class EMEulerExplorer(EM3DSymModel,Animator):
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 mouseReleaseEvent(self,event):
if self.events_mode == "inspect":
if self.current_hit != None:
self.updateGL() # there needs to be a clear or something in order for the picking to work. This is bit of hack but our rendering function doesn't take long anyhow
hit = self.get_hit(event)
if hit == self.current_hit:
self.emit(QtCore.SIGNAL("point_selected"),self.current_hit,event)
else:
#EM3DSymModel.mouseReleaseEvent(self,event)
EM3DModel.mouseReleaseEvent(self, event) #behavior in EM3DSymModel is not what we want (needed in sibling classes?)
self.current_hit = None
else:
#EM3DSymModel.mouseReleaseEvent(self,event)
EM3DModel.mouseReleaseEvent(self, event) #behavior in EM3DSymModel is not what we want (needed in sibling classes?)
def mouseMoveEvent(self,event):
if self.events_mode == "inspect" and self.current_hit:
pass
else:
EM3DSymModel.mouseMoveEvent(self,event)
def get_hit(self,event):
v = self.vdtools.wview.tolist()
self.get_gl_widget().makeCurrent() # prevents a stack underflow
# x = event.x()
# y = v[-1]-event.y()
# glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT | GL_STENCIL_BUFFER_BIT )
# vals = self.render(color_picking=True)
# glFlush()
# vv = glReadPixels(x,y,1,1,GL_RGB,GL_FLOAT)
# reslt = Vec3f(float(vv[0][0][0]),float(vv[0][0][1]),float(vv[0][0][2]))
# for i,val in enumerate(vals):
## print val,reslt,(reslt-val).length(),vv[0][0]
# if (reslt-val).length() < 0.01:
# print i
## print (reslt-val).length()
# return i
# print vv
#
# the problem with this approach is that depth testing is not part of picking
sb = [0 for i in xrange(0,512)]
glSelectBuffer(512)
glRenderMode(GL_SELECT)
glInitNames()
glMatrixMode(GL_PROJECTION)
glPushMatrix()
glLoadIdentity()
gluPickMatrix(event.x(),v[-1]-event.y(),5,5,v)
self.get_gl_widget().load_perspective()
glMatrixMode(GL_MODELVIEW)
glInitNames()
self.render()
glMatrixMode(GL_PROJECTION)
glPopMatrix()
glMatrixMode(GL_MODELVIEW)
glFlush()
intersection = None
hits = list(glRenderMode(GL_RENDER))
for hit in hits:
a,b,c=hit
if len(c) > 0:
intersection = c[0]-1
break
return intersection
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=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
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 = 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.au_selected(au,cls)
self.mirror_eulers = True
self.init_lock = False
self.force_update=True # Force a display udpdate in EMImage3DSymModule
QtCore.QObject.connect(self, QtCore.SIGNAL("point_selected"), self.au_point_selected)
def __del__(self):
EM3DSymModel.__del__(self) # this is here for documentation purposes - beware that the del function is important
def initializeGL(self):
glEnable(GL_NORMALIZE)
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 get_data_dims(self):
return (2*self.radius,2*self.radius,2*self.radius)
def width(self): return 2*self.radius
def height(self): return 2*self.radius
def depth(self): return 2*self.radius
def gen_refinement_data(self):
dirs,files = get_files_and_directories()
dirs.sort()
for i in range(len(dirs)-1,-1,-1):
if dirs[i][:7] != "refine_" and dirs[i][:6]!="multi_" and dirs[i][:11]!="multinoali_":
dirs.pop(i)
else:
try: int(dirs[i][7:])
except: dirs.pop(i)
self.dirs = dirs
print(dirs)
self.au_data = {}
for dir in self.dirs:
d = self.check_refine_db_dir(dir)
if len(d) != 0 and len(d[dir]) != 0: self.au_data.update(d)
def check_refine_db_dir(self,dir,s1="classes",s2=None,s3="cls_result",s4="threed",s5="projections"):
# s2 used to be class_indices
names = [s1,s2,s3,s4,s5]
data = {}
data[dir] = []
register_js_name = "{}/0_refine_parms.json".format(dir)
files=os.listdir(dir)
try:
nums=[int(i[7:9]) for i in files if "threed" in i and "even" not in i and "odd" not in i]
maxnum=max(nums)
except :
print("Nothing in ",dir)
return {}
for i in xrange(1,maxnum+1):
exte="_{:02d}_even.hdf".format(i)
exto="_{:02d}_odd.hdf".format(i)
data[dir].append([sadd(dir,s1,exte),sadd(dir,s2,exte),sadd(dir,s3,exte),sadd(dir,s4,exte),sadd(dir,s5,exte)])
data[dir].append([sadd(dir,s1,exto),sadd(dir,s2,exto),sadd(dir,s3,exto),sadd(dir,s4,exto),sadd(dir,s5,exto)])
return data
def set_projection_file(self,projection_file): self.projection_file = projection_file
def get_inspector(self):
if not self.inspector :
if (self.au_data == None or len(self.au_data) == 0) and self.mirror_eulers == False: #self.mirror_eulers thing is a little bit of a hack, it's tied to the sparse_mode flag in the init function, which is used by euler_display in EMAN2.py
self.inspector=EMAsymmetricUnitInspector(self,True,True)
else:
self.inspector=EMAsymmetricUnitInspector(self)
QtCore.QObject.connect(self.inspector,QtCore.SIGNAL("au_selected"),self.au_selected)
return self.inspector
def au_selected(self,refine_dir,cls):
self.refine_dir = refine_dir
get_application().setOverrideCursor(Qt.BusyCursor)
data = []
for d in self.au_data[refine_dir]:
if d[0] == cls:
data = d;
break
if len(data) == 0:
error("error, no data for %s %s, returning" %(refine_dir,cls))
# print "error, no data for",au,cls,"returning"
self.events_handlers["inspect"].reset()
get_application().setOverrideCursor(Qt.ArrowCursor)
return
if not self.readfrom:
try :
self.particle_file=js_open_dict(refine_dir+"/0_refine_parms.json")["input"]
except:
error("No data in "+refine_dir )
self.events_handlers["inspect"].reset()
get_application().setOverrideCursor(Qt.ArrowCursor)
return
self.average_file = cls
self.projection_file = data[4]
self.alignment_file = data[2]
self.clsdb = data[1]
self.dx = None
self.dy = None
self.da = None
self.dflip = None
self.classes = None
eulers = get_eulers_from(self.average_file)
#s = Symmetries.get("d7")
#eulers = s.gen_orientations("rand",{"n":EMUtil.get_image_count(self.average_file)})
self.specify_eulers(eulers)
#from emimagemx import EMDataListCache
#a = EMData.read_images(self.average_file)
#a = [test_image() for i in range(EMUtil.get_image_count(self.average_file))]
#print len(a),len(eulers)
#b = [a[i].set_attr("xform.projection",eulers[i]) for i in range(len(eulers))]
#b = [a[i].set_attr("ptcl_repr",1) for i in range(len(eulers))]
self.set_emdata_list_as_data(EMLightWeightParticleCache.from_file(self.average_file),"ptcl_repr")
#self.set_emdata_list_as_data(EMDataListCache(self.average_file),"ptcl_repr")
# self.set_emdata_list_as_data(a,"ptcl_repr")
self.force_update = True
self.au_point_selected(self.class_idx,None)
# if we have the same number of Eulers we can update everything
# if self.previous_len == len(eulers) : self.events_handlers["inspect"].repeat_event()
# else:self.events_handlers["inspect"].reset()
self.previous_len = len(eulers)
if not self.init_lock:self.updateGL()
get_application().setOverrideCursor(Qt.ArrowCursor)
def __get_file_headers(self,filename):
headers = []
n = EMUtil.get_image_count(filename)
for i in range(n):
e = EMData()
e.read_image(filename,i,True)
headers.append(e)
return headers
def au_point_selected(self,i,event=None):
if self.readfrom:
return
if i == None:
if event != None and event.modifiers()&Qt.ShiftModifier:
if self.special_euler != None:
self.special_euler = None
if not self.init_lock:self.regen_dl()
return
# self.arc_anim_points = None
self.projection = None
if self.euler_data:
# db = db_open_dict(self.average_file)
# a = db.get(i)
# print a["nx"]
# print self.average_file,i
# self.average = EMData(self.average_file,i)
# self.average["nx"]
self.average = self.euler_data[i]#
self.projection = EMData(self.projection_file,self.average.get_attr("projection_image_idx"))
self.average.process_inplace("normalize.toimage",{"to":self.projection})
try:
self.class_idx = self.average.get_attr("projection_image_idx")
print("%d (%d)"%(self.class_idx,self.average["ptcl_repr"]))
except:
self.class_idx = -1
else: return
#if self.projection == None and self.average == None: return
first = False
if self.proj_class_viewer == None:
first = True
self.proj_class_viewer = EMImageMXWidget(data=None,application=get_application())
# self.proj_class_viewer = EMImage2DWidget(image=None,application=get_application())
QtCore.QObject.connect(self.proj_class_viewer,QtCore.SIGNAL("module_closed"),self.on_mx_view_closed)
# self.proj_class_viewer.set_mouse_mode("App" )
QtCore.QObject.connect(self.proj_class_viewer,QtCore.SIGNAL("mx_image_selected"), self.mx_image_selected)
get_application().show_specific(self.proj_class_viewer)
self.proj_class_single = EMImage2DWidget(image=None,application=get_application())
QtCore.QObject.connect(self.proj_class_single,QtCore.SIGNAL("module_closed"),self.on_mx_view_closed)
# QtCore.QObject.connect(self.proj_class_single,QtCore.SIGNAL("mx_image_selected"), self.mx_image_selected)
get_application().show_specific(self.proj_class_single)
disp = []
if self.projection != None: disp.append(self.projection)
if self.average != None and self.projection!=None:
# ok, this really should be put into its own processor
#dataf = self.projection.do_fft()
#apix=self.projection["apix_x"]
#curve = dataf.calc_radial_dist(dataf["ny"], 0, 0.5,True)
#curve=[i/(dataf["nx"]*dataf["ny"])**2 for i in curve]
#xcurve=[i/(apix*2.0*dataf["ny"]) for i in range(len(curve))]
#xyd=XYData()
#xyd.set_xy_list(xcurve,curve)
#filt=self.average.process("filter.setstrucfac",{"apix":apix,"strucfac":xyd})
#filt.process_inplace("normalize.toimage",{"to":self.average})
self.projection["apix_x"]=self.average["apix_x"]
self.projection["apix_y"]=self.average["apix_y"]
self.projection["apix_z"]=self.average["apix_z"]
filt=self.projection.process("threshold.notzero")
filt.mult(self.average)
filt.process_inplace("filter.matchto",{"to":self.projection})
disp.append(filt)
if self.average!=None:
disp.append(self.average)
self.proj_class_viewer.set_data(disp)
self.proj_class_single.set_data(disp)
self.proj_class_viewer.updateGL()
self.proj_class_single.updateGL()
if self.particle_viewer != None:
self.mx_image_selected(None,None)
if first: self.proj_class_viewer.optimally_resize()
if i != self.special_euler:
self.special_euler = i
self.force_update = True
if not self.init_lock: self.updateGL()
def on_mx_view_closed(self):
self.proj_class_viewer = None
self.proj_class_single = None
def on_particle_mx_view_closed(self):
self.particle_viewer = None
def animation_done_event(self,animation):
pass
def alignment_time_animation(self,transforms):
if len(transforms) < 2: return
animation = OrientationListAnimation(self,transforms,self.radius)
self.register_animatable(animation)
def particle_selected(self,event,lc):
if lc != None:
d = lc[3]
ptcl_idx = d["Img #"]
data = self.au_data[self.refine_dir]
prj = []
cls_result = []
for l in data:
for s in l:
stag = base_name(s)
if len(stag) > 11 and stag[:11] == "projections":
prj.append(s)
elif len(stag) > 10 and stag[:10] == "cls_result":
cls_result.append(s)
transforms = []
if len(prj) != len(cls_result): RunTimeError("The number of cls_result files does not match the number of projection files?")
e = EMData()
for i,cr in enumerate(cls_result):
r = Region(0,ptcl_idx,1,1)
e.read_image(cr,0,False,r)
p = int(e.get(0))
e.read_image(prj[i],p,True)
transforms.append(e["xform.projection"])
self.alignment_time_animation(transforms)
def mx_image_selected(self,event,lc):
# self.arc_anim_points = None
get_application().setOverrideCursor(Qt.BusyCursor)
if lc != None: self.sel = lc[0]
if self.average != None:
included = []
if self.average.has_attr("class_ptcl_idxs"):
included = self.average["class_ptcl_idxs"]
excluded = []
if self.average.has_attr("exc_class_ptcl_idxs"):
excluded = self.average["exc_class_ptcl_idxs"]
all = included + excluded
#all.sort()
bdata = []
data = []
idx_included = []
running_idx = 0
from emimagemx import ApplyAttribute
for val in included:
bdata.append([self.particle_file,val,[ApplyAttribute("Img #",val)]])
idx_included.append(running_idx)
running_idx += 1
idx_excluded = []
for val in excluded:
bdata.append([self.particle_file,val,[ApplyAttribute("Img #",val)]])
idx_excluded.append(running_idx)
running_idx += 1
data = EMLightWeightParticleCache(bdata)
first = False
if self.particle_viewer == None:
first = True
self.particle_viewer = EMImageMXWidget(data=None,application=get_application())
self.particle_viewer.set_mouse_mode("App" )
QtCore.QObject.connect(self.particle_viewer,QtCore.SIGNAL("module_closed"),self.on_particle_mx_view_closed)
QtCore.QObject.connect(self.particle_viewer,QtCore.SIGNAL("mx_image_selected"), self.particle_selected)
get_application().show_specific(self.particle_viewer)
self.check_images_in_memory()
if self.sel== 0 or self.alignment_file == None:
self.particle_viewer.set_data(data)
else:
for i,[name,idx,f] in enumerate(bdata):
index = -1
if self.classes.get_xsize() == 1:
index = 0 # just assume it's the first one - this is potentially fatal assumption, but in obscure situations only
else:
for j in range(self.classes.get_xsize()):
if int(self.classes.get(j,idx)) == self.class_idx:
index = j
break
if index == -1:
print("couldn't find")
get_application().setOverrideCursor(Qt.ArrowCursor)
return
x = self.dx.get(index,idx)
y = self.dy.get(index,idx)
a = self.da.get(index,idx)
m = self.dflip.get(index,idx)
t = Transform({"type":"2d","alpha":a,"mirror":int(m)})
t.set_trans(x,y)
from emimagemx import ApplyTransform
f.append(ApplyTransform(t))
#data[i].transform(t)
self.particle_viewer.set_data(data)
if first:
self.particle_viewer.updateGL()
self.particle_viewer.optimally_resize()
self.particle_viewer.clear_sets(False)
self.particle_viewer.enable_set("Excluded",idx_excluded,True,False)
self.particle_viewer.enable_set("Included",idx_included,False,False)
self.particle_viewer.updateGL()
get_application().setOverrideCursor(Qt.ArrowCursor)
self.updateGL()
def check_images_in_memory(self):
if self.alignment_file != None:
if self.dx == None:
self.dx = EMData(self.alignment_file,2)
if self.dy == None:
self.dy = EMData(self.alignment_file,3)
if self.da == None:
self.da = EMData(self.alignment_file,4)
if self.dflip == None:
self.dflip = EMData(self.alignment_file,5)
if self.classes == None:
self.classes = EMData(self.alignment_file,0)
if self.inclusions == None:
self.inclusions = EMData(self.alignment_file,1)
def set_events_mode(self,mode):
if not mode in self.events_mode_list:
print("error, unknown events mode", mode)
return
else:
self.events_mode = mode
def closeEvent(self,event):
if self.inspector !=None: self.inspector.close()
if self.proj_class_viewer !=None: self.proj_class_viewer.close()
if self.proj_class_single !=None: self.proj_class_single.close()
if self.particle_viewer != None: self.particle_viewer.close()
get_application().close_specific(self)
self.emit(QtCore.SIGNAL("module_closed")) # this signal is
class EMEulerExplorer(EM3DSymModel,Animator):
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 mouseReleaseEvent(self,event):
if self.events_mode == "inspect":
if self.current_hit != None:
self.updateGL() # there needs to be a clear or something in order for the picking to work. This is bit of hack but our rendering function doesn't take long anyhow
hit = self.get_hit(event)
if hit == self.current_hit:
self.emit(QtCore.SIGNAL("point_selected"),self.current_hit,event)
else:
#EM3DSymModel.mouseReleaseEvent(self,event)
EM3DModel.mouseReleaseEvent(self, event) #behavior in EM3DSymModel is not what we want (needed in sibling classes?)
self.current_hit = None
else:
#EM3DSymModel.mouseReleaseEvent(self,event)
EM3DModel.mouseReleaseEvent(self, event) #behavior in EM3DSymModel is not what we want (needed in sibling classes?)
def mouseMoveEvent(self,event):
if self.events_mode == "inspect" and self.current_hit:
pass
else:
EM3DSymModel.mouseMoveEvent(self,event)
def get_hit(self,event):
v = self.vdtools.wview.tolist()
self.get_gl_widget().makeCurrent() # prevents a stack underflow
# x = event.x()
# y = v[-1]-event.y()
# glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT | GL_STENCIL_BUFFER_BIT )
# vals = self.render(color_picking=True)
# glFlush()
# vv = glReadPixels(x,y,1,1,GL_RGB,GL_FLOAT)
# reslt = Vec3f(float(vv[0][0][0]),float(vv[0][0][1]),float(vv[0][0][2]))
# for i,val in enumerate(vals):
## print val,reslt,(reslt-val).length(),vv[0][0]
# if (reslt-val).length() < 0.01:
# print i
## print (reslt-val).length()
# return i
# print vv
#
# the problem with this approach is that depth testing is not part of picking
sb = [0 for i in xrange(0,512)]
glSelectBuffer(512)
glRenderMode(GL_SELECT)
glInitNames()
glMatrixMode(GL_PROJECTION)
glPushMatrix()
glLoadIdentity()
gluPickMatrix(event.x(),v[-1]-event.y(),5,5,v)
self.get_gl_widget().load_perspective()
glMatrixMode(GL_MODELVIEW)
glInitNames()
self.render()
glMatrixMode(GL_PROJECTION)
glPopMatrix()
glMatrixMode(GL_MODELVIEW)
glFlush()
intersection = None
hits = list(glRenderMode(GL_RENDER))
for hit in hits:
a,b,c=hit
if len(c) > 0:
intersection = c[0]-1
break
return intersection
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=None, auto=True,sparse_mode=False, file_name = ""):
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 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
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 = 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.au_selected(au,cls)
self.mirror_eulers = True
self.init_lock = False
self.force_update=True # Force a display udpdate in EMImage3DSymModule
QtCore.QObject.connect(self, QtCore.SIGNAL("point_selected"), self.au_point_selected)
def __del__(self):
EM3DSymModel.__del__(self) # this is here for documentation purposes - beware that the del function is important
def initializeGL(self):
glEnable(GL_NORMALIZE)
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 get_data_dims(self):
return (2*self.radius,2*self.radius,2*self.radius)
def width(self): return 2*self.radius
def height(self): return 2*self.radius
def depth(self): return 2*self.radius
def gen_refinement_data(self):
dirs,files = get_files_and_directories()
dirs.sort()
for i in range(len(dirs)-1,-1,-1):
if len(dirs[i]) != 9:
dirs.pop(i)
elif dirs[i][:7] != "refine_":
dirs.pop(i)
else:
try: int(dirs[i][7:])
except: dirs.pop(i)
self.dirs = dirs
print dirs
self.au_data = {}
for dir in self.dirs:
d = self.check_refine_db_dir(dir)
if len(d) != 0 and len(d[dir]) != 0: self.au_data.update(d)
def check_refine_db_dir(self,dir,s1="classes",s2=None,s3="cls_result",s4="threed",s5="projections"):
# s2 used to be class_indices
names = [s1,s2,s3,s4,s5]
data = {}
data[dir] = []
register_js_name = "{}/0_refine_parms.json".format(dir)
files=os.listdir(dir)
try:
nums=[int(i[7:9]) for i in files if "threed" in i and "even" not in i and "odd" not in i]
maxnum=max(nums)
except :
print "Nothing in ",dir
return {}
for i in xrange(1,maxnum+1):
exte="_{:02d}_even.hdf".format(i)
exto="_{:02d}_odd.hdf".format(i)
data[dir].append([sadd(dir,s1,exte),sadd(dir,s2,exte),sadd(dir,s3,exte),sadd(dir,s4,exte),sadd(dir,s5,exte)])
data[dir].append([sadd(dir,s1,exto),sadd(dir,s2,exto),sadd(dir,s3,exto),sadd(dir,s4,exto),sadd(dir,s5,exto)])
return data
def set_projection_file(self,projection_file): self.projection_file = projection_file
def get_inspector(self):
if not self.inspector :
if (self.au_data == None or len(self.au_data) == 0) and self.mirror_eulers == False: #self.mirror_eulers thing is a little bit of a hack, it's tied to the sparse_mode flag in the init function, which is used by euler_display in EMAN2.py
self.inspector=EMAsymmetricUnitInspector(self,True,True)
else:
self.inspector=EMAsymmetricUnitInspector(self)
QtCore.QObject.connect(self.inspector,QtCore.SIGNAL("au_selected"),self.au_selected)
return self.inspector
def au_selected(self,refine_dir,cls):
self.refine_dir = refine_dir
get_application().setOverrideCursor(Qt.BusyCursor)
data = []
for d in self.au_data[refine_dir]:
if d[0] == cls:
data = d;
break
if len(data) == 0:
error("error, no data for %s %s, returning" %(refine_dir,cls))
# print "error, no data for",au,cls,"returning"
self.events_handlers["inspect"].reset()
get_application().setOverrideCursor(Qt.ArrowCursor)
return
try :
self.particle_file=js_open_dict(refine_dir+"/0_refine_parms.json")["input"]
except:
error("No data in "+refine_dir )
self.events_handlers["inspect"].reset()
get_application().setOverrideCursor(Qt.ArrowCursor)
return
self.average_file = cls
self.projection_file = data[4]
self.alignment_file = data[2]
self.clsdb = data[1]
self.dx = None
self.dy = None
self.da = None
self.dflip = None
self.classes = None
eulers = get_eulers_from(self.average_file)
#s = Symmetries.get("d7")
#eulers = s.gen_orientations("rand",{"n":EMUtil.get_image_count(self.average_file)})
self.specify_eulers(eulers)
#from emimagemx import EMDataListCache
#a = EMData.read_images(self.average_file)
#a = [test_image() for i in range(EMUtil.get_image_count(self.average_file))]
#print len(a),len(eulers)
#b = [a[i].set_attr("xform.projection",eulers[i]) for i in range(len(eulers))]
#b = [a[i].set_attr("ptcl_repr",1) for i in range(len(eulers))]
self.set_emdata_list_as_data(EMLightWeightParticleCache.from_file(self.average_file),"ptcl_repr")
#self.set_emdata_list_as_data(EMDataListCache(self.average_file),"ptcl_repr")
# self.set_emdata_list_as_data(a,"ptcl_repr")
self.force_update = True
self.au_point_selected(self.class_idx,None)
# if we have the same number of Eulers we can update everything
# if self.previous_len == len(eulers) : self.events_handlers["inspect"].repeat_event()
# else:self.events_handlers["inspect"].reset()
self.previous_len = len(eulers)
if not self.init_lock:self.updateGL()
get_application().setOverrideCursor(Qt.ArrowCursor)
def __get_file_headers(self,filename):
headers = []
n = EMUtil.get_image_count(filename)
for i in range(n):
e = EMData()
e.read_image(filename,i,True)
headers.append(e)
return headers
def au_point_selected(self,i,event=None):
if i == None:
if event != None and event.modifiers()&Qt.ShiftModifier:
if self.special_euler != None:
self.special_euler = None
if not self.init_lock:self.regen_dl()
return
# self.arc_anim_points = None
self.projection = None
if self.euler_data:
# db = db_open_dict(self.average_file)
# a = db.get(i)
# print a["nx"]
# print self.average_file,i
# self.average = EMData(self.average_file,i)
# self.average["nx"]
self.average = self.euler_data[i]#
self.projection = EMData(self.projection_file,self.average.get_attr("projection_image_idx"))
self.average.process_inplace("normalize.toimage",{"to":self.projection})
try:
self.class_idx = self.average.get_attr("projection_image_idx")
print "%d (%d)"%(self.class_idx,self.average["ptcl_repr"])
except:
self.class_idx = -1
else: return
#if self.projection == None and self.average == None: return
first = False
if self.proj_class_viewer == None:
first = True
self.proj_class_viewer = EMImageMXWidget(data=None,application=get_application())
# self.proj_class_viewer = EMImage2DWidget(image=None,application=get_application())
QtCore.QObject.connect(self.proj_class_viewer,QtCore.SIGNAL("module_closed"),self.on_mx_view_closed)
# self.proj_class_viewer.set_mouse_mode("App" )
QtCore.QObject.connect(self.proj_class_viewer,QtCore.SIGNAL("mx_image_selected"), self.mx_image_selected)
get_application().show_specific(self.proj_class_viewer)
self.proj_class_single = EMImage2DWidget(image=None,application=get_application())
QtCore.QObject.connect(self.proj_class_single,QtCore.SIGNAL("module_closed"),self.on_mx_view_closed)
# QtCore.QObject.connect(self.proj_class_single,QtCore.SIGNAL("mx_image_selected"), self.mx_image_selected)
get_application().show_specific(self.proj_class_single)
disp = []
if self.projection != None: disp.append(self.projection)
if self.average != None and self.projection!=None:
# ok, this really should be put into its own processor
#dataf = self.projection.do_fft()
#apix=self.projection["apix_x"]
#curve = dataf.calc_radial_dist(dataf["ny"], 0, 0.5,True)
#curve=[i/(dataf["nx"]*dataf["ny"])**2 for i in curve]
#xcurve=[i/(apix*2.0*dataf["ny"]) for i in range(len(curve))]
#xyd=XYData()
#xyd.set_xy_list(xcurve,curve)
#filt=self.average.process("filter.setstrucfac",{"apix":apix,"strucfac":xyd})
#filt.process_inplace("normalize.toimage",{"to":self.average})
self.projection["apix_x"]=self.average["apix_x"]
self.projection["apix_y"]=self.average["apix_y"]
self.projection["apix_z"]=self.average["apix_z"]
filt=self.projection.process("threshold.notzero")
filt.mult(self.average)
filt.process_inplace("filter.matchto",{"to":self.projection})
disp.append(filt)
if self.average!=None:
disp.append(self.average)
self.proj_class_viewer.set_data(disp)
self.proj_class_single.set_data(disp)
self.proj_class_viewer.updateGL()
self.proj_class_single.updateGL()
if self.particle_viewer != None:
self.mx_image_selected(None,None)
if first: self.proj_class_viewer.optimally_resize()
if i != self.special_euler:
self.special_euler = i
self.force_update = True
if not self.init_lock: self.updateGL()
def on_mx_view_closed(self):
self.proj_class_viewer = None
self.proj_class_single = None
def on_particle_mx_view_closed(self):
self.particle_viewer = None
def animation_done_event(self,animation):
pass
def alignment_time_animation(self,transforms):
if len(transforms) < 2: return
animation = OrientationListAnimation(self,transforms,self.radius)
self.register_animatable(animation)
def particle_selected(self,event,lc):
if lc != None:
d = lc[3]
ptcl_idx = d["Img #"]
data = self.au_data[self.refine_dir]
prj = []
cls_result = []
for l in data:
for s in l:
stag = base_name(s)
if len(stag) > 11 and stag[:11] == "projections":
prj.append(s)
elif len(stag) > 10 and stag[:10] == "cls_result":
cls_result.append(s)
transforms = []
if len(prj) != len(cls_result): RunTimeError("The number of cls_result files does not match the number of projection files?")
e = EMData()
for i,cr in enumerate(cls_result):
r = Region(0,ptcl_idx,1,1)
e.read_image(cr,0,False,r)
p = int(e.get(0))
e.read_image(prj[i],p,True)
transforms.append(e["xform.projection"])
self.alignment_time_animation(transforms)
def mx_image_selected(self,event,lc):
# self.arc_anim_points = None
get_application().setOverrideCursor(Qt.BusyCursor)
if lc != None: self.sel = lc[0]
if self.average != None:
included = []
if self.average.has_attr("class_ptcl_idxs"):
included = self.average["class_ptcl_idxs"]
excluded = []
if self.average.has_attr("exc_class_ptcl_idxs"):
excluded = self.average["exc_class_ptcl_idxs"]
all = included + excluded
#all.sort()
bdata = []
data = []
idx_included = []
running_idx = 0
from emimagemx import ApplyAttribute
for val in included:
bdata.append([self.particle_file,val,[ApplyAttribute("Img #",val)]])
idx_included.append(running_idx)
running_idx += 1
idx_excluded = []
for val in excluded:
bdata.append([self.particle_file,val,[ApplyAttribute("Img #",val)]])
idx_excluded.append(running_idx)
running_idx += 1
data = EMLightWeightParticleCache(bdata)
first = False
if self.particle_viewer == None:
first = True
self.particle_viewer = EMImageMXWidget(data=None,application=get_application())
self.particle_viewer.set_mouse_mode("App" )
QtCore.QObject.connect(self.particle_viewer,QtCore.SIGNAL("module_closed"),self.on_particle_mx_view_closed)
QtCore.QObject.connect(self.particle_viewer,QtCore.SIGNAL("mx_image_selected"), self.particle_selected)
get_application().show_specific(self.particle_viewer)
self.check_images_in_memory()
if self.sel== 0 or self.alignment_file == None:
self.particle_viewer.set_data(data)
else:
for i,[name,idx,f] in enumerate(bdata):
index = -1
if self.classes.get_xsize() == 1:
index = 0 # just assume it's the first one - this is potentially fatal assumption, but in obscure situations only
else:
for j in range(self.classes.get_xsize()):
if int(self.classes.get(j,idx)) == self.class_idx:
index = j
break
if index == -1:
print "couldn't find"
get_application().setOverrideCursor(Qt.ArrowCursor)
return
x = self.dx.get(index,idx)
y = self.dy.get(index,idx)
a = self.da.get(index,idx)
m = self.dflip.get(index,idx)
t = Transform({"type":"2d","alpha":a,"mirror":int(m)})
t.set_trans(x,y)
from emimagemx import ApplyTransform
f.append(ApplyTransform(t))
#data[i].transform(t)
self.particle_viewer.set_data(data)
if first:
self.particle_viewer.updateGL()
self.particle_viewer.optimally_resize()
self.particle_viewer.clear_sets(False)
self.particle_viewer.enable_set("Excluded",idx_excluded,True,False)
self.particle_viewer.enable_set("Included",idx_included,False,False)
self.particle_viewer.updateGL()
get_application().setOverrideCursor(Qt.ArrowCursor)
self.updateGL()
def check_images_in_memory(self):
if self.alignment_file != None:
if self.dx == None:
self.dx = EMData(self.alignment_file,2)
if self.dy == None:
self.dy = EMData(self.alignment_file,3)
if self.da == None:
self.da = EMData(self.alignment_file,4)
if self.dflip == None:
self.dflip = EMData(self.alignment_file,5)
if self.classes == None:
self.classes = EMData(self.alignment_file,0)
if self.inclusions == None:
self.inclusions = EMData(self.alignment_file,1)
def set_events_mode(self,mode):
if not mode in self.events_mode_list:
print "error, unknown events mode", mode
return
else:
self.events_mode = mode
def closeEvent(self,event):
if self.inspector !=None: self.inspector.close()
if self.proj_class_viewer !=None: self.proj_class_viewer.close()
if self.proj_class_single !=None: self.proj_class_single.close()
if self.particle_viewer != None: self.particle_viewer.close()
get_application().close_specific(self)
self.emit(QtCore.SIGNAL("module_closed")) # this signal is
class ParticlesWindow:
def __init__(self, rctwidget):
self.rctwidget = rctwidget
self.window=EMImageMXWidget(application=self.rctwidget.parent_window)
self.window.set_display_values(["tilt","PImg#"])
self.window.set_mouse_mode("App")
self.window.setWindowTitle("Particles")
self.window.optimally_resize()
self.connect_signals()
self.listsofparts = []
self.numlists = 0
self.closed = False
def addlist(self, name):
data = []
data.append(name)
data.append(0)
data.append([])
self.listsofparts.append(data)
self.numlists = len(self.listsofparts)
def update_particles(self, particles, idx):
#print self.listsofparts[idx][0]
# reset the relevent list of particles
self.listsofparts[idx][1] = len(particles)
self.listsofparts[idx][2] = particles
# get the number of lists and the minimum number of particles in a given list..
listlength = 1e308
for lst in self.listsofparts:
listlength = min(listlength, lst[1])
i = 0
self.totparts = []
for part in xrange(listlength):
for lst in xrange(self.numlists):
self.listsofparts[lst][2][part].set_attr("tilt", self.listsofparts[lst][0])
self.listsofparts[lst][2][part].set_attr("PImg#", part)
self.totparts.append(self.listsofparts[lst][2][part])
i += 1
if self.totparts != []:
self.window.set_data(self.totparts)
self.window.updateGL()
def connect_signals(self):
QtCore.QObject.connect(self.window,QtCore.SIGNAL("mx_image_selected"),self.box_selected)
QtCore.QObject.connect(self.window,QtCore.SIGNAL("mx_mousedrag"),self.box_moved)
QtCore.QObject.connect(self.window,QtCore.SIGNAL("mx_mouseup"),self.box_released)
QtCore.QObject.connect(self.window,QtCore.SIGNAL("mx_boxdeleted"),self.box_image_deleted)
QtCore.QObject.connect(self.window,QtCore.SIGNAL("module_closed"),self.module_closed)
def box_selected(self,event,lc):
if lc == None or lc[0] == None: return
self.moving_box_data = [event.x(),event.y(),lc[0]]
def box_moved(self,event,scale):
winidx = self.moving_box_data[2] % self.numlists
ppidx = int(self.moving_box_data[2]/self.numlists)
if self.moving_box_data:
dx = 0.2*(event.x() - self.moving_box_data[0])
dy = 0.2*(self.moving_box_data[1] - event.y())
self.rctwidget.windowlist[winidx].boxes.move_box(ppidx,dx,dy)
self.rctwidget.windowlist[winidx].update_mainwin()
self.rctwidget.windowlist[winidx].update_particles()
def box_released(self, event,lc):
pass
def box_image_deleted(self,event,lc):
if lc == None or lc[0] == None: return
#delete all particle pairs
ppidx = int(lc[0]/self.numlists)
for i,window in enumerate(self.rctwidget.windowlist):
window.boxes.remove_box(ppidx,self.rctwidget.boxsize)
window.update_mainwin()
window.update_particles()
def module_closed(self):
E2saveappwin("e2rctboxer","particles",self.window.qt_parent)
pass
