save thresholds, read me

Controller.py

@@ -36,11 +36,11 @@ class Controller:
         self.stim_values = {}
         self.recording_times = {}
 
-    def save_parameters(self):
+    def save_parameters(self, folder_path):
         header = "trial_index,threshold,min_window,step_size\n"
         for repro in self.thresholds.keys():
             # TODO change '.' to self.data_path after testing:
-            with open("." + "/{}_thresholds.csv".format(repro), "w") as threshold_file:
+            with open(folder_path + "/{}_thresholds.csv".format(repro), "w") as threshold_file:
                 threshold_file.write(header)
                 for i in range(len(self.sorting[repro])):
                     if len(self.thresholds[repro][i]) == 0:
@@ -53,7 +53,14 @@ class Controller:
                         step = self.thresholds[repro][i][2]
                         threshold_file.write("{},{},{},{}\n".format(i, thresh, min_window, step))
         print("Thresholds saved!")
+
+    def save_redetected_spikes(self, folder_path):
         # TODO save redetected spikes:
+        header = "trial_index,threshold,min_window,step_size\n"
+        for repro in self.thresholds.keys():
+            # TODO change '.' to self.data_path after testing:
+            with open(folder_path + "/{}_thresholds.csv".format(repro), "w") as threshold_file:
+                threshold_file.write(header)
 
     def get_repros(self):
         return self.parser.get_measured_repros()

ReadMe.md

@@ -0,0 +1,15 @@
+# Spike redetector
+
+###redetection parameters:
+
+- **Threshold**: number of standard deviations between a maximum and a minimum to count as a spike.
+- **Min window size**: The minimum size of a window (as number of indices) in which spikes are detected. The voltage trace is split into parts 
+  if the maximum or minimum of the next part are too different from the current part. 
+  This makes the estimation of the STD a lot more stable between trials where the absolute voltage might wander.
+- **step size**: The number of indices that are used in each step while trying to increase the size of the window.
+
+### plot controls:
+
+- Drag and drop with LMB
+
+- zoom control with RMB -> press and hold; up down is zoom on y-axis while left right is zoom on x-axis

SpikeRedetectGui.py

@@ -106,7 +106,6 @@ class SpikeRedetectGui(QWidget):
         self.grouping_checkbox.setText("Group by Stimulus Value:")
         panel_layout.addWidget(self.grouping_checkbox)
 
-
         trial_label = QLabel("Trial:")
         panel_layout.addWidget(trial_label)
         self.trial_spinbox = QSpinBox(self)
@@ -156,6 +155,11 @@ class SpikeRedetectGui(QWidget):
         button.clicked.connect(self.save_threshold_parameters)
         panel_layout.addWidget(button)
 
+        button = QPushButton('Save redetected spikes!', self)
+        button.setToolTip('Save redetected spikes with the accepted thresholds.')
+        button.clicked.connect(self.save_redetected_spikes)
+        panel_layout.addWidget(button)
+
         panel.setLayout(panel_layout)
         middle.addWidget(panel)
 
@@ -202,18 +206,31 @@ class SpikeRedetectGui(QWidget):
         for val in self.controller.get_stim_values(repro):
             self.stim_val_box.addItem(str(val))
 
-
-
     @pyqtSlot()
     def accept_redetection(self):
         params = (self.threshold_spinbox.value(), self.window_spinbox.value(), self.step_spinbox.value())
-        self.controller.set_redetection_params(self.repro_box.currentText(), self.trial_idx, params)
+        if not self.grouping_checkbox.isChecked():
-
+            self.controller.set_redetection_params(self.repro_box.currentText(), self.trial_idx, params)
-        self.trial_change(self.trial_idx + 1)
+            self.trial_change(self.trial_idx + 1)
+        else:
+            # TODO set params for all trials of the current stim value
+            #   also choose next trial idx that has no accepted params yet and update stim_val_box
+            pass
 
     @pyqtSlot()
     def save_threshold_parameters(self):
-        self.controller.save_parameters()
+        # TODO add question for save_path
+        data_path = QFileDialog.getExistingDirectory(self, directory=self.controller.data_path, caption='Select a folder to save the parameters:')
+        if data_path is None:
+            return
+        self.controller.save_parameters(data_path)
+
+    @pyqtSlot()
+    def save_redetected_spikes(self):
+        data_path = QFileDialog.getExistingDirectory(self, directory=self.controller.data_path, caption='Select a folder to save the redetected spikes:')
+        if data_path is None:
+            return
+        self.controller.save_redetected_spikes(data_path)
 
 
 class PlotCanvas(FigureCanvas):
@@ -329,7 +346,8 @@ class PlotCanvas(FigureCanvas):
         ax.eventplot(spiketimes, lineoffsets=max(trace) + 2, colors="black")
         redetect = detect_spiketimes(time, trace, redetection_vars[0], redetection_vars[1], redetection_vars[2])
         ax.eventplot(redetect, lineoffsets=max(trace) + 1, colors="red")
-        ax.set_title('Trial XYZ')
+        ax.plot(redetect, trace[np.round(np.array((redetect + recording_times[0]) / sampling_interval)).astype(int)], 'o', color='red')
+        ax.set_title('Trial')
 
         if self.current_repro == repro:
             ax.set_xlim(xlim)

main.py

@@ -14,7 +14,7 @@ sam_file  = "../neuronModel/data/final_sam/2011-10-25-ad-invivo-1"
 def main():
     app = QApplication(sys.argv)
 
-    ex = SpikeRedetectGui(sam_file)
+    ex = SpikeRedetectGui(test_file)
     sys.exit(app.exec_())