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ModularImageAnalysis (MIA) is an ImageJ plugin which provides a modular framework for assembling image and object analysis workflows. Detected objects can be transformed, filtered, measured and related. Analysis workflows are batch-enabled by default, allowing easy processing of high-content datasets.

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package io.github.mianalysis.mia.module.images.transform;

import ij.ImagePlus;
import io.github.mianalysis.mia.module.Module;
import io.github.mianalysis.mia.module.Modules;
import io.github.mianalysis.mia.module.Module;
import org.scijava.Priority;
import org.scijava.plugin.Plugin;
import io.github.mianalysis.mia.module.Category;
import io.github.mianalysis.mia.module.Categories;
import io.github.mianalysis.mia.object.Workspace;
import io.github.mianalysis.mia.object.image.Image;
import io.github.mianalysis.mia.object.image.ImageFactory;
import io.github.mianalysis.mia.object.parameters.InputImageP;
import io.github.mianalysis.mia.object.parameters.Parameters;
import io.github.mianalysis.mia.object.refs.collections.ImageMeasurementRefs;
import io.github.mianalysis.mia.object.refs.collections.MetadataRefs;
import io.github.mianalysis.mia.object.refs.collections.ObjMeasurementRefs;
import io.github.mianalysis.mia.object.refs.collections.ObjMetadataRefs;
import io.github.mianalysis.mia.object.refs.collections.ParentChildRefs;
import io.github.mianalysis.mia.object.refs.collections.PartnerRefs;
import io.github.mianalysis.mia.object.system.Status;


/**
* This module duplicates an image into another, existing, image.  
This is useful when dealing with optional modules, where a specific input is required later on.
*/
@Plugin(type = Module.class, priority=Priority.LOW, visible=true)
public class ReplaceImage extends Module {
    public static final String INPUT_IMAGE1 = "Input image 1 (to be replaced)";

	/**
	* The image to copy pixel intensities from
	*/
    public static final String INPUT_IMAGE2 = "Input image 2";

    public ReplaceImage(Modules modules) {
        super("Replace image",modules);
    }



    @Override
    public Category getCategory() {
        return Categories.IMAGES_TRANSFORM;
    }

    @Override
    public String getVersionNumber() {
        return "1.0.0";
    }

    @Override
    public String getDescription() {
        return "This module duplicates an image into another, existing, image.  " +
                "\nThis is useful when dealing with optional modules, where a specific input is required later on.";
    }

    @Override
    public Status process(Workspace workspace) {
        // Getting input images
        String inputImageName1 = parameters.getValue(INPUT_IMAGE1,workspace);
        Image inputImage1 = workspace.getImages().get(inputImageName1);

        String inputImageName2 = parameters.getValue(INPUT_IMAGE2,workspace);
        Image inputImage2 = workspace.getImages().get(inputImageName2);
        ImagePlus inputImagePlus2 = inputImage2.getImagePlus();

        inputImage1.setImagePlus(inputImagePlus2);

        return Status.PASS;

    }

    @Override
    protected void initialiseParameters() {
        parameters.add(new InputImageP(INPUT_IMAGE1,this,"","Pixel intensities for this image will be replaced."));
        parameters.add(new InputImageP(INPUT_IMAGE2,this,"","The image to copy pixel intensities from"));

    }

    @Override
    public Parameters updateAndGetParameters() {
Workspace workspace = null;
        return parameters;
    }

    @Override
    public ImageMeasurementRefs updateAndGetImageMeasurementRefs() {
return null;
    }

    @Override
public ObjMeasurementRefs updateAndGetObjectMeasurementRefs() {
return null;
    }

    @Override
    public ObjMetadataRefs updateAndGetObjectMetadataRefs() {  
	return null; 
    }

    @Override
    public MetadataRefs updateAndGetMetadataReferences() {
return null;
    }

    @Override
    public ParentChildRefs updateAndGetParentChildRefs() {
return null;
    }

    @Override
    public PartnerRefs updateAndGetPartnerRefs() {
return null;
    }

    @Override
    public boolean verify() {
        return true;
    }
}