From 2e9c25af9cd4898789a57f05380bf466d12c5311 Mon Sep 17 00:00:00 2001
From: Egor Sobolev <egor.sobolev@xfel.eu>
Date: Fri, 28 Jul 2023 18:03:27 +0200
Subject: [PATCH] Add script to refine geometry using SFX data
---
pyproject.toml | 1 +
src/geomtools/detector/crystfel_frm.py | 2 +-
src/geomtools/sfx/optimiser.py | 45 ++++++++++++++++++++++++++
3 files changed, 47 insertions(+), 1 deletion(-)
create mode 100644 src/geomtools/sfx/optimiser.py
diff --git a/pyproject.toml b/pyproject.toml
index 2da8bbf..7d1bfe7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -29,3 +29,4 @@ dependencies = [
]
[project.scripts]
geomtools-push = "geomtools.sfx.report:push_geometry"
+geomtools-refine-sfx = "geomtools.sfx.optimiser:refine"
diff --git a/src/geomtools/detector/crystfel_frm.py b/src/geomtools/detector/crystfel_frm.py
index 6418112..77d94d6 100644
--- a/src/geomtools/detector/crystfel_frm.py
+++ b/src/geomtools/detector/crystfel_frm.py
@@ -6,7 +6,7 @@ from natsort import natsorted
HEADER_TEMPLATE = """\
-; {detector} geometry file written by geomtools-optimiser-sfx
+; {detector} geometry file written by geomtools
; You may need to edit this file to add:
; - data and mask locations in the file
; - mask_good & mask_bad values to interpret the mask
diff --git a/src/geomtools/sfx/optimiser.py b/src/geomtools/sfx/optimiser.py
new file mode 100644
index 0000000..c0d55c0
--- /dev/null
+++ b/src/geomtools/sfx/optimiser.py
@@ -0,0 +1,45 @@
+import argparse
+import pathlib
+import tempfile
+
+from .refine import refine_geometry
+from .crystfelio import extract_geometry, read_crystfel_streamfile
+from ..detector import read_crystfel_geom, write_crystfel_geom
+
+
+def refine():
+ parser = argparse.ArgumentParser(
+ description='Makes the detector geometry report')
+ parser.add_argument('-i', '--stream', type=pathlib.Path, required=True,
+ help="Crystfel stream file")
+ parser.add_argument('-c', '--connected', default="modules",
+ help="Collection of rigid groups to pose")
+ parser.add_argument('-o', '--output', type=pathlib.Path,
+ default=pathlib.Path("refined.geom"),
+ help="File to store refined geometry")
+
+ args = parser.parse_args()
+
+ stream_filename = args.stream.absolute()
+ geom_file = extract_geometry(stream_filename)
+
+ temp_geom_file = tempfile.NamedTemporaryFile("w+t", prefix='geomtools')
+ temp_geom_file.write(geom_file.read())
+ geom_file.seek(0)
+
+ panels, beam = read_crystfel_geom(
+ temp_geom_file.name, indexes={'modno': 1})
+
+ temp_geom_file.close()
+
+ fr, pe, la, re, ma = read_crystfel_streamfile(
+ stream_filename, panels, args.connected, disp=True)
+
+ panels_new, transform, clen = refine_geometry(ma, panels, 1.0)
+
+ with open(args.output.absolute(), "w") as f:
+ write_crystfel_geom(f, panels_new, beam, ["modules", "quads"])
+
+
+if __name__ == "__main__":
+ refine()
--
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