ibl-neuropixel 1.8.0__tar.gz → 1.8.1__tar.gz

{ibl_neuropixel-1.8.0/src/ibl_neuropixel.egg-info → ibl_neuropixel-1.8.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ibl-neuropixel
-Version: 1.8.0
+Version: 1.8.1
 Summary: Collection of tools for Neuropixel 1.0 and 2.0 probes data
 Home-page: https://github.com/int-brain-lab/ibl-neuropixel
 Author: The International Brain Laboratory

{ibl_neuropixel-1.8.0 → ibl_neuropixel-1.8.1}/setup.py

@@ -8,7 +8,7 @@ with open("requirements.txt") as f:
 
 setuptools.setup(
     name="ibl-neuropixel",
-    version="1.8.0",
+    version="1.8.1",
     author="The International Brain Laboratory",
     description="Collection of tools for Neuropixel 1.0 and 2.0 probes data",
     long_description=long_description,

{ibl_neuropixel-1.8.0 → ibl_neuropixel-1.8.1/src/ibl_neuropixel.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ibl-neuropixel
-Version: 1.8.0
+Version: 1.8.1
 Summary: Collection of tools for Neuropixel 1.0 and 2.0 probes data
 Home-page: https://github.com/int-brain-lab/ibl-neuropixel
 Author: The International Brain Laboratory

{ibl_neuropixel-1.8.0 → ibl_neuropixel-1.8.1}/src/ibldsp/voltage.py

@@ -456,8 +456,9 @@ def decompress_destripe_cbin(
     :param nbatch: (optional) batch size
     :param nprocesses: (optional) number of parallel processes to run, defaults to number or processes detected with joblib
      interp 3:outside of brain and discard
-    :param reject_channels: (True) detects noisy or bad channels and interpolate them. Channels outside of the brain are left
-     untouched
+    :param reject_channels: (True) True | False | np.array()
+      If True, detects noisy or bad channels and interpolate them, zero out the channels outside the brain.
+      If the labels are already computed, they can be provided as a numpy array.
     :param k_kwargs: (None) arguments for the kfilter function
     :param reader_kwargs: (None) optional arguments for the spikeglx Reader instance
     :param k_filter: (True) True | False | None | custom function.
@@ -475,8 +476,11 @@ def decompress_destripe_cbin(
     # handles input parameters
     reader_kwargs = {} if reader_kwargs is None else reader_kwargs
     sr = spikeglx.Reader(sr_file, open=True, **reader_kwargs)
-    if reject_channels:  # get bad channels if option is on
+    if reject_channels is True:  # get bad channels if option is on
         channel_labels = detect_bad_channels_cbin(sr)
+    elif isinstance(reject_channels, np.ndarray):
+        channel_labels = reject_channels
+        reject_channels = True
     assert isinstance(sr_file, str) or isinstance(sr_file, Path)
     butter_kwargs, k_kwargs, spatial_fcn = _get_destripe_parameters(
         sr.fs, butter_kwargs, k_kwargs, k_filter
@@ -502,7 +506,6 @@ def decompress_destripe_cbin(
     DEPHAS = np.exp(
         1j * np.angle(fft_object(dephas)) * h["sample_shift"][:, np.newaxis]
     )
-
     # if we want to compute the rms ap across the session as well as the saturation
     if compute_rms:
         # creates a saturation memmap, this is a nsamples vector of booleans
@@ -772,7 +775,23 @@ def detect_bad_channels(
         )
     )[0]
     # the channels outside of the brains are the contiguous channels below the threshold on the trend coherency
-    ioutside = np.where(xfeats["xcor_lf"] < -0.75)[0]  # fixme: hardcoded threshold
+
+    signal_noisy = xfeats["xcor_lf"]
+    # Filter signal
+    window_size = 25  # Choose based on desired smoothing (e.g., 25 samples)
+    kernel = np.ones(window_size) / window_size
+    # Apply convolution
+    signal_filtered = np.convolve(signal_noisy, kernel, mode='same')
+
+    diff_x = np.diff(signal_filtered)
+    indx = np.where(diff_x < -0.02)[0]  # hardcoded threshold
+    if indx.size > 0:
+        indx_threshold = np.floor(np.median(indx)).astype(int)
+        threshold = signal_noisy[indx_threshold]
+        ioutside = np.where(signal_noisy < threshold)[0]
+    else:
+        ioutside = np.array([])
+
     if ioutside.size > 0 and ioutside[-1] == (nc - 1):
         a = np.cumsum(np.r_[0, np.diff(ioutside) - 1])
         ioutside = ioutside[a == np.max(a)]