From eb41a3157c79c31120926ea65be8d2d41e926df0 Mon Sep 17 00:00:00 2001
From: Gaelle <gaelle.chapuis.ibl@gmail.com>
Date: Tue, 24 Oct 2023 12:38:59 +0200
Subject: [PATCH] doc raw data probe geometry

---
 .../loading_data/loading_raw_ephys_data.ipynb | 57 +++++++++----------
 1 file changed, 28 insertions(+), 29 deletions(-)

diff --git a/examples/loading_data/loading_raw_ephys_data.ipynb b/examples/loading_data/loading_raw_ephys_data.ipynb
index 9394b675e..56716f450 100644
--- a/examples/loading_data/loading_raw_ephys_data.ipynb
+++ b/examples/loading_data/loading_raw_ephys_data.ipynb
@@ -152,7 +152,7 @@
     "\n",
     "# Use spikeglx reader to read in the whole raw data\n",
     "sr = spikeglx.Reader(bin_file)\n",
-    "sr.shape\n"
+    "print(sr.shape)"
    ]
   },
   {
@@ -328,57 +328,56 @@
   },
   {
    "cell_type": "markdown",
-   "id": "723df072",
-   "metadata": {},
    "source": [
     "## Get the probe geometry"
-   ]
+   ],
+   "metadata": {
+    "collapsed": false
+   }
   },
   {
    "cell_type": "markdown",
-   "id": "35a0db60",
-   "metadata": {},
    "source": [
     "### Using the `eid` and `probe` information"
-   ]
+   ],
+   "metadata": {
+    "collapsed": false
+   }
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c2335beb",
-   "metadata": {},
    "outputs": [],
    "source": [
     "from brainbox.io.one import load_channel_locations\n",
-    "from one.api import ONE\n",
-    "import spikeglx\n",
-    "import numpy as np\n",
-    "one = ONE()\n",
-    "\n",
-    "pid = 'da8dfec1-d265-44e8-84ce-6ae9c109b8bd'\n",
-    "eid, probe = one.pid2eid(pid)\n",
-    "channels = load_channel_locations(eid, probe)[probe]\n",
-    "channel_geometry = np.c_[channels['axial_um'], channels['lateral_um']]"
-   ]
+    "channels = load_channel_locations(eid, probe)\n",
+    "channels[probe][\"localCoordinates\"]"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
   },
   {
    "cell_type": "markdown",
-   "id": "360f668c",
-   "metadata": {},
    "source": [
     "### Using the reader and the `.cbin` file"
-   ]
+   ],
+   "metadata": {
+    "collapsed": false
+   }
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "763d6ac8",
-   "metadata": {},
    "outputs": [],
    "source": [
-    "sr = spikeglx.Reader(bin_file)\n",
+    "# You would have loaded the bin file as per the loading example above\n",
+    "# sr = spikeglx.Reader(bin_file)\n",
     "sr.geometry"
-   ]
+   ],
+   "metadata": {
+    "collapsed": false
+   }
   },
   {
    "cell_type": "markdown",
@@ -397,9 +396,9 @@
  "metadata": {
   "celltoolbar": "Edit Metadata",
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python [conda env:iblenv] *",
    "language": "python",
-   "name": "python3"
+   "name": "conda-env-iblenv-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -411,7 +410,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.16"
+   "version": "3.9.7"
   }
  },
  "nbformat": 4,