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Added Preview function for on-the-fly update ROIs #12

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Added Preview function for on-the-fly update ROIs #12

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cbcb25d
Added Preview function for on-the-fly update ROIs
hkmoon Jul 8, 2021
4d73d7c
Handle RoiManager.getInstance() null case
hkmoon Jul 9, 2021
6bca302
Removed the Labelled roi for simplicity
hkmoon Jul 9, 2021
da559fa
Changed preview checkbox to button
hkmoon Jul 9, 2021
24dcd19
Added Previewable implementation for on-the-fly ROI update
hkmoon Jul 11, 2021
fce718b
Used the given parameters for calling refresh()
hkmoon Jul 21, 2021
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2 changes: 2 additions & 0 deletions src/main/java/de/csbdresden/stardist/Opt.java
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Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,7 @@ public class Opt {
public static final String SHOW_PROB_DIST = "Show CNN Output";
public static final String SET_THRESHOLDS = "Set optimized postprocessing thresholds (for selected model)";
public static final String RESTORE_DEFAULTS = "Restore Defaults";
public static final String PREVIEW = "Preview";

// TODO: add descriptions for all options

Expand All @@ -56,6 +57,7 @@ public class Opt {
DEFAULTS.put(VERBOSE, false);
DEFAULTS.put(CSBDEEP_PROGRESS_WINDOW, false);
DEFAULTS.put(SHOW_PROB_DIST, false);
DEFAULTS.put(PREVIEW, false);
}

static Object getDefault(final String key) {
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68 changes: 67 additions & 1 deletion src/main/java/de/csbdresden/stardist/StarDist2D.java
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Original file line number Diff line number Diff line change
Expand Up @@ -16,11 +16,15 @@
import java.util.stream.IntStream;

import javax.swing.JOptionPane;
import javax.swing.SwingUtilities;

import ij.plugin.frame.RoiManager;
import org.scijava.Cancelable;
import org.scijava.ItemIO;
import org.scijava.ItemVisibility;
import org.scijava.command.Command;
import org.scijava.command.CommandModule;
import org.scijava.command.Previewable;
import org.scijava.menu.MenuConstants;
import org.scijava.plugin.Menu;
import org.scijava.plugin.Parameter;
Expand Down Expand Up @@ -49,7 +53,7 @@
@Menu(label = "StarDist"),
@Menu(label = "StarDist 2D", weight = 1)
})
public class StarDist2D extends StarDist2DBase implements Command {
public class StarDist2D extends StarDist2DBase implements Command, Previewable, Cancelable {

@Parameter(label="", visibility=ItemVisibility.MESSAGE, initializer="checkForCSBDeep")
private final String msgTitle = "<html>" +
Expand Down Expand Up @@ -147,6 +151,12 @@ public class StarDist2D extends StarDist2DBase implements Command {
@Parameter(label=Opt.RESTORE_DEFAULTS, callback="restoreDefaults")
private Button restoreDefaults;

@Parameter(label=Opt.PREVIEW)
private boolean preview = (boolean) Opt.getDefault(Opt.PREVIEW);

// @Parameter(label=Opt.PREVIEW, callback="refreshROI")
// private Button updateROI;

// ---------

private void restoreDefaults() {
Expand All @@ -163,6 +173,7 @@ private void restoreDefaults() {
verbose = (boolean) Opt.getDefault(Opt.VERBOSE);
showCsbdeepProgress = (boolean) Opt.getDefault(Opt.CSBDEEP_PROGRESS_WINDOW);
showProbAndDist = (boolean) Opt.getDefault(Opt.SHOW_PROB_DIST);
preview = (boolean) Opt.getDefault(Opt.PREVIEW);
}

private void percentileBottomChanged() {
Expand Down Expand Up @@ -400,4 +411,59 @@ public static void main(final String... args) throws Exception {
ij.command().run(StarDist2D.class, true, params);
}

private void refresh() {
final HashMap<String, Object> params = new HashMap<>();

params.put("input", input);
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For timelapse input data: should the preview only be for the current frame (how to even get that?) or the entire sequence (potentially slow)?

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It depends on the actual processing logic of StarDist. Does it probably take into account of whole timeseries of the input image? Then, it will be slow as you expected. How do you handle ROIs over time in this case?

params.put("modelChoice", modelChoice);
params.put("normalizeInput", normalizeInput);
params.put("percentileBottom", percentileBottom);
params.put("percentileTop", percentileTop);
params.put("probThresh", probThresh);
params.put("nmsThresh", nmsThresh);
params.put("outputType", "ROI Manager");
params.put("nTiles", nTiles);
params.put("excludeBoundary", excludeBoundary);
params.put("roiPosition", Opt.ROI_POSITION_AUTO);

command.run(StarDist2D.class, false, params);
}

private void refreshROI() {
if (!SwingUtilities.isEventDispatchThread()) {
SwingUtilities.invokeLater(this::refresh);
} else {
refresh();
}
}

@Override
public void preview() {
if (preview) {
refreshROI();
}
}

@Override
public void cancel() {
}

@Override
public boolean isCanceled() {
return false;
}

@Override
public void cancel(String s) {
if (RoiManager.getInstance() == null) {
new RoiManager().reset();
} else {
RoiManager.getInstance().reset();
}
}

@Override
public String getCancelReason() {
return null;
}
}
7 changes: 5 additions & 2 deletions src/main/java/de/csbdresden/stardist/StarDist2DBase.java
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Original file line number Diff line number Diff line change
Expand Up @@ -112,9 +112,12 @@ protected void exportROIs(Candidates polygons, int framePosition, long numFrames
roiManager.add(bboxRoi, -1);
}
}
if (roiManager.isVisible()) roiManager.repaint();
if (roiManager.isVisible()) {
roiManager.repaint();
roiManager.runCommand("show all");
}
}

protected void setRoiPosition(Roi roi, int framePosition, String roiPosition) {
switch (roiPosition) {
case Opt.ROI_POSITION_STACK:
Expand Down