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

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

Griffa, Michele
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>

Diese Mitteilung ist ausschliesslich für die als Empfänger aufgeführte Person(en) oder Firma bestimmt. Sie kann persönliche und/oder vertrauliche Informationen enthalten. Sollten Sie diese Mitteilung irrtümlicherweise erhalten haben, bitten wir Sie, uns umgehend per E-Mail zu informieren, sämtliche Ausdrucke zu vernichten und die E-Mail-Dateien zu löschen.

This message is intended for the exclusive use of the individual(s) or entity to whom it is addressed. It may contain information that is privileged and/or confidential. Should you have received this message erroneously, please notify us immediately by e-mail, destroy any printouts and delete all electronic files contained in this message.
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Mark Hiner-2
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Re: Continuation of "Open image sequence - significative slow down - Latest update of Fiji"

Mark Hiner-2
Hi Michele,

This sounds like a problem with SCIFIO, which is a beta image I/O component
that we enabled by default a few months ago.

If you don't mind, could you please file a Fiji bug
<http://wiki.imagej.net/Report_a_Bug> report and upload your dataset with
the "Help > Upload Sample Image" command?

In the mean time you can disable SCIFIO
<http://wiki.imagej.net/Bug_reporting_best_practices#Disable_SCIFIO> to
return to the old functionality, which should fix the problem for you.

Thanks,
Mark


On Sun, Aug 10, 2014 at 10:52 AM, Griffa, Michele <[hidden email]>
wrote:

> 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>
>
> Diese Mitteilung ist ausschliesslich für die als Empfänger aufgeführte
> Person(en) oder Firma bestimmt. Sie kann persönliche und/oder vertrauliche
> Informationen enthalten. Sollten Sie diese Mitteilung irrtümlicherweise
> erhalten haben, bitten wir Sie, uns umgehend per E-Mail zu informieren,
> sämtliche Ausdrucke zu vernichten und die E-Mail-Dateien zu löschen.
>
> This message is intended for the exclusive use of the individual(s) or
> entity to whom it is addressed. It may contain information that is
> privileged and/or confidential. Should you have received this message
> erroneously, please notify us immediately by e-mail, destroy any printouts
> and delete all electronic files contained in this message.
>
> -----------------------------------------------------------------------------------------------
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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