stim values extraction but without functionality

Controller.py

@@ -3,6 +3,7 @@ from DatParser import DatParser
 
 import numpy as np
 from warnings import warn
+import os
 import matplotlib.pyplot as plt
 
 
@@ -32,6 +33,7 @@ class Controller:
 
         self.sorting = {}
         self.thresholds = {}
+        self.stim_values = {}
         self.recording_times = {}
 
     def save_parameters(self):
@@ -84,9 +86,10 @@ class Controller:
             [time_traces, v1_traces, eod_traces, local_eod_traces, stimulus_traces] = self.get_unsorted_traces(repro)
             (spiketimes, metadata) = self.get_unsorted_spiketimes(repro)
 
+        repro_stim_values = self.extract_stim_values(repro, metadata)
+        self.stim_values[repro] = repro_stim_values
         if len(v1_traces) != len(spiketimes):
-            warn("get_traces_with_spiketimes():Unequal number of traces and spiketimes for repro {}!"
-                 "Returning only according to the number of traces!".format(repro))
+            warn("get_traces_with_spiketimes():Unequal number of traces ({}) and spiketimes ({}) for repro {}! Returning only according to the number of traces!".format(len(v1_traces), len(spiketimes), repro))
 
         ash = calculate_distance_matrix_traces_spikes(v1_traces, spiketimes, self.parser.get_sampling_interval(), before)
 
@@ -102,13 +105,35 @@ class Controller:
         return v1_traces, sorted_spiketimes, (before, after)
 
     def get_stim_values(self, repro):
+        return sorted(np.unique(self.stim_values[repro]))
+
+    def extract_stim_values(self, repro, metadata_list):
+        stim_values = []
         if repro == "BaselineActivity":
-            return ["None"]
+            for i in range(len(metadata_list)):
+                stim_values.append("None")
         elif repro == "FICurve":
-            # TODO other function that just provides the contrasts
-            return sorted([str(x[0]) for x in self.parser.get_fi_curve_contrasts()])
+            current_intensity = None
+            for i in range(len(metadata_list)):
+                if len(metadata_list[i]) != 0:
+                    current_intensity = float(metadata_list[i][-1]["intensity"][:-2])
+
+                stim_values.append(current_intensity)
+
+        elif repro == "FileStimulus":
+            for i in range(len(metadata_list)):
+                stim_values.append(os.path.basename(metadata_list[i][0]["file"]))
+
+        elif repro == "SAM":
+            for i in range(len(metadata_list)):
+                deltaf = metadata_list[i][0]["----- Stimulus -------------------------------------------------------"]["deltaf"]
+                contrast = metadata_list[i][0]["----- Stimulus -------------------------------------------------------"]["contrast"]
+                stim_values.append("{} {}".format(deltaf, contrast))
+
+        if len(stim_values) == 0:
+            return ["Stimulus values of repro not supported"]
 
-        return ["repro not supported"]
+        return stim_values
 
     def get_trials(self, repro, stimulus_value):
         pass

SpikeRedetectGui.py

@@ -1,7 +1,7 @@
 
 from PyQt5.QtWidgets import QWidget, QPushButton, QSizePolicy, QLineEdit,\
     QMessageBox, QVBoxLayout, QHBoxLayout, QGridLayout, QLabel, QFrame,\
-    QDoubleSpinBox, QComboBox, QSpinBox, QCheckBox
+    QDoubleSpinBox, QComboBox, QSpinBox, QCheckBox, QFileDialog
 from PyQt5.QtCore import pyqtSlot
 
 import numpy as np
@@ -14,9 +14,13 @@ from redetector import detect_spiketimes
 
 class SpikeRedetectGui(QWidget):
 
-    def __init__(self, controller: Controller):
+    def __init__(self, data_path=None):
         super().__init__()
-        self.controller = controller
+
+        if data_path is None:
+            data_path = QFileDialog.getExistingDirectory(self, caption='Select a cell directory:')
+
+        self.controller = Controller(data_path)
         self.title = 'Spike Redetection'
         self.left = 10
         self.top = 10
@@ -188,6 +192,9 @@ class SpikeRedetectGui(QWidget):
     def repro_change(self):
         repro = self.repro_box.currentText()
 
+        redetection = (self.threshold_spinbox.value(), self.window_spinbox.value(), self.step_spinbox.value())
+        self.canvas.plot(self.trial_idx, self.repro_box.currentText(), self.controller, redetection)
+
         # reset trials and stim values
         self.trial_change(0)
         self.stim_val_box.clear()
@@ -195,8 +202,7 @@ class SpikeRedetectGui(QWidget):
         for val in self.controller.get_stim_values(repro):
             self.stim_val_box.addItem(str(val))
 
-        redetection = (self.threshold_spinbox.value(), self.window_spinbox.value(), self.step_spinbox.value())
-        self.canvas.plot(self.trial_idx, self.repro_box.currentText(), self.controller, redetection)
+
 
     @pyqtSlot()
     def accept_redetection(self):
@@ -320,9 +326,9 @@ class PlotCanvas(FigureCanvas):
         ax.clear()
         time = np.arange(len(trace)) * sampling_interval - recording_times[0]
         ax.plot(time, trace)
-        ax.eventplot(spiketimes, lineoffsets=max(trace) + 1, colors="black")
+        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) + 2, colors="red")
+        ax.eventplot(redetect, lineoffsets=max(trace) + 1, colors="red")
         ax.set_title('Trial XYZ')
 
         if self.current_repro == repro:

main.py

@@ -1,28 +1,21 @@
 
 import sys
-import os
 
-from PyQt5.QtWidgets import QApplication, QFileDialog
+from PyQt5.QtWidgets import QApplication
 
-from Controller import Controller
 from SpikeRedetectGui import SpikeRedetectGui
 
+
 test_file = "../neuronModel/data/final_sam/2010-11-08-al-invivo-1"
+sam_file  = "../neuronModel/data/final_sam/2011-10-25-ad-invivo-1"
+# TODO CLI
 
 
 def main():
     app = QApplication(sys.argv)
-    data_path = QFileDialog.getExistingDirectory(caption='Select a directory')
-    if os.path.isdir(data_path):
-        data_provider = Controller(data_path)
-    else:
-        print("Cell loading didn't work!\n Cell folder: {}".format(data_path))
-        return
-        #data_provider = Controller(test_file)
-    ex = SpikeRedetectGui(data_provider)
-    sys.exit(app.exec_())
-
 
+    ex = SpikeRedetectGui(sam_file)
+    sys.exit(app.exec_())
 
 
 if __name__ == '__main__':

redetector.py

@@ -16,14 +16,14 @@ def detect_spike_indices_automatic_split(v1, threshold, min_length=5000, split_s
     break_threshold = 0.25
     splits = []
 
-    if len(v1) < min_length:
+    if len(v1) <= min_length:
         splits = [(0, len(v1))]
     else:
         last_max = max(v1[0:min_length])
         last_min = min(v1[0:min_length])
         idx = min_length
 
-        while idx < len(v1):
+        while idx <= len(v1):
             if idx + step_size > len(v1):
                 splits.append((split_start, len(v1)))
                 break