[ome-users] bfconvert command

Fri Aug 24 15:45:57 BST 2018

Mohanapriya,

you will have to show us more exactly what you are trying including
all the steps, so that we can help you. Additionally, we suggest
upgrading to a newer version of Bio-Formats. The most recent is 5.9.1.
The documentation for the bftools are available at:
https://docs.openmicroscopy.org/bio-formats/5.9.1/users/comlinetools/index.html#command-line-environment

~Josh

On Fri, Aug 24, 2018 at 4:28 PM Narapareddy, Mohanapriya
<mohanapriya.narapareddy at emory.edu> wrote:
>
> i tried setting environment variable but still i am getting the following error.
>
> CellSensReader initializing OS-1.vsi
>
> [CellSens VSI] -> sample1-%s.tif [Tagged Image File Format]
>
> Tile size = 512 x 512
>
> Series 0: converted 1/1 planes (100%)
>
> Tile size = 512 x 512
>
> /opt/bftools/bf.sh: line 77:    33 Killed                  java $BF_FLAGS -cp "$BF_DIR:$BF_CP" $BF_PROG "$@"
>
>
> Please solve this issue.
> Thanks, Mohanapriya
> ________________________________
> From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk> on behalf of David Gault (Staff) <d.gault at dundee.ac.uk>
> Sent: Friday, August 24, 2018 9:51:20 AM
> To: OME User Support List
> Subject: Re: [ome-users] bfconvert command
>
> Hi Mohanapriya,
>
> You can configure the maximum heap size for bfconvert by setting the BF_MAX_MEM environment variable, the default value is 512m.
> This can be done by setting the value before the call to bfconver, for example as below:
>
> export BF_MAX_MEM=4g
>
> With Thanks,
> David Gault
>
> On 24 Aug 2018, at 14:34, Narapareddy, Mohanapriya <mohanapriya.narapareddy at emory.edu> wrote:
>
> Thanks for your reply.
> Can you please tell me how can i configure how much bfconvert can use?
>
> Thanks
>
> mohanapriya
> ________________________________
> From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk> on behalf of Douglas Russell <douglas_russell at hms.harvard.edu>
> Sent: Thursday, August 23, 2018 2:23:30 PM
> To: OME User Support List
> Subject: Re: [ome-users] Fw: bfconvert command
>
> 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 $(curl -Ls -o
> /dev/null -w %{url_effective}
> http://downloads.openmicroscopy.org/latest/bio-formats)/artifacts/bftools.zip
> RUN apt-get install -y unzip RUN unzip -d /opt bftools.zip && rm
> bftools.zip RUN chmod a+rx /opt/bftools/* RUN useradd -m bf USER bf
> RUN echo 'export PATH=/opt/bftools:$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