Make StarDist (and other problematic IJ2 plugins) accessible from IJ1 Macro

pom.xml

@@ -144,5 +144,17 @@
 			<artifactId>csbdeep</artifactId>
 			<version>0.3.5-SNAPSHOT</version>
 		</dependency>
+		<dependency>
+			<groupId>com.google.code.gson</groupId>
+			<artifactId>gson</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.commons</groupId>
+			<artifactId>commons-lang3</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.commons</groupId>
+			<artifactId>commons-text</artifactId>
+		</dependency>
 	</dependencies>
 </project>

src/main/java/de/csbdresden/CommandFromMacro.java

@@ -0,0 +1,267 @@
+package de.csbdresden;
+
+import java.io.File;
+import java.lang.reflect.Field;
+import java.lang.reflect.InvocationTargetException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.concurrent.ExecutionException;
+
+import org.apache.commons.lang3.ClassUtils;
+import org.apache.commons.text.StringEscapeUtils;
+import org.scijava.ItemVisibility;
+import org.scijava.Named;
+import org.scijava.command.Command;
+import org.scijava.command.CommandInfo;
+import org.scijava.command.CommandModule;
+import org.scijava.command.CommandService;
+import org.scijava.log.LogService;
+import org.scijava.module.ModuleItem;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+import org.scijava.service.Service;
+import org.scijava.ui.UIService;
+
+import com.google.gson.Gson;
+
+import de.csbdresden.stardist.StarDist2D;
+import ij.ImagePlus;
+import ij.WindowManager;
+import ij.plugin.frame.Recorder;
+import net.imagej.Dataset;
+import net.imagej.ImageJ;
+import net.imglib2.RandomAccessibleInterval;
+
+
+@Plugin(type = Command.class, label = "Command From Macro", menuPath = "Plugins > StarDist > Other > Command From Macro")
+public class CommandFromMacro implements Command {
+
+    private static final List<ItemVisibility> SKIP_VISIBILITY = Arrays.asList(ItemVisibility.MESSAGE, ItemVisibility.INVISIBLE);
+
+    @Parameter
+    private String command;
+
+    @Parameter
+    private String args;
+
+    @Parameter
+    private boolean process;
+
+    // ---------
+
+    @Parameter
+    private UIService ui;
+
+    @Parameter
+    private CommandService cmd;
+
+    @Parameter
+    private LogService log;
+
+    // ---------
+
+    @Override
+    public void run() {
+
+        CommandInfo info = cmd.getCommand(command);
+        if (info == null) {
+            for (CommandInfo c: cmd.getCommands()) {
+                try {
+                    if (command.equals(c.getMenuPath().getLeaf().getName())) {
+                        info = c;
+                        command = info.getClassName();
+                        break;
+                    }
+                } catch (NullPointerException e) {}
+            }
+            if (info == null) {
+                log.error(String.format("Command \"%s\" not found.", command));
+                return;
+            }
+        }
+
+        final Map<String,Object> params = new LinkedHashMap<>();
+        final List<String> outputs = new ArrayList<>();
+
+        Map<?,?> argsMap = new Gson().fromJson("{"+args+"}", Map.class);
+        // System.out.println(argsMap);
+
+        for (Object keyO : argsMap.keySet()) {
+            final String key = String.valueOf(keyO);
+            final String value = String.valueOf(argsMap.get(keyO));
+            ModuleItem<?> item = null;
+
+            item = info.getInput(key);
+            if (item != null) {
+                Class<?> clazz = item.getType();
+                if (clazz.isPrimitive())
+                    clazz = ClassUtils.primitiveToWrapper(clazz);
+                params.put(key, toParameter(value, clazz));
+            } else {
+                item = info.getOutput(key);
+                if (item != null) {
+                    outputs.add(key);
+                } else {
+                    log.warn(String.format("Ignoring argument \"%s\" since neither an input or output of this command.", key));
+                }
+            }
+        }
+
+        try {
+            final CommandModule result = cmd.run(command, process, params).get();
+            for (String name : outputs) {
+                final Object output = result.getOutput(name);
+                if (output != null) ui.show(output);
+            }
+        } catch (InterruptedException | ExecutionException e) {
+            e.printStackTrace();
+        }
+    }
+
+
+    private Object toParameter(final String value, final Class<?> clazz) {
+        // some special classes (TODO: incomplete)
+        if (clazz == String.class)
+            return value;
+        if (clazz == File.class)
+            return new File(value);
+        // all typical number types and boolean are covered by this
+        if (clazz.getName().startsWith("java.lang.")) {
+            try {
+                return clazz.getDeclaredMethod("valueOf", String.class).invoke(null, value);
+            } catch (NoSuchMethodException | SecurityException | IllegalAccessException | IllegalArgumentException | InvocationTargetException e) {
+                e.printStackTrace();
+            }
+        }
+        // ImagePlus and typical imagej2 image types (all that implement RAI)
+        if (clazz == ImagePlus.class || RandomAccessibleInterval.class.isAssignableFrom(clazz)) {
+            final ImagePlus imp = WindowManager.getImage(value);
+            if (imp == null)
+                log.error(String.format("Could not find input image with name/title \"%s\".", value));
+            return imp;
+        }
+        log.error(String.format("Cannot process arguments of class \"%s\".", clazz.getName()));
+        return null;
+    }
+
+
+    public static boolean record(final Command command, final CommandService commandService) {
+        return record(command, commandService, false);
+    }    
+
+    public static boolean record(final Command command, final CommandService commandService, final boolean process) {
+        if (Recorder.getInstance() == null)
+            return false;
+        final String recorded = Recorder.getCommand();
+        final CommandInfo info = commandService.getCommand(command.getClass());
+        // only proceed if this command is being recorded
+        final String name = info.getMenuPath().getLeaf().getName();
+        // System.out.printf("RECORDED: %s, COMMAND: %s\n", recorded, name);
+        if (recorded==null || !recorded.equals(name))
+            return false;
+        // prevent automatic recording
+        Recorder.setCommand(null);
+        // record manually
+        Recorder.recordString(getMacroString(command, commandService, process));
+        return true;
+    }
+
+
+    private static String getMacroString(final Command command, final CommandService commandService, final boolean process) {
+        final Class<?> commandClass = command.getClass();
+        final CommandInfo info = commandService.getCommand(command.getClass());
+        final Map<String,String> args = new LinkedHashMap<>();
+
+        // add input parameters as arguments
+        for (final ModuleItem<?> item : info.inputs()) {
+            final String name = item.getName();
+            final Class<?> clazz = item.getType();
+            if (SKIP_VISIBILITY.contains(item.getVisibility()) || // skip items that shouldn't be recorded
+                Service.class.isAssignableFrom(clazz))            // skip all (injected) services
+                continue;
+            try {
+                final Field field = commandClass.getDeclaredField(name);
+                if (!field.isAccessible()) field.setAccessible(true);
+                final Object value = field.get(command);
+                // skip unassigned items (includes buttons)
+                if (value == null)
+                    continue;
+                if (Named.class.isAssignableFrom(clazz)) // ImgPlus and Dataset
+                    args.put(name, ((Named)value).getName());
+                else if (clazz == ImagePlus.class)
+                    args.put(name, ((ImagePlus)value).getTitle());
+                else
+                    args.put(name, String.valueOf(value));
+            } catch (NoSuchFieldException | SecurityException | IllegalArgumentException | IllegalAccessException e) {
+                e.printStackTrace();
+            }
+        }
+
+        // designate assigned outputs to be shown
+        for (final ModuleItem<?> item : info.outputs()) {
+            final String name = item.getName();
+            try {
+                final Field field = commandClass.getDeclaredField(name);
+                if (!field.isAccessible()) field.setAccessible(true);
+                final Object value = field.get(command);
+                // skip unassigned outputs
+                if (value == null)
+                    continue;
+                args.put(name, "");
+            } catch (NoSuchFieldException | SecurityException | IllegalArgumentException | IllegalAccessException e) {
+                e.printStackTrace();
+            }
+        }
+
+        // convert to json and remove curly braces
+        String argsStr = new Gson().toJson(args);
+        argsStr = argsStr.substring(1, argsStr.length()-1);
+        // to make the macro string look nicer (otherwise have to escape all double quotes):
+        // replace double quotes around json keys/values with single quotes
+        // technically not correct json, but can be parsed by Gson
+        final StringBuilder sb = new StringBuilder(argsStr);
+        int p = 0;
+        for (Entry<String, String> arg: args.entrySet()) {
+            final int k = StringEscapeUtils.escapeJava(arg.getKey()).length();
+            final int v = StringEscapeUtils.escapeJava(arg.getValue()).length();
+            sb.replace(p, p+1, "'"); p+=1+k;
+            sb.replace(p, p+1, "'"); p+=2;
+            sb.replace(p, p+1, "'"); p+=1+v;
+            sb.replace(p, p+1, "'"); p+=2;            
+        }
+        argsStr = sb.toString();
+
+        final String execName = commandService.getCommand(CommandFromMacro.class).getMenuPath().getLeaf().getName();
+        return String.format("run(\"%s\", \"command=[%s], args=[%s], process=[%s]\");\n",
+                execName, commandClass.getName(), argsStr, String.valueOf(process));
+    }
+
+
+    public static void main(final String... args) throws Exception {
+
+        final ImageJ ij = new ImageJ();
+        ij.launch(args);
+
+        Dataset input = ij.scifio().datasetIO().open(StarDist2D.class.getClassLoader().getResource("yeast_crop.tif").getFile());
+        ij.ui().show(input);
+
+//        Dataset input2 = ij.scifio().datasetIO().open(StarDist2D.class.getClassLoader().getResource("yeast_timelapse.tif").getFile());
+//        ij.ui().show(input2);
+
+        Recorder recorder = new Recorder();
+        recorder.show();
+
+        final Map<String, Object> params = new LinkedHashMap<>();
+        // params.put("input", input);
+        ij.command().run(StarDist2D.class, true, params);
+
+
+//        IJ.run("CommandFromMacro", "args=[\"input\":\"yeast_crop.tif\", \"label\":\"\"], process=[false], command=[de.csbdresden.stardist.StarDist2D]");
+    }
+
+
+}

src/main/java/de/csbdresden/stardist/StarDist2D.java

@@ -29,6 +29,7 @@
 import org.scijava.widget.ChoiceWidget;
 import org.scijava.widget.NumberWidget;
 
+import de.csbdresden.CommandFromMacro;
 import ij.IJ;
 import ij.ImagePlus;
 import net.imagej.Dataset;
@@ -47,7 +48,7 @@
         @Menu(label = MenuConstants.PLUGINS_LABEL, weight = MenuConstants.PLUGINS_WEIGHT, mnemonic = MenuConstants.PLUGINS_MNEMONIC),
         @Menu(label = "StarDist"),
         @Menu(label = "StarDist 2D", weight = 1)
-}) 
+})
 public class StarDist2D extends StarDist2DBase implements Command {
 
     @Parameter(label="", visibility=ItemVisibility.MESSAGE, initializer="checkForCSBDeep")
@@ -317,6 +318,9 @@ public void run() {
                 final Future<CommandModule> futureNMS = command.run(StarDist2DNMS.class, false, paramsNMS);
                 label = (Dataset) futureNMS.get().getOutput("label");
             }
+            // call at the end of the run() method
+            CommandFromMacro.record(this, this.command);
+
         } catch (InterruptedException | ExecutionException | IOException e) {
             e.printStackTrace();
         } finally {
@@ -384,6 +388,9 @@ public static void main(final String... args) throws Exception {
 //        Dataset input = ij.scifio().datasetIO().open(StarDist2D.class.getClassLoader().getResource("yeast_timelapse.tif").getFile());
         Dataset input = ij.scifio().datasetIO().open(StarDist2D.class.getClassLoader().getResource("yeast_crop.tif").getFile());
         ij.ui().show(input);
+
+//        Recorder recorder = new Recorder();
+//        recorder.show();
 
         final HashMap<String, Object> params = new HashMap<>();
         ij.command().run(StarDist2D.class, true, params);

src/main/java/de/csbdresden/stardist/StarDist2DBase.java

@@ -163,7 +163,6 @@ protected Dataset labelImageToDataset(String outputType) {
             return Utils.raiToDataset(dataset, Opt.LABEL_IMAGE, labelImg, axes);
         } else {
             return null;
-        }
-
+        }        
     }
 }

src/main/java/de/csbdresden/stardist/StarDist2DNMS.java

@@ -16,6 +16,7 @@
 import org.scijava.widget.ChoiceWidget;
 import org.scijava.widget.NumberWidget;
 
+import de.csbdresden.CommandFromMacro;
 import ij.IJ;
 import ij.ImagePlus;
 import net.imagej.Dataset;
@@ -117,6 +118,9 @@ public void run() {
         }
 
         label = labelImageToDataset(outputType);
+
+        // call at the end of the run() method
+        CommandFromMacro.record(this, this.command);
     }