From 971f501a56f56dd726ebb54c7a58f4791567f1db Mon Sep 17 00:00:00 2001
From: olivier <olivier.winter@hotmail.fr>
Date: Mon, 19 Jun 2023 11:32:02 +0100
Subject: [PATCH] spikeglx.Reader(): add option to specify meta-data file

---
 release_notes.md |  3 +++
 setup.py         |  2 +-
 src/spikeglx.py  | 12 ++++++------
 3 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/release_notes.md b/release_notes.md
index 82bd7b4..760a839 100644
--- a/release_notes.md
+++ b/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
 - 
diff --git a/setup.py b/setup.py
index 94223c9..a2ab78c 100644
--- a/setup.py
+++ b/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,
diff --git a/src/spikeglx.py b/src/spikeglx.py
index 5f9fbc7..fa955c9 100644
--- a/src/spikeglx.py
+++ b/src/spikeglx.py
@@ -39,7 +39,7 @@ 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
@@ -47,8 +47,8 @@ def __init__(self, sglx_file, open=True, nc=None, ns=None, fs=None, dtype='int16
         """
         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: