add functions to read SAM behaviour of data cells

CellData.py

@@ -41,6 +41,15 @@ class CellData:
         self.time_axes = None
         # self.metadata = None
 
+        self.sam_spiketimes = None
+        self.sam_contrasts = None
+        self.sam_delta_fs = None
+        self.sam_eod_freqs = None
+        self.sam_durations = None
+        self.sam_trans_amplitudes = None
+
+
+
         self.sampling_interval = self.parser.get_sampling_interval()
         self.recording_times = self.parser.get_recording_times()
 
@@ -100,6 +109,30 @@ class CellData:
 
         return contrast
 
+    def get_sam_spiketimes(self):
+        self.__read_sam_info__()
+        return self.sam_spiketimes
+
+    def get_sam_contrasts(self):
+        self.__read_sam_info__()
+        return self.sam_contrasts
+
+    def get_sam_delta_frequencies(self):
+        self.__read_sam_info__()
+        return self.sam_delta_fs
+
+    def get_sam_durations(self):
+        self.__read_sam_info__()
+        return self.sam_durations
+
+    def get_sam_eod_frequencies(self):
+        self.__read_sam_info__()
+        return self.sam_eod_freqs
+
+    def get_sam_trans_amplitudes(self):
+        self.__read_sam_info__()
+        return self.sam_trans_amplitudes
+
     def get_mean_fi_curve_isi_frequencies(self):
         if self.mean_isi_frequencies is None:
             self.time_axes, self.mean_isi_frequencies = hf.all_calculate_mean_isi_frequency_traces(
@@ -172,6 +205,17 @@ class CellData:
             self.fi_intensities, self.fi_spiketimes, self.fi_trans_amplitudes = hf.merge_similar_intensities(
                 intensities, spiketimes, trans_amplitudes)
 
+    def __read_sam_info__(self):
+        if self.sam_spiketimes is None:
+            spiketimes, contrasts, delta_fs, eod_freqs, durations, trans_amplitudes = self.parser.get_sam_info()
+
+            self.sam_spiketimes = spiketimes
+            self.sam_contrasts = contrasts
+            self.sam_delta_fs = delta_fs
+            self.sam_eod_freqs = eod_freqs
+            self.sam_durations = durations
+            self.sam_trans_amplitudes = trans_amplitudes
+
     # def get_metadata(self):
     #     self.__read_metadata__()
     #     return self.metadata

DataParserFactory.py

@@ -13,8 +13,8 @@ MODEL = 2
 
 class AbstractParser:
 
-    def cell_get_metadata(self):
-        raise NotImplementedError("NOT YET OVERRIDDEN FROM ABSTRACT CLASS")
+    # def cell_get_metadata(self):
+    #     raise NotImplementedError("NOT YET OVERRIDDEN FROM ABSTRACT CLASS")
 
     def get_baseline_traces(self):
         raise NotImplementedError("NOT YET OVERRIDDEN FROM ABSTRACT CLASS")
@@ -31,6 +31,9 @@ class AbstractParser:
     def get_fi_frequency_traces(self):
         raise NotImplementedError("NOT YET OVERRIDDEN FROM ABSTRACT CLASS")
 
+    def get_sam_info(self):
+        raise NotImplementedError("NOT YET OVERRIDDEN FROM ABSTRACT CLASS")
+
     def get_sampling_interval(self):
         raise NotImplementedError("NOT YET OVERRIDDEN FROM ABSTRACT CLASS")
 
@@ -53,6 +56,7 @@ class DatParser(AbstractParser):
         self.base_path = dir_path
         self.fi_file = self.base_path + "/fispikes1.dat"
         self.baseline_file = self.base_path + "/basespikes1.dat"
+        self.sam_file = self.base_path + "/samallspikes1.dat"
         self.stimuli_file = self.base_path + "/stimuli.dat"
         self.__test_data_file_existence__()
 
@@ -156,6 +160,58 @@ class DatParser(AbstractParser):
 
         return trans_amplitudes, intensities, spiketimes
 
+    def get_sam_info(self):
+        contrasts = []
+        delta_fs = []
+        spiketimes = []
+        durations = []
+        eod_freqs = []
+        trans_amplitudes = []
+        index = -1
+        for metadata, key, data in Dl.iload(self.sam_file):
+            factor = 1
+            if key[0][0] == 'time':
+                if key[1][0] == 'ms':
+                    factor = 1/1000
+                elif key[1][0] == 's':
+                    factor = 1
+                else:
+                    print("DataParser Dat: Unknown time notation:", key[1][0])
+            if len(metadata) != 0:
+
+                stimulus_dict = metadata[0]["----- Stimulus -------------------------------------------------------"]
+                analysis_dict = metadata[0]["----- Analysis -------------------------------------------------------"]
+                eod_freq = float(metadata[0]["EOD rate"][:-2])  # in Hz
+                trans_amplitude = metadata[0]["trans. amplitude"][:-2]  # in mV
+
+                duration = float(stimulus_dict["duration"][:-2]) * factor  # normally saved in ms? so change it with the factor
+                contrast = float(stimulus_dict["contrast"][:-1])  # in percent
+                delta_f = float(stimulus_dict["deltaf"][:-2])
+
+                # delta_f = metadata[0]["true deltaf"]
+                # contrast = metadata[0]["true contrast"]
+
+                contrasts.append(contrast)
+                delta_fs.append(delta_f)
+                durations.append(duration)
+                eod_freqs.append(eod_freq)
+                trans_amplitudes.append(trans_amplitude)
+                spiketimes.append([])
+                index += 1
+
+            if data.shape[1] != 1:
+                raise RuntimeError("DatParser:get_sam_spiketimes():\n read data has more than one dimension!")
+
+            spike_time_data = data[:, 0] * factor  # saved in ms so use the factor to change it.
+            if len(spike_time_data) < 10:
+                continue
+            if spike_time_data[-1] < 0.1:
+                print("# ignoring spike-train that ends before one tenth of a second.")
+                continue
+            spiketimes[index].append(spike_time_data)
+
+        return spiketimes, contrasts, delta_fs, eod_freqs, durations, trans_amplitudes
+
     def __get_traces__(self, repro):
         time_traces = []
         v1_traces = []
@@ -242,7 +298,8 @@ class DatParser(AbstractParser):
             raise RuntimeError(self.stimuli_file + " file doesn't exist!")
         if not exists(self.fi_file):
             raise RuntimeError(self.fi_file + " file doesn't exist!")
-
+        if not exists(self.sam_file):
+            raise RuntimeError(self.sam_file + " file doesn't exist!")
 
 # MODEL PARSER: ------------------------------