INFO 2025-06-26 20:18:43,666 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2005 --end_year 2014 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 20:18:43,666 process.py process_mission():434 [1] dorado_info[mission]["comment"] = San Pedro Bay CANON-ECOHAB - ctdToUse = ctd1 INFO 2025-06-26 20:18:43,666 process.py process_mission():449 [1] Processing CANON April 2014 mission 2014.104.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:18:43,666 process.py download_process():165 [1] Download and processing steps for 2014.104.01 INFO 2025-06-26 20:18:43,666 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014104/2014.104.01 INFO 2025-06-26 20:18:43,666 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014104/2014.104.01 to /data/auv_data/dorado/missionlogs/2014.104.01 INFO 2025-06-26 20:18:48,339 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.104.01 INFO 2025-06-26 20:18:48,339 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.104.01/ctdDriver.log (8692038 bytes) INFO 2025-06-26 20:18:48,976 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.104.01/ctdDriver2.log (8692127 bytes) INFO 2025-06-26 20:18:49,594 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.104.01/gps.log (178412 bytes) INFO 2025-06-26 20:18:49,620 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.104.01/hydroscatlog.log (7612522 bytes) INFO 2025-06-26 20:18:50,399 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.104.01/navigation.log (32579010 bytes) INFO 2025-06-26 20:18:52,675 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.104.01/isuslog.log (563733 bytes) INFO 2025-06-26 20:18:52,734 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.104.01/parosci.log (10686614 bytes) INFO 2025-06-26 20:18:53,632 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.104.01/tailCone.log (5440987 bytes) INFO 2025-06-26 20:18:54,291 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.104.01/biolume.log (6333622 bytes) INFO 2025-06-26 20:18:54,897 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:18:55,203 logs2netcdfs.py download_process_logs():807 [1] Time to process: 6.86 seconds INFO 2025-06-26 20:18:55,204 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.104.01/lopc.bin (61119352 bytes) INFO 2025-06-26 20:18:55,204 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:18:55 2025 INFO 2025-06-26 20:18:55,204 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.104.01/parosci.nc INFO 2025-06-26 20:18:55,204 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:18:55,204 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.104.01/parosci.nc INFO 2025-06-26 20:18:55,207 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1397489061.1, sensor_off_time = 1397511729.0 INFO 2025-06-26 20:18:55,207 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 22667 seconds. Expecting to read 45334 L frames from the lopc.bin file. INFO 2025-06-26 20:18:55,207 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 45334 records from the lopc.bin file. INFO 2025-06-26 20:18:55,474 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-04-14 15:24:21 Z and endTime = 2014-04-14 21:42:09 Z with 45334 records expected to be read from lopc.bin INFO 2025-06-26 20:18:55,475 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.104.01/lopc.bin INFO 2025-06-26 20:18:55,475 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.104.01/lopc.nc INFO 2025-06-26 20:18:55,475 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.104.01/lopc.nc INFO 2025-06-26 20:18:55,476 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.104.01 INFO 2025-06-26 20:18:55,476 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 20:18:55,536 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:18:55,536 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:18:55,536 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:18:56,096 lopcToNetCDF.py main():2340 [1] UnicodeDecodeError: 'utf-8' codec can't decode byte 0x87 in position 0: invalid start byte INFO 2025-06-26 20:18:56,096 lopcToNetCDF.py main():2341 [1] Failed to decode all of lopc.bin - resulting lopc.nc file likely incomplete INFO 2025-06-26 20:18:56,096 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.104.01/parosci.nc INFO 2025-06-26 20:18:56,096 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:18:56,096 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.104.01/parosci.nc INFO 2025-06-26 20:18:56,099 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1397489061.1, sensor_off_time = 1397511729.0 INFO 2025-06-26 20:18:56,100 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 22667 seconds. Expecting to read 45334 L frames from the lopc.bin file. INFO 2025-06-26 20:18:56,100 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 45334 records from the lopc.bin file. INFO 2025-06-26 20:18:56,100 lopcToNetCDF.py constructTimestampList():1340 [1] Calling correctSampleCountList() with sampleCountList[0] = 1 and len(sampleCountList) = 307 INFO 2025-06-26 20:18:56,100 lopcToNetCDF.py correctSampleCountList():1737 [1] Found overflows at indices: [] INFO 2025-06-26 20:18:56,100 lopcToNetCDF.py correctSampleCountList():1745 [1] Original sampleCountList = [ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 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1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2] INFO 2025-06-26 20:18:56,102 lopcToNetCDF.py deSpike():1590 [1] Found 0 spike indicators at indices: [] INFO 2025-06-26 20:18:56,103 lopcToNetCDF.py correctSampleCountList():1805 [1] After despike() sampleCountList = [ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 308] INFO 2025-06-26 20:18:56,104 lopcToNetCDF.py constructTimestampList():1347 [1] correctSampleCountList() returned correctedSampleCountList = [ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 308] with len(correctedSampleCountList) = 307 INFO 2025-06-26 20:18:56,105 lopcToNetCDF.py constructTimestampList():1358 [1] Subtracting 1 from all values of correctedSampleCountList INFO 2025-06-26 20:18:56,105 lopcToNetCDF.py constructTimestampList():1363 [1] Constructing timestampArray from instrument corrected sampleCount and constant deltaT = 0.500000 INFO 2025-06-26 20:18:56,105 lopcToNetCDF.py constructTimestampList():1368 [1] New re-zeroed correctedSampleCountList = [ 0. 0.5 1. 1.5 2. 2.5 3. 3.5 4. 4.5 5. 5.5 6. 6.5 7. 7.5 8. 8.5 9. 9.5 10. 10.5 11. 11.5 12. 12.5 13. 13.5 14. 14.5 15. 15.5 16. 16.5 17. 17.5 18. 18.5 19. 19.5 20. 20.5 21. 21.5 22. 22.5 23. 23.5 24. 24.5 25. 25.5 26. 26.5 27. 27.5 28. 28.5 29. 29.5 30. 30.5 31. 31.5 32. 32.5 33. 33.5 34. 34.5 35. 35.5 36. 36.5 37. 37.5 38. 38.5 39. 39.5 40. 40.5 41. 41.5 42. 42.5 43. 43.5 44. 44.5 45. 45.5 46. 46.5 47. 47.5 48. 48.5 49. 49.5 50. 50.5 51. 51.5 52. 52.5 53. 53.5 54. 54.5 55. 55.5 56. 56.5 57. 57.5 58. 58.5 59. 59.5 60. 60.5 61. 61.5 62. 62.5 63. 63.5 64. 64.5 65. 65.5 66. 66.5 67. 67.5 68. 68.5 69. 69.5 70. 70.5 71. 71.5 72. 72.5 73. 73.5 74. 74.5 75. 75.5 76. 76.5 77. 77.5 78. 78.5 79. 79.5 80. 80.5 81. 81.5 82. 82.5 83. 83.5 84. 84.5 85. 85.5 86. 86.5 87. 87.5 88. 88.5 89. 89.5 90. 90.5 91. 91.5 92. 92.5 93. 93.5 94. 94.5 95. 95.5 96. 96.5 97. 97.5 98. 98.5 99. 99.5 100. 100.5 101. 101.5 102. 102.5 103. 103.5 104. 104.5 105. 105.5 106. 106.5 107. 107.5 108. 108.5 109. 109.5 110. 110.5 111. 111.5 112. 112.5 113. 113.5 114. 114.5 115. 115.5 116. 116.5 117. 117.5 118. 118.5 119. 119.5 120. 120.5 121. 121.5 122. 122.5 123. 123.5 124. 124.5 125. 125.5 126. 126.5 127. 127.5 128. 128.5 129. 129.5 130. 130.5 131. 131.5 132. 132.5 133. 133.5 134. 134.5 135. 135.5 136. 136.5 137. 137.5 138. 138.5 139. 139.5 140. 140.5 141. 141.5 142. 142.5 143. 143.5 144. 144.5 145. 145.5 146. 146.5 147. 147.5 148. 148.5 149. 149.5 150. 150.5 151. 151.5 152. 152.5 153.5] INFO 2025-06-26 20:18:56,107 lopcToNetCDF.py constructTimestampList():1379 [1] timestampArray = [1.39748906e+09 1.39748906e+09 1.39748906e+09 1.39748906e+09 1.39748906e+09 1.39748906e+09 1.39748906e+09 1.39748906e+09 1.39748907e+09 1.39748907e+09 1.39748907e+09 1.39748907e+09 1.39748907e+09 1.39748907e+09 1.39748907e+09 1.39748907e+09 1.39748907e+09 1.39748907e+09 1.39748907e+09 1.39748907e+09 1.39748907e+09 1.39748907e+09 1.39748907e+09 1.39748907e+09 1.39748907e+09 1.39748907e+09 1.39748907e+09 1.39748907e+09 1.39748908e+09 1.39748908e+09 1.39748908e+09 1.39748908e+09 1.39748908e+09 1.39748908e+09 1.39748908e+09 1.39748908e+09 1.39748908e+09 1.39748908e+09 1.39748908e+09 1.39748908e+09 1.39748908e+09 1.39748908e+09 1.39748908e+09 1.39748908e+09 1.39748908e+09 1.39748908e+09 1.39748908e+09 1.39748908e+09 1.39748909e+09 1.39748909e+09 1.39748909e+09 1.39748909e+09 1.39748909e+09 1.39748909e+09 1.39748909e+09 1.39748909e+09 1.39748909e+09 1.39748909e+09 1.39748909e+09 1.39748909e+09 1.39748909e+09 1.39748909e+09 1.39748909e+09 1.39748909e+09 1.39748909e+09 1.39748909e+09 1.39748909e+09 1.39748909e+09 1.39748910e+09 1.39748910e+09 1.39748910e+09 1.39748910e+09 1.39748910e+09 1.39748910e+09 1.39748910e+09 1.39748910e+09 1.39748910e+09 1.39748910e+09 1.39748910e+09 1.39748910e+09 1.39748910e+09 1.39748910e+09 1.39748910e+09 1.39748910e+09 1.39748910e+09 1.39748910e+09 1.39748910e+09 1.39748910e+09 1.39748911e+09 1.39748911e+09 1.39748911e+09 1.39748911e+09 1.39748911e+09 1.39748911e+09 1.39748911e+09 1.39748911e+09 1.39748911e+09 1.39748911e+09 1.39748911e+09 1.39748911e+09 1.39748911e+09 1.39748911e+09 1.39748911e+09 1.39748911e+09 1.39748911e+09 1.39748911e+09 1.39748911e+09 1.39748911e+09 1.39748912e+09 1.39748912e+09 1.39748912e+09 1.39748912e+09 1.39748912e+09 1.39748912e+09 1.39748912e+09 1.39748912e+09 1.39748912e+09 1.39748912e+09 1.39748912e+09 1.39748912e+09 1.39748912e+09 1.39748912e+09 1.39748912e+09 1.39748912e+09 1.39748912e+09 1.39748912e+09 1.39748912e+09 1.39748912e+09 1.39748913e+09 1.39748913e+09 1.39748913e+09 1.39748913e+09 1.39748913e+09 1.39748913e+09 1.39748913e+09 1.39748913e+09 1.39748913e+09 1.39748913e+09 1.39748913e+09 1.39748913e+09 1.39748913e+09 1.39748913e+09 1.39748913e+09 1.39748913e+09 1.39748913e+09 1.39748913e+09 1.39748913e+09 1.39748913e+09 1.39748914e+09 1.39748914e+09 1.39748914e+09 1.39748914e+09 1.39748914e+09 1.39748914e+09 1.39748914e+09 1.39748914e+09 1.39748914e+09 1.39748914e+09 1.39748914e+09 1.39748914e+09 1.39748914e+09 1.39748914e+09 1.39748914e+09 1.39748914e+09 1.39748914e+09 1.39748914e+09 1.39748914e+09 1.39748914e+09 1.39748915e+09 1.39748915e+09 1.39748915e+09 1.39748915e+09 1.39748915e+09 1.39748915e+09 1.39748915e+09 1.39748915e+09 1.39748915e+09 1.39748915e+09 1.39748915e+09 1.39748915e+09 1.39748915e+09 1.39748915e+09 1.39748915e+09 1.39748915e+09 1.39748915e+09 1.39748915e+09 1.39748915e+09 1.39748915e+09 1.39748916e+09 1.39748916e+09 1.39748916e+09 1.39748916e+09 1.39748916e+09 1.39748916e+09 1.39748916e+09 1.39748916e+09 1.39748916e+09 1.39748916e+09 1.39748916e+09 1.39748916e+09 1.39748916e+09 1.39748916e+09 1.39748916e+09 1.39748916e+09 1.39748916e+09 1.39748916e+09 1.39748916e+09 1.39748916e+09 1.39748917e+09 1.39748917e+09 1.39748917e+09 1.39748917e+09 1.39748917e+09 1.39748917e+09 1.39748917e+09 1.39748917e+09 1.39748917e+09 1.39748917e+09 1.39748917e+09 1.39748917e+09 1.39748917e+09 1.39748917e+09 1.39748917e+09 1.39748917e+09 1.39748917e+09 1.39748917e+09 1.39748917e+09 1.39748917e+09 1.39748918e+09 1.39748918e+09 1.39748918e+09 1.39748918e+09 1.39748918e+09 1.39748918e+09 1.39748918e+09 1.39748918e+09 1.39748918e+09 1.39748918e+09 1.39748918e+09 1.39748918e+09 1.39748918e+09 1.39748918e+09 1.39748918e+09 1.39748918e+09 1.39748918e+09 1.39748918e+09 1.39748918e+09 1.39748918e+09 1.39748919e+09 1.39748919e+09 1.39748919e+09 1.39748919e+09 1.39748919e+09 1.39748919e+09 1.39748919e+09 1.39748919e+09 1.39748919e+09 1.39748919e+09 1.39748919e+09 1.39748919e+09 1.39748919e+09 1.39748919e+09 1.39748919e+09 1.39748919e+09 1.39748919e+09 1.39748919e+09 1.39748919e+09 1.39748919e+09 1.39748920e+09 1.39748920e+09 1.39748920e+09 1.39748920e+09 1.39748920e+09 1.39748920e+09 1.39748920e+09 1.39748920e+09 1.39748920e+09 1.39748920e+09 1.39748920e+09 1.39748920e+09 1.39748920e+09 1.39748920e+09 1.39748920e+09 1.39748920e+09 1.39748920e+09 1.39748920e+09 1.39748920e+09 1.39748920e+09 1.39748921e+09 1.39748921e+09 1.39748921e+09 1.39748921e+09 1.39748921e+09 1.39748921e+09 1.39748921e+09 1.39748921e+09 1.39748921e+09 1.39748921e+09 1.39748921e+09 1.39748921e+09 1.39748921e+09 1.39748921e+09 1.39748921e+09 1.39748921e+09 1.39748921e+09 1.39748921e+09 1.39748921e+09] INFO 2025-06-26 20:18:56,110 lopcToNetCDF.py constructTimestampList():1380 [1] timestampArray[:2] = [1397489061.1 1397489061.6, ..., timestampArray[-2:] = 1397489213.6 1397489214.6] INFO 2025-06-26 20:18:56,110 lopcToNetCDF.py constructTimestampList():1389 [1] timestampList[:2] = [np.float64(1397489061.1119602), np.float64(1397489061.6119602)], ..., timestampList[-2:] = [np.float64(1397489213.6119602), np.float64(1397489214.6119602)]] INFO 2025-06-26 20:18:56,110 lopcToNetCDF.py constructTimestampList():1394 [1] Subsampling correctedSampleCountList (len = 307) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 20:18:56,110 lopcToNetCDF.py constructTimestampList():1399 [1] lFrameCountWrittenList[:2] = [20, 41], ... lFrameCountWrittenList[-2:] = [272, 293] INFO 2025-06-26 20:18:56,110 lopcToNetCDF.py constructTimestampList():1420 [1] len(subSampledCorrectedSampleCountList) = 14 INFO 2025-06-26 20:18:56,110 lopcToNetCDF.py constructTimestampList():1439 [1] len(timestampList) = 307 INFO 2025-06-26 20:18:56,110 lopcToNetCDF.py constructTimestampList():1440 [1] timestampList[:2] = [np.float64(1397489061.1119602), np.float64(1397489061.6119602)], ..., timestampList[-2:] = [np.float64(1397489213.6119602), np.float64(1397489214.6119602)]] INFO 2025-06-26 20:18:56,110 lopcToNetCDF.py constructTimestampList():1446 [1] Subsampling timestampList (len = 307) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 20:18:56,110 lopcToNetCDF.py constructTimestampList():1457 [1] Taking indices [[np.int32(19), np.int32(40)] ... [np.int32(271), np.int32(292)]] from timestampList to create subSampledTimestampList INFO 2025-06-26 20:18:56,111 lopcToNetCDF.py constructTimestampList():1463 [1] len(subSampledTimestampList) = 14 INFO 2025-06-26 20:18:56,111 lopcToNetCDF.py constructTimestampList():1477 [1] Finding elements of cFrameEsecsList that != -9999 ERROR 2025-06-26 20:18:56,111 lopcToNetCDF.py constructTimestampList():1501 [1] Cannot interpolate to cFrameEsecsListInterpolated: array of sample points is empty INFO 2025-06-26 20:18:56,112 lopcToNetCDF.py closeNetCDFFile():2096 [1] Writing time axis for len(tsList) = 14 INFO 2025-06-26 20:18:56,112 lopcToNetCDF.py closeNetCDFFile():2099 [1] tsList[:1] = [np.float64(1397489070.6119602)], ..., tsList[-2:] = [np.float64(1397489196.6119602), np.float64(1397489207.1119602)] INFO 2025-06-26 20:18:56,112 lopcToNetCDF.py closeNetCDFFile():2100 [1] Begin time = 2014-04-14 15:24:30 Z INFO 2025-06-26 20:18:56,112 lopcToNetCDF.py closeNetCDFFile():2103 [1] End time = 2014-04-14 15:26:47 Z INFO 2025-06-26 20:18:56,112 lopcToNetCDF.py closeNetCDFFile():2107 [1] Writing time axis for len(cFrameEsecsList) = 307 INFO 2025-06-26 20:18:56,112 lopcToNetCDF.py closeNetCDFFile():2111 [1] cFrameEsecsList[:1] = [-9999], ..., cFrameEsecsList[-2:] = [-9999, -9999] INFO 2025-06-26 20:18:56,112 lopcToNetCDF.py closeNetCDFFile():2116 [1] Begin time = 1969-12-31 21:13:21 Z INFO 2025-06-26 20:18:56,113 lopcToNetCDF.py closeNetCDFFile():2120 [1] End time = 1969-12-31 21:13:21 Z INFO 2025-06-26 20:18:56,116 lopcToNetCDF.py main():2381 [1] Created file: /data/auv_data/dorado/missionnetcdfs/2014.104.01/lopc.nc INFO 2025-06-26 20:18:56,116 lopcToNetCDF.py main():2384 [1] Processing finished: Thu Jun 26 20:18:56 2025 Elapsed processing time from start of processing = 0 seconds INFO 2025-06-26 20:18:56,117 process.py calibrate():227 [1] Calibration steps for 2014.104.01 INFO 2025-06-26 20:18:56,310 calibrate.py _nudge_pos():1680 [1] seg# end_sec_diff end_lon_diff end_lat_diff len(segi) seg_min u_drift (cm/s) v_drift (cm/s) start datetime of segment INFO 2025-06-26 20:18:56,312 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:18:56,995 calibrate.py _nudge_pos():1806 [1] 110: 0.050 -0.0000330 0.0001028 1045 3.48 -1.465 5.475 2014-04-14T15:29:36.860329984 INFO 2025-06-26 20:18:57,911 calibrate.py _nudge_pos():1806 [1] 207: 0.050 0.0006879 -0.0003340 7455 24.85 4.273 -2.491 2014-04-14T15:56:03.861613056 INFO 2025-06-26 20:18:58,862 calibrate.py _nudge_pos():1806 [1] 308: 0.050 0.0007600 -0.0005616 9700 32.33 3.629 -3.219 2014-04-14T16:30:03.861863424 INFO 2025-06-26 20:18:59,800 calibrate.py _nudge_pos():1806 [1] 407: 0.050 -0.0014041 -0.0000037 7910 26.36 -8.223 -0.026 2014-04-14T16:58:03.866775296 INFO 2025-06-26 20:19:00,756 calibrate.py _nudge_pos():1806 [1] 508: 0.060 -0.0040404 0.0006330 6820 22.73 -27.450 5.161 2014-04-14T17:22:27.866484480 INFO 2025-06-26 20:19:01,491 calibrate.py _nudge_pos():1806 [1] 585: 0.060 -0.0041211 0.0007511 8770 29.23 -21.777 4.762 2014-04-14T17:52:57.861121280 INFO 2025-06-26 20:19:02,426 calibrate.py _nudge_pos():1806 [1] 684: 0.060 -0.0015229 0.0005350 6530 21.76 -10.810 4.556 2014-04-14T18:16:21.864940288 INFO 2025-06-26 20:19:03,966 calibrate.py _nudge_pos():1806 [1] 846: 0.060 -0.0076205 0.0040256 10055 33.51 -35.118 22.258 2014-04-14T18:52:33.866148096 INFO 2025-06-26 20:19:04,909 calibrate.py _nudge_pos():1806 [1] 946: 0.080 -0.0087312 0.0034867 10155 33.85 -39.829 19.089 2014-04-14T19:28:03.860233216 INFO 2025-06-26 20:19:05,648 calibrate.py _nudge_pos():1806 [1] 1024: 0.070 0.0000302 -0.0000130 20 0.06 73.522 -38.084 2014-04-14T19:29:24.864684032 INFO 2025-06-26 20:19:05,677 calibrate.py _nudge_pos():1806 [1] 1027: 0.080 -0.0069962 0.0029048 10175 33.91 -31.843 15.872 2014-04-14T20:03:21.865140224 INFO 2025-06-26 20:19:06,389 calibrate.py _nudge_pos():1806 [1] 1102: 0.090 -0.0040032 0.0018131 9530 31.76 -19.450 10.577 2014-04-14T20:36:21.859501056 INFO 2025-06-26 20:19:07,100 calibrate.py _nudge_pos():1806 [1] 1176: 0.090 -0.0034900 0.0016054 9655 32.18 -16.734 9.244 2014-04-14T21:09:45.862217728 INFO 2025-06-26 20:19:07,901 calibrate.py _nudge_pos():1806 [1] 1259: 0.090 -0.0007246 0.0007067 2530 8.43 -13.263 15.535 2014-04-14T21:19:33.861936896 INFO 2025-06-26 20:19:08,822 calibrate.py _nudge_pos():1806 [1] 1354: 0.090 0.0001186 -0.0000487 640 2.13 8.589 -4.240 2014-04-14T21:23:15.866728448 INFO 2025-06-26 20:19:08,832 calibrate.py _nudge_pos():1806 [1] 1355: 0.090 0.0000009 -0.0000622 110 0.36 0.398 -31.700 2014-04-14T21:23:37.865221376 INFO 2025-06-26 20:19:19,637 calibrate.py _nudge_pos():1862 [1] 2419: - - - 1 0.00 - - INFO 2025-06-26 20:19:19,637 calibrate.py _nudge_pos():1868 [1] Points in final series = 113113 INFO 2025-06-26 20:19:20,632 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:19:21,470 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 34 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:19:22,141 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 34 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:19:22,143 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.104.01/ctd1.nc INFO 2025-06-26 20:19:22,145 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:19:22,145 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd1_salinity', Range(min=30, max=40))] INFO 2025-06-26 20:19:22,145 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:19:22,939 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 34 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:19:23,638 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 34 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:19:23,640 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.104.01/ctd2.nc INFO 2025-06-26 20:19:23,642 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:19:23,642 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd2_salinity', Range(min=30, max=40))] INFO 2025-06-26 20:19:23,642 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 20:19:23,678 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:19:24,696 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63 64 65] INFO 2025-06-26 20:19:24,890 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:19:45,311 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.104.01 INFO 2025-06-26 20:19:45,399 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.104.01/dorado_2014.104.01_cal.nc INFO 2025-06-26 20:19:45,554 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_time, isus_nitrate, isus_quality, isus_temp, isus_time, lopc_LCcount, lopc_countListSum, lopc_flowSpeed, lopc_nonTransCount, lopc_time, lopc_transCount, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_posx, navigation_posy, navigation_roll, navigation_time, navigation_yaw, nudged_latitude, nudged_longitude, tailcone_propRpm, tailcone_time, time INFO 2025-06-26 20:19:45,559 process.py align():251 [1] Alignment steps for 2014.104.01 INFO 2025-06-26 20:19:45,601 align.py process_cal():139 [1] Processing dorado_2014.104.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.104.01 INFO 2025-06-26 20:19:45,633 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:19:45,637 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:19:45,715 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:19:45,721 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:19:45,795 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:19:45,801 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:19:45,845 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:19:45,845 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:19:45,874 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:19:45,879 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:19:45,952 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.104.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:19:45,956 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:19:46,021 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.104.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:19:46,026 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:19:46,090 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.104.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:19:46,095 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:19:46,160 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.104.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:19:46,164 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:19:46,231 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.104.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:19:46,236 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:19:46,302 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.104.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:19:46,307 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:19:46,372 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.104.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:19:46,377 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:19:46,441 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.104.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:19:46,446 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:19:46,510 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.104.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:19:46,515 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:19:46,580 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.104.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:19:46,585 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:19:46,653 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.104.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:19:46,657 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:19:46,720 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.104.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:19:46,725 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:19:46,791 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.104.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:19:46,796 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:19:46,860 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.104.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:19:46,864 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:19:46,931 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.104.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:19:46,936 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:19:47,000 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.104.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:19:47,006 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:19:47,074 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.104.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:19:47,079 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:19:47,145 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.104.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:19:47,150 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:19:47,217 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.104.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:19:47,222 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:19:47,288 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.104.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:19:47,294 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:19:47,362 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.104.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:19:47,367 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:19:47,432 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.104.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:19:47,437 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:19:47,518 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:19:47,579 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:19:47,636 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:19:47,695 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:19:47,756 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:19:47,855 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 20:19:48,414 align.py process_cal():249 [1] lopc_countListSum: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:19:48,465 align.py process_cal():249 [1] lopc_transCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:19:48,514 align.py process_cal():249 [1] lopc_nonTransCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:19:48,566 align.py process_cal():249 [1] lopc_LCcount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:19:48,618 align.py process_cal():249 [1] lopc_flowSpeed: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:19:48,671 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:19:48,725 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.104.01/dorado_2014.104.01_align.nc INFO 2025-06-26 20:19:48,888 align.py write_netcdf():342 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_latitude, hs2_longitude, hs2_time, isus_depth, isus_latitude, isus_longitude, isus_nitrate, isus_quality, isus_temp, isus_time, lopc_LCcount, lopc_countListSum, lopc_depth, lopc_flowSpeed, lopc_latitude, lopc_longitude, lopc_nonTransCount, lopc_time, lopc_transCount, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time INFO 2025-06-26 20:19:48,891 process.py resample():273 [1] Resampling steps for 2014.104.01 INFO 2025-06-26 20:19:48,892 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:19:48,930 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.104.01/dorado_2014.104.01_align.nc mission netCDF file INFO 2025-06-26 20:19:48,938 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.104.01/dorado_2014.104.01_align.nc mission netCDF file INFO 2025-06-26 20:19:48,939 resample.py get_mission_start_end():1145 [1] navigation: 2014-04-14T15:25:06.678838784 to 2014-04-14T21:42:09.059099392 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:19:48,941 resample.py get_mission_start_end():1145 [1] hs2 : 2014-04-14T15:24:26.631582208 to 2014-04-14T21:42:08.829115392 (0 days 00:00:00.229984 before mission_end) INFO 2025-06-26 20:19:48,943 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-04-14T15:24:55.699590912 to 2014-04-14T21:42:08.969105664 (0 days 00:00:00.089993728 before mission_end) INFO 2025-06-26 20:19:48,945 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-04-14T15:24:55.299618304 to 2014-04-14T21:42:09.039100928 (0 days 00:00:00.019998464 before mission_end) INFO 2025-06-26 20:19:48,946 resample.py get_mission_start_end():1145 [1] isus : 2014-04-14T15:25:34.966900736 to 2014-04-14T21:42:08.749120768 (0 days 00:00:00.309978624 before mission_end) INFO 2025-06-26 20:19:48,948 resample.py get_mission_start_end():1145 [1] biolume : 2014-04-14T15:24:19.292050688 to 2014-04-14T21:42:08.379111680 (0 days 00:00:00.679987712 before mission_end) INFO 2025-06-26 20:19:48,949 resample.py get_mission_start_end():1145 [1] lopc : 2014-04-14T15:24:30.611960064 to 2014-04-14T15:26:47.111960064 (0 days 06:15:21.947139328 before mission_end) WARNING 2025-06-26 20:19:48,950 resample.py get_mission_start_end():1156 [1] Instrument lopc has a gap > 5 minutes at the end of the mission: 0 days 06:15:21.947139328 INFO 2025-06-26 20:19:48,952 resample.py get_mission_start_end():1145 [1] tailcone : 2014-04-14T15:24:20.621993728 to 2014-04-14T21:42:08.939107584 (0 days 00:00:00.119991808 before mission_end) INFO 2025-06-26 20:19:48,953 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.104.01/dorado_2014.104.01_align.nc mission netCDF file INFO 2025-06-26 20:19:48,954 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:49,193 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:49,234 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:49,274 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:49,315 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:49,353 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:49,388 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:49,423 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:49,457 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:49,493 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:49,526 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:49,558 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:49,591 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:49,623 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:49,655 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:49,686 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:49,717 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:49,749 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:49,782 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:49,817 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:49,850 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:49,883 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:49,917 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:49,950 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:49,985 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:50,002 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:50,018 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:50,033 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:50,047 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:50,061 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:50,066 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:19:50,066 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:19:50,840 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:19:50,987 resample.py add_biolume_proxies():633 [1] Zero flow values found: 22670 of 22670 - replaced with 350 ml/s INFO 2025-06-26 20:19:50,988 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:19:51,066 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:19:51,102 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:19:51,131 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:19:51,131 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:19:51,147 resample.py resample_variable():1031 [1] Resampling lopc_countListSum with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:51,147 resample.py resample_variable():1038 [1] Padding lopc_countListSum with 0 days 06:15:21.947139328 of NaNs to the end of mission INFO 2025-06-26 20:19:51,158 resample.py resample_variable():1031 [1] Resampling lopc_transCount with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:51,158 resample.py resample_variable():1038 [1] Padding lopc_transCount with 0 days 06:15:21.947139328 of NaNs to the end of mission INFO 2025-06-26 20:19:51,167 resample.py resample_variable():1031 [1] Resampling lopc_nonTransCount with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:51,167 resample.py resample_variable():1038 [1] Padding lopc_nonTransCount with 0 days 06:15:21.947139328 of NaNs to the end of mission INFO 2025-06-26 20:19:51,176 resample.py resample_variable():1031 [1] Resampling lopc_LCcount with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:51,176 resample.py resample_variable():1038 [1] Padding lopc_LCcount with 0 days 06:15:21.947139328 of NaNs to the end of mission INFO 2025-06-26 20:19:51,185 resample.py resample_variable():1031 [1] Resampling lopc_flowSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:51,185 resample.py resample_variable():1038 [1] Padding lopc_flowSpeed with 0 days 06:15:21.947139328 of NaNs to the end of mission INFO 2025-06-26 20:19:51,223 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:19:51,480 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.104.01/dorado_2014.104.01_1S.nc INFO 2025-06-26 20:19:53,809 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:20:05,745 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.104.01/dorado_2014.104.01_1S_Gulper.txt INFO 2025-06-26 20:20:05,745 process.py archive():337 [1] Archiving steps for 2014.104.01 INFO 2025-06-26 20:20:05,745 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.104.01/dorado_2014.104.01, BASE_PATH = /data/auv_data INFO 2025-06-26 20:20:05,747 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.104.01/dorado_2014.104.01 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:20:05,748 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.104.01_1S.nc INFO 2025-06-26 20:20:05,772 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.104.01/dorado_2014.104.01_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:20:05,773 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.104.01_cal.nc INFO 2025-06-26 20:20:06,090 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.104.01/dorado_2014.104.01_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:20:06,091 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.104.01_align.nc INFO 2025-06-26 20:20:06,309 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.104.01/dorado_2014.104.01_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:20:06,339 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.104.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014104/2014.104.01 done. INFO 2025-06-26 20:20:06,365 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.104.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014104/2014.104.01 done. INFO 2025-06-26 20:20:06,370 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.104.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014104/2014.104.01 done. INFO 2025-06-26 20:20:06,394 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.104.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014104/2014.104.01 done. INFO 2025-06-26 20:20:06,493 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.104.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014104/2014.104.01 done. INFO 2025-06-26 20:20:06,500 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.104.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014104/2014.104.01 done. INFO 2025-06-26 20:20:06,532 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.104.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014104/2014.104.01 done. INFO 2025-06-26 20:20:06,556 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.104.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014104/2014.104.01 done. INFO 2025-06-26 20:20:06,618 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.104.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014104/2014.104.01 done. INFO 2025-06-26 20:20:06,624 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.104.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014104/2014.104.01 done. INFO 2025-06-26 20:20:06,625 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:20:06,626 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.104.01_1S_Gulper.txt INFO 2025-06-26 20:20:06,630 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.104.01/dorado_2014.104.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:20:06,630 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.104.01/dorado_2014.104.01_processing.log /Volumes/AUVCTD/surveys/2014/netcdf