From ffe7d8fe9d1b2fda266e9769f13ccded3980a5a3 Mon Sep 17 00:00:00 2001
From: Egor Sobolev <egor.sobolev@xfel.eu>
Date: Sat, 1 Jun 2024 20:10:46 +0200
Subject: [PATCH] Add minimal number of peaks which is needed to refine a panel
---
src/geomtools/sfx/optimiser.py | 9 ++++++---
src/geomtools/sfx/refine.py | 6 ++++--
2 files changed, 10 insertions(+), 5 deletions(-)
diff --git a/src/geomtools/sfx/optimiser.py b/src/geomtools/sfx/optimiser.py
index c0d55c0..f5ae944 100644
--- a/src/geomtools/sfx/optimiser.py
+++ b/src/geomtools/sfx/optimiser.py
@@ -2,9 +2,9 @@ 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
+from .crystfelio import extract_geometry, read_crystfel_streamfile
+from .refine import refine_geometry
def refine():
@@ -14,6 +14,8 @@ def refine():
help="Crystfel stream file")
parser.add_argument('-c', '--connected', default="modules",
help="Collection of rigid groups to pose")
+ parser.add_argument('-m', '--min-counts', type=int, default=50,
+ help="Minimum counts per group")
parser.add_argument('-o', '--output', type=pathlib.Path,
default=pathlib.Path("refined.geom"),
help="File to store refined geometry")
@@ -35,7 +37,8 @@ def refine():
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)
+ panels_new, transform, clen = refine_geometry(
+ ma, panels, 1.0, args.min_counts)
with open(args.output.absolute(), "w") as f:
write_crystfel_geom(f, panels_new, beam, ["modules", "quads"])
diff --git a/src/geomtools/sfx/refine.py b/src/geomtools/sfx/refine.py
index c1d8fb7..96cc9d1 100644
--- a/src/geomtools/sfx/refine.py
+++ b/src/geomtools/sfx/refine.py
@@ -1,11 +1,11 @@
import time
+
import numpy as np
import pandas as pd
-
from natsort import natsorted
-def refine_geometry(matches, panels, clen_scale=1.,
+def refine_geometry(matches, panels, clen_scale=1., min_counts=50,
rigid_group="modules", disp=True):
transform = {}
clen = panels.clen[0]
@@ -21,6 +21,8 @@ def refine_geometry(matches, panels, clen_scale=1.,
groups = matches[columns].groupby(rigid_group)
for modname, mp in natsorted(groups):
count = len(mp)
+ if count < min_counts:
+ continue
# AGIPD1M layout
ss_p = mp.ss_p + (np.round(mp.ss_p) // 64) * 2
--
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