[ImageJ-bugs] [Bug 1019] New: Align image by Line ROI results in Java error
bugzilla at fiji.sc
bugzilla at fiji.sc
Wed Mar 4 10:06:17 CST 2015
http://fiji.sc/bugzilla/show_bug.cgi?id=1019
Bug ID: 1019
Summary: Align image by Line ROI results in Java error
Product: Fiji
Version: unspecified
Hardware: PC
OS: Windows
Status: NEW
Severity: normal
Priority: P4
Component: Plugins
Assignee: imagej-bugs at imagej.net
Reporter: amc910 at bham.ac.uk
CC: amc910 at bham.ac.uk
Hi there,
I'm trying to run the 'Align image by line ROI' utility, and I keep getting a
Java error.
The following macro results in the same error:
-----------------
run("Dot Blot (7K)");
run("Dot Blot (7K)");
selectWindow("Dot_Blot.jpg");
makeLine(116, 256, 475, 97);
selectWindow("Dot_Blot-1.jpg");
makeLine(106, 111, 404, 172);
run("Align Image by line ROI");
-----------------
Hit 'OK' and the following Java error is printed:
-----------------
(Fiji Is Just) ImageJ 2.0.0-rc-25/1.49p; Java 1.6.0_24 [64-bit]; Windows 7 6.1;
100MB of 5971MB (1%)
java.lang.NullPointerException
at Align_Image.align(Align_Image.java:139)
at Align_Image.run(Align_Image.java:83)
at ij.IJ.runUserPlugIn(IJ.java:199)
at ij.IJ.runPlugIn(IJ.java:163)
at ij.Executer.runCommand(Executer.java:131)
at ij.Executer.run(Executer.java:64)
at ij.IJ.run(IJ.java:275)
at ij.IJ.run(IJ.java:250)
at ij.macro.Functions.doRun(Functions.java:593)
at ij.macro.Functions.doFunction(Functions.java:89)
at ij.macro.Interpreter.doStatement(Interpreter.java:226)
at ij.macro.Interpreter.doStatements(Interpreter.java:214)
at ij.macro.Interpreter.run(Interpreter.java:111)
at ij.macro.Interpreter.run(Interpreter.java:81)
at ij.macro.Interpreter.run(Interpreter.java:92)
at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:153)
at ij.IJ.runMacro(IJ.java:116)
at ij.IJ.runMacro(IJ.java:105)
at net.imagej.legacy.IJ1Helper.runMacro(IJ1Helper.java:794)
at net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:116)
at net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:160)
at org.scijava.script.ScriptModule.run(ScriptModule.java:175)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
at
org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:164)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:662)
-------------
>From the first two lines in the error log I'm assuming it has to do with lines
139 and 83 in Align_image.java:
131: float dx1 = line1.x2 - line1.x1;
83: ImageProcessor result = align(source.getProcessor(), line1,
target.getProcessor(), line2, withScaling, withRotation);
From: https://github.com/fiji/VIB/blob/master/src/main/java/Align_Image.java
I'm afraid I'm not really sure where to go from here, any ideas?
Information about your version of Java:
os.arch => amd64
os.name => Windows 7
os.version => 6.1
java.version => 1.6.0_24
java.vendor => Sun Microsystems Inc.
java.runtime.name => Java(TM) SE Runtime Environment
java.runtime.version => 1.6.0_24-b07
java.vm.name => Java HotSpot(TM) 64-Bit Server VM
java.vm.version => 19.1-b02
java.vm.vendor => Sun Microsystems Inc.
java.vm.info => mixed mode
java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
java.specification.name => Java Platform API Specification
java.specification.version => 1.6
sun.cpu.endian => little
sun.desktop => windows
file.separator => \
The up-to-date check says: REMIND_LATER
Information relevant to JAVA_HOME related problems:
JAVA_HOME is set to: C:\Work\FIJI-W~1\Fiji.app/java/win64/jdk1.6.0_24//jre
imagej.dir => C:\Work\FIJI-W~1\Fiji.app
Information about the version of each plugin:
Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150302042523)
Fiji: http://fiji.sc/update/ (last check:20150302225742)
Files not up-to-date:
b0038cbf (MODIFIED) 20150304154358 jars/ij-1.49m.jar
1ad3be0d (LOCAL_ONLY) 20140201185146 jars/jpedalSTD.jar
c7660983 (LOCAL_ONLY) 20140731142918 macros/Angus1.ijm
c55dde81 (LOCAL_ONLY) 20140731142926 macros/Angus2.ijm
0be8846e (LOCAL_ONLY) 20141210131404 macros/BatchScale.ijm
0a23f9af (LOCAL_ONLY) 20140729120848 macros/Bleach Correction.ijm
d71b3fa8 (LOCAL_ONLY) 20150217134500 macros/Confocal1.ijm
9078abc5 (LOCAL_ONLY) 20150120131532 macros/Cropping.ijm
6eeac28f (LOCAL_ONLY) 20141204141336 macros/DateLastModified.ijm
19ddd309 (LOCAL_ONLY) 20140626124302 macros/FullScan_100x.ijm
35e3bd87 (LOCAL_ONLY) 20140626124325 macros/FullScan_200x.ijm
6727eb24 (LOCAL_ONLY) 20140626124218 macros/FullScan_25x.ijm
470b2083 (LOCAL_ONLY) 20140626124344 macros/FullScan_500x.ijm
23e828fb (LOCAL_ONLY) 20140626124239 macros/FullScan_50x.ijm
51565b01 (LOCAL_ONLY) 20141209172107 macros/LoggerDataExtract.ijm
3b8be573 (LOCAL_ONLY) 20140624092005 macros/MultiOpen.ijm
c2c3c8fa (LOCAL_ONLY) 20141209172109 macros/ScannertoRGBij.ijm
20c298a4 (LOCAL_ONLY) 20140604130515 macros/StackReg.ijm
54bc1cc8 (LOCAL_ONLY) 20140731181111 macros/Timelapse overlay.ijm
0e90592c (LOCAL_ONLY) 20140624161002 macros/Timelapse1.ijm
0ea65c05 (LOCAL_ONLY) 20140804113436 macros/VirtualDubMacro.ijm
05337381 (LOCAL_ONLY) 20140804144053 macros/WB Single.ijm
76215538 (LOCAL_ONLY) 20140804144725 macros/WB Stack.ijm
b0408dbd (LOCAL_ONLY) 20150126154553 macros/WhiteBalanceAreaMean.ijm
83f01961 (LOCAL_ONLY) 20140729120800 plugins/Bleach Correction.ijm
e532d82b (LOCAL_ONLY) 20140626175231 plugins/FullScan_100x.ijm
553b12f8 (LOCAL_ONLY) 20140626175259 plugins/FullScan_200x.ijm
842dac39 (LOCAL_ONLY) 20140626175242 plugins/FullScan_25x.ijm
b90fcf8c (LOCAL_ONLY) 20140626175540 plugins/FullScan_500x.ijm
fb0ea92b (LOCAL_ONLY) 20140626175247 plugins/FullScan_50x.ijm
29aa129b (LOCAL_ONLY) 20140530113502 plugins/MeasureStack.class
698e201e (LOCAL_ONLY) 20140530113502 plugins/MeasureStackReviewer.class
db437772 (LOCAL_ONLY) 20140530113502 plugins/Measure_Stack.class
2b893d8c (LOCAL_ONLY) 20140624133848 plugins/MultiOpen.ijm
b7e36bf5 (LOCAL_ONLY) 20140804104151 plugins/RXTXcomm.jar
b3b73e80 (LOCAL_ONLY) 20141210131339 plugins/Scan_.jar
6aca4c14 (LOCAL_ONLY) 20140804151315 plugins/WB Single.ijm
ff703cc6 (LOCAL_ONLY) 20140610111222 plugins/ij-dcraw_.jar
27598922 (LOCAL_ONLY) 20140804103936 plugins/serial_ext.jar
dcb0f1b8 (LOCAL_ONLY) 20141210131339
plugins/uk.co.mmscomputing.device.twain.jar
--
You are receiving this mail because:
You are the assignee for the bug.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://imagej.net/pipermail/imagej-bugs/attachments/20150304/6f93b289/attachment.html>
More information about the Imagej-bugs
mailing list