[ome-devel] How to use masks for Rois ?

[Thomas Boudier]

Hi Dominik,

Thanks a lot four reply and thanks for the tip about the channels.

In omero.web 5.4.6 I can see some previews of the mask and it looks ok, but since the mask is the same as the binary image I was not sure it was working, because I cannot see any difference when show is checked or not. Here is a snapshot of the data.

Hi Curtis,

Thanks for the link, I will definitely have a look, because there is no pint for me writing duplicate code ;) .

cheers

Thomas

On 23/05/18 23:16, Dominik Lindner (Staff) wrote:
Hi Thomas,

I think your code looks alright.
OMERO.Insight doesn't support the display of mask ROIs unfortunately. But the
new web viewer (OMERO.iViewer) should. Can you try that?

Just as a precaution: There's a bug in the Java Gateway's ROIFacility [1]. You're
not setting 'c' when you create the MaskData, i.e. the mask applies to all channels.
That should be fine. But just in case you want to set it deliberately to 'all channels', i. e.
setC(-1), this will basically result in setting it to the first channel, like setC(0) would do.
The Z/T/C setters and getters of the ShapeData class don't handle the '-1' case properly at
the moment. If you want to deliberately set Z, C, T to "all", then you have to access the
underlying Ice object directly, something like:
((MaskI) maskData.asIObject()).setC(null)
(In the MaskI object it has to be set to null to indicate "all").
Z/T accordingly.

Regards,
Dominik

1) https://github.com/openmicroscopy/openmicroscopy/pull/5761



On 23 May 2018, at 00:54, Thomas Boudier <boudier.t at wehi.edu.au<mailto:boudier.t at wehi.edu.au>> wrote:


Dear OME developers,

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 :

ImageInt seg = object3D.createSegImage(0, 0, 0);
byte[][] mask = new byte[seg.sizeZ][seg.sizeXY];
int offX = seg.offsetX;
int offY = seg.offsetY;
int offZ = seg.offsetZ;

for (int z = 0; z < seg.sizeZ; z++) {
    byte[] img = mask[z];
    int c = 0;
    for (int y = 0; y < seg.sizeY; y++) {
        for (int x = 0; x < seg.sizeX; x++) {
            if (seg.getPixel(x, y, z) > 0)
                img[c] = (byte) 255;
            else
                img[c] = (byte) 0;
            c++;
        }
    }
}
ROIData data = new ROIData();
data.setImage(image.asImage());
for (int z = 0; z < seg.sizeZ; z++) {
    MaskData maskData = new MaskData(offX, offY, seg.sizeX, seg.sizeY, mask[z]);
    maskData.setZ(z + offZ);
    maskData.setT(T);
    maskData.setText(object3D.getName() + "_" + object3D.getValue());
    data.addShapeData(maskData);
}
// Save ROI
DataManagerFacility dm = gateway.getFacility(DataManagerFacility.class);
ROIFacility roifac = gateway.getFacility(ROIFacility.class);
ROIData roiData = roifac.saveROIs(ctx, image.getId(), Arrays.asList(data)).iterator().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


--
/***************************************************************/
      Thomas Boudier, Senior Research Officer,
      BioImage Analyst, Dynamic Imaging Centre,
      Walter and Eliza Hall Institute (WEHI), Australia.
/**************************************************************/


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--
/***************************************************************/
      Thomas Boudier, Senior Research Officer,
      BioImage Analyst, Dynamic Imaging Centre,
      Walter and Eliza Hall Institute (WEHI), Australia.
/**************************************************************/


_______________________________________________

The information in this email is confidential and intended solely for the addressee.
You must not disclose, forward, print or use it without the permission of the sender.

The Walter and Eliza Hall Institute acknowledges the Wurundjeri people of the Kulin
Nation as the traditional owners of the land where our campuses are located and
the continuing connection to country and community.
_______________________________________________
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