def __init__(self,
gl_widget,
projection_file=None,
simmx_file=None,
particle_file=None):
self.init_lock = True # a lock indicated that we are still in the __init__ function
self.au_data = None # This will be a dictionary, keys will be refinement directories, values will be something like available iterations for visual study
EM3DSymModel.__init__(self, gl_widget)
self.window_title = "SimmxXplor"
#InputEventsManager.__init__(self)
self.projection_file = projection_file # a projection file produced by e2project3d
self.particle_file = particle_file # A file containing particles to be examined
self.current_particle = -1 # keep track of the current particle
self.current_projection = None # keep track of the current projection
self.ptcl_display = None # display all particles
self.mx_display = None # mx display module for displaying projection and aligned particle
self.lay = None # 2d plot for displaying comparison between particle and projection
self.simcmp = "dot:normalize=1"
self.align = "rotate_translate_flip"
self.aligncmp = "dot"
self.refine = "refine"
self.refinecmp = "dot:normalize=1"
self.shrink = 1
def generate_current_display_list(self, force=False):
'''
Redefinition of EMImage3DSymModule.generate_current_display_list
'''
if self.init_lock: return 0
if self.au_data == None or len(self.au_data) == 0:
EM3DSymModel.generate_current_display_list(self, force)
self.init_basic_shapes()
if self.nomirror == True: val = 0
else: val = 1
self.trace_great_arcs(self.sym_object.get_asym_unit_points(val))
self.trace_great_triangles(val)
self.eulers = self.specified_eulers
if self.eulers == None: return 0
# if not self.colors_specified: self.point_colors = []
# else: self.point_colors = self.specified_colors
# self.points = []
# for i in self.eulers:
# p = i.transpose()*Vec3f(0,0,self.radius)
# self.points.append(p)
# if not self.colors_specified: self.point_colors.append((0.34615, 0.3143, 0.0903,1))
self.make_sym_dl_list(self.eulers)
return 1
def update_cmp(self):
cmpopt = parsemodopt(self.simcmp)
progress = QtGui.QProgressDialog("Computing similarities", "Abort", 0,
len(self.proj_data), None)
progress.show()
ptcl = self.ptcl_data[self.current_particle]
for i, p in enumerate(self.proj_data):
ali = p.copy()
ali.transform(p["ptcl.align2d"])
try:
p["cmp"] = -ptcl.cmp(cmpopt[0], ali, cmpopt[1])
except:
print(traceback.print_exc())
QtGui.QMessageBox.warning(
None, "Error",
"Invalid similarity metric string, or other comparison error"
)
progress.close()
return
progress.setValue(i)
QtGui.qApp.processEvents()
progress.close()
self.set_emdata_list_as_data(self.proj_data, "cmp")
# self.regen_dl(True)
EM3DSymModel.render(self)
def mousePressEvent(self, event):
if self.events_mode == "inspect":
self.current_hit = self.get_hit(event)
if self.current_hit == None:
EM3DSymModel.mousePressEvent(self, event)
else:
EM3DSymModel.mousePressEvent(self, event)
def render(self): if self.inspector == None: self.get_inspector() if self.projections == None: try:self.init_vitals() except: return #except: # self.get_inspector() # print "failed to initialize vital information" # return EM3DSymModel.render(self)
def keyPressEvent(self, event):
if event.key() == Qt.Key_F1:
self.display_web_help(
"http://blake.bcm.edu/emanwiki/EMAN2/Programs/e2eulerxplor")
elif event.key() == Qt.Key_F:
if self.flatten > 0: self.flatten = 0.0
else: self.flatten = 1.0
self.generate_current_display_list(True)
self.updateGL()
else:
EM3DSymModel.keyPressEvent(self, event)
def __init__(self, gl_widget, projection_file=None,simmx_file=None,particle_file=None): self.init_lock = True # a lock indicated that we are still in the __init__ function self.au_data = None # This will be a dictionary, keys will be refinement directories, values will be something like available iterations for visual study EM3DSymModel.__init__(self, gl_widget) self.window_title = "SimmxXplor" self.projection_file = projection_file # a projection file produced by e2project3d self.simmx_file = simmx_file # a similarity matrix produced by e2simmx or by e2classaverage - should have the same number of columns (nx) as the number of projections self.particle_file = particle_file # a similarity matrix produced by e2simmx or by e2classaverage - should have the same number of columns (nx) as the number of projections self.num_particles = None # keep track of the total number of particles ( the y dimension of the simmx file) self.current_particle = 0 # keep track of the current particle self.current_projection = None # keep track of the current projection self.projections = None # a list of the projections - the initial design keeps them all in memory - this could be overcome self.mx_display = None # mx display widget for displaying projection and aligned particle self.frc_display = None # 2d plot for displaying comparison between particle and projection self.mirror_eulers = True # If True the drawn Eulers are are also rendered on the opposite side of the sphere - see EM3DSymModel.make_sym_dl_lis
def render(self): if self.inspector == None: self.get_inspector() EM3DSymModel.render(self)
def __del__(self):
EM3DSymModel.__del__(
self
) # this is here for documentation purposes - beware that the del function is important
def __init__(self,
gl_widget=None,
auto=True,
sparse_mode=False,
file_name="",
read_from=None):
self.current_hit = None
self.events_mode_list = ["navigate", "inspect"]
self.events_mode = self.events_mode_list[1]
self.init_lock = True # a lock indicated that we are still in the __init__ function
self.au_data = None # This will be a dictionary, keys will be refinement directories, values will be something like available iterations for visual study
if len(read_from) == 0:
read_from = None
self.readfrom = read_from
if self.readfrom:
file_name = ""
auto = False
datalst = []
for rr in self.readfrom:
datalst.append([rr, None, None, None, rr])
self.au_data = {"data": datalst}
if auto: # this a flag that tells the eulerxplorer to search for refinement data and automatically add elements to the inspector, if so
self.gen_refinement_data()
EM3DSymModel.__init__(self, gl_widget, eulerfilename=file_name)
Animator.__init__(self)
self.height_scale = 8.0 # This is a value used in EM3DSymModel which scales the height of the displayed cylinders - I made it 8 because it seemed fine. The user can change it anyhow
self.projection_file = None # This is a string - the name of the projection images file
self.average_file = None # This is a string - the name of the class averages file
self.proj_class_viewer = None # This will be an EMImageMXWidget that shows the class and/or projection
self.particle_viewer = None # This will be an EMImageMXWidget that shows the particles in a class
self.clsdb = None # I think this will become redundant - it used to be the old database that stores which particles are in a class, but now that's stored in the header
self.particle_file = None # This will be a string - the name of the file that has the particle files in it. This might be made redundant with the new approach
self.alignment_file = None # This will be a string - the name of the file containing the alignment parameters - this is essential if you we want to show the aligned particles
self.refine_dir = None # This will be a string - the name of the current refinement directory that is being studied
self.dx = None # This is an EMData object storing the x shifts of the alignments for all particles. Generated by e2classaverage
self.dy = None # This is an EMData object storing the y shifts of the alignments for all particles. Generated by e2classaverage
self.da = None # This is an EMData object storing the angle of the alignments for all particles. Generated by e2classaverage
self.dflip = None # This is an EMData object storing whether or not tthe alignment involved a flip, for all particles. Generated by e2classaverage
self.classes = None # This is an EMData object storing which class(es) a particle belongs to. Generated by e2classaverage
self.inclusions = None # This is and EMDAta storing a boolean that indicates the particle was actually included in the final average. Generated by e2classaverage
self.average = None # This the class average itself, an EMData object
self.projection = None # This is the projection itelse, an EMData object
self.class_idx = None # This is the idx of the current class being studied in the interface
self.previous_len = -1 # To keep track of the number of class averages that were previously viewable. This helps to make sure we can switch to the same class average in the context of a different refinement iteration
module_closed = QtCore.pyqtSignal()
self.mirror_eulers = False
if sparse_mode:
self.mirror_eulers = True # If True the drawn Eulers are are also rendered on the opposite side of the sphere - see EM3DSymModel.make_sym_dl_lis
# Grab the symmetry from the workflow database if possible
sym = "c1"
if js_check_dict("refine_01/0_refine_parms.json"):
try:
sym = str(js_open_dict("refine_01/0_refine_parms.json")["sym"])
except:
pass
# Have to tell the EM3DSymModel that there is a new sym
self.set_symmetry(sym)
# this object will have
if self.au_data != None:
combo_entries = list(self.au_data.keys())
combo_entries.sort()
combo_entries.reverse()
if len(combo_entries) > 0:
au = combo_entries[0]
cls = self.au_data[au][0][0]
self.on_au_selected(au, cls)
self.mirror_eulers = True
self.init_lock = False
self.force_update = True # Force a display udpdate in EMImage3DSymModule
self.point_selected.connect(self.au_point_selected)
def mouseMoveEvent(self, event):
if self.events_mode == "inspect" and self.current_hit:
pass
else:
EM3DSymModel.mouseMoveEvent(self, event)