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Aliaksandr Halavatyi
AutoMicTools
Commits
4b7c890f
Commit
4b7c890f
authored
Aug 03, 2020
by
Aliaksandr Halavatyi
Browse files
debugging autofocus with LineScan
parent
9135315c
Changes
4
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Inline
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pom.xml
View file @
4b7c890f
...
...
@@ -14,7 +14,7 @@
-->
<groupId>
embl.almf
</groupId>
<artifactId>
AutoMicTools_
</artifactId>
<version>
1.1.1
4
-SNAPSHOT
</version>
<version>
1.1.1
5
-SNAPSHOT
</version>
<name>
plugins/AutoMicTools_.jar
</name>
<description>
Collection of tools for automated (feedback) microscopy data acquisition and analysis
</description>
...
...
@@ -290,11 +290,6 @@
<artifactId>
imglib2-meta
</artifactId>
<version>
2.0.0-beta-26
</version>
</dependency>
<dependency>
<groupId>
ome
</groupId>
<artifactId>
bioformats_package
</artifactId>
<version>
6.0.0
</version>
</dependency>
<dependency>
<groupId>
com.github.mcib3d
</groupId>
<artifactId>
mcib3d-core
</artifactId>
...
...
@@ -320,7 +315,12 @@
<artifactId>
ilastik4ij
</artifactId>
<version>
1.7.2
</version>
</dependency>
<dependency>
<groupId>
ome
</groupId>
<artifactId>
bioformats_package
</artifactId>
<version>
6.5.0
</version>
</dependency>
</dependencies>
</dependencyManagement>
...
...
src/main/java/automic/online/jobs/common/Job_AutofocusInit_ZenBlue.java
View file @
4b7c890f
...
...
@@ -157,7 +157,7 @@ public class Job_AutofocusInit_ZenBlue extends Job_Default{
Job_AutofocusInit_ZenBlue
testJob
=
new
Job_AutofocusInit_ZenBlue
();
testJob
.
initialise
(
null
,
"AFocus"
,
false
);
testJob
.
testImageFile
(
new
File
(
"X:\\group\\Aliaksandr\\t
mp
\\AF--W0000--P0001-T0001.czi"
));
testJob
.
testImageFile
(
new
File
(
"X:\\group\\Aliaksandr\\t
est-Tobias-auto-20200724\\20200724-150541\\AF
\\AF--W0000--P0001-T0001.czi"
));
//testJob.testJobMicTable(0, tblPth, tblFnm);
}
...
...
src/main/java/automic/online/jobs/common/Job_Autofocus_ZenBlue.java
View file @
4b7c890f
...
...
@@ -92,7 +92,7 @@ public class Job_Autofocus_ZenBlue extends Job_Default{
@Override
public
void
postProcessSuccess
()
throws
Exception
{
ZeissLSM800
.
submitJobPixels
(
newImgFile
,
"spindle-LZ"
,
new
Point3D
[]{
new
Point3D
(
null
,
null
,(
double
)
maxind
)
}
);
ZeissLSM800
.
submitJobPixels
(
newImgFile
,
"spindle-LZ"
,
new
Point3D
(
null
,
null
,(
double
)
maxind
));
Roi
[]
rs
=
getOverlay
().
toArray
();
if
(!
ROIManipulator2D
.
isEmptyRoiArr
(
rs
))
saveRoisForImage
(
newImgFile
,
rs
);
...
...
@@ -100,7 +100,7 @@ public class Job_Autofocus_ZenBlue extends Job_Default{
@Override
public
void
postProcessOffline
()
throws
Exception
{
ZeissLSM800
.
submitJobPixels
(
newImgFile
,
"spindle-LZ"
,
new
Point3D
[]{
new
Point3D
(
null
,
null
,(
double
)
maxind
)
}
);
ZeissLSM800
.
submitJobPixels
(
newImgFile
,
"spindle-LZ"
,
new
Point3D
(
null
,
null
,(
double
)
maxind
));
Roi
[]
rs
=
getOverlay
().
toArray
();
if
(!
ROIManipulator2D
.
isEmptyRoiArr
(
rs
))
saveRoisForImage
(
newImgFile
,
rs
);
...
...
src/main/java/automic/utils/imagefiles/ImageOpenerWithBioformats.java
View file @
4b7c890f
...
...
@@ -80,7 +80,7 @@ public class ImageOpenerWithBioformats {
ImagePlus
img
=
imgs
[
0
];
if
(
turnLineScans
&&((
img
.
getWidth
()==
1
)||(
img
.
getHeight
()==
1
)))
{
img
=
new
Turn
().
run
(
Image
.
wrap
(
img
),
0
,
0
,
1
).
imageplus
();
//img.duplicate();
img
=
new
Turn
().
run
(
Image
.
wrap
(
img
),
0
,
0
,
-
1
).
imageplus
();
//img.duplicate();
//IJ.run(transformedImage, "TransformJ Turn", "z-angle=0 y-angle=0 x-angle=90");
}
...
...
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