private void runDiscreteUpdateComponent(File f1)
throws ContentError, IOException, ParseError, ConnectionError, RuntimeError {
String stxt = FileUtil.readStringFromFile(f1);
XMLElementReader exmlr = new XMLElementReader(stxt + " ");
XMLElement xel = exmlr.getRootElement();
LemsLiteFactory lf = new LemsLiteFactory();
LemsLite lemsLite = lf.buildLemsFromXMLElement(xel);
E.info("lemsLite model read: " + lemsLite.getSummary());
// XMLSerializer xs = new XMLSerializer();
// String sx = xs.serialize(lemsLite);
File fdir = f1.getParentFile();
LemsLiteSimulation lls = new LemsLiteSimulation(lemsLite);
FileDataSource fds = new FileDataSource(fdir);
lls.run(fds);
}
public void generateMainScript(File localFile)
throws LEMSException, IOException, GenerationException, ModelFeatureSupportException,
NeuroMLException {
Lems lems = Utils.readLemsNeuroMLFile(FileUtil.readStringFromFile(localFile)).getLems();
System.out.println("Loaded from: " + localFile);
PyNNWriter mw = new PyNNWriter(lems);
String mod = mw.generateMainScriptAndCellFiles(AppTest.getTempDir());
for (File genFile : mw.allGeneratedFiles) {
assertTrue(genFile.exists());
System.out.println(
"------------------"
+ genFile.getAbsolutePath()
+ "------------------------------------");
System.out.println(FileUtil.readStringFromFile(genFile));
}
}
public void generateMainScript(File localFile)
throws LEMSException, GenerationException, IOException, ModelFeatureSupportException,
NeuroMLException {
Lems lems = Utils.readLemsNeuroMLFile(FileUtil.readStringFromFile(localFile)).getLems();
System.out.println("Loaded from: " + localFile);
CWriter cw = new CWriter(lems);
String code = cw.getMainScript();
System.out.println(code);
File cFile = new File(AppTest.getTempDir(), localFile.getName().replaceAll(".xml", ".c"));
FileUtil.writeStringToFile(code, cFile);
assertTrue(cFile.exists());
File mFile = new File(AppTest.getTempDir(), "Makefile");
String makefile = cw.getMakefile();
FileUtil.writeStringToFile(makefile, mFile);
}
public String getMainScript() throws GenerationException, IOException {
StringBuilder mainRunScript = new StringBuilder();
addComment(
mainRunScript,
format + " simulator compliant export for:\n\n" + lems.textSummary(false, false));
try {
List<File> files = dlemsw.convert();
for (File file : files) {
E.info("Writing " + format + " files to: " + this.getOutputFolder());
if (file.getName().equals(mainDlemsFile)) {
VelocityUtils.initializeVelocity();
VelocityContext context = new VelocityContext();
VelocityEngine ve = VelocityUtils.getVelocityEngine();
String dlems = FileUtil.readStringFromFile(file);
DLemsWriter.putIntoVelocityContext(dlems, context);
addComment(
mainRunScript,
"Using the following distilled version of the LEMS model description for the script below:\n\n"
+ dlems);
StringWriter sw1 = new StringWriter();
boolean generationStatus =
ve.evaluate(
context,
sw1,
"LOG",
VelocityUtils.getTemplateAsReader(VelocityUtils.vertexRunTemplateFile));
mainRunScript.append(sw1);
} else if (file.getName().indexOf(".synapse.") > 0) {
StringBuilder synapseScript = new StringBuilder();
addComment(
synapseScript,
format + " simulator compliant export for:\n\n" + lems.textSummary(false, false));
E.info(" ==== Handling DLEMS file: " + file.getAbsolutePath());
VelocityUtils.initializeVelocity();
VelocityContext context = new VelocityContext();
VelocityEngine ve = VelocityUtils.getVelocityEngine();
String dlems = FileUtil.readStringFromFile(file);
DLemsWriter.putIntoVelocityContext(dlems, context);
StringWriter sw2 = new StringWriter();
boolean generationStatus2 =
ve.evaluate(
context,
sw2,
"LOG",
VelocityUtils.getTemplateAsReader(VelocityUtils.vertexSynapseTemplateFile));
addComment(
synapseScript,
"Using the following distilled version of the LEMS model description for the script below:\n\n"
+ dlems);
synapseScript.append(sw2);
String name = (String) context.internalGet(DLemsKeywords.NAME.get());
E.info("Name: " + name);
File synapseScriptFile =
new File(this.getOutputFolder(), "SynapseModel_" + name.toLowerCase() + ".m");
FileUtil.writeStringToFile(synapseScript.toString(), synapseScriptFile);
outputFiles.add(synapseScriptFile);
} else {
StringBuilder cellScript = new StringBuilder();
addComment(
cellScript,
format + " simulator compliant export for:\n\n" + lems.textSummary(false, false));
E.info(" ==== Handling DLEMS file: " + file.getAbsolutePath());
VelocityUtils.initializeVelocity();
VelocityContext context = new VelocityContext();
VelocityEngine ve = VelocityUtils.getVelocityEngine();
String dlems = FileUtil.readStringFromFile(file);
DLemsWriter.putIntoVelocityContext(dlems, context);
StringWriter sw2 = new StringWriter();
boolean generationStatus2 =
ve.evaluate(
context,
sw2,
"LOG",
VelocityUtils.getTemplateAsReader(VelocityUtils.vertexCellTemplateFile));
addComment(
cellScript,
"Using the following distilled version of the LEMS model description for the script below:\n\n"
+ dlems);
cellScript.append(sw2);
String name = (String) context.internalGet(DLemsKeywords.NAME.get());
E.info("Name: " + name);
File cellScriptFile =
new File(this.getOutputFolder(), "PointNeuronModel_" + name.toLowerCase() + ".m");
FileUtil.writeStringToFile(cellScript.toString(), cellScriptFile);
outputFiles.add(cellScriptFile);
}
}
} catch (IOException e1) {
throw new GenerationException("Problem converting LEMS to dLEMS", e1);
} catch (VelocityException e) {
throw new GenerationException("Problem using Velocity template", e);
}
return mainRunScript.toString();
}