enh: add notebook demonstrating access to data from Imaging Data Commons

[fedorov]

Description

This notebook demonstrates how to load images and segmentations from Imaging Data Commons.

Checks

• Avoid including large-size files in the PR.
• Clean up long text outputs from code cells in the notebook.
• For security purposes, please check the contents and remove any sensitive info such as user names and private key.
• Ensure (1) hyperlinks and markdown anchors are working (2) use relative paths for tutorial repo files (3) put figure and graphs in the ./figure folder
• Notebook runs automatically ./runner.sh -t <path to .ipynb file>

Summary by CodeRabbit

• Documentation
  • Added a tutorial notebook showing how to query/download IDC cancer imaging data and load DICOM images and segmentations into MONAI; removed a stray non‑ASCII line in the docs.
• Chores
  • Updated CI rules to skip executing the new tutorial notebook during automated runs to avoid long or incompatible executions.

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No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 256e0836-00ef-47d1-89a5-17b614b1f648

📥 Commits

Reviewing files that changed from the base of the PR and between c5d0658 and 9113b01.

📒 Files selected for processing (2)

• README.md
• modules/idc_dataset.ipynb

🚧 Files skipped from review as they are similar to previous changes (1)

• README.md

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Walkthrough

README updated to add an idc_dataset Modules notebook entry describing IDC querying/downloading and DICOM/DICOM-SEG loading into MONAI. runner.sh updated to exclude idc_dataset.ipynb from max_epochs checks and to skip it during papermill runs.

Changes

Single cohesive update (docs + runner plumbing)

Layer / File(s)	Summary
Documentation README.md	Adds idc_dataset notebook entry under Modules describing use of idc-index to query/download NCI IDC data and load DICOM/DICOM-SEG into MONAI; removes a stray non-ASCII line near VISTA2D.
Execution Wiring runner.sh	Adds idc_dataset.ipynb to doesnt_contain_max_epochs exclusion and to skip_run_papermill patterns so the notebook is not executed via papermill and bypasses the max_epochs keyword check.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~3 minutes

Poem

🐰 A tutorial hops into view,
IDC images, DICOM true,
MONAI learns the segmented art,
Runner skips the running part,
Docs updated — a joyful queue!

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly and specifically describes the main change: adding a new notebook demonstrating access to Imaging Data Commons data, which aligns with the README update, runner.sh modifications, and overall PR objectives.
Description check	✅ Passed	The description provides a brief explanation of the notebook's purpose and includes a completed checklist covering all required template sections: file size, output cleanup, security, links/paths/figures, and runner.sh automation.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

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Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@README.md`:
- Line 391: Remove the garbled artifact line containing "ECHO�� �����Ǿ� �ֽ��ϴ�."
from the README; simply delete that exact text (the stray ECHO plus non-ASCII
characters) so the file no longer contains the corrupted Windows echo artifact,
then verify the README renders correctly (preview or lint) to ensure no other
non-ASCII artifacts remain.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: d9a7dea9-c32f-4a1f-9fd0-f3000898b7f8

📥 Commits

Reviewing files that changed from the base of the PR and between 5c908aa and c5d0658.

📒 Files selected for processing (3)

• README.md
• modules/idc_dataset.ipynb
• runner.sh