[Bug]: Unable to run topostats with my .gwy files

[hjbsmith]

Checklist

• Find the offending file in the output. If processing halts, re-run analysis with topostats --core 1 process.
• Describe the bug.
• Include the configuration file.
• Copy of the log-file from running with topostats --log-level debug <command>.
• The exact command that failed. This is what you typed at the command line, including any options.
• TopoStats version, this is reported by topostats --version
• Operating System and Python Version

Describe the bug

Topostats version: 2.3.1
MacOS Sequoia 12.6.1
Python version 3.11.13

I'm not able to run topostats using my dataset that has been cropped and converted using Gwyddion into .gwy files. They are all cropped to perfect squares.

Copy of the log-file from running with topostats --log-level debug <command>

BacHU_Analysis-2025-09-24-15-30-52.log

Include the configuration file

config.yaml

To Reproduce

On the Pyne group Xdrive, it can be found under HU > BacHU> BacHU_Analysis

TopoStats Version

Git main branch

Python Version

3.11

Operating System

MacOS M1/M2 (post-2021)

Python Packages

No response