PhysioNet

A collection of tools for working with the PhysioNet repository.

Installation

pip install physionet

Usage

PhysioNet "Preflight"

Validate your dataset before submission to PhysioNet:

# Validate a dataset
physionet validate /path/to/dataset

# Run specific checks only
physionet validate /path/to/dataset --checks filesystem,privacy

# Disable sampling for complete validation (slower)
physionet validate /path/to/dataset --no-sampling

The validator checks for:

• File naming issues (spaces, special characters, long names)
• Proprietary formats (suggests open alternatives)
• Missing documentation (README.md)
• CSV integrity (structure, encoding, duplicate columns)
• Data quality (missing values, out-of-range data)
• Privacy concerns (PHI patterns, sensitive files)

A validation report (PHYSIONET_REPORT.md) is automatically saved in your dataset folder.

API Client

Interact with the PhysioNet API to explore and search published projects:

from physionet import PhysioNetClient

# Create a client instance
client = PhysioNetClient()

# List all published projects
projects = client.projects.list_published()
print(f"Total projects: {len(projects)}")

# Display first few projects
for project in projects[:5]:
    print(f"{project.slug} v{project.version}: {project.title}")

# Search for projects
ecg_projects = client.projects.search('ECG')
print(f"Found {len(ecg_projects)} ECG-related projects")

# Get all versions of a project
versions = client.projects.list_versions('mimic-iv-demo')
for version in versions:
    print(f"Version {version.version}: {version.title}")

# Get detailed information about a specific version
details = client.projects.get_details('mimic-iv-demo', '2.2')
print(f"Title: {details.title}")
print(f"DOI: {details.doi}")
print(f"Published: {details.publish_datetime}")
print(f"Size: {details.main_storage_size} bytes")

Authenticated Requests

For endpoints that require authentication (e.g., downloading checksums):

from physionet import PhysioNetClient

# Create client with authentication
client = PhysioNetClient(
    username='your_username',
    password='your_password'
)

# Download checksums file
client.projects.download_checksums(
    'mimic-iv-demo',
    '2.2',
    'checksums.txt'
)

# Or use environment variables
# Set PHYSIONET_USERNAME and PHYSIONET_PASSWORD
from physionet.api.utils import get_credentials_from_env

username, password = get_credentials_from_env()
client = PhysioNetClient(username=username, password=password)

Using Context Manager

from physionet import PhysioNetClient

# Automatically close session when done
with PhysioNetClient() as client:
    projects = client.projects.list_published()
    print(f"Found {len(projects)} projects")

Utility Functions

from physionet.api.utils import format_size

# Format bytes to human-readable size
size = format_size(16224447)
print(size)  # "15.47 MB"

Error Handling

from physionet import PhysioNetClient
from physionet.api.exceptions import NotFoundError, RateLimitError, ForbiddenError

client = PhysioNetClient()

try:
    details = client.projects.get_details('nonexistent-project', '1.0')
except NotFoundError:
    print("Project not found")
except RateLimitError:
    print("Rate limit exceeded, please wait before retrying")
except ForbiddenError:
    print("Access denied - check credentials or project permissions")

Contributing

Contributions are welcome!

License

This project is licensed under the MIT License - see the LICENSE file for details.