public static void main(String[] args) throws ProjectFileParsingException, EquationException {

    Project testProj =
        Project.loadProject(
            new File("examples/Ex5-Networks/Ex5-Networks.neuro.xml"),
            new ProjectEventListener() {
              public void tableDataModelUpdated(String tableModelName) {};

              public void tabUpdated(String tabName) {};

              public void cellMechanismUpdated() {};
            });

    SynapticProperties sp = new SynapticProperties("Syn1");
    sp.setDelayGenerator(new NumberGenerator(33));
    WeightGenerator wg = new WeightGenerator("r*r", true);

    sp.setWeightsGenerator(wg);

    SynapticPropertiesDialog dlg = new SynapticPropertiesDialog(new Frame(), sp, testProj);

    //    Dimension dlgSize = dlg.getPreferredSize();
    dlg.setModal(true);
    dlg.pack();
    dlg.setVisible(true);

    System.out.println("wg: " + sp.getWeightsGenerator());
  }
  public static void main(String[] args) {
    try {
      Project p =
          Project.loadProject(
              new File(ProjectStructure.getnCExamplesDir(), "Ex5_Networks/Ex5_Networks.ncx"), null);

      GeneratedElecInputs gei = new GeneratedElecInputs(p);

      System.out.println("Internal info: \n" + gei.toString());

      // IClamp ic = new IClamp(2,3,4, true);

      gei.addSingleInput("Input_0", "IClamp", "cg1", 3, 3, 3, null);
      gei.addSingleInput("Input_0", "IClamp", "cg1", 38, 3, 3, null);
      gei.addSingleInput("Input_2", "IClamp", "cg3", 3, 38, 39, null);

      System.out.println("Internal info: \n" + gei.toString());

      File f = new File("../temp/tempp.txt");

      gei.saveToFile(f);

      GeneratedElecInputs cpr2 = new GeneratedElecInputs(null);

      System.out.println(
          "----  v1.8.1: \n"
              + gei.getNetworkMLElement(UnitConverter.GENESIS_SI_UNITS)
                  .getXMLString("    ", false));

      ArrayList<SimpleXMLEntity> els =
          gei.getNetworkMLEntities(
              UnitConverter.GENESIS_SI_UNITS,
              NeuroMLConstants.NeuroMLVersion.NEUROML_VERSION_2_ALPHA,
              null);

      System.out.println("----  v2.0 alpha: ");
      for (SimpleXMLEntity el : els) System.out.println(el.getXMLString("    ", false));

      els =
          gei.getNetworkMLEntities(
              UnitConverter.GENESIS_SI_UNITS,
              NeuroMLConstants.NeuroMLVersion.getLatestVersion(),
              null);

      System.out.println("----  v2.0 beta: ");
      for (SimpleXMLEntity el : els) System.out.println(el.getXMLString("    ", false));

      System.out.println("-------------- ");

    } catch (Exception ex) {
      ex.printStackTrace();
    }
  }
Ejemplo n.º 3
0
  public static void main(String args[]) {

    try {

      logger.logComment("Sys prop: " + System.getProperty("java.library.path"), true);

      // File projFile = new File("../copyNcModels/NewGranCellLayer/NewGranCellLayer.neuro.xml");

      // File projFile = new File("../nC_projects/Bignet/Bignet.neuro.xml");
      File projFile = new File("testProjects/TestNetworkML/TestNetworkML.neuro.xml");

      // Project testProj = Project.loadProject(new File("projects/Parall/Parall.neuro.xml"),null);
      // Project testProj = Project.loadProject(new
      // File("examples/Ex5-Networks/Ex5-Networks.neuro.xml"),null);
      Project testProj = Project.loadProject(projFile, null);

      // File h5File = new File(projFile.getParentFile().getAbsolutePath()+
      // "/savedNetworks/hhh.h5");
      // File h5File = new File(projFile.getParentFile().getAbsolutePath()+
      // "/savedNetworks/nnnn.h5");

      File h5File = new File("testProjects/TestNetworkML/savedNetworks/small.h5");

      // logger.logComment("Loading netml cell from "+ h5File.getAbsolutePath(), true);

      NetworkMLReader nmlReader = new NetworkMLReader(testProj);

      nmlReader.parse(h5File);

      logger.logComment("Contents: " + testProj.generatedCellPositions);
      logger.logComment("Net conns: " + testProj.generatedNetworkConnections);
      logger.logComment("Inputs: " + testProj.generatedElecInputs.details(false));

    } catch (Exception e) {
      e.printStackTrace();
      System.exit(0);
    }
  }
Ejemplo n.º 4
0
  public static void generateMainPage(File mainFile, File sourceProjDir)
      throws IOException, ProjectFileParsingException, NeuroMLException {
    SimpleXMLElement root = new SimpleXMLElement("document");
    SimpleXMLElement header = new SimpleXMLElement("header");
    root.addChildElement(header);

    SimpleXMLElement title = new SimpleXMLElement("title");
    header.addChildElement(title);

    SimpleXMLElement body = new SimpleXMLElement("body");
    root.addChildElement(body);
    SimpleXMLElement intro = new SimpleXMLElement("p");
    body.addChildElement(intro);

    if (!mainFile.getParentFile().exists()) mainFile.getParentFile().mkdir();

    File targetDownloadDir = new File(mainFile.getParentFile(), "downloads");
    if (!targetDownloadDir.exists()) targetDownloadDir.mkdir();

    if (sourceProjDir.getName().indexOf("examples") >= 0) {
      title.addContent("neuroConstruct example projects");

      intro.addContent(
          "Downloadable neuroConstruct example projects. These <strong>illustrate the core "
              + "functionality of neuroConstruct</strong>, as opposed to providing electrophysiologically accurate "
              + "models. Projects based on published conductance based models can be found <a href=\"../models/index.html\">here</a>");
    }
    if (sourceProjDir.getName().indexOf("models") >= 0) {
      title.addContent("neuroConstruct projects based on published neuronal and network models");

      intro.addContent(
          "Downloadable neuroConstruct projects <strong>based on published conductance based models</strong>. "
              + "Some examples to illustrate the core functionality of neuroConstruct, as opposed to "
              + "providing electrophysiologically accurate models can be found <a href=\"../samples/index.html\">here</a>."
              + "<p>Note: These models are currently being moved to a repository to allow open source, collaborative development of NeuroML models.</p>"
              + "<p>See the <a href=\"http://www.opensourcebrain.org\">Open Source Brain</a> website for full details.&nbsp;&nbsp;&nbsp;&nbsp;"
              + "<img alt=\"Open Source Brain\" src=\"http://www.opensourcebrain.org/images/logo.png\"/></p>");
    }
    File[] fileArray = sourceProjDir.listFiles();

    fileArray = GeneralUtils.reorderAlphabetically(fileArray, true);

    ArrayList<File> files = GeneralUtils.toArrayList(fileArray);
    // if (files.contains(""))

    ArrayList<String> toIgnore = new ArrayList<String>();
    // toIgnore.add("Thalamocortical"); // temporarily
    // toIgnore.add("CA1PyramidalCell"); // temporarily
    // toIgnore.add("SolinasEtAl-GolgiCell"); // temporarily

    for (File exProjDir : files) {
      File morphDir = new File(exProjDir, "cellMechanisms");

      if (morphDir.isDirectory() && !toIgnore.contains(exProjDir.getName())) {
        String projName = exProjDir.getName();
        SimpleXMLElement section = new SimpleXMLElement("section");
        body.addChildElement(section);

        SimpleXMLElement secTitle = new SimpleXMLElement("title");
        section.addChildElement(secTitle);
        secTitle.addContent(projName);

        SimpleXMLElement anchor = new SimpleXMLElement("anchor");
        section.addChildElement(anchor);
        anchor.addAttribute("id", projName);

        SimpleXMLElement table = new SimpleXMLElement("table");

        section.addChildElement(table);

        SimpleXMLElement row = new SimpleXMLElement("tr");
        table.addChildElement(row);

        String largeImg = "large.png";
        String smallImg = "small.png";

        File targetImageDir = new File(mainFile.getParentFile(), "images");
        if (!targetImageDir.exists()) targetImageDir.mkdir();

        File targetProjImageDir = new File(targetImageDir, projName);

        if (!targetProjImageDir.exists()) targetProjImageDir.mkdir();

        File smallImgFile = new File(exProjDir, "images/" + smallImg);
        File largeImgFile = new File(exProjDir, "images/" + largeImg);

        if (smallImgFile.exists()) {
          GeneralUtils.copyFileIntoDir(smallImgFile, targetProjImageDir);

          SimpleXMLElement col2 = new SimpleXMLElement("td");
          row.addChildElement(col2);
          col2.addAttribute("width", "120");

          SimpleXMLElement secImg = new SimpleXMLElement("p");
          col2.addChildElement(secImg);

          SimpleXMLElement img = new SimpleXMLElement("img");
          img.addAttribute("src", "images/" + projName + "/small.png");
          img.addAttribute("alt", "Screenshot of " + projName);

          if (largeImgFile.exists()) {
            GeneralUtils.copyFileIntoDir(largeImgFile, targetProjImageDir);

            SimpleXMLElement imgRef = new SimpleXMLElement("a");
            img.addAttribute("title", "Click to enlarge");
            imgRef.addAttribute("href", "images/" + projName + "/" + largeImg);
            imgRef.addChildElement(img);
            secImg.addChildElement(imgRef);
          } else {
            secImg.addChildElement(img);
          }
        }

        SimpleXMLElement secIntro = new SimpleXMLElement("p");
        SimpleXMLElement colMid = new SimpleXMLElement("td");
        SimpleXMLElement colRight = new SimpleXMLElement("td");
        row.addChildElement(colMid);
        row.addChildElement(colRight);
        colRight.addAttribute("width", "150");
        colMid.addChildElement(secIntro);
        secIntro.addContent("Project name: <strong>" + projName + "</strong>");

        File projFile = ProjectStructure.findProjectFile(exProjDir);

        Project project = Project.loadProject(projFile, null);
        String descFull = project.getProjectDescription();
        String breakpoint = "\n\n";
        String descShort = new String(descFull);

        if (descFull.indexOf(breakpoint) > 0) {
          descShort = descFull.substring(0, descFull.indexOf(breakpoint));
        }

        SimpleXMLElement desc = new SimpleXMLElement("p");
        colMid.addChildElement(desc);
        desc.addContent(GeneralUtils.parseForHyperlinks(descShort));

        SimpleXMLElement modified = new SimpleXMLElement("p");
        colMid.addChildElement(modified);

        SimpleDateFormat formatter = new SimpleDateFormat("EEEE MMMM d, yyyy");

        java.util.Date date = new java.util.Date(projFile.lastModified());

        modified.addContent("Project last modified: " + formatter.format(date));

        File zipFile = null;
        String zipFileName =
            targetDownloadDir.getAbsolutePath()
                + "/"
                + projName
                + ProjectStructure.getNewProjectZipFileExtension();

        ArrayList<String> ignore = new ArrayList<String>();
        ArrayList<String> ignoreNone = new ArrayList<String>();
        ArrayList<String> ignoreExtns = new ArrayList<String>();

        ignore.add("i686");
        ignore.add("x86_64");
        ignore.add(".svn");
        ignore.add("simulations");
        ignore.add("generatedNEURON");
        ignore.add("generatedNeuroML");
        ignore.add("generatedGENESIS");
        ignore.add("generatedMOOSE");
        ignore.add("generatedPyNN");
        ignore.add("generatedPSICS");
        ignore.add("dataSets");
        ignoreExtns.add("bak");

        zipFile = ZipUtils.zipUp(exProjDir, zipFileName, ignore, ignoreExtns);

        logger.logComment(
            "The zip file: "
                + zipFile.getAbsolutePath()
                + " ("
                + zipFile.length()
                + " bytes)  contains all of the project files");

        SimpleXMLElement downloads = new SimpleXMLElement("p");
        colRight.addChildElement(downloads);
        downloads.addContent("Downloads<a href=\"#downloadInfo\">*</a>:");

        SimpleXMLElement downloadProj = new SimpleXMLElement("p");
        colRight.addChildElement(downloadProj);

        SimpleXMLElement link = new SimpleXMLElement("a");
        link.addAttribute("href", "downloads/" + zipFile.getName());
        link.addContent("neuroConstruct project");
        link.addAttribute("title", "Download full project for loading into neuroConstruct");
        downloadProj.addChildElement(link);

        ArrayList<String> noNeuroML = new ArrayList<String>();
        noNeuroML.add("Ex3_Morphology");
        noNeuroML.add("DentateGyrus");
        noNeuroML.add("RothmanEtAl_KoleEtAl_PyrCell");

        if (!noNeuroML.contains(projName)) {
          project.neuromlFileManager.generateNeuroMLFiles(
              null, new OriginalCompartmentalisation(), 1234, false);

          File neuroMLDir = ProjectStructure.getNeuroML1Dir(project.getProjectMainDirectory());

          String nmlZipFileName =
              targetDownloadDir.getAbsolutePath() + "/" + projName + "_NeuroML.zip";

          zipFile = ZipUtils.zipUp(neuroMLDir, nmlZipFileName, ignoreNone, ignoreNone);

          SimpleXMLElement downloadNml = new SimpleXMLElement("p");
          colRight.addChildElement(downloadNml);
          // downloadNml.addContent("Download project as pure NeuroML: ");

          SimpleXMLElement img = new SimpleXMLElement("img");
          img.addAttribute("src", "../images/NeuroMLSmall.png");
          String info = "Download core project elements in NeuroML format";
          img.addAttribute("alt", info);

          SimpleXMLElement imgRef = new SimpleXMLElement("a");
          img.addAttribute("title", info);
          imgRef.addAttribute("href", "downloads/" + zipFile.getName());
          imgRef.addChildElement(img);

          downloadNml.addChildElement(imgRef);
        }
      }
    }

    SimpleXMLElement end = new SimpleXMLElement("p");
    body.addChildElement(end);
    end.addContent("&nbsp;");

    SimpleXMLElement infoDlanchor = new SimpleXMLElement("anchor");
    body.addChildElement(infoDlanchor);
    end.addAttribute("id", "downloadInfo");

    SimpleXMLElement infoDl = new SimpleXMLElement("p");
    body.addChildElement(infoDl);
    end.addContent(
        "* Note: neuroConstruct project downloads (most of which are included with the standard software distribution) "
            + "can be loaded directly into neuroConstruct to generate cell and network scripts for NEURON, GENESIS, etc.,"
            + " but NeuroML downloads just consist of the core elements of the project"
            + " (morphologies, channels, etc.) which have been exported in NeuroML format. The latter can be useful for testing NeuroML compliant applications. "
            + "If no NeuroML download link is present, this usually indicates that the model is mainly implemented using channel/synapse mechanisms in a simulator's "
            + "native language (e.g. mod files) which have not fully been converted to ChannelML yet.");

    SimpleXMLElement end2 = new SimpleXMLElement("p");
    body.addChildElement(end2);
    end2.addContent("&nbsp;");

    FileWriter fw = null;
    try {

      fw = new FileWriter(mainFile);
      fw.write("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"); // quick hack, todo: add to
      // SimpleXMLDoc...

      fw.write(
          "<!DOCTYPE document PUBLIC \"-//APACHE//DTD Documentation V2.0//EN\" \"http://forrest.apache.org/dtd/document-v20.dtd\">\n\n");
      fw.write(root.getXMLString("", false));

      fw.flush();
      fw.close();

    } catch (IOException ex) {
      logger.logError("Problem: ", ex);
      fw.close();
    }

    /*
             <header>
      <title>Examples of neuroConstruct in use</title>
    </header>
    <body>
        <p>Some screenshots of neuroConstruct in action are given below.
        Click on the thumbnails to see a full size version of the screenshots</p>

      <section>
        <title>Examples included with distribution</title>*/

  }