Basic Java/Matlab Interface (#2327)

* Adding basic Java Interface and example.

* Add basic matlab example

* Update matlab example that generates ellipsoids

* Add Matlab README.md

* Add docs for Java/Matlab

Examples/Java/JavaExample.java

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+import java.util.List;
+import java.util.Map;
+import edu.utah.sci.shapeworks.ShapeWorksProject;
+import java.io.*;
+
+public class JavaExample {
+    public static void main(String[] args) {
+
+        // Create a new ShapeWorksProject object
+        ShapeWorksProject project = new ShapeWorksProject();
+
+        // Define the list of shapes to be processed
+        List<String> filenames = List.of("meshes/ellipsoid_00.vtk", "meshes/ellipsoid_01.vtk",
+                "meshes/ellipsoid_02.vtk", "meshes/ellipsoid_03.vtk");
+        project.setShapes(filenames);
+
+        // Define grooming parameters
+        Map<String, String> groomingParameters = Map.of(
+                "alignment_enabled", "true",
+                "alignment_method", "Center"
+        // Add more parameters as needed
+        );
+        project.setGroomingParameters(groomingParameters);
+
+        // Define optimization parameters
+        Map<String, String> optimizationParameters = Map.of(
+                "number_of_particles", "128",
+                "initial_relative_weighting", "0.05"
+        // Add more parameters as needed
+        );
+        project.setOptimizationParameters(optimizationParameters);
+
+        System.out.println("Saving project...");
+        project.save("project.swproj");
+
+        // demonstrate loading
+        System.out.println("Loading project...");
+        project.load("project.swproj");
+
+        System.out.println("Running groom...");
+        project.groom();
+        System.out.println("Running optimize...");
+        project.optimize();
+        System.out.println("Opening ShapeWorksStudio...");
+        project.analyze();
+    }
+}

Examples/Java/README.md

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+See http://sciinstitute.github.io/ShapeWorks/latest/java/java.html

Examples/Matlab/MatlabExample.m

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+% ShapeWorks Matlab Example
+
+% Add the required directory to MATLAB's dynamic class path
+javaaddpath('/Users/amorris/sci/shapeworks/code/Java');
+
+% Add the shapeworks binary directory to the system path
+setenv('PATH', [getenv('PATH') ':/Users/amorris/sci/shapeworks/bin/bin']);
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import edu.utah.sci.shapeworks.ShapeWorksProject;
+
+% Create a new ShapeWorksProject object
+project = ShapeWorksProject();
+
+% Create a set of ellipsoid meshes to be processed, save as STL files
+for i=0:3
+    % vary radius using i for one of the ellipsoids directions
+    [x,y,z]=ellipsoid(0,0,0,50+i*10,50,50);
+    fv = surf2patch(x, y, z, 'triangles');
+    TR = triangulation(fv.faces, fv.vertices);
+    stlwrite(TR, sprintf('ellipsoid_%02d.stl', i));
+end
+
+
+% Define the list of shapes to be processed
+filenames = ArrayList();
+filenames.add('ellipsoid_00.stl');
+filenames.add('ellipsoid_01.stl');
+filenames.add('ellipsoid_02.stl');
+filenames.add('ellipsoid_03.stl');
+project.setShapes(filenames);
+
+% Define grooming parameters (using HashMap)
+groomingParameters = HashMap();
+groomingParameters.put('alignment_enabled', 'true');
+groomingParameters.put('alignment_method', 'Center');
+% Add more parameters as needed
+project.setGroomingParameters(groomingParameters);
+
+% Define optimization parameters (using HashMap)
+optimizationParameters = HashMap();
+optimizationParameters.put('number_of_particles', '128');
+optimizationParameters.put('initial_relative_weighting', '0.05');
+% Add more parameters as needed
+project.setOptimizationParameters(optimizationParameters);
+
+% Save the project
+disp('Saving project...');
+project.save('project.swproj');
+
+% Demonstrate loading the project
+disp('Loading project...');
+project.load('project.swproj');
+
+% Run the groom, optimize, and analyze steps
+disp('Running groom...');
+project.groom();
+disp('Running optimize...');
+project.optimize();
+disp('Opening ShapeWorksStudio...');
+project.analyze();

Examples/Matlab/README.md

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+See http://sciinstitute.github.io/ShapeWorks/latest/java/matlab.html

Java/ShapeWorksProject.java

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+package edu.utah.sci.shapeworks;
+
+import java.io.*;
+import java.util.*;
+
+public class ShapeWorksProject {
+    private List<String> shapes;
+    private Map<String, String> groomingParameters;
+    private Map<String, String> optimizationParameters;
+
+    public void setShapes(List<String> filenames) {
+        this.shapes = filenames;
+    }
+
+    public void setGroomingParameters(Map<String, String> groomingParameters) {
+        this.groomingParameters = groomingParameters;
+    }
+
+    public void setOptimizationParameters(Map<String, String> optimizationParameters) {
+        this.optimizationParameters = optimizationParameters;
+    }
+
+    public void save(String filename) {
+        try (PrintWriter writer = new PrintWriter(new FileOutputStream(filename))) {
+            writer.println("{");
+            writer.println("\"data\": [");
+            for (int i = 0; i < shapes.size(); i++) {
+                writer.println(
+                        " {\"shape_" + (i + 1) + "\": \"" + shapes.get(i) + "\"}" + (i < shapes.size() - 1 ? "," : ""));
+            }
+            writer.println("],");
+            writer.println("\"groom\": {");
+            writer.println(" \"1\": {");
+            int i = 0;
+            for (Map.Entry<String, String> entry : groomingParameters.entrySet()) {
+                writer.println("   \"" + entry.getKey() + "\": \"" + entry.getValue() + "\""
+                        + ((i < groomingParameters.size() - 1) ? "," : ""));
+                i++;
+            }
+            writer.println(" }");
+            writer.println("},");
+            writer.println("\"optimize\": {");
+            i = 0;
+            for (Map.Entry<String, String> entry : optimizationParameters.entrySet()) {
+                writer.println(" \"" + entry.getKey() + "\": \"" + entry.getValue() + "\""
+                        + ((i < optimizationParameters.size() - 1) ? "," : ""));
+                i++;
+            }
+            writer.println("},");
+            writer.println("\"project\": {");
+            writer.println(" \"version\": \"2\"");
+            writer.println("}");
+            writer.println("}");
+        } catch (IOException e) {
+            e.printStackTrace();
+        }
+    }
+
+    public void load(String filename) {
+        try (BufferedReader reader = new BufferedReader(new FileReader(filename))) {
+            StringBuilder jsonBuilder = new StringBuilder();
+            String line;
+            while ((line = reader.readLine()) != null) {
+                jsonBuilder.append(line.trim());
+            }
+            String json = jsonBuilder.toString();
+
+            // Basic JSON parsing (Note: This is a simplistic parser; real-world scenarios
+            // should use a complete library)
+            this.shapes = new ArrayList<>();
+            this.groomingParameters = new HashMap<>();
+            this.optimizationParameters = new HashMap<>();
+
+            // Parse data
+            int dataStart = json.indexOf("\"data\": [") + 8;
+            int dataEnd = json.indexOf("]", dataStart);
+            String dataContent = json.substring(dataStart, dataEnd);
+            String[] dataEntries = dataContent.split("},\\s*\\{");
+            for (String entry : dataEntries) {
+                shapes.add(entry.split(":")[1].replace("\"", "").replace("}", "").replace("{", "").trim());
+            }
+
+            // Parse groom
+            int groomStart = json.indexOf("\"groom\": {") + 10;
+            int groomEnd = json.indexOf("}", groomStart) + 1;
+            String groomContent = json.substring(groomStart, groomEnd);
+            String[] groomEntries = groomContent.split(",");
+            for (String entry : groomEntries) {
+                String[] keyValue = entry.split(":");
+                if (keyValue.length == 2) {
+                    groomingParameters.put(keyValue[0].replace("\"", "").trim(), keyValue[1].replace("\"", "").trim());
+                }
+            }
+            // Parse optimize
+            int optimizeStart = json.indexOf("\"optimize\": {") + 12;
+            int optimizeEnd = json.indexOf("}", optimizeStart);
+            String optimizeContent = json.substring(optimizeStart, optimizeEnd);
+            String[] optimizeEntries = optimizeContent.split(",");
+            for (String entry : optimizeEntries) {
+                String[] keyValue = entry.split(":");
+                if (keyValue.length == 2) {
+                    optimizationParameters.put(keyValue[0].replace("\"", "").trim(),
+                            keyValue[1].replace("\"", "").trim());
+                }
+            }
+        } catch (IOException e) {
+            e.printStackTrace();
+        }
+    }
+
+    public void groom() {
+        runSystemCommand("shapeworks groom --name project.swproj");
+    }
+
+    public void optimize() {
+        runSystemCommand("shapeworks optimize --name project.swproj");
+    }
+
+    public void analyze() {
+        runSystemCommand("shapeworksstudio project.swproj");
+    }
+
+    private void runSystemCommand(String command) {
+        try {
+            Process process = Runtime.getRuntime().exec(command);
+            process.waitFor();
+        } catch (IOException | InterruptedException e) {
+            e.printStackTrace();
+        }
+    }
+}

docs/java/java.md

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+# Using the ShapeWorks Java Interface
+
+This example Java program demonstrates how to use the ShapeWorks Java interface to perform the following tasks:
+
+1. Create a ShapeWorks project
+2. Add a shape to the project
+3. Set grooming parameters
+4. Set correspondence parameters
+5. Save/Load the project
+6. Run the ShapeWorks grooming pipeline
+7. Run the ShapeWorks correspondence optimization
+8. Launch the ShapeWorks Analysis GUI
+
+# Building the ShapeWorks Java Interface
+
+The ShapeWorks Java interface is built using the Java Compiler.  To build it:
+
+```
+cd shapeworks/Java
+javac -d . *.java
+```
+
+This will place the compiled classes in the `shapeworks/Java` directory.
+
+# Building the Example Java Program
+
+```
+cd shapeworks/Examples/Java
+javac -cp ../../Java *.java
+```
+
+# Running the Example Java Program
+
+Note: The example Java program assumes that the ShapeWorks executable is in $PATH.  Ensure that you can run `shapeworks` from the command line before running the example Java program.
+
+```
+java -cp ../../Java:. JavaExample
+```
+
+This will run the example Java program. The output should look like this:
+
+```
+Saving project...
+Loading project...
+Running groom...
+Running optimize...
+Opening ShapeWorksStudio...
+```
+
+And the ShapeWorks Analysis GUI will open.
+
+From here you can change to the analysis module and examine the shape model.
+
+![Studio Java Example](java_example.png){: width="600" }
+
+

docs/java/matlab.md

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+# Using the ShapeWorks Matlab Interface
+
+This example Matlab program demonstrates how to use the ShapeWorks Matlab interface via Java to perform the following tasks:
+
+1. Create a ShapeWorks project
+2. Generate Ellipsoids
+3. Add shapes to the project
+4. Set grooming parameters
+5. Set correspondence parameters
+6. Save/Load the project
+7. Run the ShapeWorks grooming pipeline
+8. Run the ShapeWorks correspondence optimization
+9. Launch the ShapeWorks Analysis GUI
+
+# Building the ShapeWorks Java Interface
+
+The ShapeWorks Java interface is built using the Java Compiler.  To build it:
+
+```
+cd shapeworks/Java
+javac -d . *.java
+```
+
+This will place the compiled classes in the `shapeworks/Java` directory.
+
+# Building the Example Java Program
+
+```
+cd shapeworks/Examples/Java
+javac -cp ../../Java *.java
+```
+
+# Running the Example Matlab Program
+
+Note: The example Matlab program uses the Java interface and needs the paths to the ShapeWorks executables.  Ensure that you update the paths in the start of the script.
+
+# Running the Example Matlab Program
+
+From the Matlab terminal, run the following:
+
+```
+cd shapeworks/Examples/Matlab
+javaaddpath('../../Java')
+MatlabExample
+```
+
+![Matlab Example](matlab_example1.png){: width="600" }
+
+
+![Studio Matlab Example](matlab_example2.png){: width="600" }
+
+

mkdocs.yml

@@ -131,6 +131,10 @@ nav:
    - Classes:    'api/Classes/index_classes.md'
    - Files:      'api/Files/index_files.md'
 
+- Java/Matlab Interface:
+   - Java Interface: 'java/java.md'
+   - Matlab Interface: 'java/matlab.md'
+
 - About:
    - 'Meet ShapeWorkers!':  'about/team.md'
    - 'Release Notes':      'about/release-notes.md'