def onRun(self, e):
# Run full processing
self.init_settings()
if self.sanity_check():
prime_phil = master_phil.format(python_object=self.pparams)
with Capturing() as output:
prime_phil.show()
txt_out = ''
for one_output in output:
txt_out += one_output + '\n'
source_dir = os.path.dirname(self.out_dir)
prime_file = os.path.join(source_dir, self.prime_filename)
out_file = os.path.join(self.out_dir, 'stdout.log')
with open(prime_file, 'w') as pf:
pf.write(txt_out)
self.prime_run_window = frm.PRIMERunWindow(self,
-1,
title='PRIME Output',
params=self.pparams,
prime_file=prime_file)
self.prime_run_window.prev_pids = easy_run.fully_buffered(
'pgrep -u {} {}'
''.format(user, python)).stdout_lines
self.prime_run_window.place_and_size(set_by='parent')
self.prime_run_window.Show(True)
def run_proc(args, data, info, filename, number=1):
processor = ZMQProcessor(last_stage=args.last_stage, phil_file=args.phil)
with Capturing() as junk:
t_start = time.time()
info = processor.run(data, filename, info)
proc_time = time.time() - t_start
n_spots = info["n_spots"]
if args.verbose:
print("\n*** channel # {}".format(number))
print("{} spots found".format(n_spots))
print("Trial: {}. Time: {:.2f} sec".format(number, proc_time))
return proc_time
def reset_settings(self):
self.prime_phil = master_phil
self.pparams = self.prime_phil.extract()
self.input_window.inp_box.delete_all()
self.input_window.out_box.reset_default()
self.input_window.project_title.reset_default()
self.input_window.opt_chk_useref.SetValue(False)
self.input_window.opt_spc_nproc.reset_default()
self.input_window.opt_spc_nres.reset_default()
# Generate Python object and text of parameters
with Capturing() as txt_output:
master_phil.show()
self.phil_string = ''
for one_output in txt_output:
self.phil_string += one_output + '\n'
def onSaveScript(self, e):
self.init_settings()
# Generate text of params
final_phil = master_phil.format(python_object=self.pparams)
with Capturing() as txt_output:
final_phil.show()
txt_out = ''
for one_output in txt_output:
txt_out += one_output + '\n'
# Save param file
save_dlg = wx.FileDialog(self,
message="Save PRIME Script",
defaultDir=os.curdir,
defaultFile="*.phil",
wildcard="*.phil",
style=wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT)
if save_dlg.ShowModal() == wx.ID_OK:
with open(save_dlg.GetPath(), 'w') as savefile:
savefile.write(txt_out)
save_dlg.Destroy()
def run(self, idx, img):
if self.meta_parent.terminated:
raise IOTATermination(
'IOTA_TRACKER: SPF Termination signal received!')
else:
with Capturing() as junk_output:
fail = False
sg = None
uc = None
try:
experiments = ExperimentListFactory.from_filenames([img
])[0]
observed = self.processor.find_spots(
experiments=experiments)
except Exception:
fail = True
observed = []
pass
# TODO: Indexing / lattice determination very slow (how to speed up?)
if self.run_indexing:
if not fail:
try:
experiments, indexed = self.processor.index(
experiments=experiments, reflections=observed)
except Exception:
fail = True
pass
if not fail:
try:
solution = self.processor.refine_bravais_settings(
reflections=indexed, experiments=experiments)
# Only reindex if higher-symmetry solution found
if solution is not None:
experiments, indexed = self.processor.reindex(
reflections=indexed,
experiments=experiments,
solution=solution)
lat = experiments[0].crystal.get_space_group(
).info()
sg = str(lat).replace(' ', '')
except Exception:
fail = True
pass
if not fail:
unit_cell = experiments[0].crystal.get_unit_cell(
).parameters()
uc = ' '.join(['{:.4f}'.format(i) for i in unit_cell])
if self.run_integration:
if not fail:
try:
# Run refinement
experiments, indexed = self.processor.refine(
experiments=experiments, centroids=indexed)
except Exception:
fail = True
pass
if not fail:
try:
print(experiments)
print(indexed)
integrated = self.processor.integrate(
experiments=experiments, indexed=indexed)
except Exception:
pass
return [idx, int(len(observed)), img, sg, uc]
def generate_phil_string(self):
with Capturing() as txt_output:
self.prime_phil.show()
self.phil_string = ''
for one_output in txt_output:
self.phil_string += one_output + '\n'
def process_image(self):
if os.path.isfile(self.termfile):
raise IOTATermination('IOTA_TRACKER: Termination signal received!')
else:
with Capturing() as junk_output:
# if True:
err = []
start = time.time()
fail = False
sg = None
uc = None
status = None
score = 0
try:
datablock = DataBlockFactory.from_filenames([self.img])[0]
observed = self.processor.find_spots(datablock=datablock)
status = 'spots found'
except Exception, e:
fail = True
observed = []
err.append('SPOTFINDING ERROR: {}'.format(e))
pass
# TODO: Indexing / lattice determination very slow (how to speed up?)
if self.run_indexing:
if not fail:
try:
experiments, indexed = self.processor.index(
datablock=datablock, reflections=observed)
score = len(indexed)
except Exception, e:
fail = True
err.append('INDEXING ERROR: {}'.format(e))
pass
if not fail:
try:
solution = self.processor.refine_bravais_settings(
reflections=indexed, experiments=experiments)
# Only reindex if higher-symmetry solution found
if solution is not None:
experiments, indexed = self.processor.reindex(
reflections=indexed,
experiments=experiments,
solution=solution)
obs = experiments
lat = experiments[0].crystal.get_space_group(
).info()
sg = str(lat).replace(' ', '')
status = 'indexed'
except Exception, e:
fail = True
err.append('LATTICE ERROR: {}'.format(e))
pass
if not fail:
unit_cell = experiments[0].crystal.get_unit_cell(
).parameters()
uc = ' '.join(['{:.4f}'.format(i) for i in unit_cell])
if self.run_integration:
if not fail:
try:
# Run refinement
experiments, indexed = self.processor.refine(
experiments=experiments, centroids=indexed)
except Exception, e:
fail = True
err.append('REFINEMENT ERROR: {}'.format(e))
pass
if not fail:
try:
print(experiments)
print(indexed)
integrated = self.processor.integrate(
experiments=experiments, indexed=indexed)
frame = ConstructFrame(
integrated, experiments[0]).make_frame()
status = 'integrated'
except Exception, e:
err.append('INTEGRATION ERROR: {}'.format(e))
pass