<div dir="ltr"><div>Hi Thomas & everyone,</div><div><br></div><div>Relatedly, I'd like to draw your attention to the ImageJ-OMERO project [1]. It now supports upload/download of ImgLib2-style ROIs (part of the imglib2-roi since 0.5.0 released in February) to/from OMERO; a new release of ImageJ-OMERO is forthcoming, and we will be presenting it during the OME Users conference in Dundee next week.</div><div><br></div><div>Regards,</div><div>Curtis</div><div><br></div>[1] <a href="https://github.com/imagej/imagej-omero">https://github.com/imagej/imagej-omero</a><br><div><br></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><span style="font-size:12.8px">--</span></div><div><span style="font-size:12.8px">Curtis Rueden</span><br></div><div><span style="font-size:12.8px">LOCI software architect - <a href="https://loci.wisc.edu/software" target="_blank">https://loci.wisc.edu/software</a></span></div><div>ImageJ2 lead, Fiji maintainer - <span style="font-size:12.8px"><a href="https://imagej.net/User:Rueden" target="_blank">https://imagej.net/User:Rueden</a></span></div><div>Did you know ImageJ has a forum? <a href="http://forum.imagej.net/" target="_blank">http://forum.imagej.net/</a></div><div><br></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Tue, May 22, 2018 at 6:54 PM, Thomas Boudier <span dir="ltr"><<a href="mailto:boudier.t@wehi.edu.au" target="_blank">boudier.t@wehi.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<p>Dear OME developers,</p>
<p>I am trying to write some java code to create kinda 3D Rois, but I am not sure how to create MaskData, this is my code :
<br>
</p>
<pre style="background-color:#ffffff;color:#000000;font-family:'DejaVu Sans Mono';font-size:10.5pt">ImageInt seg = object3D.createSegImage(<span style="color:#0000ff">0</span>, <span style="color:#0000ff">0</span>, <span style="color:#0000ff">0</span>);
<span style="color:#000080;font-weight:bold">byte</span>[][] mask = <span style="color:#000080;font-weight:bold">new byte</span>[seg.<span style="color:#660e7a;font-weight:bold">sizeZ</span>][seg.<span style="color:#660e7a;font-weight:bold">sizeXY</span>];
<span style="color:#000080;font-weight:bold">int </span>offX = seg.<span style="color:#660e7a;font-weight:bold">offsetX</span>;
<span style="color:#000080;font-weight:bold">int </span>offY = seg.<span style="color:#660e7a;font-weight:bold">offsetY</span>;
<span style="color:#000080;font-weight:bold">int </span>offZ = seg.<span style="color:#660e7a;font-weight:bold">offsetZ</span>;
<span style="color:#000080;font-weight:bold">for </span>(<span style="color:#000080;font-weight:bold">int </span>z = <span style="color:#0000ff">0</span>; z < seg.<span style="color:#660e7a;font-weight:bold">sizeZ</span>; z++) {
<span style="color:#000080;font-weight:bold">byte</span>[] img = mask[z];
<span style="color:#000080;font-weight:bold">int </span>c = <span style="color:#0000ff">0</span>;
<span style="color:#000080;font-weight:bold">for </span>(<span style="color:#000080;font-weight:bold">int </span>y = <span style="color:#0000ff">0</span>; y < seg.<span style="color:#660e7a;font-weight:bold">sizeY</span>; y++) {
<span style="color:#000080;font-weight:bold">for </span>(<span style="color:#000080;font-weight:bold">int </span>x = <span style="color:#0000ff">0</span>; x < seg.<span style="color:#660e7a;font-weight:bold">sizeX</span>; x++) {
<span style="color:#000080;font-weight:bold">if </span>(seg.getPixel(x, y, z) > <span style="color:#0000ff">0</span>)
img[c] = (<span style="color:#000080;font-weight:bold">byte</span>) <span style="color:#0000ff">255</span>;
<span style="color:#000080;font-weight:bold">else
</span><span style="color:#000080;font-weight:bold"> </span>img[c] = (<span style="color:#000080;font-weight:bold">byte</span>) <span style="color:#0000ff">0</span>;
c++;
}
}
}
ROIData data = <span style="color:#000080;font-weight:bold">new </span>ROIData();
data.setImage(image.asImage())<wbr>;
<span style="color:#000080;font-weight:bold">for </span>(<span style="color:#000080;font-weight:bold">int </span>z = <span style="color:#0000ff">0</span>; z < seg.<span style="color:#660e7a;font-weight:bold">sizeZ</span>; z++) {
MaskData maskData = <span style="color:#000080;font-weight:bold">new </span>MaskData(offX, offY, seg.<span style="color:#660e7a;font-weight:bold">sizeX</span>, seg.<span style="color:#660e7a;font-weight:bold">sizeY</span>, mask[z]);
maskData.setZ(z + offZ);
maskData.setT(T);
maskData.setText(object3D.<wbr>getName() + <span style="color:#008000;font-weight:bold">"_" </span>+ object3D.getValue());
data.addShapeData(maskData);
}
<span style="color:#808080;font-style:italic">// Save ROI
</span>DataManagerFacility dm = <span style="color:#660e7a;font-weight:bold">gateway</span>.getFacility(<wbr>DataManagerFacility.<span style="color:#000080;font-weight:bold">class</span>);
ROIFacility roifac = <span style="color:#660e7a;font-weight:bold">gateway</span>.getFacility(<wbr>ROIFacility.<span style="color:#000080;font-weight:bold">class</span>);
ROIData roiData = roifac.saveROIs(<span style="color:#660e7a;font-weight:bold">ctx</span>, image.getId(), Arrays.<span style="font-style:italic">asList</span>(data)).iterator(<wbr>).next();
Actually I am not sure how such Mask Roi should display inside OMERO, it seems I can only see the bounding box but not the actual mask.
Thanks for any hints.
Best,
Thomas
</pre>
<pre class="m_-4189061808703441442moz-signature" cols="72">--
/*****************************<wbr>******************************<wbr>****/
Thomas Boudier, Senior Research Officer,
BioImage Analyst, Dynamic Imaging Centre,
Walter and Eliza Hall Institute (WEHI), Australia.
/*****************************<wbr>******************************<wbr>***/
</pre>
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