/**
* Get list of series for each sample in array
*
* @return
*/
public static ArrayList<ITridasSeries> getSeries(ArrayList<Sample> sampleList) {
ArrayList<ITridasSeries> serList = new ArrayList<ITridasSeries>();
for (Sample s : sampleList) {
serList.add(s.getSeries());
}
return serList;
}
/**
* Parse the specified legacy data file for series
*
* @param file
* @param fileType
*/
private void parseFile(File file, AbstractDendroFormat format) {
ArrayList<Sample> sampleList = new ArrayList<Sample>();
// Create a reader based on the file type supplied
AbstractDendroFileReader reader = TridasIO.getFileReaderFromFormat(format);
if (reader == null) {
Alert.error(containerFrame, "Error", "Unknown file type");
return;
}
// Try and load the file
try {
reader.loadFile(file.getAbsolutePath());
} catch (IOException e) {
Alert.errorLoading(file.getAbsolutePath(), e);
return;
} catch (InvalidDendroFileException e) {
Alert.error(
containerFrame,
"Error",
"The selected file is not a valid "
+ format.getShortName()
+ " file.\nPlease check and try again");
return;
} catch (NullPointerException e) {
Alert.error(containerFrame, "Invalid File", e.getLocalizedMessage());
}
TridasTridas tc = reader.getTridasContainer();
log.debug("Project count: " + tc.getProjects().size());
Boolean hideWarningsFlag = false;
for (TridasProject p : tc.getProjects()) {
for (TridasObject o : p.getObjects()) {
for (TridasElement e : TridasUtils.getElementList(o)) {
log.debug("Element count: " + o.getElements().size());
for (TridasSample s : e.getSamples()) {
for (TridasRadius r : s.getRadiuses()) {
for (TridasMeasurementSeries ms : r.getMeasurementSeries()) {
Sample sample =
EditorFactory.createSampleFromSeries(ms, e, file, format, hideWarningsFlag);
if (sample == null) {
hideWarningsFlag = true;
} else {
sampleList.add(sample);
}
}
}
}
}
}
for (TridasDerivedSeries ds : p.getDerivedSeries()) {
Sample sample =
EditorFactory.createSampleFromSeries(ds, null, file, format, hideWarningsFlag);
if (sample == null) {
hideWarningsFlag = true;
} else {
sampleList.add(sample);
}
}
}
Boolean unitsSet = false;
for (ITridasSeries ser : getSeries(sampleList)) {
for (TridasValues tv : ser.getValues()) {
if (tv.isSetUnit()) {
if (tv.getUnit().isSetNormalTridas()) {
unitsSet = true;
}
}
}
}
if (unitsSet == false && sampleList.size() > 0 && unitsIfNotSpecified == null) {
Object[] possibilities = {"1/1000th mm", "1/100th mm", "1/50th mm", "1/20th mm", "1/10th mm"};
Object s =
JOptionPane.showInputDialog(
containerFrame,
"One or more series has no units defined.\n" + "Please specify units below:",
"Set Units",
JOptionPane.PLAIN_MESSAGE,
null,
possibilities,
"1/1000th mm");
if (s.equals("1/1000th mm")) {
unitsIfNotSpecified = NormalTridasUnit.MICROMETRES;
} else if (s.equals("1/100th mm")) {
unitsIfNotSpecified = NormalTridasUnit.HUNDREDTH_MM;
} else if (s.equals("1/50th mm")) {
unitsIfNotSpecified = NormalTridasUnit.FIFTIETH_MM;
} else if (s.equals("1/20th mm")) {
unitsIfNotSpecified = NormalTridasUnit.TWENTIETH_MM;
} else if (s.equals("1/10th mm")) {
unitsIfNotSpecified = NormalTridasUnit.TENTH_MM;
} else {
Alert.error(containerFrame, "Error", "Invalid measurement units specified");
return;
}
}
for (Sample sample : sampleList) {
ITridasSeries series = sample.getSeries();
try {
for (int i = 0; i < series.getValues().size(); i++) {
TridasValues tv = series.getValues().get(i);
if (tv.isSetUnit()) {
if (!tv.getUnit().isSetNormalTridas()) {
tv.getUnit().setNormalTridas(unitsIfNotSpecified);
}
} else {
TridasUnit unit = new TridasUnit();
unit.setNormalTridas(unitsIfNotSpecified);
tv.setUnit(unit);
tv.setUnitless(null);
}
tv = UnitUtils.convertTridasValues(NormalTridasUnit.MICROMETRES, tv, true);
TridasUnit unit = new TridasUnit();
unit.setNormalTridas(NormalTridasUnit.MICROMETRES);
tv.setUnit(unit);
series.getValues().set(i, tv);
}
} catch (NumberFormatException e) {
Alert.error("Error", "One or more data values are not numbers.");
return;
} catch (ConversionWarningException e) {
Alert.error("Error", "Error converting units");
return;
}
}
for (Sample s : sampleList) {
SeriesIdentity id = new SeriesIdentity(file, format, s);
model.addItem(id);
}
}