[reproclasses, FIData] reading data from old-style files works

fishbook/reproclasses.py

@@ -63,7 +63,8 @@ class BaselineData:
         if not self.__dataset:
             return
         self.__repros = RePro.find("BaselineActivity", cell_id=self.__cell.id)
-        for r in self.__repros:
+        for i in tqdm(range(len(self.__repros)), desc="loading data"):
+            r = self.__repros[i]
             sd = self.__read_spike_data(r)
             if sd is not None and len(sd) > 1:
                 self.__spike_data.append(sd)
@@ -399,9 +400,11 @@ class FIData:
             sd, c, eods, time = self.__read_spike_data(r)
             if sd is not None and len(sd) > 1:
                 self.__spike_data.extend(sd)
-                self.__eod_data.extend(eods)
+                if eods:
+                    self.__eod_data.extend(eods)
                 self.__contrasts.extend(c)
-                self.__eod_times.extend(time)
+                if time:
+                    self.__eod_times.extend(time)
             else:
                 continue
 
@@ -414,9 +417,7 @@ class FIData:
         if self.__dataset.has_nix:
             return self.__read_spikes_from_nix(repro)
         else:
-            print("Sorry, so far only from nix!!!")
-            pass
-        return None, None, None, None
+            return self.__read_spikes_from_directory(repro)
 
     def __do_read_spike_data_from_nix(self, mtag: nix.pycore.MultiTag, stimulus: Stimulus, repro: RePro):
         r_settings = repro.settings.split("\n")
@@ -458,10 +459,9 @@ class FIData:
         data_source = os.path.join(self.__dataset.data_source, self.__dataset.id + ".nix")
         if not os.path.exists(data_source):
             print("Data not found! Trying from directory")
-            return self.__read_spike_data_from_directory(repro)
+            return self.__read_spikes_from_directory(repro)
         f = nix.File.open(data_source, nix.FileMode.ReadOnly)
         b = f.blocks[0]
-
         mt = None
         for i in tqdm(range(len(stimuli)), desc="Loading data"):
             s = stimuli[i]
@@ -476,9 +476,40 @@ class FIData:
         f.close()
         return spikes, contrasts, eods, time
 
-    def __read_spikes_from_directory(self, repro = RePro):
+    def __do_read_data_block(self, f, l):
+        spikes = []
+        while len(l.strip()) > 0 and "#" not in l:
+            spikes.append(float(l.strip()))
+            l = f.readline()
+        return spikes, l
 
-        pass
+    def __read_spikes_from_directory(self, repro: RePro):
+        spikes = []
+        contrasts = []
+        print("Warning! Exact reconstruction of stimulus order not possible for old relacs files!")
+        data_source = os.path.join(self.__dataset.data_source, "fispikes1.dat")
+        if os.path.exists(data_source):
+            with open(data_source, 'r') as f:
+                l = f.readline()
+                fish_intensity = None
+                stim_intensity = None
+                while l:
+                    l = l.strip().lower()
+                    if "index" in l:
+                        fish_intensity = None
+                        stim_intensity = None
+                    if "intensity = " in l:
+                        if "true intensity = " in l:
+                            fish_intensity = float(l.split("=")[-1].strip()[:-2])
+                        elif "pre" not in l:
+                            stim_intensity = float(l.split("=")[-1].strip()[:-2])
+                    if len(l) > 0  and "#" not in l:  # data line
+                        sp, l = self.__do_read_data_block(f, l)
+                        spikes.append(sp)
+                        contrasts.append((stim_intensity/fish_intensity-1)*100)
+                        continue
+                    l = f.readline()
+        return spikes, contrasts, None, None
 
     @property
     def size(self) -> int:
@@ -508,6 +539,9 @@ class FIData:
         :param index: the index of the trial. Default of -1 indicates that all data should be returned.
         :return: Either two vectors representing time and the local eod or two lists of such vectors
         """
+        if len(self.__eod_data) == 0:
+            print("EOD data not available for old-style relacs data.")
+            return None, None
         if 0 <= index < self.size:
             return self.__eod_times[index], self.__eod_data[index]
         else:
@@ -516,7 +550,7 @@ class FIData:
     def contrast(self, index=-1):
         """
         The stimulus contrast used in the respective trial(s).
-        \
+
         :param index:  the index of the trial. Default of -1 indicates that all data should be returned.
         :return: Either a single scalar representing the contrast, or a list of such scalars, one entry for each trial.
         """
@@ -577,10 +611,9 @@ class FIData:
         return boltzmann_fit
 
 
-
 if __name__ == "__main__":
-    #dataset = Dataset(dataset_id='2011-06-14-ag')
-    dataset = Dataset(dataset_id="2018-01-19-ac-invivo-1")
-    # dataset = Dataset(dataset_id='2018-11-09-aa-invivo-1')
-    baseline = BaselineData(dataset)
+    # dataset = Dataset(dataset_id='2011-06-14-ag')
+    # dataset = Dataset(dataset_id="2018-01-19-ac-invivo-1")
+    dataset = Dataset(dataset_id='2013-04-18-ac')
+    fi_curve = FIData(dataset)
     embed()