Defaults Module

defaults.py

Central registry of all pipeline parameters, their default values, and the short abbreviations used in checkpoint filenames.

When a parameter is set to its default value, it is omitted from filenames entirely. Only non-default values appear, keeping names concise for typical runs.

Pipeline stages

  1. Padding — load raw images onto a common padded canvas

  2. Boundary alignment — phase correlation + ICP on tissue boundary

  3. Interior alignment — SIFT feature matching on tissue interior

  4. Diagnostics — diagnostic plots, scale estimation, difference image

Stage 4 always generates the five diagnostic plots and a difference image using the Moffat-fit scale estimate. When scale_percentile or manual_scale are set, stage 4 additionally computes difference images for those alternative scales and overplots them on the excess heatmap.

exo2micro.defaults.build_suffix(params, stage)[source]

Build the non-default parameter suffix for a checkpoint filename.

Only parameters relevant to the given stage (and all upstream stages) that differ from their defaults are included.

Parameters:

  • params (dict) – Current parameter values (keys must match PARAMETER_REGISTRY names).

  • stage (int) – Pipeline stage number (1-4).

Returns:

Suffix string like ‘_bw20_bs15’, or ‘’ if all relevant params are at their defaults.

Return type:

str

exo2micro.defaults.params_from_suffix(suffix)[source]

Parse a filename suffix back into a dict of non-default parameter values.

Parameters:

suffix (str) – The suffix portion of a filename, e.g. ‘_bw20_bs15’.

Returns:

Parameter names and their parsed values.

Return type:

dict