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Diffstat (limited to 'silx/gui/data/NXdataWidgets.py')
| -rw-r--r-- | silx/gui/data/NXdataWidgets.py | 523 |
1 files changed, 523 insertions, 0 deletions
diff --git a/silx/gui/data/NXdataWidgets.py b/silx/gui/data/NXdataWidgets.py new file mode 100644 index 0000000..343c7f9 --- /dev/null +++ b/silx/gui/data/NXdataWidgets.py @@ -0,0 +1,523 @@ +# coding: utf-8 +# /*########################################################################## +# +# Copyright (c) 2017 European Synchrotron Radiation Facility +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in +# all copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +# THE SOFTWARE. +# +# ###########################################################################*/ +"""This module defines widgets used by _NXdataView. +""" +__authors__ = ["P. Knobel"] +__license__ = "MIT" +__date__ = "20/03/2017" + +import numpy + +from silx.gui import qt +from silx.gui.data.NumpyAxesSelector import NumpyAxesSelector +from silx.gui.plot import Plot1D, Plot2D, StackView + +from silx.math.calibration import ArrayCalibration, NoCalibration, LinearCalibration + + +class ArrayCurvePlot(qt.QWidget): + """ + Widget for plotting a curve from a multi-dimensional signal array + and a 1D axis array. + + The signal array can have an arbitrary number of dimensions, the only + limitation being that the last dimension must have the same length as + the axis array. + + The widget provides sliders to select indices on the first (n - 1) + dimensions of the signal array, and buttons to add/replace selected + curves to the plot. + + This widget also handles simple 2D or 3D scatter plots (third dimension + displayed as colour of points). + """ + def __init__(self, parent=None): + """ + + :param parent: Parent QWidget + """ + super(ArrayCurvePlot, self).__init__(parent) + + self.__signal = None + self.__signal_name = None + self.__signal_errors = None + self.__axis = None + self.__axis_name = None + self.__axis_errors = None + self.__values = None + + self.__first_curve_added = False + + self._plot = Plot1D(self) + self._plot.setDefaultColormap( # for scatters + {"name": "viridis", + "vmin": 0., "vmax": 1., # ignored (autoscale) but mandatory + "normalization": "linear", + "autoscale": True}) + + self.selectorDock = qt.QDockWidget("Data selector", self._plot) + # not closable + self.selectorDock.setFeatures(qt.QDockWidget.DockWidgetMovable | + qt.QDockWidget.DockWidgetFloatable) + self._selector = NumpyAxesSelector(self.selectorDock) + self._selector.setNamedAxesSelectorVisibility(False) + self.__selector_is_connected = False + self.selectorDock.setWidget(self._selector) + self._plot.addTabbedDockWidget(self.selectorDock) + + layout = qt.QGridLayout() + layout.setContentsMargins(0, 0, 0, 0) + layout.addWidget(self._plot, 0, 0) + + self.setLayout(layout) + + def setCurveData(self, y, x=None, values=None, + yerror=None, xerror=None, + ylabel=None, xlabel=None, title=None): + """ + + :param y: dataset to be represented by the y (vertical) axis. + For a scatter, this must be a 1D array and x and values must be + 1-D arrays of the same size. + In other cases, it can be a n-D array whose last dimension must + have the same length as x (and values must be None) + :param x: 1-D dataset used as the curve's x values. If provided, + its lengths must be equal to the length of the last dimension of + ``y`` (and equal to the length of ``value``, for a scatter plot). + :param values: Values, to be provided for a x-y-value scatter plot. + This will be used to compute the color map and assign colors + to the points. + :param yerror: 1-D dataset of errors for y, or None + :param xerror: 1-D dataset of errors for x, or None + :param ylabel: Label for Y axis + :param xlabel: Label for X axis + :param title: Graph title + """ + self.__signal = y + self.__signal_name = ylabel + self.__signal_errors = yerror + self.__axis = x + self.__axis_name = xlabel + self.__axis_errors = xerror + self.__values = values + + if self.__selector_is_connected: + self._selector.selectionChanged.disconnect(self._updateCurve) + self.__selector_is_connected = False + self._selector.setData(y) + self._selector.setAxisNames([ylabel or "Y"]) + + if len(y.shape) < 2: + self.selectorDock.hide() + else: + self.selectorDock.show() + + self._plot.setGraphTitle(title or "") + self._plot.setGraphXLabel(self.__axis_name or "X") + self._plot.setGraphYLabel(self.__signal_name or "Y") + self._updateCurve() + + if not self.__selector_is_connected: + self._selector.selectionChanged.connect(self._updateCurve) + self.__selector_is_connected = True + + def _updateCurve(self): + y = self._selector.selectedData() + x = self.__axis + if x is None: + x = numpy.arange(len(y)) + elif numpy.isscalar(x) or len(x) == 1: + # constant axis + x = x * numpy.ones_like(y) + elif len(x) == 2 and len(y) != 2: + # linear calibration a + b * x + x = x[0] + x[1] * numpy.arange(len(y)) + legend = self.__signal_name + "[" + for sl in self._selector.selection(): + if sl == slice(None): + legend += ":, " + else: + legend += str(sl) + ", " + legend = legend[:-2] + "]" + if self.__signal_errors is not None: + y_errors = self.__signal_errors[self._selector.selection()] + else: + y_errors = None + + self._plot.remove(kind=("curve", "scatter")) + + # values: x-y-v scatter + if self.__values is not None: + self._plot.addScatter(x, y, self.__values, + legend=legend, + xerror=self.__axis_errors, + yerror=y_errors) + + # x monotonically increasing: curve + elif numpy.all(numpy.diff(x) > 0): + self._plot.addCurve(x, y, legend=legend, + xerror=self.__axis_errors, + yerror=y_errors) + + # scatter + else: + self._plot.addScatter(x, y, value=numpy.ones_like(y), + legend=legend, + xerror=self.__axis_errors, + yerror=y_errors) + self._plot.resetZoom() + self._plot.setGraphXLabel(self.__axis_name) + self._plot.setGraphYLabel(self.__signal_name) + + def clear(self): + self._plot.clear() + + +class ArrayImagePlot(qt.QWidget): + """ + Widget for plotting an image from a multi-dimensional signal array + and two 1D axes array. + + The signal array can have an arbitrary number of dimensions, the only + limitation being that the last two dimensions must have the same length as + the axes arrays. + + Sliders are provided to select indices on the first (n - 2) dimensions of + the signal array, and the plot is updated to show the image corresponding + to the selection. + + If one or both of the axes does not have regularly spaced values, the + the image is plotted as a coloured scatter plot. + """ + def __init__(self, parent=None): + """ + + :param parent: Parent QWidget + """ + super(ArrayImagePlot, self).__init__(parent) + + self.__signal = None + self.__signal_name = None + self.__x_axis = None + self.__x_axis_name = None + self.__y_axis = None + self.__y_axis_name = None + + self._plot = Plot2D(self) + self._plot.setDefaultColormap( + {"name": "viridis", + "vmin": 0., "vmax": 1., # ignored (autoscale) but mandatory + "normalization": "linear", + "autoscale": True}) + + self.selectorDock = qt.QDockWidget("Data selector", self._plot) + # not closable + self.selectorDock.setFeatures(qt.QDockWidget.DockWidgetMovable | + qt.QDockWidget.DockWidgetFloatable) + self._legend = qt.QLabel(self) + self._selector = NumpyAxesSelector(self.selectorDock) + self._selector.setNamedAxesSelectorVisibility(False) + self.__selector_is_connected = False + + layout = qt.QVBoxLayout() + layout.addWidget(self._plot) + layout.addWidget(self._legend) + self.selectorDock.setWidget(self._selector) + self._plot.addTabbedDockWidget(self.selectorDock) + + self.setLayout(layout) + + def setImageData(self, signal, + x_axis=None, y_axis=None, + signal_name=None, + xlabel=None, ylabel=None, + title=None): + """ + + :param signal: n-D dataset, whose last 2 dimensions are used as the + image's 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 signal_name: Label used in the legend + :param xlabel: Label for X axis + :param ylabel: Label for Y axis + :param title: Graph title + """ + if self.__selector_is_connected: + self._selector.selectionChanged.disconnect(self._updateImage) + 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._selector.setData(signal) + self._selector.setAxisNames([ylabel or "Y", xlabel or "X"]) + + if len(signal.shape) < 3: + self.selectorDock.hide() + else: + self.selectorDock.show() + + self._plot.setGraphTitle(title or "") + self._plot.setGraphXLabel(self.__x_axis_name or "X") + self._plot.setGraphYLabel(self.__y_axis_name or "Y") + + self._updateImage() + + if not self.__selector_is_connected: + self._selector.selectionChanged.connect(self._updateImage) + self.__selector_is_connected = True + + def _updateImage(self): + 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) + + img = self._selector.selectedData() + x_axis = self.__x_axis + y_axis = self.__y_axis + + if x_axis is None and y_axis is None: + xcalib = NoCalibration() + ycalib = NoCalibration() + else: + if x_axis is None: + # no calibration + x_axis = numpy.arange(img.shape[-1]) + elif numpy.isscalar(x_axis) or len(x_axis) == 1: + # constant axis + x_axis = x_axis * numpy.ones((img.shape[-1], )) + elif len(x_axis) == 2: + # linear calibration + x_axis = x_axis[0] * numpy.arange(img.shape[-1]) + x_axis[1] + + if y_axis is None: + y_axis = numpy.arange(img.shape[-2]) + elif numpy.isscalar(y_axis) or len(y_axis) == 1: + y_axis = y_axis * numpy.ones((img.shape[-2], )) + elif len(y_axis) == 2: + y_axis = y_axis[0] * numpy.arange(img.shape[-2]) + y_axis[1] + + xcalib = ArrayCalibration(x_axis) + ycalib = ArrayCalibration(y_axis) + + self._plot.remove(kind=("scatter", "image")) + if xcalib.is_affine() and ycalib.is_affine(): + # regular image + xorigin, xscale = xcalib(0), xcalib.get_slope() + yorigin, yscale = ycalib(0), ycalib.get_slope() + origin = (xorigin, yorigin) + scale = (xscale, yscale) + + self._plot.addImage(img, legend=legend, + origin=origin, scale=scale) + else: + scatterx, scattery = numpy.meshgrid(x_axis, y_axis) + self._plot.addScatter(numpy.ravel(scatterx), + numpy.ravel(scattery), + numpy.ravel(img), + legend=legend) + self._plot.setGraphXLabel(self.__x_axis_name) + self._plot.setGraphYLabel(self.__y_axis_name) + self._plot.resetZoom() + + def clear(self): + self._plot.clear() + + +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 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([ylabel or "Y", xlabel or "X", zlabel or "Z"]) + + self._stack_view.setGraphTitle(title or "") + # by default, the z axis is the image position (dimension not plotted) + self._stack_view.setGraphXLabel(self.__x_axis_name or "X") + self._stack_view.setGraphYLabel(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): + self._stack_view.clear() |