Commit 4b7c890f authored by Aliaksandr Halavatyi's avatar Aliaksandr Halavatyi
Browse files

debugging autofocus with LineScan

parent 9135315c
......@@ -14,7 +14,7 @@
-->
<groupId>embl.almf</groupId>
<artifactId>AutoMicTools_</artifactId>
<version>1.1.14-SNAPSHOT</version>
<version>1.1.15-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>
......
......@@ -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\\tmp\\AF--W0000--P0001-T0001.czi"));
testJob.testImageFile(new File("X:\\group\\Aliaksandr\\test-Tobias-auto-20200724\\20200724-150541\\AF\\AF--W0000--P0001-T0001.czi"));
//testJob.testJobMicTable(0, tblPth, tblFnm);
}
......
......@@ -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);
......
......@@ -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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