HTML reporting

Simple example.

Example on how to aggregate QC information in an HTML report. See user guide for details.

Data

Let’s first get some data to display. Here ‘step 1’ is composed of an image with an overlay and a table, and ‘step 2’ is composed of a carousel of two images.

import pandas as pd
from pathlib import Path

from brainprep.datasets import git_download


working_dir = Path("/tmp/brainprep-reporting")
working_dir.mkdir(parents=True, exist_ok=True)


git_download(
    url=("https://raw.githubusercontent.com/brainprepdesk/brainprep/"
         "dev/doc/logos/brainprep.png"),
    destination=working_dir / "im1.png",
)
git_download(
    url=("https://raw.githubusercontent.com/brainprepdesk/brainprep/"
         "dev/doc/logos/brainprep.png"),
    destination=working_dir / "im2.png",
)

data = [
  {
    "name": "Step 1",
    "content": working_dir / "im1.png",
    "overlay": working_dir / "im2.png",
    "tables": pd.DataFrame(
        data={'col1': [1, 2], 'col2': [4, 3]}
    ),
  },
  {
    "name": "Step 2",
    "content": [
        working_dir / "im1.png",
        working_dir / "im2.png",
    ],
  },
]

Reporting

Now let’s generate the HTML report.

from brainprep.reporting import generate_qc_report

report = generate_qc_report(
  title="Simple QC Example",
  docstring="""
  This is a simple example.

  ..note::
      Please adapt this code.
  """,
  version="0.0.0",
  date="01.01.2000",
  data=data,
)
report
report.save_as_html(working_dir / "report.html")

Estimated memory usage: 115 MB