Add generation of bad pixels mask in the optimiser

src/geomtools/sfx/optimiser.py

@@ -2,8 +2,11 @@ import argparse
 import pathlib
 import tempfile
 
+import h5py
+
 from ..detector import read_crystfel_geom, write_crystfel_geom
 from .crystfelio import extract_geometry, read_crystfel_streamfile
+from .misc import badpixels_mask, get_detector_shape, pixels_to_image
 from .refine import refine_geometry
 
 
@@ -40,9 +43,18 @@ def refine():
     panels_new, transform, clen = refine_geometry(
         ma, panels, 1.0, args.min_counts)
 
-    with open(args.output.absolute(), "w") as f:
+    px = badpixels_mask(pe, panels)
+    shape = get_detector_shape(panels)
+    msk = pixels_to_image(shape, px)
+
+    geom_fn = args.output
+    with open(geom_fn.absolute(), "w") as f:
         write_crystfel_geom(f, panels_new, beam, ["modules", "quads"])
 
+    mask_fn = geom_fn.parent / (geom_fn.stem + "_mask.h5")
+    with h5py.File(mask_fn, "w") as f:
+        f["/entry_1/data_1/mask"] = msk.astype("u2")
+
 
 if __name__ == "__main__":
     refine()