diff --git a/src/geomtools/__init__.py b/src/geomtools/__init__.py
index 28a9d3ea297692a2b9681e2b30aa9d2e9c6b6b00..5652b69a86571e3702f10db83b36801d962ffe68 100644
--- a/src/geomtools/__init__.py
+++ b/src/geomtools/__init__.py
@@ -1,10 +1,11 @@
# flake8: noqa E401
from .sfx import (
parse_crystfel_streamfile, read_crystfel_streamfile, extract_geometry,
- plot_center_shift, plot_cell_parameters, plot_peakogram, plot_powder,
- ph_en_to_lambda, get_q_from_xyz, get_min_bragg_dist, spacing,
- gauss2d_fit, ellipse, parse_xwiz_summary, get_peak_position,
- plot_geoptimiser_errormap, avg_pixel_displacement, rmsd_per_group,
+ extract_cell, plot_center_shift, plot_cell_parameters, plot_peakogram,
+ plot_powder, ph_en_to_lambda, get_q_from_xyz, get_min_bragg_dist,
+ spacing, cell_volume, gauss2d_fit, ellipse, parse_xwiz_summary,
+ get_peak_position, plot_geoptimiser_errormap, avg_pixel_displacement,
+ rmsd_per_group, read_crystfel_cell,
)
from .detector import (
read_crystfel_geom, get_pixel_positions, assemble_data,
diff --git a/src/geomtools/sfx/__init__.py b/src/geomtools/sfx/__init__.py
index 5095366d7bf516e0f47b2bdb7bad8e37eda215d3..56452e10030127ce53d9aca1c72a5be6a15650fa 100644
--- a/src/geomtools/sfx/__init__.py
+++ b/src/geomtools/sfx/__init__.py
@@ -1,13 +1,15 @@
# flake8: noqa E401
from .crystfelio import (
parse_crystfel_streamfile, read_crystfel_streamfile, extract_geometry,
+ extract_cell,
)
from .draw import (
plot_center_shift, plot_cell_parameters, plot_peakogram, plot_powder,
plot_geoptimiser_errormap,
)
from .lattice import (
- spacing, ph_en_to_lambda, get_q_from_xyz, get_min_bragg_dist,
+ cell_volume, spacing, ph_en_to_lambda, get_q_from_xyz,
+ get_min_bragg_dist, read_crystfel_cell,
)
from .misc import (
gauss2d_fit, ellipse, get_peak_position, avg_pixel_displacement,
diff --git a/src/geomtools/sfx/crystfelio.py b/src/geomtools/sfx/crystfelio.py
index 2adc6fe910ea73cd160d949f308fee0a7916aa3b..232e5b03fce718903bf95256ce55324149965d49 100644
--- a/src/geomtools/sfx/crystfelio.py
+++ b/src/geomtools/sfx/crystfelio.py
@@ -13,6 +13,8 @@ from cfelpyutils.crystfel_stream import (
GEOM_START_MARKER = "----- Begin geometry file -----"
GEOM_END_MARKER = "----- End geometry file -----"
+CELL_START_MARKER = "----- Begin unit cell -----"
+CELL_END_MARKER = "----- End unit cell -----"
PEAK_COLUMN_MAP = {
"fs/px": "fs", "ss/px": "ss", "(1/d)/nm^-1": "res",
@@ -49,7 +51,8 @@ def match_reflexes_to_peaks(reflexes, peaks, lattices,
# 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', 'reflno']].copy()
+ re = reflexes[['fs', 'ss', 'panel', 'frame', 'cryst', 'reflno',
+ 'xa', 'ya']].copy()
if group_name != 'panel':
re = re.join(panels[[group_name]], on='panel')
re = re.join(get_peak_position(re, panels))
@@ -83,7 +86,8 @@ def match_reflexes_to_peaks(reflexes, peaks, lattices,
def parse_crystfel_streamfile(stream_filename, panels, connected_groups,
begin=0, end=None):
- lattice_params = ['lattice_type', 'centering', 'unique_axis']
+ lattice_params = ['lattice_type', 'centering', 'unique_axis',
+ 'astar', 'bstar', 'cstar']
lattice_arrays = {
'Cell parameters/lengths': ['a', 'b', 'c'],
'Cell parameters/angles': ['alpha', 'beta', 'gamma'],
@@ -143,12 +147,22 @@ def parse_crystfel_streamfile(stream_filename, panels, connected_groups,
1. / res_avg, clen_avg, lmd, cell)
lattices.append(la)
+
la_kwargs = dict((name, la[name]) for name in cell_columns)
re = crystal['reflections']
re['res'] = np.sqrt(spacing(
re.h.values, re.k.values, re.l.values, **la_kwargs))
+ M = np.array([
+ crystal['astar'], crystal['bstar'], crystal['cstar']
+ ])
+ hkl = np.array([re.h.values, re.k.values, re.l.values])
+ u, v, w = M.T @ hkl
+ s = clen / (1e-9 / lmd + w) / 200e-6
+ re['xa'] = u * s
+ re['ya'] = v * s
+
re['frame'] = frame_ix
re['cryst'] = cryst_ix
reflexes.append(re)
@@ -176,29 +190,63 @@ def parse_crystfel_streamfile(stream_filename, panels, connected_groups,
return frames, peaks, lattices, reflexes, match
-def extract_geometry(stream_filename):
- """Extracts geometry from Crystfel stream file.
+def extract_chunk(stream_filename, start_marker, end_marker):
+ """Extracts text bracketed with markers from Crystfel stream file.
Input
-----
stream_filename: str
Crystfel stream file name
+ start_marker: str
+ String indicated begin of the text
+ end_marker: str
+ String indicated end of the text
Returns
-------
- StringIO buffer with geometry file
+ StringIO buffer with text
"""
with open(stream_filename, 'r') as f:
line = f.readline()
- while line and line.strip() != GEOM_START_MARKER:
+ while line and line.strip() != start_marker:
if line.strip() == CHUNK_START_MARKER:
return
line = f.readline()
- geom = _buffer_to_line(f, GEOM_END_MARKER)
+ geom = _buffer_to_line(f, end_marker)
return geom
+def extract_geometry(stream_filename):
+ """Extracts geometry from Crystfel stream file.
+
+ Input
+ -----
+ stream_filename: str
+ Crystfel stream file name
+
+ Returns
+ -------
+ StringIO buffer with geometry file
+ """
+ return extract_chunk(stream_filename, GEOM_START_MARKER, GEOM_END_MARKER)
+
+
+def extract_cell(stream_filename):
+ """Extracts unit cell from Crystfel stream file.
+
+ Input
+ -----
+ stream_filename: str
+ Crystfel stream file name
+
+ Returns
+ -------
+ StringIO buffer with crystfel cell file
+ """
+ return extract_chunk(stream_filename, CELL_START_MARKER, CELL_END_MARKER)
+
+
def _split_file(filename, nproc=20, partsize=None, nbytes=None):
"""Split file on portions."""
if nbytes is None: