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SarthakJariwalaSarthakJariwala
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added .QUA file type compatibility for analysis
1 parent 3bc7b4e commit bda05b2

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Lines changed: 171 additions & 171 deletions

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‎PythonGUI_apps/PLQE_analysis/plqe_analysis.py‎

Lines changed: 171 additions & 171 deletions
Original file line numberDiff line numberDiff line change
@@ -5,9 +5,7 @@
55
from pyqtgraph import exporters
66
from pyqtgraph.Qt import QtCore, QtGui, QtWidgets
77
import matplotlib.pyplot as plt
8-
import pandas as pd
98
import numpy as np
10-
import time
119

1210
# local modules
1311

@@ -30,183 +28,185 @@
3028
plt.rc('axes', linewidth = 3.5)
3129

3230
class MainWindow(TemplateBaseClass):
33-
34-
def __init__(self):
35-
super(TemplateBaseClass, self).__init__()
36-
37-
# Create the main window
38-
self.ui = WindowTemplate()
39-
self.ui.setupUi(self)
40-
41-
#setup uv vis plot
42-
self.plot = self.ui.plotWidget.getPlotItem()
43-
self.plot.setTitle(title="Wavelength vs. Intensity")
44-
self.plot.setLabel('bottom', 'Wavelength', unit='nm')
45-
self.plot.setLabel('left', 'Intensity', unit='a.u.')
46-
self.plot.setLogMode(x=None, y=1)
47-
48-
#setup line rois for laser and emission
49-
self.laser_region = pg.LinearRegionItem(brush=QtGui.QBrush(QtGui.QColor(255, 0, 0, 50)))
50-
self.laser_region.sigRegionChanged.connect(self.update_laser_spinBoxes)
51-
self.emission_region = pg.LinearRegionItem()
52-
self.emission_region.sigRegionChanged.connect(self.update_emission_spinBoxes)
53-
self.laser_region.setRegion((200, 400))
54-
self.emission_region.setRegion((700, 800))
55-
56-
#setup ui signals
57-
self.ui.load_data_pushButton.clicked.connect(self.open_data_file)
58-
self.ui.plot_pushButton.clicked.connect(self.plot_intensity)
59-
self.ui.clear_pushButton.clicked.connect(self.clear)
60-
self.ui.calculate_plqe_pushButton.clicked.connect(self.calculate_plqe)
61-
self.ui.laser_start_spinBox.valueChanged.connect(self.update_laser_region)
62-
self.ui.laser_stop_spinBox.valueChanged.connect(self.update_laser_region)
63-
self.ui.emission_start_spinBox.valueChanged.connect(self.update_emission_region)
64-
self.ui.emission_stop_spinBox.valueChanged.connect(self.update_emission_region)
65-
66-
self.show()
67-
68-
def open_data_file(self):
69-
""" Open data file """
70-
try:
71-
self.filename = QtWidgets.QFileDialog.getOpenFileName(self)
72-
#self.data = np.loadtxt(self.filename[0], delimiter = '\t', skiprows = 1)
73-
if ".txt" in self.filename[0]:
74-
self.data = np.loadtxt(self.filename[0], delimiter = '\t', skiprows = 1)
75-
elif ".csv" in self.filename[0]:
76-
self.data = np.loadtxt(self.filename[0], delimiter = ',', skiprows = 1)
77-
self.cs_window = ColSelectionWindow(self.data)
78-
self.cs_window.col_selection_signal.connect(self.open_with_col_selection)
79-
self.nm = np.copy(self.data[:,0])
80-
#self.ref_data = np.copy(self.data[:,1])
81-
#self.inpath_data = np.copy(self.data[:,2])
82-
#self.outpath_data = np.copy(self.data[:,3])
83-
except Exception as err:
84-
print(format(err))
85-
86-
def open_with_col_selection(self):
87-
ref_data_col = self.cs_window.ui.ref_spinBox.value() - 1 #subtract since spinboxes refer to column num and not index
88-
inpath_data_col = self.cs_window.ui.inpath_spinBox.value() - 1
89-
outpath_data_col = self.cs_window.ui.outpath_spinBox.value() - 1
90-
self.ref_data = np.copy(self.data[:,ref_data_col])
91-
self.inpath_data = np.copy(self.data[:,inpath_data_col])
92-
self.outpath_data = np.copy(self.data[:,outpath_data_col])
93-
94-
def update_laser_spinBoxes(self):
95-
""" Update laser spinboxes based on line rois """
96-
self.laser_start, self.laser_stop = self.laser_region.getRegion()
97-
self.ui.laser_start_spinBox.setValue(self.laser_start)
98-
self.ui.laser_stop_spinBox.setValue(self.laser_stop)
99-
100-
101-
def update_emission_spinBoxes(self):
102-
""" Update emission spinboxes based on line rois """
103-
self.emission_start, self.emission_stop = self.emission_region.getRegion()
104-
self.ui.emission_start_spinBox.setValue(self.emission_start)
105-
self.ui.emission_stop_spinBox.setValue(self.emission_stop)
106-
107-
def update_laser_region(self):
108-
""" Update laser line rois based on spinboxes """
109-
laser_start = self.ui.laser_start_spinBox.value()
110-
laser_stop = self.ui.laser_stop_spinBox.value()
111-
self.laser_region.setRegion((laser_start, laser_stop))
112-
113-
def update_emission_region(self):
114-
""" Update emission line rois based on spinboxes """
115-
emission_start = self.ui.emission_start_spinBox.value()
116-
emission_stop = self.ui.emission_stop_spinBox.value()
117-
self.emission_region.setRegion((emission_start, emission_stop))
118-
119-
def plot_intensity(self):
120-
try:
121-
self.plot.plot(self.nm, self.inpath_data)
122-
self.plot.addItem(self.laser_region, ignoreBounds=True)
123-
self.plot.addItem(self.emission_region, ignoreBounds=True)
124-
except Exception as err:
125-
print(format(err))
126-
127-
def find_nearest(self,array,value):
128-
idx = (np.abs(array-value)).argmin()
129-
return idx
130-
131-
def calculate_plqe(self):
132-
133-
nm_interp_step = 1
134-
nm_interp_start = np.ceil(self.nm[0] / nm_interp_step) * nm_interp_step
135-
nm_interp_stop = np.floor(self.nm[len(self.nm) - 1] / nm_interp_step) * nm_interp_step
136-
nm_interp = np.arange(nm_interp_start, nm_interp_stop + nm_interp_step, nm_interp_step)
137-
138-
ref_interp = np.interp(nm_interp, self.nm, self.ref_data)
139-
140-
141-
inpath_interp = np.interp(nm_interp, self.nm, self.inpath_data)
142-
outpath_interp = np.interp(nm_interp, self.nm, self.outpath_data)
143-
144-
145-
"""L_x is area under laser profile for experiment x"""
146-
"""P_x_ is area under emission profile for experiment x"""
147-
148-
149-
#plt.semilogy(nm, a1_outpath_data[:,1])
150-
151-
emission_start_idx = self.find_nearest(nm_interp, self.emission_start)
152-
emission_stop_idx = self.find_nearest(nm_interp, self.emission_stop)
153-
154-
laser_start_idx = self.find_nearest(nm_interp, self.laser_start)
155-
laser_stop_idx = self.find_nearest(nm_interp, self.laser_stop)
156-
157-
la = np.trapz(ref_interp[laser_start_idx: laser_stop_idx], x = nm_interp[laser_start_idx:laser_stop_idx])
158-
lb = np.trapz(outpath_interp[laser_start_idx: laser_stop_idx], x = nm_interp[laser_start_idx:laser_stop_idx])
159-
lc = np.trapz(inpath_interp[laser_start_idx: laser_stop_idx], x = nm_interp[laser_start_idx:laser_stop_idx])
160-
161-
pa = np.trapz(ref_interp[emission_start_idx:emission_stop_idx], x = nm_interp[emission_start_idx:emission_stop_idx])
162-
pb = np.trapz(outpath_interp[emission_start_idx:emission_stop_idx], x = nm_interp[emission_start_idx:emission_stop_idx])
163-
pc = np.trapz(inpath_interp[emission_start_idx:emission_stop_idx], x = nm_interp[emission_start_idx:emission_stop_idx])
164-
165-
absorb = 1.0 - (lc / lb)
166-
167-
plqe = 100 * (pc - ((1.0 - absorb) * pb)) / (la * absorb)
168-
#print('PLQE Percent = %.3f' %(plqe))
169-
#return plqe
170-
self.ui.plqe_label.setText("%.3f" %(plqe))
171-
172-
def clear(self):
173-
self.plot.clear()
31+
32+
def __init__(self):
33+
super(TemplateBaseClass, self).__init__()
34+
35+
# Create the main window
36+
self.ui = WindowTemplate()
37+
self.ui.setupUi(self)
38+
39+
#setup uv vis plot
40+
self.plot = self.ui.plotWidget.getPlotItem()
41+
self.plot.setTitle(title="Wavelength vs. Intensity")
42+
self.plot.setLabel('bottom', 'Wavelength', unit='nm')
43+
self.plot.setLabel('left', 'Intensity', unit='a.u.')
44+
self.plot.setLogMode(x=None, y=1)
45+
46+
#setup line rois for laser and emission
47+
self.laser_region = pg.LinearRegionItem(brush=QtGui.QBrush(QtGui.QColor(255, 0, 0, 50)))
48+
self.laser_region.sigRegionChanged.connect(self.update_laser_spinBoxes)
49+
self.emission_region = pg.LinearRegionItem()
50+
self.emission_region.sigRegionChanged.connect(self.update_emission_spinBoxes)
51+
self.laser_region.setRegion((200, 400))
52+
self.emission_region.setRegion((700, 800))
53+
54+
#setup ui signals
55+
self.ui.load_data_pushButton.clicked.connect(self.open_data_file)
56+
self.ui.plot_pushButton.clicked.connect(self.plot_intensity)
57+
self.ui.clear_pushButton.clicked.connect(self.clear)
58+
self.ui.calculate_plqe_pushButton.clicked.connect(self.calculate_plqe)
59+
self.ui.laser_start_spinBox.valueChanged.connect(self.update_laser_region)
60+
self.ui.laser_stop_spinBox.valueChanged.connect(self.update_laser_region)
61+
self.ui.emission_start_spinBox.valueChanged.connect(self.update_emission_region)
62+
self.ui.emission_stop_spinBox.valueChanged.connect(self.update_emission_region)
63+
64+
self.show()
65+
66+
def open_data_file(self):
67+
""" Open data file """
68+
try:
69+
self.filename = QtWidgets.QFileDialog.getOpenFileName(self)
70+
#self.data = np.loadtxt(self.filename[0], delimiter = '\t', skiprows = 1)
71+
if ".txt" in self.filename[0]:
72+
self.data = np.loadtxt(self.filename[0], delimiter = '\t', skiprows = 1, usecols = (0,1,2,3))
73+
elif ".csv" in self.filename[0]:
74+
self.data = np.loadtxt(self.filename[0], delimiter = ',', skiprows = 1)
75+
elif ".qua" in self.filename[0]:
76+
self.data = np.genfromtxt(self.filename[0], delimiter = '\t', skip_header = 12, usecols = (0,1,2,3))
77+
self.cs_window = ColSelectionWindow(self.data)
78+
self.cs_window.col_selection_signal.connect(self.open_with_col_selection)
79+
self.nm = np.copy(self.data[:,0])
80+
#self.ref_data = np.copy(self.data[:,1])
81+
#self.inpath_data = np.copy(self.data[:,2])
82+
#self.outpath_data = np.copy(self.data[:,3])
83+
except Exception as err:
84+
print(format(err))
85+
86+
def open_with_col_selection(self):
87+
ref_data_col = self.cs_window.ui.ref_spinBox.value() - 1 #subtract since spinboxes refer to column num and not index
88+
inpath_data_col = self.cs_window.ui.inpath_spinBox.value() - 1
89+
outpath_data_col = self.cs_window.ui.outpath_spinBox.value() - 1
90+
self.ref_data = np.copy(self.data[:,ref_data_col])
91+
self.inpath_data = np.copy(self.data[:,inpath_data_col])
92+
self.outpath_data = np.copy(self.data[:,outpath_data_col])
93+
94+
def update_laser_spinBoxes(self):
95+
""" Update laser spinboxes based on line rois """
96+
self.laser_start, self.laser_stop = self.laser_region.getRegion()
97+
self.ui.laser_start_spinBox.setValue(self.laser_start)
98+
self.ui.laser_stop_spinBox.setValue(self.laser_stop)
99+
100+
101+
def update_emission_spinBoxes(self):
102+
""" Update emission spinboxes based on line rois """
103+
self.emission_start, self.emission_stop = self.emission_region.getRegion()
104+
self.ui.emission_start_spinBox.setValue(self.emission_start)
105+
self.ui.emission_stop_spinBox.setValue(self.emission_stop)
106+
107+
def update_laser_region(self):
108+
""" Update laser line rois based on spinboxes """
109+
laser_start = self.ui.laser_start_spinBox.value()
110+
laser_stop = self.ui.laser_stop_spinBox.value()
111+
self.laser_region.setRegion((laser_start, laser_stop))
112+
113+
def update_emission_region(self):
114+
""" Update emission line rois based on spinboxes """
115+
emission_start = self.ui.emission_start_spinBox.value()
116+
emission_stop = self.ui.emission_stop_spinBox.value()
117+
self.emission_region.setRegion((emission_start, emission_stop))
118+
119+
def plot_intensity(self):
120+
try:
121+
self.plot.plot(self.nm, self.inpath_data)
122+
self.plot.addItem(self.laser_region, ignoreBounds=True)
123+
self.plot.addItem(self.emission_region, ignoreBounds=True)
124+
except Exception as err:
125+
print(format(err))
126+
127+
def find_nearest(self,array,value):
128+
idx = (np.abs(array-value)).argmin()
129+
return idx
130+
131+
def calculate_plqe(self):
132+
133+
nm_interp_step = 1
134+
nm_interp_start = np.ceil(self.nm[0] / nm_interp_step) * nm_interp_step
135+
nm_interp_stop = np.floor(self.nm[len(self.nm) - 1] / nm_interp_step) * nm_interp_step
136+
nm_interp = np.arange(nm_interp_start, nm_interp_stop + nm_interp_step, nm_interp_step)
137+
138+
ref_interp = np.interp(nm_interp, self.nm, self.ref_data)
139+
140+
141+
inpath_interp = np.interp(nm_interp, self.nm, self.inpath_data)
142+
outpath_interp = np.interp(nm_interp, self.nm, self.outpath_data)
143+
144+
145+
"""L_x is area under laser profile for experiment x"""
146+
"""P_x_ is area under emission profile for experiment x"""
147+
148+
149+
#plt.semilogy(nm, a1_outpath_data[:,1])
150+
151+
emission_start_idx = self.find_nearest(nm_interp, self.emission_start)
152+
emission_stop_idx = self.find_nearest(nm_interp, self.emission_stop)
153+
154+
laser_start_idx = self.find_nearest(nm_interp, self.laser_start)
155+
laser_stop_idx = self.find_nearest(nm_interp, self.laser_stop)
156+
157+
la = np.trapz(ref_interp[laser_start_idx: laser_stop_idx], x = nm_interp[laser_start_idx:laser_stop_idx])
158+
lb = np.trapz(outpath_interp[laser_start_idx: laser_stop_idx], x = nm_interp[laser_start_idx:laser_stop_idx])
159+
lc = np.trapz(inpath_interp[laser_start_idx: laser_stop_idx], x = nm_interp[laser_start_idx:laser_stop_idx])
160+
161+
pa = np.trapz(ref_interp[emission_start_idx:emission_stop_idx], x = nm_interp[emission_start_idx:emission_stop_idx])
162+
pb = np.trapz(outpath_interp[emission_start_idx:emission_stop_idx], x = nm_interp[emission_start_idx:emission_stop_idx])
163+
pc = np.trapz(inpath_interp[emission_start_idx:emission_stop_idx], x = nm_interp[emission_start_idx:emission_stop_idx])
164+
165+
absorb = 1.0 - (lc / lb)
166+
167+
plqe = 100 * (pc - ((1.0 - absorb) * pb)) / (la * absorb)
168+
#print('PLQE Percent = %.3f' %(plqe))
169+
#return plqe
170+
self.ui.plqe_label.setText("%.3f" %(plqe))
171+
172+
def clear(self):
173+
self.plot.clear()
174174

175175
"""Table view GUI"""
176176
ui_file_path = (base_path / "column_selection_gui.ui").resolve()
177177
col_selection_WindowTemplate, col_selection_TemplateBaseClass = pg.Qt.loadUiType(ui_file_path)
178178

179179
class ColSelectionWindow(col_selection_TemplateBaseClass):
180-
181-
col_selection_signal = QtCore.pyqtSignal() #signal to help with pass info back to MainWindow
182-
183-
def __init__(self, data):
184-
col_selection_TemplateBaseClass.__init__(self)
185-
# Create the param window
186-
self.ui = col_selection_WindowTemplate()
187-
self.ui.setupUi(self)
188-
self.ui.done_pushButton.clicked.connect(self.done)
189-
190-
self.table_widget = pg.TableWidget()
191-
self.ui.data_preview_groupBox.layout().addWidget(self.table_widget)
192-
193-
self.table_widget.setData(data)
194-
195-
#self.setWindowFlag(QtCore.Qt.WindowCloseButtonHint, False)
196-
self.show()
197-
198-
def done(self):
199-
self.col_selection_signal.emit()
200-
self.ui.textBrowser.setText("Data successfully loaded.")
201-
#self.close()
202-
203-
def closeEvent(self, event):
204-
self.col_selection_signal.emit()
180+
181+
col_selection_signal = QtCore.pyqtSignal() #signal to help with pass info back to MainWindow
182+
183+
def __init__(self, data):
184+
col_selection_TemplateBaseClass.__init__(self)
185+
# Create the param window
186+
self.ui = col_selection_WindowTemplate()
187+
self.ui.setupUi(self)
188+
self.ui.done_pushButton.clicked.connect(self.done)
189+
190+
self.table_widget = pg.TableWidget()
191+
self.ui.data_preview_groupBox.layout().addWidget(self.table_widget)
192+
193+
self.table_widget.setData(data)
194+
195+
#self.setWindowFlag(QtCore.Qt.WindowCloseButtonHint, False)
196+
self.show()
197+
198+
def done(self):
199+
self.col_selection_signal.emit()
200+
self.ui.textBrowser.setText("Data successfully loaded.")
201+
#self.close()
202+
203+
def closeEvent(self, event):
204+
self.col_selection_signal.emit()
205205

206206
"""Run the Main Window"""
207207
def run():
208-
win = MainWindow()
209-
QtGui.QApplication.instance().exec_()
210-
return win
208+
win = MainWindow()
209+
QtGui.QApplication.instance().exec_()
210+
return win
211211

212212
#run()

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