Updates for compatibility with spikeinterface version 0.101

.ipynb_checkpoints/0-reference_files-checkpoint.ipynb

@@ -25,8 +25,8 @@
     "from ceciestunepipe.file import bcistructure as et\n",
     "\n",
     "sess_par = {\n",
-    "    'bird': 'z_r5r13_24',\n",
-    "    'sess': '2024-08-08'\n",
+    "    'bird': 'z_c7r3_24',\n",
+    "    'sess': '2024-10-27'\n",
     "}\n",
     "\n",
     "rig_dict_path = et.get_exp_struct(sess_par['bird'],sess_par['sess'])['files']['rig']"
@@ -50,7 +50,8 @@
     "            'microphone_M': 'adc-00',\n",
     "            'microphone_F': 'adc-05',\n",
     "            'wav_stim': 'adc-01',\n",
-    "            'wav_syn': 'adc-02'\n",
+    "            'wav_syn': 'adc-02',\n",
+    "            'opto_stim': 'adc-06'\n",
     "        },\n",
     "        'port': {\n",
     "            'probe_0': 'A-'\n",
@@ -59,7 +60,7 @@
     "    'probe': {\n",
     "        'probe_0': { # will always be probe_0 unless multiple recordings from different probes on the same day\n",
     "            'model': 'NP2013',\n",
-    "            'serial': '22420013432', # update every time\n",
+    "            'serial': '22420015061', # update every time\n",
     "            'headstage': '23280347'\n",
     "        }\n",
     "    }\n",

.ipynb_checkpoints/1.3-get_IMEC_lengths-checkpoint.ipynb

@@ -0,0 +1,168 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Look up lengths of IMEC recordings\n",
+    "\n",
+    "For recordings you want to concatenate, look up lengths of individual segments and stitch them together in 2-curate_acoustics\n",
+    "\n",
+    "Use the environment **songproc** to run this notebook"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "h5py version > 2.10.0. Some extractors might not work properly. It is recommended to downgrade to version 2.10.0: \n",
+      ">>> pip install h5py==2.10.0\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/mnt/cube/lo/envs/songproc/lib/python3.8/site-packages/spikeextractors/__init__.py:21: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.\n",
+      "  if StrictVersion(h5py.__version__) > '2.10.0':\n"
+     ]
+    }
+   ],
+   "source": [
+    "%matplotlib widget\n",
+    "import numpy as np\n",
+    "import sys\n",
+    "sys.path.append('/mnt/cube/lo/envs/ceciestunepipe')\n",
+    "from ceciestunepipe.file import bcistructure as et\n",
+    "from ceciestunepipe.util import sglxutil as sglu\n",
+    "from ceciestunepipe.util import sglxsync as sy\n",
+    "from ceciestunepipe.util.spikeextractors.extractors.spikeglxrecordingextractor import spikeglxrecordingextractor as sglex"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Set parameters"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# single session params\n",
+    "sess_par = {\n",
+    "    'bird':'z_c7r3_24',\n",
+    "    'sess':'2024-10-26',\n",
+    "    'stim_sess':[], # sessions where stimuli were presented\n",
+    "    'mic_list':['microphone_M','microphone_F'], # list of mics of interest, by signal name in rig.json\n",
+    "    'adc_list':[], # list of adc channels of interest\n",
+    "    'stim_list':[], # list of adc chans with the stimulus\n",
+    "    'nidq_ttl_list':[], # list of TTL signals form the nidq digital inputs to extract (besides the 'sync')\n",
+    "    'ref_stream':'ap_0', # what to synchronize everything to (sglx only, oe already synced)\n",
+    "    'trial_tag_chan':2, # sglx, what was the tag channel in the stimulus wave (this should come from meta et. al)\n",
+    "    'on_signal':1, # sglx, whether signal on is hi or lo\n",
+    "    'sort':'sort_0', # sort index\n",
+    "    'ephys_software':'sglx'\n",
+    "}"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "['1146_g0', '1201_g0', '1330_g0', '1403_g0', '1425_g0']\n"
+     ]
+    }
+   ],
+   "source": [
+    "# get epochs\n",
+    "sess_epochs = et.list_ephys_epochs(sess_par)\n",
+    "print(sess_epochs)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Display lengths of recordings"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Epoch 1146_g0: 27083876 samples\n",
+      "Epoch 1201_g0: 158552049 samples\n",
+      "Epoch 1330_g0: 13797107 samples\n",
+      "Epoch 1403_g0: 38425270 samples\n",
+      "Epoch 1425_g0: 235757801 samples\n",
+      "Sampling rate: 29999.68717785555 Hz\n"
+     ]
+    }
+   ],
+   "source": [
+    "for epoch in sess_epochs:\n",
+    "    sess_par['epoch'] = epoch\n",
+    "\n",
+    "    epoch_struct = et.sgl_struct(sess_par,sess_par['epoch'],ephys_software=sess_par['ephys_software'])\n",
+    "\n",
+    "    # get epoch files\n",
+    "    sgl_folders, sgl_files = sglu.sgl_file_struct(epoch_struct['folders']['sglx'])\n",
+    "    run_meta_files = {k:v[0] for k,v in sgl_files.items()}\n",
+    "    run_recordings = {k:sglex.SpikeGLXRecordingExtractor(sglu.get_data_meta_path(v)[0]) for k,v in run_meta_files.items()}\n",
+    "\n",
+    "    # get streams, from raw recording extractors and preprocessed data\n",
+    "    all_streams = list(run_recordings.keys()) #+ ['wav'] ### might want to just remove this\n",
+    "    all_syn_dict = {k:sy.get_syn_pattern(run_recordings,epoch_struct,k,force=False) for k in all_streams}\n",
+    "    \n",
+    "    # display n_samples\n",
+    "    print('Epoch {}: {} samples'.format(epoch, np.shape(all_syn_dict['ap_0']['t_0'])[0]))\n",
+    "    \n",
+    "print('Sampling rate:',all_syn_dict['ap_0']['s_f'],'Hz')"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "songproc",
+   "language": "python",
+   "name": "songproc"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.16"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}