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grp-almf
feedback-fly-embryo-crocker
Commits
4c3acdb9
Commit
4c3acdb9
authored
Dec 09, 2020
by
Aliaksandr Halavatyi
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Plain Diff
resolve an issue when the well is the whole image
parent
f76a3e39
Changes
4
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4 changed files
with
40 additions
and
24 deletions
+40
-24
src/main/java/feedback/fly/embryo/jobs/Job_SelectMultipleEmbryosAuto.java
...edback/fly/embryo/jobs/Job_SelectMultipleEmbryosAuto.java
+14
-4
src/main/java/feedback/fly/embryo/jobs/Job_SelectMultipleEmbryosManual3D.java
...ck/fly/embryo/jobs/Job_SelectMultipleEmbryosManual3D.java
+6
-2
src/test/java/jobdistributors/run/debug/RunJobDistributor.java
...est/java/jobdistributors/run/debug/RunJobDistributor.java
+20
-0
src/test/java/jobdistributors/run/debug/RunManualDistributorRotationSplit.java
...ributors/run/debug/RunManualDistributorRotationSplit.java
+0
-18
No files found.
src/main/java/feedback/fly/embryo/jobs/Job_SelectMultipleEmbryosAuto.java
View file @
4c3acdb9
...
...
@@ -215,9 +215,14 @@ public class Job_SelectMultipleEmbryosAuto extends Job_Default{
this
.
showDebug
(
_embryoImage
,
"Image for embryo segmentation"
,
true
);
//exclude particles outside ROI by filling with 0
embryoProcessor
.
setColor
(
0
);
embryoProcessor
.
fillOutside
(
wellRoi
);
long
imageSize
=
embryoProcessor
.
getWidth
()*
embryoProcessor
.
getHeight
();
embryoProcessor
.
setRoi
(
wellRoi
);
long
roiSize
=(
long
)
embryoProcessor
.
getStats
().
area
;
embryoProcessor
.
setRoi
((
Roi
)
null
);
if
(
roiSize
<
imageSize
)
{
//check if there is any area on the image outside Roi
embryoProcessor
.
setColor
(
0
);
embryoProcessor
.
fillOutside
(
wellRoi
);
}
ImageProcessor
maskProcessor
=
new
MaximumFinder
().
findMaxima
(
embryoProcessor
,
watershedTolerance
,
embryoFluorThreshold
,
MaximumFinder
.
SEGMENTED
,
false
,
false
);
ImagePlus
watershedMaskImage
=
new
ImagePlus
(
"Embryo Mask Image"
,
maskProcessor
);
...
...
@@ -309,7 +314,12 @@ public class Job_SelectMultipleEmbryosAuto extends Job_Default{
//saveRoiForImage(newImgFile,saveRoi);
this
.
setSharedValue
(
"Zoom Points"
,
selectedPoints
);
this
.
setSharedValue
(
"Zoom Counter"
,
-
1
);
if
(
this
.
getSharedValue
(
"Zoom Counter"
)==
null
)
{
this
.
setSharedValue
(
"Zoom Counter"
,
-
1
);
}
if
(
this
.
getSharedValue
(
"Table Row Counter"
)==
null
)
{
this
.
setSharedValue
(
"Table Row Counter"
,
-
1
);
}
this
.
setSharedValue
(
"Selected Embryo Rois"
,
selectedEmbryoRois
);
}
...
...
src/main/java/feedback/fly/embryo/jobs/Job_SelectMultipleEmbryosManual3D.java
View file @
4c3acdb9
...
...
@@ -177,8 +177,12 @@ public class Job_SelectMultipleEmbryosManual3D extends Job_Default{
saveRoiForImage
(
newImgFile
,
saveRoi
);
this
.
setSharedValue
(
"Zoom Counter"
,
-
1
);
this
.
setSharedValue
(
"Table Row Counter"
,
-
1
);
if
(
this
.
getSharedValue
(
"Zoom Counter"
)==
null
)
{
this
.
setSharedValue
(
"Zoom Counter"
,
-
1
);
}
if
(
this
.
getSharedValue
(
"Table Row Counter"
)==
null
)
{
this
.
setSharedValue
(
"Table Row Counter"
,
-
1
);
}
}
...
...
src/test/java/jobdistributors/run/debug/RunJobDistributor.java
0 → 100644
View file @
4c3acdb9
package
jobdistributors.run.debug
;
import
feedback.fly.embryo.jobdistributors.JobDistributor_AutoSelectionMultiple_AFocus_Rotation_Split
;
//import feedback.fly.embryo.jobdistributors.JobDistributor_ManualSelection3DMultiple_AFocus_Rotation_Split;
import
ij.IJ
;
import
net.imagej.ImageJ
;
public
class
RunJobDistributor
{
public
static
void
main
(
String
[]
args
)
{
//Class<?> clazz = JobDistributor_ManualSelection3DMultiple_AFocus_Rotation_Split.class;
Class
<?>
clazz
=
JobDistributor_AutoSelectionMultiple_AFocus_Rotation_Split
.
class
;
// start ImageJ
ImageJ
ij2
=
new
ImageJ
();
ij2
.
ui
().
showUI
();
//IJ.runPlugIn(clazz.getName(),"Debug run");
IJ
.
runPlugIn
(
clazz
.
getName
(),
""
);
}
}
src/test/java/jobdistributors/run/debug/RunManualDistributorRotationSplit.java
deleted
100644 → 0
View file @
f76a3e39
package
jobdistributors.run.debug
;
import
feedback.fly.embryo.jobdistributors.JobDistributor_ManualSelection3DMultiple_AFocus_Rotation_Split
;
import
ij.IJ
;
import
net.imagej.ImageJ
;
public
class
RunManualDistributorRotationSplit
{
public
static
void
main
(
String
[]
args
)
{
Class
<?>
clazz
=
JobDistributor_ManualSelection3DMultiple_AFocus_Rotation_Split
.
class
;
// start ImageJ
ImageJ
ij2
=
new
ImageJ
();
ij2
.
ui
().
showUI
();
IJ
.
runPlugIn
(
clazz
.
getName
(),
"Debug run"
);
//IJ.runPlugIn(clazz.getName(),"");
}
}
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