[Bug]: TopoStats not processing .jpk-qi-image file #175
Description
Describe the bug
We have tried processing a .jpk-qi-image through TopoStats (and have set file_ext in the config file to .jpk-qi-image) but TopoStats still seems to be looking for .spm files.
Copy of the output
[Mon, 10 Nov 2025 12:11:48] [INFO ] [topostats] [init.py] [287] TopoStats version : 2.3.2rc3.dev13+gd98553cf7
[Mon, 10 Nov 2025 12:11:48] [INFO ] [topostats] [init.py] [288] Commit : d98553cf7
[Mon, 10 Nov 2025 12:11:48] [ERROR ] [topostats] [io.py] [157] while parsing a block mapping
in "my_config.yaml", line 4, column 1
did not find expected key
in "my_config.yaml", line 4, column 17
[Mon, 10 Nov 2025 12:11:48] [INFO ] [topostats] [validation.py] [32] The YAML configuration file is valid.
[Mon, 10 Nov 2025 12:11:48] [INFO ] [topostats] [validation.py] [32] The YAML plotting configuration file is valid.
[Mon, 10 Nov 2025 12:11:48] [INFO ] [topostats] [processing.py] [1554] Configuration run options are consistent, processing can proceed.
[Mon, 10 Nov 2025 12:11:48] [INFO ] [topostats] [run_modules.py] [95] Configuration file loaded from : my_config.yaml
[Mon, 10 Nov 2025 12:11:48] [INFO ] [topostats] [run_modules.py] [96] Scanning for images in : C:\Users\MSP25KAW\Documents\TopoStats\notebooks
[Mon, 10 Nov 2025 12:11:48] [INFO ] [topostats] [run_modules.py] [97] Output directory : output
[Mon, 10 Nov 2025 12:11:48] [INFO ] [topostats] [run_modules.py] [98] Looking for images with extension : .spm
[Mon, 10 Nov 2025 12:11:48] [INFO ] [topostats] [run_modules.py] [99] Images with extension .spm in C:\Users\MSP25KAW\Documents\TopoStats\notebooks : 0
[Mon, 10 Nov 2025 12:11:48] [ERROR ] [topostats] [run_modules.py] [101] No images with extension .spm in C:\Users\MSP25KAW\Documents\TopoStats\notebooks
[Mon, 10 Nov 2025 12:11:48] [ERROR ] [topostats] [run_modules.py] [102] Please check your configuration and directories.
To Reproduce
No response
AFMReader Version
0.1.0
Python Version
3.11
Operating System
Windows
Python Packages
No response