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<div class="moz-forward-container">Dear Curtis,<br>
<div class="moz-cite-prefix"> <br>
> there is nothing "wrong" per se with calling
"imagej.Main.launch()" if what you really want is for the ImageJ
application to pop up. So no worries there.<br>
That is good news, it is exactly what I am trying to do.<br>
<br>
I wrote previously : <br>
"If I use this instance to open an lsm image with 2 channels,
the image isn't loaded properly, only one channel is visable and
trying to split channels will ask me for arguments and won't be
done." <br>
<br>
When I was trying to regenerate the problem with minimal code, I
figured out that the problem was due to wrong loading of imageJ
in the following way: <br>
<br>
public class launchij2 {<br>
launchij2()<br>
{ <br>
ImageJ ij = new ImageJ();<br>
ij = imagej.Main.launch();<br>
}<br>
<br>
public static void main(String args[])<br>
{<br>
new launchij2();<br>
} <br>
}<br>
<br>
I learned that <ij = mageJ.Main.launch();> doesn't replace
the <ij = new ImageJ();>; but somehow mix things together.
Is this an expected behaviour?<br>
<br>
Best Regards,<br>
Mohamed Tleis<br>
<br>
On 06/25/2013 09:03 PM, Curtis Rueden wrote:<br>
</div>
<blockquote
cite="mid:CADN69y=jzfit8FdnHZ8gAJemPvKkdoAN5w8F7wZZ=-1TogQsBw@mail.gmail.com"
type="cite">
<div dir="ltr">
<div>Hi Mohamed and everyone,</div>
<div><br>
</div>
I agree with Johannes that using "new ImageJ()" is better for
programmatic use, in that it is more flexible. That said,
there is nothing "wrong" per se with calling
"imagej.Main.launch()" if what you really want is for the
ImageJ application to pop up. So no worries there.
<div> <br>
</div>
<div>As for your reported problem, I have a couple of
questions:</div>
<div><br>
</div>
<div>
<div>> If I use this instance to open an lsm image with 2
channels</div>
<div><br>
</div>
<div style="">Please note that ImageJ2 does not support LSM
out of the box. You need either Bio-Formats or LSM_Reader
for that (which at the moment are ImageJ1 plugins, and
will be run using the IJ2's legacy layer). If you open an
LSM with File > Open right now, I believe it will open
as a vanilla TIFF file, which may not read all the
metadata, and may misinterpret some Zeiss-specific image
parameters.</div>
<div style=""><br>
</div>
<div style="">> Note that opening the imageJ from the
provided executable works fine.</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">Hmm, you mean if you launch ImageJ2
from the launcher, then open your LSM file, it behaves as
expected? Then there may indeed be a bug lurking here
somewhere. Do you have a sample non-working image file you
can upload via the Help > Upload Sample Image command?
That, along with specific brief instructions about what
doesn't work, would be very helpful to diagnose and fix
the problem.</div>
<div class="gmail_extra"><br>
Thanks,</div>
<div class="gmail_extra">Curtis</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Mon, Jun 24, 2013 at 9:54 AM,
Mohamed Tleis <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:mohammedtleis@hotmail.com"
target="_blank">mohammedtleis@hotmail.com</a>></span>
wrote:<br>
<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">Dear
Developers,<br>
<br>
from inside my code I am calling imageJ through<br>
<br>
ImageJ ij = new ImageJ.Main.launch();<br>
<br>
If I use this instance to open an lsm image with 2
channels, the image isn't loaded properly, only one
channel is visable and trying to split channels will
ask me for arguments and won't be done.<br>
Note that opening the imageJ from the provided
executable works fine. I suppose the launch method
needs some arguments to be passed. Can you please show
me an example to how to do this?<br>
<br>
Best Regards,<br>
M. Tleis<br>
<br>
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</blockquote>
</div>
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</blockquote>
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