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#/*##########################################################################
#
# The PyMca X-Ray Fluorescence Toolkit
#
# 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. Armando Sole - ESRF"
__contact__ = "sole@esrf.fr"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
import sys
import numpy
from PyMca5.PyMcaGui import PyMcaQt as qt
from PyMca5.PyMcaGui.plotting import PyMca_Icons
IconDict = PyMca_Icons.IconDict
from PyMca5.PyMcaGui.plotting import PlotWindow
from PyMca5.PyMcaMath.fitting import RateLaw
class RateLawWindow(qt.QMainWindow):
def __init__(self, parent=None, backend=None):
super(RateLawWindow, self).__init__(parent)
self.setWindowTitle("RateLaw Window")
if parent is not None:
# behave as a widget
self.setWindowFlags(qt.Qt.Widget)
self.mdiArea = RateLawMdiArea(self, backend=backend)
self.setCentralWidget(self.mdiArea)
# connect
#self.mdiArea.sigRateLawMdiAreaSignal.connect(self._update)
def setSpectrum(self, x, y, **kw):
self.mdiArea.setSpectrum(x, y, **kw)
class RateLawMdiArea(qt.QMdiArea):
sigRateLawMdiAreaSignal = qt.pyqtSignal(object)
def __init__(self, parent=None, backend=None):
super(RateLawMdiArea, self).__init__(parent)
self._windowDict = {}
self._windowList = ["Original", "Zero",
"First", "Second"]
self._windowList.reverse()
for title in self._windowList:
plot = PlotWindow.PlotWindow(self,
position=True,
backend=backend)
plot.setWindowTitle(title)
self.addSubWindow(plot)
self._windowDict[title] = plot
plot.setDataMargins(0, 0, 0.025, 0.025)
self._windowList.reverse()
self.setActivationOrder(qt.QMdiArea.StackingOrder)
self.tileSubWindows()
def setSpectrum(self, x, y, legend=None, sigmay=None,
xlabel=None, ylabel=None):
for key in self._windowDict:
self._windowDict[key].clearCurves()
self._windowDict["Original"].addCurve(x,
y,
legend=legend,
xlabel=xlabel,
ylabel=ylabel,
yerror=sigmay,
symbol="o")
self.update()
def update(self):
plot = self._windowDict["Original"]
activeCurve = plot.getActiveCurve()
if not len(activeCurve):
return
[x, y, legend, info] = activeCurve[:4]
xmin, xmax = plot.getGraphXLimits()
ymin, ymax = plot.getGraphYLimits()
result = RateLaw.rateLaw(x, y, sigmay=None)
labels = ["Zero", "First", "Second"]
for key in labels:
plot = self._windowDict[key]
workingResult = result[key.lower()]
if workingResult is None:
# no fit was performed
plot.clear()
continue
intercept = workingResult["intercept"]
slope = workingResult["slope"]
sigma_intercept = workingResult["sigma_intercept"]
sigma_slope = workingResult["sigma_slope"]
r_value = workingResult["r_value"]
stderr = workingResult["stderr"]
xw = workingResult["x"]
yw = workingResult["y"]
xlabel = info["ylabel"]
ylabel = info["ylabel"]
title = "r = %.5f slope = %.3E +/- %.2E" % (r_value, slope, sigma_slope)
fit_legend = "%.3g * x + %.3g" % (slope, intercept)
if key == "First":
ylabel = "log(%s)" % ylabel
elif key == "Second":
ylabel = "1 / %s" % ylabel
plot.addCurve(xw, yw,
legend="Data",
replace=True, replot=False,
symbol="o",
linestyle=" ",
ylabel=ylabel)
plot.setGraphTitle(title)
plot.addCurve(xw, intercept + slope * xw,
legend=fit_legend,
replace=False,
replot=True,
symbol=None,
color="red",
ylabel=ylabel)
plot.resetZoom()
self.sigRateLawMdiAreaSignal.emit(result)
def main(argv=None):
if argv is None:
argv = sys.argv
if len(argv) < 2:
# 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
# second order, k = 1.3e-02
#x = [0, 900, 1800, 3600, 6000]
#y = [1.72e-2, 1.43e-2, 1.23e-2, 9.52e-3, 7.3e-3]
#order = "second"
#slope = "0.013"
elif len(argv) > 1:
# assume we have got a two column csv file
data = numpy.loadtxt(argv[1])
x = data[:, 0]
y = data[:, 1]
if data.shape[1] > 2:
sigmay = data[:, 2]
else:
sigmay = None
else:
print("RateLaw [csv_file_name]")
return
w = RateLawWindow()
w.show()
w.setSpectrum(x, y, sigmay = sigmay)
return w
if __name__ == "__main__":
app = qt.QApplication([])
w = main()
app.exec()
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