def load_reflections_file(self,
file_name,
set_array=True,
data_only=False):
file_name = to_str(file_name)
if (file_name != ""):
from iotbx.reflection_file_reader import any_reflection_file
self.viewer.isnewfile = True
#self.params.NGL_HKLviewer.mergedata = None
self.viewer.iarray = -1
self.viewer.colour_scene_id = -1
self.viewer.radii_scene_id = -1
self.viewer.match_valarrays = []
self.viewer.proc_arrays = []
self.spacegroup_choices = []
display.reset_settings()
self.settings = display.settings()
self.viewer.settings = self.params.NGL_HKLviewer.viewer
self.viewer.mapcoef_fom_dict = {}
try:
hkl_file = any_reflection_file(file_name)
arrays = hkl_file.as_miller_arrays(
merge_equivalents=False,
) #observation_type_callback=misc_dialogs.get_shelx_file_data_type)
#arrays = f.file_server.miller_arrays
except Exception as e:
self.NewFileLoaded = False
self.mprint(to_str(e))
arrays = []
valid_arrays = []
self.array_infostrs = []
self.array_infotpls = []
for array in arrays:
#if array.is_hendrickson_lattman_array() :
# continue
#elif (data_only) :
if (not array.is_real_array()) and (not array.is_complex_array()) \
and (not array.is_integer_array()) and (not array.is_bool_array()) :
self.mprint('Ignoring miller array \"%s\" of %s' \
%(array.info().label_string(), type(array.data()[0]) ) )
continue
self.array_infostrs.append(
ArrayInfo(array, self.mprint).infostr)
self.array_infotpls.append(
ArrayInfo(array, self.mprint).infotpl)
valid_arrays.append(array)
self.valid_arrays = valid_arrays
self.mprint("Miller arrays in this file:")
for e in self.array_infostrs:
self.mprint("%s" % e)
self.NewFileLoaded = True
if (len(valid_arrays) == 0):
msg = "No arrays of the supported types in this file."
self.mprint(msg)
self.NewFileLoaded = False
return False
elif (len(valid_arrays) >= 1):
if (set_array):
self.set_miller_array()
return True
def make_new_miller_array(self):
miller_array_operations_lst = eval(self.params.NGL_HKLviewer.miller_array_operations)
unique_miller_array_operations_lst = []
for (operation, label, arrid1, arrid2) in miller_array_operations_lst:
isunique = True
for arr in self.procarrays:
if label in arr.info().label_string():
self.mprint(label + " is already labelling one of the original miller arrays")
isunique = False
break
if isunique:
unique_miller_array_operations_lst.append( (operation, label, arrid1, arrid2) )
self.params.NGL_HKLviewer.miller_array_operations = str(unique_miller_array_operations_lst)
from copy import deepcopy
millarr1 = deepcopy(self.procarrays[arrid1])
newarray = None
if arrid2:
millarr2 = deepcopy(self.procarrays[arrid2])
newarray = self.viewer.OperateOn2MillerArrays(millarr1, millarr2, operation)
else:
newarray = self.viewer.OperateOn1MillerArray(millarr1, operation)
if newarray:
newarray.set_info(millarr1._info )
newarray._info.labels = [ label ]
procarray, procarray_info = self.process_miller_array(newarray)
self.procarrays.append(procarray)
self.viewer.proc_arrays = self.procarrays
self.viewer.has_new_miller_array = True
self.viewer.array_infostrs.append( ArrayInfo(procarray, self.mprint).infostr )
self.viewer.array_infotpls.append( ArrayInfo(procarray, self.mprint).infotpl )
mydict = { "array_infotpls": self.viewer.array_infotpls, "NewHKLscenes" : True, "NewMillerArray" : True}
self.SendInfoToGUI(mydict)
def make_new_miller_array(self):
miller_array_operations_lst = eval(self.params.miller_array_operations)
unique_miller_array_operations_lst = []
for (operation, label, arrid1, arrid2) in miller_array_operations_lst:
for arr in self.procarrays:
if label in arr.info().label_string() or label in [ "", None]:
raise Sorry("Provide an unambiguous label for your new miller array!")
unique_miller_array_operations_lst.append( (operation, label, arrid1, arrid2) )
self.params.miller_array_operations = str(unique_miller_array_operations_lst)
from copy import deepcopy
millarr1 = deepcopy(self.procarrays[arrid1])
newarray = None
if arrid2 != -1:
millarr2 = deepcopy(self.procarrays[arrid2])
newarray = self.viewer.OperateOn2MillerArrays(millarr1, millarr2, operation)
else:
newarray = self.viewer.OperateOn1MillerArray(millarr1, operation)
if newarray is not None:
newarray.set_info(millarr1._info )
newarray._info.labels = [ label ]
procarray, procarray_info = self.process_miller_array(newarray)
self.procarrays.append(procarray)
self.viewer.proc_arrays = self.procarrays
self.viewer.has_new_miller_array = True
self.viewer.array_infostrs.append( ArrayInfo(procarray, self.mprint).infostr )
self.viewer.array_infotpls.append( ArrayInfo(procarray, self.mprint).infotpl )
#self.viewer.SupersetMillerArrays()
hkls = self.origarrays["HKLs"]
nanarr = flex.double(len(hkls), float("nan"))
m = miller.match_indices(hkls, procarray.indices() )
indices_of_matched_hkls = m.pairs().column(0)
for i,e in enumerate(indices_of_matched_hkls):
nanarr[e] = procarray.data()[i]
self.origarrays[label] = list(nanarr)
mydict = { "array_infotpls": self.viewer.array_infotpls, "NewHKLscenes" : True, "NewMillerArray" : True}
self.SendInfoToGUI(mydict)
def LoadReflectionsFile(self, file_name, set_array=True, data_only=False):
file_name = to_str(file_name)
if (file_name != ""):
from iotbx.reflection_file_reader import any_reflection_file
self.viewer.isnewfile = True
self.viewer.iarray = 0
self.viewer.icolourcol = 0
self.viewer.iradiicol = 0
display.reset_settings()
self.settings = display.settings()
self.viewer.settings = self.settings
self.viewer.mapcoef_fom_dict = {}
try:
hkl_file = any_reflection_file(file_name)
except Exception, e:
raise Sorry(to_str(e))
arrays = hkl_file.as_miller_arrays(
merge_equivalents=False,
) #observation_type_callback=misc_dialogs.get_shelx_file_data_type)
#arrays = f.file_server.miller_arrays
valid_arrays = []
self.array_info = []
for array in arrays:
#if array.is_hendrickson_lattman_array() :
# continue
#elif (data_only) :
if (data_only):
if (not array.is_real_array()) and (
not array.is_complex_array()):
continue
self.array_info.append(ArrayInfo(array).infostr)
valid_arrays.append(array)
self.valid_arrays = valid_arrays
for i, e in enumerate(self.array_info):
self.mprint("%d, %s" % (i, e))
if (len(valid_arrays) == 0):
msg = "No arrays of the supported types in this file."
raise Sorry(msg)
elif (len(valid_arrays) == 1):
if (set_array):
self.set_miller_array(valid_arrays[0])
return valid_arrays[0]
def finish_dataloading(self, arrays):
valid_arrays = []
self.viewer.array_infostrs = []
self.viewer.array_infotpls = []
for i,array in enumerate(arrays) :
arrayinfo = ArrayInfo(array, self.mprint)
self.viewer.array_infostrs.append( arrayinfo.infostr )
self.viewer.array_infotpls.append( arrayinfo.infotpl )
if i==0:
mydict = { "spacegroup_info": arrayinfo.spginf, "unitcell_info": arrayinfo.ucellinf }
self.SendInfoToGUI(mydict)
valid_arrays.append(array)
self.valid_arrays = valid_arrays
self.mprint("%d Miller arrays in this data set:" %len(arrays))
for e in self.viewer.array_infostrs:
self.mprint("%s" %e)
self.mprint("\n")
self.NewFileLoaded = True
if (len(valid_arrays) == 0):
msg = "No arrays of the supported types present."
self.mprint(msg)
self.NewFileLoaded=False
elif (len(valid_arrays) >= 1):
self.set_miller_array()
self.update_space_group_choices(0) # get the default spacegroup choice
mydict = { "info": self.infostr,
"array_infotpls": self.viewer.array_infotpls,
"bin_infotpls": self.viewer.bin_infotpls,
"html_url": self.viewer.url,
"tncsvec": self.tncsvec,
"merge_data": self.params.merge_data,
"spacegroups": [e.symbol_and_number() for e in self.spacegroup_choices],
"NewFileLoaded": self.NewFileLoaded,
"file_name": self.params.openfilename
}
self.SendInfoToGUI(mydict)
self.params.openfilename = None
def load_reflections_file(self, file_name, set_array=True, data_only=False):
file_name = to_str(file_name)
if (file_name != ""):
self.mprint("Reading file...")
from iotbx.reflection_file_reader import any_reflection_file
self.viewer.isnewfile = True
#self.params.NGL_HKLviewer.mergedata = None
self.params.NGL_HKLviewer.viewer.scene_id = None
self.viewer.colour_scene_id = None
self.viewer.radii_scene_id = None
self.viewer.match_valarrays = []
self.viewer.proc_arrays = []
self.spacegroup_choices = []
display.reset_settings()
self.settings = display.settings()
self.viewer.settings = self.params.NGL_HKLviewer.viewer
self.viewer.mapcoef_fom_dict = {}
self.hklfile_history = []
self.tncsvec = None
try :
hkl_file = any_reflection_file(file_name)
arrays = hkl_file.as_miller_arrays(merge_equivalents=False,
)#observation_type_callback=misc_dialogs.get_shelx_file_data_type)
#arrays = f.file_server.miller_arrays
if hkl_file._file_type == 'ccp4_mtz':
self.hklfile_history = list(hkl_file._file_content.history())
for e in self.hklfile_history:
if "TNCS NMOL" in e and "VECTOR" in e:
svec = e.split()[-3:]
t1 = float(svec[0])
t2 = float(svec[1])
t3 = float(svec[2])
if (t1*t1 + t2*t2 + t3*t3) > 0.0:
self.tncsvec = [ t1, t2, t3 ]
self.mprint("tNCS vector found in header of mtz file: %s" %str(svec) )
except Exception as e :
self.NewFileLoaded=False
self.mprint(to_str(e))
arrays = []
valid_arrays = []
self.viewer.array_infostrs = []
self.viewer.array_infotpls = []
for array in arrays :
#if array.is_hendrickson_lattman_array() :
# continue
#elif (data_only) :
if (not array.is_real_array()) and (not array.is_complex_array()) \
and (not array.is_integer_array()) and (not array.is_bool_array()) :
self.mprint('Ignoring miller array \"%s\" of %s' \
%(array.info().label_string(), type(array.data()[0]) ) )
continue
self.viewer.array_infostrs.append( ArrayInfo(array, self.mprint).infostr )
self.viewer.array_infotpls.append( ArrayInfo(array, self.mprint).infotpl )
valid_arrays.append(array)
self.valid_arrays = valid_arrays
self.mprint("Miller arrays in this file:")
for e in self.viewer.array_infostrs:
self.mprint("%s" %e)
self.mprint("\n")
self.NewFileLoaded = True
if (len(valid_arrays) == 0):
msg = "No arrays of the supported types in this file."
self.mprint(msg)
self.NewFileLoaded=False
return False
elif (len(valid_arrays) >= 1):
if (set_array):
self.set_miller_array()
self.viewer.superset_all_miller_arrays()
mydict = { "info": self.infostr,
"array_infotpls": self.viewer.array_infotpls,
"bin_infotpls": self.viewer.bin_infotpls,
"html_url": self.viewer.url,
"tncsvec": self.tncsvec,
"merge_data": self.params.NGL_HKLviewer.merge_data,
"spacegroups": [e.symbol_and_number() for e in self.spacegroup_choices],
"NewFileLoaded": self.NewFileLoaded
}
self.SendInfoToGUI(mydict)
return True