diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 7a4648d..ea08c7d 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -1,13 +1,14 @@ version: 2 build: - image: latest + os: ubuntu-20.04 + tools: + python: "3.10" sphinx: configuration: doc/conf.py python: - version: 3.8 install: - method: pip path: . diff --git a/src/probeinterface/io.py b/src/probeinterface/io.py index ea279db..78b3cdb 100644 --- a/src/probeinterface/io.py +++ b/src/probeinterface/io.py @@ -730,9 +730,9 @@ def write_csv(file, probe): "ap_hp_filters", ), }, - # Neuropixels 2.0 - Single Shank + # Neuropixels 2.0 - Single Shank - Prototype 21: { - "probe_name": "Neuropixels 2.0 - Single Shank", + "probe_name": "Neuropixels 2.0 - Single Shank - Prototype", "x_pitch": 32, "y_pitch": 15, "contact_width": 12, @@ -743,8 +743,72 @@ def write_csv(file, probe): "polygon": polygon_description["default"], "fields_in_imro_table": ("channel_ids", "banks", "references", "elec_ids"), }, - # Neuropixels 2.0 - Four Shank + # Neuropixels 2.0 - Four Shank - Prototype 24: { + "probe_name": "Neuropixels 2.0 - Four Shank - Prototype", + "x_pitch": 32, + "y_pitch": 15, + "contact_width": 12, + "stagger": 0.0, + "shank_pitch": 250, + "shank_number": 4, + "ncol": 2, + "polygon": polygon_description["default"], + "fields_in_imro_table": ( + "channel_ids", + "shank_id", + "banks", + "references", + "elec_ids", + ), + }, + # Neuropixels 2.0 - Single Shank - Commercial without metal cap + 2003: { + "probe_name": "Neuropixels 2.0 - Single Shank", + "x_pitch": 32, + "y_pitch": 15, + "contact_width": 12, + "stagger": 0.0, + "shank_pitch": 0, + "shank_number": 1, + "ncol": 2, + "polygon": polygon_description["default"], + "fields_in_imro_table": ("channel_ids", "banks", "references", "elec_ids"), + }, + # Neuropixels 2.0 - Single Shank - Commercial with metal cap + 2004: { + "probe_name": "Neuropixels 2.0 - Single Shank", + "x_pitch": 32, + "y_pitch": 15, + "contact_width": 12, + "stagger": 0.0, + "shank_pitch": 0, + "shank_number": 1, + "ncol": 2, + "polygon": polygon_description["default"], + "fields_in_imro_table": ("channel_ids", "banks", "references", "elec_ids"), + }, + # Neuropixels 2.0 - Four Shank - Commercial without metal cap + 2013: { + "probe_name": "Neuropixels 2.0 - Four Shank", + "x_pitch": 32, + "y_pitch": 15, + "contact_width": 12, + "stagger": 0.0, + "shank_pitch": 250, + "shank_number": 4, + "ncol": 2, + "polygon": polygon_description["default"], + "fields_in_imro_table": ( + "channel_ids", + "shank_id", + "banks", + "references", + "elec_ids", + ), + }, + # Neuropixels 2.0 - Four Shank - Commercial with metal cap + 2014: { "probe_name": "Neuropixels 2.0 - Four Shank", "x_pitch": 32, "y_pitch": 15, @@ -1157,6 +1221,8 @@ def read_spikeglx(file: str | Path) -> Probe: if saved_chans.size != probe.get_contact_count(): # slice if needed probe = probe.get_slice(saved_chans) + # wire it + probe.set_device_channel_indices(np.arange(probe.get_contact_count())) return probe diff --git a/tests/data/openephys/OE_Neuropix-PXI-opto-with-sync/settings.xml b/tests/data/openephys/OE_Neuropix-PXI-opto-with-sync/settings.xml new file mode 100644 index 0000000..17155d5 --- /dev/null +++ b/tests/data/openephys/OE_Neuropix-PXI-opto-with-sync/settings.xml @@ -0,0 +1,655 @@ + + + + + 0.6.0 + 8 + 30 Aug 2023 23:41:36 + Windows 10 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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diff --git a/tests/test_io/test_openephys.py b/tests/test_io/test_openephys.py index 0ef312e..edc3b46 100644 --- a/tests/test_io/test_openephys.py +++ b/tests/test_io/test_openephys.py @@ -24,7 +24,7 @@ def test_NP1_subset(): assert probe_ap.get_shank_count() == 1 assert "1.0" in probe_ap.model_name - assert len(probe_ap.contact_positions) == 200 + assert probe_ap.get_contact_count() == 200 probe_lf = read_openephys( data_path / "OE_Neuropix-PXI-subset" / "settings.xml", stream_name="ProbeA-LFP" @@ -95,6 +95,14 @@ def test_multiple_probes(): assert np.min(ypos) >= 0 +def test_np_otpo_with_sync(): + probe = read_openephys(data_path / "OE_Neuropix-PXI-opto-with-sync" / "settings.xml") + assert probe.model_name == "Neuropixels Opto" + assert probe.get_shank_count() == 1 + assert probe.get_contact_count() == 384 + + + def test_older_than_06_format(): ## Test with the open ephys < 0.6 format diff --git a/tests/test_io/test_spikeglx.py b/tests/test_io/test_spikeglx.py index 80cdad1..e22cc55 100644 --- a/tests/test_io/test_spikeglx.py +++ b/tests/test_io/test_spikeglx.py @@ -37,12 +37,6 @@ def test_NP1(): assert "1.0" in probe.model_name -def test_NP2_1_shanks(): - probe = read_spikeglx(data_path / "p2_g0_t0.imec0.ap.meta") - assert "2.0" in probe.model_name - assert probe.get_shank_count() == 1 - - def test_NP_phase3A(): # Data provided by rtraghavan probe = read_spikeglx(data_path / "phase3a.imec.ap.meta") @@ -62,10 +56,17 @@ def test_NP_phase3A(): assert np.all(probe.contact_shape_params == {"width": contact_width}) assert np.all(probe.contact_shapes == contact_shape) + +def test_NP2_1_shanks(): + probe = read_spikeglx(data_path / "p2_g0_t0.imec0.ap.meta") + assert "2.0" in probe.model_name + assert probe.get_shank_count() == 1 + + def test_NP2_4_shanks(): probe = read_spikeglx(data_path / "NP2_4_shanks.imec0.ap.meta") - assert probe.model_name == "Neuropixels 2.0 - Four Shank" + assert probe.model_name == "Neuropixels 2.0 - Four Shank - Prototype" assert probe.manufacturer == "IMEC" assert probe.annotations["probe_type"] == 24 @@ -85,11 +86,61 @@ def test_NP2_4_shanks(): assert np.min(ypos) == pytest.approx(0) +def test_NP2_2013_all(): + # Data provided by Jennifer Colonell + probe = read_spikeglx(data_path / "NP2_2013_all_channels.imec0.ap.meta") + + assert probe.model_name == "Neuropixels 2.0 - Four Shank" + assert probe.manufacturer == "IMEC" + assert probe.annotations["probe_type"] == 2013 + + assert probe.ndim == 2 + # all channels are from the first shank + assert probe.get_shank_count() == 1 + assert probe.get_contact_count() == 384 + + # Test contact geometry + contact_width = 12.0 + contact_shape = "square" + + assert np.all(probe.contact_shape_params == {"width": contact_width}) + assert np.all(probe.contact_shapes == contact_shape) + + # This file does not save the channnels from 0 as the one above (NP2_4_shanks_g0_t0.imec0.ap.meta) + ypos = probe.contact_positions[:, 1] + assert np.min(ypos) == pytest.approx(0) + + +def test_NP2_2013_subset(): + # Data provided by Jennifer Colonell + probe = read_spikeglx(data_path / "NP2_2013_subset_channels.imec0.ap.meta") + + assert probe.model_name == "Neuropixels 2.0 - Four Shank" + assert probe.manufacturer == "IMEC" + assert probe.annotations["probe_type"] == 2013 + + assert probe.ndim == 2 + # all channels are from the first shank + assert probe.get_shank_count() == 1 + assert probe.get_contact_count() == 120 + + # Test contact geometry + contact_width = 12.0 + contact_shape = "square" + + assert np.all(probe.contact_shape_params == {"width": contact_width}) + assert np.all(probe.contact_shapes == contact_shape) + + # This file does not save the channnels from 0 as the one above (NP2_4_shanks_g0_t0.imec0.ap.meta) + ypos = probe.contact_positions[:, 1] + assert np.min(ypos) == pytest.approx(0) + + def test_NP2_4_shanks_with_different_electrodes_saved(): # Data provided by Jennifer Colonell probe = read_spikeglx(data_path / "NP2_4_shanks_save_different_electrodes.imec0.ap.meta") - assert probe.model_name == "Neuropixels 2.0 - Four Shank" + assert probe.model_name == "Neuropixels 2.0 - Four Shank - Prototype" assert probe.manufacturer == "IMEC" assert probe.annotations["probe_type"] == 24 @@ -275,4 +326,5 @@ def test_CatGT_NP1(): if __name__ == "__main__": - test_NP1() + test_NP2_2013_all() + test_NP2_2013_subset()