[d4881f6a] | 1 | """ |
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| 2 | This module provides the intelligence behind the gui interface for Corfunc. |
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| 3 | """ |
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| 4 | # pylint: disable=E1101 |
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| 5 | |
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| 6 | # global |
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[e90988c] | 7 | from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg \ |
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| 8 | as FigureCanvas |
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[4b796b8] | 9 | from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT |
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[e90988c] | 10 | from matplotlib.figure import Figure |
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| 11 | from numpy.linalg.linalg import LinAlgError |
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| 12 | |
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[d4881f6a] | 13 | from PyQt5 import QtCore |
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| 14 | from PyQt5 import QtGui, QtWidgets |
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| 15 | |
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| 16 | # sas-global |
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| 17 | # pylint: disable=import-error, no-name-in-module |
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| 18 | import sas.qtgui.Utilities.GuiUtils as GuiUtils |
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| 19 | from sas.sascalc.corfunc.corfunc_calculator import CorfuncCalculator |
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| 20 | # pylint: enable=import-error, no-name-in-module |
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| 21 | |
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| 22 | # local |
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| 23 | from .UI.CorfuncPanel import Ui_CorfuncDialog |
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| 24 | from .CorfuncUtils import WIDGETS as W |
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| 25 | |
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| 26 | |
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| 27 | class MyMplCanvas(FigureCanvas): |
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| 28 | """Ultimately, this is a QWidget (as well as a FigureCanvasAgg, etc.).""" |
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| 29 | def __init__(self, model, width=5, height=4, dpi=100): |
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| 30 | self.model = model |
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| 31 | self.fig = Figure(figsize=(width, height), dpi=dpi) |
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| 32 | self.axes = self.fig.add_subplot(111) |
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| 33 | |
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| 34 | FigureCanvas.__init__(self, self.fig) |
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| 35 | |
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| 36 | self.data = None |
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| 37 | self.extrap = None |
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[9913448] | 38 | self.setMinimumSize(300, 300) |
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[d4881f6a] | 39 | |
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| 40 | def draw_q_space(self): |
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| 41 | """Draw the Q space data in the plot window |
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| 42 | |
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| 43 | This draws the q space data in self.data, as well |
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| 44 | as the bounds set by self.qmin, self.qmax1, and self.qmax2. |
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| 45 | It will also plot the extrpolation in self.extrap, if it exists.""" |
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| 46 | |
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[cb4d219] | 47 | # TODO: add interactivity to axvlines so qlimits are immediately updated! |
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[d4881f6a] | 48 | self.fig.clf() |
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| 49 | |
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| 50 | self.axes = self.fig.add_subplot(111) |
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| 51 | self.axes.set_xscale("log") |
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| 52 | self.axes.set_yscale("log") |
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[0ffdf6e] | 53 | self.axes.set_xlabel("Q [$\AA^{-1}$]") |
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| 54 | self.axes.set_ylabel("I(Q) [cm$^{-1}$]") |
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[3beadede] | 55 | self.axes.set_title("Scattering data") |
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[0ffdf6e] | 56 | self.fig.tight_layout() |
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[d4881f6a] | 57 | |
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| 58 | qmin = float(self.model.item(W.W_QMIN).text()) |
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| 59 | qmax1 = float(self.model.item(W.W_QMAX).text()) |
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| 60 | qmax2 = float(self.model.item(W.W_QCUTOFF).text()) |
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| 61 | |
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| 62 | if self.data: |
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[3beadede] | 63 | # self.axes.plot(self.data.x, self.data.y, label="Experimental Data") |
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| 64 | self.axes.errorbar(self.data.x, self.data.y, yerr=self.data.dy, label="Experimental Data") |
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[d4881f6a] | 65 | self.axes.axvline(qmin) |
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| 66 | self.axes.axvline(qmax1) |
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| 67 | self.axes.axvline(qmax2) |
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| 68 | self.axes.set_xlim(min(self.data.x) / 2, |
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| 69 | max(self.data.x) * 1.5 - 0.5 * min(self.data.x)) |
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[d215517] | 70 | self.axes.set_ylim(min(self.data.y) / 2, |
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| 71 | max(self.data.y) * 1.5 - 0.5 * min(self.data.y)) |
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[3beadede] | 72 | |
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[d4881f6a] | 73 | if self.extrap: |
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[3beadede] | 74 | self.axes.plot(self.extrap.x, self.extrap.y, label="Extrapolation") |
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| 75 | |
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| 76 | if self.data or self.extrap: |
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| 77 | self.axes.legend() |
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[d4881f6a] | 78 | |
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| 79 | self.draw() |
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| 80 | |
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| 81 | def draw_real_space(self): |
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| 82 | """ |
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| 83 | This function draws the real space data onto the plot |
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| 84 | |
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| 85 | The 1d correlation function in self.data, the 3d correlation function |
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| 86 | in self.data3, and the interface distribution function in self.data_idf |
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| 87 | are all draw in on the plot in linear cooredinates.""" |
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| 88 | self.fig.clf() |
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| 89 | |
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| 90 | self.axes = self.fig.add_subplot(111) |
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| 91 | self.axes.set_xscale("linear") |
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| 92 | self.axes.set_yscale("linear") |
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[0ffdf6e] | 93 | self.axes.set_xlabel("Z [$\AA$]") |
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| 94 | self.axes.set_ylabel("Correlation") |
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[3beadede] | 95 | self.axes.set_title("Real Space Correlations") |
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[0ffdf6e] | 96 | self.fig.tight_layout() |
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[d4881f6a] | 97 | |
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| 98 | if self.data: |
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| 99 | data1, data3, data_idf = self.data |
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| 100 | self.axes.plot(data1.x, data1.y, label="1D Correlation") |
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| 101 | self.axes.plot(data3.x, data3.y, label="3D Correlation") |
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| 102 | self.axes.plot(data_idf.x, data_idf.y, |
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| 103 | label="Interface Distribution Function") |
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[f7e6b30] | 104 | self.axes.set_xlim(0, max(data1.x) / 4) |
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[d4881f6a] | 105 | self.axes.legend() |
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| 106 | |
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| 107 | self.draw() |
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| 108 | |
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| 109 | |
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| 110 | class CorfuncWindow(QtWidgets.QDialog, Ui_CorfuncDialog): |
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| 111 | """Displays the correlation function analysis of sas data.""" |
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| 112 | name = "Corfunc" # For displaying in the combo box |
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| 113 | |
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| 114 | trigger = QtCore.pyqtSignal(tuple) |
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| 115 | |
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| 116 | # pylint: disable=unused-argument |
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| 117 | def __init__(self, parent=None): |
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| 118 | super(CorfuncWindow, self).__init__() |
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| 119 | self.setupUi(self) |
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| 120 | |
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| 121 | self.setWindowTitle("Corfunc Perspective") |
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| 122 | |
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[cb4d219] | 123 | self.parent = parent |
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[d4881f6a] | 124 | self.mapper = None |
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| 125 | self.model = QtGui.QStandardItemModel(self) |
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| 126 | self.communicate = GuiUtils.Communicate() |
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| 127 | self._calculator = CorfuncCalculator() |
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[e9359e0a] | 128 | self._allow_close = False |
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[cb4d219] | 129 | self._model_item = None |
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| 130 | self.txtLowerQMin.setText("0.0") |
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| 131 | self.txtLowerQMin.setEnabled(False) |
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[d4881f6a] | 132 | |
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| 133 | self._canvas = MyMplCanvas(self.model) |
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[28c2586] | 134 | self.plotLayout.insertWidget(0, self._canvas) |
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[4b796b8] | 135 | self.plotLayout.insertWidget(1, NavigationToolbar2QT(self._canvas, self)) |
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[84fa015] | 136 | self._realplot = MyMplCanvas(self.model) |
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[4b796b8] | 137 | self.plotLayout.insertWidget(2, self._realplot) |
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| 138 | self.plotLayout.insertWidget(3, NavigationToolbar2QT(self._realplot, self)) |
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[d4881f6a] | 139 | |
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[a7a0def] | 140 | self.gridLayout_8.setColumnStretch(0, 1) |
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| 141 | self.gridLayout_8.setColumnStretch(1, 3) |
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| 142 | |
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[d4881f6a] | 143 | # Connect buttons to slots. |
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| 144 | # Needs to be done early so default values propagate properly. |
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| 145 | self.setup_slots() |
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| 146 | |
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| 147 | # Set up the model. |
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| 148 | self.setup_model() |
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| 149 | |
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| 150 | # Set up the mapper |
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| 151 | self.setup_mapper() |
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| 152 | |
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| 153 | def setup_slots(self): |
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| 154 | """Connect the buttons to their appropriate slots.""" |
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[cb4d219] | 155 | self.cmdExtrapolate.clicked.connect(self.extrapolate) |
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| 156 | self.cmdExtrapolate.setEnabled(False) |
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| 157 | self.cmdTransform.clicked.connect(self.transform) |
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| 158 | self.cmdTransform.setEnabled(False) |
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[d4881f6a] | 159 | |
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[cb4d219] | 160 | self.cmdCalculateBg.clicked.connect(self.calculate_background) |
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| 161 | self.cmdCalculateBg.setEnabled(False) |
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[e90988c] | 162 | self.cmdHelp.clicked.connect(self.showHelp) |
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[d4881f6a] | 163 | |
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| 164 | self.model.itemChanged.connect(self.model_changed) |
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| 165 | |
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| 166 | self.trigger.connect(self.finish_transform) |
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| 167 | |
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| 168 | def setup_model(self): |
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| 169 | """Populate the model with default data.""" |
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| 170 | self.model.setItem(W.W_QMIN, |
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| 171 | QtGui.QStandardItem("0.01")) |
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| 172 | self.model.setItem(W.W_QMAX, |
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| 173 | QtGui.QStandardItem("0.20")) |
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| 174 | self.model.setItem(W.W_QCUTOFF, |
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| 175 | QtGui.QStandardItem("0.22")) |
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| 176 | self.model.setItem(W.W_BACKGROUND, |
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| 177 | QtGui.QStandardItem("0")) |
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[cb4d219] | 178 | #self.model.setItem(W.W_TRANSFORM, |
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| 179 | # QtGui.QStandardItem("Fourier")) |
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[d4881f6a] | 180 | self.model.setItem(W.W_GUINIERA, |
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| 181 | QtGui.QStandardItem("0.0")) |
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| 182 | self.model.setItem(W.W_GUINIERB, |
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| 183 | QtGui.QStandardItem("0.0")) |
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| 184 | self.model.setItem(W.W_PORODK, |
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| 185 | QtGui.QStandardItem("0.0")) |
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| 186 | self.model.setItem(W.W_PORODSIGMA, |
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| 187 | QtGui.QStandardItem("0.0")) |
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| 188 | self.model.setItem(W.W_CORETHICK, QtGui.QStandardItem(str(0))) |
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| 189 | self.model.setItem(W.W_INTTHICK, QtGui.QStandardItem(str(0))) |
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| 190 | self.model.setItem(W.W_HARDBLOCK, QtGui.QStandardItem(str(0))) |
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| 191 | self.model.setItem(W.W_CRYSTAL, QtGui.QStandardItem(str(0))) |
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| 192 | self.model.setItem(W.W_POLY, QtGui.QStandardItem(str(0))) |
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| 193 | self.model.setItem(W.W_PERIOD, QtGui.QStandardItem(str(0))) |
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| 194 | |
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| 195 | def model_changed(self, _): |
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| 196 | """Actions to perform when the data is updated""" |
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| 197 | if not self.mapper: |
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| 198 | return |
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| 199 | self.mapper.toFirst() |
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| 200 | self._canvas.draw_q_space() |
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| 201 | |
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| 202 | def _update_calculator(self): |
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| 203 | self._calculator.lowerq = float(self.model.item(W.W_QMIN).text()) |
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| 204 | qmax1 = float(self.model.item(W.W_QMAX).text()) |
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| 205 | qmax2 = float(self.model.item(W.W_QCUTOFF).text()) |
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| 206 | self._calculator.upperq = (qmax1, qmax2) |
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| 207 | self._calculator.background = \ |
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| 208 | float(self.model.item(W.W_BACKGROUND).text()) |
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| 209 | |
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| 210 | def extrapolate(self): |
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| 211 | """Extend the experiemntal data with guinier and porod curves.""" |
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| 212 | self._update_calculator() |
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| 213 | try: |
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| 214 | params, extrapolation, _ = self._calculator.compute_extrapolation() |
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[cb4d219] | 215 | self.model.setItem(W.W_GUINIERA, QtGui.QStandardItem("{:.3g}".format(params['A']))) |
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| 216 | self.model.setItem(W.W_GUINIERB, QtGui.QStandardItem("{:.3g}".format(params['B']))) |
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| 217 | self.model.setItem(W.W_PORODK, QtGui.QStandardItem("{:.3g}".format(params['K']))) |
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[d4881f6a] | 218 | self.model.setItem(W.W_PORODSIGMA, |
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[cb4d219] | 219 | QtGui.QStandardItem("{:.4g}".format(params['sigma']))) |
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[d4881f6a] | 220 | |
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| 221 | self._canvas.extrap = extrapolation |
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| 222 | self._canvas.draw_q_space() |
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[cb4d219] | 223 | self.cmdTransform.setEnabled(True) |
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[d4881f6a] | 224 | except (LinAlgError, ValueError): |
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| 225 | message = "These is not enough data in the fitting range. "\ |
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| 226 | "Try decreasing the upper Q, increasing the "\ |
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| 227 | "cutoff Q, or increasing the lower Q." |
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| 228 | QtWidgets.QMessageBox.warning(self, "Calculation Error", |
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| 229 | message) |
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| 230 | self._canvas.extrap = None |
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| 231 | self._canvas.draw_q_space() |
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| 232 | |
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| 233 | |
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| 234 | def transform(self): |
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| 235 | """Calculate the real space version of the extrapolation.""" |
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[cb4d219] | 236 | #method = self.model.item(W.W_TRANSFORM).text().lower() |
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| 237 | |
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| 238 | method = "fourier" |
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[d4881f6a] | 239 | |
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| 240 | extrap = self._canvas.extrap |
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| 241 | background = float(self.model.item(W.W_BACKGROUND).text()) |
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| 242 | |
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| 243 | def updatefn(msg): |
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| 244 | """Report progress of transformation.""" |
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| 245 | self.communicate.statusBarUpdateSignal.emit(msg) |
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| 246 | |
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| 247 | def completefn(transforms): |
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| 248 | """Extract the values from the transforms and plot""" |
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| 249 | self.trigger.emit(transforms) |
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| 250 | |
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| 251 | self._update_calculator() |
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| 252 | self._calculator.compute_transform(extrap, method, background, |
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| 253 | completefn, updatefn) |
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| 254 | |
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| 255 | |
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| 256 | def finish_transform(self, transforms): |
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| 257 | params = self._calculator.extract_parameters(transforms[0]) |
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[cb4d219] | 258 | self.model.setItem(W.W_CORETHICK, QtGui.QStandardItem("{:.3g}".format(params['d0']))) |
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| 259 | self.model.setItem(W.W_INTTHICK, QtGui.QStandardItem("{:.3g}".format(params['dtr']))) |
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| 260 | self.model.setItem(W.W_HARDBLOCK, QtGui.QStandardItem("{:.3g}".format(params['Lc']))) |
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| 261 | self.model.setItem(W.W_CRYSTAL, QtGui.QStandardItem("{:.3g}".format(params['fill']))) |
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| 262 | self.model.setItem(W.W_POLY, QtGui.QStandardItem("{:.3g}".format(params['A']))) |
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| 263 | self.model.setItem(W.W_PERIOD, QtGui.QStandardItem("{:.3g}".format(params['max']))) |
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[84fa015] | 264 | self._realplot.data = transforms |
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[cb4d219] | 265 | |
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| 266 | self.update_real_space_plot(transforms) |
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| 267 | |
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[84fa015] | 268 | self._realplot.draw_real_space() |
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[cb4d219] | 269 | |
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| 270 | def update_real_space_plot(self, datas): |
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| 271 | """take the datas tuple and create a plot in DE""" |
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| 272 | |
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| 273 | assert isinstance(datas, tuple) |
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| 274 | plot_id = id(self) |
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| 275 | titles = ['1D Correlation', '3D Correlation', 'Interface Distribution Function'] |
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| 276 | for i, plot in enumerate(datas): |
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| 277 | plot_to_add = self.parent.createGuiData(plot) |
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| 278 | # set plot properties |
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| 279 | title = plot_to_add.title |
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| 280 | plot_to_add.scale = 'linear' |
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| 281 | plot_to_add.symbol = 'Line' |
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| 282 | plot_to_add._xaxis = "x" |
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| 283 | plot_to_add._xunit = "A" |
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| 284 | plot_to_add._yaxis = "\Gamma" |
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| 285 | if i < len(titles): |
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| 286 | title = titles[i] |
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| 287 | plot_to_add.name = titles[i] |
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| 288 | GuiUtils.updateModelItemWithPlot(self._model_item, plot_to_add, title) |
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| 289 | #self.axes.set_xlim(min(data1.x), max(data1.x) / 4) |
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| 290 | pass |
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[d4881f6a] | 291 | |
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| 292 | def setup_mapper(self): |
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| 293 | """Creating mapping between model and gui elements.""" |
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| 294 | self.mapper = QtWidgets.QDataWidgetMapper(self) |
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| 295 | self.mapper.setOrientation(QtCore.Qt.Vertical) |
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| 296 | self.mapper.setModel(self.model) |
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| 297 | |
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[cb4d219] | 298 | self.mapper.addMapping(self.txtLowerQMax, W.W_QMIN) |
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| 299 | self.mapper.addMapping(self.txtUpperQMin, W.W_QMAX) |
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| 300 | self.mapper.addMapping(self.txtUpperQMax, W.W_QCUTOFF) |
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| 301 | self.mapper.addMapping(self.txtBackground, W.W_BACKGROUND) |
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| 302 | #self.mapper.addMapping(self.transformCombo, W.W_TRANSFORM) |
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[d4881f6a] | 303 | |
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[cb4d219] | 304 | self.mapper.addMapping(self.txtGuinierA, W.W_GUINIERA) |
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| 305 | self.mapper.addMapping(self.txtGuinierB, W.W_GUINIERB) |
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| 306 | self.mapper.addMapping(self.txtPorodK, W.W_PORODK) |
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| 307 | self.mapper.addMapping(self.txtPorodSigma, W.W_PORODSIGMA) |
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[d4881f6a] | 308 | |
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[cb4d219] | 309 | self.mapper.addMapping(self.txtAvgCoreThick, W.W_CORETHICK) |
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| 310 | self.mapper.addMapping(self.txtAvgIntThick, W.W_INTTHICK) |
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| 311 | self.mapper.addMapping(self.txtAvgHardBlock, W.W_HARDBLOCK) |
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| 312 | self.mapper.addMapping(self.txtPolydisp, W.W_POLY) |
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| 313 | self.mapper.addMapping(self.txtLongPeriod, W.W_PERIOD) |
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| 314 | self.mapper.addMapping(self.txtLocalCrystal, W.W_CRYSTAL) |
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[d4881f6a] | 315 | |
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| 316 | self.mapper.toFirst() |
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| 317 | |
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| 318 | def calculate_background(self): |
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| 319 | """Find a good estimate of the background value.""" |
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| 320 | self._update_calculator() |
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| 321 | try: |
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| 322 | background = self._calculator.compute_background() |
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[cb4d219] | 323 | temp = QtGui.QStandardItem("{:.4g}".format(background)) |
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[d4881f6a] | 324 | self.model.setItem(W.W_BACKGROUND, temp) |
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| 325 | except (LinAlgError, ValueError): |
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| 326 | message = "These is not enough data in the fitting range. "\ |
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| 327 | "Try decreasing the upper Q or increasing the cutoff Q" |
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| 328 | QtWidgets.QMessageBox.warning(self, "Calculation Error", |
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| 329 | message) |
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| 330 | |
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| 331 | |
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| 332 | # pylint: disable=invalid-name |
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[e90988c] | 333 | def showHelp(self): |
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| 334 | """ |
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| 335 | Opens a webpage with help on the perspective |
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| 336 | """ |
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| 337 | """ Display help when clicking on Help button """ |
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[aed0532] | 338 | treeLocation = "/user/qtgui/Perspectives/Corfunc/corfunc_help.html" |
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[e90988c] | 339 | self.parent.showHelp(treeLocation) |
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| 340 | |
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[d4881f6a] | 341 | @staticmethod |
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| 342 | def allowBatch(): |
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| 343 | """ |
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| 344 | We cannot perform corfunc analysis in batch at this time. |
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| 345 | """ |
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| 346 | return False |
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| 347 | |
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| 348 | def setData(self, data_item, is_batch=False): |
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| 349 | """ |
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| 350 | Obtain a QStandardItem object and dissect it to get Data1D/2D |
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| 351 | Pass it over to the calculator |
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| 352 | """ |
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| 353 | if not isinstance(data_item, list): |
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| 354 | msg = "Incorrect type passed to the Corfunc Perpsective" |
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| 355 | raise AttributeError(msg) |
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| 356 | |
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| 357 | if not isinstance(data_item[0], QtGui.QStandardItem): |
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| 358 | msg = "Incorrect type passed to the Corfunc Perspective" |
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| 359 | raise AttributeError(msg) |
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| 360 | |
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| 361 | model_item = data_item[0] |
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| 362 | data = GuiUtils.dataFromItem(model_item) |
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[cb4d219] | 363 | self._model_item = model_item |
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[d4881f6a] | 364 | self._calculator.set_data(data) |
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[cb4d219] | 365 | self.cmdCalculateBg.setEnabled(True) |
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| 366 | self.cmdExtrapolate.setEnabled(True) |
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[d4881f6a] | 367 | |
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| 368 | self.model.setItem(W.W_GUINIERA, QtGui.QStandardItem("")) |
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| 369 | self.model.setItem(W.W_GUINIERB, QtGui.QStandardItem("")) |
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| 370 | self.model.setItem(W.W_PORODK, QtGui.QStandardItem("")) |
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| 371 | self.model.setItem(W.W_PORODSIGMA, QtGui.QStandardItem("")) |
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| 372 | self.model.setItem(W.W_CORETHICK, QtGui.QStandardItem("")) |
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| 373 | self.model.setItem(W.W_INTTHICK, QtGui.QStandardItem("")) |
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| 374 | self.model.setItem(W.W_HARDBLOCK, QtGui.QStandardItem("")) |
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| 375 | self.model.setItem(W.W_CRYSTAL, QtGui.QStandardItem("")) |
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| 376 | self.model.setItem(W.W_POLY, QtGui.QStandardItem("")) |
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| 377 | self.model.setItem(W.W_PERIOD, QtGui.QStandardItem("")) |
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| 378 | |
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| 379 | self._canvas.data = data |
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| 380 | self._canvas.extrap = None |
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| 381 | self._canvas.draw_q_space() |
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[cb4d219] | 382 | self.cmdTransform.setEnabled(False) |
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[d4881f6a] | 383 | |
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[84fa015] | 384 | self._realplot.data = None |
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| 385 | self._realplot.draw_real_space() |
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[d4881f6a] | 386 | |
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| 387 | def setClosable(self, value=True): |
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| 388 | """ |
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| 389 | Allow outsiders close this widget |
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| 390 | """ |
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| 391 | assert isinstance(value, bool) |
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| 392 | |
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| 393 | self._allow_close = value |
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| 394 | |
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| 395 | def closeEvent(self, event): |
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| 396 | """ |
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| 397 | Overwrite QDialog close method to allow for custom widget close |
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| 398 | """ |
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| 399 | if self._allow_close: |
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| 400 | # reset the closability flag |
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| 401 | self.setClosable(value=False) |
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| 402 | # Tell the MdiArea to close the container |
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[50bfab0] | 403 | if self.parent: |
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| 404 | self.parentWidget().close() |
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[d4881f6a] | 405 | event.accept() |
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| 406 | else: |
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| 407 | event.ignore() |
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| 408 | # Maybe we should just minimize |
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| 409 | self.setWindowState(QtCore.Qt.WindowMinimized) |
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| 410 | |
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| 411 | def title(self): |
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| 412 | """ |
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| 413 | Window title function used by certain error messages. |
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| 414 | Check DataExplorer.py, line 355 |
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| 415 | """ |
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| 416 | return "Corfunc Perspective" |
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| 417 | # pylint: enable=invalid-name |
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