DC initialization from file by drbergman · Pull Request #357 · MathCancer/PhysiCell

drbergman · 2025-02-02T11:22:20Z

provide a CSV file with similar structure to the substrate ICs csv header row: x,y,z,<substrate_01>,<substrate_02>,... where the list of substrates need not be all the substrates, only those with DCs being set. Each subsequent row is:

<x_coord>,<y_coord>,<z_coord>,<val_01>,<val_02>,...

where the coords must be specified and the vals can either be empty (<val_01>,,<val_03>,...) or a number

If empty, then nothing chagnes for the substrate in that column at that voxel
If a number, then the DC activation for that voxel-substrate pairing is set to the number

If the XML sets DCs, this will overwrite those values for which a number is supplied in the CSV. In other words, if a voxel on the boundary has a DC set to ON by the XML, parsing the CSV file can only change the value of the DC, not turn it OFF.

a sample project in sample_projects/dirichlet_from_file is provided. try it with make dirichlet-from-file-sample

provide a CSV file with similar structure to the substrate ICs csv header row: x,y,z,<substrate_01>,<substrate_02>,... where the list of substrates need not be all the substrates, only those with DCs being set each subsequent row is: <x_coord>,<y_coord>,<z_coord>,<val_01>,<val_02>,... where the coords must be specified and the vals can either be empty (<val_01>,,<val_03>,...) or a number If empty, then nothing chagnes for the substrate in that column at that voxel If a number, then the DC activation for that voxel-substrate pairing is set to the number

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Makefile: Language not supported
sample_projects/Makefile-default: Language not supported
sample_projects/dirichlet_from_file/Makefile: Language not supported
sample_projects/dirichlet_from_file/config/PhysiCell_settings.xml: Language not supported
sample_projects/dirichlet_from_file/config/cell_rules.csv: Language not supported
sample_projects/dirichlet_from_file/config/cells.csv: Language not supported
sample_projects/dirichlet_from_file/config/dcs.csv: Language not supported

Comments suppressed due to low confidence (1)

BioFVM/BioFVM_microenvironment.cpp:1735

The function update_dirichlet_node is invoked here but it is not declared or defined in the provided diffs. Consider replacing this call with a defined function such as set_substrate_dirichlet_activation (or implementing update_dirichlet_node) to ensure the dirichlet condition is updated correctly.

microenvironment.update_dirichlet_node(voxel_ind, substrate_indices[ci], data[ci + 3]);

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Pull Request Overview

This PR introduces functionality for initializing Dirichlet conditions from a CSV file. Key changes include updates to the main simulation and configuration files, new parsing routines for CSV‐based Dirichlet conditions in the BioFVM module, and corresponding build system modifications.

Reviewed Changes

Copilot reviewed 16 out of 16 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
sample_projects/dirichlet_from_file/main.cpp	Updates to main simulation code to invoke DC initialization
sample_projects/dirichlet_from_file/custom_modules/.h,.cpp	Custom module updates with minimal changes
config/*.csv, config/PhysiCell_settings.xml	New configuration files (CSV and XML) supporting DC initialization
Makefile, Makefile-default	Build files updated to support the new project configuration
modules/PhysiCell_settings.cpp	Added XML parsing logic for Dirichlet condition file settings
BioFVM/BioFVM_vector.{h,cpp}	New function (dirichlet_csv_to_vector) to parse CSV rows for DC data
BioFVM/BioFVM_microenvironment.{h,cpp}	Updates and new functions for setting and loading Dirichlet conditions

#70) Merging development into feature-dc-init-file dropped both trim_cr calls from load_initial_conditions_from_csv. The two functions are near-identical copies, so the resolution landed development's additions on the dirichlet copy and kept the feature branch's untouched version of the substrate copy. A CRLF substrates.csv with a header therefore fails again with "Substrate <name> not found in the BioFVM microenvironment", since the final column name carries the trailing carriage return. Both csv row processors also indexed their parsed row without consulting its length, which is out of bounds for a malformed row: - a blank or whitespace-only line leaves csv_to_vector's output empty, so data[0..2] reads past the end (and the churn loop itself walks past the terminator looking for a digit). - substrate_indices is sized from the header, so a short row runs data[ci + 3] off the end. - dirichlet_csv_to_vector writes is_missing[ind] and data[ind] once per comma with no bound, so a row with more fields than the header established writes past the end of both vectors. Blank lines are now skipped in both, matching load_cells_csv_v1 and process_csv_v2_line, and a row whose column count disagrees with the header is a hard error rather than a silent partial write. Ordering the substrate guard ahead of the existing warning also stops data.size() - 3 from underflowing on a short row. dirichlet_csv_to_vector additionally treats a whitespace-only field as omitted rather than feeding it to std::stod, and reports a field that is not a complete number instead of letting std::stod throw uncaught or silently accepting "1.5abc" as 1.5. Co-authored-by: Claude Opus 5 <noreply@anthropic.com>

drbergman · 2026-08-21T23:46:53Z

After merging this and #386, there is some opportunity to reduce the codebase through DRY principles. Not worth stacking them here, so will just wait on that.

drbergman force-pushed the feature-dc-init-file branch from 0cec57e to c7860b4 Compare February 2, 2025 11:31

drbergman requested a review from Copilot April 4, 2025 15:07

Copilot AI reviewed Apr 4, 2025

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