docs: formatting update to config page

docs/config.md

@@ -44,45 +44,45 @@ N.B. that all section/subsection headers must be present even if no values in th
 
 This section is for options that affect the general features of ReX.
 
-mask_value = 0
+`mask_value = 0`
 
 Masking value for mutations, can be either an integer, float or one of the following built-in occlusions 'spectral', 'min', 'mean'.
 Default: 0.
 
-seed = 42
+`seed = 42`
 
 Random seed, only set for reproducibility.
 Default: None.
 
-gpu = true
+`gpu = true`
 
 Whether to use gpu or not.
 Default: true.
 
-batch_size = 64
+`batch_size = 64`
 
 Batch size for the model.
 Default: 1.
 
 ### [rex.onnx] section
 
-means = [0.485, 0.456, 0.406]
+`means = [0.485, 0.456, 0.406]`
 
 Means for min-max normalization.
 Default: None.
 
-stds = [0.229, 0.224, 0.225]
+`stds = [0.229, 0.224, 0.225]`
 
 Standard deviations for min-max normalization.
 Default: None.
 
-binary_threshold = 0.5
+`binary_threshold = 0.5`
 
 Binary model confidence threshold.
 Anything >= threshold will be classified as 1, otherwise 0.
 Default: None.
 
-norm
+`norm`
 <!-- unclear to me what this is used for -->
 
 Optional.
@@ -92,49 +92,49 @@ Default: None.
 
 This section is for options that control the appearance of the progress bar and output data visualisation.
 
-progress_bar = false
+`progress_bar = false`
 
 Whether to show progress bar in the terminal.
 Defaults: true.
 
-resize = true
+`resize = true`
 
 Resize the explanation to the size of the original image.
 This uses cubic interpolation and will not be as visually accurate as not resizing.
 Default: false.
 
-info = false
+`info = false`
 
 Include classification and confidence information in title of plot.
 Default: true.
 
-raw = false
+`raw = false`
 
 Produce unvarnished image with actual masking value.
 Defaults: false.
 
-colour = 150
+`colour = 150`
 
 Pretty printing colour for explanations.
 Defaults: 200.
 
-heatmap = 'coolwarm'
+`heatmap = 'coolwarm'`
 
 Matplotlib colourscheme for responsibility map plotting.
 Default: 'magma'.
 See the [Matplotlib documentation](https://matplotlib.org/stable/users/explain/colors/colormaps.html) for a list of all possible colourmaps.
 
-alpha = 0.2
+`alpha = 0.2`
 
 Alpha blend for main image (PIL Image.blend parameter).
 Default: 0.2.
 
-grid = false
+`grid = false`
 
 Overlay a 10*10 grid on an explanation.
 Defaults: false.
 
-mark_segments = false
+`mark_segments = false`
 
 Mark quickshift segmentation on image.
 Default: false.
@@ -143,76 +143,76 @@ Default: false.
 
 This sections is for options relevant to the causal responsibility calculations.
 
-tree_depth = 30
+`tree_depth = 30`
 
 Maximum depth of tree.
 Default: 10.
 Note that search can actually go beyond this number on occasion, as the check only occurs at the end of an iteration.
 
-search_limit = 1000
+`search_limit = 1000`
 
 Limit on the number of combinations to consider *per iteration*.
 Optional.
 Default: None.
 It is **not** the total work done by ReX over all iterations.
 Leaving the search limit at none can potentially be very expensive.
 
-iters = 30
+`iters = 30`
 
 Number of times to run the algorithm.
 Defaults: 20.
 <!-- from code looks like default is actually 30 -->
 
-min_box_size = 10
+`min_box_size = 10`
 
 Minimum child size, in pixels.
 Default: 10.
-<!-- is this width or area? -->
+<!-- how to interpret - is this width or area? -->
 
-confidence_filter = 0.5
+`confidence_filter = 0.5`
 
 Remove passing mutants which have a confidence less than `confidence_filter`.
 Default: 0.0 (meaning all mutants are considered).
 
-weighted = false
+`weighted = false`
 
 Whether to weight responsibility by prediction confidence.
 Default: false.
 
-queue_style = "area"
+`queue_style = "area"`
 
 queue_style = "intersection" | "area" | "all" | "dc"
 Default: "area".
 
-queue_len = 1
+`queue_len = 1`
 
 Maximum number of things to hold in search queue, either an integer or 'all'.
 Default: 1.
 
-concentrate = false
+`concentrate = false`
 
 Weight responsibility by size and depth of passing partition.
 Default: false.
 
-segmentation
+`segmentation`
 
 Default: false.
 
 ### [causal.distribution] section
 
 This section is for options that control the distribution used to split boxes.
 
-distribution = 'uniform'
+`distribution = 'uniform'`
 
 Distribution for splitting the box.
 Default: 'uniform'.
 Possible choices are 'uniform' | 'binom' | 'betabinom' | 'adaptive'.
 
-blend = 0.5
+`blend = 0.5`
 
 Default: 0.0.
 
-dist_args = [1.1, 1.1]
+`dist_args = [1.1, 1.1]`
 
 Supplemental arguments for distribution creation, these are ignored if `distribution` does not take any parameters.
 Optional.
@@ -222,25 +222,26 @@ Default: None.
 
 This section is for options related to identifying the explanation(s).
 
-chunk = 10
+`chunk = 10`
 
 Iterate through pixel ranking in chunks, defaults to `causal.min_box_size`.
+<!-- Is default correct? from code seems to be set to 10 -->
 
 ### [explanation.spatial] section
 
 This section is for options used for spatial search for explanations.
 
-initial_radius = 25
+`initial_radius = 25`
 
 Initial search radius.
 Default: 25.
 
-radius_eta = 0.2
+`radius_eta = 0.2`
 
 Increment to change radius.
 Default: 0.2.
 
-no_expansions = 50
+`no_expansions = 50`
 
 Number of times to expand before quitting
 Default: 1.
@@ -253,35 +254,35 @@ method = 'spotlight'
 
 Multi-explanation method (only spotlight is currently implemented).
 
-spotlights = 10
+`spotlights = 10`
 
 Number of spotlights to launch.
 Default: 10.
 
-spotlight_size = 24
+`spotlight_size = 24`
 
 Default size of spotlight.
 Default: 20.
 
-spotlight_eta = 0.2
+`spotlight_eta = 0.2`
 
 Decrease spotlight by this amount.
 Default: 0.2
 
-obj_function = 'mean'
+`obj_function = 'mean'`
 
 Objective function for spotlight search.
 Possible options 'mean' | 'max' | 'min'.
 
-spotlight_step
+`spotlight_step = 5`
 
 Default: 5.
 
 ### [explanation.evaluation] section
 
 These options are used if ReX is run with the `--analyse` option.
 
-insertion_step = 100
+`insertion_step = 100`
 
 Insertion/deletion curve step size.
 Default: 100.