Source code for silx.gui.plot.actions.histogram

# coding: utf-8
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"""
:mod:`silx.gui.plot.actions.histogram` provides actions relative to histograms
for :class:`.PlotWidget`.

The following QAction are available:

- :class:`PixelIntensitiesHistoAction`
"""

from __future__ import division

__authors__ = ["V.A. Sole", "T. Vincent", "P. Knobel"]
__date__ = "01/12/2020"
__license__ = "MIT"

from typing import Optional, Tuple
import numpy
import logging
import weakref

from .PlotToolAction import PlotToolAction

from silx.math.histogram import Histogramnd
from silx.math.combo import min_max
from silx.gui import qt
from silx.gui.plot import items
from silx.gui.widgets.ElidedLabel import ElidedLabel
from silx.gui.widgets.RangeSlider import RangeSlider
from silx.utils.deprecation import deprecated

_logger = logging.getLogger(__name__)


class _ElidedLabel(ElidedLabel):
    """QLabel with a default size larger than what is displayed."""

    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)
        self.setTextInteractionFlags(qt.Qt.TextSelectableByMouse)

    def sizeHint(self):
        hint = super().sizeHint()
        nbchar = max(len(self.getText()), 12)
        width = self.fontMetrics().boundingRect('#' * nbchar).width()
        return qt.QSize(max(hint.width(), width), hint.height())


class _StatWidget(qt.QWidget):
    """Widget displaying a name and a value

    :param parent:
    :param name:
    """

    def __init__(self, parent=None, name: str=''):
        super().__init__(parent)
        layout = qt.QHBoxLayout(self)
        layout.setContentsMargins(0, 0, 0, 0)

        keyWidget = qt.QLabel(parent=self)
        keyWidget.setText("<b>" + name.capitalize() + ":<b>")
        layout.addWidget(keyWidget)
        self.__valueWidget = _ElidedLabel(parent=self)
        self.__valueWidget.setText("-")
        self.__valueWidget.setTextInteractionFlags(
            qt.Qt.TextSelectableByMouse | qt.Qt.TextSelectableByKeyboard)
        layout.addWidget(self.__valueWidget)

    def setValue(self, value: Optional[float]):
        """Set the displayed value

        :param value:
        """
        self.__valueWidget.setText(
            "-" if value is None else "{:.5g}".format(value))


class _IntEdit(qt.QLineEdit):
    """QLineEdit for integers with a default value and update on validation.

    :param QWidget parent:
    """

    sigValueChanged = qt.Signal(int)
    """Signal emitted when the value has changed (on editing finished)"""

    def __init__(self, parent=None):
        super().__init__(parent)
        self.__value = None
        self.setAlignment(qt.Qt.AlignRight)
        validator = qt.QIntValidator()
        self.setValidator(validator)
        validator.bottomChanged.connect(self.__updateSize)
        validator.topChanged.connect(self.__updateSize)
        self.__updateSize()

        self.textEdited.connect(self.__textEdited)

    def __updateSize(self, *args):
        """Update widget's maximum size according to bounds"""
        bottom, top = self.getRange()
        nbchar = max(len(str(bottom)), len(str(top)))
        font = self.font()
        font.setStyle(qt.QFont.StyleItalic)
        fontMetrics = qt.QFontMetrics(font)
        self.setMaximumWidth(
            fontMetrics.boundingRect('0' * (nbchar + 1)).width()
        )
        self.setMaxLength(nbchar)

    def __textEdited(self, _):
        if self.font().style() != qt.QFont.StyleItalic:
            font = self.font()
            font.setStyle(qt.QFont.StyleItalic)
            self.setFont(font)

    # Use events rather than editingFinished to also trigger with empty text

    def focusOutEvent(self, event):
        self.__commitValue()
        return super().focusOutEvent(event)

    def keyPressEvent(self, event):
        if event.key() in (qt.Qt.Key_Enter, qt.Qt.Key_Return):
            self.__commitValue()
        return super().keyPressEvent(event)

    def __commitValue(self):
        """Update the value returned by :meth:`getValue`"""
        value = self.getCurrentValue()
        if value is None:
            value = self.getDefaultValue()
            if value is None:
                return  # No value, keep previous one

        if self.font().style() != qt.QFont.StyleNormal:
            font = self.font()
            font.setStyle(qt.QFont.StyleNormal)
            self.setFont(font)

        if value != self.__value:
            self.__value = value
            self.sigValueChanged.emit(value)

    def getValue(self) -> Optional[int]:
        """Return current value (None if never set)."""
        return self.__value

    def setRange(self, bottom: int, top: int):
        """Set the range of valid values"""
        self.validator().setRange(bottom, top)

    def getRange(self) -> Tuple[int, int]:
        """Returns the current range of valid values

        :returns: (bottom, top)
        """
        return self.validator().bottom(), self.validator().top()

    def __validate(self, value: int, extend_range: bool):
        """Ensure value is in range

        :param int value:
        :param bool extend_range:
            True to extend range if needed.
            False to clip value if needed.
        """
        if extend_range:
            bottom, top = self.getRange()
            self.setRange(min(value, bottom), max(value, top))
        return numpy.clip(value, *self.getRange())

    def setDefaultValue(self, value: int, extend_range: bool=False):
        """Set default value when QLineEdit is empty

        :param int value:
        :param bool extend_range:
            True to extend range if needed.
            False to clip value if needed
        """
        self.setPlaceholderText(str(self.__validate(value, extend_range)))
        if self.getCurrentValue() is None:
            self.__commitValue()

    def getDefaultValue(self) -> Optional[int]:
        """Return the default value or the bottom one if not set"""
        try:
            return int(self.placeholderText())
        except ValueError:
            return None

    def setCurrentValue(self, value: int, extend_range: bool=False):
        """Set the currently displayed value

        :param int value:
        :param bool extend_range:
            True to extend range if needed.
            False to clip value if needed
        """
        self.setText(str(self.__validate(value, extend_range)))
        self.__commitValue()

    def getCurrentValue(self) -> Optional[int]:
        """Returns the displayed value or None if not correct"""
        try:
            return int(self.text())
        except ValueError:
            return None


[docs]class HistogramWidget(qt.QWidget): """Widget displaying a histogram and some statistic indicators""" _SUPPORTED_ITEM_CLASS = items.ImageBase, items.Scatter def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) self.setWindowTitle('Histogram') self.__itemRef = None # weakref on the item to track layout = qt.QVBoxLayout(self) layout.setContentsMargins(0, 0, 0, 0) layout.setSpacing(0) # Plot # Lazy import to avoid circular dependencies from silx.gui.plot.PlotWindow import Plot1D self.__plot = Plot1D(self) layout.addWidget(self.__plot) self.__plot.setDataMargins(0.1, 0.1, 0.1, 0.1) self.__plot.getXAxis().setLabel("Value") self.__plot.getYAxis().setLabel("Count") posInfo = self.__plot.getPositionInfoWidget() posInfo.setSnappingMode(posInfo.SNAPPING_CURVE) # Histogram controls controlsWidget = qt.QWidget(self) layout.addWidget(controlsWidget) controlsLayout = qt.QHBoxLayout(controlsWidget) controlsLayout.setContentsMargins(4, 4, 4, 4) controlsLayout.addWidget(qt.QLabel("<b>Histogram:<b>")) controlsLayout.addWidget(qt.QLabel("N. bins:")) self.__nbinsLineEdit = _IntEdit(self) self.__nbinsLineEdit.setRange(2, 9999) self.__nbinsLineEdit.sigValueChanged.connect( self.__updateHistogramFromControls) controlsLayout.addWidget(self.__nbinsLineEdit) self.__rangeLabel = qt.QLabel("Range:") controlsLayout.addWidget(self.__rangeLabel) self.__rangeSlider = RangeSlider(parent=self) self.__rangeSlider.sigValueChanged.connect( self.__updateHistogramFromControls) self.__rangeSlider.sigValueChanged.connect(self.__rangeChanged) controlsLayout.addWidget(self.__rangeSlider) controlsLayout.addStretch(1) # Stats display statsWidget = qt.QWidget(self) layout.addWidget(statsWidget) statsLayout = qt.QHBoxLayout(statsWidget) statsLayout.setContentsMargins(4, 4, 4, 4) self.__statsWidgets = dict( (name, _StatWidget(parent=statsWidget, name=name)) for name in ("min", "max", "mean", "std", "sum")) for widget in self.__statsWidgets.values(): statsLayout.addWidget(widget) statsLayout.addStretch(1)
[docs] def getPlotWidget(self): """Returns :class:`PlotWidget` use to display the histogram""" return self.__plot
[docs] def resetZoom(self): """Reset PlotWidget zoom""" self.getPlotWidget().resetZoom()
[docs] def reset(self): """Clear displayed information""" self.getPlotWidget().clear() self.setStatistics()
[docs] def getItem(self) -> Optional[items.Item]: """Returns item used to display histogram and statistics.""" return None if self.__itemRef is None else self.__itemRef()
[docs] def setItem(self, item: Optional[items.Item]): """Set item from which to display histogram and statistics. :param item: """ previous = self.getItem() if previous is not None: previous.sigItemChanged.disconnect(self.__itemChanged) self.__itemRef = None if item is None else weakref.ref(item) if item is not None: if isinstance(item, self._SUPPORTED_ITEM_CLASS): # Only listen signal for supported items item.sigItemChanged.connect(self.__itemChanged) self._updateFromItem()
def __itemChanged(self, event): """Handle update of the item""" if event in (items.ItemChangedType.DATA, items.ItemChangedType.MASK): self._updateFromItem() def __updateHistogramFromControls(self, *args): """Handle udates coming from histogram control widgets""" hist = self.getHistogram(copy=False) if hist is not None: count, edges = hist if (len(count) == self.__nbinsLineEdit.getValue() and (edges[0], edges[-1]) == self.__rangeSlider.getValues()): return # Nothing has changed self._updateFromItem() def __rangeChanged(self, first, second): """Handle change of histogram range from the range slider""" tooltip = "Histogram range:\n[%g, %g]" % (first, second) self.__rangeSlider.setToolTip(tooltip) self.__rangeLabel.setToolTip(tooltip) def _updateFromItem(self): """Update histogram and stats from the item""" item = self.getItem() if item is None: self.reset() return if not isinstance(item, self._SUPPORTED_ITEM_CLASS): _logger.error("Unsupported item", item) self.reset() return # Compute histogram and stats array = item.getValueData(copy=False) if array.size == 0: self.reset() return xmin, xmax = min_max(array, min_positive=False, finite=True) if xmin is None or xmax is None: # All not finite data self.reset() return guessed_nbins = min(1024, int(numpy.sqrt(array.size))) # bad hack: get 256 bins in the case we have a B&W if numpy.issubdtype(array.dtype, numpy.integer): if guessed_nbins > xmax - xmin: guessed_nbins = xmax - xmin guessed_nbins = max(2, guessed_nbins) # Set default nbins self.__nbinsLineEdit.setDefaultValue(guessed_nbins, extend_range=True) # Set slider range: do not keep the range value, but the relative pos. previousPositions = self.__rangeSlider.getPositions() if xmin == xmax: # Enlarge range is none if xmin == 0: range_ = -0.01, 0.01 else: range_ = sorted((xmin * .99, xmin * 1.01)) else: range_ = xmin, xmax self.__rangeSlider.setRange(*range_) self.__rangeSlider.setPositions(*previousPositions) histogram = Histogramnd( array.ravel().astype(numpy.float32), n_bins=max(2, self.__nbinsLineEdit.getValue()), histo_range=self.__rangeSlider.getValues(), ) if len(histogram.edges) != 1: _logger.error("Error while computing the histogram") self.reset() return self.setHistogram(histogram.histo, histogram.edges[0]) self.resetZoom() self.setStatistics( min_=xmin, max_=xmax, mean=numpy.nanmean(array), std=numpy.nanstd(array), sum_=numpy.nansum(array))
[docs] def setHistogram(self, histogram, edges): """Set displayed histogram :param histogram: Bin values (N) :param edges: Bin edges (N+1) """ # Only useful if setHistogram is called directly # TODO #nbins = len(histogram) #if nbins != self.__nbinsLineEdit.getDefaultValue(): # self.__nbinsLineEdit.setValue(nbins, extend_range=True) #self.__rangeSlider.setValues(edges[0], edges[-1]) self.getPlotWidget().addHistogram( histogram=histogram, edges=edges, legend='histogram', fill=True, color='#66aad7', resetzoom=False)
[docs] def getHistogram(self, copy: bool=True): """Returns currently displayed histogram. :param copy: True to get a copy, False to get internal representation (Do not modify!) :return: (histogram, edges) or None """ for item in self.getPlotWidget().getItems(): if item.getName() == 'histogram': return (item.getValueData(copy=copy), item.getBinEdgesData(copy=copy)) else: return None
[docs] def setStatistics(self, min_: Optional[float] = None, max_: Optional[float] = None, mean: Optional[float] = None, std: Optional[float] = None, sum_: Optional[float] = None): """Set displayed statistic indicators.""" self.__statsWidgets['min'].setValue(min_) self.__statsWidgets['max'].setValue(max_) self.__statsWidgets['mean'].setValue(mean) self.__statsWidgets['std'].setValue(std) self.__statsWidgets['sum'].setValue(sum_)
[docs]class PixelIntensitiesHistoAction(PlotToolAction): """QAction to plot the pixels intensities diagram :param plot: :class:`.PlotWidget` instance on which to operate :param parent: See :class:`QAction` """ def __init__(self, plot, parent=None): PlotToolAction.__init__(self, plot, icon='pixel-intensities', text='pixels intensity', tooltip='Compute image intensity distribution', parent=parent) def _connectPlot(self, window): plot = self.plot if plot is not None: selection = plot.selection() selection.sigSelectedItemsChanged.connect(self._selectedItemsChanged) self._updateSelectedItem() PlotToolAction._connectPlot(self, window) def _disconnectPlot(self, window): plot = self.plot if plot is not None: selection = self.plot.selection() selection.sigSelectedItemsChanged.disconnect(self._selectedItemsChanged) PlotToolAction._disconnectPlot(self, window) self.getHistogramWidget().setItem(None) def _updateSelectedItem(self): """Synchronises selected item with plot widget.""" plot = self.plot if plot is not None: selected = plot.selection().getSelectedItems() # Give priority to image over scatter for klass in (items.ImageBase, items.Scatter): for item in selected: if isinstance(item, klass): # Found a matching item, use it self.getHistogramWidget().setItem(item) return self.getHistogramWidget().setItem(None) def _selectedItemsChanged(self): if self._isWindowInUse(): self._updateSelectedItem() @deprecated(since_version='0.15.0') def computeIntensityDistribution(self): self.getHistogramWidget()._updateFromItem()
[docs] def getHistogramWidget(self): """Returns the widget displaying the histogram""" return self._getToolWindow()
@deprecated(since_version='0.15.0', replacement='getHistogramWidget().getPlotWidget()') def getHistogramPlotWidget(self): return self._getToolWindow().getPlotWidget() def _createToolWindow(self): return HistogramWidget(self.plot, qt.Qt.Window)
[docs] def getHistogram(self) -> Optional[numpy.ndarray]: """Return the last computed histogram :return: the histogram displayed in the HistogramWidget """ histogram = self.getHistogramWidget().getHistogram() return None if histogram is None else histogram[0]