Re: [micro-manager-general] Spam (8.588):Re: Spam (12.588):Re: Steps to get a functional plugin, lesson n+1

[Nico S. <nic...@uc...>]

Hi Carlos,

> a friendly reminder that I got stuck on a couple of issues on the last
> thread.

No worries, did not realize that it was my turn. Ccing the mailing list.

>
>> Couple of things missing to make it a real usefull tool though:
>>
>> * marking on the window.
>> Something that has bothered me, but not much, is a bluish rectangle that
>> uM puts in the data window. I don't know where it comes from, nor what
>> it represent. But trying to use the ImageJ processor to mark the ROIs
>> did not work.
>>
>> 	processor.setLineWidth(1);
>> 	processor.setColor(Color.red);
>>
>> 	processor.setRoi(roi_[i]);
>> 	v = processor.getStats().mean;
>> 	data[i].add((double)imagesReceived_, v, false);
>> 	processor.draw(roi_[i]);
>>
>> That, or drawRoi(), do not make it.

This is drawn by mageJ, to indicate that you are (slightly) zoomed in 
and can pan the image around. It is a known bug that is hard to solve, 
see: https://github.com/micro-manager/micro-manager/issues/238.

>> * ROI set saving.
>> The ROI set should go into the datastore somehow, so the data can be
>> reproduced afterwards. I have't looked at that part yet, but I'm trying
>> to maximize the SNR of this message :)

You will need to add these to the metadata.  This goes something like:

Metadata md = image.getMetadata();
PropertyMap.Builder pMapBuilder = md.getUserData().getCopyBuilder();
pMapBuilder.putRectangleList("YourKey", 
ListofYourRoisTransformedToRectangles);
newMd = 
md.copyBuilderPreservingUUID().userData(pMapBuilder.build()).build();
Image storeThisOne = image.copyWithMetadat(newMd);

Typing this without IDE, so doubtlessly errors.  This is a bit 
complicated, but the design has the advantage that each object is 
immutable.

Hope it makes sense!


Best,


Nico