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danv61danv61
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Merge pull request #1666 from virtualcell/dan-ss-display2
Dan ss display2
2 parents 5f63e06 + 6ef5bfd commit c5f4f2c

8 files changed

Lines changed: 498 additions & 211 deletions

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‎vcell-client/src/main/java/cbit/plot/gui/AbstractPlotPanel.java‎

Lines changed: 65 additions & 190 deletions
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‎vcell-client/src/main/java/cbit/plot/gui/PlotRenderers.java‎

Lines changed: 358 additions & 0 deletions
Original file line numberDiff line numberDiff line change
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package cbit.plot.gui;
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import org.apache.logging.log4j.LogManager;
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import org.apache.logging.log4j.Logger;
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import java.awt.*;
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import java.awt.geom.Path2D;
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import static cbit.plot.gui.AbstractPlotPanel.*;
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public final class PlotRenderers {
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private static final Logger lg = LogManager.getLogger(PlotRenderers.class);
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// Generic renderer interface
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protected interface SeriesRenderer {
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void draw(Graphics2D g2,
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int x0, int x1, int y0, int y1,
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int plotWidth, int plotHeight,
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double xMaxRounded, double yMaxRounded, double yMinRounded,
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double dt);
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/**
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* Returns the closest pixel-space point to (mouseX, mouseY),
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* or null if this renderer does not support snapping.
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*/
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default Point getClosestPoint(int mouseX, int mouseY) {
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return null; // default: no snapping
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}
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String getSeriesName();
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}
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// -------------------------------------------------------------------------------------------------
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// AVG renderer: polyline
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protected static class AvgRenderer implements SeriesRenderer {
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final String seriesName; // for legend and hover highlighting
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final double[] time;
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final double[] values;
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final Color color;
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final AbstractPlotPanel parent;
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private int[] xs;
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private int[] ys;
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AvgRenderer(String seriesName, double[] time, double[] values, Color color, AbstractPlotPanel parent) {
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this.seriesName = seriesName;
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this.time = time;
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this.values = values;
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this.color = color;
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this.parent = parent;
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}
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public String getSeriesName() { return seriesName; }
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@Override
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public void draw(Graphics2D g2,
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int x0, int x1, int y0, int y1,
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int plotWidth, int plotHeight,
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double xMaxRounded, double yMaxRounded, double yMinRounded,
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double dt) {
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int n = values.length;
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if (n < 2) return;
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xs = new int[n];
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ys = new int[n];
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for (int i = 0; i < n; i++) {
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double t = (time != null ? time[i] : i * dt);
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xs[i] = x0 + (int)Math.round((t / xMaxRounded) * plotWidth);
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double v = values[i];
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double norm = (v - yMinRounded) / (yMaxRounded - yMinRounded);
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ys[i] = y0 - (int)Math.round(norm * plotHeight);
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}
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Color c = color;
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// Dim this line if hovering another series
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if (parent.hoveredSeriesName != null) {
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if (!parent.hoveredSeriesName.equals(seriesName)) {
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c = new Color(c.getRed(), c.getGreen(), c.getBlue(), DIMMED_LINE_ALPHA);
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}
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}
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// Unite the poins as a polyline or as steps, depending on the setting
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if(parent.getShowLines()) {
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if (!parent.stepAvg) { // draw the polyline (unite the data points directly)
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g2.setColor(c);
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g2.setStroke(new BasicStroke(CURVE_STROKE, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND));
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g2.drawPolyline(xs, ys, n);
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} else { // unite the data points as steps
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// step function: horizontal line from (time[i], values[i]) to (time[i+1], values[i]),
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// then vertical jump at time[i+1]
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g2.setColor(c);
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g2.setStroke(new BasicStroke(CURVE_STROKE, BasicStroke.CAP_BUTT, BasicStroke.JOIN_BEVEL));
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for (int i = 0; i < n - 1; i++) {
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int xStart = xs[i];
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int yStart = ys[i];
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int xEnd = xs[i + 1];
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int yEnd = ys[i + 1];
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g2.drawLine(xStart, yStart, xEnd, yStart); // horizontal segment
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g2.drawLine(xEnd, yStart, xEnd, yEnd); // vertical jump
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}
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}
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}
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// Draw nodes if enabled
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if (parent.getShowNodes()) { // parent is the AbstractPlotPanel
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g2.setColor(c);
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int diameter = parent.nodeDiameter; // small, unobtrusive
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if(!parent.getShowLines()) {
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diameter += 2; // if no lines, make nodes bigger to be more visible
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}
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int radius = diameter / 2;
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for (int i = 0; i < n; i++) {
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int cx = xs[i] - radius;
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int cy = ys[i] - radius;
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g2.fillOval(cx, cy, diameter, diameter);
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}
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}
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}
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@Override
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public Point getClosestPoint(int mouseX, int mouseY) {
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if (xs == null || ys == null) return null;
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int bestIndex = -1;
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double bestDist2 = Double.POSITIVE_INFINITY;
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for (int i = 0; i < xs.length; i++) {
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double dx = xs[i] - mouseX;
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double dy = ys[i] - mouseY;
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double d2 = dx*dx + dy*dy;
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if (d2 < bestDist2) {
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bestDist2 = d2;
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bestIndex = i;
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}
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}
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if (bestIndex < 0) return null;
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return new Point(xs[bestIndex], ys[bestIndex]);
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}
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}
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// -------------------------------------------------------------------------------------------------
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// Band renderer: min/max or sd (envelope)
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protected static class BandRenderer implements SeriesRenderer {
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final String seriesName; // for legend and hover highlighting
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final double[] time;
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final double[] upper;
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final double[] lower;
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final Color fillColor;
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final AbstractPlotPanel parent;
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BandRenderer(String seriesName, double[] time, double[] lower, double[] upper, Color fillColor, AbstractPlotPanel parent) {
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this.seriesName = seriesName;
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this.time = time;
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this.upper = upper;
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this.lower = lower;
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this.fillColor = fillColor;
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this.parent = parent;
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}
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public String getSeriesName() { return seriesName; }
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@Override
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public void draw(Graphics2D g2,
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int x0, int x1, int y0, int y1,
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int plotWidth, int plotHeight,
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double xMaxRounded, double yMaxRounded, double yMinRounded,
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double dt) {
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int n = upper.length;
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if (n < 2) return;
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Path2D path = new Path2D.Double();
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double t0 = (time != null ? time[0] : 0.0);
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double v0 = upper[0];
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double norm0 = (v0 - yMinRounded) / (yMaxRounded - yMinRounded);
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int xStart = x0 + (int)Math.round((t0 / xMaxRounded) * plotWidth);
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int yStart = y0 - (int)Math.round(norm0 * plotHeight);
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path.moveTo(xStart, yStart);
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for (int i = 1; i < n; i++) {
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double t = (time != null ? time[i] : i * dt);
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double v = upper[i];
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double norm = (v - yMinRounded) / (yMaxRounded - yMinRounded);
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int x = x0 + (int)Math.round((t / xMaxRounded) * plotWidth);
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int y = y0 - (int)Math.round(norm * plotHeight);
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path.lineTo(x, y);
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}
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for (int i = n - 1; i >= 0; i--) {
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double t = (time != null ? time[i] : i * dt);
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double v = lower[i];
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double norm = (v - yMinRounded) / (yMaxRounded - yMinRounded);
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int x = x0 + (int)Math.round((t / xMaxRounded) * plotWidth);
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int y = y0 - (int)Math.round(norm * plotHeight);
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path.lineTo(x, y);
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}
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path.closePath();
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Color c = fillColor;
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// If hovering, dim all bands except the hovered one
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if (parent.hoveredSeriesName != null) {
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if (!parent.hoveredSeriesName.equals(parent.getSeriesNameForRenderer(this))) {
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// Dim this band heavily
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c = new Color(c.getRed(), c.getGreen(), c.getBlue(), DIMMED_BAND_ALPHA);
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}
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}
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if (!parent.stepBand) {
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// your existing Path2D polygon
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g2.setColor(c);
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g2.fill(path);
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} else {
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// step function: horizontal line from (time[i], value[i]) to (time[i+1], value[i]),
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// then vertical jump at time[i+1]; do this for both upper and lower, then connect the ends
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Path2D step = new Path2D.Double();
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// ---- UPPER BOUNDARY (left → right) ----
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// Start at first upper point
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double t0u = (time != null ? time[0] : 0.0);
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double v0u = upper[0];
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double norm0u = (v0u - yMinRounded) / (yMaxRounded - yMinRounded);
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int x0u = x0 + (int)Math.round((t0u / xMaxRounded) * plotWidth);
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int y0u = y0 - (int)Math.round(norm0u * plotHeight);
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step.moveTo(x0u, y0u);
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for (int i = 0; i < n - 1; i++) {
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// current point
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double tA = (time != null ? time[i] : i * dt);
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double vA = upper[i];
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double normA = (vA - yMinRounded) / (yMaxRounded - yMinRounded);
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int xA = x0 + (int)Math.round((tA / xMaxRounded) * plotWidth);
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int yA = y0 - (int)Math.round(normA * plotHeight);
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// next point
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double tB = (time != null ? time[i+1] : (i+1) * dt);
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double vB = upper[i+1];
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double normB = (vB - yMinRounded) / (yMaxRounded - yMinRounded);
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int xB = x0 + (int)Math.round((tB / xMaxRounded) * plotWidth);
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int yB = y0 - (int)Math.round(normB * plotHeight);
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// horizontal segment: (xA, yA) → (xB, yA)
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step.lineTo(xB, yA);
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// vertical segment: (xB, yA) → (xB, yB)
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step.lineTo(xB, yB);
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}
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// VERTICAL SEGMENT from last upper point to first lower point
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// compute first lower point at the rightmost x
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double tLast = (time != null ? time[n - 1] : (n - 1) * dt);
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double vLastLower = lower[n - 1];
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double normLastLower = (vLastLower - yMinRounded) / (yMaxRounded - yMinRounded);
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int xLast = x0 + (int)Math.round((tLast / xMaxRounded) * plotWidth);
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int yLastLower = y0 - (int)Math.round(normLastLower * plotHeight);
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// vertical segment from last upper point to first lower point
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step.lineTo(xLast, yLastLower);
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// ---- LOWER BOUNDARY (right → left) ----
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for (int i = n - 1; i > 0; i--) {
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// current point
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double tA = (time != null ? time[i] : i * dt);
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double vA = lower[i];
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double normA = (vA - yMinRounded) / (yMaxRounded - yMinRounded);
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int xA = x0 + (int)Math.round((tA / xMaxRounded) * plotWidth);
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int yA = y0 - (int)Math.round(normA * plotHeight);
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// previous point
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double tB = (time != null ? time[i-1] : (i-1) * dt);
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double vB = lower[i-1];
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double normB = (vB - yMinRounded) / (yMaxRounded - yMinRounded);
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int xB = x0 + (int)Math.round((tB / xMaxRounded) * plotWidth);
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int yB = y0 - (int)Math.round(normB * plotHeight);
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// horizontal segment: (xA, yA) → (xB, yA)
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step.lineTo(xB, yA);
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// vertical segment: (xB, yA) → (xB, yB)
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step.lineTo(xB, yB);
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}
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step.closePath();
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g2.setColor(c);
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g2.fill(step);
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}
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}
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}
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// ------------------------------------------------------------------
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protected static class BarRenderer implements SeriesRenderer {
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final String seriesName;
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final double[] time;
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final double[] upper;
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final double[] lower;
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final Color color;
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final AbstractPlotPanel parent;
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public BarRenderer(String seriesName,
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double[] time,
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double[] lower,
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double[] upper,
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Color color,
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AbstractPlotPanel parent) {
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this.seriesName = seriesName;
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this.time = time;
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this.upper = upper;
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this.lower = lower;
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this.color = color;
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this.parent = parent;
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}
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@Override
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public String getSeriesName() {
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return seriesName;
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}
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@Override
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public void draw(Graphics2D g2,
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int x0, int x1, int y0, int y1,
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int plotWidth, int plotHeight,
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double xMaxRounded, double yMaxRounded, double yMinRounded,
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double dt) {
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int n = upper.length;
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if (n == 0) return;
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Color c = color;
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if (parent.hoveredSeriesName != null && // dimming logic is the same as in BandRenderer
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!parent.hoveredSeriesName.equals(parent.getSeriesNameForRenderer(this))) {
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c = new Color(c.getRed(), c.getGreen(), c.getBlue(), AbstractPlotPanel.DIMMED_BAND_ALPHA);
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}
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g2.setColor(c);
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g2.setStroke(new BasicStroke(2.0f));
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for (int i = 0; i < n; i++) {
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double t = (time != null ? time[i] : i * dt);
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double vLow = lower[i];
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double vHigh = upper[i];
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double vAvg = (vLow + vHigh) / 2.0;
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double normLow = (vLow - yMinRounded) / (yMaxRounded - yMinRounded);
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double normAvg = (vAvg - yMinRounded) / (yMaxRounded - yMinRounded);
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double normHigh = (vHigh - yMinRounded) / (yMaxRounded - yMinRounded);
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int x = x0 + (int)Math.round((t / xMaxRounded) * plotWidth);
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int yLowPix = y0 - (int)Math.round(normLow * plotHeight);
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int yAvgPix = y0 - (int)Math.round(normAvg * plotHeight);
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int yHighPix = y0 - (int)Math.round(normHigh * plotHeight);
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if (parent.getShowLines()) {
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g2.drawLine(x, yLowPix, x, yHighPix); // vertical SD bar
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g2.drawLine(x - 3, yLowPix, x + 3, yLowPix); // optional caps
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g2.drawLine(x - 3, yHighPix, x + 3, yHighPix);
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} else {
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// only upper half
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g2.drawLine(x, yAvgPix, x, yHighPix); // vertical SD bar
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// diamond at top
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int d = 4; // diamond radius
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int[] dx = { x, x + d, x, x - d };
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int[] dy = { yHighPix - d, yHighPix, yHighPix + d, yHighPix };
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g2.fillPolygon(dx, dy, 4);
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}
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}
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}
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}
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}

‎vcell-client/src/main/java/cbit/vcell/solver/ode/gui/AbstractVisualizationPanel.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -26,13 +26,13 @@ public LineIcon(Color color) {
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@Override
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public void paintIcon(Component c, Graphics g, int x, int y) {
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Graphics2D g2 = (Graphics2D)g;
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g2.setStroke(new BasicStroke(4.0f));
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g2.setStroke(new BasicStroke(6.0f));
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g2.setPaint(color);
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int midY = y + getIconHeight() / 2;
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g2.drawLine(x, midY, x + getIconWidth(), midY);
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}
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@Override
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public int getIconWidth() { return 50; }
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public int getIconWidth() { return 80; }
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@Override
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public int getIconHeight() {
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return 4; // more vertical room for a wider stroke

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