add time series check

src/pynwb/base.py

@@ -1,10 +1,12 @@
 from warnings import warn
 from collections.abc import Iterable
-import numpy as np
 from typing import NamedTuple
 
+import numpy as np
+
 from hdmf.utils import docval, getargs, popargs, call_docval_func, get_docval
 from hdmf.common import DynamicTable, VectorData
+from hdmf.utils import get_data_shape
 
 from . import register_class, CORE_NAMESPACE
 from .core import NWBDataInterface, MultiContainerInterface, NWBData
@@ -146,6 +148,24 @@ def __init__(self, **kwargs):
                 "control",
                 "control_description",
                 "continuity")
+
+        data_shape = get_data_shape(data=kwargs["data"], strict_no_data_load=True)
+        timestamps_shape = get_data_shape(data=kwargs["timestamps"], strict_no_data_load=True)
+        if (
+            # check that the shape is known
+            data_shape is not None and timestamps_shape is not None
+
+            # check for scalars. Should never happen
+            and (len(data_shape) > 0 and len(timestamps_shape) > 0)
+
+            # check that the length of the first dimension is known
+            and (data_shape[0] is not None and timestamps_shape[0] is not None)
+
+            # check that the data and timestamps match
+            and (data_shape[0] != timestamps_shape[0])
+        ):
+            warn("Length of data does not match length of timestamps. Your data may be transposed. Time should be on "
+                 "the 0th dimension")
         for key in keys:
             val = kwargs.get(key)
             if val is not None:

src/pynwb/ecephys.py

@@ -1,7 +1,9 @@
 from collections.abc import Iterable
+import warnings
 
 from hdmf.utils import docval, getargs, popargs, call_docval_func, get_docval
 from hdmf.data_utils import DataChunkIterator, assertEqualShape
+from hdmf.utils import get_data_shape
 
 from . import register_class, CORE_NAMESPACE
 from .base import TimeSeries
@@ -78,6 +80,19 @@ class ElectricalSeries(TimeSeries):
     def __init__(self, **kwargs):
         name, electrodes, data, channel_conversion, filtering = popargs('name', 'electrodes', 'data',
                                                                         'channel_conversion', 'filtering', kwargs)
+        data_shape = get_data_shape(data, strict_no_data_load=True)
+        if (
+            data_shape is not None
+            and len(data_shape) == 2
+            and data_shape[1] != len(electrodes.data)
+        ):
+            if data_shape[0] == len(electrodes.data):
+                warnings.warn("The second dimension of data does not match the length of electrodes, but instead the "
+                              "first does. Data is oriented incorrectly and should be transposed.")
+            else:
+                warnings.warn("The second dimension of data does not match the length of electrodes. Your data may be "
+                              "transposed.")
+
         super(ElectricalSeries, self).__init__(name, data, 'volts', **kwargs)
         self.electrodes = electrodes
         self.channel_conversion = channel_conversion

src/pynwb/ophys.py

@@ -2,7 +2,7 @@
 import numpy as np
 import warnings
 
-from hdmf.utils import docval, getargs, popargs, call_docval_func, get_docval
+from hdmf.utils import docval, getargs, popargs, call_docval_func, get_docval, get_data_shape
 
 from . import register_class, CORE_NAMESPACE
 from .base import TimeSeries
@@ -342,6 +342,26 @@ class RoiResponseSeries(TimeSeries):
                         'comments', 'description', 'control', 'control_description'))
     def __init__(self, **kwargs):
         rois = popargs('rois', kwargs)
+
+        data_shape = get_data_shape(data=kwargs["data"], strict_no_data_load=True)
+        rois_shape = get_data_shape(data=rois.data, strict_no_data_load=True)
+        if (
+            data_shape is not None and rois_shape is not None
+
+            # check that data is 2d and rois is 1d
+            and len(data_shape) == 2 and len(rois_shape) == 1
+
+            # check that key dimensions are known
+            and data_shape[1] is not None and rois_shape[0] is not None
+
+            and data_shape[1] != rois_shape
+        ):
+            if data_shape[0] == rois_shape[0]:
+                warnings.warn("The second dimension of data does not match the length of rois, but instead the "
+                              "first does. Data is oriented incorrectly and should be transposed.")
+            else:
+                warnings.warn("The second dimension of data does not match the length of rois. Your data may be "
+                              "transposed.")
         call_docval_func(super(RoiResponseSeries, self).__init__, kwargs)
         self.rois = rois
 

tests/unit/test_base.py

@@ -1,3 +1,5 @@
+import warnings
+
 import numpy as np
 
 from pynwb.base import ProcessingModule, TimeSeries, Images, Image, TimeSeriesReferenceVectorData, TimeSeriesReference
@@ -203,6 +205,22 @@ def test_conflicting_time_args(self):
             TimeSeries('test_ts2', [10, 11, 12, 13, 14, 15], 'grams',
                        starting_time=30., timestamps=[.3, .4, .5, .6, .7, .8])
 
+    def test_dimension_warning(self):
+        with warnings.catch_warnings(record=True) as w:
+            # Cause all warnings to always be triggered.
+            warnings.simplefilter("always")
+            TimeSeries(
+                name='test_ts2',
+                data=[10, 11, 12],
+                unit='grams',
+                timestamps=[.3, .4, .5, .6, .7, .8],
+            )
+            assert len(w) == 1
+            assert (
+                "Length of data does not match length of timestamps. Your data may be "
+                "transposed. Time should be on the 0th dimension"
+                   ) in str(w[-1].message)
+
 
 class TestImage(TestCase):
 

tests/unit/test_ecephys.py

@@ -1,3 +1,5 @@
+import warnings
+
 import numpy as np
 
 from pynwb.ecephys import ElectricalSeries, SpikeEventSeries, EventDetection, Clustering, EventWaveform,\
@@ -66,6 +68,38 @@ def test_invalid_data_shape(self):
                                                 "2)', expected '((None,), (None, None), (None, None, None))')")):
             ElectricalSeries('test_ts1', np.ones((2, 2, 2, 2)), region, timestamps=[0.0, 0.1, 0.2, 0.3, 0.4, 0.5])
 
+    def test_dimensions_warning(self):
+        table = make_electrode_table()
+        region = DynamicTableRegion('electrodes', [0, 2], 'the first and third electrodes', table)
+        with warnings.catch_warnings(record=True) as w:
+            # Cause all warnings to always be triggered.
+            warnings.simplefilter("always")
+            ElectricalSeries(
+                name="test_ts1",
+                data=np.ones((6, 3)),
+                electrodes=region,
+                timestamps=[0.0, 0.1, 0.2, 0.3, 0.4, 0.5]
+            )
+            self.assertEqual(len(w), 1)
+            assert (
+                "The second dimension of data does not match the length of electrodes. Your data may be transposed."
+                ) in str(w[-1].message)
+
+        with warnings.catch_warnings(record=True) as w:
+            # Cause all warnings to always be triggered.
+            warnings.simplefilter("always")
+            ElectricalSeries(
+                name="test_ts1",
+                data=np.ones((2, 6)),
+                electrodes=region,
+                rate=30000.,
+            )
+            self.assertEqual(len(w), 1)
+            assert (
+               "The second dimension of data does not match the length of electrodes, but instead the first does. Data "
+               "is oriented incorrectly and should be transposed."
+                   ) in str(w[-1].message)
+
 
 class SpikeEventSeriesConstructor(TestCase):
 

tests/unit/test_ophys.py

@@ -1,3 +1,5 @@
+import warnings
+
 import numpy as np
 
 from pynwb.base import TimeSeries
@@ -289,6 +291,41 @@ def test_init(self):
         self.assertEqual(ts.unit, 'unit')
         self.assertEqual(ts.rois, rt_region)
 
+    def test_warnings(self):
+        ps = create_plane_segmentation()
+        rt_region = ps.create_roi_table_region(description='the second ROI', region=[0, 1])
+
+        with warnings.catch_warnings(record=True) as w:
+            # Cause all warnings to always be triggered.
+            warnings.simplefilter("always")
+            RoiResponseSeries(
+                name="test_ts1",
+                data=np.ones((6, 3)),
+                rois=rt_region,
+                unit="n.a.",
+                timestamps=[0.0, 0.1, 0.2, 0.3, 0.4, 0.5]
+            )
+            self.assertEqual(len(w), 1)
+            assert (
+                    "The second dimension of data does not match the length of rois. Your data may be transposed."
+                ) in str(w[-1].message)
+
+        with warnings.catch_warnings(record=True) as w:
+            # Cause all warnings to always be triggered.
+            warnings.simplefilter("always")
+            RoiResponseSeries(
+                name="test_ts1",
+                data=np.ones((2, 6)),
+                rois=rt_region,
+                rate=30000.,
+                unit="n.a.",
+            )
+            self.assertEqual(len(w), 1)
+            assert (
+               "The second dimension of data does not match the length of rois, but instead the first does. "
+               "Data is oriented incorrectly and should be transposed."
+                   ) in str(w[-1].message)
+
 
 class DfOverFConstructor(TestCase):
     def test_init(self):