fix(workflow): 🐛 wire dilate_labels' use_gpu through cfg["dilate_gpu"]

build_fn called dilate_labels(fn, iterations=dilate) with no way to reach
its use_gpu flag from YAML, so GPU dilation on the cluster was silently
unreachable despite the API supporting it. Adds cfg["dilate_gpu"] (bool,
default False) and documents it in both example configs.

Author: lguerard

workflow/config/config.yaml

@@ -30,7 +30,8 @@ empty_threshold: null # null → Otsu; or a number
 
 # ---- segmentation -----------------------------------------------------------
 method: "cellpose" # "cellpose" (GPU), "threshold" (no GPU; testing), "custom"
-# dilate: 2 # optional: pixels to grow labels by after segmentation, any method
+# dilate: 2       # optional: pixels to grow labels by after segmentation, any method
+# dilate_gpu: true # optional: dilate via cupy instead of scipy, needs a GPU
 # Also namespaces this run's intermediate files under work_dir/<label_name>/,
 # so a second segmentation (different label_name, e.g. nuclei vs cytoplasm)
 # can safely target the same work_dir — see docs/guide/snakemake.md

workflow/config/config_cilia.yaml

@@ -25,7 +25,8 @@ skip_empty: true
 empty_threshold: null
 
 method: "custom"
-# dilate: 2 # optional: pixels to grow labels by after segmentation
+# dilate: 2       # optional: pixels to grow labels by after segmentation
+# dilate_gpu: true # optional: dilate via cupy instead of scipy, needs a GPU
 label_name: "cilia_labels"
 custom:
   module: "patchworks.plugins.dog"

workflow/scripts/_pw.py

@@ -136,7 +136,10 @@ def build_fn(cfg):
         function (``cfg["custom"] = {module, function, kwargs}``). Optional
         ``cfg["dilate"]``: int, pixels to grow labels by after segmentation
         (via ``patchworks.dilate_labels``), applied regardless of ``method``.
-        Omitted/0 disables dilation.
+        Omitted/0 disables dilation. ``cfg["dilate_gpu"]``: bool, dilate via
+        cupyx instead of scipy (default ``False``); only takes effect when
+        ``dilate`` is set, and needs a GPU allocated for the segment job
+        (independent of whether ``method`` itself uses one).
 
     Returns
     -------
@@ -149,7 +152,7 @@ def build_fn(cfg):
     if dilate:
         from patchworks import dilate_labels
 
-        fn = dilate_labels(fn, iterations=dilate)
+        fn = dilate_labels(fn, iterations=dilate, use_gpu=cfg.get("dilate_gpu", False))
 
     return fn