<div dir="ltr">Hi Jacob,<div><br></div><div><br></div><div><div>> I have been trying to convert some files in the proprietary jpeg2000</div><div>> format used by PICTools medical into tiffs--is there some utility that</div>
<div>> can do this in batch method (all files in directory x)?</div><div><br></div><div style>Here are two macros that might work for you:</div><div style><div><a href="https://github.com/openmicroscopy/bioformats/blob/v4.4.5/components/loci-plugins/utils/macros/recursiveTiffConvert.txt">https://github.com/openmicroscopy/bioformats/blob/v4.4.5/components/loci-plugins/utils/macros/recursiveTiffConvert.txt</a><br>
</div><div><a href="https://github.com/openmicroscopy/bioformats/blob/v4.4.5/components/loci-plugins/utils/macros/batchTiffConvert.txt">https://github.com/openmicroscopy/bioformats/blob/v4.4.5/components/loci-plugins/utils/macros/batchTiffConvert.txt</a></div>
</div><div><br></div><div>I found both of these on the page at:</div><div><a href="http://openmicroscopy.org/site/support/bio-formats/users/imagej">http://openmicroscopy.org/site/support/bio-formats/users/imagej</a><br></div>
<div><br></div><div style><div><div><br class="">> These files are readable by fiji but not plain imagej<br></div><div><br></div><div style>The reason you can read them in Fiji is because Fiji bundles the Bio-Formats plugins, which can read JP2. To read them in plain ImageJ, you would need to install Bio-Formats first, as described here: <a href="http://openmicroscopy.org/site/support/bio-formats/users/imagej/installing.html">http://openmicroscopy.org/site/support/bio-formats/users/imagej/installing.html</a></div>
<div><br></div><div><br></div><div>> I wrote a macro in fiji but which keeps prompting me with a dialog for</div><div>> every image.</div></div><div><br></div></div></div><div style>Your macro looks OK to me. Using Plugins > Macros > Record I created a similar macro (which uses the open() and saveAs() functions), and it works without popping up any dialog boxes, even if the output image already exists. So I am not sure what is causing your problem. That said, hopefully one of the above macros will work for you and the issue will be moot.</div>
<div style><br></div><div style>Good luck,</div><div style>Curtis</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Jan 16, 2013 at 11:18 AM, Keller, Jacob <span dir="ltr"><<a href="mailto:kellerj@janelia.hhmi.org" target="_blank">kellerj@janelia.hhmi.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-size:10pt;font-family:Courier New">
Dear List,
<div><br>
</div>
<div>I have been trying to convert some files in the proprietary jpeg2000 format used by PICTools medical into tiffs--is there some utility that can do this in batch method (all files in directory x)? These files are readable by fiji but not plain imagej, and
I wrote a macro in fiji but which keeps prompting me with a dialog for every image. Here is the macro:</div>
<div><br>
</div>
<div><br style="color:rgb(34,34,34);font-family:arial,sans-serif">
<span style="color:rgb(34,34,34);font-family:arial,sans-serif"> for (i=0; i<10; i++) {</span><br style="color:rgb(34,34,34);font-family:arial,sans-serif">
<span style="color:rgb(34,34,34);font-family:arial,sans-serif"> for (j=0; j<10; j++) {</span><br style="color:rgb(34,34,34);font-family:arial,sans-serif">
<span style="color:rgb(34,34,34);font-family:arial,sans-serif"> for (k=0; k<10; k++) {</span><br style="color:rgb(34,34,34);font-family:arial,sans-serif">
<span style="color:rgb(34,34,34);font-family:arial,sans-serif">one = d2s(i, 0);</span><br style="color:rgb(34,34,34);font-family:arial,sans-serif">
<span style="color:rgb(34,34,34);font-family:arial,sans-serif">two = d2s(j, 0);</span><br style="color:rgb(34,34,34);font-family:arial,sans-serif">
<span style="color:rgb(34,34,34);font-family:arial,sans-serif">thr = d2s(k, 0);</span><br style="color:rgb(34,34,34);font-family:arial,sans-serif">
<span style="color:rgb(34,34,34);font-family:arial,sans-serif">setBatchMode(true);</span><br style="color:rgb(34,34,34);font-family:arial,sans-serif">
<span style="color:rgb(34,34,34);font-family:arial,sans-serif">filename = "C:\\Users\\Jacob\\Desktop\\</span><u></u><span style="color:rgb(34,34,34);font-family:arial,sans-serif">ZfishBrains\\SPC00_TM00"+one+</span><u></u><span style="color:rgb(34,34,34);font-family:arial,sans-serif">two+thr+"_ANG000_CM0_CHN00_</span><u></u><span style="color:rgb(34,34,34);font-family:arial,sans-serif">PH0.jp2";</span><br style="color:rgb(34,34,34);font-family:arial,sans-serif">
<span style="color:rgb(34,34,34);font-family:arial,sans-serif">print(filename);</span><br style="color:rgb(34,34,34);font-family:arial,sans-serif">
<span style="color:rgb(34,34,34);font-family:arial,sans-serif">open(filename);</span><br style="color:rgb(34,34,34);font-family:arial,sans-serif">
<span style="color:rgb(34,34,34);font-family:arial,sans-serif">saveAs("Tiff", "X:\\Zebrafish_Brain_Images\\</span><u></u><span style="color:rgb(34,34,34);font-family:arial,sans-serif">tifs\\SPC00_TM00"+one+two+thr+</span><u></u><span style="color:rgb(34,34,34);font-family:arial,sans-serif">"_ANG000_CM0_CHN00_PH0x.tif");</span><br style="color:rgb(34,34,34);font-family:arial,sans-serif">
<span style="color:rgb(34,34,34);font-family:arial,sans-serif">close();</span></div>
<div><br>
</div>
<div><br>
</div>
<div>Jacob<br>
<div><br>
<div style="font-family:Tahoma;font-size:13px">
<div><font face="Courier New">*******************************************</font></div>
<div><font face="Courier New">Jacob Pearson Keller, PhD</font></div>
<div><font face="Courier New">Postdoctoral Associate</font></div>
<div><font face="Courier New">HHMI Janelia Farms Research Campus</font></div>
<div><font face="Courier New">email: <a href="mailto:j-keller2@northwestern.edu" target="_blank">j-keller2@northwestern.edu</a></font></div>
<div><font face="Courier New">*******************************************</font></div>
</div>
</div>
</div>
</div>
</div>
<br>_______________________________________________<br>
ome-users mailing list<br>
<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
<br></blockquote></div><br></div>