1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
|
#/*##########################################################################
# Copyright (C) 2004-2019 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.
#
#############################################################################*/
"""
This plugin provides 3 methods:
- subtract a SNIP1D background from the active curve
- apply a Savitsky-Golay filter on the active curve
- smooth and replace current curve by its SNIP1D background (deglitch)
"""
__author__ = "V.A. Sole - ESRF Data Analysis"
__contact__ = "sole@esrf.fr"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
import numpy
from PyMca5 import Plugin1DBase
from PyMca5.PyMcaGui import SGWindow
from PyMca5.PyMcaGui import SNIPWindow
from PyMca5.PyMcaGui import PyMca_Icons
class BackgroundScanPlugin(Plugin1DBase.Plugin1DBase):
def __init__(self, plotWindow, **kw):
Plugin1DBase.Plugin1DBase.__init__(self, plotWindow, **kw)
SGtext = "Replace active curve by a\n"
SGtext += "Savitsky-Golay treated one."
SNIP1Dtext = "Replace active curve by a\n"
SNIP1Dtext += "SNIP1D treated one."
self.methodDict = {}
function = self.replaceActiveCurveWithSavitzkyGolayFiltering
info = SGtext
icon = PyMca_Icons.substract
self.methodDict["Savitzky-Golay Filtering"] =[function,
info,
icon]
function = self.subtract1DSnipBackgroundFromActiveCurve
info = SNIP1Dtext
self.methodDict["Subtract SNIP 1D Background"] =[function,
info,
icon]
function = self.deglitchActiveCurveWith1DSnipBackground
info = "Smooth and replace current curve\n"
info += "by its SNIP1D background."
self.methodDict["Deglitch with SNIP 1D Background"] =[function,
info,
PyMca_Icons.smooth]
self.__methodKeys = ["Subtract SNIP 1D Background",
"Savitzky-Golay Filtering",
"Deglitch with SNIP 1D Background"]
self.subtract1DSnipParameters = None
self.deglitch1DSnipParameters = 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, ...
"""
if 0:
names = self.methodDict.keys()
names.sort()
return names
else:
return self.__methodKeys
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 replaceActiveCurveWithSavitzkyGolayFiltering(self):
activeCurve = self.getActiveCurve()
if activeCurve is None:
return
x, spectrum, legend, info = activeCurve[:4]
snipWindow = SGWindow.SGDialog(None,
spectrum, x=x)
snipWindow.graph.setGraphXLabel(info['xlabel'])
snipWindow.graph.setGraphYLabel(info['ylabel'])
#snipWindow.setModal(True)
snipWindow.show()
ret = snipWindow.exec()
if ret:
ydata = snipWindow.parametersWidget.background
xdata = snipWindow.parametersWidget.xValues
operations = info.get("operations", [])
operations.append("SG Filtered")
info['operations'] = operations
self.addCurve(xdata, ydata, legend=legend, info=info, replot=True)
def subtract1DSnipBackgroundFromActiveCurve(self, smooth=False):
activeCurve = self.getActiveCurve()
if activeCurve is None:
return
x, spectrum, legend, info = activeCurve[:4]
snipWindow = SNIPWindow.SNIPDialog(None,
spectrum, x=x, smooth=False)
if self.subtract1DSnipParameters is not None:
snipWindow.setParameters(self.subtract1DSnipParameters)
snipWindow.graph.setGraphXLabel(info['xlabel'])
snipWindow.graph.setGraphYLabel(info['ylabel'])
snipWindow.show()
ret = snipWindow.exec()
if ret:
ydata = snipWindow.parametersWidget.spectrum -\
snipWindow.parametersWidget.background
xdata = snipWindow.parametersWidget.xValues
operations = info.get("operations", [])
operations.append("SNIP Background Removal")
info['operations'] = operations
# we cannot aford to change the name of the curve in order to properly
# handle the calibration in an MCA window
if "McaCalib" not in info:
self.removeCurve(legend, replot=False)
legend = legend + " Net"
self.addCurve(xdata, ydata, legend=legend, info=info, replot=True)
self.subtract1DSnipParameters = snipWindow.getParameters()
def deglitchActiveCurveWith1DSnipBackground(self):
activeCurve = self.getActiveCurve()
if activeCurve is None:
return
x, spectrum, legend, info = activeCurve[:4]
snipWindow = SNIPWindow.SNIPDialog(None,
spectrum, x=x, smooth=True)
if self.deglitch1DSnipParameters is not None:
snipWindow.setParameters(self.deglitch1DSnipParameters)
snipWindow.graph.setGraphXLabel(info['xlabel'])
snipWindow.graph.setGraphYLabel(info['ylabel'])
snipWindow.show()
ret = snipWindow.exec()
if ret:
ydata = snipWindow.parametersWidget.background
xdata = snipWindow.parametersWidget.xValues
operations = info.get("operations", [])
operations.append("SNIP Deglith")
info['operations'] = operations
self.addCurve(xdata, ydata, legend=legend, info=info, replot=True)
self.deglitch1DSnipParameters = snipWindow.getParameters()
MENU_TEXT = "Background subtraction tools"
def getPlugin1DInstance(plotWindow, **kw):
ob = BackgroundScanPlugin(plotWindow)
return ob
if __name__ == "__main__":
from PyMca5.PyMcaGui import PyMcaQt as qt
app = qt.QApplication([])
from PyMca5.PyMcaGraph import Plot
x = numpy.arange(100.)
y = x * x
plot = Plot.Plot()
plot.addCurve(x, y, "dummy")
plot.addCurve(x+100, -x*x)
plugin = getPlugin1DInstance(plot)
for method in plugin.getMethods():
print(method, ":", plugin.getMethodToolTip(method))
plugin.applyMethod(plugin.getMethods()[0])
curves = plugin.getAllCurves()
for curve in curves:
print(curve[2])
print("LIMITS = ", plugin.getGraphYLimits())
#app = qt.QApplication()
|
