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#/*##########################################################################
# Copyright (C) 2004-2013 European Synchrotron Radiation Facility
#
# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
# the ESRF by the Software group.
#
# This toolkit is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the Free
# Software Foundation; either version 2 of the License, or (at your option)
# any later version.
#
# PyMca is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details.
#
# You should have received a copy of the GNU General Public License along with
# PyMca; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
# PyMca follows the dual licensing model of Riverbank's PyQt and cannot be
# used as a free plugin for a non-free program.
#
# Please contact the ESRF industrial unit (industry@esrf.fr) if this license
# is a problem for you.
#############################################################################*/
__author__ = "T. Rueter - ESRF Data Analysis Unit"
from PyMca import Plugin1DBase
from PyMca.PyMcaSciPy.signal import medfilt1d
from PyMca import PyMcaQt as qt
import numpy
DEBUG = 0
class MedianFilterScanDeglitchPlugin(Plugin1DBase.Plugin1DBase):
def __init__(self, plotWindow, **kw):
Plugin1DBase.Plugin1DBase.__init__(self, plotWindow, **kw)
self.methodDict = {
'Apply to active curve':
[self.removeSpikesActive,
'Apply sliding median filter to active curve',
None],
'Apply to all curves':
[self.removeSpikesAll,
'Apply sliding median filter to all curves',
None],
'Configure median filter':
[self.configureFilter,
'Set threshold and width of the filter',
None]
}
self._methodList = ['Configure median filter',
'Apply to active curve',
'Apply to all curves']
self.threshold = 0.66
self.width = 9
self._widget = None
#Methods to be implemented by the plugin
def getMethods(self, plottype=None):
"""
A list with the NAMES associated to the callable methods
that are applicable to the specified plot.
Plot type can be "SCAN", "MCA", None, ...
"""
return list(self._methodList)
def getMethodToolTip(self, name):
"""
Returns the help associated to the particular method name or None.
"""
return self.methodDict[name][1]
def getMethodPixmap(self, name):
"""
Returns the pixmap associated to the particular method name or None.
"""
return self.methodDict[name][2]
def applyMethod(self, name):
"""
The plugin is asked to apply the method associated to name.
"""
self.methodDict[name][0]()
return
def configureFilter(self):
if self._widget is None:
msg = qt.QDialog()
msg.setWindowTitle("Deglitch Configuration")
msgLayout = qt.QGridLayout()
buttonLayout = qt.QHBoxLayout()
inpThreshold = qt.QDoubleSpinBox()
inpThreshold.setRange(0.,10.)
inpThreshold.setSingleStep(.1)
inpThreshold.setValue(self.threshold)
inpThreshold.setToolTip('Increase width for broad spikes')
inpWidth = qt.QSpinBox()
inpWidth.setRange(1,101)
inpWidth.setSingleStep(2)
inpWidth.setValue(self.width)
inpWidth.setToolTip('Set low threshold for multiple spikes of different markedness')
labelWidth = qt.QLabel('Width (must be odd)')
labelThreshold = qt.QLabel('Threshold (multiple of deviation)')
buttonOK = qt.QPushButton('Ok')
buttonOK.clicked.connect(msg.accept)
buttonCancel = qt.QPushButton('Cancel')
buttonCancel.clicked.connect(msg.reject)
allActiveBG = qt.QButtonGroup()
buttonAll = qt.QCheckBox('Apply to All')
buttonActive = qt.QCheckBox('Apply to Active')
allActiveBG.addButton(buttonAll, 0)
allActiveBG.addButton(buttonActive, 1)
buttonActive.setChecked(True)
buttonLayout.addWidget(qt.HorizontalSpacer())
buttonLayout.addWidget(buttonOK)
buttonLayout.addWidget(buttonCancel)
msgLayout.addWidget(labelWidth,0,0)
msgLayout.addWidget(inpWidth,0,1)
msgLayout.addWidget(labelThreshold,1,0)
msgLayout.addWidget(inpThreshold,1,1)
msgLayout.addWidget(buttonActive,2,0)
msgLayout.addWidget(buttonAll,2,1)
msgLayout.addLayout(buttonLayout,3,0,1,2)
msg.setLayout(msgLayout)
self._widget = msg
self._widget.inputWidth = inpWidth
self._widget.inputThreshold = inpThreshold
self._widget.applyToAll = buttonAll
if self._widget.exec_():
self.threshold = float(self._widget.inputThreshold.value())
self.width = int(self._widget.inputWidth.value())
if not (self.width%2):
self.width += 1
if buttonActive.isChecked():
if DEBUG:
print('ActiveChecked')
self.removeSpikesActive()
if buttonAll.isChecked():
if DEBUG:
print('AllChecked')
self.removeSpikesAll()
def removeSpikesAll(self):
self.medianThresholdFilter(False, self.threshold, self.width)
def removeSpikesActive(self):
self.medianThresholdFilter(True, self.threshold, self.width)
def medianThresholdFilter(self, activeOnly, threshold, length):
if activeOnly:
active = self._plotWindow.getActiveCurve()
if not active:
return
else:
x, y, legend, info = active
self.removeCurve(legend)
spectra = [active]
else:
spectra = self._plotWindow.getAllCurves()
for (idx, spec) in enumerate(spectra):
x, y, legend, info = spec
filtered = medfilt1d(y, length)
diff = filtered-y
mean = diff.mean()
sigma = (x-mean)**2
sigma = numpy.sqrt(sigma.sum()/len(sigma))
ynew = numpy.where(abs(diff) > threshold * sigma, filtered, y)
legend = info.get('selectionlegend','') + ' SR'
if (idx==0) and (len(spectra)!=1):
self.addCurve(x,ynew,legend,info,replace=True, replot=False)
elif idx == (len(spectra)- 1):
self.addCurve(x,ynew,legend,info, replot=True)
else:
self.addCurve(x,ynew,legend,info, replot=False)
MENU_TEXT = "Remove glitches from curves"
def getPlugin1DInstance(plotWindow, **kw):
ob = MedianFilterScanDeglitchPlugin(plotWindow)
return ob
if __name__ == "__main__":
from PyMca import ScanWindow
from PyMca import PyMcaQt as qt
import numpy
app = qt.QApplication([])
sw = ScanWindow.ScanWindow()
x = numpy.arange(1000.)
y0 = 10 * x + 10000. * numpy.exp(-0.5*(x-500)*(x-500)/400) + 1500 * numpy.random.random(1000.)
y1 = 10 * x + 10000. * numpy.exp(-0.5*(x-600)*(x-600)/400) + 1500 * numpy.random.random(1000.)
y2 = 10 * x + 10000. * numpy.exp(-0.5*(x-400)*(x-400)/400) + 1500 * numpy.random.random(1000.)
y3 = 10 * x + 10000. * numpy.exp(-0.5*(x-700)*(x-700)/400) + 1500 * numpy.random.random(1000.)
y0[320:322] = 50000.
y2[400:405] = 12300.
y2[200:205] = 10400.
y1[620:623] = 16300.
y1[800:803] = 50000.
y3[664:666] = 16950.
y3[699:701] = 20000.
y3[730:733] = 20000.
sw.addCurve(x, y0, legend="Curve0")
sw.addCurve(x, y1, legend="Curve1")
sw.addCurve(x, y2, legend="Curve2")
sw.addCurve(x, y3, legend="Curve3")
plugin = getPlugin1DInstance(sw)
plugin.configureFilter()
sw.show()
app.exec_()
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