http://imagej.273.s1.nabble.com/Fiji-Bio-Formats-is-not-opening-large-czi-tp5011842p5011878.html
> Hi Mario,
>
> > Stephan Preibisch might be right that opening the files just takes
> > forever. But why? The network mount is reasonably fast, it achieves
> > easily 100MB/s.
>
> There are multiple sorts of "fast" at work here: burst throughput,
> sustained throughput, latency, etc.
>
> If you really want to know why it is slow, then take a few stack traces
> while you are waiting for the files to be read. Just press Ctrl+\ while
> showinf is thinking. Cut and paste them from your console, saving them to
> files. Look for the string "loci.formats." and find out which Bio-Formats
> classes/method/lines are being hit. That will be 90% likely to answer your
> "why" question in this instance.
>
> Regards,
> Curtis
>
> On Wed, Mar 4, 2015 at 9:26 AM, Mario Emmenlauer <
[hidden email]>
> wrote:
>
> > Hi Curtis,
> >
> > On 03.03.2015 17:11, Curtis Rueden wrote:
> > >> Fiji shows "Analyzing XXX" in the status bar, then nothing happens.
> > >> I've waited 20 minutes now, then gave up.
> > >
> > > Did you try reading it with the Bio-Formats showinf command line tool?
> > >
http://openmicroscopy.org/info/bio-formats/users/comlinetools/> >
> > I tried that now, and it seems Stephan Preibisch might be right that
> > opening the files just takes forever. But why? The network mount is
> > reasonably fast, it achieves easily 100MB/s. Zeiss Zen 2012 opens the
> > file in ~30sec, and I can scroll through the timepoints and stacks at
> > reasonable speed. I opened the czi with "Open files individually" and
> > "Use virtual stack" in Fiji, and I hoped this might speed things up.
> >
> > So in Fiji, I can select the thumbnails finally after > 2hrs. Thats
> > 25% of the time it would take to read *all* the files over the 100MB/s
> > network. I can not think Bio-Formats would not read 25% of the 4TB
> > data, just to show thumbnails?
> >
> >
> > When using showinf, it prints first:
> > Checking file format [Zeiss CZI]
> > Initializing reader
> > ZeissCZIReader initializing L:\MarioEmmenlauer\Lightsheet_RAW\drlGFP
> > lmo2Red 7ss .czi
> >
> > ... and then after around 1 hour, it fails with out-of-memory. Can
> > it really take >2 hrs before I can see anything? Should the option
> > "Open files individually" not limit it to the first timepoint?
> >
> > Cheers,
> >
> > Mario
> >
> >
> >
> > > Did you check out the "Debugging JVM hangs" section of the Debugging
> > page?
> > >
http://imagej.net/Debugging#Debugging_JVM_hangs> > >
> > > Getting a stack trace will tell you more about what is going on --
> i.e.,
> > > what Bio-Formats is doing internally, whether it has crashed, etc.
> > >
> > > Did you try with the Bio-Formats update site enabled? This enables the
> > > 5.1.x development builds, which contain additional bug-fixes.
> > >
http://fiji.sc/Bio-Formats#Daily_builds> > >
> > > If this is a bug in Bio-Formats (if showinf also does not work, etc.),
> > then
> > > please report this bug to the OME team.
> > >
http://openmicroscopy.org/info/bio-formats/about/bug-reporting.html> > >
> > > Regards,
> > > Curtis
> > >
> > > On Tue, Mar 3, 2015 at 8:45 AM, Mario Emmenlauer <
[hidden email]>
> > > wrote:
> > >
> > >> Hi,
> > >>
> > >> I have a 85 GB CZI file (one out of a series of 40 files in the
> > >> same folder) that I wanted to open with latest Fiji (updates from
> > >> today, on Win7 x64 with 42GB RAM, Sun Java 7, -Xmx 12GB. I tried:
> > >> Plugins > Bio-Formats > Bio-Formats Importer
> > >>
> > >> with options:
> > >> - View with Hyperstack
> > >> - Open files individually
> > >> - Use virtual stack
> > >> - all other options unchecked
> > >>
> > >> Fiji shows "Analyzing XXX" in the status bar, then nothing happens.
> > >> I've waited 20 minutes now, then gave up. About Bio-Formats says
> > >> "5.0.7 built 3.2.2015 revision 274796b".
> > >>
> > >> The file opens fine in Zeiss ZEN 2012 in ~30sec. I tried Fiji with
> > >> the --debug option, but the command prompt console does not show any
> > >> messages (to track down whats happening).
> > >>
> > >> Thanks for your help, and all the best,
> > >>
> > >> Mario
> > >>
> > >>
> > >>
> > >>
> > >> --
> > >> Mario Emmenlauer BioDataAnalysis Mobil:
> +49-(0)151-68108489
> > >> Balanstrasse 43 mailto: mario.emmenlauer *
> unibas.ch
> > >> D-81669 München
>
http://www.biodataanalysis.de/> > >>
> > >> --
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http://imagej.nih.gov/ij/list.html> > >>
> > >
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> > --
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> > > Q: Are you sure?
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> > >>> Q: Why is top posting annoying in email?
> >
> > Mario Emmenlauer BioDataAnalysis Mobil: +49-(0)151-68108489
> > Balanstrasse 43 mailto: mario.emmenlauer * unibas.ch
> > D-81669 München
http://www.biodataanalysis.de/> >
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