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

import ij.ImagePlus;
import ij.plugin.Resizer;
import ij.process.ImageProcessor;
import io.github.mianalysis.mia.MIA;
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.ChoiceP;
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 23/03/2018.
 */

/**
* Interpolates Z-axis of image to match XY spatial calibration
*/
@Plugin(type = Module.class, priority=Priority.LOW, visible=true)
public class InterpolateZAxis extends Module {

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

	/**
	* Input image to which the Z-axis interpolation will be applied.
	*/
    public static final String INPUT_IMAGE = "Input image";

	/**
	* Output image with Z-axis interpolation applied.  This image will be stored in the workspace and be accessible using this name.
	*/
    public static final String OUTPUT_IMAGE = "Output image";


	/**
	* 
	*/
    public static final String INTERPOLATION_SEPARATOR = "Interpolation options";

	/**
	* Controls how interpolated pixel values are calculated.
	*/
    public static final String INTERPOLATION_MODE = "Interpolation mode";

    public interface InterpolationModes {
        String NONE = "None";
        String BICUBIC = "Bicubic";
        String BILINEAR = "Bilinear";

        String[] ALL = new String[] { NONE, BICUBIC, BILINEAR };

    }

    public InterpolateZAxis(Modules modules) {
        super("Interpolate Z axis", modules);
    }

    public static ImagePlus matchZToXY(ImagePlus inputImagePlus, String interpolationMode) {
        // Calculating scaling
        int nSlices = inputImagePlus.getNSlices();
        double distPerPxXY = inputImagePlus.getCalibration().pixelWidth;
        double distPerPxZ = inputImagePlus.getCalibration().pixelDepth;
        if (Double.isNaN(distPerPxXY) || Double.isNaN(distPerPxZ)) {
            MIA.log.writeWarning("XY or Z spatial calibration missing.  Interpolation not applied");
            return inputImagePlus.duplicate();
        }

        int finalNSlices = (int) Math.round(nSlices * distPerPxZ / distPerPxXY);

        // Checking if interpolation is necessary
        if (finalNSlices == nSlices)
            return inputImagePlus;

        Resizer resizer = new Resizer();
        resizer.setAverageWhenDownsizing(true);

        int interpolation = ImageProcessor.NONE;
        switch (interpolationMode) {
            case InterpolationModes.BICUBIC:
                interpolation = ImageProcessor.BICUBIC;
                break;
            case InterpolationModes.BILINEAR:
                interpolation = ImageProcessor.BILINEAR;
                break;
        }
        ImagePlus resized = resizer.zScale(inputImagePlus, finalNSlices, interpolation + Resizer.IN_PLACE);
        resized.setDimensions(inputImagePlus.getNChannels(), finalNSlices, inputImagePlus.getNFrames());

        return resized;

    }

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

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

    @Override
    public String getDescription() {
        return "Interpolates Z-axis of image to match XY spatial calibration";
    }

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

        // Getting parameters
        String outputImageName = parameters.getValue(OUTPUT_IMAGE,workspace);
        String interpolationMode = parameters.getValue(INTERPOLATION_MODE,workspace);

        ImagePlus outputImagePlus = matchZToXY(inputImagePlus, interpolationMode);

        Image outputImage = ImageFactory.createImage(outputImageName, outputImagePlus);
        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 OutputImageP(OUTPUT_IMAGE, this));

        parameters.add(new SeparatorP(INTERPOLATION_SEPARATOR, this));
        parameters.add(new ChoiceP(INTERPOLATION_MODE, this, InterpolationModes.BILINEAR, InterpolationModes.ALL));

        addParameterDescriptions();

    }

    @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;
    }

    void addParameterDescriptions() {
        parameters.get(INPUT_IMAGE).setDescription("Input image to which the Z-axis interpolation will be applied.");

        parameters.get(OUTPUT_IMAGE).setDescription(
                "Output image with Z-axis interpolation applied.  This image will be stored in the workspace and be accessible using this name.");

        parameters.get(INTERPOLATION_MODE).setDescription("Controls how interpolated pixel values are calculated.");
    }
}