probe.name > probe.dscription for NP

Author: samuelgarcia

resources/generate_neuropixels_library.py

@@ -80,7 +80,7 @@ def generate_all_npx():
         n = probe.get_contact_count()
 
         title = f"{probe.manufacturer} - {model_name}"
-        title += f"\n{probe.name}"
+        title += f"\n{probe.description}"
         title += f"\n {n}ch"
         if probe.shank_ids is not None:
             num_shank = probe.get_shank_count()

src/probeinterface/neuropixels_tools.py

@@ -90,20 +90,21 @@ def _load_np_probe_features():
 }
 
 # Map from ProbeInterface to ProbeTable naming conventions
-pi_to_pt_names = {
-    "x_pitch": "electrode_pitch_horz_um",
-    "y_pitch": "electrode_pitch_vert_um",
-    "contact_width": "electrode_size_horz_direction_um",
-    "shank_pitch": "shank_pitch_um",
-    "shank_number": "num_shanks",
-    "ncols_per_shank": "cols_per_shank",
-    "nrows_per_shank": "rows_per_shank",
-    "adc_bit_depth": "adc_bit_depth",
-    "model_name": "description",
-    "num_readout_channels": "num_readout_channels",
-    "shank_width_um": "shank_width_um",
-    "tip_length_um": "tip_length_um",
-}
+# @Chris : is this necessary ?
+# pi_to_pt_names = {
+#     "x_pitch": "electrode_pitch_horz_um",
+#     "y_pitch": "electrode_pitch_vert_um",
+#     "contact_width": "electrode_size_horz_direction_um",
+#     "shank_pitch": "shank_pitch_um",
+#     "shank_number": "num_shanks",
+#     "ncols_per_shank": "cols_per_shank",
+#     "nrows_per_shank": "rows_per_shank",
+#     "adc_bit_depth": "adc_bit_depth",
+#     "model_name": "description",
+#     "num_readout_channels": "num_readout_channels",
+#     "shank_width_um": "shank_width_um",
+#     "tip_length_um": "tip_length_um",
+# }
 
 
 def get_probe_length(probe_part_number: str) -> int:
@@ -271,9 +272,8 @@ def _make_npx_probe_from_description(probe_description, model_name, elec_ids, sh
     positions = np.stack((x_pos, y_pos), axis=1)
 
     # construct Probe object
-    probe = Probe(
-        ndim=2, si_units="um", model_name=model_name, manufacturer="imec", name=probe_description["description"]
-    )
+    probe = Probe(ndim=2, si_units="um", model_name=model_name, manufacturer="imec")
+    probe.description = probe_description["description"]
     probe.set_contacts(
         positions=positions,
         shapes="square",
@@ -905,14 +905,12 @@ def read_openephys(
         )
         num_shanks = pt_metadata["num_shanks"]
 
-        model_name = pt_metadata.get("description")
-        if model_name is None:
-            model_name = "Unknown"
+        description = pt_metadata.get("description")
 
         elec_ids = []
         for i, pos in enumerate(positions):
             # Do not calculate contact ids if the model name is not known
-            if model_name == "Unknown":
+            if description is None:
                 elec_ids = None
                 break
 
@@ -1060,6 +1058,7 @@ def read_openephys(
         pt_metadata, probe_part_number, elec_ids, shank_ids=shank_ids, mux_table=mux_table
     )
     probe.serial_number = np_probe_info["serial_number"]
+    probe.name = np_probe_info["name"]
 
     probe.annotate(
         part_number=np_probe_info["part_number"],

src/probeinterface/probe.py

@@ -201,6 +201,18 @@ def manufacturer(self, value):
             # we remove the annotation if it exists
             _ = self.annotations.pop("manufacturer", None)
 
+    @property
+    def description(self):
+        return self.annotations.get("description", None)
+
+    @description.setter
+    def description(self, value):
+        if value is not None:
+            self.annotate(description=value)
+        else:
+            # we remove the annotation if it exists
+            _ = self.annotations.pop("description", None)
+
     def get_title(self) -> str:
         if self.contact_positions is None:
             txt = "Undefined probe"

tests/test_io/test_openephys.py

@@ -85,15 +85,15 @@ def test_NP1_subset():
     validate_probe_dict(probe_dict)
 
     assert probe_ap.get_shank_count() == 1
-    assert "1.0" in probe_ap.name
+    assert "1.0" in probe_ap.description
     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.name
+    assert "1.0" in probe_lf.description
     assert len(probe_lf.contact_positions) == 200
 
     # Not specifying the stream_name should raise an Exception, because both the ProbeA-AP and
@@ -109,7 +109,7 @@ def test_multiple_probes():
     validate_probe_dict(probe_dict)
 
     assert probeA.get_shank_count() == 1
-    assert "1.0" in probeA.name
+    assert "1.0" in probeA.description
 
     probeB = read_openephys(
         data_path / "OE_Neuropix-PXI-multi-probe" / "settings.xml",

tests/test_io/test_spikeglx.py

@@ -43,7 +43,7 @@ def test_get_saved_channel_indices_from_spikeglx_meta():
 
 def test_NP1():
     probe = read_spikeglx(data_path / "Noise_g0_t0.imec0.ap.meta")
-    assert "1.0" in probe.name
+    assert "1.0" in probe.description
 
 
 def test_NP_phase3A():
@@ -66,7 +66,7 @@ def test_NP_phase3A():
 
 def test_NP2_1_shanks():
     probe = read_spikeglx(data_path / "p2_g0_t0.imec0.ap.meta")
-    assert "2.0" in probe.name
+    assert "2.0" in probe.description
     assert probe.get_shank_count() == 1
 
 
@@ -163,7 +163,7 @@ def test_NP2_4_shanks_with_different_electrodes_saved():
 def test_NP1_large_depth_span():
     # Data provided by Tom Bugnon NP1 with large Depth span
     probe = read_spikeglx(data_path / "allan-longcol_g0_t0.imec0.ap.meta")
-    assert "1.0" in probe.name
+    assert "1.0" in probe.description
     assert probe.get_shank_count() == 1
     ypos = probe.contact_positions[:, 1]
     assert (np.max(ypos) - np.min(ypos)) > 7600
@@ -173,7 +173,7 @@ def test_NP1_other_example():
     # Data provided by Tom Bugnon NP1
     probe = read_spikeglx(data_path / "doppio-checkerboard_t0.imec0.ap.meta")
     print(probe)
-    assert "1.0" in probe.name
+    assert "1.0" in probe.description
     assert probe.get_shank_count() == 1
     ypos = probe.contact_positions[:, 1]
     assert (np.max(ypos) - np.min(ypos)) > 7600
@@ -317,7 +317,7 @@ def test_ultra_probe():
 
 def test_CatGT_NP1():
     probe = read_spikeglx(data_path / "catgt.meta")
-    assert "1.0" in probe.name
+    assert "1.0" in probe.description
 
 
 def test_snsGeomMap():