/usr/lib/python2.7/dist-packages/PyMca/PyMcaPlugins/BackgroundStackPlugin.py is in pymca 4.7.1+dfsg-2.
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) 2004-2012 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__ = "V.A. Sole - ESRF Data Analysis"
"""
A Stack plugin is a module that will be automatically added to the PyMca
stack windows in order to perform user defined operations on the data stack.
These plugins will be compatible with any stack window that provides the
functions:
#data related
getStackDataObject
getStackData
getStackInfo
setStack
#images related
addImage
removeImage
replaceImage
#mask related
setSelectionMask
getSelectionMask
#displayed curves
getActiveCurve
getGraphXLimits
getGraphYLimits
#information method
stackUpdated
selectionMaskUpdated
"""
try:
from PyMca import StackPluginBase
from PyMca import SGWindow
from PyMca import SNIPWindow
import PyMca.PyMca_Icons as PyMca_Icons
except ImportError:
print("Plugin importing from somewhere else")
import StackPluginBase
import SGWindow
import SNIPWindow
import PyMca_Icons
import numpy
DEBUG = 0
class BackgroundStackPlugin(StackPluginBase.StackPluginBase):
def __init__(self, stackWindow, **kw):
StackPluginBase.DEBUG = DEBUG
StackPluginBase.StackPluginBase.__init__(self, stackWindow, **kw)
SGtext = "Replace current stack by a\n"
SGtext += "Savitsky-Golay treated one."
SNIP1Dtext = "Replace current stack by a\n"
SNIP1Dtext += "SNIP1D treated one."
SNIP2Dtext = "Replace current stack by a\n"
SNIP2Dtext += "SNIP2D treated one."
self.methodDict = {}
function = self.replaceStackWithSavitzkyGolayFiltering
info = SGtext
icon = PyMca_Icons.substract
self.methodDict["Savitzky-Golay Filtering"] = [function, info, icon]
function = self.subtract1DSnipBackground
info = SNIP1Dtext
self.methodDict["Subtract SNIP 1D Background"] = [function, info, icon]
function = self.replaceWith1DSnipBackground
info = "Smooth and replace current stack\n"
info += "by its SNIP1D background."
self.methodDict["Deglitch with SNIP 1D Background"] = [function,
info,
PyMca_Icons.smooth]
function = self.subtract2DSnipBackground
info = SNIP2Dtext
self.methodDict["Subtract SNIP 2D Background"] = [function, info, icon]
function = self.subtractActiveCurve
info = "Replace current stack by one in which\nthe active curve has been subtracted"
self.methodDict["Subtract active curve"] = [function, info, icon]
self.__methodKeys = ["Savitzky-Golay Filtering",
"Deglitch with SNIP 1D Background",
"Subtract SNIP 1D Background",
"Subtract SNIP 2D Background",
"Subtract active curve"]
def stackUpdated(self):
self.dialogWidget = None
#Methods implemented by the plugin
def getMethods(self):
return self.__methodKeys
def getMethodToolTip(self, name):
return self.methodDict[name][1]
def getMethodPixmap(self, name):
return self.methodDict[name][2]
def applyMethod(self, name):
return self.methodDict[name][0]()
def replaceStackWithSavitzkyGolayFiltering(self):
activeCurve = self.getActiveCurve()
if activeCurve is None:
return
x, spectrum, legend, info = activeCurve
snipWindow = SGWindow.SGDialog(None,
spectrum, x=x)
snipWindow.graph.setGraphXTitle(info['xlabel'])
snipWindow.graph.setGraphYTitle(info['ylabel'])
#snipWindow.setModal(True)
snipWindow.show()
ret = snipWindow.exec_()
if ret:
snipParametersDict = snipWindow.getParameters()
snipWindow.close()
function = snipParametersDict['function']
arguments = snipParametersDict['arguments']
stack = self.getStackDataObject()
function(stack, *arguments)
self.setStack(stack)
def subtract1DSnipBackground(self, smooth=False):
activeCurve = self.getActiveCurve()
if activeCurve is None:
return
x, spectrum, legend, info = activeCurve
snipWindow = SNIPWindow.SNIPDialog(None,
spectrum, x=x, smooth=smooth)
snipWindow.graph.setGraphXTitle(info['xlabel'])
snipWindow.graph.setGraphYTitle(info['ylabel'])
#snipWindow.setModal(True)
snipWindow.show()
ret = snipWindow.exec_()
if ret:
snipParametersDict = snipWindow.getParameters()
snipWindow.close()
function = snipParametersDict['function']
arguments = snipParametersDict['arguments']
stack = self.getStackDataObject()
function(stack, *arguments)
self.setStack(stack)
def replaceWith1DSnipBackground(self):
return self.subtract1DSnipBackground(smooth=True)
def subtract2DSnipBackground(self):
imageList = self.getStackROIImagesAndNames()
if imageList is None:
return
imageList, imageNames = imageList
if not len(imageList):
return
snipWindow = SNIPWindow.SNIPDialog(None,
imageList[0] * 1)
#snipWindow.setModal(True)
snipWindow.show()
ret = snipWindow.exec_()
if ret:
snipParametersDict = snipWindow.getParameters()
snipWindow.close()
function = snipParametersDict['function']
arguments = snipParametersDict['arguments']
stack = self.getStackDataObject()
function(stack, *arguments)
self.setStack(stack)
def subtractActiveCurve(self):
curve = self.getActiveCurve()
if curve is None:
raise ValueError("No active curve")
x, y = curve[0:2]
stack = self.getStackDataObject()
if not isinstance(stack.data, numpy.ndarray):
text = "This method does not work with dynamically loaded stacks"
raise TypeError(text)
mcaIndex = stack.info.get('McaIndex', -1)
if mcaIndex in [-1, 2]:
for i in range(stack.data.shape[-1]):
stack.data[:, :, i] -= y[i]
elif mcaIndex == 0:
for i in range(stack.data.shape[0]):
stack.data[i] -= y[i]
else:
raise ValueError("Invalid 1D index %d" % mcaIndex)
self.setStack(stack)
MENU_TEXT = "Stack Filtering Options"
def getStackPluginInstance(stackWindow, **kw):
ob = BackgroundStackPlugin(stackWindow)
return ob
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