Extend available NP2 probe types

.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: .

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
 

tests/data/spikeglx/NP2_2013_subset_channels.imec0.ap.meta

@@ -0,0 +1,62 @@
+acqApLfSy=384,0,1
+appVersion=20230815
+fileCreateTime=2023-09-04T16:03:26
+fileName=F://chan_below_r65_sync_g0/chan_below_r65_sync_g0_imec0/chan_below_r65_sync_g0_t0.imec0.ap.bin
+fileSHA1=8A7F08D4C8AA82589527E6DFC19ACEA0E6E2665B
+fileSizeBytes=75511260
+fileTimeSecs=10.401
+firstSample=920506
+gateMode=Immediate
+imAiRangeMax=0.62
+imAiRangeMin=-0.62
+imAnyChanFullBand=true
+imCalibrated=false
+imChan0apGain=100
+imDatApi=3.62
+imDatBs_fw=2.0.169
+imDatBsc_fw=3.2.189
+imDatBsc_hw=1.9
+imDatBsc_pn=NP2_QBSC_00
+imDatBsc_sn=175
+imDatFx_hw=0.1
+imDatFx_pn=NPM_FLEX_01
+imDatFx_sn=23100013
+imDatHs_hw=3.2
+imDatHs_pn=NPM_HS_31
+imDatHs_sn=23100013
+imDatPrb_dock=1
+imDatPrb_pn=NP2013
+imDatPrb_port=1
+imDatPrb_slot=6
+imDatPrb_sn=12345601012
+imDatPrb_type=2013
+imErrFlags_IS_CT_SR_LK_PP_SY=0 0 0 0 0 0
+imIsSvyRun=false
+imLEDEnable=false
+imLowLatency=false
+imMaxInt=2048
+imSampRate=30000
+imStdby=
+imSvyMaxBnk=-1
+imSvySecPerBnk=60
+imTipLength=206
+imTrgRising=true
+imTrgSource=0
+imroFile=F:/16_box_pat.imro
+nDataDirs=1
+nSavedChans=121
+snsApLfSy=120,0,1
+snsSaveChanSubset=0:35,72:95,192:227,264:287,384
+syncImInputSlot=6
+syncSourceIdx=2
+syncSourcePeriod=1
+trigMode=Immediate
+typeImEnabled=1
+typeNiEnabled=1
+typeObEnabled=0
+typeThis=imec
+userNotes=
+~imroTbl=(2013,384)(0 0 0 0 0)(1 0 0 0 1)(2 0 0 0 2)(3 0 0 0 3)(4 0 0 0 4)(5 0 0 0 5)(6 0 0 0 6)(7 0 0 0 7)(8 0 0 0 8)(9 0 0 0 9)(10 0 0 0 10)(11 0 0 0 11)(12 0 0 0 12)(13 0 0 0 13)(14 0 0 0 14)(15 0 0 0 15)(16 0 0 0 16)(17 0 0 0 17)(18 0 0 0 18)(19 0 0 0 19)(20 0 0 0 20)(21 0 0 0 21)(22 0 0 0 22)(23 0 0 0 23)(24 2 0 0 120)(25 2 0 0 121)(26 2 0 0 122)(27 2 0 0 123)(28 2 0 0 124)(29 2 0 0 125)(30 2 0 0 126)(31 2 0 0 127)(32 2 0 0 128)(33 2 0 0 129)(34 2 0 0 130)(35 2 0 0 131)(36 2 0 0 132)(37 2 0 0 133)(38 2 0 0 134)(39 2 0 0 135)(40 2 0 0 136)(41 2 0 0 137)(42 2 0 0 138)(43 2 0 0 139)(44 2 0 0 140)(45 2 0 0 141)(46 2 0 0 142)(47 2 0 0 143)(48 1 1 0 384)(49 1 1 0 385)(50 1 1 0 386)(51 1 1 0 387)(52 1 1 0 388)(53 1 1 0 389)(54 1 1 0 390)(55 1 1 0 391)(56 1 1 0 392)(57 1 1 0 393)(58 1 1 0 394)(59 1 1 0 395)(60 1 1 0 396)(61 1 1 0 397)(62 1 1 0 398)(63 1 1 0 399)(64 1 1 0 400)(65 1 1 0 401)(66 1 1 0 402)(67 1 1 0 403)(68 1 1 0 404)(69 1 1 0 405)(70 1 1 0 406)(71 1 1 0 407)(72 1 0 0 24)(73 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+~muxTbl=(24,16)(0 1 32 33 64 65 96 97 128 129 160 161 192 193 224 225 256 257 288 289 320 321 352 353)(2 3 34 35 66 67 98 99 130 131 162 163 194 195 226 227 258 259 290 291 322 323 354 355)(4 5 36 37 68 69 100 101 132 133 164 165 196 197 228 229 260 261 292 293 324 325 356 357)(6 7 38 39 70 71 102 103 134 135 166 167 198 199 230 231 262 263 294 295 326 327 358 359)(8 9 40 41 72 73 104 105 136 137 168 169 200 201 232 233 264 265 296 297 328 329 360 361)(10 11 42 43 74 75 106 107 138 139 170 171 202 203 234 235 266 267 298 299 330 331 362 363)(12 13 44 45 76 77 108 109 140 141 172 173 204 205 236 237 268 269 300 301 332 333 364 365)(14 15 46 47 78 79 110 111 142 143 174 175 206 207 238 239 270 271 302 303 334 335 366 367)(16 17 48 49 80 81 112 113 144 145 176 177 208 209 240 241 272 273 304 305 336 337 368 369)(18 19 50 51 82 83 114 115 146 147 178 179 210 211 242 243 274 275 306 307 338 339 370 371)(20 21 52 53 84 85 116 117 148 149 180 181 212 213 244 245 276 277 308 309 340 341 372 373)(22 23 54 55 86 87 118 119 150 151 182 183 214 215 246 247 278 279 310 311 342 343 374 375)(24 25 56 57 88 89 120 121 152 153 184 185 216 217 248 249 280 281 312 313 344 345 376 377)(26 27 58 59 90 91 122 123 154 155 186 187 218 219 250 251 282 283 314 315 346 347 378 379)(28 29 60 61 92 93 124 125 156 157 188 189 220 221 252 253 284 285 316 317 348 349 380 381)(30 31 62 63 94 95 126 127 158 159 190 191 222 223 254 255 286 287 318 319 350 351 382 383)
+~snsChanMap=(384,0,1)(AP0;0:0)(AP1;1:1)(AP2;2:2)(AP3;3:3)(AP4;4:4)(AP5;5:5)(AP6;6:6)(AP7;7:7)(AP8;8:8)(AP9;9:9)(AP10;10:10)(AP11;11:11)(AP12;12:12)(AP13;13:13)(AP14;14:14)(AP15;15:15)(AP16;16:16)(AP17;17:17)(AP18;18:18)(AP19;19:19)(AP20;20:20)(AP21;21:21)(AP22;22:22)(AP23;23:23)(AP24;24:216)(AP25;25:217)(AP26;26:218)(AP27;27:219)(AP28;28:220)(AP29;29:221)(AP30;30:222)(AP31;31:223)(AP32;32:224)(AP33;33:225)(AP34;34:226)(AP35;35:227)(AP72;72:72)(AP73;73:73)(AP74;74:74)(AP75;75:75)(AP76;76:76)(AP77;77:77)(AP78;78:78)(AP79;79:79)(AP80;80:80)(AP81;81:81)(AP82;82:82)(AP83;83:83)(AP84;84:84)(AP85;85:85)(AP86;86:86)(AP87;87:87)(AP88;88:88)(AP89;89:89)(AP90;90:90)(AP91;91:91)(AP92;92:92)(AP93;93:93)(AP94;94:94)(AP95;95:95)(AP192;192:192)(AP193;193:193)(AP194;194:194)(AP195;195:195)(AP196;196:196)(AP197;197:197)(AP198;198:198)(AP199;199:199)(AP200;200:200)(AP201;201:201)(AP202;202:202)(AP203;203:203)(AP204;204:204)(AP205;205:205)(AP206;206:206)(AP207;207:207)(AP208;208:208)(AP209;209:209)(AP210;210:210)(AP211;211:211)(AP212;212:212)(AP213;213:213)(AP214;214:214)(AP215;215:215)(AP216;216:24)(AP217;217:25)(AP218;218:26)(AP219;219:27)(AP220;220:28)(AP221;221:29)(AP222;222:30)(AP223;223:31)(AP224;224:32)(AP225;225:33)(AP226;226:34)(AP227;227:35)(AP264;264:264)(AP265;265:265)(AP266;266:266)(AP267;267:267)(AP268;268:268)(AP269;269:269)(AP270;270:270)(AP271;271:271)(AP272;272:272)(AP273;273:273)(AP274;274:274)(AP275;275:275)(AP276;276:276)(AP277;277:277)(AP278;278:278)(AP279;279:279)(AP280;280:280)(AP281;281:281)(AP282;282:282)(AP283;283:283)(AP284;284:284)(AP285;285:285)(AP286;286:286)(AP287;287:287)(SY0;384:384)
+~snsGeomMap=(NP2013,4,250,70)(0:27:0:1)(0:59:0:1)(0:27:15:1)(0:59:15:1)(0:27:30:1)(0:59:30:1)(0:27:45:1)(0:59:45:1)(0:27:60:1)(0:59:60:1)(0:27:75:1)(0:59:75:1)(0:27:90:1)(0:59:90:1)(0:27:105:1)(0:59:105:1)(0:27:120:1)(0:59:120:1)(0:27:135:1)(0:59:135:1)(0:27:150:1)(0:59:150:1)(0:27:165:1)(0:59:165:1)(2:27:900:1)(2:59:900:1)(2:27:915:1)(2:59:915:1)(2:27:930:1)(2:59:930:1)(2:27:945:1)(2:59:945:1)(2:27:960:1)(2:59:960:1)(2:27:975:1)(2:59:975:1)(1:27:180:1)(1:59:180:1)(1:27:195:1)(1:59:195:1)(1:27:210:1)(1:59:210:1)(1:27:225:1)(1:59:225:1)(1:27:240:1)(1:59:240:1)(1:27:255:1)(1:59:255:1)(1:27:270:1)(1:59:270:1)(1:27:285:1)(1:59:285:1)(1:27:300:1)(1:59:300:1)(1:27:315:1)(1:59:315:1)(1:27:330:1)(1:59:330:1)(1:27:345:1)(1:59:345:1)(2:27:0:1)(2:59:0:1)(2:27:15:1)(2:59:15:1)(2:27:30:1)(2:59:30:1)(2:27:45:1)(2:59:45:1)(2:27:60:1)(2:59:60:1)(2:27:75:1)(2:59:75:1)(2:27:90:1)(2:59:90:1)(2:27:105:1)(2:59:105:1)(2:27:120:1)(2:59:120:1)(2:27:135:1)(2:59:135:1)(2:27:150:1)(2:59:150:1)(2:27:165:1)(2:59:165:1)(0:27:900:1)(0:59:900:1)(0:27:915:1)(0:59:915:1)(0:27:930:1)(0:59:930:1)(0:27:945:1)(0:59:945:1)(0:27:960:1)(0:59:960:1)(0:27:975:1)(0:59:975:1)(3:27:180:1)(3:59:180:1)(3:27:195:1)(3:59:195:1)(3:27:210:1)(3:59:210:1)(3:27:225:1)(3:59:225:1)(3:27:240:1)(3:59:240:1)(3:27:255:1)(3:59:255:1)(3:27:270:1)(3:59:270:1)(3:27:285:1)(3:59:285:1)(3:27:300:1)(3:59:300:1)(3:27:315:1)(3:59:315:1)(3:27:330:1)(3:59:330:1)(3:27:345:1)(3:59:345:1)

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
 

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()