Merge pull request #1127 from apdavison/irrsig-in-neomatlabio

Add support for IrregularlySampledSignal in NeoMatlabIO

Author: JuliaSprenger

neo/io/neomatlabio.py

@@ -37,8 +37,8 @@
         SCIPY_ERR = None
 
 from neo.io.baseio import BaseIO
-from neo.core import (Block, Segment, AnalogSignal, Event, Epoch, SpikeTrain,
-                      objectnames, class_by_name)
+from neo.core import (Block, Segment, AnalogSignal, IrregularlySampledSignal,
+                      Event, Epoch, SpikeTrain, objectnames, class_by_name)
 
 classname_lower_to_upper = {}
 for k in objectnames:
@@ -190,7 +190,8 @@ class NeoMatlabIO(BaseIO):
     is_readable = True
     is_writable = True
 
-    supported_objects = [Block, Segment, AnalogSignal, Epoch, Event, SpikeTrain]
+    supported_objects = [Block, Segment, AnalogSignal, IrregularlySampledSignal,
+                         Epoch, Event, SpikeTrain]
     readable_objects = [Block]
     writeable_objects = [Block]
 
@@ -251,6 +252,10 @@ def write_block(self, bl, **kargs):
                 anasig_struct = self.create_struct_from_obj(anasig)
                 seg_struct['analogsignals'].append(anasig_struct)
 
+            for irrsig in seg.irregularlysampledsignals:
+                irrsig_struct = self.create_struct_from_obj(irrsig)
+                seg_struct['irregularlysampledsignals'].append(irrsig_struct)
+
             for ea in seg.events:
                 ea_struct = self.create_struct_from_obj(ea)
                 seg_struct['events'].append(ea_struct)
@@ -348,7 +353,13 @@ def create_ob_from_struct(self, struct, classname):
                 else:
                     data_complement["t_start"] = 0.0
 
-            ob = cl(arr, **data_complement)
+            if "times" in (at[0] for at in cl._necessary_attrs) and quantity_attr != "times":
+                # handle IrregularlySampledSignal
+                times = getattr(struct, "times")
+                data_complement["time_units"] = getattr(struct, "times_units")
+                ob = cl(times, arr, **data_complement)
+            else:
+                ob = cl(arr, **data_complement)
         else:
             ob = cl()
 

neo/test/iotest/test_neomatlabio.py

@@ -3,8 +3,11 @@
 """
 
 import unittest
-
+from numpy.testing import assert_array_equal
 import quantities as pq
+
+from neo.core.analogsignal import AnalogSignal
+from neo.core.irregularlysampledsignal import IrregularlySampledSignal
 from neo import Block, Segment, SpikeTrain
 from neo.test.iotest.common_io_test import BaseTestIO
 from neo.io.neomatlabio import NeoMatlabIO, HAVE_SCIPY
@@ -21,8 +24,12 @@ def test_write_read_single_spike(self):
         seg = Segment('segment1')
         spiketrain1 = SpikeTrain([1] * pq.s, t_stop=10 * pq.s, sampling_rate=1 * pq.Hz)
         spiketrain1.annotate(yep='yop')
+        sig1 = AnalogSignal([4, 5, 6] * pq.A, sampling_period=1 * pq.ms)
+        irrsig1 = IrregularlySampledSignal([0, 1, 2] * pq.ms, [4, 5, 6] * pq.A)
         block1.segments.append(seg)
         seg.spiketrains.append(spiketrain1)
+        seg.analogsignals.append(sig1)
+        seg.irregularlysampledsignals.append(irrsig1)
 
         # write block
         filename = self.get_local_path('matlabiotestfile.mat')
@@ -36,6 +43,14 @@ def test_write_read_single_spike(self):
         self.assertEqual(block1.segments[0].spiketrains[0],
                          block2.segments[0].spiketrains[0])
 
+        assert_array_equal(block1.segments[0].analogsignals[0],
+                            block2.segments[0].analogsignals[0])
+
+        assert_array_equal(block1.segments[0].irregularlysampledsignals[0].magnitude,
+                           block2.segments[0].irregularlysampledsignals[0].magnitude)
+        assert_array_equal(block1.segments[0].irregularlysampledsignals[0].times,
+                           block2.segments[0].irregularlysampledsignals[0].times)
+
         # test annotations
         spiketrain2 = block2.segments[0].spiketrains[0]
         assert 'yep' in spiketrain2.annotations