = [sig.name for sig in blk.segments[0].analogsignals]
@@ -207,7 +207,7 @@ def test_multi_segment(self):
 
         filename = self.get_filename_path('episodic.axgd')
         reader = AxographIO(filename=filename)
-        blk = reader.read_block()
+        blk = reader.read_block(signal_group_mode='split-all')
         assert_equal(len(blk.segments), 30)
         assert_equal(len(blk.channel_indexes), 2)
 
@@ -216,7 +216,7 @@ def test_force_single_segment(self):
 
         filename = self.get_filename_path('episodic.axgd')
         reader = AxographIO(filename=filename, force_single_segment=True)
-        blk = reader.read_block()
+        blk = reader.read_block(signal_group_mode='split-all')
         assert_equal(len(blk.segments), 1)
         assert_equal(len(blk.channel_indexes), 60)
 
diff --git a/neo/test/iotest/test_exampleio.py b/neo/test/iotest/test_exampleio.py
@@ -62,7 +62,7 @@ def test_read_block(self):
         r = ExampleIO(filename=None)
         bl = r.read_block(lazy=True)
         assert len(bl.list_units) == 3
-        assert len(bl.channel_indexes) == 1 + 3  # signals grouped + units
+        assert len(bl.channel_indexes) == 1 + 1  # signals grouped + units grouped
 
     def test_read_segment_with_time_slice(self):
         r = ExampleIO(filename=None)
