def load_script(self, out_dir):
''' Loads PRIME script '''
import iotbx.phil as ip
script = os.path.join(out_dir, self.prime_filename)
user_phil = ip.parse(open(script).read())
self.pparams = master_phil.fetch(sources=[user_phil]).extract()
self.input_window.pparams = self.pparams
self.input_window.inp_box.ctr.SetValue(str(self.pparams.data[0]))
current_dir = os.path.dirname(self.pparams.run_no)
self.input_window.out_box.ctr.SetValue(str(current_dir))
if str(self.input_window.out_box.ctr.GetValue).lower() == '':
self.input_window.out_box.ctr.SetValue(self.out_dir)
if str(self.pparams.title).lower() != 'none':
self.input_window.title_box.ctr.SetValue(str(self.pparams.title))
if str(self.pparams.hklisoin).lower() != 'none':
self.input_window.ref_box.ctr.SetValue(str(self.pparams.hklisoin))
elif str(self.pparams.hklrefin).lower() != 'none':
self.input_window.ref_box.ctr.SetValue(str(self.pparams.hklrefin))
self.input_window.opt_chk_useref.SetValue(True)
if str(self.pparams.n_residues).lower() == 'none':
self.input_window.opt_spc_nres.SetValue(500)
else:
self.input_window.opt_spc_nres.SetValue(int(self.pparams.n_residues))
self.input_window.opt_spc_nproc.SetValue(int(self.pparams.n_processors))
def regenerate_params(self, phil=None):
if phil is not None:
self.prime_phil = master_phil.fetch(source=phil)
else:
self.prime_phil = master_phil
# Generate Python object and text of parameters
self.generate_phil_string(self.prime_phil)
self.pparams = self.prime_phil.extract()
def onRecovery(self, e):
# Find finished runs and display results
p_folder = os.path.abspath('{}/prime'.format(os.curdir))
if not os.path.isdir(p_folder):
open_dlg = wx.DirDialog(self, "Choose the integration run:",
style=wx.DD_DEFAULT_STYLE)
if open_dlg.ShowModal() == wx.ID_OK:
p_folder = open_dlg.GetPath()
open_dlg.Destroy()
else:
open_dlg.Destroy()
return
paths = [os.path.join(p_folder, p) for p in os.listdir(p_folder)]
paths = [p for p in paths if (os.path.isdir(p) and
os.path.basename(p).isdigit())]
path_dlg = dlg.RecoveryDialog(self)
path_dlg.insert_paths(paths)
if path_dlg.ShowModal() == wx.ID_OK:
selected = path_dlg.selected
recovery = path_dlg.recovery_mode
prime_path = selected[1]
prime_status = selected[0]
settings_file = os.path.join(prime_path, 'settings.phil')
# If neither log-file nor stat file are found, terminate; otherwise
# import settings
if not os.path.isfile(settings_file):
wx.MessageBox('Cannot Import This Run \n(No Files Found!)',
'Info', wx.OK | wx.ICON_ERROR)
return
else:
self.reset_settings()
with open(settings_file, 'r') as sf:
phil_string = sf.read()
read_phil = ip.parse(phil_string)
self.prime_phil = master_phil.fetch(source=read_phil)
self.pparams = self.prime_phil.extract()
self.input_window.regenerate_params(self.prime_phil)
self.update_input_window()
# If any cycles (or full run) were completed, show results
if prime_status == 'Unknown':
return
if recovery == 0:
self.prime_run_window = frm.PRIMERunWindow(self, -1,
title='PRIME Output',
params=self.pparams,
prime_file=settings_file,
recover=True)
self.prime_run_window.Show(True)
self.prime_run_window.recover()
def load_script(self, out_dir):
''' Loads PRIME script '''
script = os.path.join(out_dir, self.prime_filename)
with open(script, 'r') as sf:
phil_string = sf.read()
self.reset_settings()
user_phil = ip.parse(phil_string)
self.pparams = master_phil.fetch(source=user_phil).extract()
self.input_window.pparams = self.pparams
self.input_window.phil_string = phil_string
self.update_input_window()
def test_phil(self, filepath):
''' Tests incoming PHIL file to try and determine what it's for '''
import iotbx.phil as ip
try:
test_phil = ip.parse(open(filepath).read())
# Test if IOTA parameter file
from iota.components.iota_input import master_phil as iota_phil
new_phil, unused = iota_phil.fetch(sources=[test_phil],
track_unused_definitions=True)
if len(unused) == 0:
return 'IOTA settings'
# Test if PRIME parameter file
from prime.postrefine.mod_input import master_phil as prime_phil
new_phil, unused = prime_phil.fetch(sources=[test_phil],
track_unused_definitions=True)
if len(unused) == 0:
return 'PRIME settings'
# Test if LABELIT target file
from labelit.phil_preferences import iotbx_defs, libtbx_defs
labelit_phil = ip.parse(input_string=iotbx_defs + libtbx_defs,
process_includes=True)
new_phil, unused = labelit_phil.fetch(sources=[test_phil],
track_unused_definitions=True)
if len(unused) == 0:
return 'LABELIT target'
# Test if DIALS target file
from dials.command_line.stills_process import control_phil_str, \
dials_phil_str
dials_phil = ip.parse(control_phil_str + dials_phil_str,
process_includes=True)
new_phil, unused = dials_phil.fetch(sources=[test_phil],
track_unused_definitions=True)
if len(unused) == 0:
return 'DIALS target'
else:
return 'text'
except Exception:
return 'text'
def onAdvancedOptions(self, e):
advanced = dlg.PRIMEAdvancedOptions(self,
title='Advanced PRIME Options',
style=wx.DEFAULT_DIALOG_STYLE
| wx.RESIZE_BORDER)
advanced.Fit()
# Populate the PHIL textbox
advanced.phil.ctr.SetValue(self.phil_string)
# Set values to default parameters
advanced.res.high.SetValue('{:4.2f}'.format(
self.pparams.postref.allparams.d_max))
advanced.res.low.SetValue('{:4.2f}'.format(
self.pparams.postref.allparams.d_min))
advanced.sg.spacegroup.SetValue(str(self.pparams.target_space_group))
if str(self.pparams.target_unit_cell).lower() != 'none':
uc = ' '.join(
list(map(str, self.pparams.target_unit_cell.parameters())))
advanced.uc.unit_cell.SetValue(uc)
else:
advanced.uc.unit_cell.SetValue(str(self.pparams.target_unit_cell))
advanced.anom.SetValue(self.pparams.target_anomalous_flag)
advanced.cc.cc_cutoff.SetValue(str(self.pparams.frame_accept_min_cc))
advanced.pix.pixel_size.SetValue(str(self.pparams.pixel_size_mm))
advanced.cycles.ctr.SetValue(int(self.pparams.n_postref_cycle))
if advanced.ShowModal() == wx.ID_OK:
# Read PHIL string from window, convert to params
self.phil_string = advanced.phil.ctr.GetValue()
new_phil = ip.parse(self.phil_string)
self.pparams = master_phil.fetch(sources=[new_phil]).extract()
# Param controls will override the PHIL string (clunky, but for now)
if advanced.res_override.GetValue():
self.pparams.scale.d_max = float(advanced.res.high.GetValue())
self.pparams.scale.d_min = float(advanced.res.low.GetValue())
self.pparams.merge.d_max = float(advanced.res.high.GetValue())
self.pparams.merge.d_min = float(advanced.res.low.GetValue())
self.pparams.postref.scale.d_max = float(
advanced.res.high.GetValue())
self.pparams.postref.scale.d_min = float(
advanced.res.low.GetValue())
self.pparams.postref.crystal_orientation.d_max = float(
advanced.res.high.GetValue())
self.pparams.postref.crystal_orientation.d_min = float(
advanced.res.low.GetValue())
self.pparams.postref.reflecting_range.d_max = float(
advanced.res.high.GetValue())
self.pparams.postref.reflecting_range.d_min = float(
advanced.res.low.GetValue())
self.pparams.postref.unit_cell.d_max = float(
advanced.res.high.GetValue())
self.pparams.postref.unit_cell.d_min = float(
advanced.res.low.GetValue())
self.pparams.postref.allparams.d_max = float(
advanced.res.high.GetValue())
self.pparams.postref.allparams.d_min = float(
advanced.res.low.GetValue())
self.pparams.target_space_group = advanced.sg.spacegroup.GetValue()
if advanced.uc.unit_cell.GetValue().lower() != 'none':
uc = str_split(advanced.uc.unit_cell.GetValue())
self.pparams.target_unit_cell = unit_cell(list(map(float, uc)))
else:
self.pparams.target_unit_cell = None
self.pparams.target_anomalous_flag = advanced.anom.GetValue()
if advanced.cc.cc_cutoff.GetValue().lower() != 'none':
self.pparams.frame_accept_min_cc = float(
advanced.cc.cc_cutoff.GetValue())
else:
self.pparams.frame_accept_min_cc = None
if advanced.pix.pixel_size.GetValue().lower() != 'none':
self.pparams.pixel_size_mm = float(
advanced.pix.pixel_size.GetValue())
else:
self.pparams.pixel_size_mm = None
self.pparams.n_postref_cycle = int(advanced.cycles.ctr.GetValue())
self.regenerate_params(self.pparams)
advanced.Destroy()
e.Skip()
def test_phil(self, filepath):
"""Tests incoming PHIL file to try and determine what it's for."""
from iotbx import phil as ip
from iotbx.file_reader import any_file as af
try:
if af(filepath).file_type == "phil":
test_phil = ip.parse(open(filepath).read())
else:
test_phil = None
except RuntimeError: # If not a PHIL file or a bad PHIL file
return "text"
else:
if test_phil:
# Test if IOTA parameter file
from iota.init.iota_input import master_phil as iota_phil
new_phil, unused = iota_phil.fetch(
sources=[test_phil], track_unused_definitions=True)
len_test = len(
test_phil.all_definitions(suppress_multiple=True))
percent_fit = (1 - len(unused) / len_test) * 100
if percent_fit >= 50:
return "IOTA settings"
# Test if PRIME parameter file
from prime.postrefine.mod_input import master_phil as prime_phil
new_phil, unused = prime_phil.fetch(
sources=[test_phil], track_unused_definitions=True)
len_test = len(
test_phil.all_definitions(suppress_multiple=True))
percent_fit = (1 - len(unused) / len_test) * 100
if percent_fit >= 50:
return "PRIME settings"
# Test if LABELIT target file (LABELIT not always available)
try:
from labelit.phil_preferences import iotbx_defs, libtbx_defs
except ImportError:
pass
else:
labelit_phil = ip.parse(input_string=iotbx_defs +
libtbx_defs,
process_includes=True)
new_phil, unused = labelit_phil.fetch(
sources=[test_phil], track_unused_definitions=True)
len_test = len(
test_phil.all_definitions(suppress_multiple=True))
percent_fit = (1 - len(unused) / len_test) * 100
if percent_fit >= 50:
return "LABELIT target"
# Test if DIALS target file
from dials.command_line.stills_process import (
control_phil_str,
dials_phil_str,
)
dials_phil = ip.parse(control_phil_str + dials_phil_str,
process_includes=True)
new_phil, unused = dials_phil.fetch(
sources=[test_phil], track_unused_definitions=True)
len_test = len(
test_phil.all_definitions(suppress_multiple=True))
percent_fit = (1 - len(unused) / len_test) * 100
if percent_fit >= 50:
return "DIALS target"
else:
return "text"
else:
return "text"
def onAdvancedOptions(self, e):
advanced = PRIMEAdvancedOptions(self,
title='Advanced PRIME Options',
style=wx.DEFAULT_DIALOG_STYLE | wx.RESIZE_BORDER)
advanced.Fit()
# Populate the PHIL textbox
advanced.phil.ctr.SetValue(self.phil_string)
# Set values to default parameters
advanced.res.high.SetValue('{:4.2f}'.format(self.pparams.scale.d_max))
advanced.res.low.SetValue('{:4.2f}'.format(self.pparams.scale.d_min))
advanced.sg.spacegroup.SetValue(str(self.pparams.target_space_group))
if str(self.pparams.target_unit_cell).lower() != 'none':
uc = ' '.join(list(map(str, self.pparams.target_unit_cell.parameters())))
advanced.uc.unit_cell.SetValue(uc)
else:
advanced.uc.unit_cell.SetValue(str(self.pparams.target_unit_cell))
advanced.uc_override.SetValue(self.pparams.flag_override_unit_cell)
advanced.anom.SetValue(self.pparams.target_anomalous_flag)
advanced.cc.cc_cutoff.SetValue(str(self.pparams.frame_accept_min_cc))
advanced.pix.pixel_size.SetValue(str(self.pparams.pixel_size_mm))
advanced.cycles.ctr.SetValue(int(self.pparams.n_postref_cycle))
if advanced.ShowModal() == wx.ID_OK:
# Read PHIL string from window, convert to params
self.phil_string = advanced.phil.ctr.GetValue()
new_phil = ip.parse(self.phil_string)
self.pparams = master_phil.fetch(sources=[new_phil]).extract()
# Param controls will override the PHIL string (clunky, but for now)
self.pparams.scale.d_max = float(advanced.res.high.GetValue())
self.pparams.scale.d_min = float(advanced.res.low.GetValue())
self.pparams.merge.d_max = float(advanced.res.high.GetValue())
self.pparams.merge.d_min = float(advanced.res.low.GetValue())
self.pparams.postref.scale.d_max = float(advanced.res.high.GetValue())
self.pparams.postref.scale.d_min = float(advanced.res.low.GetValue())
self.pparams.postref.crystal_orientation.d_max = \
float(advanced.res.high.GetValue())
self.pparams.postref.crystal_orientation.d_min = \
float(advanced.res.low.GetValue())
self.pparams.postref.reflecting_range.d_max = \
float(advanced.res.high.GetValue())
self.pparams.postref.reflecting_range.d_min = \
float(advanced.res.low.GetValue())
self.pparams.postref.unit_cell.d_max = float(advanced.res.high.GetValue())
self.pparams.postref.unit_cell.d_min = float(advanced.res.low.GetValue())
self.pparams.postref.allparams.d_max = float(advanced.res.high.GetValue())
self.pparams.postref.allparams.d_min = float(advanced.res.low.GetValue())
self.pparams.target_space_group = advanced.sg.spacegroup.GetValue()
if advanced.uc.unit_cell.GetValue().lower() != 'none':
uc = str_split(advanced.uc.unit_cell.GetValue())
self.pparams.target_unit_cell = unit_cell(list(map(float, uc)))
else:
self.pparams.target_unit_cell = None
self.pparams.flag_override_unit_cell = advanced.uc_override.GetValue()
self.pparams.target_anomalous_flag = advanced.anom.GetValue()
if advanced.cc.cc_cutoff.GetValue().lower() != 'none':
self.pparams.frame_accept_min_cc = float(advanced.cc.cc_cutoff.GetValue())
else:
self.pparams.frame_accept_min_cc = None
if advanced.pix.pixel_size.GetValue().lower() != 'none':
self.pparams.pixel_size_mm = float(advanced.pix.pixel_size.GetValue())
else:
self.pparams.pixel_size_mm = None
self.pparams.n_postref_cycle = int(advanced.cycles.ctr.GetValue())
self.regenerate_params(self.pparams)
advanced.Destroy()
e.Skip()
