Hi Josh,<div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><br>I've got a proprietary format which stores absolute date-timestamps in<br>
a footer for each frame, and I have written an ImageJ plugin to open<br>these files, and post the timestamps as a list in the Show Info<br>dialog, however now I want to display the timestamps on the image or<br>in a table (user option). I've come across the following macro, which<br>
extracts timestamps from Bio-Formats:<br><a href="https://github.com/openmicroscopy/bioformats/blob/develop/components/loci-plugins/utils/macros/planeTimings.txt" target="_blank">https://github.com/openmicroscopy/bioformats/blob/develop/components/loci-plugins/utils/macros/planeTimings.txt</a><br>
</blockquote><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"> </blockquote><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
Perhaps someone knows how they implement this, or where to look in the<br>code. Is there any other way to accomplish my goal?</blockquote><div><br></div><div>Bio-Formats is able to perform this operation in a format-agnostic way because it standardizes metadata from the proprietary file format (PFF) into the standard OME-XML data model. For details, see the section "A brief overview of metadata" at:</div>
<div> <a href="http://loci.wisc.edu/bio-formats/about">http://loci.wisc.edu/bio-formats/about</a></div><div><br></div><div>Your question is becoming a frequently asked one; see these messages from the ImageJ archive:</div>
<div> <a href="https://list.nih.gov/cgi-bin/wa.exe?A2=IMAGEJ;e1955de4.1206">https://list.nih.gov/cgi-bin/wa.exe?A2=IMAGEJ;e1955de4.1206</a></div><div> <a href="https://list.nih.gov/cgi-bin/wa.exe?A2=IMAGEJ;6e754ad5.1206">https://list.nih.gov/cgi-bin/wa.exe?A2=IMAGEJ;6e754ad5.1206</a><br>
<br>In short, you can make calls to the makeText macro function within your plugin to write your timestamps onto the image planes:</div><div> <a href="http://rsb.info.nih.gov/ij/developer/macro/functions.html#makeText">http://rsb.info.nih.gov/ij/developer/macro/functions.html#makeText</a></div>
<div><br></div><div>If you think your file format reader is of general interest (and from Aaron Hendrickson's reply, it sounds like it could be), we would be delighted to include it with Bio-Formats. See the Bio-Formats File Format Reader Guide for information on how to create a Bio-Formats reader:</div>
<div> <a href="https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats/doc/reader-guide.txt">https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats/doc/reader-guide.txt</a></div>
<div><br></div><div>You can use GitHub to good effect here, forking the Bio-Formats project (from <a href="https://github.com/openmicroscopy/bioformats">https://github.com/openmicroscopy/bioformats</a>) into your own project space, implementing your reader on a branch there, and then filing a "Pull Request" to submit your changes back upstream.</div>
<div><br></div><div>Alternately, you could send us your existing ImageJ plugin and we can convert it to a Bio-Formats file reader as our time allows.<br><br>Regards,</div><div>Curtis</div><div><br><br><div class="gmail_quote">
On Thu, Jul 12, 2012 at 11:06 AM, Josh Doe <span dir="ltr"><<a href="mailto:josh@joshdoe.com" target="_blank">josh@joshdoe.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I've got a proprietary format which stores absolute date-timestamps in<br>
a footer for each frame, and I have written an ImageJ plugin to open<br>
these files, and post the timestamps as a list in the Show Info<br>
dialog, however now I want to display the timestamps on the image or<br>
in a table (user option). I've come across the following macro, which<br>
extracts timestamps from Bio-Formats:<br>
<a href="https://github.com/openmicroscopy/bioformats/blob/develop/components/loci-plugins/utils/macros/planeTimings.txt" target="_blank">https://github.com/openmicroscopy/bioformats/blob/develop/components/loci-plugins/utils/macros/planeTimings.txt</a><br>
<br>
Perhaps someone knows how they implement this, or where to look in the<br>
code. Is there any other way to accomplish my goal?<br>
<br>
Maybe the concept of frame metadata can be implemented in ImageJ,<br>
which can consist of simple key value pairs, and perhaps even have a<br>
few standard keys like microseconds since the Unix epoch, comment,<br>
etc. An integrated or plugin metadata viewer would then update the<br>
metadata whenever the stack's current frame is changed.<br>
<br>
Thanks,<br>
-Josh<br>
<br>
--<br>
ImageJ mailing list: <a href="http://imagej.nih.gov/ij/list.html" target="_blank">http://imagej.nih.gov/ij/list.html</a><br>
</blockquote></div><br></div>