[ome-users] Fw: bfconvert command

Douglas Russell douglas_russell at hms.harvard.edu
Thu Aug 23 19:23:30 BST 2018 

It's a Java heap space error. How much memory is available to Docker? You
also might need to configure how much bfconvert can use:
https://docs.openmicroscopy.org/bio-formats/5.9.1/users/comlinetools/index.html#command-line-environment

Cheers,

Douglas

On Thu, 23 Aug 2018 at 13:32 Narapareddy, Mohanapriya <
mohanapriya.narapareddy at emory.edu> wrote:

> Hello when i am trying to run the bftools dockerfile on a alpine base
> image i am getting the below error.
>
> CellSensReader initializing OS-1.vsi
>
> [CellSens VSI] -> sample-%s.tif [Tagged Image File Format]
>
> Tile size = 512 x 512
>
> Series 0: converted 1/1 planes (100%)
>
> Tile size = 512 x 512
>
> Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
>
> at java.util.Arrays.copyOf(Arrays.java:3236)
>
> at
> java.io.ByteArrayOutputStream.toByteArray(ByteArrayOutputStream.java:191)
>
> at loci.formats.tiff.TiffSaver.writeImage(TiffSaver.java:384)
>
> at loci.formats.tiff.TiffSaver.writeImage(TiffSaver.java:277)
>
> at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:270)
>
> at
> loci.formats.tools.ImageConverter.convertTilePlane(ImageConverter.java:748)
>
> at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:634)
>
> at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:563)
>
> at loci.formats.tools.ImageConverter.main(ImageConverter.java:884)
>
> Below is my docker file.
>
>
> FROM alpine:3.5
>
>
>
> RUN apk -Uuv add bash openjdk8-jre \
>
>         && mkdir /opt \
>
>         && wget
> http://downloads.openmicroscopy.org/latest/bio-formats5.6/artifacts/bftools.zip
> \
>
>         && unzip bftools.zip -x '*.bat' -d /opt/ \
>
>         && rm /var/cache/apk/*
>
>
> ENV PATH $PATH:/opt/bftools/
>
>
> WORKDIR /tmp
>
> ~
>
> Please resolve this issue. Look forward to hear from you.
>
>
>
> Thanks,
>
> Mohanapriya
> ------------------------------
> *From:* ome-users <ome-users-bounces at lists.openmicroscopy.org.uk> on
> behalf of Manuel Stritt <manuel.stritt at idorsia.com>
> *Sent:* Thursday, August 16, 2018 10:17:29 AM
>
> *To:* OME User Support List
> *Subject:* Re: [ome-users] Fw: bfconvert command
> Dear Mohanapriya,
>
> an VSI file contains one or several scenes. Each scene /series is stored
> in a ets file.
> For that reason you should have a subdirectory at the location of your VSI
> file which is
> names like the VSI file (with a "_" at the start and end). Probably you
> moved/copied the
> VSI file but not the corresponding ets subdirectory.
>
> Regards,
> Manuel
>
>
> Hello Josh,
>
>
> i have done the change to "%s" and executed again but i still getting the
> same result.
>
> bf at fc435e6036f7:~/data$ bfconvert -bigtiff -compression LZW OS-1.vsi
> sample1-%s.tif
>
> OS-1.vsi
>
> CellSensReader initializing OS-1.vsi
>
> Missing expected .ets files in /home/bf/data/_OS-1_
>
> [CellSens VSI] -> sample1-%s.tif [Tagged Image File Format]
>
> Converted 1/1 planes (100%)
>
> [done]
>
> 5.339s elapsed (35.0+4022.0ms per plane, 1267ms overhead)
>
>
>
> can u please let me know
>
> "Missing expected .ets files in /home/bf/data/_OS-1_" what does this mean
>
> Look forward to hear from you.
>
>
> Thanks,
>
> Mohanapriya
> ------------------------------
> *From:* ome-users <ome-users-bounces at lists.openmicroscopy.org.uk> on
> behalf of Josh Moore <josh at glencoesoftware.com>
> *Sent:* Thursday, August 16, 2018 4:04:22 AM
> *To:* OME User Support List
> *Cc:* Narapareddy, Mohanapriya
> *Subject:* Re: [ome-users] Fw: bfconvert command
>
> Hi Mohan,
>
> Thanks for the details. It looks like there is a typo in the command
> line you are using in docker:
>
> bfconvert -bigtiff -compression LZW OS-1.vsi sample1-s%.tif
>
> Here "s%" should be "%s".
>
> All the best,
> ~Josh
>
>
> ---------- Forwarded message ----------
> From: Narapareddy, Mohanapriya <mohanapriya.narapareddy at emory.edu>
> Date: Wed, Aug 15, 2018 at 8:12 PM
> Subject: Re: ome-users mailing list email
> To: Josh Moore <j.a.moore at dundee.ac.uk>
>
>
> Hello Josh Moore,
>
> Thanks for your reply.
>
> i have used java version 7 and bio formats version 5.8.2 .
> docker run -it -v ~/Desktop/dir:/home/bf/data test
>                                             ]This is my docker run
> command. and inside the container i am executing the following
> command.
>                                                              bfconvert
> -bigtiff -compression LZW OS-1.vsi sample1-s%.tif
> FROM java:7 MAINTAINER ome-devel at lists.openmicroscopy.org.uk RUN
> apt-get install -y curl RUN curl -o bftools.zip $(curl -Ls -o
> /dev/null -w %{url_effective}
>
> http://downloads.openmicroscopy.org/latest/bio-formats)/artifacts/bftools.zip
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__downloads.openmicroscopy.org_latest_bio-2Dformats-29_artifacts_bftools.zip&d=DwMFAg&c=WO-RGvefibhHBZq3fL85hQ&r=hG980ESxUhpWXeq9BOrnOv3CUpq5lW8uGu7OdRUzoVI&m=voky8_dW4UwOtkK0WpmWnZzp7BaSnvyFxatV-lr3kbQ&s=4ETZLRNOcMDE7VxI5PFQsud3HfmoF9cG0Bnp2yPu36w&e=>
> RUN apt-get install -y unzip RUN unzip -d /opt bftools.zip && rm
> bftools.zip RUN chmod a+rx /opt/bftools/* RUN useradd -m bf USER bf
> RUN echo 'export PATH=/opt/bftools:$PATH' >> /home/bf/.bashrc ENV HOME
> /home/bf WORKDIR /home/bf CMD bash
>
>
>
> The above is my docker file.
>
>
> 4. I dont see any error messages but i am getting the following out put.
>
>
> bf at 935e7d25059c:~/data$ bfconvert -bigtiff -compression LZW OS-1.vsi
> sample1-s%.tif
>
> OS-1.vsi
>
> CellSensReader initializing OS-1.vsi
>
> Missing expected .ets files in /home/bf/data/_OS-1_
>
> [CellSens VSI] -> sample1-s%.tif [Tagged Image File Format]
>
> Converted 1/1 planes (100%)
>
> [done]
>
> 6.95s elapsed (69.0+5815.0ms per plane, 1053ms overhead)
>
>
>
>
> look forward to hear from you.
>
> Thanks,
>
> Mohanapriya
>
> On Tue, Aug 14, 2018 at 10:59 PM, Narapareddy, Mohanapriya
> <mohanapriya.narapareddy at emory.edu> wrote:
> >
> >
> > mohanapriya
> >
> >
> >
> > ________________________________
> > From: Narapareddy, Mohanapriya
> > Sent: Tuesday, August 14, 2018 4:39 PM
> > To: ome-users-bounces at lists.openmicroscopy.org.uk
> > Subject: bfconvert command
> >
> >
> >  I am trying to execute this command
> >  bfconvert -bigtiff -compression LZW <input file.vsi> <outfile>-%s.tif
> >
> > its working fine in centOs , i am getting multiple image planes,
> >  but when i am trying to execute in docker container i am getting only a
> > single image plane. Please resolve this issue.
> >
> >
> > Thanks,
> >
> > Mohanapriya
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