Merge pull request #96 from holoviz-topics/public-docs-multi-ts

Draft public docs for Multi-Channel timeseries set of workflows

benchmarks/create_ephys_data.ipynb

@@ -13,7 +13,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -29,7 +29,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -142,6 +142,76 @@
     "    mr.save_recording_generator(recgen, f'data/ephys_sim_neuropixels_{dur}s_384ch.h5')"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Add channel names object"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 16,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "/Users/droumis/data/ephys_sim_neuropixels/ephys_sim_neuropixels_1s_384ch.h5 num_channels: 384\n",
+      "channels object already present.\n",
+      "/Users/droumis/data/ephys_sim_neuropixels/ephys_sim_neuropixels_10s_384ch.h5 num_channels: 384\n",
+      "channels object already present.\n",
+      "/Users/droumis/data/ephys_sim_neuropixels/ephys_sim_neuropixels_100s_384ch.h5 num_channels: 384\n",
+      "channels object added successfully.\n",
+      "channels object already present.\n",
+      "/Users/droumis/data/ephys_sim_neuropixels/ephys_sim_neuropixels_200s_384ch.h5 num_channels: 384\n",
+      "channels object added successfully.\n",
+      "channels object already present.\n"
+     ]
+    }
+   ],
+   "source": [
+    "import h5py\n",
+    "from pathlib import Path\n",
+    "\n",
+    "durations = [1, 10, 100, 200]\n",
+    "\n",
+    "for dur in durations:\n",
+    "    # Open the existing HDF5 file in append mode\n",
+    "    H5_PATH = Path(f'~/data/ephys_sim_neuropixels/ephys_sim_neuropixels_{dur}s_384ch.h5').expanduser()\n",
+    "    with h5py.File(H5_PATH, 'a') as f:\n",
+    "        num_channels = f['channel_positions'].shape[0]\n",
+    "        print(H5_PATH, 'num_channels:', num_channels)\n",
+    "        # skip if 'channels' object already exists\n",
+    "        if 'channels' in f:\n",
+    "            print(\"channels object already present.\")\n",
+    "        else:\n",
+    "            f.create_dataset('channels', data=list(range(384)))\n",
+    "            print(\"channels object added successfully.\") \n",
+    "    "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "PosixPath('/Users/droumis/data/ephys_sim_neuropixels_10s_384ch.h5')"
+      ]
+     },
+     "execution_count": 9,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "H5_PATH"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -152,7 +222,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "neuro-eeg-viewer",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -166,9 +236,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "version": "3.11.8"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

workflows/image_stack/workflow_image-stack.ipynb

@@ -370,16 +370,6 @@
     "# TODO: Consider including additional advanced versions are in 231218_backup_workflow_image-stack.ipynb"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "4905ce20-3c49-4631-b4b7-6676faa2d9e7",
-   "metadata": {},
-   "source": [
-    "## Conclusion\n",
-    "\n",
-    "This workflow represents our efforts to create a performant and easily adaptable tool for neuroscience imaging data visualization."
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -405,7 +395,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.18"
+   "version": "3.12.3"
   }
  },
  "nbformat": 4,