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Merge pull request #210 from mianalysis/develop
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Updated ClassSelector colour seed
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@sjcross
sjcross authored Nov 28, 2024
2 parents e14a13d + 2ec54eb commit 93212f5
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Showing 13 changed files with 219 additions and 113 deletions.
33 changes: 22 additions & 11 deletions mia-core/src/main/java/io/github/mianalysis/mia/object/image/Image.java
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Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,17 @@ public abstract class Image<T extends RealType<T> & NativeType<T>> implements Me
protected String name;
protected LinkedHashMap<String, Measurement> measurements = new LinkedHashMap<>();

public interface DisplayModes {
String COLOUR = "Colour";
String COMPOSITE = "Composite";
String COMPOSITE_INVERT = "Composite (invert)";
String COMPOSITE_MAX = "Composite (max)";
String COMPOSITE_MIN = "Composite (min)";

String[] ALL = new String[]{COLOUR, COMPOSITE, COMPOSITE_INVERT, COMPOSITE_MAX, COMPOSITE_MIN};

}

// Abstract methods

public abstract ImageRenderer getRenderer();
Expand All @@ -46,9 +57,9 @@ public abstract class Image<T extends RealType<T> & NativeType<T>> implements Me

public abstract void setRenderer(ImageRenderer imageRenderer);

public abstract void show(String title, @Nullable LUT lut, boolean normalise, boolean composite);
public abstract void show(String title, @Nullable LUT lut, boolean normalise, String displayMode);

public abstract void show(String title, @Nullable LUT lut, boolean normalise, boolean composite,
public abstract void show(String title, @Nullable LUT lut, boolean normalise, String displayMode,
Overlay overlay);

public abstract long getWidth();
Expand Down Expand Up @@ -134,11 +145,11 @@ public Measurement getMeasurement(String name) {
}

public void show(String title, LUT lut, Overlay overlay) {
show(title, lut, true, false, overlay);
show(title, lut, true, DisplayModes.COLOUR, overlay);
}

public void show(String title, LUT lut) {
show(title, lut, true, false);
show(title, lut, true, DisplayModes.COLOUR);
}

public void show(String title) {
Expand All @@ -158,28 +169,28 @@ public void show(Overlay overlay) {
}

public void show(boolean normalise) {
show(name, null, normalise, false);
show(name, null, normalise, DisplayModes.COLOUR);
}

@Deprecated
public void showImage(String title, @Nullable LUT lut, boolean normalise, boolean composite) {
show(title, lut, normalise, composite);
public void showImage(String title, @Nullable LUT lut, boolean normalise, String displayMode) {
show(title, lut, normalise, displayMode);
}

@Deprecated
public void showImage(String title, @Nullable LUT lut, boolean normalise, boolean composite,
public void showImage(String title, @Nullable LUT lut, boolean normalise, String displayMode,
Overlay overlay) {
show(title, lut, normalise, composite, overlay);
show(title, lut, normalise, displayMode, overlay);
}

@Deprecated
public void showImage(String title, LUT lut, Overlay overlay) {
show(title, lut, true, false, overlay);
show(title, lut, true, DisplayModes.COLOUR, overlay);
}

@Deprecated
public void showImage(String title, LUT lut) {
show(title, lut, true, false);
show(title, lut, true, DisplayModes.COLOUR);
}

@Deprecated
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8 changes: 4 additions & 4 deletions mia-core/src/main/java/io/github/mianalysis/mia/object/image/ImagePlusImage.java
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Expand Up @@ -192,14 +192,14 @@ public void addObjectCentroid(Obj obj, float hue) {
}
}

public void show(String title, @Nullable LUT lut, boolean normalise, boolean composite) {
public void show(String title, @Nullable LUT lut, boolean normalise, String displayMode) {
// Show using this overlay
Overlay overlay = imagePlus.getOverlay() == null ? null : imagePlus.getOverlay().duplicate();
show(title, lut, normalise, composite, overlay);
show(title, lut, normalise, displayMode, overlay);
}

public void show(String title, @Nullable LUT lut, boolean normalise, boolean composite, Overlay overlay) {
getRenderer().render(this, title, lut, normalise, composite, overlay);
public void show(String title, @Nullable LUT lut, boolean normalise, String displayMode, Overlay overlay) {
getRenderer().render(this, title, lut, normalise, displayMode, overlay);
}

public ImagePlusImage duplicate(String outputImageName) {
Expand Down
8 changes: 4 additions & 4 deletions mia-core/src/main/java/io/github/mianalysis/mia/object/image/ImgPlusImage.java
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Original file line number Diff line number Diff line change
Expand Up @@ -257,13 +257,13 @@ public static <T extends RealType<T> & NativeType<T>> void setCalibration(ImageP
}
}

public void show(String title, @Nullable LUT lut, boolean normalise, boolean composite) {
public void show(String title, @Nullable LUT lut, boolean normalise, String displayMode) {
// Show using this overlay
show(title, lut, normalise, composite, overlay);
show(title, lut, normalise, displayMode, overlay);
}

public void show(String title, @Nullable LUT lut, boolean normalise, boolean composite, Overlay overlay) {
getRenderer().render(this, title, lut, normalise, composite, overlay);
public void show(String title, @Nullable LUT lut, boolean normalise, String displayMode, Overlay overlay) {
getRenderer().render(this, title, lut, normalise, displayMode, overlay);

}

Expand Down
36 changes: 29 additions & 7 deletions mia-core/src/main/java/io/github/mianalysis/mia/object/image/renderer/ImagePlusRenderer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,8 @@

public class ImagePlusRenderer implements ImageRenderer {
@Override
public void render(Image image, String title, @Nullable LUT lut, boolean normalise, boolean composite, Overlay overlay) {
public void render(Image image, String title, @Nullable LUT lut, boolean normalise, String displayMode,
Overlay overlay) {
ImagePlus imagePlus = image.getImagePlus();

// Adds the specified overlay rather than the overlay associated with this image
Expand All @@ -27,13 +28,34 @@ public void render(Image image, String title, @Nullable LUT lut, boolean normali
if (lut != null && dispIpl.getBitDepth() != 24)
dispIpl.setLut(lut);

if (composite && dispIpl.getNChannels() > 1)
dispIpl.setDisplayMode(CompositeImage.COMPOSITE);
else
dispIpl.setDisplayMode(CompositeImage.COLOR);
switch (displayMode) {
case Image.DisplayModes.COLOUR:
dispIpl.setDisplayMode(CompositeImage.COLOR);
break;

case Image.DisplayModes.COMPOSITE:
dispIpl.setDisplayMode(CompositeImage.COMPOSITE);
dispIpl.setProp("CompositeProjection", "Sum");
break;

case Image.DisplayModes.COMPOSITE_INVERT:
dispIpl.setDisplayMode(CompositeImage.COMPOSITE);
dispIpl.setProp("CompositeProjection", "Invert");
break;

case Image.DisplayModes.COMPOSITE_MAX:
dispIpl.setDisplayMode(CompositeImage.COMPOSITE);
dispIpl.setProp("CompositeProjection", "Max");
break;

case Image.DisplayModes.COMPOSITE_MIN:
dispIpl.setDisplayMode(CompositeImage.COMPOSITE);
dispIpl.setProp("CompositeProjection", "Min");
break;
}

dispIpl.repaintWindow();
dispIpl.show();
}

}
}
2 changes: 1 addition & 1 deletion mia-core/src/main/java/io/github/mianalysis/mia/object/image/renderer/ImageRenderer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,5 +7,5 @@
import io.github.mianalysis.mia.object.image.Image;

public interface ImageRenderer {
public void render(Image image, String title, @Nullable LUT lut, boolean normalise, boolean composite, Overlay overlay);
public void render(Image image, String title, @Nullable LUT lut, boolean normalise, String displayMode, Overlay overlay);
}
46 changes: 34 additions & 12 deletions mia-core/src/main/java/io/github/mianalysis/mia/object/image/renderer/ImgPlusRenderer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -12,26 +12,48 @@
public class ImgPlusRenderer implements ImageRenderer {

@Override
public void render(Image image, String title, LUT lut, boolean normalise, boolean composite, Overlay overlay) {
ImagePlus ipl = ImageJFunctions.show(image.getImgPlus());
public void render(Image image, String title, LUT lut, boolean normalise, String displayMode, Overlay overlay) {
ImagePlus dispIpl = ImageJFunctions.show(image.getImgPlus());

// Adds the specified overlay rather than the overlay associated with this image
// ImagePlus ipl = image.getImagePlus();
ImgPlus img = image.getImgPlus();

if (lut != null && ipl.getBitDepth() != 24)
ipl.setLut(lut);
if (lut != null && dispIpl.getBitDepth() != 24)
dispIpl.setLut(lut);

if (composite && ipl.getNChannels() > 1)
ipl.setDisplayMode(CompositeImage.COMPOSITE);
else
ipl.setDisplayMode(CompositeImage.COLOR);
switch (displayMode) {
case Image.DisplayModes.COLOUR:
dispIpl.setDisplayMode(CompositeImage.COLOR);
break;

ImgPlusImage.setCalibration(ipl, img);
ipl.setOverlay(overlay);
case Image.DisplayModes.COMPOSITE:
dispIpl.setDisplayMode(CompositeImage.COMPOSITE);
dispIpl.setProp("CompositeProjection", "Sum");
break;

ipl.setTitle(title);
case Image.DisplayModes.COMPOSITE_INVERT:
dispIpl.setDisplayMode(CompositeImage.COMPOSITE);
dispIpl.setProp("CompositeProjection", "Invert");
break;

ipl.show();
case Image.DisplayModes.COMPOSITE_MAX:
dispIpl.setDisplayMode(CompositeImage.COMPOSITE);
dispIpl.setProp("CompositeProjection", "Max");
break;

case Image.DisplayModes.COMPOSITE_MIN:
dispIpl.setDisplayMode(CompositeImage.COMPOSITE);
dispIpl.setProp("CompositeProjection", "Min");
break;
}

ImgPlusImage.setCalibration(dispIpl, img);
dispIpl.setOverlay(overlay);

dispIpl.setTitle(title);

dispIpl.show();

}
}
4 changes: 2 additions & 2 deletions ...dules/src/main/java/io/github/mianalysis/mia/module/images/configure/SetDisplayRange.java
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Original file line number Diff line number Diff line change
Expand Up @@ -304,11 +304,11 @@ public Status process(Workspace workspace) {
Image outputImage = ImageFactory.createImage(outputImageName, inputImagePlus);
workspace.addImage(outputImage);
if (showOutput)
outputImage.show(outputImageName, null, false, true);
outputImage.show(outputImageName, null, false, Image.DisplayModes.COMPOSITE);

} else {
if (showOutput)
inputImage.show(inputImageName, null, false, true);
inputImage.show(inputImageName, null, false, Image.DisplayModes.COMPOSITE);

}

Expand Down
46 changes: 43 additions & 3 deletions ...odules/src/main/java/io/github/mianalysis/mia/module/images/configure/SetLookupTable.java
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Original file line number Diff line number Diff line change
@@ -1,12 +1,19 @@
package io.github.mianalysis.mia.module.images.configure;

import java.awt.Color;
import java.io.File;
import java.util.Arrays;
import java.util.TreeMap;
import java.util.TreeSet;

import org.apache.commons.lang.WordUtils;
import org.scijava.Priority;
import org.scijava.plugin.Plugin;

import ij.CompositeImage;
import ij.IJ;
import ij.ImagePlus;
import ij.plugin.LutLoader;
import ij.process.LUT;
import io.github.mianalysis.mia.module.Categories;
import io.github.mianalysis.mia.module.Category;
Expand All @@ -15,6 +22,7 @@
import io.github.mianalysis.mia.object.Workspace;
import io.github.mianalysis.mia.object.image.Image;
import io.github.mianalysis.mia.object.imagej.LUTs;
import io.github.mianalysis.mia.object.parameters.BooleanP;
import io.github.mianalysis.mia.object.parameters.ChoiceP;
import io.github.mianalysis.mia.object.parameters.InputImageP;
import io.github.mianalysis.mia.object.parameters.Parameters;
Expand Down Expand Up @@ -97,6 +105,12 @@ public class SetLookupTable extends Module {
*/
public static final String DISPLAY_MODE = "Display mode";

public static final String INVERT_LUT = "Invert LUT";


TreeMap<String,String> imageJLUTs;
// TreeMap<String, String> allLUTs;

public SetLookupTable(Modules modules) {
super("Set lookup table", modules);
}
Expand Down Expand Up @@ -261,6 +275,7 @@ public Status process(Workspace workspace) {
int channel = parameters.getValue(CHANNEL, workspace);
String displayMode = parameters.getValue(DISPLAY_MODE, workspace);
double wavelengthNM = parameters.getValue(WAVELENGTH, workspace);
boolean invertLUT = parameters.getValue(INVERT_LUT, workspace);

// If this image doesn't exist, skip this module. This returns true, because
// this isn't terminal for the analysis.
Expand All @@ -275,13 +290,23 @@ public Status process(Workspace workspace) {
switch (channelMode) {
case ChannelModes.ALL_CHANNELS:
case ChannelModes.SPECIFIC_CHANNELS:
LUT lut = getLUT(lookupTableName, wavelengthNM);
LUT lut;
if (imageJLUTs.keySet().contains(lookupTableName))
lut = LutLoader.openLut(IJ.getDir("luts") + lookupTableName + ".lut");
else
lut = getLUT(lookupTableName, wavelengthNM);

switch (displayMode) {
case DisplayModes.SET_ZERO_TO_BLACK:
lut = setZeroToBlack(lut);
break;
}

if (invertLUT)
lut = lut.createInvertedLut();

setLUT(inputImage, lut, channelMode, channel);

break;
case ChannelModes.COPY_FROM_IMAGE:
Image referenceImage = workspace.getImage(referenceImageName);
Expand All @@ -292,7 +317,7 @@ public Status process(Workspace workspace) {
inputImage.getImagePlus().updateChannelAndDraw();

if (showOutput)
inputImage.show(inputImageName, null, false, true);
inputImage.show(inputImageName, null, false, Image.DisplayModes.COMPOSITE);

return Status.PASS;

Expand All @@ -307,9 +332,22 @@ protected void initialiseParameters() {
parameters.add(new ChoiceP(CHANNEL_MODE, this, ChannelModes.ALL_CHANNELS, ChannelModes.ALL));
parameters.add(new InputImageP(REFERENCE_IMAGE, this));
parameters.add(new IntegerP(CHANNEL, this, 1));
parameters.add(new ChoiceP(LOOKUP_TABLE, this, LookupTables.GREY, LookupTables.ALL));

TreeSet<String> allLUTs = new TreeSet<>();
imageJLUTs = new TreeMap<>();

String[] lutFiles = new File(IJ.getDirectory("luts")).list();
if (lutFiles != null)
Arrays.stream(lutFiles).forEach(v -> imageJLUTs.put(WordUtils.capitalize(v.replace(".lut", "")),v));

allLUTs.addAll(imageJLUTs.keySet());
Arrays.stream(LookupTables.ALL).forEach(v -> allLUTs.add(v));

parameters.add(new ChoiceP(LOOKUP_TABLE, this, LookupTables.GREY,
allLUTs.toArray(new String[allLUTs.size()])));
parameters.add(new DoubleP(WAVELENGTH, this, 405));
parameters.add(new ChoiceP(DISPLAY_MODE, this, DisplayModes.FULL_RANGE, DisplayModes.ALL));
parameters.add(new BooleanP(INVERT_LUT, this, false));

addParameterDescriptions();

Expand All @@ -332,6 +370,7 @@ public Parameters updateAndGetParameters() {
if (((String) parameters.getValue(LOOKUP_TABLE, workspace)).equals(LookupTables.FROM_WAVELENGTH))
returnedParameters.add(parameters.getParameter(WAVELENGTH));
returnedParameters.add(parameters.getParameter(DISPLAY_MODE));
returnedParameters.add(parameters.getParameter(INVERT_LUT));
break;
case ChannelModes.COPY_FROM_IMAGE:
returnedParameters.add(parameters.getParameter(REFERENCE_IMAGE));
Expand All @@ -342,6 +381,7 @@ public Parameters updateAndGetParameters() {
if (((String) parameters.getValue(LOOKUP_TABLE, workspace)).equals(LookupTables.FROM_WAVELENGTH))
returnedParameters.add(parameters.getParameter(WAVELENGTH));
returnedParameters.add(parameters.getParameter(DISPLAY_MODE));
returnedParameters.add(parameters.getParameter(INVERT_LUT));
break;
}

Expand Down
4 changes: 2 additions & 2 deletions ...ules/src/main/java/io/github/mianalysis/mia/module/images/process/NormaliseIntensity.java
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Original file line number Diff line number Diff line change
Expand Up @@ -328,11 +328,11 @@ public Status process(Workspace workspace) {
Image outputImage = ImageFactory.createImage(outputImageName, inputImagePlus);
workspace.addImage(outputImage);
if (showOutput)
outputImage.show(outputImageName, LUT.createLutFromColor(Color.WHITE), false, true);
outputImage.show(outputImageName, LUT.createLutFromColor(Color.WHITE), false, Image.DisplayModes.COMPOSITE);

} else {
if (showOutput)
inputImage.show(inputImageName, LUT.createLutFromColor(Color.WHITE), false, true);
inputImage.show(inputImageName, LUT.createLutFromColor(Color.WHITE), false, Image.DisplayModes.COMPOSITE);

}

Expand Down
2 changes: 1 addition & 1 deletion ...modules/src/main/java/io/github/mianalysis/mia/module/objects/relate/RelateManyToOne.java
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Original file line number Diff line number Diff line change
Expand Up @@ -744,7 +744,7 @@ public Status process(Workspace workspace) {
HashMap<Integer, Float> hues2 = ColourFactory.getParentIDHues(childObjects, parentObjectName, false);
Image childImage = childObjects.convertToImage(childObjectName, hues2, 32, false);
SetDisplayRange.setDisplayRangeManual(childImage, new double[] { 0, maxID });
childImage.show(childObjectName, LUTs.Random(true, false), false, false);
childImage.show(childObjectName, LUTs.Random(true, false), false, Image.DisplayModes.COLOUR);

}

Expand Down
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