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Draft public docs for Multi-Channel timeseries and Large Image workflows #96

Merged
merged 14 commits into from
Jun 12, 2024
171 changes: 72 additions & 99 deletions README.md

Large diffs are not rendered by default.

80 changes: 75 additions & 5 deletions benchmarks/create_ephys_data.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -29,7 +29,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -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,
Expand All @@ -152,7 +222,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "neuro-eeg-viewer",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -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
}
12 changes: 1 addition & 11 deletions workflows/image_stack/workflow_image-stack.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand All @@ -405,7 +395,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.18"
"version": "3.12.3"
}
},
"nbformat": 4,
Expand Down
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