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Aliaksandr Halavatyi
AutoMicTools
Commits
ed4eebc9
Commit
ed4eebc9
authored
Sep 29, 2020
by
Aliaksandr Halavatyi
Browse files
cleaning procedures for line and frame acquisitions
parent
6db677b6
Changes
2
Hide whitespace changes
Inline
Side-by-side
pom.xml
View file @
ed4eebc9
...
...
@@ -14,7 +14,7 @@
-->
<groupId>
embl.almf
</groupId>
<artifactId>
AutoMicTools_
</artifactId>
<version>
1.1.1
6
-SNAPSHOT
</version>
<version>
1.1.1
7
-SNAPSHOT
</version>
<name>
plugins/AutoMicTools_.jar
</name>
<description>
Collection of tools for automated (feedback) microscopy data acquisition and analysis
</description>
...
...
src/main/java/automic/online/jobs/common/Job_AutofocusInit_ZenBlue.java
View file @
ed4eebc9
...
...
@@ -8,7 +8,6 @@ import automic.online.jobs.Job_Default;
import
automic.online.microscope.ZeissLSM800
;
import
automic.utils.imagefiles.ImageOpenerWithBioformats
;
import
automic.utils.roi.ROIManipulator2D
;
import
ij.IJ
;
import
ij.ImageJ
;
import
ij.ImagePlus
;
import
ij.ImageStack
;
...
...
@@ -16,8 +15,6 @@ import ij.gui.Line;
import
ij.gui.Overlay
;
import
ij.gui.ProfilePlot
;
import
ij.gui.Roi
;
import
imagescience.transform.Turn
;
import
imagescience.image.Image
;
public
class
Job_AutofocusInit_ZenBlue
extends
Job_Default
{
//private static final Roi nullRoi=null;
...
...
@@ -44,6 +41,7 @@ public class Job_AutofocusInit_ZenBlue extends Job_Default{
Exper_nm
=
Exper_nm
.
substring
(
0
,
Exper_nm
.
indexOf
(
fileTag
));
this
.
setSharedValue
(
"Experiment Name"
,
Exper_nm
);
TimeUnit
.
MILLISECONDS
.
sleep
(
1000
);
ImageOpenerWithBioformats
.
turnLineScans
=
true
;
img
=
ImageOpenerWithBioformats
.
openImage
(
newImgFile
);
isLineScan
=(
img
.
getWidth
()==
1
)||(
img
.
getHeight
()==
1
);
}
...
...
@@ -51,21 +49,51 @@ public class Job_AutofocusInit_ZenBlue extends Job_Default{
@Override
protected
void
preProcessOffline
()
throws
Exception
{
//img=ImageOpenerWithBioformats.openImage(currentTable.getFile(curDInd, imgColumnNm, "IMG"));
ImageOpenerWithBioformats
.
turnLineScans
=
true
;
img
=
ImageOpenerWithBioformats
.
openImage
(
newImgFile
);
isLineScan
=(
img
.
getWidth
()==
1
)||(
img
.
getHeight
()==
1
);
}
@Override
protected
boolean
runProcessing
()
throws
Exception
{
if
(
isLineScan
)
maxind
=
getFocusValueLine
(
img
);
else
{
maxind
=
getFocusValueFrameStack
(
img
);
}
return
true
;
}
private
int
getFocusValueLine
(
ImagePlus
_image
)
{
//find focus and send to the microscope macro
_image
.
setRoi
(
0
,
0
,
_image
.
getWidth
(),
_image
.
getHeight
());
double
[]
vals
=
new
ProfilePlot
(
_image
,
true
).
getProfile
();
_image
.
setRoi
((
Roi
)
null
);
int
npoints
=
vals
.
length
;
double
maxv
=
0
;
int
max_id
=-
1
;
for
(
int
i
=
0
;
i
<
npoints
;
i
++){
if
(
vals
[
i
]>
maxv
){
max_id
=
i
;
maxv
=
vals
[
i
];
}
}
return
max_id
;
}
private
int
getFocusValueFrameStack
(
ImagePlus
_image
)
{
//find focus and send to the microscope macro
//img.setRoi(0,0,img.getWidth(), img.getHeight());
//double [] vals=new ProfilePlot(img,true).getProfile();
//img.setRoi((Roi)null);
//int npoints=vals.length;
_image
.
setRoi
((
Roi
)
null
);
/*
double
maxv
=
0
;
maxi
n
d=-1;
int
max
_
id
=-
1
;
ImageStack
stack
=
img
.
getStack
();
int
nSlices
=
stack
.
getSize
();
...
...
@@ -74,40 +102,21 @@ public class Job_AutofocusInit_ZenBlue extends Job_Default{
for
(
int
i
=
0
;
i
<
nSlices
;
i
++){
currentValue
=
stack
.
getProcessor
(
i
+
1
).
getStatistics
().
mean
;
if
(
currentValue
>
maxv
){
maxi
n
d=i;
max
_
id
=
i
;
maxv
=
currentValue
;
}
}
//ln=new Line(0,maxind,img.getWidth(),maxind);
//ln.setStrokeColor(Color.ORANGE);
*/
//find focus and send to the microscope macro
img
.
setRoi
(
0
,
0
,
img
.
getWidth
(),
img
.
getHeight
());
double
[]
vals
=
new
ProfilePlot
(
img
,
true
).
getProfile
();
img
.
setRoi
((
Roi
)
null
);
int
npoints
=
vals
.
length
;
double
maxv
=
0
;
maxind
=-
1
;
for
(
int
i
=
0
;
i
<
npoints
;
i
++){
if
(
vals
[
i
]>
maxv
){
maxind
=
i
;
maxv
=
vals
[
i
];
}
}
return
max_id
;
return
true
;
}
@Override
protected
Overlay
createOverlay
(){
Overlay
o
=
new
Overlay
();
//if(isLineScan&&(maxind>0))
if
(
maxind
>
0
)
if
(
isLineScan
&&(
maxind
>
0
))
o
.
add
(
new
Line
(
0
,
maxind
,
img
.
getWidth
()-
1
,
maxind
));
return
o
;
}
...
...
@@ -115,18 +124,10 @@ public class Job_AutofocusInit_ZenBlue extends Job_Default{
@Override
public
void
visualise
(
int
_xvis
,
int
_yvis
){
this
.
visualiseImg
(
img
,
getOverlay
(),
_xvis
,
_yvis
);
/*
if (isLineScan) {
ImagePlus transformedImage=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");
this.visualiseImg(transformedImage, getOverlay(), _xvis, _yvis);
}else{
this.visualiseImg(img, getOverlay(), _xvis, _yvis);
if (maxind>0)
img.setSlice(maxind);
if
((!
isLineScan
)
&&
(
maxind
>
0
))
{
img
.
setSlice
(
maxind
);
}
*/
}
...
...
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