// ## 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;
}