private void updateHistogramGraph(double min, double max) {
xAxis.clear();
currentMaxMin.max = max;
currentMaxMin.min = min;
histogramFunc.setMinMax(min, max);
histogramFunc.setIgnoreOutliers(true);
// sanity check if there is actually a histogram live
List<? extends Dataset> newHistogram = histogramFunc.value(data);
Dataset histogram = newHistogram.get(0);
if (histograms != null && histograms.size() > 1) {
histograms.set(histograms.size() - 1, histogram);
} else {
histograms = new ArrayList<Dataset>();
histograms.add(histogram);
}
// Some logging to check on the histograms size
logger.debug("number of histograms stored is {}", histograms.size());
if (histograms.size() > 10) {
logger.warn(
"Number of stored histograms is over expected levels, now at {}", histograms.size());
}
xAxis.setValues(
DatasetUtils.linSpace(min, max, Math.max(1, histogram.getSize() + 1), Dataset.FLOAT64));
histogramPlotter.setXAxisValues(xAxis, 1);
generateHistogramUpdate();
updateChannelGraphs();
histogramPlotter.refresh(true);
}
public void setGraphLines(boolean checked) {
if (histogramPlotter != null) {
Plot1DGraphTable table = histogramPlotter.getColourTable();
for (int i = 0; i < 4; i++) table.getLegendEntry(i).setVisible(checked);
}
histogramPlotter.updateAllAppearance();
histogramPlotter.refresh(false);
}
@Override
public Object execute(ExecutionEvent event) throws ExecutionException {
String viewID = event.getParameter("uk.ac.diamond.scisoft.analysis.command.sourceView");
if (viewID != null) {
final AbstractPlotView apv =
(AbstractPlotView)
PlatformUI.getWorkbench().getActiveWorkbenchWindow().getActivePage().findView(viewID);
DataSetPlotter plotter = apv.getPlotter();
if (plotter != null) {
plotter.setYAxisScaling(ScaleType.LN);
}
return Boolean.TRUE;
}
return Boolean.FALSE;
}
@Override
public void dispose() {
// store current settings back into preferences
IPreferenceStore preferenceStore = AnalysisRCPActivator.getDefault().getPreferenceStore();
String pName = getPartName();
Integer setting = colourSettings.get(pName);
if (setting != null)
preferenceStore.setValue(
pName + "." + PreferenceConstants.PLOT_VIEW_PLOT2D_COLOURMAP, setting);
preferenceStore.setValue(
pName + "." + PreferenceConstants.PLOT_VIEW_PLOT2D_SCALING, (useLog ? 1 : 0));
deleteIObservers();
if (histogramPlotter != null) histogramPlotter.cleanUp();
data = null;
if (histogramUI != null) {
histogramUI.deactivate(false);
histogramUI.dispose();
}
if (!cmbAlpha.isDisposed()) cmbAlpha.removeSelectionListener(this);
if (!cmbRedColour.isDisposed()) cmbRedColour.removeSelectionListener(this);
if (!cmbGreenColour.isDisposed()) cmbGreenColour.removeSelectionListener(this);
if (!cmbBlueColour.isDisposed()) cmbBlueColour.removeSelectionListener(this);
if (!btnGreenInverse.isDisposed()) btnGreenInverse.removeSelectionListener(this);
if (!btnBlueInverse.isDisposed()) btnBlueInverse.removeSelectionListener(this);
if (!btnAlphaInverse.isDisposed()) btnAlphaInverse.removeSelectionListener(this);
if (!btnRedInverse.isDisposed()) btnRedInverse.removeSelectionListener(this);
super.dispose();
}
private void autoRangeHistogram() {
histogramPlotter.clearZoomHistory();
double[] m;
if (autoContrast && data.getRank() == 2) {
try {
final int[] shape = data.getShape();
if (shape[0] > 512 && shape[1] > 512) {
int yReduce = (int) Math.ceil(shape[0] / 512.0);
int xReduce = (int) Math.ceil(shape[1] / 512.0);
Downsample sample = new Downsample(DownsampleMode.MAXIMUM, xReduce, yReduce);
m =
Stats.quantile(
(Dataset) sample.value(data).get(0),
getPreferenceAutoContrastLo(),
getPreferenceAutoContrastHi());
} else
m = Stats.quantile(data, getPreferenceAutoContrastLo(), getPreferenceAutoContrastHi());
} catch (Exception e) {
m = new double[] {data.min().doubleValue(), data.max().doubleValue()};
}
} else {
m = new double[] {data.min().doubleValue(), data.max().doubleValue()};
}
if (Double.compare(m[1], m[0]) <= 0)
m[1] = m[0] + PreferenceConstants.MINIMUM_CONTRAST_DELTA / 100.0;
currentMaxMin.max = m[1];
currentMaxMin.min = m[0];
}
protected void buildGradientImage() {
GlobalColourMaps.mappingFunctions.get(0);
AbstractMapFunction redFunc =
GlobalColourMaps.mappingFunctions.get(cmbRedColour.getSelectionIndex());
AbstractMapFunction greenFunc =
GlobalColourMaps.mappingFunctions.get(cmbGreenColour.getSelectionIndex());
AbstractMapFunction blueFunc =
GlobalColourMaps.mappingFunctions.get(cmbBlueColour.getSelectionIndex());
AbstractMapFunction alphaFunc =
GlobalColourMaps.mappingFunctions.get(cmbAlpha.getSelectionIndex());
boolean negRed = btnRedInverse.getSelection();
boolean negGreen = btnGreenInverse.getSelection();
boolean negBlue = btnBlueInverse.getSelection();
boolean negAlpha = btnAlphaInverse.getSelection();
histogramPlotter.applyColourCast(
redFunc, greenFunc, blueFunc, alphaFunc, negRed, negGreen, negBlue, negAlpha, 0, 256);
histogramPlotter.refresh(false);
}
public void setScaling(ScaleType newScaling) {
useLog = (newScaling != ScaleType.LINEAR);
histogramPlotter.setYAxisScaling(newScaling);
}
protected void updateChannelGraphs() {
if (histograms != null && histograms.size() > 1) {
// remove red channel graph
histograms.remove(0);
// remove green channel graph
histograms.remove(0);
// remove blue channel graph
histograms.remove(0);
// remove alpha channel graph
histograms.remove(0);
}
AbstractMapFunction redFunc = GlobalColourMaps.mappingFunctions.get(curRedSelect);
AbstractMapFunction greenFunc = GlobalColourMaps.mappingFunctions.get(curGreenSelect);
AbstractMapFunction blueFunc = GlobalColourMaps.mappingFunctions.get(curBlueSelect);
AbstractMapFunction alphaFunc = GlobalColourMaps.mappingFunctions.get(curAlphaSelect);
double maxValue = histograms.get(0).max().doubleValue();
int currentSize = histograms.get(0).getSize();
DoubleDataset redChannel = new DoubleDataset(currentSize);
DoubleDataset greenChannel = new DoubleDataset(currentSize);
DoubleDataset blueChannel = new DoubleDataset(currentSize);
DoubleDataset alphaChannel = new DoubleDataset(currentSize);
for (int i = 0; i < currentSize; i++) {
double value = i / (double) currentSize;
double redvalue = redFunc.getPoint(value);
if (curRedInverse) redvalue = 1.0 - redvalue;
redvalue *= maxValue;
double greenvalue = greenFunc.getPoint(value);
if (curGreenInverse) greenvalue = 1.0 - greenvalue;
greenvalue *= maxValue;
double bluevalue = blueFunc.getPoint(value);
if (curBlueInverse) bluevalue = 1.0 - bluevalue;
bluevalue *= maxValue;
double alphavalue = alphaFunc.getPoint(value);
if (curAlphaInverse) alphavalue = 1.0 - alphavalue;
alphavalue *= maxValue;
redChannel.set(Math.max(redvalue, 0.0), i);
greenChannel.set(Math.max(greenvalue, 0.0), i);
blueChannel.set(Math.max(bluevalue, 0.0), i);
alphaChannel.set(Math.max(alphavalue, 0.0), i);
}
histograms.add(0, alphaChannel);
histograms.add(0, blueChannel);
histograms.add(0, greenChannel);
histograms.add(0, redChannel);
// Some logging to check on the histograms size
logger.debug("number of histograms stored is {}", histograms.size());
if (histograms.size() > 10) {
logger.warn(
"Number of stored histograms is over expected levels, now at {}", histograms.size());
}
try {
histogramPlotter.replaceAllPlots(histograms);
} catch (PlotException e) {
e.printStackTrace();
}
}
@Override
public void widgetSelected(SelectionEvent e) {
if (e.getSource().equals(cmbRedColour)
|| e.getSource().equals(cmbGreenColour)
|| e.getSource().equals(cmbBlueColour)
|| e.getSource().equals(cmbAlpha)
|| e.getSource().equals(btnRedInverse)
|| e.getSource().equals(btnGreenInverse)
|| e.getSource().equals(btnBlueInverse)
|| e.getSource().equals(btnAlphaInverse)) {
curAlphaSelect = cmbAlpha.getSelectionIndex();
curRedSelect = cmbRedColour.getSelectionIndex();
curGreenSelect = cmbGreenColour.getSelectionIndex();
curBlueSelect = cmbBlueColour.getSelectionIndex();
curAlphaInverse = btnAlphaInverse.getSelection();
curRedInverse = btnRedInverse.getSelection();
curGreenInverse = btnGreenInverse.getSelection();
curBlueInverse = btnBlueInverse.getSelection();
if (hasData()) {
if (e.getSource().equals(cmbRedColour)) handleChange(0);
else if (e.getSource().equals(cmbGreenColour)) handleChange(1);
else if (e.getSource().equals(cmbBlueColour)) handleChange(2);
else if (e.getSource().equals(cmbAlpha)) handleChange(3);
updateChannelGraphs();
generateHistogramUpdate();
}
if (e.getSource().equals(cmbGreenColour)
|| e.getSource().equals(cmbRedColour)
|| e.getSource().equals(btnRedInverse)
|| e.getSource().equals(btnGreenInverse)
|| e.getSource().equals(btnBlueInverse)
|| e.getSource().equals(btnAlphaInverse)) histogramPlotter.refresh(true);
buildGradientImage();
} else if (e.getSource().equals(cmbColourMap)) {
colourSettings.put(getPartName(), cmbColourMap.getSelectionIndex());
buildSelection();
handleChange(0);
handleChange(1);
handleChange(2);
if (hasData()) {
updateChannelGraphs();
generateHistogramUpdate();
}
histogramPlotter.refresh(true);
buildGradientImage();
if (cmbColourMap.getItem(cmbColourMap.getSelectionIndex()).equals("Mark's special")) {
spnMinValue.setSelection((int) (specialMinThreshold * 100));
spnMaxValue.setSelection((int) (specialMaxThreshold * 100));
threshPanel.setVisible(true);
((GridData) threshPanel.getLayoutData()).exclude = false;
} else {
threshPanel.setVisible(false);
((GridData) threshPanel.getLayoutData()).exclude = true;
}
container.layout();
} else if (e.getSource().equals(spnMinValue) || e.getSource().equals(spnMaxValue)) {
SpecialExposureFunction redFunc =
(SpecialExposureFunction)
GlobalColourMaps.mappingFunctions.get(cmbRedColour.getSelectionIndex());
SpecialExposureFunction greenFunc =
(SpecialExposureFunction)
GlobalColourMaps.mappingFunctions.get(cmbGreenColour.getSelectionIndex());
SpecialExposureFunction blueFunc =
(SpecialExposureFunction)
GlobalColourMaps.mappingFunctions.get(cmbBlueColour.getSelectionIndex());
redFunc.setThresholds(spnMinValue.getSelection() / 100.0, spnMaxValue.getSelection() / 100.0);
greenFunc.setThresholds(
spnMinValue.getSelection() / 100.0, spnMaxValue.getSelection() / 100.0);
blueFunc.setThresholds(
spnMinValue.getSelection() / 100.0, spnMaxValue.getSelection() / 100.0);
specialMaxThreshold = spnMaxValue.getSelection() / 100.0;
specialMinThreshold = spnMinValue.getSelection() / 100.0;
updateChannelGraphs();
generateHistogramUpdate();
histogramPlotter.refresh(true);
} else if (e.getSource().equals(spnRangeStart.getControl())
|| e.getSource().equals(spnRangeStop.getControl())) {
final double min = spnRangeStart.getDouble();
final double max = spnRangeStop.getDouble();
updateHistogramGraph(min, max);
} else if (e.getSource().equals(sldMinValue) || e.getSource().equals(sldMaxValue)) {
final double min =
spnRangeStart.getMinimum()
+ spnRangeStart.getRange()
* (sldMinValue.getSelection() / (double) sldMinValue.getMaximum());
final double max =
spnRangeStart.getMinimum()
+ spnRangeStart.getRange()
* (sldMaxValue.getSelection() / (double) sldMaxValue.getMaximum());
spnRangeStart.setDouble(min);
spnRangeStop.setDouble(max);
if (hasData()) updateHistogramGraph(min, max);
} else if (e.getSource().equals(btnExpertMode)) {
expertGroup.setVisible(btnExpertMode.getSelection());
((GridData) expertGroup.getLayoutData()).exclude = !btnExpertMode.getSelection();
container.layout();
}
}
@Override
public void createPartControl(Composite parent) {
this.parent = parent;
container = new Composite(parent, SWT.NONE);
container.setLayout(new GridLayout(1, false));
final Composite top = new Composite(container, SWT.NONE);
top.setLayout(new GridLayout(3, false));
top.setLayoutData(new GridData(SWT.FILL, SWT.CENTER, true, false));
final Label scheme = new Label(top, SWT.NONE);
scheme.setText("Colour Scheme");
cmbColourMap = new CCombo(top, SWT.BORDER | SWT.READ_ONLY);
cmbColourMap.setToolTipText("Change the color scheme.");
cmbColourMap.setLayoutData(new GridData(SWT.FILL, SWT.CENTER, true, false));
btnExpertMode = new Button(top, SWT.CHECK);
btnExpertMode.setText("Expert");
btnExpertMode.setToolTipText("Enable expert mode for customising colour channels");
btnExpertMode.addSelectionListener(this);
advancedComp = new Composite(container, SWT.NONE);
// controlGroup.setText("RGB Settings"); // Looks a bit busy with this label
advancedComp.setLayoutData(new GridData(SWT.FILL, SWT.TOP, true, false));
advancedComp.setLayout(new GridLayout(3, false));
expertGroup = new Group(advancedComp, SWT.NONE);
expertGroup.setLayoutData(new GridData(SWT.FILL, SWT.TOP, true, false, 2, 1));
expertGroup.setLayout(new GridLayout(3, false));
{
Label lblRed = new Label(expertGroup, SWT.NONE);
lblRed.setText("Red");
cmbRedColour = new CCombo(expertGroup, SWT.BORDER | SWT.READ_ONLY);
btnRedInverse = new Button(expertGroup, SWT.CHECK);
btnRedInverse.setText("Inverse");
btnRedInverse.addSelectionListener(this);
Label lblGreen = new Label(expertGroup, SWT.NONE);
lblGreen.setText("Green");
cmbGreenColour = new CCombo(expertGroup, SWT.BORDER | SWT.READ_ONLY);
btnGreenInverse = new Button(expertGroup, SWT.CHECK);
btnGreenInverse.setText("Inverse");
btnGreenInverse.addSelectionListener(this);
Label lblBlue = new Label(expertGroup, SWT.NONE);
lblBlue.setText("Blue");
cmbBlueColour = new CCombo(expertGroup, SWT.BORDER | SWT.READ_ONLY);
btnBlueInverse = new Button(expertGroup, SWT.CHECK);
btnBlueInverse.setText("Inverse");
btnBlueInverse.addSelectionListener(this);
Label lblAlpha = new Label(expertGroup, SWT.NONE);
lblAlpha.setText("Alpha");
cmbAlpha = new CCombo(expertGroup, SWT.BORDER | SWT.READ_ONLY);
btnAlphaInverse = new Button(expertGroup, SWT.CHECK);
btnAlphaInverse.setText("Inverse");
btnAlphaInverse.addSelectionListener(this);
}
expertGroup.setVisible(getPreferenceColourMapExpertMode());
((GridData) expertGroup.getLayoutData()).exclude = !getPreferenceColourMapExpertMode();
threshPanel = new Group(advancedComp, SWT.NONE);
threshPanel.setText("Mark's special threshhold"); // Looks a bit busy with this label
threshPanel.setLayoutData(new GridData(SWT.FILL, SWT.TOP, false, false));
threshPanel.setLayout(new GridLayout(2, false));
{
Label lblMinValue = new Label(threshPanel, SWT.NONE);
lblMinValue.setText("Min threshold");
spnMinValue = new Spinner(threshPanel, SWT.BORDER);
spnMinValue.setMinimum(0);
spnMinValue.setMaximum(100);
spnMinValue.addSelectionListener(this);
Label lblMaxValue = new Label(threshPanel, SWT.NONE);
lblMaxValue.setText("Max threshold");
spnMaxValue = new Spinner(threshPanel, SWT.BORDER);
spnMaxValue.setMinimum(0);
spnMaxValue.setMaximum(100);
spnMaxValue.addSelectionListener(this);
}
threshPanel.setVisible(false);
((GridData) threshPanel.getLayoutData()).exclude = true;
rangePanel = new Group(container, SWT.NONE);
rangePanel.setLayoutData(new GridData(SWT.FILL, SWT.CENTER, true, false));
rangePanel.setLayout(new GridLayout(3, false));
rangePanel.setText("Histogram range");
{
Label lblStartValue = new Label(rangePanel, SWT.NONE);
lblStartValue.setText("Minimum");
spnRangeStart = new FloatSpinner(rangePanel, SWT.BORDER);
GridData gridData = new GridData(SWT.NONE, SWT.NONE, true, false);
spnRangeStart.setLayoutData(gridData);
spnRangeStart.addSelectionListener(this);
sldMinValue = new Slider(rangePanel, SWT.BORDER);
gridData = new GridData(SWT.FILL, SWT.NONE, true, false);
gridData.minimumWidth = 90;
sldMinValue.setLayoutData(gridData);
sldMinValue.addSelectionListener(this);
sldMinValue.setMinimum(0);
sldMinValue.setMaximum(SLIDERSECTIONS);
sldMinValue.setIncrement(1);
Label lblStopValue = new Label(rangePanel, SWT.NONE);
lblStopValue.setText("Maximum");
gridData = new GridData(SWT.NONE, SWT.NONE, true, false);
spnRangeStop = new FloatSpinner(rangePanel, SWT.BORDER);
spnRangeStop.setLayoutData(gridData);
spnRangeStop.addSelectionListener(this);
spnRangeStart.setEnabled(false);
spnRangeStop.setEnabled(false);
sldMaxValue = new Slider(rangePanel, SWT.BORDER);
gridData = new GridData(SWT.FILL, SWT.NONE, true, false);
gridData.minimumWidth = 90;
sldMaxValue.setLayoutData(gridData);
sldMaxValue.addSelectionListener(this);
sldMaxValue.setMinimum(0);
sldMaxValue.setMaximum(SLIDERSECTIONS);
sldMaxValue.setIncrement(1);
spnRangeStart.setEnabled(false);
spnRangeStop.setEnabled(false);
sldMinValue.setEnabled(false);
sldMaxValue.setEnabled(false);
}
{
composite = new Composite(container, SWT.NONE);
composite.setLayoutData(new GridData(SWT.FILL, SWT.FILL, true, true));
composite.setLayout(new FillLayout());
histogramPlotter = new DataSetPlotter(PlottingMode.BARCHART, composite, false);
histogramPlotter.setXAxisLabel("Intensity Value");
histogramPlotter.setYAxisLabel("Count");
histogramPlotter.setAxisModes(AxisMode.CUSTOM, AxisMode.LINEAR, AxisMode.LINEAR);
histogramPlotter.setXTickLabelFormat(TickFormatting.plainMode);
histogramPlotter.setXAxisValues(xAxis, 1);
Plot1DGraphTable colourTable = histogramPlotter.getColourTable();
Plot1DAppearance plotApp = new Plot1DAppearance(Color.RED, Plot1DStyles.SOLID, "");
colourTable.addEntryOnLegend(plotApp);
plotApp = new Plot1DAppearance(Color.GREEN, Plot1DStyles.SOLID, "");
colourTable.addEntryOnLegend(plotApp);
plotApp = new Plot1DAppearance(Color.BLUE, Plot1DStyles.SOLID, "");
colourTable.addEntryOnLegend(plotApp);
plotApp = new Plot1DAppearance(Color.ORANGE, Plot1DStyles.SOLID, "");
colourTable.addEntryOnLegend(plotApp);
}
cmbColourMap.addSelectionListener(this);
cmbRedColour.addSelectionListener(this);
cmbGreenColour.addSelectionListener(this);
cmbBlueColour.addSelectionListener(this);
cmbAlpha.addSelectionListener(this);
buildToolbar();
GlobalColourMaps.InitializeColourMaps();
fillupColourComboBoxes();
fillupColourMapBox();
buildGradientImage();
}
protected void buildToolbar() {
IActionBars toolBar = getViewSite().getActionBars();
histogramUI = new HistogramUI(this, toolBar, histogramPlotter);
histogramUI.addIObserver(this);
histogramPlotter.registerUI(histogramUI);
}