def exercise_spots_xds():
txt = """\
1104.20 1290.27 2.20 632. -4 -3 -1
912.22 1303.37 3.49 346. 0 0 0
1427.55 1339.93 3.34 259. 7 3 -1
1380.54 1187.54 3.58 243. 4 3 4
1222.32 1220.09 3.95 241. -1 0 2
1491.71 1322.33 2.72 237. 9 4 0
1053.50 1227.71 2.87 221. -6 -4 1
"""
f = open_tmp_file(suffix="SPOTS.XDS", mode="wb")
f.write(txt)
f.close()
spots_in = spot_xds.reader()
spots_in.read_file(f.name)
assert approx_equal(
spots_in.centroid,
[[1104.2, 1290.27, 2.2], [912.22, 1303.37, 3.49],
[1427.55, 1339.93, 3.34], [1380.54, 1187.54, 3.58],
[1222.32, 1220.09, 3.95], [1491.71, 1322.33, 2.72],
[1053.5, 1227.71, 2.87]])
assert approx_equal(
spots_in.intensity,
[632.0, 346.0, 259.0, 243.0, 241.0, 237.0, 221.0])
assert approx_equal(
spots_in.miller_index,
[[-4, -3, -1], [0, 0, 0], [7, 3, -1], [4, 3, 4],
[-1, 0, 2], [9, 4, 0], [-6, -4, 1]])
spots_out = spot_xds.writer(
spots_in.centroid, spots_in.intensity, spots_in.miller_index)
f = open_tmp_file(suffix="SPOTS.XDS", mode="wb")
f.close()
spots_out.write_file(filename=f.name)
spots_in = spot_xds.reader()
spots_in.read_file(f.name)
assert approx_equal(spots_in.centroid, spots_out.centroids)
assert approx_equal(spots_in.intensity, spots_out.intensities)
assert approx_equal(spots_in.miller_index, spots_out.miller_indices)
# now without miller indices
spots_out = spot_xds.writer(spots_in.centroid, spots_in.intensity)
f = open_tmp_file(suffix="SPOTS.XDS", mode="wb")
f.close()
spots_out.write_file(filename=f.name)
spots_in = spot_xds.reader()
spots_in.read_file(f.name)
assert approx_equal(spots_in.centroid, spots_out.centroids)
assert approx_equal(spots_in.intensity, spots_out.intensities)
assert len(spots_in.miller_index) == 0
def exercise_spots_xds():
txt = """\
1104.20 1290.27 2.20 632. -4 -3 -1
912.22 1303.37 3.49 346. 0 0 0
1427.55 1339.93 3.34 259. 7 3 -1
1380.54 1187.54 3.58 243. 4 3 4
1222.32 1220.09 3.95 241. -1 0 2
1491.71 1322.33 2.72 237. 9 4 0
1053.50 1227.71 2.87 221. -6 -4 1
"""
f = open_tmp_file(suffix="SPOTS.XDS", mode="wb")
f.write(txt)
f.close()
spots_in = spot_xds.reader()
spots_in.read_file(f.name)
assert approx_equal(spots_in.centroid,
[[1104.2, 1290.27, 2.2], [912.22, 1303.37, 3.49],
[1427.55, 1339.93, 3.34], [1380.54, 1187.54, 3.58],
[1222.32, 1220.09, 3.95], [1491.71, 1322.33, 2.72],
[1053.5, 1227.71, 2.87]])
assert approx_equal(spots_in.intensity,
[632.0, 346.0, 259.0, 243.0, 241.0, 237.0, 221.0])
assert approx_equal(spots_in.miller_index,
[[-4, -3, -1], [0, 0, 0], [7, 3, -1], [4, 3, 4],
[-1, 0, 2], [9, 4, 0], [-6, -4, 1]])
spots_out = spot_xds.writer(spots_in.centroid, spots_in.intensity,
spots_in.miller_index)
f = open_tmp_file(suffix="SPOTS.XDS", mode="wb")
f.close()
spots_out.write_file(filename=f.name)
spots_in = spot_xds.reader()
spots_in.read_file(f.name)
assert approx_equal(spots_in.centroid, spots_out.centroids)
assert approx_equal(spots_in.intensity, spots_out.intensities)
assert approx_equal(spots_in.miller_index, spots_out.miller_indices)
# now without miller indices
spots_out = spot_xds.writer(spots_in.centroid, spots_in.intensity)
f = open_tmp_file(suffix="SPOTS.XDS", mode="wb")
f.close()
spots_out.write_file(filename=f.name)
spots_in = spot_xds.reader()
spots_in.read_file(f.name)
assert approx_equal(spots_in.centroid, spots_out.centroids)
assert approx_equal(spots_in.intensity, spots_out.intensities)
assert len(spots_in.miller_index) == 0
def export_spot_xds(reflections, filename):
if reflections is not None and len(reflections) > 0:
centroids = reflections["xyzobs.px.value"]
intensities = reflections["intensity.sum.value"]
miller_indices = None
if "miller_index" in reflections:
miller_indices = reflections["miller_index"]
selection = miller_indices != (0, 0, 0)
miller_indices = miller_indices.select(selection)
if len(miller_indices) == 0:
miller_indices = None
else:
centroids = centroids.select(selection)
intensities = intensities.select(selection)
xds_writer = spot_xds.writer(
centroids=centroids, intensities=intensities, miller_indices=miller_indices
)
logger.info("Exporting spot list as %s", filename)
xds_writer.write_file(filename=filename)
def export_spot_xds(reflections, filename):
from iotbx.xds import spot_xds
if reflections is not None and len(reflections) > 0:
centroids = reflections['xyzobs.px.value']
intensities = reflections['intensity.sum.value']
miller_indices = None
if 'miller_index' in reflections:
miller_indices = reflections['miller_index']
selection = miller_indices != (0, 0, 0)
miller_indices = miller_indices.select(selection)
if len(miller_indices) == 0:
miller_indices = None
else:
centroids = centroids.select(selection)
intensities = intensities.select(selection)
xds_writer = spot_xds.writer(centroids=centroids,
intensities=intensities,
miller_indices=miller_indices)
print "Exporting spot list as %s" %filename
xds_writer.write_file(filename=filename)
def export_spot_xds(reflections, filename):
from iotbx.xds import spot_xds
if reflections is not None and len(reflections) > 0:
centroids = reflections['xyzobs.px.value']
intensities = reflections['intensity.sum.value']
miller_indices = None
if 'miller_index' in reflections:
miller_indices = reflections['miller_index']
selection = miller_indices != (0, 0, 0)
miller_indices = miller_indices.select(selection)
if len(miller_indices) == 0:
miller_indices = None
else:
centroids = centroids.select(selection)
intensities = intensities.select(selection)
xds_writer = spot_xds.writer(centroids=centroids,
intensities=intensities,
miller_indices=miller_indices)
print "Exporting spot list as %s" %filename
xds_writer.write_file(filename=filename)
