From 38681df9522f910b45a7d0a0dad1d470a24837da Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Thu, 22 Sep 2022 13:40:56 +0100
Subject: [PATCH] tweak(logfile_parser): migrate examples
---
examples/cExperiment_log_001.txt | 276 ++++++++++++
examples/example_multiDGUI_acq.txt | 46 ++
examples/example_multiDGUI_log.txt | 651 +++++++++++++++++++++++++++++
3 files changed, 973 insertions(+)
create mode 100644 examples/cExperiment_log_001.txt
create mode 100644 examples/example_multiDGUI_acq.txt
create mode 100644 examples/example_multiDGUI_log.txt
diff --git a/examples/cExperiment_log_001.txt b/examples/cExperiment_log_001.txt
new file mode 100644
index 00000000..8db3a2e4
--- /dev/null
+++ b/examples/cExperiment_log_001.txt
@@ -0,0 +1,276 @@
+
+
+=====================
+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.
+---------------------
diff --git a/examples/example_multiDGUI_acq.txt b/examples/example_multiDGUI_acq.txt
new file mode 100644
index 00000000..e2d1e9b4
--- /dev/null
+++ b/examples/example_multiDGUI_acq.txt
@@ -0,0 +1,46 @@
+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
diff --git a/examples/example_multiDGUI_log.txt b/examples/example_multiDGUI_log.txt
new file mode 100644
index 00000000..e4a242ca
--- /dev/null
+++ b/examples/example_multiDGUI_log.txt
@@ -0,0 +1,651 @@
+Swain Lab microscope experiment log file
+Swain lab microscope control software - MultiDGUI commit number:05903fb3769ccf612e7801b46e2248644ce7ca28
+Warning! - there are uncommitted changes - software may be different from the above commit
+29-Feb-2020
+Microscope name is: Batman
+Acquisition settings are saved in:
+C:\path\to\example_multiDGUI_log.txt
+Experiment details:
+Aim: Strain: Comments:
+Microscope setup for used channels:
+Brightfield:
+White LED
+->(Polariser + Prism + condenser)]
+->Filter block:[Dual GFP/mCherry exciter (59022x),Dual dichroic (89021bs),No emission filter]
+->Emission filter wheel:[No filter in emission wheel]
+GFPFast:
+470nm LED
+->Combiner cube:[480/40 exciter, 515LP dichroic->(455LP dichroic)]
+->Filter block:[Dual GFP/mCherry exciter (59022x),Dual dichroic (89021bs),No emission filter]
+->Emission filter wheel:[520/40 emission filter]
+mCherry:
+White LED
+->Combiner cube:[No exciter, No reflecting dichroic->(515LP and 455LP dichroics)]
+->Filter block:[Dual GFP/mCherry exciter (59022x),Dual dichroic (89021bs),No emission filter]
+->Emission filter wheel:[632/60 emission filter]
+Micromanager config file:C:\path\to\config_file.cfg
+Omero project:
+SteadystateGlucose
+Omero tags:
+29-Feb-2020,Batman,3 chamber,GFP,mCherry,1106.Mig2-GFP Mig1-mCherry,900.Mig1-GFP Msn2-mCherry,898.Msn2-GFP Mig1-mCherry,0.1% glucose,2% glucose,
+Experiment started at:29-Feb-2020 01:16:51
+
+------Time point_1------
+Memory available for all arrays: 14141227008
+Memory used by Matlab: 2237132800
+Switching pumps at 29-Feb-2020 01:16:52. Fast infusion/withdrawal step: Rate=100. Volume=50
+Pump switch complete at:29-Feb-2020 01:16:52
+Dominant pump is now: COM8 pumping at 4ul/min
+Dominant medium is now: 0.1% glucose in SC
+Position:1,pos001
+Position group:1
+Channel configuration set to: Brightfield: 29-Feb-2020 01:16:52
+Moved to X:568, Y:1302
+Call to readDrift after moving to position1
+Setting PFS offset to :122.45
+readDrift script. Reference z position is:1876.5
+readDrift script. Cumulative drift is:-5.9
+Channel configuration set to: Brightfield: 29-Feb-2020 01:17:01
+Channel:Brightfield set at:29-Feb-2020 01:17:01
+Exposure time:30ms
+Channel configuration set to: GFPFast: 29-Feb-2020 01:17:06
+Channel:GFPFast set at:29-Feb-2020 01:17:06
+Exposure time:30ms
+Exposure time:30ms
+captureStack (Batman). Z drive position before stack capture is: 1870.575. 29-Feb-2020 01:17:10
+captureStack (Batman). Starting PIFOC position is: 0. 29-Feb-2020 01:17:10
+captureStackMM2 (Batmanl). Z drive position before stack capture is: 1870.575. 29-Feb-2020 01:17:10
+captureStack (Batgirl). Starting Z stage position is: 50. 29-Feb-2020 01:17:10
+Channel configuration set to: mCherry: 29-Feb-2020 01:17:12
+Channel:mCherry set at:29-Feb-2020 01:17:12
+Exposure time:100ms
+Exposure time:100ms
+captureStack (Batman). Z drive position before stack capture is: 1870.575. 29-Feb-2020 01:17:12
+captureStack (Batman). Starting PIFOC position is: 0. 29-Feb-2020 01:17:12
+captureStackMM2 (Batmanl). Z drive position before stack capture is: 1870.55. 29-Feb-2020 01:17:13
+captureStack (Batgirl). Starting Z stage position is: 50. 29-Feb-2020 01:17:13
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Position:2,pos002
+Position group:1
+Channel configuration set to: Brightfield: 29-Feb-2020 01:17:18
+Moved to X:1267, Y:1302
+Call to readDrift after moving to position2
+Setting PFS offset to :119.95
+readDrift script. Reference z position is:1880.125
+readDrift script. Cumulative drift is:-9.725
+Channel configuration set to: Brightfield: 29-Feb-2020 01:17:27
+Channel:Brightfield set at:29-Feb-2020 01:17:27
+Exposure time:30ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Channel configuration set to: GFPFast: 29-Feb-2020 01:17:32
+Channel:GFPFast set at:29-Feb-2020 01:17:32
+Exposure time:30ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Channel configuration set to: mCherry: 29-Feb-2020 01:17:37
+Channel:mCherry set at:29-Feb-2020 01:17:38
+Exposure time:100ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Position:3,pos003
+Position group:1
+Channel configuration set to: Brightfield: 29-Feb-2020 01:17:43
+Moved to X:1026, Y:977
+Call to readDrift after moving to position3
+Setting PFS offset to :120.1
+readDrift script. Reference z position is:1877.575
+readDrift script. Cumulative drift is:-5.925
+Channel configuration set to: Brightfield: 29-Feb-2020 01:17:52
+Channel:Brightfield set at:29-Feb-2020 01:17:52
+Exposure time:30ms
+Exposure time:30ms
+captureStack (Batman). Z drive position before stack capture is: 1870.925. 29-Feb-2020 01:17:57
+captureStack (Batman). Starting PIFOC position is: 0. 29-Feb-2020 01:17:57
+captureStackMM2 (Batmanl). Z drive position before stack capture is: 1870.9. 29-Feb-2020 01:17:58
+captureStack (Batgirl). Starting Z stage position is: 50. 29-Feb-2020 01:17:58
+Channel configuration set to: GFPFast: 29-Feb-2020 01:18:00
+Channel:GFPFast set at:29-Feb-2020 01:18:00
+Exposure time:30ms
+Exposure time:30ms
+captureStack (Batman). Z drive position before stack capture is: 1870.925. 29-Feb-2020 01:18:01
+captureStack (Batman). Starting PIFOC position is: 0. 29-Feb-2020 01:18:01
+captureStackMM2 (Batmanl). Z drive position before stack capture is: 1870.925. 29-Feb-2020 01:18:01
+captureStack (Batgirl). Starting Z stage position is: 50. 29-Feb-2020 01:18:01
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Channel configuration set to: mCherry: 29-Feb-2020 01:18:06
+Channel:mCherry set at:29-Feb-2020 01:18:07
+Exposure time:100ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Position:4,pos004
+Position group:2
+Channel configuration set to: Brightfield: 29-Feb-2020 01:18:14
+Moved to X:540, Y:-347
+Call to readDrift after moving to position4
+Setting PFS offset to :121.2
+readDrift script. Reference z position is:1868.725
+readDrift script. Cumulative drift is:3.65
+PFS not locked. Waiting for lock...
+PFS took 0.650000 seconds to lock.
+Channel configuration set to: Brightfield: 29-Feb-2020 01:18:18
+Channel:Brightfield set at:29-Feb-2020 01:18:18
+Exposure time:30ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Channel configuration set to: GFPFast: 29-Feb-2020 01:18:23
+Channel:GFPFast set at:29-Feb-2020 01:18:23
+Exposure time:30ms
+Exposure time:30ms
+captureStack (Batman). Z drive position before stack capture is: 1862.575. 29-Feb-2020 01:18:28
+captureStack (Batman). Starting PIFOC position is: 0. 29-Feb-2020 01:18:28
+captureStackMM2 (Batmanl). Z drive position before stack capture is: 1862.55. 29-Feb-2020 01:18:28
+captureStack (Batgirl). Starting Z stage position is: 50. 29-Feb-2020 01:18:28
+Channel configuration set to: mCherry: 29-Feb-2020 01:18:31
+Channel:mCherry set at:29-Feb-2020 01:18:31
+Exposure time:100ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Position:5,pos005
+Position group:2
+Channel configuration set to: Brightfield: 29-Feb-2020 01:18:37
+Moved to X:510, Y:-687
+Call to readDrift after moving to position5
+Setting PFS offset to :122.9
+readDrift script. Reference z position is:1867.15
+readDrift script. Cumulative drift is:-6.05
+Channel configuration set to: Brightfield: 29-Feb-2020 01:18:44
+Channel:Brightfield set at:29-Feb-2020 01:18:44
+Exposure time:30ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Channel configuration set to: GFPFast: 29-Feb-2020 01:18:49
+Channel:GFPFast set at:29-Feb-2020 01:18:49
+Exposure time:30ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Channel configuration set to: mCherry: 29-Feb-2020 01:18:54
+Channel:mCherry set at:29-Feb-2020 01:18:55
+Exposure time:100ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Position:6,pos006
+Position group:2
+Channel configuration set to: Brightfield: 29-Feb-2020 01:19:00
+Moved to X:-187, Y:-470
+Call to readDrift after moving to position6
+Setting PFS offset to :119.6
+readDrift script. Reference z position is:1864.05
+readDrift script. Cumulative drift is:-4.725
+Channel configuration set to: Brightfield: 29-Feb-2020 01:19:05
+Channel:Brightfield set at:29-Feb-2020 01:19:05
+Exposure time:30ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Channel configuration set to: GFPFast: 29-Feb-2020 01:19:10
+Channel:GFPFast set at:29-Feb-2020 01:19:10
+Exposure time:30ms
+Exposure time:30ms
+captureStack (Batman). Z drive position before stack capture is: 1859.075. 29-Feb-2020 01:19:13
+captureStack (Batman). Starting PIFOC position is: 0. 29-Feb-2020 01:19:13
+captureStackMM2 (Batmanl). Z drive position before stack capture is: 1859.05. 29-Feb-2020 01:19:13
+captureStack (Batgirl). Starting Z stage position is: 50. 29-Feb-2020 01:19:13
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Channel configuration set to: mCherry: 29-Feb-2020 01:19:18
+Channel:mCherry set at:29-Feb-2020 01:19:18
+Exposure time:100ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Position:7,pos007
+Position group:3
+Channel configuration set to: Brightfield: 29-Feb-2020 01:19:25
+Moved to X:-731, Y:916
+Call to readDrift after moving to position7
+Setting PFS offset to :117.05
+readDrift script. Reference z position is:1867.05
+readDrift script. Cumulative drift is:-7.625
+Channel configuration set to: Brightfield: 29-Feb-2020 01:19:33
+Channel:Brightfield set at:29-Feb-2020 01:19:33
+Exposure time:30ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Channel configuration set to: GFPFast: 29-Feb-2020 01:19:38
+Channel:GFPFast set at:29-Feb-2020 01:19:39
+Exposure time:30ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Channel configuration set to: mCherry: 29-Feb-2020 01:19:44
+Channel:mCherry set at:29-Feb-2020 01:19:44
+Exposure time:100ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Position:8,pos008
+Position group:3
+Channel configuration set to: Brightfield: 29-Feb-2020 01:19:49
+Moved to X:-1003, Y:1178
+Call to readDrift after moving to position8
+Setting PFS offset to :121.7
+readDrift script. Reference z position is:1866.425
+readDrift script. Cumulative drift is:-4.275
+Channel configuration set to: Brightfield: 29-Feb-2020 01:19:54
+Channel:Brightfield set at:29-Feb-2020 01:19:54
+Exposure time:30ms
+Exposure time:30ms
+captureStack (Batman). Z drive position before stack capture is: 1861.825. 29-Feb-2020 01:19:58
+captureStack (Batman). Starting PIFOC position is: 0. 29-Feb-2020 01:19:58
+captureStackMM2 (Batmanl). Z drive position before stack capture is: 1861.85. 29-Feb-2020 01:19:58
+captureStack (Batgirl). Starting Z stage position is: 50. 29-Feb-2020 01:19:58
+Channel configuration set to: GFPFast: 29-Feb-2020 01:20:03
+Channel:GFPFast set at:29-Feb-2020 01:20:03
+Exposure time:30ms
+Exposure time:30ms
+captureStack (Batman). Z drive position before stack capture is: 1861.8. 29-Feb-2020 01:20:06
+captureStack (Batman). Starting PIFOC position is: 0. 29-Feb-2020 01:20:06
+captureStackMM2 (Batmanl). Z drive position before stack capture is: 1861.825. 29-Feb-2020 01:20:07
+captureStack (Batgirl). Starting Z stage position is: 50. 29-Feb-2020 01:20:07
+Channel configuration set to: mCherry: 29-Feb-2020 01:20:08
+Channel:mCherry set at:29-Feb-2020 01:20:09
+Exposure time:100ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Position:9,pos009
+Position group:3
+Channel configuration set to: Brightfield: 29-Feb-2020 01:20:14
+Moved to X:-568, Y:1157
+Call to readDrift after moving to position9
+readDrift script. Reference z position is:1868.45
+readDrift script. Cumulative drift is:-5.525
+Channel configuration set to: Brightfield: 29-Feb-2020 01:20:22
+Channel:Brightfield set at:29-Feb-2020 01:20:23
+Exposure time:30ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Channel configuration set to: GFPFast: 29-Feb-2020 01:20:28
+Channel:GFPFast set at:29-Feb-2020 01:20:28
+Exposure time:30ms
+Exposure time:30ms
+captureStack (Batman). Z drive position before stack capture is: 1862.95. 29-Feb-2020 01:20:31
+captureStack (Batman). Starting PIFOC position is: 0. 29-Feb-2020 01:20:31
+captureStackMM2 (Batmanl). Z drive position before stack capture is: 1862.95. 29-Feb-2020 01:20:31
+captureStack (Batgirl). Starting Z stage position is: 50. 29-Feb-2020 01:20:31
+Channel configuration set to: mCherry: 29-Feb-2020 01:20:32
+Channel:mCherry set at:29-Feb-2020 01:20:33
+Exposure time:100ms
+Exposure time:100ms
+captureStack (Batman). Z drive position before stack capture is: 1863. 29-Feb-2020 01:20:33
+captureStack (Batman). Starting PIFOC position is: 0. 29-Feb-2020 01:20:33
+captureStackMM2 (Batmanl). Z drive position before stack capture is: 1863. 29-Feb-2020 01:20:33
+captureStack (Batgirl). Starting Z stage position is: 50. 29-Feb-2020 01:20:33
+Position group_1. Channel:Brightfield
+Maximum intensity measured in position group_1_is:0
+Channel does not use Smart EM camera mode. Settings remain unchanged.
+Position group_1. Channel:GFPFast
+Maximum intensity measured in position group_1_is:0
+Channel does not use Smart EM camera mode. Settings remain unchanged.
+Position group_1. Channel:mCherry
+Maximum intensity measured in position group_1_is:0
+Channel does not use Smart EM camera mode. Settings remain unchanged.
+Position group_1. Channel:Brightfield
+Maximum intensity measured in position group_1_is:0
+Channel does not use Smart EM camera mode. Settings remain unchanged.
+Position group_1. Channel:GFPFast
+Maximum intensity measured in position group_1_is:0
+Channel does not use Smart EM camera mode. Settings remain unchanged.
+Position group_1. Channel:mCherry
+Maximum intensity measured in position group_1_is:0
+Channel does not use Smart EM camera mode. Settings remain unchanged.
+Position group_1. Channel:Brightfield
+Maximum intensity measured in position group_1_is:0
+Channel does not use Smart EM camera mode. Settings remain unchanged.
+Position group_1. Channel:GFPFast
+Maximum intensity measured in position group_1_is:0
+Channel does not use Smart EM camera mode. Settings remain unchanged.
+Position group_1. Channel:mCherry
+Maximum intensity measured in position group_1_is:0
+Channel does not use Smart EM camera mode. Settings remain unchanged.
+Timepoint:1 completed at:29-Feb-2020 01:20:35
+Time since start of timelapse:224.2978
+PFS is locked
+Time to next time point:-104.2112
+
+------Time point_2------
+Memory available for all arrays: 13728235520
+Memory used by Matlab: 2301521920
+Position:1,pos001
+Position group:1
+Channel configuration set to: Brightfield: 29-Feb-2020 01:20:36
+Moved to X:568, Y:1302
+Call to readDrift after moving to position1
+Setting PFS offset to :122.45
+readDrift script. Reference z position is:1876.5
+readDrift script. Cumulative drift is:-6
+Channel configuration set to: Brightfield: 29-Feb-2020 01:20:40
+Channel:Brightfield set at:29-Feb-2020 01:20:40
+Exposure time:30ms
+Exposure time:30ms
+captureStack (Batman). Z drive position before stack capture is: 1870.6. 29-Feb-2020 01:20:41
+captureStack (Batman). Starting PIFOC position is: 0. 29-Feb-2020 01:20:41
+captureStackMM2 (Batmanl). Z drive position before stack capture is: 1870.575. 29-Feb-2020 01:20:41
+captureStack (Batgirl). Starting Z stage position is: 50. 29-Feb-2020 01:20:41
+Channel configuration set to: GFPFast: 29-Feb-2020 01:20:42
+Channel:GFPFast set at:29-Feb-2020 01:20:42
+Exposure time:30ms
+Exposure time:30ms
+captureStack (Batman). Z drive position before stack capture is: 1870.575. 29-Feb-2020 01:20:43
+captureStack (Batman). Starting PIFOC position is: 0. 29-Feb-2020 01:20:43
+captureStackMM2 (Batmanl). Z drive position before stack capture is: 1870.575. 29-Feb-2020 01:20:43
+captureStack (Batgirl). Starting Z stage position is: 50. 29-Feb-2020 01:20:43
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Channel configuration set to: mCherry: 29-Feb-2020 01:20:48
+Channel:mCherry set at:29-Feb-2020 01:20:48
+Exposure time:100ms
+Exposure time:100ms
+captureStack (Batman). Z drive position before stack capture is: 1870.575. 29-Feb-2020 01:20:52
+captureStack (Batman). Starting PIFOC position is: 0. 29-Feb-2020 01:20:52
+captureStackMM2 (Batmanl). Z drive position before stack capture is: 1870.575. 29-Feb-2020 01:20:52
+captureStack (Batgirl). Starting Z stage position is: 50. 29-Feb-2020 01:20:52
+Position:2,pos002
+Position group:1
+Channel configuration set to: Brightfield: 29-Feb-2020 01:20:56
+Moved to X:1267, Y:1302
+Call to readDrift after moving to position2
+Setting PFS offset to :119.95
+readDrift script. Reference z position is:1880.125
+readDrift script. Cumulative drift is:-9.375
+Channel configuration set to: Brightfield: 29-Feb-2020 01:21:04
+Channel:Brightfield set at:29-Feb-2020 01:21:04
+Exposure time:30ms
+Exposure time:30ms
+captureStack (Batman). Z drive position before stack capture is: 1870.9. 29-Feb-2020 01:21:10
+captureStack (Batman). Starting PIFOC position is: 0. 29-Feb-2020 01:21:10
+captureStackMM2 (Batmanl). Z drive position before stack capture is: 1870.9. 29-Feb-2020 01:21:10
+captureStack (Batgirl). Starting Z stage position is: 50. 29-Feb-2020 01:21:10
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Channel configuration set to: GFPFast: 29-Feb-2020 01:21:15
+Channel:GFPFast set at:29-Feb-2020 01:21:15
+Exposure time:30ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Channel configuration set to: mCherry: 29-Feb-2020 01:21:20
+Channel:mCherry set at:29-Feb-2020 01:21:21
+Exposure time:100ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Position:3,pos003
+Position group:1
+Channel configuration set to: Brightfield: 29-Feb-2020 01:21:27
+Moved to X:1026, Y:977
+Call to readDrift after moving to position3
+Setting PFS offset to :120.1
+readDrift script. Reference z position is:1877.575
+readDrift script. Cumulative drift is:-2.825
+Channel configuration set to: Brightfield: 29-Feb-2020 01:21:35
+Channel:Brightfield set at:29-Feb-2020 01:21:35
+Exposure time:30ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Channel configuration set to: GFPFast: 29-Feb-2020 01:21:40
+Channel:GFPFast set at:29-Feb-2020 01:21:41
+Exposure time:30ms
+Exposure time:30ms
+captureStack (Batman). Z drive position before stack capture is: 1874.825. 29-Feb-2020 01:21:41
+captureStack (Batman). Starting PIFOC position is: 0. 29-Feb-2020 01:21:41
+captureStackMM2 (Batmanl). Z drive position before stack capture is: 1874.75. 29-Feb-2020 01:21:42
+captureStack (Batgirl). Starting Z stage position is: 50. 29-Feb-2020 01:21:42
+Channel configuration set to: mCherry: 29-Feb-2020 01:21:43
+Channel:mCherry set at:29-Feb-2020 01:21:43
+Exposure time:100ms
+Exposure time:100ms
+captureStack (Batman). Z drive position before stack capture is: 1874.775. 29-Feb-2020 01:21:44
+captureStack (Batman). Starting PIFOC position is: 0. 29-Feb-2020 01:21:44
+captureStackMM2 (Batmanl). Z drive position before stack capture is: 1874.75. 29-Feb-2020 01:21:44
+captureStack (Batgirl). Starting Z stage position is: 50. 29-Feb-2020 01:21:44
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Position:4,pos004
+Position group:2
+Channel configuration set to: Brightfield: 29-Feb-2020 01:21:50
+Moved to X:540, Y:-347
+Call to readDrift after moving to position4
+Setting PFS offset to :121.2
+readDrift script. Reference z position is:1868.725
+readDrift script. Cumulative drift is:3.175
+Channel configuration set to: Brightfield: 29-Feb-2020 01:21:55
+Channel:Brightfield set at:29-Feb-2020 01:21:55
+Exposure time:30ms
+Exposure time:30ms
+captureStack (Batman). Z drive position before stack capture is: 1863.425. 29-Feb-2020 01:21:55
+captureStack (Batman). Starting PIFOC position is: 0. 29-Feb-2020 01:21:55
+captureStackMM2 (Batmanl). Z drive position before stack capture is: 1863.45. 29-Feb-2020 01:21:56
+captureStack (Batgirl). Starting Z stage position is: 50. 29-Feb-2020 01:21:56
+Channel configuration set to: GFPFast: 29-Feb-2020 01:21:56
+Channel:GFPFast set at:29-Feb-2020 01:21:57
+Exposure time:30ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Channel configuration set to: mCherry: 29-Feb-2020 01:22:02
+Channel:mCherry set at:29-Feb-2020 01:22:02
+Exposure time:100ms
+Exposure time:100ms
+captureStack (Batman). Z drive position before stack capture is: 1863.4. 29-Feb-2020 01:22:04
+captureStack (Batman). Starting PIFOC position is: 0. 29-Feb-2020 01:22:04
+captureStackMM2 (Batmanl). Z drive position before stack capture is: 1863.4. 29-Feb-2020 01:22:04
+captureStack (Batgirl). Starting Z stage position is: 50. 29-Feb-2020 01:22:04
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Position:5,pos005
+Position group:2
+Channel configuration set to: Brightfield: 29-Feb-2020 01:22:11
+Moved to X:510, Y:-687
+Call to readDrift after moving to position5
+Setting PFS offset to :122.9
+readDrift script. Reference z position is:1867.15
+readDrift script. Cumulative drift is:-4.2
+Channel configuration set to: Brightfield: 29-Feb-2020 01:22:19
+Channel:Brightfield set at:29-Feb-2020 01:22:19
+Exposure time:30ms
+Exposure time:30ms
+captureStack (Batman). Z drive position before stack capture is: 1863.275. 29-Feb-2020 01:22:22
+captureStack (Batman). Starting PIFOC position is: 0. 29-Feb-2020 01:22:22
+captureStackMM2 (Batmanl). Z drive position before stack capture is: 1863.275. 29-Feb-2020 01:22:23
+captureStack (Batgirl). Starting Z stage position is: 50. 29-Feb-2020 01:22:23
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Channel configuration set to: GFPFast: 29-Feb-2020 01:22:28
+Channel:GFPFast set at:29-Feb-2020 01:22:28
+Exposure time:30ms
+Exposure time:30ms
+captureStack (Batman). Z drive position before stack capture is: 1863.275. 29-Feb-2020 01:22:31
+captureStack (Batman). Starting PIFOC position is: 0. 29-Feb-2020 01:22:31
+captureStackMM2 (Batmanl). Z drive position before stack capture is: 1863.275. 29-Feb-2020 01:22:32
+captureStack (Batgirl). Starting Z stage position is: 50. 29-Feb-2020 01:22:32
+Channel configuration set to: mCherry: 29-Feb-2020 01:22:34
+Channel:mCherry set at:29-Feb-2020 01:22:35
+Exposure time:100ms
+Exposure time:100ms
+captureStack (Batman). Z drive position before stack capture is: 1863.275. 29-Feb-2020 01:22:35
+captureStack (Batman). Starting PIFOC position is: 0. 29-Feb-2020 01:22:35
+captureStackMM2 (Batmanl). Z drive position before stack capture is: 1863.275. 29-Feb-2020 01:22:35
+captureStack (Batgirl). Starting Z stage position is: 50. 29-Feb-2020 01:22:35
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Position:6,pos006
+Position group:2
+Channel configuration set to: Brightfield: 29-Feb-2020 01:22:42
+Moved to X:-187, Y:-470
+Call to readDrift after moving to position6
+Setting PFS offset to :119.6
+readDrift script. Reference z position is:1864.05
+readDrift script. Cumulative drift is:-2
+Channel configuration set to: Brightfield: 29-Feb-2020 01:22:50
+Channel:Brightfield set at:29-Feb-2020 01:22:51
+Exposure time:30ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Channel configuration set to: GFPFast: 29-Feb-2020 01:22:56
+Channel:GFPFast set at:29-Feb-2020 01:22:56
+Exposure time:30ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Channel configuration set to: mCherry: 29-Feb-2020 01:23:01
+Channel:mCherry set at:29-Feb-2020 01:23:01
+Exposure time:100ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Position:7,pos007
+Position group:3
+Channel configuration set to: Brightfield: 29-Feb-2020 01:23:07
+Moved to X:-731, Y:916
+Call to readDrift after moving to position7
+Setting PFS offset to :117.05
+readDrift script. Reference z position is:1867.05
+readDrift script. Cumulative drift is:-6.275
+Channel configuration set to: Brightfield: 29-Feb-2020 01:23:16
+Channel:Brightfield set at:29-Feb-2020 01:23:16
+Exposure time:30ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Channel configuration set to: GFPFast: 29-Feb-2020 01:23:21
+Channel:GFPFast set at:29-Feb-2020 01:23:21
+Exposure time:30ms
+Exposure time:30ms
+captureStack (Batman). Z drive position before stack capture is: 1860.775. 29-Feb-2020 01:23:22
+captureStack (Batman). Starting PIFOC position is: 0. 29-Feb-2020 01:23:22
+captureStackMM2 (Batmanl). Z drive position before stack capture is: 1860.775. 29-Feb-2020 01:23:23
+captureStack (Batgirl). Starting Z stage position is: 50. 29-Feb-2020 01:23:23
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Channel configuration set to: mCherry: 29-Feb-2020 01:23:28
+Channel:mCherry set at:29-Feb-2020 01:23:28
+Exposure time:100ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Position:8,pos008
+Position group:3
+Channel configuration set to: Brightfield: 29-Feb-2020 01:23:34
+Moved to X:-1003, Y:1178
+Call to readDrift after moving to position8
+Setting PFS offset to :121.7
+readDrift script. Reference z position is:1866.425
+readDrift script. Cumulative drift is:-2.825
+PFS not locked. Waiting for lock...
+PFS took 0.600000 seconds to lock.
+Channel configuration set to: Brightfield: 29-Feb-2020 01:23:43
+Channel:Brightfield set at:29-Feb-2020 01:23:43
+Exposure time:30ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Channel configuration set to: GFPFast: 29-Feb-2020 01:23:48
+Channel:GFPFast set at:29-Feb-2020 01:23:49
+Exposure time:30ms
+Exposure time:30ms
+captureStack (Batman). Z drive position before stack capture is: 1862.925. 29-Feb-2020 01:23:54
+captureStack (Batman). Starting PIFOC position is: 0. 29-Feb-2020 01:23:54
+captureStackMM2 (Batmanl). Z drive position before stack capture is: 1862.925. 29-Feb-2020 01:23:54
+captureStack (Batgirl). Starting Z stage position is: 50. 29-Feb-2020 01:23:54
+Channel configuration set to: mCherry: 29-Feb-2020 01:23:55
+Channel:mCherry set at:29-Feb-2020 01:23:55
+Exposure time:100ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Position:9,pos009
+Position group:3
+Channel configuration set to: Brightfield: 29-Feb-2020 01:24:01
+Moved to X:-568, Y:1157
+Call to readDrift after moving to position9
+readDrift script. Reference z position is:1868.45
+readDrift script. Cumulative drift is:-6.2
+Channel configuration set to: Brightfield: 29-Feb-2020 01:24:10
+Channel:Brightfield set at:29-Feb-2020 01:24:10
+Exposure time:30ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Channel configuration set to: GFPFast: 29-Feb-2020 01:24:15
+Channel:GFPFast set at:29-Feb-2020 01:24:15
+Exposure time:30ms
+Exposure time:30ms
+captureStack (Batman). Z drive position before stack capture is: 1862.2. 29-Feb-2020 01:24:18
+captureStack (Batman). Starting PIFOC position is: 0. 29-Feb-2020 01:24:18
+captureStackMM2 (Batmanl). Z drive position before stack capture is: 1862.2. 29-Feb-2020 01:24:18
+captureStack (Batgirl). Starting Z stage position is: 50. 29-Feb-2020 01:24:18
+Channel configuration set to: mCherry: 29-Feb-2020 01:24:19
+Channel:mCherry set at:29-Feb-2020 01:24:19
+Exposure time:100ms
+WARNING - ERROR CAUGHT - NO IMAGE CAPTURED TO THIS CHANNEL AND TIMEPOINT. Error message:Java exception occurred:
+java.lang.Exception: Wait for device "XYStage" timed out after 5000ms
+ at mmcorej.MMCoreJJNI.CMMCore_waitForSystem(Native Method)
+Position group_1. Channel:Brightfield
+Maximum intensity measured in position group_1_is:0
+Channel does not use Smart EM camera mode. Settings remain unchanged.
+Position group_1. Channel:GFPFast
+Maximum intensity measured in position group_1_is:0
+Channel does not use Smart EM camera mode. Settings remain unchanged.
+Position group_1. Channel:mCherry
+Maximum intensity measured in position group_1_is:0
+Channel does not use Smart EM camera mode. Settings remain unchanged.
+Position group_1. Channel:Brightfield
+Maximum intensity measured in position group_1_is:0
+Channel does not use Smart EM camera mode. Settings remain unchanged.
+Position group_1. Channel:GFPFast
+Maximum intensity measured in position group_1_is:0
+Channel does not use Smart EM camera mode. Settings remain unchanged.
+Position group_1. Channel:mCherry
+Maximum intensity measured in position group_1_is:0
+Channel does not use Smart EM camera mode. Settings remain unchanged.
+Position group_1. Channel:Brightfield
+Maximum intensity measured in position group_1_is:0
+Channel does not use Smart EM camera mode. Settings remain unchanged.
+Position group_1. Channel:GFPFast
+Maximum intensity measured in position group_1_is:0
+Channel does not use Smart EM camera mode. Settings remain unchanged.
+Position group_1. Channel:mCherry
+Maximum intensity measured in position group_1_is:0
+Channel does not use Smart EM camera mode. Settings remain unchanged.
+Timepoint:2 completed at:29-Feb-2020 01:24:25
+Time since start of timelapse:454.3878
+PFS is locked
+Time to next time point:-110.0053
+Experiment completed
--
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