[ome-users] bfconvert command
Josh Moore
josh at glencoesoftware.com
Fri Aug 24 16:13:35 BST 2018
On Fri, Aug 24, 2018 at 5:09 PM, Narapareddy, Mohanapriya
<mohanapriya.narapareddy at emory.edu> wrote:
> Hello Josh,
Hi Mohanapriya,
> This is my dockerfile
...
> Later I tried setting environment variable export BF_MAX_MEM=4g, but
> still i am getting the following error.
Thanks for all the previous detail, but you haven't showed us how you
set BF_MAX_MEM? Also, back to Douglas' question, how much memory is
available on this machine? Also, did you try upgrading to a newer
version of Bio-Formats?
Cheers,
~Josh
> 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
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