Add validation for Open Ephys and SpikeGadgets tests

Author: alejoe91

tests/test_io/test_openephys.py

@@ -1,17 +1,21 @@
 from pathlib import Path
 
 import numpy as np
+import glob
 
 import pytest
 
 from probeinterface import read_openephys
+from probeinterface.testing import validate_probe_dict
 
 data_path = Path(__file__).absolute().parent.parent / "data" / "openephys"
 
 
 def test_NP2_OE_1_0():
     # NP2 1-shank
     probeA = read_openephys(data_path / "OE_1.0_Neuropix-PXI-multi-probe" / "settings.xml", probe_name="ProbeA")
+    probe_dict = probeA.to_dict(array_as_list=True)
+    validate_probe_dict(probe_dict)
     assert probeA.get_shank_count() == 1
     assert "2.0" in probeA.model_name
     assert probeA.get_contact_count() == 384
@@ -20,13 +24,17 @@ def test_NP2_OE_1_0():
 def test_NP2():
     # NP2
     probe = read_openephys(data_path / "OE_Neuropix-PXI" / "settings.xml")
+    probe_dict = probe.to_dict(array_as_list=True)
+    validate_probe_dict(probe_dict)
     assert probe.get_shank_count() == 1
     assert "2.0 - Single Shank" in probe.model_name
 
 
 def test_NP2_four_shank():
     # NP2
     probe = read_openephys(data_path / "OE_Neuropix-PXI-NP2-4shank" / "settings.xml")
+    probe_dict = probe.to_dict(array_as_list=True)
+    validate_probe_dict(probe_dict)
     # on this case, only shanks 2-3 are used
     assert probe.get_shank_count() == 2
     assert "2.0 - Four Shank" in probe.model_name
@@ -38,6 +46,8 @@ def test_NP_Ultra():
         data_path / "OE_Neuropix-PXI-NP-Ultra" / "settings.xml",
         probe_name="ProbeA",
     )
+    probe_dict = probeA.to_dict(array_as_list=True)
+    validate_probe_dict(probe_dict)
     assert "Ultra" in probeA.model_name
     assert probeA.get_shank_count() == 1
     assert probeA.get_contact_count() == 384
@@ -46,6 +56,8 @@ def test_NP_Ultra():
         data_path / "OE_Neuropix-PXI-NP-Ultra" / "settings.xml",
         probe_name="ProbeB",
     )
+    probe_dict = probeB.to_dict(array_as_list=True)
+    validate_probe_dict(probe_dict)
     assert "Ultra" in probeB.model_name
     assert probeB.get_shank_count() == 1
     assert probeB.get_contact_count() == 384
@@ -54,6 +66,8 @@ def test_NP_Ultra():
         data_path / "OE_Neuropix-PXI-NP-Ultra" / "settings.xml",
         probe_name="ProbeF",
     )
+    probe_dict = probeF.to_dict(array_as_list=True)
+    validate_probe_dict(probe_dict)
     assert "Ultra" in probeF.model_name
     assert probeF.get_shank_count() == 1
     assert probeF.get_contact_count() == 384
@@ -62,6 +76,8 @@ def test_NP_Ultra():
         data_path / "OE_Neuropix-PXI-NP-Ultra" / "settings.xml",
         probe_name="ProbeD",
     )
+    probe_dict = probeD.to_dict(array_as_list=True)
+    validate_probe_dict(probe_dict)
     assert "Ultra" in probeD.model_name and "Type 2" in probeD.model_name
     assert probeD.get_shank_count() == 1
     assert probeD.get_contact_count() == 384
@@ -72,12 +88,16 @@ def test_NP_Ultra():
 def test_NP1_subset():
     # NP1 - 200 channels selected by recording_state in Record Node
     probe_ap = read_openephys(data_path / "OE_Neuropix-PXI-subset" / "settings.xml", stream_name="ProbeA-AP")
+    probe_dict = probe_ap.to_dict(array_as_list=True)
+    validate_probe_dict(probe_dict)
 
     assert probe_ap.get_shank_count() == 1
     assert "1.0" in probe_ap.model_name
     assert probe_ap.get_contact_count() == 200
 
     probe_lf = read_openephys(data_path / "OE_Neuropix-PXI-subset" / "settings.xml", stream_name="ProbeA-LFP")
+    probe_dict = probe_lf.to_dict(array_as_list=True)
+    validate_probe_dict(probe_dict)
 
     assert probe_lf.get_shank_count() == 1
     assert "1.0" in probe_lf.model_name
@@ -92,6 +112,8 @@ def test_NP1_subset():
 def test_multiple_probes():
     # multiple probes
     probeA = read_openephys(data_path / "OE_Neuropix-PXI-multi-probe" / "settings.xml", probe_name="ProbeA")
+    probe_dict = probeA.to_dict(array_as_list=True)
+    validate_probe_dict(probe_dict)
 
     assert probeA.get_shank_count() == 1
     assert "1.0" in probeA.model_name
@@ -100,17 +122,23 @@ def test_multiple_probes():
         data_path / "OE_Neuropix-PXI-multi-probe" / "settings.xml",
         stream_name="RecordNode#ProbeB",
     )
+    probe_dict = probeB.to_dict(array_as_list=True)
+    validate_probe_dict(probe_dict)
 
     assert probeB.get_shank_count() == 1
 
     probeC = read_openephys(
         data_path / "OE_Neuropix-PXI-multi-probe" / "settings.xml",
         serial_number="20403311714",
     )
+    probe_dict = probeC.to_dict(array_as_list=True)
+    validate_probe_dict(probe_dict)
 
     assert probeC.get_shank_count() == 1
 
     probeD = read_openephys(data_path / "OE_Neuropix-PXI-multi-probe" / "settings.xml", probe_name="ProbeD")
+    probe_dict = probeD.to_dict(array_as_list=True)
+    validate_probe_dict(probe_dict)
 
     assert probeD.get_shank_count() == 1
 
@@ -146,11 +174,16 @@ def test_multiple_probes_enabled():
     probe = read_openephys(
         data_path / "OE_6.7_enabled_disabled_Neuropix-PXI" / "settings_enabled-enabled.xml", probe_name="ProbeA"
     )
+    probe_dict = probe.to_dict(array_as_list=True)
+    validate_probe_dict(probe_dict)
+
     assert probe.get_shank_count() == 1
 
     probe = read_openephys(
         data_path / "OE_6.7_enabled_disabled_Neuropix-PXI" / "settings_enabled-enabled.xml", probe_name="ProbeB"
     )
+    probe_dict = probe.to_dict(array_as_list=True)
+    validate_probe_dict(probe_dict)
     assert probe.get_shank_count() == 4
 
 
@@ -159,7 +192,8 @@ def test_multiple_probes_disabled():
     probe = read_openephys(
         data_path / "OE_6.7_enabled_disabled_Neuropix-PXI" / "settings_enabled-disabled.xml", probe_name="ProbeA"
     )
-
+    probe_dict = probe.to_dict(array_as_list=True)
+    validate_probe_dict(probe_dict)
     assert probe.get_shank_count() == 1
 
     # Fail as this is disabled:
@@ -173,6 +207,8 @@ def test_multiple_probes_disabled():
 
 def test_np_opto_with_sync():
     probe = read_openephys(data_path / "OE_Neuropix-PXI-opto-with-sync" / "settings.xml")
+    probe_dict = probe.to_dict(array_as_list=True)
+    validate_probe_dict(probe_dict)
     assert probe.model_name == "Neuropixels Opto"
     assert probe.get_shank_count() == 1
     assert probe.get_contact_count() == 384
@@ -182,7 +218,8 @@ def test_older_than_06_format():
     ## Test with the open ephys < 0.6 format
 
     probe = read_openephys(data_path / "OE_5_Neuropix-PXI-multi-probe" / "settings.xml", probe_name="100.0")
-
+    probe_dict = probe.to_dict(array_as_list=True)
+    validate_probe_dict(probe_dict)
     assert probe.get_shank_count() == 4
     assert "2.0 - Four Shank" in probe.model_name
     ypos = probe.contact_positions[:, 1]
@@ -193,6 +230,8 @@ def test_multiple_signal_chains():
     # tests that the probe information can be loaded even if the Neuropix-PXI plugin
     # is not in the first signalchain
     probe = read_openephys(data_path / "OE_Neuropix-PXI-multiple-signalchains" / "settings.xml")
+    probe_dict = probe.to_dict(array_as_list=True)
+    validate_probe_dict(probe_dict)
     assert probe.model_name == "Neuropixels 1.0"
 
 

tests/test_io/test_spikegadgets.py

@@ -1,10 +1,10 @@
 from pathlib import Path
 from xml.etree import ElementTree
 
-import pytest
-
 from probeinterface import read_spikegadgets
 from probeinterface.io import parse_spikegadgets_header
+from probeinterface.testing import validate_probe_dict
+
 
 data_path = Path(__file__).absolute().parent.parent / "data" / "spikegadgets"
 test_file = "SpikeGadgets_test_data_2xNpix1.0_20240318_173658_header_only.rec"
@@ -22,6 +22,8 @@ def test_neuropixels_1_reader():
     probe_group = read_spikegadgets(data_path / test_file, raise_error=False)
     assert len(probe_group.probes) == 2
     for probe in probe_group.probes:
+        probe_dict = probe.to_dict(array_as_list=True)
+        validate_probe_dict(probe_dict)
         assert "1.0" in probe.model_name
         assert probe.get_shank_count() == 1
         assert probe.get_contact_count() == 384