automate saving of transformation matrices file

[tischi]

@miura

Would it be possible to automate saving of the transformation matrices?
Right now, the macro recorder only records "save" without the path...
For automation it would be great if that could be recorded such that no UI will pop up and one can reload the transformation file automatically as well.

run("MultiStackReg", "stack_1=C2-input action_1=Align file_1=[] stack_2=None action_2=Ignore file_2=[] transformation=[Rigid Body] save");

[tischi]

Just to clarify what my workflow would be (the issue is that I cannot know the transformationPath):

//
// Correct rotational jitter in a multi-channel image, based on registration of one of the channels
// Author: Christian Tischer (EMBL, CBA)
// Christian.Tischer@EMBL.DE 
//


//
// USER INPUT (could be modified)
//

referenceChannelId = 2;

//
// CODE (do not modify)
//
title = getTitle();
getDimensions(w, h, channels, slices, frames);

rename("input");
run("Split Channels");

run("MultiStackReg", "stack_1=C"+referenceChannelId+"-input action_1=Align file_1=[] stack_2=None action_2=Ignore file_2=[] transformation=[Rigid Body] save");

transformationPath = "/Users/tischer/Documents/isabelle-schneider-3d-rotational-jitter-correction/data/TransformationMatrices.txt";

for (i = 1; i < channels; i++) 
{
	if ( i != referenceChannelId )
	{
		run("MultiStackReg", "stack_1=C"+i+"-input action_1=Align file_1=["+transformationPath+"] stack_2=None action_2=Ignore file_2=[] transformation=[Rigid Body]");
	}
}

run("Merge Channels...", "c1=C1-input c2=C2-input c3=C3-input create");

rename( title );

[tischi]

I realize another option might be to add the multi-channel logic into the java code.
The functionality would be that one can select one reference channel and all channels get aligned accordingly.

I could do this however I am not sure how to handle it such that the UI does not get super complex...

[miura]

Hi @tischi

I don't have time to do this now, but I think the easiest way is below line 217 of MultiStackReg_.java something like

gd.addStringField("Path","",20);

That the path manually set in the string field will become the destination of the output. The aim is to have the path be recorded in the command recorder. Path then can be modified within the macro.

Then add a line below line 246

savepath = gd.getNextString();

presuming that you will also add savepath as a static field value.

savepath can then be integrated within the scope of if (saveTransform){ from line 314.

[tischi]

Sounds perfect! I'll do it and submit a PR :)

[tischi]

While looking into the code in order to add the changes I figured out that it actually works already, like this:

run("MultiStackReg", "stack_1=moving-dot.tif action_1=Align file_1=/Users/tischer/Desktop/tmp01/transformations.txt stack_2=None action_2=Ignore file_2=[] transformation=[Rigid Body]");

In this case file_1 is considered the saving path of the transformations.