@Override
public ImageServiceBean createBeanFromPreferences() {
ImageServiceBean imageServiceBean = new ImageServiceBean();
if (Platform.getPreferencesService() != null) { // Normally
IPreferenceStore store =
new ScopedPreferenceStore(InstanceScope.INSTANCE, "org.dawnsci.plotting");
imageServiceBean.setOrigin(
ImageOrigin.forLabel(store.getString(BasePlottingConstants.ORIGIN_PREF)));
imageServiceBean.setHistogramType(
HistoType.forLabel(store.getString(BasePlottingConstants.HISTO_PREF)));
imageServiceBean.setMinimumCutBound(
HistogramBound.fromString(store.getString(BasePlottingConstants.MIN_CUT)));
imageServiceBean.setMaximumCutBound(
HistogramBound.fromString(store.getString(BasePlottingConstants.MAX_CUT)));
imageServiceBean.setNanBound(
HistogramBound.fromString(store.getString(BasePlottingConstants.NAN_CUT)));
imageServiceBean.setLo(store.getDouble(BasePlottingConstants.HISTO_LO));
imageServiceBean.setHi(store.getDouble(BasePlottingConstants.HISTO_HI));
try {
IPaletteService pservice = ServiceLoader.getPaletteService();
if (pservice != null) {
final String scheme = store.getString(BasePlottingConstants.COLOUR_SCHEME);
if (store.getBoolean(BasePlottingConstants.USE_PALETTE_FUNCTIONS)) {
FunctionContainer container = pservice.getFunctionContainer(scheme);
if (container != null) {
imageServiceBean.setFunctionObject(container);
} else {
imageServiceBean.setPalette(pservice.getDirectPaletteData(scheme));
}
} else {
// if 8-bit, set direct palette, otherwise set palette functions.
PaletteData pd;
try {
pd = pservice.getDirectPaletteData(scheme);
} catch (final IllegalArgumentException e) { // scheme does not exist
final String defaultScheme = pservice.getColorSchemes().iterator().next();
pd = pservice.getDirectPaletteData(defaultScheme);
store.setValue(BasePlottingConstants.COLOUR_SCHEME, defaultScheme);
}
imageServiceBean.setPalette(pd);
}
}
} catch (Exception e) {
// Ignored
}
} else { // Hard code something
imageServiceBean.setOrigin(ImageOrigin.TOP_LEFT);
imageServiceBean.setHistogramType(HistoType.OUTLIER_VALUES);
imageServiceBean.setMinimumCutBound(HistogramBound.DEFAULT_MINIMUM);
imageServiceBean.setMaximumCutBound(HistogramBound.DEFAULT_MAXIMUM);
imageServiceBean.setNanBound(HistogramBound.DEFAULT_NAN);
imageServiceBean.setLo(00.01);
imageServiceBean.setHi(99.99);
imageServiceBean.setPalette(makeJetPalette());
}
return imageServiceBean;
}
/**
* Fast statistics as a rough guide - this is faster than Dataset.getMin() and getMax() which may
* cache but slows the opening of images too much. The return array[2] was added in "Updated for
* Diffraction Tool." commit, but no trace of such usage. However it should not be removed,
* because it is useful as return array[3].
*
* @param bean
* @return [0] = min [1] = max(=mean*constant) [2] = mean [3] max
*/
public double[] getFastStatistics(ImageServiceBean bean) {
Dataset image = getImageLoggedData(bean);
if (bean.getHistogramType() == HistoType.OUTLIER_VALUES && !bean.isLogColorScale()) {
double[] ret = null;
try {
double[] stats = Stats.outlierValues(image, bean.getLo(), bean.getHi(), -1);
ret = new double[] {stats[0], stats[1], -1};
} catch (IllegalArgumentException iae) {
bean.setLo(10);
bean.setHi(90);
double[] stats = Stats.outlierValues(image, bean.getLo(), bean.getHi(), -1);
ret = new double[] {stats[0], stats[1], -1};
}
if (bean.isLogColorScale() && ret != null) {
ret = new double[] {Math.pow(10, ret[0]), Math.pow(10, ret[1]), -1};
}
return ret;
}
double min = Double.MAX_VALUE;
double max = -Double.MAX_VALUE;
double sum = 0.0;
int size = 0;
BooleanDataset mask =
bean.getMask() != null
? (BooleanDataset) DatasetUtils.cast(bean.getMask(), Dataset.BOOL)
: null;
// Big loop warning:
final IndexIterator it = image.getIterator();
final IndexIterator mit = mask == null ? null : mask.getIterator();
while (it.hasNext()) {
final double val = image.getElementDoubleAbs(it.index);
if (mit != null && mit.hasNext()) {
if (!mask.getElementBooleanAbs(mit.index)) {
continue; // Masked!
}
}
if (Double.isNaN(val)) continue;
if (!bean.isInBounds(val)) continue;
sum += val;
if (val < min) min = val;
if (val > max) max = val;
size++;
}
double retMax = Double.NaN;
double retExtra = Double.NaN;
if (bean.getHistogramType() == HistoType.MEDIAN) {
double median = Double.NaN;
try {
median = ((Number) Stats.median(image)).doubleValue(); // SLOW
} catch (Exception ne) {
median = ((Number) Stats.median(image.cast(Dataset.INT16))).doubleValue(); // SLOWER
}
retMax = 2 * median;
retExtra = median;
} else { // Use mean based histo
double mean = sum / size;
retMax = (Math.E) * mean; // Not statistical, E seems to be better than 3...
retExtra = mean;
}
if (retMax > max) retMax = max;
if (bean.isLogColorScale()) {
return new double[] {Math.pow(10, min), Math.pow(10, retMax), Math.pow(10, retExtra)};
}
return new double[] {min, retMax, retExtra, max};
}
