def summary(self, block_size, block_size_units):
''' Print a summary of the integration stuff. '''
from libtbx.table_utils import format as table
from dials.util.command_line import heading
from logging import info
# Compute the task table
if self._experiments.all_stills():
rows = [["#", "Group", "Frame From", "Frame To"]]
for i in range(len(self)):
job = self._manager.job(i)
group = job.index()
f0, f1 = job.frames()
rows.append([str(i), str(group), str(f0), str(f1)])
elif self._experiments.all_sweeps():
rows = [["#", "Group", "Frame From", "Frame To", "Angle From", "Angle To"]]
for i in range(len(self)):
job = self._manager.job(i)
group = job.index()
expr = job.expr()
f0, f1 = job.frames()
scan = self._experiments[expr[0]].scan
p0 = scan.get_angle_from_array_index(f0)
p1 = scan.get_angle_from_array_index(f1)
rows.append([str(i), str(group), str(f0), str(f1), str(p0), str(p1)])
else:
raise RuntimeError('Experiments must be all sweeps or all stills')
task_table = table(rows, has_header=True, justify="right", prefix=" ")
def summary(self):
'''
Get a summary of the processing
'''
from libtbx.table_utils import format as table
# Compute the task table
if self.experiments.all_stills():
rows = [["#",
"Group",
"Frame From",
"Frame To",
"# Reflections"]]
for i in range(len(self)):
job = self.manager.job(i)
group = job.index()
f0, f1 = job.frames()
n = self.manager.num_reflections(i)
rows.append([str(i), str(group), str(f0), str(f1), str(n)])
elif self.experiments.all_sweeps():
rows = [["#",
"Group",
"Frame From",
"Frame To",
"Angle From",
"Angle To",
"# Reflections"]]
for i in range(len(self)):
job = self.manager.job(i)
group = job.index()
expr = job.expr()
f0, f1 = job.frames()
scan = self.experiments[expr[0]].scan
p0 = scan.get_angle_from_array_index(f0)
p1 = scan.get_angle_from_array_index(f1)
n = self.manager.num_reflections(i)
rows.append([str(i), str(group), str(f0), str(f1), str(p0), str(p1), str(n)])
else:
raise RuntimeError('Experiments must be all sweeps or all stills')
# The job table
task_table = table(rows, has_header=True, justify="right", prefix=" ")
# The format string
if self.params.block.size is None:
block_size = "auto"
else:
block_size = str(self.params.block.size)
fmt = (
'Processing reflections in the following blocks of images:\n'
'\n'
' block_size: %s %s\n'
'\n'
'%s\n'
)
return fmt % (block_size, self.params.block.units, task_table)
def __str__(self):
''' Convert to string. '''
from libtbx.table_utils import format as table
rows = [
["Read time" , "%.2f seconds" % (self.read) ],
["Pre-process time" , "%.2f seconds" % (self.initialize) ],
["Process time" , "%.2f seconds" % (self.process) ],
["Post-process time", "%.2f seconds" % (self.finalize) ],
["Total time" , "%.2f seconds" % (self.total) ],
["User time" , "%.2f seconds" % (self.user) ],
]
return table(rows, justify='right', prefix=' ')
def __str__(self):
''' Convert to string. '''
from libtbx.table_utils import format as table
rows = [
["Read time" , "%.2f seconds" % (self.read) ],
["Pre-process time" , "%.2f seconds" % (self.initialize) ],
["Process time" , "%.2f seconds" % (self.process) ],
["Post-process time", "%.2f seconds" % (self.finalize) ],
["Total time" , "%.2f seconds" % (self.total) ],
["User time" , "%.2f seconds" % (self.user) ],
]
return table(rows, justify='right', prefix=' ')
def __str__(self):
""" Convert to string. """
from libtbx.table_utils import format as table
rows = [
["Read time", "%.2f seconds" % (self.read)],
["Extract time", "%.2f seconds" % (self.extract)],
["Pre-process time",
"%.2f seconds" % (self.initialize)],
["Process time", "%.2f seconds" % (self.process)],
["Post-process time",
"%.2f seconds" % (self.finalize)],
["Total time", "%.2f seconds" % (self.total)],
["User time", "%.2f seconds" % (self.user)],
]
return table(rows, justify="right", prefix=" ")
def as_str(self, prefix=''):
'''
Return the table as a string
:return: The string
'''
from libtbx.table_utils import format as table
rows = [[col[1] for col in self.cols]]
for i, row in enumerate(self.rows):
rows.append([str(x) for x in row])
text = [
prefix + self.title,
table(rows, has_header=True, justify='left', prefix=prefix), ''
]
return '\n'.join(text)
def as_str(self, prefix=''):
'''
Return the table as a string
:return: The string
'''
from libtbx.table_utils import format as table
rows = [[col[1] for col in self.cols]]
for i in range(len(self.rows)):
rows.append([str(x) for x in self.rows[i]])
text = [
prefix + self.title,
table(rows, has_header=True, justify='left', prefix=prefix),
''
]
return '\n'.join(text)
def as_str(self, prefix=""):
"""
Return the table as a string
:return: The string
"""
from libtbx.table_utils import format as table
rows = [[col[1] for col in self.cols]]
for i, row in enumerate(self.rows):
rows.append([str(x) for x in row])
text = [
prefix + self.title,
table(rows, has_header=True, justify="left", prefix=prefix),
"",
]
return "\n".join(text)
def summary(self, block_size, block_size_units):
''' Print a summary of the integration stuff. '''
from libtbx.table_utils import format as table
from dials.util.command_line import heading
# Compute the task table
if self._experiments.all_stills():
rows = [["#", "Group", "Frame From", "Frame To"]]
for i in range(len(self)):
job = self._manager.job(i)
group = job.index()
f0, f1 = job.frames()
rows.append([str(i), str(group), str(f0), str(f1)])
elif self._experiments.all_sweeps():
rows = [[
"#", "Group", "Frame From", "Frame To", "Angle From",
"Angle To"
]]
for i in range(len(self)):
job = self._manager.job(i)
group = job.index()
expr = job.expr()
f0, f1 = job.frames()
scan = self._experiments[expr[0]].scan
p0 = scan.get_angle_from_array_index(f0)
p1 = scan.get_angle_from_array_index(f1)
rows.append(
[str(i),
str(group),
str(f0),
str(f1),
str(p0),
str(p1)])
else:
raise RuntimeError('Experiments must be all sweeps or all stills')
task_table = table(rows, has_header=True, justify="right", prefix=" ")
def run(self):
'''Execute the script.'''
from dials.util.options import flatten_datablocks
from time import time
from dials.util import log
from libtbx.utils import Sorry
import datetime
start_time = time()
# Parse the command line
params, options = self.parser.parse_args(show_diff_phil=False)
# Configure the logging
log.config(
params.verbosity,
info=params.output.log,
debug=params.output.debug_log)
from dials.util.version import dials_version
logger.info(dials_version())
# Log the diff phil
diff_phil = self.parser.diff_phil.as_str()
if diff_phil is not '':
logger.info('The following parameters have been modified:\n')
logger.info(diff_phil)
# Ensure we have a data block
datablocks = flatten_datablocks(params.input.datablock)
if len(datablocks) == 0:
self.parser.print_help()
return
# Extend the first datablock
datablock = datablocks[0]
for db in datablocks[1:]:
if datablock.format_class() != db.format_class():
raise Sorry("Datablocks must have the same format")
datablock.extend(db)
# Get the imagesets and sweeps
stills = datablock.extract_stills()
sweeps = datablock.extract_sweeps()
if len(stills) > 0:
raise Sorry("Sets of still images are currently unsupported")
logger.info("Number of sweeps = %d" % len(sweeps))
# Sort the sweeps by timestamps
logger.info("Sorting sweeps based on timestamp")
sweeps = sorted(sweeps, key=lambda x: x.get_scan().get_epochs()[0])
# Count the number of datasets from each day
from collections import Counter
counter = Counter()
for s in sweeps:
timestamp = s.get_scan().get_epochs()[0]
timestamp = datetime.datetime.fromtimestamp(timestamp)
timestamp = timestamp.strftime('%Y-%m-%d')
counter[timestamp] += 1
# Print the number of datasets on each day
for timestamp in sorted(counter.keys()):
logger.info("%d datasets collected on %s" % (counter[timestamp], timestamp))
# Loop though and see if any models might be shared
b_list = [ s.get_beam() for s in sweeps ]
d_list = [ s.get_detector() for s in sweeps ]
g_list = [ s.get_goniometer() for s in sweeps ]
b_index = []
d_index = []
g_index = []
for i in range(len(sweeps)):
b = b_list[i]
d = d_list[i]
g = g_list[i]
bn = i
dn = i
gn = i
if i > 0:
bj = b_index[-1]
dj = d_index[-1]
gj = g_index[-1]
if b.is_similar_to(b_list[bj]):
bn = bj
if d.is_similar_to(d_list[dj]):
dn = dj
if g.is_similar_to(g_list[gj]):
gn = gj
b_index.append(bn)
d_index.append(dn)
g_index.append(gn)
# Print a table of possibly shared models
from libtbx.table_utils import format as table
rows = [["Sweep", "ID", "Beam", "Detector", "Goniometer", "Date", "Time"]]
for i in range(len(sweeps)):
timestamp = sweeps[i].get_scan().get_epochs()[0]
timestamp = datetime.datetime.fromtimestamp(timestamp)
date_str = timestamp.strftime('%Y-%m-%d')
time_str = timestamp.strftime('%H:%M:%S')
row = [
'%s' % sweeps[i].get_template(),
'%s' % i,
'%s' % b_index[i],
'%s' % d_index[i],
'%s' % g_index[i],
'%s' % date_str,
'%s' % time_str]
rows.append(row)
logger.info(table(rows, has_header=True, justify='left', prefix=' '))
# Print the time
logger.info("Time Taken: %f" % (time() - start_time))
def run(self):
"""Execute the script."""
from dials.util.options import flatten_experiments
from dxtbx.imageset import ImageSequence
from time import time
from dials.util import log
import datetime
start_time = time()
# Parse the command line
params, options = self.parser.parse_args(show_diff_phil=False)
# Configure the logging
log.config(verbosity=options.verbose, logfile=params.output.log)
from dials.util.version import dials_version
logger.info(dials_version())
# Log the diff phil
diff_phil = self.parser.diff_phil.as_str()
if diff_phil != "":
logger.info("The following parameters have been modified:\n")
logger.info(diff_phil)
# Ensure we have a data block
experiments = flatten_experiments(params.input.experiments)
if len(experiments) == 0:
self.parser.print_help()
return
# Get the list of sequences
sequences = []
for experiment in experiments:
if isinstance(experiment.imageset, ImageSequence):
sequences.append(experiment.imageset)
logger.info("Number of sequences = %d" % len(sequences))
# Sort the sequences by timestamps
logger.info("Sorting sequences based on timestamp")
sequences = sorted(sequences,
key=lambda x: x.get_scan().get_epochs()[0])
# Count the number of datasets from each day
from collections import Counter
counter = Counter()
for s in sequences:
timestamp = s.get_scan().get_epochs()[0]
timestamp = datetime.datetime.fromtimestamp(timestamp)
timestamp = timestamp.strftime("%Y-%m-%d")
counter[timestamp] += 1
# Print the number of datasets on each day
for timestamp in sorted(counter.keys()):
logger.info("%d datasets collected on %s" %
(counter[timestamp], timestamp))
# Loop though and see if any models might be shared
b_list = [s.get_beam() for s in sequences]
d_list = [s.get_detector() for s in sequences]
g_list = [s.get_goniometer() for s in sequences]
b_index = []
d_index = []
g_index = []
for i in range(len(sequences)):
b = b_list[i]
d = d_list[i]
g = g_list[i]
bn = i
dn = i
gn = i
if i > 0:
bj = b_index[-1]
dj = d_index[-1]
gj = g_index[-1]
if b.is_similar_to(b_list[bj]):
bn = bj
if d.is_similar_to(d_list[dj]):
dn = dj
if g.is_similar_to(g_list[gj]):
gn = gj
b_index.append(bn)
d_index.append(dn)
g_index.append(gn)
# Print a table of possibly shared models
from libtbx.table_utils import format as table
rows = [[
"Sequence", "ID", "Beam", "Detector", "Goniometer", "Date", "Time"
]]
for i in range(len(sequences)):
timestamp = sequences[i].get_scan().get_epochs()[0]
timestamp = datetime.datetime.fromtimestamp(timestamp)
date_str = timestamp.strftime("%Y-%m-%d")
time_str = timestamp.strftime("%H:%M:%S")
row = [
"%s" % sequences[i].get_template(),
"%s" % i,
"%s" % b_index[i],
"%s" % d_index[i],
"%s" % g_index[i],
"%s" % date_str,
"%s" % time_str,
]
rows.append(row)
logger.info(table(rows, has_header=True, justify="left", prefix=" "))
# Print the time
logger.info("Time Taken: %f" % (time() - start_time))
def run(self):
'''Execute the script.'''
from dials.array_family import flex
from dials.util.options import flatten_datablocks
from time import time
from dials.util import log
from libtbx.utils import Sorry
import datetime
start_time = time()
# Parse the command line
params, options = self.parser.parse_args(show_diff_phil=False)
# Configure the logging
log.config(
params.verbosity,
info=params.output.log,
debug=params.output.debug_log)
from dials.util.version import dials_version
logger.info(dials_version())
# Log the diff phil
diff_phil = self.parser.diff_phil.as_str()
if diff_phil is not '':
logger.info('The following parameters have been modified:\n')
logger.info(diff_phil)
# Ensure we have a data block
datablocks = flatten_datablocks(params.input.datablock)
if len(datablocks) == 0:
self.parser.print_help()
return
# Extend the first datablock
datablock = datablocks[0]
for db in datablocks[1:]:
if datablock.format_class() != db.format_class():
raise Sorry("Datablocks must have the same format")
datablock.extend(db)
# Get the imagesets and sweeps
stills = datablock.extract_stills()
sweeps = datablock.extract_sweeps()
if len(stills) > 0:
raise Sorry("Sets of still images are currently unsupported")
logger.info("Number of sweeps = %d" % len(sweeps))
# Sort the sweeps by timestamps
logger.info("Sorting sweeps based on timestamp")
sweeps = sorted(sweeps, key=lambda x: x.get_scan().get_epochs()[0])
# Count the number of datasets from each day
from collections import Counter
counter = Counter()
for s in sweeps:
timestamp = s.get_scan().get_epochs()[0]
timestamp = datetime.datetime.fromtimestamp(timestamp)
timestamp = timestamp.strftime('%Y-%m-%d')
counter[timestamp] += 1
# Print the number of datasets on each day
for timestamp in sorted(counter.keys()):
logger.info("%d datasets collected on %s" % (counter[timestamp], timestamp))
# Loop though and see if any models might be shared
b_list = [ s.get_beam() for s in sweeps ]
d_list = [ s.get_detector() for s in sweeps ]
g_list = [ s.get_goniometer() for s in sweeps ]
b_index = []
d_index = []
g_index = []
for i in range(len(sweeps)):
b = b_list[i]
d = d_list[i]
g = g_list[i]
bn = i
dn = i
gn = i
if i > 0:
bj = b_index[-1]
dj = d_index[-1]
gj = g_index[-1]
if b.is_similar_to(b_list[bj]):
bn = bj
if d.is_similar_to(d_list[dj]):
dn = dj
if g.is_similar_to(g_list[gj]):
gn = gj
b_index.append(bn)
d_index.append(dn)
g_index.append(gn)
# Print a table of possibly shared models
from libtbx.table_utils import format as table
rows = [["Sweep", "ID", "Beam", "Detector", "Goniometer", "Date", "Time"]]
for i in range(len(sweeps)):
timestamp = sweeps[i].get_scan().get_epochs()[0]
timestamp = datetime.datetime.fromtimestamp(timestamp)
date_str = timestamp.strftime('%Y-%m-%d')
time_str = timestamp.strftime('%H:%M:%S')
row = [
'%s' % sweeps[i].get_template(),
'%s' % i,
'%s' % b_index[i],
'%s' % d_index[i],
'%s' % g_index[i],
'%s' % date_str,
'%s' % time_str]
rows.append(row)
logger.info(table(rows, has_header=True, justify='left', prefix=' '))
# Print the time
logger.info("Time Taken: %f" % (time() - start_time))