def print_params():
""" Print out master parameters for IOTA """
help_out = convert_phil_to_text(master_phil, att_level=1)
txt_out = convert_phil_to_text(master_phil)
return help_out, txt_out
def onOutputScript(self, e):
# Determine param filepath
save_dlg = wx.FileDialog(self,
message="Save IOTA Script",
defaultDir=os.curdir,
defaultFile="*.param",
wildcard="*",
style=wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT)
if save_dlg.ShowModal() == wx.ID_OK:
script_filepath = save_dlg.GetPath()
# Finalize settings
self.init_settings()
self.gparams = self.iota_phil.extract()
# Save target PHIL file, if a PHIL script exists
if self.target_phil is not None:
if self.gparams.advanced.processing_backend == 'ha14':
phil_filepath = os.path.join(
os.path.dirname(script_filepath), 'cctbx_ha14.phil')
self.gparams.cctbx_ha14.target = phil_filepath
if self.gparams.advanced.processing_backend == 'cctbx.xfel':
phil_filepath = os.path.join(
os.path.dirname(script_filepath), 'cctbx_xfel.phil')
self.gparams.cctbx_xfel.target = phil_filepath
# Generate text of params
final_phil = self.iota_phil.format(python_object=self.gparams)
final_phil_txt = util.convert_phil_to_text(final_phil,
script_filepath)
if self.target_phil is not None:
with open(phil_filepath, 'w') as phil_file:
phil_file.write(self.target_phil)
def initialize_main_log(self):
""" Initialize main log (iota.log) and record starting parameters
:return: True if successful, False if fails
"""
try:
# Generate text of params
self.iota_phil_string = util.convert_phil_to_text(self.iota_phil)
# Initialize main log
self.logfile = os.path.abspath(os.path.join(self.int_base, 'iota.log'))
# Log starting info
util.main_log(self.logfile, '{:*^80} \n'.format(' IOTA MAIN LOG '))
util.main_log(self.logfile, '{:-^80} \n'.format(' SETTINGS FOR THIS RUN '))
util.main_log(self.logfile, self.iota_phil_string)
# Log cctbx.xfel / DIALS settings
util.main_log(self.logfile, '{:-^80} \n'.format('BACKEND SETTINGS'))
util.main_log(self.logfile, self.target_phil)
return True, 'IOTA_INIT: MAIN LOG INITIALIZED'
except Exception as e:
return False, 'IOTA_INIT_ERROR: MAIN LOG NOT INITIALIZED, {}'.format(e)
def make_prime_input(self,
filename='prime.phil',
run_zero=False):
""" Imports default PRIME input parameters, modifies correct entries and
prints out a starting PHIL file to be used with PRIME
"""
pixel_size = self.final_objects[0].final['pixel_size']
try:
sg = str(self.cons_pg).replace(" ", "")
except AttributeError as e:
print ('PRIME INPUT ERROR, SPACE GROUP: ', e)
sg = 'P1'
sym = crystal.symmetry(space_group_symbol=sg)
crystal_system = str(sym.space_group().crystal_system())
# Determine number of images for indexing ambiguity resolution
# My default: 1/2 of images or 300, whichever is smaller
if len(self.final_objects) >= 600:
idx_ambiguity_sample = 300
idx_ambiguity_selected = 100
else:
idx_ambiguity_sample = int(round(len(self.final_objects) / 2))
idx_ambiguity_selected = int(round(idx_ambiguity_sample / 3))
prime_params = mod_input.master_phil.extract()
if run_zero:
run_no = '000'
else:
run_no = '001'
# Populate pertinent data parameters
prime_params.run_no = os.path.join(os.path.dirname(self.prime_data_path),
'prime/{}'.format(run_no))
prime_params.data = [self.prime_data_path]
prime_params.title = 'Auto-generated by IOTA v{} on {}'.format(self.ver, self.now)
prime_params.scale.d_min = np.mean(self.hres)
prime_params.scale.d_max = 8
prime_params.postref.scale.d_min = np.mean(self.hres)
prime_params.postref.scale.d_max = np.max(self.lres)
prime_params.postref.crystal_orientation.d_min = np.mean(self.hres)
prime_params.postref.crystal_orientation.d_max = np.max(self.lres)
prime_params.postref.reflecting_range.d_min = np.mean(self.hres)
prime_params.postref.reflecting_range.d_max = np.max(self.lres)
prime_params.postref.unit_cell.d_min = np.mean(self.hres)
prime_params.postref.unit_cell.d_max = np.max(self.lres)
prime_params.postref.allparams.d_min = np.mean(self.hres)
prime_params.postref.allparams.d_max = np.max(self.lres)
prime_params.merge.d_min = np.mean(self.hres)
prime_params.merge.d_max = np.max(self.lres)
prime_params.target_unit_cell = uctbx.unit_cell(self.cons_uc)
prime_params.target_space_group = sg
prime_params.target_crystal_system = crystal_system
prime_params.pixel_size_mm = pixel_size
prime_params.n_residues = 500
prime_params.indexing_ambiguity.n_sample_frames = idx_ambiguity_sample
prime_params.indexing_ambiguity.n_selected_frames = idx_ambiguity_selected
# Determine which queue to run on (i.e. match IOTA queue)
# Modify specific options based in IOTA settings
# Queue options
if (
self.params.mp.method == 'lsf' and
self.params.mp.queue is not None
):
prime_params.queue.mode = 'bsub'
prime_params.queue.qname = self.params.mp.queue
# Number of processors (automatically, 1/2 of IOTA procs)
prime_params.n_processors = int(self.params.mp.n_processors / 2)
# Generate PRIME param PHIL
prime_phil = mod_input.master_phil.format(python_object=prime_params)
prime_file = os.path.join(self.output_dir, filename)
prime_phil_txt = util.convert_phil_to_text(prime_phil, prime_file)
return prime_phil
params.cctbx_ha14.image_conversion.rename_pickle_prefix = args.prefix
#Check -s option to bypass grid search and run selection/integration only
if args.select:
params.cctbx_ha14.selection.select_only.flag_on = True
# Check if grid search is turned off; if so, set everything to zero
if str(params.cctbx_ha14.grid_search.type).lower() == 'none':
params.cctbx_ha14.grid_search.area_range = 0
params.cctbx_ha14.grid_search.height_range = 0
params.cctbx_ha14.grid_search.sig_height_search = False
final_phil = master_phil.format(python_object=params)
if mode == 'auto':
txt_out = convert_phil_to_text(final_phil)
write_defaults(os.path.abspath(os.curdir), txt_out,
params.advanced.processing_backend)
return final_phil
def write_defaults(current_path=None, txt_out=None, method='current',
write_target_file=True, write_param_file=True):
""" Generates list of default parameters for a reasonable target file:
- old cctbx.xfel (HA14) now deprecated, but can still be used
- also writes out the IOTA parameter file.
:param current_path: path to current output folder
:param txt_out: text of IOTA parameters
:param method: which backend is used (default = cctbx.xfel AB18)