Diffusion

[vcaldas]

I'm stuck in the line 191.

The code generate 3 new tables (Results, Diffusion Coefficient, Mean Squase Displacement) - You should be able to call them via WindowManager.getNonImageTitles().

Then, I want to save every table as "filename_trajectories.csv, filename_DiffCoeff, etc" For example. Input [red]flat.peaks => [red]flat.DiffCoeff.

[cmpunter]

I assume that this is in DiffusioOperation.java? Do we need to store the intermediate results also? (fitted peaks etc). Alternatively we can implement this as seperate steps so that the end user first needs to run the peak fitter, then the peak tracker and then the mean square displacement plugin. How do you envision this?

[cmpunter]

I updated the SMB plugins! I'm currently using the following code to access all the result tables:

            TextWindow window1 = (TextWindow)WindowManager.getWindow("Diffusion Coefficients");
            TextWindow window2 = (TextWindow)WindowManager.getWindow("mean square displacements");
            TextWindow window3 = (TextWindow)WindowManager.getWindow("square displacements");
            ResultsTable table1 = window1.getTextPanel().getResultsTable();
            ResultsTable table2 = window2.getTextPanel().getResultsTable();
            ResultsTable table3 = window3.getTextPanel().getResultsTable();

            table1.save("table1.csv"); // needs to be changed of course
            table2.save("table2.csv");
            table3.save("table3.csv");  

[vcaldas]

The intermediate results don't need to be stored, but fitted values may be used later.

I would say that separating the steps is better. This way we can call every separated plugin with the input we want and save. Is better to separate and assemale the analysis strategy later than make one black box to do it all.we never now how the inputs look like and what intermediate steps will be necessary.

About the sm plugins. Great! S soon as possible ill take care of setting up the updates for Isbatch and the plugins on Fiji.