Exemplo n.º 1
0
def plot3Dsilx(nodeData):
    from silx.gui.plot import StackView

    saveType = nodeData[0]
    plot = StackView()
    plot.setColormap('viridis')
    plot.setGraphTitle(nodeData[1] + ' ' + saveType)
    plot.setLabels(nodeData[3])

    savedColumns = nodeData[4]
    for fname, props in savedColumns.items():
        maps = read3D(saveType, fname, props)

    # applied only to one (first) 3D map:
    v = maps[0]
    plot.setStack(v)
    # plot.saveGraph('test.png')
    plot.show()  # end plot3Dsilx
Exemplo n.º 2
0
class ArrayStackPlot(qt.QWidget):
    """
    Widget for plotting a n-D array (n >= 3) as a stack of images.
    Three axis arrays can be provided to calibrate the axes.

    The signal array can have an arbitrary number of dimensions, the only
    limitation being that the last 3 dimensions must have the same length as
    the axes arrays.

    Sliders are provided to select indices on the first (n - 3) dimensions of
    the signal array, and the plot is updated to load the stack corresponding
    to the selection.
    """
    def __init__(self, parent=None):
        """

        :param parent: Parent QWidget
        """
        super(ArrayStackPlot, self).__init__(parent)

        self.__signal = None
        self.__signal_name = None
        # the Z, Y, X axes apply to the last three dimensions of the signal
        # (in that order)
        self.__z_axis = None
        self.__z_axis_name = None
        self.__y_axis = None
        self.__y_axis_name = None
        self.__x_axis = None
        self.__x_axis_name = None

        self._stack_view = StackView(self)
        self._hline = qt.QFrame(self)
        self._hline.setFrameStyle(qt.QFrame.HLine)
        self._hline.setFrameShadow(qt.QFrame.Sunken)
        self._legend = qt.QLabel(self)
        self._selector = NumpyAxesSelector(self)
        self._selector.setNamedAxesSelectorVisibility(False)
        self.__selector_is_connected = False

        layout = qt.QVBoxLayout()
        layout.addWidget(self._stack_view)
        layout.addWidget(self._hline)
        layout.addWidget(self._legend)
        layout.addWidget(self._selector)

        self.setLayout(layout)

    def getStackView(self):
        """Returns the plot used for the display

        :rtype: StackView
        """
        return self._stack_view

    def setStackData(self,
                     signal,
                     x_axis=None,
                     y_axis=None,
                     z_axis=None,
                     signal_name=None,
                     xlabel=None,
                     ylabel=None,
                     zlabel=None,
                     title=None):
        """

        :param signal: n-D dataset, whose last 3 dimensions are used as the
            3D stack values.
        :param x_axis: 1-D dataset used as the image's x coordinates. If
            provided, its lengths must be equal to the length of the last
            dimension of ``signal``.
        :param y_axis: 1-D dataset used as the image's y. If provided,
            its lengths must be equal to the length of the 2nd to last
            dimension of ``signal``.
        :param z_axis: 1-D dataset used as the image's z. If provided,
            its lengths must be equal to the length of the 3rd to last
            dimension of ``signal``.
        :param signal_name: Label used in the legend
        :param xlabel: Label for X axis
        :param ylabel: Label for Y axis
        :param zlabel: Label for Z axis
        :param title: Graph title
        """
        if self.__selector_is_connected:
            self._selector.selectionChanged.disconnect(self._updateStack)
            self.__selector_is_connected = False

        self.__signal = signal
        self.__signal_name = signal_name or ""
        self.__x_axis = x_axis
        self.__x_axis_name = xlabel
        self.__y_axis = y_axis
        self.__y_axis_name = ylabel
        self.__z_axis = z_axis
        self.__z_axis_name = zlabel

        self._selector.setData(signal)
        self._selector.setAxisNames(["Y", "X", "Z"])

        self._stack_view.setGraphTitle(title or "")
        # by default, the z axis is the image position (dimension not plotted)
        self._stack_view.getPlotWidget().getXAxis().setLabel(self.__x_axis_name
                                                             or "X")
        self._stack_view.getPlotWidget().getYAxis().setLabel(self.__y_axis_name
                                                             or "Y")

        self._updateStack()

        ndims = len(signal.shape)
        self._stack_view.setFirstStackDimension(ndims - 3)

        # the legend label shows the selection slice producing the volume
        # (only interesting for ndim > 3)
        if ndims > 3:
            self._selector.setVisible(True)
            self._legend.setVisible(True)
            self._hline.setVisible(True)
        else:
            self._selector.setVisible(False)
            self._legend.setVisible(False)
            self._hline.setVisible(False)

        if not self.__selector_is_connected:
            self._selector.selectionChanged.connect(self._updateStack)
            self.__selector_is_connected = True

    @staticmethod
    def _get_origin_scale(axis):
        """Assuming axis is a regularly spaced 1D array,
        return a tuple (origin, scale) where:
            - origin = axis[0]
            - scale = (axis[n-1] - axis[0]) / (n -1)
        :param axis: 1D numpy array
        :return: Tuple (axis[0], (axis[-1] - axis[0]) / (len(axis) - 1))
        """
        return axis[0], (axis[-1] - axis[0]) / (len(axis) - 1)

    def _updateStack(self):
        """Update displayed stack according to the current axes selector
        data."""
        stk = self._selector.selectedData()
        x_axis = self.__x_axis
        y_axis = self.__y_axis
        z_axis = self.__z_axis

        calibrations = []
        for axis in [z_axis, y_axis, x_axis]:

            if axis is None:
                calibrations.append(NoCalibration())
            elif len(axis) == 2:
                calibrations.append(
                    LinearCalibration(y_intercept=axis[0], slope=axis[1]))
            else:
                calibrations.append(ArrayCalibration(axis))

        legend = self.__signal_name + "["
        for sl in self._selector.selection():
            if sl == slice(None):
                legend += ":, "
            else:
                legend += str(sl) + ", "
        legend = legend[:-2] + "]"
        self._legend.setText("Displayed data: " + legend)

        self._stack_view.setStack(stk, calibrations=calibrations)
        self._stack_view.setLabels(labels=[
            self.__z_axis_name, self.__y_axis_name, self.__x_axis_name
        ])

    def clear(self):
        old = self._selector.blockSignals(True)
        self._selector.clear()
        self._selector.blockSignals(old)
        self._stack_view.clear()
Exemplo n.º 3
0
class ArrayStackPlot(qt.QWidget):
    """
    Widget for plotting a n-D array (n >= 3) as a stack of images.
    Three axis arrays can be provided to calibrate the axes.

    The signal array can have an arbitrary number of dimensions, the only
    limitation being that the last 3 dimensions must have the same length as
    the axes arrays.

    Sliders are provided to select indices on the first (n - 3) dimensions of
    the signal array, and the plot is updated to load the stack corresponding
    to the selection.
    """
    def __init__(self, parent=None):
        """

        :param parent: Parent QWidget
        """
        super(ArrayStackPlot, self).__init__(parent)

        self.__signal = None
        self.__signal_name = None
        # the Z, Y, X axes apply to the last three dimensions of the signal
        # (in that order)
        self.__z_axis = None
        self.__z_axis_name = None
        self.__y_axis = None
        self.__y_axis_name = None
        self.__x_axis = None
        self.__x_axis_name = None

        self._stack_view = StackView(self)
        self._hline = qt.QFrame(self)
        self._hline.setFrameStyle(qt.QFrame.HLine)
        self._hline.setFrameShadow(qt.QFrame.Sunken)
        self._legend = qt.QLabel(self)
        self._selector = NumpyAxesSelector(self)
        self._selector.setNamedAxesSelectorVisibility(False)
        self.__selector_is_connected = False

        layout = qt.QVBoxLayout()
        layout.addWidget(self._stack_view)
        layout.addWidget(self._hline)
        layout.addWidget(self._legend)
        layout.addWidget(self._selector)

        self.setLayout(layout)

    def getStackView(self):
        """Returns the plot used for the display

        :rtype: StackView
        """
        return self._stack_view

    def setStackData(self, signal,
                     x_axis=None, y_axis=None, z_axis=None,
                     signal_name=None,
                     xlabel=None, ylabel=None, zlabel=None,
                     title=None):
        """

        :param signal: n-D dataset, whose last 3 dimensions are used as the
            3D stack values.
        :param x_axis: 1-D dataset used as the image's x coordinates. If
            provided, its lengths must be equal to the length of the last
            dimension of ``signal``.
        :param y_axis: 1-D dataset used as the image's y. If provided,
            its lengths must be equal to the length of the 2nd to last
            dimension of ``signal``.
        :param z_axis: 1-D dataset used as the image's z. If provided,
            its lengths must be equal to the length of the 3rd to last
            dimension of ``signal``.
        :param signal_name: Label used in the legend
        :param xlabel: Label for X axis
        :param ylabel: Label for Y axis
        :param zlabel: Label for Z axis
        :param title: Graph title
        """
        if self.__selector_is_connected:
            self._selector.selectionChanged.disconnect(self._updateStack)
            self.__selector_is_connected = False

        self.__signal = signal
        self.__signal_name = signal_name or ""
        self.__x_axis = x_axis
        self.__x_axis_name = xlabel
        self.__y_axis = y_axis
        self.__y_axis_name = ylabel
        self.__z_axis = z_axis
        self.__z_axis_name = zlabel

        self._selector.setData(signal)
        self._selector.setAxisNames(["Y", "X", "Z"])

        self._stack_view.setGraphTitle(title or "")
        # by default, the z axis is the image position (dimension not plotted)
        self._stack_view.getPlot().getXAxis().setLabel(self.__x_axis_name or "X")
        self._stack_view.getPlot().getYAxis().setLabel(self.__y_axis_name or "Y")

        self._updateStack()

        ndims = len(signal.shape)
        self._stack_view.setFirstStackDimension(ndims - 3)

        # the legend label shows the selection slice producing the volume
        # (only interesting for ndim > 3)
        if ndims > 3:
            self._selector.setVisible(True)
            self._legend.setVisible(True)
            self._hline.setVisible(True)
        else:
            self._selector.setVisible(False)
            self._legend.setVisible(False)
            self._hline.setVisible(False)

        if not self.__selector_is_connected:
            self._selector.selectionChanged.connect(self._updateStack)
            self.__selector_is_connected = True

    @staticmethod
    def _get_origin_scale(axis):
        """Assuming axis is a regularly spaced 1D array,
        return a tuple (origin, scale) where:
            - origin = axis[0]
            - scale = (axis[n-1] - axis[0]) / (n -1)
        :param axis: 1D numpy array
        :return: Tuple (axis[0], (axis[-1] - axis[0]) / (len(axis) - 1))
        """
        return axis[0], (axis[-1] - axis[0]) / (len(axis) - 1)

    def _updateStack(self):
        """Update displayed stack according to the current axes selector
        data."""
        stk = self._selector.selectedData()
        x_axis = self.__x_axis
        y_axis = self.__y_axis
        z_axis = self.__z_axis

        calibrations = []
        for axis in [z_axis, y_axis, x_axis]:

            if axis is None:
                calibrations.append(NoCalibration())
            elif len(axis) == 2:
                calibrations.append(
                        LinearCalibration(y_intercept=axis[0],
                                          slope=axis[1]))
            else:
                calibrations.append(ArrayCalibration(axis))

        legend = self.__signal_name + "["
        for sl in self._selector.selection():
            if sl == slice(None):
                legend += ":, "
            else:
                legend += str(sl) + ", "
        legend = legend[:-2] + "]"
        self._legend.setText("Displayed data: " + legend)

        self._stack_view.setStack(stk, calibrations=calibrations)
        self._stack_view.setLabels(
                labels=[self.__z_axis_name,
                        self.__y_axis_name,
                        self.__x_axis_name])

    def clear(self):
        old = self._selector.blockSignals(True)
        self._selector.clear()
        self._selector.blockSignals(old)
        self._stack_view.clear()