These are chat archives for fiji/fiji

16th
Jun 2016
Ivan Ruiz
@ivanfrustrado_twitter
Jun 16 2016 09:00
Hello guys. Is there a way to work with images larger that 4 gb? I'm using a 4.3 gb tiff image with 38 layers and using the bio-formats importer always gives me an error. I increased the memory with no success :(
Jan Eglinger
@imagejan
Jun 16 2016 10:59
@ivanfrustrado_twitter I'm working with 20gb images without problems. As long as a single plane is not larger than 2 Gigapixels, which creates problems with the ImageJ 1.x pixel arrays in Java. Why don't you post the error message you're getting (and possibly a link to an example image) to http://forum.imagej.net ?
Nienke Hesen
@NienkeHesen_twitter
Jun 16 2016 12:28
Is it possible to lock the FIJI screen on foreground?
Stefan Helfrich
@stelfrich
Jun 16 2016 12:36
@NienkeHesen_twitter I think that has been discussed on the mailinglist: http://imagej.1557.x6.nabble.com/ImageJ-window-Always-on-Top-tp3694763p3694770.html
Nienke Hesen
@NienkeHesen_twitter
Jun 16 2016 12:46
@stelfrich Thanks! How should I do the ctrl-j? It does not do anything and if I press the run button it gives an error: unrecognized IJ function...
Stefan Helfrich
@stelfrich
Jun 16 2016 12:50
Ah! That thread has been sitting there for quite some time ;)
Open the script editor with [ and change the language to JavaScript
importClass(Packages.ij.IJ);
IJ.getInstance().setAlwaysOnTop(true);
And try to run that script
(the parameter you want is true obviously)
Nienke Hesen
@NienkeHesen_twitter
Jun 16 2016 12:58
@stelfrich Thanks so much it worked!!! :D
Sorry but it does not work... -.-
Stefan Helfrich
@stelfrich
Jun 16 2016 13:02
Which OS?
Nienke Hesen
@NienkeHesen_twitter
Jun 16 2016 13:02
How can I fix this? The file I created is in the plugins folder, but it does not say that it is an executable jar file like all other plugins in the folder...
windows 10
Stefan Helfrich
@stelfrich
Jun 16 2016 13:03
So it did work when you executed the script from the script editor?
Nienke Hesen
@NienkeHesen_twitter
Jun 16 2016 13:03
ImageJ 1.51c
yes it worked when i did that
Stefan Helfrich
@stelfrich
Jun 16 2016 13:04
Is there a _ in your script's filename?
Nienke Hesen
@NienkeHesen_twitter
Jun 16 2016 13:05
No, I just copied what you typed...
Stefan Helfrich
@stelfrich
Jun 16 2016 13:06
Now I am confused..
It is not working anymore?
Jan Eglinger
@imagejan
Jun 16 2016 13:07
@NienkeHesen_twitter you saved under which filename?
Nienke Hesen
@NienkeHesen_twitter
Jun 16 2016 13:12
I saved it under Always_on_Top
in the plugins folder
I copied what you typed and pressed run, then it worked, then i saved it under Always_on_Top in the plugins folder and restarted FIJI but now it does not work anymore...
Jan Eglinger
@imagejan
Jun 16 2016 13:14
It should be Always_on_Top.js if you want it to be a runnable JavaScript file
Then it'll appear as 'Always on Top' in the plugins menu (or anywhere else if you put it into ./plugins/Scripts/Your/Menu/Submenu)
Ivan Ruiz
@ivanfrustrado_twitter
Jun 16 2016 14:06
@imagejan it's a subset of a worldview-2 image with the 8 spectral bands, I added some extra bands with spatial info (27 bands) in total 35 bands and 4.3 gb tiff file. I get an opener window saying: File is not in a supported format, a reader plugin is not available, or it was not found.
when I try to load it via the bioformats plugin I get this: loci.formats.FormatException: loci.common.ReflectException: Cannot execute method: getNumPages
at loci.formats.in.TiffJAIReader.initFile(TiffJAIReader.java:149)
at loci.formats.FormatReader.setId(FormatReader.java:1426)
at loci.formats.DelegateReader.setId(DelegateReader.java:298)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:505)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)
at loci.plugins.in.Importer.showDialogs(Importer.java:140)
at loci.plugins.in.Importer.run(Importer.java:76)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:216)
at ij.IJ.runPlugIn(IJ.java:180)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:745)
Caused by: loci.common.ReflectException: Cannot execute method: getNumPages
at loci.common.ReflectedUniverse.exec(ReflectedUniverse.java:316)
at loci.formats.in.TiffJAIReader.initFile(TiffJAIReader.java:146)
... 12 more
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at loci.common.ReflectedUniverse.exec(ReflectedUniverse.java:311)
... 13 more
Caused by: java.io.IOException: Bad magic number, should be 42.
at com.sun.media.jai.codecimpl.CodecUtils.toIOException(CodecUtils.java:76)
at com.sun.media.jai.codecimpl.TIFFImageDecoder.getNumPages(TIFFImageDecoder.java:98)
... 18 more
Caused by: java.lang.IllegalArgumentException: Bad magic number, should be 42.
at com.sun.media.jai.codec.TIFFDirectory.getNumDirectories(TIFFDirectory.java:601)
at com.sun.media.jai.codecimpl.TIFFImageDecoder.getNumPages(TIFFImageDecoder.java:96)
... 18 more
Oh my god its too long didn't realize it before , I'm sorry
I tried with smaller tiff files and its ok
Jan Eglinger
@imagejan
Jun 16 2016 15:07
@ivanfrustrado_twitter as I said, please continue the discussion on forum.imagej.net, where it will be more visible to others having the same issue in the future.
Nienke Hesen
@NienkeHesen_twitter
Jun 16 2016 15:14
@imagejan @stelfrich Thanks guys! It works now! I changed the name to .js
Curtis Rueden
@ctrueden
Jun 16 2016 15:30
@ivanfrustrado_twitter java.io.IOException: Bad magic number, should be 42. sounds like a corrupt TIFF file. And I agree with @imagejan: discussing on the forum will involve more people, including Bio-Formats people. :-)