spikeglx.Reader(): add option to specify meta-data file

release_notes.md

@@ -1,4 +1,7 @@
 # 0.6.0
+## 0.6.2 2023-06-19
+- add option to specify meta-data file for spikeglx.Reader
+
 ## 0.6.1 2023-06-06
 - Fix bug in ADC cycles sampling for Neuropixel 1.0 probes
 - 

setup.py

@@ -8,7 +8,7 @@
 
 setuptools.setup(
     name="ibl-neuropixel",
-    version="0.6.1",
+    version="0.6.2",
     author="The International Brain Laboratory",
     description="Collection of tools for Neuropixel 1.0 and 2.0 probes data",
     long_description=long_description,

src/spikeglx.py

@@ -39,16 +39,16 @@ class Reader:
     """
 
     def __init__(self, sglx_file, open=True, nc=None, ns=None, fs=None, dtype='int16', s2v=None,
-                 nsync=None, ignore_warnings=False):
+                 nsync=None, ignore_warnings=False, meta_file=None):
         """
         An interface for reading data from a SpikeGLX file
         :param sglx_file: Path to a SpikeGLX file (compressed or otherwise), or to a meta-data file
         :param open: when True the file is opened
         """
         self.ignore_warnings = ignore_warnings
         sglx_file = Path(sglx_file)
-        file_meta_data = sglx_file.with_suffix('.meta')
-        if file_meta_data == sglx_file:
+        meta_file = meta_file or sglx_file.with_suffix('.meta')
+        if meta_file == sglx_file:
             # if a meta-data file is provided, try to get the binary file
             self.file_bin = sglx_file.with_suffix('.cbin') if sglx_file.with_suffix('.cbin').exists() else None
             self.file_bin = sglx_file.with_suffix('.bin') if sglx_file.with_suffix('.bin').exists() else None
@@ -57,7 +57,7 @@ def __init__(self, sglx_file, open=True, nc=None, ns=None, fs=None, dtype='int16
         self.nbytes = self.file_bin.stat().st_size if self.file_bin else None
         self.dtype = np.dtype(dtype)
 
-        if not file_meta_data.exists():
+        if not meta_file.exists():
             # if no meta-data file is provided, try to get critical info from the binary file
             # by seeing if filesize checks out with neuropixel 384 channels
             if self.file_bin.stat().st_size / 384 % 2 == 0:
@@ -85,8 +85,8 @@ def __init__(self, sglx_file, open=True, nc=None, ns=None, fs=None, dtype='int16
                 self.channel_conversion_sample2v['samples'][-nsync:] = 1
         else:
             # normal case we continue reading and interpreting the metadata file
-            self.file_meta_data = file_meta_data
-            self.meta = read_meta_data(file_meta_data)
+            self.file_meta_data = meta_file
+            self.meta = read_meta_data(meta_file)
             self.channel_conversion_sample2v = _conversion_sample2v_from_meta(self.meta)
             self._raw = None
         if open and self.file_bin: