A groovy script to batch test param for cellpose

RUN_mulitpleParam_Cellpose.groovy

#@File file_path

IJ.run("Close All", "");

// the folder containing the lif
dir = file_path.getParent()
// a subfolder to save images
output_dir = new File( dir ,"outputRom1PC")
output_dir.mkdir()

imp = IJ.openImage( file_path.toString() );

mb_ch = 1
//diam_array = [120,90,60,30]
//nucCh_array = [-1,2]
//model_array = ["cyto", "cyto2"]
diam_array = [60,90,100,110]
nucCh_array = [0,2]
model_array = ["cyto","cyto2","cyto2_omni"]


ImagePlus[] channels_imp = ChannelSplitter.split(imp);
mb_imp = channels_imp[0].duplicate();
mb_imp.setTitle("mb")
mb_imp.show()

nucCh_array.each{ nucCh ->
	diam_array.each{ diam ->
		model_array.each{ model ->
		
			// Here is the Cellpose Magic 
			Cellpose_SegmentImgPlusAdvanced cellCellpose = new Cellpose_SegmentImgPlusAdvanced();
			cellCellpose.imp = imp;
			cellCellpose.diameter = diam;
			cellCellpose.cellproba_threshold = 0;
			cellCellpose.flow_threshold = 0.4;
			cellCellpose.model = model;
			cellCellpose.nuclei_channel = nucCh ;
			cellCellpose.cyto_channel = 1 ;
			cellCellpose.dimensionMode  = "3D";
			cellCellpose.run();
			
			cell_cellpose_imp = cellCellpose.cellpose_imp ;
			cell_cellpose_imp.show()
			IJ.run(cell_cellpose_imp, "glasbey_inverted", "");
			IJ.run(cell_cellpose_imp, mb_imp.getBitDepth()+"-bit", "");// to merge with input mb use same BitDepth
			cell_cellpose_imp.setTitle("cellpose")
			cell_cellpose_imp.changes = false
			
			IJ.run( "Merge Channels...", "c1=[mb] c2=[cellpose]  create keep");
			merged_imp = IJ.getImage();
			
			IJ.saveAs(merged_imp, "Tiff", new File ( output_dir, imp.getTitle()+"-"+nucCh.toString()+"-"+diam.toString()+"-"+model+".tif").toString() )
			
			//close currents images
			merged_imp.close()
			cell_cellpose_imp.close()
			
		}
	}
}

return

//IJ.run( "Merge Channels...", "c1=["+enhancedMb_imp.getTitle()+"] c2=["+dapi_imp.getTitle()+"]  create keep");
//dapi_enhanced_imp = IJ.getImage();

import ij.*
import ch.epfl.biop.wrappers.cellpose.ij2commands.Cellpose_SegmentImgPlusAdvanced
import ij.process.*
import ij.gui.*
import java.awt.*
import ij.plugin.*
import ij.io.FileSaver
import ij.process.StackStatistics