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#/*##########################################################################
# Copyright (C) 2004-2022 European Synchrotron Radiation Facility
#
# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
# the ESRF.
#
# 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"
__contact__ = "sole@esrf.fr"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
import numpy
try:
from PyMca5 import Plugin1DBase
except ImportError:
from . import Plugin1DBase
try:
from PyMca5.PyMcaGui.math.fitting import RateLawWindow
except ImportError:
print("KineticsPlugin problem")
class KineticsPlugin(Plugin1DBase.Plugin1DBase):
'''Calculate Rate Laws plot and Arrhenius plot'''
def __init__(self, plotWindow, **kw):
Plugin1DBase.Plugin1DBase.__init__(self, plotWindow, **kw)
self.methodDict = {}
text = "Graphical calculation of Rate Laws"
function = self.rateLaw
info = text
icon = None
self.methodDict["Rate Law Plots"] =[function,
info,
icon]
text = "Replace current (x, y) plot by (1/x, log(y)) plot"
info = text
icon = None
function = self.arrhenius
method = "Arrhenius Plot"
self.methodDict[method] = [function,
info,
icon]
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, ...
"""
names = list(self.methodDict.keys())
names.sort()
return names
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 rateLaw(self):
#get active curve
activeCurve = self.getActiveCurve()
if activeCurve is None:
raise ValueError("Please select an active curve")
return
x, y, legend0, info = activeCurve[:4]
xmin, xmax = self.getGraphXLimits()
idx = (x >= xmin) & (x <= xmax)
x = x[idx]
y = y[idx]
if self.widget is None:
parent = None
self.widget = RateLawWindow.RateLawWindow(parent)
self.widget.setSpectrum(x, y,
legend=legend0,
xlabel=info["xlabel"],
ylabel=info["ylabel"])
self.widget.show()
self.widget.raise_()
def arrhenius(self):
curves = self.getMonotonicCurves()
nCurves = len(curves)
if nCurves < 1:
raise ValueError("At least one curve needed")
return
# get legend of active curve
try:
activeCurveLegend = self.getActiveCurve()[2]
if activeCurveLegend is None:
activeCurveLegend = curves[0][2]
for curve in curves:
if curve[2] == activeCurveLegend:
activeCurve = curve
break
except:
activeCurve = curves[0]
activeCurveLegend = curves[0][2]
# apply between graph limits
xmin, xmax =self.getGraphXLimits()
toPlot = []
for curve in curves:
x0, y0, legend, info = curve[:4]
idx = numpy.nonzero((x0 >= xmin) & (x0 <= xmax) & (x0 != 0))[0]
x = numpy.take(x0, idx)
y = numpy.take(y0, idx)
idx = numpy.nonzero(y > 0)[0]
x = numpy.take(x, idx)
y = numpy.take(y, idx)
if not x.size:
continue
x = 1.0 / x
y = numpy.log(y)
toPlot.append((x, y, legend, info))
for i in range(len(toPlot)):
if i == 0:
replace=True
else:
replace=False
if i == (len(toPlot) - 1):
replot = True
else:
replot=False
x, y, legend, info = toPlot[i]
self.addCurve(x, y,
legend=legend,
info=info,
ylabel="log(%s)" % info["ylabel"],
xlabel="1/%s" % info["xlabel"],
replot=replot,
replace=replace)
self.setActiveCurve(activeCurveLegend)
MENU_TEXT = "Kinetics Tools"
def getPlugin1DInstance(plotWindow, **kw):
ob = KineticsPlugin(plotWindow)
return ob
if __name__ == "__main__":
import os
from PyMca5.PyMcaGui import PyMcaQt as qt
from PyMca5.PyMcaGui import PlotWindow
# first order, k = 4.820e-04
x = [0, 600, 1200, 1800, 2400, 3000, 3600]
y = [0.0365, 0.0274, 0.0206, 0.0157, 0.0117, 0.00860, 0.00640]
order = "First"
slope = "0.000482"
print("Expected order: First")
print("Expected slope: 0.000482")
sigmay = None
app = qt.QApplication([])
plot = PlotWindow.PlotWindow()
plot.setPluginDirectoryList([os.path.dirname(__file__)])
plot.getPlugins()
plot.addCurve(x, y, "Test Data")
plot.show()
plugin = getPlugin1DInstance(plot)
for method in plugin.getMethods():
print(method, ":", plugin.getMethodToolTip(method))
#plugin.applyMethod(plugin.getMethods()[1])
app.exec()
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