#/*##########################################################################
# Copyright (C) 2004-2014 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.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# 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:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# 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
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
#############################################################################*/
__author__ = "V.A. Sole - ESRF Data Analysis"
__contact__ = "sole@esrf.fr"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
"""
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
"""
import numpy
from PyMca5 import StackPluginBase
DEBUG = 0
[docs]class StackNormalizationPlugin(StackPluginBase.StackPluginBase):
def __init__(self, stackWindow, **kw):
StackPluginBase.DEBUG = DEBUG
StackPluginBase.StackPluginBase.__init__(self, stackWindow, **kw)
self.methodDict = {}
text = "Stack/I0 where I0 is the active curve\n"
function = self.divideByCurve
info = text
icon = None
self.methodDict["I/I0 Normalization"] =[function,
info,
icon]
text = "-log(Stack/I0) Normalization where I0 is the active curve\n"
function = self.logNormalizeByCurve
info = text
icon = None
self.methodDict["-log(I/I0) Normalization"] =[function,
info,
icon]
self.__methodKeys = ["I/I0 Normalization",
"-log(I/I0) Normalization"]
#Methods implemented by the plugin
[docs] def getMethods(self):
return self.__methodKeys
[docs] def getMethodPixmap(self, name):
return self.methodDict[name][2]
[docs] def applyMethod(self, name):
return self.methodDict[name][0]()
[docs] def divideByCurve(self):
stack = self.getStackDataObject()
if not isinstance(stack.data, numpy.ndarray):
text = "This method does not work with dynamically loaded stacks"
raise TypeError(text)
curve = self.getActiveCurve()
if curve is None:
text = "Please make sure to have an active curve"
raise TypeError(text)
x, y, legend, info = self.getActiveCurve()
yWork = y[y!=0].astype(numpy.float)
mcaIndex = stack.info.get('McaIndex', -1)
if mcaIndex in [-1, 2]:
for i, value in enumerate(yWork):
stack.data[:, :, i] = stack.data[:,:,i]/value
elif mcaIndex == 0:
for i, value in enumerate(yWork):
stack.data[i, :, :] = stack.data[i,:,:]/value
elif mcaIndex == 1:
for i, value in enumerate(yWork):
stack.data[:, i, :] = stack.data[:,i,:]/value
else:
raise ValueError("Invalid 1D index %d" % mcaIndex)
self.setStack(stack)
[docs] def logNormalizeByCurve(self):
stack = self.getStackDataObject()
if not isinstance(stack.data, numpy.ndarray):
text = "This method does not work with dynamically loaded stacks"
raise TypeError(text)
curve = self.getActiveCurve()
if curve is None:
text = "Please make sure to have an active curve"
raise TypeError(text)
x, y, legend, info = self.getActiveCurve()
yWork = y[y>0]
mcaIndex = stack.info.get('McaIndex', -1)
if mcaIndex in [-1, 2]:
for i, value in enumerate(yWork):
stack.data[:, :, i] = -numpy.log(stack.data[:,:,i]/value)
elif mcaIndex == 0:
for i, value in enumerate(yWork):
stack.data[i, :, :] = -numpy.log(stack.data[i,:,:]/value)
elif mcaIndex == 1:
for i, value in enumerate(yWork):
stack.data[:, i, :] = -numpy.log(stack.data[:,i,:]/value)
else:
raise ValueError("Invalid 1D index %d" % mcaIndex)
self.setStack(stack)
MENU_TEXT = "Stack Normalization"
[docs]def getStackPluginInstance(stackWindow, **kw):
ob = StackNormalizationPlugin(stackWindow)
return ob