fix the docs

int-brain-lab · Oct 19, 2023 · 21233e3 · 21233e3
1 parent 183a68d
commit 21233e3
Showing 1 changed file with 27 additions and 25 deletions.
diff --git a/examples/loading_data/loading_raw_ephys_data.ipynb b/examples/loading_data/loading_raw_ephys_data.ipynb
@@ -328,55 +328,57 @@
   },
   {
    "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",
-    "channels = load_channel_locations(eid, probe)\n",
-    "channels[probe][\"localCoordinates\"]"
-   ],
-   "metadata": {
-    "collapsed": false
-   }
+    "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']]"
+   ]
   },
   {
    "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",
     "sr.geometry"
-   ],
-   "metadata": {
-    "collapsed": false
-   }
+   ]
   },
   {
    "cell_type": "markdown",
@@ -395,9 +397,9 @@
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+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
-   "name": "conda-env-iblenv-py"
+   "name": "python3"
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   "language_info": {
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@@ -409,7 +411,7 @@
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    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
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+   "version": "3.9.16"
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