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 = EMImage2DWidget()
# self.mx_display = EMImageMXWidget()
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 = EMPlot2DWidget()
# 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 plot(files, app):
from emplot2d import EMPlot2DWidget
plotw = EMPlot2DWidget(application=app)
for f in files:
plotw.set_data_from_file(f, quiet=True)
plotw.setWindowTitle("2D Plot")
app.show_specific(plotw)
return plotw
def __init__(self, mode=0, cs=0., twod=False):
QtGui.QMainWindow.__init__(self)
if twod:
self.twodview = EMImage2DWidget()
widget = Microscope(self, None, None, self.twodview, mode, cs)
else:
self.imgview = EMImage2DWidget()
self.pltview = EMPlot2DWidget()
widget = Microscope(self, self.imgview, self.pltview, None, mode,
cs)
#widget = Microscope(self, None, None, None, mode, cs)
#widget = Microscope(self, None, None)
self.closeEvent = widget.closeEvent
self.setCentralWidget(widget)
def main():
progname = os.path.basename(sys.argv[0])
usage = """prog [options]
This is a program to compute the resolution of a n averaged subtomogram. Right now it is very simple simple divide the aligned
subtomos into even/odd classes, average and then compute the FSC. In the future this program will be extended to compute
resolution of an averged subtomo vs a reference and hopefuly of a single sub/tomogram.
"""
parser = EMArgumentParser(usage=usage,version=EMANVERSION)
parser.add_pos_argument(name="tomodir",help="The refinement directory to use for tomoresolution.", default="", guitype='dirbox', dirbasename='spt_', row=0, col=0,rowspan=1, colspan=2)
parser.add_header(name="tomoresoheader", help='Options below this label are specific to e2tomoresolution', title="### e2tomoresolution options ###", row=1, col=0, rowspan=1, colspan=2)
parser.add_argument("--averager",type=str,help="The averager used to generate the averages. Default is \'mean\'.",default="mean", guitype='combobox', choicelist='dump_averagers_list()', row=2, col=0, rowspan=1, colspan=2)
parser.add_argument("--sym", type=str,help="The recon symmetry", default="c1", guitype='symbox', row=3, col=0, rowspan=1, colspan=2)
parser.add_argument("--mask", type=str,help="The mask to apply before FSC calculation", default=None, guitype='comboparambox', choicelist='re_filter_list(dump_processors_list(),\'mask\')', row=4, col=0, rowspan=1, colspan=2)
parser.add_argument("--ppid", type=int, help="Set the PID of the parent process, used for cross platform PPID",default=-1)
(options, args) = parser.parse_args()
if options.mask: options.mask = parsemodopt(options.mask)
logid=E2init(sys.argv,options.ppid)
fscstrategy = EvenOddReso(args[0], options)
fscstrategy.execute()
results_db = db_open_dict("bdb:%s#convergence.results"%args[0])
results_db["tomo_fsc"] = [fscstrategy.getFreq(),fscstrategy.getFSC(),fscstrategy.getError()]
results_db.close()
E2end(logid)
# Plot FSC
app = EMApp()
plot = EMPlot2DWidget()
plot.set_data((fscstrategy.getFreq(),fscstrategy.getFSC()))
plot.show()
app.exec_()
def __init__(self,
application,
apix=1.0,
voltage=300.0,
cs=4.1,
ac=10.0,
samples=256):
"""CTF simulation dialog
"""
try:
from emimage2d import EMImage2DWidget
except:
print "Cannot import EMAN image GUI objects (EMImage2DWidget)"
sys.exit(1)
try:
from emplot2d import EMPlot2DWidget
except:
print "Cannot import EMAN plot GUI objects (is matplotlib installed?)"
sys.exit(1)
self.app = weakref.ref(application)
self.df_voltage = voltage
self.df_apix = apix
self.df_cs = cs
self.df_ac = ac
self.df_samples = samples
self.img = None
QtGui.QWidget.__init__(self, None)
self.setWindowIcon(QtGui.QIcon(get_image_directory() + "ctf.png"))
self.data = []
self.curset = 0
self.plotmode = 0
self.guiim = EMImage2DWidget(application=self.app())
self.guiiminit = True # a flag that's used to auto resize the first time the gui's set_data function is called
self.guiplot = EMPlot2DWidget(application=self.app())
# self.guirealim=EMImage2DWidget(application=self.app()) # This will show the original particle images
# self.guirealim.connect(self.guirealim,QtCore.SIGNAL("keypress"),self.realimgkey)
self.guiim.connect(self.guiim, QtCore.SIGNAL("mousedown"),
self.imgmousedown)
self.guiim.connect(self.guiim, QtCore.SIGNAL("mousedrag"),
self.imgmousedrag)
self.guiim.connect(self.guiim, QtCore.SIGNAL("mouseup"),
self.imgmouseup)
self.guiplot.connect(self.guiplot, QtCore.SIGNAL("mousedown"),
self.plotmousedown)
self.guiim.mmode = "app"
# This object is itself a widget we need to set up
self.hbl = QtGui.QHBoxLayout(self)
self.hbl.setMargin(0)
self.hbl.setSpacing(6)
self.hbl.setObjectName("hbl")
# plot list and plot mode combobox
self.vbl2 = QtGui.QVBoxLayout()
self.setlist = MyListWidget(self)
self.setlist.setSizePolicy(QtGui.QSizePolicy.Preferred,
QtGui.QSizePolicy.Expanding)
self.vbl2.addWidget(self.setlist)
self.splotmode = QtGui.QComboBox(self)
self.splotmode.addItem("Amplitude")
self.splotmode.addItem("Intensity")
self.splotmode.addItem("Int w sum")
self.splotmode.addItem("Amp w sum")
self.vbl2.addWidget(self.splotmode)
self.hbl.addLayout(self.vbl2)
# ValSliders for CTF parameters
self.vbl = QtGui.QVBoxLayout()
self.vbl.setMargin(0)
self.vbl.setSpacing(6)
self.vbl.setObjectName("vbl")
self.hbl.addLayout(self.vbl)
#self.samp = ValSlider(self,(0,5.0),"Amp:",0)
#self.vbl.addWidget(self.samp)
self.imginfo = QtGui.QLabel("Info", self)
self.vbl.addWidget(self.imginfo)
self.sdefocus = ValSlider(self, (0, 5), "Defocus:", 0, 90)
self.vbl.addWidget(self.sdefocus)
self.sbfactor = ValSlider(self, (0, 1600), "B factor:", 0, 90)
self.vbl.addWidget(self.sbfactor)
self.sdfdiff = ValSlider(self, (0, 1), "DF Diff:", 0, 90)
self.vbl.addWidget(self.sdfdiff)
self.sdfang = ValSlider(self, (0, 180), "Df Angle:", 0, 90)
self.vbl.addWidget(self.sdfang)
self.sampcont = ValSlider(self, (0, 100), "% AC", 0, 90)
self.vbl.addWidget(self.sampcont)
self.sapix = ValSlider(self, (.2, 10), "A/Pix:", 2, 90)
self.vbl.addWidget(self.sapix)
self.svoltage = ValSlider(self, (0, 1000), "Voltage (kV):", 0, 90)
self.vbl.addWidget(self.svoltage)
self.scs = ValSlider(self, (0, 5), "Cs (mm):", 0, 90)
self.vbl.addWidget(self.scs)
self.ssamples = ValSlider(self, (32, 1024), "# Samples:", 0, 90)
self.ssamples.setIntonly(True)
self.vbl.addWidget(self.ssamples)
self.hbl_buttons = QtGui.QHBoxLayout()
self.newbut = QtGui.QPushButton("New")
self.hbl_buttons.addWidget(self.newbut)
self.vbl.addLayout(self.hbl_buttons)
self.on_new_but()
QtCore.QObject.connect(self.sdefocus, QtCore.SIGNAL("valueChanged"),
self.newCTF)
QtCore.QObject.connect(self.sbfactor, QtCore.SIGNAL("valueChanged"),
self.newCTF)
QtCore.QObject.connect(self.sdfdiff, QtCore.SIGNAL("valueChanged"),
self.newCTF)
QtCore.QObject.connect(self.sdfang, QtCore.SIGNAL("valueChanged"),
self.newCTF)
QtCore.QObject.connect(self.sapix, QtCore.SIGNAL("valueChanged"),
self.newCTF)
QtCore.QObject.connect(self.sampcont, 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.ssamples, QtCore.SIGNAL("valueChanged"),
self.newCTF)
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.splotmode,
QtCore.SIGNAL("currentIndexChanged(int)"),
self.newPlotMode)
QtCore.QObject.connect(self.newbut, QtCore.SIGNAL("clicked(bool)"),
self.on_new_but)
self.resize(
720, 380
) # figured these values out by printing the width and height in resize event
E2loadappwin("e2ctfsim", "main", self)
E2loadappwin("e2ctfsim", "image", self.guiim.qt_parent)
# E2loadappwin("e2ctf","realimage",self.guirealim.qt_parent)
E2loadappwin("e2ctfsim", "plot", self.guiplot.qt_parent)
self.setWindowTitle("CTF")
def __init__(self, application, data):
"""Implements the CTF fitting dialog using various EMImage and EMPlot2D widgets
'data' is a list of (filename,ctf,im_1d,bg_1d,im_2d,bg_2d)
"""
try:
from emimage2d import EMImage2DWidget
except:
print "Cannot import EMAN image GUI objects (EMImage2DWidget)"
sys.exit(1)
try:
from emplot2d import EMPlot2DWidget
except:
print "Cannot import EMAN plot GUI objects (is matplotlib installed?)"
sys.exit(1)
self.app = weakref.ref(application)
QtGui.QWidget.__init__(self, None)
self.setWindowIcon(QtGui.QIcon(get_image_directory() + "ctf.png"))
self.data = data
self.curset = 0
self.plotmode = 0
self.guiim = EMImage2DWidget(application=self.app())
self.guiplot = EMPlot2DWidget(application=self.app())
self.guiim.connect(self.guiim, QtCore.SIGNAL("mousedown"),
self.imgmousedown)
self.guiim.connect(self.guiim, QtCore.SIGNAL("mousedrag"),
self.imgmousedrag)
self.guiim.connect(self.guiim, QtCore.SIGNAL("mouseup"),
self.imgmouseup)
self.guiplot.connect(self.guiplot, QtCore.SIGNAL("mousedown"),
self.plotmousedown)
self.guiim.mmode = "app"
# This object is itself a widget we need to set up
self.hbl = QtGui.QHBoxLayout(self)
self.hbl.setMargin(0)
self.hbl.setSpacing(6)
self.hbl.setObjectName("hbl")
# plot list and plot mode combobox
self.vbl2 = QtGui.QVBoxLayout()
self.setlist = QtGui.QListWidget(self)
self.setlist.setSizePolicy(QtGui.QSizePolicy.Preferred,
QtGui.QSizePolicy.Expanding)
self.vbl2.addWidget(self.setlist)
self.splotmode = QtGui.QComboBox(self)
self.splotmode.addItem("Bgsub & fit")
self.splotmode.addItem("Ptcl & BG power")
self.splotmode.addItem("SNR")
self.splotmode.addItem("Smoothed SNR")
self.splotmode.addItem("Integrated SNR")
self.splotmode.addItem("Total CTF")
self.vbl2.addWidget(self.splotmode)
self.hbl.addLayout(self.vbl2)
# ValSliders for CTF parameters
self.vbl = QtGui.QVBoxLayout()
self.vbl.setMargin(0)
self.vbl.setSpacing(6)
self.vbl.setObjectName("vbl")
self.hbl.addLayout(self.vbl)
#self.samp = ValSlider(self,(0,5.0),"Amp:",0)
#self.vbl.addWidget(self.samp)
self.sdefocus = ValSlider(self, (0, 5), "Defocus:", 0, 90)
self.vbl.addWidget(self.sdefocus)
self.sbfactor = ValSlider(self, (0, 1600), "B factor:", 0, 90)
self.vbl.addWidget(self.sbfactor)
self.sampcont = ValSlider(self, (0, 100), "% AC", 0, 90)
self.vbl.addWidget(self.sampcont)
# self.sapix=ValSlider(self,(.2,10),"A/Pix:",2,90)
# self.vbl.addWidget(self.sapix)
self.svoltage = ValSlider(self, (0, 500), "Voltage (kV):", 0, 90)
self.vbl.addWidget(self.svoltage)
self.scs = ValSlider(self, (0, 5), "Cs (mm):", 0, 90)
self.vbl.addWidget(self.scs)
self.hbl_buttons = QtGui.QHBoxLayout()
self.saveparms = QtGui.QPushButton("Save parms")
self.recallparms = QtGui.QPushButton("Recall")
self.output = QtGui.QPushButton("Output")
self.hbl_buttons.addWidget(self.saveparms)
self.hbl_buttons.addWidget(self.recallparms)
self.hbl_buttons2 = QtGui.QHBoxLayout()
self.hbl_buttons2.addWidget(self.output)
self.vbl.addLayout(self.hbl_buttons)
self.vbl.addLayout(self.hbl_buttons2)
QtCore.QObject.connect(self.sdefocus, QtCore.SIGNAL("valueChanged"),
self.newCTF)
QtCore.QObject.connect(self.sbfactor, QtCore.SIGNAL("valueChanged"),
self.newCTF)
# QtCore.QObject.connect(self.sapix, QtCore.SIGNAL("valueChanged"), self.newCTF)
QtCore.QObject.connect(self.sampcont, 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.setlist,
QtCore.SIGNAL("currentRowChanged(int)"),
self.newSet)
QtCore.QObject.connect(self.splotmode,
QtCore.SIGNAL("currentIndexChanged(int)"),
self.newPlotMode)
QtCore.QObject.connect(self.saveparms, QtCore.SIGNAL("clicked(bool)"),
self.on_save_params)
QtCore.QObject.connect(self.recallparms,
QtCore.SIGNAL("clicked(bool)"),
self.on_recall_params)
QtCore.QObject.connect(self.output, QtCore.SIGNAL("clicked(bool)"),
self.on_output)
self.update_data()
self.update_data()
self.resize(
460, 380
) # figured these values out by printing the width and height in resize event
self.setWindowTitle("CTF")
def menu_add_plotwin(self):
if self.viewer == None: return
self.viewer.append(EMPlot2DWidget())
self.viewer[-1].show()
self.needupdate = 1
def __init__(self,images,voltage=None,apix=None,cs=None,ac=10.0,box=512,usefoldername=False,constbfactor=-1,fitastig=False):
"""Implements the CTF fitting dialog using various EMImage and EMPlot2D widgets
'data' is a list of (filename,ctf,im_1d,bg_1d,quality)
'parms' is [box size,ctf,box coord,set of excluded boxnums,quality,oversampling]
"""
try:
from emimage2d import EMImage2DWidget
except:
print "Cannot import EMAN image GUI objects (EMImage2DWidget)"
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.fitastig=fitastig
self.nodir=not usefoldername
self.data=None
self.curset=0
self.calcmode=1
self.f2dmode=0
self.f2danmode=0
self.plotmode=0
self.curfilename = None
self.ringrad=1
self.xpos1=(10,0)
self.xpos2=(0,10)
# self.db = db_open_dict('bdb:mgquality')
self.defaultvoltage=voltage
self.defaultapix=apix
self.defaultcs=cs
self.defaultac=ac
self.constbfactor=constbfactor
# Per image parameters to keep track of
# for each image [box size,ctf,box coord,set of excluded boxnums,quality,oversampling]
self.parms=[]
# db_fparms=db_open_dict("bdb:e2ctf.frameparms",True)
# This little block of code deals with Z stacks of images and multiple image files,
# rewriting the name(s) with an enumeration including ;number or ,number
newimages=[]
for i in images:
n=EMUtil.get_image_count(i)
if n!=1:
for j in xrange(n): newimages.append(i+",%d"%j)
else:
h=EMData(i,0,True) # read header
n=h["nz"]
if n!=1:
for j in xrange(n): newimages.append(i+";%d"%j)
else : newimages.append(i)
images=newimages
# Now we try to restore old image information
for i in images:
try:
pd=js_open_dict(info_name(i,nodir=self.nodir))
parms=pd["ctf_frame"]
parms[4]=pd["quality"]
if box>=64 and parms[0]!=box:
parms[0]=box
parms[3]=set()
# if parms==None : raise Exception
except:
ctf = EMAN2Ctf()
ctf.from_dict({'defocus':0.0,'dfdiff':0.0,'dfang':0.0,'bfactor':200.0,'ampcont':self.defaultac,'voltage':200.0,'cs':4.1,'apix':1.0,'dsbg':-1})
if self.defaultvoltage!=None : ctf.voltage=self.defaultvoltage
if self.defaultcs!=None : ctf.cs=self.defaultcs
if self.defaultapix!=None : ctf.apix=self.defaultapix
parms=[int(box),ctf,(256,256),set(),5,1]
print "Initialize new parms for: ",base_name(i)
if self.constbfactor>0 : parms[1].bfactor=self.constbfactor
if parms[0]<64 :
parms[0]=512
parms[3]=set()
self.parms.append(parms)
self.wimage=EMImage2DWidget()
self.wimage.setWindowTitle("e2evalimage - Micrograph")
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.wfft.connect(self.wfft,QtCore.SIGNAL("mousedown"),self.fftmousedown)
self.wfft.connect(self.wfft,QtCore.SIGNAL("mousedrag"),self.fftmousedrag)
self.wfft.connect(self.wfft,QtCore.SIGNAL("mouseup") ,self.fftmouseup)
self.wplot.connect(self.wplot,QtCore.SIGNAL("mousedown"),self.plotmousedown)
self.wimage.mmode="app"
self.wfft.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.lcalcmode=QtGui.QLabel("Region:",self)
self.gbl.addWidget(self.lcalcmode,10,0)
self.scalcmode=QtGui.QComboBox(self)
self.scalcmode.addItem("Single Region")
self.scalcmode.addItem("Tiled Boxes")
self.scalcmode.setCurrentIndex(1)
self.gbl.addWidget(self.scalcmode,10,1)
self.lcalcmode=QtGui.QLabel("2D FFT:",self)
self.gbl.addWidget(self.lcalcmode,11,0)
self.s2dmode=QtGui.QComboBox(self)
self.s2dmode.addItem("Power Spectrum")
self.s2dmode.addItem("Bg Subtracted")
self.s2dmode.addItem("Background")
self.gbl.addWidget(self.s2dmode,11,1)
self.lcalcmode=QtGui.QLabel("Annotate:",self)
self.gbl.addWidget(self.lcalcmode,12,0)
self.s2danmode=QtGui.QComboBox(self)
self.s2danmode.addItem("Ctf Zeroes")
self.s2danmode.addItem("Resolution Ring")
self.s2danmode.addItem("2-D Xtal")
self.s2danmode.addItem("None")
self.gbl.addWidget(self.s2danmode,12,1)
self.lcalcmode=QtGui.QLabel("Plot:",self)
self.gbl.addWidget(self.lcalcmode,13,0)
self.splotmode=QtGui.QComboBox(self)
self.splotmode.addItem("Bgsub and Fit")
self.splotmode.addItem("Fg and Bg")
self.splotmode.addItem("Bgsub, 45 deg slices")
self.splotmode.addItem("Fg, 45 deg slices")
self.splotmode.addItem("SSNR (NOT BY PTCL !)")
self.gbl.addWidget(self.splotmode,13,1)
# ValSliders for CTF parameters
#self.samp = ValSlider(self,(0,5.0),"Amp:",0)
#self.vbl.addWidget(self.samp)
self.sdefocus=ValSlider(self,(0,5),"Defocus:",0.0,90)
self.gbl.addWidget(self.sdefocus,0,2,1,3)
self.sbfactor=ValSlider(self,(0,1600),"B factor:",200.0,90)
self.gbl.addWidget(self.sbfactor,1,2,1,3)
self.sdfdiff=ValSlider(self,(0,1),"DF Diff:",0,90)
self.gbl.addWidget(self.sdfdiff,2,2,1,3)
self.sdfang=ValSlider(self,(0,180),"Df Angle:",0,90)
self.gbl.addWidget(self.sdfang,3,2,1,3)
self.sampcont=ValSlider(self,(0,100),"% AC",10.0,90)
if self.defaultac!=None : self.sampcont.setValue(self.defaultac)
self.gbl.addWidget(self.sampcont,4,2,1,3)
self.sang45=ValSlider(self,(-22.5,22.5),"45 mode ang",0.0,90)
self.gbl.addWidget(self.sang45,5,2,1,3)
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("Refit")
self.gbl.addWidget(self.brefit,7,2)
self.cbgadj=CheckBox(None,"CTF BG Adj",1)
self.gbl.addWidget(self.cbgadj,7,3)
# self.sapix=ValSlider(self,(.2,10),"A/Pix:",2,90)
# self.vbl.addWidget(self.sapix)
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,(128,1024),"Box Size:",512,90)
self.sboxsize.intonly=True
self.gbl.addWidget(self.sboxsize,13,2)
# self.soversamp=ValBox(self,(0,500),"Oversample:",1,90)
# self.soversamp.intonly=True
# self.gbl.addWidget(self.soversamp,14,2) # disable oversampling for now, not properly integrated with save/recall mechanism, and not clear if it's really useful
# this is just a spacer
self.gbl.setColumnStretch(3,2)
self.bbox=QtGui.QGroupBox("Project")
self.gbl.addWidget(self.bbox,10,4,4,1)
self.bvbl=QtGui.QVBoxLayout()
self.bbox.setLayout(self.bvbl)
self.bimport=QtGui.QPushButton("Import")
self.bvbl.addWidget(self.bimport)
self.cinvert=CheckBox(None,"Invert")
self.bvbl.addWidget(self.cinvert)
self.cxray=CheckBox(None,"X-ray Pixels")
self.bvbl.addWidget(self.cxray)
QtCore.QObject.connect(self.bimport, QtCore.SIGNAL("clicked(bool)"),self.doImport)
QtCore.QObject.connect(self.brefit, QtCore.SIGNAL("clicked(bool)"),self.doRefit)
QtCore.QObject.connect(self.cbgadj, QtCore.SIGNAL("valueChanged"),self.bgAdj)
QtCore.QObject.connect(self.sdefocus, QtCore.SIGNAL("valueChanged"), self.newCTF)
QtCore.QObject.connect(self.sbfactor, QtCore.SIGNAL("valueChanged"), self.newCTF)
QtCore.QObject.connect(self.sdfdiff, QtCore.SIGNAL("valueChanged"), self.newCTF)
QtCore.QObject.connect(self.sdfang, QtCore.SIGNAL("valueChanged"), self.newCTF)
QtCore.QObject.connect(self.sapix, QtCore.SIGNAL("valueChanged"), self.newCTF)
QtCore.QObject.connect(self.sampcont, 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.sang45, QtCore.SIGNAL("valueChanged"), self.recalc_real)
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.scalcmode,QtCore.SIGNAL("currentIndexChanged(int)"),self.newCalcMode)
QtCore.QObject.connect(self.s2dmode,QtCore.SIGNAL("currentIndexChanged(int)"),self.new2DMode)
QtCore.QObject.connect(self.s2danmode,QtCore.SIGNAL("currentIndexChanged(int)"),self.new2DAnMode)
QtCore.QObject.connect(self.splotmode,QtCore.SIGNAL("currentIndexChanged(int)"),self.newPlotMode)
#QtCore.QObject.connect(self.saveparms,QtCore.SIGNAL("clicked(bool)"),self.on_save_params)
#QtCore.QObject.connect(self.recallparms,QtCore.SIGNAL("clicked(bool)"),self.on_recall_params)
#QtCore.QObject.connect(self.refit,QtCore.SIGNAL("clicked(bool)"),self.on_refit)
#QtCore.QObject.connect(self.output,QtCore.SIGNAL("clicked(bool)"),self.on_output)
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("e2evalimage - Control Panel")
self.wimage.show()
self.wfft.show()
self.wplot.show()
E2loadappwin("e2evalimage","main",self)
E2loadappwin("e2evalimage","image",self.wimage.qt_parent)
E2loadappwin("e2evalimage","fft",self.wfft.qt_parent)
E2loadappwin("e2evalimage","plot",self.wplot.qt_parent)
def __new__(cls,
data=None,
old=None,
app=None,
force_2d=False,
force_plot=False,
filename="",
replace=True):
"""This will create a new EMImage* object depending on the type of 'data'. If
old= is provided, and of the appropriate type, it will be used rather than creating
a new instance.
"""
if isinstance(data, EMData) and data.get_size() == 0:
raise RuntimeError(
"Can not display an EMData object that has no pixels")
from EMAN2 import remove_directories_from_name
if force_plot and force_2d:
# ok this sucks but it suffices for the time being
print(
"Error, the force_plot and force_2d options are mutually exclusive"
)
return None
if force_plot or (isinstance(data, EMData) and data.get_zsize() == 1
and data.get_ysize() == 1):
from emplot2d import EMPlot2DWidget
if old:
if isinstance(old, EMPlot2DWidget):
old.set_data(data, remove_directories_from_name(filename),
replace)
return old
widget = EMPlot2DWidget(application=app)
widget.set_data(data, remove_directories_from_name(filename),
replace)
return widget
elif force_2d or (isinstance(data, EMData) and data.get_zsize() == 1):
from emimage2d import EMImage2DWidget
if old:
if isinstance(old, EMImage2DWidget):
old.set_data(data, filename)
return old
widget = EMImage2DWidget(application=app)
widget.set_data(data, filename)
return widget
elif isinstance(data, EMData):
if isinstance(old, EMScene3D): widget = old
else: widget = EMScene3D()
data = EMDataItem3D(data, transform=Transform())
#data.setSelectedItem(True)
isosurface = EMIsosurface(data, transform=Transform())
widget.insertNewNode(os.path.basename(filename),
data,
parentnode=widget)
widget.insertNewNode("Iso", isosurface, parentnode=data)
return widget
elif isinstance(data, list) and isinstance(data[0], EMData):
from emimagemx import EMImageMXWidget
if old:
if isinstance(old, EMImageMXWidget):
old.set_data(data, filename)
return old
widget = EMImageMXWidget(application=app)
widget.set_data(data, filename)
return widget
elif isinstance(data, list):
from emplot3d import EMPlot3DWidgetNew
if (isinstance(data[0], list)
or isinstance(data[0], tuple)) and len(data) > 2:
if old:
if isinstance(old, EMPlot3DWidgetNew):
old.set_data(data,
remove_directories_from_name(filename),
replace)
return old
widget = EMPlot3DWidgetNew()
widget.set_data(data, remove_directories_from_name(filename),
replace)
return widget
else:
from emplot2d import EMPlot2DWidget
if old:
if isinstance(old, EMPlot2DWidget):
old.set_data(data,
remove_directories_from_name(filename),
replace)
return old
widget = EMPlot2DWidget(application=app)
widget.set_data(data, remove_directories_from_name(filename),
replace)
return widget
else:
raise Exception(
"data must be a single EMData object or a list of EMData objects"
)
def __new__(cls,
filename,
application,
force_plot=False,
force_2d=False,
old=None):
file_type = Util.get_filename_ext(filename)
em_file_type = EMUtil.get_image_ext_type(file_type)
if not file_exists(filename): return None
if force_plot and force_2d:
# ok this sucks but it suffices for the time being
print(
"Error, the force_plot and force_2d options are mutually exclusive"
)
return None
if force_plot:
from emplot2d import EMPlot2DWidget
if isinstance(old, EMPlot2DWidget): widget = old
else: widget = EMPlot2DWidget(application=application)
widget.set_data_from_file(filename)
return widget
if em_file_type != IMAGE_UNKNOWN or filename[:4] == "bdb:":
n = EMUtil.get_image_count(filename)
nx, ny, nz = gimme_image_dimensions3D(filename)
if n > 1 and nz == 1:
if force_2d:
a = EMData()
data = a.read_images(filename)
else:
data = None # This is like a flag - the ImageMXWidget only needs the file name
elif nz == 1:
data = [EMData(filename, 0)]
else:
data = EMData()
data.read_image(
filename, 0, not force_2d
) # This should be 3-D. We read the header-only here
data = [data]
if data != None and len(data) == 1: data = data[0]
if force_2d or isinstance(data, EMData) and data.get_zsize() == 1:
if isinstance(data, list) or data.get_ysize() != 1:
from emimage2d import EMImage2DWidget
if isinstance(old, EMImage2DWidget): widget = old
else: widget = EMImage2DWidget(application=application)
else:
from emplot2d import EMPlot2DWidget
if isinstance(old, EMPlot2DWidget): widget = old
else: widget = EMPlot2DWidget(application=application)
widget.set_data_from_file(filename)
return widget
elif isinstance(data, EMData):
if isinstance(old, EMScene3D): widget = old
else: widget = EMScene3D()
# print n,data
for ii in xrange(n):
data = EMData(filename, ii)
datai = EMDataItem3D(data, transform=Transform())
widget.insertNewNode(os.path.basename(filename),
datai,
parentnode=widget)
isosurface = EMIsosurface(datai, transform=Transform())
widget.insertNewNode("Iso", isosurface, parentnode=datai)
return widget
elif data == None or isinstance(data, list):
from emimagemx import EMImageMXWidget
if isinstance(old, EMImageMXWidget): widget = old
else: widget = EMImageMXWidget(application=application)
data = filename
else:
print(filename)
raise # weirdness, this should never happen
widget.set_data(data, filename)
return widget
else:
from emplot2d import EMPlot2DWidget
if isinstance(old, EMPlot2DWidget): widget = old
else: widget = EMPlot2DWidget(application=application)
widget.set_data_from_file(filename)
return widget
def __init__(self, app):
self.app = app
QtGui.QWidget.__init__(self, None)
self.synthplot = EMPlot2DWidget(self.app)
self.synthplot.show()
# overall layout
self.vbl1 = QtGui.QVBoxLayout()
self.setLayout(self.vbl1)
# First row contains general purpose controls
self.hbl1 = QtGui.QHBoxLayout()
self.vbl1.addLayout(self.hbl1)
self.vcell = ValBox(self, (0, 128.0), "Cell:", 64)
self.hbl1.addWidget(self.vcell)
self.vncells = ValBox(self, (0, 128.0), "n Cells:", 1)
self.hbl1.addWidget(self.vncells)
self.voversamp = ValBox(self, (0, 128.0), "Oversample:", 1)
self.hbl1.addWidget(self.voversamp)
self.targfn = None
self.vnsin = ValBox(self, (1, 64), "# Sin:", 16)
self.vnsin.intonly = 1
self.hbl1.addWidget(self.vnsin)
self.cbshowall = QtGui.QCheckBox("Show All")
self.hbl1.addWidget(self.cbshowall)
self.cbshifted = QtGui.QCheckBox("Shifted")
self.hbl1.addWidget(self.cbshifted)
self.cbtargfn = QtGui.QComboBox(self)
self.cbtargfn.addItem("None")
self.cbtargfn.addItem("triangle")
self.cbtargfn.addItem("square")
self.cbtargfn.addItem("square imp")
self.cbtargfn.addItem("delta")
self.cbtargfn.addItem("noise")
self.cbtargfn.addItem("saw")
self.cbtargfn.addItem("sin")
self.cbtargfn.addItem("modsin")
self.cbtargfn.addItem("modsin2")
self.cbtargfn.addItem("modsin3")
self.cbtargfn.addItem("sin low")
self.cbtargfn.addItem("doubledelta")
self.cbtargfn.addItem("sin bad f")
self.cbtargfn.addItem("sin bad f2")
self.hbl1.addWidget(self.cbtargfn)
# Widget containing valsliders
self.wapsliders = QtGui.QWidget(self)
# self.wapsliders.setMinimumSize(800,640)
self.gblap = QtGui.QGridLayout()
self.gblap.setSizeConstraint(QtGui.QLayout.SetMinAndMaxSize)
self.gblap.setColumnMinimumWidth(0, 250)
self.gblap.setColumnMinimumWidth(1, 250)
self.wapsliders.setLayout(self.gblap)
# ScrollArea providing view on slider container widget
self.wapsarea = QtGui.QScrollArea(self)
self.wapsarea.setWidgetResizable(True)
self.wapsarea.setWidget(self.wapsliders)
self.vbl1.addWidget(self.wapsarea)
QtCore.QObject.connect(self.vcell, QtCore.SIGNAL("valueChanged"),
self.recompute)
QtCore.QObject.connect(self.vncells, QtCore.SIGNAL("valueChanged"),
self.recompute)
QtCore.QObject.connect(self.voversamp, QtCore.SIGNAL("valueChanged"),
self.recompute)
QtCore.QObject.connect(self.vnsin, QtCore.SIGNAL("valueChanged"),
self.nsinchange)
QtCore.QObject.connect(self.cbshowall,
QtCore.SIGNAL("stateChanged(int)"),
self.recompute)
QtCore.QObject.connect(self.cbshifted,
QtCore.SIGNAL("stateChanged(int)"),
self.recompute)
QtCore.QObject.connect(self.cbtargfn, QtCore.SIGNAL("activated(int)"),
self.newtargfn)
self.wamp = []
self.wpha = []
self.curves = []
self.xvals = []
for i in range(65):
self.wamp.append(ValSlider(self, (0.0, 1.0), "%2d:" % i, 0.0))
self.gblap.addWidget(self.wamp[-1], i, 0)
QtCore.QObject.connect(self.wamp[-1],
QtCore.SIGNAL("valueChanged"),
self.recompute)
self.wpha.append(ValSlider(self, (-180.0, 180.0), "%2d:" % i, 0.0))
self.gblap.addWidget(self.wpha[-1], i, 1)
QtCore.QObject.connect(self.wpha[-1],
QtCore.SIGNAL("valueChanged"),
self.recompute)
self.curves.append(EMData(64, 1))
if self.cbshowall.isChecked():
self.synthplot
self.total = EMData(64, 1)
self.nsinchange()
def main():
progname = os.path.basename(sys.argv[0])
usage = """prog Refinement directory [options]
Plot FSC curvers produced by e2refine, eotest, etc.
>"""
parser = EMArgumentParser(usage=usage,version=EMANVERSION)
#dirbasename='refine|frealign',
#parser.add_pos_argument(name="plot_files",help="List the directories to plot here.", default="", guitype='filebox', browser="EMBrowserWidget(withmodal=True,multiselect=True)", row=0, col=0,rowspan=1, colspan=2)
parser.add_header(name="filterheader", help='There is no help', title="This program is currently not functional. The table below is still useful,\n but for actual plots, suggest using e2evalrefine.py for now.", row=0, col=0, rowspan=1, colspan=2)
parser.add_pos_argument(name="fscdir",help="The refinement directory to use for FSC plotting.", default="", guitype='fsctable', row=1, col=0,rowspan=1, colspan=2)
parser.add_header(name="filterheader", help='Options below this label are specific to e2plotFSC', title="### e2plotFSC options ###", row=2, col=0, rowspan=1, colspan=2)
parser.add_argument("--plote2res",action="store_false",help="Plot curves from e2resoltion",default=True,guitype='boolbox',row=3,col=0,rowspan=1,colspan=1)
parser.add_argument("--plote2eotest",action="store_false",help="Plot curves from e2eotest",default=True,guitype='boolbox',row=3,col=1,rowspan=1,colspan=1)
parser.add_argument("--plotconvergence",action="store_false",help="Plot curves from refinement convergence",default=True,guitype='boolbox',row=4,col=0,rowspan=1,colspan=1)
parser.add_argument("--ploteoconvergence",action="store_false",help="Plot curves from refine_even_odd convergence",default=True,guitype='boolbox',row=4,col=1,rowspan=1,colspan=1)
parser.add_argument("--ppid", type=int, help="Set the PID of the parent process, used for cross platform PPID",default=-1)
(options, args) = parser.parse_args()
# Make the QT app
app = EMApp()
# display table
if len(args) == 0:
fsctable = PMFSCTableWidget("fsc","",None,resize=True)
fsctable.show()
# or let user choose FSC plotting pars
else:
module = EMPlot2DWidget()
# Get data from data base
db_name = "bdb:"+args[0]+"#convergence.results"
if not db_check_dict(db_name):
print "Rubbish!!!, no FSC curves found!!!"
return
db = db_open_dict(db_name,ro=True)
keys = db.keys()
# Load desired FSC curves
res = []
eo = []
conv = []
eoconv = []
# Method to the maddness, I use not here because I need to only plot when open is not presented AND I need to keep presentation on in the GUI
if not options.plote2res: res= get_e2resolution_results_list(keys)
if not options.plote2eotest: eo = get_e2eotest_results_list(keys)
if not options.plotconvergence: conv = get_convergence_results_list(keys)
if not options.ploteoconvergence: eoconv = get_e2refine_even_odd_results_list(keys)
# Plot FSC curves
i = 0
max = len(colortypes)
for k in conv:
module.set_data(db[k],k,color=(i%max),linewidth=1) # there are only a ceratin number of colors
i += 1
# plot e2refine_even_odd curves
for k in eoconv:
module.set_data(db[k],k,color=(i%max),linewidth=2) # there are only a ceratin number of colors
i += 1
#plot eo test and res
for plot in [eo,res]:
for k in plot:
module.set_data(db[k],k,color=(i%max),linewidth=3) # there are only a ceratin number of colors
i += 1
module.show()
app.exec_()