io.github.mianalysis.mia.module.images.transform.MergeChannels 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.
package io.github.mianalysis.mia.module.images.transform;
import java.util.Arrays;
import java.util.LinkedHashMap;
import org.scijava.Priority;
import org.scijava.plugin.Plugin;
import ij.ImagePlus;
import ij.plugin.Duplicator;
import ij.plugin.HyperStackConverter;
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.ParameterGroup;
import io.github.mianalysis.mia.object.parameters.Parameters;
import io.github.mianalysis.mia.object.parameters.text.IntegerP;
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;
import io.github.mianalysis.mia.process.imagej.IntensityMinMax;
import net.imagej.ImgPlus;
import net.imagej.axis.Axes;
import net.imagej.axis.CalibratedAxis;
import net.imagej.axis.IdentityAxis;
import net.imglib2.Cursor;
import net.imglib2.cache.img.DiskCachedCellImgFactory;
import net.imglib2.img.display.imagej.ImageJFunctions;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.view.Views;
/**
* Created by sc13967 on 22/02/2018.
*/
/**
* DEPRECATED: This Module has been superseeded by the more generalised "Concatenate stacks" Module. It will be removed in a future release.
Combines image stacks as different channels. Output is automatically converted to a composite image.
*/
@Plugin(type = Module.class, priority=Priority.LOW, visible=true)
public class MergeChannels & NativeType> extends Module {
/**
* Add another image to be included in output merged image. All added images must have the same X,Y,Z and T dimensions.
*/
public static final String ADD_INPUT_IMAGE = "Add image";
public static final String INPUT_IMAGE = "Input image";
/**
* Controls where the output image is stored:
- "Create new image" Stores the merged image as a new image in the workspace with the name specified by "Output image".
- "Overwrite image" Overwrite the image specified by the index "Image index to overwrite (greater than or equal to 1)" in the workspace with the merged image.
*/
public static final String OVERWRITE_MODE = "Overwrite mode";
/**
* Name for the output merged image to be stored in the workspace with.
*/
public static final String OUTPUT_IMAGE = "Output image";
public static final String IMAGE_INDEX_TO_OVERWRITE = "Image index to overwrite (>= 1)";
public MergeChannels(Modules modules) {
super("Merge channels", modules);
deprecated = true;
}
public interface OverwriteModes {
String CREATE_NEW = "Create new image";
String OVERWRITE_IMAGE = "Overwrite image";
String[] ALL = new String[] { CREATE_NEW, OVERWRITE_IMAGE };
}
public Image combineImages(Image[] inputImages, String outputImageName) {
// Processing first two images
Image outputImage = combineImages(inputImages[0], inputImages[1], outputImageName);
// Appending any additional images
for (int i = 2; i < inputImages.length; i++) {
outputImage = combineImages(outputImage, inputImages[i], outputImageName);
}
return outputImage;
}
public Image combineImages(Image inputImage1, Image inputImage2, String outputImageName) {
ImgPlus img1 = inputImage1.getImgPlus();
ImgPlus img2 = inputImage2.getImgPlus();
int xDim1 = img1.dimensionIndex(Axes.X);
int yDim1 = img1.dimensionIndex(Axes.Y);
int cDim1 = img1.dimensionIndex(Axes.CHANNEL);
int zDim1 = img1.dimensionIndex(Axes.Z);
int tDim1 = img1.dimensionIndex(Axes.TIME);
int xDim2 = img2.dimensionIndex(Axes.X);
int yDim2 = img2.dimensionIndex(Axes.Y);
int cDim2 = img2.dimensionIndex(Axes.CHANNEL);
int zDim2 = img2.dimensionIndex(Axes.Z);
int tDim2 = img2.dimensionIndex(Axes.TIME);
long[] dimsIn1 = new long[5];
long[] dimsIn2 = new long[5];
long[] dimsOut = new long[5];
long[] offsetOut1 = new long[5];
long[] offsetOut2 = new long[5];
dimsIn1[0] = xDim1 == -1 ? 1 : img1.dimension(xDim1);
dimsIn1[1] = yDim1 == -1 ? 1 : img1.dimension(yDim1);
dimsIn1[2] = cDim1 == -1 ? 1 : img1.dimension(cDim1);
dimsIn1[3] = zDim1 == -1 ? 1 : img1.dimension(zDim1);
dimsIn1[4] = tDim1 == -1 ? 1 : img1.dimension(tDim1);
dimsIn2[0] = xDim2 == -1 ? 1 : img2.dimension(xDim2);
dimsIn2[1] = yDim2 == -1 ? 1 : img2.dimension(yDim2);
dimsIn2[2] = cDim2 == -1 ? 1 : img2.dimension(cDim2);
dimsIn2[3] = zDim2 == -1 ? 1 : img2.dimension(zDim2);
dimsIn2[4] = tDim2 == -1 ? 1 : img2.dimension(tDim2);
dimsOut[0] = xDim1 == -1 ? 1 : img1.dimension(xDim1);
dimsOut[1] = yDim1 == -1 ? 1 : img1.dimension(yDim1);
dimsOut[2] = (cDim1 == -1 ? 1 : img1.dimension(cDim1)) + (cDim2 == -1 ? 1 : img2.dimension(cDim2));
dimsOut[3] = zDim1 == -1 ? 1 : img1.dimension(zDim1);
dimsOut[4] = tDim1 == -1 ? 1 : img1.dimension(tDim1);
Arrays.fill(offsetOut1, 0);
Arrays.fill(offsetOut2, 0);
offsetOut2[2] = dimsIn1[2];
// Creating the composite image
T type = img1.firstElement();
DiskCachedCellImgFactory factory = new DiskCachedCellImgFactory(type);
ImgPlus mergedImg = new ImgPlus<>(factory.create(dimsOut));
// Assigning the relevant dimensions
CalibratedAxis xAxis = xDim1 == -1 ? new IdentityAxis(Axes.X) : img1.axis(xDim1);
mergedImg.setAxis(xAxis, 0);
CalibratedAxis yAxis = yDim1 == -1 ? new IdentityAxis(Axes.Y) : img1.axis(yDim1);
mergedImg.setAxis(yAxis, 1);
CalibratedAxis cAxis = cDim1 == -1 ? new IdentityAxis(Axes.CHANNEL) : img1.axis(cDim1);
mergedImg.setAxis(cAxis, 2);
CalibratedAxis zAxis = zDim1 == -1 ? new IdentityAxis(Axes.Z) : img1.axis(zDim1);
mergedImg.setAxis(zAxis, 3);
CalibratedAxis tAxis = tDim1 == -1 ? new IdentityAxis(Axes.TIME) : img1.axis(tDim1);
mergedImg.setAxis(tAxis, 4);
Cursor cursorIn = img1.cursor();
Cursor cursorOut = Views.offsetInterval(mergedImg, offsetOut1, dimsIn1).cursor();
while (cursorIn.hasNext())
cursorOut.next().set(cursorIn.next());
cursorIn = img2.cursor();
cursorOut = Views.offsetInterval(mergedImg, offsetOut2, dimsIn2).cursor();
while (cursorIn.hasNext())
cursorOut.next().set(cursorIn.next());
ImagePlus ipl = ImageJFunctions.wrap(mergedImg, outputImageName);
ipl = new Duplicator().run(HyperStackConverter.toHyperStack(ipl, ipl.getNChannels(), ipl.getNSlices(),
ipl.getNFrames(), "xyczt", "Composite"));
// Updating the display range to help show all the colours
IntensityMinMax.run(ipl, true, 0.001, 0.001, IntensityMinMax.PROCESS_FAST);
// Spatial calibration has to be reapplied, as it's lost in the translation
// between ImagePlus and ImgPlus
ipl.setCalibration(inputImage1.getImagePlus().getCalibration());
ipl.setPosition(1, 1, 1);
ipl.updateChannelAndDraw();
return ImageFactory.createImage(outputImageName, ipl);
}
@Override
public Category getCategory() {
return Categories.IMAGES_TRANSFORM;
}
@Override
public String getVersionNumber() {
return "1.0.0";
}
@Override
public String getDescription() {
return "DEPRECATED: This Module has been superseeded by the more generalised \"Concatenate stacks\" Module. It will "
+ "be removed in a future release.
"
+ "Combines image stacks as different channels. Output is automatically converted to a composite image.";
}
@Override
public Status process(Workspace workspace) {
// Getting parameters
String overwriteMode = parameters.getValue(OVERWRITE_MODE,workspace);
String outputImageName = parameters.getValue(OUTPUT_IMAGE,workspace);
// Creating a collection of images
LinkedHashMap collections = parameters.getValue(ADD_INPUT_IMAGE,workspace);
Image[] inputImages = new Image[collections.size()];
int i = 0;
for (Parameters collection : collections.values()) {
inputImages[i++] = workspace.getImage(collection.getValue(INPUT_IMAGE,workspace));
}
Image mergedImage = combineImages(inputImages, outputImageName);
// If the image is being saved as a new image, adding it to the workspace
switch (overwriteMode) {
case OverwriteModes.CREATE_NEW:
Image outputImage = ImageFactory.createImage(outputImageName, mergedImage.getImagePlus());
workspace.addImage(outputImage);
break;
case OverwriteModes.OVERWRITE_IMAGE:
inputImages[i - 1].setImagePlus(mergedImage.getImagePlus());
break;
}
if (showOutput)
mergedImage.show();
return Status.PASS;
}
@Override
protected void initialiseParameters() {
Parameters collection = new Parameters();
collection.add(new InputImageP(INPUT_IMAGE, this));
parameters.add(new ParameterGroup(ADD_INPUT_IMAGE, this, collection, 2));
parameters.add(new ChoiceP(OVERWRITE_MODE, this, OverwriteModes.CREATE_NEW, OverwriteModes.ALL));
parameters.add(new OutputImageP(OUTPUT_IMAGE, this));
parameters.add(new IntegerP(IMAGE_INDEX_TO_OVERWRITE, this, 1));
addParameterDescriptions();
}
@Override
public Parameters updateAndGetParameters() {
Workspace workspace = null;
Parameters returnedParameters = new Parameters();
returnedParameters.add(parameters.getParameter(ADD_INPUT_IMAGE));
returnedParameters.add(parameters.getParameter(OVERWRITE_MODE));
switch ((String) parameters.getValue(OVERWRITE_MODE,workspace)) {
case OverwriteModes.CREATE_NEW:
returnedParameters.add(parameters.getParameter(OUTPUT_IMAGE));
break;
case OverwriteModes.OVERWRITE_IMAGE:
returnedParameters.add(parameters.getParameter(IMAGE_INDEX_TO_OVERWRITE));
break;
}
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 collection = ((ParameterGroup) parameters.get(ADD_INPUT_IMAGE)).getTemplateParameters();
collection.get(INPUT_IMAGE).setDescription("Image from workspace to add to output merged image.");
parameters.get(ADD_INPUT_IMAGE).setDescription(
"Add another image to be included in output merged image. All added images must have the same X,Y,Z and T dimensions.");
parameters.get(OVERWRITE_MODE).setDescription("Controls where the output image is stored:
"
+ "- \"" + OverwriteModes.CREATE_NEW
+ "\" Stores the merged image as a new image in the workspace with the name specified by \""
+ OUTPUT_IMAGE + "\".
"
+ "- \"" + OverwriteModes.OVERWRITE_IMAGE + "\" Overwrite the image specified by the index \""
+ IMAGE_INDEX_TO_OVERWRITE + "\" in the workspace with the merged image.
");
parameters.get(OUTPUT_IMAGE)
.setDescription("Name for the output merged image to be stored in the workspace with.");
parameters.get(IMAGE_INDEX_TO_OVERWRITE).setDescription(
"If overwriting one of the input images, the image specified by this index (numbering starting at 1) will be overwritten.");
}
}