<div dir="ltr">Hi Roy,<div><br></div><div>Ok I found the problem.</div><div><br></div><div>The tables return their item sorted by time (spot, edges at least). So you need to make sure that you compute the time feature for edges if you don't want to to fail.This means in your script add:</div><div><br></div><div><div><br></div><div># Edge analyzer</div><div>settings.addEdgeAnalyzer(EdgeTargetAnalyzer())</div><div>settings.addEdgeAnalyzer(EdgeTimeLocationAnalyzer())</div></div><div><br></div><div>(without Target, you cannot save the TrackMate file btw)</div><div><br></div><div>and then </div><div><br></div><div>ExportStatsToIJAction().execute(trackmate)<br></div><div><br></div><div>will work.</div><div><br></div><div>best</div><div>jy</div><div><br></div><div><br></div><div><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sat, Jun 13, 2015 at 5:16 PM, Roy Francis <span dir="ltr"><<a href="mailto:roy.m.francis@outlook.com" target="_blank">roy.m.francis@outlook.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><div dir="ltr"><font color="#666666" size="2" face="Tahoma, sans-serif">Hi Jean,</font><div><font color="#666666" size="2" face="Tahoma, sans-serif">Thank you for your quick reply. ExportStatsToIJAction().execute(trackmate) doesn't seem to work. It doesn't matter what approach is used. Is there any way to save the three output data to a text file during batch process using script? If there is no way to do that, how can I have the result tables be opened in new windows during batch process so that I can manually save them at the end?</font></div><div><font color="#666666" size="2" face="Tahoma, sans-serif">Thanks,</font></div><div><font color="#666666" size="2" face="Tahoma, sans-serif">Roy <br></font><br><br><div><hr>Date: Sat, 13 Jun 2015 16:31:10 +0200<br>Subject: Re: Exporting trackmate data using ImageJ/Jython script<br>From: <a href="mailto:jeanyves.tinevez@gmail.com" target="_blank">jeanyves.tinevez@gmail.com</a><br>To: <a href="mailto:roy.m.francis@outlook.com" target="_blank">roy.m.francis@outlook.com</a><div><div class="h5"><br><br><div dir="ltr"><br><div><br><div>On Sat, Jun 13, 2015 at 4:17 PM, Roy Francis <span dir="ltr"><<a href="mailto:roy.m.francis@outlook.com" target="_blank">roy.m.francis@outlook.com</a>></span> wrote:<br><blockquote style="border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div><div dir="ltr"><font face="Verdana,sans-serif" size="1" style="font-size:8pt" color="#666666"><br></font>Hi,<div>I am using trackmate to track some cells in image files. They seem to work fine using the GUI. But, I have a folder full of files and wish to run trackmate non-interactively as a batch.</div><div><br></div><div>I am using ImageJ macros to load images, convert avi to tiff sequence, convert to hyper stacks (for z-stack to time-stack) and then feed to the trackmate function which I created as a plugin based on instructions this page</div><div><br></div><div><a href="http://fiji.sc/Scripting_TrackMate" target="_blank">http://fiji.sc/Scripting_TrackMate</a></div><div><br></div><div>Painfully, I have got it all to work except for the final part. The data exporting. Using the GUI, there is a button that opens three data tables for spot results, connections and track results. And once this is open it can be saved using IMJ macros.</div><div><br></div><div>How can I open these data and/or save them to a text file either using IMJ or Jython? I have the feeling the answer is <span style="font-size:12pt">ExportStatsToIJAction(). But, I have no idea how to use it. The help page </span></div><div><a href="http://javadoc.imagej.net/Fiji/fiji/plugin/trackmate/action/ExportStatsToIJAction.html" target="_blank">http://javadoc.imagej.net/Fiji/fiji/plugin/trackmate/action/ExportStatsToIJAction.html</a></div><div><span style="font-size:12pt">is utterly unreadable and doesn't explain anything.</span></div><div><span style="font-size:12pt"><br></span></div><div><span style="font-size:12pt">Any help is greatly appreciated. </span><span style="font-size:12pt">Full script below if required.</span></div><div></div></div></div></blockquote></div><br></div><div><br></div><div>Hi Roy</div><div><br></div><div>I am afraid the action you mention cannot be used in an headless mode. It just generates the tables on ImageJ then you have to save them manually</div><div><br></div><div>If it is still what you want to to, try something in the lione of:</div><div><br></div><div><span style="font-size:12pt">ExportStatsToIJAction().execute(trackmate)</span></div><div><span style="font-size:12pt"><br></span></div><div><span style="font-size:12pt">best</span></div><div><span style="font-size:12pt">jy</span></div></div></div></div></div></div> </div></div>
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