Merge branch 'master' into sgrawio_chan_fix

Author: zm711

neo/io/__init__.py

@@ -453,7 +453,7 @@ def list_candidate_ios(file_or_folder, ignore_patterns=["*.ini", "README.txt", "
 
     elif file_or_folder.is_dir():
         # scan files in folder to determine io type
-        filenames = [f for f in file_or_folder.glob("*") if f.is_file()]
+        filenames = [f for f in file_or_folder.glob("**/*") if f.is_file()]
         # keep only relevant filenames
         filenames = [f for f in filenames if f.suffix and not any([f.match(p) for p in ignore_patterns])]
 

neo/rawio/intanrawio.py

@@ -107,7 +107,7 @@ def __init__(self, filename, pl2_dll_file_path=None):
         # download default PL2 dll once if not yet available
         if pl2_dll_file_path is None:
             architecture = platform.architecture()[0]
-            if architecture == "64bit" and platform.system() == "Windows":
+            if architecture == "64bit" and platform.system() in ["Windows", "Darwin"]:
                 file_name = "PL2FileReader64.dll"
             else:  # Apparently wine uses the 32 bit version in linux
                 file_name = "PL2FileReader.dll"
@@ -120,16 +120,26 @@ def __init__(self, filename, pl2_dll_file_path=None):
                 dist = urlopen(url=url)
 
                 with open(pl2_dll_file_path, "wb") as f:
-                    print(f"Downloading plexon dll to {pl2_dll_file_path}")
+                    warnings.warn(f"dll file does not exist, downloading plexon dll to {pl2_dll_file_path}")
                     f.write(dist.read())
 
         # Instantiate wrapper for Windows DLL
         from neo.rawio.plexon2rawio.pypl2.pypl2lib import PyPL2FileReader
 
         self.pl2reader = PyPL2FileReader(pl2_dll_file_path=pl2_dll_file_path)
 
-        # Open the file.
-        self.pl2reader.pl2_open_file(self.filename)
+        reading_attempts = 10
+        for attempt in range(reading_attempts):
+            self.pl2reader.pl2_open_file(self.filename)
+
+            # Verify the file handle is valid.
+            if self.pl2reader._file_handle.value != 0:
+                # File handle is valid, exit the loop early
+                break
+            else:
+                if attempt == reading_attempts - 1:
+                    self.pl2reader._print_error()
+                    raise IOError(f"Opening {self.filename} failed after {reading_attempts} attempts.")
 
     def _source_name(self):
         return self.filename
@@ -146,7 +156,6 @@ def _parse_header(self):
         Source = namedtuple("Source", "id name sampling_rate n_samples")
         for c in range(self.pl2reader.pl2_file_info.m_TotalNumberOfAnalogChannels):
             achannel_info = self.pl2reader.pl2_get_analog_channel_info(c)
-
             # only consider active channels
             if not achannel_info.m_ChannelEnabled:
                 continue
@@ -262,8 +271,10 @@ def _parse_header(self):
                     # python is 1..12 https://docs.python.org/3/library/datetime.html#datetime.datetime
                     # so month needs to be tm_mon+1; also tm_sec could cause problems in the case of leap
                     # seconds, but this is harder to defend against.
+                    year = tmo.tm_year  # This has base 1900 in the c++ struct specification so we need to add 1900
+                    year += 1900
                     dt = datetime(
-                        year=tmo.tm_year,
+                        year=year,
                         month=tmo.tm_mon + 1,
                         day=tmo.tm_mday,
                         hour=tmo.tm_hour,
@@ -317,7 +328,6 @@ def _parse_header(self):
                 "m_OneBasedChannelInTrode",
                 "m_Source",
                 "m_Channel",
-                "m_Name",
                 "m_MaximumNumberOfFragments",
             ]
 

neo/rawio/plexon2rawio/plexon2rawio.py

@@ -25,7 +25,10 @@
 
     from zugbruecke import CtypesSession
 
-    ctypes = CtypesSession(log_level=100)
+    if platform.system() == "Darwin":
+        ctypes = CtypesSession(log_level=100, arch="win64")
+    else:
+        ctypes = CtypesSession(log_level=100)
 
 
 class tm(ctypes.Structure):
@@ -610,7 +613,7 @@ def pl2_get_spike_channel_info_by_name(self, channel_name):
 
         self.pl2_dll.PL2_GetSpikeChannelInfoByName.argtypes = (
             ctypes.c_int,
-            ctypes.c_char * len(channel_name),
+            ctypes.POINTER(ctypes.c_char),
             ctypes.POINTER(PL2SpikeChannelInfo),
         )
 
@@ -629,11 +632,9 @@ def pl2_get_spike_channel_info_by_name(self, channel_name):
         result = self.pl2_dll.PL2_GetSpikeChannelInfoByName(
             self._file_handle, channel_name, ctypes.byref(pl2_spike_channel_info)
         )
-
         if not result:
             self._print_error()
             return None
-
         return pl2_spike_channel_info
 
     def pl2_get_spike_channel_info_by_source(self, source_id, one_based_channel_index_in_source):
@@ -744,7 +745,7 @@ def pl2_get_spike_channel_data_by_name(self, channel_name):
 
         self.pl2_dll.PL2_GetSpikeChannelDataByName.argtypes = (
             ctypes.c_int,
-            ctypes.c_char,
+            ctypes.POINTER(ctypes.c_char),
             ctypes.POINTER(ctypes.c_ulonglong),
             ctypes.POINTER(ctypes.c_ulonglong),
             ctypes.POINTER(ctypes.c_ushort),

neo/rawio/plexon2rawio/pypl2/pypl2lib.py

@@ -95,14 +95,14 @@ def _parse_header(self):
         )
 
         # dsp channels header = spikes and waveforms
-        nb_unit_chan = global_header["NumDSPChannels"]
+        nb_unit_chan = int(global_header["NumDSPChannels"])
         offset1 = np.dtype(GlobalHeader).itemsize
         dspChannelHeaders = np.memmap(
             self.filename, dtype=DspChannelHeader, mode="r", offset=offset1, shape=(nb_unit_chan,)
         )
 
         # event channel header
-        nb_event_chan = global_header["NumEventChannels"]
+        nb_event_chan = int(global_header["NumEventChannels"])
         offset2 = offset1 + np.dtype(DspChannelHeader).itemsize * nb_unit_chan
         eventHeaders = np.memmap(
             self.filename,
@@ -113,7 +113,7 @@ def _parse_header(self):
         )
 
         # slow channel header = signal
-        nb_sig_chan = global_header["NumSlowChannels"]
+        nb_sig_chan = int(global_header["NumSlowChannels"])
         offset3 = offset2 + np.dtype(EventChannelHeader).itemsize * nb_event_chan
         slowChannelHeaders = np.memmap(
             self.filename, dtype=SlowChannelHeader, mode="r", offset=offset3, shape=(nb_sig_chan,)
@@ -136,7 +136,9 @@ def _parse_header(self):
 
         while pos < data.size:
             bl_header = data[pos : pos + 16].view(DataBlockHeader)[0]
-            length = bl_header["NumberOfWaveforms"] * bl_header["NumberOfWordsInWaveform"] * 2 + 16
+            number_of_waveforms = int(bl_header["NumberOfWaveforms"])
+            number_of_words_in_waveform = int(bl_header["NumberOfWordsInWaveform"])
+            length = (number_of_waveforms * number_of_words_in_waveform * 2) + 16
             bl_type = int(bl_header["Type"])
             chan_id = int(bl_header["Channel"])
             block_pos[bl_type][chan_id].append(pos)

neo/rawio/plexonrawio.py

@@ -387,61 +387,71 @@ def parse_spikeglx_fname(fname):
     Consider the filenames: `Noise4Sam_g0_t0.nidq.bin` or `Noise4Sam_g0_t0.imec0.lf.bin`
     The filenames consist of 3 or 4 parts separated by `.`
     1. "Noise4Sam_g0_t0" will be the `name` variable. This choosen by the user at recording time.
-    2. "_g0_" is the "gate_num"
-    3. "_t0_" is the "trigger_num"
+    2. "g0" is the "gate_num"
+    3. "t0" is the "trigger_num"
     4. "nidq" or "imec0" will give the `device`
     5. "lf" or "ap" will be the `stream_kind`
-        `stream_name` variable is the concatenation of `device.stream_kind`
+       `stream_name` variable is the concatenation of `device.stream_kind`
+
+    If CatGT is used, then the trigger numbers in the file names ("t0"/"t1"/etc.)
+    will be renamed to "tcat". In this case, the parsed "trigger_num" will be set to "cat".
 
     This function is copied/modified from Graham Findlay.
 
     Notes:
-       * Sometimes the original file name is modified by the user and "_gt0_" or "_t0_"
+        * Sometimes the original file name is modified by the user and "_g0_" or "_t0_"
           are manually removed. In that case gate_name and trigger_num will be None.
 
     Parameters
     ---------
     fname: str
         The filename to parse without the extension, e.g. "my-run-name_g0_t1.imec2.lf"
+
     Returns
     -------
     run_name: str
         The run name, e.g. "my-run-name".
     gate_num: int or None
         The gate identifier, e.g. 0.
-    trigger_num: int or None
-        The trigger identifier, e.g. 1.
+    trigger_num: int | str or None
+        The trigger identifier, e.g. 1. If CatGT is used, then the trigger_num will be set to "cat".
     device: str
         The probe identifier, e.g. "imec2"
     stream_kind: str or None
         The data type identifier, "lf" or "ap" or None
     """
-    r = re.findall(r"(\S*)_g(\d*)_t(\d*)\.(\S*).(ap|lf)", fname)
-    if len(r) == 1:
+    re_standard = re.findall(r"(\S*)_g(\d*)_t(\d*)\.(\S*).(ap|lf)", fname)
+    re_tcat = re.findall(r"(\S*)_g(\d*)_tcat.(\S*).(ap|lf)", fname)
+    re_nidq = re.findall(r"(\S*)_g(\d*)_t(\d*)\.(\S*)", fname)
+    if len(re_standard) == 1:
         # standard case with probe
-        run_name, gate_num, trigger_num, device, stream_kind = r[0]
+        run_name, gate_num, trigger_num, device, stream_kind = re_standard[0]
+    elif len(re_tcat) == 1:
+        # tcat case
+        run_name, gate_num, device, stream_kind = re_tcat[0]
+        trigger_num = "cat"
+    elif len(re_nidq) == 1:
+        # case for nidaq
+        run_name, gate_num, trigger_num, device = re_nidq[0]
+        stream_kind = None
     else:
-        r = re.findall(r"(\S*)_g(\d*)_t(\d*)\.(\S*)", fname)
-        if len(r) == 1:
-            # case for nidaq
-            run_name, gate_num, trigger_num, device = r[0]
-            stream_kind = None
+        # the naming do not correspond lets try something more easy
+        # example: sglx_xxx.imec0.ap
+        re_else = re.findall(r"(\S*)\.(\S*).(ap|lf)", fname)
+        re_else_nidq = re.findall(r"(\S*)\.(\S*)", fname)
+        if len(re_else) == 1:
+            run_name, device, stream_kind = re_else_nidq[0]
+            gate_num, trigger_num = None, None
+        elif len(re_else_nidq) == 1:
+            # easy case for nidaq, example: sglx_xxx.nidq
+            run_name, device = re_else_nidq[0]
+            gate_num, trigger_num, stream_kind = None, None, None
         else:
-            # the naming do not correspond lets try something more easy
-            # example: sglx_xxx.imec0.ap
-            r = re.findall(r"(\S*)\.(\S*).(ap|lf)", fname)
-            if len(r) == 1:
-                run_name, device, stream_kind = r[0]
-                gate_num, trigger_num = None, None
-            else:
-                # easy case for nidaq, example: sglx_xxx.nidq
-                r = re.findall(r"(\S*)\.(\S*)", fname)
-                run_name, device = r[0]
-                gate_num, trigger_num, stream_kind = None, None, None
+            raise ValueError(f"Cannot parse filename {fname}")
 
     if gate_num is not None:
         gate_num = int(gate_num)
-    if trigger_num is not None:
+    if trigger_num is not None and trigger_num != "cat":
         trigger_num = int(trigger_num)
 
     return (run_name, gate_num, trigger_num, device, stream_kind)

neo/rawio/spikeglxrawio.py

@@ -32,6 +32,13 @@ class TestSpikeGLXRawIO(BaseTestRawIO, unittest.TestCase):
         "spikeglx/NP2_subset_with_sync",
         # NP-ultra
         "spikeglx/np_ultra_stub",
+        # CatGT
+        "spikeglx/multi_trigger_multi_gate/CatGT/CatGT-A",
+        "spikeglx/multi_trigger_multi_gate/CatGT/CatGT-B",
+        "spikeglx/multi_trigger_multi_gate/CatGT/CatGT-C",
+        "spikeglx/multi_trigger_multi_gate/CatGT/CatGT-D",
+        "spikeglx/multi_trigger_multi_gate/CatGT/CatGT-E",
+        "spikeglx/multi_trigger_multi_gate/CatGT/Supercat-A",
     ]
 
     def test_with_location(self):