Package aQute.maven

Examples of aQute.maven.MavenRepository$Project


public class TrakEM2_Add_Balls implements PlugIn {

  public void run(String arg) {

    // 1 - Obtain an open TrakEM2 project: the one selected in the ControlWindow
    final Project project = ControlWindow.getActive();

    if (null == project) {
      Utils.log("Open or create a TrakEM2 project first!");
      return;
    }
    // Else, you could create a project like:
    // Project project = Project.newFSProject("blank", null, "/path/to/storage_folder/");


    // 2 - Define two sets of x,y,z,r coordinates to import as 3D-positioned balls of radius r

          //   X    Y    Z   R

    final double[][] set1 = {{ 100, 100,   0, 25 },
                       { 130, 120,   1, 30 },
           { 110, 150,   0, 15 }};

    final double[][] set2 = {{ 200, 200,   1, 45 },
                       { 240, 190,   0, 35 },
           { 220, 250,   1, 55 }};

    // 3 - Insert each set as a Ball object, each containing 3 x,y,z,r spheres:
    Ball b1 = addBallObject(project, set1, "Set 1");
    Ball b2 = addBallObject(project, set2, "Set 2");

    // 4 - Change colors and settings:
    b1.setColor(Color.green);
    b2.setColor(Color.magenta); // yellow is default color
    // NOTICE that the color cues will paint each individual ball red in the previous layer,
    // and blue in the next one -- the color is used to paint in the actual layer where it lives.
    // (Scroll through the stack to see the effect -- the color cues help in noticing whether
    // a ball already exists at the location in the previous or next slice/Layer).
    // You can TURN OFF color cues with the 'p' keyboard shortcut on a Display,
    // or programmatically by:
    //      project.setProperty("no_color_cues", true);


    // 5 - Add nodes automatically to the Template and Project trees (REQUIRED):
    // (can be rearranged manually later, or could be added with way more precision programmatically)
    ArrayList al = new ArrayList();
    al.add(b1);
    al.add(b2);
    project.getProjectTree().insertSegmentations(project, al);

    // 6 - Automatically scroll LayerSet to the first layer of the first ball (OPTIONAL):
    Display.getFront().setLayer(b1.getFirstLayer());

    // 7 - Show the balls in 3D (OPTIONAL):
    ProjectThing p1 = project.findProjectThing(b1); // a Project tree node
    ProjectThing p2 = project.findProjectThing(b2); // a Project tree node
    Future<List<Content>> fu1 = Display3D.show(p1, true, 1); // wait, and resample 1 ( but resample only affects image volumes and AreaList meshes!)
    Future<List<Content>> fu2 = Display3D.show(p2, true, 1); //  If not waiting, then since its threaded, the saveAsWaveFront below would find nothing to save.

    // WAIT until added, so we know the Display3D has been created
    try {
      fu1.get();
      fu2.get();
    } catch (InterruptedException ie) {
      //
    } catch (ExecutionException ee) {
      ee.printStackTrace();
    }

    // 8 - Export the balls meshes to a .obj wavefront file (OPTIONAL):
    // (This will export all the current contents of the Display3D that can be exported as meshes.
    // One could refine what to export with:
    //    Content c1 = univ.getContent(Display3D.makeTitle(b1)); // by title
    //    Content c2 = ...
    // ... and then adding them to a Collection.
    //
    Image3DUniverse univ = Display3D.getDisplay(project.getRootLayerSet()).getUniverse();
    Collection all = univ.getContents();
    MeshExporter.saveAsWaveFront(all); // pops up file dialog to save
  }
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            // first, we must map up any schedules, etc.
            processBuildDefinitions( projectGroup.getBuildDefinitions(), schedules );

            for ( Iterator j = projectGroup.getProjects().iterator(); j.hasNext(); )
            {
                Project project = (Project) j.next();

                processBuildDefinitions( project.getBuildDefinitions(), schedules );
            }

            PlexusJdoUtils.addObject( pmf.getPersistenceManager(), projectGroup );
        }
        pmf.close();
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            // first, we must map up any schedules, etc.
            processBuildDefinitions( projectGroup.getBuildDefinitions(), schedules );

            for ( Iterator j = projectGroup.getProjects().iterator(); j.hasNext(); )
            {
                Project project = (Project) j.next();

                processBuildDefinitions( project.getBuildDefinitions(), schedules );
            }

            PlexusJdoUtils.addObject( pmf.getPersistenceManager(), projectGroup );
        }
        pmf.close();
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            // first, we must map up any schedules, etc.
            processBuildDefinitions( projectGroup.getBuildDefinitions(), schedules );

            for ( Iterator j = projectGroup.getProjects().iterator(); j.hasNext(); )
            {
                Project project = (Project) j.next();

                processBuildDefinitions( project.getBuildDefinitions(), schedules );
            }

            PlexusJdoUtils.addObject( pmf.getPersistenceManager(), projectGroup );
        }
        pmf.close();
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            // first, we must map up any schedules, etc.
            processBuildDefinitions( projectGroup.getBuildDefinitions(), schedules );

            for ( Iterator j = projectGroup.getProjects().iterator(); j.hasNext(); )
            {
                Project project = (Project) j.next();

                processBuildDefinitions( project.getBuildDefinitions(), schedules );
            }

            PlexusJdoUtils.addObject( pmf.getPersistenceManager(), projectGroup );
        }
        pmf.close();
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            // first, we must map up any schedules, etc.
            processBuildDefinitions( projectGroup.getBuildDefinitions(), schedules );

            for ( Iterator j = projectGroup.getProjects().iterator(); j.hasNext(); )
            {
                Project project = (Project) j.next();

                processBuildDefinitions( project.getBuildDefinitions(), schedules );
            }

            PlexusJdoUtils.addObject( pmf.getPersistenceManager(), projectGroup );
        }
        pmf.close();
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    {
      InputStream inputStream = new FileInputStream(path);

      JAXBContext jc = JAXBContext.newInstance(Project.class);
      Unmarshaller um = jc.createUnmarshaller();
      Project project = ((Project) um.unmarshal(inputStream));

      Configuration configuration = project.getConfiguration();

      if (configuration != null)
      {
        Data data = configuration.getData();
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