Post Processing

Post Processing

The postprocessing/ folder contains analysis and plotting utilities for simulation outputs in result_files/ (CSV, pickle, and VTK-derived signals).

Main Scripts

• report_focad.py
  • Loads simulation pickle or VTK data and exports focal adhesion metrics/polarity time series to CSV.
  • Builds summary tables (including last-20% statistics) and generates diagnostic plots.
• report_cell_population.py
  • Tracks per-step cell counts (total, alive/dead, proliferation proxy, death by cause) from pickle or VTK outputs.
  • Generates population time-series plots and CSV reports.
• report_matrix_remodeling.py
  • Tracks FNODE count, degradation, reinforcement, net remodeling, and elastic energy per step.
  • Produces time-series plots and CSV reports from pickle or VTK outputs.
• compare_linc_runs.py
  • Compares tagged LINC OFF/ON CSV outputs and produces comparison tables and figures.
• plot_migration_results.py
  • Plots CELL migration metrics (speed, trajectories) from pickle files.
  • Supports optional target CSV for reference comparison lines.
• plot_migration_comparison.py
  • Compares migration results across one or two conditions via violin plots and 3D trajectory plots.
  • Computes and plots directionality ratio curves per cell type.
• plot_migration_diff_profiles_comparison.py
  • Produces a fixed 2×4 figure comparing migration metrics, directionality, and diffusion-profile evolution for two conditions.
• plot_organoid_metrics.py
  • Plots organoid growth metrics over time (radius of gyration, sphericity, span, cell count per type).
  • Supports single or dual-condition comparison.
• plot_boundary_results.py
  • Loads boundary-related outputs from pickle and produces force/position/shear visualizations.
• plot_diffusion_results.py
  • Demonstrates time-series plotting for concentration variables from VTK-derived datasets.

Typical Outputs

• Time-series CSV files for metrics and polarity indicators.
• Summary CSV files for run-level comparison.
• PNG figures for trends, diagnostics, and side-by-side run comparisons.

Recommended Usage

1. Run simulation and generate outputs in result_files/.
2. Use report_focad.py for baseline focal adhesion reports.
3. Use report_cell_population.py and report_matrix_remodeling.py for population and matrix diagnostics.
4. Use migration plotting scripts for speed and trajectory analysis.
5. Use compare_linc_runs.py for condition-to-condition analysis.
6. Use boundary/diffusion plotting scripts for targeted diagnostics.