@Override
@SuppressWarnings("SleepWhileHoldingLock")
public void run() {
try {
// initialize the statusbar
status.removeAll();
JProgressBar progress = new JProgressBar();
progress.setMinimum(0);
progress.setMaximum(doc.getLength());
status.add(progress);
status.revalidate();
// start writing
Writer out = new FileWriter(f);
Segment text = new Segment();
text.setPartialReturn(true);
int charsLeft = doc.getLength();
int offset = 0;
while (charsLeft > 0) {
doc.getText(offset, Math.min(4096, charsLeft), text);
out.write(text.array, text.offset, text.count);
charsLeft -= text.count;
offset += text.count;
progress.setValue(offset);
try {
Thread.sleep(10);
} catch (InterruptedException e) {
Logger.getLogger(FileSaver.class.getName()).log(Level.SEVERE, null, e);
}
}
out.flush();
out.close();
} catch (IOException e) {
final String msg = e.getMessage();
SwingUtilities.invokeLater(
new Runnable() {
public void run() {
JOptionPane.showMessageDialog(
getFrame(),
"Could not save file: " + msg,
"Error saving file",
JOptionPane.ERROR_MESSAGE);
}
});
} catch (BadLocationException e) {
System.err.println(e.getMessage());
}
// we are done... get rid of progressbar
status.removeAll();
status.revalidate();
}
/** Test of evaluateAt method, of class ParameterisedGroup. */
@Test
public void testEvaluateAt() throws ParameterException {
System.out.println("--- testEvaluateAt...");
// SegmentLocation loc1 = new PostSynapticTerminalLocation(d2.getSegmentId(), 0.5f);
assertEquals(0.5, pg1.evaluateAt(cell, d2, 0.5f), 0);
assertEquals(15, pg2.evaluateAt(cell, d2, 0.5f), 0);
//////// assertEquals(15, pg5.evaluateAt(cell, loc1), 0);
// SegmentLocation loc2 = new PostSynapticTerminalLocation(d3.getSegmentId(), 0.5f);
assertEquals(5d / 6d, pg1.evaluateAt(cell, d3, 0.5f), 1e-7);
assertEquals(25, pg2.evaluateAt(cell, d3, 0.5f), 0);
assertEquals(0.5, pg3.evaluateAt(cell, d3, 0.5f), 0);
assertEquals(0, pg4.evaluateAt(cell, d3, 0), 0);
assertEquals(5, pg4.evaluateAt(cell, d3, 0.5f), 0);
SegmentLocation sl1 = new SegmentLocation(d3.getSegmentId(), 0.5f);
assertEquals(
25,
pg5.evaluateAt(cell, cell.getSegmentWithId(sl1.getSegmentId()), sl1.getFractAlong()),
0);
assertEquals(30, pg5.evaluateAt(cell, d3, 1), 0);
GenesisCompartmentalisation g = new GenesisCompartmentalisation();
Cell gCell = g.getCompartmentalisation(cell);
System.out.println(CellTopologyHelper.printDetails(cell, null));
System.out.println(
"Changed from morph: " + cell.getMorphSummary() + ", to morph: " + gCell.getMorphSummary());
System.out.println("getSegmentMapper: " + g.getSegmentMapper());
System.out.println(CellTopologyHelper.printDetails(gCell, null));
SegmentLocation sl1_g = g.getSegmentMapper().mapSegmentLocation(sl1);
System.out.println("Mapped: " + sl1 + " to " + sl1_g);
assertEquals(
25,
pg5.evaluateAt(gCell, gCell.getSegmentWithId(sl1_g.getSegmentId()), sl1_g.getFractAlong()),
0);
}
@Before
public void setUp() {
System.out.println("--------------- setUp() ParameterisedGroupTest");
cell = new OneSegment("Simple");
d1 =
cell.addDendriticSegment(
1, "d1", new Point3f(10, 0, 0), cell.getFirstSomaSegment(), 1, "Sec1", false);
d2 = cell.addDendriticSegment(2, "d2", new Point3f(20, 0, 0), d1, 1, "Sec2", false);
d3 = cell.addDendriticSegment(7, "d3", new Point3f(20, 10, 0), d2, 1, "Sec3", false);
d3.getSection().setStartRadius(3);
d1.getSection().setNumberInternalDivisions(4);
d2.getSection().setNumberInternalDivisions(3);
d3.getSection().setNumberInternalDivisions(5);
d3.getSection().addToGroup(tipSection);
pg1 =
new ParameterisedGroup(
"ZeroToOne",
Section.DENDRITIC_GROUP,
Metric.PATH_LENGTH_FROM_ROOT,
ProximalPref.MOST_PROX_AT_0,
DistalPref.MOST_DIST_AT_1,
"p1");
pg2 =
new ParameterisedGroup(
"StartToEnd",
Section.DENDRITIC_GROUP,
Metric.PATH_LENGTH_FROM_ROOT,
ProximalPref.NO_TRANSLATION,
DistalPref.NO_NORMALISATION,
"p2");
pg3 =
new ParameterisedGroup(
"TipZeroToOne",
tipSection,
Metric.PATH_LENGTH_FROM_ROOT,
ProximalPref.MOST_PROX_AT_0,
DistalPref.MOST_DIST_AT_1,
"p3");
pg4 =
new ParameterisedGroup(
"TipToEnd",
tipSection,
Metric.PATH_LENGTH_FROM_ROOT,
ProximalPref.MOST_PROX_AT_0,
DistalPref.NO_NORMALISATION,
"p4");
pg5 =
new ParameterisedGroup(
"TipToEnd_PathFromRoot",
tipSection,
Metric.PATH_LENGTH_FROM_ROOT,
ProximalPref.NO_TRANSLATION,
DistalPref.NO_NORMALISATION,
"p5");
/*
pg5 = new ParameterisedGroup("3DDistZeroToOne",
Section.ALL,
Metric.THREE_D_RADIAL_POSITION,
ProximalPref.MOST_PROX_AT_0,
DistalPref.MOST_DIST_AT_1);*/
}