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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.visualise.overlays;
import java.awt.Color;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.apache.commons.lang.time.DurationFormatUtils;
import org.scijava.Priority;
import org.scijava.plugin.Plugin;
import ij.ImagePlus;
import ij.gui.TextRoi;
import ij.plugin.Duplicator;
import ij.plugin.HyperStackConverter;
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.BooleanP;
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.ParameterState;
import io.github.mianalysis.mia.object.parameters.Parameters;
import io.github.mianalysis.mia.object.parameters.SeparatorP;
import io.github.mianalysis.mia.object.parameters.text.IntegerP;
import io.github.mianalysis.mia.object.parameters.text.MessageP;
import io.github.mianalysis.mia.object.parameters.text.StringP;
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.Colours;
import io.github.mianalysis.mia.object.system.Preferences;
import io.github.mianalysis.mia.object.system.Status;
import io.github.mianalysis.mia.object.units.TemporalUnit;
import io.github.mianalysis.mia.process.ColourFactory;
import io.github.mianalysis.mia.process.string.CommaSeparatedStringInterpreter;
import ome.units.UNITS;
/**
* Adds an overlay to the specified input image showing a fixed text label. Slice and frame indices can be dynamically inserted into the text using keywords.
*/
@Plugin(type = Module.class, priority = Priority.LOW, visible = true)
public class AddText extends AbstractOverlay {
TextRoi textRoi = null;
/**
*
*/
public static final String INPUT_SEPARATOR = "Image input/output";
/**
* Image onto which overlay will be rendered. Input image will only be updated if "Apply to input image" is enabled, otherwise the image containing the overlay will be stored as a new image with name specified by "Output image".
*/
public static final String INPUT_IMAGE = "Input image";
/**
* Image onto which overlay will be rendered. Input image will only be updated if "Apply to input image" is enabled, otherwise the image containing the overlay will be stored as a new image with name specified by "Output image".
*/
public static final String APPLY_TO_INPUT = "Apply to input image";
/**
* If the modifications (overlay) aren't being applied directly to the input image, this control will determine if a separate image containing the overlay should be saved to the workspace.
*/
public static final String ADD_OUTPUT_TO_WORKSPACE = "Add output image to workspace";
/**
* The name of the new image to be saved to the workspace (if not applying the changes directly to the input image).
*/
public static final String OUTPUT_IMAGE = "Output image";
/**
*
*/
public static final String RENDERING_SEPARATOR = "Overlay rendering";
/**
* Fixed text to be displayed. The current slice and frame numbers can be inserted using "D{SLICE}" and "D{FRAME}". Similarly, it's possible to insert the elapsed frame time in the form "T{HH:mm:ss.SSS}" (where this example would give hours:minutes:seconds.millis). The full description of supported time values can be found here.
*/
public static final String TEXT = "Text";
/**
*
*/
public static final String DYNAMIC_VALUES = "Available dynamic values";
/**
* Horizontal location of the text to be displayed. Specified in pixel units relative to the left of the image (x=0).
*/
public static final String X_POSITION = "X-position";
/**
* Vertical location of the text to be displayed. Specified in pixel units relative to the top of the image (y=0).
*/
public static final String Y_POSITION = "Y-position";
/**
* Z-slices on which to display the text. This is specified as a comma-separated list of slice indices. The keyword "end" is used to denote the final slice in the stack and will be interpreted automatically. Accepted formats are "[VALUE]" for a single index, "[RANGE START]-[RANGE END]" for a complete range of indices and "[RANGE START]-[RANGE-END]-[INTERVAL]" for indices evenly spaced at the specified interval.
*/
public static final String Z_RANGE = "Z-range";
/**
* Frames on which to display the text. This is specified as a comma-separated list of frame indices. The keyword "end" is used to denote the final frame in the stack and will be interpreted automatically. Accepted formats are "[VALUE]" for a single index, "[RANGE START]-[RANGE END]" for a complete range of indices and "[RANGE START]-[RANGE-END]-[INTERVAL]" for indices evenly spaced at the specified interval.
*/
public static final String FRAME_RANGE = "Frame-range";
/**
* When selected, text will be centred on the specified XY coordinate. Otherwise, text will be based with its top-left corner at the specified coordinate.
*/
public static final String CENTRE_TEXT = "Centre text";
/**
* Font size of the text label.
*/
public static final String LABEL_SIZE = "Label size";
/**
* Colour of the text label. Choices are: White, Black, Red, Orange, Yellow, Green, Cyan, Blue, Violet, Magenta.
*/
public static final String LABEL_COLOUR = "Label colour";
public AddText(Modules modules) {
super("Add text", modules);
}
public static void addOverlay(ImagePlus ipl, String text, Color color, int labelSize, double opacity, int xPosition,
int yPosition, int[] zRange, int[] frameRange, boolean centreText) {
// If necessary, turning the image into a HyperStack (if 2 dimensions=1 it will
// be a standard ImagePlus)
if (!ipl.isComposite() & (ipl.getNSlices() > 1 | ipl.getNFrames() > 1 | ipl.getNChannels() > 1))
ipl = HyperStackConverter.toHyperStack(ipl, ipl.getNChannels(), ipl.getNSlices(), ipl.getNFrames());
// Getting frame interval in second units
long frameIntervalMs = TemporalUnit.getOMEUnit()
.convertValue(ipl.getCalibration().frameInterval, UNITS.MILLISECOND).longValue();
for (int z : zRange) {
for (int f : frameRange) {
String replacedText = replaceDynamicValues(text, f, z);
replacedText = replaceTimeValues(replacedText, frameIntervalMs, f);
double[] location = new double[] { xPosition, yPosition, z };
AddLabels.addOverlay(ipl, replacedText, location, f, color, labelSize, centreText);
}
}
}
public static String replaceDynamicValues(String text, int f, int z) {
text = text.replace("D{FRAME}", String.valueOf(f));
return text.replace("D{SLICE}", String.valueOf(z));
}
public static String replaceTimeValues(String text, long frameIntervalMs, int f) {
Pattern pattern = Pattern.compile("T\\{([^\\{}]+)}");
Matcher matcher = pattern.matcher(text);
if (matcher.matches()) {
String format = matcher.group(1);
String formatted = DurationFormatUtils.formatDuration(frameIntervalMs * (f-1), format);
text = text.replace("T{" + format + "}", formatted);
}
return text;
}
@Override
public Category getCategory() {
return Categories.VISUALISATION_OVERLAYS;
}
@Override
public String getVersionNumber() {
return "1.0.0";
}
@Override
public String getDescription() {
return "Adds an overlay to the specified input image showing a fixed text label. Slice and frame indices can be dynamically inserted into the text using keywords.";
}
@Override
protected Status process(Workspace workspace) {
// Getting parameters
boolean applyToInput = parameters.getValue(APPLY_TO_INPUT, workspace);
boolean addOutputToWorkspace = parameters.getValue(ADD_OUTPUT_TO_WORKSPACE, workspace);
String outputImageName = parameters.getValue(OUTPUT_IMAGE, workspace);
// Getting input image
String inputImageName = parameters.getValue(INPUT_IMAGE, workspace);
Image inputImage = workspace.getImages().get(inputImageName);
ImagePlus ipl = inputImage.getImagePlus();
// Getting label settings
double opacity = parameters.getValue(OPACITY, workspace);
String text = parameters.getValue(TEXT, workspace);
int xPosition = parameters.getValue(X_POSITION, workspace);
int yPosition = parameters.getValue(Y_POSITION, workspace);
String zRangeString = parameters.getValue(Z_RANGE, workspace);
String frameRangeString = parameters.getValue(FRAME_RANGE, workspace);
int labelSize = parameters.getValue(LABEL_SIZE, workspace);
boolean centreText = parameters.getValue(CENTRE_TEXT, workspace);
String labelColour = parameters.getValue(LABEL_COLOUR, workspace);
Color color = ColourFactory.getColour(labelColour);
// Only add output to workspace if not applying to input
if (applyToInput)
addOutputToWorkspace = false;
// Duplicating the image, so the original isn't altered
if (!applyToInput)
ipl = new Duplicator().run(ipl);
// Converting slice and frame ranges to numbers
int[] zRange = CommaSeparatedStringInterpreter.interpretIntegers(zRangeString, true, ipl.getNSlices());
int[] frameRange = CommaSeparatedStringInterpreter.interpretIntegers(frameRangeString, true, ipl.getNFrames());
addOverlay(ipl, text, color, labelSize, opacity, xPosition, yPosition, zRange, frameRange, centreText);
Image outputImage = ImageFactory.createImage(outputImageName, ipl);
// If necessary, adding output image to workspace. This also allows us to show
// it.
if (addOutputToWorkspace)
workspace.addImage(outputImage);
if (showOutput)
outputImage.show();
return Status.PASS;
}
@Override
protected void initialiseParameters() {
super.initialiseParameters();
parameters.add(new SeparatorP(INPUT_SEPARATOR, this));
parameters.add(new InputImageP(INPUT_IMAGE, this));
parameters.add(new BooleanP(APPLY_TO_INPUT, this, false));
parameters.add(new BooleanP(ADD_OUTPUT_TO_WORKSPACE, this, false));
parameters.add(new OutputImageP(OUTPUT_IMAGE, this));
parameters.add(new SeparatorP(RENDERING_SEPARATOR, this));
parameters.add(new StringP(TEXT, this));
parameters.add(new MessageP(DYNAMIC_VALUES, this,
"The current slice and/or frame can be inserted into the rendered text by including one of the following: D{FRAME}, D{SLICE}. Elapsed time can be inserted in the form T{HH:mm:ss.SSS}.",
ParameterState.MESSAGE));
parameters.add(new IntegerP(X_POSITION, this, 0));
parameters.add(new IntegerP(Y_POSITION, this, 0));
parameters.add(new StringP(Z_RANGE, this, "1-end"));
parameters.add(new StringP(FRAME_RANGE, this, "1-end"));
parameters.add(new BooleanP(CENTRE_TEXT, this, false));
parameters.add(new IntegerP(LABEL_SIZE, this, 8));
parameters.add(new ChoiceP(LABEL_COLOUR, this, SingleColours.BLACK, SingleColours.ALL));
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(ADD_OUTPUT_TO_WORKSPACE));
if ((boolean) parameters.getValue(ADD_OUTPUT_TO_WORKSPACE, workspace)) {
returnedParameters.add(parameters.getParameter(OUTPUT_IMAGE));
}
}
returnedParameters.add(parameters.getParameter(RENDERING_SEPARATOR));
returnedParameters.add(parameters.getParameter(TEXT));
returnedParameters.add(parameters.getParameter(DYNAMIC_VALUES));
returnedParameters.add(parameters.getParameter(X_POSITION));
returnedParameters.add(parameters.getParameter(Y_POSITION));
returnedParameters.add(parameters.getParameter(Z_RANGE));
returnedParameters.add(parameters.getParameter(FRAME_RANGE));
returnedParameters.add(parameters.getParameter(CENTRE_TEXT));
returnedParameters.add(parameters.getParameter(LABEL_SIZE));
returnedParameters.add(parameters.getParameter(LABEL_COLOUR));
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;
}
@Override
protected void addParameterDescriptions() {
super.addParameterDescriptions();
parameters.get(INPUT_IMAGE)
.setDescription("Image onto which overlay will be rendered. Input image will only be updated if \""
+ APPLY_TO_INPUT
+ "\" is enabled, otherwise the image containing the overlay will be stored as a new image with name specified by \""
+ OUTPUT_IMAGE + "\".");
parameters.get(APPLY_TO_INPUT)
.setDescription("Image onto which overlay will be rendered. Input image will only be updated if \""
+ APPLY_TO_INPUT
+ "\" is enabled, otherwise the image containing the overlay will be stored as a new image with name specified by \""
+ OUTPUT_IMAGE + "\".");
parameters.get(ADD_OUTPUT_TO_WORKSPACE).setDescription(
"If the modifications (overlay) aren't being applied directly to the input image, this control will determine if a separate image containing the overlay should be saved to the workspace.");
parameters.get(OUTPUT_IMAGE).setDescription(
"The name of the new image to be saved to the workspace (if not applying the changes directly to the input image).");
parameters.get(TEXT).setDescription("Fixed text to be displayed. The current slice and frame numbers can be inserted using \"D{SLICE}\" and \"D{FRAME}\". Similarly, it's possible to insert the elapsed frame time in the form \"T{HH:mm:ss.SSS}\" (where this example would give hours:minutes:seconds.millis). The full description of supported time values can be found here.");
parameters.get(X_POSITION).setDescription(
"Horizontal location of the text to be displayed. Specified in pixel units relative to the left of the image (x=0).");
parameters.get(Y_POSITION).setDescription(
"Vertical location of the text to be displayed. Specified in pixel units relative to the top of the image (y=0).");
parameters.get(Z_RANGE).setDescription(
"Z-slices on which to display the text. This is specified as a comma-separated list of slice indices. The keyword \"end\" is used to denote the final slice in the stack and will be interpreted automatically. Accepted formats are \"[VALUE]\" for a single index, \"[RANGE START]-[RANGE END]\" for a complete range of indices and \"[RANGE START]-[RANGE-END]-[INTERVAL]\" for indices evenly spaced at the specified interval.");
parameters.get(FRAME_RANGE).setDescription(
"Frames on which to display the text. This is specified as a comma-separated list of frame indices. The keyword \"end\" is used to denote the final frame in the stack and will be interpreted automatically. Accepted formats are \"[VALUE]\" for a single index, \"[RANGE START]-[RANGE END]\" for a complete range of indices and \"[RANGE START]-[RANGE-END]-[INTERVAL]\" for indices evenly spaced at the specified interval.");
parameters.get(CENTRE_TEXT).setDescription(
"When selected, text will be centred on the specified XY coordinate. Otherwise, text will be based with its top-left corner at the specified coordinate.");
parameters.get(LABEL_SIZE).setDescription("Font size of the text label.");
parameters.get(LABEL_COLOUR).setDescription(
"Colour of the text label. Choices are: " + String.join(", ", SingleColours.ALL) + ".");
}
}