def test_decide_pointgroup(self):
meta = {'beam': (120.55726144764847, 119.44351135718689),
'detector': 'EIGER_9M',
'detector_class': 'eiger 9M',
'directory': '/mnt/optane/hbernstein/CollinsLaccases/data/CataApo05/5/NSLS2-18_10',
'distance': 200.04000666485112,
'end': 50,
'exposure_time': 0.05000000074505806,
'extra_text': 'LIB=/usr/local/crys-local/ccp4-7.0/bin/../lib/eiger2cbf.so\n',
'matching': [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30,
31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,
46, 47, 48, 49, 50],
'oscillation': (0.0, 0.20000000298023224),
'oscillation_axis': 'Omega_I_guess',
'phi_end': 0.20000000298023224,
'phi_start': 0.0,
'phi_width': 0.20000000298023224,
'pixel': (0.07500000356230885, 0.07500000356230885),
'saturation': 92461.0,
'sensor': 0.44999999227002263,
'serial_number': 0,
'size': (3269, 3110),
'start': 1,
'template': 'CataApo05_1444_??????.h5',
'wavelength': 0.9201257824897766}
p1_unit_cell = (199.7, 200.9, 202.5, 108.0, 109.9, 109.6)
input_spacegroup = None
self.assertEqual(decide_pointgroup(p1_unit_cell, meta, input_spacegroup), ((232.96666666666667, 232.96666666666667, 232.96666666666667, 90.0, 90.0, 90.0), 197, 6.492))
def process(self):
'''Main routine, chain together all of the steps imported from
autoindex, integrate, pointgroup, scale and merge.'''
try:
hostname = os.environ['HOSTNAME'].split('.')[0]
if version == 2:
try:
write('Running on: %s' % hostname)
except:
pass
else:
write('Running on: {}'.format(hostname))
except Exception:
pass
# check input frame limits
if not self._first_image is None:
if self._metadata['start'] < self._first_image:
start = self._metadata['start']
self._metadata['start'] = self._first_image
self._metadata['phi_start'] += self._metadata['phi_width'] * \
(self._first_image - start)
if not self._last_image is None:
if self._metadata['end'] > self._last_image:
self._metadata['end'] = self._last_image
# first if the number of jobs was set to 0, decide something sensible.
# this should be jobs of a minimum of 5 degrees, 10 frames.
if self._n_jobs == 0:
phi = self._metadata['oscillation'][1]
if phi == 0.0:
if version == 2:
try:
raise RuntimeError, 'grid scan data'
except:
pass
else:
raise RuntimeError('grid scan data')
wedge = max(10, int(round(5.0 / phi)))
frames = self._metadata['end'] - self._metadata['start'] + 1
n_jobs = int(round(frames / wedge))
if self._max_n_jobs > 0:
if n_jobs > self._max_n_jobs:
n_jobs = self._max_n_jobs
self.set_n_jobs(n_jobs)
if version == 2:
try:
write('Number of jobs: %d' % self._n_jobs)
write('Number of cores: %d' % self._n_cores)
except:
pass
else:
write('Number of jobs: {}'.format(self._n_jobs))
write('Number of cores: {}'.format(self._n_cores))
step_time = time.time()
if version == 2:
try:
write('Processing images: %d -> %d' %
(self._metadata['start'], self._metadata['end']))
except:
pass
else:
write('Processing images: {} -> {}'.format(self._metadata['start'],
self._metadata['end']))
phi_end = self._metadata['phi_start'] + self._metadata['phi_width'] * \
(self._metadata['end'] - self._metadata['start'] + 1)
if version == 2:
try:
write('Phi range: %.2f -> %.2f' %
(self._metadata['phi_start'], phi_end))
write('Template: %s' % self._metadata['template'])
write('Wavelength: %.5f' % self._metadata['wavelength'])
write('Working in: %s' % os.getcwd())
except:
pass
else:
write('Phi range: {:.2f} -> {:.2f}'.format(
self._metadata['phi_start'], phi_end))
write('Template: {}'.format(self._metadata['template']))
write('Wavelength: {:.5f}'.format(self._metadata['wavelength']))
write('Working in: {}'.format(os.getcwd()))
if self._plugin_library != " " and self._plugin_library != "None" and self._plugin_library != "none":
oet = self._metadata['extra_text']
et = None
for line in oet.split('\n'):
if line[0:3] != "LIB=":
if et == None:
et = line + "\n"
else:
et = et + line + "\n"
if et == None:
self._metadata[
'extra_text'] = "LIB=" + self._plugin_library + "\n"
else:
self._metadata[
'extra_text'] = et + "LIB=" + self._plugin_library + "\n"
elif self._plugin_library == "None" or self._plugin_library == "none":
oet = self._metadata['extra_text']
et = None
for line in oet.split('\n'):
if line[0:3] != "LIB=":
if et == None:
et = line + "\n"
else:
et = et + line + "\n"
self._metadata['extra_text'] = et
if version == 2:
try:
write('Extra commands: %s' % self._metadata['extra_text'])
except:
pass
else:
write('Extra commands: {}'.format(self._metadata['extra_text']))
try:
self._p1_unit_cell = autoindex(self._metadata,
input_cell=self._input_cell_p1)
except Exception as e:
traceback.print_exc(file=open('fast_dp.error', 'w'))
if version == 2:
try:
write('Autoindexing error: %s' % e)
except:
pass
else:
write('Autoindexing error: {}'.format(e))
fdpelogpath = get_afilepath()
fdpelogprefix = get_afileprefix()
if fdpelogpath:
if version == 2:
try:
try:
shutil.copyfile(
'fast_dp.error',
os.path.join(fdpelogpath,
fdpelogprefix + 'fast_dp.error'))
write('Archived fast_dp.error to %s' %
os.path.join(fdpelogpath, fdpelogprefix +
'fast_dp.error'))
except:
write('fast_dp.error not archived to %s' %
os.path.join(fdpelogpath, fdpelogprefix +
'fast_dp.error'))
except:
pass
else:
try:
shutil.copyfile(
'fast_dp.error',
os.path.join(fdpelogpath,
fdpelogprefix + 'fast_dp.error'))
write('Archived fast_dp.error to {}'.format(
os.path.join(fdpelogpath,
fdpelogprefix + 'fast_dp.error')))
except:
write('fast_dp.error not archived to {}'.format(
os.path.join(fdpelogpath,
fdpelogprefix + 'fast_dp.error')))
return
try:
mosaics = integrate(self._metadata, self._p1_unit_cell,
self._resolution_low, self._n_jobs,
self._n_cores)
if version == 2:
try:
write('Mosaic spread: %.2f < %.2f < %.2f' % tuple(mosaics))
except:
pass
else:
write('Mosaic spread: {0[0]:.2f} < {0[1]:.2f} < {0[2]:.2f}'.
format(tuple(mosaics)))
except RuntimeError as e:
traceback.print_exc(file=open('fast_dp.error', 'w'))
if version == 2:
try:
write('Integration error: %s' % e)
except:
pass
else:
write('Integration error: {}'.format(e))
fdpelogpath = get_afilepath()
fdpelogprefix = get_afileprefix()
if fdpelogpath:
if version == 2:
try:
try:
shutil.copyfile(
'fast_dp.error',
os.path.join(fdpelogpath,
fdpelogprefix + 'fast_dp.error'))
write('Archived fast_dp.error to %s' %
os.path.join(fdpelogpath, fdpelogprefix +
'fast_dp.error'))
except:
write('fast_dp.error not archived to %s' %
os.path.join(fdpelogpath, fdpelogprefix +
'fast_dp.error'))
except:
pass
else:
try:
shutil.copyfile(
'fast_dp.error',
os.path.join(fdpelogpath,
fdpelogprefix + 'fast_dp.error'))
write('Archived fast_dp.error to {}'.format(
os.path.join(fdpelogpath,
fdpelogprefix + 'fast_dp.error')))
except:
write('fast_dp.error not archived to {}'.format(
os.path.join(fdpelogpath,
fdpelogprefix + 'fast_dp.error')))
return
try:
# FIXME in here will need a mechanism to take the input
# spacegroup, determine the corresponding pointgroup
# and then apply this (or verify that it is allowed then
# select)
metadata = copy.deepcopy(self._metadata)
cell, sg_num, resol = decide_pointgroup(
self._p1_unit_cell,
metadata,
input_spacegroup=self._input_spacegroup)
self._unit_cell = cell
self._space_group_number = sg_num
if not self._resolution_high:
self._resolution_high = resol
except RuntimeError as e:
if version == 2:
try:
write('Pointgroup error: %s' % e)
except:
pass
else:
write('Pointgroup error: {}'.format(e))
return
try:
self._unit_cell, self._space_group, self._nref, beam_pixels = \
scale(self._unit_cell, self._metadata, self._space_group_number, \
self._resolution_high, self._resolution_low, self._n_jobs,
self._n_cores)
self._refined_beam = (self._metadata['pixel'][1] * beam_pixels[1],
self._metadata['pixel'][0] * beam_pixels[0])
except RuntimeError as e:
if version == 2:
try:
write('Scaling error: %s' % e)
except:
pass
else:
write('Scaling error: {}'.format(e))
return
try:
n_images = self._metadata['end'] - self._metadata['start'] + 1
self._xml_results = merge()
mtzlogpath = get_afilepath()
mtzlogprefix = get_afileprefix()
if mtzlogpath:
if version == 2:
try:
try:
shutil.copyfile(
'fast_dp.mtz',
os.path.join(mtzlogpath,
mtzlogprefix + 'fast_dp.mtz'))
write('Archived fast_dp.mtz to %s' % os.path.join(
mtzlogpath, mtzlogprefix + 'fast_dp.mtz'))
except:
write('fast_dp.mtz not archived to %s' %
os.path.join(mtzlogpath,
mtzlogprefix + 'fast_dp.mtz'))
except:
pass
else:
try:
shutil.copyfile(
'fast_dp.mtz',
os.path.join(mtzlogpath,
mtzlogprefix + 'fast_dp.mtz'))
write('Archived fast_dp.mtz to {}'.format(
os.path.join(mtzlogpath,
mtzlogprefix + 'fast_dp.mtz')))
except:
write('fast_dp.mtz not archived to {}'.format(
os.path.join(mtzlogpath,
mtzlogprefix + 'fast_dp.mtz')))
except RuntimeError as e:
if version == 2:
try:
write('Merging error: %s' % e)
except:
pass
else:
write('Merging error: {}'.format(e))
return
if version == 2:
try:
write('Merging point group: %s' % self._space_group)
write('Unit cell: %6.2f %6.2f %6.2f %6.2f %6.2f %6.2f' % \
self._unit_cell)
duration = time.time() - step_time
write('Processing took %s (%d s) [%d reflections]' %
(time.strftime('%Hh %Mm %Ss', time.gmtime(duration)),
duration, self._nref))
write('RPS: %.1f' % (float(self._nref) / duration))
except:
pass
else:
write('Merging point group: {}'.format(self._space_group))
write(
'Unit cell: {0[0]:6.2f} {0[1]:6.2f} {0[2]:6.2f} {0[3]:6.2f} {0[4]:6.2f} {0[5]:6.2f}'
.format(self._unit_cell))
duration = time.time() - step_time
write('Processing took {} ({:d} s) [{:d} reflections]'.format(
time.strftime('%Hh %Mm %Ss', time.gmtime(duration)),
int(duration), self._nref))
write('RPS: {:.1f}'.format((float(self._nref) / duration)))
# write out json and xml
for func in (output.write_json, output.write_ispyb_xml):
func(self._commandline, self._space_group, self._unit_cell,
self._xml_results, self._start_image, self._refined_beam)
def reprocess(self):
'''Main routine, chain together last few steps of processing i.e.
pointgroup, scale and merge.'''
try:
hostname = os.environ['HOSTNAME'].split('.')[0]
if version == 2:
try:
write('Running on: %s' % hostname)
except:
pass
else:
write('Running on: {}'.format(hostname))
except Exception:
pass
# check input frame limits
if not self._first_image is None:
if self._metadata['start'] < self._first_image:
start = self._metadata['start']
self._metadata['start'] = self._first_image
self._metadata['phi_start'] += self._metadata['phi_width'] * \
(self._first_image - start)
if not self._last_image is None:
if self._metadata['end'] > self._last_image:
self._metadata['end'] = self._last_image
step_time = time.time()
if version == 2:
try:
write('Processing images: %d -> %d' % (self._metadata['start'],
self._metadata['end']))
except:
pass
else:
write('Processing images: {} -> {}'.format(
self._metadata['start'], self._metadata['end']))
phi_end = self._metadata['phi_start'] + self._metadata['phi_width'] * \
(self._metadata['end'] - self._metadata['start'] + 1)
if version == 2:
try:
write('Phi range: %.2f -> %.2f' % (self._metadata['phi_start'],
phi_end))
write('Template: %s' % self._metadata['template'])
write('Wavelength: %.5f' % self._metadata['wavelength'])
write('Working in: %s' % os.getcwd())
except:
pass
else:
write('Phi range: {:.2f} -> {:.2f}'.format(
self._metadata['phi_start'], phi_end))
write('Template: {}'.format(self._metadata['template']))
write('Wavelength: {:.5f}'.format(self._metadata['wavelength']))
write('Working in: {}'.format(os.getcwd()))
# just for information for the user, print all options for indexing
# FIXME should be able to run the same from CORRECT.LP which would
# work better....
from xds_reader import read_xds_idxref_lp
from cell_spacegroup import spacegroup_to_lattice
results = read_xds_idxref_lp('IDXREF.LP')
write('For reference, all indexing results:')
if version == 2:
try:
write('%3s %6s %6s %6s %6s %6s %6s' % \
('Lattice', 'a', 'b', 'c', 'alpha', 'beta', 'gamma'))
except:
pass
else:
write('{:3s} {:6s} {:6s} {:6s} {:6s} {:6s} {:6s}'.format(
'Lattice ', 'a', 'b', 'c', 'alpha', 'beta', 'gamma'))
for r in reversed(sorted(results)):
if not type(r) == type(1):
continue
cell = results[r][1]
if version == 2:
try:
write('%7s %6.2f %6.2f %6.2f %6.2f %6.2f %6.2f' % \
(spacegroup_to_lattice(r), cell[0], cell[1], cell[2],
cell[3], cell[4], cell[5]))
except:
pass
else:
write('{:7s} {:6.2f} {:6.2f} {:6.2f} {:6.2f} {:6.2f} {:6.2f}'.format(
spacegroup_to_lattice(r), cell[0], cell[1], cell[2],
cell[3], cell[4], cell[5]))
try:
# FIXME in here will need a mechanism to take the input
# spacegroup, determine the corresponding pointgroup
# and then apply this (or verify that it is allowed then
# select)
metadata = copy.deepcopy(self._metadata)
cell, sg_num, resol = decide_pointgroup(
self._p1_unit_cell, metadata,
input_spacegroup = self._input_spacegroup)
self._unit_cell = cell
self._space_group_number = sg_num
if not self._resolution_high:
self._resolution_high = resol
except RuntimeError as e:
if version == 2:
try:
write('Pointgroup error: %s' % e)
except:
pass
else:
write('Pointgroup error: {}'.format(e))
return
try:
self._unit_cell, self._space_group, self._nref, beam_pixels = \
scale(self._unit_cell, self._metadata, self._space_group_number, \
self._resolution_high, self._resolution_low, self._n_jobs,
self._n_cores)
self._refined_beam = (self._metadata['pixel'][1] * beam_pixels[1],
self._metadata['pixel'][0] * beam_pixels[0])
except RuntimeError as e:
if version == 2:
try:
write('Scaling error: %s' % e)
except:
pass
else:
write('Scaling error: {}'.format(e))
return
try:
n_images = self._metadata['end'] - self._metadata['start'] + 1
self._xml_results = merge(hklout='fast_rdp.mtz',
aimless_log='aimless_rerun.log')
except RuntimeError as e:
if version == 2:
try:
write('Merging error: %s' % e)
except:
pass
else:
write('Merging error: {}'.format(e))
return
if version == 2:
try:
write('Merging point group: %s' % self._space_group)
write('Unit cell: %6.2f %6.2f %6.2f %6.2f %6.2f %6.2f' % \
self._unit_cell)
duration = time.time() - step_time
write('Reprocessing took %s (%d s) [%d reflections]' %
(time.strftime('%Hh %Mm %Ss',
time.gmtime(duration)), duration,
self._nref))
except:
pass
else:
write('Merging point group: {}'.format(self._space_group))
write('Unit cell: {:6.2f} {:6.2f} {:6.2f} {:6.2f} {:6.2f} {:6.2f}'.format(
self._unit_cell))
duration = time.time() - step_time
write('Reprocessing took {} ({} s) [{} reflections]'.format(
(time.strftime('%Hh %Mm %Ss',
time.gmtime(duration)), duration,
self._nref)))
# write out json and xml
for func, filename in [ (output.write_json, 'fast_rdp.json'),
(output.write_ispyb_xml, 'fast_rdp.xml') ]:
func(self._commandline, self._space_group,
self._unit_cell, self._xml_results,
self._start_image, self._refined_beam,
filename=filename)