# coding: utf-8
#/*##########################################################################
# Copyright (C) 2004-2020 V.A. Sole, European Synchrotron Radiation Facility
#
# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
# the ESRF by the Software group.
#
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# of this software and associated documentation files (the "Software"), to deal
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# 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:
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# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
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# 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
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# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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"""This module provides a background configuration widget
:class:`BackgroundWidget` and a corresponding dialog window
:class:`BackgroundDialog`.
.. image:: img/BackgroundDialog.png
:height: 300px
"""
import sys
import numpy
from silx.gui import qt
from silx.gui.plot import PlotWidget
from silx.math.fit import filters
__authors__ = ["V.A. Sole", "P. Knobel"]
__license__ = "MIT"
__date__ = "28/06/2017"
class HorizontalSpacer(qt.QWidget):
def __init__(self, *args):
qt.QWidget.__init__(self, *args)
self.setSizePolicy(qt.QSizePolicy(qt.QSizePolicy.Expanding,
qt.QSizePolicy.Fixed))
class BackgroundParamWidget(qt.QWidget):
"""Background configuration composite widget.
Strip and snip filters parameters can be adjusted using input widgets.
Updating the widgets causes :attr:`sigBackgroundParamWidgetSignal` to
be emitted.
"""
sigBackgroundParamWidgetSignal = qt.pyqtSignal(object)
def __init__(self, parent=None):
qt.QWidget.__init__(self, parent)
self.mainLayout = qt.QGridLayout(self)
self.mainLayout.setColumnStretch(1, 1)
# Algorithm choice ---------------------------------------------------
self.algorithmComboLabel = qt.QLabel(self)
self.algorithmComboLabel.setText("Background algorithm")
self.algorithmCombo = qt.QComboBox(self)
self.algorithmCombo.addItem("Strip")
self.algorithmCombo.addItem("Snip")
self.algorithmCombo.activated[int].connect(
self._algorithmComboActivated)
# Strip parameters ---------------------------------------------------
self.stripWidthLabel = qt.QLabel(self)
self.stripWidthLabel.setText("Strip Width")
self.stripWidthSpin = qt.QSpinBox(self)
self.stripWidthSpin.setMaximum(100)
self.stripWidthSpin.setMinimum(1)
self.stripWidthSpin.valueChanged[int].connect(self._emitSignal)
self.stripIterLabel = qt.QLabel(self)
self.stripIterLabel.setText("Strip Iterations")
self.stripIterValue = qt.QLineEdit(self)
validator = qt.QIntValidator(self.stripIterValue)
self.stripIterValue._v = validator
self.stripIterValue.setText("0")
self.stripIterValue.editingFinished[()].connect(self._emitSignal)
self.stripIterValue.setToolTip(
"Number of iterations for strip algorithm.\n" +
"If greater than 999, an 2nd pass of strip filter is " +
"applied to remove artifacts created by first pass.")
# Snip parameters ----------------------------------------------------
self.snipWidthLabel = qt.QLabel(self)
self.snipWidthLabel.setText("Snip Width")
self.snipWidthSpin = qt.QSpinBox(self)
self.snipWidthSpin.setMaximum(300)
self.snipWidthSpin.setMinimum(0)
self.snipWidthSpin.valueChanged[int].connect(self._emitSignal)
# Smoothing parameters -----------------------------------------------
self.smoothingFlagCheck = qt.QCheckBox(self)
self.smoothingFlagCheck.setText("Smoothing Width (Savitsky-Golay)")
self.smoothingFlagCheck.toggled.connect(self._smoothingToggled)
self.smoothingSpin = qt.QSpinBox(self)
self.smoothingSpin.setMinimum(3)
#self.smoothingSpin.setMaximum(40)
self.smoothingSpin.setSingleStep(2)
self.smoothingSpin.valueChanged[int].connect(self._emitSignal)
# Anchors ------------------------------------------------------------
self.anchorsGroup = qt.QWidget(self)
anchorsLayout = qt.QHBoxLayout(self.anchorsGroup)
anchorsLayout.setSpacing(2)
anchorsLayout.setContentsMargins(0, 0, 0, 0)
self.anchorsFlagCheck = qt.QCheckBox(self.anchorsGroup)
self.anchorsFlagCheck.setText("Use anchors")
self.anchorsFlagCheck.setToolTip(
"Define X coordinates of points that must remain fixed")
self.anchorsFlagCheck.stateChanged[int].connect(
self._anchorsToggled)
anchorsLayout.addWidget(self.anchorsFlagCheck)
maxnchannel = 16384 * 4 # Fixme ?
self.anchorsList = []
num_anchors = 4
for i in range(num_anchors):
anchorSpin = qt.QSpinBox(self.anchorsGroup)
anchorSpin.setMinimum(0)
anchorSpin.setMaximum(maxnchannel)
anchorSpin.valueChanged[int].connect(self._emitSignal)
anchorsLayout.addWidget(anchorSpin)
self.anchorsList.append(anchorSpin)
# Layout ------------------------------------------------------------
self.mainLayout.addWidget(self.algorithmComboLabel, 0, 0)
self.mainLayout.addWidget(self.algorithmCombo, 0, 2)
self.mainLayout.addWidget(self.stripWidthLabel, 1, 0)
self.mainLayout.addWidget(self.stripWidthSpin, 1, 2)
self.mainLayout.addWidget(self.stripIterLabel, 2, 0)
self.mainLayout.addWidget(self.stripIterValue, 2, 2)
self.mainLayout.addWidget(self.snipWidthLabel, 3, 0)
self.mainLayout.addWidget(self.snipWidthSpin, 3, 2)
self.mainLayout.addWidget(self.smoothingFlagCheck, 4, 0)
self.mainLayout.addWidget(self.smoothingSpin, 4, 2)
self.mainLayout.addWidget(self.anchorsGroup, 5, 0, 1, 4)
# Initialize interface -----------------------------------------------
self._setAlgorithm("strip")
self.smoothingFlagCheck.setChecked(False)
self._smoothingToggled(is_checked=False)
self.anchorsFlagCheck.setChecked(False)
self._anchorsToggled(is_checked=False)
def _algorithmComboActivated(self, algorithm_index):
self._setAlgorithm("strip" if algorithm_index == 0 else "snip")
def _setAlgorithm(self, algorithm):
"""Enable/disable snip and snip input widgets, depending on the
chosen algorithm.
:param algorithm: "snip" or "strip"
"""
if algorithm not in ["strip", "snip"]:
raise ValueError(
"Unknown background filter algorithm %s" % algorithm)
self.algorithm = algorithm
self.stripWidthSpin.setEnabled(algorithm == "strip")
self.stripIterValue.setEnabled(algorithm == "strip")
self.snipWidthSpin.setEnabled(algorithm == "snip")
def _smoothingToggled(self, is_checked):
"""Enable/disable smoothing input widgets, emit dictionary"""
self.smoothingSpin.setEnabled(is_checked)
self._emitSignal()
def _anchorsToggled(self, is_checked):
"""Enable/disable all spin widgets defining anchor X coordinates,
emit signal.
"""
for anchor_spin in self.anchorsList:
anchor_spin.setEnabled(is_checked)
self._emitSignal()
def setParameters(self, ddict):
"""Set values for all input widgets.
:param dict ddict: Input dictionary, must have the same
keys as the dictionary output by :meth:`getParameters`
"""
if "algorithm" in ddict:
self._setAlgorithm(ddict["algorithm"])
if "SnipWidth" in ddict:
self.snipWidthSpin.setValue(int(ddict["SnipWidth"]))
if "StripWidth" in ddict:
self.stripWidthSpin.setValue(int(ddict["StripWidth"]))
if "StripIterations" in ddict:
self.stripIterValue.setText("%d" % int(ddict["StripIterations"]))
if "SmoothingFlag" in ddict:
self.smoothingFlagCheck.setChecked(bool(ddict["SmoothingFlag"]))
if "SmoothingWidth" in ddict:
self.smoothingSpin.setValue(int(ddict["SmoothingWidth"]))
if "AnchorsFlag" in ddict:
self.anchorsFlagCheck.setChecked(bool(ddict["AnchorsFlag"]))
if "AnchorsList" in ddict:
anchorslist = ddict["AnchorsList"]
if anchorslist in [None, 'None']:
anchorslist = []
for spin in self.anchorsList:
spin.setValue(0)
i = 0
for value in anchorslist:
self.anchorsList[i].setValue(int(value))
i += 1
def getParameters(self):
"""Return dictionary of parameters defined in the GUI
The returned dictionary contains following values:
- *algorithm*: *"strip"* or *"snip"*
- *StripWidth*: width of strip iterator
- *StripIterations*: number of iterations
- *StripThreshold*: curvature parameter (currently fixed to 1.0)
- *SnipWidth*: width of snip algorithm
- *SmoothingFlag*: flag to enable/disable smoothing
- *SmoothingWidth*: width of Savitsky-Golay smoothing filter
- *AnchorsFlag*: flag to enable/disable anchors
- *AnchorsList*: list of anchors (X coordinates of fixed values)
"""
stripitertext = self.stripIterValue.text()
stripiter = int(stripitertext) if len(stripitertext) else 0
return {"algorithm": self.algorithm,
"StripThreshold": 1.0,
"SnipWidth": self.snipWidthSpin.value(),
"StripIterations": stripiter,
"StripWidth": self.stripWidthSpin.value(),
"SmoothingFlag": self.smoothingFlagCheck.isChecked(),
"SmoothingWidth": self.smoothingSpin.value(),
"AnchorsFlag": self.anchorsFlagCheck.isChecked(),
"AnchorsList": [spin.value() for spin in self.anchorsList]}
def _emitSignal(self, dummy=None):
self.sigBackgroundParamWidgetSignal.emit(
{'event': 'ParametersChanged',
'parameters': self.getParameters()})
[docs]class BackgroundDialog(qt.QDialog):
"""QDialog window featuring a :class:`BackgroundWidget`"""
def __init__(self, parent=None):
qt.QDialog.__init__(self, parent)
self.setWindowTitle("Strip and Snip Configuration Window")
self.mainLayout = qt.QVBoxLayout(self)
self.mainLayout.setContentsMargins(0, 0, 0, 0)
self.mainLayout.setSpacing(2)
self.parametersWidget = BackgroundWidget(self)
self.mainLayout.addWidget(self.parametersWidget)
hbox = qt.QWidget(self)
hboxLayout = qt.QHBoxLayout(hbox)
hboxLayout.setContentsMargins(0, 0, 0, 0)
hboxLayout.setSpacing(2)
self.okButton = qt.QPushButton(hbox)
self.okButton.setText("OK")
self.okButton.setAutoDefault(False)
self.dismissButton = qt.QPushButton(hbox)
self.dismissButton.setText("Cancel")
self.dismissButton.setAutoDefault(False)
hboxLayout.addWidget(HorizontalSpacer(hbox))
hboxLayout.addWidget(self.okButton)
hboxLayout.addWidget(self.dismissButton)
self.mainLayout.addWidget(hbox)
self.dismissButton.clicked.connect(self.reject)
self.okButton.clicked.connect(self.accept)
self.output = {}
"""Configuration dictionary containing following fields:
- *SmoothingFlag*
- *SmoothingWidth*
- *StripWidth*
- *StripIterations*
- *StripThreshold*
- *SnipWidth*
- *AnchorsFlag*
- *AnchorsList*
"""
# self.parametersWidget.parametersWidget.sigBackgroundParamWidgetSignal.connect(self.updateOutput)
# def updateOutput(self, ddict):
# self.output = ddict
[docs] def accept(self):
"""Update :attr:`output`, then call :meth:`QDialog.accept`
"""
self.output = self.getParameters()
super(BackgroundDialog, self).accept()
[docs] def sizeHint(self):
return qt.QSize(int(1.5*qt.QDialog.sizeHint(self).width()),
qt.QDialog.sizeHint(self).height())
[docs] def setData(self, x, y, xmin=None, xmax=None):
"""See :meth:`BackgroundWidget.setData`"""
return self.parametersWidget.setData(x, y, xmin, xmax)
[docs] def getParameters(self):
"""See :meth:`BackgroundWidget.getParameters`"""
return self.parametersWidget.getParameters()
[docs] def setParameters(self, ddict):
"""See :meth:`BackgroundWidget.setPrintGeometry`"""
return self.parametersWidget.setParameters(ddict)
[docs] def setDefault(self, ddict):
"""Alias for :meth:`setPrintGeometry`"""
return self.setParameters(ddict)
def getBgDialog(parent=None, default=None, modal=True):
"""Instantiate and return a bg configuration dialog, adapted
for configuring standard background theories from
:mod:`silx.math.fit.bgtheories`.
:return: Instance of :class:`BackgroundDialog`
"""
bgd = BackgroundDialog(parent=parent)
# apply default to newly added pages
bgd.setParameters(default)
return bgd
def main():
# synthetic data
from silx.math.fit.functions import sum_gauss
x = numpy.arange(5000)
# (height1, center1, fwhm1, ...) 5 peaks
params1 = (50, 500, 100,
20, 2000, 200,
50, 2250, 100,
40, 3000, 75,
23, 4000, 150)
y0 = sum_gauss(x, *params1)
# random values between [-1;1]
noise = 2 * numpy.random.random(5000) - 1
# make it +- 5%
noise *= 0.05
# 2 gaussians with very large fwhm, as background signal
actual_bg = sum_gauss(x, 15, 3500, 3000, 5, 1000, 1500)
# Add 5% random noise to gaussians and add background
y = y0 + numpy.average(y0) * noise + actual_bg
# Open widget
a = qt.QApplication(sys.argv)
a.lastWindowClosed.connect(a.quit)
def mySlot(ddict):
print(ddict)
w = BackgroundDialog()
w.parametersWidget.parametersWidget.sigBackgroundParamWidgetSignal.connect(mySlot)
w.setData(x, y)
w.exec_()
#a.exec_()
if __name__ == "__main__":
main()
