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  • swain-lab/aliby/aliby-mirror
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extraction/examples/pos_example.py → examples/extraction/pos_example.py
View file @ 95958192
from extraction.core.parameters import Parameters
from extraction.core.extractor import Extractor
import numpy as np
from extraction.core.parameters import Parameters
params = Parameters(
tree={
......@@ -15,6 +14,4 @@ params = Parameters(
ext = Extractor(params, omero_id=19310)
# ext.extract_exp(tile_size=117)
d=ext.extract_tp(tp=1,tile_size=117)
d = ext.extract_tp(tp=1, tile_size=117)
examples/extraction/tiler_error.py 0 → 100644
View file @ 95958192
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()
examples/logfile_parser/cExperiment_log_001.txt 0 → 100644
View file @ 95958192
=====================
06-Jan-2020 18:30:59 Start creating new experiment using parameters:
Omero experiment name: 001
Temporary working directory: C:06-Jan-2020 18:30:59 Processing position 2 (1108_002)
06-Jan-2020 18:31:00 Processing position 3 (1108_003)
06-Jan-2020 18:31:01 Processing position 4 (1109_004)
06-Jan-2020 18:31:02 Processing position 5 (1109_005)
06-Jan-2020 18:31:04 Processing position 6 (1109_006)
06-Jan-2020 18:31:05 Processing position 7 (1110_007)
06-Jan-2020 18:31:06 Processing position 8 (1110_008)
06-Jan-2020 18:31:07 Processing position 9 (1110_009)
06-Jan-2020 18:31:10 Successfully completed creating new experiment in 11 secs.
---------------------
=====================
06-Jan-2020 18:31:33 Start selecting traps...
06-Jan-2020 18:31:33 Processing position 1 (1108_001)
06-Jan-2020 18:31:40 Remove trap at 550 1188
06-Jan-2020 18:31:40 Remove trap at 733 1179
06-Jan-2020 18:31:41 Remove trap at 384 1189
06-Jan-2020 18:31:42 Remove trap at 201 1186
06-Jan-2020 18:31:47 Processing position 2 (1108_002)
06-Jan-2020 18:31:52 Remove trap at 384 1060
06-Jan-2020 18:31:54 Remove trap at 1081 571
06-Jan-2020 18:32:01 Processing position 3 (1108_003)
06-Jan-2020 18:32:05 Remove trap at 948 1140
06-Jan-2020 18:32:06 Remove trap at 1141 1174
06-Jan-2020 18:32:17 Remove trap at 139 1111
06-Jan-2020 18:32:18 Add trap at 130 1138
06-Jan-2020 18:32:26 Processing position 4 (1109_004)
06-Jan-2020 18:32:32 Remove trap at 1176 388
06-Jan-2020 18:32:39 Processing position 5 (1109_005)
06-Jan-2020 18:32:44 Remove trap at 1141 1135
06-Jan-2020 18:32:51 Remove trap at 955 379
06-Jan-2020 18:32:55 Processing position 6 (1109_006)
06-Jan-2020 18:33:00 Remove trap at 676 1177
06-Jan-2020 18:33:01 Remove trap at 1111 1147
06-Jan-2020 18:33:14 Processing position 7 (1110_007)
06-Jan-2020 18:33:20 Remove trap at 46 46
06-Jan-2020 18:33:28 Remove trap at 1150 84
06-Jan-2020 18:33:34 Processing position 8 (1110_008)
06-Jan-2020 18:33:49 Processing position 9 (1110_009)
06-Jan-2020 18:33:55 Add trap at 1153 1129
06-Jan-2020 18:33:57 Remove trap at 1135 1141
06-Jan-2020 18:33:57 Remove trap at 1176 1095
06-Jan-2020 18:34:15 Successfully completed selecting traps in 2.7 mins.
---------------------
=====================
06-Jan-2020 18:34:28 Start setting extraction parameters using parameters:
extractionParameters: {
extractFunction: extractCellDataStandardParfor
functionParameters: {
type: max
channels: 2 3
nuclearMarkerChannel: NaN
maxPixOverlap: 5
maxAllowedOverlap: 25
}
}
06-Jan-2020 18:34:28 Processing position 1 (1108_001)
06-Jan-2020 18:34:28 Processing position 2 (1108_002)
06-Jan-2020 18:34:29 Processing position 3 (1108_003)
06-Jan-2020 18:34:29 Processing position 4 (1109_004)
06-Jan-2020 18:34:30 Processing position 5 (1109_005)
06-Jan-2020 18:34:30 Processing position 6 (1109_006)
06-Jan-2020 18:34:30 Processing position 7 (1110_007)
06-Jan-2020 18:34:31 Processing position 8 (1110_008)
06-Jan-2020 18:34:31 Processing position 9 (1110_009)
06-Jan-2020 18:34:33 Successfully completed setting extraction parameters in 5 secs.
---------------------
=====================
07-Jan-2020 13:17:43 Start tracking traps in time...
07-Jan-2020 13:17:43 Processing position 1 (1108_001)
07-Jan-2020 13:23:31 Processing position 2 (1108_002)
07-Jan-2020 13:29:21 Processing position 3 (1108_003)
07-Jan-2020 13:35:13 Processing position 4 (1109_004)
07-Jan-2020 13:41:19 Processing position 5 (1109_005)
07-Jan-2020 13:47:09 Processing position 6 (1109_006)
07-Jan-2020 13:52:57 Processing position 7 (1110_007)
07-Jan-2020 13:58:41 Processing position 8 (1110_008)
07-Jan-2020 14:04:41 Processing position 9 (1110_009)
07-Jan-2020 14:10:38 Successfully completed tracking traps in time in 52.9 mins.
---------------------
=====================
07-Jan-2020 14:10:38 Start baby segmentation...
07-Jan-2020 14:10:39 Processing position 1 (1108_001)
07-Jan-2020 14:14:32 cTimelapse: 210.344 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 14:18:30 cTimelapse: 240.345 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 14:22:31 cTimelapse: 272.459 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 14:26:32 cTimelapse: 303.876 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 14:30:34 cTimelapse: 336.470 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 14:32:32 Processing position 2 (1108_002)
07-Jan-2020 14:36:22 cTimelapse: 206.699 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 14:40:12 cTimelapse: 235.726 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 14:44:13 cTimelapse: 268.814 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 14:48:27 cTimelapse: 306.046 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 14:52:43 cTimelapse: 343.681 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 14:54:44 Processing position 3 (1108_003)
07-Jan-2020 14:58:47 cTimelapse: 214.895 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 15:02:44 cTimelapse: 247.137 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 15:06:47 cTimelapse: 280.902 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 15:10:51 cTimelapse: 314.796 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 15:15:13 cTimelapse: 354.774 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 15:17:16 Processing position 4 (1109_004)
07-Jan-2020 15:21:06 cTimelapse: 222.663 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 15:25:09 cTimelapse: 253.596 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 15:29:16 cTimelapse: 286.597 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 15:33:46 cTimelapse: 325.040 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 15:38:35 cTimelapse: 369.190 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 15:40:50 Processing position 5 (1109_005)
07-Jan-2020 15:45:01 cTimelapse: 235.110 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 15:49:23 cTimelapse: 268.760 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 15:53:50 cTimelapse: 304.703 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 15:58:15 cTimelapse: 339.861 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:02:47 cTimelapse: 377.877 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:04:53 Processing position 6 (1109_006)
07-Jan-2020 16:08:32 cTimelapse: 205.246 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:12:09 cTimelapse: 231.500 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:15:49 cTimelapse: 259.276 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:19:45 cTimelapse: 291.813 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:24:03 cTimelapse: 331.193 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:26:11 Processing position 7 (1110_007)
07-Jan-2020 16:29:30 cTimelapse: 222.990 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:32:46 cTimelapse: 238.288 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:36:03 cTimelapse: 255.524 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:39:21 cTimelapse: 275.165 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:42:40 cTimelapse: 297.244 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:44:14 Processing position 8 (1110_008)
07-Jan-2020 16:47:32 cTimelapse: 215.583 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:50:51 cTimelapse: 235.959 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:54:09 cTimelapse: 256.409 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 16:57:25 cTimelapse: 275.563 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 17:00:43 cTimelapse: 296.390 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 17:02:13 Processing position 9 (1110_009)
07-Jan-2020 17:05:35 cTimelapse: 225.847 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 17:08:54 cTimelapse: 245.291 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 17:12:17 cTimelapse: 266.060 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 17:15:41 cTimelapse: 288.448 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 17:19:04 cTimelapse: 311.290 MB; posOverviewGUI: 741.580 MB
07-Jan-2020 17:20:36 Successfully completed baby segmentation in 3.2 hours.
---------------------
=====================
07-Jan-2020 17:20:37 Start tracking cells using parameters:
Tracking threshold: 10
07-Jan-2020 17:20:39 Processing position 1 (1108_001)
07-Jan-2020 17:21:23 Processing position 2 (1108_002)
07-Jan-2020 17:22:06 Processing position 3 (1108_003)
07-Jan-2020 17:22:49 Processing position 4 (1109_004)
07-Jan-2020 17:23:33 Processing position 5 (1109_005)
07-Jan-2020 17:24:18 Processing position 6 (1109_006)
07-Jan-2020 17:24:58 Processing position 7 (1110_007)
07-Jan-2020 17:25:25 Processing position 8 (1110_008)
07-Jan-2020 17:25:55 Processing position 9 (1110_009)
07-Jan-2020 17:26:25 Successfully completed tracking cells in 5.8 mins.
---------------------
=====================
07-Jan-2020 17:26:25 Start autoselecting cells using parameters:
Fraction of timelapse that cells are present for: 0.5
Number of frames a cell must be present: 540
Cell must appear by frame: 540
Cell must still be present by frame: 1
Maximum number of cells: Inf
07-Jan-2020 17:26:27 Processing position 1 (1108_001)
07-Jan-2020 17:26:42 Processing position 2 (1108_002)
07-Jan-2020 17:26:58 Processing position 3 (1108_003)
07-Jan-2020 17:27:14 Processing position 4 (1109_004)
07-Jan-2020 17:27:31 Processing position 5 (1109_005)
07-Jan-2020 17:27:48 Processing position 6 (1109_006)
07-Jan-2020 17:28:03 Processing position 7 (1110_007)
07-Jan-2020 17:28:13 Processing position 8 (1110_008)
07-Jan-2020 17:28:25 Processing position 9 (1110_009)
07-Jan-2020 17:28:36 Successfully completed autoselecting cells in 2.2 mins.
---------------------
=====================
07-Jan-2020 17:28:37 Start extracting cell information...
07-Jan-2020 17:28:39 Processing position 1 (1108_001)
07-Jan-2020 17:58:38 Processing position 2 (1108_002)
07-Jan-2020 18:28:43 Processing position 3 (1108_003)
07-Jan-2020 18:58:45 Processing position 4 (1109_004)
07-Jan-2020 19:29:03 Processing position 5 (1109_005)
07-Jan-2020 19:59:31 Processing position 6 (1109_006)
07-Jan-2020 20:29:01 Processing position 7 (1110_007)
07-Jan-2020 20:56:05 Processing position 8 (1110_008)
07-Jan-2020 21:23:53 Processing position 9 (1110_009)
07-Jan-2020 21:51:15 Successfully completed extracting cell information in 4.4 hours.
---------------------
=====================
07-Jan-2020 21:51:16 Start baby lineage extraction...
07-Jan-2020 21:51:18 Processing position 1 (1108_001)
07-Jan-2020 21:52:37 Processing position 2 (1108_002)
07-Jan-2020 21:53:57 Processing position 3 (1108_003)
07-Jan-2020 21:55:16 Processing position 4 (1109_004)
07-Jan-2020 21:56:36 Processing position 5 (1109_005)
07-Jan-2020 21:57:59 Processing position 6 (1109_006)
07-Jan-2020 21:59:08 Processing position 7 (1110_007)
07-Jan-2020 21:59:50 Processing position 8 (1110_008)
07-Jan-2020 22:00:41 Processing position 9 (1110_009)
07-Jan-2020 22:01:26 Successfully completed baby lineage extraction in 10.2 mins.
---------------------
=====================
07-Jan-2020 22:01:26 Start compiling cell information...
07-Jan-2020 22:01:28 Processing position 1 (1108_001)
07-Jan-2020 22:01:30 Processing position 2 (1108_002)
07-Jan-2020 22:01:33 Processing position 3 (1108_003)
07-Jan-2020 22:01:35 Processing position 4 (1109_004)
07-Jan-2020 22:01:38 Processing position 5 (1109_005)
07-Jan-2020 22:01:40 Processing position 6 (1109_006)
07-Jan-2020 22:01:42 Processing position 7 (1110_007)
07-Jan-2020 22:01:44 Processing position 8 (1110_008)
07-Jan-2020 22:01:46 Processing position 9 (1110_009)
07-Jan-2020 22:02:20 Successfully completed compiling cell information in 54 secs.
---------------------
examples/logfile_parser/example_multiDGUI_acq.txt 0 → 100644
View file @ 95958192
Channels:
Channel name, Exposure time, Skip, Z sect., Start time, Camera mode, EM gain, Voltage
Brightfield, 30, 1, 1, 1, 2, 270, 1.000
GFPFast, 30, 1, 1, 1, 2, 270, 3.500
mCherry, 100, 1, 1, 1, 2, 270, 2.500
Z_sectioning:
Sections,Spacing,PFSon?,AnyZ?,Drift,Method
3, 0.80, 1, 1, 0, 2
Time_settings:
1,120,660,79200
Points:
Position name, X position, Y position, Z position, PFS offset, Group, Brightfield, GFPFast, mCherry
pos001, 568.00, 1302.00, 1876.500, 122.450, 1, 30, 30, 100
pos002, 1267.00, 1302.00, 1880.125, 119.950, 1, 30, 30, 100
pos003, 1026.00, 977.00, 1877.575, 120.100, 1, 30, 30, 100
pos004, 540.00, -347.00, 1868.725, 121.200, 2, 30, 30, 100
pos005, 510.00, -687.00, 1867.150, 122.900, 2, 30, 30, 100
pos006, -187.00, -470.00, 1864.050, 119.600, 2, 30, 30, 100
pos007, -731.00, 916.00, 1867.050, 117.050, 3, 30, 30, 100
pos008, -1003.00, 1178.00, 1866.425, 121.700, 3, 30, 30, 100
pos009, -568.00, 1157.00, 1868.450, 119.350, 3, 30, 30, 100
Flow_control:
Syringe pump details: 2 pumps.
Pump states at beginning of experiment:
Pump port, Diameter, Current rate, Direction, Running, Contents
COM7, 14.43, 0.00, INF, 1, 2% glucose in SC
COM8, 14.43, 4.00, INF, 1, 0.1% glucose in SC
Dynamic flow details:
Number of pump changes:
1
Switching parameters:
Infuse/withdraw volumes:
50
Infuse/withdraw rates:
100
Times:
0
Switched to:
2
Switched from:
1
Flow post switch:
0
4
examples/logfile_parser/example_multiDGUI_log.txt 0 → 100644
View file @ 95958192
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
examples/parsers/swainlab_logfile_header_example.log 0 → 100644
View file @ 95958192
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-----
examples/tiler/pypipeline_unit_test_00_000001_Brightfield_003.tif 0 → 100755
View file @ 95958192
File added
examples/tiler/pypipeline_unit_test_00_000001_Brightfield_003_square.tif 0 → 100755
View file @ 95958192
File added
extraction/core/__init__.py deleted 100644 → 0
View file @ 21d8d578
#!/usr/bin/env python
extraction/core/extractor.py deleted 100644 → 0
View file @ 21d8d578
import os
from pathlib import Path, PosixPath
import pkg_resources
from collections.abc import Iterable
# from copy import copy
from typing import Union, List, Dict, Callable
from datetime import datetime
import numpy as np
import pandas as pd
from scipy.sparse import dok_matrix, vstack, issparse
from tqdm import tqdm
from extraction.core.functions.loaders import (
load_funs,
load_custom_args,
load_redfuns,
load_mergefuns,
)
from extraction.core.functions.defaults import exparams_from_meta
from extraction.core.functions.distributors import trap_apply, reduce_z
from extraction.core.functions.utils import depth
from agora.abc import ProcessABC, ParametersABC
from agora.io.writer import Writer, load_attributes
from agora.io.cells import Cells
from agora.tile.tiler import Tiler
CELL_FUNS, TRAPFUNS, FUNS = load_funs()
CUSTOM_FUNS, CUSTOM_ARGS = load_custom_args()
RED_FUNS = load_redfuns()
MERGE_FUNS = load_mergefuns()
# Assign datatype depending on the metric used
m2type = {"mean": np.float32, "median": np.ubyte, "imBackground": np.ubyte}
class ExtractorParameters(ParametersABC):
"""
Base class to define parameters for extraction
:tree: dict of depth n. If not of depth three tree will be filled with Nones
str channel -> U(function,None) reduction -> str metric
"""
def __init__(
self,
tree: Dict[Union[str, None], Dict[Union[Callable, None], List[str]]] = None,
sub_bg: set = set(),
multichannel_ops: Dict = {},
):
self.tree = fill_tree(tree)
self.sub_bg = sub_bg
self.multichannel_ops = multichannel_ops
@staticmethod
def guess_from_meta(store_name: str, suffix="fast"):
"""
Make a guess on the parameters using the hdf5 metadata
Add anything as a suffix, default "fast"
Parameters:
store_name : str or Path indicating the results' storage.
suffix : str to add at the end of the predicted parameter set
"""
with h5py.open(store_name, "r") as f:
microscope = f["/"].attrs.get("microscope") # TODO Check this with Arin
assert microscope, "No metadata found"
return "_".join((microscope, suffix))
@classmethod
def default(cls):
return cls({})
@classmethod
def from_meta(cls, meta):
return cls(**exparams_from_meta(meta))
class Extractor(ProcessABC):
"""
Base class to perform feature extraction.
Parameters
----------
parameters: core.extractor Parameters
Parameters that include with channels, reduction and
b extraction functions to use.
store: str
Path to hdf5 storage file. Must contain cell outlines.
tiler: pipeline-core.core.segmentation tiler
Class that contains or fetches the image to be used for segmentation.
"""
default_meta = {"pixel_size": 0.236, "z_size": 0.6, "spacing": 0.6}
def __init__(self, parameters: ExtractorParameters, store: str, tiler: Tiler):
self.params = parameters
self.local = store
self.load_meta()
self.tiler = tiler
self.load_funs()
@classmethod
def from_tiler(cls, parameters: ExtractorParameters, store: str, tiler: Tiler):
return cls(parameters, store=store, tiler=tiler)
@classmethod
def from_img(cls, parameters: ExtractorParameters, store: str, img_meta: tuple):
return cls(parameters, store=store, tiler=Tiler(*img_meta))
# @classmethod
# def from_store(cls, parameters: ExtractorParameters, store: str, img_meta: tuple):
# return cls(parameters, store=store, tiler=Tiler(*img_meta))
@property
def channels(self):
if not hasattr(self, "_channels"):
if type(self.params.tree) is dict:
self._channels = tuple(self.params.tree.keys())
return self._channels
@property
def current_position(self):
return self.local.split("/")[-1][:-3]
@property
def group(self): # Path within hdf5
if not hasattr(self, "_out_path"):
self._group = "/extraction/"
return self._group
@property
def pos_file(self, store_name="store.h5"):
if not hasattr(self, "_pos_file"):
return self.local
def load_custom_funs(self):
"""
Load parameters of functions that require them from expt.
These must be loaded within the Extractor instance because their parameters
depend on their experiment's metadata.
"""
funs = set(
[
fun
for ch in self.params.tree.values()
for red in ch.values()
for fun in red
]
)
funs = funs.intersection(CUSTOM_FUNS.keys())
ARG_VALS = {
k: {k2: self.get_meta(k2) for k2 in v} for k, v in CUSTOM_ARGS.items()
}
# self._custom_funs = {trap_apply(CUSTOM_FUNS[fun],])
self._custom_funs = {}
for k, f in CUSTOM_FUNS.items():
def tmp(f):
return lambda m, img: trap_apply(f, m, img, **ARG_VALS.get(k, {}))
self._custom_funs[k] = tmp(f)
def load_funs(self):
self.load_custom_funs()
self._all_cell_funs = set(self._custom_funs.keys()).union(CELL_FUNS)
self._all_funs = {**self._custom_funs, **FUNS}
def load_meta(self):
self.meta = load_attributes(self.local)
def get_traps(
self, tp: int, channels: list = None, z: list = None, **kwargs
) -> tuple:
if channels is None:
channel_ids = list(range(len(self.tiler.channels)))
elif len(channels):
channel_ids = [self.tiler.get_channel_index(ch) for ch in channels]
else:
channel_ids = None
if z is None:
z = list(range(self.tiler.shape[-1]))
traps = (
self.tiler.get_traps_timepoint(tp, channels=channel_ids, z=z, **kwargs)
if channel_ids
else None
)
return traps
def extract_traps(
self,
traps: List[np.array],
masks: List[np.array],
metric: str,
labels: List[int] = None,
) -> dict:
"""
Apply a function for a whole position.
:traps: List[np.array] list of images
:masks: List[np.array] list of masks
:metric:str metric to extract
:labels: List[int] cell Labels to use as indices for output DataFrame
:pos_info: bool Whether to add the position as index or not
returns
:d: Dictionary of dataframe
"""
if labels is None:
raise Warning("No labels given. Sorting cells using index.")
cell_fun = True if metric in self._all_cell_funs else False
idx = []
results = []
for trap_id, (mask_set, trap, lbl_set) in enumerate(
zip(masks, traps, labels.values())
):
if len(mask_set): # ignore empty traps
result = self._all_funs[metric](mask_set, trap)
if cell_fun:
for lbl, val in zip(lbl_set, result):
results.append(val)
idx.append((trap_id, lbl))
else:
results.append(result)
idx.append(trap_id)
return (tuple(results), tuple(idx))
def extract_funs(
self, traps: List[np.array], masks: List[np.array], metrics: List[str], **kwargs
) -> dict:
"""
Extract multiple metrics from a timepoint
"""
d = {
metric: self.extract_traps(
traps=traps, masks=masks, metric=metric, **kwargs
)
for metric in metrics
}
return d
def reduce_extract(
self, traps: Union[np.array, None], masks: list, red_metrics: dict, **kwargs
) -> dict:
"""
:param red_metrics: dict in which keys are reduction funcions and
values are strings indicating the metric function
:**kwargs: All other arguments, must include masks and traps.
"""
reduced_traps = {}
if traps is not None:
for red_fun in red_metrics.keys():
reduced_traps[red_fun] = [
self.reduce_dims(trap, method=RED_FUNS[red_fun]) for trap in traps
]
d = {
red_fun: self.extract_funs(
metrics=metrics,
traps=reduced_traps.get(red_fun, [None for _ in masks]),
masks=masks,
**kwargs,
)
for red_fun, metrics in red_metrics.items()
}
return d
def reduce_dims(self, img: np.array, method=None) -> np.array:
# assert len(img.shape) == 3, "Incorrect number of dimensions"
if method is None:
return img
return reduce_z(img, method)
def extract_tp(
self, tp: int, tree: dict = None, tile_size: int = 117, **kwargs
) -> dict:
"""
:param tp: int timepoint from which to extract results
:param tree: dict of dict {channel : {reduction_function : metrics}}
:**kwargs: Must include masks and preferably labels.
"""
if tree is None:
tree = self.params.tree
ch_tree = {ch: v for ch, v in tree.items() if ch != "general"}
tree_chs = (*ch_tree,)
cells = Cells.hdf(self.local)
# labels
raw_labels = cells.labels_at_time(tp)
labels = {
trap_id: raw_labels.get(trap_id, []) for trap_id in range(cells.ntraps)
}
# masks
raw_masks = cells.at_time(tp, kind="mask")
masks = {trap_id: [] for trap_id in range(cells.ntraps)}
for trap_id, cells in raw_masks.items():
if len(cells):
masks[trap_id] = np.dstack(np.array(cells)).astype(bool)
masks = [np.array(v) for v in masks.values()]
# traps
traps = self.get_traps(tp, tile_size=tile_size, channels=tree_chs)
self.img_bgsub = {}
if self.params.sub_bg:
bg = [
~np.sum(m, axis=2).astype(bool)
if np.any(m)
else np.zeros((tile_size, tile_size))
for m in masks
]
d = {}
for ch, red_metrics in tree.items():
img = None
# ch != is necessary for threading
if ch != "general" and traps is not None and len(traps):
img = traps[:, tree_chs.index(ch), 0]
d[ch] = self.reduce_extract(
red_metrics=red_metrics, traps=img, masks=masks, labels=labels, **kwargs
)
if (
ch in self.params.sub_bg and img is not None
): # Calculate metrics with subtracted bg
ch_bs = ch + "_bgsub"
self.img_bgsub[ch_bs] = []
for trap, maskset in zip(img, bg):
cells_fl = np.zeros_like(trap)
is_cell = np.where(maskset)
if len(is_cell[0]): # skip calculation for empty traps
cells_fl = np.median(trap[is_cell], axis=0)
self.img_bgsub[ch_bs].append(trap - cells_fl)
d[ch_bs] = self.reduce_extract(
red_metrics=ch_tree[ch],
traps=self.img_bgsub[ch_bs],
masks=masks,
labels=labels,
**kwargs,
)
# Additional operations between multiple channels (e.g. pH calculations)
for name, (chs, merge_fun, red_metrics) in self.params.multichannel_ops.items():
if len(
set(chs).intersection(set(self.img_bgsub.keys()).union(tree_chs))
) == len(chs):
imgs = [self.get_imgs(ch, traps, tree_chs) for ch in chs]
merged = MERGE_FUNS[merge_fun](*imgs)
d[name] = self.reduce_extract(
red_metrics=red_metrics,
traps=merged,
masks=masks,
labels=labels,
**kwargs,
)
del traps, masks
return d
def get_imgs(self, channel, traps, channels=None):
"""
Returns the image from a correct source, either raw or bgsub
:channel: str name of channel to get
:img: ndarray (trap_id, channel, tp, tile_size, tile_size, n_zstacks) of standard channels
:channels: List of channels
"""
if channels is None:
channels = (*self.params.tree,)
if channel in channels:
return traps[:, channels.index(channel), 0]
elif channel in self.img_bgsub:
return self.img_bgsub[channel]
def run(self, tree=None, tps: List[int] = None, save=True, **kwargs) -> dict:
if tree is None:
tree = self.params.tree
if tps is None:
tps = list(range(self.meta["time_settings/ntimepoints"]))
d = {}
for tp in tps:
new = flatten_nest(
self.extract_tp(tp=tp, tree=tree, **kwargs),
to="series",
tp=tp,
)
for k in new.keys():
n = new[k]
d[k] = pd.concat((d.get(k, None), n), axis=1)
for k in d.keys():
indices = ["experiment", "position", "trap", "cell_label"]
idx = (
indices[-d[k].index.nlevels :]
if d[k].index.nlevels > 1
else [indices[-2]]
)
d[k].index.names = idx
toreturn = d
if save:
self.save_to_hdf(toreturn)
return toreturn
def extract_pos(
self, tree=None, tps: List[int] = None, save=True, **kwargs
) -> dict:
if tree is None:
tree = self.params.tree
if tps is None:
tps = list(range(self.meta["time_settings/ntimepoints"]))
d = {}
for tp in tps:
new = flatten_nest(
self.extract_tp(tp=tp, tree=tree, **kwargs),
to="series",
tp=tp,
)
for k in new.keys():
n = new[k]
d[k] = pd.concat((d.get(k, None), n), axis=1)
for k in d.keys():
indices = ["experiment", "position", "trap", "cell_label"]
idx = (
indices[-d[k].index.nlevels :]
if d[k].index.nlevels > 1
else [indices[-2]]
)
d[k].index.names = idx
toreturn = d
if save:
self.save_to_hdf(toreturn)
return toreturn
def save_to_hdf(self, group_df, path=None):
if path is None:
path = self.local
self.writer = Writer(path)
for path, df in group_df.items():
dset_path = "/extraction/" + path
self.writer.write(dset_path, df)
self.writer.id_cache.clear()
def get_meta(self, flds):
if not hasattr(flds, "__iter__"):
flds = [flds]
meta_short = {k.split("/")[-1]: v for k, v in self.meta.items()}
return {f: meta_short.get(f, self.default_meta.get(f, None)) for f in flds}
### Helpers
def flatten_nest(nest: dict, to="series", tp: int = None) -> dict:
"""
Convert a nested extraction dict into a dict of series
:param nest: dict contained the nested results of extraction
:param to: str = 'series' Determine output format, either list or pd.Series
:param tp: int timepoint used to name the series
"""
d = {}
for k0, v0 in nest.items():
for k1, v1 in v0.items():
for k2, v2 in v1.items():
d["/".join((k0, k1, k2))] = (
pd.Series(*v2, name=tp) if to == "series" else v2
)
return d
def fill_tree(tree):
if tree is None:
return None
tree_depth = depth(tree)
if depth(tree) < 3:
d = {None: {None: {None: []}}}
for _ in range(2 - tree_depth):
d = d[None]
d[None] = tree
tree = d
return tree
extraction/core/functions/cell.py deleted 100644 → 0
View file @ 21d8d578
"""
Base functions to extract information from a single cell
These functions are automatically read, so only add new functions with
the same arguments as the existing ones.
Input:
:cell_mask: (x,y) 2-D cell mask
:trap_image: (x,y) 2-D or (x,y,z) 3-D cell mask
np.where is used to cover for cases where z>1
"""
import math
import numpy as np
from scipy import ndimage
from sklearn.cluster import KMeans
def area(cell_mask, trap_image=None):
return np.sum(cell_mask, dtype=int)
def mean(cell_mask, trap_image):
return np.mean(trap_image[np.where(cell_mask)], dtype=float)
def median(cell_mask, trap_image):
return np.median(trap_image[np.where(cell_mask)])
def max2p5pc(cell_mask, trap_image):
npixels = cell_mask.sum()
top_pixels = int(np.ceil(npixels * 0.025))
sorted_vals = np.sort(trap_image[np.where(cell_mask)], axis=None)
top_vals = sorted_vals[-top_pixels:]
max2p5pc = np.mean(top_vals, dtype=float)
return max2p5pc
def max5px(cell_mask, trap_image):
sorted_vals = np.sort(trap_image[np.where(cell_mask)], axis=None)
top_vals = sorted_vals[-5:]
max5px = np.mean(top_vals, dtype=float)
return max5px
def std(cell_mask, trap_image):
return np.std(trap_image[np.where(cell_mask)], dtype=float)
def k2_top_median(cell_mask, trap_image):
# Use kmeans to cluster the contents of a cell in two, return the high median
# Useful when a big non-tagged organelle (e.g. vacuole) occupies a big fraction
# of the cell
if not np.any(cell_mask):
return np.nan
X = trap_image[np.where(cell_mask)].reshape(-1, 1)
kmeans = KMeans(n_clusters=2, random_state=0).fit(X)
high_clust_id = kmeans.cluster_centers_.argmax()
major_cluster = X[kmeans.predict(X) == high_clust_id]
k2_top_median = np.median(major_cluster, axis=None)
return k2_top_median
def membraneMax5(cell_mask, trap_image):
pass
def membraneMedian(cell_mask, trap_image):
pass
def volume(cell_mask, trap_image=None):
"""Volume from a cell mask, assuming an ellipse.
Assumes the mask is the median plane of the ellipsoid.
Assumes rotational symmetry around the major axis.
"""
min_ax, maj_ax = min_maj_approximation(cell_mask, trap_image)
return (4 * math.pi * min_ax**2 * maj_ax) / 3
def conical_volume(cell_mask, trap_image=None):
padded = np.pad(cell_mask, 1, mode='constant', constant_values=0)
nearest_neighbor = ndimage.morphology.distance_transform_edt(
padded == 1) * padded
return 4 * (nearest_neighbor.sum())
def spherical_volume(cell_mask, trap_image=None):
area = cell_mask.sum()
r = np.sqrt(area / np.pi)
return (4 * np.pi * r**3) / 3
def min_maj_approximation(cell_mask, trap_image=None):
"""Length approximation of minor and major axes of an ellipse from mask.
:param cell_mask:
:param trap_image:
:return:
"""
padded = np.pad(cell_mask,1, mode='constant', constant_values=0)
nn = ndimage.morphology.distance_transform_edt(padded == 1) * padded
dn = ndimage.morphology.distance_transform_edt(nn - nn.max()) * padded
cone_top = ndimage.morphology.distance_transform_edt(dn == 0) * padded
min_ax = np.round(nn.max())
maj_ax = np.round(dn.max() + cone_top.sum()/2)
return min_ax, maj_ax
def eccentricity(cell_mask, trap_image=None):
min_ax, maj_ax = min_maj_approximation(cell_mask)
return np.sqrt(maj_ax**2 - min_ax**2)/maj_ax
extraction/core/functions/defaults.py deleted 100644 → 0
View file @ 21d8d578
# File with defaults for ease of use
from typing import Union
from pathlib import PosixPath, Path
import json
def exparams_from_meta(meta: Union[dict, PosixPath, str], extras=["ph"]):
"""
Obtain parameters from metadata of hdf5 file
"""
meta = meta if isinstance(meta, dict) else load_attributes(meta)
base = {
"tree": {"general": {"None": ["area", "volume"]}},
"multichannel_ops": {},
}
av_channels = {
"Citrine",
"GFP",
"GFPFast",
"mCherry",
"pHluorin405",
"Flavin",
"Cy5",
"mKO2",
}
default_reductions = {"np_max"}
default_metrics = {"mean", "median", "imBackground", "max2p5pc"}
default_rm = {r: default_metrics for r in default_reductions}
av_flch = av_channels.intersection(meta["channels/channel"]).difference(
{"Brightfield, DIC"}
)
for ch in av_flch:
base["tree"][ch] = default_rm
base["sub_bg"] = av_flch
# Additional extraction
if "ph" in extras and {"pHluorin405", "GFPFast"}.issubset(av_flch):
sets = {
b + a: (x, y)
for a, x in zip(
["", "_bgsub"],
(
["GFPFast", "pHluorin405"],
["GFPFast_bgsub", "pHluorin405_bgsub"],
),
)
for b, y in zip(["em_ratio", "gsum"], ["div0", "np_add"])
}
for i, v in sets.items():
base["multichannel_ops"][i] = [
*v,
default_rm,
]
return base
def load_attributes(file: str, group="/"):
with h5py.File(file, "r") as f:
meta = dict(f[group].attrs.items())
return meta
extraction/core/functions/distributors.py deleted 100644 → 0
View file @ 21d8d578
import numpy as np
def trap_apply(cell_fun, cell_masks, trap_image, **kwargs):
"""
Apply a cell_function to a mask, trap_image pair
:param cell_fun: function to apply to a cell (from extraction/cell.py)
:param cell_masks: (numpy 3d array) cells' segmentation mask
:param trap_image: the image for the trap in which the cell is (all
channels)
:**kwargs: parameters to pass if needed for custom functions
"""
cells_iter = (*range(cell_masks.shape[2]),)
return [cell_fun(cell_masks[..., i], trap_image, **kwargs) for i in cells_iter]
def reduce_z(trap_image, fun):
# Optimise the reduction function if possible
if isinstance(fun, np.ufunc):
return fun.reduce(trap_image, axis=2)
else:
return np.apply_along_axis(fun, 2, trap_image)
extraction/core/functions/io.py deleted 100644 → 0
View file @ 21d8d578
from yaml import load, dump
def dict_to_yaml(d, f):
with open(f, "w") as f:
dump(d, f)
def add_attrs(hdfile, path, files):
group = hdfile.create_group(path)
for k, v in files:
group.attrs[k] = v