Closing windows created by Coloc2 in macro

[BrazilianFIJItsu]

Hello,

I have a simple question regarding the "Coloc 2" plugin in FIJI.

Assume I have two images named "tmp0" and "tmp1", when I use the Coloc2, even though I don't check any box on the dialog window, there are two result windows show up. one is the text "Log" window which I use to retrieve the R value. the other is titled "Colocalization tmp1 vs tmp0" which contained similar information as in the "Log" window, this one can also be saved as a pdf file.

My question is how to avoid the "Colocalisation tmp1 vs tmp0" window showing up. When I wrote a macro to batch process, I only need the "Log" window to retrieve information. And in the macro, selectWindow("Coloclisation tmp1 vs tmp0") function can select the window, but neither close() or run("Close") function can close it. This causes a pile-up of such "Colocalization ..." windows at the end of the macro.

Thanks for the help.

[etadobson]

Hi @BrazilianFIJItsu -

At the moment - I am not able to come up with a quick workaround to this issue (tested some mini-macros myself and haven't found a solution). Perhaps others on this repo will have some tips? @chalkie666 ?? @tomka ?? @imagejan ??

Too - don't forget to post on the ImageJ Forum in the future ... there is a wider audience reviewing posts there for user questions such as this.

Saying that - will keep this issue in mind though for future updates/fixes to ease batch processing for Coloc 2.

eta

[imagejan]

one is the text "Log" window which I use to retrieve the R value.

To make this part more configurable, Coloc 2 should use the SciJava LogService instead of IJ.log() in the future.

the other is titled "Colocalization tmp1 vs tmp0"

This one is currently hard-coded in SingleWindowDisplay.java and will always be shown because the code mixes processing and UI display. Nevertheless, I guess the window display can be made optional by introducing an additional config flag here.

In the long term, Coloc_2 (or whatever the name will be) will hopefully do all the processing via Ops and separate the UI from the processing (as discussed here), but this still requires some effort.

[jackyko1991]

Any update after many years of the issue report?

I am working on Fiji macro for Coloc2 for thousands of cells...really hope that we can opt for the output format.

[chalkie666]

Hi @jackyko1991 the coloc2 code is unlikely to get the fix you need any time soon. But no problem, as the same algorithms are implemeted as "ops" and with those you can format the output however you like.