/usr/share/pyshared/PyMca/SNIPWindow.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) 2004-2011 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.
#############################################################################*/
__author__ = "V.A. Sole - ESRF Data Analysis"
import PyMcaQt as qt
from PyMca_Icons import IconDict
import MaskImageWidget
#RGBCorrelatorGraph
import ScanWindow
import sys
import SNIPModule
OBJECT3D = False
try:
from Object3D import Object3DScene
OBJECT3D = True
except:
OBJECT3D = False
class HorizontalSpacer(qt.QWidget):
def __init__(self, *args):
qt.QWidget.__init__(self, *args)
self.setSizePolicy(qt.QSizePolicy(qt.QSizePolicy.Expanding,
qt.QSizePolicy.Fixed))
class SNIP1DParametersWidget(qt.QWidget):
def __init__(self, parent = None, length=2000, smooth=False):
qt.QWidget.__init__(self, parent)
self.mainLayout = qt.QGridLayout(self)
self.mainLayout.setMargin(0)
self.mainLayout.setSpacing(2)
i = 0
self.parametersDict = {'roi_min':0,
'roi_max':length,
'width':min(30, length/10),
'smoothing':1}
textLabels = ["SNIP background width (2 to 3 times fwhm) :",
"Minimum channel considered:",
"Maximum channel considered:",
"Preliminar smoothing level:"]
if smooth:
textLabels[0] = "SNIP width :"
self.parametersDict['width'] = 3
for text in textLabels:
label = qt.QLabel(self)
label.setText(text)
self.mainLayout.addWidget(label, i, 0)
#self.mainLayout.addWidget(HorizontalSpacer(self), i, 1)
i +=1
i = 0
self.widgetDict = {}
for key in ['width', 'roi_min', 'roi_max', 'smoothing']:
self.widgetDict[key] = qt.QSpinBox(self)
self.widgetDict[key].setMinimum(0)
self.widgetDict[key].setMaximum(self.parametersDict['roi_max'])
self.widgetDict[key].setValue(self.parametersDict[key])
self.connect(self.widgetDict[key],
qt.SIGNAL("valueChanged(int)"),
self._updateParameters)
self.mainLayout.addWidget(self.widgetDict[key], i, 1)
i += 1
self.widgetDict['smoothing'].setMaximum(100)
def _updateParameters(self, val):
for key in ['width', 'roi_min', 'roi_max', 'smoothing']:
self.parametersDict[key] = self.widgetDict[key].value()
ddict = {}
ddict['event']='SNIPParametersChanged'
ddict.update(self.parametersDict)
self.emit(qt.SIGNAL('SNIPParametersSignal'), ddict)
def getParameters(self):
return self.parametersDict
def setParameters(self, ddict=None):
if ddict is None:
return
actualKeys = self.widgetDict.keys()
for key in ddict.keys():
if key in actualKeys:
w = self.widgetDict[key]
#w.setMaximum(max(ddict[key], w.value()))
#w.setMinimum(min(ddict[key], w.value()))
w.setValue(ddict[key])
self._updateParameters("dummy")
class SNIP2DParametersWidget(qt.QWidget):
def __init__(self, parent = None, shape=(4000,4000)):
qt.QWidget.__init__(self, parent)
self.mainLayout = qt.QGridLayout(self)
self.mainLayout.setMargin(0)
self.mainLayout.setSpacing(2)
i = 0
self.parametersDict = {'roi_min':[0,0],
'roi_max':[shape[0], shape[1]],
'width':min(30, int(min(shape)/10)),
'smoothing':1}
for text in ["SNIP background width (2 to 3 times fwhm) :",
"Minimum ROI channels considered:",
"Maximum ROI channels considered:",
"Pleliminar smoothing level:"]:
label = qt.QLabel(self)
label.setText(text)
self.mainLayout.addWidget(label, i, 0)
#self.mainLayout.addWidget(HorizontalSpacer(self), i, 1)
i +=1
i = 0
self.widgetDict = {}
for key in ['width', 'roi_min', 'roi_max', 'smoothing']:
if key in ['width', 'smoothing']:
spinBox = qt.QSpinBox(self)
spinBox.setMinimum(0)
spinBox.setMaximum(min(self.parametersDict['roi_max']))
spinBox.setValue(self.parametersDict[key])
self.connect(spinBox,
qt.SIGNAL("valueChanged(int)"),
self._updateParameters)
self.mainLayout.addWidget(spinBox, i, 2)
self.widgetDict[key] = spinBox
elif 1:
lineEdit = qt.QLineEdit(self)
validator = qt.QIntValidator(lineEdit)
lineEdit.setValidator(validator)
lineEdit._validator = validator
lineEdit.setText("%d" % self.parametersDict[key][0])
self.connect(lineEdit,
qt.SIGNAL("editingFinished()"),
self._updateParameters)
self.mainLayout.addWidget(lineEdit, i, 1)
self.widgetDict[key] = [lineEdit]
lineEdit = qt.QLineEdit(self)
validator = qt.QIntValidator(lineEdit)
lineEdit.setValidator(validator)
lineEdit._validator = validator
lineEdit.setText("%d" % self.parametersDict[key][1])
self.connect(lineEdit,
qt.SIGNAL("editingFinished()"),
self._updateParameters)
self.mainLayout.addWidget(lineEdit, i, 2)
self.widgetDict[key].append(lineEdit)
else:
spinBox = qt.QSpinBox(self)
spinBox.setMinimum(0)
spinBox.setMaximum(self.parametersDict['roi_max'][0])
spinBox.setValue(self.parametersDict[key][0])
self.connect(spinBox,
qt.SIGNAL("valueChanged(int)"),
self._updateParameters)
self.mainLayout.addWidget(spinBox, i, 1)
self.widgetDict[key] = [spinBox]
spinBox = qt.QSpinBox(self)
spinBox.setMinimum(0)
spinBox.setMaximum(self.parametersDict['roi_max'][1])
spinBox.setValue(self.parametersDict[key][1])
self.connect(spinBox,
qt.SIGNAL("valueChanged(int)"),
self._updateParameters)
self.mainLayout.addWidget(spinBox, i, 2)
self.widgetDict[key].append(spinBox)
i += 1
self.widgetDict['smoothing'].setMaximum(100)
def _updateParameters(self, val=None):
for key in ['width', 'smoothing']:
self.parametersDict[key] = self.widgetDict[key].value()
for key in ['roi_min', 'roi_max']:
self.parametersDict[key] = [int(self.widgetDict[key][0].text()),
int(self.widgetDict[key][1].text())]
ddict = {}
ddict['event']='SNIPParametersChanged'
ddict.update(self.parametersDict)
self.emit(qt.SIGNAL('SNIPParametersSignal'), ddict)
def getParameters(self):
return self.parametersDict
def setParameters(self):
raise NotImplemented("Set parameters not implemented for SNIP 2D")
class SNIPWindow(qt.QWidget):
def __init__(self, parent, data, image=None, x=None, smooth=False):
qt.QWidget.__init__(self, parent)
self.setWindowTitle("SNIP Configuration Window")
self.mainLayout = qt.QVBoxLayout(self)
self.mainLayout.setMargin(0)
self.mainLayout.setSpacing(2)
if image is None:
image = False
if data.shape == 2:
if 1 not in data.shape:
image = True
else:
spectrum = data.ravel()
else:
spectrum = data
elif not image:
spectrum = data
self.__smooth = smooth
self.__image = image
if self.__image:
self.spectrum = None
else:
if x is None:
self.xValues = range(len(spectrum))
else:
self.xValues = x
if self.__image:
self.image = data
self.graphWidget = MaskImageWidget.MaskImageWidget(self,
colormap=True,
selection=False,
imageicons=False,
standalonesave=True)
self.parametersWidget = SNIP2DParametersWidget(self, shape=self.image.shape)
self.graph = self.graphWidget.graphWidget.graph
self.graphWidget.setImageData(data)
self.mainLayout.addWidget(self.parametersWidget)
self.mainLayout.addWidget(self.graphWidget)
self.o3dScene = None
else:
self.image = None
self.spectrum = spectrum
self.parametersWidget = SNIP1DParametersWidget(self,
length=len(spectrum),
smooth=smooth)
self.graph = ScanWindow.ScanWindow(self)
self.graph.newCurve(self.xValues,
spectrum, "Spectrum", replace=True)
self.mainLayout.addWidget(self.parametersWidget)
self.mainLayout.addWidget(self.graph)
self.xMarkers = []
self.yMarkers = []
self.getParameters = self.parametersWidget.getParameters
self.setParameters = self.parametersWidget.setParameters
self.connect(self.parametersWidget,
qt.SIGNAL('SNIPParametersSignal'),
self.updateGraph)
self.updateGraph(self.getParameters())
def updateGraph(self, ddict):
width = ddict['width']
roi_min = ddict['roi_min']
roi_max = ddict['roi_max']
smoothing = ddict['smoothing']
if self.__image:
if self.xMarkers == []:
xMin, xMax = self.graph.getX1AxisLimits()
yMin, yMax = self.graph.getY1AxisLimits()
xMean = 0.5 * (xMin + xMax)
yMean = 0.5 * (yMin + yMax)
self.xMarkers.append(self.graph.insertX1Marker(roi_min[1], yMean, label='C Min'))
self.xMarkers.append(self.graph.insertX1Marker(roi_max[1], yMean, label='C Max'))
self.yMarkers.append(self.graph.insertY1Marker(xMean, roi_min[0], label='R Min'))
self.yMarkers.append(self.graph.insertY1Marker(xMean, roi_max[0], label='R Max'))
else:
self.graph.markersdict[self.xMarkers[0]]['marker'].setXValue(roi_min[1])
self.graph.markersdict[self.xMarkers[1]]['marker'].setXValue(roi_max[1])
self.graph.markersdict[self.yMarkers[0]]['marker'].setYValue(roi_min[0])
self.graph.markersdict[self.yMarkers[1]]['marker'].setYValue(roi_max[0])
self.background = SNIPModule.getImageBackground(self.image, width,
roi_min=roi_min,
roi_max=roi_max,
smoothing=smoothing)
difference = self.image-self.background
self.graphWidget.setImageData(difference)
if OBJECT3D:
if self.o3dScene is None:
self.o3dScene = Object3DScene.Object3DScene()
self.o3dScene.show()
if 0:
imageData =(self.image * 1).astype(numpy.float32)
backgroundData = (self.background * 1).astype(numpy.float32)
self.o3dScene.mesh(imageData, z=imageData * 1, legend='Data', update_scene=True)
self.o3dScene.mesh(backgroundData, z=backgroundData , legend='Background', update_scene=True)
else:
self.o3dScene.mesh(difference, z=difference, legend='Data-Background')
self.o3dScene.show()
else:
self.background = SNIPModule.getSpectrumBackground(self.spectrum, width,
roi_min=roi_min,
roi_max=roi_max,
smoothing=smoothing)
if self.__smooth:
legend0 = "Smoothed Spectrum"
else:
legend0 = "Background"
self.graph.newCurve(self.xValues,
self.background, legend0, replace=False)
#Force information update
legend = self.graph.getActiveCurve(just_legend=True)
if legend.startswith(legend0[0:5]):
self.graph.setActiveCurve(legend)
class SNIPDialog(qt.QDialog):
def __init__(self, parent, data, x=None, smooth=False):
qt.QDialog.__init__(self, parent)
self.setWindowTitle("SNIP Configuration Dialog")
self.mainLayout = qt.QVBoxLayout(self)
self.mainLayout.setMargin(10)
self.mainLayout.setSpacing(2)
self.__image = False
self.__smooth = smooth
if len(data.shape) == 2:
if 1 not in data.shape:
image = data
self.__image = True
else:
spectrum = data.ravel()
else:
spectrum = data
if self.__image:
self.parametersWidget = SNIPWindow(self, image, image=True, x=x)
else:
self.parametersWidget = SNIPWindow(self, spectrum, image=False,
x=x, smooth=smooth)
self.graph = self.parametersWidget.graph
self.mainLayout.addWidget(self.parametersWidget)
hbox = qt.QWidget(self)
hboxLayout = qt.QHBoxLayout(hbox)
hboxLayout.setMargin(0)
hboxLayout.setSpacing(0)
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(self.okButton)
hboxLayout.addWidget(HorizontalSpacer(hbox))
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 getParameters(self):
parametersDict = self.parametersWidget.getParameters()
if self.__image:
parametersDict['function'] = SNIPModule.subtractSnip2DBackgroundFromStack
elif self.__smooth:
parametersDict['function'] = SNIPModule.replaceStackWithSnip1DBackground
else:
parametersDict['function'] = SNIPModule.subtractSnip1DBackgroundFromStack
parametersDict['arguments'] = [parametersDict['width'],
parametersDict['roi_min'],
parametersDict['roi_max'],
parametersDict['smoothing']]
return parametersDict
def setParameters(self, ddict0):
if 'arguments' in ddict0:
ddict = {}
ddict['width'] = ddict0['arguments'][0]
ddict['roi_min'] = ddict0['arguments'][1]
ddict['roi_max'] = ddict0['arguments'][2]
ddict['smoothing'] = ddict0['arguments'][3]
self.parametersWidget.setParameters(ddict)
else:
self.parametersWidget.setParameters(ddict0)
if __name__ == "__main__":
import numpy
app = qt.QApplication([])
if 0:
noise = numpy.random.randn(1000.)
y=numpy.arange(1000.)
w = SNIPDialog(None, y+numpy.sqrt(y)* noise)
elif len(sys.argv) > 1:
import EdfFile
edf = EdfFile.EdfFile(sys.argv[1])
data = edf.GetData(0)
w = SNIPDialog(None, data)
else:
x, y = numpy.ogrid[0:200:200j, 0:200:200j]
data = 50 * numpy.exp(-(x-64)*(x-64)/20.) +\
50 * numpy.exp(-(y-128)*(y-128)/20.) +\
100 * numpy.exp(-(1./20) * ((x-64)*(x-64) + (y-128)*(y-128)))
w = SNIPDialog(None, data)
w.show()
ret=w.exec_()
if ret:
print(w.getParameters())
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