/usr/share/pyshared/PyMca/StripBackgroundWidget.py is in pymca 4.5.0-4.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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# Copyright (C) 2004-2010 European Synchrotron Radiation Facility
#
# This file is part of the PyMCA X-ray Fluorescence Toolkit developed at
# the ESRF by the Beamline Instrumentation Software Support (BLISS) 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., 59 Temple Place,
# Suite 330, Boston, MA 02111-1307, USA.
#
# PyMCA follows the dual licensing model of Trolltech's Qt and 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.
#############################################################################*/
import sys
import PyMcaQt as qt
try:
import ScanWindow
SCANWINDOW = True
except ImportError:
import Plot1DMatplotlib
SCANWINDOW = False
import numpy
import SpecfitFuns
class HorizontalSpacer(qt.QWidget):
def __init__(self, *args):
qt.QWidget.__init__(self, *args)
self.setSizePolicy(qt.QSizePolicy(qt.QSizePolicy.Expanding,
qt.QSizePolicy.Fixed))
class VerticalSpacer(qt.QWidget):
def __init__(self, *args):
qt.QWidget.__init__(self, *args)
self.setSizePolicy(qt.QSizePolicy(qt.QSizePolicy.Fixed,
qt.QSizePolicy.Expanding))
class StripParametersWidget(qt.QWidget):
def __init__(self, parent=None):
qt.QWidget.__init__(self, parent)
self.build()
def build(self):
self.mainLayout = qt.QGridLayout(self)
self.mainLayout.setMargin(11)
self.mainLayout.setSpacing(6)
#strip algorithm
self.stripComboLabel = qt.QLabel(self)
self.stripComboLabel.setText("Non-analytical (or estimation) background algorithm")
self.stripCombo = qt.QComboBox(self)
self.stripCombo.addItem(str("Strip"))
self.stripCombo.addItem(str("SNIP"))
self.connect(self.stripCombo,
qt.SIGNAL("activated(int)"),
self._stripComboActivated)
#SNIP width
self.snipWidthLabel = qt.QLabel(self)
self.snipWidthLabel.setText(str("SNIP Background Width"))
self.snipWidthSpin = qt.QSpinBox(self)
self.snipWidthSpin.setMaximum(300)
self.snipWidthSpin.setMinimum(0)
self.connect(self.snipWidthSpin,
qt.SIGNAL('valueChanged(int)'),
self._emitSignal)
#Strip width
self.stripWidthLabel = qt.QLabel(self)
self.stripWidthLabel.setText(str("Strip Background Width"))
self.stripWidthSpin = qt.QSpinBox(self)
self.stripWidthSpin.setMaximum(100)
self.stripWidthSpin.setMinimum(1)
self.connect(self.stripWidthSpin,
qt.SIGNAL('valueChanged(int)'),
self._emitSignal)
#Strip iterations
self.stripIterLabel = qt.QLabel(self)
self.stripIterLabel.setText(str("Strip Background Iterations"))
self.stripIterValue = qt.QLineEdit(self)
validator = qt.QIntValidator(self.stripIterValue)
self.stripIterValue._v = validator
self.connect(self.stripIterValue,
qt.SIGNAL('editingFinished()'),
self._emitSignal)
#Strip smoothing
self.stripFilterLabel = qt.QLabel(self)
self.stripFilterLabel.setText(str("Strip Background Smoothing Width (Savitsky-Golay)"))
self.stripFilterSpin = qt.QSpinBox(self)
self.stripFilterSpin.setMinimum(1)
self.stripFilterSpin.setMaximum(40)
self.stripFilterSpin.setSingleStep(2)
self.connect(self.stripFilterSpin,
qt.SIGNAL('valueChanged(int)'),
self._emitSignal)
#anchors
self.anchorsContainer = qt.QWidget(self)
anchorsContainerLayout = qt.QHBoxLayout(self.anchorsContainer)
anchorsContainerLayout.setMargin(0)
anchorsContainerLayout.setSpacing(2)
self.stripAnchorsFlagCheck = qt.QCheckBox(self.anchorsContainer)
self.stripAnchorsFlagCheck.setText(str("Strip Background use Anchors"))
self.connect(self.stripAnchorsFlagCheck,
qt.SIGNAL('stateChanged(int)'),
self._emitSignal)
anchorsContainerLayout.addWidget(self.stripAnchorsFlagCheck)
#self.iterSpin = qt.QSpinBox(self)
#self.iterSpin.setMinimum(1)
maxnchannel = 16384*4
self.stripAnchorsList = []
for i in range(4):
anchorSpin = qt.QSpinBox(self.anchorsContainer)
anchorSpin.setMinimum(0)
anchorSpin.setMaximum(maxnchannel)
self.connect(anchorSpin,
qt.SIGNAL('valueChanged(int)'),
self._emitSignal)
anchorsContainerLayout.addWidget(anchorSpin)
self.stripAnchorsList.append(anchorSpin)
self.mainLayout.setColumnStretch(0, 1)
row = 0
self.mainLayout.addWidget(self.stripComboLabel, row, 0)
self.mainLayout.addWidget(self.stripCombo, row, 4)
row += 1
self.mainLayout.addWidget(self.snipWidthLabel,row, 0)
self.mainLayout.addWidget(self.snipWidthSpin, row, 4)
row += 1
self.mainLayout.addWidget(self.stripWidthLabel, row, 0)
self.mainLayout.addWidget(self.stripWidthSpin, row, 4)
row += 1
self.mainLayout.addWidget(self.stripIterLabel, row, 0)
self.mainLayout.addWidget(self.stripIterValue, row, 4)
row += 1
self.mainLayout.addWidget(self.stripFilterLabel, row, 0)
self.mainLayout.addWidget(self.stripFilterSpin, row, 4)
row += 1
self.mainLayout.addWidget(self.anchorsContainer, row, 0, 1, 5)
self._stripComboActivated(0)
def _stripComboActivated(self, iValue):
if iValue == 1:
self.setSNIP(True)
else:
self.setSNIP(False)
def setSNIP(self, bValue):
if bValue:
self.snipWidthSpin.setEnabled(True)
self.stripWidthSpin.setEnabled(False)
#self.stripFilterSpin.setEnabled(False)
self.stripIterValue.setEnabled(False)
self.stripCombo.setCurrentIndex(1)
else:
self.snipWidthSpin.setEnabled(False)
#self.stripFilterSpin.setEnabled(True)
self.stripWidthSpin.setEnabled(True)
self.stripIterValue.setEnabled(True)
self.stripCombo.setCurrentIndex(0)
def setParameters(self, ddict):
if 'fit' in ddict:
pars = ddict['fit']
else:
pars = ddict
key = "stripalgorithm"
if key in pars:
stripAlgorithm = int(pars[key])
self.setSNIP(stripAlgorithm)
key = "snipwidth"
if key in pars:
self.snipWidthSpin.setValue(int(pars[key]))
key = "stripwidth"
if key in pars:
self.stripWidthSpin.setValue(int(pars[key]))
key = "stripiterations"
if key in pars:
self.stripIterValue.setText("%d" % int(pars[key]))
key = "stripfilterwidth"
if key in pars:
self.stripFilterSpin.setValue(int(pars[key]))
key = "stripanchorsflag"
if key in pars:
self.stripAnchorsFlagCheck.setChecked(int(pars[key]))
key = "stripanchorslist"
if key in pars:
anchorslist = pars[key]
if anchorslist in [None, 'None']:
anchorslist = []
for spin in self.stripAnchorsList:
spin.setValue(0)
i = 0
for value in anchorslist:
self.stripAnchorsList[i].setValue(int(value))
i += 1
def getParameters(self):
pars = {}
pars["stripalgorithm"] = int(self.stripCombo.currentIndex())
pars["stripconstant"]= 1.0
pars["snipwidth"] = self.snipWidthSpin.value()
txt = str(self.stripIterValue.text())
if len(txt):
pars["stripiterations"]= int(txt)
else:
pars["stripiterations"] = 0
pars["stripwidth"]= self.stripWidthSpin.value()
pars["stripfilterwidth"] = self.stripFilterSpin.value()
pars["stripanchorsflag"] = int(self.stripAnchorsFlagCheck.isChecked())
pars["stripanchorslist"] = []
for spin in self.stripAnchorsList:
pars["stripanchorslist"].append(spin.value())
return pars
def _emitSignal(self, dummy=None):
ddict= {}
ddict['event']='ParametersChanged'
ddict['parameters'] = self.getParameters()
self.emit(qt.SIGNAL('StripParametersWidgetSignal'), ddict)
class StripBackgroundWidget(qt.QWidget):
def __init__(self, parent=None):
qt.QWidget.__init__(self, parent)
self.setWindowTitle("Strip and SNIP Configuration Window")
self.mainLayout = qt.QVBoxLayout(self)
self.mainLayout.setMargin(0)
self.mainLayout.setSpacing(2)
self.parametersWidget = StripParametersWidget(self)
if SCANWINDOW:
self.graphWidget = ScanWindow.ScanWindow(self)
else:
self.graphWidget = Plot1DMatplotlib.Plot1DMatplotlib(self)
try:
self.graphWidget.fitButton.hide()
self.graphWidget.scanWindowInfoWidget.hide()
except:
pass
self.mainLayout.addWidget(self.parametersWidget)
self.mainLayout.addWidget(self.graphWidget)
self.getParameters = self.parametersWidget.getParameters
self.setParameters = self.parametersWidget.setParameters
self._x = None
self._y = None
self.connect(self.parametersWidget,
qt.SIGNAL('StripParametersWidgetSignal'),
self._slot)
def setData(self, x, y):
self._x = x
self._y = y
self.update()
def _slot(self, ddict):
self.update()
def update(self):
if self._y is None:
return
pars = self.getParameters()
#smoothed data
y = numpy.ravel(numpy.array(self._y)).astype(numpy.float)
ysmooth = SpecfitFuns.SavitskyGolay(y, pars['stripfilterwidth'])
f=[0.25,0.5,0.25]
ysmooth[1:-1]=numpy.convolve(ysmooth,f,mode=0)
ysmooth[0]=0.5*(ysmooth[0]+ysmooth[1])
ysmooth[-1]=0.5*(ysmooth[-1]+ysmooth[-2])
#loop for anchors
x = self._x
niter = pars['stripiterations']
anchorslist = []
if pars['stripanchorsflag']:
if pars['stripanchorslist'] is not None:
ravelled = x
for channel in pars['stripanchorslist']:
if channel <= ravelled[0]:continue
index = numpy.nonzero(ravelled >= channel)[0]
if len(index):
index = min(index)
if index > 0:
anchorslist.append(index)
if niter > 1000:
stripBackground = SpecfitFuns.subac(ysmooth,
pars['stripconstant'],
niter,
pars['stripwidth'],
anchorslist)
#final smoothing
stripBackground = SpecfitFuns.subac(stripBackground,
pars['stripconstant'],
500,1,
anchorslist)
elif niter > 0:
stripBackground = SpecfitFuns.subac(ysmooth,
pars['stripconstant'],
niter,
pars['stripwidth'],
anchorslist)
else:
stripBackground = 0.0 * ysmooth + ysmooth.min()
if len(anchorslist) == 0:
anchorslist = [0, len(ysmooth)-1]
anchorslist.sort()
snipBackground = 0.0 * ysmooth
lastAnchor = 0
width = pars['snipwidth']
for anchor in anchorslist:
if (anchor > lastAnchor) and (anchor < len(ysmooth)):
snipBackground[lastAnchor:anchor] =\
SpecfitFuns.snip1d(ysmooth[lastAnchor:anchor], width, 0)
lastAnchor = anchor
if lastAnchor < len(ysmooth):
snipBackground[lastAnchor:] =\
SpecfitFuns.snip1d(ysmooth[lastAnchor:], width, 0)
self.graphWidget.newCurve(x, y, 'Input Data')
self.graphWidget.newCurve(x, stripBackground, 'Strip Background')
self.graphWidget.newCurve(x, snipBackground, 'SNIP Background')
class StripBackgroundDialog(qt.QDialog):
def __init__(self, parent=None):
qt.QDialog.__init__(self, parent)
self.setWindowTitle("Strip and SNIP Configuration Window")
self.mainLayout = qt.QVBoxLayout(self)
self.mainLayout.setMargin(0)
self.mainLayout.setSpacing(2)
self.parametersWidget = StripBackgroundWidget(self)
self.setData = self.parametersWidget.setData
self.getParameters = self.parametersWidget.getParameters
self.setParameters = self.parametersWidget.setParameters
self.mainLayout.addWidget(self.parametersWidget)
hbox = qt.QWidget(self)
hboxLayout = qt.QHBoxLayout(hbox)
hboxLayout.setMargin(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.connect(self.dismissButton, qt.SIGNAL("clicked()"), self.reject)
self.connect(self.okButton, qt.SIGNAL("clicked()"), self.accept)
def sizeHint(self):
return qt.QSize(int(1.5*qt.QDialog.sizeHint(self).width()),
qt.QDialog.sizeHint(self).height())
if __name__ == "__main__":
a = qt.QApplication(sys.argv)
qt.QObject.connect(a,qt.SIGNAL("lastWindowClosed()"),a,qt.SLOT("quit()"))
w = StripBackgroundDialog()
def mySlot(ddict):
print(ddict)
qt.QObject.connect(w.parametersWidget, qt.SIGNAL('StripParametersWidgetSignal'), mySlot)
x = numpy.arange(1000.).astype(numpy.float32)
y = 100 + x + 100 * numpy.exp(-0.5*(x-500) * (x-500)/ 30.)
w.setData(x, y)
w.exec_()
#a.exec_()
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