docs: regenerate pipeline DAG from current workflow#118
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Add docs/images/make_dag.py, a small matplotlib generator that renders the pipeline overview (docs/images/dag.png) so the figure is reproducible and stays in sync with the Snakemake rules. Regenerate the DAG to match the current workflow: input modalities (T1w/T2w/FLAIR/ct) -> synthsr / n4_bias_correction -> norm_im / regmni2sub -> resample_im / mni2subfids / download_cnn_model -> applyfidmodel -> regqc / stereotaxy / fidqc -> all, including the 'if SynthSR' branch feeding the detector directly. Keeps the existing rulegraph-style layout and colour scheme.
Measure each label's actual rendered extent and size its box to fit (plus padding), and disable patch clipping so no box is cut at the axes edge. Fixes text spilling out of the resample_im / mni2subfids / download_cnn_model boxes.
Redraw the norm_im -> applyfidmodel dashed branch as a rounded bracket that exits norm_im to the left, runs down the left margin beside the 'if SynthSR' label, and enters applyfidmodel from the left, instead of curving through the resample_im column.
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Summary
Refreshes the pipeline overview figure (
docs/images/dag.png) so it reflects the current Snakemake workflow, and adds a small generator script so the figure is reproducible going forward.What changed
docs/images/make_dag.py— a minimal matplotlib generator (python docs/images/make_dag.py) that renders the DAG directly from the rule set. No new runtime dependencies.docs/images/dag.png— regenerated to match the current rules.Architecture (unchanged in spirit, kept the existing rulegraph style)
Input modalities (T1w / T2w / FLAIR / ct) →
synthsr/n4_bias_correction→norm_im/regmni2sub→resample_im/mni2subfids/download_cnn_model→applyfidmodel→regqc/stereotaxy/fidqc→all, including theif SynthSRbranch that feeds the detector directly for non-T1w inputs.Same rounded-box layout and colour scheme as before — just reproducible and in sync with the code.