add functionality to parse baseline spiketimes

CellData.py

@@ -33,6 +33,7 @@ class CellData:
         self.parser = dpf.get_parser(data_path)
 
         self.base_traces = None
+        self.base_spikes = None
         # self.fi_traces = None
         self.fi_intensities = None
         self.fi_spiketimes = None
@@ -41,7 +42,6 @@ class CellData:
         self.time_axes = None
         # self.metadata = None
 
-
         self.sampling_interval = self.parser.get_sampling_interval()
         self.recording_times = self.parser.get_recording_times()
 
@@ -57,6 +57,12 @@ class CellData:
         else:
             return self.base_traces[trace_type]
 
+    def get_base_spikes(self):
+        if self.base_spikes is None:
+            self.base_spikes = self.parser.get_baseline_spiketimes()
+
+        return self.base_spikes
+
     def get_fi_traces(self):
         raise NotImplementedError("CellData:get_fi_traces():\n" +
                                   "Getting the Fi-Traces currently overflows the RAM and causes swapping! Reimplement if really needed!")

DataParserFactory.py

@@ -18,6 +18,9 @@ class AbstractParser:
     def get_baseline_traces(self):
         raise NotImplementedError("NOT YET OVERRIDDEN FROM ABSTRACT CLASS")
 
+    def get_baseline_spiketimes(self):
+        raise NotImplementedError("NOT YET OVERRIDDEN FROM ABSTRACT CLASS")
+
     def get_fi_curve_traces(self):
         raise NotImplementedError("NOT YET OVERRIDDEN FROM ABSTRACT CLASS")
 
@@ -48,6 +51,7 @@ class DatParser(AbstractParser):
     def __init__(self, dir_path):
         self.base_path = dir_path
         self.fi_file = self.base_path + "/fispikes1.dat"
+        self.baseline_file = self.base_path + "/basespikes1.dat"
         self.stimuli_file = self.base_path + "/stimuli.dat"
         self.__test_data_file_existence__()
 
@@ -63,9 +67,6 @@ class DatParser(AbstractParser):
     def spiketimes_available(self) -> bool:
         return True
 
-    def cell_get_metadata(self):
-        raise NotImplementedError("NOT YET OVERRIDDEN FROM ABSTRACT CLASS")
-
     def get_sampling_interval(self):
         if self.sampling_interval == -1:
             self.__read_sampling_interval__()
@@ -80,6 +81,15 @@ class DatParser(AbstractParser):
     def get_baseline_traces(self):
         return self.__get_traces__("BaselineActivity")
 
+    def get_baseline_spiketimes(self):
+        spiketimes = []
+
+        for metadata, key, data in Dl.iload(self.baseline_file):
+            spikes = data[:, 0]
+            spiketimes.append(spikes)
+
+        return spiketimes
+
     def get_fi_curve_traces(self):
         return self.__get_traces__("FICurve")