Changed output CSV names and added basic / full option in config

[tobyallwood]

TopoStats Pull Requests

Changed the main output CSV names:

• all_statistics.csv -> grain_statistics.csv
• image_stats.csv -> image_statistics.csv
• all_mol_stats -> molecule_statistics.csv
• all_disordered_segment_stats -> branch_statistics.csv

A new option in config has also been added called output_stats_file which can be set to full or basic. full will cause all four csvs to output and basic will ignore molecule_statistics.csv and branch_statistics.csv and only output grain_statistics.csv and image_statistics.csv.

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Before submitting a Pull Request please check the following.

• Existing tests pass.
• Documentation has been updated and builds. Remember to update as required...
  • docs/configuration.md
  • docs/usage.md
  • docs/data_dictionary.md
  • docs/advanced.md and new pages it should link to.
• Pre-commit checks pass.

topostats/default_config.yaml

If adding options to topostats/default_config.yaml please ensure.

• There is a comment adjacent to the option explaining what it is and the valid values.
• A check is made in topostats/validation.py to ensure entries are valid.
• Add the option to the relevant sub-parser in topostats/entry_point.py.

[ns-rse]

Thanks for addressing the output files here @tobyallwood

I think the output_stats_file could be misleading (as I've also noted in the comments below) as reading that makes me think that its a file-name parameter that the statistics are written to. Dropping the suffix _file would leave output_stats which is more representative in my view (it could just be me though).

[ns-rse]

Thanks for going through these @tobyallwood

I've marked the previous conversations as "Resolved" but spotted a few minor things that have been introduced (comments inline).

If you make these changes locally then you can avoid making another "Addressing PR feedback" commit by using git commit --amend and then, because no one else is likely to have touched this branch on GitHub or anywhere else you can git push --force to force push the changes to the branch on GitHub and the pull request will be updated (this helps keep the history cleaner and avoids lots of small commits, if you want to read more on this the Git With It material I wrote and occassionally deliver has details).

[ns-rse]

Missing The amount of

Suggested change

	| `output_stats` | | string | `full` | statistics to write to `.csv` files, options are `full` (all information on grains as well as branch and molecule statistics) or `basic` (just grain level statistics) |
	| `output_stats` | | string | `full` | The amount of statistics to write to `.csv` files, options are `full` (all information on grains as well as branch and molecule statistics) or `basic` (just grain level statistics) |

[ns-rse]

Thanks @tobyallwood, hopefully the nomenclature will stick going forward.

This can be merged now 👍

[SylviaWhittle]

:)