file_parsing_utils

Utilities for reading the simple ipnode/ipelem/ipfiel file formats used by the project. The functions here are intentionally small and strict — they perform basic validation of file names and convert the 1-based indexing of the input files to the 0-based indexing used internally.

Functions

read_nodes(filename)

Parse a .ipnode file and return a dictionary mapping node ids (0-based) to their (x, y, z) coordinates. Performs basic filename validation and converts coordinates to floats. Parameters ———- filename : str

Path to a .ipnode file. The function validates the extension and expects the format used by the project’s mesh exporter.

dict

Mapping node_index -> [x, y, z] with 0-based node indices.

>>> nodes = read_nodes('placenta.ipnode')

read_elements(filename)

Parse a .ipelem file and return a list of element tuples (node_from, node_to) using 0-based node indices.

filenamestr

Path to a .ipelem file.

list of tuple

Each element is (node_from_index, node_to_index) with 0-based indices.

define_fields_from_files(files)

Read one or more .ipfiel files that encode per-element/per-node fields (for example a radius or resistance field). The input is a dictionary mapping field names to filenames and the return value is a dict mapping field names to dictionaries of element indices -> values.

filesdict

Dictionary mapping field names (str) to filenames (str) of corresponding .ipfiel files.

dict

Mapping field name to a dict of element indices -> numeric value.

The function performs minimal validation of the ipfiel format and will raise TypeError for unexpected extensions.

Notes and limitations

• The parser expects the original simple text formats used in the project. If you need to support other mesh/file formats consider converting them upstream or adding another helper.

• The functions validate file extensions and will raise TypeError for unexpected extensions.

Examples

nodes = read_nodes('placenta.ipnode')
elements = read_elements('placenta.ipelem')
fields = define_fields_from_files({'radius':'radius.ipfiel'})

API reference

read_nodes

filenamestr

Path to a .ipnode file. The function validates the extension and expects the format used by the project’s mesh exporter.

dict

Mapping node_index -> [x, y, z] with 0-based node indices.

read_elements

filenamestr

Path to a .ipelem file. The function validates the extension and returns a list of tuples describing element connectivity.

list of tuple

Each element is (node_from_index, node_to_index) with 0-based indices.

define_fields_from_files

filesdict

Dictionary mapping field names (str) to filenames (str) of corresponding .ipfiel files.

dict

Mapping field name to a dict of element indices -> numeric value.

Notes

These functions are intentionally strict; if you need to import other mesh formats create a lightweight converter that outputs the simple .ipnode/.ipelem format and call the helpers here. See FetoFlow.geometry_utils for how parsed nodes/elements are used to construct the graph.

Examples

nodes = read_nodes('input/placenta.ipnode')
elements = read_elements('input/placenta.ipelem')
fields = define_fields_from_files({'radius':'input/radius.ipfiel'})