treewide: Allow to inject a SweepTable

The SweepTable was the first icephys table for grouping different patch
clamp series together, see NeurodataWithoutBorders/pynwb@21f91920 (Add a
SweepTable for icephys data, 2018-11-02) for pynwb 0.6.0.

This was superseeded by the icephys metadata tables introduced in pynwb
2.0.0 and finally removed in 3.0.0.

While migrating to the icephys metadata tables is on the list [1], we
don't want to do this here now.

So let's add a nasty hack for injecting a sweep table.

[1]: AllenInstitute/IPNWB#47

Author: t-b

ipfx/utilities.py

@@ -6,6 +6,8 @@
 from ipfx.stimulus import StimulusOntology
 from ipfx.dataset.ephys_data_set import EphysDataSet
 
+from pynwb.icephys import SweepTable
+import pynwb
 
 def drop_failed_sweeps(
         dataset: EphysDataSet,
@@ -41,3 +43,12 @@ def drop_failed_sweeps(
 
     dataset.sweep_info = sweep_features
 
+def inject_sweep_table(nwbfile: pynwb.NWBFile):
+    """
+    Allows us to keep using the SweepTable which can not be constructed anymore in pynwb 3.0.
+    """
+
+    sweep_table = SweepTable.__new__(SweepTable, parent=nwbfile, in_construct_mode=True)
+    sweep_table.__init__(name='sweep_table')
+    sweep_table._in_construct_mode = False
+    nwbfile.sweep_table = sweep_table

ipfx/x_to_nwb/ABFConverter.py

@@ -21,6 +21,7 @@
 from ipfx.x_to_nwb.conversion_utils import PLACEHOLDER, V_CLAMP_MODE, I_CLAMP_MODE, I0_CLAMP_MODE, \
      parseUnit, getStimulusSeriesClass, getAcquiredSeriesClass, createSeriesName, convertDataset, \
      getPackageInfo, createCycleID
+from ipfx.utilities import inject_sweep_table
 
 log = logging.getLogger(__name__)
 
@@ -78,6 +79,8 @@ def __init__(self, inFileOrFolder, outFile, outputFeedbackChannel, compression=T
         electrodes = self._createElectrodes(device)
         nwbFile.add_icephys_electrode(electrodes)
 
+        inject_sweep_table(nwbfile)
+
         for i in self._createStimulusSeries(electrodes):
             nwbFile.add_stimulus(i, use_sweep_table=True)
 

ipfx/x_to_nwb/DatConverter.py

@@ -16,6 +16,7 @@
 from ipfx.x_to_nwb.conversion_utils import PLACEHOLDER, V_CLAMP_MODE, I_CLAMP_MODE, \
      parseUnit, getStimulusSeriesClass, getAcquiredSeriesClass, createSeriesName, convertDataset, \
      getPackageInfo, getStimulusRecordIndex, createCycleID, clampModeToString
+from ipfx.utilities import inject_sweep_table
 
 log = logging.getLogger(__name__)
 
@@ -70,6 +71,8 @@ def generateList(multipleGroupsPerFile, pul):
             electrodes = self._createElectrodes(device)
             nwbFile.add_icephys_electrode(electrodes)
 
+            inject_sweep_table(nwbfile)
+
             for i in self._createAcquiredSeries(electrodes, elem):
                 nwbFile.add_acquisition(i, use_sweep_table=True)
 

tests/attach_metadata/test_cli.py

@@ -12,7 +12,7 @@
 import pynwb
 import numpy as np
 import pytest
-
+from ipfx.utilities import inject_sweep_table
 
 class CliRunner:
 
@@ -56,6 +56,9 @@ def simple_nwb(base_path):
         identifier='test session',
         session_start_time=datetime.now()
     )
+
+    inject_sweep_table(nwbfile)
+
     nwbfile.add_acquisition(
         pynwb.TimeSeries(
             name="a timeseries", 

tests/attach_metadata/test_nwb2_sink.py

@@ -16,6 +16,7 @@
 import h5py
 
 from ipfx.attach_metadata.sink import nwb2_sink
+from ipfx.utilities import inject_sweep_table
 
 
 @pytest.fixture
@@ -42,6 +43,7 @@ def nwbfile():
           electrode=ice,
           sweep_number=12
     )
+    inject_sweep_table(_nwbfile)
     _nwbfile.add_acquisition(series, use_sweep_table=True)
     _nwbfile.subject = pynwb.file.Subject()
 

tests/dataset/test_ephys_nwb_data.py

@@ -6,6 +6,7 @@
 import pynwb
 from pynwb.icephys import CurrentClampStimulusSeries, CurrentClampSeries
 import numpy as np
+from ipfx.utilities import inject_sweep_table
 
 from dictdiffer import diff
 
@@ -58,6 +59,7 @@ def nwbfile_to_test():
         **stimulus_meta_data
     )
 
+    inject_sweep_table(nwbfile)
     nwbfile.add_stimulus(stimulus_series, use_sweep_table=True)
 
     response_data = [1, 2, 3, 4, 5]