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Add BrickMic burst analysis
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tpeulen committed Feb 17, 2025
1 parent c11399a commit 692b4c1
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Showing 7 changed files with 878 additions and 610 deletions.
87 changes: 69 additions & 18 deletions chisurf/gui/widgets/wizard/tttr_burst_finder.py
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Original file line number Diff line number Diff line change
Expand Up @@ -168,6 +168,7 @@ def create_bur_summary(start_stop, filename, tttr, windows, detectors):


class CommaSeparatedIntegersValidator(QValidator):

def validate(self, input_str, pos):
# Allow empty input
if not input_str:
Expand Down Expand Up @@ -742,9 +743,27 @@ def update_pie_windows(self):
self.update_parameter()

@chisurf.gui.decorators.init_with_ui("tttr_burst_finder.ui")
def __init__(self, *args, windows, detectors, callback_function=None, **kwargs):
def __init__(self, *args,
windows,
detectors,
callback_function=None,
show_dT=True,
show_burst_histogram=True,
show_mcs=True,
show_decay=True,
show_filter=True,
initial_trace_bin_width: float = 1.0,
initial_photon_threshold: int = 100,
initial_tw_size: float = 1.0,
initial_max_gap: int = 6,
initial_decay_coarse: int = 16,
initial_number_of_burst_bins: int = 50,
initial_dT_min: float = 0.0001,
initial_dT_max: float = 0.15,
**kwargs):
self.setTitle("Photon filter / burst finder")

# Store the windows and detectors dictionaries and update corresponding UI elements.
self.windows = windows
self.detectors = detectors
self.fill_detectors(detectors)
Expand Down Expand Up @@ -777,41 +796,52 @@ def cc():
self.setSizePolicy(sizePolicy)

self.tttr = None

# Set default dT values (which will later be overridden by any passed initial_dT_min/max)
self._dT_min = 0.0001
self._dT_max = 0.15

# Plot widget: Burst size histogram
self.pw_burst_histogram = pg.plot()
self.plot_burst_histogram = self.pw_burst_histogram.getPlotItem()
# self.pw_burst_histogram.setLabel('left', 'Counts')
# self.pw_burst_histogram.setLabel('bottom', 'Burst Length (time)')
self.pw_burst_histogram.resize(100, 80)

# Define common pens for the plots.
color_all = QtGui.QColor(255, 255, 0, 64)
color_selected = QtGui.QColor(0, 255, 255, 255)
pen2 = pg.mkPen(color_all, width=1, style=QtCore.Qt.SolidLine)
pen1 = pg.mkPen(color_selected, width=1, style=QtCore.Qt.SolidLine)

# Plot widget: delta macro time plot
# Plot widget: Burst size histogram
self.pw_burst_histogram = pg.plot()
self.plot_burst_histogram = self.pw_burst_histogram.getPlotItem()
self.pw_burst_histogram.resize(100, 80)
self.pw_burst_histogram.setVisible(show_burst_histogram)

# Plot widget: Delta macro time plot
self.pw_dT = pg.plot()
self.plot_item_dt = self.pw_dT.getPlotItem()
self.plot_unselected = self.plot_item_dt.plot(x=[1.0], y=[1.0], pen=pen2)
self.plot_selected = self.plot_item_dt.plot(x=[1.0], y=[1.0], pen=pen1)
self.pw_dT.resize(200, 40)
self.pw_dT.setVisible(show_dT)

# Plot widget: MCS trace
self.pw_mcs = pg.plot()
self.plot_item_mcs = self.pw_mcs.getPlotItem()
# Set axis labels for MCS trace plot
self.plot_item_mcs.setLabel('bottom', 'Time (s)')
self.plot_item_mcs.setLabel('left', 'Intensity')
self.plot_mcs_all = self.plot_item_mcs.plot(x=[1.0], y=[1.0], pen=pen2)
self.plot_mcs_selected = self.plot_item_mcs.plot(x=[1.0], y=[1.0], pen=pen1)
self.pw_mcs.resize(200, 80)
self.pw_mcs.setVisible(show_mcs)

# Plot widget: Fluorescence decay
self.pw_decay = pg.plot()
self.plot_item_decay = self.pw_decay.getPlotItem()
# Set axis labels for decay plot
self.plot_item_decay.setLabel('bottom', 'Time (ns)')
self.plot_item_decay.setLabel('left', 'Counts')
self.plot_decay_all = self.plot_item_decay.plot(x=[1.0], y=[1.0], pen=pen2)
self.plot_decay_selected = self.plot_item_decay.plot(x=[1.0], y=[1.0], pen=pen1)
self.pw_decay.resize(200, 80)
self.pw_decay.setVisible(show_decay)

# Plot widget: Filtered photons
self.pw_filter = pg.plot()
Expand All @@ -821,6 +851,7 @@ def cc():
self.plot_item_sel = self.pw_filter.getPlotItem()
self.plot_select = self.plot_item_sel.plot(x=[1.0], y=[1.0])
self.pw_filter.resize(200, 20)
self.pw_filter.setVisible(show_filter)

self.plot_item_dt.setLogMode(False, True)
self.plot_item_decay.setLogMode(False, True)
Expand Down Expand Up @@ -851,13 +882,34 @@ def onRegionUpdate(evt):

self.region_selector.sigRegionChangeFinished.connect(onRegionUpdate)

self.gridLayout_6.addWidget(self.pw_dT, 0, 0, 1, 3) # (widget, row, column, rowSpan, columnSpan)
self.gridLayout_6.addWidget(self.pw_filter, 1, 0, 1, 3) # (widget, row, column, rowSpan, columnSpan)
self.gridLayout_6.addWidget(self.pw_mcs, 2, 0, 1, 1) # (widget, row, column, rowSpan, columnSpan)
self.gridLayout_6.addWidget(self.pw_decay, 2, 1, 1, 1) # (widget, row, column, rowSpan, columnSpan)
self.gridLayout_6.addWidget(self.pw_burst_histogram, 0, 1, 2, 1) # (widget, row, column, rowSpan, columnSpan)

# Connect actions
# --- Add new initial settings for burst selection parameters ---
# Set the initial trace bin width (time window) for the MCS trace.
self.doubleSpinBox_4.setValue(initial_trace_bin_width)
# Set the photon number threshold.
self.spinBox.setValue(initial_photon_threshold)
# Set the maximum gap (for gap filling in burst selection).
self.spinBox_7.setValue(initial_max_gap)
# Set the decay coarse binning.
self.spinBox_5.setValue(initial_decay_coarse)
# Set the number of burst bins for the histogram.
self.spinBox_6.setValue(initial_number_of_burst_bins)
# Set the lower and upper limits for dT (delta macro time) filtering.
self._dT_min = initial_dT_min
self._dT_max = initial_dT_max
self.doubleSpinBox_2.setValue(initial_dT_min)
self.doubleSpinBox_3.setValue(initial_dT_max)
# Update the region selector to match the new dT limits.
self.doubleSpinBox.setValue(initial_tw_size)
self.region_selector.setRegion((np.log10(initial_dT_min), np.log10(initial_dT_max)))

# Add widgets to layout.
self.gridLayout_6.addWidget(self.pw_dT, 0, 0, 1, 3)
self.gridLayout_6.addWidget(self.pw_filter, 1, 0, 1, 3)
self.gridLayout_6.addWidget(self.pw_mcs, 2, 0, 1, 1)
self.gridLayout_6.addWidget(self.pw_decay, 2, 1, 1, 1)
self.gridLayout_6.addWidget(self.pw_burst_histogram, 0, 1, 2, 1)

# Connect actions.
self.actionUpdate_Values.triggered.connect(self.update_parameter)
self.actionUpdateUI.triggered.connect(self.updateUI)
self.actionFile_changed.triggered.connect(self.read_tttr)
Expand All @@ -873,9 +925,8 @@ def onRegionUpdate(evt):
self.comboBox_2.currentTextChanged.connect(self.update_detectors)
self.comboBox_3.currentTextChanged.connect(self.update_pie_windows)

# Set the custom validator
# Set the custom validator.
validator = CommaSeparatedIntegersValidator()
self.lineEdit_4.setValidator(validator)

self.update_parameter()

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