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Commit 38681df9 authored by Alán Muñoz's avatar Alán Muñoz
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tweak(logfile_parser): migrate examples

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examples/cExperiment_log_001.txt 0 → 100644
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View file @ 38681df9
=====================
06-Jan-2020 18:30:59 Start creating new experiment using parameters:
Omero experiment name: 001
Temporary working directory: C:06-Jan-2020 18:30:59 Processing position 2 (1108_002)
06-Jan-2020 18:31:00 Processing position 3 (1108_003)
06-Jan-2020 18:31:01 Processing position 4 (1109_004)
06-Jan-2020 18:31:02 Processing position 5 (1109_005)
06-Jan-2020 18:31:04 Processing position 6 (1109_006)
06-Jan-2020 18:31:05 Processing position 7 (1110_007)
06-Jan-2020 18:31:06 Processing position 8 (1110_008)
06-Jan-2020 18:31:07 Processing position 9 (1110_009)
06-Jan-2020 18:31:10 Successfully completed creating new experiment in 11 secs.
---------------------
=====================
06-Jan-2020 18:31:33 Start selecting traps...
06-Jan-2020 18:31:33 Processing position 1 (1108_001)
06-Jan-2020 18:31:40 Remove trap at 550 1188
06-Jan-2020 18:31:40 Remove trap at 733 1179
06-Jan-2020 18:31:41 Remove trap at 384 1189
06-Jan-2020 18:31:42 Remove trap at 201 1186
06-Jan-2020 18:31:47 Processing position 2 (1108_002)
06-Jan-2020 18:31:52 Remove trap at 384 1060
06-Jan-2020 18:31:54 Remove trap at 1081 571
06-Jan-2020 18:32:01 Processing position 3 (1108_003)
06-Jan-2020 18:32:05 Remove trap at 948 1140
06-Jan-2020 18:32:06 Remove trap at 1141 1174
06-Jan-2020 18:32:17 Remove trap at 139 1111
06-Jan-2020 18:32:18 Add trap at 130 1138
06-Jan-2020 18:32:26 Processing position 4 (1109_004)
06-Jan-2020 18:32:32 Remove trap at 1176 388
06-Jan-2020 18:32:39 Processing position 5 (1109_005)
06-Jan-2020 18:32:44 Remove trap at 1141 1135
06-Jan-2020 18:32:51 Remove trap at 955 379
06-Jan-2020 18:32:55 Processing position 6 (1109_006)
06-Jan-2020 18:33:00 Remove trap at 676 1177
06-Jan-2020 18:33:01 Remove trap at 1111 1147
06-Jan-2020 18:33:14 Processing position 7 (1110_007)
06-Jan-2020 18:33:20 Remove trap at 46 46
06-Jan-2020 18:33:28 Remove trap at 1150 84
06-Jan-2020 18:33:34 Processing position 8 (1110_008)
06-Jan-2020 18:33:49 Processing position 9 (1110_009)
06-Jan-2020 18:33:55 Add trap at 1153 1129
06-Jan-2020 18:33:57 Remove trap at 1135 1141
06-Jan-2020 18:33:57 Remove trap at 1176 1095
06-Jan-2020 18:34:15 Successfully completed selecting traps in 2.7 mins.
---------------------
=====================
06-Jan-2020 18:34:28 Start setting extraction parameters using parameters:
extractionParameters: {
extractFunction: extractCellDataStandardParfor
functionParameters: {
type: max
channels: 2 3
nuclearMarkerChannel: NaN
maxPixOverlap: 5
maxAllowedOverlap: 25
}
}
06-Jan-2020 18:34:28 Processing position 1 (1108_001)
06-Jan-2020 18:34:28 Processing position 2 (1108_002)
06-Jan-2020 18:34:29 Processing position 3 (1108_003)
06-Jan-2020 18:34:29 Processing position 4 (1109_004)
06-Jan-2020 18:34:30 Processing position 5 (1109_005)
06-Jan-2020 18:34:30 Processing position 6 (1109_006)
06-Jan-2020 18:34:30 Processing position 7 (1110_007)
06-Jan-2020 18:34:31 Processing position 8 (1110_008)
06-Jan-2020 18:34:31 Processing position 9 (1110_009)
06-Jan-2020 18:34:33 Successfully completed setting extraction parameters in 5 secs.
---------------------
=====================
07-Jan-2020 13:17:43 Start tracking traps in time...
07-Jan-2020 13:17:43 Processing position 1 (1108_001)
07-Jan-2020 13:23:31 Processing position 2 (1108_002)
07-Jan-2020 13:29:21 Processing position 3 (1108_003)
07-Jan-2020 13:35:13 Processing position 4 (1109_004)
07-Jan-2020 13:41:19 Processing position 5 (1109_005)
07-Jan-2020 13:47:09 Processing position 6 (1109_006)
07-Jan-2020 13:52:57 Processing position 7 (1110_007)
07-Jan-2020 13:58:41 Processing position 8 (1110_008)
07-Jan-2020 14:04:41 Processing position 9 (1110_009)
07-Jan-2020 14:10:38 Successfully completed tracking traps in time in 52.9 mins.
---------------------
=====================
07-Jan-2020 14:10:38 Start baby segmentation...
07-Jan-2020 14:10:39 Processing position 1 (1108_001)
07-Jan-2020 14:14:32 cTimelapse: 210.344 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 14:18:30 cTimelapse: 240.345 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 14:22:31 cTimelapse: 272.459 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 14:26:32 cTimelapse: 303.876 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 14:30:34 cTimelapse: 336.470 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 14:32:32 Processing position 2 (1108_002)
07-Jan-2020 14:36:22 cTimelapse: 206.699 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 14:40:12 cTimelapse: 235.726 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 14:44:13 cTimelapse: 268.814 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 14:48:27 cTimelapse: 306.046 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 14:52:43 cTimelapse: 343.681 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 14:54:44 Processing position 3 (1108_003)
07-Jan-2020 14:58:47 cTimelapse: 214.895 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 15:02:44 cTimelapse: 247.137 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 15:06:47 cTimelapse: 280.902 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 15:10:51 cTimelapse: 314.796 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 15:15:13 cTimelapse: 354.774 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 15:17:16 Processing position 4 (1109_004)
07-Jan-2020 15:21:06 cTimelapse: 222.663 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 15:25:09 cTimelapse: 253.596 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 15:29:16 cTimelapse: 286.597 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 15:33:46 cTimelapse: 325.040 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 15:38:35 cTimelapse: 369.190 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 15:40:50 Processing position 5 (1109_005)
07-Jan-2020 15:45:01 cTimelapse: 235.110 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 15:49:23 cTimelapse: 268.760 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 15:53:50 cTimelapse: 304.703 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 15:58:15 cTimelapse: 339.861 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:02:47 cTimelapse: 377.877 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:04:53 Processing position 6 (1109_006)
07-Jan-2020 16:08:32 cTimelapse: 205.246 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:12:09 cTimelapse: 231.500 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:15:49 cTimelapse: 259.276 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:19:45 cTimelapse: 291.813 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:24:03 cTimelapse: 331.193 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:26:11 Processing position 7 (1110_007)
07-Jan-2020 16:29:30 cTimelapse: 222.990 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:32:46 cTimelapse: 238.288 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:36:03 cTimelapse: 255.524 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:39:21 cTimelapse: 275.165 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:42:40 cTimelapse: 297.244 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:44:14 Processing position 8 (1110_008)
07-Jan-2020 16:47:32 cTimelapse: 215.583 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:50:51 cTimelapse: 235.959 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:54:09 cTimelapse: 256.409 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:57:25 cTimelapse: 275.563 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 17:00:43 cTimelapse: 296.390 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 17:02:13 Processing position 9 (1110_009)
07-Jan-2020 17:05:35 cTimelapse: 225.847 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 17:08:54 cTimelapse: 245.291 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 17:12:17 cTimelapse: 266.060 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 17:15:41 cTimelapse: 288.448 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 17:19:04 cTimelapse: 311.290 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 17:20:36 Successfully completed baby segmentation in 3.2 hours.
---------------------
=====================
07-Jan-2020 17:20:37 Start tracking cells using parameters:
Tracking threshold: 10
07-Jan-2020 17:20:39 Processing position 1 (1108_001)
07-Jan-2020 17:21:23 Processing position 2 (1108_002)
07-Jan-2020 17:22:06 Processing position 3 (1108_003)
07-Jan-2020 17:22:49 Processing position 4 (1109_004)
07-Jan-2020 17:23:33 Processing position 5 (1109_005)
07-Jan-2020 17:24:18 Processing position 6 (1109_006)
07-Jan-2020 17:24:58 Processing position 7 (1110_007)
07-Jan-2020 17:25:25 Processing position 8 (1110_008)
07-Jan-2020 17:25:55 Processing position 9 (1110_009)
07-Jan-2020 17:26:25 Successfully completed tracking cells in 5.8 mins.
---------------------
=====================
07-Jan-2020 17:26:25 Start autoselecting cells using parameters:
Fraction of timelapse that cells are present for: 0.5
Number of frames a cell must be present: 540
Cell must appear by frame: 540
Cell must still be present by frame: 1
Maximum number of cells: Inf
07-Jan-2020 17:26:27 Processing position 1 (1108_001)
07-Jan-2020 17:26:42 Processing position 2 (1108_002)
07-Jan-2020 17:26:58 Processing position 3 (1108_003)
07-Jan-2020 17:27:14 Processing position 4 (1109_004)
07-Jan-2020 17:27:31 Processing position 5 (1109_005)
07-Jan-2020 17:27:48 Processing position 6 (1109_006)
07-Jan-2020 17:28:03 Processing position 7 (1110_007)
07-Jan-2020 17:28:13 Processing position 8 (1110_008)
07-Jan-2020 17:28:25 Processing position 9 (1110_009)
07-Jan-2020 17:28:36 Successfully completed autoselecting cells in 2.2 mins.
---------------------
=====================
07-Jan-2020 17:28:37 Start extracting cell information...
07-Jan-2020 17:28:39 Processing position 1 (1108_001)
07-Jan-2020 17:58:38 Processing position 2 (1108_002)
07-Jan-2020 18:28:43 Processing position 3 (1108_003)
07-Jan-2020 18:58:45 Processing position 4 (1109_004)
07-Jan-2020 19:29:03 Processing position 5 (1109_005)
07-Jan-2020 19:59:31 Processing position 6 (1109_006)
07-Jan-2020 20:29:01 Processing position 7 (1110_007)
07-Jan-2020 20:56:05 Processing position 8 (1110_008)
07-Jan-2020 21:23:53 Processing position 9 (1110_009)
07-Jan-2020 21:51:15 Successfully completed extracting cell information in 4.4 hours.
---------------------
=====================
07-Jan-2020 21:51:16 Start baby lineage extraction...
07-Jan-2020 21:51:18 Processing position 1 (1108_001)
07-Jan-2020 21:52:37 Processing position 2 (1108_002)
07-Jan-2020 21:53:57 Processing position 3 (1108_003)
07-Jan-2020 21:55:16 Processing position 4 (1109_004)
07-Jan-2020 21:56:36 Processing position 5 (1109_005)
07-Jan-2020 21:57:59 Processing position 6 (1109_006)
07-Jan-2020 21:59:08 Processing position 7 (1110_007)
07-Jan-2020 21:59:50 Processing position 8 (1110_008)
07-Jan-2020 22:00:41 Processing position 9 (1110_009)
07-Jan-2020 22:01:26 Successfully completed baby lineage extraction in 10.2 mins.
---------------------
=====================
07-Jan-2020 22:01:26 Start compiling cell information...
07-Jan-2020 22:01:28 Processing position 1 (1108_001)
07-Jan-2020 22:01:30 Processing position 2 (1108_002)
07-Jan-2020 22:01:33 Processing position 3 (1108_003)
07-Jan-2020 22:01:35 Processing position 4 (1109_004)
07-Jan-2020 22:01:38 Processing position 5 (1109_005)
07-Jan-2020 22:01:40 Processing position 6 (1109_006)
07-Jan-2020 22:01:42 Processing position 7 (1110_007)
07-Jan-2020 22:01:44 Processing position 8 (1110_008)
07-Jan-2020 22:01:46 Processing position 9 (1110_009)
07-Jan-2020 22:02:20 Successfully completed compiling cell information in 54 secs.
---------------------
examples/example_multiDGUI_acq.txt 0 → 100644
+ 46
− 0
View file @ 38681df9
Channels:
Channel name, Exposure time, Skip, Z sect., Start time, Camera mode, EM gain, Voltage
Brightfield, 30, 1, 1, 1, 2, 270, 1.000
GFPFast, 30, 1, 1, 1, 2, 270, 3.500
mCherry, 100, 1, 1, 1, 2, 270, 2.500
Z_sectioning:
Sections,Spacing,PFSon?,AnyZ?,Drift,Method
3, 0.80, 1, 1, 0, 2
Time_settings:
1,120,660,79200
Points:
Position name, X position, Y position, Z position, PFS offset, Group, Brightfield, GFPFast, mCherry
pos001, 568.00, 1302.00, 1876.500, 122.450, 1, 30, 30, 100
pos002, 1267.00, 1302.00, 1880.125, 119.950, 1, 30, 30, 100
pos003, 1026.00, 977.00, 1877.575, 120.100, 1, 30, 30, 100
pos004, 540.00, -347.00, 1868.725, 121.200, 2, 30, 30, 100
pos005, 510.00, -687.00, 1867.150, 122.900, 2, 30, 30, 100
pos006, -187.00, -470.00, 1864.050, 119.600, 2, 30, 30, 100
pos007, -731.00, 916.00, 1867.050, 117.050, 3, 30, 30, 100
pos008, -1003.00, 1178.00, 1866.425, 121.700, 3, 30, 30, 100
pos009, -568.00, 1157.00, 1868.450, 119.350, 3, 30, 30, 100
Flow_control:
Syringe pump details: 2 pumps.
Pump states at beginning of experiment:
Pump port, Diameter, Current rate, Direction, Running, Contents
COM7, 14.43, 0.00, INF, 1, 2% glucose in SC
COM8, 14.43, 4.00, INF, 1, 0.1% glucose in SC
Dynamic flow details:
Number of pump changes:
1
Switching parameters:
Infuse/withdraw volumes:
50
Infuse/withdraw rates:
100
Times:
0
Switched to:
2
Switched from:
1
Flow post switch:
0
4
examples/example_multiDGUI_log.txt 0 → 100644
+ 651
− 0
View file @ 38681df9
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