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<p style="margin-top:0;margin-bottom:0">Hello Josh,</p>
<p style="margin-top:0;margin-bottom:0">This is my dockerfile</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0"></p>
<p style="margin: 0px; font: 12px "Helvetica Neue"; color: rgb(69, 69, 69);">FROM alpine:3.5</p>
<p style="margin: 0px; font: 12px "Helvetica Neue"; color: rgb(69, 69, 69); min-height: 14px;">
<span class="Apple-converted-space"> </span></p>
<p style="margin: 0px; font: 12px "Helvetica Neue"; color: rgb(69, 69, 69);">RUN apk add openjdk8 \</p>
<p style="margin: 0px; font: 12px "Helvetica Neue"; color: rgb(69, 69, 69);"><span class="Apple-converted-space">
</span>&& mkdir /opt \</p>
<p style="margin: 0px; font: 12px "Helvetica Neue"; color: rgb(69, 69, 69);"><span class="Apple-converted-space">
</span>&& wget http://downloads.openmicroscopy.org/latest/bio-formats5.6/artifacts/bftools.zip \</p>
<p style="margin: 0px; font: 12px "Helvetica Neue"; color: rgb(69, 69, 69);"><span class="Apple-converted-space">
</span>&& unzip bftools.zip -x '*.bat' -d /opt/ \</p>
<p style="margin: 0px; font: 12px "Helvetica Neue"; color: rgb(69, 69, 69);"><span class="Apple-converted-space">
</span>&& rm /var/cache/apk/*</p>
<p style="margin: 0px; font: 12px "Helvetica Neue"; color: rgb(69, 69, 69); min-height: 14px;">
<br>
</p>
<p style="margin: 0px; font: 12px "Helvetica Neue"; color: rgb(69, 69, 69);">ENV PATH $PATH:/opt/bftools/</p>
<p style="margin: 0px; font: 12px "Helvetica Neue"; color: rgb(69, 69, 69); min-height: 14px;">
<br>
</p>
<p style="margin: 0px; font: 12px "Helvetica Neue"; color: rgb(69, 69, 69);">WORKDIR /tmp</p>
<br>
<p></p>
<p style="margin-top:0;margin-bottom:0">The below is my command</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0"></p>
<p style="margin: 0px; font: 12px "Helvetica Neue"; color: rgb(69, 69, 69);"><span style="font-size: 12pt;">b</span><span style="font-size: 12pt;">fconvert -bigtiff -compression LZW OS-1.vsi sample1-%s.tif</span></p>
<p style="margin: 0px; font: 12px "Helvetica Neue"; color: rgb(69, 69, 69);"><br>
</p>
<p style="margin: 0px; font: 12px "Helvetica Neue"; color: rgb(69, 69, 69);"><span style="font-size: 12pt;">Intially when i tried to execute i got the below output:</span></p>
<p style="margin: 0px; font: 12px "Helvetica Neue"; color: rgb(69, 69, 69);"><br>
</p>
<p style="margin: 0px; font: 12px "Helvetica Neue"; color: rgb(69, 69, 69);"></p>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 16px; margin: 0px;">
<font color="black"><span style="font-size: 9pt;">CellSensReader initializing OS-1.vsi</span></font></div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 16px; margin: 0px;">
<font color="black"><span style="font-size: 9pt;">[CellSens VSI] -> sample-%s.tif [Tagged Image File Format]</span></font></div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 16px; margin: 0px;">
<font color="black"><span style="font-size: 9pt;">Tile size = 512 x 512</span></font></div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 16px; margin: 0px;">
<font color="black"><span style="font-size: 9pt;">Series 0: converted 1/1 planes (100%)</span></font></div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 16px; margin: 0px;">
<font color="black"><span style="font-size: 9pt;">Tile size = 512 x 512</span></font></div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 16px; margin: 0px;">
<font color="black"><span style="font-size: 9pt;">Exception in thread "main" java.lang.OutOfMemoryError: Java heap space</span></font></div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 16px; margin: 0px;">
<font color="black"><span style="font-size: 9pt;">at java.util.Arrays.copyOf(Arrays.java:3236)</span></font></div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 16px; margin: 0px;">
<font color="black"><span style="font-size: 9pt;">at java.io.ByteArrayOutputStream.toByteArray(ByteArrayOutputStream.java:191)</span></font></div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 16px; margin: 0px;">
<font color="black"><span style="font-size: 9pt;">at loci.formats.tiff.TiffSaver.writeImage(TiffSaver.java:384)</span></font></div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 16px; margin: 0px;">
<font color="black"><span style="font-size: 9pt;">at loci.formats.tiff.TiffSaver.writeImage(TiffSaver.java:277)</span></font></div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 16px; margin: 0px;">
<font color="black"><span style="font-size: 9pt;">at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:270)</span></font></div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 16px; margin: 0px;">
<font color="black"><span style="font-size: 9pt;">at loci.formats.tools.ImageConverter.convertTilePlane(ImageConverter.java:748)</span></font></div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 16px; margin: 0px;">
<font color="black"><span style="font-size: 9pt;">at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:634)</span></font></div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 16px; margin: 0px;">
<font color="black"><span style="font-size: 9pt;">at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:563)</span></font></div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 16px; margin: 0px;">
<font color="black"><span style="font-size: 9pt;">at loci.formats.tools.ImageConverter.main(ImageConverter.java:884)</span></font></div>
<div><font color="black"><br>
</font></div>
<p></p>
<p style="margin: 0px; font: 12px "Helvetica Neue"; color: rgb(69, 69, 69);"><span style="font-size: 12pt;"> Later I
</span><span style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;"> tried setting </span><font face="Calibri" color="#37474F" style="font-size: 16px;"><span style="font-size: 12pt;">environment variable
<font face="arial,sans-serif" size="2" color="#545454">export </font><font face="arial,sans-serif" size="2" color="#6A6A6A"><b>BF_MAX_MEM</b></font><font face="arial,sans-serif" size="2" color="#545454">=4g, </font>but still i am getting the following error.</span></font><span style="font-family: Calibri, Helvetica, sans-serif; font-size: 16px;"></span></p>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 16px;"><font face="Calibri" color="#37474F"><br>
</font></div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 16px;">
<div style="margin: 0px;"><font face="Calibri" color="black">CellSensReader initializing OS-1.vsi</font></div>
<div style="margin: 0px;"><font face="Calibri" color="black">[CellSens VSI] -> sample1-%s.tif [Tagged Image File Format]</font></div>
<div style="margin: 0px;"><font face="Calibri" color="black">Tile size = 512 x 512</font></div>
<div style="margin: 0px;"><font face="Calibri" color="black">Series 0: converted 1/1 planes (100%)</font></div>
<div style="margin: 0px;"><font face="Calibri" color="black">Tile size = 512 x 512</font></div>
<div style="margin: 0px;"><font face="Calibri" color="black">/opt/bftools/bf.sh: line 77: 33 Killed java $BF_FLAGS -cp "$BF_DIR:$BF_CP" $BF_PROG "$@"</font></div>
<font face="Calibri" color="#37474F"><br>
</font></div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 16px;"><font face="Calibri" color="#37474F">Please solve this issue. </font></div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 16px;"><font face="Calibri" color="#37474F">Thanks, Mohanapriya</font></div>
<p></p>
<br>
<p></p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<div id="Signature">
<p>mohanapriya</p>
</div>
</div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> ome-users <ome-users-bounces@lists.openmicroscopy.org.uk> on behalf of Josh Moore <josh@glencoesoftware.com><br>
<b>Sent:</b> Friday, August 24, 2018 10:45:57 AM<br>
<b>To:</b> OME Users<br>
<b>Subject:</b> Re: [ome-users] bfconvert command</font>
<div> </div>
</div>
<div class="BodyFragment"><font size="2"><span style="font-size:11pt;">
<div class="PlainText">Mohanapriya,<br>
<br>
you will have to show us more exactly what you are trying including<br>
all the steps, so that we can help you. Additionally, we suggest<br>
upgrading to a newer version of Bio-Formats. The most recent is 5.9.1.<br>
The documentation for the bftools are available at:<br>
<a href="https://docs.openmicroscopy.org/bio-formats/5.9.1/users/comlinetools/index.html#command-line-environment">https://docs.openmicroscopy.org/bio-formats/5.9.1/users/comlinetools/index.html#command-line-environment</a><br>
<br>
~Josh<br>
<br>
<br>
<br>
On Fri, Aug 24, 2018 at 4:28 PM Narapareddy, Mohanapriya<br>
<mohanapriya.narapareddy@emory.edu> wrote:<br>
><br>
> i tried setting environment variable but still i am getting the following error.<br>
><br>
> CellSensReader initializing OS-1.vsi<br>
><br>
> [CellSens VSI] -> sample1-%s.tif [Tagged Image File Format]<br>
><br>
> Tile size = 512 x 512<br>
><br>
> Series 0: converted 1/1 planes (100%)<br>
><br>
> Tile size = 512 x 512<br>
><br>
> /opt/bftools/bf.sh: line 77: 33 Killed java $BF_FLAGS -cp "$BF_DIR:$BF_CP" $BF_PROG "$@"<br>
><br>
><br>
> Please solve this issue.<br>
> Thanks, Mohanapriya<br>
> ________________________________<br>
> From: ome-users <ome-users-bounces@lists.openmicroscopy.org.uk> on behalf of David Gault (Staff) <d.gault@dundee.ac.uk><br>
> Sent: Friday, August 24, 2018 9:51:20 AM<br>
> To: OME User Support List<br>
> Subject: Re: [ome-users] bfconvert command<br>
><br>
> Hi Mohanapriya,<br>
><br>
> You can configure the maximum heap size for bfconvert by setting the BF_MAX_MEM environment variable, the default value is 512m.<br>
> This can be done by setting the value before the call to bfconver, for example as below:<br>
><br>
> export BF_MAX_MEM=4g<br>
><br>
> With Thanks,<br>
> David Gault<br>
><br>
> On 24 Aug 2018, at 14:34, Narapareddy, Mohanapriya <mohanapriya.narapareddy@emory.edu> wrote:<br>
><br>
> Thanks for your reply.<br>
> Can you please tell me how can i configure how much bfconvert can use?<br>
><br>
> Thanks<br>
><br>
> mohanapriya<br>
> ________________________________<br>
> From: ome-users <ome-users-bounces@lists.openmicroscopy.org.uk> on behalf of Douglas Russell <douglas_russell@hms.harvard.edu><br>
> Sent: Thursday, August 23, 2018 2:23:30 PM<br>
> To: OME User Support List<br>
> Subject: Re: [ome-users] Fw: bfconvert command<br>
><br>
> 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:
<a href="https://docs.openmicroscopy.org/bio-formats/5.9.1/users/comlinetools/index.html#command-line-environment">
https://docs.openmicroscopy.org/bio-formats/5.9.1/users/comlinetools/index.html#command-line-environment</a><br>
><br>
> Cheers,<br>
><br>
> Douglas<br>
><br>
> On Thu, 23 Aug 2018 at 13:32 Narapareddy, Mohanapriya <mohanapriya.narapareddy@emory.edu> wrote:<br>
><br>
> Hello when i am trying to run the bftools dockerfile on a alpine base image i am getting the below error.<br>
><br>
> CellSensReader initializing OS-1.vsi<br>
> [CellSens VSI] -> sample-%s.tif [Tagged Image File Format]<br>
> Tile size = 512 x 512<br>
> Series 0: converted 1/1 planes (100%)<br>
> Tile size = 512 x 512<br>
> Exception in thread "main" java.lang.OutOfMemoryError: Java heap space<br>
> at java.util.Arrays.copyOf(Arrays.java:3236)<br>
> at java.io.ByteArrayOutputStream.toByteArray(ByteArrayOutputStream.java:191)<br>
> at loci.formats.tiff.TiffSaver.writeImage(TiffSaver.java:384)<br>
> at loci.formats.tiff.TiffSaver.writeImage(TiffSaver.java:277)<br>
> at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:270)<br>
> at loci.formats.tools.ImageConverter.convertTilePlane(ImageConverter.java:748)<br>
> at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:634)<br>
> at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:563)<br>
> at loci.formats.tools.ImageConverter.main(ImageConverter.java:884)<br>
><br>
> Below is my docker file.<br>
><br>
> FROM alpine:3.5<br>
><br>
><br>
><br>
> RUN apk -Uuv add bash openjdk8-jre \<br>
> && mkdir /opt \<br>
> && wget <a href="http://downloads.openmicroscopy.org/latest/bio-formats5.6/artifacts/bftools.zip">
http://downloads.openmicroscopy.org/latest/bio-formats5.6/artifacts/bftools.zip</a> \<br>
> && unzip bftools.zip -x '*.bat' -d /opt/ \<br>
> && rm /var/cache/apk/*<br>
><br>
> ENV PATH $PATH:/opt/bftools/<br>
><br>
> WORKDIR /tmp<br>
> ~<br>
><br>
> Please resolve this issue. Look forward to hear from you.<br>
><br>
><br>
><br>
> Thanks,<br>
> Mohanapriya<br>
> ________________________________<br>
> From: ome-users <ome-users-bounces@lists.openmicroscopy.org.uk> on behalf of Manuel Stritt <manuel.stritt@idorsia.com><br>
> Sent: Thursday, August 16, 2018 10:17:29 AM<br>
><br>
> To: OME User Support List<br>
> Subject: Re: [ome-users] Fw: bfconvert command<br>
> Dear Mohanapriya,<br>
><br>
> an VSI file contains one or several scenes. Each scene /series is stored in a ets file.<br>
> For that reason you should have a subdirectory at the location of your VSI file which is<br>
> names like the VSI file (with a "_" at the start and end). Probably you moved/copied the<br>
> VSI file but not the corresponding ets subdirectory.<br>
><br>
> Regards,<br>
> Manuel<br>
><br>
><br>
> Hello Josh,<br>
><br>
> i have done the change to "%s" and executed again but i still getting the same result.<br>
><br>
> bf@fc435e6036f7:~/data$ bfconvert -bigtiff -compression LZW OS-1.vsi sample1-%s.tif<br>
> OS-1.vsi<br>
> CellSensReader initializing OS-1.vsi<br>
> Missing expected .ets files in /home/bf/data/_OS-1_<br>
> [CellSens VSI] -> sample1-%s.tif [Tagged Image File Format]<br>
> Converted 1/1 planes (100%)<br>
> [done]<br>
> 5.339s elapsed (35.0+4022.0ms per plane, 1267ms overhead)<br>
><br>
><br>
> can u please let me know<br>
> "Missing expected .ets files in /home/bf/data/_OS-1_" what does this mean<br>
><br>
> Look forward to hear from you.<br>
><br>
> Thanks,<br>
> Mohanapriya<br>
> ________________________________<br>
> From: ome-users <ome-users-bounces@lists.openmicroscopy.org.uk> on behalf of Josh Moore <josh@glencoesoftware.com><br>
> Sent: Thursday, August 16, 2018 4:04:22 AM<br>
> To: OME User Support List<br>
> Cc: Narapareddy, Mohanapriya<br>
> Subject: Re: [ome-users] Fw: bfconvert command<br>
><br>
> Hi Mohan,<br>
><br>
> Thanks for the details. It looks like there is a typo in the command<br>
> line you are using in docker:<br>
><br>
> bfconvert -bigtiff -compression LZW OS-1.vsi sample1-s%.tif<br>
><br>
> Here "s%" should be "%s".<br>
><br>
> All the best,<br>
> ~Josh<br>
><br>
><br>
> ---------- Forwarded message ----------<br>
> From: Narapareddy, Mohanapriya <mohanapriya.narapareddy@emory.edu><br>
> Date: Wed, Aug 15, 2018 at 8:12 PM<br>
> Subject: Re: ome-users mailing list email<br>
> To: Josh Moore <j.a.moore@dundee.ac.uk><br>
><br>
><br>
> Hello Josh Moore,<br>
><br>
> Thanks for your reply.<br>
><br>
> i have used java version 7 and bio formats version 5.8.2 .<br>
> docker run -it -v ~/Desktop/dir:/home/bf/data test<br>
> ]This is my docker run<br>
> command. and inside the container i am executing the following<br>
> command.<br>
> bfconvert<br>
> -bigtiff -compression LZW OS-1.vsi sample1-s%.tif<br>
> FROM java:7 MAINTAINER ome-devel@lists.openmicroscopy.org.uk RUN<br>
> apt-get install -y curl RUN curl -o bftools.zip $(curl -Ls -o<br>
> /dev/null -w %{url_effective}<br>
> <a href="http://downloads.openmicroscopy.org/latest/bio-formats)/artifacts/bftools.zip">
http://downloads.openmicroscopy.org/latest/bio-formats)/artifacts/bftools.zip</a><br>
> RUN apt-get install -y unzip RUN unzip -d /opt bftools.zip && rm<br>
> bftools.zip RUN chmod a+rx /opt/bftools/* RUN useradd -m bf USER bf<br>
> RUN echo 'export PATH=/opt/bftools:$PATH' >> /home/bf/.bashrc ENV HOME<br>
> /home/bf WORKDIR /home/bf CMD bash<br>
><br>
><br>
><br>
> The above is my docker file.<br>
><br>
><br>
> 4. I dont see any error messages but i am getting the following out put.<br>
><br>
><br>
> bf@935e7d25059c:~/data$ bfconvert -bigtiff -compression LZW OS-1.vsi<br>
> sample1-s%.tif<br>
><br>
> OS-1.vsi<br>
><br>
> CellSensReader initializing OS-1.vsi<br>
><br>
> Missing expected .ets files in /home/bf/data/_OS-1_<br>
><br>
> [CellSens VSI] -> sample1-s%.tif [Tagged Image File Format]<br>
><br>
> Converted 1/1 planes (100%)<br>
><br>
> [done]<br>
><br>
> 6.95s elapsed (69.0+5815.0ms per plane, 1053ms overhead)<br>
><br>
><br>
><br>
><br>
> look forward to hear from you.<br>
><br>
> Thanks,<br>
><br>
> Mohanapriya<br>
><br>
> On Tue, Aug 14, 2018 at 10:59 PM, Narapareddy, Mohanapriya<br>
> <mohanapriya.narapareddy@emory.edu> wrote:<br>
> ><br>
> ><br>
> > mohanapriya<br>
> ><br>
> ><br>
> ><br>
> > ________________________________<br>
> > From: Narapareddy, Mohanapriya<br>
> > Sent: Tuesday, August 14, 2018 4:39 PM<br>
> > To: ome-users-bounces@lists.openmicroscopy.org.uk<br>
> > Subject: bfconvert command<br>
> ><br>
> ><br>
> > I am trying to execute this command<br>
> > bfconvert -bigtiff -compression LZW <input file.vsi> <outfile>-%s.tif<br>
> ><br>
> > its working fine in centOs , i am getting multiple image planes,<br>
> > but when i am trying to execute in docker container i am getting only a<br>
> > single image plane. Please resolve this issue.<br>
> ><br>
> ><br>
> > Thanks,<br>
> ><br>
> > Mohanapriya<br>
_______________________________________________<br>
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