Ejemplo n.º 1
0
  public static void main(String[] args) {
    new ExampleProjects();

    try {

      File exsDir = new File("osb/showcase/neuroConstructShowcase");

      File mainFile = new File("docs/XML/xmlForHtml/samples/index.xml");

      logger.logComment("Going to create docs at: " + mainFile.getCanonicalPath(), true);

      generateMainPage(mainFile, exsDir);

      logger.logComment("Created doc at: " + mainFile.getCanonicalPath(), true);
      /*
      File modelsDir = new File("nCmodels");
      mainFile = new File("docs/XML/xmlForHtml/models/index.xml");


      generateMainPage(mainFile, modelsDir);

      logger.logComment("Created doc at: "+ mainFile.getCanonicalPath(), true);

       */
    } catch (Exception e) {
      e.printStackTrace();
    }
  }
  public void loadFromFile(File positionFile) throws java.io.IOException {
    logger.logComment("Loading position records from file: " + positionFile.getAbsolutePath());

    this.reset();

    Reader in = new FileReader(positionFile);
    LineNumberReader reader = new LineNumberReader(in);
    String nextLine = null;

    String currentInputRef = null;

    while ((nextLine = reader.readLine()) != null) {
      // logger.logComment("Parsing line: "+ nextLine);

      if (nextLine.endsWith(":")) {
        currentInputRef = nextLine.substring(0, nextLine.length() - 1);
        logger.logComment("currentInputRef: " + currentInputRef);
      } else {
        SingleElectricalInput input = new SingleElectricalInput(nextLine);
        this.addSingleInput(currentInputRef, input);
      }
    }
    in.close();

    logger.logComment("Finished loading cell info. Internal state: " + this.toString());
  }
  public void saveToFile(File inputsFile) throws java.io.IOException {
    logger.logComment(
        "Saving "
            + this.getNumberSingleInputs()
            + " inputs to file: "
            + inputsFile.getAbsolutePath());

    // will create the parent dir if it doesn't exist.
    if (!inputsFile.exists()) {
      logger.logComment("File: " + inputsFile + " doesn't exist.");
      if (!inputsFile.getParentFile().exists()) {
        logger.logComment("Parent dir: " + inputsFile.getParentFile() + " doesn't exist.");
        // String parentDirName = inputsFile.getParentFile().getCanonicalPath();
        File projectDir = inputsFile.getParentFile().getParentFile();

        if (!projectDir.exists()) {
          throw new FileNotFoundException(
              "Project dir doesn't exist: " + projectDir.getAbsolutePath());
        }
        // logger.logComment("Going to create dir: "+ parentDirName +" in dir :"+ projectDir);

        logger.logComment("Going to create dir: " + inputsFile.getParentFile());

        inputsFile.getParentFile().mkdir();

        logger.logComment("Success? " + inputsFile.getParentFile().exists());
      }
    }

    FileWriter fw = new FileWriter(inputsFile);

    Enumeration keys = this.myElecInputs.keys();

    while (keys.hasMoreElements()) {
      String input = (String) keys.nextElement();
      ArrayList<SingleElectricalInput> inputs = getInputLocations(input);

      fw.write(input + ":\n");

      for (int i = 0; i < inputs.size(); i++) {
        fw.write(inputs.get(i) + "\n");
      }
    }
    logger.logComment("Finished saving data to file: " + inputsFile.getAbsolutePath());
    fw.flush();
    fw.close();
  }
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>*/

  }
  public ArrayList<SimpleXMLEntity> getNetworkMLEntities(
      int unitSystem, NeuroMLConstants.NeuroMLVersion version, SimpleXMLElement topLevelCompElement)
      throws NeuroMLException {
    ArrayList<SimpleXMLEntity> entities = new ArrayList<SimpleXMLEntity>();

    Units timeUnits = UnitConverter.timeUnits[unitSystem];
    Units currentUnits = UnitConverter.currentUnits[unitSystem];

    SimpleXMLElement inputsElement = null;
    try {
      logger.logComment(
          "Going to save file in NeuroML format: "
              + this.getNumberSingleInputs()
              + " inputs in total");

      if (getNumberSingleInputs() == 0) {
        SimpleXMLComment comm =
            new SimpleXMLComment("There are no electrical inputs present in the network");
        entities.add(comm);
        return entities;
      }

      boolean nml2 = version.isVersion2();
      boolean nml2alpha = version.isVersion2alpha();

      if (!nml2) {
        inputsElement = new SimpleXMLElement(NetworkMLConstants.INPUTS_ELEMENT);
        entities.add(inputsElement);

        if (unitSystem == UnitConverter.GENESIS_PHYSIOLOGICAL_UNITS) {
          inputsElement.addAttribute(
              new SimpleXMLAttribute(
                  NetworkMLConstants.UNITS_ATTR, NetworkMLConstants.UNITS_PHYSIOLOGICAL));
        } else if (unitSystem == UnitConverter.GENESIS_SI_UNITS) {
          inputsElement.addAttribute(
              new SimpleXMLAttribute(NetworkMLConstants.UNITS_ATTR, NetworkMLConstants.UNITS_SI));
        }
      }

      Enumeration keys = myElecInputs.keys();

      while (keys.hasMoreElements()) {
        String inputReference = (String) keys.nextElement();
        ArrayList<SingleElectricalInput> inputsHere = getInputLocations(inputReference);

        logger.logComment("Adding " + inputsHere.size() + " inputs");

        StimulationSettings nextStim = project.elecInputInfo.getStim(inputReference);

        ElectricalInput myElectricalInput = nextStim.getElectricalInput();

        SimpleXMLElement inputElement = new SimpleXMLElement(NetworkMLConstants.INPUT_ELEMENT);

        inputElement.addAttribute(
            new SimpleXMLAttribute(NetworkMLConstants.INPUT_NAME_ATTR, inputReference));

        if (myElectricalInput instanceof IClamp) {
          IClamp ic = (IClamp) myElectricalInput;

          float delay = ic.getDel().getNominalNumber();
          float duration = ic.getDur().getNominalNumber();
          float amplitude = ic.getAmp().getNominalNumber();

          SimpleXMLElement inputTypeElement =
              new SimpleXMLElement(NetworkMLConstants.PULSEINPUT_ELEMENT);

          float del =
              (float) UnitConverter.getTime(delay, UnitConverter.NEUROCONSTRUCT_UNITS, unitSystem);
          float dur =
              (float)
                  UnitConverter.getTime(duration, UnitConverter.NEUROCONSTRUCT_UNITS, unitSystem);
          float amp =
              (float)
                  UnitConverter.getCurrent(
                      amplitude, UnitConverter.NEUROCONSTRUCT_UNITS, unitSystem);

          inputTypeElement.addAttribute(
              new SimpleXMLAttribute(NetworkMLConstants.INPUT_DELAY_ATTR, del + ""));

          inputTypeElement.addAttribute(
              new SimpleXMLAttribute(NetworkMLConstants.INPUT_DUR_ATTR, dur + ""));

          inputTypeElement.addAttribute(
              new SimpleXMLAttribute(NetworkMLConstants.INPUT_AMP_ATTR, amp + ""));

          inputElement.addChildElement(inputTypeElement);

          inputElement.addContent("\n        ");

          if (nml2) {
            SimpleXMLElement pulseGenElement =
                new SimpleXMLElement(NetworkMLConstants.NEUROML2_PULSE_GEN_ELEMENT);
            pulseGenElement.addAttribute(NeuroMLConstants.NEUROML_ID_V2, inputReference);
            pulseGenElement.addAttribute(
                NetworkMLConstants.INPUT_DELAY_ATTR, del + timeUnits.getNeuroML2Symbol());
            pulseGenElement.addAttribute(
                NetworkMLConstants.INPUT_DUR_ATTR, dur + timeUnits.getNeuroML2Symbol());
            pulseGenElement.addAttribute(
                NetworkMLConstants.INPUT_AMP_ATTR, amp + currentUnits.getNeuroML2Symbol());

            topLevelCompElement.addContent("\n\n    ");
            topLevelCompElement.addChildElement(pulseGenElement);
            topLevelCompElement.addContent("\n\n    ");
          }

        } else if (myElectricalInput instanceof RandomSpikeTrain) {
          RandomSpikeTrain rst = (RandomSpikeTrain) myElectricalInput;

          float stimFreq = rst.getRate().getNominalNumber();
          String stimMech = rst.getSynapseType();

          SimpleXMLElement inputTypeElement =
              new SimpleXMLElement(NetworkMLConstants.RANDOMSTIM_ELEMENT);
          float rate =
              (float)
                  UnitConverter.getRate(stimFreq, UnitConverter.NEUROCONSTRUCT_UNITS, unitSystem);
          inputTypeElement.addAttribute(
              new SimpleXMLAttribute(
                  NetworkMLConstants.RND_STIM_FREQ_ATTR,
                  (float)
                          UnitConverter.getRate(
                              stimFreq, UnitConverter.NEUROCONSTRUCT_UNITS, unitSystem)
                      + ""));

          inputTypeElement.addAttribute(
              new SimpleXMLAttribute(NetworkMLConstants.RND_STIM_MECH_ATTR, stimMech));
          inputElement.addChildElement(inputTypeElement);
          inputElement.addContent("\n        ");

          if (nml2 && !nml2alpha) {
            SimpleXMLElement spikeGenElement =
                new SimpleXMLElement(NetworkMLConstants.NEUROML2_SPIKE_GEN_POISSON_ELEMENT);
            spikeGenElement.addAttribute(NeuroMLConstants.NEUROML_ID_V2, inputReference);
            spikeGenElement.addAttribute(
                NetworkMLConstants.NEUROML2_SPIKE_GEN_POISSON_RATE_ATTR,
                rate
                    + " "
                    + UnitConverter.rateUnits[UnitConverter.NEUROCONSTRUCT_UNITS]
                        .getNeuroML2Symbol()
                    + "");

            topLevelCompElement.addContent("\n\n    ");
            topLevelCompElement.addChildElement(spikeGenElement);
            topLevelCompElement.addContent("\n\n    ");
          }
        } else {
          throw new NeuroMLException(
              "Error trying to save input "
                  + inputReference
                  + ". Cannot save in NeuroML an input of type: "
                  + myElectricalInput.getType());
        }

        SimpleXMLElement inputTargetElement =
            new SimpleXMLElement(NetworkMLConstants.INPUT_TARGET_ELEMENT);

        inputTargetElement.addAttribute(
            new SimpleXMLAttribute(
                NetworkMLConstants.INPUT_TARGET_POPULATION_ATTR, nextStim.getCellGroup()));

        inputElement.addChildElement(inputTargetElement);
        inputTargetElement.addContent("\n            ");

        SimpleXMLElement inputTargetSitesElement =
            new SimpleXMLElement(NetworkMLConstants.INPUT_TARGET_SITES_ELEMENT);

        inputTargetSitesElement.addAttribute(
            new SimpleXMLAttribute(
                NetworkMLConstants.INPUT_SITES_SIZE_ATTR, inputsHere.size() + ""));

        inputTargetElement.addChildElement(inputTargetSitesElement);

        SimpleXMLElement stimProjElement = null;

        if (version.isVersion2betaOrLater()) {

          if (myElectricalInput instanceof IClamp) {
            SimpleXMLElement inputListElement =
                new SimpleXMLElement(NetworkMLConstants.NEUROML2_INPUT_LIST_ELEMENT);
            entities.add(inputListElement);
            inputListElement.addAttribute(NeuroMLConstants.NEUROML_ID_V2, nextStim.getReference());
            inputListElement.addAttribute(
                NetworkMLConstants.NEUROML2_INPUT_COMPONENT, inputReference);
            inputListElement.addAttribute(
                NetworkMLConstants.NEUROML2_INPUT_POPULATION, nextStim.getCellGroup());

            // inputElement.addContent("\n    ");
            inputTargetSitesElement = inputListElement;

          } else if (myElectricalInput instanceof RandomSpikeTrain) {
            SimpleXMLElement popElement =
                new SimpleXMLElement(NetworkMLConstants.POPULATION_ELEMENT);
            entities.add(0, popElement);
            popElement.addAttribute(
                NeuroMLConstants.NEUROML_ID_V2, nextStim.getReference() + "_population");
            popElement.addAttribute(
                NetworkMLConstants.NEUROML2_POPULATION_COMPONENT,
                nextStim.getReference() + "_population");
            popElement.addAttribute(
                NetworkMLConstants.NEUROML2_POPULATION_SIZE, inputsHere.size() + "");

            stimProjElement = new SimpleXMLElement(NetworkMLConstants.PROJECTION_ELEMENT);
            stimProjElement.addAttribute(
                NeuroMLConstants.NEUROML_ID_V2, nextStim.getReference() + "_projection");
            entities.add(stimProjElement);
          }
        }

        // Iterate around the list of sites
        for (int i = 0; i < inputsHere.size(); i++) {
          inputTargetSitesElement.addContent("\n                ");

          SingleElectricalInput sei = inputsHere.get(i);

          SimpleXMLElement inputTargetSiteElement =
              new SimpleXMLElement(NetworkMLConstants.INPUT_TARGET_SITE_ELEMENT);

          inputTargetSiteElement.addAttribute(
              new SimpleXMLAttribute(
                  NetworkMLConstants.INPUT_SITE_CELLID_ATTR, sei.getCellNumber() + ""));
          inputTargetSiteElement.addAttribute(
              new SimpleXMLAttribute(
                  NetworkMLConstants.INPUT_SITE_SEGID_ATTR, sei.getSegmentId() + ""));
          inputTargetSiteElement.addAttribute(
              new SimpleXMLAttribute(
                  NetworkMLConstants.INPUT_SITE_FRAC_ATTR, sei.getFractionAlong() + ""));

          if (!nml2) inputTargetSitesElement.addChildElement(inputTargetSiteElement);

          if (nml2 && !nml2alpha) {
            if (myElectricalInput instanceof RandomSpikeTrain) {
              String connElName = NetworkMLConstants.CONNECTION_ELEMENT;

              SimpleXMLElement connElement = new SimpleXMLElement(connElName);

              connElement.addAttribute(
                  new SimpleXMLAttribute(NetworkMLConstants.CONNECTION_ID_ATTR, i + ""));
              stimProjElement.addContent("\n    ");
              stimProjElement.addChildElement(connElement);
              stimProjElement.addContent("\n    ");
            }
          }

          if (sei.getInstanceProps() != null) {
            inputTargetSiteElement.addContent("\n                ");
            inputTargetSiteElement.addComment("Adding the site specific props");

            if (sei.getInstanceProps() instanceof IClampInstanceProps) {
              IClampInstanceProps ic = (IClampInstanceProps) sei.getInstanceProps();

              float delay =
                  (float)
                      UnitConverter.getTime(
                          ic.getDelay(), UnitConverter.NEUROCONSTRUCT_UNITS, unitSystem);
              float duration =
                  (float)
                      UnitConverter.getTime(
                          ic.getDuration(), UnitConverter.NEUROCONSTRUCT_UNITS, unitSystem);
              float amp =
                  (float)
                      UnitConverter.getCurrent(
                          ic.getAmplitude(), UnitConverter.NEUROCONSTRUCT_UNITS, unitSystem);

              if (!nml2) {
                SimpleXMLElement inputTypeElement =
                    new SimpleXMLElement(NetworkMLConstants.PULSEINPUT_INSTANCE_ELEMENT);

                inputTypeElement.addAttribute(
                    new SimpleXMLAttribute(NetworkMLConstants.INPUT_DELAY_ATTR, delay + ""));

                inputTypeElement.addAttribute(
                    new SimpleXMLAttribute(NetworkMLConstants.INPUT_DUR_ATTR, duration + ""));

                // System.out.println("Converted "+amp+" to "+ a);
                inputTypeElement.addAttribute(
                    new SimpleXMLAttribute(NetworkMLConstants.INPUT_AMP_ATTR, amp + ""));

                inputTargetSiteElement.addContent("                    ");
                inputTargetSiteElement.addChildElement(inputTypeElement);

                inputTargetSiteElement.addContent("\n                ");
              } else {
                SimpleXMLElement pulseGenElement =
                    new SimpleXMLElement(NetworkMLConstants.NEUROML2_PULSE_GEN_ELEMENT);
                pulseGenElement.addAttribute(
                    NeuroMLConstants.NEUROML_ID_V2, inputReference + "__" + i);
                pulseGenElement.addAttribute(
                    NetworkMLConstants.INPUT_DELAY_ATTR, delay + timeUnits.getNeuroML2Symbol());
                pulseGenElement.addAttribute(
                    NetworkMLConstants.INPUT_DUR_ATTR, duration + timeUnits.getNeuroML2Symbol());
                pulseGenElement.addAttribute(
                    NetworkMLConstants.INPUT_AMP_ATTR, amp + currentUnits.getNeuroML2Symbol());

                topLevelCompElement.addContent("\n\n    ");
                topLevelCompElement.addChildElement(pulseGenElement);
                topLevelCompElement.addContent("\n\n    ");

                if (version.isVersion2alpha()) {
                  String target = nextStim.getCellGroup() + "[" + sei.getCellNumber() + "]";
                  SimpleXMLElement expInputElement =
                      new SimpleXMLElement(NetworkMLConstants.NEUROML2_EXP_INPUT_ELEMENT);
                  expInputElement.addAttribute(
                      NetworkMLConstants.NEUROML2_EXP_INPUT_TARGET_ATTR, target);
                  expInputElement.addAttribute(
                      NetworkMLConstants.NEUROML2_EXP_INPUT_INPUT_ATTR, inputReference + "__" + i);

                  entities.add(expInputElement);
                } else {
                  String target =
                      "../"
                          + nextStim.getCellGroup()
                          + "/"
                          + sei.getCellNumber()
                          + "/"
                          + project.cellGroupsInfo.getCellType(nextStim.getCellGroup());
                  SimpleXMLElement expInputElement =
                      new SimpleXMLElement(NetworkMLConstants.NEUROML2_INPUT_LIST_ELEMENT);
                  expInputElement.addAttribute(
                      NetworkMLConstants.NEUROML2_EXP_INPUT_TARGET_ATTR, target);
                  expInputElement.addAttribute(
                      NetworkMLConstants.NEUROML2_EXP_INPUT_INPUT_ATTR, inputReference + "__" + i);

                  entities.add(expInputElement);
                }
              }
            } else if (sei.getInstanceProps() instanceof RandomSpikeTrainInstanceProps) {
              RandomSpikeTrainInstanceProps rst =
                  (RandomSpikeTrainInstanceProps) sei.getInstanceProps();

              float stimFreq = rst.getRate();
              // String stimMech = rst.get;

              SimpleXMLElement inputTypeElement =
                  new SimpleXMLElement(NetworkMLConstants.RANDOMSTIM_INSTANCE_ELEMENT);

              inputTypeElement.addAttribute(
                  new SimpleXMLAttribute(
                      NetworkMLConstants.RND_STIM_FREQ_ATTR,
                      (float)
                              UnitConverter.getRate(
                                  stimFreq, UnitConverter.NEUROCONSTRUCT_UNITS, unitSystem)
                          + ""));

              // inputTypeElement.addAttribute(new
              // SimpleXMLAttribute(NetworkMLConstants.RND_STIM_MECH_ATTR, stimMech));

              inputTargetSiteElement.addContent("                    ");
              inputTargetSiteElement.addChildElement(inputTypeElement);
              inputTargetSiteElement.addContent("\n                ");

            } else {
              throw new NeuroMLException(
                  "Error trying to save input "
                      + inputReference
                      + ". Cannot save in NeuroML an input of type: "
                      + myElectricalInput.getType());
            }
          } else {
            if (nml2) {
              if (version.isVersion2alpha()) {
                String target = nextStim.getCellGroup() + "[" + sei.getCellNumber() + "]";
                SimpleXMLElement expInputElement =
                    new SimpleXMLElement(NetworkMLConstants.NEUROML2_EXP_INPUT_ELEMENT);
                expInputElement.addAttribute(
                    NetworkMLConstants.NEUROML2_EXP_INPUT_TARGET_ATTR, target);
                expInputElement.addAttribute(
                    NetworkMLConstants.NEUROML2_EXP_INPUT_INPUT_ATTR, inputReference);

                entities.add(expInputElement);
              } else {
                String target =
                    "../"
                        + nextStim.getCellGroup()
                        + "/"
                        + sei.getCellNumber()
                        + "/"
                        + project.cellGroupsInfo.getCellType(nextStim.getCellGroup());
                SimpleXMLElement expInputElement =
                    new SimpleXMLElement(NetworkMLConstants.NEUROML2_INPUT_ELEMENT);
                expInputElement.addAttribute(NeuroMLConstants.NEUROML_ID_V2, i + "");
                expInputElement.addAttribute(
                    NetworkMLConstants.NEUROML2_EXP_INPUT_TARGET_ATTR, target);
                expInputElement.addAttribute(
                    NetworkMLConstants.NEUROML2_INPUT_DESTINATION,
                    NetworkMLConstants.NEUROML2_INPUT_DESTINATION_DEFAULT);

                inputTargetSitesElement.addChildElement(expInputElement);
              }
            }
          }

          if (i == inputsHere.size() - 1) inputTargetSitesElement.addContent("\n            ");

          // Next Site
        }
        inputTargetElement.addContent("\n        ");

        if (!nml2) {
          inputsElement.addChildElement(inputElement);
          inputElement.addContent("\n    ");
        }
      }
      logger.logComment("Finished saving data to inputs element");

    } catch (Exception ex) {
      ex.printStackTrace();
      throw new NeuroMLException("Problem creating inputs element file", ex);
    }
    return entities;
  }