From 157fe57d4921ce39d88236eec9813d77cf64fb7d Mon Sep 17 00:00:00 2001
From: Egor Sobolev <egor.sobolev@xfel.eu>
Date: Sat, 17 Jun 2023 03:45:24 +0200
Subject: [PATCH] Look for the closest reflex over connected group
---
src/geomtools/sfx/crystfelio.py | 41 ++++++++++++++++++++++-----------
src/geomtools/sfx/misc.py | 6 ++++-
src/geomtools/sfx/report.ipynb | 11 +++++++--
src/geomtools/sfx/report.py | 4 ++++
4 files changed, 45 insertions(+), 17 deletions(-)
diff --git a/src/geomtools/sfx/crystfelio.py b/src/geomtools/sfx/crystfelio.py
index a635b73..2adc6fe 100644
--- a/src/geomtools/sfx/crystfelio.py
+++ b/src/geomtools/sfx/crystfelio.py
@@ -42,22 +42,27 @@ def _buffer_to_line(f, marker):
return s
-def match_reflexes_to_peaks(reflexes, peaks, lattices, panels):
+def match_reflexes_to_peaks(reflexes, peaks, lattices,
+ panels, group_name='panel'):
"""Looks for matches of reflexes to peaks"""
# 1. distance
# 2. one reflex to one peak
# 3. one peak to one reflex in the same crystal
# but to can also match refelex in other crystals
- re = reflexes[['fs', 'ss', 'panel', 'frame', 'cryst']].copy()
- re['reflno'] = re.index
+ re = reflexes[['fs', 'ss', 'panel', 'frame', 'cryst', 'reflno']].copy()
+ if group_name != 'panel':
+ re = re.join(panels[[group_name]], on='panel')
re = re.join(get_peak_position(re, panels))
- pe = peaks[['fs', 'ss', 'panel', 'frame']].copy()
- pe['peakno'] = pe.index
+ pe = peaks[['fs', 'ss', 'panel', 'frame', 'peakno']]
+ if group_name != 'panel':
+ pe = pe.join(panels[[group_name]], on='panel')
pe = pe.join(get_peak_position(pe, panels))
- match = pe.join(re.set_index(['frame', 'panel']), on=['frame', 'panel'],
- lsuffix='_p', rsuffix='_r', how='inner')
+ match = pe.join(re.set_index(['frame', group_name]),
+ on=['frame', group_name],
+ lsuffix='_p', rsuffix='_r',
+ how='inner')
match = match.join(lattices[['xc', 'yc', 'rmin']], on='cryst')
@@ -68,12 +73,16 @@ def match_reflexes_to_peaks(reflexes, peaks, lattices, panels):
r2max = 0.25 * match.rmin * match.rmin
match = match[match.r2 < r2max]
- match = match.loc[match.groupby(['frame', 'cryst', 'reflno']).r2.idxmin()]
+
+ # this line applies condition 3, remove it to be like geoptimiser
+ # match = match.loc[match[['reflno', 'r2']].groupby('reflno').r2.idxmin()]
+ match = match.sort_values("r2").groupby("reflno", as_index=False).first()
return match
-def parse_crystfel_streamfile(stream_filename, panels, begin=0, end=None):
+def parse_crystfel_streamfile(stream_filename, panels, connected_groups,
+ begin=0, end=None):
lattice_params = ['lattice_type', 'centering', 'unique_axis']
lattice_arrays = {
'Cell parameters/lengths': ['a', 'b', 'c'],
@@ -161,7 +170,8 @@ def parse_crystfel_streamfile(stream_filename, panels, begin=0, end=None):
lattices = pd.DataFrame(lattices)
frames = pd.DataFrame(frames)
- match = match_reflexes_to_peaks(reflexes, peaks, lattices, panels)
+ match = match_reflexes_to_peaks(reflexes, peaks, lattices,
+ panels, connected_groups)
return frames, peaks, lattices, reflexes, match
@@ -208,17 +218,20 @@ def _split_file(filename, nproc=20, partsize=None, nbytes=None):
class StreamReader:
- def __init__(self, filename, panels):
+ def __init__(self, filename, panels, connected_groups):
self.filename = filename
self.panels = panels
+ self.connected_groups = connected_groups
def read_part(self, args):
begin, end = args
return parse_crystfel_streamfile(
- self.filename, self.panels, begin=begin, end=end)
+ self.filename, self.panels, self.connected_groups,
+ begin=begin, end=end)
-def read_crystfel_streamfile(stream_filename, panels, disp=False):
+def read_crystfel_streamfile(stream_filename, panels,
+ connected_groups, disp=False):
"""Read Crystfel stream file in parallel.
Input
@@ -240,7 +253,7 @@ def read_crystfel_streamfile(stream_filename, panels, disp=False):
if disp:
print(f"nproc: {nproc} nslice: {nslice}")
- rdr = StreamReader(stream_filename, panels)
+ rdr = StreamReader(stream_filename, panels, connected_groups)
with mp.Pool(min(nproc, nslice)) as pool:
res = pool.imap(rdr.read_part, slices)
diff --git a/src/geomtools/sfx/misc.py b/src/geomtools/sfx/misc.py
index 8d5e9c3..39f968f 100644
--- a/src/geomtools/sfx/misc.py
+++ b/src/geomtools/sfx/misc.py
@@ -53,7 +53,11 @@ def get_peak_position(peaks, panels):
def avg_pixel_displacement(match, panels):
- pxdispl = match[['dx', 'dy', 'peakno', 'panel']].copy()
+ if 'panel_p' in match.columns:
+ pxdispl = match[['dx', 'dy', 'peakno', 'panel_p']].copy()
+ pxdispl = pxdispl.rename(columns={'panel_p': 'panel'})
+ else:
+ pxdispl = match[['dx', 'dy', 'peakno', 'panel']].copy()
pxdispl['fsi'] = np.floor(match['fs_p']).astype(int)
pxdispl['ssi'] = np.floor(match['ss_p']).astype(int)
diff --git a/src/geomtools/sfx/report.ipynb b/src/geomtools/sfx/report.ipynb
index 9724be3..078cbe7 100644
--- a/src/geomtools/sfx/report.ipynb
+++ b/src/geomtools/sfx/report.ipynb
@@ -16,7 +16,8 @@
"summary_file = \"\"\n",
"prefix=prefix = \"\"\n",
"output_dir = \"\"\n",
- "geometry_file = \"\""
+ "geometry_file = \"\"\n",
+ "connected_groups = \"\""
]
},
{
@@ -52,12 +53,18 @@
"\n",
"panels, beam = read_crystfel_geom(geometry_file, indexes={'modno': 1})\n",
"\n",
+ "panel_columns = panels.columns.tolist() + ['panel']\n",
+ "if connected_groups not in panel_columns:\n",
+ " raise ValueError(\n",
+ " f\"Connected groups '{connected_groups}' are not defined\")\n",
+ "\n",
"photon_energy = beam['photon_energy']\n",
"clen = panels.clen.unique()\n",
"if len(clen) == 1:\n",
" clen = clen[0]\n",
"\n",
- "fr, pe, la, re, ma = read_crystfel_streamfile(stream_file, panels, disp=False)"
+ "fr, pe, la, re, ma = read_crystfel_streamfile(\n",
+ " stream_file, panels, connected_groups, disp=False)"
]
},
{
diff --git a/src/geomtools/sfx/report.py b/src/geomtools/sfx/report.py
index 14e35bb..3e8a35d 100644
--- a/src/geomtools/sfx/report.py
+++ b/src/geomtools/sfx/report.py
@@ -53,6 +53,7 @@ def push_geometry():
help="EXtra-xwiz summary file")
parser.add_argument('-i', '--stream', type=pathlib.Path,
help="Crystfel stream file")
+ parser.add_argument('-c', '--connected', default="modules")
parser.add_argument('-r', '--report-only', action="store_true")
parser.add_argument('detector', choices=DET.keys())
parser.add_argument('tag')
@@ -105,6 +106,7 @@ def push_geometry():
date = dc.run_metadata()['creationDate']
day, _, tm = date.partition('T')
print("Data: ", day)
+ print("Connected groups:", args.connected)
geom_id = '_'.join([args.detector, day, args.tag])
if not args.report_only:
@@ -130,6 +132,7 @@ def push_geometry():
'runs': runs,
'method': 'sfx',
'tool': 'geoptimiser',
+ 'connected_groups': args.connected,
'sample': args.sample,
'date': date,
'motors': motor_pos,
@@ -158,6 +161,7 @@ def push_geometry():
stream_file=str(stream_file.absolute()),
summary_file=str(summary_file.absolute()),
geometry_file=str(geom_file.absolute()),
+ connected_groups=args.connected,
prefix=prefix,
output_dir=str(output_dir.absolute()),
)
--
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