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Viewer2D: Allow fixed range in all axes
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See https://forum.image.sc/t/snt-problem-with-inconsistent-scale-on-x-axis-in-multiple-reconstruction-plotter/105520
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@tferr
tferr committed Dec 1, 2024
1 parent 8b7d542 commit 23ae70e
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Showing 3 changed files with 108 additions and 9 deletions.
2 changes: 1 addition & 1 deletion src/main/java/sc/fiji/snt/analysis/MultiTreeColorMapper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -218,7 +218,7 @@ private String getNormalizedMeasurementInternal(final String measurement) {
final String normMeasurement = tryReallyHardToGuessMetric(measurement);
if (!measurement.equals(normMeasurement)) {
SNTUtils.log("\"" + normMeasurement + "\" assumed");
if ("unknonwn".equals(normMeasurement)) {
if ("unknown".equals(normMeasurement)) {
throw new IllegalArgumentException("Unrecognizable measurement! "
+ "Maybe you meant one of the following?: " + Arrays.toString(MULTI_TREE_FLAGS));
}
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87 changes: 79 additions & 8 deletions src/main/java/sc/fiji/snt/viewer/MultiViewer2D.java
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Original file line number Diff line number Diff line change
Expand Up @@ -138,6 +138,28 @@ public void setOutlineVisible(final boolean visible) {
outlineVisible = visible;
}

/**
* Sets a manual range for the viewers' X-axis. Calling {@code setXrange(-1, -1)} enables auto-range (the default).
* Must be called before Viewer is fully assembled.
*
* @param xMin the lower-limit for the X-axis
* @param xMax the upper-limit for the X-axis
*/
public void setXrange(final double xMin, final double xMax) {
viewers.forEach( v -> v.setXrange(xMin, xMax));
}

/**
* Sets a manual range for the viewers' Y-axis. Calling {@code setYrange(-1, -1)} enables auto-range (the default).
* Must be called before Viewer is fully assembled.
*
* @param yMin the lower-limit for the Y-axis
* @param yMax the upper-limit for the Y-axis
*/
public void setYrange(final double yMin, final double yMax) {
viewers.forEach( v -> v.setYrange(yMin, yMax));
}

public <T extends sc.fiji.snt.analysis.ColorMapper> void setColorBarLegend(final T colorMapper) {
final double[] minMax = colorMapper.getMinMax();
setColorBarLegend(colorMapper.getColorTable(), minMax[0], minMax[1], (colorMapper.isIntegerScale()) ? 0 : 2);
Expand Down Expand Up @@ -239,8 +261,32 @@ private String getTitlesAsString(final List<Viewer2D> viewers) {
return null;
}

private SNTChart getMergedChart(final List<Viewer2D> viewers, final String style) {
private double[] getFixedXRange(final List<Viewer2D> viewers) {
final double min = viewers.get(0).getPlot().xAxis().getMin();
final double max = viewers.get(0).getPlot().xAxis().getMax();
if (min == max) return null;
for (int i = 1; i < viewers.size(); i++) {
if (min != viewers.get(i).getPlot().xAxis().getMin() && max != viewers.get(i).getPlot().xAxis().getMax())
return null;
}
return new double[]{min, max};
}

private double[] getFixedYRange(final List<Viewer2D> viewers) {
final double min = viewers.get(0).getPlot().yAxis().getMin();
final double max = viewers.get(0).getPlot().yAxis().getMax();
if (min == max) return null;
for (int i = 1; i < viewers.size(); i++) {
if (min != viewers.get(i).getPlot().yAxis().getMin() && max != viewers.get(i).getPlot().yAxis().getMax())
return null;
}
return new double[]{min, max};
}

private SNTChart getMergedChart(final List<Viewer2D> viewers, final String style) {
JFreeChart result;
final double[] fixedXrange = getFixedXRange(viewers);
final double[] fixedYrange = getFixedYRange(viewers);
if (style != null && style.toLowerCase().startsWith("c")) { // column
final CombinedRangeXYPlot mergedPlot = new CombinedRangeXYPlot();
for (final Viewer2D viewer : viewers) {
Expand All @@ -250,18 +296,43 @@ private SNTChart getMergedChart(final List<Viewer2D> viewers, final String style
plot.setDomainGridlinesVisible(gridVisible);
plot.setRangeGridlinesVisible(gridVisible);
plot.setOutlineVisible(outlineVisible);
if (fixedXrange != null) {
plot.getDomainAxis().setRange(fixedXrange[0], fixedXrange[1]);
plot.getDomainAxis().setAutoRange(false);
}
if (fixedYrange != null) {
plot.getRangeAxis().setRange(fixedYrange[0], fixedYrange[1]);
plot.getRangeAxis().setAutoRange(false);
}
mergedPlot.add(plot, 1);
if (fixedYrange != null) {
mergedPlot.getRangeAxis().setRange(fixedYrange[0], fixedYrange[1]);
mergedPlot.getRangeAxis().setAutoRange(false);
}
}
result = new JFreeChart(null, mergedPlot);
} else {
final CombinedDomainXYPlot mergedPlot = new CombinedDomainXYPlot();
for (final Viewer2D viewer : viewers) {
mergedPlot.add(viewer.getChart().getChart().getXYPlot(), 1);
final XYPlot plot = viewer.getJFreeChart().getXYPlot();
if (fixedXrange != null) {
plot.getDomainAxis().setRange(fixedXrange[0], fixedXrange[1]);
plot.getDomainAxis().setAutoRange(false);
}
if (fixedYrange != null) {
plot.getRangeAxis().setRange(fixedYrange[0], fixedYrange[1]);
plot.getRangeAxis().setAutoRange(false);
}
mergedPlot.add(plot, 1);
if (fixedXrange != null) {
mergedPlot.getDomainAxis().setRange(fixedXrange[0], fixedXrange[1]);
mergedPlot.getDomainAxis().setAutoRange(false);
}
}
result = new JFreeChart(null, mergedPlot);
}
if (legend != null && viewers.contains(colorLegendViewer)) {
if (gridCols >= this.viewers.size()) {
if (gridCols >= viewers.size()) {
legend.setPosition(RectangleEdge.RIGHT);
legend.setMargin(50, 5, 50, 5);
} else {
Expand Down Expand Up @@ -290,7 +361,7 @@ public static void main(final String... args) {

// Color code each cell and assign a hue ramp to the group
final MultiTreeColorMapper mapper = new MultiTreeColorMapper(trees);
mapper.map("tips", ColorTables.ICE);
mapper.map("no. of tips", ColorTables.ICE);

// Assemble a multi-panel Viewer2D from the color mapper
final MultiViewer2D viewer1 = mapper.getMultiViewer();
Expand All @@ -300,8 +371,7 @@ public static void main(final String... args) {
viewer1.setAxesVisible(false);
viewer1.show();

// Sholl mapping //TODO: The API for this feels clunky
// and everything is really slow. Optimization needed!
// Sholl mapping
final List<Viewer2D> viewers = new ArrayList<>();
double min = Double.MAX_VALUE;
double max = Double.MIN_VALUE;
Expand All @@ -325,9 +395,10 @@ public static void main(final String... args) {
viewer2.setLayoutColumns(0);
viewer2.setGridlinesVisible(false);
viewer2.setOutlineVisible(false);
viewer2.setAxesVisible(false);
viewer2.setAxesVisible(true);
viewer2.setXrange(-100, 100);
viewer2.setYrange(-200, 200);
viewer2.show();

}

}
28 changes: 28 additions & 0 deletions src/main/java/sc/fiji/snt/viewer/Viewer2D.java
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Original file line number Diff line number Diff line change
Expand Up @@ -513,6 +513,34 @@ public String getTitle() {
return title;
}

/**
* Sets a manual range for the viewers' X-axis. Calling {@code setXrange(-1, -1)} enables auto-range (the default).
* Must be called before Viewer is fully assembled.
*
* @param xMin the lower-limit for the X-axis
* @param xMax the upper-limit for the X-axis
*/
public void setXrange(final double xMin, final double xMax) {
if (xMin == xMax && xMin == -1)
plot.xAxis().setAutoRange();
else
plot.xAxis().setManualRange(xMin, xMax);
}

/**
* Sets a manual range for the viewers' Y-axis. Calling {@code setYrange(-1, -1)} enables auto-range (the default).
* Must be called before Viewer is fully assembled.
*
* @param yMin the lower-limit for the Y-axis
* @param yMax the upper-limit for the Y-axis
*/
public void setYrange(final double yMin, final double yMax) {
if (yMin == yMax && yMin == -1)
plot.yAxis().setAutoRange();
else
plot.yAxis().setManualRange(yMin, yMax);
}

/**
* @deprecated Use {@link #show()} instead.
*/
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1 comment on commit 23ae70e

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This commit has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/snt-problem-with-inconsistent-scale-on-x-axis-in-multiple-reconstruction-plotter/105520/2

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