Merge branch 'main' of github.com:int-brain-lab/ibl-neuropixel

int-brain-lab · Jul 2, 2024 · c358990 · c358990
2 parents 3641c1e + e49f6c5
commit c358990
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diff --git a/release_notes.md b/release_notes.md
@@ -1,3 +1,7 @@
+# 1.1.0
+## 1.1.1 2024-06-07
+-  Add support for NP2.0 prototype probe with probetype 1030
+
 # 1.0.0
 ## 1.0.1 2024-05-29: support for waveform extraction on non-standard electrode layouts
   - bugfix waveform extraction: the probe channel layout is inferred from the spikeglx metadata by default

diff --git a/setup.py b/setup.py
@@ -8,7 +8,7 @@
 
 setuptools.setup(
     name="ibl-neuropixel",
-    version="1.1.0a02",
+    version="1.1.1",
     author="The International Brain Laboratory",
     description="Collection of tools for Neuropixel 1.0 and 2.0 probes data",
     long_description=long_description,

diff --git a/src/ibldsp/voltage.py b/src/ibldsp/voltage.py
@@ -740,7 +740,7 @@ def nxcor(x, ref):
         )
     )[0]
     # the channels outside of the brains are the contiguous channels below the threshold on the trend coherency
-    ioutside = np.where(xfeats["xcor_lf"] < -0.75)[0]
+    ioutside = np.where(xfeats["xcor_lf"] < -0.75)[0]  # fixme: hardcoded threshold
     if ioutside.size > 0 and ioutside[-1] == (nc - 1):
         a = np.cumsum(np.r_[0, np.diff(ioutside) - 1])
         ioutside = ioutside[a == np.max(a)]

diff --git a/src/spikeglx.py b/src/spikeglx.py
@@ -545,6 +545,8 @@ def _get_max_int_from_meta(md, neuropixel_version=None):
 def _get_neuropixel_version_from_meta(md):
     """
     Get neuropixel version tag (3A, 3B1, 3B2) from the metadata dictionary
+    A useful resource is the following link:
+    https://billkarsh.github.io/SpikeGLX/help/parsing/
     """
     if "typeEnabled" in md.keys():
         return "3A"
@@ -556,7 +558,7 @@ def _get_neuropixel_version_from_meta(md):
         else:
             return "3B1"
     # Neuropixel 2.0 single shank
-    elif prb_type == 21:
+    elif prb_type == 21 or prb_type == 1030:
         return "NP2.1"
     # Neuropixel 2.0 four shank
     elif prb_type == 24 or prb_type == 2013:

diff --git a/src/tests/unit/cpu/fixtures/sampleNP2.1_prototype.ap.meta b/src/tests/unit/cpu/fixtures/sampleNP2.1_prototype.ap.meta
@@ -0,0 +1,51 @@
+acqApLfSy=384,384,1
+appVersion=20201012
+fileCreateTime=2021-08-03T13:48:51
+fileName=C:/SGL_DATA/210803_133520_Alfie_g0/210803_133520_Alfie_g0_imec1/210803_133520_Alfie_g0_t0.imec1.ap.bin
+fileSHA1=6F56A3A1E5C31822B234D3D6323C71779BEEC480
+fileSizeBytes=206258928260
+fileTimeSecs=8928.957933333333
+firstSample=422882
+gateMode=Immediate
+imAiRangeMax=0.6
+imAiRangeMin=-0.6
+imCalibrated=true
+imDatApi=3.31
+imDatBs_fw=2.0.137
+imDatBsc_fw=3.2.176
+imDatBsc_hw=5.1
+imDatBsc_pn=NP2_HS_30
+imDatBsc_sn=586
+imDatFx_hw=3.6
+imDatFx_pn=NPNH_AFLEX_00
+imDatHs_fw=5.1
+imDatHs_pn=NP2_HS_30
+imDatHs_sn=922
+imDatPrb_dock=1
+imDatPrb_pn=NP1030
+imDatPrb_port=2
+imDatPrb_slot=2
+imDatPrb_sn=19445518081
+imDatPrb_type=1030
+imLEDEnable=false
+imMaxInt=512
+imRoFile=
+imSampRate=30000
+imStdby=
+imTrgRising=true
+imTrgSource=0
+nDataDirs=1
+nSavedChans=385
+snsApLfSy=384,0,1
+snsSaveChanSubset=0:383,768
+syncImInputSlot=2
+syncSourceIdx=0
+syncSourcePeriod=1
+trigMode=Immediate
+typeImEnabled=2
+typeNiEnabled=1
+typeThis=imec
+userNotes=
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+~snsChanMap=(384,384,1)(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;24:24)(AP25;25:25)(AP26;26:26)(AP27;27:27)(AP28;28:28)(AP29;29:29)(AP30;30:30)(AP31;31:31)(AP32;32:32)(AP33;33:33)(AP34;34:34)(AP35;35:35)(AP36;36:36)(AP37;37:37)(AP38;38:38)(AP39;39:39)(AP40;40:40)(AP41;41:41)(AP42;42:42)(AP43;43:43)(AP44;44:44)(AP45;45:45)(AP46;46:46)(AP47;47:47)(AP48;48:48)(AP49;49:49)(AP50;50:50)(AP51;51:51)(AP52;52:52)(AP53;53:53)(AP54;54:54)(AP55;55:55)(AP56;56:56)(AP57;57:57)(AP58;58:58)(AP59;59:59)(AP60;60:60)(AP61;61:61)(AP62;62:62)(AP63;63:63)(AP64;64:64)(AP65;65:65)(AP66;66:66)(AP67;67:67)(AP68;68:68)(AP69;69:69)(AP70;70:70)(AP71;71:71)(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)(AP96;96:96)(AP97;97:97)(AP98;98:98)(AP99;99:99)(AP100;100:100)(AP101;101:101)(AP102;102:102)(AP103;103:103)(AP104;104:104)(AP105;105:105)(AP106;106:106)(AP107;107:107)(AP108;108:108)(AP109;109:109)(AP110;110:110)(AP111;111:111)(AP112;112:112)(AP113;113:113)(AP114;114:114)(AP115;115:115)(AP116;116:116)(AP117;117:117)(AP118;118:118)(AP119;119:119)(AP120;120:120)(AP121;121:121)(AP122;122:122)(AP123;123:123)(AP124;124:124)(AP125;125:125)(AP126;126:126)(AP127;127:127)(AP128;128:128)(AP129;129:129)(AP130;130:130)(AP131;131:131)(AP132;132:132)(AP133;133:133)(AP134;134:134)(AP135;135:135)(AP136;136:136)(AP137;137:137)(AP138;138:138)(AP139;139:139)(AP140;140:140)(AP141;141:141)(AP142;142:142)(AP143;143:143)(AP144;144:144)(AP145;145:145)(AP146;146:146)(AP147;147:147)(AP148;148:148)(AP149;149:149)(AP150;150:150)(AP151;151:151)(AP152;152:152)(AP153;153:153)(AP154;154:154)(AP155;155:155)(AP156;156:156)(AP157;157:157)(AP158;158:158)(AP159;159:159)(AP160;160:160)(AP161;161:161)(AP162;162:162)(AP163;163:163)(AP164;164:164)(AP165;165:165)(AP166;166:166)(AP167;167:167)(AP168;168:168)(AP169;169:169)(AP170;170:170)(AP171;171:171)(AP172;172:172)(AP173;173:173)(AP174;174:174)(AP175;175:175)(AP176;176:176)(AP177;177:177)(AP178;178:178)(AP179;179:179)(AP180;180:180)(AP181;181:181)(AP182;182:182)(AP183;183:183)(AP184;184:184)(AP185;185:185)(AP186;186:186)(AP187;187:187)(AP188;188:188)(AP189;189:189)(AP190;190:190)(AP191;191:191)(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;216:216)(AP217;217:217)(AP218;218:218)(AP219;219:219)(AP220;220:220)(AP221;221:221)(AP222;222:222)(AP223;223:223)(AP224;224:224)(AP225;225:225)(AP226;226:226)(AP227;227:227)(AP228;228:228)(AP229;229:229)(AP230;230:230)(AP231;231:231)(AP232;232:232)(AP233;233:233)(AP234;234:234)(AP235;235:235)(AP236;236:236)(AP237;237:237)(AP238;238:238)(AP239;239:239)(AP240;240:240)(AP241;241:241)(AP242;242:242)(AP243;243:243)(AP244;244:244)(AP245;245:245)(AP246;246:246)(AP247;247:247)(AP248;248:248)(AP249;249:249)(AP250;250:250)(AP251;251:251)(AP252;252:252)(AP253;253:253)(AP254;254:254)(AP255;255:255)(AP256;256:256)(AP257;257:257)(AP258;258:258)(AP259;259:259)(AP260;260:260)(AP261;261:261)(AP262;262:262)(AP263;263:263)(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)(AP288;288:288)(AP289;289:289)(AP290;290:290)(AP291;291:291)(AP292;292:292)(AP293;293:293)(AP294;294:294)(AP295;295:295)(AP296;296:296)(AP297;297:297)(AP298;298:298)(AP299;299:299)(AP300;300:300)(AP301;301:301)(AP302;302:302)(AP303;303:303)(AP304;304:304)(AP305;305:305)(AP306;306:306)(AP307;307:307)(AP308;308:308)(AP309;309:309)(AP310;310:310)(AP311;311:311)(AP312;312:312)(AP313;313:313)(AP314;314:314)(AP315;315:315)(AP316;316:316)(AP317;317:317)(AP318;318:318)(AP319;319:319)(AP320;320:320)(AP321;321:321)(AP322;322:322)(AP323;323:323)(AP324;324:324)(AP325;325:325)(AP326;326:326)(AP327;327:327)(AP328;328:328)(AP329;329:329)(AP330;330:330)(AP331;331:331)(AP332;332:332)(AP333;333:333)(AP334;334:334)(AP335;335:335)(AP336;336:336)(AP337;337:337)(AP338;338:338)(AP339;339:339)(AP340;340:340)(AP341;341:341)(AP342;342:342)(AP343;343:343)(AP344;344:344)(AP345;345:345)(AP346;346:346)(AP347;347:347)(AP348;348:348)(AP349;349:349)(AP350;350:350)(AP351;351:351)(AP352;352:352)(AP353;353: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+~snsShankMap=(1,2,2208)(0:0:0:1)(0:1:0:1)(0:0:1:1)(0:1:1:1)(0:0:2:1)(0:1:2:1)(0:0:3:1)(0:1:3:1)(0:0:4:1)(0:1:4:1)(0:0:5:1)(0:1:5:1)(0:0:6:1)(0:1:6:1)(0:0:7:1)(0:1:7:1)(0:0:8:1)(0:1:8:1)(0:0:9:1)(0:1:9:1)(0:0:10:1)(0:1:10:1)(0:0:11:1)(0:1:11:1)(0:0:12:1)(0:1:12:1)(0:0:13:1)(0:1:13:1)(0:0:14:1)(0:1:14:1)(0:0:15:1)(0:1:15:1)(0:0:16:1)(0:1:16:1)(0:0:17:1)(0:1:17:1)(0:0:18:1)(0:1:18:1)(0:0:19:1)(0:1:19:1)(0:0:20:1)(0:1:20:1)(0:0:21:1)(0:1:21:1)(0:0:22:1)(0:1:22:1)(0:0:23:1)(0:1:23:1)(0:0:24:1)(0:1:24:1)(0:0:25:1)(0:1:25:1)(0:0:26:1)(0:1:26:1)(0:0:27:1)(0:1:27:1)(0:0:28:1)(0:1:28:1)(0:0:29:1)(0:1:29:1)(0:0:30:1)(0:1:30:1)(0:0:31:1)(0:1:31:1)(0:0:32:1)(0:1:32:1)(0:0:33:1)(0:1:33:1)(0:0:34:1)(0:1:34:1)(0:0:35:1)(0:1:35:1)(0:0:36:1)(0:1:36:1)(0:0:37:1)(0:1:37:1)(0:0:38:1)(0:1:38:1)(0:0:39:1)(0:1:39:1)(0:0:40:1)(0:1:40:1)(0:0:41:1)(0:1:41:1)(0:0:42:1)(0:1:42:1)(0:0:43:1)(0:1:43:1)(0:0:44:1)(0:1:44:1)(0:0:45:1)(0:1:45:1)(0:0:46:1)(0:1:46:1)(0:0:47:1)(0:1:47:1)(0:0:48:1)(0:1:48:1)(0:0:49:1)(0:1:49:1)(0:0:50:1)(0:1:50:1)(0:0:51:1)(0:1:51:1)(0:0:52:1)(0:1:52:1)(0:0:53:1)(0:1:53:1)(0:0:54:1)(0:1:54:1)(0:0:55:1)(0:1:55:1)(0:0:56:1)(0:1:56:1)(0:0:57:1)(0:1:57:1)(0:0:58:1)(0:1:58:1)(0:0:59:1)(0:1:59:1)(0:0:60:1)(0:1:60:1)(0:0:61:1)(0:1:61:1)(0:0:62:1)(0:1:62:1)(0:0:63:1)(0:1:63:1)(0:0:64:1)(0:1:64:1)(0:0:65:1)(0:1:65:1)(0:0:66:1)(0:1:66:1)(0:0:67:1)(0:1:67:1)(0:0:68:1)(0:1:68:1)(0:0:69:1)(0:1:69:1)(0:0:70:1)(0:1:70:1)(0:0:71:1)(0:1:71:1)(0:0:72:1)(0:1:72:1)(0:0:73:1)(0:1:73:1)(0:0:74:1)(0:1:74:1)(0:0:75:1)(0:1:75:1)(0:0:76:1)(0:1:76:1)(0:0:77:1)(0:1:77:1)(0:0:78:1)(0:1:78:1)(0:0:79:1)(0:1:79:1)(0:0:80:1)(0:1:80:1)(0:0:81:1)(0:1:81:1)(0:0:82:1)(0:1:82:1)(0:0:83:1)(0:1:83:1)(0:0:84:1)(0:1:84:1)(0:0:85:1)(0:1:85:1)(0:0:86:1)(0:1:86:1)(0:0:87:1)(0:1:87:1)(0:0:88:1)(0:1:88:1)(0:0:89:1)(0:1:89:1)(0:0:90:1)(0:1:90:1)(0:0:91:1)(0:1:91:1)(0:0:92:1)(0:1:92:1)(0:0:93:1)(0:1:93:1)(0:0:94:1)(0:1:94:1)(0:0:95:1)(0:1:95:0)(0:0:96:1)(0:1:96:1)(0:0:97:1)(0:1:97:1)(0:0:98:1)(0:1:98:1)(0:0:99:1)(0:1:99:1)(0:0:100:1)(0:1:100:1)(0:0:101:1)(0:1:101:1)(0:0:102:1)(0:1:102:1)(0:0:103:1)(0:1:103:1)(0:0:104:1)(0:1:104:1)(0:0:105:1)(0:1:105:1)(0:0:106:1)(0:1:106:1)(0:0:107:1)(0:1:107:1)(0:0:108:1)(0:1:108:1)(0:0:109:1)(0:1:109:1)(0:0:110:1)(0:1:110:1)(0:0:111:1)(0:1:111:1)(0:0:112:1)(0:1:112:1)(0:0:113:1)(0:1:113:1)(0:0:114:1)(0:1:114:1)(0:0:115:1)(0:1:115:1)(0:0:116:1)(0:1:116:1)(0:0:117:1)(0:1:117:1)(0:0:118:1)(0:1:118:1)(0:0:119:1)(0:1:119:1)(0:0:120:1)(0:1:120:1)(0:0:121:1)(0:1:121:1)(0:0:122:1)(0:1:122:1)(0:0:123:1)(0:1:123:1)(0:0:124:1)(0:1:124:1)(0:0:125:1)(0:1:125:1)(0:0:126:1)(0:1:126:1)(0:0:127:1)(0:1:127:1)(0:0:128:1)(0:1:128:1)(0:0:129:1)(0:1:129:1)(0:0:130:1)(0:1:130:1)(0:0:131:1)(0:1:131:1)(0:0:132:1)(0:1:132:1)(0:0:133:1)(0:1:133:1)(0:0:134:1)(0:1:134:1)(0:0:135:1)(0:1:135:1)(0:0:136:1)(0:1:136:1)(0:0:137:1)(0:1:137:1)(0:0:138:1)(0:1:138:1)(0:0:139:1)(0:1:139:1)(0:0:140:1)(0:1:140:1)(0:0:141:1)(0:1:141:1)(0:0:142:1)(0:1:142:1)(0:0:143:1)(0:1:143:1)(0:0:144:1)(0:1:144:1)(0:0:145:1)(0:1:145:1)(0:0:146:1)(0:1:146:1)(0:0:147:1)(0:1:147:1)(0:0:148:1)(0:1:148:1)(0:0:149:1)(0:1:149:1)(0:0:150:1)(0:1:150:1)(0:0:151:1)(0:1:151:1)(0:0:152:1)(0:1:152:1)(0:0:153:1)(0:1:153:1)(0:0:154:1)(0:1:154:1)(0:0:155:1)(0:1:155:1)(0:0:156:1)(0:1:156:1)(0:0:157:1)(0:1:157:1)(0:0:158:1)(0:1:158:1)(0:0:159:1)(0:1:159:1)(0:0:160:1)(0:1:160:1)(0:0:161:1)(0:1:161:1)(0:0:162:1)(0:1:162:1)(0:0:163:1)(0:1:163:1)(0:0:164:1)(0:1:164:1)(0:0:165:1)(0:1:165:1)(0:0:166:1)(0:1:166:1)(0:0:167:1)(0:1:167:1)(0:0:168:1)(0:1:168:1)(0:0:169:1)(0:1:169:1)(0:0:170:1)(0:1:170:1)(0:0:171:1)(0:1:171:1)(0:0:172:1)(0:1:172:1)(0:0:173:1)(0:1:173:1)(0:0:174:1)(0:1:174:1)(0:0:175:1)(0:1:175:1)(0:0:176:1)(0:1:176:1)(0:0:177:1)(0:1:177:1)(0:0:178:1)(0:1:178:1)(0:0:179:1)(0:1:179:1)(0:0:180:1)(0:1:180:1)(0:0:181:1)(0:1:181:1)(0:0:182:1)(0:1:182:1)(0:0:183:1)(0:1:183:1)(0:0:184:1)(0:1:184:1)(0:0:185:1)(0:1:185:1)(0:0:186:1)(0:1:186:1)(0:0:187:1)(0:1:187:1)(0:0:188:1)(0:1:188:1)(0:0:189:1)(0:1:189:1)(0:0:190:1)(0:1:190:1)(0:0:191:1)(0:1:191:1)
diff --git a/src/tests/unit/cpu/test_spikeglx.py b/src/tests/unit/cpu/test_spikeglx.py
@@ -371,6 +371,17 @@ def test_read_3B(self):
             )
             self.assert_read_glx(bin_3b)
 
+    def test_read_NP20_prototype(self):
+        with tempfile.TemporaryDirectory(prefix="glx_test") as tdir:
+            bin_3b = spikeglx._mock_spikeglx_file(
+                Path(tdir).joinpath("sampleNP2.1_prototype.ap.bin"),
+                self.workdir / "sampleNP2.1_prototype.ap.meta",
+                ns=32,
+                nc=385,
+                sync_depth=16,
+            )
+            self.assert_read_glx(bin_3b)
+
     def test_read_NP21(self):
         with tempfile.TemporaryDirectory(prefix="glx_test") as tdir:
             bin_3b = spikeglx._mock_spikeglx_file(