Error loading an imec Dataset , .imec..bin gets added to filename about neuropixel-utils

[djoshea]

Hi Janna, thanks for filing the issue. Sorry you're having issues, which I'm fairly confident are minor issues related to newer versions of the SpikeGLX software than what I'd originally developed these tools with.

First, I made some assumptions about the structure of the filenames so that datasets could be automatically linked together (LF and AP x bin and meta). Originally my files were ended with imec.ap.bin, so if the code doesn't see that at the end, it (incorrectly) assumes you're specifying the common prefix not including .imec.ap.bin, so that's why it's being added. I think this would be simple to address by just looking for imec and some number in the stem.

Second, it looks like the contents of the .meta file have changed. Would you mind posting the contents of the imec0.ap.meta file so I can see what fields have changed? (Or you can email me at my github name at stanford dot edu.)

[JannaAarse]

Hey,

thanks for your fast help.
This is the content of my meta file (I tried also to attach it in case that is easier to work with):

acqApLfSy=384,384,1
appVersion=20190413
fileCreateTime=2020-04-02T13:11:31
fileName=D:/20200402_JA0033_Light_g0/20200402_JA0033_Light_g0_imec0/20200402_JA0033_Light_g0_t0.imec0.ap.bin
fileSHA1=E9C2100E5E0373A04A15A4EF0AB655D77C20B941
fileSizeBytes=10520637050
fileTimeSecs=455.4365593234114
firstSample=2286347
gateMode=Immediate
imAiRangeMax=0.6
imAiRangeMin=-0.6
imCalibrated=true
imDatApi=1.20
imDatBs_fw=1.1.123
imDatBsc_fw=1.0.151
imDatBsc_hw=1.9
imDatBsc_pn=NP2_QBSC_00
imDatBsc_sn=161
imDatFx_hw=1.2
imDatFx_pn=NP2_FLEX_0
imDatHs_fw=5.1
imDatHs_pn=NP2_HS_30
imDatHs_sn=290
imDatPrb_pn=PRB_1_4_0480_1
imDatPrb_port=3
imDatPrb_slot=2
imDatPrb_sn=19051008241
imDatPrb_type=0
imLEDEnable=false
imRoFile=C:/SpikeGLX/Release_v20190413-phase3B2/Release_v20190413-phase3B2/SpikeGLX/default.imro
imSampRate=30000.149791
imStdby=
imTrgRising=true
imTrgSource=0
nSavedChans=385
snsApLfSy=384,0,1
snsSaveChanSubset=0:383,768
syncImInputSlot=2
syncSourceIdx=0
syncSourcePeriod=1
trigMode=Immediate
typeImEnabled=1
typeNiEnabled=0
typeThis=imec
userNotes=
~imroTbl=(0,384)(0 0 0 500 250 1)(1 0 0 500 250 1)(2 0 0 500 250 1)(3 0 0 500 250 1)(4 0 0 500 250 1)(5 0 0 500 250 1)(6 0 0 500 250 1)(7 0 0 500 250 1)(8 0 0 500 250 1)(9 0 0 500 250 1)(10 0 0 500 250 1)(11 0 0 500 250 1)(12 0 0 500 250 1)(13 0 0 500 250 1)(14 0 0 500 250 1)(15 0 0 500 250 1)(16 0 0 500 250 1)(17 0 0 500 250 1)(18 0 0 500 250 1)(19 0 0 500 250 1)(20 0 0 500 250 1)(21 0 0 500 250 1)(22 0 0 500 250 1)(23 0 0 500 250 1)(24 0 0 500 250 1)(25 0 0 500 250 1)(26 0 0 500 250 1)(27 0 0 500 250 1)(28 0 0 500 250 1)(29 0 0 500 250 1)(30 0 0 500 250 1)(31 0 0 500 250 1)(32 0 0 500 250 1)(33 0 0 500 250 1)(34 0 0 500 250 1)(35 0 0 500 250 1)(36 0 0 500 250 1)(37 0 0 500 250 1)(38 0 0 500 250 1)(39 0 0 500 250 1)(40 0 0 500 250 1)(41 0 0 500 250 1)(42 0 0 500 250 1)(43 0 0 500 250 1)(44 0 0 500 250 1)(45 0 0 500 250 1)(46 0 0 500 250 1)(47 0 0 500 250 1)(48 0 0 500 250 1)(49 0 0 500 250 1)(50 0 0 500 250 1)(51 0 0 500 250 1)(52 0 0 500 250 1)(53 0 0 500 250 1)(54 0 0 500 250 1)(55 0 0 500 250 1)(56 0 0 500 250 1)(57 0 0 500 250 1)(58 0 0 500 250 1)(59 0 0 500 250 1)(60 0 0 500 250 1)(61 0 0 500 250 1)(62 0 0 500 250 1)(63 0 0 500 250 1)(64 0 0 500 250 1)(65 0 0 500 250 1)(66 0 0 500 250 1)(67 0 0 500 250 1)(68 0 0 500 250 1)(69 0 0 500 250 1)(70 0 0 500 250 1)(71 0 0 500 250 1)(72 0 0 500 250 1)(73 0 0 500 250 1)(74 0 0 500 250 1)(75 0 0 500 250 1)(76 0 0 500 250 1)(77 0 0 500 250 1)(78 0 0 500 250 1)(79 0 0 500 250 1)(80 0 0 500 250 1)(81 0 0 500 250 1)(82 0 0 500 250 1)(83 0 0 500 250 1)(84 0 0 500 250 1)(85 0 0 500 250 1)(86 0 0 500 250 1)(87 0 0 500 250 1)(88 0 0 500 250 1)(89 0 0 500 250 1)(90 0 0 500 250 1)(91 0 0 500 250 1)(92 0 0 500 250 1)(93 0 0 500 250 1)(94 0 0 500 250 1)(95 0 0 500 250 1)(96 0 0 500 250 1)(97 0 0 500 250 1)(98 0 0 500 250 1)(99 0 0 500 250 1)(100 0 0 500 250 1)(101 0 0 500 250 1)(102 0 0 500 250 1)(103 0 0 500 250 1)(104 0 0 500 250 1)(105 0 0 500 250 1)(106 0 0 500 250 1)(107 0 0 500 250 1)(108 0 0 500 250 1)(109 0 0 500 250 1)(110 0 0 500 250 1)(111 0 0 500 250 1)(112 0 0 500 250 1)(113 0 0 500 250 1)(114 0 0 500 250 1)(115 0 0 500 250 1)(116 0 0 500 250 1)(117 0 0 500 250 1)(118 0 0 500 250 1)(119 0 0 500 250 1)(120 0 0 500 250 1)(121 0 0 500 250 1)(122 0 0 500 250 1)(123 0 0 500 250 1)(124 0 0 500 250 1)(125 0 0 500 250 1)(126 0 0 500 250 1)(127 0 0 500 250 1)(128 0 0 500 250 1)(129 0 0 500 250 1)(130 0 0 500 250 1)(131 0 0 500 250 1)(132 0 0 500 250 1)(133 0 0 500 250 1)(134 0 0 500 250 1)(135 0 0 500 250 1)(136 0 0 500 250 1)(137 0 0 500 250 1)(138 0 0 500 250 1)(139 0 0 500 250 1)(140 0 0 500 250 1)(141 0 0 500 250 1)(142 0 0 500 250 1)(143 0 0 500 250 1)(144 0 0 500 250 1)(145 0 0 500 250 1)(146 0 0 500 250 1)(147 0 0 500 250 1)(148 0 0 500 250 1)(149 0 0 500 250 1)(150 0 0 500 250 1)(151 0 0 500 250 1)(152 0 0 500 250 1)(153 0 0 500 250 1)(154 0 0 500 250 1)(155 0 0 500 250 1)(156 0 0 500 250 1)(157 0 0 500 250 1)(158 0 0 500 250 1)(159 0 0 500 250 1)(160 0 0 500 250 1)(161 0 0 500 250 1)(162 0 0 500 250 1)(163 0 0 500 250 1)(164 0 0 500 250 1)(165 0 0 500 250 1)(166 0 0 500 250 1)(167 0 0 500 250 1)(168 0 0 500 250 1)(169 0 0 500 250 1)(170 0 0 500 250 1)(171 0 0 500 250 1)(172 0 0 500 250 1)(173 0 0 500 250 1)(174 0 0 500 250 1)(175 0 0 500 250 1)(176 0 0 500 250 1)(177 0 0 500 250 1)(178 0 0 500 250 1)(179 0 0 500 250 1)(180 0 0 500 250 1)(181 0 0 500 250 1)(182 0 0 500 250 1)(183 0 0 500 250 1)(184 0 0 500 250 1)(185 0 0 500 250 1)(186 0 0 500 250 1)(187 0 0 500 250 1)(188 0 0 500 250 1)(189 0 0 500 250 1)(190 0 0 500 250 1)(191 0 0 500 250 1)(192 0 0 500 250 1)(193 0 0 500 250 1)(194 0 0 500 250 1)(195 0 0 500 250 1)(196 0 0 500 250 1)(197 0 0 500 250 1)(198 0 0 500 250 1)(199 0 0 500 250 1)(200 0 0 500 250 1)(201 0 0 500 250 1)(202 0 0 500 250 1)(203 0 0 500 250 1)(204 0 0 500 250 1)(205 0 0 500 250 1)(206 0 0 500 250 1)(207 0 0 500 250 1)(208 0 0 500 250 1)(209 0 0 500 250 1)(210 0 0 500 250 1)(211 0 0 500 250 1)(212 0 0 500 250 1)(213 0 0 500 250 1)(214 0 0 500 250 1)(215 0 0 500 250 1)(216 0 0 500 250 1)(217 0 0 500 250 1)(218 0 0 500 250 1)(219 0 0 500 250 1)(220 0 0 500 250 1)(221 0 0 500 250 1)(222 0 0 500 250 1)(223 0 0 500 250 1)(224 0 0 500 250 1)(225 0 0 500 250 1)(226 0 0 500 250 1)(227 0 0 500 250 1)(228 0 0 500 250 1)(229 0 0 500 250 1)(230 0 0 500 250 1)(231 0 0 500 250 1)(232 0 0 500 250 1)(233 0 0 500 250 1)(234 0 0 500 250 1)(235 0 0 500 250 1)(236 0 0 500 250 1)(237 0 0 500 250 1)(238 0 0 500 250 1)(239 0 0 500 250 1)(240 0 0 500 250 1)(241 0 0 500 250 1)(242 0 0 500 250 1)(243 0 0 500 250 1)(244 0 0 500 250 1)(245 0 0 500 250 1)(246 0 0 500 250 1)(247 0 0 500 250 1)(248 0 0 500 250 1)(249 0 0 500 250 1)(250 0 0 500 250 1)(251 0 0 500 250 1)(252 0 0 500 250 1)(253 0 0 500 250 1)(254 0 0 500 250 1)(255 0 0 500 250 1)(256 0 0 500 250 1)(257 0 0 500 250 1)(258 0 0 500 250 1)(259 0 0 500 250 1)(260 0 0 500 250 1)(261 0 0 500 250 1)(262 0 0 500 250 1)(263 0 0 500 250 1)(264 0 0 500 250 1)(265 0 0 500 250 1)(266 0 0 500 250 1)(267 0 0 500 250 1)(268 0 0 500 250 1)(269 0 0 500 250 1)(270 0 0 500 250 1)(271 0 0 500 250 1)(272 0 0 500 250 1)(273 0 0 500 250 1)(274 0 0 500 250 1)(275 0 0 500 250 1)(276 0 0 500 250 1)(277 0 0 500 250 1)(278 0 0 500 250 1)(279 0 0 500 250 1)(280 0 0 500 250 1)(281 0 0 500 250 1)(282 0 0 500 250 1)(283 0 0 500 250 1)(284 0 0 500 250 1)(285 0 0 500 250 1)(286 0 0 500 250 1)(287 0 0 500 250 1)(288 0 0 500 250 1)(289 0 0 500 250 1)(290 0 0 500 250 1)(291 0 0 500 250 1)(292 0 0 500 250 1)(293 0 0 500 250 1)(294 0 0 500 250 1)(295 0 0 500 250 1)(296 0 0 500 250 1)(297 0 0 500 250 1)(298 0 0 500 250 1)(299 0 0 500 250 1)(300 0 0 500 250 1)(301 0 0 500 250 1)(302 0 0 500 250 1)(303 0 0 500 250 1)(304 0 0 500 250 1)(305 0 0 500 250 1)(306 0 0 500 250 1)(307 0 0 500 250 1)(308 0 0 500 250 1)(309 0 0 500 250 1)(310 0 0 500 250 1)(311 0 0 500 250 1)(312 0 0 500 250 1)(313 0 0 500 250 1)(314 0 0 500 250 1)(315 0 0 500 250 1)(316 0 0 500 250 1)(317 0 0 500 250 1)(318 0 0 500 250 1)(319 0 0 500 250 1)(320 0 0 500 250 1)(321 0 0 500 250 1)(322 0 0 500 250 1)(323 0 0 500 250 1)(324 0 0 500 250 1)(325 0 0 500 250 1)(326 0 0 500 250 1)(327 0 0 500 250 1)(328 0 0 500 250 1)(329 0 0 500 250 1)(330 0 0 500 250 1)(331 0 0 500 250 1)(332 0 0 500 250 1)(333 0 0 500 250 1)(334 0 0 500 250 1)(335 0 0 500 250 1)(336 0 0 500 250 1)(337 0 0 500 250 1)(338 0 0 500 250 1)(339 0 0 500 250 1)(340 0 0 500 250 1)(341 0 0 500 250 1)(342 0 0 500 250 1)(343 0 0 500 250 1)(344 0 0 500 250 1)(345 0 0 500 250 1)(346 0 0 500 250 1)(347 0 0 500 250 1)(348 0 0 500 250 1)(349 0 0 500 250 1)(350 0 0 500 250 1)(351 0 0 500 250 1)(352 0 0 500 250 1)(353 0 0 500 250 1)(354 0 0 500 250 1)(355 0 0 500 250 1)(356 0 0 500 250 1)(357 0 0 500 250 1)(358 0 0 500 250 1)(359 0 0 500 250 1)(360 0 0 500 250 1)(361 0 0 500 250 1)(362 0 0 500 250 1)(363 0 0 500 250 1)(364 0 0 500 250 1)(365 0 0 500 250 1)(366 0 0 500 250 1)(367 0 0 500 250 1)(368 0 0 500 250 1)(369 0 0 500 250 1)(370 0 0 500 250 1)(371 0 0 500 250 1)(372 0 0 500 250 1)(373 0 0 500 250 1)(374 0 0 500 250 1)(375 0 0 500 250 1)(376 0 0 500 250 1)(377 0 0 500 250 1)(378 0 0 500 250 1)(379 0 0 500 250 1)(380 0 0 500 250 1)(381 0 0 500 250 1)(382 0 0 500 250 1)(383 0 0 500 250 1)
~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;353:353)(AP354;354:354)(AP355;355:355)(AP356;356:356)(AP357;357:357)(AP358;358:358)(AP359;359:359)(AP360;360:360)(AP361;361:361)(AP362;362:362)(AP363;363:363)(AP364;364:364)(AP365;365:365)(AP366;366:366)(AP367;367:367)(AP368;368:368)(AP369;369:369)(AP370;370:370)(AP371;371:371)(AP372;372:372)(AP373;373:373)(AP374;374:374)(AP375;375:375)(AP376;376:376)(AP377;377:377)(AP378;378:378)(AP379;379:379)(AP380;380:380)(AP381;381:381)(AP382;382:382)(AP383;383:383)(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)(0:0:68:1)(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)

20200402_JA0033_Light_g0_t0.imec0.ap.txt

[JannaAarse]

I am really sorry to bother , I am think my matlab skills are probably rather moderate than anything else, I tried to work with putting 'imec*.' as an indicator (imec = Neuropixel.ImecDataset('Z:\Users\Janna\IMECDATASET\20200402\001\NP\20200402_JA0033_Light_g0_t0.imec*');) I also tried different versions, none of them worked, at some point I started looking into different variables in the code and setting a breaking point at line 98 (which is the error message I am getting at the moment) , I can run that one by hand and it is fine, the file is the correct one , but if I manually run line 102 after that
[df.pathRoot, df.fileStem, df.fileTypeAP] = Neuropixel.ImecDataset.parseImecFileName(file);

df.fileTypeAP is an empty chart, could this also be due to some changes in how the .imec.ap.bin files are saved ?

also some other variables are already wrong, the attachement shows APfile which is looking for and additional .imec..bin to the name, I tried to work around the number in the imec by adding the asterics, I did it with and without in both cases it still tries to add the additional ending which I don't understand why.

[djoshea]

Hey Janna, thanks for trying to work through this. I think I've resolved the underlying issue by gracefully handling the new file names in a037119. To keep from breaking things working on the master branch, I've been making a bunch of improvements and fixing other issue on the markSplitOnly branch. Would you mind switching to that branch ( git checkout markSplitOnly) and then try your loading command again:

imec = Neuropixel.ImecDataset('Z:\Users\Janna\IMECDATASET\20200402\001\NP\20200402_JA0033_Light_g0_t0.imec0.ap.bin');

If you run into new issues with this branch, I can try to cherry pick back to the master branch, but I know I've since fixed a bunch of issues since then.

Let me know how it goes!
Dan

[JannaAarse]

Hey Dan,

thank you so much for all your help. I got the other branch and was running it, I was able to load two different imec datasets that were recorded in the same animal the same day. Whichis already pretty nice :) I was able to make an imec List and tried to run the writeConcatenatedFileMatchGains function. Unfortunately it gives me another error message when I run it:

imecList = {imec1, imec2};
imecOut = Neuropixel.ImecDataset.writeConcatenatedFileMatchGains(Output_folder, imecList);
Error using cellfun
Input #2 expected to be a cell array, was char instead.

Error in Neuropixel.ImecDataset.writeConcatenatedFileMatchGains (line 2354)
stemList = cellfun(@(imec) imec.fileStem, imecList, 'UniformOutput', false);

I first thought that maybe my imec List is not ok , this is how I did run the imec sets
imec1 = Neuropixel.ImecDataset('Z:\Users\Janna\IMECDATASET\20200402\001\NP\20200402_JA0033_Light_g0_t0.imec0.ap.bin', 'channelMap', channelMapFile);
imec2 = Neuropixel.ImecDataset('Z:\Users\Janna\IMECDATASET\20200402\003\NP\20200402_JA0033_dark_g0_t0.imec0.ap.bin', 'channelMap', channelMapFile);

this gives me a 1x2 cell, so I did run it with the debugging and checked line line 2354 by hand and when I check what the imecList is at that moment it is equivalent to the outPath and therefore a char and not a cell
I attached a snip of what is shown.

Did I used the part wrong ? Or do I have to run it with a handle function ? I did run it without because I thought if I want to have the whole files concatenated as unprocessed raw data I probably should not add a handle.

Best,
Janna

[JannaAarse]

Hey Dan,

I was working on the error message a bit more and figured out that the order of the variables was just mixed up, so instead of
imecOut = Neuropixel.ImecDataset.writeConcatenatedFileMatchGains(Output_folder, imecList);
I used
imecOut = Neuropixel.ImecDataset.writeConcatenatedFileMatchGains(imecList,Output_folder);

So I was running the two files I used to try it out, it did run through both with 100% but at the end still gave me an error message:

All files have common gain of 500
Writing AP meta file .imec.ap.meta
Writing AP bin file Z:\Users\Janna\IMECDATASET\ConcenatedFiles.imec.ap.bin
Writing contents of 20200402_JA0033_Light_g0_t0
Copying ap file 1 / 2: 20200402_JA0033_Light_g0_t0 : 100% []
Writing contents of 20200402_JA0033_dark_g0_t0
Copying ap file 2 / 2: 20200402_JA0033_dark_g0_t0 : 100% []
Error using Neuropixel.ImecDataset (line 140)
Could not find AP bin file Z:\Users\Janna\IMECDATASET\ConcenatedFiles.imec.ap.bin.imec..bin

Error in Neuropixel.ImecDataset.writeConcatenatedFileMatchGains (line 2548)
imecOut = Neuropixel.ImecDataset(outFile, 'channelMap', imecList{1}.channelMapFile, 'sourceDatasets', cat(1, imecList{:}));

I checked my outputfolder which contains two files but they are named imec.ap.bin , so they are missing the additional .imec..bin , I will try to see if I can figure it out but I get the feeling it is a similar problem to what it was in the other part of the code at the beginning maybe?

[djoshea]

Hey Janna, sorry for the delay. Great, glad the order of the args was the issue in the first one. An error message would be probably be helpful there, and indeed I do have it backwards in my documentation.

As for the second, it certainly looks like an issue with paths again. I'm trying to think through the issue. However this line 2548 is simply trying to hand you back a reference to the concatenated dataset, but all the work has completed successfully by this point. Can you try simply accessing it directly by saying:

imecCat = Neuropixel.ImecDataset('Z:\Users\Janna\IMECDATASET\ConcenatedFiles.imec.ap.bin');

Does that work?