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

[Carlos G M. <tr...@ac...>]

Hey Nico,

Nico Stuurman @ 21/04/2020 20:05 -0300 dixit:
> Hi Carlos,
> 
> Finally got around playing with your plugin.  The idea is really nice,
> but I quickly run into problems, and was never able to get a plot of a
> time-lapse.  Specifically:
> 
> 2020-04-21T15:56:41.089398 tid12468 [IFO,App]
> java.lang.NullPointerException
> 2020-04-21T15:56:41.089398 tid12468 [IFO,App]   at
> org.micromanager.plugins.rtintensities.RTIntensitiesFrame$4$1.run(RTIntensitiesFrame.java:177)
> 
> 2020-04-21T15:56:41.089398 tid12468 [IFO,App]   at
> java.lang.Thread.run(Thread.java:748)

That's ... unexpected.
That line is (AFAIK):

 if (studio.acquisitions().getAcquisitionSettings().intervalMs < 1000) {

Code has just started a new acquisition (by pressing the plugin's "Run
Acquisition") and is accessing the MDA period to "dampen" the refresh
cycle if frequency > 1Hz. I did not expect intervalMs to be null.

This or I've changed the code between my publishing it and now, which I
don't recall but it could be. I should start versioning... (In fact I
have already, but do not know if published jar corresponds to latest)


> 
> Also, it would be nice if ROI intensity plotting was available for a
> live window.

Noted. I do not have knowledge of actual usage, but I can imagine that
seeing the evolution of intensities in some ROIs "just to get an idea"
could be useful.

> 
> Does the plugin work with images with multiple channels?
> 

Nope, it could. In that case it would be nice to have an obvious
relation between corresponding lines (may be same color dotted?), and
different scales ? But I would need some sense of usefulness from
someone to work in that.

> Is there a way of getting the intensity data out (copying to the
> clipboard or saving)?


THIS question I got from the guy I'm helping, and it actually confused
me. The DATA is in the images, the plot is only showing it. All you
would need to reproduce the plot is to document the ROIs, and that's why
I would like to embedd that info in the image set.
Afterwards, there are tons of tools to do other analysis and pretier
graphs and...


>> My issue is that I want to show the ROIs in the display, and that the
>> code that I thought would do it, does not.
> 
> That may be harder than it should be.  MM handles the display an
> overlays, so most likely, the ImageJ way to draw ROIs no longer works in
> the MM display.  Looks for Overlay plugins in the MM source code.

Ah, this seems my mantra. It seems I got it wrong when I thought that
Micro-Manager used ImageJ for all analysis. There there is a ROI Manager
and I thought a ROI set could be easily embedded in an Image set.
Sounded like the logical way to documenting things.

> 
>> Will ImageJ be able to understand those tags afterwards ?
> 
> No, ImageJ may (or may not?) have its own way of saving ROIs in images. 
> The Micro-Manager API has no access to those.  However, your plugin
> could look for those tags in open Micro-Manager datasets, and
> reconstruct the ROIs.

Yep, what I thought ROI Manager would do.

> 
> 
> Best,
> 
> 
> Nico
> 
Thanks,

-- 
-- 
Carlos G Mendioroz  <tr...@ac...>