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 __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)
class GUIFourierSynth(QtGui.QWidget):
"""This class represents an application for interactive Fourier synthesis"""
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 newtargfn(self, index):
"This function has a number of hardcoded 'target' functions"
if index == 0:
self.targfn = None
else:
nx = int(self.vcell.getValue())
self.targfn = EMData(nx, 1)
if index == 1: # triangle
for i in xrange(nx / 2):
self.targfn[i] = -1.0 + 4.0 * i / nx
for i in xrange(nx / 2, nx):
self.targfn[i] = 3.0 - 4.0 * i / nx
elif index == 2: # square
for i in xrange(nx / 4):
self.targfn[i] = -1.0
for i in xrange(nx / 4, nx * 3 / 4):
self.targfn[i] = 1.0
for i in xrange(nx * 3 / 4, nx):
self.targfn[i] = -1.0
elif index == 3: # square impulse
self.targfn.to_zero()
for i in xrange(nx / 4, nx / 2):
self.targfn[i] = 1.0
elif index == 4: # delta
self.targfn.to_zero()
self.targfn[nx * 2 / 5] = 1.0
elif index == 5: # noise
self.targfn.process_inplace("testimage.noise.gauss",
{"seed": 0})
elif index == 6: # saw
self.targfn.to_zero()
for i in xrange(nx / 4, nx / 2):
self.targfn[i] = 4.0 * (i - nx / 4.0) / nx
for i in xrange(nx / 2, nx * 3 / 4):
self.targfn[i] = -1 + 4.0 * (i - nx / 2.0) / nx
elif index == 7: # sin
for i in xrange(nx):
self.targfn[i] = sin(i * pi / 4.0)
elif index == 8: # modulated sine
for i in xrange(nx):
self.targfn[i] = sin(i * pi / 4.0) * sin(i * pi / 32)
elif index == 9: # modulated sine 2
for i in xrange(nx):
self.targfn[i] = sin(i * pi / 4.0) * sin(i * pi / 29)
elif index == 10: # modulated sine 3
for i in xrange(nx):
self.targfn[i] = sin(i * pi / 4.0) * sin(i * pi / 126)
elif index == 11: # sin low
for i in xrange(nx):
self.targfn[i] = sin(i * pi / 16.0)
elif index == 12: # double delta
self.targfn.to_zero()
self.targfn[nx / 16] = 4.0
self.targfn[nx * 15 / 16] = 4.0
elif index == 13: # sin bad f
for i in xrange(nx):
self.targfn[i] = sin(i * pi / 15.5)
elif index == 14: # sin bad f2
for i in xrange(nx):
self.targfn[i] = sin(i * pi / 19)
self.target2sliders()
self.recompute()
def target2sliders(self):
nsin = int(self.vnsin.getValue())
# cp=self.targfn.process("xform.phaseorigin.tocenter")
cp = self.targfn.copy()
fft = cp.do_fft()
fft[0] = fft[0] / 2.0
fft[fft["nx"] / 2 - 1] = fft[fft["nx"] / 2 - 1] / 2.0
fft.ri2ap()
for i in xrange(min(fft["nx"] / 2, nsin + 1)):
# print fft[i]
amp = fft[i].real
if fabs(amp) < 1.0e-5: amp = 0.0
self.wamp[i].setValue(amp * 2 / (fft["nx"] - 2), quiet=1)
self.wpha[i].setValue(fft[i].imag * 180.0 / pi + 90.0, quiet=1)
def nsinchange(self, value=None):
if value == None: value = int(self.vnsin.getValue())
for i in range(65):
if i > value:
self.wamp[i].hide()
self.wpha[i].hide()
else:
self.wamp[i].show()
self.wpha[i].show()
if self.targfn != None:
self.target2sliders()
self.recompute()
def recompute(self, value=None):
nsin = int(self.vnsin.getValue())
cell = int(self.vcell.getValue())
ncells = self.vncells.getValue()
oversamp = int(self.voversamp.getValue())
samples = int(cell * ncells * oversamp)
self.xvals = [xn / float(oversamp) for xn in range(samples)]
self.total.set_size(samples)
self.total.to_zero()
for i in range(nsin + 1):
self.curves[i].set_size(samples)
if i == 0:
self.curves[i].to_one()
if self.wpha[0].getValue() > 180.0: self.curves[i].mult(-1.0)
else:
self.curves[i].process_inplace(
"testimage.sinewave", {
"wavelength": cell * oversamp / float(i),
"phase": self.wpha[i].getValue() * pi / 180.0
})
self.curves[i].mult(self.wamp[i].getValue())
self.total.add(self.curves[i])
self.synthplot.set_data((self.xvals, self.total.get_data_as_vector()),
"Sum",
replace=True,
quiet=True,
linewidth=2)
if self.targfn != None:
self.synthplot.set_data(self.targfn,
"Target",
quiet=True,
linewidth=1,
linetype=2,
symtype=0)
if self.cbshowall.isChecked():
csum = self.total["minimum"] * 1.1
for i in range(nsin):
if self.wamp[i].getValue() == 0: continue
csum -= self.wamp[i].getValue() * 1.1
if self.cbshifted.isChecked(): self.curves[i].add(csum)
self.synthplot.set_data(
(self.xvals, self.curves[i].get_data_as_vector()),
"%d" % i,
quiet=True,
linewidth=1,
color=2)
csum -= self.wamp[i].getValue() * 1.1
self.synthplot.updateGL()
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)
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.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()
class GUIFourierSynth(QtGui.QWidget):
"""This class represents an application for interactive Fourier synthesis"""
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.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 newtargfn(self,index):
"This function has a number of hardcoded 'target' functions"
if index==0 :
self.targfn=None
else :
nx=int(self.vcell.getValue())
self.targfn=EMData(nx,1)
if index==1 : # triangle
for i in xrange(nx/2):
self.targfn[i]=-1.0+4.0*i/nx
for i in xrange(nx/2,nx):
self.targfn[i]=3.0-4.0*i/nx
elif index==2 : # square
for i in xrange(nx/4): self.targfn[i]=-1.0
for i in xrange(nx/4,nx*3/4): self.targfn[i]=1.0
for i in xrange(nx*3/4,nx): self.targfn[i]=-1.0
elif index==3 : # square impulse
self.targfn.to_zero()
for i in xrange(nx/4,nx/2): self.targfn[i]=1.0
elif index==4 : # delta
self.targfn.to_zero()
self.targfn[nx*2/5]=1.0
elif index==5 : # noise
self.targfn.process_inplace("testimage.noise.gauss",{"seed":0})
elif index==6 : # saw
self.targfn.to_zero()
for i in xrange(nx/4,nx/2): self.targfn[i]=4.0*(i-nx/4.0)/nx
for i in xrange(nx/2,nx*3/4): self.targfn[i]=-1+4.0*(i-nx/2.0)/nx
elif index==7 : # sin
for i in xrange(nx): self.targfn[i]=sin(i*pi/4.0)
elif index==8 : # modulated sine
for i in xrange(nx): self.targfn[i]=sin(i*pi/4.0)*sin(i*pi/32)
elif index==9 : # modulated sine 2
for i in xrange(nx): self.targfn[i]=sin(i*pi/4.0)*sin(i*pi/29)
elif index==10 : # modulated sine 3
for i in xrange(nx): self.targfn[i]=sin(i*pi/4.0)*sin(i*pi/126)
elif index==11 : # sin low
for i in xrange(nx): self.targfn[i]=sin(i*pi/16.0)
elif index==12 : # double delta
self.targfn.to_zero()
self.targfn[nx/16]=4.0
self.targfn[nx*15/16]=4.0
self.target2sliders()
self.recompute()
def target2sliders(self):
nsin=int(self.vnsin.getValue())
# cp=self.targfn.process("xform.phaseorigin.tocenter")
cp=self.targfn.copy()
fft=cp.do_fft()
fft[0]=fft[0]/2.0
fft[fft["nx"]/2-1]=fft[fft["nx"]/2-1]/2.0
fft.ri2ap()
for i in xrange(min(fft["nx"]/2,nsin+1)):
# print fft[i]
amp=fft[i].real
if fabs(amp)<1.0e-5 : amp=0.0
self.wamp[i].setValue(amp*2/(fft["nx"]-2),quiet=1)
self.wpha[i].setValue(fft[i].imag*180.0/pi+90.0,quiet=1)
def nsinchange(self,value=None):
if value==None : value=int(self.vnsin.getValue())
for i in range(65):
if i>value:
self.wamp[i].hide()
self.wpha[i].hide()
else :
self.wamp[i].show()
self.wpha[i].show()
if self.targfn!=None :
self.target2sliders()
self.recompute()
def recompute(self,value=None):
nsin=int(self.vnsin.getValue())
cell=int(self.vcell.getValue())
ncells=self.vncells.getValue()
oversamp=int(self.voversamp.getValue())
samples=int(cell*ncells*oversamp)
self.xvals=[xn/float(oversamp) for xn in range(samples)]
self.total.set_size(samples)
self.total.to_zero()
for i in range(nsin+1):
self.curves[i].set_size(samples)
if i==0:
self.curves[i].to_one()
if self.wpha[0].getValue()>180.0 : self.curves[i].mult(-1.0)
else: self.curves[i].process_inplace("testimage.sinewave",{"wavelength":cell*oversamp/float(i),"phase":self.wpha[i].getValue()*pi/180.0})
self.curves[i].mult(self.wamp[i].getValue())
self.total.add(self.curves[i])
self.synthplot.set_data((self.xvals,self.total.get_data_as_vector()),"Sum",replace=True,quiet=True,linewidth=2)
if self.targfn!=None:
self.synthplot.set_data(self.targfn,"Target",quiet=True,linewidth=1,linetype=2,symtype=0)
if self.cbshowall.isChecked() :
csum=self.total["minimum"]*1.1
for i in range(nsin):
if self.wamp[i].getValue()==0: continue
csum-=self.wamp[i].getValue()*1.1
if self.cbshifted.isChecked() : self.curves[i].add(csum)
self.synthplot.set_data((self.xvals,self.curves[i].get_data_as_vector()),"%d"%i,quiet=True,linewidth=1,color=2)
csum-=self.wamp[i].getValue()*1.1
self.synthplot.updateGL()
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)
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)
