public static LineageData loadNucFiles(final ProductionInfo productionInfo) {
final TableLineageData tableLineageData =
new TableLineageData(
allCellNames,
productionInfo.getXScale(),
productionInfo.getYScale(),
productionInfo.getZScale());
try {
// accounts for first tld.addFrame() added when reading from JAR --> from dir name first entry
// match
tableLineageData.addTimeFrame();
URL url;
for (int i = 1; i <= productionInfo.getTotalTimePoints(); i++) {
if (i < 10) {
url =
AceTreeTableLineageLoader.class.getResource(
ENTRY_PREFIX + T + TWO_ZERO_PAD + i + ENTRY_EXT);
if (url != null) {
process(tableLineageData, i, url.openStream());
} else {
System.out.println(
"Could not process file: " + ENTRY_PREFIX + T + TWO_ZERO_PAD + i + ENTRY_EXT);
}
} else if (i >= 10 && i < 100) {
url =
AceTreeTableLineageLoader.class.getResource(
ENTRY_PREFIX + T + ONE_ZERO_PAD + i + ENTRY_EXT);
if (url != null) {
process(tableLineageData, i, url.openStream());
} else {
System.out.println(
"Could not process file: " + ENTRY_PREFIX + T + ONE_ZERO_PAD + i + ENTRY_EXT);
}
} else if (i >= 100) {
url = AceTreeTableLineageLoader.class.getResource(ENTRY_PREFIX + T + i + ENTRY_EXT);
if (url != null) {
process(tableLineageData, i, url.openStream());
} else {
System.out.println("Could not process file: " + ENTRY_PREFIX + T + i + ENTRY_EXT);
}
}
}
} catch (IOException ioe) {
ioe.printStackTrace();
}
// translate all cells to center around (0,0,0)
setOriginToZero(tableLineageData, true);
return tableLineageData;
}
private static void makeNucleus(
final TableLineageData tableLineageData, final int time, final String[] tokens) {
try {
tableLineageData.addNucleus(
time,
tokens[ID],
parseInt(tokens[XCOR]),
parseInt(tokens[YCOR]),
round(parseDouble(tokens[ZCOR])),
parseInt(tokens[DIAMETER]));
} catch (NumberFormatException nfe) {
System.out.println("Incorrect format in nucleus file for time " + time + ".");
}
}
private static void process(
final TableLineageData tableLineageData, final int time, final InputStream input) {
tableLineageData.addTimeFrame();
try (InputStreamReader isr = new InputStreamReader(input);
BufferedReader reader = new BufferedReader(isr)) {
String line;
while ((line = reader.readLine()) != null) {
String[] tokens = new String[TOKEN_ARRAY_SIZE];
StringTokenizer tokenizer = new StringTokenizer(line, ",");
int k = 0;
while (tokenizer.hasMoreTokens()) {
tokens[k++] = tokenizer.nextToken().trim();
}
if (parseInt(tokens[VALID]) == 1) {
makeNucleus(tableLineageData, time, tokens);
}
}
} catch (IOException e) {
System.out.println("Error in processing input stream");
}
}
