flatironinstitute / ironclust

Spike sorting software being developed at Flatiron Institute, based on JRCLUST (Janelia Rocket Cluster)
Apache License 2.0
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error running .bin files #41

Closed WeissShahaf closed 4 years ago

WeissShahaf commented 4 years ago

Hey James, when trying to run irc2 i get the following error:

ran command: irc2 GL383_20190830_CIRCLE_g0_t0.imec0.ap.bin

error message: Index in position 1 exceeds array bounds (must not exceed 1). Error in irc2>readmdapaged (line 4445) if ~isempty(viSite2Chan), out = out(P.viSite2Chan,:); end Error in irc2>detect_ (line 3551) [mrWav_T1, nlim_wav1, fDone] = readmdapaged(); var_size1 = varsize(mrWavT1); Error in irc2 (line 175) S0 = detect(P);

debug line 4445> if ~isempty(viSite2Chan), out = out(P.viSite2Chan,:); end

K>> whos out Name Size Bytes Class Attributes

out 1x125000300 250000600 int16

jamesjun commented 4 years ago

this is because the probe file is not specified. i will add this feature today and let you specify a probe file. for Neuropixels probes this is not needed.

-James

On Feb 5, 2020, at 4:52 AM, WeissShahaf notifications@github.com wrote:

 Hey James, when trying to run irc2 i get the following error:

ran command: irc2 GL383_20190830_CIRCLE_g0_t0.imec0.ap.bin

error message: Index in position 1 exceeds array bounds (must not exceed 1). Error in irc2>readmdapaged (line 4445) if ~isempty(viSite2Chan), out = out(P.viSite2Chan,:); end Error in irc2>detect_ (line 3551) [mrWav_T1, nlim_wav1, fDone] = readmdapaged(); var_size1 = varsize(mrWavT1); Error in irc2 (line 175) S0 = detect(P);

debug line 4445> if ~isempty(viSite2Chan), out = out(P.viSite2Chan,:); end

K>> whos out Name Size Bytes Class Attributes

out 1x125000300 250000600 int16

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WeissShahaf commented 4 years ago

thank you. btw this was a neuropixels 1.0 probe.

WeissShahaf commented 4 years ago

i tried it again with irc2 version v5.6.8 (02/05/2020) installed, MD5: feba6fd83541b522f855c3e8a9cd1518

commandline output: irc2 GL383_20190830_CIRCLE_g0_t0.imec0.ap.bin irc2: cleared all Running irc2.m (v5.6.8) nTime_batch = 15 (batch_sec_drift = 300.0 s) nTime_drift = 104688 (step_sec_drift = 20.0 s) Created irc2\raw_geom.prm Cleared irc2\raw_geom.prm Index in position 1 exceeds array bounds (must not exceed 1). Error in irc2>readmdapaged (line 4577) if ~isempty(viSite2Chan), out = out(P.viSite2Chan,:); end Error in irc2>detect_ (line 3683) [mrWav_T1, nlim_wav1, fDone] = readmdapaged(); var_size1 = varsize(mrWavT1); Error in irc2 (line 177) S0 = detect(P);

K>> size(out) ans = 1 125000300 size(P_.viSite2Chan) ans = 1 383

when i use irc2 import-spikeglx i get the following error Index in position 1 exceeds array bounds (must not exceed 1). Error in irc2>readmdapaged (line 4577) if ~isempty(viSite2Chan), out = out(P.viSite2Chan,:); end Error in irc2>detect_ (line 3683) [mrWav_T1, nlim_wav1, fDone] = readmdapaged(); var_size1 = varsize(mrWavT1); Error in irc2 (line 177) S0 = detect(P);

now , i see the default prb file it's looking for in S_meta.vcProbe is "imec3_opt384.prb". this file does not exist in the ironclust\matlab\prb folder, but even when i specify a correct .prb file i get and error Index in position 1 exceeds array bounds (must not exceed 1). Error in irc2>importspikeglx (line 7840) writemda_fid(fidmda, mr(S_prb.viSite2Chan,:)); Error in irc2 (line 57) case 'import-spikeglx', importspikeglx(vcArg1, vcArg2, vcArg3); return;

another odd thing is that S_meta.nChans==1, s_meta.nSites==0

jamesjun commented 4 years ago

Thank you very much for trying out. The error has to do with the new .meta file standard. Unfortunately, the latest .meta file I have is two years old. I would greatly appreciate it if you could post the content of your .meta file associate with your probe.

-James

On Thu, Feb 6, 2020 at 7:41 AM WeissShahaf notifications@github.com wrote:

i tried it again with irc2 version v5.6.8 (02/05/2020) installed, MD5: feba6fd83541b522f855c3e8a9cd1518

commandline output: irc2 GL383_20190830_CIRCLE_g0_t0.imec0.ap.bin irc2: cleared all Running irc2.m (v5.6.8) nTime_batch = 15 (batch_sec_drift = 300.0 s) nTime_drift = 104688 (step_sec_drift = 20.0 s) Created irc2\raw_geom.prm Cleared irc2\raw_geom.prm Index in position 1 exceeds array bounds (must not exceed 1). Error in irc2>readmdapaged (line 4577) if ~isempty(viSite2Chan), out = out(P.viSite2Chan,:); end Error in irc2>detect_ (line 3683) [mrWav_T1, nlim_wav1, fDone] = readmdapaged(); var_size1 = varsize(mrWavT1); Error in irc2 (line 177) S0 = detect(P);

K>> size(out) ans = 1 125000300 size(P_.viSite2Chan) ans = 1 383

when i use irc2 import-spikeglx i get the following error

irc2 import-spikeglx GL383_20190830_CIRCLE_g0_t0.imec0.ap.bin 4913 S_meta.vcProbe = sprintf('imec3_opt%d', vnIMRO(3)); Wrote to mda\params.json Wrote to mda\geom.csv Index in position 1 exceeds array bounds (must not exceed 1). Error in irc2>importspikeglx (line 7840) writemda_fid(fidmda, mr(S_prb.viSite2Chan,:)); Error in irc2 (line 57) case 'import-spikeglx', importspikeglx(vcArg1, vcArg2, vcArg3); return;

now , i see the default prb file it's looking for in S_meta.vcProbe is "imec3_opt384.prb". this file does not exist in the ironclust\matlab\prb folder, but even when i specify a correct .prb file the error persists**

another odd thing is that S_meta.nChans==1, s_meta.nSites==0

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WeissShahaf commented 4 years ago

example of meta file contents: acqApLfSy=384,384,1 appVersion=20190413 catGTCmdline0=<CatGT -dir=\gpfs.corp.brain.mpg.de\laur\experiments\neuropixels\GL383\20190815\openfield -run=GL383_20190815_OF -g=0 -t=0,0 -prb_fld -t_miss_ok -prb=0 -ap -aphipass=300 -gbldmx> catTVals=0,0 fileCreateTime=2020-01-13T14:25:48 fileCreateTime_original=2019-08-15T11:46:22 fileName=//gpfs.corp.brain.mpg.de/laur/experiments/neuropixels/GL383/20190815/openfield/GL383_20190815_OF_g0/GL383_20190815_OF_g0_imec0/GL383_20190815_OF_g0_tcat.imec0.ap.bin fileSHA1=0 fileSizeBytes=90120339540 fileTimeSecs=3901.268968837841 firstSample=1879790 gateMode=Immediate imAiRangeMax=0.6 imAiRangeMin=-0.6 imCalibrated=true imDatApi=1.20 imDatBs_fw=1.1.128 imDatBsc_fw=1.0.151 imDatBsc_hw=1.9 imDatBsc_pn=NP2_QBSC_00 imDatBsc_sn=73 imDatFx_hw=1.2 imDatFx_pn=NP2_FLEX_0 imDatHs_fw=5.1 imDatHs_pn=NP2_HS_30 imDatHs_sn=255 imDatPrb_pn=PRB_1_4_0480_1_C imDatPrb_port=3 imDatPrb_slot=2 imDatPrb_sn=18408411092 imDatPrb_type=0 imLEDEnable=false imRoFile=C:/SpikeGLX/Release_v20190413-phase3B2/SpikeGLX/channelMaps/default.imro imSampRate=30000.341667 imStdby=136,238,251,258,272 imTrgRising=true imTrgSource=0 nSavedChans=385 snsApLfSy=384,0,1 snsSaveChanSubset=0:383,768 syncImInputSlot=2 syncSourceIdx=3 syncSourcePeriod=1 trgTTLAIChan=3 trgTTLBit=1 trgTTLInarow=1 trgTTLIsAnalog=false trgTTLIsNInf=true trgTTLMarginS=1 trgTTLMode=2 trgTTLNH=10 trgTTLRefractS=0.5 trgTTLStream=nidq trgTTLTH=0.5 trgTTLThresh=1.1 trigMode=TTL typeImEnabled=1 typeNiEnabled=1 typeThis=imec userNotes= ~imroTbl=(0,384)(0 0 0 500 500 0)(1 0 0 500 500 0)(2 0 0 500 500 0)(3 0 0 500 500 0)(4 0 0 500 500 0)(5 0 0 500 500 0)(6 0 0 500 500 0)(7 0 0 500 500 0)(8 0 0 500 500 0)(9 0 0 500 500 0)(10 0 0 500 500 0)(11 0 0 500 500 0)(12 0 0 500 500 0)(13 0 0 500 500 0)(14 0 0 500 500 0)(15 0 0 500 500 0)(16 0 0 500 500 0)(17 0 0 500 500 0)(18 0 0 500 500 0)(19 0 0 500 500 0)(20 0 0 500 500 0)(21 0 0 500 500 0)(22 0 0 500 500 0)(23 0 0 500 500 0)(24 0 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~snsChanMap=(384,384,1)(AP0;0:383)(AP1;1:382)(AP2;2:381)(AP3;3:380)(AP4;4:379)(AP5;5:378)(AP6;6:377)(AP7;7:376)(AP8;8:375)(AP9;9:374)(AP10;10:373)(AP11;11:372)(AP12;12:371)(AP13;13:370)(AP14;14:369)(AP15;15:368)(AP16;16:367)(AP17;17:366)(AP18;18:365)(AP19;19:364)(AP20;20:363)(AP21;21:362)(AP22;22:361)(AP23;23:360)(AP24;24:359)(AP25;25:358)(AP26;26:357)(AP27;27:356)(AP28;28:355)(AP29;29:354)(AP30;30:353)(AP31;31:352)(AP32;32:351)(AP33;33:350)(AP34;34:349)(AP35;35:348)(AP36;36:347)(AP37;37:346)(AP38;38:345)(AP39;39:344)(AP40;40:343)(AP41;41:342)(AP42;42:341)(AP43;43:340)(AP44;44:339)(AP45;45:338)(AP46;46:337)(AP47;47:336)(AP48;48:335)(AP49;49:334)(AP50;50:333)(AP51;51:332)(AP52;52:331)(AP53;53:330)(AP54;54:329)(AP55;55:328)(AP56;56:327)(AP57;57:326)(AP58;58:325)(AP59;59:324)(AP60;60:323)(AP61;61:322)(AP62;62:321)(AP63;63:320)(AP64;64:319)(AP65;65:318)(AP66;66:317)(AP67;67:316)(AP68;68:315)(AP69;69:314)(AP70;70:313)(AP71;71:312)(AP72;72:311)(AP73;73:310)(AP74;74:309)(AP75;75:308)(AP76;76:307)(AP77;77:306)(AP78;78:305)(AP79;79:304)(AP80;80:303)(AP81;81:302)(AP82;82:301)(AP83;83:300)(AP84;84:299)(AP85;85:298)(AP86;86:297)(AP87;87:296)(AP88;88:295)(AP89;89:294)(AP90;90:293)(AP91;91:292)(AP92;92:291)(AP93;93:290)(AP94;94:289)(AP95;95:288)(AP96;96:287)(AP97;97:286)(AP98;98:285)(AP99;99:284)(AP100;100:283)(AP101;101:282)(AP102;102:281)(AP103;103:280)(AP104;104:279)(AP105;105:278)(AP106;106:277)(AP107;107:276)(AP108;108:275)(AP109;109:274)(AP110;110:273)(AP111;111:272)(AP112;112:271)(AP113;113:270)(AP114;114:269)(AP115;115:268)(AP116;116:267)(AP117;117:266)(AP118;118:265)(AP119;119:264)(AP120;120:263)(AP121;121:262)(AP122;122:261)(AP123;123:260)(AP124;124:259)(AP125;125:258)(AP126;126:257)(AP127;127:256)(AP128;128:255)(AP129;129:254)(AP130;130:253)(AP131;131:252)(AP132;132:251)(AP133;133:250)(AP134;134:249)(AP135;135:248)(AP136;136:247)(AP137;137:246)(AP138;138:245)(AP139;139:244)(AP140;140:243)(AP141;141:242)(AP142;142:241)(AP143;143:240)(AP144;144:239)(AP145;145:238)(AP146;146:237)(AP147;147:236)(AP148;148:235)(AP149;149:234)(AP150;150:233)(AP151;151:232)(AP152;152:231)(AP153;153:230)(AP154;154:229)(AP155;155:228)(AP156;156:227)(AP157;157:226)(AP158;158:225)(AP159;159:224)(AP160;160:223)(AP161;161:222)(AP162;162:221)(AP163;163:220)(AP164;164:219)(AP165;165:218)(AP166;166:217)(AP167;167:216)(AP168;168:215)(AP169;169:214)(AP170;170:213)(AP171;171:212)(AP172;172:211)(AP173;173:210)(AP174;174:209)(AP175;175:208)(AP176;176:207)(AP177;177:206)(AP178;178:205)(AP179;179:204)(AP180;180:203)(AP181;181:202)(AP182;182:201)(AP183;183:200)(AP184;184:199)(AP185;185:198)(AP186;186:197)(AP187;187:196)(AP188;188:195)(AP189;189:194)(AP190;190:193)(AP191;191:192)(AP192;192:191)(AP193;193:190)(AP194;194:189)(AP195;195:188)(AP196;196:187)(AP197;197:186)(AP198;198:185)(AP199;199:184)(AP200;200:183)(AP201;201:182)(AP202;202:181)(AP203;203:180)(AP204;204:179)(AP205;205:178)(AP206;206:177)(AP207;207:176)(AP208;208:175)(AP209;209:174)(AP210;210:173)(AP211;211:172)(AP212;212:171)(AP213;213:170)(AP214;214:169)(AP215;215:168)(AP216;216:167)(AP217;217:166)(AP218;218:165)(AP219;219:164)(AP220;220:163)(AP221;221:162)(AP222;222:161)(AP223;223:160)(AP224;224:159)(AP225;225:158)(AP226;226:157)(AP227;227:156)(AP228;228:155)(AP229;229:154)(AP230;230:153)(AP231;231:152)(AP232;232:151)(AP233;233:150)(AP234;234:149)(AP235;235:148)(AP236;236:147)(AP237;237:146)(AP238;238:145)(AP239;239:144)(AP240;240:143)(AP241;241:142)(AP242;242:141)(AP243;243:140)(AP244;244:139)(AP245;245:138)(AP246;246:137)(AP247;247:136)(AP248;248:135)(AP249;249:134)(AP250;250:133)(AP251;251:132)(AP252;252:131)(AP253;253:130)(AP254;254:129)(AP255;255:128)(AP256;256:127)(AP257;257:126)(AP258;258:125)(AP259;259:124)(AP260;260:123)(AP261;261:122)(AP262;262:121)(AP263;263:120)(AP264;264:119)(AP265;265:118)(AP266;266:117)(AP267;267:116)(AP268;268:115)(AP269;269:114)(AP270;270:113)(AP271;271:112)(AP272;272:111)(AP273;273:110)(AP274;274:109)(AP275;275:108)(AP276;276:107)(AP277;277:106)(AP278;278:105)(AP279;279:104)(AP280;280:103)(AP281;281:102)(AP282;282:101)(AP283;283:100)(AP284;284:99)(AP285;285:98)(AP286;286:97)(AP287;287:96)(AP288;288:95)(AP289;289:94)(AP290;290:93)(AP291;291:92)(AP292;292:91)(AP293;293:90)(AP294;294:89)(AP295;295:88)(AP296;296:87)(AP297;297:86)(AP298;298:85)(AP299;299:84)(AP300;300:83)(AP301;301:82)(AP302;302:81)(AP303;303:80)(AP304;304:79)(AP305;305:78)(AP306;306:77)(AP307;307:76)(AP308;308:75)(AP309;309:74)(AP310;310:73)(AP311;311:72)(AP312;312:71)(AP313;313:70)(AP314;314:69)(AP315;315:68)(AP316;316:67)(AP317;317:66)(AP318;318:65)(AP319;319:64)(AP320;320:63)(AP321;321:62)(AP322;322:61)(AP323;323:60)(AP324;324:59)(AP325;325:58)(AP326;326:57)(AP327;327:56)(AP328;328:55)(AP329;329:54)(AP330;330:53)(AP331;331:52)(AP332;332:51)(AP333;333:50)(AP334;334:49)(AP335;335:48)(AP336;336:47)(AP337;337:46)(AP338;338:45)(AP339;339:44)(AP340;340:43)(AP341;341:42)(AP342;342:41)(AP343;343:40)(AP344;344:39)(AP345;345:38)(AP346;346:37)(AP347;347:36)(AP348;348:35)(AP349;349:34)(AP350;350:33)(AP351;351:32)(AP352;352:31)(AP353;353:30)(AP354;354:29)(AP355;355:28)(AP356;356:27)(AP357;357:26)(AP358;358:25)(AP359;359:24)(AP360;360:23)(AP361;361:22)(AP362;362:21)(AP363;363:20)(AP364;364:19)(AP365;365:18)(AP366;366:17)(AP367;367:16)(AP368;368:15)(AP369;369:14)(AP370;370:13)(AP371;371:12)(AP372;372:11)(AP373;373:10)(AP374;374:9)(AP375;375:8)(AP376;376:7)(AP377;377:6)(AP378;378:5)(AP379;379:4)(AP380;380:3)(AP381;381:2)(AP382;382:1)(AP383;383:0)(SY0;768:768) ~snsShankMap=(1,2,480)(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)(0:0:68:0)(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)(0:0:119:0)(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)(0:1:125:0)(0:0:126:1)(0:1:126:1)(0:0:127:1)(0:1:127:1)(0:0:128:1)(0:1:128:1)(0:0:129:0)(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)(0:0:136:0)(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)

WeissShahaf commented 4 years ago

example 2 acqApLfSy=384,384,1 appVersion=20190413 catGTCmdline0=<CatGT -dir=U:\GL847\20191122\openfield -run=GL847_20191122_OF -g=0 -t=0,0 -prb_fld -t_miss_ok -prb=0:3 -ap -aphipass=300 -gbldmx> catTVals=0,0 fileCreateTime=2020-01-21T15:31:45 fileCreateTime_original=2019-11-22T15:00:22 fileName=U:/GL847/20191122/openfield/GL847_20191122_OF_g0/GL847_20191122_OF_g0_imec3/GL847_20191122_OF_g0_tcat.imec3.ap.bin fileSHA1=0 fileSizeBytes=69438298160 fileTimeSecs=3005.986933333333 firstSample=1456960 gateMode=Immediate imAiRangeMax=0.6 imAiRangeMin=-0.6 imCalibrated=true imDatApi=1.20 imDatBs_fw=1.1.128 imDatBsc_fw=1.0.151 imDatBsc_hw=1.9 imDatBsc_pn=NP2_QBSC_00 imDatBsc_sn=73 imDatFx_hw=1.2 imDatFx_pn=NP2_FLEX_0 imDatHs_fw=5.1 imDatHs_pn=NP2_HS_30 imDatHs_sn=414 imDatPrb_pn=PRB_1_4_0480_1 imDatPrb_port=4 imDatPrb_slot=2 imDatPrb_sn=19051009532 imDatPrb_type=0 imLEDEnable=false imRoFile=C:/SpikeGLX/Release_v20190413-phase3B2/SpikeGLX/channelMaps/default_Tip.imro imSampRate=30000 imStdby= imTrgRising=false imTrgSource=0 nSavedChans=385 snsApLfSy=384,0,1 snsSaveChanSubset=0:383,768 syncImInputSlot=2 syncSourceIdx=3 syncSourcePeriod=1 trgTTLAIChan=3 trgTTLBit=1 trgTTLInarow=1 trgTTLIsAnalog=false trgTTLIsNInf=true trgTTLMarginS=1 trgTTLMode=2 trgTTLNH=10 trgTTLRefractS=0.5 trgTTLStream=nidq trgTTLTH=0.5 trgTTLThresh=1.1 trigMode=TTL typeImEnabled=4 typeNiEnabled=1 typeThis=imec userNotes= ~imroTbl=(0,384)(0 0 1 1000 500 0)(1 0 1 1000 500 0)(2 0 1 1000 500 0)(3 0 1 1000 500 0)(4 0 1 1000 500 0)(5 0 1 1000 500 0)(6 0 1 1000 500 0)(7 0 1 1000 500 0)(8 0 1 1000 500 0)(9 0 1 1000 500 0)(10 0 1 1000 500 0)(11 0 1 1000 500 0)(12 0 1 1000 500 0)(13 0 1 1000 500 0)(14 0 1 1000 500 0)(15 0 1 1000 500 0)(16 0 1 1000 500 0)(17 0 1 1000 500 0)(18 0 1 1000 500 0)(19 0 1 1000 500 0)(20 0 1 1000 500 0)(21 0 1 1000 500 0)(22 0 1 1000 500 0)(23 0 1 1000 500 0)(24 0 1 1000 500 0)(25 0 1 1000 500 0)(26 0 1 1000 500 0)(27 0 1 1000 500 0)(28 0 1 1000 500 0)(29 0 1 1000 500 0)(30 0 1 1000 500 0)(31 0 1 1000 500 0)(32 0 1 1000 500 0)(33 0 1 1000 500 0)(34 0 1 1000 500 0)(35 0 1 1000 500 0)(36 0 1 1000 500 0)(37 0 1 1000 500 0)(38 0 1 1000 500 0)(39 0 1 1000 500 0)(40 0 1 1000 500 0)(41 0 1 1000 500 0)(42 0 1 1000 500 0)(43 0 1 1000 500 0)(44 0 1 1000 500 0)(45 0 1 1000 500 0)(46 0 1 1000 500 0)(47 0 1 1000 500 0)(48 0 1 1000 500 0)(49 0 1 1000 500 0)(50 0 1 1000 500 0)(51 0 1 1000 500 0)(52 0 1 1000 500 0)(53 0 1 1000 500 0)(54 0 1 1000 500 0)(55 0 1 1000 500 0)(56 0 1 1000 500 0)(57 0 1 1000 500 0)(58 0 1 1000 500 0)(59 0 1 1000 500 0)(60 0 1 1000 500 0)(61 0 1 1000 500 0)(62 0 1 1000 500 0)(63 0 1 1000 500 0)(64 0 1 1000 500 0)(65 0 1 1000 500 0)(66 0 1 1000 500 0)(67 0 1 1000 500 0)(68 0 1 1000 500 0)(69 0 1 1000 500 0)(70 0 1 1000 500 0)(71 0 1 1000 500 0)(72 0 1 1000 500 0)(73 0 1 1000 500 0)(74 0 1 1000 500 0)(75 0 1 1000 500 0)(76 0 1 1000 500 0)(77 0 1 1000 500 0)(78 0 1 1000 500 0)(79 0 1 1000 500 0)(80 0 1 1000 500 0)(81 0 1 1000 500 0)(82 0 1 1000 500 0)(83 0 1 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WeissShahaf commented 4 years ago

i just noticed the 2 files i uploaded are result of a CAR preprocessing. the original file for the last probe: acqApLfSy=384,384,1 appVersion=20190413 fileCreateTime=2019-11-22T15:00:22 fileName=D:/SpikeGLX_Data/GL847_20191122_OF_g0/GL847_20191122_OF_g0_imec3/GL847_20191122_OF_g0_t0.imec3.ap.bin fileSHA1=0806E6D834C1CBE6E3F5F1AAC0224352B8CF7CDF fileSizeBytes=69438298160 fileTimeSecs=3005.986933333333 firstSample=1456960 gateMode=Immediate imAiRangeMax=0.6 imAiRangeMin=-0.6 imCalibrated=true imDatApi=1.20 imDatBs_fw=1.1.128 imDatBsc_fw=1.0.151 imDatBsc_hw=1.9 imDatBsc_pn=NP2_QBSC_00 imDatBsc_sn=73 imDatFx_hw=1.2 imDatFx_pn=NP2_FLEX_0 imDatHs_fw=5.1 imDatHs_pn=NP2_HS_30 imDatHs_sn=414 imDatPrb_pn=PRB_1_4_0480_1 imDatPrb_port=4 imDatPrb_slot=2 imDatPrb_sn=19051009532 imDatPrb_type=0 imLEDEnable=false imRoFile=C:/SpikeGLX/Release_v20190413-phase3B2/SpikeGLX/channelMaps/default_Tip.imro imSampRate=30000 imStdby= imTrgRising=false imTrgSource=0 nSavedChans=385 snsApLfSy=384,0,1 snsSaveChanSubset=0:383,768 syncImInputSlot=2 syncSourceIdx=3 syncSourcePeriod=1 trgTTLAIChan=3 trgTTLBit=1 trgTTLInarow=1 trgTTLIsAnalog=false trgTTLIsNInf=true trgTTLMarginS=1 trgTTLMode=2 trgTTLNH=10 trgTTLRefractS=0.5 trgTTLStream=nidq trgTTLTH=0.5 trgTTLThresh=1.1 trigMode=TTL typeImEnabled=4 typeNiEnabled=1 typeThis=imec userNotes= ~imroTbl=(0,384)(0 0 1 1000 500 0)(1 0 1 1000 500 0)(2 0 1 1000 500 0)(3 0 1 1000 500 0)(4 0 1 1000 500 0)(5 0 1 1000 500 0)(6 0 1 1000 500 0)(7 0 1 1000 500 0)(8 0 1 1000 500 0)(9 0 1 1000 500 0)(10 0 1 1000 500 0)(11 0 1 1000 500 0)(12 0 1 1000 500 0)(13 0 1 1000 500 0)(14 0 1 1000 500 0)(15 0 1 1000 500 0)(16 0 1 1000 500 0)(17 0 1 1000 500 0)(18 0 1 1000 500 0)(19 0 1 1000 500 0)(20 0 1 1000 500 0)(21 0 1 1000 500 0)(22 0 1 1000 500 0)(23 0 1 1000 500 0)(24 0 1 1000 500 0)(25 0 1 1000 500 0)(26 0 1 1000 500 0)(27 0 1 1000 500 0)(28 0 1 1000 500 0)(29 0 1 1000 500 0)(30 0 1 1000 500 0)(31 0 1 1000 500 0)(32 0 1 1000 500 0)(33 0 1 1000 500 0)(34 0 1 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jamesjun commented 4 years ago

Thank you very much for sharing.

Please pull version 5.6.9 and try again.

I also added a phy exporter: irc2 export-phy path_to_prm_file

-James

On Thu, Feb 6, 2020 at 8:40 AM WeissShahaf notifications@github.com wrote:

i just noticed the 2 files i uploaded are result of a CAR preprocessing. the original file for the last probe: acqApLfSy=384,384,1 appVersion=20190413 fileCreateTime=2019-11-22T15:00:22

fileName=D:/SpikeGLX_Data/GL847_20191122_OF_g0/GL847_20191122_OF_g0_imec3/GL847_20191122_OF_g0_t0.imec3.ap.bin fileSHA1=0806E6D834C1CBE6E3F5F1AAC0224352B8CF7CDF fileSizeBytes=69438298160 fileTimeSecs=3005.986933333333 firstSample=1456960 gateMode=Immediate imAiRangeMax=0.6 imAiRangeMin=-0.6 imCalibrated=true imDatApi=1.20 imDatBs_fw=1.1.128 imDatBsc_fw=1.0.151 imDatBsc_hw=1.9 imDatBsc_pn=NP2_QBSC_00 imDatBsc_sn=73 imDatFx_hw=1.2 imDatFx_pn=NP2_FLEX_0 imDatHs_fw=5.1 imDatHs_pn=NP2_HS_30 imDatHs_sn=414 imDatPrb_pn=PRB_1_4_0480_1 imDatPrb_port=4 imDatPrb_slot=2 imDatPrb_sn=19051009532 imDatPrb_type=0 imLEDEnable=false

imRoFile=C:/SpikeGLX/Release_v20190413-phase3B2/SpikeGLX/channelMaps/default_Tip.imro imSampRate=30000 imStdby= imTrgRising=false imTrgSource=0 nSavedChans=385 snsApLfSy=384,0,1 snsSaveChanSubset=0:383,768 syncImInputSlot=2 syncSourceIdx=3 syncSourcePeriod=1 trgTTLAIChan=3 trgTTLBit=1 trgTTLInarow=1 trgTTLIsAnalog=false trgTTLIsNInf=true trgTTLMarginS=1 trgTTLMode=2 trgTTLNH=10 trgTTLRefractS=0.5 trgTTLStream=nidq trgTTLTH=0.5 trgTTLThresh=1.1 trigMode=TTL typeImEnabled=4 typeNiEnabled=1 typeThis=imec userNotes= ~imroTbl=(0,384)(0 0 1 1000 500 0)(1 0 1 1000 500 0)(2 0 1 1000 500 0)(3 0 1 1000 500 0)(4 0 1 1000 500 0)(5 0 1 1000 500 0)(6 0 1 1000 500 0)(7 0 1 1000 500 0)(8 0 1 1000 500 0)(9 0 1 1000 500 0)(10 0 1 1000 500 0)(11 0 1 1000 500 0)(12 0 1 1000 500 0)(13 0 1 1000 500 0)(14 0 1 1000 500 0)(15 0 1 1000 500 0)(16 0 1 1000 500 0)(17 0 1 1000 500 0)(18 0 1 1000 500 0)(19 0 1 1000 500 0)(20 0 1 1000 500 0)(21 0 1 1000 500 0)(22 0 1 1000 500 0)(23 0 1 1000 500 0)(24 0 1 1000 500 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WeissShahaf commented 4 years ago

should i be using the irc2 import-spikeglx or the irc2 command?

and how do i rerun the sorting without recreating the prm file in the process?

jamesjun commented 4 years ago

For neuropixels import-spikeglx is not needed. You can run irc2 [path_to_prm_file] once the prm file is created. To find out which prm file is created type irc2 which.

WeissShahaf commented 4 years ago

thanks for the effort,

unfortunately, it crashed when i did irc2 . i think there the code is missing the fclose command for "raw_geomet_fet###.irc" i got this error:

Detecting 221/360: 14855 spikes found (1087.2 spikes/s, 17.8 MB/s, took 13.7 s) Rejecting 3.920 % of time due to motion Detecting 222/360: 3610 spikes found (292.8 spikes/s, 19.7 MB/s, took 12.3 s) Rejecting 4.196 % of time due to motion Detecting 223/360: 5866 spikes found (473.4 spikes/s, 19.6 MB/s, took 12.4 s) Rejecting 2.167 % of time due to motion Detecting 224/360: 3156 spikes found (260.9 spikes/s, 20.1 MB/s, took 12.1 s) Rejecting 8.324 % of time due to motion Detecting 225/360: 3564 spikes found (288.9 spikes/s, 19.7 MB/s, took 12.3 s) Rejecting 3.228 % of time due to motion Error using fwrite Invalid file identifier. Use fopen to generate a valid file identifier. Error in irc2>writebin (line 5993) Error in irc2>save_paged_fetsite (line 3931) Error in irc2>detect_pagedsave (line 3900) Error in irc2>detect_ (line 3701) Error in irc2 (line 177) Too many open files. Close files to prevent MATLAB instability. Caused by: Message Catalog MATLAB:builtins was not loaded from the file. Please check file location, format or contents

also when i try to use the prm file that was created i get:

irc2 raw_geom.prm irc2: cleared all Running irc2.m (5.6.9)

**Error using irc2>makeParam_ (line 4672) raw_geom.prm\raw.mda does not exist

Error in irc2 (line 170) P = makeParam_(vcDir_in, vcDir_out, vcFile_arg, fParfor);**

jamesjun commented 4 years ago

Thanks for testing. I made sure that the files are closed after writing. I left the file open to be read later for optimization purpose but your error made me realize that it's not worth the risk for a small performance gain.

-James

On Feb 7, 2020, at 3:12 AM, WeissShahaf notifications@github.com wrote:



thanks for the effort,

unfortunately, it crashed when i did irc2 . i think there the code is missing the fclose command for "raw_geomet_fet###.irc" i got this error:

Detecting 221/360: 14855 spikes found (1087.2 spikes/s, 17.8 MB/s, took 13.7 s) Rejecting 3.920 % of time due to motion Detecting 222/360: 3610 spikes found (292.8 spikes/s, 19.7 MB/s, took 12.3 s) Rejecting 4.196 % of time due to motion Detecting 223/360: 5866 spikes found (473.4 spikes/s, 19.6 MB/s, took 12.4 s) Rejecting 2.167 % of time due to motion Detecting 224/360: 3156 spikes found (260.9 spikes/s, 20.1 MB/s, took 12.1 s) Rejecting 8.324 % of time due to motion Detecting 225/360: 3564 spikes found (288.9 spikes/s, 19.7 MB/s, took 12.3 s) Rejecting 3.228 % of time due to motion

Error using fwrite Invalid file identifier. Use fopen to generate a valid file identifier. Error in irc2>writebin (line 5993) Error in irc2>save_paged_fetsite (line 3931) Error in irc2>detect_pagedsave (line 3900) Error in irc2>detect_ (line 3701) Error in irc2 (line 177) Too many open files. Close files to prevent MATLAB instability. Caused by: Message Catalog MATLAB:builtins was not loaded from the file. Please check file location, format or contents

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WeissShahaf commented 4 years ago

1)sorting now works, although i cannot get manual curation to load. it takes a full day to load and then runs out of memory


Summary of irc2\raw_geom.prm

Recording format Recording file: GL383_20190815_OF_g0_t0.imec0.ap.bin Probe file: imec3_opt3.prb Recording Duration: 3901.3s Data Type: int16

Channels in file: 385

#Sites:                 374
#Shanks:                1

Pre-processing Filter type: bandpass Filter range (Hz): [300.0, NaN] Matched Filter: 1 Common ref: trimmean Whiten: 0 FFT threshold: 8 blank threshold: 30 Events

Spikes: 3344395

Feature extracted:      gpca
#Sites/event:           18
maxDist_site_um:        50
maxDist_site_spk_um:    100
spkLim_ms:              [-1.500, 1.500]
#Features/event:        45
#PC/chan:               2.500000e+00

Cluster

Clusters: 62

#Unique events:         2243234
min. spk/clu:           30
Cluster method:         drift-knn
knn:                    30
step_sec_drift:         20.0s
batch_sec_drift:        300.0s

Auto-merge delta_cut: 1.000 maxWavCor: 0.985 cc_merge_thresh: 0.900 Runtime (s) Detect + feature (s): 2873.8s Cluster runtime (s): 405.5s merge runtime (s): 138.4s Total runtime (s): 3417.7s Runtime speed: x1.1 realtime Processing speed: 978.6 spikes/s memory usage (GiB): 0.310 detect: -0.006 sort: 0.310 auto-merge: 0.256 Execution irc2 version: 5.6.11 fGpu (GPU use): 1 fParfor (parfor use): 0 fLargeRecording: 0 Parameter file: irc2\raw_geom.prm

Wrote to irc2\firings.mda, took 0.2s

irc2 manual E:\runfolder\irc2\raw_geom.prm irc2 (5.6.11) opening E:\runfolder\irc2\raw_geom.prm Loading irc2\raw_geom.prm... took 7.6s Loading feature 1...callirc2: Requested 9x18x292032512 (176.2GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information. Error using rethrow Input must be a structure. Error in irc2_ui>callirc2 (line 1219) rethrow ME; Error in irc2_ui>loadfet (line 1299) function varargout = loadfet(varargin), cell_out = callirc2(dbstack(), varargin, nargout); varargout = cell_out; end Error in irc2_ui (line 12) S0.trPc_spk = loadfet(S0, P, 1); % Error in irc2 (line 131) case {'manual', 'ui'}, irc2_ui(P); return;

2) in raw_geom.prm, is it normal for uv_per_Bit to equal "Inf" after command irc2 ? i guess it doesn't get it from the meta file. So i've been manually entering my values.