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Thanks for the summary Sebastien.
<div class="">I’ll try and get a PR together when I can.</div>
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<div class="">Best </div>
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<div class="">Ian<br class="">
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<div class="">On 31 Jul 2018, at 13:39, Sebastien Besson (Staff) <<a href="mailto:s.besson@dundee.ac.uk" class="">s.besson@dundee.ac.uk</a>> wrote:</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Hi Ian and Romain,</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">having briefly discussed the state of the things internally, here is a summary:</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">- there is nothing in FormatWriter that handles file existing i.e. the writer will write to the</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""> specified output stream</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">- handling file deletion prior to writing is the responsiblity of the caller of the low-level</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""> writer API</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">- the `bfconvert` command-line utility contains some logic to detect the output file</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""> existence and overwrite it either via an interactive opt-in or via the `-overwrite` option<br class="">
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">- the `bfsave.m` MATLAB utility does not contain any such logic at the moment. Until</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""> Bio-Formats 5.9.0 it is the responsibility of the bfsave caller to handle file existence.</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Implementing some overwriting logic at the MATLAB level probably controlled by a</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">key/value option would probably be a reasonable choice if this helped addressing the</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">issues you and Romain faced. In this case, feel free to suggest your changes as a</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Pull Request against the Bio-Formats source code repository.<br class="">
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Best,</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Sebastien<br class="">
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<font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>ome-devel <<a href="mailto:ome-devel-bounces@lists.openmicroscopy.org.uk" class="">ome-devel-bounces@lists.openmicroscopy.org.uk</a>>
on behalf of Munro, Ian <<a href="mailto:i.munro@imperial.ac.uk" class="">i.munro@imperial.ac.uk</a>><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Monday, July 30, 2018 8:48:04 PM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>OME External Developer List<br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [ome-devel] OME.tiff with FLIM time gates that are not equally spaced in time</font>
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<div class="">Hi All</div>
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<div class="">Since sending the mail below Romain has been in touch to say </div>
<div class="">“ <span class="" style="font-family: Calibri, sans-serif; font-size: 11pt;">There’s just a small problem is that I think it doesn’t overwrite files properly when there’s already a file with the same name.</span></div>
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I got some weird results doing that so I made sure they’re created each time."</div>
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<div class="">This suggests that a the problem of overwriting existing files, addressed by the 2nd of the 2 code snippets below, remains an issue.</div>
<div class="">My feeling is that this should be addressed in either the bio-formats Matlab plugin or at an even lower level?</div>
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<div class="">What does the OME team think?</div>
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<div class="">Best Wishes</div>
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<div class="">On 17 Jul 2018, at 13:20, Munro, Ian <<a href="mailto:i.munro@imperial.ac.uk" class="">i.munro@imperial.ac.uk</a>> wrote:</div>
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<div class="">Hi Romain</div>
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<div class="">Attached is a little Matlab script to create a FLIM OME-TIFF.</div>
<div class="">The first section just creates some dummy data.</div>
<div class="">The second part (after the tic at line 28) uses the bio-formats Matlab plugin to write this to a file.</div>
<div class="">Note that the variable “delays’ can contain any strings not just the regularly spaced ones used here.</div>
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<div class="">This is quite old code now so maybe someone from the core OME team could have a quick look and see if it’s still ok?</div>
<div class="">In particular this line:</div>
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<span class="" style="font-size: 13px; line-height: normal;">java.lang.System.setProperty(</span><span class="">'javax.xml.transform.TransformerFactory'</span><span class="" style="font-size: 13px; line-height: normal;">,</span><span class="">'com.sun.org.apache.xalan.internal.xsltc.trax.TransformerFactoryImpl’</span><span class="" style="font-size: 13px; line-height: normal;">);</span></div>
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<div class="" style="margin: 0px; line-height: normal;">may no longer be required.</div>
<div class="" style="margin: 0px; line-height: normal;">Also we used to have problems when overwriting existing files. If this has since been addressed,</div>
<div class="" style="margin: 0px; line-height: normal;">then this section:</div>
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<div class="" style="font-family: Menlo; margin: 0px; line-height: normal;"><span class="" style="font-size: 11px; line-height: normal; color: rgb(187, 44, 162);">if</span><span class=""><span class="Apple-converted-space"> </span>exist(outputPath,<span class="Apple-converted-space"> </span></span><span class="" style="font-size: 11px; line-height: normal; color: rgb(39, 42, 216);">'file'</span><span class="">)
==<span class="Apple-converted-space"> </span></span><span class="" style="font-size: 11px; line-height: normal; color: rgb(39, 42, 216);">2</span></div>
<div class="" style="font-family: Menlo; margin: 0px; line-height: normal;"><span class=""> delete(outputPath);</span></div>
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<div class="" style="margin: 0px; line-height: normal;"><span class="">May no longer be required.</span></div>
<div class="" style="margin: 0px; line-height: normal;"><span class="">Hope that helps.</span></div>
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<div class="" style="margin: 0px; line-height: normal;"><span class="">Best wishes.</span></div>
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<div class="" style="margin: 0px; line-height: normal;"><span class="">Ian</span></div>
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