Add IJM macro compatible commands

There is a bug somewhere in the SciJava IJ1 compatibility layer.
An output ImagePlus or Dataset is not properly recognized in IJM scripts.
It's unlikely that this bug will be fixed soon. So I provide a work
around for Labkit.

src/main/java/sc/fiji/labkit/ui/plugin/CalculateProbabilityMapWithLabkitIJ1Plugin.java

@@ -0,0 +1,99 @@
+/*-
+ * #%L
+ * The Labkit image segmentation tool for Fiji.
+ * %%
+ * Copyright (C) 2017 - 2023 Matthias Arzt
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package sc.fiji.labkit.ui.plugin;
+
+import ij.ImagePlus;
+import net.imglib2.img.VirtualStackAdapter;
+import net.imglib2.img.display.imagej.ImageJFunctions;
+import org.scijava.Cancelable;
+import org.scijava.Context;
+import org.scijava.ItemIO;
+import org.scijava.app.StatusService;
+import org.scijava.command.Command;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+import sc.fiji.labkit.ui.segmentation.SegmentationTool;
+import sc.fiji.labkit.ui.utils.progress.StatusServiceProgressWriter;
+
+import java.io.File;
+
+/**
+ * @author Robert Haase
+ * @author Matthias Arzt
+ */
+@Plugin(type = Command.class,
+	menuPath = "Plugins > Labkit > Macro Recordable > Calculate Probability Map With Labkit (IJ1)")
+public class CalculateProbabilityMapWithLabkitIJ1Plugin implements Command, Cancelable {
+
+	@Parameter
+	private Context context;
+
+	@Parameter
+	private StatusService statusService;
+
+	@Parameter
+	private ImagePlus input;
+
+	@Parameter
+	private File segmenter_file;
+
+	@Parameter(type = ItemIO.OUTPUT)
+	private ImagePlus output;
+
+	@Parameter(required = false)
+	private Boolean use_gpu = false;
+
+	@Override
+	public void run() {
+		SegmentationTool segmenter = new SegmentationTool();
+		segmenter.setContext(context);
+		segmenter.openModel(segmenter_file.getAbsolutePath());
+		segmenter.setUseGpu(use_gpu);
+		segmenter.setProgressWriter(new StatusServiceProgressWriter(statusService));
+		output = ImageJFunctions.wrap(
+			segmenter.probabilityMap(VirtualStackAdapter.wrap(input)), "");
+		output.show();
+	}
+
+	@Override
+	public boolean isCanceled() {
+		return false;
+	}
+
+	@Override
+	public void cancel(String reason) {
+
+	}
+
+	@Override
+	public String getCancelReason() {
+		return null;
+	}
+}

src/main/java/sc/fiji/labkit/ui/plugin/CalculateProbabilityMapWithLabkitPlugin.java

@@ -6,13 +6,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -29,26 +29,16 @@
 
 package sc.fiji.labkit.ui.plugin;
 
-import bdv.export.ProgressWriterConsole;
 import net.imagej.Dataset;
 import net.imagej.DatasetService;
-import net.imagej.ImgPlus;
-import net.imglib2.img.Img;
-import net.imglib2.type.numeric.real.FloatType;
-import net.imglib2.util.Intervals;
 import org.scijava.Cancelable;
 import org.scijava.Context;
 import org.scijava.ItemIO;
 import org.scijava.app.StatusService;
 import org.scijava.command.Command;
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
-import sc.fiji.labkit.ui.inputimage.DatasetInputImage;
 import sc.fiji.labkit.ui.segmentation.SegmentationTool;
-import sc.fiji.labkit.ui.segmentation.SegmentationUtils;
-import sc.fiji.labkit.ui.segmentation.Segmenter;
-import sc.fiji.labkit.ui.segmentation.weka.TrainableSegmentationSegmenter;
-import sc.fiji.labkit.ui.utils.ParallelUtils;
 import sc.fiji.labkit.ui.utils.progress.StatusServiceProgressWriter;
 
 import java.io.File;

src/main/java/sc/fiji/labkit/ui/plugin/SegmentImageWithLabkitIJ1Plugin.java

@@ -0,0 +1,97 @@
+/*-
+ * #%L
+ * The Labkit image segmentation tool for Fiji.
+ * %%
+ * Copyright (C) 2017 - 2023 Matthias Arzt
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package sc.fiji.labkit.ui.plugin;
+
+import java.io.File;
+
+import ij.ImagePlus;
+import net.imglib2.img.VirtualStackAdapter;
+import net.imglib2.img.display.imagej.ImageJFunctions;
+import org.scijava.Cancelable;
+import org.scijava.Context;
+import org.scijava.ItemIO;
+import org.scijava.app.StatusService;
+import org.scijava.command.Command;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+import sc.fiji.labkit.ui.segmentation.SegmentationTool;
+import sc.fiji.labkit.ui.utils.progress.StatusServiceProgressWriter;
+
+/**
+ * @author Matthias Arzt
+ */
+@Plugin(type = Command.class,
+	menuPath = "Plugins > Labkit > Macro Recordable > Segment Image With Labkit (IJ1)")
+public class SegmentImageWithLabkitIJ1Plugin implements Command, Cancelable {
+
+	@Parameter
+	private Context context;
+
+	@Parameter
+	private StatusService statusService;
+
+	@Parameter
+	private ImagePlus input;
+
+	@Parameter
+	private File segmenter_file;
+
+	@Parameter(type = ItemIO.OUTPUT)
+	private ImagePlus output;
+
+	@Parameter(required = false)
+	private Boolean use_gpu = false;
+
+	@Override
+	public void run() {
+		SegmentationTool segmenter = new SegmentationTool();
+		segmenter.setContext(context);
+		segmenter.setUseGpu(use_gpu);
+		segmenter.setProgressWriter(new StatusServiceProgressWriter(statusService));
+		segmenter.openModel(segmenter_file.getAbsolutePath());
+		output = ImageJFunctions.wrap(segmenter.segment(VirtualStackAdapter.wrap(input)), "");
+		output.show();
+	}
+
+	@Override
+	public boolean isCanceled() {
+		return false;
+	}
+
+	@Override
+	public void cancel(String reason) {
+
+	}
+
+	@Override
+	public String getCancelReason() {
+		return null;
+	}
+}

src/test/java/sc/fiji/labkit/ui/plugin/CalculateProbabilityMapWithLabkitIJ1PluginTest.java

@@ -0,0 +1,47 @@
+package sc.fiji.labkit.ui.plugin;
+
+import static org.junit.Assert.assertTrue;
+
+import java.io.File;
+import java.io.IOException;
+
+import ij.IJ;
+import ij.ImagePlus;
+import ij.macro.Interpreter;
+import net.imglib2.img.VirtualStackAdapter;
+import net.imglib2.test.ImgLib2Assert;
+import org.junit.Test;
+import sc.fiji.labkit.pixel_classification.utils.SingletonContext;
+
+public class CalculateProbabilityMapWithLabkitIJ1PluginTest {
+
+	@Test
+	public void test() throws IOException {
+		SingletonContext.getInstance();
+		String inputImage = fullPath("/blobs.tif");
+		String blobsModel = fullPath("/blobs.classifier");
+		String source = fullPath("/blobs_probability_map.tif");
+		File outputImage = File.createTempFile("labkit-segmentation-test", ".tif");
+		String macroTemplate = "close('*');\n" +
+			"open('INPUT_TIF');\n" +
+			"run('Calculate Probability Map With Labkit (IJ1)', 'segmenter_file=SEGMENTER_FILE use_gpu=false');\n" +
+			"selectImage('probability map for blobs.tif');\n" +
+			"saveAs('Tiff', 'OUTPUT_TIF');\n" +
+			"close('*');\n";
+		String macro = macroTemplate
+			.replace('\'', '"')
+			.replace("INPUT_TIF", inputImage)
+			.replace("SEGMENTER_FILE", blobsModel)
+			.replace("OUTPUT_TIF", outputImage.getAbsolutePath());
+		new Interpreter().run(macro);
+		assertTrue(outputImage.exists());
+		ImagePlus expected = IJ.openImage(source);
+		ImagePlus result = IJ.openImage(outputImage.getAbsolutePath());
+		ImgLib2Assert.assertImageEquals(VirtualStackAdapter.wrap(expected), VirtualStackAdapter.wrap(result), Object::equals);
+	}
+
+	private String fullPath(String name) {
+		return SegmentImageWithLabkitPluginTest.class.getResource(
+			name).getFile();
+	}
+}

src/test/java/sc/fiji/labkit/ui/plugin/SegmentImageWithLabkitIJ1PluginTest.java

@@ -0,0 +1,47 @@
+package sc.fiji.labkit.ui.plugin;
+
+import static org.junit.Assert.assertTrue;
+
+import java.io.File;
+import java.io.IOException;
+
+import ij.IJ;
+import ij.ImagePlus;
+import ij.macro.Interpreter;
+import net.imglib2.img.VirtualStackAdapter;
+import net.imglib2.test.ImgLib2Assert;
+import org.junit.Test;
+import sc.fiji.labkit.pixel_classification.utils.SingletonContext;
+
+public class SegmentImageWithLabkitIJ1PluginTest {
+
+	@Test
+	public void test() throws IOException {
+		SingletonContext.getInstance();
+		String inputImage = fullPath("/blobs.tif");
+		String blobsModel = fullPath("/blobs.classifier");
+		String source = fullPath("/blobs_segmentation.tif");
+		File outputImage = File.createTempFile("labkit-segmentation-test", ".tif");
+		String macroTemplate = "close('*');\n" +
+			"open('INPUT_TIF');\n" +
+			"run('Segment Image With Labkit (IJ1)', 'segmenter_file=SEGMENTER_FILE use_gpu=false');\n" +
+			"selectImage('segmentation of blobs.tif');\n" +
+			"saveAs('Tiff', 'OUTPUT_TIF');\n" +
+			"close('*');\n";
+		String macro = macroTemplate
+			.replace('\'', '"')
+			.replace("INPUT_TIF", inputImage)
+			.replace("SEGMENTER_FILE", blobsModel)
+			.replace("OUTPUT_TIF", outputImage.getAbsolutePath());
+		new Interpreter().run(macro);
+		assertTrue(outputImage.exists());
+		ImagePlus expected = IJ.openImage(source);
+		ImagePlus result = IJ.openImage(outputImage.getAbsolutePath());
+		ImgLib2Assert.assertImageEquals(VirtualStackAdapter.wrap(expected), VirtualStackAdapter.wrap(result), Object::equals);
+	}
+
+	private String fullPath(String name) {
+		return SegmentImageWithLabkitPluginTest.class.getResource(
+			name).getFile();
+	}
+}

src/test/java/sc/fiji/labkit/ui/utils/TestResources.java

@@ -0,0 +1,2 @@
+package sc.fiji.labkit.ui.utils;public class TestResources {
+}