DPI settings from config override the plotting dictionary #807
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ns-rse
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Feb 28, 2024
Closes #807 Current process is... 1. `topostats/entry_point.create_parser` : get arguments from commandline via the `process_parser` subparser (includes DPI) 2. `topostats/run_topostats.run_topostats()` : loads the dictionary and updates it with any values from `arg`, will update `savefig_dpi` with `--savefig-dpi` value. 3. Validate the updated configuration. 4. Load the default `topostats/plotting_dictionary.yaml` to the main `config["plotting"]["plot_dict"]"`. This adds in all the image specific settings such as title and importantly DPI values for each image. 5. Validate the `config["plotting"]` configuration. 6. Update the plotting configuration with via `utils.update_plotting_config()`. This adds all the options _not_ defined in the `plotting_dictionary` with those from `topostats/default_config.yaml`. I think this is wrong because we have `plotting_config["plot_dict"][image] = {**options, **main_config}` and so the options from `**main_config` override those from `**options` as you can not have dictionaries with duplicate keys. This has been fixed by... 1. Updating the values from `plot_dictionary` with any that exist in the `default_config.yaml` under the `plotting` section. Importantly this means that if any are `None` they do not update, logic that already existed in `update_config()`. 2. Then adding to each image within `plot_dictionary` any values from the `plotting` section of `default_config.yaml` that do _not_ already exist. This avoids replacing the defaults from `plot_dictionary` with `None` values from the `plotting` section of `default_config.yaml`. Tests included which check equality of dictionaries and that `LOGGER.info()` is included when changes are made to the DPI. Other Changes + `LOGGER.info()` to `LOGGER.debug()` in `topostats.io.dict_to_hdf5` as I don't think printing the keys is that informative.
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The value was added to
topostats/default_config.yamlto allow users to over-ride the defaults.Ideally we want...
if plotting["savefig_dpi"] is None... use the values intopostats/plotting_dictionary.yaml.else:... use the values fromtopostats/default_config.yaml/command line.The text was updated successfully, but these errors were encountered: