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Continuation of "Open image sequence - significative slow down - Latest update of Fiji"

Posted by Griffa, Michele on Aug 10, 2014; 3:50pm
URL: http://imagej.273.s1.nabble.com/Continuation-of-Open-image-sequence-significative-slow-down-Latest-update-of-Fiji-tp5009082.html

Dear ImageJ developers, just a small appendix to my previous thread titled

"Open image sequence" significative slow down - Latest update of Fiji"

Once the stack of images is finally loaded up, I notice that the memory used by ImageJ is much larger than the actual size of the stack.
For a stack of 1760 8 bit images of size 2048 x 2048, the occupied memory is about 35 GBytes, while the datasets would require about 7040 MBytes.
This is valid even when I execute the loading as the first operation of ImageJ, such that there is no residue of previous operations, in terms of memory occupancy.

If I save the stack then as a single TIFF file, close Fiji, re-open it and try to load the single TIFF file I get the following error message, which did not appear at all with the previous versions of Fiji/ImageJ:

(Fiji Is Just) ImageJ 2.0.0-rc-11/1.49e; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 7094MB of 98219MB (7%)
java.lang.IndexOutOfBoundsException: Index: 1, Size: 1
                at java.util.ArrayList.RangeCheck(ArrayList.java:547)
                at java.util.ArrayList.get(ArrayList.java:322)
                at io.scif.formats.MinimalTIFFFormat$Reader.openPlane(MinimalTIFFFormat.java:612)
                at io.scif.formats.MinimalTIFFFormat$Reader.openPlane(MinimalTIFFFormat.java:534)
                at io.scif.AbstractReader.openPlane(AbstractReader.java:167)
                at io.scif.filters.ChannelFiller.openPlane(ChannelFiller.java:170)
                at io.scif.filters.ChannelFiller.openPlane(ChannelFiller.java:151)
                at io.scif.filters.PlaneSeparator.openPlane(PlaneSeparator.java:297)
                at io.scif.filters.AbstractReaderFilter.openPlane(AbstractReaderFilter.java:244)
                at io.scif.img.ImgOpener.read(ImgOpener.java:813)
                at io.scif.img.ImgOpener.read(ImgOpener.java:793)
                at io.scif.img.ImgOpener.read(ImgOpener.java:775)
                at io.scif.img.ImgOpener.readPlanes(ImgOpener.java:761)
                at io.scif.img.ImgOpener.openImgs(ImgOpener.java:362)
                at io.scif.img.ImgOpener.openImgs(ImgOpener.java:257)
                at io.scif.img.ImgOpener.openImgs(ImgOpener.java:145)
                at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:266)
                at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:250)
                at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:78)
                at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:50)
                at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:136)
                at net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:335)
                at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:152)
                at ij.IJ.runPlugIn(IJ.java)
                at ij.Executer.runCommand(Executer.java:131)
                at ij.Executer.run(Executer.java:64)
                at java.lang.Thread.run(Thread.java:662)

Thanks a lot in advance for the help.

Best regards,

Michele
---------------------------------------------------------------------------------------------
Michele Griffa, PhD
Senior Research Scientist

Concrete and Construction Chemistry Laboratory
and
Center for X-Ray Analytics

Empa
Swiss Federal Laboratories for Materials Science and Technology
ETH Domain

Überlandstrasse 129
8600 Dübendorf
Switzerland

Tel +41 58 765 4360
Fax +41 58 765 4035
[hidden email]
www.empa.ch<http://www.empa.ch/>
www.empa.ch/x-ray<http://www.empa.ch/x-ray>

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