diff --git a/examples/extraction/pairs_data/pos010_trap001_tp0001_Brightfield.png b/examples/extraction/pairs_data/pos010_trap001_tp0001_Brightfield.png
deleted file mode 100644
index d50e92fbf3a744f01fd44993720c2b2d38b3fb0b..0000000000000000000000000000000000000000
Binary files a/examples/extraction/pairs_data/pos010_trap001_tp0001_Brightfield.png and /dev/null differ
diff --git a/examples/extraction/pairs_data/pos010_trap001_tp0001_GFP.png b/examples/extraction/pairs_data/pos010_trap001_tp0001_GFP.png
deleted file mode 100644
index 2b50663f26ed9c7f0305c35339d23fbbc1b529d8..0000000000000000000000000000000000000000
Binary files a/examples/extraction/pairs_data/pos010_trap001_tp0001_GFP.png and /dev/null differ
diff --git a/examples/extraction/pairs_data/pos010_trap001_tp0001_segoutlines.png b/examples/extraction/pairs_data/pos010_trap001_tp0001_segoutlines.png
deleted file mode 100644
index eb29a60c11d99411cad09711b046d1cb32318e4d..0000000000000000000000000000000000000000
Binary files a/examples/extraction/pairs_data/pos010_trap001_tp0001_segoutlines.png and /dev/null differ
diff --git a/examples/extraction/pairs_data/pos010_trap050_tp0001_Brightfield.png b/examples/extraction/pairs_data/pos010_trap050_tp0001_Brightfield.png
deleted file mode 100644
index 9f26817ea8dffffd33f360dd39031ee59830d673..0000000000000000000000000000000000000000
Binary files a/examples/extraction/pairs_data/pos010_trap050_tp0001_Brightfield.png and /dev/null differ
diff --git a/examples/extraction/pairs_data/pos010_trap050_tp0001_GFP.png b/examples/extraction/pairs_data/pos010_trap050_tp0001_GFP.png
deleted file mode 100644
index a600fefdf7dff067a3274f808d359491babca203..0000000000000000000000000000000000000000
Binary files a/examples/extraction/pairs_data/pos010_trap050_tp0001_GFP.png and /dev/null differ
diff --git a/examples/extraction/pairs_data/pos010_trap050_tp0001_segoutlines.png b/examples/extraction/pairs_data/pos010_trap050_tp0001_segoutlines.png
deleted file mode 100644
index 8dc7a456ee8df34e09e6bee62008ecb5653ff24f..0000000000000000000000000000000000000000
Binary files a/examples/extraction/pairs_data/pos010_trap050_tp0001_segoutlines.png and /dev/null differ
diff --git a/examples/extraction/pairs_data/pos010_trap081_tp0001_Brightfield.png b/examples/extraction/pairs_data/pos010_trap081_tp0001_Brightfield.png
deleted file mode 100644
index 5670a02a388cd94fdbcf9974295b766caa09632c..0000000000000000000000000000000000000000
Binary files a/examples/extraction/pairs_data/pos010_trap081_tp0001_Brightfield.png and /dev/null differ
diff --git a/examples/extraction/pairs_data/pos010_trap081_tp0001_GFP.png b/examples/extraction/pairs_data/pos010_trap081_tp0001_GFP.png
deleted file mode 100644
index 7b5702fc7a99653930bd22aa3ef520ac2c2749f3..0000000000000000000000000000000000000000
Binary files a/examples/extraction/pairs_data/pos010_trap081_tp0001_GFP.png and /dev/null differ
diff --git a/examples/extraction/pairs_data/pos010_trap081_tp0001_segoutlines.png b/examples/extraction/pairs_data/pos010_trap081_tp0001_segoutlines.png
deleted file mode 100644
index 909cfe00ec9dedd03e2f8bd565eaa2c18f6a5e02..0000000000000000000000000000000000000000
Binary files a/examples/extraction/pairs_data/pos010_trap081_tp0001_segoutlines.png and /dev/null differ
diff --git a/examples/extraction/pos_example.py b/examples/extraction/pos_example.py
deleted file mode 100644
index da44f464b54d81dbba3f5902125d1f7b1fe4abc9..0000000000000000000000000000000000000000
--- a/examples/extraction/pos_example.py
+++ /dev/null
@@ -1,17 +0,0 @@
-from extraction.core.extractor import Extractor
-from extraction.core.parameters import Parameters
-
-params = Parameters(
- tree={
- "general": {"None": ["area"]},
- "GFPFast": {"np_max": ["mean", "median", "imBackground"]},
- "pHluorin405": {"np_max": ["mean", "median", "imBackground"]},
- "mCherry": {
- "np_max": ["mean", "median", "imBackground", "max5px", "max2p5pc"]
- },
- }
-)
-
-
-ext = Extractor(params, omero_id=19310)
-d = ext.extract_tp(tp=1, tile_size=117)
diff --git a/examples/extraction/tiler_error.py b/examples/extraction/tiler_error.py
deleted file mode 100644
index 78619c8f5fd4111d412ea0b9962a56049c6586e4..0000000000000000000000000000000000000000
--- a/examples/extraction/tiler_error.py
+++ /dev/null
@@ -1,39 +0,0 @@
-import matplotlib.pyplot as plt
-from core.experiment import Experiment
-from core.segment import Tiler
-
-expt = Experiment.from_source(
- 19310, # Experiment ID on OMERO
- "upload", # OMERO Username
- "***REMOVED***", # OMERO Password
- "islay.bio.ed.ac.uk", # OMERO host
- port=4064, # This is default
-)
-
-
-# Load whole position
-img = expt[0, 0, :, :, 2]
-plt.imshow(img[0, 0, ..., 0])
-plt.show()
-
-# Manually get template
-tilesize = 117
-x0 = 827
-y0 = 632
-trap_template = img[0, 0, x0 : x0 + tilesize, y0 : y0 + tilesize, 0]
-plt.imshow(trap_template)
-plt.show()
-
-tiler = Tiler(expt, template=trap_template)
-
-# Load images (takes about 5 mins)
-trap_tps = tiler.get_tiles_timepoint(0, tile_size=117, z=[2])
-
-# Plot found traps
-nrows, ncols = (5, 5)
-fig, axes = plt.subplots(nrows, ncols)
-for i in range(nrows):
- for j in range(ncols):
- if i * nrows + j < trap_tps.shape[0]:
- axes[i, j].imshow(trap_tps[i * nrows + j, 0, 0, ..., 0])
-plt.show()
diff --git a/examples/logfile_parser/cExperiment_log_001.txt b/examples/logfile_parser/cExperiment_log_001.txt
deleted file mode 100644
index 8db3a2e4b899c5ee597f79569caa8a531607a9ea..0000000000000000000000000000000000000000
--- a/examples/logfile_parser/cExperiment_log_001.txt
+++ /dev/null
@@ -1,276 +0,0 @@
-
-
-=====================
-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/logfile_parser/example_multiDGUI_acq.txt b/examples/logfile_parser/example_multiDGUI_acq.txt
deleted file mode 100644
index e2d1e9b462c12a5f21878b6dd3b6738df7e9e51b..0000000000000000000000000000000000000000
--- a/examples/logfile_parser/example_multiDGUI_acq.txt
+++ /dev/null
@@ -1,46 +0,0 @@
-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/logfile_parser/example_multiDGUI_log.txt b/examples/logfile_parser/example_multiDGUI_log.txt
deleted file mode 100644
index e4a242ca9bc785e92a432b8b7965b7e0e581a6dc..0000000000000000000000000000000000000000
--- a/examples/logfile_parser/example_multiDGUI_log.txt
+++ /dev/null
@@ -1,651 +0,0 @@
-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
diff --git a/examples/parsers/swainlab_logfile_header_example.log b/examples/parsers/swainlab_logfile_header_example.log
deleted file mode 100644
index 8a7197bf9c0f4811afe252499ff5ba2deb53354a..0000000000000000000000000000000000000000
--- a/examples/parsers/swainlab_logfile_header_example.log
+++ /dev/null
@@ -1,123 +0,0 @@
-2022-10-10 15:31:27,350 - INFO
-Swain Lab microscope experiment log file
-GIT commit: e5d5e33 fix: changes to a few issues with focus control on Batman.
-Microscope name: Batman
-Date: 022-10-10 15:31:27
-Log file path: D:\AcquisitionDataBatman\Swain Lab\Ivan\RAW DATA\2022\Oct\10-Oct-2022\pH_med_to_low00\pH_med_to_low.log
-Micromanager config file: C:\Users\Public\Microscope control\Micromanager config files\Batman_python_15_4_22.cfg
-Omero project: Default project
-Omero tags:
-Experiment details: Effect on growth and cytoplasmic pH of switch from normal pH (4.25) media to higher pH (5.69). Switching is run using the Oxygen software
------Acquisition settings-----
-
-2022-10-10 15:31:27,350 - INFO Image Configs:
-Image config,Channel,Description,Exposure (ms), Number of Z sections,Z spacing (um),Sectioning method
-brightfield1,Brightfield,Default bright field config,30,5,0.6,PIFOC
-pHluorin405_0_4,pHluorin405,Phluorin excitation from 405 LED 0.4v and 10ms exposure,5,1,0.6,PIFOC
-pHluorin488_0_4,GFPFast,Phluorin excitation from 488 LED 0.4v,10,1,0.6,PIFOC
-cy5,cy5,Default cy5,30,1,0.6,PIFOC
-
-Device properties:
-Image config,device,property,value
-pHluorin405_0_4,DTOL-DAC-1,Volts,0.4
-pHluorin488_0_4,DTOL-DAC-2,Volts,0.4
-cy5,DTOL-DAC-3,Volts,4
-
-2022-10-10 15:31:27,353 - INFO
-group: YST_247 field: position
-Name, X, Y, Z, Autofocus offset
-YST_247_001,-8968,-3319,2731.125040696934,123.25
-YST_247_002,-8953,-3091,2731.3000406995416,123.25
-YST_247_003,-8954,-2849,2731.600040704012,122.8
-YST_247_004,-8941,-2611,2730.7750406917185,122.8
-YST_247_005,-8697,-2541,2731.4500407017767,118.6
-group: YST_247 field: time
-start: 0
-interval: 300
-frames: 180
-
-group: YST_247 field: config
-brightfield1: 0xfffffffffffffffffffffffffffffffffffffffffffff
-pHluorin405_0_4: 0xfffffffffffffffffffffffffffffffffffffffffffff
-pHluorin488_0_4: 0xfffffffffffffffffffffffffffffffffffffffffffff
-cy5: 0xfffffffffffffffffffffffffffffffffffffffffffff
-
-2022-10-10 15:31:27,356 - INFO
-group: YST_1510 field: position
-Name,X,Y,Z,Autofocus offset
-YST_1510_001,-6450,-230,2343.300034917891,112.55
-YST_1510_002,-6450,-436,2343.350034918636,112.55
-YST_1510_003,-6450,-639,2344.000034928322,116.8
-YST_1510_004,-6450,-831,2344.250034932047,116.8
-YST_1510_005,-6848,-536,2343.3250349182636,110
-group: YST_1510 field: time
-start: 0
-interval: 300
-frames: 180
-
-group: YST_1510 field: config
-brightfield1: 0xfffffffffffffffffffffffffffffffffffffffffffff
-pHluorin405_0_4: 0xfffffffffffffffffffffffffffffffffffffffffffff
-pHluorin488_0_4: 0xfffffffffffffffffffffffffffffffffffffffffffff
-cy5: 0xfffffffffffffffffffffffffffffffffffffffffffff
-2022-10-10 15:31:27,359 - INFO
-group: YST_1511 field: position
-Name, X, Y, Z, Autofocus offset
-YST_1511_001,-10618,-1675,2716.900040484965,118.7
-YST_1511_002,-10618,-1914,2717.2250404898077,122.45
-YST_1511_003,-10367,-1695,2718.2500405050814,120.95
-YST_1511_004,-10367,-1937,2718.8250405136496,120.95
-YST_1511_005,-10092,-1757,2719.975040530786,119.45
-
-group: YST_1511 field: time
-start: 0
-interval: 300
-frames: 180
-
-group: YST_1511 field: config
-brightfield1: 0xfffffffffffffffffffffffffffffffffffffffffffff
-pHluorin405_0_4: 0xfffffffffffffffffffffffffffffffffffffffffffff
-pHluorin488_0_4: 0xfffffffffffffffffffffffffffffffffffffffffffff
-cy5: 0xfffffffffffffffffffffffffffffffffffffffffffff
-
-2022-10-10 15:31:27,362 - INFO
-group: YST_1512 field: position
-Name,X,Y,Z,Autofocus offset
-YST_1512_001,-8173,-2510,2339.0750348549336,115.65
-YST_1512_002,-8173,-2718,2338.0250348392874,110.8
-YST_1512_003,-8173,-2963,2336.625034818426,110.8
-YST_1512_004,-8457,-2963,2336.350034814328,110.9
-YST_1512_005,-8481,-2706,2337.575034832582,113.3
-group: YST_1512 field: time
-start: 0
-interval: 300
-frames: 180
-
-group: YST_1512 field: config
-brightfield1: 0xfffffffffffffffffffffffffffffffffffffffffffff
-pHluorin405_0_4: 0xfffffffffffffffffffffffffffffffffffffffffffff
-pHluorin488_0_4: 0xfffffffffffffffffffffffffffffffffffffffffffff
-cy5: 0xfffffffffffffffffffffffffffffffffffffffffffff
-
-2022-10-10 15:31:27,365 - INFO
-group: YST_1513 field: position
-Name,X,Y,Z,Autofocus offset
-YST_1513_001,-6978,-2596,2339.8750348668545,113.3
-YST_1513_002,-6978,-2380,2340.500034876168,113.3
-YST_1513_003,-6971,-2163,2340.8750348817557,113.3
-YST_1513_004,-6971,-1892,2341.2500348873436,113.3
-YST_1513_005,-6692,-1892,2341.550034891814,113.3
-group: YST_1513 field: time
-start: 0
-interval: 300
-frames: 180
-
-group: YST_1513 field: config
-brightfield1: 0xfffffffffffffffffffffffffffffffffffffffffffff
-pHluorin405_0_4: 0xfffffffffffffffffffffffffffffffffffffffffffff
-pHluorin488_0_4: 0xfffffffffffffffffffffffffffffffffffffffffffff
-cy5: 0xfffffffffffffffffffffffffffffffffffffffffffff
-
-2022-10-10 15:31:27,365 - INFO
-2022-10-10 15:31:27,365 - INFO
------Experiment started-----
diff --git a/examples/run_jura.py b/examples/run_jura.py
new file mode 100644
index 0000000000000000000000000000000000000000..93a08a95292927d2c77aa5e064edb9f58df276e0
--- /dev/null
+++ b/examples/run_jura.py
@@ -0,0 +1,16 @@
+from aliby.pipeline import PipelineParameters, Pipeline
+
+params = PipelineParameters.default(
+ general={
+ "expt_id": 2172,
+ "distributed": 0,
+ "directory": ".",
+ "host": "staffa.bio.ed.ac.uk",
+ "username": pass,
+ "password": pass,
+ }
+)
+# specify OMERO_channels if the channels on OMERO have a different order from the logfiles
+p = Pipeline(params)
+
+p.run()
diff --git a/examples/run_local.py b/examples/run_local.py
new file mode 100644
index 0000000000000000000000000000000000000000..214e9311a89081bda291d1f3381b2d04011fd452
--- /dev/null
+++ b/examples/run_local.py
@@ -0,0 +1,27 @@
+from pathlib import Path
+
+from aliby.pipeline import Pipeline, PipelineParameters
+from postprocessor.grouper import Grouper
+
+omid = "25681_2022_04_30_flavin_htb2_glucose_10mgpL_01_00"
+
+h5dir = "/Users/pswain/wip/aliby_output/"
+omero_dir = "/Users/pswain/wip/aliby_input/"
+
+# setup and run pipeline
+params = PipelineParameters.default(
+ general={
+ "expt_id": omero_dir + omid,
+ "distributed": 2,
+ "directory": h5dir,
+ # specify position to segment
+ "filter": "fy4_007",
+ # specify final time point
+ # "tps": 4,
+ },
+)
+
+
+# initialise and run pipeline
+p = Pipeline(params, OMERO_channels=["Brightfield", "Flavin"])
+p.run()
diff --git a/examples/tiler/pypipeline_unit_test_00_000001_Brightfield_003.tif b/examples/tiler/pypipeline_unit_test_00_000001_Brightfield_003.tif
deleted file mode 100755
index 569f33a72ab18f65c79e28e38869a4f17cd30cca..0000000000000000000000000000000000000000
Binary files a/examples/tiler/pypipeline_unit_test_00_000001_Brightfield_003.tif and /dev/null differ
diff --git a/examples/tiler/pypipeline_unit_test_00_000001_Brightfield_003_square.tif b/examples/tiler/pypipeline_unit_test_00_000001_Brightfield_003_square.tif
deleted file mode 100755
index f813c15a9c8aef8a6e629ff17e460aef4acdb630..0000000000000000000000000000000000000000
Binary files a/examples/tiler/pypipeline_unit_test_00_000001_Brightfield_003_square.tif and /dev/null differ