Beispiel #1
0
  // ## operation Chemkin(double,double,String)
  public Chemkin(double p_rtol, double p_atol, String p_reactorType) {
    // #[ operation Chemkin(double,double,String)
    if (p_rtol < 0 || p_atol < 0)
      throw new InvalidChemkinParameterException("Negative rtol or atol!");
    if (p_reactorType == null) throw new NullPointerException();

    String dir = System.getProperty("RMG.workingDirectory");

    // create the documentTypesDefinitions
    File docFile = new File("chemkin/documentTypeDefinitions");
    docFile.mkdir();
    copyFiles(
        dir + "/software/reactorModel/documentTypeDefinitions/reactorInput.dtd",
        "chemkin/documentTypeDefinitions/reactorInput.dtd");
    copyFiles(
        dir + "/software/reactorModel/documentTypeDefinitions/reactorOutput.dtd",
        "chemkin/documentTypeDefinitions/reactorOutput.dtd");

    rtol = p_rtol;
    atol = p_atol;
    reactorType = p_reactorType;
  }
  /*
   * Carries out a number of tests, generates NEURON, GENESIS and NeuroML code etc.
   */
  private static void doTests(neuronEditorFrame nef, String fileName) {
    System.out.println(
        "Testing Cvapp/NeuroMorpho.Org by generating NEURON, GENESIS and NeuroML files for "
            + fileName);
    File tempDir = new File("temp");
    if (!tempDir.exists()) tempDir.mkdir();

    neuronEditorPanel nep = nef.getNeuronEditorPanel();

    String rootFileName = fileName;
    if (rootFileName.toLowerCase().endsWith(".swc")) {
      rootFileName = rootFileName.substring(0, rootFileName.length() - 4);
    }

    if (rootFileName.lastIndexOf(System.getProperty("file.separator")) > 0) {
      rootFileName =
          rootFileName.substring(
              rootFileName.lastIndexOf(System.getProperty("file.separator")) + 1);
    }

    // NEURON save...

    String neuronFileName = rootFileName + ".hoc";
    File neuronFile = new File(tempDir, neuronFileName);
    File neuronTestFile = new File(tempDir, rootFileName + "_test.hoc");

    nep.writeStringToFile(nep.getCell().HOCwriteNS(), neuronFile.getAbsolutePath());

    StringBuilder sbNeuTest = new StringBuilder();
    sbNeuTest.append("load_file(\"nrngui.hoc\")\n");
    sbNeuTest.append("load_file(\"../neuronUtils/nCtools.hoc\")\n");
    sbNeuTest.append("load_file(\"../neuronUtils/cellCheck.hoc\")\n");
    sbNeuTest.append("load_file(\"nrngui.hoc\")\n");
    sbNeuTest.append("load_file(\"" + neuronFileName + "\")\n\n");
    sbNeuTest.append("forall morph()\n");
    System.out.println("--------------------------------------------------------------");
    nep.writeStringToFile(sbNeuTest.toString(), neuronTestFile.getAbsolutePath());

    System.out.println(
        "Saved NEURON representation of the file to: "
            + neuronFile.getAbsolutePath()
            + ": "
            + neuronFile.exists());
    System.out.println("--------------------------------------------------------------");

    // GENESIS save...

    String genesisFileName = rootFileName + ".p";
    File genesisFile = new File(tempDir, genesisFileName);
    File genesisTestFile = new File(tempDir, rootFileName + "_test.g");

    nep.writeStringToFile(nep.getCell().GENESISwriteHR(), genesisFile.getAbsolutePath());

    StringBuilder sbGenTest = new StringBuilder();

    sbGenTest.append("include compartments \n");
    sbGenTest.append("create neutral /library\n");
    sbGenTest.append("disable /library\n");
    sbGenTest.append("ce /library\n");
    sbGenTest.append("make_cylind_compartment\n");
    sbGenTest.append("make_cylind_symcompartment\n");
    sbGenTest.append("make_sphere_compartment\n");
    sbGenTest.append("ce /\n");
    sbGenTest.append(
        "echo \"Prototype compartments created, reading cell from " + genesisFileName + "\"\n");
    sbGenTest.append("readcell " + genesisFileName + " /mycell\n\n");

    sbGenTest.append("create xform /form [0,0,400,400] -nolabel\n");
    sbGenTest.append(
        "create xdraw /form/draw [0,0,100%,100%] -wx 0.002 -wy 0.002 -transform ortho3d -bg white\n");
    sbGenTest.append(
        "setfield /form/draw xmin -3.0E-4 xmax 3.0E-4 ymin -3.0E-4 ymax 3.0E-4 vx 0.0 vy 0.0 vz -0.002\n");
    sbGenTest.append(
        "create xcell /form/draw/cell -path \"/mycell/##[][TYPE=compartment],/mycell/##[][TYPE=symcompartment]\" -colfield Vm -colmin -0.07 -colmax 0.03 -diarange -5\n");
    sbGenTest.append("xcolorscale hot\n");
    sbGenTest.append("xshow /form\n\n");
    sbGenTest.append("showfield /mycell/##[][TYPE=compartment] **\n\n");

    nep.writeStringToFile(sbGenTest.toString(), genesisTestFile.getAbsolutePath());

    System.out.println(
        "Saved GENESIS representation of the file to: "
            + genesisFile.getAbsolutePath()
            + ": "
            + genesisFile.exists());
    System.out.println("--------------------------------------------------------------");

    // NeuroML save...

    String nml1FileName = rootFileName + ".xml";
    File nml1File = new File(tempDir, nml1FileName);

    nep.writeStringToFile(nep.getCell().writeNeuroML_v1_8_1(), nml1File.getAbsolutePath());

    System.out.println(
        "Saved NeuroML representation of the file to: "
            + nml1File.getAbsolutePath()
            + ": "
            + nml1File.exists());

    File v1schemaFile = new File("Schemas/v1.8.1/Level3/NeuroML_Level3_v1.8.1.xsd");

    validateXML(nml1File, v1schemaFile);

    String nml2FileName = rootFileName + ".cell.nml";

    if (Character.isDigit(nml2FileName.charAt(0))) {
      nml2FileName = "Cell_" + nml2FileName;
    }
    File nml2File = new File(tempDir, nml2FileName);

    nep.writeStringToFile(nep.getCell().writeNeuroML_v2beta(), nml2File.getAbsolutePath());

    System.out.println(
        "Saved NeuroML representation of the file to: "
            + nml2File.getAbsolutePath()
            + ": "
            + nml2File.exists());

    validateXMLWithURL(nml2File, "Schemas/v2/NeuroML_v2beta4.xsd");
  }
  public static boolean transform(
      File origXmlFileOrDir, File xslFile, File targetDir, String extension) {
    logger.logComment(
        "Going to transform " + origXmlFileOrDir + " into dir " + targetDir + " using: " + xslFile,
        true);

    if (!origXmlFileOrDir.exists()) {
      GuiUtils.showErrorMessage(
          logger,
          "Warning, XML file/directory: " + origXmlFileOrDir + " doesn't exist",
          null,
          null);
      return false;
    }

    if (!xslFile.exists()) {
      GuiUtils.showErrorMessage(
          logger, "Warning, XSL file: " + xslFile + " doesn't exist", null, null);
      return false;
    }

    if (!targetDir.exists()) {
      GuiUtils.showErrorMessage(
          logger, "Warning, target directory: " + targetDir + " doesn't exist", null, null);
      return false;
    }

    if (origXmlFileOrDir.isDirectory()) {
      logger.logComment("That file is a directory. Converting all of the XML files in it");
      File[] files = origXmlFileOrDir.listFiles();

      boolean totalSuccess = true;
      for (int i = 0; i < files.length; i++) {
        if (!files[i].isDirectory()
            && (files[i].getName().endsWith(".xml") || files[i].getName().endsWith(".XML"))) {
          boolean partialSuccess = transform(files[i], xslFile, targetDir, extension);

          totalSuccess = totalSuccess || partialSuccess;
        } else if (files[i].isDirectory() && !GeneralUtils.isVersionControlDir(files[i])) {
          File newFolder = new File(targetDir, files[i].getName());
          newFolder.mkdir();

          logger.logComment(
              "Found a sub folder. Going to convert all there into: " + newFolder + "...");

          transform(files[i], xslFile, newFolder, extension);
        }
      }
      return totalSuccess;
    }

    String result = transform(origXmlFileOrDir, xslFile);

    String newName = origXmlFileOrDir.getName();

    if (newName.endsWith(".xml") || newName.endsWith(".XML")) {
      newName = newName.substring(0, newName.length() - 4) + extension;
    }
    File targetFile = new File(targetDir, newName);

    try {
      FileWriter fw = new FileWriter(targetFile);
      fw.write(result);
      fw.close();
    } catch (IOException ex) {
      GuiUtils.showErrorMessage(logger, "Exception writing to file: " + targetFile, ex, null);
      return false;
    }

    logger.logComment("The result is in " + targetFile + " *************");

    return result != null;
  }