Companion repository for the manuscript Anatomy-Informed Modeling of the Fetal Umbilical Circulation Across Gestation (Tang, Peng and Ho; in preparation). It collects everything behind the paper in one place, in three folders.
| Folder | What it holds | Live viewer |
|---|---|---|
atlas/ |
MR-digitised fetal anatomy atlas of a single fetus: 26 source meshes forming 23 named structures, one STL per part, parsing and assembly scripts | atlas viewer |
umbilical-geometry/ |
Digitised cord and umbilical-vein centreline, synthetic paired umbilical arteries, cord sheath and placenta; geometry-generation scripts; the two viewers | geometry viewer, cardiac-cycle flow viewer |
solver/ |
1-D compliant pulsatile umbilical-artery solver (Lax-Wendroff, RCR Windkessel), reduced UV return model, calibration to PI/RI, sensitivity, path-length and Womersley analyses, stored results, tests | none |
atlas -> the specimen’s UV, cord and placenta surfaces -> umbilical-geometry/ (UV centreline, synthetic UA pair, growth curves) -> UA length and radius used by solver/ -> pressure and flow fields exported to umbilical-geometry/viewer/flow_data.js (solver/figures/export_flow_data.py).
pip install -r requirements.txt
python -m pytest solver/tests -q # 22 tests, about 1 min
python solver/reproduce_check.py 25 # re-runs the 25-week production solve and compares with the stored results
The viewers are self-contained HTML: open the files directly, or use the live links above. Each folder has its own README with provenance and reproduction steps; see solver/README.md for the model and the saved results.
solver/data/). Patient-level Doppler records are not included. solver/calibration/pi_information_analysis.py needs the cohort workbook (path via the UA_COHORT_XLSX environment variable); its aggregate output is stored in solver/results/.solver/data/norway_cord_length_percentiles_SOURCE.txt.The repository accompanies a manuscript under preparation. A Zenodo DOI will be added after acceptance. The 23-week gestation-dependent cord-length fit did not converge, so solver/results/ga_dependent_length/GA23.json is marked on_target: false (PI 1.30 vs target 1.19) and is not used in the paper.
MIT (LICENSE).