Parse spikeGLX meta files that have been processed by catGT
Closed this issue · 3 comments
emilyasterjones commented
CatGT adds its command string to the .ap.meta and .lf.meta files when it's run. The command string contains several '=', which breaks this line in parse_spikeglx_meta (key, val = line.split('=')). The code is expecting to unpack 2 values from line.split, but receives many more than that.
This could be fixed by adding:
if 'catGTCmdline0' in line:
continue
before this line.
alejoe91 commented
Thanks @emilyasterjones
Could you share a meta file modified by CatGT so we can add some additional tests?
brandonStell commented
We're seeing the same issue. Here is a .meta (the third line seems to be the problem):
acqApLfSy=384,384,1
appVersion=20230120
catGTCmdline0=<CatGT -dir=/media/setups/bsinvivo3/neuropixels/2023_04_27 -run=77.230125_2023-04-27 -g=0 -t=0 -prb_fld -ni -ap -lf -prb=0 -gblcar -dest=/media/bs/tmp_working/ecephys -out_prb_fld>
catGVals=0,0
catNFiles=1
catTVals=0,0
fileCreateTime=2023-06-05T17:20:39
fileCreateTime_original=2023-04-27T15:21:38
fileName=/media/bs/tmp_working/ecephys/catgt_77.230125_2023-04-27_g0/77.230125_2023-04-27_g0_imec0/77.230125_2023-04-27_g0_tcat.imec0.ap.bin
fileSHA1=0
fileSizeBytes=98624725430
fileTimeSecs=4269.447345892785
firstSample=48994605
gateMode=Immediate
imAiRangeMax=0.6
imAiRangeMin=-0.6
imCalibrated=true
imDatApi=3.57
imDatBs_fw=2.0.169
imDatBsc_fw=3.2.176
imDatBsc_hw=2.2
imDatBsc_pn=NP2_QBSC_00
imDatBsc_sn=22030965
imDatFx_hw=4.13
imDatFx_pn=NP2_FLEX_0
imDatFx_sn=0
imDatHs_hw=5.1
imDatHs_pn=NP2_HS_30
imDatHs_sn=852
imDatPrb_dock=1
imDatPrb_pn=PRB_1_4_0480_1_C
imDatPrb_port=1
imDatPrb_slot=4
imDatPrb_sn=19454409771
imDatPrb_type=0
imIsSvyRun=false
imLEDEnable=false
imMaxInt=512
imSampRate=30000.149579831934
imStdby=
imSvyMaxBnk=-1
imSvySecPerBnk=35
imTrgRising=true
imTrgSource=0
imroFile=C:/Users/bs_spikeglx/Desktop/trst.imro
nDataDirs=1
nSavedChans=385
snsApLfSy=384,0,1
snsSaveChanSubset=0:383,768
syncImInputSlot=4
syncSourceIdx=3
syncSourcePeriod=1
trigMode=Immediate
typeImEnabled=1
typeNiEnabled=1
typeObEnabled=0
typeThis=imec
userNotes=
~imroTbl=(0,384)(0 0 1 500 50 1)(1 0 1 500 50 1)(2 0 1 500 50 1)(3 0 1 500 50 1)(4 0 1 500 50 1)(5 0 1 500 50 1)(6 0 1 500 50 1)(7 0 1 500 50 1)(8 0 1 500 50 1)(9 0 1 500 50 1)(10 0 1 500 50 1)(11 0 1 500 50 1)(12 0 1 500 50 1)(13 0 1 500 50 1)(14 0 1 500 50 1)(15 0 1 500 50 1)(16 0 1 500 50 1)(17 0 1 500 50 1)(18 0 1 500 50 1)(19 0 1 500 50 1)(20 0 1 500 50 1)(21 0 1 500 50 1)(22 0 1 500 50 1)(23 0 1 500 50 1)(24 0 1 500 50 1)(25 0 1 500 50 1)(26 0 1 500 50 1)(27 0 1 500 50 1)(28 0 1 500 50 1)(29 0 1 500 50 1)(30 0 1 500 50 1)(31 0 1 500 50 1)(32 0 1 500 50 1)(33 0 1 500 50 1)(34 0 1 500 50 1)(35 0 1 500 50 1)(36 0 1 500 50 1)(37 0 1 500 50 1)(38 0 1 500 50 1)(39 0 1 500 50 1)(40 0 1 500 50 1)(41 0 1 500 50 1)(42 0 1 500 50 1)(43 0 1 500 50 1)(44 0 1 500 50 1)(45 0 1 500 50 1)(46 0 1 500 50 1)(47 0 1 500 50 1)(48 0 1 500 50 1)(49 0 1 500 50 1)(50 0 1 500 50 1)(51 0 1 500 50 1)(52 0 1 500 50 1)(53 0 1 500 50 1)(54 0 1 500 50 1)(55 0 1 500 50 1)(56 0 1 500 50 1)(57 0 1 500 50 1)(58 0 1 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~muxTbl=(32,12)(0 1 24 25 48 49 72 73 96 97 120 121 144 145 168 169 192 193 216 217 240 241 264 265 288 289 312 313 336 337 360 361)(2 3 26 27 50 51 74 75 98 99 122 123 146 147 170 171 194 195 218 219 242 243 266 267 290 291 314 315 338 339 362 363)(4 5 28 29 52 53 76 77 100 101 124 125 148 149 172 173 196 197 220 221 244 245 268 269 292 293 316 317 340 341 364 365)(6 7 30 31 54 55 78 79 102 103 126 127 150 151 174 175 198 199 222 223 246 247 270 271 294 295 318 319 342 343 366 367)(8 9 32 33 56 57 80 81 104 105 128 129 152 153 176 177 200 201 224 225 248 249 272 273 296 297 320 321 344 345 368 369)(10 11 34 35 58 59 82 83 106 107 130 131 154 155 178 179 202 203 226 227 250 251 274 275 298 299 322 323 346 347 370 371)(12 13 36 37 60 61 84 85 108 109 132 133 156 157 180 181 204 205 228 229 252 253 276 277 300 301 324 325 348 349 372 373)(14 15 38 39 62 63 86 87 110 111 134 135 158 159 182 183 206 207 230 231 254 255 278 279 302 303 326 327 350 351 374 375)(16 17 40 41 64 65 88 89 112 113 136 137 160 161 184 185 208 209 232 233 256 257 280 281 304 305 328 329 352 353 376 377)(18 19 42 43 66 67 90 91 114 115 138 139 162 163 186 187 210 211 234 235 258 259 282 283 306 307 330 331 354 355 378 379)(20 21 44 45 68 69 92 93 116 117 140 141 164 165 188 189 212 213 236 237 260 261 284 285 308 309 332 333 356 357 380 381)(22 23 46 47 70 71 94 95 118 119 142 143 166 167 190 191 214 215 238 239 262 263 286 287 310 311 334 335 358 359 382 383)
~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;353:3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alejoe91 commented
@brandonStell @emilyasterjones
Should be fixed here: #193
@brandonStell I added the file you provided in the test files. Is that ok?