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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
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‎Examples/Java/JavaExample.java

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

‎Examples/Java/README.md

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

‎Examples/Java/meshes/ellipsoid_00.vtk

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‎Examples/Java/meshes/ellipsoid_01.vtk

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‎Examples/Java/meshes/ellipsoid_02.vtk

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‎Examples/Java/meshes/ellipsoid_03.vtk

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‎Examples/Matlab/MatlabExample.m

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% ShapeWorks Matlab Example
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% Add the required directory to MATLAB's dynamic class path
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javaaddpath('/Users/amorris/sci/shapeworks/code/Java');
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% Add the shapeworks binary directory to the system path
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setenv('PATH', [getenv('PATH') ':/Users/amorris/sci/shapeworks/bin/bin']);
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import java.util.ArrayList;
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import java.util.HashMap;
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import edu.utah.sci.shapeworks.ShapeWorksProject;
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% Create a new ShapeWorksProject object
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project = ShapeWorksProject();
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% Create a set of ellipsoid meshes to be processed, save as STL files
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for i=0:3
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% vary radius using i for one of the ellipsoids directions
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[x,y,z]=ellipsoid(0,0,0,50+i*10,50,50);
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fv = surf2patch(x, y, z, 'triangles');
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TR = triangulation(fv.faces, fv.vertices);
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stlwrite(TR, sprintf('ellipsoid_%02d.stl', i));
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end
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% Define the list of shapes to be processed
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filenames = ArrayList();
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filenames.add('ellipsoid_00.stl');
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filenames.add('ellipsoid_01.stl');
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filenames.add('ellipsoid_02.stl');
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filenames.add('ellipsoid_03.stl');
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project.setShapes(filenames);
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% Define grooming parameters (using HashMap)
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groomingParameters = HashMap();
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groomingParameters.put('alignment_enabled', 'true');
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groomingParameters.put('alignment_method', 'Center');
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% Add more parameters as needed
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project.setGroomingParameters(groomingParameters);
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% Define optimization parameters (using HashMap)
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optimizationParameters = HashMap();
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optimizationParameters.put('number_of_particles', '128');
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optimizationParameters.put('initial_relative_weighting', '0.05');
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% Add more parameters as needed
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project.setOptimizationParameters(optimizationParameters);
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% Save the project
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disp('Saving project...');
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project.save('project.swproj');
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% Demonstrate loading the project
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disp('Loading project...');
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project.load('project.swproj');
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% Run the groom, optimize, and analyze steps
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disp('Running groom...');
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project.groom();
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disp('Running optimize...');
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project.optimize();
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disp('Opening ShapeWorksStudio...');
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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;
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import java.io.*;
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import java.util.*;
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public class ShapeWorksProject {
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private List<String> shapes;
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private Map<String, String> groomingParameters;
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private Map<String, String> optimizationParameters;
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public void setShapes(List<String> filenames) {
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this.shapes = filenames;
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}
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public void setGroomingParameters(Map<String, String> groomingParameters) {
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this.groomingParameters = groomingParameters;
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}
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public void setOptimizationParameters(Map<String, String> optimizationParameters) {
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this.optimizationParameters = optimizationParameters;
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}
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public void save(String filename) {
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try (PrintWriter writer = new PrintWriter(new FileOutputStream(filename))) {
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writer.println("{");
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writer.println("\"data\": [");
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for (int i = 0; i < shapes.size(); i++) {
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writer.println(
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" {\"shape_" + (i + 1) + "\": \"" + shapes.get(i) + "\"}" + (i < shapes.size() - 1 ? "," : ""));
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}
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writer.println("],");
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writer.println("\"groom\": {");
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writer.println(" \"1\": {");
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int i = 0;
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for (Map.Entry<String, String> entry : groomingParameters.entrySet()) {
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writer.println(" \"" + entry.getKey() + "\": \"" + entry.getValue() + "\""
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+ ((i < groomingParameters.size() - 1) ? "," : ""));
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i++;
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}
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writer.println(" }");
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writer.println("},");
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writer.println("\"optimize\": {");
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i = 0;
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for (Map.Entry<String, String> entry : optimizationParameters.entrySet()) {
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writer.println(" \"" + entry.getKey() + "\": \"" + entry.getValue() + "\""
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+ ((i < optimizationParameters.size() - 1) ? "," : ""));
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i++;
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}
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writer.println("},");
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writer.println("\"project\": {");
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writer.println(" \"version\": \"2\"");
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writer.println("}");
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writer.println("}");
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} catch (IOException e) {
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e.printStackTrace();
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}
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}
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public void load(String filename) {
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try (BufferedReader reader = new BufferedReader(new FileReader(filename))) {
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StringBuilder jsonBuilder = new StringBuilder();
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String line;
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while ((line = reader.readLine()) != null) {
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jsonBuilder.append(line.trim());
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}
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String json = jsonBuilder.toString();
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// Basic JSON parsing (Note: This is a simplistic parser; real-world scenarios
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// should use a complete library)
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this.shapes = new ArrayList<>();
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this.groomingParameters = new HashMap<>();
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this.optimizationParameters = new HashMap<>();
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// Parse data
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int dataStart = json.indexOf("\"data\": [") + 8;
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int dataEnd = json.indexOf("]", dataStart);
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String dataContent = json.substring(dataStart, dataEnd);
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String[] dataEntries = dataContent.split("},\\s*\\{");
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for (String entry : dataEntries) {
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shapes.add(entry.split(":")[1].replace("\"", "").replace("}", "").replace("{", "").trim());
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}
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// Parse groom
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int groomStart = json.indexOf("\"groom\": {") + 10;
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int groomEnd = json.indexOf("}", groomStart) + 1;
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String groomContent = json.substring(groomStart, groomEnd);
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String[] groomEntries = groomContent.split(",");
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for (String entry : groomEntries) {
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String[] keyValue = entry.split(":");
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if (keyValue.length == 2) {
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groomingParameters.put(keyValue[0].replace("\"", "").trim(), keyValue[1].replace("\"", "").trim());
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}
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}
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// Parse optimize
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int optimizeStart = json.indexOf("\"optimize\": {") + 12;
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int optimizeEnd = json.indexOf("}", optimizeStart);
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String optimizeContent = json.substring(optimizeStart, optimizeEnd);
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String[] optimizeEntries = optimizeContent.split(",");
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for (String entry : optimizeEntries) {
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String[] keyValue = entry.split(":");
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if (keyValue.length == 2) {
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optimizationParameters.put(keyValue[0].replace("\"", "").trim(),
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keyValue[1].replace("\"", "").trim());
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}
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}
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} catch (IOException e) {
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e.printStackTrace();
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}
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}
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public void groom() {
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runSystemCommand("shapeworks groom --name project.swproj");
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}
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public void optimize() {
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runSystemCommand("shapeworks optimize --name project.swproj");
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}
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public void analyze() {
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runSystemCommand("shapeworksstudio project.swproj");
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}
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private void runSystemCommand(String command) {
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try {
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Process process = Runtime.getRuntime().exec(command);
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process.waitFor();
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} catch (IOException | InterruptedException e) {
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e.printStackTrace();
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}
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}
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}

‎docs/java/java.md

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

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‎docs/java/matlab.md

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

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‎docs/java/matlab_example2.png

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‎mkdocs.yml

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- Classes: 'api/Classes/index_classes.md'
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- Files: 'api/Files/index_files.md'
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- Java/Matlab Interface:
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- Java Interface: 'java/java.md'
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- Matlab Interface: 'java/matlab.md'
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- About:
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- 'Meet ShapeWorkers!': 'about/team.md'
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- 'Release Notes': 'about/release-notes.md'

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