DC initialization from file #357

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

Copilot

Copilot reviewed 9 out of 16 changed files in this pull request and generated no comments.

Files not reviewed (7)

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]);

drbergman · 2025-05-22T12:02:43Z

BioFVM/BioFVM_microenvironment.cpp

+	return;
+}
+
+void load_initial_conditions_from_matlab(std::string filename)


This function is unchanged except that the error at the bottom now goes to std::cerr rather than std::cout. It is green here only because the set_microenvironment_initial_condition function is refactored and that moved things around too much for git to track well.

drbergman · 2025-05-22T12:07:15Z

BioFVM/BioFVM_microenvironment.cpp

+	return;
+}
+
+void load_initial_conditions_from_csv(std::string filename)


This function is unchanged except the comment // Do not include a header row. has been removed since you can (and probably should) included a header row. See comment on load_initial_conditions_from_matlab.

Note: you should include a header row to explicitly declare the substrates you are setting, rather than relying on their index in the substrate list.

In reviewing this PR, I found an error when loading DCs from a CSV without a header row. That mistake was traced back to the code for reading in substrates from a CSV (written by yours truly). So, that has been fixed here.

drbergman · 2025-05-22T12:08:40Z

BioFVM/BioFVM_microenvironment.cpp

+	return;
+}
+
+void get_row_from_substrate_initial_condition_csv(std::vector<int> &voxel_set, const std::string line, const std::vector<int> substrate_indices, const bool header_provided)


This function is entirely unchanged. See comment on load_initial_conditions_from_matlab.

drbergman · 2025-05-22T12:10:59Z

BioFVM/BioFVM_microenvironment.cpp

+	set_dirichlet_boundaries_from_file();
+}
+
+void set_dirichlet_boundaries_from_XML( void )


This new function is just the old end to set_microenvironment_initial_condition, refactored into its own function for simplicity and clarity of logic. This is especially useful as its caller (set_dirichlet_initial_condition) handles the loading of DC conditions from both XML and file.

drbergman · 2025-05-22T12:12:09Z

BioFVM/BioFVM_microenvironment.cpp

 }

-void load_initial_conditions_from_matlab(std::string filename)
+void set_dirichlet_boundaries_from_file( void )


See comment on load_initial_conditions_from_matlab. This is a new function, not a rework of load_initial_conditions_from_matlab. It just shares enough code that git thinks it is reworking this.

Copilot

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

Copilot · 2025-05-22T13:08:06Z

BioFVM/BioFVM_vector.cpp

+    while( i < strlen( buffer ) )
+    {
+        if(buffer[i] == ',')
+        {


Inside 'dirichlet_csv_to_vector', the index 'ind' is incremented without checking whether it has reached the allocated size of the 'is_missing' and 'data' vectors, which could lead to an out-of-bounds access if the CSV row contains more fields than expected. Consider adding a bounds check before writing to these vectors.

Suggested change

{

{

if (ind >= is_missing.size())

{

std::cerr << "Error: Too many fields in the CSV row. Expected at most " << is_missing.size() << " fields." << std::endl;

std::cerr << "\tRow: " << buffer << std::endl;

exit(-1);

}

Copilot · 2025-05-22T13:08:07Z

BioFVM/BioFVM_microenvironment.cpp

 				  << "\tExpected: " << microenvironment.number_of_voxels() << std::endl
 				  << "\tFound: " << data.size() - 3 << std::endl


The warning message incorrectly prints the expected value using 'microenvironment.number_of_voxels()' even though the check compares against (number_of_densities() + 3). This could be confusing; revise the error message to correctly reference the expected number of density data columns.

Suggested change

<< "\tExpected: " << microenvironment.number_of_voxels() << std::endl

<< "\tFound: " << data.size() - 3 << std::endl

<< "\tExpected: " << (microenvironment.number_of_densities() + 3) << " columns (3 for position + " << microenvironment.number_of_densities() << " for substrates)" << std::endl

<< "\tFound: " << data.size() << " columns" << std::endl

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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drbergman commented May 22, 2025

View reviewed changes

- fix logic reading in substrates.csv without a header

8f96226

drbergman self-assigned this May 22, 2025

drbergman requested a review from Copilot May 22, 2025 13:07

drbergman assigned drbergman and unassigned drbergman May 22, 2025

Copilot AI reviewed May 22, 2025

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drbergman mentioned this pull request May 22, 2025

simplified dc functions #369

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DC initialization from file #357

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drbergman commented Feb 2, 2025 •

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-        {
+        {
+            if (ind >= is_missing.size())
+            {
+                std::cerr << "Error: Too many fields in the CSV row. Expected at most " << is_missing.size() << " fields." << std::endl;
+                std::cerr << "\tRow: " << buffer << std::endl;
+                exit(-1);
+            }

		<< "\tExpected: " << microenvironment.number_of_voxels() << std::endl
		<< "\tFound: " << data.size() - 3 << std::endl

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drbergman commented Feb 2, 2025 •

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