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 __init__(self, *args, **kwds):
self.valid_arrays = []
self.spacegroup_choices = []
self.array_infostrs = []
self.array_infotpls = []
self.procarrays = []
self.merge_answer = [None]
self.dmin = -1
self.settings = display.settings()
self.verbose = 0
if 'verbose' in kwds:
self.verbose = kwds['verbose']
kwds['settings'] = self.settings
kwds['mprint'] = self.mprint
self.infostr = ""
self.guiSocketPort = None
if 'useGuiSocket' in kwds:
self.guiSocketPort = kwds['useGuiSocket']
self.context = zmq.Context()
self.guisocket = self.context.socket(zmq.PAIR)
self.guisocket.connect("tcp://127.0.0.1:%s" % self.guiSocketPort)
self.STOP = False
print("starting socketthread")
self.msgqueuethrd = threading.Thread(target=self.zmq_listen)
self.msgqueuethrd.daemon = True
self.msgqueuethrd.start()
kwds['guisocket'] = self.guisocket
kwds['websockport'] = self.find_free_port()
self.viewer = view_3d.hklview_3d(**kwds)
self.ResetPhilandViewer()
self.NewFileLoaded = False
def __init__ (self, *args, **kwds) :
self.miller_array = None
self.valid_arrays = []
self.spacegroup_choices = []
self.array_infostrs = []
self.array_infotpls = []
self.merge_answer = [None]
self.dmin = -1
self.settings = display.settings()
self.verbose = True
if kwds.has_key('verbose'):
self.verbose = kwds['verbose']
kwds['settings'] = self.settings
kwds['mprint'] = self.mprint
self.viewer = view_3d.hklview_3d( **kwds )
self.ResetPhilandViewer()
self.NewFileLoaded = False
self.infostr = ""
self.useSocket=False
if kwds.has_key('useSocket'):
self.useSocket = kwds['useSocket']
self.context = zmq.Context()
self.socket = self.context.socket(zmq.PAIR)
self.socket.connect("tcp://127.0.0.1:7895")
self.STOP = False
print "starting socketthread"
self.msgqueuethrd = threading.Thread(target = self.zmq_listen )
self.msgqueuethrd.daemon = True
self.msgqueuethrd.start()
def __init__ (self, *args, **kwds) :
self.valid_arrays = []
self.spacegroup_choices = []
self.procarrays = []
self.origarrays = {}
self.merge_answer = [None]
self.dmin = -1
self.settings = display.settings()
self.verbose = 0
if 'verbose' in kwds:
self.verbose = eval(kwds['verbose'])
self.guiSocketPort=None
self.mprint("kwds= " +str(kwds), 1)
self.mprint("args= " + str(args), 1)
kwds['settings'] = self.settings
kwds['mprint'] = self.mprint
self.infostr = ""
self.hklfile_history = []
self.tncsvec = None
self.uservectors = []
self.new_miller_array_operations_lst = []
self.copyrightpaths = [("CCTBX copyright", libtbx.env.under_root(os.path.join("modules","cctbx_project","COPYRIGHT.txt"))),
("NGL copyright", libtbx.env.under_root(os.path.join("modules","cctbx_project","crys3d","hklview","License_for_NGL.txt"))),
("html2canvas copyright", libtbx.env.under_root(os.path.join("modules","cctbx_project","crys3d","hklview","LICENSE_for_html2canvas.txt")))
]
self.zmqsleeptime = 0.1
if 'useGuiSocket' in kwds:
self.guiSocketPort = eval(kwds['useGuiSocket'])
self.context = zmq.Context()
self.guisocket = self.context.socket(zmq.PAIR)
self.guisocket.connect("tcp://127.0.0.1:%s" %self.guiSocketPort )
self.STOP = False
self.mprint("starting socketthread", 1)
# name this thread to ensure any asyncio functions are called only from main thread
self.msgqueuethrd = threading.Thread(target = self.zmq_listen, name="HKLviewerZmqThread" )
self.msgqueuethrd.daemon = True
kwds['send_info_to_gui'] = self.SendInfoToGUI # function also used by hklview_3d
pyversion = "cctbx.python.version: " + str(sys.version_info[0])
# tell gui what python version we are
self.SendInfoToGUI(pyversion )
self.SendInfoToGUI({"copyrights": self.copyrightpaths } )
kwds['websockport'] = self.find_free_port()
kwds['parent'] = self
self.viewer = view_3d.hklview_3d( **kwds )
self.ResetPhilandViewer()
self.idx_data = None
self.NewFileLoaded = False
self.loaded_file_name = ""
self.hklin = None
if 'hklin' in kwds or 'HKLIN' in kwds:
self.hklin = kwds.get('hklin', kwds.get('HKLIN') )
self.LoadReflectionsFile(self.hklin)
if 'useGuiSocket' in kwds:
self.msgqueuethrd.start()
def __init__(self, *args, **kwds):
self.miller_array = None
self.valid_arrays = []
self.spacegroup_choices = []
self.procarrays = []
self.array_info = []
self.dmin = -1
self.settings = display.settings()
self.verbose = True
if kwds.has_key('verbose'):
self.verbose = kwds['verbose']
kwds['settings'] = self.settings
kwds['mprint'] = self.mprint
self.viewer = view_3d.hklview_3d(**kwds)
def prepare_dataloading(self):
self.viewer.isnewfile = True
#self.params.mergedata = None
self.params.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 = []
self.origarrays = {}
display.reset_settings()
self.settings = display.settings()
self.viewer.settings = self.params.viewer
self.viewer.mapcoef_fom_dict = {}
self.viewer.sceneid_from_arrayid = []
self.hklfile_history = []
self.tncsvec = None
self.loaded_file_name = ""
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 __init__ (self, *args, **kwds) :
self.valid_arrays = []
self.spacegroup_choices = []
self.procarrays = []
self.merge_answer = [None]
self.dmin = -1
self.settings = display.settings()
self.verbose = 0
if 'verbose' in kwds:
self.verbose = eval(kwds['verbose'])
self.guiSocketPort=None
self.mprint("kwds= " +str(kwds), 1)
self.mprint("args= " + str(args), 1)
kwds['settings'] = self.settings
kwds['mprint'] = self.mprint
self.infostr = ""
self.hklfile_history = []
self.tncsvec = None
self.new_miller_array_operations_lst = []
self.zmqsleeptime = 0.1
if 'useGuiSocket' in kwds:
self.guiSocketPort = eval(kwds['useGuiSocket'])
self.context = zmq.Context()
self.guisocket = self.context.socket(zmq.PAIR)
self.guisocket.connect("tcp://127.0.0.1:%s" %self.guiSocketPort )
self.STOP = False
self.mprint("starting socketthread", 1)
self.msgqueuethrd = threading.Thread(target = self.zmq_listen )
self.msgqueuethrd.daemon = True
self.msgqueuethrd.start()
kwds['send_info_to_gui'] = self.SendInfoToGUI # function also used by hklview_3d
kwds['websockport'] = self.find_free_port()
kwds['parent'] = self
self.viewer = view_3d.hklview_3d( **kwds )
self.ResetPhilandViewer()
self.idx_data = None
self.NewFileLoaded = False
self.loaded_file_name = ""
self.hklin = None
if 'hklin' in kwds or 'HKLIN' in kwds:
self.hklin = kwds.get('hklin', kwds.get('HKLIN') )
self.LoadReflectionsFile(self.hklin)
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
