class ErasingPanel: # copied for ideas for the morph panel
def __init__(self, target, erase_radius=128):
self.busy = True
self.erase_radius = erase_radius
self.target = weakref.ref(target)
self.erase_rad_edit = None
self.widget = None
self.busy = False
def set_erase_radius(self, erase_rad_edit):
self.busy = True
self.erase_radius = erase_rad_edit
if self.erase_rad_edit != None:
self.erase_rad_edit.setValue(erase_rad_edit)
self.busy = False
def get_widget(self):
if self.widget == None:
from PyQt4 import QtCore, QtGui, Qt
self.widget = QtGui.QWidget()
vbl = QtGui.QVBoxLayout(self.widget)
vbl.setMargin(0)
vbl.setSpacing(6)
vbl.setObjectName("vbl")
hbl = QtGui.QHBoxLayout()
hbl.addWidget(QtGui.QLabel("Erase Radius:"))
from eman2_gui.valslider import ValSlider
self.erase_rad_edit = ValSlider(None, (0.0, 1000.0), "")
self.erase_rad_edit.setValue(int(self.erase_radius))
self.erase_rad_edit.setEnabled(True)
hbl.addWidget(self.erase_rad_edit)
self.unerase = QtGui.QCheckBox("Unerase")
self.unerase.setChecked(False)
vbl.addLayout(hbl)
vbl.addWidget(self.unerase)
QtCore.QObject.connect(self.erase_rad_edit,
QtCore.SIGNAL("sliderReleased"),
self.new_erase_radius)
QtCore.QObject.connect(self.unerase,
QtCore.SIGNAL("clicked(bool)"),
self.unerase_checked)
return self.widget
def new_erase_radius(self, erase_rad_edit):
if self.busy: return
self.target().set_erase_radius(erase_rad_edit)
def unerase_checked(self, val):
if self.busy: return
self.target().toggle_unerase(val)
class GUIctfsim(QtGui.QWidget):
module_closed = QtCore.pyqtSignal()
def __init__(self,
application,
apix=1.0,
voltage=300.0,
cs=4.1,
ac=10.0,
samples=256,
apply=None):
"""CTF simulation dialog
"""
try:
from eman2_gui.emimage2d import EMImage2DWidget
except:
print("Cannot import EMAN image GUI objects (EMImage2DWidget)")
sys.exit(1)
try:
from eman2_gui.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
if apply == None:
self.apply = None
self.applyim = None
else:
self.apply = EMData(apply, 0)
self.df_apix = self.apply["apix_x"]
print("A/pix reset to ", self.df_apix)
self.applyim = EMImage2DWidget(application=self.app())
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.guiim.mousedown.connect(self.imgmousedown)
self.guiim.mousedrag.connect(self.imgmousedrag)
self.guiim.mouseup.connect(self.imgmouseup)
self.guiplot.mousedown.connect(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:", 100, 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.sphase = ValSlider(self, (0, 1), "Phase/pi", 0, 90)
self.vbl.addWidget(self.sphase)
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()
self.sdefocus.valueChanged.connect(self.newCTF)
self.sbfactor.valueChanged.connect(self.newCTF)
self.sdfdiff.valueChanged.connect(self.newCTF)
self.sdfang.valueChanged.connect(self.newCTF)
self.sapix.valueChanged.connect(self.newCTF)
self.sampcont.valueChanged.connect(self.newCTFac)
self.sphase.valueChanged.connect(self.newCTFpha)
self.svoltage.valueChanged.connect(self.newCTF)
self.scs.valueChanged.connect(self.newCTF)
self.ssamples.valueChanged.connect(self.newCTF)
self.setlist.currentRowChanged[int].connect(self.newSet)
self.setlist.keypress.connect(self.listkey)
self.splotmode.currentIndexChanged[int].connect(self.newPlotMode)
self.newbut.clicked[bool].connect(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 listkey(self, event):
if event.key() >= Qt.Key_0 and event.key() <= Qt.Key_9:
q = int(event.key()) - Qt.Key_0
self.squality.setValue(q)
elif event.key() == Qt.Key_Left:
self.sdefocus.setValue(self.sdefocus.getValue() - 0.01)
elif event.key() == Qt.Key_Right:
self.sdefocus.setValue(self.sdefocus.getValue() + 0.01)
elif event.key() == Qt.Key_R:
self.on_recall_params()
def on_new_but(self):
ctf = EMAN2Ctf()
ctf.defocus = 1.0
ctf.bfactor = 100.0
ctf.voltage = self.df_voltage
ctf.apix = self.df_apix
ctf.cs = self.df_cs
ctf.ac = self.df_ac
ctf.samples = self.df_samples
self.data.append((str(len(self.setlist) + 1), ctf))
self.curset = len(self.data)
self.update_data()
def show_guis(self):
if self.guiim != None:
self.app().show_specific(self.guiim)
if self.applyim != None:
self.app().show_specific(self.applyim)
if self.guiplot != None:
self.app().show_specific(self.guiplot)
#if self.guirealim != None:
#self.app().show_specific(self.guirealim)
self.show()
def closeEvent(self, event):
# QtGui.QWidget.closeEvent(self,event)
# self.app.app.closeAllWindows()
E2saveappwin("e2ctf", "main", self)
if self.guiim != None:
E2saveappwin("e2ctf", "image", self.guiim.qt_parent)
self.app().close_specific(self.guiim)
self.guiim = None
if self.applyim != None:
self.app().close_specific(self.applyim)
self.applyim = None
if self.guiplot != None:
E2saveappwin("e2ctf", "plot", self.guiplot.qt_parent)
self.app().close_specific(self.guiplot)
#if self.guirealim != None:
#E2saveappwin("e2ctf","realimage",self.guirealim.qt_parent)
#self.app().close_specific(self.guirealim)
event.accept()
self.app().close_specific(self)
self.module_closed.emit(
) # this signal is important when e2ctf is being used by a program running its own event loop
def update_data(self):
"""This will make sure the various widgets properly show the current data sets"""
self.setlist.clear()
for i, j in enumerate(self.data):
self.setlist.addItem(j[0])
self.setlist.setCurrentRow(self.curset)
def update_plot(self):
if self.guiplot == None: return # it's closed/not visible
for d in range(len(self.data)):
ctf = self.data[d][1]
ds = old_div(1.0, (ctf.apix * 2.0 * ctf.samples))
s = arange(0, ds * ctf.samples, ds)
curve = array(ctf.compute_1d(len(s) * 2, ds, Ctf.CtfType.CTF_AMP))
if self.plotmode == 1 or self.plotmode == 2:
curve = curve**2
if self.plotmode == 2 or self.plotmode == 3:
if d == 0: avg = curve[:]
else:
if len(curve) != len(avg):
print(
"Number of samples must be fixed to compute an average ({})"
.format(d + 1))
else:
avg += curve
self.guiplot.set_data((s, curve),
self.data[d][0],
d == 0,
True,
color=d + 1)
if self.plotmode in (2, 3):
self.guiplot.set_data((s, avg), "Sum", False, True, color=0)
self.guiplot.setAxisParms("s (1/$\AA$)", "CTF")
ctf.compute_2d_complex(self.img, Ctf.CtfType.CTF_AMP, None)
self.guiim.set_data(self.img)
if self.applyim != None:
applyf = self.apply.do_fft()
ctfmul = applyf.copy()
ctf.compute_2d_complex(ctfmul, Ctf.CtfType.CTF_AMP)
ctfsgn = applyf.copy()
ctf.compute_2d_complex(ctfsgn, Ctf.CtfType.CTF_SIGN)
applyf.mult(ctfmul)
apply2 = applyf.do_ift()
apply2.mult(
5.0
) # roughly compensate for contrast reduction so apply comparable
applyf.mult(ctfsgn)
apply3 = applyf.do_ift()
apply3.mult(5.0)
self.applyim.set_data([apply2, apply3, self.apply])
def newSet(self, val=0):
"called when a new data set is selected from the list"
self.curset = val
self.sdefocus.setValue(self.data[val][1].defocus, True)
self.sbfactor.setValue(self.data[val][1].bfactor, True)
self.sapix.setValue(self.data[val][1].apix, True)
self.sampcont.setValue(self.data[val][1].ampcont, True)
self.sphase.setValue(old_div(self.data[val][1].get_phase(), pi), True)
self.svoltage.setValue(self.data[val][1].voltage, True)
self.scs.setValue(self.data[val][1].cs, True)
self.sdfdiff.setValue(self.data[val][1].dfdiff, True)
self.sdfang.setValue(self.data[val][1].dfang, True)
self.ssamples.setValue(self.data[val][1].samples, True)
# make new image if necessary
if self.img == None or self.img["ny"] != self.data[val][1].samples:
self.img = EMData(self.data[val][1].samples + 2,
self.data[val][1].samples)
self.img.to_zero()
self.img.set_complex(1)
self.guiim.set_data(self.img)
# self.imginfo.setText("%s particles SNR = %s"%(ptcl,ssnr))
#if self.guiim != None:
## print self.data
#self.guiim.set_data(self.data[val][4])
#if self.guiiminit:
#self.guiim.optimally_resize()
#self.guiiminit = False
#self.guiim.updateGL()
#self.update_plot()
# print "self.data[val]=",self.data[val][0].split('#')[-1]
self.guiim.qt_parent.setWindowTitle("e2ctfsim - 2D FFT - " +
self.data[val][0])
# self.guirealim.qt_parent.setWindowTitle("e2ctf - "+self.data[val][0].split('#')[-1])
self.guiplot.qt_parent.setWindowTitle("e2ctfsim - Plot ")
#n=EMUtil.get_image_count(self.data[val][0])
#if n>1:
#self.ptcldata=EMData.read_images(self.data[val][0],range(0,min(20,n)))
#im=sum(self.ptcldata)
#im.mult(1.0/len(self.ptcldata))
#self.ptcldata.insert(0,im)
#self.guirealim.set_data(self.ptcldata)
#else : self.guirealim.set_data([EMData()])
self.update_plot()
def newPlotMode(self, mode):
self.plotmode = mode
self.update_plot()
def newCTF(self):
# print traceback.print_stack()
self.data[self.curset][1].defocus = self.sdefocus.value
self.data[self.curset][1].bfactor = self.sbfactor.value
self.data[self.curset][1].dfdiff = self.sdfdiff.value
self.data[self.curset][1].dfang = self.sdfang.value
self.data[self.curset][1].apix = self.sapix.value
self.data[self.curset][1].ampcont = self.sampcont.value
# self.data[self.curset][1].set_phase(self.sphase.value)*pi
self.data[self.curset][1].voltage = self.svoltage.value
self.data[self.curset][1].cs = self.scs.value
self.data[self.curset][1].samples = self.ssamples.value
if self.img == None or self.img["ny"] != self.ssamples.value:
self.img = EMData(self.ssamples.value + 2, self.ssamples.value)
self.img.to_zero()
self.img.set_complex(1)
self.guiim.set_data(self.img)
self.update_plot()
def newCTFac(self):
# print traceback.print_stack()
self.data[self.curset][1].ampcont = self.sampcont.value
self.sphase.setValue(
old_div(self.data[self.curset][1].get_phase(), pi), True)
if self.img == None or self.img["ny"] != self.ssamples.value:
self.img = EMData(self.ssamples.value + 2, self.ssamples.value)
self.img.to_zero()
self.img.set_complex(1)
self.guiim.set_data(self.img)
self.update_plot()
def newCTFpha(self):
# print traceback.print_stack()
self.data[self.curset][1].set_phase(self.sphase.value * pi)
self.sampcont.setValue(self.data[self.curset][1].ampcont, True)
if self.img == None or self.img["ny"] != self.ssamples.value:
self.img = EMData(self.ssamples.value + 2, self.ssamples.value)
self.img.to_zero()
self.img.set_complex(1)
self.guiim.set_data(self.img)
self.update_plot()
def imgmousedown(self, event):
m = self.guiim.scr_to_img((event.x(), event.y()))
#self.guiim.add_shape("cen",["rect",.9,.9,.4,x0,y0,x0+2,y0+2,1.0])
def imgmousedrag(self, event):
m = self.guiim.scr_to_img((event.x(), event.y()))
# box deletion when shift held down
#if event.modifiers()&Qt.ShiftModifier:
#for i,j in enumerate(self.boxes):
def imgmouseup(self, event):
m = self.guiim.scr_to_img((event.x(), event.y()))
def plotmousedown(self, event):
m = self.guiim.scr_to_img((event.x(), event.y()))
def run(self):
"""If you make your own application outside of this object, you are free to use
your own local app.exec_(). This is a convenience for ctf-only programs."""
self.app.exec_()
# E2saveappwin("boxer","imagegeom",self.guiim)
# try:
# E2setappval("boxer","imcontrol",self.guiim.inspector.isVisible())
# if self.guiim.inspector.isVisible() : E2saveappwin("boxer","imcontrolgeom",self.guiim.inspector)
# except : E2setappval("boxer","imcontrol",False)
return
class GUIctf(QtGui.QWidget):
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 eman2_gui.emimage2d import EMImage2DWidget
except:
ERROR("Cannot import EMAN image GUI objects (EMImage2DWidget)")
return
try:
from eman2_gui.emplot2d import EMPlot2DWidget
except:
ERROR(
"Cannot import EMAN plot GUI objects (is matplotlib installed?)"
)
return
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.mousedown.connect(self.imgmousedown)
self.guiim.mousedrag.connect(self.imgmousedrag)
self.guiim.mouseup.connect(self.imgmouseup)
self.guiplot.mousedown.connect(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)
self.sdefocus.valueChanged.connect(self.newCTF)
self.sbfactor.valueChanged.connect(self.newCTF)
# QtCore.QObject.connect(self.sapix, QtCore.SIGNAL("valueChanged"), self.newCTF)
self.sampcont.valueChanged.connect(self.newCTF)
self.svoltage.valueChanged.connect(self.newCTF)
self.scs.valueChanged.connect(self.newCTF)
self.setlist.currentRowChanged[int].connect(self.newSet)
self.splotmode.currentIndexChanged[int].connect(self.newPlotMode)
self.saveparms.clicked[bool].connect(self.on_save_params)
self.recallparms.clicked[bool].connect(self.on_recall_params)
self.output.clicked[bool].connect(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 on_save_params(self):
if len(self.setlist.selectedItems()) == 0: return
val = self.curset
name = str(self.setlist.item(val).text())
name = base_name(name)
# if not db_check_dict(name):
# print "error, the db doesn't exist:",name
#
db_parms = db_open_dict("bdb:e2ctf.parms")
ctf = self.data[val][1].to_string()
output = []
for i, val in enumerate(self.data[val]):
# ignore i == 0 it's just the filename
if i > 1:
output.append(val)
elif i == 1:
output.append(ctf)
db_parms[name] = output
def on_recall_params(self):
if len(self.setlist.selectedItems()) == 0: return
val = self.curset
name = str(self.setlist.item(val).text())
data = [name]
name = base_name(name)
db_parms = db_open_dict("bdb:e2ctf.parms")
if name not in db_parms:
sxprint("error, ctf parameters do not exist for:", name)
#
data.extend(db_parms[name])
ctf = EMAN2Ctf()
ctf.from_string(data[1])
data[1] = ctf
self.data[val] = data
self.newSet(self.curset)
# def get_output_params(self):
def on_output(self):
from eman2_gui.emsprworkflow import E2CTFOutputTaskGeneral
self.form = E2CTFOutputTaskGeneral()
self.form.run_form()
def show_guis(self):
if self.guiim != None:
self.app().show_specific(self.guiim)
if self.guiplot != None:
self.app().show_specific(self.guiplot)
self.app().show_specific(self)
def closeEvent(self, event):
# QtGui.QWidget.closeEvent(self,event)
# self.app.app.closeAllWindows()
if self.guiim != None:
self.app().close_specific(self.guiim)
self.guiim = None
if self.guiplot != None:
self.app().close_specific(self.guiplot)
event.accept()
def newData(self, data):
self.data = data
self.update_data()
def update_data(self):
"""This will make sure the various widgets properly show the current data sets"""
self.setlist.clear()
for i, j in enumerate(self.data):
self.setlist.addItem(j[0])
self.setlist.setCurrentRow(self.curset)
def update_plot(self):
val = self.curset
ctf = self.data[val][1]
ds = self.data[val][1].dsbg
s = [ds * i for i in range(len(ctf.background))]
if self.plotmode == 1:
self.guiplot.set_data((s, self.data[val][2]), "fg", True, True)
self.guiplot.set_data((s, self.data[val][3]), "bg")
self.guiplot.setAxisParms("s (1/A)", "Intensity (a.u)")
elif self.plotmode == 0:
bgsub = [
self.data[val][2][i] - self.data[val][3][i]
for i in range(len(self.data[val][2]))
]
self.guiplot.set_data((s, bgsub), "fg-bg", True, True)
fit = ctf.compute_1d(len(s) * 2, ds,
Ctf.CtfType.CTF_AMP) # The fit curve
sf = sfact(s, "ribosome", "nono")
fit = [sf[i] * fit[i]**2 for i in range(len(s))
] # squared * a generic structure factor
# auto-amplitude for b-factor adjustment
rto, nrto = 0, 0
for i in range(int(.04 / ds) + 1, min(int(0.15 / ds), len(s) - 1)):
if bgsub[i] > 0:
#rto+=fit[i]**2/fabs(bgsub[i])
#nrto+=fit[i]
#rto+=fit[i]**2
#nrto+=bgsub[i]**2
rto += fit[i]
nrto += fabs(bgsub[i])
if nrto == 0: rto = 1.0
else: rto /= nrto
fit = [fit[i] / rto for i in range(len(s))]
self.guiplot.set_data((s, fit), "fit")
self.guiplot.setAxisParms("s (1/A)", "Intensity (a.u)")
elif self.plotmode == 2:
snr = ctf.compute_1d(len(s) * 2, ds,
Ctf.CtfType.CTF_SNR) # The snr curve
self.guiplot.set_data((s, snr[:len(s)]), "snr", True)
self.guiplot.setAxisParms("s (1/A)", "SNR (intensity ratio)")
elif self.plotmode == 3:
snr = ctf.compute_1d(len(s) * 2, ds,
Ctf.CtfType.CTF_SNR) # The snr curve
self.guiplot.set_data((s, snr[:len(s)]), "snr", True)
ssnr = ctf.compute_1d(len(s) * 2, ds,
Ctf.CtfType.CTF_SNR_SMOOTH) # The fit curve
self.guiplot.set_data((s, ssnr[:len(s)]), "ssnr")
self.guiplot.setAxisParms("s (1/A)", "SNR (intensity ratio)")
elif self.plotmode == 4:
snr = ctf.compute_1d(len(s) * 2, ds,
Ctf.CtfType.CTF_SNR) # The snr curve
for i in range(1, len(snr)):
snr[i] = snr[i] * i + snr[i - 1] # integrate SNR*s
# for i in range(1,len(snr)): snr[i]/=snr[-1] # normalize
for i in range(1, len(snr)):
snr[i] /= len(
snr
) # this way the relative quality of images can be compared
self.guiplot.set_data((s, snr[:len(s)]), "snr", True)
self.guiplot.setAxisParms("s (1/A)", "Integrated SNR")
elif self.plotmode == 5:
inten = [
fabs(i)
for i in ctf.compute_1d(len(s) * 2, ds, Ctf.CtfType.CTF_AMP)
] # The snr curve
self.guiplot.set_data((s, inten[:len(s)]), "single", True)
all = [0 for i in inten]
for st in self.data:
sxprint(st)
inten = [
fabs(i) for i in st[1].compute_1d(
len(s) * 2, ds, Ctf.CtfType.CTF_AMP)
]
for i in range(len(all)):
all[i] += inten[i]
self.guiplot.set_data((s, all[:len(s)]), "total")
#bgsub=[self.data[val][2][i]-self.data[val][3][i] for i in range(len(self.data[val][2]))]
#self.guiplot.set_data("fg-bg",(s,bgsub),True,True)
#fit=[bgsub[i]/sfact(s[i]) for i in range(len(s))] # squared * a generic structure factor
#self.guiplot.set_data("fit",(s,fit))
def newSet(self, val):
"called when a new data set is selected from the list"
self.curset = val
self.sdefocus.setValue(self.data[val][1].defocus, True)
self.sbfactor.setValue(self.data[val][1].bfactor, True)
# self.sapix.setValue(self.data[val][1].apix)
self.sampcont.setValue(self.data[val][1].ampcont, True)
self.svoltage.setValue(self.data[val][1].voltage, True)
self.scs.setValue(self.data[val][1].cs, True)
self.guiim.set_data(self.data[val][4])
self.update_plot()
def newPlotMode(self, mode):
self.plotmode = mode
self.update_plot()
def newCTF(self):
self.data[self.curset][1].defocus = self.sdefocus.value
self.data[self.curset][1].bfactor = self.sbfactor.value
# self.data[self.curset][1].apix=self.sapix.value
self.data[self.curset][1].ampcont = self.sampcont.value
self.data[self.curset][1].voltage = self.svoltage.value
self.data[self.curset][1].cs = self.scs.value
self.update_plot()
def imgmousedown(self, event):
m = self.guiim.scr_to_img((event.x(), event.y()))
#self.guiim.add_shape("cen",["rect",.9,.9,.4,x0,y0,x0+2,y0+2,1.0])
def imgmousedrag(self, event):
m = self.guiim.scr_to_img((event.x(), event.y()))
# box deletion when shift held down
#if event.modifiers()&Qt.ShiftModifier:
#for i,j in enumerate(self.boxes):
def imgmouseup(self, event):
m = self.guiim.scr_to_img((event.x(), event.y()))
def plotmousedown(self, event):
m = self.guiim.scr_to_img((event.x(), event.y()))
def run(self):
"""If you make your own application outside of this object, you are free to use
your own local app.exec_(). This is a convenience for ctf-only programs."""
self.app.exec_()
# E2saveappwin("boxer","imagegeom",self.guiim)
# try:
# E2setappval("boxer","imcontrol",self.guiim.inspector.isVisible())
# if self.guiim.inspector.isVisible() : E2saveappwin("boxer","imcontrolgeom",self.guiim.inspector)
# except : E2setappval("boxer","imcontrol",False)
return
class EMTomoBoxer(QtGui.QMainWindow):
"""This class represents the EMTomoBoxer application instance. """
keypress = QtCore.pyqtSignal(QtGui.QKeyEvent)
module_closed = QtCore.pyqtSignal()
def __init__(self,application,options,datafile):
QtGui.QWidget.__init__(self)
self.initialized=False
self.app=weakref.ref(application)
self.options=options
self.yshort=False
self.apix=options.apix
self.currentset=0
self.shrink=1#options.shrink
self.setWindowTitle("Main Window (e2spt_boxer.py)")
if options.mode=="3D":
self.boxshape="circle"
else:
self.boxshape="rect"
# Menu Bar
self.mfile=self.menuBar().addMenu("File")
self.mfile_open=self.mfile.addAction("Open")
self.mfile_read_boxloc=self.mfile.addAction("Read Box Coord")
self.mfile_save_boxloc=self.mfile.addAction("Save Box Coord")
self.mfile_save_boxes_stack=self.mfile.addAction("Save Boxes as Stack")
self.mfile_quit=self.mfile.addAction("Quit")
self.setCentralWidget(QtGui.QWidget())
self.gbl = QtGui.QGridLayout(self.centralWidget())
# relative stretch factors
self.gbl.setColumnStretch(0,1)
self.gbl.setColumnStretch(1,4)
self.gbl.setColumnStretch(2,0)
self.gbl.setRowStretch(1,1)
self.gbl.setRowStretch(0,4)
# 3 orthogonal restricted projection views
self.xyview = EMImage2DWidget()
self.gbl.addWidget(self.xyview,0,1)
self.xzview = EMImage2DWidget()
self.gbl.addWidget(self.xzview,1,1)
self.zyview = EMImage2DWidget()
self.gbl.addWidget(self.zyview,0,0)
# Select Z for xy view
self.wdepth = QtGui.QSlider()
self.gbl.addWidget(self.wdepth,1,2)
### Control panel area in upper left corner
self.gbl2 = QtGui.QGridLayout()
self.gbl.addLayout(self.gbl2,1,0)
#self.wxpos = QtGui.QSlider(Qt.Horizontal)
#self.gbl2.addWidget(self.wxpos,0,0)
#self.wypos = QtGui.QSlider(Qt.Vertical)
#self.gbl2.addWidget(self.wypos,0,3,6,1)
# box size
self.wboxsize=ValBox(label="Box Size:",value=0)
self.gbl2.addWidget(self.wboxsize,2,0,1,2)
# max or mean
#self.wmaxmean=QtGui.QPushButton("MaxProj")
#self.wmaxmean.setCheckable(True)
#self.gbl2.addWidget(self.wmaxmean,3,0)
# number slices
self.wnlayers=QtGui.QSpinBox()
self.wnlayers.setMinimum(1)
self.wnlayers.setMaximum(256)
self.wnlayers.setValue(1)
self.gbl2.addWidget(self.wnlayers,3,1)
# Local boxes in side view
self.wlocalbox=QtGui.QCheckBox("Limit Side Boxes")
self.gbl2.addWidget(self.wlocalbox,3,0)
self.wlocalbox.setChecked(True)
# scale factor
self.wscale=ValSlider(rng=(.1,2),label="Sca:",value=1.0)
self.gbl2.addWidget(self.wscale,4,0,1,2)
# 2-D filters
self.wfilt = ValSlider(rng=(0,150),label="Filt:",value=0.0)
self.gbl2.addWidget(self.wfilt,5,0,1,2)
self.curbox=-1
self.boxes=[] # array of box info, each is (x,y,z,...)
self.boxesimgs=[] # z projection of each box
self.xydown=self.xzdown=self.zydown=None
self.firsthbclick = None
# coordinate display
self.wcoords=QtGui.QLabel("X: " + str(self.get_x()) + "\t\t" + "Y: " + str(self.get_y()) + "\t\t" + "Z: " + str(self.get_z()))
self.gbl2.addWidget(self.wcoords, 1, 0, 1, 2)
# file menu
self.mfile_open.triggered[bool].connect(self.menu_file_open)
self.mfile_read_boxloc.triggered[bool].connect(self.menu_file_read_boxloc)
self.mfile_save_boxloc.triggered[bool].connect(self.menu_file_save_boxloc)
self.mfile_save_boxes_stack.triggered[bool].connect(self.save_boxes)
self.mfile_quit.triggered[bool].connect(self.menu_file_quit)
# all other widgets
self.wdepth.valueChanged[int].connect(self.event_depth)
self.wnlayers.valueChanged[int].connect(self.event_nlayers)
self.wboxsize.valueChanged.connect(self.event_boxsize)
#self.wmaxmean.clicked[bool].connect(self.event_projmode)
self.wscale.valueChanged.connect(self.event_scale)
self.wfilt.valueChanged.connect(self.event_filter)
self.wlocalbox.stateChanged[int].connect(self.event_localbox)
self.xyview.mousemove.connect(self.xy_move)
self.xyview.mousedown.connect(self.xy_down)
self.xyview.mousedrag.connect(self.xy_drag)
self.xyview.mouseup.connect(self.xy_up)
self.xyview.mousewheel.connect(self.xy_wheel)
self.xyview.signal_set_scale.connect(self.xy_scale)
self.xyview.origin_update.connect(self.xy_origin)
self.xzview.mousedown.connect(self.xz_down)
self.xzview.mousedrag.connect(self.xz_drag)
self.xzview.mouseup.connect(self.xz_up)
self.xzview.signal_set_scale.connect(self.xz_scale)
self.xzview.origin_update.connect(self.xz_origin)
self.zyview.mousedown.connect(self.zy_down)
self.zyview.mousedrag.connect(self.zy_drag)
self.zyview.mouseup.connect(self.zy_up)
self.zyview.signal_set_scale.connect(self.zy_scale)
self.zyview.origin_update.connect(self.zy_origin)
self.xyview.keypress.connect(self.key_press)
self.datafilename=datafile
self.basename=base_name(datafile)
p0=datafile.find('__')
if p0>0:
p1=datafile.rfind('.')
self.filetag=datafile[p0:p1]
if self.filetag[-1]!='_':
self.filetag+='_'
else:
self.filetag="__"
data=EMData(datafile)
self.set_data(data)
# Boxviewer subwidget (details of a single box)
self.boxviewer=EMBoxViewer()
#self.app().attach_child(self.boxviewer)
# Boxes Viewer (z projections of all boxes)
self.boxesviewer=EMImageMXWidget()
#self.app().attach_child(self.boxesviewer)
self.boxesviewer.show()
self.boxesviewer.set_mouse_mode("App")
self.boxesviewer.setWindowTitle("Particle List")
self.boxesviewer.rzonce=True
self.setspanel=EMTomoSetsPanel(self)
self.optionviewer=EMTomoBoxerOptions(self)
self.optionviewer.add_panel(self.setspanel,"Sets")
self.optionviewer.show()
# Average viewer shows results of background tomographic processing
# self.averageviewer=EMAverageViewer(self)
#self.averageviewer.show()
self.boxesviewer.mx_image_selected.connect(self.img_selected)
self.jsonfile=info_name(datafile)
info=js_open_dict(self.jsonfile)
self.sets={}
self.boxsize={}
if "class_list" in info:
clslst=info["class_list"]
for k in sorted(clslst.keys()):
if type(clslst[k])==dict:
self.sets[int(k)]=str(clslst[k]["name"])
self.boxsize[int(k)]=int(clslst[k]["boxsize"])
else:
self.sets[int(k)]=str(clslst[k])
self.boxsize[int(k)]=boxsize
clr=QtGui.QColor
self.setcolors=[clr("blue"),clr("green"),clr("red"),clr("cyan"),clr("purple"),clr("orange"), clr("yellow"),clr("hotpink"),clr("gold")]
self.sets_visible={}
if "boxes_3d" in info:
box=info["boxes_3d"]
for i,b in enumerate(box):
#### X-center,Y-center,Z-center,method,[score,[class #]]
bdf=[0,0,0,"manual",0.0, 0]
for j,bi in enumerate(b): bdf[j]=bi
if bdf[5] not in list(self.sets.keys()):
clsi=int(bdf[5])
self.sets[clsi]="particles_{:02d}".format(clsi)
self.boxsize[clsi]=boxsize
self.boxes.append(bdf)
###### this is the new (2018-09) metadata standard..
### now we use coordinates at full size from center of tomogram so it works for different binning and clipping
### have to make it compatible with older versions though..
if "apix_unbin" in info:
self.apix_unbin=info["apix_unbin"]
self.apix_cur=apix=data["apix_x"]
for b in self.boxes:
b[0]=b[0]/apix*self.apix_unbin+data["nx"]//2
b[1]=b[1]/apix*self.apix_unbin+data["ny"]//2
b[2]=b[2]/apix*self.apix_unbin+data["nz"]//2
for k in self.boxsize.keys():
self.boxsize[k]=self.boxsize[k]/apix*self.apix_unbin
else:
self.apix_unbin=-1
info.close()
if len(self.sets)==0:
self.new_set("particles_00")
self.sets_visible[list(self.sets.keys())[0]]=0
self.currentset=sorted(self.sets.keys())[0]
self.setspanel.update_sets()
self.wboxsize.setValue(self.get_boxsize())
print(self.sets)
for i in range(len(self.boxes)):
self.update_box(i)
self.update_all()
self.initialized=True
def set_data(self,data):
self.data=data
self.apix=data["apix_x"]
self.datasize=(data["nx"],data["ny"],data["nz"])
self.wdepth.setRange(0,self.datasize[2]-1)
self.boxes=[]
self.curbox=-1
self.wdepth.setValue(old_div(self.datasize[2],2))
if self.initialized:
self.update_all()
def eraser_width(self):
return int(self.optionviewer.eraser_radius.getValue())
def get_cube(self,x,y,z, centerslice=False, boxsz=-1):
"""Returns a box-sized cube at the given center location"""
if boxsz<0:
bs=self.get_boxsize()
else:
bs=boxsz
if centerslice:
bz=1
else:
bz=bs
if ((x<-bs//2) or (y<-bs//2) or (z<-bz//2)
or (x>self.data["nx"]+bs//2) or (y>self.data["ny"]+bs//2) or (z>self.data["nz"]+bz//2) ):
r=EMData(bs,bs,bz)
else:
r=self.data.get_clip(Region(x-bs//2,y-bs//2,z-bz//2,bs,bs,bz))
if self.apix!=0 :
r["apix_x"]=self.apix
r["apix_y"]=self.apix
r["apix_z"]=self.apix
#if options.normproc:
#r.process_inplace(options.normproc)
return r
def get_slice(self,n,xyz):
"""Reads a slice either from a file or the preloaded memory array.
xyz is the axis along which 'n' runs, 0=x (yz), 1=y (xz), 2=z (xy)"""
if xyz==0:
r=self.data.get_clip(Region(n,0,0,1,self.datasize[1],self.datasize[2]))
r.set_size(self.datasize[1],self.datasize[2],1)
elif xyz==1:
r=self.data.get_clip(Region(0,n,0,self.datasize[0],1,self.datasize[2]))
r.set_size(self.datasize[0],self.datasize[2],1)
else:
r=self.data.get_clip(Region(0,0,n,self.datasize[0],self.datasize[1],1))
if self.apix!=0 :
r["apix_x"]=self.apix
r["apix_y"]=self.apix
r["apix_z"]=self.apix
return r
def event_boxsize(self):
if self.get_boxsize()==int(self.wboxsize.getValue()):
return
self.boxsize[self.currentset]=int(self.wboxsize.getValue())
cb=self.curbox
self.initialized=False
for i in range(len(self.boxes)):
if self.boxes[i][5]==self.currentset:
self.update_box(i)
self.update_box(cb)
self.initialized=True
self.update_all()
def event_projmode(self,state):
"""Projection mode can be simple average (state=False) or maximum projection (state=True)"""
self.update_all()
def event_scale(self,newscale):
self.xyview.set_scale(newscale)
self.xzview.set_scale(newscale)
self.zyview.set_scale(newscale)
def event_depth(self):
if self.initialized:
self.update_xy()
def event_nlayers(self):
self.update_all()
def event_filter(self):
self.update_all()
def event_localbox(self,tog):
self.update_sides()
def get_boxsize(self, clsid=-1):
if clsid<0:
return int(self.boxsize[self.currentset])
else:
try:
ret= int(self.boxsize[clsid])
except:
print("No box size saved for {}..".format(clsid))
ret=32
return ret
def nlayers(self):
return int(self.wnlayers.value())
def depth(self):
return int(self.wdepth.value())
def scale(self):
return self.wscale.getValue()
def get_x(self):
return self.get_coord(0)
def get_y(self):
return self.get_coord(1)
def get_z(self):
return self.depth()
def get_coord(self, coord_index):
if len(self.boxes) > 1:
if self.curbox:
return self.boxes[self.curbox][coord_index]
else:
return self.boxes[-1][coord_index]
else:
return 0
def menu_file_open(self,tog):
QtGui.QMessageBox.warning(None,"Error","Sorry, in the current version, you must provide a file to open on the command-line.")
def load_box_yshort(self, boxcoords):
if options.yshort:
return [boxcoords[0], boxcoords[2], boxcoords[1]]
else:
return boxcoords
def menu_file_read_boxloc(self):
fsp=str(QtGui.QFileDialog.getOpenFileName(self, "Select output text file"))
f=file(fsp,"r")
for b in f:
b2=[old_div(int(float(i)),self.shrink) for i in b.split()[:3]]
bdf=[0,0,0,"manual",0.0, self.currentset]
for j in range(len(b2)):
bdf[j]=b2[j]
self.boxes.append(bdf)
self.update_box(len(self.boxes)-1)
f.close()
def menu_file_save_boxloc(self):
shrinkf=self.shrink #jesus
fsp=str(QtGui.QFileDialog.getSaveFileName(self, "Select output text file"))
out=file(fsp,"w")
for b in self.boxes:
out.write("%d\t%d\t%d\n"%(b[0]*shrinkf,b[1]*shrinkf,b[2]*shrinkf))
out.close()
def save_boxes(self, clsid=[]):
if len(clsid)==0:
defaultname="ptcls.hdf"
else:
defaultname="_".join([self.sets[i] for i in clsid])+".hdf"
name,ok=QtGui.QInputDialog.getText( self, "Save particles", "Filename suffix:", text=defaultname)
if not ok:
return
name=self.filetag+str(name)
if name[-4:].lower()!=".hdf" :
name+=".hdf"
if self.options.mode=="3D":
dr="particles3d"
is2d=False
else:
dr="particles"
is2d=True
if not os.path.isdir(dr):
os.mkdir(dr)
fsp=os.path.join(dr,self.basename)+name
print("Saving {} particles to {}".format(self.options.mode, fsp))
if os.path.isfile(fsp):
print("{} exist. Overwritting...".format(fsp))
os.remove(fsp)
progress = QtGui.QProgressDialog("Saving", "Abort", 0, len(self.boxes),None)
boxsz=-1
for i,b in enumerate(self.boxes):
if len(clsid)>0:
if int(b[5]) not in clsid:
continue
#img=self.get_cube(b[0],b[1],b[2])
bs=self.get_boxsize(b[5])
if boxsz<0:
boxsz=bs
else:
if boxsz!=bs:
print("Inconsistant box size in the particles to save.. Using {:d}..".format(boxsz))
bs=boxsz
sz=[s//2 for s in self.datasize]
img=self.get_cube(b[0], b[1], b[2], centerslice=is2d, boxsz=bs)
if is2d==False:
img.process_inplace('normalize')
img["ptcl_source_image"]=self.datafilename
img["ptcl_source_coord"]=(b[0]-sz[0], b[1]-sz[1], b[2]-sz[2])
if is2d==False: #### do not invert contrast for 2D images
img.mult(-1)
img.write_image(fsp,-1)
progress.setValue(i+1)
if progress.wasCanceled():
break
def menu_file_quit(self):
self.close()
def transform_coords(self, point, xform):
xvec = xform.get_matrix()
return [xvec[0]*point[0] + xvec[4]*point[1] + xvec[8]*point[2] + xvec[3], xvec[1]*point[0] + xvec[5]*point[1] + xvec[9]*point[2] + xvec[7], xvec[2]*point[0] + xvec[6]*point[1] + xvec[10]*point[2] + xvec[11]]
def get_averager(self):
"""returns an averager of the appropriate type for generating projection views"""
#if self.wmaxmean.isChecked() : return Averagers.get("minmax",{"max":1})
return Averagers.get("mean")
def update_sides(self):
"""updates xz and yz views due to a new center location"""
#print "\n\n\n\n\nIn update sides, self.datafile is", self.datafile
#print "\n\n\n\n"
if self.data==None:
return
if self.curbox==-1 :
x=self.datasize[0]//2
y=self.datasize[1]//2
z=0
else:
x,y,z=self.boxes[self.curbox][:3]
self.cury=y
self.curx=x
# update shape display
if self.wlocalbox.isChecked():
xzs=self.xzview.get_shapes()
for i in range(len(self.boxes)):
bs=self.get_boxsize(self.boxes[i][5])
if self.boxes[i][1]<self.cury+old_div(bs,2) and self.boxes[i][1]>self.cury-old_div(bs,2) and self.boxes[i][5] in self.sets_visible:
xzs[i][0]=self.boxshape
else:
xzs[i][0]="hidden"
zys=self.zyview.get_shapes()
for i in range(len(self.boxes)):
bs=self.get_boxsize(self.boxes[i][5])
if self.boxes[i][0]<self.curx+old_div(bs,2) and self.boxes[i][0]>self.curx-old_div(bs,2) and self.boxes[i][5] in self.sets_visible:
zys[i][0]=self.boxshape
else:
zys[i][0]="hidden"
else :
xzs=self.xzview.get_shapes()
zys=self.zyview.get_shapes()
for i in range(len(self.boxes)):
bs=self.get_boxsize(self.boxes[i][5])
if self.boxes[i][5] in self.sets_visible:
xzs[i][0]=self.boxshape
zys[i][0]=self.boxshape
else:
xzs[i][0]="hidden"
zys[i][0]="hidden"
self.xzview.shapechange=1
self.zyview.shapechange=1
# yz
avgr=self.get_averager()
for x in range(x-(self.nlayers()//2),x+((self.nlayers()+1)//2)):
slc=self.get_slice(x,0)
avgr.add_image(slc)
av=avgr.finish()
if not self.yshort:
av.process_inplace("xform.transpose")
if self.wfilt.getValue()!=0.0:
av.process_inplace("filter.lowpass.gauss",{"cutoff_freq":old_div(1.0,self.wfilt.getValue()),"apix":self.apix})
self.zyview.set_data(av)
# xz
avgr=self.get_averager()
for y in range(y-old_div(self.nlayers(),2),y+old_div((self.nlayers()+1),2)):
slc=self.get_slice(y,1)
avgr.add_image(slc)
av=avgr.finish()
if self.wfilt.getValue()!=0.0:
av.process_inplace("filter.lowpass.gauss",{"cutoff_freq":old_div(1.0,self.wfilt.getValue()),"apix":self.apix})
self.xzview.set_data(av)
def update_xy(self):
"""updates xy view due to a new slice range"""
#print "\n\n\n\n\nIn update_xy, self.datafile is", self.datafile
#print "\n\n\n\n"
if self.data==None:
return
# Boxes should also be limited by default in the XY view
if len(self.boxes) > 0:
zc=self.wdepth.value()
#print "The current depth is", self.wdepth.value()
xys=self.xyview.get_shapes()
for i in range(len(self.boxes)):
bs=self.get_boxsize(self.boxes[i][5])
zdist=abs(self.boxes[i][2] - zc)
if self.options.mode=="3D":
zthr=bs/2
xys[i][6]=bs//2-zdist
else:
zthr=1
if zdist < zthr and self.boxes[i][5] in self.sets_visible:
xys[i][0]=self.boxshape
else :
xys[i][0]="hidden"
self.xyview.shapechange=1
#if self.wmaxmean.isChecked():
#avgr=Averagers.get("minmax",{"max":1})
#else:
avgr=Averagers.get("mean")
slc=EMData()
for z in range(self.wdepth.value()-self.nlayers()//2,self.wdepth.value()+(self.nlayers()+1)//2):
slc=self.get_slice(z,2)
avgr.add_image(slc)
av=avgr.finish()
#print "\n\nIn update xy, av and type are", av, type(av)
if self.wfilt.getValue()!=0.0:
av.process_inplace("filter.lowpass.gauss",{"cutoff_freq":old_div(1.0,self.wfilt.getValue()),"apix":self.apix})
if self.initialized:
self.xyview.set_data(av, keepcontrast=True)
else:
self.xyview.set_data(av)
def update_all(self):
"""redisplay of all widgets"""
#print "\n\n\n\n\nIn update all, self.datafile is", self.datafile
#print "\n\n\n\n"
if self.data==None:
return
self.update_xy()
self.update_sides()
self.update_boximgs()
def update_coords(self):
self.wcoords.setText("X: " + str(self.get_x()) + "\t\t" + "Y: " + str(self.get_y()) + "\t\t" + "Z: " + str(self.get_z()))
def inside_box(self,n,x=-1,y=-1,z=-1):
"""Checks to see if a point in image coordinates is inside box number n. If any value is negative, it will not be checked."""
box=self.boxes[n]
if box[5] not in self.sets_visible:
return False
bs=self.get_boxsize(box[5])/2
if self.options.mode=="3D":
rr=(x>=0)*((box[0]-x)**2) + (y>=0)*((box[1]-y) **2) + (z>=0)*((box[2]-z)**2)
else:
rr=(x>=0)*((box[0]-x)**2) + (y>=0)*((box[1]-y) **2) + (z>=0)*(box[2]!=z)*(1e3*bs**2)
return rr<=bs**2
def do_deletion(self, delids):
kpids=[i for i,b in enumerate(self.boxes) if i not in delids]
self.boxes=[self.boxes[i] for i in kpids]
self.boxesimgs=[self.boxesimgs[i] for i in kpids]
self.xyview.shapes={i:self.xyview.shapes[k] for i,k in enumerate(kpids)}
self.xzview.shapes={i:self.xzview.shapes[k] for i,k in enumerate(kpids)}
self.zyview.shapes={i:self.zyview.shapes[k] for i,k in enumerate(kpids)}
#print self.boxes, self.xyview.get_shapes()
self.curbox=-1
self.update_all()
def del_box(self,n):
"""Delete an existing box by replacing the deleted box with the last box. A bit funny, but otherwise
update after deletion is REALLY slow."""
# print "del ",n
if n<0 or n>=len(self.boxes): return
if self.boxviewer.get_data(): self.boxviewer.set_data(None)
self.curbox=-1
self.do_deletion([n])
def update_box(self,n,quiet=False):
"""After adjusting a box, call this"""
# print "upd ",n,quiet
try:
box=self.boxes[n]
except IndexError:
return
bs2=self.get_boxsize(box[5])//2
color=self.setcolors[box[5]%len(self.setcolors)].getRgbF()
if self.options.mode=="3D":
self.xyview.add_shape(n,EMShape(["circle",color[0],color[1],color[2],box[0],box[1],bs2,2]))
self.xzview.add_shape(n,EMShape(["circle",color[0],color[1],color[2],box[0],box[2],bs2,2]))
self.zyview.add_shape(n,EMShape(("circle",color[0],color[1],color[2],box[2],box[1],bs2,2)))
else:
self.xyview.add_shape(n,EMShape(["rect",color[0],color[1],color[2],
box[0]-bs2,box[1]-bs2,box[0]+bs2,box[1]+bs2,2]))
self.xzview.add_shape(n,EMShape(["rect",color[0],color[1],color[2],
box[0]-bs2,box[2]-1,box[0]+bs2,box[2]+1,2]))
self.zyview.add_shape(n,EMShape(["rect",color[0],color[1],color[2],
box[2]-1,box[1]-bs2,box[2]+1,box[1]+bs2,2]))
if self.depth()!=box[2]:
self.wdepth.setValue(box[2])
else:
self.xyview.update()
if self.initialized: self.update_sides()
# For speed, we turn off updates while dragging a box around. Quiet is set until the mouse-up
if not quiet:
# Get the cube from the original data (normalized)
proj=self.get_cube(box[0], box[1], box[2], centerslice=True, boxsz=self.get_boxsize(box[5]))
proj.process_inplace("normalize")
for i in range(len(self.boxesimgs),n+1):
self.boxesimgs.append(None)
self.boxesimgs[n]=proj
mm=[m for im,m in enumerate(self.boxesimgs) if self.boxes[im][5] in self.sets_visible]
if self.initialized: self.SaveJson()
if self.initialized:
self.update_boximgs()
if n!=self.curbox:
self.boxesviewer.set_selected((n,),True)
self.curbox=n
self.update_coords()
def update_boximgs(self):
self.boxids=[im for im,m in enumerate(self.boxesimgs) if self.boxes[im][5] in self.sets_visible]
self.boxesviewer.set_data([self.boxesimgs[i] for i in self.boxids])
self.boxesviewer.update()
return
def img_selected(self,event,lc):
#print "sel",lc[0]
lci=self.boxids[lc[0]]
if event.modifiers()&Qt.ShiftModifier:
self.del_box(lci)
else:
self.update_box(lci)
if self.curbox>=0 :
box=self.boxes[self.curbox]
self.xyview.scroll_to(box[0],box[1])
self.xzview.scroll_to(None,box[2])
self.zyview.scroll_to(box[2],None)
self.currentset=box[5]
self.setspanel.initialized=False
self.setspanel.update_sets()
def del_region_xy(self, x=-1, y=-1, z=-1, rad=-1):
if rad<0:
rad=self.eraser_width()
delids=[]
for i,b in enumerate(self.boxes):
if b[5] not in self.sets_visible:
continue
if (x>=0)*(b[0]-x)**2 + (y>=0)*(b[1]-y)**2 +(z>=0)*(b[2]-z)**2 < rad**2:
delids.append(i)
self.do_deletion(delids)
def xy_down(self,event):
x,y=self.xyview.scr_to_img((event.x(),event.y()))
x,y=int(x),int(y)
z=int(self.get_z())
self.xydown=None
if x<0 or y<0 : return # no clicking outside the image (on 2 sides)
if self.optionviewer.erasercheckbox.isChecked():
self.del_region_xy(x,y)
return
for i in range(len(self.boxes)):
if self.inside_box(i,x,y,z):
if event.modifiers()&Qt.ShiftModifier:
self.del_box(i)
self.firsthbclick = None
else:
self.xydown=(i,x,y,self.boxes[i][0],self.boxes[i][1])
self.update_box(i)
break
else:
# if x>self.get_boxsize()/2 and x<self.datasize[0]-self.get_boxsize()/2 and y>self.get_boxsize()/2 and y<self.datasize[1]-self.get_boxsize()/2 and self.depth()>self.get_boxsize()/2 and self.depth()<self.datasize[2]-self.get_boxsize()/2 :
if not event.modifiers()&Qt.ShiftModifier:
self.boxes.append(([x,y,self.depth(), 'manual', 0.0, self.currentset]))
self.xydown=(len(self.boxes)-1,x,y,x,y) # box #, x down, y down, x box at down, y box at down
self.update_box(self.xydown[0])
if self.curbox>=0:
box=self.boxes[self.curbox]
self.xzview.scroll_to(None,box[2])
self.zyview.scroll_to(box[2],None)
def xy_drag(self,event):
x,y=self.xyview.scr_to_img((event.x(),event.y()))
x,y=int(x),int(y)
if self.optionviewer.erasercheckbox.isChecked():
self.del_region_xy(x,y)
self.xyview.eraser_shape=EMShape(["circle",1,1,1,x,y,self.eraser_width(),2])
self.xyview.shapechange=1
self.xyview.update()
return
if self.xydown==None : return
dx=x-self.xydown[1]
dy=y-self.xydown[2]
self.boxes[self.xydown[0]][0]=dx+self.xydown[3]
self.boxes[self.xydown[0]][1]=dy+self.xydown[4]
self.update_box(self.curbox,True)
def xy_up (self,event):
if self.xydown!=None: self.update_box(self.curbox)
self.xydown=None
def xy_wheel (self,event):
if event.delta() > 0:
#self.wdepth.setValue(self.wdepth.value()+4)
self.wdepth.setValue(self.wdepth.value()+1) #jesus
elif event.delta() < 0:
#self.wdepth.setValue(self.wdepth.value()-4)
self.wdepth.setValue(self.wdepth.value()-1) #jesus
def xy_scale(self,news):
"xy image view has been rescaled"
self.wscale.setValue(news)
#self.xzview.set_scale(news,True)
#self.zyview.set_scale(news,True)
def xy_origin(self,newor):
"xy origin change"
xzo=self.xzview.get_origin()
self.xzview.set_origin(newor[0],xzo[1],True)
zyo=self.zyview.get_origin()
self.zyview.set_origin(zyo[0],newor[1],True)
def xy_move(self,event):
if self.optionviewer.erasercheckbox.isChecked():
x,y=self.xyview.scr_to_img((event.x(),event.y()))
#print x,y
self.xyview.eraser_shape=EMShape(["circle",1,1,1,x,y,self.eraser_width(),2])
self.xyview.shapechange=1
self.xyview.update()
else:
self.xyview.eraser_shape=None
def xz_down(self,event):
x,z=self.xzview.scr_to_img((event.x(),event.y()))
x,z=int(x),int(z)
y=int(self.get_y())
self.xzdown=None
if x<0 or z<0 : return # no clicking outside the image (on 2 sides)
if self.optionviewer.erasercheckbox.isChecked():
return
for i in range(len(self.boxes)):
if (not self.wlocalbox.isChecked() and self.inside_box(i,x,y,z)) or self.inside_box(i,x,self.cury,z) :
if event.modifiers()&Qt.ShiftModifier:
self.del_box(i)
self.firsthbclick = None
else :
self.xzdown=(i,x,z,self.boxes[i][0],self.boxes[i][2])
self.update_box(i)
break
else:
if not event.modifiers()&Qt.ShiftModifier:
self.boxes.append(([x,self.cury,z, 'manual', 0.0, self.currentset]))
self.xzdown=(len(self.boxes)-1,x,z,x,z) # box #, x down, y down, x box at down, y box at down
self.update_box(self.xzdown[0])
if self.curbox>=0 :
box=self.boxes[self.curbox]
self.xyview.scroll_to(None,box[1])
self.zyview.scroll_to(box[2],None)
def xz_drag(self,event):
if self.xzdown==None : return
x,z=self.xzview.scr_to_img((event.x(),event.y()))
x,z=int(x),int(z)
dx=x-self.xzdown[1]
dz=z-self.xzdown[2]
self.boxes[self.xzdown[0]][0]=dx+self.xzdown[3]
self.boxes[self.xzdown[0]][2]=dz+self.xzdown[4]
self.update_box(self.curbox,True)
def xz_up (self,event):
if self.xzdown!=None: self.update_box(self.curbox)
self.xzdown=None
def xz_scale(self,news):
"xy image view has been rescaled"
self.wscale.setValue(news)
#self.xyview.set_scale(news,True)
#self.zyview.set_scale(news,True)
def xz_origin(self,newor):
"xy origin change"
xyo=self.xyview.get_origin()
self.xyview.set_origin(newor[0],xyo[1],True)
#zyo=self.zyview.get_origin()
#self.zyview.set_origin(zyo[0],newor[1],True)
def zy_down(self,event):
z,y=self.zyview.scr_to_img((event.x(),event.y()))
z,y=int(z),int(y)
x=int(self.get_x())
self.xydown=None
if z<0 or y<0 : return # no clicking outside the image (on 2 sides)
for i in range(len(self.boxes)):
if (not self.wlocalbox.isChecked() and self.inside_box(i,x,y,z)) or self.inside_box(i,self.curx,y,z):
if event.modifiers()&Qt.ShiftModifier:
self.del_box(i)
self.firsthbclick = None
else :
self.zydown=(i,z,y,self.boxes[i][2],self.boxes[i][1])
self.update_box(i)
break
else:
if not event.modifiers()&Qt.ShiftModifier:
###########
self.boxes.append(([self.curx,y,z, 'manual', 0.0, self.currentset]))
self.zydown=(len(self.boxes)-1,z,y,z,y) # box #, x down, y down, x box at down, y box at down
self.update_box(self.zydown[0])
if self.curbox>=0 :
box=self.boxes[self.curbox]
self.xyview.scroll_to(box[0],None)
self.xzview.scroll_to(None,box[2])
def zy_drag(self,event):
if self.zydown==None : return
z,y=self.zyview.scr_to_img((event.x(),event.y()))
z,y=int(z),int(y)
dz=z-self.zydown[1]
dy=y-self.zydown[2]
self.boxes[self.zydown[0]][2]=dz+self.zydown[3]
self.boxes[self.zydown[0]][1]=dy+self.zydown[4]
self.update_box(self.curbox,True)
def zy_up (self,event):
if self.zydown!=None:
self.update_box(self.curbox)
self.zydown=None
def zy_scale(self,news):
"xy image view has been rescaled"
self.wscale.setValue(news)
#self.xyview.set_scale(news,True)
#self.xzview.set_scale(news,True)
def zy_origin(self,newor):
"xy origin change"
xyo=self.xyview.get_origin()
self.xyview.set_origin(xyo[0],newor[1],True)
#xzo=self.xzview.get_origin()
#self.xzview.set_origin(xzo[0],newor[1],True)
def set_current_set(self, name):
#print "set current", name
name=parse_setname(name)
self.currentset=name
self.wboxsize.setValue(self.get_boxsize())
self.update_all()
return
def hide_set(self, name):
name=parse_setname(name)
if name in self.sets_visible: self.sets_visible.pop(name)
if self.initialized:
self.update_all()
self.update_boximgs()
return
def show_set(self, name):
name=parse_setname(name)
self.sets_visible[name]=0
#self.currentset=name
self.wboxsize.setValue(self.get_boxsize())
if self.initialized:
self.update_all()
self.update_boximgs()
return
def delete_set(self, name):
name=parse_setname(name)
## idx to keep
delids=[i for i,b in enumerate(self.boxes) if b[5]==int(name)]
self.do_deletion(delids)
if name in self.sets_visible: self.sets_visible.pop(name)
if name in self.sets: self.sets.pop(name)
if name in self.boxsize: self.boxsize.pop(name)
self.curbox=-1
self.update_all()
return
def rename_set(self, oldname, newname):
name=parse_setname(oldname)
if name in self.sets:
self.sets[name]=newname
return
def new_set(self, name):
for i in range(len(self.sets)+1):
if i not in self.sets:
break
self.sets[i]=name
self.sets_visible[i]=0
if self.options.mode=="3D":
self.boxsize[i]=32
else:
self.boxsize[i]=64
return
def save_set(self):
self.save_boxes(list(self.sets_visible.keys()))
return
def key_press(self,event):
if event.key() == 96:
self.wdepth.setValue(self.wdepth.value()+1)
elif event.key() == 49:
self.wdepth.setValue(self.wdepth.value()-1)
else:
self.keypress.emit(event)
def SaveJson(self):
info=js_open_dict(self.jsonfile)
sx,sy,sz=(self.data["nx"]//2,self.data["ny"]//2,self.data["nz"]//2)
if "apix_unbin" in info:
bxs=[]
for b0 in self.boxes:
b=[ (b0[0]-sx)*self.apix_cur/self.apix_unbin,
(b0[1]-sy)*self.apix_cur/self.apix_unbin,
(b0[2]-sz)*self.apix_cur/self.apix_unbin,
b0[3], b0[4], b0[5] ]
bxs.append(b)
bxsz={}
for k in self.boxsize.keys():
bxsz[k]=self.boxsize[k]*self.apix_cur/self.apix_unbin
else:
bxs=self.boxes
bxsz=self.boxsize
info["boxes_3d"]=bxs
clslst={}
for key in list(self.sets.keys()):
clslst[int(key)]={
"name":self.sets[key],
"boxsize":int(bxsz[key]),
}
info["class_list"]=clslst
info.close()
def closeEvent(self,event):
print("Exiting")
self.SaveJson()
self.boxviewer.close()
self.boxesviewer.close()
self.optionviewer.close()
self.xyview.close()
self.xzview.close()
self.zyview.close()
self.module_closed.emit() # this signal is important when e2ctf is being used by a program running its own event loop
class EMHelloWorldInspector(QtWidgets.QWidget):
def __init__(self, target):
QtWidgets.QWidget.__init__(self, None)
self.target = target
self.vbl = QtWidgets.QVBoxLayout(self)
self.vbl.setContentsMargins(0, 0, 0, 0)
self.vbl.setSpacing(6)
self.vbl.setObjectName("vbl")
self.hbl = QtWidgets.QHBoxLayout()
self.hbl.setContentsMargins(0, 0, 0, 0)
self.hbl.setSpacing(6)
self.hbl.setObjectName("hbl")
self.vbl.addLayout(self.hbl)
self.vbl2 = QtWidgets.QVBoxLayout()
self.vbl2.setContentsMargins(0, 0, 0, 0)
self.vbl2.setSpacing(6)
self.vbl2.setObjectName("vbl2")
self.hbl.addLayout(self.vbl2)
self.wiretog = QtWidgets.QPushButton("Wire")
self.wiretog.setCheckable(1)
self.vbl2.addWidget(self.wiretog)
self.lighttog = QtWidgets.QPushButton("Light")
self.lighttog.setCheckable(1)
self.vbl2.addWidget(self.lighttog)
self.tabwidget = QtWidgets.QTabWidget()
self.maintab = None
self.tabwidget.addTab(self.get_main_tab(), "Main")
self.tabwidget.addTab(self.get_GL_tab(), "GL")
self.vbl.addWidget(self.tabwidget)
self.n3_showing = False
self.scale.valueChanged.connect(target.set_scale)
self.az.valueChanged.connect(self.slider_rotate)
self.alt.valueChanged.connect(self.slider_rotate)
self.phi.valueChanged.connect(self.slider_rotate)
self.cbb.currentIndexChanged[str].connect(target.setColor)
self.src.currentIndexChanged[str].connect(self.set_src)
self.x_trans.valueChanged[double].connect(target.set_cam_x)
self.y_trans.valueChanged[double].connect(target.set_cam_y)
self.z_trans.valueChanged[double].connect(target.set_cam_z)
self.wiretog.toggled[bool].connect(target.toggle_wire)
self.lighttog.toggled[bool].connect(target.toggle_light)
self.glcontrast.valueChanged.connect(target.set_GL_contrast)
self.glbrightness.valueChanged.connect(target.set_GL_brightness)
def get_GL_tab(self):
self.gltab = QtWidgets.QWidget()
gltab = self.gltab
gltab.vbl = QtWidgets.QVBoxLayout(self.gltab)
gltab.vbl.setContentsMargins(0, 0, 0, 0)
gltab.vbl.setSpacing(6)
gltab.vbl.setObjectName("Main")
self.glcontrast = ValSlider(gltab, (1.0, 5.0), "GLShd:")
self.glcontrast.setObjectName("GLShade")
self.glcontrast.setValue(1.0)
gltab.vbl.addWidget(self.glcontrast)
self.glbrightness = ValSlider(gltab, (-1.0, 0.0), "GLBst:")
self.glbrightness.setObjectName("GLBoost")
self.glbrightness.setValue(0.1)
self.glbrightness.setValue(0.0)
gltab.vbl.addWidget(self.glbrightness)
return gltab
def get_main_tab(self):
if (self.maintab == None):
self.maintab = QtWidgets.QWidget()
maintab = self.maintab
maintab.vbl = QtWidgets.QVBoxLayout(self.maintab)
maintab.vbl.setContentsMargins(0, 0, 0, 0)
maintab.vbl.setSpacing(6)
maintab.vbl.setObjectName("Main")
self.scale = ValSlider(maintab, (0.01, 30.0), "Zoom:")
self.scale.setObjectName("scale")
self.scale.setValue(1.0)
maintab.vbl.addWidget(self.scale)
self.hbl_color = QtWidgets.QHBoxLayout()
self.hbl_color.setContentsMargins(0, 0, 0, 0)
self.hbl_color.setSpacing(6)
self.hbl_color.setObjectName("Material")
maintab.vbl.addLayout(self.hbl_color)
self.color_label = QtWidgets.QLabel()
self.color_label.setText('Material')
self.hbl_color.addWidget(self.color_label)
self.cbb = QtWidgets.QComboBox(maintab)
self.hbl_color.addWidget(self.cbb)
self.hbl_trans = QtWidgets.QHBoxLayout()
self.hbl_trans.setContentsMargins(0, 0, 0, 0)
self.hbl_trans.setSpacing(6)
self.hbl_trans.setObjectName("Trans")
maintab.vbl.addLayout(self.hbl_trans)
self.x_label = QtWidgets.QLabel()
self.x_label.setText('x')
self.hbl_trans.addWidget(self.x_label)
self.x_trans = QtWidgets.QDoubleSpinBox(self)
self.x_trans.setMinimum(-10000)
self.x_trans.setMaximum(10000)
self.x_trans.setValue(0.0)
self.hbl_trans.addWidget(self.x_trans)
self.y_label = QtWidgets.QLabel()
self.y_label.setText('y')
self.hbl_trans.addWidget(self.y_label)
self.y_trans = QtWidgets.QDoubleSpinBox(maintab)
self.y_trans.setMinimum(-10000)
self.y_trans.setMaximum(10000)
self.y_trans.setValue(0.0)
self.hbl_trans.addWidget(self.y_trans)
self.z_label = QtWidgets.QLabel()
self.z_label.setText('z')
self.hbl_trans.addWidget(self.z_label)
self.z_trans = QtWidgets.QDoubleSpinBox(maintab)
self.z_trans.setMinimum(-10000)
self.z_trans.setMaximum(10000)
self.z_trans.setValue(0.0)
self.hbl_trans.addWidget(self.z_trans)
self.hbl_src = QtWidgets.QHBoxLayout()
self.hbl_src.setContentsMargins(0, 0, 0, 0)
self.hbl_src.setSpacing(6)
self.hbl_src.setObjectName("hbl")
maintab.vbl.addLayout(self.hbl_src)
self.label_src = QtWidgets.QLabel()
self.label_src.setText('Rotation Convention')
self.hbl_src.addWidget(self.label_src)
self.src = QtWidgets.QComboBox(maintab)
self.load_src_options(self.src)
self.hbl_src.addWidget(self.src)
# set default value -1 ensures that the val slider is updated the first time it is created
self.az = ValSlider(self, (-360.0, 360.0), "az", -1)
self.az.setObjectName("az")
maintab.vbl.addWidget(self.az)
self.alt = ValSlider(self, (-180.0, 180.0), "alt", -1)
self.alt.setObjectName("alt")
maintab.vbl.addWidget(self.alt)
self.phi = ValSlider(self, (-360.0, 360.0), "phi", -1)
self.phi.setObjectName("phi")
maintab.vbl.addWidget(self.phi)
self.current_src = EULER_EMAN
return self.maintab
def set_xy_trans(self, x, y):
self.x_trans.setValue(x)
self.y_trans.setValue(y)
def set_xyz_trans(self, x, y, z):
self.x_trans.setValue(x)
self.y_trans.setValue(y)
self.z_trans.setValue(z)
def set_translate_scale(self, xscale, yscale, zscale):
self.x_trans.setSingleStep(xscale)
self.y_trans.setSingleStep(yscale)
self.z_trans.setSingleStep(zscale)
def update_rotations(self, t3d):
convention = str(self.src.currentText())
#FIXME: Transform.get_rotation() wants a string sometimes and a EulerType other times
try:
rot = t3d.get_rotation(str(self.src_map[convention]))
except Exception as e: #doing a quick fix
print(e)
print(
"Developers: This catches a large range of exceptions... a better way surely exists"
)
rot = t3d.get_rotation(self.src_map[convention])
if (self.src_map[convention] == EULER_SPIN):
self.n3.setValue(rot[self.n3.getLabel()], True)
self.az.setValue(rot[self.az.getLabel()], True)
self.alt.setValue(rot[self.alt.getLabel()], True)
self.phi.setValue(rot[self.phi.getLabel()], True)
def slider_rotate(self):
self.target.load_rotation(self.get_current_rotation())
def get_current_rotation(self):
convention = self.src.currentText()
rot = {}
if (self.current_src == EULER_SPIN):
rot[self.az.getLabel()] = self.az.getValue()
n1 = self.alt.getValue()
n2 = self.phi.getValue()
n3 = self.n3.getValue()
norm = sqrt(n1 * n1 + n2 * n2 + n3 * n3)
n1 /= norm
n2 /= norm
n3 /= norm
rot[self.alt.getLabel()] = n1
rot[self.phi.getLabel()] = n2
rot[self.n3.getLabel()] = n3
else:
rot[self.az.getLabel()] = self.az.getValue()
rot[self.alt.getLabel()] = self.alt.getValue()
rot[self.phi.getLabel()] = self.phi.getValue()
return Transform(self.current_src, rot)
def set_src(self, val):
t3d = self.get_current_rotation()
if (self.n3_showing):
self.vbl.removeWidget(self.n3)
self.n3.deleteLater()
self.n3_showing = False
self.az.setRange(-360, 360)
self.alt.setRange(-180, 180)
self.phi.setRange(-360, 660)
if (self.src_map[str(val)] == EULER_SPIDER):
self.az.setLabel('phi')
self.alt.setLabel('theta')
self.phi.setLabel('psi')
elif (self.src_map[str(val)] == EULER_EMAN):
self.az.setLabel('az')
self.alt.setLabel('alt')
self.phi.setLabel('phi')
elif (self.src_map[str(val)] == EULER_IMAGIC):
self.az.setLabel('alpha')
self.alt.setLabel('beta')
self.phi.setLabel('gamma')
elif (self.src_map[str(val)] == EULER_XYZ):
self.az.setLabel('xtilt')
self.alt.setLabel('ytilt')
self.phi.setLabel('ztilt')
elif (self.src_map[str(val)] == EULER_MRC):
self.az.setLabel('phi')
self.alt.setLabel('theta')
self.phi.setLabel('omega')
elif (self.src_map[str(val)] == EULER_SPIN):
self.az.setLabel('omega')
self.alt.setRange(-1, 1)
self.phi.setRange(-1, 1)
self.alt.setLabel('n1')
self.phi.setLabel('n2')
self.n3 = ValSlider(self, (-360.0, 360.0), "n3", -1)
self.n3.setRange(-1, 1)
self.n3.setObjectName("n3")
self.vbl.addWidget(self.n3)
self.n3.valueChanged.connect(self.slider_rotate)
self.n3_showing = True
self.current_src = self.src_map[str(val)]
self.update_rotations(t3d)
def load_src_options(self, widgit):
self.load_src()
for i in self.src_strings:
widgit.addItem(i)
# read src as 'supported rotation conventions'
def load_src(self):
# supported_rot_conventions
src_flags = []
src_flags.append(EULER_EMAN)
src_flags.append(EULER_SPIDER)
src_flags.append(EULER_IMAGIC)
src_flags.append(EULER_MRC)
src_flags.append(EULER_SPIN)
src_flags.append(EULER_XYZ)
self.src_strings = []
self.src_map = {}
for i in src_flags:
self.src_strings.append(str(i))
self.src_map[str(i)] = i
def setColors(self, colors, current_color):
a = 0
for i in colors:
self.cbb.addItem(i)
if (i == current_color):
self.cbb.setCurrentIndex(a)
a += 1
def set_scale(self, newscale):
self.scale.setValue(newscale)