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Make StarDist2D macro-recordable #6

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Make StarDist2D macro-recordable #6

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82af25c
ignore IntelliJ files
Mar 29, 2020
a8466a9
added a mediator plugin for StarDist
Mar 29, 2020
a1a29c3
disabled nonfunctional Macro recording
Mar 29, 2020
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2 changes: 2 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -2,3 +2,5 @@
/.project
/.settings/
/target/
/.idea/
*.iml
36 changes: 35 additions & 1 deletion src/main/java/de/csbdresden/stardist/StarDist2D.java
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Expand Up @@ -16,6 +16,7 @@

import javax.swing.JOptionPane;

import ij.plugin.frame.Recorder;
import org.scijava.ItemIO;
import org.scijava.ItemVisibility;
import org.scijava.command.Command;
Expand Down Expand Up @@ -200,6 +201,7 @@ private void checkForCSBDeep() {

@Override
public void run() {
record();
checkForCSBDeep();
if (!checkInputs()) return;

Expand Down Expand Up @@ -314,7 +316,39 @@ public void run() {
}
}
}


private void record() {
if (Recorder.getInstance() == null) {
return;
}

// prevent recording of run("Star Dist 2D");
Recorder.setCommand(null);

// record by hand
Recorder.recordString("run(\"" +
"StarDist 2D (from Macro)" +
"\", \"" +
"input=[" + IJ.getImage().getTitle() + "] " +
"modelChoice=[" + modelChoice + "] " +
"modelFile=[" + modelFile + "] " +
"modelUrl=[" + modelUrl + "] " +
(normalizeInput?"normalizeinput ":"") +
"percentileBottom=" + percentileBottom + " " +
"percentileTop=" + percentileTop + " " +
"probThresh=" + probThresh + " " +
"nmsThresh=" + nmsThresh + " " +
"outputType=" + outputType + " " +
"nTiles=" + nTiles + " " +
"excludeBoundary=" + excludeBoundary + " " +
(verbose?"verbose ":"") +
(showCsbdeepProgress?"showcsbdeepprogress ":"") +
(showProbAndDist?"showprobanddist ":"") +
"\");\n"
);

}

// this function is very cumbersome... is there a better way to do this?
private Pair<Dataset, Dataset> splitPrediction(final Dataset prediction) {
final RandomAccessibleInterval<FloatType> predictionRAI = (RandomAccessibleInterval<FloatType>) prediction.getImgPlus();
Expand Down
200 changes: 200 additions & 0 deletions src/main/java/de/csbdresden/stardist/StarDist2DFromMacro.java
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@@ -0,0 +1,200 @@
package de.csbdresden.stardist;

import ij.ImagePlus;
import ij.gui.GenericDialog;
import ij.plugin.filter.PlugInFilter;
import ij.process.ImageProcessor;
import net.imagej.Data;
import net.imagej.Dataset;
import net.imagej.ImageJ;
import org.ojalgo.series.primitive.DataSeries;
import org.scijava.ItemIO;
import org.scijava.ItemVisibility;
import org.scijava.command.Command;
import org.scijava.command.CommandModule;
import org.scijava.command.CommandService;
import org.scijava.menu.MenuConstants;
import org.scijava.plugin.Menu;
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;
import org.scijava.ui.UIService;
import org.scijava.widget.Button;
import org.scijava.widget.ChoiceWidget;
import org.scijava.widget.NumberWidget;

import java.awt.*;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.io.File;
import java.io.IOException;
import java.net.URI;
import java.net.URISyntaxException;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.Future;

import static de.csbdresden.stardist.StarDist2DModel.MODEL_DSB2018_HEAVY_AUGMENTATION;
import static de.csbdresden.stardist.StarDist2DModel.MODEL_DSB2018_PAPER;
import static org.apache.log4j.helpers.Loader.getResource;

/**
* This class serves calls from the ImageJ Macro language. It's just a mediator which calls the real StartDist2D plugin.
*
* @author: haesleinhuepf
* March 2020
*/
@Plugin(type = Command.class, menu = {
@org.scijava.plugin.Menu(label = MenuConstants.PLUGINS_LABEL, weight = MenuConstants.PLUGINS_WEIGHT, mnemonic = MenuConstants.PLUGINS_MNEMONIC),
@org.scijava.plugin.Menu(label = "StarDist"),
@org.scijava.plugin.Menu(label = "Other"),
@Menu(label = "StarDist 2D (from Macro)", weight = 2)})
public class StarDist2DFromMacro implements Command {

@Parameter
private CommandService commandService;

@Parameter
private UIService uiService;

@Parameter
private Dataset input;

/* // It really doesn't work with scijava dialogs :-(
@Parameter
private String modelChoice = (String) Opt.getDefault(Opt.MODEL);

@Parameter
private boolean normalizeInput = (boolean) Opt.getDefault(Opt.NORMALIZE_IMAGE);

@Parameter
private double percentileBottom = (double) Opt.getDefault(Opt.PERCENTILE_LOW);

@Parameter
private double percentileTop = (double) Opt.getDefault(Opt.PERCENTILE_HIGH);

@Parameter
private double probThresh = (double) Opt.getDefault(Opt.PROB_THRESH);

@Parameter
private double nmsThresh = (double) Opt.getDefault(Opt.NMS_THRESH);

@Parameter
private String outputType = (String) Opt.getDefault(Opt.OUTPUT_TYPE);

@Parameter(required=false)
private String modelFile = "";

@Parameter(required=false)
protected String modelUrl = "";

@Parameter
private int nTiles = (int) Opt.getDefault(Opt.NUM_TILES);

@Parameter
private int excludeBoundary = (int) Opt.getDefault(Opt.EXCLUDE_BNDRY);

@Parameter
private boolean verbose = (boolean) Opt.getDefault(Opt.VERBOSE);

@Parameter
private boolean showCsbdeepProgress = (boolean) Opt.getDefault(Opt.CSBDEEP_PROGRESS_WINDOW);

@Parameter
private boolean showProbAndDist = (boolean) Opt.getDefault(Opt.SHOW_PROB_DIST);
*/


@Override
public void run() {
// Build an ImageJ1 generic dialog
String modelChoice = (String) Opt.getDefault(Opt.MODEL);
boolean normalizeInput = (boolean) Opt.getDefault(Opt.NORMALIZE_IMAGE);
double percentileBottom = (double) Opt.getDefault(Opt.PERCENTILE_LOW);
double percentileTop = (double) Opt.getDefault(Opt.PERCENTILE_HIGH);
double probThresh = (double) Opt.getDefault(Opt.PROB_THRESH);
double nmsThresh = (double) Opt.getDefault(Opt.NMS_THRESH);
String outputType = (String) Opt.getDefault(Opt.OUTPUT_TYPE);
String modelFile = "";
String modelUrl = "";
int nTiles = (int) Opt.getDefault(Opt.NUM_TILES);
int excludeBoundary = (int) Opt.getDefault(Opt.EXCLUDE_BNDRY);
boolean verbose = (boolean) Opt.getDefault(Opt.VERBOSE);
boolean showCsbdeepProgress = (boolean) Opt.getDefault(Opt.CSBDEEP_PROGRESS_WINDOW);
boolean showProbAndDist = (boolean) Opt.getDefault(Opt.SHOW_PROB_DIST);

GenericDialog gd = new GenericDialog("StarDist2D (From Macro)");
gd.addMessage("This plugin is thought for being called via ImageJ scripting only. Use 'StarDist 2D' instead.");

gd.addStringField("modelChoice", modelChoice);
gd.addCheckbox("normalizeInput", normalizeInput);
gd.addNumericField("percentileBottom", percentileBottom, 3);
gd.addNumericField("percentileTop", percentileTop, 3);
gd.addNumericField("probThresh", probThresh, 3);
gd.addNumericField("nmsThresh", nmsThresh, 3);
gd.addStringField("outputType", outputType);
gd.addStringField("modelFile", modelFile);
gd.addStringField("modelUrl", modelUrl);
gd.addNumericField("nTiles", nTiles, 0);
gd.addNumericField("excludeBoundary", excludeBoundary, 0);
gd.addCheckbox("verbose", verbose);
gd.addCheckbox("showCsbdeepProgress", showCsbdeepProgress);
gd.addCheckbox("showProbAndDist", showProbAndDist);

gd.showDialog();

if (gd.wasCanceled()) {
return;
}

modelChoice = gd.getNextString();
normalizeInput = gd.getNextBoolean();
percentileBottom = gd.getNextNumber();
percentileTop = gd.getNextNumber();
probThresh = gd.getNextNumber();
nmsThresh = gd.getNextNumber();
outputType = gd.getNextString();
modelFile = gd.getNextString();
modelUrl = gd.getNextString();
nTiles = (int)gd.getNextNumber();
excludeBoundary = (int)gd.getNextNumber();
verbose = gd.getNextBoolean();
showCsbdeepProgress = gd.getNextBoolean();
showProbAndDist = gd.getNextBoolean();

System.out.println("normalizeInput was "+ normalizeInput);

Future module = commandService.run(StarDist2D.class, false,
"input", input,
"modelChoice", modelChoice,
"modelFile", (modelFile!=null?new File(modelFile):""),
"modelUrl", (modelUrl!=null?modelUrl:""),
"normalizeInput", new Boolean(normalizeInput),
"percentileBottom", percentileBottom,
"percentileTop", percentileTop,
"probThresh", probThresh,
"nmsThresh", nmsThresh,
"outputType", outputType,
"nTiles", nTiles,
"excludeBoundary", excludeBoundary,
"verbose", verbose,
"showCsbdeepProgress", showCsbdeepProgress,
"showProbAndDist", showProbAndDist
);

CommandModule res = null;

try {
res = (CommandModule) module.get();
} catch (InterruptedException e) {
e.printStackTrace();
} catch (ExecutionException e) {
e.printStackTrace();
}

System.out.println("RES: " + res.toString());
System.out.println("RES class: " + res.getClass());

Dataset label = (Dataset) res.getOutput("label");
uiService.show(label);
}
}