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ALMF
feedback-fly-embryo-crocker
Commits
4af06eda
Commit
4af06eda
authored
Feb 04, 2021
by
Aliaksandr Halavatyi
Browse files
debugging auto selection workflow
parent
ce60b956
Changes
2
Hide whitespace changes
Inline
Side-by-side
pom.xml
View file @
4af06eda
...
...
@@ -15,7 +15,7 @@
<groupId>
embl.almf
</groupId>
<version>
1.0.
3
</version>
<version>
1.0.
6-snapshot
</version>
<name>
Fly_Embryo_Feedback
</name>
<inceptionYear>
2017
</inceptionYear>
...
...
src/main/java/feedback/fly/embryo/jobs/Job_SelectMultipleEmbryosAuto.java
View file @
4af06eda
...
...
@@ -11,12 +11,14 @@ import automic.parameters.ParameterCollection;
import
automic.parameters.ParameterType
;
import
automic.utils.ArrIndUtils
;
import
automic.utils.DebugVisualiserSettings
;
import
automic.utils.FileUtils
;
import
automic.utils.roi.ParticleFilterer
;
import
automic.utils.roi.ROIManipulator2D
;
import
ij.IJ
;
import
ij.ImageJ
;
import
ij.ImagePlus
;
import
ij.gui.Overlay
;
import
ij.gui.PointRoi
;
import
ij.gui.Roi
;
import
ij.plugin.Duplicator
;
import
ij.plugin.ZProjector
;
...
...
@@ -104,8 +106,11 @@ public class Job_SelectMultipleEmbryosAuto extends Job_Default{
protected
void
preProcessOnline
()
throws
Exception
{
currentTable
.
setFileAbsolutePath
(
newImgFile
,
curDInd
,
imgColumnNm
,
"IMG"
);
String
oldExperimentName
=(
String
)
this
.
getSharedValue
(
"Experiment Name"
);
String
Exper_nm
=
newImgFile
.
getName
();
Exper_nm
=
Exper_nm
.
substring
(
0
,
Exper_nm
.
indexOf
(
fileTag
));
if
(!
Exper_nm
.
equals
(
oldExperimentName
))
super
.
clearSharedData
();
this
.
setSharedValue
(
"Experiment Name"
,
Exper_nm
);
TimeUnit
.
MILLISECONDS
.
sleep
(
imageOpeningTimeDelay
);
...
...
@@ -291,6 +296,7 @@ public class Job_SelectMultipleEmbryosAuto extends Job_Default{
@Override
public
void
postProcessSuccess
()
throws
Exception
{
//PointRoi saveRoi=null;
//form comma-separated strings with coordinates
String
xstr
=
""
,
ystr
=
""
,
zstr
=
""
;
...
...
@@ -305,6 +311,11 @@ public class Job_SelectMultipleEmbryosAuto extends Job_Default{
xstr
+=
selectedPoints
[
i
].
x
;
ystr
+=
selectedPoints
[
i
].
y
;
zstr
+=
img
.
getNSlices
()/
2
;
//central slice by default
currentTable
.
setNumericValue
(
selectedPoints
[
i
].
x
,
0
,
"Zoom.X"
);
currentTable
.
setNumericValue
(
selectedPoints
[
i
].
y
,
0
,
"Zoom.Y"
);
this
.
recordSummaryDataset
(
true
);
}
...
...
@@ -320,7 +331,7 @@ public class Job_SelectMultipleEmbryosAuto extends Job_Default{
if
(
this
.
getSharedValue
(
"Table Row Counter"
)==
null
)
{
this
.
setSharedValue
(
"Table Row Counter"
,
-
1
);
}
this
.
setSharedValue
(
"Selected Embryo Rois"
,
selectedEmbryoRois
);
//
this.setSharedValue("Selected Embryo Rois", selectedEmbryoRois);
}
@Override
...
...
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