Add clear blink interval feature

README.md

@@ -10,7 +10,7 @@ FRET (smFRET) fast and efficiently. The key feature is reverse-loading of ASCII
 - Memory-free movie batch loading
 - Distribution plotting and fitting
 - Backwards-compatibility with iSMS-exported data
-- Manual blinking interval selection and export
+- Manual blinking interval selection, clearing and export
 
 If you'd like to play around with just the Keras/TensorFlow model, please go to https://github.com/komodovaran/DeepFRET-Model
 

src/main/python/ui/MenuBar.ui

@@ -135,6 +135,7 @@
       <string>Manually Select Blinking</string>
      </property>
      <addaction name="actionSelect_Blink_Interval"/>
+     <addaction name="actionClear_Blink_Intervals"/>
     </widget>
     <widget class="QMenu" name="menuPredict_Trace_Type">
      <property name="title">
@@ -598,6 +599,14 @@
     <string>Blink Interval</string>
    </property>
   </action>
+  <action name="actionClear_Blink_Intervals">
+   <property name="enabled">
+    <bool>false</bool>
+   </property>
+   <property name="text">
+    <string>Clear Blink Intervals</string>
+   </property>
+  </action>
   <action name="actionAdvanced_Sort">
    <property name="enabled">
     <bool>false</bool>

src/main/python/ui/_MenuBar.py

@@ -224,6 +224,11 @@ def setupUi(self, MenuBar):
         self.actionSelect_Blink_Interval.setObjectName(
             "actionSelect_Blink_Interval"
         )
+        self.actionClear_Blink_Intervals = QtWidgets.QAction(MenuBar)
+        self.actionClear_Blink_Intervals.setEnabled(False)
+        self.actionClear_Blink_Intervals.setObjectName(
+            "actionClear_Blink_Intervals"
+        )
         self.actionAdvanced_Sort = QtWidgets.QAction(MenuBar)
         self.actionAdvanced_Sort.setEnabled(False)
         self.actionAdvanced_Sort.setObjectName("actionAdvanced_Sort")
@@ -285,6 +290,9 @@ def setupUi(self, MenuBar):
         self.menuManually_Select_Blinking.addAction(
             self.actionSelect_Blink_Interval
         )
+        self.menuManually_Select_Blinking.addAction(
+            self.actionClear_Blink_Intervals
+        )
         self.menuPredict_Trace_Type.addAction(
             self.actionPredict_Selected_Traces
         )
@@ -518,6 +526,9 @@ def retranslateUi(self, MenuBar):
         self.actionSelect_Blink_Interval.setText(
             _translate("MenuBar", "Blink Interval")
         )
+        self.actionClear_Blink_Intervals.setText(
+            _translate("MenuBar", "Clear Blink Intervals")
+        )
         self.actionAdvanced_Sort.setText(_translate("MenuBar", "Advanced Sort"))
         self.actionCheck_All.setText(_translate("MenuBar", "Check All"))
         self.actionCheck_All.setShortcut(

src/main/python/widgets/base_window.py

@@ -178,6 +178,10 @@ def setupMenuBarActions(self):
         for f in (self.triggerBlink, self.refreshPlot):
             self.ui.actionSelect_Blink_Interval.triggered.connect(f)
 
+        self.ui.actionClear_Blink_Intervals.triggered.connect(
+            self.clearBlinkIntervals
+        )
+
         # self.ui.actionFit_Hmm_Current.triggered.connect(
         #     partial(self.fitSingleTraceHiddenMarkovModel, True)
         # )
@@ -922,6 +926,10 @@ def triggerBlink(self):
         """Override in subclass."""
         pass
 
+    def clearBlinkIntervals(self):
+        """Override in subclass."""
+        pass
+
     def triggerBleach(self, color):
         """Override in subclass."""
         pass

src/main/python/widgets/trace_window.py

@@ -118,6 +118,7 @@ def enablePerWindow(self):
             self.ui.actionSelect_Bleach_Red_Channel,
             self.ui.actionSelect_Bleach_Green_Channel,
             self.ui.actionSelect_Blink_Interval,
+            self.ui.actionClear_Blink_Intervals,
             self.ui.actionFit_Hmm_Selected,
             self.ui.actionPredict_Selected_Traces,
             self.ui.actionPredict_All_traces,
@@ -767,6 +768,29 @@ def clearCorrectionFactors(self):
         self.clearMarkerLines()
         self.refreshPlot()
 
+    def clearBlinkIntervals(self):
+        """Clear manually selected blink intervals for the current trace."""
+        if self.currName is not None:
+            trace = self.currentTrace()
+            trace.blink_intervals = []
+            trace.hmm = None
+
+            self.refreshPlot()
+
+            histogram_window = self.windows[gvars.HistogramWindow]
+            transition_density_window = self.windows[gvars.TransitionDensityWindow]
+
+            histogram_window.getHistogramData()
+            histogram_window.gauss_params = None
+            if histogram_window.isVisible():
+                histogram_window.refreshPlot()
+
+            histogram_window.setPooledLifetimes()
+            transition_density_window.setClusteredTransitions()
+
+            if transition_density_window.isVisible():
+                transition_density_window.refreshPlot()
+
     def getCurrentLines(self, ax):
         """Get labels of currently plotted lines"""
         if self.currName is not None: