Merge pull request #778 from AFM-SPM/derollins/tiff_validation

Add the option to save as a `tif` file

docs/configuration.md

@@ -263,10 +263,13 @@ topostats process --cmap rainbow
 
 Matplotlib, and by extension TopoStats, supports saving images in a range of different formats including `png`
 ([Portable Network Graphic](https://en.wikipedia.org/wiki/PNG)), `svg` ([Scalable Vector
-Graphics](https://en.wikipedia.org/wiki/SVG)) and `pdf` ([Portable Document
-Format](https://en.wikipedia.org/wiki/PDF)). The default is `png` but, as with both DPI and Colormap, these can be
-easily changed via a custom configuration file or command line options to change these without having to edit
-the [Matplotlib Style file](matplotlib-style).
+Graphics](https://en.wikipedia.org/wiki/SVG)), `pdf` ([Portable Document
+Format](https://en.wikipedia.org/wiki/PDF)), and `tif` ([Tag Image File
+Format](https://en.wikipedia.org/wiki/TIFF)). The default is `png` but, as with both DPI and Colormap, these can be
+easily changed via a custom configuration file or command line options to change these without having to edit the
+[Matplotlib Style file](matplotlib-style). If using `tif` it is worth being aware that although the image will be saved,
+this will be without metadata since this is not supported for `tif` files (see the note under `metadata` of [Matplotlib
+savefig](https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.savefig.html)).
 
 If you want to modify the output file format that is used you have two options. Firstly you can [generate a
 configuration](generating-a-configuration) file and modify the field `savefig_format` to your choice. The example below

topostats/default_config.yaml

@@ -61,7 +61,7 @@ dnatracing:
 plotting:
   run: true # Options : true, false
   style: topostats.mplstyle # Options : topostats.mplstyle or path to a matplotlibrc params file
-  savefig_format: null # Options : null (defaults to png) or see https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.savefig.html
+  savefig_format: null # Options : null, png, svg or pdf. tif is also available although no metadata will be saved. (defaults to png) See https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.savefig.html
   savefig_dpi: null # Options : null (defaults to figure) see https://afm-spm.github.io/TopoStats/main/configuration.html#further-customisation and https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.savefig.html
   pixel_interpolation: null # Options : https://matplotlib.org/stable/gallery/images_contours_and_fields/interpolation_methods.html
   image_set: core # Options : all, core

topostats/validation.py

@@ -897,7 +897,9 @@ def validate_config(config: dict, schema: Schema, config_type: str) -> None:
             "png",
             "pdf",
             "svg",
-            error=("Invalid value in config 'savefig_format', valid values are 'png', 'pdf' or 'svg' "),
+            "tiff",
+            "tif",
+            error=("Invalid value in config 'savefig_format', valid values are 'png', 'pdf', 'svg' or 'tif'"),
         ),
         "pickle_plots": Or(
             True,