def run(args):
user_phil = []
for arg in args:
try:
user_phil.append(parse(arg))
except Exception as e:
raise Sorry("Unrecognized argument %s" % arg)
params = phil_scope.fetch(sources=user_phil).extract()
app = xfel_db_application(params)
runs = []
all_results = []
if params.rungroup is None:
assert len(params.run) == 0
trial = app.get_trial(trial_number=params.trial)
for rungroup in trial.rungroups:
for run in rungroup.runs:
stats = HitrateStats(app, run.run, trial.trial, rungroup.id,
params.d_min)()
if len(stats[0]) > 0:
runs.append(run.run)
all_results.append(stats)
else:
for run_no in params.run:
runs.append(run_no)
all_results.append(
HitrateStats(app, run_no, params.trial, params.rungroup,
params.d_min)())
plot_multirun_stats(all_results, runs, params.d_min, n_strong_cutoff=params.n_strong_cutoff, \
i_sigi_cutoff=params.i_sigi_cutoff, run_tags=params.run_tags, title=params.title, \
minimalist=params.minimalist, interactive=True, compress_runs=params.compress_runs)
def run(args):
user_phil = []
for arg in args:
try:
user_phil.append(parse(arg))
except Exception as e:
raise Sorry("Unrecognized argument %s" % arg)
params = phil_scope.fetch(sources=user_phil).extract()
app = xfel_db_application(params)
if params.tag is not None and len(params.tag) > 0:
tags = []
for tag in app.get_all_tags():
for t in params.tag:
if t == tag.name:
tags.append(tag)
extra_title = ",".join([t.name for t in tags])
else:
tags = None
extra_title = None
if params.run is not None and len(params.run) > 0:
assert params.rungroup is not None
runs = [app.get_run(run_number=r) for r in params.run]
rungroup = app.get_rungroup(rungroup_id=params.rungroup)
else:
runs = None
rungroup = None
if extra_title is None and runs is not None:
extra_title = "%s" % (",".join(["%s" % r.run for r in runs]))
trial = app.get_trial(trial_number=params.trial)
info = []
print("Reading data...")
cells = app.get_stats(trial=trial,
tags=tags,
isigi_cutoff=1.0,
tag_selection_mode=params.tag_selection_mode,
selected_runs=runs,
selected_rungroup=rungroup)()
for cell in cells:
info.append({
'a': cell.cell_a,
'b': cell.cell_b,
'c': cell.cell_c,
'alpha': cell.cell_alpha,
'beta': cell.cell_beta,
'gamma': cell.cell_gamma,
'n_img': 0
})
import xfel.ui.components.xfel_gui_plotter as pltr
plotter = pltr.PopUpCharts()
plotter.plot_uc_histogram(info_list=[info],
extra_title=extra_title,
legend_list=[""],
iqr_ratio=params.iqr_ratio)
plotter.plot_uc_3Dplot(info=info, iqr_ratio=params.iqr_ratio)
plotter.plt.show()
def run(args):
user_phil = []
for arg in args:
try:
user_phil.append(parse(arg))
except Exception as e:
raise Sorry("Unrecognized argument %s" % arg)
params = phil_scope.fetch(sources=user_phil).extract()
app = xfel_db_application(params)
trial = app.get_trial(trial_number=params.trial)
jobs = app.get_all_jobs()
for rungroup in trial.rungroups:
for run in rungroup.runs:
if params.output_folder is None:
job = None
all_path = None
else:
job_found = None
for job in jobs:
if job.trial.id == trial.id and job.rungroup.id == rungroup.id and job.run.id == run.id:
all_path = os.path.join(
os.path.sep.join(job.get_log_path().split(
os.path.sep)[:-2]), "all")
assert job_found is None
job_found = job
assert job_found is not None
job = job_found
where = "WHERE event.n_strong >= %d" % params.hit_cutoff
events = app.get_all_events(trial=trial,
runs=[run],
only_indexed=False,
where=where)
for e in events:
t = e.timestamp
ts = t[0:4] + t[5:7] + t[8:10] + t[11:13] + t[14:16] + t[
17:19] + t[20:23]
if all_path is None:
print "%04d" % run.run, ts
else:
print os.path.join(all_path, "shot-" + ts + ".pickle")
def run(args):
user_phil = []
for arg in args:
try:
user_phil.append(parse(arg))
except Exception as e:
raise Sorry("Unrecognized argument %s"%arg)
params = phil_scope.fetch(sources=user_phil).extract()
print("Printing results for trial", params.trial, "using a hit cutoff of", params.n_strong_cutoff, "reflections")
print()
print(" Run N Drop Hits (%) N Hits (%) N Indexed (%) N Lattices N High qual (%) %HQR N Frames")
drop_hits_total = 0
hit_total = 0
indexed_total = 0
lattices_total = 0
high_quality_total = 0
overall_total = 0
ratio_cutoff = 1
app = xfel_db_application(params)
if params.run is None or len(params.run) == 0:
trial = app.get_trial(trial_number=params.trial)
runs = []
run_ids = []
rungroups = []
for rg in trial.rungroups:
for run in rg.runs:
if run.id in run_ids: continue
runs.append(run.run)
run_ids.append(run.id)
rungroups.append(rg.id)
else:
runs = params.run
assert params.rungroup is not None
rungroups = [params.rungroup] * len(runs)
for run_no, rungroup_id in zip(runs, rungroups):
try:
timestamps, two_theta_low, two_theta_high, n_strong, average_i_sigi, n_lattices = HitrateStats(app, run_no, params.trial, rungroup_id, params.d_min)()
except Exception as e:
print("Couldn't get run", run_no)
continue
n_hit = (n_strong >= params.n_strong_cutoff).count(True)
n_indexed = (n_lattices > 0).count(True)
n_lattices = flex.sum(n_lattices)
n_total = len(timestamps)
n_high_quality = ((average_i_sigi > 0) & (n_strong >= params.n_strong_cutoff)).count(True)
invalid = (two_theta_low <= 0) or (two_theta_high < 0) # <= to prevent /0
numerator = two_theta_high.set_selected(invalid, 0)
denominator = two_theta_low.set_selected(two_theta_low == 0, 1) # prevent /0
drop_ratios = numerator/denominator
drop_hits = drop_ratios >= ratio_cutoff
n_drop_hits = drop_hits.count(True)
try:
print("% 20s % 7d % 5.1f % 7d % 5.1f % 7d % 5.1f % 7d % 7d % 5.1f % 5.1f % 7d " % (run_no, n_drop_hits, 100*n_drop_hits/n_total, n_hit, 100*n_hit/n_total, n_indexed, 100*n_indexed/n_total, n_lattices, n_high_quality, 100*n_high_quality/n_total, 100*n_high_quality/n_indexed, n_total))
except ZeroDivisionError:
print("% 20s % 7d % 5.1f % 7d % 5.1f % 7d % 5.1f % 7d % 7d % 5.1f % 5.1f % 7d " % (run_no, n_drop_hits, 0, n_hit, 0, n_indexed, 0, n_lattices, n_high_quality, 0, 0, n_total))
drop_hits_total += n_drop_hits
hit_total += n_hit
indexed_total += n_indexed
lattices_total += n_lattices
high_quality_total += n_high_quality
overall_total += n_total
if len(runs) > 1:
print("-" * 80)
try:
print("Total % 7d % 5.1f % 7d % 5.1f % 7d % 5.1f % 7d % 7d % 5.1f % 5.1f % 7d " % (drop_hits_total, 100*drop_hits_total/overall_total, hit_total, 100*hit_total/overall_total, indexed_total, 100*indexed_total/overall_total, lattices_total, high_quality_total, 100*high_quality_total/overall_total, 100*high_quality_total/indexed_total, overall_total))
except ZeroDivisionError:
if overall_total == 0:
print("Total % 7d % 5.1f % 7d % 5.1f % 7d % 5.1f % 7d % 7d % 5.1f % 5.1f % 7d " % (drop_hits_total, 0, hit_total, 0, indexed_total, 0, lattices_total, 0, 0, 0, overall_total))
else:
print("Total % 7d % 5.1f % 7d % 5.1f % 7d % 5.1f % 7d % 7d % 5.1f % 5.1f % 7d " % (drop_hits_total, 100*drop_hits_total/overall_total, hit_total, 100*hit_total/overall_total, indexed_total, 100*indexed_total/overall_total, lattices_total, high_quality_total, 100*high_quality_total/overall_total, 0, overall_total))
.type = bool
.help = When plotting multiple runs, adjust timestamps so there is no blank space between them.
.help = Thise mode is not compatible with fetching events from timestamps.
"""
phil_scope = parse(phil_str + db_phil_str)
def run(args):
user_phil = []
for arg in args:
try:
user_phil.append(parse(arg))
except Exception, e:
raise Sorry("Unrecognized argument %s"%arg)
params = phil_scope.fetch(sources=user_phil).extract()
app = xfel_db_application(params)
runs = []
all_results = []
if params.rungroup is None:
assert len(params.run) == 0
trial = app.get_trial(trial_number = params.trial)
for rungroup in trial.rungroups:
for run in rungroup.runs:
stats = HitrateStats(app, run.run, trial.trial, rungroup.id, params.d_min)()
if len(stats[0]) > 0:
runs.append(run.run)
all_results.append(stats)
else:
for run_no in params.run:
runs.append(run_no)
all_results.append(HitrateStats(app, run_no, params.trial, params.rungroup, params.d_min)())
.type = float
.help = Interquartile range multiplier for outlier rejection. Use None to disable outlier rejection.
"""
phil_scope = parse(phil_str + db_phil_str)
def run(args):
user_phil = []
for arg in args:
try:
user_phil.append(parse(arg))
except Exception, e:
raise Sorry("Unrecognized argument %s" % arg)
params = phil_scope.fetch(sources=user_phil).extract()
app = xfel_db_application(params)
if params.tag is not None and len(params.tag) > 0:
tags = []
for tag in app.get_all_tags():
for t in params.tag:
if t == tag.name:
tags.append(tag)
extra_title = ",".join([t.name for t in tags])
else:
tags = None
extra_title = None
if params.run is not None and len(params.run) > 0:
assert params.rungroup is not None
runs = [app.get_run(run_number=r) for r in params.run]
def run(args):
user_phil = []
for arg in args:
try:
user_phil.append(parse(arg))
except Exception as e:
raise Sorry("Unrecognized argument %s" % arg)
params = phil_scope.fetch(sources=user_phil).extract()
app = xfel_db_application(params)
trial_ni = app.get_trial(trial_number=params.trial_noisoforms)
trial_i = app.get_trial(trial_number=params.trial_isoforms)
tags = []
if params.tag is not None and len(params.tag) > 0:
for tag in app.get_all_tags():
if params.tag == tag.name:
tags.append(tag)
extra_title = ",".join([t.name for t in tags])
tag_ids = [t.id for t in tags]
runs_ni = [
r for r in trial_ni.runs if any([t.id in tag_ids for t in r.tags])
]
runs_i = [
r for r in trial_i.runs if any([t.id in tag_ids for t in r.tags])
]
else:
extra_title = None
runs_ni = trial_ni.runs
runs_i = trial_i.runs
runs_ni_str = "(%s)" % (", ".join([str(r.id) for r in runs_ni]))
exp_tag = params.experiment_tag
isoforms = app.get_trial_isoforms(trial_i.id)
print "Reading data..."
info_list = []
legend_list = []
for isoform in isoforms:
events_i = app.get_all_events(trial=trial_i,
runs=runs_i,
isoform=isoform)
if len(events_i) == 0:
print "No events of isoform %s found" % isoform.name
continue
legend_list.append(isoform.name)
events_i_str = "(%s)" % (", ".join(
["'%s'" % e.timestamp for e in events_i]))
query = """SELECT crystal.cell_id FROM `%s_crystal` crystal
JOIN `%s_experiment` exp ON exp.crystal_id = crystal.id
JOIN `%s_imageset` imgset ON imgset.id = exp.imageset_id
JOIN `%s_imageset_event` ie ON ie.imageset_id = imgset.id
JOIN `%s_event` evt ON evt.id = ie.event_id
JOIN `%s_trial` trial ON trial.id = evt.trial_id
JOIN `%s_run` run ON run.id = evt.run_id
WHERE run.id in %s AND trial.id = %d AND evt.timestamp IN %s""" % (
exp_tag, exp_tag, exp_tag, exp_tag, exp_tag, exp_tag, exp_tag,
runs_ni_str, trial_ni.id, events_i_str)
cell_ids = [str(i[0]) for i in app.execute_query(query).fetchall()]
if len(cell_ids) == 0:
cells = []
else:
from xfel.ui.db.experiment import Cell
cells = app.get_all_x(Cell,
'cell',
where="WHERE id IN (%s)" %
", ".join(cell_ids))
print len(cells)
info = []
for cell in cells:
info.append({
'a': cell.cell_a,
'b': cell.cell_b,
'c': cell.cell_c,
'alpha': cell.cell_alpha,
'beta': cell.cell_beta,
'gamma': cell.cell_gamma,
'n_img': 0
})
info_list.append(info)
import xfel.ui.components.xfel_gui_plotter as pltr
plotter = pltr.PopUpCharts()
plotter.plot_uc_histogram(info_list=info_list,
legend_list=legend_list,
extra_title=extra_title)
plotter.plt.show()