vr behaviour implemented

pixels/configs.py

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+import logging
+
+from wavpack_numcodecs import WavPack
+from numcodecs import Blosc
+import spikeinterface as si
+
+# Configure logging to include a timestamp with seconds
+logging.basicConfig(
+    level=logging.INFO,
+    format='''\n%(asctime)s %(levelname)s: %(message)s\
+            \n[in %(filename)s:%(lineno)d]''',
+    datefmt='%Y%m%d %H:%M:%S',
+)
+
+#logging.info('This is an info message.')
+#logging.warning('This is a warning message.')
+#logging.error('This is an error message.')
+
+# set si job_kwargs
+job_kwargs = dict(
+    pool_engine="thread", # instead of default "process"
+    #pool_engine="process",# does not work on 2025 oct 14
+    mp_context="fork", # linux
+    #mp_context="spawn", # mac & win
+    progress_bar=True,
+    n_jobs=0.8,
+    chunk_duration='1s',
+    max_threads_per_worker=8,
+)
+si.set_global_job_kwargs(**job_kwargs)
+
+# instantiate WavPack compressor
+wv_compressor = WavPack(
+    level=3, # high compression
+    bps=None, # lossless
+)
+
+# use blosc compressor for generic zarr
+compressor = Blosc(
+    cname="zstd",
+    clevel=5,
+    shuffle=Blosc.BITSHUFFLE,
+)
+
+# kilosort 4 singularity image names
+ks4_0_30_image_name = "si103.0_ks4-0-30_with_wavpack.sif"
+#ks4_0_30_image_name = "si102.3_ks4-0-30_with_wavpack.sif"
+ks4_0_18_image_name = "ks4-0-18_with_wavpack.sif"
+ks4_image_name = ks4_0_30_image_name

pixels/constants.py

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+"""
+This file contains some constants parameters for the pixels pipeline.
+"""
+import numpy as np
+
+SAMPLE_RATE = 2000 # Hz
+
+freq_bands = {
+    "ap":[300, 9000],
+    "lfp":[0.5, 500],
+    "theta":[4, 11], # from Tom
+    "gamma":[30, 80], # from Tom
+    "ripple":[110, 220], # from Tom
+}
+
+BEHAVIOUR_HZ = 25000
+
+np.random.seed(BEHAVIOUR_HZ)
+
+REPEATS = 100
+
+# latency of luminance change evoked spike
+# NOTE: usually it should be between 40-60ms. now we use 500ms just to test
+V1_SPIKE_LATENCY = 500 # ms #60
+V1_LFP_LATENCY = 40 # ms
+LGN_SPIKE_LATENCY = 30 # ms
+
+# chunking for zarr
+SMALL_CHUNKS = 64
+BIG_CHUNKS = 1024
+
+ALPHA = 0.05
+
+# position bin sizes
+POSITION_BIN = 1 # cm
+BIG_POSITION_BIN = 10 # cm