Merge pull request #1041 from JuliaSprenger/enh/neuralynx_multi_rate

[Neuralynx] Add multiple streams

Author: samuelgarcia

neo/io/neuralynxio.py

@@ -35,6 +35,9 @@ def __init__(self, dirname='', filename='', use_cache=False, cache_path='same_as
         ----------
         dirname : str
             Directory containing data files
+        filename : str
+            Name of a single ncs, nse, nev, or ntt file to include in dataset. Will be ignored,
+            if dirname is provided.
         use_cache : bool, optional
             Cache results of initial file scans for faster loading in subsequent runs.
             Default: False

neo/rawio/neuralynxrawio/ncssections.py

@@ -27,6 +27,17 @@ def __hash__(self):
         return (f'{self.sampFreqUsed};{self.microsPerSampUsed};'
                f'{[s.__hash__() for s in self.sects]}').__hash__()
 
+    def is_equivalent(self, other, rel_tol=0, abs_tol=0):
+        if len(self.sects) != len(other.sects):
+            return False
+        else:
+            # do not check for gaps if only a single section is present
+            for sec_id in range(len(self.sects) - 1):
+                if not self.sects[sec_id].is_equivalent(
+                        other.sects[sec_id], rel_tol=rel_tol, abs_tol=abs_tol):
+                    return False
+            return True
+
 
 class NcsSection:
     """
@@ -66,6 +77,12 @@ def __hash__(self):
         s = f'{self.startRec};{self.startTime};{self.endRec};{self.endTime};{self.n_samples}'
         return s.__hash__()
 
+    def is_equivalent(self, other, rel_tol=0, abs_tol=0):
+        eq_start = math.isclose(self.startTime, other.startTime, rel_tol=rel_tol, abs_tol=abs_tol)
+        eq_end = math.isclose(self.endTime, other.endTime, rel_tol=rel_tol, abs_tol=abs_tol)
+        return eq_start & eq_end
+
+
     def before_time(self, rhb):
         """
         Determine if this section is completely before another section in time.
@@ -211,9 +228,9 @@ def _buildGivenActualFrequency(ncsMemMap, actualSampFreq, reqFreq):
             raise IOError("Sampling frequency in first record doesn't agree with header.")
         chanNum = ncsMemMap['channel_id'][0]
 
-        nb = NcsSections()
-        nb.sampFreqUsed = actualSampFreq
-        nb.microsPerSampUsed = NcsSectionsFactory.get_micros_per_samp_for_freq(actualSampFreq)
+        secs = NcsSections()
+        secs.sampFreqUsed = actualSampFreq
+        secs.microsPerSampUsed = NcsSectionsFactory.get_micros_per_samp_for_freq(actualSampFreq)
 
         # check if file is one block of records, which is often the case, and avoid full parse
         lastBlkI = ncsMemMap.shape[0] - 1
@@ -231,15 +248,15 @@ def _buildGivenActualFrequency(ncsMemMap, actualSampFreq, reqFreq):
             n_samples = NcsSection._RECORD_SIZE * lastBlkI
             curBlock = NcsSection(0, ts0, lastBlkI, lastBlkEndTime, n_samples)
 
-            nb.sects.append(curBlock)
-            return nb
+            secs.sects.append(curBlock)
+            return secs
 
         # otherwise need to scan looking for breaks
         else:
             blkOnePredTime = NcsSectionsFactory.calc_sample_time(actualSampFreq, ts0, nb0)
             curBlock = NcsSection(0, ts0, -1, -1, -1)
-            nb.sects.append(curBlock)
-            return NcsSectionsFactory._parseGivenActualFrequency(ncsMemMap, nb, chanNum, reqFreq,
+            secs.sects.append(curBlock)
+            return NcsSectionsFactory._parseGivenActualFrequency(ncsMemMap, secs, chanNum, reqFreq,
                                                                  blkOnePredTime)
 
     @staticmethod
@@ -369,7 +386,7 @@ def _buildForMaxGap(ncsMemMap, nomFreq):
             endTime = NcsSectionsFactory.calc_sample_time(nomFreq, lts, lnb)
             curBlock = NcsSection(0, ts0, lastBlkI, endTime, numSampsForPred)
             nb.sects.append(curBlock)
-            nb.sampFreqUsed = numSampsForPred / (lts - ts0) * 1e6
+            nb.sampFreqUsed = (numSampsForPred + lnb) / (endTime - ts0) * 1e6
             nb.microsPerSampUsed = NcsSectionsFactory.get_micros_per_samp_for_freq(nb.sampFreqUsed)
 
         # otherwise parse records to determine blocks using default maximum gap length