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
class GUIBoxer(QtGui.QWidget):
# Dictionary of autopickers
# to add a new one, provide name:(Qt_setup_function,picker_execution_function)
# Qt_setup_function(self,empty_grid_layout)
# picker_execution_function(self,...
aboxmodes = [ ("by Ref","auto_ref",boxerByRef), ("Gauss","auto_gauss",boxerGauss) ]
boxcolors = { "selected":(0.9,0.9,0.9), "manual":(0,0,0), "refgood":(0,0.8,0), "refbad":(0.8,0,0), "unknown":[.4,.4,.1], "auto_ref":(.1,.1,.4), "auto_gauss":(.4,.1,.4) }
def __init__(self,imagenames,voltage=None,apix=None,cs=None,ac=10.0,box=256,ptcl=200):
"""The 'new' e2boxer interface.
"""
QtGui.QWidget.__init__(self,None)
# self.setWindowIcon(QtGui.QIcon(get_image_directory() + "ctf.png"))
self.data=None
self.curfilename = None # current selected file for boxing
self.filenames=imagenames # list of available filenames
self.micrograph=None
self.boxes=None
self.defaultvoltage=voltage
self.defaultapix=apix
self.defaultcs=cs
self.defaultac=ac
self.db = None # open JSON file for current image
self.wimage=EMImage2DWidget()
self.wimage.setWindowTitle("Micrograph")
self.wparticles=EMImageMXWidget()
self.wparticles.setWindowTitle("Particles")
self.wrefs=EMImageMXWidget()
self.wrefs.setWindowTitle("Box Refs")
self.wbadrefs=EMImageMXWidget()
self.wbadrefs.setWindowTitle("Bad Box Refs")
#self.wfft=EMImage2DWidget()
#self.wfft.setWindowTitle("e2evalimage - 2D FFT")
#self.wplot=EMPlot2DWidget()
#self.wplot.setWindowTitle("e2evalimage - Plot")
self.wimage.connect(self.wimage,QtCore.SIGNAL("mousedown"),self.imgmousedown)
self.wimage.connect(self.wimage,QtCore.SIGNAL("mousedrag"),self.imgmousedrag)
self.wimage.connect(self.wimage,QtCore.SIGNAL("mouseup") ,self.imgmouseup)
self.wparticles.connect(self.wparticles,QtCore.SIGNAL("mousedown"),self.ptclmousedown)
self.wparticles.connect(self.wparticles,QtCore.SIGNAL("mousedrag"),self.ptclmousedrag)
self.wparticles.connect(self.wparticles,QtCore.SIGNAL("mouseup") ,self.ptclmouseup)
self.wrefs.connect(self.wparticles,QtCore.SIGNAL("mousedown"),self.refmousedown)
self.wrefs.connect(self.wparticles,QtCore.SIGNAL("mousedrag"),self.refmousedrag)
self.wrefs.connect(self.wparticles,QtCore.SIGNAL("mouseup") ,self.refmouseup)
self.wimage.mmode="app"
self.wparticles.mmode="app"
# This object is itself a widget we need to set up
self.gbl = QtGui.QGridLayout(self)
self.gbl.setMargin(8)
self.gbl.setSpacing(6)
# Micrograph list
self.setlist=QtGui.QListWidget(self)
self.setlist.setSizePolicy(QtGui.QSizePolicy.Preferred,QtGui.QSizePolicy.Expanding)
for i in imagenames:
self.setlist.addItem(i)
self.gbl.addWidget(self.setlist,0,0,12,2)
self.setlist.connect(self.setlist,QtCore.SIGNAL("currentRowChanged(int)"),self.newSet)
self.setlist.connect(self.setlist,QtCore.SIGNAL("keypress"),self.listKey)
# Mouse Modes
self.mmode="manual"
self.boxmm=QtGui.QGroupBox("Mouse Mode",self)
self.boxmm.setFlat(False)
self.gbl.addWidget(self.boxmm,0,2,3,2)
self.hbl0=QtGui.QHBoxLayout(self.boxmm)
self.bmmanual=QtGui.QPushButton("Manual")
self.bmmanual.setToolTip("Manual selection of particles. No impact on autoselection.")
self.bmmanual.setAutoExclusive(True)
self.bmmanual.setCheckable(True)
self.bmmanual.setChecked(True)
self.hbl0.addWidget(self.bmmanual)
self.bmdel=QtGui.QPushButton("Delete")
self.bmdel.setToolTip("Delete particles from any mode. Can also shift-click in other mouse modes.")
self.bmdel.setAutoExclusive(True)
self.bmdel.setCheckable(True)
self.hbl0.addWidget(self.bmdel)
self.bmgref=QtGui.QPushButton("Good Refs")
self.bmgref.setToolTip("Identify some good particles. Available to all autoboxers.")
self.bmgref.setAutoExclusive(True)
self.bmgref.setCheckable(True)
self.hbl0.addWidget(self.bmgref)
self.bmbref=QtGui.QPushButton("Bad Refs")
self.bmbref.setToolTip("Identify regions which should not be selected as particles.")
self.bmbref.setAutoExclusive(True)
self.bmbref.setCheckable(True)
self.hbl0.addWidget(self.bmbref)
QtCore.QObject.connect(self.bmmanual,QtCore.SIGNAL("clicked(bool)"),self.setMouseManual)
QtCore.QObject.connect(self.bmdel,QtCore.SIGNAL("clicked(bool)"),self.setMouseDel)
QtCore.QObject.connect(self.bmgref,QtCore.SIGNAL("clicked(bool)"),self.setMouseGoodRef)
QtCore.QObject.connect(self.bmbref,QtCore.SIGNAL("clicked(bool)"),self.setMouseBadRef)
# Global parameters
self.boxparm=QtGui.QGroupBox("Parameters",self)
self.boxparm.setFlat(False)
self.gbl.addWidget(self.boxparm,3,2,3,3)
self.gbl1=QtGui.QGridLayout(self.boxparm)
self.gbl1.setMargin(8)
self.gbl1.setSpacing(6)
self.vbbsize = ValBox(label="Box Size:",value=box)
self.gbl1.addWidget(self.vbbsize,0,0)
self.vbbpsize = ValBox(label="Ptcl Size:",value=ptcl)
self.gbl1.addWidget(self.vbbpsize,0,1)
self.vbbapix = ValBox(label="A/pix:",value=apix)
self.gbl1.addWidget(self.vbbapix,0,2)
self.vbvoltage = ValBox(label="Voltage:",value=voltage)
self.gbl1.addWidget(self.vbvoltage,1,0)
self.vbbac = ValBox(label="% AC:",value=ac)
self.gbl1.addWidget(self.vbbac,1,1)
self.vbcs = ValBox(label="Cs:",value=cs)
self.gbl1.addWidget(self.vbcs,1,2)
# Autoboxing Tabs
self.autolbl = QtGui.QLabel("Autoboxing Methods:")
self.gbl.addWidget(self.autolbl,7,2)
self.autotab = QtGui.QTabWidget()
self.gbl.addWidget(self.autotab,8,2,6,3)
self.bautobox = QtGui.QPushButton("Autobox")
self.gbl.addWidget(self.bautobox,7,4)
QtCore.QObject.connect(self.bautobox,QtCore.SIGNAL("clicked(bool)"),self.doAutoBox)
# Individual tabs from Dictionary
self.abwid=[]
for name,bname,cls in GUIBoxer.aboxmodes:
w=QtGui.QWidget()
gl=QtGui.QGridLayout(w)
self.abwid.append((w,gl))
cls.setup_gui(gl)
self.autotab.addTab(w,name)
self.setWindowTitle("e2boxer21 - Control Panel")
self.wimage.show()
# self.wfft.show()
# self.wplot.show()
E2loadappwin("e2boxer21","main",self)
E2loadappwin("e2boxer21","image",self.wimage.qt_parent)
E2loadappwin("e2boxer21","particles",self.wparticles.qt_parent)
E2loadappwin("e2boxer21","refs",self.wrefs.qt_parent)
E2loadappwin("e2boxer21","badrefs",self.wbadrefs.qt_parent)
self.newSet(0)
#QWidget *firstPageWidget = new QWidget;
#QWidget *secondPageWidget = new QWidget;
#QWidget *thirdPageWidget = new QWidget;
#QStackedWidget *stackedWidget = new QStackedWidget;
#stackedWidget->addWidget(firstPageWidget);
#stackedWidget->addWidget(secondPageWidget);
#stackedWidget->addWidget(thirdPageWidget);
#QVBoxLayout *layout = new QVBoxLayout;
#layout->addWidget(stackedWidget);
#setLayout(layout);
#QComboBox *pageComboBox = new QComboBox;
#pageComboBox->addItem(tr("Page 1"));
#pageComboBox->addItem(tr("Page 2"));
#pageComboBox->addItem(tr("Page 3"));
#connect(pageComboBox, SIGNAL(activated(int)),stackedWidget, SLOT(setCurrentIndex(int)));
#self.lboxmode=QtGui.QLabel("Mode:",self)
#self.gbl.addWidget(self.lboxmode,10,0)
#self.sboxmode=QtGui.QComboBox(self)
#self.sboxmode.addItem("Manual")
#self.sboxmode.addItem("Reference")
#self.sboxmode.setCurrentIndex(1)
#self.gbl.addWidget(self.sboxmode,10,1)
#self.lanmode=QtGui.QLabel("Annotate:",self)
#self.gbl.addWidget(self.lanmode,12,0)
#self.sanmode=QtGui.QComboBox(self)
#self.sanmode.addItem("Box")
#self.sanmode.addItem("Box+dot")
#self.sanmode.addItem("Circle")
#self.sanmode.addItem("None")
#self.gbl.addWidget(self.sanmode,12,1)
#self.sdefocus=ValSlider(self,(0,5),"Defocus:",0.0,90)
#self.gbl.addWidget(self.sdefocus,0,2,1,3)
#self.squality=ValSlider(self,(0,9),"Quality (0-9):",0,90)
#self.squality.setIntonly(True)
#self.gbl.addWidget(self.squality,6,2,1,3)
#self.brefit=QtGui.QPushButton("Autobox")
#self.gbl.addWidget(self.brefit,7,2)
#self.bclrauto=QtGui.QPushButton("Clear Auto")
#self.gbl.addWidget(self.bclrauto,7,3)
#self.bclrall=QtGui.QPushButton("Clear All")
#self.gbl.addWidget(self.bclrall,7,4)
#self.sapix=ValBox(self,(0,500),"A/pix:",1.0,90)
#if self.defaultapix!=None : self.sapix.setValue(self.defaultapix)
#self.gbl.addWidget(self.sapix,10,2)
#self.svoltage=ValBox(self,(0,500),"Voltage (kV):",200,90)
#if self.defaultvoltage!=None : self.svoltage.setValue(self.defaultvoltage)
#self.gbl.addWidget(self.svoltage,11,2)
#self.scs=ValBox(self,(0,5),"Cs (mm):",4.1,90)
#if self.defaultcs!=None : self.scs.setValue(self.defaultcs)
#self.gbl.addWidget(self.scs,12,2)
#self.sboxsize=ValBox(self,(0,500),"Box Size:",256,90)
#self.sboxsize.intonly=True
#self.gbl.addWidget(self.sboxsize,13,2)
#self.sptclsize=ValBox(self,(0,500),"Ptcl Size:",256,90)
#self.sptclsize.intonly=True
#self.gbl.addWidget(self.sptclsize,14,2)
#QtCore.QObject.connect(self.sdefocus, QtCore.SIGNAL("valueChanged"), self.newCTF)
#QtCore.QObject.connect(self.sapix, QtCore.SIGNAL("valueChanged"), self.newCTF)
#QtCore.QObject.connect(self.svoltage, QtCore.SIGNAL("valueChanged"), self.newCTF)
#QtCore.QObject.connect(self.scs, QtCore.SIGNAL("valueChanged"), self.newCTF)
#QtCore.QObject.connect(self.sboxsize, QtCore.SIGNAL("valueChanged"), self.newBox)
## QtCore.QObject.connect(self.soversamp, QtCore.SIGNAL("valueChanged"), self.newBox)
#QtCore.QObject.connect(self.squality,QtCore.SIGNAL("valueChanged"),self.newQualityFactor)
#QtCore.QObject.connect(self.setlist,QtCore.SIGNAL("currentRowChanged(int)"),self.newSet)
#QtCore.QObject.connect(self.setlist,QtCore.SIGNAL("keypress"),self.listkey)
#QtCore.QObject.connect(self.sboxmode,QtCore.SIGNAL("currentIndexChanged(int)"),self.newBoxMode)
#self.resize(720,380) # figured these values out by printing the width and height in resize event
#### This section is responsible for background updates
#self.busy=False
#self.needupdate=True
#self.needredisp=False
#self.procthread=None
#self.errors=None # used to communicate errors back from the reprocessing thread
#self.timer=QTimer()
#QtCore.QObject.connect(self.timer, QtCore.SIGNAL("timeout()"), self.timeOut)
#self.timer.start(100)
# self.recalc()
def setMouseManual(self,x):
self.mmode="manual"
def setMouseDel(self,x):
self.mmode="del"
def setMouseGoodRef(self,x):
self.mmode="refgood"
def setMouseBadRef(self,x):
self.mmode="refbad"
def imgmousedown(self,event) :
m=self.wimage.scr_to_img((event.x(),event.y()))
boxsize2=self.vbbsize.getValue()//2
ptclsize=self.vbbpsize.getValue()
self.curbox=0
# check to see if click was inside an existing box, in which case we move it
for i in self.boxes:
if abs(m.x-i[0])<boxsize2 and abs(m.y-i[1])<boxsize2 :
self.curbox=i
break
else :
# Create a new box
if self.mmode=="del" : return # This is for creating a new box, so clearly not desirable in delete mode
self.curbox=len(self.boxes)
self.boxes.append((m[0],m[1],self.mmode))
self.__addBox(self.curbox,self.boxes[-1])
#self.guiim.add_shape("cen",["rect",.9,.9,.4,x0,y0,x0+2,y0+2,1.0])
def imgmousedrag(self,event) :
if self.calcmode==0:
m=self.wimage.scr_to_img((event.x(),event.y()))
parms=self.parms[self.curset]
parms[2]=(m[0]-parms[0]/2,m[1]-parms[0]/2)
self.needredisp=True
self.recalc()
# box deletion when shift held down
#if event.modifiers()&Qt.ShiftModifier:
#for i,j in enumerate(self.boxes):
def imgmouseup(self,event) :
m=self.wimage.scr_to_img((event.x(),event.y()))
if self.calcmode==1:
parms=self.parms[self.curset]
nx=self.data["nx"]/parms[0]-1
grid=int((m[0]-parms[0]/2)/parms[0])+int((m[1]-parms[0]/2)/parms[0])*nx
if grid in parms[3] : parms[3].remove(grid)
else: parms[3].add(grid)
self.needredisp=True
self.recalc()
def ptclmousedown(self,event) :
return
def ptclmousedrag(self,event) :
return
def ptclmouseup(self,event) :
return
def refmousedown(self,event) :
return
def refmousedrag(self,event) :
return
def refmouseup(self,event) :
return
def newSet(self,val):
"called when a new data set is selected from the list"
first=True
newfilename=str(self.setlist.item(val).text())
if newfilename==self.curfilename : return
# Write the current image parameters to the database
if self.curfilename!=None and self.boxes!=None :
self.save_boxes()
first=False
self.micrograph=load_micrograph(newfilename)
self.wimage.set_data(self.micrograph)
if first : E2loadappwin("e2boxer21","image",self.wimage.qt_parent)
self.curfilename=newfilename
self.restore_boxes()
def save_boxes(self):
js=js_open_dict(info_name(self.curfilename))
js["boxes"]=self.boxes
def restore_boxes(self):
# first we restore the list of box locations
js=js_open_dict(info_name(self.curfilename))
try: self.boxes=js["boxes"]
except: self.boxes=[]
boxsize=self.vbbsize.getValue()
ptclsize=self.vbbpsize.getValue()
micro=self.wimage.get_data()
self.wimage.del_shapes()
if len(self.boxes)==0 :
self.wparticles.set_data([])
return
# Then we extract the actual boxed out particles
goodrefs=[]
badrefs=[]
self.particles=[]
for i,box in enumerate(self.boxes):
self.__addBox(i,box)
# extract the data
boxim=self.micrograph.get_clip(Region(box[0]-boxsize//2,box[1]-boxsize//2,boxsize,boxsize))
boxim["ptcl_source_coord"]=(box[0],box[1])
if box[2]=="refgood":
goodrefs.append(boxim)
elif box[2]=="refbad":
badrefs.append(boxim)
else:
self.particles.append(boxim)
# finally redisplay as appropriate
self.wimage.update()
self.wparticles.set_data(self.particles)
if len(self.particles)>0 : self.wparticles.show()
if len(goodrefs)+len(badrefs)!=0:
self.goodrefs=goodrefs
self.badrefs=badrefs
self.wrefs.set_data(self.goodrefs)
self.wbadrefs.set_data(self.badrefs)
if len(self.goodrefs)>0 : self.wrefs.show()
if len(self.badrefs)>0 : self.wbadrefs.show()
def __addBox(self,i,box):
"""takes the number of the box in self.boxes and the (x,y,mode) tuple and displays it"""
# Display the actual box
boxsize=self.vbbsize.getValue()
ptclsize=self.vbbpsize.getValue()
try: color=self.boxcolors[box[2]]
except: color=self.boxcolors["unknown"]
self.wimage.add_shape("box{}".format(i),EMShape(("rect",color[0],color[1],color[2],box[0]-boxsize//2,box[1]-boxsize//2,box[0]+boxsize//2,box[1]+boxsize//2,2)))
self.wimage.add_shape("cir{}".format(i),EMShape(("circle",color[0],color[1],color[2],box[0],box[1],ptclsize/2,1.5)))
def listKey(self,event):
pass
#if event.key()>=Qt.Key_0 and event.key()<=Qt.Key_9 :
#q=int(event.key())-Qt.Key_0
#self.squality.setValue(q)
#elif event.key() == Qt.Key_Left:
#self.sdefocus.setValue(self.sdefocus.getValue()-0.03)
#elif event.key() == Qt.Key_Right:
#self.sdefocus.setValue(self.sdefocus.getValue()+0.03)
#elif event.key()==Qt.Key_I :
#self.doImport()
#elif event.key()==Qt.Key_U :
#self.unImport()
def doAutoBox(self,b):
"""Autobox button pressed, find the right algorithm and call it"""
name,bname,fn1=self.aboxmodes[self.autotab.currentIndex()]
print name," called"
def closeEvent(self,event):
# QtGui.QWidget.closeEvent(self,event)
E2saveappwin("e2boxer21","main",self)
E2saveappwin("e2boxer21","image",self.wimage.qt_parent)
E2saveappwin("e2boxer21","particles",self.wparticles.qt_parent)
E2saveappwin("e2boxer21","refs",self.wrefs.qt_parent)
E2saveappwin("e2boxer21","badrefs",self.wbadrefs.qt_parent)
#self.writeCurParm()
event.accept()
QtGui.qApp.exit(0)
class GUIBoxer(QtGui.QWidget):
# Dictionary of autopickers
# to add a new one, provide name:(Qt_setup_function,picker_execution_function)
# Qt_setup_function(self,empty_grid_layout)
# picker_execution_function(self,...
aboxmodes = [("by Ref", "auto_ref", boxerByRef),
("Gauss", "auto_gauss", boxerGauss)]
boxcolors = {
"selected": (0.9, 0.9, 0.9),
"manual": (0, 0, 0),
"refgood": (0, 0.8, 0),
"refbad": (0.8, 0, 0),
"unknown": [.4, .4, .1],
"auto_ref": (.1, .1, .4),
"auto_gauss": (.4, .1, .4)
}
def __init__(self,
imagenames,
voltage=None,
apix=None,
cs=None,
ac=10.0,
box=256,
ptcl=200):
"""The 'new' e2boxer interface.
"""
QtGui.QWidget.__init__(self, None)
# self.setWindowIcon(QtGui.QIcon(get_image_directory() + "ctf.png"))
self.data = None
self.curfilename = None # current selected file for boxing
self.filenames = imagenames # list of available filenames
self.micrograph = None
self.boxes = None
self.defaultvoltage = voltage
self.defaultapix = apix
self.defaultcs = cs
self.defaultac = ac
self.db = None # open JSON file for current image
self.wimage = EMImage2DWidget()
self.wimage.setWindowTitle("Micrograph")
self.wparticles = EMImageMXWidget()
self.wparticles.setWindowTitle("Particles")
self.wrefs = EMImageMXWidget()
self.wrefs.setWindowTitle("Box Refs")
self.wbadrefs = EMImageMXWidget()
self.wbadrefs.setWindowTitle("Bad Box Refs")
#self.wfft=EMImage2DWidget()
#self.wfft.setWindowTitle("e2evalimage - 2D FFT")
#self.wplot=EMPlot2DWidget()
#self.wplot.setWindowTitle("e2evalimage - Plot")
self.wimage.connect(self.wimage, QtCore.SIGNAL("mousedown"),
self.imgmousedown)
self.wimage.connect(self.wimage, QtCore.SIGNAL("mousedrag"),
self.imgmousedrag)
self.wimage.connect(self.wimage, QtCore.SIGNAL("mouseup"),
self.imgmouseup)
self.wparticles.connect(self.wparticles, QtCore.SIGNAL("mousedown"),
self.ptclmousedown)
self.wparticles.connect(self.wparticles, QtCore.SIGNAL("mousedrag"),
self.ptclmousedrag)
self.wparticles.connect(self.wparticles, QtCore.SIGNAL("mouseup"),
self.ptclmouseup)
self.wrefs.connect(self.wparticles, QtCore.SIGNAL("mousedown"),
self.refmousedown)
self.wrefs.connect(self.wparticles, QtCore.SIGNAL("mousedrag"),
self.refmousedrag)
self.wrefs.connect(self.wparticles, QtCore.SIGNAL("mouseup"),
self.refmouseup)
self.wimage.mmode = "app"
self.wparticles.mmode = "app"
# This object is itself a widget we need to set up
self.gbl = QtGui.QGridLayout(self)
self.gbl.setMargin(8)
self.gbl.setSpacing(6)
# Micrograph list
self.setlist = QtGui.QListWidget(self)
self.setlist.setSizePolicy(QtGui.QSizePolicy.Preferred,
QtGui.QSizePolicy.Expanding)
for i in imagenames:
self.setlist.addItem(i)
self.gbl.addWidget(self.setlist, 0, 0, 12, 2)
self.setlist.connect(self.setlist,
QtCore.SIGNAL("currentRowChanged(int)"),
self.newSet)
self.setlist.connect(self.setlist, QtCore.SIGNAL("keypress"),
self.listKey)
# Mouse Modes
self.mmode = "manual"
self.boxmm = QtGui.QGroupBox("Mouse Mode", self)
self.boxmm.setFlat(False)
self.gbl.addWidget(self.boxmm, 0, 2, 3, 2)
self.hbl0 = QtGui.QHBoxLayout(self.boxmm)
self.bmmanual = QtGui.QPushButton("Manual")
self.bmmanual.setToolTip(
"Manual selection of particles. No impact on autoselection.")
self.bmmanual.setAutoExclusive(True)
self.bmmanual.setCheckable(True)
self.bmmanual.setChecked(True)
self.hbl0.addWidget(self.bmmanual)
self.bmdel = QtGui.QPushButton("Delete")
self.bmdel.setToolTip(
"Delete particles from any mode. Can also shift-click in other mouse modes."
)
self.bmdel.setAutoExclusive(True)
self.bmdel.setCheckable(True)
self.hbl0.addWidget(self.bmdel)
self.bmgref = QtGui.QPushButton("Good Refs")
self.bmgref.setToolTip(
"Identify some good particles. Available to all autoboxers.")
self.bmgref.setAutoExclusive(True)
self.bmgref.setCheckable(True)
self.hbl0.addWidget(self.bmgref)
self.bmbref = QtGui.QPushButton("Bad Refs")
self.bmbref.setToolTip(
"Identify regions which should not be selected as particles.")
self.bmbref.setAutoExclusive(True)
self.bmbref.setCheckable(True)
self.hbl0.addWidget(self.bmbref)
QtCore.QObject.connect(self.bmmanual, QtCore.SIGNAL("clicked(bool)"),
self.setMouseManual)
QtCore.QObject.connect(self.bmdel, QtCore.SIGNAL("clicked(bool)"),
self.setMouseDel)
QtCore.QObject.connect(self.bmgref, QtCore.SIGNAL("clicked(bool)"),
self.setMouseGoodRef)
QtCore.QObject.connect(self.bmbref, QtCore.SIGNAL("clicked(bool)"),
self.setMouseBadRef)
# Global parameters
self.boxparm = QtGui.QGroupBox("Parameters", self)
self.boxparm.setFlat(False)
self.gbl.addWidget(self.boxparm, 3, 2, 3, 3)
self.gbl1 = QtGui.QGridLayout(self.boxparm)
self.gbl1.setMargin(8)
self.gbl1.setSpacing(6)
self.vbbsize = ValBox(label="Box Size:", value=box)
self.gbl1.addWidget(self.vbbsize, 0, 0)
self.vbbpsize = ValBox(label="Ptcl Size:", value=ptcl)
self.gbl1.addWidget(self.vbbpsize, 0, 1)
self.vbbapix = ValBox(label="A/pix:", value=apix)
self.gbl1.addWidget(self.vbbapix, 0, 2)
self.vbvoltage = ValBox(label="Voltage:", value=voltage)
self.gbl1.addWidget(self.vbvoltage, 1, 0)
self.vbbac = ValBox(label="% AC:", value=ac)
self.gbl1.addWidget(self.vbbac, 1, 1)
self.vbcs = ValBox(label="Cs:", value=cs)
self.gbl1.addWidget(self.vbcs, 1, 2)
# Autoboxing Tabs
self.autolbl = QtGui.QLabel("Autoboxing Methods:")
self.gbl.addWidget(self.autolbl, 7, 2)
self.autotab = QtGui.QTabWidget()
self.gbl.addWidget(self.autotab, 8, 2, 6, 3)
self.bautobox = QtGui.QPushButton("Autobox")
self.gbl.addWidget(self.bautobox, 7, 4)
QtCore.QObject.connect(self.bautobox, QtCore.SIGNAL("clicked(bool)"),
self.doAutoBox)
# Individual tabs from Dictionary
self.abwid = []
for name, bname, cls in GUIBoxer.aboxmodes:
w = QtGui.QWidget()
gl = QtGui.QGridLayout(w)
self.abwid.append((w, gl))
cls.setup_gui(gl)
self.autotab.addTab(w, name)
self.setWindowTitle("e2boxer21 - Control Panel")
self.wimage.show()
# self.wfft.show()
# self.wplot.show()
E2loadappwin("e2boxer21", "main", self)
E2loadappwin("e2boxer21", "image", self.wimage.qt_parent)
E2loadappwin("e2boxer21", "particles", self.wparticles.qt_parent)
E2loadappwin("e2boxer21", "refs", self.wrefs.qt_parent)
E2loadappwin("e2boxer21", "badrefs", self.wbadrefs.qt_parent)
self.newSet(0)
#QWidget *firstPageWidget = new QWidget;
#QWidget *secondPageWidget = new QWidget;
#QWidget *thirdPageWidget = new QWidget;
#QStackedWidget *stackedWidget = new QStackedWidget;
#stackedWidget->addWidget(firstPageWidget);
#stackedWidget->addWidget(secondPageWidget);
#stackedWidget->addWidget(thirdPageWidget);
#QVBoxLayout *layout = new QVBoxLayout;
#layout->addWidget(stackedWidget);
#setLayout(layout);
#QComboBox *pageComboBox = new QComboBox;
#pageComboBox->addItem(tr("Page 1"));
#pageComboBox->addItem(tr("Page 2"));
#pageComboBox->addItem(tr("Page 3"));
#connect(pageComboBox, SIGNAL(activated(int)),stackedWidget, SLOT(setCurrentIndex(int)));
#self.lboxmode=QtGui.QLabel("Mode:",self)
#self.gbl.addWidget(self.lboxmode,10,0)
#self.sboxmode=QtGui.QComboBox(self)
#self.sboxmode.addItem("Manual")
#self.sboxmode.addItem("Reference")
#self.sboxmode.setCurrentIndex(1)
#self.gbl.addWidget(self.sboxmode,10,1)
#self.lanmode=QtGui.QLabel("Annotate:",self)
#self.gbl.addWidget(self.lanmode,12,0)
#self.sanmode=QtGui.QComboBox(self)
#self.sanmode.addItem("Box")
#self.sanmode.addItem("Box+dot")
#self.sanmode.addItem("Circle")
#self.sanmode.addItem("None")
#self.gbl.addWidget(self.sanmode,12,1)
#self.sdefocus=ValSlider(self,(0,5),"Defocus:",0.0,90)
#self.gbl.addWidget(self.sdefocus,0,2,1,3)
#self.squality=ValSlider(self,(0,9),"Quality (0-9):",0,90)
#self.squality.setIntonly(True)
#self.gbl.addWidget(self.squality,6,2,1,3)
#self.brefit=QtGui.QPushButton("Autobox")
#self.gbl.addWidget(self.brefit,7,2)
#self.bclrauto=QtGui.QPushButton("Clear Auto")
#self.gbl.addWidget(self.bclrauto,7,3)
#self.bclrall=QtGui.QPushButton("Clear All")
#self.gbl.addWidget(self.bclrall,7,4)
#self.sapix=ValBox(self,(0,500),"A/pix:",1.0,90)
#if self.defaultapix!=None : self.sapix.setValue(self.defaultapix)
#self.gbl.addWidget(self.sapix,10,2)
#self.svoltage=ValBox(self,(0,500),"Voltage (kV):",200,90)
#if self.defaultvoltage!=None : self.svoltage.setValue(self.defaultvoltage)
#self.gbl.addWidget(self.svoltage,11,2)
#self.scs=ValBox(self,(0,5),"Cs (mm):",4.1,90)
#if self.defaultcs!=None : self.scs.setValue(self.defaultcs)
#self.gbl.addWidget(self.scs,12,2)
#self.sboxsize=ValBox(self,(0,500),"Box Size:",256,90)
#self.sboxsize.intonly=True
#self.gbl.addWidget(self.sboxsize,13,2)
#self.sptclsize=ValBox(self,(0,500),"Ptcl Size:",256,90)
#self.sptclsize.intonly=True
#self.gbl.addWidget(self.sptclsize,14,2)
#QtCore.QObject.connect(self.sdefocus, QtCore.SIGNAL("valueChanged"), self.newCTF)
#QtCore.QObject.connect(self.sapix, QtCore.SIGNAL("valueChanged"), self.newCTF)
#QtCore.QObject.connect(self.svoltage, QtCore.SIGNAL("valueChanged"), self.newCTF)
#QtCore.QObject.connect(self.scs, QtCore.SIGNAL("valueChanged"), self.newCTF)
#QtCore.QObject.connect(self.sboxsize, QtCore.SIGNAL("valueChanged"), self.newBox)
## QtCore.QObject.connect(self.soversamp, QtCore.SIGNAL("valueChanged"), self.newBox)
#QtCore.QObject.connect(self.squality,QtCore.SIGNAL("valueChanged"),self.newQualityFactor)
#QtCore.QObject.connect(self.setlist,QtCore.SIGNAL("currentRowChanged(int)"),self.newSet)
#QtCore.QObject.connect(self.setlist,QtCore.SIGNAL("keypress"),self.listkey)
#QtCore.QObject.connect(self.sboxmode,QtCore.SIGNAL("currentIndexChanged(int)"),self.newBoxMode)
#self.resize(720,380) # figured these values out by printing the width and height in resize event
#### This section is responsible for background updates
#self.busy=False
#self.needupdate=True
#self.needredisp=False
#self.procthread=None
#self.errors=None # used to communicate errors back from the reprocessing thread
#self.timer=QTimer()
#QtCore.QObject.connect(self.timer, QtCore.SIGNAL("timeout()"), self.timeOut)
#self.timer.start(100)
# self.recalc()
def setMouseManual(self, x):
self.mmode = "manual"
def setMouseDel(self, x):
self.mmode = "del"
def setMouseGoodRef(self, x):
self.mmode = "refgood"
def setMouseBadRef(self, x):
self.mmode = "refbad"
def imgmousedown(self, event):
m = self.wimage.scr_to_img((event.x(), event.y()))
boxsize2 = self.vbbsize.getValue() // 2
ptclsize = self.vbbpsize.getValue()
self.curbox = 0
# check to see if click was inside an existing box, in which case we move it
for i in self.boxes:
if abs(m.x - i[0]) < boxsize2 and abs(m.y - i[1]) < boxsize2:
self.curbox = i
break
else:
# Create a new box
if self.mmode == "del":
return # This is for creating a new box, so clearly not desirable in delete mode
self.curbox = len(self.boxes)
self.boxes.append((m[0], m[1], self.mmode))
self.__addBox(self.curbox, self.boxes[-1])
#self.guiim.add_shape("cen",["rect",.9,.9,.4,x0,y0,x0+2,y0+2,1.0])
def imgmousedrag(self, event):
if self.calcmode == 0:
m = self.wimage.scr_to_img((event.x(), event.y()))
parms = self.parms[self.curset]
parms[2] = (m[0] - parms[0] / 2, m[1] - parms[0] / 2)
self.needredisp = True
self.recalc()
# box deletion when shift held down
#if event.modifiers()&Qt.ShiftModifier:
#for i,j in enumerate(self.boxes):
def imgmouseup(self, event):
m = self.wimage.scr_to_img((event.x(), event.y()))
if self.calcmode == 1:
parms = self.parms[self.curset]
nx = self.data["nx"] / parms[0] - 1
grid = int((m[0] - parms[0] / 2) / parms[0]) + int(
(m[1] - parms[0] / 2) / parms[0]) * nx
if grid in parms[3]: parms[3].remove(grid)
else: parms[3].add(grid)
self.needredisp = True
self.recalc()
def ptclmousedown(self, event):
return
def ptclmousedrag(self, event):
return
def ptclmouseup(self, event):
return
def refmousedown(self, event):
return
def refmousedrag(self, event):
return
def refmouseup(self, event):
return
def newSet(self, val):
"called when a new data set is selected from the list"
first = True
newfilename = str(self.setlist.item(val).text())
if newfilename == self.curfilename: return
# Write the current image parameters to the database
if self.curfilename != None and self.boxes != None:
self.save_boxes()
first = False
self.micrograph = load_micrograph(newfilename)
self.wimage.set_data(self.micrograph)
if first: E2loadappwin("e2boxer21", "image", self.wimage.qt_parent)
self.curfilename = newfilename
self.restore_boxes()
def save_boxes(self):
js = js_open_dict(info_name(self.curfilename))
js["boxes"] = self.boxes
def restore_boxes(self):
# first we restore the list of box locations
js = js_open_dict(info_name(self.curfilename))
try:
self.boxes = js["boxes"]
except:
self.boxes = []
boxsize = self.vbbsize.getValue()
ptclsize = self.vbbpsize.getValue()
micro = self.wimage.get_data()
self.wimage.del_shapes()
if len(self.boxes) == 0:
self.wparticles.set_data([])
return
# Then we extract the actual boxed out particles
goodrefs = []
badrefs = []
self.particles = []
for i, box in enumerate(self.boxes):
self.__addBox(i, box)
# extract the data
boxim = self.micrograph.get_clip(
Region(box[0] - boxsize // 2, box[1] - boxsize // 2, boxsize,
boxsize))
boxim["ptcl_source_coord"] = (box[0], box[1])
if box[2] == "refgood":
goodrefs.append(boxim)
elif box[2] == "refbad":
badrefs.append(boxim)
else:
self.particles.append(boxim)
# finally redisplay as appropriate
self.wimage.update()
self.wparticles.set_data(self.particles)
if len(self.particles) > 0: self.wparticles.show()
if len(goodrefs) + len(badrefs) != 0:
self.goodrefs = goodrefs
self.badrefs = badrefs
self.wrefs.set_data(self.goodrefs)
self.wbadrefs.set_data(self.badrefs)
if len(self.goodrefs) > 0: self.wrefs.show()
if len(self.badrefs) > 0: self.wbadrefs.show()
def __addBox(self, i, box):
"""takes the number of the box in self.boxes and the (x,y,mode) tuple and displays it"""
# Display the actual box
boxsize = self.vbbsize.getValue()
ptclsize = self.vbbpsize.getValue()
try:
color = self.boxcolors[box[2]]
except:
color = self.boxcolors["unknown"]
self.wimage.add_shape(
"box{}".format(i),
EMShape(("rect", color[0], color[1], color[2],
box[0] - boxsize // 2, box[1] - boxsize // 2,
box[0] + boxsize // 2, box[1] + boxsize // 2, 2)))
self.wimage.add_shape(
"cir{}".format(i),
EMShape(("circle", color[0], color[1], color[2], box[0], box[1],
ptclsize / 2, 1.5)))
def listKey(self, event):
pass
#if event.key()>=Qt.Key_0 and event.key()<=Qt.Key_9 :
#q=int(event.key())-Qt.Key_0
#self.squality.setValue(q)
#elif event.key() == Qt.Key_Left:
#self.sdefocus.setValue(self.sdefocus.getValue()-0.03)
#elif event.key() == Qt.Key_Right:
#self.sdefocus.setValue(self.sdefocus.getValue()+0.03)
#elif event.key()==Qt.Key_I :
#self.doImport()
#elif event.key()==Qt.Key_U :
#self.unImport()
def doAutoBox(self, b):
"""Autobox button pressed, find the right algorithm and call it"""
name, bname, fn1 = self.aboxmodes[self.autotab.currentIndex()]
print name, " called"
def closeEvent(self, event):
# QtGui.QWidget.closeEvent(self,event)
E2saveappwin("e2boxer21", "main", self)
E2saveappwin("e2boxer21", "image", self.wimage.qt_parent)
E2saveappwin("e2boxer21", "particles", self.wparticles.qt_parent)
E2saveappwin("e2boxer21", "refs", self.wrefs.qt_parent)
E2saveappwin("e2boxer21", "badrefs", self.wbadrefs.qt_parent)
#self.writeCurParm()
event.accept()
QtGui.qApp.exit(0)
class GUIBoxer(QtGui.QWidget):
def __init__(self,
images,
voltage=None,
apix=None,
cs=None,
ac=10.0,
box=512):
"""The 'new' e2boxer interface.
"""
try:
from emimage2d import EMImage2DWidget
except:
print "Cannot import EMAN image GUI objects (EMImage2DWidget)"
sys.exit(1)
try:
from emimagemx import EMImageMXWidget
except:
print "Cannot import EMAN image GUI objects (EMImageMXWidget)"
sys.exit(1)
try:
from emplot2d import EMPlot2DWidget
except:
print "Cannot import EMAN plot GUI objects (is matplotlib installed?)"
sys.exit(1)
QtGui.QWidget.__init__(self, None)
self.setWindowIcon(QtGui.QIcon(get_image_directory() + "ctf.png"))
self.data = None
self.curfilename = None
self.defaultvoltage = voltage
self.defaultapix = apix
self.defaultcs = cs
self.defaultac = ac
self.wimage = EMImage2DWidget()
self.wimage.setWindowTitle("Micrograph")
self.wparticles = EMImageMXWidget()
self.wparticles.setWindowTitle("Particles")
#self.wfft=EMImage2DWidget()
#self.wfft.setWindowTitle("e2evalimage - 2D FFT")
#self.wplot=EMPlot2DWidget()
#self.wplot.setWindowTitle("e2evalimage - Plot")
self.wimage.connect(QtCore.SIGNAL("mousedown"), self.imgmousedown)
self.wimage.connect(QtCore.SIGNAL("mousedrag"), self.imgmousedrag)
self.wimage.connect(QtCore.SIGNAL("mouseup"), self.imgmouseup)
self.wparticles.connect(QtCore.SIGNAL("mousedown"), self.ptclmousedown)
self.wparticles.connect(QtCore.SIGNAL("mousedrag"), self.ptclmousedrag)
self.wparticles.connect(QtCore.SIGNAL("mouseup"), self.ptclmouseup)
self.wimage.mmode = "app"
self.wparticles.mmode = "app"
# This object is itself a widget we need to set up
self.gbl = QtGui.QGridLayout(self)
self.gbl.setMargin(8)
self.gbl.setSpacing(6)
# plot list and plot mode combobox
self.setlist = e2ctf.MyListWidget(self)
self.setlist.setSizePolicy(QtGui.QSizePolicy.Preferred,
QtGui.QSizePolicy.Expanding)
for i in images:
self.setlist.addItem(i)
self.gbl.addWidget(self.setlist, 0, 0, 10, 2)
self.lboxmode = QtGui.QLabel("Mode:", self)
self.gbl.addWidget(self.lboxmode, 10, 0)
self.sboxmode = QtGui.QComboBox(self)
self.sboxmode.addItem("Manual")
self.sboxmode.addItem("Reference")
self.sboxmode.setCurrentIndex(1)
self.gbl.addWidget(self.sboxmode, 10, 1)
self.lanmode = QtGui.QLabel("Annotate:", self)
self.gbl.addWidget(self.lanmode, 12, 0)
self.sanmode = QtGui.QComboBox(self)
self.sanmode.addItem("Box")
self.sanmode.addItem("Box+dot")
self.sanmode.addItem("Circle")
self.sanmode.addItem("None")
self.gbl.addWidget(self.sanmode, 12, 1)
self.sdefocus = ValSlider(self, (0, 5), "Defocus:", 0.0, 90)
self.gbl.addWidget(self.sdefocus, 0, 2, 1, 3)
self.squality = ValSlider(self, (0, 9), "Quality (0-9):", 0, 90)
self.squality.setIntonly(True)
self.gbl.addWidget(self.squality, 6, 2, 1, 3)
self.brefit = QtGui.QPushButton("Autobox")
self.gbl.addWidget(self.brefit, 7, 2)
self.bclrauto = QtGui.QPushButton("Clear Auto")
self.gbl.addWidget(self.bclrauto, 7, 3)
self.bclrall = QtGui.QPushButton("Clear All")
self.gbl.addWidget(self.bclrall, 7, 4)
self.sapix = ValBox(self, (0, 500), "A/pix:", 1.0, 90)
if self.defaultapix != None: self.sapix.setValue(self.defaultapix)
self.gbl.addWidget(self.sapix, 10, 2)
self.svoltage = ValBox(self, (0, 500), "Voltage (kV):", 200, 90)
if self.defaultvoltage != None:
self.svoltage.setValue(self.defaultvoltage)
self.gbl.addWidget(self.svoltage, 11, 2)
self.scs = ValBox(self, (0, 5), "Cs (mm):", 4.1, 90)
if self.defaultcs != None: self.scs.setValue(self.defaultcs)
self.gbl.addWidget(self.scs, 12, 2)
self.sboxsize = ValBox(self, (0, 500), "Box Size:", 256, 90)
self.sboxsize.intonly = True
self.gbl.addWidget(self.sboxsize, 13, 2)
self.sptclsize = ValBox(self, (0, 500), "Ptcl Size:", 256, 90)
self.sptclsize.intonly = True
self.gbl.addWidget(self.sptclsize, 14, 2)
QtCore.QObject.connect(self.sdefocus, QtCore.SIGNAL("valueChanged"),
self.newCTF)
QtCore.QObject.connect(self.sapix, QtCore.SIGNAL("valueChanged"),
self.newCTF)
QtCore.QObject.connect(self.svoltage, QtCore.SIGNAL("valueChanged"),
self.newCTF)
QtCore.QObject.connect(self.scs, QtCore.SIGNAL("valueChanged"),
self.newCTF)
QtCore.QObject.connect(self.sboxsize, QtCore.SIGNAL("valueChanged"),
self.newBox)
# QtCore.QObject.connect(self.soversamp, QtCore.SIGNAL("valueChanged"), self.newBox)
QtCore.QObject.connect(self.squality, QtCore.SIGNAL("valueChanged"),
self.newQualityFactor)
QtCore.QObject.connect(self.setlist,
QtCore.SIGNAL("currentRowChanged(int)"),
self.newSet)
QtCore.QObject.connect(self.setlist, QtCore.SIGNAL("keypress"),
self.listkey)
QtCore.QObject.connect(self.sboxmode,
QtCore.SIGNAL("currentIndexChanged(int)"),
self.newBoxMode)
self.resize(
720, 380
) # figured these values out by printing the width and height in resize event
### This section is responsible for background updates
self.busy = False
self.needupdate = True
self.needredisp = False
self.procthread = None
self.errors = None # used to communicate errors back from the reprocessing thread
self.timer = QTimer()
QtCore.QObject.connect(self.timer, QtCore.SIGNAL("timeout()"),
self.timeOut)
self.timer.start(100)
self.setWindowTitle("e2boxer21 - Control Panel")
self.wimage.show()
self.wfft.show()
self.wplot.show()
E2loadappwin("e2boxer21", "main", self)
E2loadappwin("e2boxer21", "image", self.wimage.qt_parent)
E2loadappwin("e2boxer21", "particles", self.wparticles.qt_parent)
# self.recalc()
def listkey(self, event):
if event.key() >= Qt.Key_0 and event.key() <= Qt.Key_9:
q = int(event.key()) - Qt.Key_0
self.squality.setValue(q)
#elif event.key() == Qt.Key_Left:
#self.sdefocus.setValue(self.sdefocus.getValue()-0.03)
#elif event.key() == Qt.Key_Right:
#self.sdefocus.setValue(self.sdefocus.getValue()+0.03)
#elif event.key()==Qt.Key_I :
#self.doImport()
#elif event.key()==Qt.Key_U :
#self.unImport()
def closeEvent(self, event):
# QtGui.QWidget.closeEvent(self,event)
E2saveappwin("e2evalimage", "main", self)
E2saveappwin("e2evalimage", "image", self.wimage.qt_parent)
E2saveappwin("e2evalimage", "particles", self.wparticles.qt_parent)
#self.writeCurParm()
event.accept()
QtGui.qApp.exit(0)
#app=QtGui.qApp
#if self.wimage != None:
#app.close_specific(self.wimage)
#self.wimage = None
#if self.wfft != None:
#app.close_specific(self.wfft)
#if self.wplot != None:
#app.close_specific(self.wplot)
#app.close_specific(self)
# self.emit(QtCore.SIGNAL("module_closed")) # this signal is important when e2ctf is being used by a program running its own event loop
def update_plot(self):
# if self.wplot == None: return # it's closed/not visible
if self.incalc: return # no plot updates during a recomputation
parms = self.parms[self.curset]
apix = self.sapix.getValue()
ds = 1.0 / (apix * parms[0] * parms[5])
ctf = parms[1]
bg1d = array(ctf.background)
r = len(ctf.background)
s = arange(0, ds * r, ds)
# This updates the FFT CTF-zero circles
if self.f2danmode == 0:
fit = ctf.compute_1d(len(s) * 2, ds, Ctf.CtfType.CTF_AMP)
shp = {}
nz = 0
for i in range(1, len(fit)):
if fit[i - 1] * fit[i] <= 0.0:
nz += 1
shp["z%d" % i] = EMShape(
("circle", 0.0, 0.0, 1.0 / nz, r, r, i, 1.0))
self.wfft.del_shapes()
self.wfft.add_shapes(shp)
self.wfft.updateGL()
# Single measurement circle mode
elif self.f2danmode == 1:
self.wfft.del_shapes()
if self.ringrad == 0: self.ringrad = 1.0
self.wfft.add_shape(
"ring",
EMShape(("circle", 0.2, 1.0, 0.2, r, r, self.ringrad, 1.0)))
self.wfft.add_shape(
"ringlbl",
EMShape(("scrlabel", 0.2, 1.0, 0.2, 10, 10,
"r=%d pix -> 1/%1.2f 1/A (%1.4f)" %
(self.ringrad, 1.0 /
(self.ringrad * ds), self.ringrad * ds), 24.0, 2.0)))
self.wfft.updateGL()
# 2-D Crystal mode
elif self.f2danmode == 2:
shp = {}
for a in range(-5, 6):
for b in range(-5, 6):
shp["m%d%d" % (a, b)] = EMShape(
("circle", 1.0, 0.0, 0.0, a * self.xpos1[0] +
b * self.xpos2[0] + self.fft["nx"] / 2 - 1,
a * self.xpos1[1] + b * self.xpos2[1] +
self.fft["ny"] / 2, 3, 1.0))
self.wfft.del_shapes()
self.wfft.add_shapes(shp)
self.wfft.add_shape(
"xtllbl",
EMShape(("scrlabel", 1.0, 0.3, 0.3, 10, 10,
"Unit Cell: %1.2f,%1.2f" %
(1.0 / (hypot(*self.xpos1) * ds), 1.0 /
(hypot(*self.xpos2) * ds)), 60.0, 2.0)))
# except: pass
self.wfft.updateGL()
else:
self.wfft.del_shapes()
self.wfft.updateGL()
# Now update the plots for the correct plot mode
if self.plotmode == 0:
try:
bgsub = self.fft1d - bg1d
except:
print "Error computing bgsub on this image"
return
self.wplot.set_data((s, bgsub), "fg-bg", quiet=True, color=0)
fit = array(ctf.compute_1d(len(s) * 2, ds,
Ctf.CtfType.CTF_AMP)) # The fit curve
fit = fit * fit # squared
# auto-amplitude for b-factor adjustment
rto, nrto = 0, 0
for i in range(int(.04 / ds) + 1, min(int(0.15 / ds), len(s) - 1)):
if bgsub[i] > 0:
rto += fit[i]
nrto += fabs(bgsub[i])
if nrto == 0: rto = 1.0
else: rto /= nrto
fit = [fit[i] / rto for i in range(len(s))]
# print ctf_cmp((self.sdefocus.value,self.sbfactor.value,rto),(ctf,bgsub,int(.04/ds)+1,min(int(0.15/ds),len(s)-1),ds,self.sdefocus.value))
self.wplot.set_data((s, fit), "fit", color=1)
self.wplot.setAxisParms("s (1/" + "$\AA$" + ")", "Intensity (a.u)")
elif self.plotmode == 1:
self.wplot.set_data((s[1:], self.fft1d[1:]),
"fg",
quiet=True,
color=1)
self.wplot.set_data((s[1:], bg1d[1:]), "bg", color=0)
self.wplot.setAxisParms("s (1/" + "$\AA$" + ")", "Intensity (a.u)")
elif self.plotmode == 2:
if self.fft1dang == None: self.recalc_real()
bgsub = self.fft1d - bg1d
bgsuba = [array(self.fft1dang[i]) - bg1d for i in xrange(4)]
# Write the current image parameters to the database
# for i in xrange(4): bgsuba[i][0]=0
self.wplot.set_data((s, bgsub), "fg", quiet=True, color=0)
self.wplot.set_data((s[3:], bgsuba[0][3:]),
"fg 0-45",
quiet=True,
color=2)
self.wplot.set_data((s[3:], bgsuba[1][3:]),
"fg 45-90",
quiet=True,
color=3)
self.wplot.set_data((s[3:], bgsuba[2][3:]),
"fg 90-135",
quiet=True,
color=4)
self.wplot.set_data((s[3:], bgsuba[3][3:]),
"fg 135-180",
quiet=True,
color=6)
fit = array(ctf.compute_1d(len(s) * 2, ds,
Ctf.CtfType.CTF_AMP)) # The fit curve
fit = fit * fit # squared
# auto-amplitude for b-factor adjustment
rto, nrto = 0, 0
for i in range(int(.04 / ds) + 1, min(int(0.15 / ds), len(s) - 1)):
if bgsub[i] > 0:
rto += fit[i]
nrto += fabs(bgsub[i])
if nrto == 0: rto = 1.0
else: rto /= nrto
fit /= rto
self.wplot.set_data((s, fit), "fit", color=1)
self.wplot.setAxisParms("s (1/" + "$\AA$" + ")", "Intensity (a.u)")
elif self.plotmode == 3:
if self.fft1dang == None: self.recalc_real()
#bgsub=self.fft1d-bg1d
#bgsuba=[array(self.fft1dang[i])-bg1d for i in xrange(4)]
fg = self.fft1d
fga = [array(self.fft1dang[i]) for i in xrange(4)]
for i in xrange(4):
fga[i][0] = 0
self.wplot.set_data((s, fg), "fg", quiet=True, color=0)
self.wplot.set_data((s, fga[0]), "fg 0-45", quiet=True, color=2)
self.wplot.set_data((s, fga[1]), "fg 45-90", quiet=True, color=3)
self.wplot.set_data((s, fga[2]), "fg 90-135", quiet=True, color=4)
self.wplot.set_data((s, fga[3]), "fg 135-180", quiet=True, color=6)
#fit=array(ctf.compute_1d(len(s)*2,ds,Ctf.CtfType.CTF_AMP)) # The fit curve
#fit=fit*fit # squared
## auto-amplitude for b-factor adjustment
#rto,nrto=0,0
#for i in range(int(.04/ds)+1,min(int(0.15/ds),len(s)-1)):
#if bgsub[i]>0 :
#rto+=fit[i]
#nrto+=fabs(bgsub[i])
#if nrto==0 : rto=1.0
#else : rto/=nrto
#fit/=rto
#self.wplot.set_data((s,fit),"fit",color=1)
#self.wplot.setAxisParms("s (1/"+ "$\AA$" + ")","Intensity (a.u)")
if self.plotmode == 4:
if min(bg1d) <= 0.0: bg1d += min(bg1d) + max(bg1d) / 10000.0
ssnr = (self.fft1d - bg1d) / bg1d
self.wplot.set_data((s, ssnr), "SSNR", quiet=True, color=0)
#fit=array(ctf.compute_1d(len(s)*2,ds,Ctf.CtfType.CTF_AMP)) # The fit curve
#fit=fit*fit # squared
## auto-amplitude for b-factor adjustment
#rto,nrto=0,0
#for i in range(int(.04/ds)+1,min(int(0.15/ds),len(s)-1)):
#if bgsub[i]>0 :
#rto+=fit[i]
#nrto+=fabs(bgsub[i])
#if nrto==0 : rto=1.0
#else : rto/=nrto
#fit=[fit[i]/rto for i in range(len(s))]
## print ctf_cmp((self.sdefocus.value,self.sbfactor.value,rto),(ctf,bgsub,int(.04/ds)+1,min(int(0.15/ds),len(s)-1),ds,self.sdefocus.value))
#self.wplot.set_data((s,fit),"fit",color=1)
self.wplot.setAxisParms("s (1/" + "$\AA$" + ")", "Est. SSNR")
def timeOut(self):
if self.busy: return
# Redisplay before spawning thread for more interactive display
if self.needredisp:
try:
self.redisplay()
except:
pass
# Spawn a thread to reprocess the data
if self.needupdate and self.procthread == None:
self.procthread = threading.Thread(target=self.recalc_real)
self.procthread.start()
if self.errors:
QtGui.QMessageBox.warning(
None, "Error",
"The following processors encountered errors during processing of 1 or more images:"
+ "\n".join(self.errors))
self.errors = None
def doRefit(self):
parms = self.parms[self.curset]
apix = self.sapix.getValue()
ds = 1.0 / (apix * parms[0] * parms[5])
try:
parms[1] = e2ctf.ctf_fit(self.fft1d,
parms[1].background,
parms[1].background,
self.fft,
self.fftbg,
parms[1].voltage,
parms[1].cs,
parms[1].ampcont,
apix,
bgadj=False,
autohp=True,
verbose=1)
except:
print "CTF Autofit Failed"
traceback.print_exc()
parms[1].defocus = 1.0
self.sdefocus.setValue(parms[1].defocus, True)
self.sbfactor.setValue(parms[1].bfactor, True)
self.sampcont.setValue(parms[1].ampcont, True)
self.update_plot()
def unImport(self, val=None):
print "unimport ", base_name(self.setlist.item(self.curset).text())
item = base_name(self.setlist.item(self.curset).text())
try:
os.unlink("micrographs/%s.hdf" % item)
except:
print "Couldn't delete micrographs/%s.hdf" % item
def doImport(self, val=None):
"""Imports the currently selected image into a project"""
print "import ", base_name(self.setlist.item(self.curset).text())
# This is just the (presumably) unique portion of the filename
item = base_name(self.setlist.item(self.curset).text())
# create directory if necessary
if not os.access("micrographs", os.R_OK):
try:
os.mkdir("micrographs")
except:
QtGui.QMessageBox.warning(
self, "Error !", "Cannot create micrographs directory")
return
#db=db_open_dict("bdb:micrographs#%s"%item)
self.data["ctf"] = self.parms[self.curset][1]
if self.cinvert.getValue() != 0: self.data.mult(-1)
if self.cxray.getValue():
self.data.process_inplace("threshold.clampminmax.nsigma", {
"nsigma": 4,
"tomean": 1
})
self.data.write_image("micrographs/%s.hdf" % item)
self.writeCurParm()
# js_open_dict(info_name(item))["ctf"]=[self.parms[val][1],None,None,None,None]
# db_parms=db_open_dict("bdb:e2ctf.parms")
# db_parms[item]=[self.parms[val][1].to_string(),self.fft1d,self.parms[val][1].background,self.parms[val][4]]
def writeCurParm(self):
"Called to store the current parameters for this image to the frameparms database"
parms = self.parms[self.curset]
js = js_open_dict(info_name(self.curfilename))
js.setval("ctf_frame", parms, True)
js.setval("quality", parms[4])
# db_fparms=db_open_dict("bdb:e2ctf.frameparms")
# curtag=item_name(str(self.setlist.item(self.curset).text()))
# db_fparms[curtag]=self.parms[self.curset]
def newSet(self, val):
"called when a new data set is selected from the list"
# Write the current image parameters to the database
if val != self.curset: self.writeCurParm()
# now set the new item
self.curset = val
# This deals with Z stacks and multi image files
fsp = str(self.setlist.item(val).text())
if "," in fsp:
fsp, n = fsp.split(",")
self.data = EMData(fsp, int(n)) # read the image from disk
elif ";" in fsp:
fsp, n = fsp.split(";")
hdr = EMData(fsp, 0, True)
self.data = EMData(fsp, 0, False,
Region(0, 0, int(n), hdr["nx"], hdr["ny"],
1)) # read the image from disk
else:
self.data = EMData(fsp, 0) # read the image from disk
self.wimage.setWindowTitle("e2evalimage - " + fsp.split("/")[-1])
self.wfft.setWindowTitle("e2evalimage - 2D FFT - " +
fsp.split("/")[-1])
self.wplot.setWindowTitle("e2evalimage - Plot - " + fsp.split("/")[-1])
if self.defaultapix != None: self.data["apix_x"] = self.defaultapix
self.wimage.set_data(self.data)
self.curfilename = str(self.setlist.item(val).text())
ctf = self.parms[val][1]
# if voltage is 0, we need to initialize
if ctf.voltage == 0:
try:
ctf.voltage = self.data["microscope_voltage"]
except:
pass
if ctf.voltage == 0: ctf.voltage = self.defaultvoltage
try:
ctf.cs = self.data["microscope_cs"]
except:
pass
if ctf.cs == 0: ctf.cs = self.defaultcs
ctf.apix = self.data["apix_x"]
ctf.defocus = 0.0 #triggers fitting
ctf.bfactor = 200.0
ctf.ampcont = self.defaultac
self.sdefocus.setValue(ctf.defocus, True)
self.sbfactor.setValue(ctf.bfactor, True)
self.sapix.setValue(ctf.apix, True)
self.sampcont.setValue(ctf.ampcont, True)
self.svoltage.setValue(ctf.voltage, True)
self.scs.setValue(ctf.cs, True)
self.sboxsize.setValue(self.parms[val][0], True)
self.squality.setValue(self.parms[val][4], True)
#if self.guiim != None:
## print self.data
#self.guiim.set_data(self.data[val][4])
#if self.guiiminit:
#self.guiim.optimally_resize()
#self.guiiminit = False
#self.guiim.updateGL()
self.recalc()
def recalc(self):
self.needupdate = True
def recalc_real(self):
"Called to recompute the power spectra, also updates plot"
self.needupdate = False
if self.data == None:
self.procthread = None
return
self.incalc = True # to avoid incorrect plot updates
# To simplify expressions
parms = self.parms[self.curset]
apix = self.sapix.getValue()
if len(parms) == 5:
parms.append(
1
) # for old projects where there was no oversampling specification
else:
parms[5] = max(1, int(parms[5]))
ds = 1.0 / (apix * parms[0] * parms[5])
# Mode where user drags the box around the parent image
if self.calcmode == 0:
# extract the data and do an fft
clip = self.data.get_clip(
Region(parms[2][0], parms[2][1], parms[0], parms[0]))
clip.process_inplace("normalize.edgemean")
if parms[5] > 1:
clip = clip.get_clip(
Region(0, 0, parms[0] * parms[5], parms[0] * parms[5])
) # since we aren't using phases, doesn't matter if we center it or not
self.fft = clip.do_fft()
# self.fft.mult(1.0/parms[0]**2)
self.fft.mult(1.0 / parms[0])
# mode where user selects/deselcts tiled image set
elif self.calcmode == 1:
# update the box display on the image
nx = self.data["nx"] / parms[0] - 1
self.fft = None
nbx = 0
for x in range(nx):
for y in range(self.data["ny"] / parms[0] - 1):
# User deselected this one
if int(x + y * nx) in parms[3]: continue
# read the data and make the FFT
clip = self.data.get_clip(
Region(x * parms[0] + parms[0] / 2,
y * parms[0] + parms[0] / 2, parms[0],
parms[0]))
clip.process_inplace("normalize.edgemean")
if parms[5] > 1:
clip = clip.get_clip(
Region(0, 0, parms[0] * parms[5],
parms[0] * parms[5])
) # since we aren't using phases, doesn't matter if we center it or not
fft = clip.do_fft()
# fft.mult(parms[0])
fft.ri2inten()
if self.fft == None: self.fft = fft
else: self.fft += fft
nbx += 1
self.fft.mult(1.0 / (nbx * parms[0]**2))
self.fft.process_inplace("math.sqrt")
self.fft[
"is_intensity"] = 0 # These 2 steps are done so the 2-D display of the FFT looks better. Things would still work properly in 1-D without it
# self.fft.mult(1.0/(nbx*parms[0]**2))
self.fftbg = self.fft.process("math.nonconvex")
self.fft1d = self.fft.calc_radial_dist(
self.fft.get_ysize() / 2, 0.0, 1.0,
1) # note that this handles the ri2inten averages properly
if self.plotmode == 2 or self.plotmode == 3:
self.fft1dang = array(
self.fft.calc_radial_dist(self.fft.get_ysize() / 2, 0.0, 1.0,
4,
self.sang45.getValue() * .017453292,
1)
) # This form generates 4 sequential power spectra representing angular ranges
self.fft1dang = self.fft1dang.reshape(
(4, self.fft.get_ysize() / 2))
else:
self.fft1dang = None
# Compute 1-D curve and background
bg_1d = e2ctf.low_bg_curve(self.fft1d, ds)
parms[1].background = bg_1d
parms[1].dsbg = ds
self.fft1d = array(self.fft1d)
self.needredisp = True
self.incalc = False
time.sleep(.2) # help make sure update has a chance
self.procthread = None
# dbquality = self.db[os.path.basename(self.curfilename)]
# print dbquality
# item=item_name(self.curfilename)
# db=db_open_dict("bdb:e2ctf.parms")
# if db[item]==None or db[item[3]]==None : db[item]=[parms[1].to_string(),self.fft1d,parms[1].background,5]
# # print item,db[item][3]
# try: self.squality.setValue(int(db[item[3]]))
# except: self.squality.setValue(5)
def redisplay(self):
if self.incalc: return
self.needredisp = False
self.busy = True
parms = self.parms[self.curset]
apix = self.sapix.getValue()
ds = 1.0 / (apix * parms[0] * parms[5])
# Fitting not done yet. Need to make 2D background somehow
if parms[1].defocus == 0:
self.doRefit()
self.wimage.show()
self.wfft.show()
self.wplot.show()
self.update_plot()
# To simplify expressions
if self.calcmode == 0:
# update the box display on the image
self.wimage.del_shapes()
self.wimage.add_shape(
"box",
EMShape(("rect", .3, .9, .3, parms[2][0], parms[2][1],
parms[2][0] + parms[0], parms[2][1] + parms[0], 1)))
self.wimage.updateGL()
elif self.calcmode == 1:
# update the box display on the image
nx = self.data["nx"] / parms[0] - 1
shp = {}
for x in range(nx):
for y in range(self.data["ny"] / parms[0] - 1):
# User deselected this one
if int(x + y * nx) in parms[3]: continue
# Make a shape for this box
shp["box%02d%02d" % (x, y)] = EMShape(
("rect", .3, .9, .3, (x + .5) * parms[0],
(y + .5) * parms[0], (x + 1.5) * parms[0],
(y + 1.5) * parms[0], 1))
self.wimage.del_shapes()
self.wimage.add_shapes(shp)
self.wimage.updateGL()
if self.f2dmode > 0:
if self.f2dmode == 1: self.wfft.set_data(self.fft - self.fftbg)
else: self.wfft.set_data(self.fftbg)
else:
self.wfft.set_data(self.fft)
self.busy = False
def newCalcMode(self, mode):
self.calcmode = mode
self.recalc()
def new2DMode(self, mode):
self.f2dmode = mode
self.recalc()
def new2DAnMode(self, mode):
self.f2danmode = mode
self.needredisp = True
def newPlotMode(self, mode):
self.plotmode = mode
self.wplot.set_data(
None, replace=True, quiet=True
) # clear the data so plots are properly redisplayed, but don't update the display
self.needredisp = True
def newBox(self):
parms = self.parms[self.curset]
parms[0] = self.sboxsize.value
# parms[5]=self.soversamp.value
parms[5] = 1
parms[3] = set()
self.recalc()
def newQualityFactor(self):
parms = self.parms[self.curset]
parms[4] = self.squality.value
def newCTF(self):
parms = self.parms[self.curset]
parms[1].defocus = self.sdefocus.value
parms[1].bfactor = self.sbfactor.value
parms[1].dfdiff = self.sdfdiff.value
parms[1].dfang = self.sdfang.value
parms[1].apix = self.sapix.value
parms[1].ampcont = self.sampcont.value
parms[1].voltage = self.svoltage.value
parms[1].cs = self.scs.value
self.needredisp = True
def imgmousedown(self, event):
if self.calcmode == 0:
m = self.wimage.scr_to_img((event.x(), event.y()))
parms = self.parms[self.curset]
parms[2] = (m[0] - parms[0] / 2, m[1] - parms[0] / 2)
self.recalc()
self.needredisp = True
#self.guiim.add_shape("cen",["rect",.9,.9,.4,x0,y0,x0+2,y0+2,1.0])
def imgmousedrag(self, event):
if self.calcmode == 0:
m = self.wimage.scr_to_img((event.x(), event.y()))
parms = self.parms[self.curset]
parms[2] = (m[0] - parms[0] / 2, m[1] - parms[0] / 2)
self.needredisp = True
self.recalc()
# box deletion when shift held down
#if event.modifiers()&Qt.ShiftModifier:
#for i,j in enumerate(self.boxes):
def imgmouseup(self, event):
m = self.wimage.scr_to_img((event.x(), event.y()))
if self.calcmode == 1:
parms = self.parms[self.curset]
nx = self.data["nx"] / parms[0] - 1
grid = int((m[0] - parms[0] / 2) / parms[0]) + int(
(m[1] - parms[0] / 2) / parms[0]) * nx
if grid in parms[3]: parms[3].remove(grid)
else: parms[3].add(grid)
self.needredisp = True
self.recalc()
def fftmousedown(self, event, m):
#m=self.wfft.scr_to_img((event.x(),event.y()))
if self.f2danmode == 1:
self.ringrad = hypot(m[0] - self.fft["nx"] / 2,
m[1] - self.fft["ny"] / 2)
self.needredisp = True
elif self.f2danmode == 2:
if (event.modifiers() & Qt.ControlModifier):
self.xpos2 = ((m[0] - self.fft["nx"] / 2) / 3.0,
(m[1] - self.fft["ny"] / 2) / 3.0)
else:
self.xpos1 = ((m[0] - self.fft["nx"] / 2) / 3.0,
(m[1] - self.fft["ny"] / 2) / 3.0)
self.needredisp = True
#self.guiim.add_shape("cen",["rect",.9,.9,.4,x0,y0,x0+2,y0+2,1.0])
def fftmousedrag(self, event, m):
#m=self.wfft.scr_to_img((event.x(),event.y()))
if self.f2danmode == 1:
self.ringrad = hypot(m[0] - self.fft["nx"] / 2,
m[1] - self.fft["ny"] / 2)
self.needredisp = True
elif self.f2danmode == 2:
if (event.modifiers() & Qt.ControlModifier):
self.xpos2 = ((m[0] - self.fft["nx"] / 2) / 3.0,
(m[1] - self.fft["ny"] / 2) / 3.0)
else:
self.xpos1 = ((m[0] - self.fft["nx"] / 2) / 3.0,
(m[1] - self.fft["ny"] / 2) / 3.0)
self.needredisp = True
# box deletion when shift held down
#if event.modifiers()&Qt.ShiftModifier:
#for i,j in enumerate(self.boxes):
def fftmouseup(self, event, m):
"up"
#m=self.wfft.scr_to_img((event.x(),event.y()))
def plotmousedown(self, event):
"mousedown in plot"
class GUIBoxer(QtGui.QWidget):
def __init__(self,images,voltage=None,apix=None,cs=None,ac=10.0,box=512):
"""The 'new' e2boxer interface.
"""
try:
from emimage2d import EMImage2DWidget
except:
print "Cannot import EMAN image GUI objects (EMImage2DWidget)"
sys.exit(1)
try:
from emimagemx import EMImageMXWidget
except:
print "Cannot import EMAN image GUI objects (EMImageMXWidget)"
sys.exit(1)
try:
from emplot2d import EMPlot2DWidget
except:
print "Cannot import EMAN plot GUI objects (is matplotlib installed?)"
sys.exit(1)
QtGui.QWidget.__init__(self,None)
self.setWindowIcon(QtGui.QIcon(get_image_directory() + "ctf.png"))
self.data=None
self.curfilename = None
self.defaultvoltage=voltage
self.defaultapix=apix
self.defaultcs=cs
self.defaultac=ac
self.wimage=EMImage2DWidget()
self.wimage.setWindowTitle("Micrograph")
self.wparticles=EMImageMXWidget()
self.wparticles.setWindowTitle("Particles")
#self.wfft=EMImage2DWidget()
#self.wfft.setWindowTitle("e2evalimage - 2D FFT")
#self.wplot=EMPlot2DWidget()
#self.wplot.setWindowTitle("e2evalimage - Plot")
self.wimage.connect(QtCore.SIGNAL("mousedown"),self.imgmousedown)
self.wimage.connect(QtCore.SIGNAL("mousedrag"),self.imgmousedrag)
self.wimage.connect(QtCore.SIGNAL("mouseup") ,self.imgmouseup)
self.wparticles.connect(QtCore.SIGNAL("mousedown"),self.ptclmousedown)
self.wparticles.connect(QtCore.SIGNAL("mousedrag"),self.ptclmousedrag)
self.wparticles.connect(QtCore.SIGNAL("mouseup") ,self.ptclmouseup)
self.wimage.mmode="app"
self.wparticles.mmode="app"
# This object is itself a widget we need to set up
self.gbl = QtGui.QGridLayout(self)
self.gbl.setMargin(8)
self.gbl.setSpacing(6)
# plot list and plot mode combobox
self.setlist=e2ctf.MyListWidget(self)
self.setlist.setSizePolicy(QtGui.QSizePolicy.Preferred,QtGui.QSizePolicy.Expanding)
for i in images:
self.setlist.addItem(i)
self.gbl.addWidget(self.setlist,0,0,10,2)
self.lboxmode=QtGui.QLabel("Mode:",self)
self.gbl.addWidget(self.lboxmode,10,0)
self.sboxmode=QtGui.QComboBox(self)
self.sboxmode.addItem("Manual")
self.sboxmode.addItem("Reference")
self.sboxmode.setCurrentIndex(1)
self.gbl.addWidget(self.sboxmode,10,1)
self.lanmode=QtGui.QLabel("Annotate:",self)
self.gbl.addWidget(self.lanmode,12,0)
self.sanmode=QtGui.QComboBox(self)
self.sanmode.addItem("Box")
self.sanmode.addItem("Box+dot")
self.sanmode.addItem("Circle")
self.sanmode.addItem("None")
self.gbl.addWidget(self.sanmode,12,1)
self.sdefocus=ValSlider(self,(0,5),"Defocus:",0.0,90)
self.gbl.addWidget(self.sdefocus,0,2,1,3)
self.squality=ValSlider(self,(0,9),"Quality (0-9):",0,90)
self.squality.setIntonly(True)
self.gbl.addWidget(self.squality,6,2,1,3)
self.brefit=QtGui.QPushButton("Autobox")
self.gbl.addWidget(self.brefit,7,2)
self.bclrauto=QtGui.QPushButton("Clear Auto")
self.gbl.addWidget(self.bclrauto,7,3)
self.bclrall=QtGui.QPushButton("Clear All")
self.gbl.addWidget(self.bclrall,7,4)
self.sapix=ValBox(self,(0,500),"A/pix:",1.0,90)
if self.defaultapix!=None : self.sapix.setValue(self.defaultapix)
self.gbl.addWidget(self.sapix,10,2)
self.svoltage=ValBox(self,(0,500),"Voltage (kV):",200,90)
if self.defaultvoltage!=None : self.svoltage.setValue(self.defaultvoltage)
self.gbl.addWidget(self.svoltage,11,2)
self.scs=ValBox(self,(0,5),"Cs (mm):",4.1,90)
if self.defaultcs!=None : self.scs.setValue(self.defaultcs)
self.gbl.addWidget(self.scs,12,2)
self.sboxsize=ValBox(self,(0,500),"Box Size:",256,90)
self.sboxsize.intonly=True
self.gbl.addWidget(self.sboxsize,13,2)
self.sptclsize=ValBox(self,(0,500),"Ptcl Size:",256,90)
self.sptclsize.intonly=True
self.gbl.addWidget(self.sptclsize,14,2)
QtCore.QObject.connect(self.sdefocus, QtCore.SIGNAL("valueChanged"), self.newCTF)
QtCore.QObject.connect(self.sapix, QtCore.SIGNAL("valueChanged"), self.newCTF)
QtCore.QObject.connect(self.svoltage, QtCore.SIGNAL("valueChanged"), self.newCTF)
QtCore.QObject.connect(self.scs, QtCore.SIGNAL("valueChanged"), self.newCTF)
QtCore.QObject.connect(self.sboxsize, QtCore.SIGNAL("valueChanged"), self.newBox)
# QtCore.QObject.connect(self.soversamp, QtCore.SIGNAL("valueChanged"), self.newBox)
QtCore.QObject.connect(self.squality,QtCore.SIGNAL("valueChanged"),self.newQualityFactor)
QtCore.QObject.connect(self.setlist,QtCore.SIGNAL("currentRowChanged(int)"),self.newSet)
QtCore.QObject.connect(self.setlist,QtCore.SIGNAL("keypress"),self.listkey)
QtCore.QObject.connect(self.sboxmode,QtCore.SIGNAL("currentIndexChanged(int)"),self.newBoxMode)
self.resize(720,380) # figured these values out by printing the width and height in resize event
### This section is responsible for background updates
self.busy=False
self.needupdate=True
self.needredisp=False
self.procthread=None
self.errors=None # used to communicate errors back from the reprocessing thread
self.timer=QTimer()
QtCore.QObject.connect(self.timer, QtCore.SIGNAL("timeout()"), self.timeOut)
self.timer.start(100)
self.setWindowTitle("e2boxer21 - Control Panel")
self.wimage.show()
self.wfft.show()
self.wplot.show()
E2loadappwin("e2boxer21","main",self)
E2loadappwin("e2boxer21","image",self.wimage.qt_parent)
E2loadappwin("e2boxer21","particles",self.wparticles.qt_parent)
# self.recalc()
def listkey(self,event):
if event.key()>=Qt.Key_0 and event.key()<=Qt.Key_9 :
q=int(event.key())-Qt.Key_0
self.squality.setValue(q)
#elif event.key() == Qt.Key_Left:
#self.sdefocus.setValue(self.sdefocus.getValue()-0.03)
#elif event.key() == Qt.Key_Right:
#self.sdefocus.setValue(self.sdefocus.getValue()+0.03)
#elif event.key()==Qt.Key_I :
#self.doImport()
#elif event.key()==Qt.Key_U :
#self.unImport()
def closeEvent(self,event):
# QtGui.QWidget.closeEvent(self,event)
E2saveappwin("e2evalimage","main",self)
E2saveappwin("e2evalimage","image",self.wimage.qt_parent)
E2saveappwin("e2evalimage","particles",self.wparticles.qt_parent)
#self.writeCurParm()
event.accept()
QtGui.qApp.exit(0)
#app=QtGui.qApp
#if self.wimage != None:
#app.close_specific(self.wimage)
#self.wimage = None
#if self.wfft != None:
#app.close_specific(self.wfft)
#if self.wplot != None:
#app.close_specific(self.wplot)
#app.close_specific(self)
# self.emit(QtCore.SIGNAL("module_closed")) # this signal is important when e2ctf is being used by a program running its own event loop
def update_plot(self):
# if self.wplot == None: return # it's closed/not visible
if self.incalc : return # no plot updates during a recomputation
parms=self.parms[self.curset]
apix=self.sapix.getValue()
ds=1.0/(apix*parms[0]*parms[5])
ctf=parms[1]
bg1d=array(ctf.background)
r=len(ctf.background)
s=arange(0,ds*r,ds)
# This updates the FFT CTF-zero circles
if self.f2danmode==0 :
fit=ctf.compute_1d(len(s)*2,ds,Ctf.CtfType.CTF_AMP)
shp={}
nz=0
for i in range(1,len(fit)):
if fit[i-1]*fit[i]<=0.0:
nz+=1
shp["z%d"%i]=EMShape(("circle",0.0,0.0,1.0/nz,r,r,i,1.0))
self.wfft.del_shapes()
self.wfft.add_shapes(shp)
self.wfft.updateGL()
# Single measurement circle mode
elif self.f2danmode==1 :
self.wfft.del_shapes()
if self.ringrad==0: self.ringrad=1.0
self.wfft.add_shape("ring",EMShape(("circle",0.2,1.0,0.2,r,r,self.ringrad,1.0)))
self.wfft.add_shape("ringlbl",EMShape(("scrlabel",0.2,1.0,0.2,10,10,"r=%d pix -> 1/%1.2f 1/A (%1.4f)"%(self.ringrad,1.0/(self.ringrad*ds),self.ringrad*ds),24.0,2.0)))
self.wfft.updateGL()
# 2-D Crystal mode
elif self.f2danmode==2 :
shp={}
for a in range(-5,6):
for b in range(-5,6):
shp["m%d%d"%(a,b)]=EMShape(("circle",1.0,0.0,0.0,a*self.xpos1[0]+b*self.xpos2[0]+self.fft["nx"]/2-1,a*self.xpos1[1]+b*self.xpos2[1]+self.fft["ny"]/2,3,1.0))
self.wfft.del_shapes()
self.wfft.add_shapes(shp)
self.wfft.add_shape("xtllbl",EMShape(("scrlabel",1.0,0.3,0.3,10,10,"Unit Cell: %1.2f,%1.2f"%(1.0/(hypot(*self.xpos1)*ds),1.0/(hypot(*self.xpos2)*ds)),60.0,2.0)))
# except: pass
self.wfft.updateGL()
else:
self.wfft.del_shapes()
self.wfft.updateGL()
# Now update the plots for the correct plot mode
if self.plotmode==0:
try: bgsub=self.fft1d-bg1d
except:
print "Error computing bgsub on this image"
return
self.wplot.set_data((s,bgsub),"fg-bg",quiet=True,color=0)
fit=array(ctf.compute_1d(len(s)*2,ds,Ctf.CtfType.CTF_AMP)) # The fit curve
fit=fit*fit # squared
# auto-amplitude for b-factor adjustment
rto,nrto=0,0
for i in range(int(.04/ds)+1,min(int(0.15/ds),len(s)-1)):
if bgsub[i]>0 :
rto+=fit[i]
nrto+=fabs(bgsub[i])
if nrto==0 : rto=1.0
else : rto/=nrto
fit=[fit[i]/rto for i in range(len(s))]
# print ctf_cmp((self.sdefocus.value,self.sbfactor.value,rto),(ctf,bgsub,int(.04/ds)+1,min(int(0.15/ds),len(s)-1),ds,self.sdefocus.value))
self.wplot.set_data((s,fit),"fit",color=1)
self.wplot.setAxisParms("s (1/"+ "$\AA$" +")","Intensity (a.u)")
elif self.plotmode==1:
self.wplot.set_data((s[1:],self.fft1d[1:]),"fg",quiet=True,color=1)
self.wplot.set_data((s[1:],bg1d[1:]),"bg",color=0)
self.wplot.setAxisParms("s (1/"+ "$\AA$" +")","Intensity (a.u)")
elif self.plotmode==2:
if self.fft1dang==None: self.recalc_real()
bgsub=self.fft1d-bg1d
bgsuba=[array(self.fft1dang[i])-bg1d for i in xrange(4)]
# Write the current image parameters to the database
# for i in xrange(4): bgsuba[i][0]=0
self.wplot.set_data((s,bgsub),"fg",quiet=True,color=0)
self.wplot.set_data((s[3:],bgsuba[0][3:]),"fg 0-45",quiet=True,color=2)
self.wplot.set_data((s[3:],bgsuba[1][3:]),"fg 45-90",quiet=True,color=3)
self.wplot.set_data((s[3:],bgsuba[2][3:]),"fg 90-135",quiet=True,color=4)
self.wplot.set_data((s[3:],bgsuba[3][3:]),"fg 135-180",quiet=True,color=6)
fit=array(ctf.compute_1d(len(s)*2,ds,Ctf.CtfType.CTF_AMP)) # The fit curve
fit=fit*fit # squared
# auto-amplitude for b-factor adjustment
rto,nrto=0,0
for i in range(int(.04/ds)+1,min(int(0.15/ds),len(s)-1)):
if bgsub[i]>0 :
rto+=fit[i]
nrto+=fabs(bgsub[i])
if nrto==0 : rto=1.0
else : rto/=nrto
fit/=rto
self.wplot.set_data((s,fit),"fit",color=1)
self.wplot.setAxisParms("s (1/"+ "$\AA$" + ")","Intensity (a.u)")
elif self.plotmode==3:
if self.fft1dang==None: self.recalc_real()
#bgsub=self.fft1d-bg1d
#bgsuba=[array(self.fft1dang[i])-bg1d for i in xrange(4)]
fg=self.fft1d
fga=[array(self.fft1dang[i]) for i in xrange(4)]
for i in xrange(4): fga[i][0]=0
self.wplot.set_data((s,fg),"fg",quiet=True,color=0)
self.wplot.set_data((s,fga[0]),"fg 0-45",quiet=True,color=2)
self.wplot.set_data((s,fga[1]),"fg 45-90",quiet=True,color=3)
self.wplot.set_data((s,fga[2]),"fg 90-135",quiet=True,color=4)
self.wplot.set_data((s,fga[3]),"fg 135-180",quiet=True,color=6)
#fit=array(ctf.compute_1d(len(s)*2,ds,Ctf.CtfType.CTF_AMP)) # The fit curve
#fit=fit*fit # squared
## auto-amplitude for b-factor adjustment
#rto,nrto=0,0
#for i in range(int(.04/ds)+1,min(int(0.15/ds),len(s)-1)):
#if bgsub[i]>0 :
#rto+=fit[i]
#nrto+=fabs(bgsub[i])
#if nrto==0 : rto=1.0
#else : rto/=nrto
#fit/=rto
#self.wplot.set_data((s,fit),"fit",color=1)
#self.wplot.setAxisParms("s (1/"+ "$\AA$" + ")","Intensity (a.u)")
if self.plotmode==4:
if min(bg1d)<=0.0 : bg1d+=min(bg1d)+max(bg1d)/10000.0
ssnr=(self.fft1d-bg1d)/bg1d
self.wplot.set_data((s,ssnr),"SSNR",quiet=True,color=0)
#fit=array(ctf.compute_1d(len(s)*2,ds,Ctf.CtfType.CTF_AMP)) # The fit curve
#fit=fit*fit # squared
## auto-amplitude for b-factor adjustment
#rto,nrto=0,0
#for i in range(int(.04/ds)+1,min(int(0.15/ds),len(s)-1)):
#if bgsub[i]>0 :
#rto+=fit[i]
#nrto+=fabs(bgsub[i])
#if nrto==0 : rto=1.0
#else : rto/=nrto
#fit=[fit[i]/rto for i in range(len(s))]
## print ctf_cmp((self.sdefocus.value,self.sbfactor.value,rto),(ctf,bgsub,int(.04/ds)+1,min(int(0.15/ds),len(s)-1),ds,self.sdefocus.value))
#self.wplot.set_data((s,fit),"fit",color=1)
self.wplot.setAxisParms("s (1/"+ "$\AA$" + ")","Est. SSNR")
def timeOut(self):
if self.busy : return
# Redisplay before spawning thread for more interactive display
if self.needredisp :
try: self.redisplay()
except: pass
# Spawn a thread to reprocess the data
if self.needupdate and self.procthread==None:
self.procthread=threading.Thread(target=self.recalc_real)
self.procthread.start()
if self.errors:
QtGui.QMessageBox.warning(None,"Error","The following processors encountered errors during processing of 1 or more images:"+"\n".join(self.errors))
self.errors=None
def doRefit(self):
parms=self.parms[self.curset]
apix=self.sapix.getValue()
ds=1.0/(apix*parms[0]*parms[5])
try:
parms[1]=e2ctf.ctf_fit(self.fft1d,parms[1].background,parms[1].background,self.fft,self.fftbg,parms[1].voltage,parms[1].cs,parms[1].ampcont,apix,bgadj=False,autohp=True,verbose=1)
except:
print "CTF Autofit Failed"
traceback.print_exc()
parms[1].defocus=1.0
self.sdefocus.setValue(parms[1].defocus,True)
self.sbfactor.setValue(parms[1].bfactor,True)
self.sampcont.setValue(parms[1].ampcont,True)
self.update_plot()
def unImport(self,val=None):
print "unimport ",base_name(self.setlist.item(self.curset).text())
item=base_name(self.setlist.item(self.curset).text())
try: os.unlink("micrographs/%s.hdf"%item)
except: print "Couldn't delete micrographs/%s.hdf"%item
def doImport(self,val=None):
"""Imports the currently selected image into a project"""
print "import ",base_name(self.setlist.item(self.curset).text())
# This is just the (presumably) unique portion of the filename
item=base_name(self.setlist.item(self.curset).text())
# create directory if necessary
if not os.access("micrographs",os.R_OK) :
try : os.mkdir("micrographs")
except:
QtGui.QMessageBox.warning(self,"Error !","Cannot create micrographs directory")
return
#db=db_open_dict("bdb:micrographs#%s"%item)
self.data["ctf"]=self.parms[self.curset][1]
if self.cinvert.getValue()!=0 : self.data.mult(-1)
if self.cxray.getValue() : self.data.process_inplace("threshold.clampminmax.nsigma",{"nsigma":4,"tomean":1})
self.data.write_image("micrographs/%s.hdf"%item)
self.writeCurParm()
# js_open_dict(info_name(item))["ctf"]=[self.parms[val][1],None,None,None,None]
# db_parms=db_open_dict("bdb:e2ctf.parms")
# db_parms[item]=[self.parms[val][1].to_string(),self.fft1d,self.parms[val][1].background,self.parms[val][4]]
def writeCurParm(self):
"Called to store the current parameters for this image to the frameparms database"
parms=self.parms[self.curset]
js=js_open_dict(info_name(self.curfilename))
js.setval("ctf_frame",parms,True)
js.setval("quality",parms[4])
# db_fparms=db_open_dict("bdb:e2ctf.frameparms")
# curtag=item_name(str(self.setlist.item(self.curset).text()))
# db_fparms[curtag]=self.parms[self.curset]
def newSet(self,val):
"called when a new data set is selected from the list"
# Write the current image parameters to the database
if val!=self.curset : self.writeCurParm()
# now set the new item
self.curset=val
# This deals with Z stacks and multi image files
fsp=str(self.setlist.item(val).text())
if "," in fsp :
fsp,n=fsp.split(",")
self.data=EMData(fsp,int(n)) # read the image from disk
elif ";" in fsp :
fsp,n=fsp.split(";")
hdr=EMData(fsp,0,True)
self.data=EMData(fsp,0,False,Region(0,0,int(n),hdr["nx"],hdr["ny"],1)) # read the image from disk
else :
self.data=EMData(fsp,0) # read the image from disk
self.wimage.setWindowTitle("e2evalimage - " + fsp.split("/")[-1])
self.wfft.setWindowTitle("e2evalimage - 2D FFT - "+fsp.split("/")[-1])
self.wplot.setWindowTitle("e2evalimage - Plot - "+fsp.split("/")[-1])
if self.defaultapix!=None : self.data["apix_x"]=self.defaultapix
self.wimage.set_data(self.data)
self.curfilename = str(self.setlist.item(val).text())
ctf=self.parms[val][1]
# if voltage is 0, we need to initialize
if ctf.voltage==0:
try: ctf.voltage=self.data["microscope_voltage"]
except: pass
if ctf.voltage==0 : ctf.voltage=self.defaultvoltage
try: ctf.cs=self.data["microscope_cs"]
except: pass
if ctf.cs==0 : ctf.cs=self.defaultcs
ctf.apix=self.data["apix_x"]
ctf.defocus=0.0 #triggers fitting
ctf.bfactor=200.0
ctf.ampcont=self.defaultac
self.sdefocus.setValue(ctf.defocus,True)
self.sbfactor.setValue(ctf.bfactor,True)
self.sapix.setValue(ctf.apix,True)
self.sampcont.setValue(ctf.ampcont,True)
self.svoltage.setValue(ctf.voltage,True)
self.scs.setValue(ctf.cs,True)
self.sboxsize.setValue(self.parms[val][0],True)
self.squality.setValue(self.parms[val][4],True)
#if self.guiim != None:
## print self.data
#self.guiim.set_data(self.data[val][4])
#if self.guiiminit:
#self.guiim.optimally_resize()
#self.guiiminit = False
#self.guiim.updateGL()
self.recalc()
def recalc(self):
self.needupdate=True
def recalc_real(self):
"Called to recompute the power spectra, also updates plot"
self.needupdate=False
if self.data==None :
self.procthread=None
return
self.incalc=True # to avoid incorrect plot updates
# To simplify expressions
parms=self.parms[self.curset]
apix=self.sapix.getValue()
if len(parms)==5 : parms.append(1) # for old projects where there was no oversampling specification
else: parms[5]=max(1,int(parms[5]))
ds=1.0/(apix*parms[0]*parms[5])
# Mode where user drags the box around the parent image
if self.calcmode==0:
# extract the data and do an fft
clip=self.data.get_clip(Region(parms[2][0],parms[2][1],parms[0],parms[0]))
clip.process_inplace("normalize.edgemean")
if parms[5]>1 :
clip=clip.get_clip(Region(0,0,parms[0]*parms[5],parms[0]*parms[5])) # since we aren't using phases, doesn't matter if we center it or not
self.fft=clip.do_fft()
# self.fft.mult(1.0/parms[0]**2)
self.fft.mult(1.0/parms[0])
# mode where user selects/deselcts tiled image set
elif self.calcmode==1:
# update the box display on the image
nx=self.data["nx"]/parms[0]-1
self.fft=None
nbx=0
for x in range(nx):
for y in range(self.data["ny"]/parms[0]-1):
# User deselected this one
if int(x+y*nx) in parms[3] : continue
# read the data and make the FFT
clip=self.data.get_clip(Region(x*parms[0]+parms[0]/2,y*parms[0]+parms[0]/2,parms[0],parms[0]))
clip.process_inplace("normalize.edgemean")
if parms[5]>1 :
clip=clip.get_clip(Region(0,0,parms[0]*parms[5],parms[0]*parms[5])) # since we aren't using phases, doesn't matter if we center it or not
fft=clip.do_fft()
# fft.mult(parms[0])
fft.ri2inten()
if self.fft==None: self.fft=fft
else: self.fft+=fft
nbx+=1
self.fft.mult(1.0/(nbx*parms[0]**2))
self.fft.process_inplace("math.sqrt")
self.fft["is_intensity"]=0 # These 2 steps are done so the 2-D display of the FFT looks better. Things would still work properly in 1-D without it
# self.fft.mult(1.0/(nbx*parms[0]**2))
self.fftbg=self.fft.process("math.nonconvex")
self.fft1d=self.fft.calc_radial_dist(self.fft.get_ysize()/2,0.0,1.0,1) # note that this handles the ri2inten averages properly
if self.plotmode==2 or self.plotmode==3:
self.fft1dang=array(self.fft.calc_radial_dist(self.fft.get_ysize()/2,0.0,1.0,4,self.sang45.getValue()*.017453292,1)) # This form generates 4 sequential power spectra representing angular ranges
self.fft1dang=self.fft1dang.reshape((4,self.fft.get_ysize()/2))
else:
self.fft1dang=None
# Compute 1-D curve and background
bg_1d=e2ctf.low_bg_curve(self.fft1d,ds)
parms[1].background=bg_1d
parms[1].dsbg=ds
self.fft1d=array(self.fft1d)
self.needredisp=True
self.incalc=False
time.sleep(.2) # help make sure update has a chance
self.procthread=None
# dbquality = self.db[os.path.basename(self.curfilename)]
# print dbquality
# item=item_name(self.curfilename)
# db=db_open_dict("bdb:e2ctf.parms")
# if db[item]==None or db[item[3]]==None : db[item]=[parms[1].to_string(),self.fft1d,parms[1].background,5]
# # print item,db[item][3]
# try: self.squality.setValue(int(db[item[3]]))
# except: self.squality.setValue(5)
def redisplay(self):
if self.incalc: return
self.needredisp=False
self.busy=True
parms=self.parms[self.curset]
apix=self.sapix.getValue()
ds=1.0/(apix*parms[0]*parms[5])
# Fitting not done yet. Need to make 2D background somehow
if parms[1].defocus==0:
self.doRefit()
self.wimage.show()
self.wfft.show()
self.wplot.show()
self.update_plot()
# To simplify expressions
if self.calcmode==0:
# update the box display on the image
self.wimage.del_shapes()
self.wimage.add_shape("box",EMShape(("rect",.3,.9,.3,parms[2][0],parms[2][1],parms[2][0]+parms[0],parms[2][1]+parms[0],1)))
self.wimage.updateGL()
elif self.calcmode==1:
# update the box display on the image
nx=self.data["nx"]/parms[0]-1
shp={}
for x in range(nx):
for y in range(self.data["ny"]/parms[0]-1):
# User deselected this one
if int(x+y*nx) in parms[3] : continue
# Make a shape for this box
shp["box%02d%02d"%(x,y)]=EMShape(("rect",.3,.9,.3,(x+.5)*parms[0],(y+.5)*parms[0],(x+1.5)*parms[0],(y+1.5)*parms[0],1))
self.wimage.del_shapes()
self.wimage.add_shapes(shp)
self.wimage.updateGL()
if self.f2dmode>0 :
if self.f2dmode==1 : self.wfft.set_data(self.fft-self.fftbg)
else : self.wfft.set_data(self.fftbg)
else :
self.wfft.set_data(self.fft)
self.busy=False
def newCalcMode(self,mode):
self.calcmode=mode
self.recalc()
def new2DMode(self,mode):
self.f2dmode=mode
self.recalc()
def new2DAnMode(self,mode):
self.f2danmode=mode
self.needredisp=True
def newPlotMode(self,mode):
self.plotmode=mode
self.wplot.set_data(None,replace=True,quiet=True) # clear the data so plots are properly redisplayed, but don't update the display
self.needredisp=True
def newBox(self):
parms=self.parms[self.curset]
parms[0]=self.sboxsize.value
# parms[5]=self.soversamp.value
parms[5]=1
parms[3]=set()
self.recalc()
def newQualityFactor(self):
parms=self.parms[self.curset]
parms[4]=self.squality.value
def newCTF(self) :
parms=self.parms[self.curset]
parms[1].defocus=self.sdefocus.value
parms[1].bfactor=self.sbfactor.value
parms[1].dfdiff=self.sdfdiff.value
parms[1].dfang=self.sdfang.value
parms[1].apix=self.sapix.value
parms[1].ampcont=self.sampcont.value
parms[1].voltage=self.svoltage.value
parms[1].cs=self.scs.value
self.needredisp=True
def imgmousedown(self,event) :
if self.calcmode==0:
m=self.wimage.scr_to_img((event.x(),event.y()))
parms=self.parms[self.curset]
parms[2]=(m[0]-parms[0]/2,m[1]-parms[0]/2)
self.recalc()
self.needredisp=True
#self.guiim.add_shape("cen",["rect",.9,.9,.4,x0,y0,x0+2,y0+2,1.0])
def imgmousedrag(self,event) :
if self.calcmode==0:
m=self.wimage.scr_to_img((event.x(),event.y()))
parms=self.parms[self.curset]
parms[2]=(m[0]-parms[0]/2,m[1]-parms[0]/2)
self.needredisp=True
self.recalc()
# box deletion when shift held down
#if event.modifiers()&Qt.ShiftModifier:
#for i,j in enumerate(self.boxes):
def imgmouseup(self,event) :
m=self.wimage.scr_to_img((event.x(),event.y()))
if self.calcmode==1:
parms=self.parms[self.curset]
nx=self.data["nx"]/parms[0]-1
grid=int((m[0]-parms[0]/2)/parms[0])+int((m[1]-parms[0]/2)/parms[0])*nx
if grid in parms[3] : parms[3].remove(grid)
else: parms[3].add(grid)
self.needredisp=True
self.recalc()
def fftmousedown(self,event,m) :
#m=self.wfft.scr_to_img((event.x(),event.y()))
if self.f2danmode==1:
self.ringrad=hypot(m[0]-self.fft["nx"]/2,m[1]-self.fft["ny"]/2)
self.needredisp=True
elif self.f2danmode==2:
if (event.modifiers()&Qt.ControlModifier): self.xpos2=((m[0]-self.fft["nx"]/2)/3.0,(m[1]-self.fft["ny"]/2)/3.0)
else: self.xpos1=((m[0]-self.fft["nx"]/2)/3.0,(m[1]-self.fft["ny"]/2)/3.0)
self.needredisp=True
#self.guiim.add_shape("cen",["rect",.9,.9,.4,x0,y0,x0+2,y0+2,1.0])
def fftmousedrag(self,event,m) :
#m=self.wfft.scr_to_img((event.x(),event.y()))
if self.f2danmode==1:
self.ringrad=hypot(m[0]-self.fft["nx"]/2,m[1]-self.fft["ny"]/2)
self.needredisp=True
elif self.f2danmode==2:
if (event.modifiers()&Qt.ControlModifier): self.xpos2=((m[0]-self.fft["nx"]/2)/3.0,(m[1]-self.fft["ny"]/2)/3.0)
else: self.xpos1=((m[0]-self.fft["nx"]/2)/3.0,(m[1]-self.fft["ny"]/2)/3.0)
self.needredisp=True
# box deletion when shift held down
#if event.modifiers()&Qt.ShiftModifier:
#for i,j in enumerate(self.boxes):
def fftmouseup(self,event,m) :
"up"
#m=self.wfft.scr_to_img((event.x(),event.y()))
def plotmousedown(self,event) :
"mousedown in plot"