Skip to content

Commit

Permalink
Merge pull request #79 from NeurodataWithoutBorders/readme
Browse files Browse the repository at this point in the history
  • Loading branch information
@rly
rly authored Jun 2, 2024
2 parents 85e7897 + e27213e commit 79d7295
Show file tree
Hide file tree
Showing 2 changed files with 210 additions and 7 deletions.
9 changes: 2 additions & 7 deletions README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -77,12 +77,7 @@ h5_url = "https://api.dandiarchive.org/api/assets/11f512ba-5bcf-4230-a8cb-dc8d36
# Create the h5py-like client
client = lindi.LindiH5pyFile.from_hdf5_file(h5_url)

# Generate a reference file system
rfs = client.to_reference_file_system()

# Save it to a file for later use
with open("example.lindi.json", "w") as f:
json.dump(rfs, f, indent=2)
client.write_lindi_file('example.lindi.json')

# See the next example for how to read this file
```
Expand Down Expand Up @@ -116,7 +111,7 @@ url = 'https://lindi.neurosift.org/dandi/dandisets/000939/assets/56d875d6-a705-4

# Load the h5py-like client for the reference file system
# in read-write mode
client = lindi.LindiH5pyFile.from_reference_file_system(url, mode="r+")
client = lindi.LindiH5pyFile.from_lindi_file(url, mode="r+")

# Edit an attribute
client.attrs['new_attribute'] = 'new_value'
Expand Down
208 changes: 208 additions & 0 deletions examples/lindi_demo.ipynb
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,208 @@
{
"cells": [
{
"cell_type": "code",
"execution_count": null,
"id": "52802664-85e7-433a-a8c3-f2645847423b",
"metadata": {
"scrolled": true
},
"outputs": [],
"source": [
"%pip install -q lindi\n",
"%pip install -q pynwb"
]
},
{
"cell_type": "markdown",
"id": "94dadefb-c04a-4aea-b906-b4cc3a263570",
"metadata": {},
"source": [
"### Lazy-load a remote NWB/HDF5 file for efficient access to metadata and data"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "65b50dec-5c6e-40cf-aa93-c18d220b74bb",
"metadata": {},
"outputs": [],
"source": [
"import pynwb\n",
"import lindi\n",
"\n",
"# URL of the remote NWB file\n",
"h5_url = \"https://api.dandiarchive.org/api/assets/11f512ba-5bcf-4230-a8cb-dc8d36db38cb/download/\"\n",
"\n",
"# Set up a local cache\n",
"local_cache = lindi.LocalCache(cache_dir='lindi_cache')\n",
"\n",
"# Create the h5py-like client\n",
"client = lindi.LindiH5pyFile.from_hdf5_file(h5_url, local_cache=local_cache)\n",
"\n",
"# Open using pynwb\n",
"with pynwb.NWBHDF5IO(file=client, mode=\"r\") as io:\n",
" nwbfile = io.read()\n",
" print(nwbfile)\n",
"\n",
"# The downloaded data will be cached locally, so subsequent reads will be faster"
]
},
{
"cell_type": "markdown",
"id": "79a2ce81-c3da-4c9c-a013-fd5fa34762f7",
"metadata": {},
"source": [
"### Represent a remote NWB/HDF5 file as a .nwb.lindi.json file"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "d11db473-ab25-4d1e-ac15-7a16654c4bcf",
"metadata": {},
"outputs": [],
"source": [
"import json\n",
"import lindi\n",
"\n",
"# URL of the remote NWB file\n",
"h5_url = \"https://api.dandiarchive.org/api/assets/11f512ba-5bcf-4230-a8cb-dc8d36db38cb/download/\"\n",
"\n",
"# Create the h5py-like client\n",
"client = lindi.LindiH5pyFile.from_hdf5_file(h5_url)\n",
"\n",
"client.write_lindi_file('example.lindi.json')\n",
"\n",
"# See the next example for how to read this file"
]
},
{
"cell_type": "markdown",
"id": "2550661e-ee88-45d8-b6b2-8c6f8fe4dfaa",
"metadata": {},
"source": [
"### Read a local or remote .nwb.lindi.json file using pynwb or other tools"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "9973c935-db2e-468f-ba9c-7f5e7153b319",
"metadata": {},
"outputs": [],
"source": [
"import pynwb\n",
"import lindi\n",
"\n",
"# URL of the remote .nwb.lindi.json file\n",
"url = 'https://lindi.neurosift.org/dandi/dandisets/000939/assets/56d875d6-a705-48d3-944c-53394a389c85/nwb.lindi.json'\n",
"\n",
"# Load the h5py-like client\n",
"client = lindi.LindiH5pyFile.from_lindi_file(url)\n",
"\n",
"# Open using pynwb\n",
"with pynwb.NWBHDF5IO(file=client, mode=\"r\") as io:\n",
" nwbfile = io.read()\n",
" print(nwbfile)"
]
},
{
"cell_type": "markdown",
"id": "ea03ad43-7d0b-4cfd-9992-bdb1ada6b13c",
"metadata": {},
"source": [
"### Edit a .nwb.lindi.json file using pynwb or other tools"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "1c66931b-3ea9-4222-afc8-a93b25457e37",
"metadata": {},
"outputs": [],
"source": [
"import json\n",
"import lindi\n",
"\n",
"# URL of the remote .nwb.lindi.json file\n",
"url = 'https://lindi.neurosift.org/dandi/dandisets/000939/assets/56d875d6-a705-48d3-944c-53394a389c85/nwb.lindi.json'\n",
"\n",
"# Load the h5py-like client for the reference file system\n",
"# in read-write mode\n",
"client = lindi.LindiH5pyFile.from_lindi_file(url, mode=\"r+\")\n",
"\n",
"# Edit an attribute\n",
"client.attrs['new_attribute'] = 'new_value'\n",
"\n",
"# Save the changes to a new .nwb.lindi.json file\n",
"client.write_lindi_file('new.nwb.lindi.json')"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "fe19e0f6-1c62-42e9-9af0-4a57c8a61364",
"metadata": {},
"outputs": [],
"source": [
"# Now load that file\n",
"client2 = lindi.LindiH5pyFile.from_lindi_file('new.nwb.lindi.json')\n",
"print(client2.attrs['new_attribute'])"
]
},
{
"cell_type": "markdown",
"id": "4a2addfc-58ed-4e79-9c64-b7ec95cb12f5",
"metadata": {},
"source": [
"### Add datasets to a .nwb.lindi.json file using a local staging area"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "6e87640d-1927-43c1-89c1-c1274a11f185",
"metadata": {},
"outputs": [],
"source": [
"import lindi\n",
"\n",
"# URL of the remote .nwb.lindi.json file\n",
"url = 'https://lindi.neurosift.org/dandi/dandisets/000939/assets/56d875d6-a705-48d3-944c-53394a389c85/nwb.lindi.json'\n",
"\n",
"# Load the h5py-like client for the reference file system\n",
"# in read-write mode with a staging area\n",
"with lindi.StagingArea.create(base_dir='lindi_staging') as staging_area:\n",
" client = lindi.LindiH5pyFile.from_lindi_file(\n",
" url,\n",
" mode=\"r+\",\n",
" staging_area=staging_area\n",
" )\n",
" # add datasets to client using pynwb or other tools\n",
" # upload the changes to the remote .nwb.lindi.json file"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.0"
}
},
"nbformat": 4,
"nbformat_minor": 5
}

0 comments on commit 79d7295

Please sign in to comment.