private Tgm getModel(GtaModelReference gtaModelReference) {
TgmDataObject tgmDO = null;
Tgm model = null;
String path = project.getProjectDirectory() + File.separator + gtaModelReference.getPath();
try {
File datasetF = new File(path);
FileObject datasetFO = FileUtil.createData(datasetF);
DataObject datasetDO = DataObject.find(datasetFO);
if (datasetDO != null) {
tgmDO = (TgmDataObject) datasetDO;
model = tgmDO.getTgm();
}
} catch (DataObjectExistsException ex) {
Exceptions.printStackTrace(ex);
} catch (IOException ex) {
Exceptions.printStackTrace(ex);
}
return model;
}
private DatasetTimp[] getDatasets(GtaDatasetContainer gtaDatasetContainer) {
TimpDatasetDataObject timpDatasetDO = null;
int numberOfDatasets = gtaDatasetContainer.getDatasets().size();
datasets = new DatasetTimp[numberOfDatasets];
for (int i = 0; i < numberOfDatasets; i++) {
GtaDataset gtaDataset = gtaDatasetContainer.getDatasets().get(i);
String path = project.getProjectDirectory() + File.separator + gtaDataset.getPath();
try {
File datasetF = new File(path);
FileObject datasetFO = FileUtil.createData(datasetF);
DataObject datasetDO = DataObject.find(datasetFO);
if (datasetDO != null) {
timpDatasetDO = (TimpDatasetDataObject) datasetDO;
datasets[i] = timpDatasetDO.getDatasetTimp();
}
} catch (DataObjectExistsException ex) {
Exceptions.printStackTrace(ex);
} catch (IOException ex) {
Exceptions.printStackTrace(ex);
}
}
return datasets;
}
private Tgm getModel(String filename, String relativeFilePath) {
TgmDataObject tgmDO;
Tgm model = null;
String newPath =
project.getProjectDirectory()
+ File.separator
+ relativeFilePath
+ File.separator
+ filename;
try {
File datasetF = new File(newPath);
FileObject datasetFO = FileUtil.createData(datasetF);
DataObject datasetDO = DataObject.find(datasetFO);
if (datasetDO != null) {
tgmDO = (TgmDataObject) datasetDO;
model = tgmDO.getTgm();
}
} catch (DataObjectExistsException ex) {
Exceptions.printStackTrace(ex);
} catch (IOException ex) {
Exceptions.printStackTrace(ex);
}
return model;
}
private void writeResults(
TimpResultDataset[] results, GtaModelReference modelReference, String[] nlsprogressResult) {
Tgm model = getModel(modelReference);
GtaResult newResultsObject = new GtaResult();
String freeResultsFilename =
FileUtil.findFreeFileName(resultsfolder, resultsfolder.getName(), "summary");
try {
writeSummary(resultsfolder, freeResultsFilename);
} catch (IOException ex) {
Exceptions.printStackTrace(ex);
}
if (nlsprogressResult != null) {
for (int i = 0; i < nlsprogressResult.length; i++) {
NlsProgress progress = new NlsProgress();
progress.setRss(nlsprogressResult[i]);
newResultsObject.getNlsprogress().add(progress);
}
}
for (int i = 0; i < results.length; i++) {
TimpResultDataset timpResultDataset = results[i];
timpResultDataset.setType(datasets[i].getType());
newResultsObject.getDatasets().add(new Dataset());
newResultsObject.getDatasets().get(i).setDatasetFile(new OutputFile());
newResultsObject
.getDatasets()
.get(i)
.getDatasetFile()
.setFilename(datasetContainer.getDatasets().get(i).getFilename());
newResultsObject
.getDatasets()
.get(i)
.getDatasetFile()
.setPath(datasetContainer.getDatasets().get(i).getPath());
newResultsObject.getDatasets().get(i).getDatasetFile().setFiletype(datasets[i].getType());
newResultsObject.getDatasets().get(i).setId(String.valueOf(i + 1));
if (model.getDat().getIrfparPanel().getLamda() != null) {
timpResultDataset.setLamdac(model.getDat().getIrfparPanel().getLamda());
}
if (datasets[i].getType().equalsIgnoreCase("flim")) {
timpResultDataset.setOrheigh(datasets[i].getOriginalHeight());
timpResultDataset.setOrwidth(datasets[i].getOriginalWidth());
timpResultDataset.setIntenceIm(datasets[i].getIntenceIm().clone());
timpResultDataset.setMaxInt(datasets[i].getMaxInt());
timpResultDataset.setMinInt(datasets[i].getMinInt());
timpResultDataset.setX(datasets[i].getX().clone());
timpResultDataset.setX2(datasets[i].getX2().clone());
}
try {
String freeFilename =
FileUtil.findFreeFileName(
resultsfolder,
resultsfolder.getName() + "_d" + (i + 1) + "_" + timpResultDataset.getDatasetName(),
"timpres");
timpResultDataset.setDatasetName(freeFilename);
writeTo = resultsfolder.createData(freeFilename, "timpres");
ObjectOutputStream stream = new ObjectOutputStream(writeTo.getOutputStream());
stream.writeObject(timpResultDataset);
stream.close();
newResultsObject.getDatasets().get(i).setResultFile(new OutputFile());
newResultsObject.getDatasets().get(i).getResultFile().setFilename(freeFilename);
newResultsObject
.getDatasets()
.get(i)
.getResultFile()
.setPath(FileUtil.getRelativePath(project.getProjectDirectory(), resultsfolder));
} catch (IOException ex) {
Exceptions.printStackTrace(ex);
}
}
try {
writeResultsXml(newResultsObject);
} catch (IOException ex) {
Exceptions.printStackTrace(ex);
}
}
private void doAnalysis() {
if (project != null) {
if (output.getIterations() != null) {
if (!output.getIterations().isEmpty()) {
numIterations = Integer.parseInt(output.getIterations());
}
} else {
numIterations = NO_OF_ITERATIONS;
}
if (output.getOutputPath() != null) {
String[] nlsprogressResult = null;
String outputPath =
project.getResultsFolder(true) + File.separator + output.getOutputPath();
File outputFolder = new File(outputPath);
if (outputFolder.exists()) {
resultsfolder = FileUtil.toFileObject(outputFolder);
if (resultsfolder.getChildren().length > 0) {
try {
resultsfolder =
FileUtil.createFolder(
resultsfolder.getParent(),
FileUtil.findFreeFolderName(
resultsfolder.getParent(), resultsfolder.getName()));
} catch (IOException ex) {
Exceptions.printStackTrace(ex);
}
}
} else {
try {
FileUtil.createFolder(outputFolder);
resultsfolder = outputFolder.exists() ? FileUtil.toFileObject(outputFolder) : null;
} catch (IOException ex) {
Exceptions.printStackTrace(ex);
}
}
datasets = getDatasets(datasetContainer);
modelCalls.add(getModelCall(modelReference, 0));
fitModelCall =
getFitModelCall(datasets, modelCalls, modelDifferences, output, numIterations);
if (isValidAnalysis(datasets, modelReference)) {
timpcontroller = Lookup.getDefault().lookup(TimpControllerInterface.class);
if (timpcontroller != null) {
results = timpcontroller.runAnalysis(datasets, modelCalls, fitModelCall);
nlsprogressResult =
timpcontroller.getStringArray(
TimpControllerInterface.NAME_OF_RESULT_OBJECT + "$nlsprogress");
}
} else {
// TODO: CoreErrorMessages warning
return;
}
if (results != null) {
writeResults(results, modelReference, nlsprogressResult);
} else {
try {
writeSummary(
resultsfolder,
FileUtil.findFreeFileName(
resultsfolder, resultsfolder.getName() + "_errorlog", "summary"));
} catch (IOException ex) {
Exceptions.printStackTrace(ex);
}
}
timpcontroller.cleanup();
}
}
}
