Load DIPY data in Python using dltHub

Build a DIPY-to-database or-dataframe pipeline in Python using dlt with automatic Cursor support.

In this guide, we'll set up a complete DIPY data pipeline from API credentials to your first data load in just 10 minutes. You'll end up with a fully declarative Python pipeline based on dlt's REST API connector, like in the partial example code below:

Example code
@dlt.source
def dipy_migration_source(access_token=dlt.secrets.value):
    config: RESTAPIConfig = {
        "client": {
            "base_url": "https://dipy.org/",
            "auth": {
                "type": "bearer",
                "token": access_token,
            },
        },
        "resources": [
            H, Add, norm
            ],
    }
    [...]
    yield from rest_api_resources(config)


def get_data() -> None:
    # Connect to destination
    pipeline = dlt.pipeline(
        pipeline_name='dipy_migration_pipeline',
        destination='duckdb',
        dataset_name='dipy_migration_data', 
    )
    # Load the data
    load_info = pipeline.run(dipy_migration_source())
    print(load_info)

Why use dltHub Workspace with LLM Context to generate Python pipelines?

  • Accelerate pipeline development with AI-native context
  • Debug pipelines, validate schemas and data with the integrated Pipeline Dashboard
  • Build Python notebooks for end users of your data
  • Low maintenance thanks to Schema evolution with type inference, resilience and self documenting REST API connectors. A shallow learning curve makes the pipeline easy to extend by any team member
  • dlt is the tool of choice for Pythonic Iceberg Lakehouses, bringing mature data loading to pythonic Iceberg with or without catalogs

What you’ll do

We’ll show you how to generate a readable and easily maintainable Python script that fetches data from dipy_migration’s API and loads it into Iceberg, DataFrames, files, or a database of your choice. Here are some of the endpoints you can load:

  • H: Represents the main functionality of the API.
  • Add: Endpoint for adding new resources or entries.
  • norm: Endpoint related to normalization processes.
  • mode: Endpoint for computing modes in data processing.
  • magn: Endpoint related to magnitudes in data.
  • trace: Endpoint for tracing computations or data flows.
  • load: Endpoint for loading specific datasets or resources.

You will then debug the DIPY pipeline using our Pipeline Dashboard tool to ensure it is copying the data correctly, before building a Notebook to explore your data and build reports.

Setup & steps to follow

💡
Before getting started, let's make sure Cursor is set up correctly:

Now you're ready to get started!

  1. ⚙️ Set up dlt Workspace

    Install dlt with duckdb support:

    pip install "dlt[workspace]"

    Initialize a dlt pipeline with DIPY support.

    dlt init dlthub:dipy_migration duckdb

    The init command will setup the necessary files and folders for the next step.

  2. 🤠 Start LLM-assisted coding

    Here’s a prompt to get you started:

    Prompt
    Please generate a REST API Source for DIPY API, as specified in @dipy_migration-docs.yaml 
Start with endpoints H and  and skip incremental loading for now. 
Place the code in dipy_migration_pipeline.py and name the pipeline dipy_migration_pipeline. 
If the file exists, use it as a starting point. 
Do not add or modify any other files. 
Use @dlt rest api as a tutorial. 
After adding the endpoints, allow the user to run the pipeline with python dipy_migration_pipeline.py and await further instructions.

  3. 🔒 Set up credentials

    DIPY uses OAuth2 for authentication, which requires setting up a connected app and obtaining an access token.

    To get the appropriate API keys, please visit the original source at https://www.dipy.org/. If you want to protect your environment secrets in a production environment, look into setting up credentials with dlt.

  4. 🏃‍♀️ Run the pipeline in the Python terminal in Cursor

    python dipy_migration_pipeline.py

    If your pipeline runs correctly, you’ll see something like the following:

    Pipeline dipy_migration load step completed in 0.26 seconds
1 load package(s) were loaded to destination duckdb and into dataset dipy_migration_data
The duckdb destination used duckdb:/dipy_migration.duckdb location to store data
Load package 1749667187.541553 is LOADED and contains no failed jobs

  5. 📈 Debug your pipeline and data with the Pipeline Dashboard

    Now that you have a running pipeline, you need to make sure it’s correct, so you do not introduce silent failures like misconfigured pagination or incremental loading errors. By launching the dlt Workspace Pipeline Dashboard, you can see various information about the pipeline to enable you to test it. Here you can see:

    • Pipeline overview: State, load metrics
    • Data’s schema: tables, columns, types, hints
    • You can query the data itself
    dlt pipeline dipy_migration_pipeline show

  6. 🐍 Build a Notebook with data explorations and reports

    With the pipeline and data partially validated, you can continue with custom data explorations and reports. To get started, paste the snippet below into a new marimo Notebook and ask your LLM to go from there. Jupyter Notebooks and regular Python scripts are supported as well.

    import dlt

data = dlt.pipeline("dipy_migration_pipeline").dataset()
# get  table as Pandas frame
data..df().head()

Running into errors?

DIPY can process large diffusion datasets, so it is recommended to use a 64-bit operating system for optimal performance. Some endpoints may require specific parameters to function correctly. Additionally, certain functionalities depend on using compatible versions of Python and external libraries like FURY.

Extra resources:

Next steps