Open derollins opened 1 year ago
You can't structure a YAML file in that manner as it introduces duplicate key names, e.g. there are now two filter
sections. Its why the configuration options that pertain to a step in processing are nested under that processes section.
We could structure it as...
basic:
base_dir: C:\Users\Work\OneDrive\Documents\Uni\Research\Data\My_Data\20230426_Sixfold
output_dir: C:\Users\Work\OneDrive\Documents\Uni\Research\Data\My_Data\20230426_Sixfold\output
file_ext: .spm
loading:
channel: Height
filter:
run: true
grains:
run: true
grainstats:
run: true
plotting:
run: true
save_format: png
image_set: core
zrange:
- -4
- 4
colorbar: true
axes: true
cmap: nanoscope
summary_stats:
run: true
---------------------------------------------------------------------------------------------------
advanced:
log_level: info
cores: 3
filter:
row_alignment_quantile: 0.2
threshold_method: std_dev
otsu_threshold_multiplier: 1.0
threshold_std_dev:
below: 10.0
above: 1.0
threshold_absolute:
below: -1.0
above: 1.0
gaussian_size: 1.0121397464510862
gaussian_mode: nearest
remove_scars:
run: true
removal_iterations: 2
threshold_low: 0.25
threshold_high: 0.666
max_scar_width: 4
min_scar_length: 16
grains:
threshold_method: std_dev
otsu_threshold_multiplier: 1.0
threshold_std_dev:
below: 10.0
above: 1.0
threshold_absolute:
below: -1.0
above: 1.0
direction: above
smallest_grain_size_nm2: 50
absolute_area_threshold:
above:
- 300
- 3000
below:
-
-
grainstats:
edge_detection_method: binary_erosion
cropped_size: 40.0
dnatracing:
run: true
plotting:
mask_cmap: blu
histogram_log_axis: false
histogram_bins: 200
dpi: 1000
summary_stats:
config:
And then combine all sections together again before config validation? It's a popular feature request by users.
Is your feature request related to a problem? Please describe. Aid usability by splitting 'basic' functional settings and 'advanced' parameters.
Describe the solution you'd like
Here is my idea:
Additional context Discussed at Pyne group meeting 27/04/2023