[ome-users] Fw: bfconvert command
Narapareddy, Mohanapriya
mohanapriya.narapareddy at emory.edu
Fri Aug 24 14:34:43 BST 2018
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<mailto: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 $PATH:/opt/bftools/
WORKDIR /tmp
~
Please resolve this issue. Look forward to hear from you.
Thanks,
Mohanapriya
________________________________
From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>> on behalf of Manuel Stritt <manuel.stritt at idorsia.com<mailto:manuel.stritt at idorsia.com>>
Sent: Thursday, August 16, 2018 10:17:29 AM
To: OME User Support List
Subject: Re: [ome-users] Fw: bfconvert command
Dear Mohanapriya,
an VSI file contains one or several scenes. Each scene /series is stored in a ets file.
For that reason you should have a subdirectory at the location of your VSI file which is
names like the VSI file (with a "_" at the start and end). Probably you moved/copied the
VSI file but not the corresponding ets subdirectory.
Regards,
Manuel
Hello Josh,
i have done the change to "%s" and executed again but i still getting the same result.
bf at fc435e6036f7:~/data$ 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<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>> on behalf of Josh Moore <josh at glencoesoftware.com<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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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