private final List<Point2D> getPointsFrom(
GraphSettings gInfo, Graph g, Year startYear, int nYears, int bottom) {
// index into our data values for this particular year
int idx = startYear.diff(g.graph.getStart().add(g.xoffset));
// make a list of points
// this is ok, because we know points are continuous
List<Point2D> points = new ArrayList<Point2D>(nYears);
// the year the plot starts
Year plotStartYear = gInfo.getDrawBounds().getStart();
// the adjusted range of this graph
Range graphRange = g.getRange();
int yearWidth = gInfo.getYearWidth();
float unitScale = gInfo.getHundredUnitHeight() / 100.0f;
for (int i = 0; i <= nYears; i++) {
// skip points that don't exist
if (!graphRange.contains(startYear.add(i))) continue;
int value = g.graph.getRingWidthData().get(idx + i).intValue();
int x = getXValue(g, plotStartYear, yearWidth, idx + i);
int y = getYValue(g, unitScale, value, bottom);
points.add(new Point2D.Float(x, y));
}
return points;
}
private final List<Point2D> getPointsFrom(
GraphSettings gInfo, Graph g, Year startYear, int nYears, int bottom) {
// make a list of points
// this is ok, because we know points are continuous
List<Point2D> points = new ArrayList<Point2D>(nYears);
int yearWidth = gInfo.getYearWidth();
float unitScale = gInfo.getHundredUnitHeight() / 100.0f;
List<? extends Number> data = g.graph.getRingWidthData();
double[] dataDbl = new double[data.size()];
for (int i = 0; i < data.size(); i++) {
Integer intval = (Integer) data.get(i);
dataDbl[i] = (double) intval;
}
int x = yearWidth * (g.graph.getStart().diff(gInfo.getDrawBounds().getStart()) + g.xoffset);
// int value1 = yTransform((float) stats.getMean());
int value1 = yTransform((float) baselineY);
int meanYVal = bottom - (int) (value1 * unitScale) - (int) (g.yoffset * unitScale);
try {
// x-position
int x1 = x;
int x2 =
yearWidth
* (g.graph.getStart().diff(gInfo.getDrawBounds().getStart())
+ g.xoffset
+ g.graph.getRingWidthData().size());
points.add(new Point2D.Float(x1, meanYVal));
points.add(new Point2D.Float(x2, meanYVal));
} catch (ClassCastException cce) {
}
return points;
}
public boolean contact(GraphSettings gInfo, Graph g, Point p, int bottom) {
// snap to year
int yearWidth = gInfo.getYearWidth();
int firstYearIdx = (p.x / yearWidth) - 1;
int nYears = 3;
// Check three years' worth of data: the year prior to and after the year the mouse is inside
Year startYear = gInfo.getDrawBounds().getStart().add(firstYearIdx);
List<Point2D> points = this.getPointsFrom(gInfo, g, startYear, nYears, bottom);
int nLines = points.size() - 1;
for (int i = 0; i < nLines; i++) {
Line2D line = new Line2D.Float(points.get(i), points.get(i + 1));
int distance = Math.round((float) line.ptSegDist(p));
if (distance <= NEAR) return true;
}
return false;
}
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);
}
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));
// If it's a chronology, point bones down
/*if(g.graph instanceof Sample)
{
if (((Sample) g.graph).getSeries() instanceof TridasDerivedSeries)
{
this.areBonesBelowLine = true;
}
}*/
// left/right
int l = g2.getClipBounds().x;
int r = l + g2.getClipBounds().width;
// 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;
}
// Draw standard line
int x = yearWidth * (g.graph.getStart().diff(gInfo.getDrawBounds().getStart()) + g.xoffset);
// int value1 = yTransform((float) getMeanValue(g));
int value1 = yTransform((float) baselineY);
int baseYVal = bottom - (int) (value1 * unitScale) - (int) (g.yoffset * unitScale);
try {
// x-position
int x1 = x;
int x2 =
yearWidth
* (g.graph.getStart().diff(gInfo.getDrawBounds().getStart())
+ g.xoffset
+ g.graph.getRingWidthData().size());
// if we're past the end, draw only as far as we need
if (x2 > r + yearWidth) {
x2 = r + yearWidth;
}
// log.debug("Drawing mean line: "+x1+", "+meanYVal+", "+x2+", "+meanYVal);
g2.drawLine(x1, baseYVal, x2, baseYVal);
// Calcs for start/end triangles
int YLineHeight = 50;
int YTriangleHeight = 25;
int XTriangleWidth = 15;
if (areBonesBelowLine) {
YLineHeight = -50;
YTriangleHeight = -25;
}
// Draw start triangle
g2.drawLine(x1, baseYVal, x1, baseYVal - YTriangleHeight);
g2.drawLine(x1, baseYVal, x1 - XTriangleWidth, baseYVal - YTriangleHeight);
g2.drawLine(x1 - XTriangleWidth, baseYVal - YTriangleHeight, x1, baseYVal - YTriangleHeight);
g2.drawLine(x1, baseYVal, x1, baseYVal - YLineHeight);
// Draw end triangle
g2.drawLine(x2, baseYVal, x2, baseYVal - YTriangleHeight);
g2.drawLine(x2, baseYVal, x2 + XTriangleWidth, baseYVal - YTriangleHeight);
g2.drawLine(x2 + XTriangleWidth, baseYVal - YTriangleHeight, x2, baseYVal - YTriangleHeight);
g2.drawLine(x2, baseYVal, x2, baseYVal - YLineHeight);
} catch (ClassCastException cce) {
}
int value;
try {
value = ((Number) g.graph.getRingWidthData().get(0)).intValue();
value = yTransform(value * g.scale);
} catch (ClassCastException cce) {
value = yTransform(0);
}
int n = g.graph.getRingWidthData().size();
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;
}
// Extract the window of interest
int ringsEitherSideOfFocus =
(App.prefs.getIntPref(PrefKey.STATS_SKELETON_PLOT_WINDOW_SIZE, 7) - 1) / 2;
// Convert to ArrayList first as its easier to handle
ArrayList<Double> ringWidths = new ArrayList<Double>();
for (int z = 0; z < n; z++) {
ringWidths.add((double) g.graph.getRingWidthData().get(z).intValue());
}
int firstind = i - 1 - ringsEitherSideOfFocus;
int lastind = i + ringsEitherSideOfFocus;
if (firstind < 0) firstind = 0;
if (lastind > n) lastind = n;
int size = lastind - firstind;
double[] window = new double[size];
int t = 0;
for (int w = firstind; w < lastind; w++) {
window[t] = ringWidths.get(w);
t++;
}
DescriptiveStatistics windowStats = new DescriptiveStatistics(window);
/*if(i<7 )
{
log.debug("Stats for ring: "+i);
try{
log.debug(" Window 0: "+window[0]);
log.debug(" Window 1: "+window[1]);
log.debug(" Window 2: "+window[2]);
log.debug(" Window 3: "+window[3]);
log.debug(" Window 4: "+window[4]);
log.debug(" Window 5: "+window[5]);
log.debug(" Window 6: "+window[6]);
} catch (ArrayIndexOutOfBoundsException e){}
log.debug(" Mean is "+i+" - "+(int) windowStats.getMean());
log.debug(" Min is "+i+" - "+(int) windowStats.getMin());
log.debug(" Std is "+i+" - "+(int) windowStats.getStandardDeviation());
log.debug(" Std/2 is "+i+" - "+(int) windowStats.getStandardDeviation()/2);
}*/
// 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?
}
int y = bottom - (int) (value * unitScale) - (int) (g.yoffset * unitScale);
// Calculate skeleton category
Integer skeletonCateogory = null;
String prefAlg =
App.prefs.getPref(
PrefKey.STATS_SKELETON_PLOT_ALGORITHM, SkeletonPlotAlgorithm.PERCENTILES.toString());
if (prefAlg.equals(SkeletonPlotAlgorithm.PERCENTILES.toString())) {
skeletonCateogory = getSkeletonCategoryFromPercentiles(value, windowStats);
} else if (prefAlg.equals(SkeletonPlotAlgorithm.CROPPER1979_0POINT5.toString())) {
skeletonCateogory = getSkeletonCategoryFromCropper1979(value, windowStats, 0.5);
} else if (prefAlg.equals(SkeletonPlotAlgorithm.CROPPER1979_0POINT75.toString())) {
skeletonCateogory = getSkeletonCategoryFromCropper1979(value, windowStats, 0.75);
}
// Draw the skeleton line
if (areBonesBelowLine) {
g2.drawLine(x, baseYVal, x, baseYVal + (skeletonCateogory * 5));
} else {
g2.drawLine(x, baseYVal, x, baseYVal - (skeletonCateogory * 5));
}
// Try and paint remark icons
try {
List<TridasRemark> remarks = g.graph.getTridasValues().get(i).getRemarks();
if (areBonesBelowLine) {
Graph.drawRemarkIcons(
g2, gInfo, remarks, g.graph.getTridasValues().get(i), x, baseYVal, false);
} else {
Graph.drawRemarkIcons(
g2, gInfo, remarks, g.graph.getTridasValues().get(i), x, baseYVal, true);
}
} catch (Exception e) {
log.error("Exception drawing icons to graph: " + e.getClass());
}
}
}