/**
* 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;
}
public void draw(
GraphSettings gInfo, Graphics2D g2, int bottom, Graph g, int thickness, int xscroll) {
// cache yearsize, we use this a lot
int yearWidth = gInfo.getYearWidth(); // the size of a year, in pixels
float unitScale = gInfo.getHundredUnitHeight() / 100.0f; // the size of 1 "unit" in pixels.
// set pen
boolean dotted = (gInfo.isDottedIndexes() && (g.graph instanceof Index));
g2.setStroke(makeStroke(thickness, dotted));
// left/right
int l = g2.getClipBounds().x;
int r = l + g2.getClipBounds().width;
// Image img1 =
// Toolkit.getDefaultToolkit().getImage("/home/pwb48/dev/java5/tellervo-desktop/src/main/resources/Icons/256x256/tellervo-application.png");
// g2.drawImage(img1, 10, 10, null);
// baseline
if (gInfo.isShowBaselines()) {
int y = bottom - (int) (g.yoffset * unitScale);
g2.drawLine(xscroll, y, xscroll + 10 * yearWidth, y); // 1 decade wide -- ok?
}
// hundred percent line
if (gInfo.isShowHundredpercentlines()
&& (g.graph instanceof Sample)
&& ((Sample) g.graph).isIndexed()) {
Color oldcolor = g2.getColor();
g2.setColor(ColorUtils.blend(oldcolor, gInfo.getBackgroundColor()));
// x is 0 if we aren't drawing graph names...
// x is the pixel at the end of the empty range if we are.
int x = (gInfo.isShowGraphNames()) ? yearWidth * (gInfo.getEmptyBounds().getSpan() - 1) : 0;
int y =
bottom - (int) (yTransform(1000 * g.scale) * unitScale) - (int) (g.yoffset * unitScale);
g2.drawLine((x > xscroll) ? x : xscroll, y, r, y);
g2.setColor(oldcolor);
}
// no data? stop.
if (g.graph.getRingWidthData().isEmpty()) return;
// compare g.getClipBounds() to [x,0]..[x+yearSize*data.size(),bottom]
tempRect.x =
yearWidth
* (g.graph.getStart().diff(gInfo.getDrawBounds().getStart())
+ g.xoffset); // REDUNDANT! see x later
tempRect.y = 0; // - g.yoffset, IF you're sure there are no negative values (but there are)
tempRect.width = yearWidth * (g.graph.getRingWidthData().size() - 1);
tempRect.height = bottom;
// TODO: compute top/bottom as min/max?
// REFACTOR: will this be obsolete with the start/end stuff below?
if (!tempRect.intersects(g2.getClipBounds())) {
// skip this graph, it's off the screen
return;
}
// compute sapwood
int sapwoodIndex, sapwoodCount = 0;
if (g.graph instanceof Sample) {
Sample sample = (Sample) g.graph;
if (sample.meta().hasSapwood()) sapwoodCount = sample.meta().getNumberOfSapwoodRings();
}
sapwoodIndex = g.graph.getRingWidthData().size() - sapwoodCount + 1;
// my path
GeneralPath p = new GeneralPath();
// x-position
int x = yearWidth * (g.graph.getStart().diff(gInfo.getDrawBounds().getStart()) + g.xoffset);
// move to the first point -- THIS IS NOT REALLY A SPECIAL CASE!
int value;
try {
value = ((Number) g.graph.getRingWidthData().get(0)).intValue();
value = yTransform(value * g.scale);
} catch (ClassCastException cce) {
value =
yTransform(0); // BAD! instead: (1) just continue now, and (2) NEXT point is a move-to.
}
p.moveTo(x, bottom - (int) (value * unitScale) - (int) (g.yoffset * unitScale));
/*
-- i really want to start at year max(graph.start, bounds.start)
-- there are 3 things going on:
---- x is the pixel position
---- i is the index into data[]
---- y is the year
-- y isn't updated each time through the loop, so that's not too bad
-- but: starting y is easy to compute; from that, i and x are easy
*/
// connect the lines through the rest of the graph
int n =
g.graph
.getRingWidthData()
.size(); // THIS is the third time it's called; why not use it above?
for (int i = 1; i < n; i++) {
// new x-position for this point
x += yearWidth;
// if we're past the end, draw what we've got, and say goodbye
// (go +_yearsize so the line going off the screen is visible)
if (x > r + yearWidth) {
break;
}
// sapwood? draw what we've got, and start a new (thicker) path
// but only do it if sapwoodThicker() is enabled!
if (gInfo.isThickerSapwood() && i == sapwoodIndex) {
g2.draw(p);
g2.setStroke(makeStroke(2 * thickness, false));
p = new GeneralPath();
p.moveTo(
yearWidth
* (i - 1 + g.graph.getStart().diff(gInfo.getDrawBounds().getStart()) + g.xoffset),
bottom - (int) (value * unitScale) - (int) (g.yoffset * unitScale));
}
// y-position for this point
try {
value = yTransform(((Number) g.graph.getRingWidthData().get(i)).intValue() * g.scale);
} catch (ClassCastException cce) {
value = yTransform(0); // e.g., if it's being edited, it's still a string
// BAD! instead: (1) draw what i've got so far, and (2) NEXT point is a move-to.
// -- try to parse String as an integer?
}
// Try and paint remark icons
try {
List<TridasRemark> remarks = g.graph.getTridasValues().get(i).getRemarks();
int xcoord = (yearWidth * (i + g.graph.getStart().diff(gInfo.getDrawBounds().getStart())));
int ycoord = (bottom - (int) (value * unitScale) - (int) (g.yoffset * unitScale));
Graph.drawRemarkIcons(g2, gInfo, remarks, g.graph.getTridasValues().get(i), xcoord, ycoord);
} catch (Exception e) {
log.error("Exception drawing icons to graph: " + e.getClass());
}
int y = bottom - (int) (value * unitScale) - (int) (g.yoffset * unitScale);
// if we're not where this sample starts, don't bother drawing yet
if (x < l - yearWidth) {
p.moveTo(x, y);
continue;
}
// if MR, draw a vertical line -- use Sample.MR, for now
if (g.graph instanceof Sample && !validValue(value)) g2.drawLine(x, y - 20, x, y + 20);
// draw a line to this point
p.lineTo(x, y);
}
// draw it!
g2.draw(p);
}
/**
* 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);
}
}
