drop in ibldsp (#729)

Co-authored-by: chris-langfield <[email protected]>

Author: chris-langfield

brainbox/behavior/dlc.py

@@ -9,7 +9,7 @@
 import scipy.interpolate as interpolate
 from scipy.stats import zscore
 
-from neurodsp.smooth import smooth_interpolate_savgol
+from ibldsp.smooth import smooth_interpolate_savgol
 from iblutil.numerical import bincount2D
 import brainbox.behavior.wheel as bbox_wheel
 

brainbox/metrics/electrode_drift.py

@@ -1,6 +1,6 @@
 import numpy as np
 
-from neurodsp import smooth, utils, fourier
+from ibldsp import smooth, utils, fourier
 from iblutil.numerical import bincount2D
 
 

examples/archive/ibllib/synchronisation_ephys.py

@@ -1,4 +1,4 @@
-import neurodsp.utils
+import ibldsp.utils
 import spikeglx
 import ibllib.io.extractors.ephys_fpga
 
@@ -15,7 +15,7 @@
 
 # if the data is needed as well, loop over the file
 # raw data contains raw ephys traces, while raw_sync contains the 16 sync traces
-wg = neurodsp.utils.WindowGenerator(sr.ns, BATCH_SIZE_SAMPLES, overlap=1)
+wg = ibldsp.utils.WindowGenerator(sr.ns, BATCH_SIZE_SAMPLES, overlap=1)
 for first, last in wg.firstlast:
     rawdata, rawsync = sr.read_samples(first, last)
     wg.print_progress()

examples/loading_data/loading_raw_ephys_data.ipynb

@@ -236,7 +236,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from neurodsp.voltage import destripe\n",
+    "from ibldsp.voltage import destripe\n",
     "# Reminder : If not done before, remove first the sync channel from raw data\n",
     "# Apply destriping algorithm to data\n",
     "destriped = destripe(raw_ap, fs=sr_ap.fs)"
@@ -445,7 +445,7 @@
    "source": [
     "## Useful modules\n",
     "* [ibllib.io.spikeglx](https://int-brain-lab.github.io/ibl-neuropixel/_autosummary/spikeglx.html)\n",
-    "* [ibllib.voltage.dsp](https://int-brain-lab.github.io/ibl-neuropixel/_autosummary/neurodsp.voltage.html)\n",
+    "* [ibllib.voltage.dsp](https://int-brain-lab.github.io/ibl-neuropixel/_autosummary/ibldsp.voltage.html)\n",
     "* [brainbox.io.spikeglx.stream](https://int-brain-lab.github.io/iblenv/_autosummary/brainbox.io.spikeglx.html#brainbox.io.spikeglx.stream)\n",
     "* [viewephys](https://github.com/oliche/viewephys) to visualise raw data snippets (Note: this package is not within `ibllib` but standalone)"
    ]

examples/one/histology/coverage_map.py

@@ -1,7 +1,7 @@
 import matplotlib.pyplot as plt
 import numpy as np
 from one.api import ONE
-from neurodsp.utils import fcn_cosine
+from ibldsp.utils import fcn_cosine
 
 import iblatlas.atlas as atlas
 from ibllib.pipes.histology import coverage

ibllib/ephys/ephysqc.py

@@ -11,7 +11,7 @@
 from iblutil.util import Bunch
 import spikeglx
 import neuropixel
-from neurodsp import fourier, utils, voltage
+from ibldsp import fourier, utils, voltage
 from tqdm import tqdm
 
 from brainbox.io.spikeglx import Streamer

ibllib/ephys/sync_probes.py

@@ -199,7 +199,7 @@ def sync_probe_front_times(t, tref, sr, display=False, type='smooth', tol=2.0):
         to the sampling rate of digital channels. The residual is fit using frequency domain
         smoothing
         """
-        import neurodsp.fourier
+        import ibldsp.fourier
         CAMERA_UPSAMPLING_RATE_HZ = 300
         PAD_LENGTH_SECS = 60
         STAT_LENGTH_SECS = 30  # median length to compute padding value
@@ -214,7 +214,7 @@ def sync_probe_front_times(t, tref, sr, display=False, type='smooth', tol=2.0):
         res_filt = np.pad(res_upsamp, lpad, mode='median',
                           stat_length=CAMERA_UPSAMPLING_RATE_HZ * STAT_LENGTH_SECS)
         fbounds = [0.001, 0.002]
-        res_filt = neurodsp.fourier.lp(res_filt, 1 / CAMERA_UPSAMPLING_RATE_HZ, fbounds)[lpad[0]:-lpad[1]]
+        res_filt = ibldsp.fourier.lp(res_filt, 1 / CAMERA_UPSAMPLING_RATE_HZ, fbounds)[lpad[0]:-lpad[1]]
         tout = np.arange(0, np.max(tref) + SYNC_SAMPLING_RATE_SECS, 20)
         sync_points = np.c_[tout, np.polyval(pol, tout) + np.interp(tout, t_upsamp, res_filt)]
         if display:

ibllib/io/extractors/camera.py

@@ -10,7 +10,7 @@
 import matplotlib.pyplot as plt
 from iblutil.util import range_str
 
-import neurodsp.utils as dsp
+import ibldsp.utils as dsp
 from ibllib.plots import squares, vertical_lines
 from ibllib.io.video import assert_valid_label, VideoStreamer
 from iblutil.numerical import within_ranges

ibllib/io/extractors/ephys_fpga.py

@@ -44,7 +44,7 @@
 from packaging import version
 
 import spikeglx
-import neurodsp.utils
+import ibldsp.utils
 import one.alf.io as alfio
 from iblutil.util import Bunch
 from iblutil.spacer import Spacer
@@ -160,11 +160,11 @@ def _sync_to_alf(raw_ephys_apfile, output_path=None, save=False, parts=''):
     file_ftcp = Path(output_path).joinpath(f'fronts_times_channel_polarity{uuid.uuid4()}.bin')
 
     # loop over chunks of the raw ephys file
-    wg = neurodsp.utils.WindowGenerator(sr.ns, int(SYNC_BATCH_SIZE_SECS * sr.fs), overlap=1)
+    wg = ibldsp.utils.WindowGenerator(sr.ns, int(SYNC_BATCH_SIZE_SECS * sr.fs), overlap=1)
     fid_ftcp = open(file_ftcp, 'wb')
     for sl in wg.slice:
         ss = sr.read_sync(sl)
-        ind, fronts = neurodsp.utils.fronts(ss, axis=0)
+        ind, fronts = ibldsp.utils.fronts(ss, axis=0)
         # a = sr.read_sync_analog(sl)
         sav = np.c_[(ind[0, :] + sl.start) / sr.fs, ind[1, :], fronts.astype(np.double)]
         sav.tofile(fid_ftcp)
@@ -775,7 +775,7 @@ def _extract(self, sync=None, chmap=None, sync_collection='raw_ephys_data',
             bpod_start = self.bpod_trials['intervals'][:, 0]
             if len(t_trial_start) > len(bpod_start) / 2:  # if least half the trial start TTLs detected
                 _logger.warning('Attempting to get protocol period from aligning trial start TTLs')
-                fcn, *_ = neurodsp.utils.sync_timestamps(bpod_start, t_trial_start)
+                fcn, *_ = ibldsp.utils.sync_timestamps(bpod_start, t_trial_start)
                 buffer = 2.5  # the number of seconds to include before/after task
                 start, end = fcn(self.bpod_trials['intervals'].flat[[0, -1]])
                 tmin = min(sync['times'][0], start - buffer)
@@ -1202,7 +1202,7 @@ def sync_bpod_clock(bpod_trials, fpga_trials, sync_field):
                 bpod_fpga_timestamps[i] = trials[sync_field]
 
         # Sync the two timestamps
-        fcn, drift, ibpod, ifpga = neurodsp.utils.sync_timestamps(*bpod_fpga_timestamps, return_indices=True)
+        fcn, drift, ibpod, ifpga = ibldsp.utils.sync_timestamps(*bpod_fpga_timestamps, return_indices=True)
 
         # If it's drifting too much throw warning or error
         _logger.info('N trials: %i bpod, %i FPGA, %i merged, sync %.5f ppm',

ibllib/io/extractors/fibrephotometry.py

@@ -25,7 +25,7 @@
 from ibllib.io.extractors.base import BaseExtractor
 from ibllib.io.raw_daq_loaders import load_channels_tdms, load_raw_daq_tdms
 from ibllib.io.extractors.training_trials import GoCueTriggerTimes
-from neurodsp.utils import rises, sync_timestamps
+from ibldsp.utils import rises, sync_timestamps
 
 _logger = logging.getLogger(__name__)