Add strict_gap_mode=True/False to handle new clock sustem in neuralynx

Author: samuelgarcia

neo/rawio/neuralynxrawio/ncssections.py

@@ -487,7 +487,7 @@ def _buildNcsGeneric(ncsMemMap, sampFreq, gapTolerance=0):
         return ncsSects
 
     @staticmethod
-    def build_for_ncs_file(ncsMemMap, nlxHdr, gapTolerance=None):
+    def build_for_ncs_file(ncsMemMap, nlxHdr, gapTolerance=None, strict_gap_mode=True):
         """
         Build an NcsSections object for an NcsFile, given as a memmap and NlxHeader,
         handling gap detection appropriately given the file type as specified by the header.
@@ -512,15 +512,25 @@ def build_for_ncs_file(ncsMemMap, nlxHdr, gapTolerance=None):
             microsPerSampUsed = math.floor(NcsSectionsFactory.get_micros_per_samp_for_freq(freq))
             sampFreqUsed = NcsSectionsFactory.get_freq_for_micros_per_samp(microsPerSampUsed)
             if gapTolerance is None:
-                gapTolerance = 0
+                if strict_gap_mode:
+                    # this is the old behavior, maybe we could put 0.9 sample interval no ?
+                    gapTolerance = 0
+                else:
+                    gapTolerance = 0
+
             ncsSects = NcsSectionsFactory._buildNcsGeneric(ncsMemMap, sampFreqUsed, gapTolerance=gapTolerance)
             ncsSects.sampFreqUsed = sampFreqUsed
             ncsSects.microsPerSampUsed = microsPerSampUsed
 
         elif acqType in ["DIGITALLYNX", "DIGITALLYNXSX", "CHEETAH64", "CHEETAH560", "RAWDATAFILE"]:
             # digital lynx style with fractional frequency and micros per samp determined from block times
             if gapTolerance is None:
-                gapTolerance = round(NcsSectionsFactory._maxGapSampFrac * 1e6 / freq)
+                if strict_gap_mode:
+                    # this is the old behavior
+                    gapTolerance = round(NcsSectionsFactory._maxGapSampFrac * 1e6 / freq)
+                else:
+                    # quarter of paquet size is tolerate
+                    gapTolerance = round(0.25 * NcsSection._RECORD_SIZE * 1e6 / freq)
             ncsSects = NcsSectionsFactory._buildNcsGeneric(ncsMemMap, freq, gapTolerance=gapTolerance)
 
 
@@ -543,8 +553,12 @@ def build_for_ncs_file(ncsMemMap, nlxHdr, gapTolerance=None):
 
         elif acqType == "BML" or acqType == "ATLAS":
             # BML & ATLAS style with fractional frequency and micros per samp
-            if gapTolerance is None:
+            if strict_gap_mode:
+                # this is the old behavior, maybe we could put 0.9 sample interval no ?
                 gapTolerance = 0
+            else:
+                # quarter of paquet size is tolerate
+                gapTolerance = round(0.25 * NcsSection._RECORD_SIZE * 1e6 / freq)
             ncsSects = NcsSectionsFactory._buildNcsGeneric(ncsMemMap, freq, gapTolerance=gapTolerance)
             ncsSects.sampFreqUsed = freq
             ncsSects.microsPerSampUsed = NcsSectionsFactory.get_micros_per_samp_for_freq(freq)

neo/rawio/neuralynxrawio/neuralynxrawio.py

@@ -85,7 +85,13 @@ class NeuralynxRawIO(BaseRawIO):
     keep_original_times: bool, default: False
         If True, keep original start time as in files,
         Otherwise set 0 of time to first time in dataset
-
+    strict_gap_mode: bool, default: True
+        Detect gaps using strict mode or not.
+          * strict_gap_mode = True then a gap is consider when timstamp difference between two 
+            consequtive data packet is more than one sample interval.
+          * strict_gap_mode = False then a gap has an increased tolerance. Some new system with different clock need this option
+            otherwise, too many gaps are detected
+    
     Notes
     -----
     * This IO supports NCS, NEV, NSE and NTT file formats (not NVT or NRD yet)
@@ -125,7 +131,7 @@ class NeuralynxRawIO(BaseRawIO):
         ("samples", "int16", (NcsSection._RECORD_SIZE)),
     ]
 
-    def __init__(self, dirname="", filename="", exclude_filename=None, keep_original_times=False, **kargs):
+    def __init__(self, dirname="", filename="", exclude_filename=None, keep_original_times=False, strict_gap_mode=True, **kargs):
 
         if dirname != "":
             self.dirname = dirname
@@ -137,6 +143,7 @@ def __init__(self, dirname="", filename="", exclude_filename=None, keep_original
             raise ValueError("One of dirname or filename must be provided.")
 
         self.keep_original_times = keep_original_times
+        self.strict_gap_mode = strict_gap_mode
         self.exclude_filename = exclude_filename
         BaseRawIO.__init__(self, **kargs)
 
@@ -790,7 +797,7 @@ def scan_stream_ncs_files(self, ncs_filenames):
 
             verify_sec_struct = NcsSectionsFactory._verifySectionsStructure
             if not chanSectMap or (not verify_sec_struct(data, chan_ncs_sections)):
-                chan_ncs_sections = NcsSectionsFactory.build_for_ncs_file(data, nlxHeader)
+                chan_ncs_sections = NcsSectionsFactory.build_for_ncs_file(data, nlxHeader, strict_gap_mode=self.strict_gap_mode)
 
             # register file section structure for all contained channels
             for chan_uid in zip(nlxHeader["channel_names"], np.asarray(nlxHeader["channel_ids"], dtype=str)):