def object_picked(self, object_number):
if object_number == self.current_projection: return
self.current_projection = object_number
resize_necessary = False
if self.mx_display == None:
self.mx_display = EMImageMXModule()
QtCore.QObject.connect(self.mx_display,
QtCore.SIGNAL("module_closed"),
self.on_mx_display_closed)
resize_necessary = True
#if self.frc_display == None:
#self.frc_display = EMPlot2DModule()
# QtCore.QObject.connect(self.frc_display,QtCore.SIGNAL("module_closed"),self.on_frc_display_closed)
self.update_display(False)
if resize_necessary:
get_application().show_specific(self.mx_display)
self.mx_display.optimally_resize()
# get_application().show_specific(self.frc_display)
# self.frc_display.optimally_resize()
else:
self.mx_display.updateGL()
# self.frc_display.updateGL()
if object_number != self.special_euler:
self.special_euler = object_number
self.regen_dl()
def object_picked(self,object_number):
if object_number == self.current_projection: return
self.current_projection = object_number
resize_necessary = False
if self.mx_display == None:
self.mx_display = EMImageMXModule()
QtCore.QObject.connect(self.mx_display,QtCore.SIGNAL("module_closed"),self.on_mx_display_closed)
resize_necessary = True
#if self.frc_display == None:
#self.frc_display = EMPlot2DModule()
# QtCore.QObject.connect(self.frc_display,QtCore.SIGNAL("module_closed"),self.on_frc_display_closed)
self.update_display(False)
if resize_necessary:
get_application().show_specific(self.mx_display)
self.mx_display.optimally_resize()
# get_application().show_specific(self.frc_display)
# self.frc_display.optimally_resize()
else:
self.mx_display.updateGL()
# self.frc_display.updateGL()
if object_number != self.special_euler:
self.special_euler = object_number
self.regen_dl()
def set_shrink(self,shrink):
"""This actually loads the data ..."""
self.shrink=shrink
# Deal with particles
n=min(EMUtil.get_image_count(self.particle_file),800)
self.ptcl_data=[i for i in EMData.read_images(self.particle_file,range(n)) if i!=None]
if self.shrink>1 :
for i in self.ptcl_data : i.process_inplace("math.meanshrink",{"n":self.shrink})
for i in self.ptcl_data : i.process_inplace("normalize.edgemean",{})
if self.ptcl_display==None :
self.ptcl_display = EMImageMXModule()
self.ptcl_display.set_mouse_mode("App")
QtCore.QObject.connect(self.ptcl_display,QtCore.SIGNAL("mx_image_selected"),self.ptcl_selected)
QtCore.QObject.connect(self.ptcl_display,QtCore.SIGNAL("module_closed"),self.on_mx_display_closed)
self.ptcl_display.set_data(self.ptcl_data)
# deal with projections
self.proj_data=EMData.read_images(self.projection_file)
if self.shrink>1 :
for i in self.proj_data : i.process_inplace("math.meanshrink",{"n":self.shrink})
for i in self.proj_data : i.process_inplace("normalize.edgemean",{})
eulers = [i["xform.projection"] for i in self.proj_data]
self.specify_eulers(eulers)
for i in self.proj_data : i["cmp"]=0.0
self.set_emdata_list_as_data(self.proj_data,"cmp")
def set_shrink(self, shrink):
"""This actually loads the data ..."""
self.shrink = shrink
# Deal with particles
n = min(EMUtil.get_image_count(self.particle_file), 800)
self.ptcl_data = [
i for i in EMData.read_images(self.particle_file, range(n))
if i != None
]
if self.shrink > 1:
for i in self.ptcl_data:
i.process_inplace("math.meanshrink", {"n": self.shrink})
for i in self.ptcl_data:
i.process_inplace("normalize.edgemean", {})
if self.ptcl_display == None:
self.ptcl_display = EMImageMXModule()
self.ptcl_display.set_mouse_mode("App")
QtCore.QObject.connect(self.ptcl_display,
QtCore.SIGNAL("mx_image_selected"),
self.ptcl_selected)
QtCore.QObject.connect(self.ptcl_display,
QtCore.SIGNAL("module_closed"),
self.on_mx_display_closed)
self.ptcl_display.set_data(self.ptcl_data)
# deal with projections
self.proj_data = EMData.read_images(self.projection_file)
if self.shrink > 1:
for i in self.proj_data:
i.process_inplace("math.meanshrink", {"n": self.shrink})
for i in self.proj_data:
i.process_inplace("normalize.edgemean", {})
eulers = [i["xform.projection"] for i in self.proj_data]
self.specify_eulers(eulers)
for i in self.proj_data:
i["cmp"] = 0.0
self.set_emdata_list_as_data(self.proj_data, "cmp")
class EMCmpExplorer(EM3DSymModel):
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 set_data(self, projections, particles):
'''
Initialize data
'''
if not file_exists(projections):
raise RuntimeError("%s does not exist" % self.projection_file)
if not file_exists(particles):
raise RuntimeError("%s does not exist" % self.particle_file)
self.projection_file = projections # a projection file produced by e2project3d
self.particle_file = particles # A file containing particles to be examined
self.set_shrink(self.shrink)
def set_shrink(self, shrink):
"""This actually loads the data ..."""
self.shrink = shrink
# Deal with particles
n = min(EMUtil.get_image_count(self.particle_file), 800)
self.ptcl_data = [
i for i in EMData.read_images(self.particle_file, range(n))
if i != None
]
if self.shrink > 1:
for i in self.ptcl_data:
i.process_inplace("math.meanshrink", {"n": self.shrink})
for i in self.ptcl_data:
i.process_inplace("normalize.edgemean", {})
if self.ptcl_display == None:
self.ptcl_display = EMImageMXModule()
self.ptcl_display.set_mouse_mode("App")
QtCore.QObject.connect(self.ptcl_display,
QtCore.SIGNAL("mx_image_selected"),
self.ptcl_selected)
QtCore.QObject.connect(self.ptcl_display,
QtCore.SIGNAL("module_closed"),
self.on_mx_display_closed)
self.ptcl_display.set_data(self.ptcl_data)
# deal with projections
self.proj_data = EMData.read_images(self.projection_file)
if self.shrink > 1:
for i in self.proj_data:
i.process_inplace("math.meanshrink", {"n": self.shrink})
for i in self.proj_data:
i.process_inplace("normalize.edgemean", {})
eulers = [i["xform.projection"] for i in self.proj_data]
self.specify_eulers(eulers)
for i in self.proj_data:
i["cmp"] = 0.0
self.set_emdata_list_as_data(self.proj_data, "cmp")
def get_num_particles(self):
if self.ptcl_data == None: return 0
return len(self.ptcl_data)
def render(self):
if self.inspector == None: self.get_inspector()
EM3DSymModel.render(self)
def object_picked(self, object_number):
if object_number == self.current_projection: return
self.current_projection = object_number
resize_necessary = False
if self.mx_display == None:
self.mx_display = EMImageMXModule()
QtCore.QObject.connect(self.mx_display,
QtCore.SIGNAL("module_closed"),
self.on_mx_display_closed)
resize_necessary = True
#if self.frc_display == None:
#self.frc_display = EMPlot2DModule()
# QtCore.QObject.connect(self.frc_display,QtCore.SIGNAL("module_closed"),self.on_frc_display_closed)
self.update_display(False)
if resize_necessary:
get_application().show_specific(self.mx_display)
self.mx_display.optimally_resize()
# get_application().show_specific(self.frc_display)
# self.frc_display.optimally_resize()
else:
self.mx_display.updateGL()
# self.frc_display.updateGL()
if object_number != self.special_euler:
self.special_euler = object_number
self.regen_dl()
def update_display(self, update=True):
'''
Uses self.current_particle and self.current_projection to udpate the self.mx_display
'''
if self.mx_display == None: return
if self.current_particle < 0 or self.current_projection == None: return
dlist = []
dlist.append(self.proj_data[
self.current_projection].copy()) # aligned projection
dlist[0].transform(dlist[0]["ptcl.align2d"])
tmp = dlist[0].process("threshold.notzero")
dlist.append(
self.ptcl_data[self.current_particle].copy()) # original particle
dlist[1].process_inplace("normalize.toimage", {"to": dlist[0]})
dlist.append(self.proj_data[
self.current_projection].copy()) # filtered projection
dlist[2].process_inplace("filter.matchto", {"to": dlist[1]})
dlist[2].mult(tmp)
dlist[2].process_inplace("normalize.toimage", {"to": dlist[1]})
dlist.append(dlist[2].copy()) # particle with projection subtracted
dlist[3].sub(dlist[1])
#dlist.append(self.ptcl_data[self.current_particle].copy()) # same as 1 and 2 above, but with a mask
#tmp=dlist[0].process("threshold.notzero")
#dlist[4].mult(tmp)
#dlist[4].process_inplace("filter.matchto",{"to":dlist[0]})
#dlist[4].mult(tmp)
#dlist[4].process_inplace("normalize.toimage",{"to":dlist[0]})
#dlist.append(dlist[3].copy())
#dlist[5].sub(dlist[0])
self.mx_display.set_data(dlist)
if update: self.mx_display.updateGL()
def on_mx_display_closed(self):
self.mx_display = None
def get_inspector(self):
if not self.inspector:
self.inspector = EMSimmxXplorInspector(self)
return self.inspector
def ptcl_selected(self, event, lc):
"""slot for image selection events from image mx"""
self.set_ptcl_idx(lc[0])
def set_alignment(self, align, aligncmp, refine, refinecmp):
"""sets alignment algorithms and recomputes"""
self.align = str(align)
self.aligncmp = str(aligncmp)
self.refine = str(refine)
self.refinecmp = str(refinecmp)
self.update_align()
def set_ptcl_idx(self, idx):
"""Select the index of the current particle to use for comparisons"""
if self.current_particle != idx:
self.current_particle = idx
self.update_align()
def update_align(self):
if self.current_particle < 0: return
ptcl = self.ptcl_data[self.current_particle]
progress = QtGui.QProgressDialog("Computing alignments", "Abort", 0,
len(self.proj_data), None)
progress.show()
# redetermines particle alignments
# then we can quickly compute a series of different similarity values
aopt = parsemodopt(self.align)
acmp = parsemodopt(self.aligncmp)
ropt = parsemodopt(self.refine)
rcmp = parsemodopt(self.refinecmp)
for i, p in enumerate(self.proj_data):
try:
ali = p.align(aopt[0], ptcl, aopt[1], acmp[0], acmp[1])
if self.refine != "":
ropt[1]["xform.align2d"] = ali["xform.align2d"]
ali = p.align(ropt[0], ptcl, ropt[1], rcmp[0], rcmp[1])
except:
print traceback.print_exc()
QtGui.QMessageBox.warning(None, "Error",
"Problem with alignment parameters")
progress.close()
return
p["ptcl.align2d"] = ali["xform.align2d"]
progress.setValue(i)
QtCore.QCoreApplication.instance().processEvents()
progress.close()
self.update_cmp()
# self.update_display(True)
def set_cmp(self, cmpstring):
"""Select the comparator. Passed as a standard name:attr=value:attr=value string"""
self.simcmp = str(cmpstring)
self.update_cmp()
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)
class EMCmpExplorer(EM3DSymModel):
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 set_data(self,projections,particles):
'''
Initialize data
'''
if not file_exists(projections): raise RuntimeError("%s does not exist" %self.projection_file)
if not file_exists(particles): raise RuntimeError("%s does not exist" %self.particle_file)
self.projection_file = projections # a projection file produced by e2project3d
self.particle_file = particles # A file containing particles to be examined
self.set_shrink(self.shrink)
def set_shrink(self,shrink):
"""This actually loads the data ..."""
self.shrink=shrink
# Deal with particles
n=min(EMUtil.get_image_count(self.particle_file),800)
self.ptcl_data=[i for i in EMData.read_images(self.particle_file,range(n)) if i!=None]
if self.shrink>1 :
for i in self.ptcl_data : i.process_inplace("math.meanshrink",{"n":self.shrink})
for i in self.ptcl_data : i.process_inplace("normalize.edgemean",{})
if self.ptcl_display==None :
self.ptcl_display = EMImageMXModule()
self.ptcl_display.set_mouse_mode("App")
QtCore.QObject.connect(self.ptcl_display,QtCore.SIGNAL("mx_image_selected"),self.ptcl_selected)
QtCore.QObject.connect(self.ptcl_display,QtCore.SIGNAL("module_closed"),self.on_mx_display_closed)
self.ptcl_display.set_data(self.ptcl_data)
# deal with projections
self.proj_data=EMData.read_images(self.projection_file)
if self.shrink>1 :
for i in self.proj_data : i.process_inplace("math.meanshrink",{"n":self.shrink})
for i in self.proj_data : i.process_inplace("normalize.edgemean",{})
eulers = [i["xform.projection"] for i in self.proj_data]
self.specify_eulers(eulers)
for i in self.proj_data : i["cmp"]=0.0
self.set_emdata_list_as_data(self.proj_data,"cmp")
def get_num_particles(self):
if self.ptcl_data==None : return 0
return len(self.ptcl_data)
def render(self):
if self.inspector == None: self.get_inspector()
EM3DSymModel.render(self)
def object_picked(self,object_number):
if object_number == self.current_projection: return
self.current_projection = object_number
resize_necessary = False
if self.mx_display == None:
self.mx_display = EMImageMXModule()
QtCore.QObject.connect(self.mx_display,QtCore.SIGNAL("module_closed"),self.on_mx_display_closed)
resize_necessary = True
#if self.frc_display == None:
#self.frc_display = EMPlot2DModule()
# QtCore.QObject.connect(self.frc_display,QtCore.SIGNAL("module_closed"),self.on_frc_display_closed)
self.update_display(False)
if resize_necessary:
get_application().show_specific(self.mx_display)
self.mx_display.optimally_resize()
# get_application().show_specific(self.frc_display)
# self.frc_display.optimally_resize()
else:
self.mx_display.updateGL()
# self.frc_display.updateGL()
if object_number != self.special_euler:
self.special_euler = object_number
self.regen_dl()
def update_display(self,update=True):
'''
Uses self.current_particle and self.current_projection to udpate the self.mx_display
'''
if self.mx_display == None : return
if self.current_particle<0 or self.current_projection==None : return
dlist=[]
dlist.append(self.proj_data[self.current_projection].copy()) # aligned projection
dlist[0].transform(dlist[0]["ptcl.align2d"])
tmp=dlist[0].process("threshold.notzero")
dlist.append(self.ptcl_data[self.current_particle].copy()) # original particle
dlist[1].process_inplace("normalize.toimage",{"to":dlist[0]})
dlist.append(self.proj_data[self.current_projection].copy()) # filtered projection
dlist[2].process_inplace("filter.matchto",{"to":dlist[1]})
dlist[2].mult(tmp)
dlist[2].process_inplace("normalize.toimage",{"to":dlist[1]})
dlist.append(dlist[2].copy()) # particle with projection subtracted
dlist[3].sub(dlist[1])
#dlist.append(self.ptcl_data[self.current_particle].copy()) # same as 1 and 2 above, but with a mask
#tmp=dlist[0].process("threshold.notzero")
#dlist[4].mult(tmp)
#dlist[4].process_inplace("filter.matchto",{"to":dlist[0]})
#dlist[4].mult(tmp)
#dlist[4].process_inplace("normalize.toimage",{"to":dlist[0]})
#dlist.append(dlist[3].copy())
#dlist[5].sub(dlist[0])
self.mx_display.set_data(dlist)
if update: self.mx_display.updateGL()
def on_mx_display_closed(self):
self.mx_display = None
def get_inspector(self):
if not self.inspector :
self.inspector=EMSimmxXplorInspector(self)
return self.inspector
def ptcl_selected(self,event,lc):
"""slot for image selection events from image mx"""
self.set_ptcl_idx(lc[0])
def set_alignment(self,align,aligncmp,refine,refinecmp):
"""sets alignment algorithms and recomputes"""
self.align = str(align)
self.aligncmp = str(aligncmp)
self.refine = str(refine)
self.refinecmp = str(refinecmp)
self.update_align()
def set_ptcl_idx(self,idx):
"""Select the index of the current particle to use for comparisons"""
if self.current_particle != idx:
self.current_particle = idx
self.update_align()
def update_align(self):
if self.current_particle<0 : return
ptcl=self.ptcl_data[self.current_particle]
progress = QtGui.QProgressDialog("Computing alignments", "Abort", 0, len(self.proj_data),None)
progress.show()
# redetermines particle alignments
# then we can quickly compute a series of different similarity values
aopt=parsemodopt(self.align)
acmp=parsemodopt(self.aligncmp)
ropt=parsemodopt(self.refine)
rcmp=parsemodopt(self.refinecmp)
for i,p in enumerate(self.proj_data):
try:
ali=p.align(aopt[0],ptcl,aopt[1],acmp[0],acmp[1])
if self.refine!="" :
ropt[1]["xform.align2d"]=ali["xform.align2d"]
ali=p.align(ropt[0],ptcl,ropt[1],rcmp[0],rcmp[1])
except:
print traceback.print_exc()
QtGui.QMessageBox.warning(None,"Error","Problem with alignment parameters")
progress.close()
return
p["ptcl.align2d"]=ali["xform.align2d"]
progress.setValue(i)
QtCore.QCoreApplication.instance().processEvents()
progress.close()
self.update_cmp()
# self.update_display(True)
def set_cmp(self,cmpstring):
"""Select the comparator. Passed as a standard name:attr=value:attr=value string"""
self.simcmp=str(cmpstring)
self.update_cmp()
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)
