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Hi Fethallah,
<div><br>
</div>
<div>the logging level is set by the following line in bfopen.m:</div>
<div><span class="n" style="box-sizing: border-box; color: rgb(51, 51, 51); font-family: Consolas, 'Liberation Mono', Courier, monospace; font-size: 12px; line-height: 18px; white-space: pre; background-color: rgb(255, 255, 255); ">loci</span><span class="p" style="box-sizing: border-box; color: rgb(51, 51, 51); font-family: Consolas, 'Liberation Mono', Courier, monospace; font-size: 12px; line-height: 18px; white-space: pre; background-color: rgb(255, 255, 255); ">.</span><span class="n" style="box-sizing: border-box; color: rgb(51, 51, 51); font-family: Consolas, 'Liberation Mono', Courier, monospace; font-size: 12px; line-height: 18px; white-space: pre; background-color: rgb(255, 255, 255); ">common</span><span class="p" style="box-sizing: border-box; color: rgb(51, 51, 51); font-family: Consolas, 'Liberation Mono', Courier, monospace; font-size: 12px; line-height: 18px; white-space: pre; background-color: rgb(255, 255, 255); ">.</span><span class="n" style="box-sizing: border-box; color: rgb(51, 51, 51); font-family: Consolas, 'Liberation Mono', Courier, monospace; font-size: 12px; line-height: 18px; white-space: pre; background-color: rgb(255, 255, 255); ">DebugTools</span><span class="p" style="box-sizing: border-box; color: rgb(51, 51, 51); font-family: Consolas, 'Liberation Mono', Courier, monospace; font-size: 12px; line-height: 18px; white-space: pre; background-color: rgb(255, 255, 255); ">.</span><span class="n" style="box-sizing: border-box; color: rgb(51, 51, 51); font-family: Consolas, 'Liberation Mono', Courier, monospace; font-size: 12px; line-height: 18px; white-space: pre; background-color: rgb(255, 255, 255); ">enableLogging</span><span class="p" style="box-sizing: border-box; color: rgb(51, 51, 51); font-family: Consolas, 'Liberation Mono', Courier, monospace; font-size: 12px; line-height: 18px; white-space: pre; background-color: rgb(255, 255, 255); ">(</span><span class="s" style="box-sizing: border-box; color: rgb(221, 17, 68); font-family: Consolas, 'Liberation Mono', Courier, monospace; font-size: 12px; line-height: 18px; white-space: pre; background-color: rgb(255, 255, 255); ">'INFO'</span><span class="p" style="box-sizing: border-box; color: rgb(51, 51, 51); font-family: Consolas, 'Liberation Mono', Courier, monospace; font-size: 12px; line-height: 18px; white-space: pre; background-color: rgb(255, 255, 255); ">);</span></div>
<div><br>
</div>
<div>To decrease the amount of verbosity while opening your image, you </div>
<div>could either increase the logging level, e.g.</div>
<div>
<div><span class="n" style="box-sizing: border-box; color: rgb(51, 51, 51); font-family: Consolas, 'Liberation Mono', Courier, monospace; font-size: 12px; line-height: 18px; white-space: pre; background-color: rgb(255, 255, 255); ">loci</span><span class="p" style="box-sizing: border-box; color: rgb(51, 51, 51); font-family: Consolas, 'Liberation Mono', Courier, monospace; font-size: 12px; line-height: 18px; white-space: pre; background-color: rgb(255, 255, 255); ">.</span><span class="n" style="box-sizing: border-box; color: rgb(51, 51, 51); font-family: Consolas, 'Liberation Mono', Courier, monospace; font-size: 12px; line-height: 18px; white-space: pre; background-color: rgb(255, 255, 255); ">common</span><span class="p" style="box-sizing: border-box; color: rgb(51, 51, 51); font-family: Consolas, 'Liberation Mono', Courier, monospace; font-size: 12px; line-height: 18px; white-space: pre; background-color: rgb(255, 255, 255); ">.</span><span class="n" style="box-sizing: border-box; color: rgb(51, 51, 51); font-family: Consolas, 'Liberation Mono', Courier, monospace; font-size: 12px; line-height: 18px; white-space: pre; background-color: rgb(255, 255, 255); ">DebugTools</span><span class="p" style="box-sizing: border-box; color: rgb(51, 51, 51); font-family: Consolas, 'Liberation Mono', Courier, monospace; font-size: 12px; line-height: 18px; white-space: pre; background-color: rgb(255, 255, 255); ">.</span><span class="n" style="box-sizing: border-box; color: rgb(51, 51, 51); font-family: Consolas, 'Liberation Mono', Courier, monospace; font-size: 12px; line-height: 18px; white-space: pre; background-color: rgb(255, 255, 255); ">enableLogging</span><span class="p" style="box-sizing: border-box; color: rgb(51, 51, 51); font-family: Consolas, 'Liberation Mono', Courier, monospace; font-size: 12px; line-height: 18px; white-space: pre; background-color: rgb(255, 255, 255); ">(</span><span class="s" style="box-sizing: border-box; color: rgb(221, 17, 68); font-family: Consolas, 'Liberation Mono', Courier, monospace; font-size: 12px; line-height: 18px; white-space: pre; background-color: rgb(255, 255, 255); ">'ERROR'</span><span class="p" style="box-sizing: border-box; color: rgb(51, 51, 51); font-family: Consolas, 'Liberation Mono', Courier, monospace; font-size: 12px; line-height: 18px; white-space: pre; background-color: rgb(255, 255, 255); ">);</span></div>
</div>
<div>or if you want no logging at all, you could comment out this line.</div>
<div><br>
</div>
<div>Hope this helps,</div>
<div>Sebastien</div>
<div><br>
<div>
<div>On 14 Jan 2014, at 15:22, Fethallah Benmansour <<a href="mailto:fethallah.benmansour@gmail.com">fethallah.benmansour@gmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div dir="ltr">Hi Sebastien,
<div><br>
</div>
<div>Indeed setGroupFiles(false), solved the problem, and I have modified my m files accordingly to make it accessible as a parameter at the openbf level. So, thanks for offering.</div>
<div>Do you know if there's an option such as verbose(0) ?Now, that I know that the images are loaded properly, I don't want to see all the details each time an image is loaded.</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>--</div>
<div>Fethallah</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br clear="all">
<div>
<div>--</div>
Fethallah Benmansour</div>
<br>
<br>
<div class="gmail_quote">On Tue, Jan 14, 2014 at 3:49 PM, Sebastien Besson <span dir="ltr">
<<a href="mailto:s.besson@dundee.ac.uk" target="_blank">s.besson@dundee.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">Hi Fetallah,
<div><br>
</div>
<div>in general, the API documentation for Bio-Formats should be browsable via the Javadocs</div>
<div>which are located at:</div>
<div><a href="http://ci.openmicroscopy.org/job/BIOFORMATS-stable/javadoc/" target="_blank">http://ci.openmicroscopy.org/job/BIOFORMATS-stable/javadoc/</a> for Bio-Formats 4.4.x</div>
<div>or </div>
<div><a href="http://ci.openmicroscopy.org/job/BIOFORMATS-5.0/javadoc/" target="_blank">http://ci.openmicroscopy.org/job/BIOFORMATS-5.0/javadoc/</a> for Bio-Formats 5.0.x</div>
<div><br>
</div>
<div>As Christophe already answered, setting setGroupFile(false) before calling setId(id) should disable</div>
<div>the file grouping. Do you think exposing this groupFile option directly in the top level bfopen would</div>
<div>be valuable for you?</div>
<div><br>
</div>
<div>Cheers,</div>
<div>Sebastien</div>
<div><br>
<div>
<div>
<div>
<div class="h5">
<div>On 14 Jan 2014, at 14:20, Fethallah Benmansour <<a href="mailto:fethallah.benmansour@gmail.com" target="_blank">fethallah.benmansour@gmail.com</a>> wrote:</div>
<br>
</div>
</div>
<blockquote type="cite">
<div>
<div class="h5">
<div dir="ltr">
<div>Thanks Christophe, you made my day :-)</div>
<div><br>
</div>
<div>I suspected something as simple as that. Where can I find the complete documentation for bf objects ?<br>
</div>
<div><br>
</div>
<div>Thanks into advance,</div>
<div><br>
</div>
<div>--</div>
<div>Fethallah</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Tue, Jan 14, 2014 at 3:12 PM, Christophe TREFOIS <span dir="ltr">
<<a href="mailto:christophe.trefois@uni.lu" target="_blank">christophe.trefois@uni.lu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div lang="FR-BE" link="#0563C1" vlink="#954F72">
<div>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Did you try setting setGroupFile(false) on the bf object?<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Best,<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">--<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Christophe<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">
<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" target="_blank">ome-users-bounces@lists.openmicroscopy.org.uk</a> [mailto:<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" target="_blank">ome-users-bounces@lists.openmicroscopy.org.uk</a>]
<b>On Behalf Of </b>Fethallah Benmansour<br>
<b>Sent:</b> mardi 14 janvier 2014 09:52<br>
<b>To:</b> <a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">
ome-users@lists.openmicroscopy.org.uk</a><br>
<b>Subject:</b> [ome-users] Opera scanner Flex files: bfopen very slow<u></u><u></u></span></p>
<div>
<div>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<div>
<div>
<p class="MsoNormal">Dear All,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">I have tried to load one flex file using the matlab function bfopen.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">If the flex file is isolated in one directory, then the function reads it immediately.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">However, if the file belongs to the plate directory with many flex files near it, then the loading take about 1.5 hours (not to say forever).<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">In fact, it does the following steps:<u></u><u></u></p>
</div>
<div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">#<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Storing well indices<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">#<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Looking for other .flex files<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">#<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Looking for files that are in the same dataset as Y:\SomeLocation\Meas_01(2014-01-09_17-02-50)\003003004.flex<u></u><u></u></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">#<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Measurement files not found.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">#<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Making sure that all .flex files are valid<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">#<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Grouping together files in the same dataset<u></u><u></u></p>
</div>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">...etc<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">The plate is huge indeed (about 20 Gigs of data).<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Is there a way to force it to read only one specific file, without extracting the metadata from the whole plate ?<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Thanks into advance,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<div>
<div>
<p class="MsoNormal">--<u></u><u></u></p>
</div>
<p class="MsoNormal">Fethallah<u></u><u></u></p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</div>
</div>
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</blockquote>
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<br>
</div>
</div>
<br>
<br>
<div><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;text-align:-webkit-auto;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;font-size:medium;white-space:normal;font-family:Helvetica;word-spacing:0px">
<div style="word-wrap:break-word"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;text-align:-webkit-auto;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;font-size:medium;white-space:normal;font-family:Helvetica;word-spacing:0px">
<div style="word-wrap:break-word">
<div>Dr Sébastien Besson</div>
<div>Open Microscopy Environment / Harvard Medical School</div>
<div>Wellcome Trust Centre for Gene Regulation and Expression,</div>
<div>College of Life Sciences, University of Dundee, Dow Street,</div>
<div>Dundee DD1 5EH Scotland UK Tel: (01382) 386364</div>
</div>
</span></div>
</span></div>
<br>
<br>
<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
</div>
</blockquote>
</div>
<br>
</div>
</blockquote>
</div>
<br>
<div><span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; ">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; ">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
<div>Dr Sébastien Besson</div>
<div>Open Microscopy Environment / Harvard Medical School</div>
<div>Wellcome Trust Centre for Gene Regulation and Expression,</div>
<div>College of Life Sciences, University of Dundee, Dow Street,</div>
<div>Dundee DD1 5EH Scotland UK Tel: (01382) 386364</div>
</div>
</span></div>
</span></span></div>
<br>
</div>
<br>
<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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