io.github.mianalysis.mia.module.images.process.InvertIntensity Maven / Gradle / Ivy

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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.process;

import org.scijava.Priority;
import org.scijava.plugin.Plugin;

import ij.ImagePlus;
import ij.ImageStack;
import ij.plugin.Duplicator;
import io.github.mianalysis.mia.module.Categories;
import io.github.mianalysis.mia.module.Category;
import io.github.mianalysis.mia.module.Module;
import io.github.mianalysis.mia.module.Modules;
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.BooleanP;
import io.github.mianalysis.mia.object.parameters.InputImageP;
import io.github.mianalysis.mia.object.parameters.OutputImageP;
import io.github.mianalysis.mia.object.parameters.Parameters;
import io.github.mianalysis.mia.object.parameters.SeparatorP;
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;

/**
 * Created by sc13967 on 17/01/2018.
 */

/**
* Invert intensity of each pixel.  This uses the stock ImageJ intensity inversion function ("Edit - Invert")
*/
@Plugin(type = Module.class, priority = Priority.LOW, visible = true)
public class InvertIntensity extends Module {

	/**
	* 
	*/
    public static final String INPUT_SEPARATOR = "Image input/output";

	/**
	* Image to be inverted.
	*/
    public static final String INPUT_IMAGE = "Input image";

	/**
	* When selected, the input image will be replaced by the inverted image in the workspace.  If disabled, the inverted image will be stored as a new image in the workspace.
	*/
    public static final String APPLY_TO_INPUT = "Apply to input image";

	/**
	* If "Apply to input image" is not selected, the inverted image will be stored as a new image in the workspace.  This is the name of the output inverted image.
	*/
    public static final String OUTPUT_IMAGE = "Output image";

    public InvertIntensity(Modules modules) {
        super("Invert image intensity", modules);
    }

    public static void process(Image inputImage) {
        process(inputImage.getImagePlus());
    }

    public static void process(ImagePlus inputImagePlus) {
        ImageStack ist = inputImagePlus.getStack();
        for (int idx=1;idx<=ist.size();idx++)
            ist.getProcessor(idx).invert();
    }

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

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

    @Override
    public String getDescription() {
        return "Invert intensity of each pixel.  This uses the stock ImageJ intensity inversion function (\"Edit > Invert\")";
    }

    @Override
    public Status process(Workspace workspace) {
        // Getting input image
        String inputImageName = parameters.getValue(INPUT_IMAGE, workspace);
        Image inputImage = workspace.getImages().get(inputImageName);
        ImagePlus inputImagePlus = inputImage.getImagePlus();

        // Getting parameters
        boolean applyToInput = parameters.getValue(APPLY_TO_INPUT, workspace);
        String outputImageName = parameters.getValue(OUTPUT_IMAGE, workspace);

        // If applying to a new image, the input image is duplicated
        if (!applyToInput) {
            inputImagePlus = new Duplicator().run(inputImagePlus);
        }

        // Applying intensity inversion
        process(inputImagePlus);

        // If the image is being saved as a new image, adding it to the workspace
        if (applyToInput) {
            inputImage.setImagePlus(inputImagePlus);
            if (showOutput)
                inputImage.show();
        } else {            
            Image outputImage = ImageFactory.createImage(outputImageName, inputImagePlus);
            workspace.addImage(outputImage);
            if (showOutput)
                outputImage.show();
        }

        return Status.PASS;

    }

    @Override
    protected void initialiseParameters() {
        parameters.add(new SeparatorP(INPUT_SEPARATOR, this));
        parameters.add(new InputImageP(INPUT_IMAGE, this));
        parameters.add(new BooleanP(APPLY_TO_INPUT, this, true));
        parameters.add(new OutputImageP(OUTPUT_IMAGE, this));

        addParameterDescriptions();

    }

    @Override
    public Parameters updateAndGetParameters() {
        Workspace workspace = null;
        Parameters returnedParameters = new Parameters();

        returnedParameters.add(parameters.getParameter(INPUT_SEPARATOR));
        returnedParameters.add(parameters.getParameter(INPUT_IMAGE));
        returnedParameters.add(parameters.getParameter(APPLY_TO_INPUT));

        if (!(boolean) parameters.getValue(APPLY_TO_INPUT, workspace)) {
            returnedParameters.add(parameters.getParameter(OUTPUT_IMAGE));
        }

        return returnedParameters;

    }

    @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;
    }

    void addParameterDescriptions() {
        parameters.get(INPUT_IMAGE).setDescription("Image to be inverted.");

        parameters.get(APPLY_TO_INPUT).setDescription(
                "When selected, the input image will be replaced by the inverted image in the workspace.  If disabled, the inverted image will be stored as a new image in the workspace.");

        parameters.get(OUTPUT_IMAGE).setDescription("If \"" + APPLY_TO_INPUT
                + "\" is not selected, the inverted image will be stored as a new image in the workspace.  This is the name of the output inverted image.");

    }
}