[ome-users] bfconvert command
Narapareddy, Mohanapriya
mohanapriya.narapareddy at emory.edu
Fri Aug 24 16:09:55 BST 2018
Hello Josh,
This is my dockerfile
FROM alpine:3.5
RUN apk add openjdk8 \
&& 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
The below is my command
bfconvert -bigtiff -compression LZW OS-1.vsi sample1-%s.tif
Intially when i tried to execute i got the below output:
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)
Later I tried setting environment variable export BF_MAX_MEM=4g, 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
mohanapriya
________________________________
From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk> on behalf of Josh Moore <josh at glencoesoftware.com>
Sent: Friday, August 24, 2018 10:45:57 AM
To: OME Users
Subject: Re: [ome-users] bfconvert command
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
_______________________________________________
ome-users mailing list
ome-users at lists.openmicroscopy.org.uk
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
________________________________
This e-mail message (including any attachments) is for the sole use of
the intended recipient(s) and may contain confidential and privileged
information. If the reader of this message is not the intended
recipient, you are hereby notified that any dissemination, distribution
or copying of this message (including any attachments) is strictly
prohibited.
If you have received this message in error, please contact
the sender by reply e-mail message and destroy all copies of the
original message (including attachments).
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20180824/5b203c0e/attachment.html>
More information about the ome-users
mailing list