def object_picked(self, object_number):
if object_number == self.current_projection: return
self.current_projection = object_number
resize_necessary = False
if self.mx_display == None:
self.mx_display = EMImage2DWidget()
# self.mx_display = EMImageMXWidget()
self.mx_display.module_closed.connect(self.on_mx_display_closed)
resize_necessary = True
if self.frc_display == None:
self.frc_display = EMPlot2DWidget()
# QtCore.QObject.connect(self.frc_display,QtCore.SIGNAL("module_closed"),self.on_frc_display_closed)
self.update_display(False)
if resize_necessary:
get_application().show_specific(self.mx_display)
self.mx_display.optimally_resize()
get_application().show_specific(self.frc_display)
# self.frc_display.optimally_resize()
else:
self.mx_display.updateGL()
self.frc_display.updateGL()
if object_number != self.special_euler:
self.special_euler = object_number
self.regen_dl()
def plot(files, app):
from eman2_gui.emplot2d import EMPlot2DWidget
plotw = EMPlot2DWidget(application=app)
for f in files:
plotw.set_data_from_file(f, quiet=True)
plotw.setWindowTitle("2D Plot")
app.show_specific(plotw)
return plotw
def __init__(self, options): QtWidgets.QMainWindow.__init__(self) if options.twod: self.twodview = EMImage2DWidget() widget = Microscope(self, options, None, None, self.twodview) else: self.imgview = EMImage2DWidget() self.pltview = EMPlot2DWidget() widget = Microscope(self, options, self.imgview, self.pltview, None) #widget = Microscope(self, None, None, None, mode, cs) #widget = Microscope(self, None, None) self.closeEvent=widget.closeEvent self.setCentralWidget(widget)
def __init__(self, mode=0, cs=0., twod=False): QtGui.QMainWindow.__init__(self) if twod: self.twodview = EMImage2DWidget() widget = Microscope(self, None, None, self.twodview, mode, cs) else: self.imgview = EMImage2DWidget() self.pltview = EMPlot2DWidget() widget = Microscope(self, self.imgview, self.pltview, None, mode, cs) #widget = Microscope(self, None, None, None, mode, cs) #widget = Microscope(self, None, None) self.closeEvent=widget.closeEvent self.setCentralWidget(widget)
def main():
progname = os.path.basename(sys.argv[0])
usage = """e2simmxptclcmp.py [options] <simmx file> ...
Plots the set of similarity quality values for a single particle from a set of simmx files.
"""
parser = EMArgumentParser(usage=usage, version=EMANVERSION)
parser.add_argument("--ptcl", type=int, help="particle number", default=0)
# parser.add_argument("--refine",type=str,default=None,help="Automatically get parameters for a refine directory")
#parser.add_argument("--output",type=str,help="Output text file",default="zvssim.txt")
#parser.add_argument("--refs",type=str,help="Reference images from the similarity matrix (projections)",default=None)
#parser.add_argument("--inimgs",type=str,help="Input image file",default=None)
#parser.add_argument("--outimgs",type=str,help="Output image file",default="imgs.hdf")
#parser.add_argument("--filtimgs",type=str,help="A python expression using Z[n], Q[n] and N[n] for selecting specific particles to output. n is the 0 indexed number of the input file",default=None)
#parser.add_argument("--ppid", type=int, help="Set the PID of the parent process, used for cross platform PPID",default=-1)
(options, args) = parser.parse_args()
app = EMApp()
from eman2_gui.emplot2d import EMPlot2DWidget
plotw = EMPlot2DWidget(application=app)
plts = []
for simmx in args:
mx = EMData(simmx, 0)
plts.append(mx.get_clip(Region(0, options.ptcl, mx["nx"], 1)))
plts[-1].process_inplace("normalize")
plotw.set_data(plts[-1], simmx)
plotw.setWindowTitle("ptcl vs similarity")
plotw.show()
try:
plotw.raise_()
except:
pass
app.exec_()
def main():
progname = os.path.basename(sys.argv[0])
usage = """prog [options]
This is a program to compute the resolution of a n averaged subtomogram. Right now it is very simple simple divide the aligned
subtomos into even/odd classes, average and then compute the FSC. In the future this program will be extended to compute
resolution of an averged subtomo vs a reference and hopefuly of a single sub/tomogram.
"""
parser = EMArgumentParser(usage=usage, version=EMANVERSION)
parser.add_pos_argument(
name="tomodir",
help="The refinement directory to use for tomoresolution.",
default="",
guitype='dirbox',
dirbasename='spt_',
row=0,
col=0,
rowspan=1,
colspan=2)
parser.add_header(
name="tomoresoheader",
help='Options below this label are specific to e2tomoresolution',
title="### e2tomoresolution options ###",
row=1,
col=0,
rowspan=1,
colspan=2)
parser.add_argument(
"--averager",
type=str,
help="The averager used to generate the averages. Default is \'mean\'.",
default="mean",
guitype='combobox',
choicelist='dump_averagers_list()',
row=2,
col=0,
rowspan=1,
colspan=2)
parser.add_argument("--sym",
type=str,
help="The recon symmetry",
default="c1",
guitype='symbox',
row=3,
col=0,
rowspan=1,
colspan=2)
parser.add_argument(
"--mask",
type=str,
help="The mask to apply before FSC calculation",
default=None,
guitype='comboparambox',
choicelist='re_filter_list(dump_processors_list(),\'mask\')',
row=4,
col=0,
rowspan=1,
colspan=2)
parser.add_argument(
"--ppid",
type=int,
help="Set the PID of the parent process, used for cross platform PPID",
default=-1)
(options, args) = parser.parse_args()
if options.mask: options.mask = parsemodopt(options.mask)
logid = E2init(sys.argv, options.ppid)
fscstrategy = EvenOddReso(args[0], options)
fscstrategy.execute()
results_db = db_open_dict("bdb:%s#convergence.results" % args[0])
results_db["tomo_fsc"] = [
fscstrategy.getFreq(),
fscstrategy.getFSC(),
fscstrategy.getError()
]
results_db.close()
E2end(logid)
# Plot FSC
app = EMApp()
plot = EMPlot2DWidget()
plot.set_data((fscstrategy.getFreq(), fscstrategy.getFSC()))
plot.show()
app.exec_()
def __init__(self,
application,
apix=1.0,
voltage=300.0,
cs=4.1,
ac=10.0,
samples=256,
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 main():
progname = os.path.basename(sys.argv[0])
usage = """prog Refinement directory [options]
Plot FSC curvers produced by e2refine, eotest, etc.
>"""
parser = EMArgumentParser(usage=usage, version=EMANVERSION)
#dirbasename='refine|frealign',
#parser.add_pos_argument(name="plot_files",help="List the directories to plot here.", default="", guitype='filebox', browser="EMBrowserWidget(withmodal=True,multiselect=True)", row=0, col=0,rowspan=1, colspan=2)
parser.add_header(
name="filterheader",
help='There is no help',
title=
"This program is currently not functional. The table below is still useful,\n but for actual plots, suggest using e2evalrefine.py for now.",
row=0,
col=0,
rowspan=1,
colspan=2)
parser.add_pos_argument(
name="fscdir",
help="The refinement directory to use for FSC plotting.",
default="",
guitype='fsctable',
row=1,
col=0,
rowspan=1,
colspan=2)
parser.add_header(
name="filterheader",
help='Options below this label are specific to e2plotFSC',
title="### e2plotFSC options ###",
row=2,
col=0,
rowspan=1,
colspan=2)
parser.add_argument("--plote2res",
action="store_false",
help="Plot curves from e2resoltion",
default=True,
guitype='boolbox',
row=3,
col=0,
rowspan=1,
colspan=1)
parser.add_argument("--plote2eotest",
action="store_false",
help="Plot curves from e2eotest",
default=True,
guitype='boolbox',
row=3,
col=1,
rowspan=1,
colspan=1)
parser.add_argument("--plotconvergence",
action="store_false",
help="Plot curves from refinement convergence",
default=True,
guitype='boolbox',
row=4,
col=0,
rowspan=1,
colspan=1)
parser.add_argument("--ploteoconvergence",
action="store_false",
help="Plot curves from refine_even_odd convergence",
default=True,
guitype='boolbox',
row=4,
col=1,
rowspan=1,
colspan=1)
parser.add_argument(
"--ppid",
type=int,
help="Set the PID of the parent process, used for cross platform PPID",
default=-1)
(options, args) = parser.parse_args()
# Make the QT app
app = EMApp()
# display table
if len(args) == 0:
fsctable = PMFSCTableWidget("fsc", "", None, resize=True)
fsctable.show()
# or let user choose FSC plotting pars
else:
module = EMPlot2DWidget()
# Get data from data base
db_name = "bdb:" + args[0] + "#convergence.results"
if not db_check_dict(db_name):
print("Rubbish!!!, no FSC curves found!!!")
return
db = db_open_dict(db_name, ro=True)
keys = db.keys()
# Load desired FSC curves
res = []
eo = []
conv = []
eoconv = []
# Method to the maddness, I use not here because I need to only plot when open is not presented AND I need to keep presentation on in the GUI
if not options.plote2res: res = get_e2resolution_results_list(keys)
if not options.plote2eotest: eo = get_e2eotest_results_list(keys)
if not options.plotconvergence:
conv = get_convergence_results_list(keys)
if not options.ploteoconvergence:
eoconv = get_e2refine_even_odd_results_list(keys)
# Plot FSC curves
i = 0
max = len(colortypes)
for k in conv:
module.set_data(
db[k], k, color=(i % max),
linewidth=1) # there are only a ceratin number of colors
i += 1
# plot e2refine_even_odd curves
for k in eoconv:
module.set_data(
db[k], k, color=(i % max),
linewidth=2) # there are only a ceratin number of colors
i += 1
#plot eo test and res
for plot in [eo, res]:
for k in plot:
module.set_data(
db[k], k, color=(i % max),
linewidth=3) # there are only a ceratin number of colors
i += 1
module.show()
app.exec_()
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 __init__(self,app):
self.app=app
QtWidgets.QWidget.__init__(self,None)
self.synthplot=EMPlot2DWidget(self.app)
self.synthplot.show()
# overall layout
self.vbl1=QtWidgets.QVBoxLayout()
self.setLayout(self.vbl1)
# First row contains general purpose controls
self.hbl1=QtWidgets.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:",32)
self.vnsin.intonly=1
self.hbl1.addWidget(self.vnsin)
self.cbshowall=QtWidgets.QCheckBox("Show All")
self.hbl1.addWidget(self.cbshowall)
self.cbshifted=QtWidgets.QCheckBox("Shifted")
self.hbl1.addWidget(self.cbshifted)
self.cbtargfn=QtWidgets.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.cbtargfn.addItem("square imp dx")
self.cbtargfn.addItem("square imp 2")
self.hbl1.addWidget(self.cbtargfn)
# Widget containing valsliders
self.wapsliders=QtWidgets.QWidget(self)
# self.wapsliders.setMinimumSize(800,640)
self.gblap=QtWidgets.QGridLayout()
self.gblap.setSizeConstraint(QtWidgets.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=QtWidgets.QScrollArea(self)
self.wapsarea.setWidgetResizable(True)
self.wapsarea.setWidget(self.wapsliders)
self.vbl1.addWidget(self.wapsarea)
self.vcell.valueChanged.connect(self.recompute)
self.vncells.valueChanged.connect(self.recompute)
self.voversamp.valueChanged.connect(self.recompute)
self.vnsin.valueChanged.connect(self.nsinchange)
self.cbshowall.stateChanged[int].connect(self.recompute)
self.cbshifted.stateChanged[int].connect(self.recompute)
self.cbtargfn.activated[int].connect(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)
self.wamp[-1].valueChanged.connect(self.recompute)
self.wpha.append(ValSlider(self,(-180.0,180.0),"%2d:"%i,0.0))
self.gblap.addWidget(self.wpha[-1],i,1)
self.wpha[-1].valueChanged.connect(self.recompute)
self.curves.append(EMData(64,1))
if self.cbshowall.isChecked() :
self.synthplot
self.total=EMData(64,1)
self.nsinchange()
def __init__(self, options):
self.path="tomograms/"
QtGui.QWidget.__init__(self,None)
self.win_size=[1000,680]
self.setMinimumSize(self.win_size[0], self.win_size[1])
# This object is itself a widget we need to set up
self.gbl = QtGui.QGridLayout(self)
self.gbl.setMargin(8)
self.gbl.setSpacing(6)
self.gbl.setColumnStretch(0,4)
self.gbl.setColumnStretch(1,1)
#self.gbl.setColumnStretch(2,1)
self.gbl.setRowStretch(0,1)
# Micrograph list
self.imglst=QtGui.QTableWidget(1, 3, self)
self.imglst.verticalHeader().hide()
self.gbl.addWidget(self.imglst,0,0,10,1)
#self.imglst.setColumnWidth(0,50)
self.imglst.setColumnWidth(1,200)
self.imglst_srtby=0
hdr=self.imglst.horizontalHeader()
self.imglst.cellClicked[int, int].connect(self.select_folder)
hdr.sectionPressed[int].connect(self.sortlst)
self.dp_folder=QtGui.QComboBox()
self.dp_folder.setToolTip("Folder suffix")
self.gbl.addWidget(self.dp_folder, 0,1,1,1)
sfxlst=["spt", "sptsgd"]
for i in sfxlst:
self.dp_folder.addItem(i)
self.dp_folder.currentIndexChanged[int].connect(self.set_sfx)
self.wg_thumbnail=EMScene3D()#parent=self)
#self.wg_thumbnail.set_scale(1)
self.wg_thumbnail_width=old_div(self.size().width(),4)*.9
self.wg_thumbnail.resize(self.wg_thumbnail_width,self.wg_thumbnail_width)
#print self.wg_thumbnail_width
self.wg_thumbnail.setMinimumHeight(330)
self.wg_thumbnail.setMinimumWidth(330)
self.gbl.addWidget(self.wg_thumbnail, 1,1,2,2)
self.wg_thumbnail.newnode=None
self.bt_showbs=QtGui.QPushButton("ShowBrowser")
self.bt_showbs.setToolTip("Show Browser")
self.gbl.addWidget(self.bt_showbs, 2,1,1,2)
self.bt_showbs.clicked[bool].connect(self.show_browser)
self.bt_plotParms=QtGui.QPushButton("PlotParams")
self.bt_plotParms.setToolTip("Examine particle orientations")
self.gbl.addWidget(self.bt_plotParms, 3,1,1,2)
self.bt_plotParms.clicked[bool].connect(self.plot_params)
self.paramplot = EMPlot2DWidget()
self.bt_plotFSC=QtGui.QPushButton("PlotFSCs")
self.bt_plotFSC.setToolTip("Examine tightly masked FSCs from this SPT refinement")
self.gbl.addWidget(self.bt_plotFSC, 4,1,1,2)
self.bt_plotFSC.clicked[bool].connect(self.plot_fscs)
self.fscplot = EMPlot2DWidget()
self.setspanel=TomoListWidget(self)
self.gbl.addWidget(self.setspanel, 5,1,5,2)
self.itemflags= Qt.ItemFlags(Qt.ItemIsSelectable)|Qt.ItemFlags(Qt.ItemIsEnabled)|Qt.ItemFlags(Qt.ItemIsUserCheckable)
#self.wg_notes=QtGui.QTextEdit(self)
#self.gbl.addWidget(self.wg_notes, 10,1,1,2)
#self.setspanel.itemChanged[QtGui.QListWidgetItem].connect(self.click_set)
#QtCore.QObject.connect(self.wg_notes,QtCore.SIGNAL("textChanged()"),self.noteupdate)
#self.wg_plot2d=EMPlot2DWidget()
self.update_files()
self.browser=SPTBrowserWidget(withmodal=False,multiselect=False)
def __init__(self, options):
self.path = "tomograms/"
QtGui.QWidget.__init__(self, None)
self.win_size = [1000, 680]
self.setMinimumSize(self.win_size[0], self.win_size[1])
# This object is itself a widget we need to set up
self.gbl = QtGui.QGridLayout(self)
self.gbl.setMargin(8)
self.gbl.setSpacing(6)
self.gbl.setColumnStretch(0, 4)
self.gbl.setColumnStretch(1, 1)
self.gbl.setColumnStretch(2, 1)
self.gbl.setRowStretch(0, 1)
# Micrograph list
self.imglst = QtGui.QTableWidget(1, 3, self)
self.imglst.verticalHeader().hide()
self.gbl.addWidget(self.imglst, 0, 0, 11, 1)
self.imglst.setColumnWidth(0, 50)
self.imglst.setColumnWidth(1, 200)
self.imglst_srtby = 0
hdr = self.imglst.horizontalHeader()
QtCore.QObject.connect(self.imglst,
QtCore.SIGNAL("cellClicked(int,int)"),
self.selimg)
QtCore.QObject.connect(hdr, QtCore.SIGNAL("sectionPressed(int)"),
self.sortlst)
self.wg_thumbnail = EMImage2DWidget(parent=self)
self.wg_thumbnail.set_scale(1)
self.wg_thumbnail_width = self.size().width() / 3 * .9
self.wg_thumbnail.resize(self.wg_thumbnail_width,
self.wg_thumbnail_width)
#print self.wg_thumbnail_width
self.wg_thumbnail.setMinimumHeight(330)
self.gbl.addWidget(self.wg_thumbnail, 0, 1, 3, 2)
self.bt_show2d = QtGui.QPushButton("Show2D")
self.bt_show2d.setToolTip("Show 2D images")
self.gbl.addWidget(self.bt_show2d, 4, 1, 1, 2)
self.bt_runboxer = QtGui.QPushButton("Boxer")
self.bt_runboxer.setToolTip("Run spt_boxer")
self.gbl.addWidget(self.bt_runboxer, 5, 1)
self.bt_refresh = QtGui.QPushButton("Refresh")
self.bt_refresh.setToolTip("Refresh")
self.gbl.addWidget(self.bt_refresh, 5, 2)
self.bt_showtlts = QtGui.QPushButton("ShowTilts")
self.bt_showtlts.setToolTip("Show raw tilt series")
self.gbl.addWidget(self.bt_showtlts, 6, 1)
self.bt_plottpm = QtGui.QPushButton("TiltParams")
self.bt_plottpm.setToolTip("Plot tilt parameters")
self.gbl.addWidget(self.bt_plottpm, 6, 2)
self.bt_plotloss = QtGui.QPushButton("PlotLoss")
self.bt_plotloss.setToolTip("Plot alignment loss")
self.gbl.addWidget(self.bt_plotloss, 7, 1)
self.bt_plotctf = QtGui.QPushButton("PlotCtf")
self.bt_plotctf.setToolTip("Plot CTF estimation")
self.gbl.addWidget(self.bt_plotctf, 7, 2)
QtCore.QObject.connect(self.bt_show2d, QtCore.SIGNAL("clicked(bool)"),
self.show2d)
QtCore.QObject.connect(self.bt_runboxer,
QtCore.SIGNAL("clicked(bool)"), self.runboxer)
QtCore.QObject.connect(self.bt_plotloss,
QtCore.SIGNAL("clicked(bool)"), self.plot_loss)
QtCore.QObject.connect(self.bt_plottpm, QtCore.SIGNAL("clicked(bool)"),
self.plot_tltparams)
QtCore.QObject.connect(self.bt_showtlts,
QtCore.SIGNAL("clicked(bool)"), self.show_tlts)
QtCore.QObject.connect(self.bt_refresh, QtCore.SIGNAL("clicked(bool)"),
self.update_files)
QtCore.QObject.connect(self.bt_plotctf, QtCore.SIGNAL("clicked(bool)"),
self.plot_ctf)
self.wg_2dimage = EMImage2DWidget()
self.wg_2dimage.setWindowTitle("Tomo2D")
self.cur_data = None
self.wg_tltimage = EMImage2DWidget()
self.wg_tltimage.setWindowTitle("Tiltseries")
self.wg_tltimage.set_scale(.2)
self.cur_tlt = None
self.setspanel = QtGui.QListWidget(self)
self.gbl.addWidget(self.setspanel, 8, 1, 2, 2)
self.itemflags = Qt.ItemFlags(Qt.ItemIsEditable) | Qt.ItemFlags(
Qt.ItemIsSelectable) | Qt.ItemFlags(
Qt.ItemIsEnabled) | Qt.ItemFlags(Qt.ItemIsUserCheckable)
self.wg_notes = QtGui.QTextEdit(self)
self.gbl.addWidget(self.wg_notes, 10, 1, 1, 2)
QtCore.QObject.connect(self.setspanel,
QtCore.SIGNAL("itemChanged(QListWidgetItem*)"),
self.clickset)
QtCore.QObject.connect(self.wg_notes, QtCore.SIGNAL("textChanged()"),
self.noteupdate)
self.wg_plot2d = EMPlot2DWidget()
self.update_files()
def __init__(self,images,voltage=None,apix=None,cs=None,ac=10.0,box=512,usefoldername=False,constbfactor=-1,fitastig=False,phaseplate=False):
"""Implements the CTF fitting dialog using various EMImage and EMPlot2D widgets
'data' is a list of (filename,ctf,im_1d,bg_1d,quality)
'parms' is [box size,ctf,box coord,set of excluded boxnums,quality,oversampling]
"""
try:
from 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)
QtWidgets.QWidget.__init__(self,None)
self.setWindowIcon(QtGui.QIcon(get_image_directory() + "ctf.png"))
self.nodir=not usefoldername
self.data=None
self.curset=0
self.calcmode=1
self.f2dmode=0
self.f2danmode=0
self.plotmode=0
self.curfilename = None
self.ringrad=1
self.xpos1=(10,0)
self.xpos2=(0,10)
# self.db = db_open_dict('bdb:mgquality')
self.defaultvoltage=voltage
self.defaultapix=apix
self.defaultcs=cs
self.defaultac=ac
self.constbfactor=constbfactor
# Per image parameters to keep track of
# for each image [box size,ctf,box coord,set of excluded boxnums,quality,oversampling]
self.parms=[]
# db_fparms=db_open_dict("bdb:e2ctf.frameparms",True)
# This little block of code deals with Z stacks of images and multiple image files,
# rewriting the name(s) with an enumeration including ;number or ,number
newimages=[]
for i in images:
n=EMUtil.get_image_count(i)
if n!=1:
for j in range(n): newimages.append(i+",%d"%j)
else:
h=EMData(i,0,True) # read header
n=h["nz"]
if n!=1:
for j in range(n): newimages.append(i+";%d"%j)
else : newimages.append(i)
images=newimages
# Now we try to restore old image information
for i in images:
try:
pd=js_open_dict(info_name(i,nodir=self.nodir))
parms=pd["ctf_frame"]
parms[4]=pd["quality"]
if box>=64 and parms[0]!=box:
parms[0]=box
parms[3]=set()
# if parms==None : raise Exception
except:
ctf = EMAN2Ctf()
ctf.from_dict({'defocus':0.0,'dfdiff':0.0,'dfang':0.0,'bfactor':200.0,'ampcont':self.defaultac,'voltage':200.0,'cs':4.1,'apix':1.0,'dsbg':-1})
if self.defaultvoltage!=None : ctf.voltage=self.defaultvoltage
if self.defaultcs!=None : ctf.cs=self.defaultcs
if self.defaultapix!=None : ctf.apix=self.defaultapix
parms=[int(box),ctf,(256,256),set(),5,1]
print("Initialize new parms for: ",base_name(i))
if self.constbfactor>0 : parms[1].bfactor=self.constbfactor
if parms[0]<64 :
parms[0]=512
parms[3]=set()
self.parms.append(parms)
self.wimage=EMImage2DWidget()
self.wimage.setWindowTitle("e2evalimage - Micrograph")
self.wfft=EMImage2DWidget()
self.wfft.setWindowTitle("e2evalimage - 2D FFT")
self.wplot=EMPlot2DWidget()
self.wplot.setWindowTitle("e2evalimage - Plot")
self.wimage.mousedown.connect(self.imgmousedown)
self.wimage.mousedrag.connect(self.imgmousedrag)
self.wimage.mouseup.connect(self.imgmouseup)
self.wfft.mousedown.connect(self.fftmousedown)
self.wfft.mousedrag.connect(self.fftmousedrag)
self.wfft.mouseup.connect(self.fftmouseup)
self.wimage.mmode="app"
self.wfft.mmode="app"
# This object is itself a widget we need to set up
self.gbl = QtWidgets.QGridLayout(self)
self.gbl.setContentsMargins(8, 8, 8, 8)
self.gbl.setSpacing(6)
# plot list and plot mode combobox
self.setlist=e2ctf.MyListWidget(self)
self.setlist.setSizePolicy(QtWidgets.QSizePolicy.Preferred,QtWidgets.QSizePolicy.Expanding)
for i in images:
self.setlist.addItem(i)
self.gbl.addWidget(self.setlist,0,0,8,2)
self.lcalcmode=QtWidgets.QLabel("Region:",self)
self.gbl.addWidget(self.lcalcmode,10,0)
self.scalcmode=QtWidgets.QComboBox(self)
self.scalcmode.addItem("Single Region")
self.scalcmode.addItem("Tiled Boxes")
self.scalcmode.setCurrentIndex(1)
self.gbl.addWidget(self.scalcmode,10,1)
self.lcalcmode=QtWidgets.QLabel("2D FFT:",self)
self.gbl.addWidget(self.lcalcmode,11,0)
self.s2dmode=QtWidgets.QComboBox(self)
self.s2dmode.addItem("Power Spectrum")
self.s2dmode.addItem("Bg Subtracted")
self.s2dmode.addItem("Background")
self.gbl.addWidget(self.s2dmode,11,1)
self.lcalcmode=QtWidgets.QLabel("Annotate:",self)
self.gbl.addWidget(self.lcalcmode,12,0)
self.s2danmode=QtWidgets.QComboBox(self)
self.s2danmode.addItem("Ctf Zeroes")
self.s2danmode.addItem("Resolution Ring")
self.s2danmode.addItem("2-D Xtal")
self.s2danmode.addItem("None")
self.gbl.addWidget(self.s2danmode,12,1)
self.lcalcmode=QtWidgets.QLabel("Plot:",self)
self.gbl.addWidget(self.lcalcmode,13,0)
self.splotmode=QtWidgets.QComboBox(self)
self.splotmode.addItem("Bgsub and Fit")
self.splotmode.addItem("Fg and Bg")
self.splotmode.addItem("Bgsub, 45 deg slices")
self.splotmode.addItem("Fg, 45 deg slices")
self.splotmode.addItem("SSNR (NOT BY PTCL !)")
self.gbl.addWidget(self.splotmode,13,1)
# ValSliders for CTF parameters
#self.samp = ValSlider(self,(0,5.0),"Amp:",0)
#self.vbl.addWidget(self.samp)
self.sdefocus=ValSlider(self,(0,5),"Defocus:",0.0,90)
self.gbl.addWidget(self.sdefocus,0,2,1,3)
self.sbfactor=ValSlider(self,(0,1600),"B factor:",200.0,90)
self.gbl.addWidget(self.sbfactor,1,2,1,3)
self.sdfdiff=ValSlider(self,(0,1),"DF Diff:",0,90)
self.gbl.addWidget(self.sdfdiff,2,2,1,3)
self.sdfang=ValSlider(self,(0,180),"Df Angle:",0,90)
self.gbl.addWidget(self.sdfang,3,2,1,3)
self.sampcont=ValSlider(self,(0,100),"% AC",10.0,90)
if self.defaultac!=None : self.sampcont.setValue(self.defaultac)
self.gbl.addWidget(self.sampcont,4,2,1,3)
self.sang45=ValSlider(self,(-22.5,22.5),"45 mode ang",0.0,90)
self.gbl.addWidget(self.sang45,5,2,1,3)
self.squality=ValSlider(self,(0,9),"Quality (0-9):",0,90)
self.squality.setIntonly(True)
self.gbl.addWidget(self.squality,6,2,1,3)
self.brefit=QtWidgets.QPushButton("Refit")
self.gbl.addWidget(self.brefit,7,2)
self.cbgadj=CheckBox(None,"CTF BG Adj",1)
self.gbl.addWidget(self.cbgadj,10,3)
self.castig=CheckBox(None,"Astig:",fitastig)
self.gbl.addWidget(self.castig,11,3)
self.cphasep=CheckBox(None,"Phaseplate:",phaseplate)
self.gbl.addWidget(self.cphasep,12,3)
# self.sapix=ValSlider(self,(.2,10),"A/Pix:",2,90)
# self.vbl.addWidget(self.sapix)
self.sapix=ValBox(self,(0,500),"A/pix:",1.0,90)
if self.defaultapix!=None : self.sapix.setValue(self.defaultapix)
self.gbl.addWidget(self.sapix,10,2)
self.svoltage=ValBox(self,(0,500),"Voltage (kV):",200,90)
if self.defaultvoltage!=None : self.svoltage.setValue(self.defaultvoltage)
self.gbl.addWidget(self.svoltage,11,2)
self.scs=ValBox(self,(0,5),"Cs (mm):",4.1,90)
if self.defaultcs!=None : self.scs.setValue(self.defaultcs)
self.gbl.addWidget(self.scs,12,2)
self.sboxsize=ValBox(self,(128,1024),"Box Size:",512,90)
self.sboxsize.intonly=True
self.gbl.addWidget(self.sboxsize,13,2)
# self.soversamp=ValBox(self,(0,500),"Oversample:",1,90)
# self.soversamp.intonly=True
# self.gbl.addWidget(self.soversamp,14,2) # disable oversampling for now, not properly integrated with save/recall mechanism, and not clear if it's really useful
# this is just a spacer
self.gbl.setColumnStretch(3,2)
self.bbox=QtWidgets.QGroupBox("Project")
self.gbl.addWidget(self.bbox,10,4,4,1)
self.bvbl=QtWidgets.QVBoxLayout()
self.bbox.setLayout(self.bvbl)
self.bimport=QtWidgets.QPushButton("Import")
self.bvbl.addWidget(self.bimport)
self.cinvert=CheckBox(None,"Invert")
self.bvbl.addWidget(self.cinvert)
self.cxray=CheckBox(None,"X-ray Pixels")
self.bvbl.addWidget(self.cxray)
self.bimport.clicked[bool].connect(self.doImport)
self.brefit.clicked[bool].connect(self.doRefit)
self.cbgadj.valueChanged.connect(self.bgAdj)
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.newCTF)
self.svoltage.valueChanged.connect(self.newCTF)
self.scs.valueChanged.connect(self.newCTF)
self.sboxsize.valueChanged.connect(self.newBox)
# QtCore.QObject.connect(self.soversamp, QtCore.SIGNAL("valueChanged"), self.newBox)
self.sang45.valueChanged.connect(self.recalc_real)
self.squality.valueChanged.connect(self.newQualityFactor)
self.setlist.currentRowChanged[int].connect(self.newSet)
self.setlist.keypress.connect(self.listkey)
self.scalcmode.currentIndexChanged[int].connect(self.newCalcMode)
self.s2dmode.currentIndexChanged[int].connect(self.new2DMode)
self.s2danmode.currentIndexChanged[int].connect(self.new2DAnMode)
self.splotmode.currentIndexChanged[int].connect(self.newPlotMode)
#QtCore.QObject.connect(self.saveparms,QtCore.SIGNAL("clicked(bool)"),self.on_save_params)
#QtCore.QObject.connect(self.recallparms,QtCore.SIGNAL("clicked(bool)"),self.on_recall_params)
#QtCore.QObject.connect(self.refit,QtCore.SIGNAL("clicked(bool)"),self.on_refit)
#QtCore.QObject.connect(self.output,QtCore.SIGNAL("clicked(bool)"),self.on_output)
self.resize(720,380) # figured these values out by printing the width and height in resize event
### This section is responsible for background updates
self.busy=False
self.needupdate=True
self.needredisp=False
self.procthread=None
self.errors=None # used to communicate errors back from the reprocessing thread
self.timer=QTimer()
self.timer.timeout.connect(self.timeOut)
self.timer.start(100)
self.setWindowTitle("e2evalimage - Control Panel")
self.wimage.show()
self.wfft.show()
self.wplot.show()
E2loadappwin("e2evalimage","main",self)
E2loadappwin("e2evalimage","image",self.wimage.qt_parent)
E2loadappwin("e2evalimage","fft",self.wfft.qt_parent)
E2loadappwin("e2evalimage","plot",self.wplot.qt_parent)
def __init__(self, application, opt):
self.options = opt
"""application is an QApplication instance. path is the path for ouput files"""
QtWidgets.QWidget.__init__(self)
self.particles = None
self.app = weakref.ref(application)
self.setWindowTitle("Main Window (e2gmm.py)")
# Menu Bar
#self.mfile=self.menuBar().addMenu("File")
#self.mfileopen=self.mfile.addAction("Select Particles")
#self.mfileopencls=self.mfile.addAction("Particles from Classes")
#self.mfileopencls.setEnabled(False)
#self.mfilequit=self.mfile.addAction("Quit")
self.setCentralWidget(QtWidgets.QWidget())
self.gbl = QtWidgets.QGridLayout(self.centralWidget())
cen = self.centralWidget()
self.gbl.setColumnStretch(0, 0)
self.gbl.setColumnStretch(2, 4)
self.gbl.setColumnStretch(4, 5)
# Plot
self.wplot2d = EMPlot2DWidget()
self.gbl.addWidget(self.wplot2d, 0, 2, 3, 1)
self.wplot2d.set_mouse_emit(True)
# 3-D View
self.wview3d = EMScene3D()
self.gbl.addWidget(self.wview3d, 0, 4, 3, 1)
# Left pane for GMM folder and parameters
self.gbll = QtWidgets.QGridLayout()
self.gbl.addLayout(self.gbll, 0, 0, 4, 1) # 4 rows tall, 1 column wide
# gmm_XX folder selection
self.gblfld = QtWidgets.QGridLayout()
self.gbll.addLayout(self.gblfld, 0, 0)
self.wlistgmm = QtWidgets.QListWidget()
self.wlistgmm.setSizePolicy(QtWidgets.QSizePolicy.Preferred,
QtWidgets.QSizePolicy.Expanding)
self.update_gmms()
self.gblfld.addWidget(self.wlistgmm, 0, 0, 1, 2)
self.wbutnewgmm = QtWidgets.QPushButton("New GMM")
self.gblfld.addWidget(self.wbutnewgmm, 1, 0)
self.wbutrefine = QtWidgets.QPushButton("refine_XX")
self.gblfld.addWidget(self.wbutrefine, 1, 1)
# run selection
self.gblrun = QtWidgets.QGridLayout()
self.gbll.addLayout(self.gblrun, 1, 0)
self.wlistrun = QtWidgets.QListWidget()
self.wlistrun.setSizePolicy(QtWidgets.QSizePolicy.Preferred,
QtWidgets.QSizePolicy.Expanding)
# self.update_runs()
self.gblrun.addWidget(self.wlistrun, 0, 0, 1, 2)
self.wbutrerun = QtWidgets.QPushButton("Rerun")
self.gblrun.addWidget(self.wbutrerun, 1, 1)
self.wbutnewrun = QtWidgets.QPushButton("New Run")
self.gblrun.addWidget(self.wbutnewrun, 1, 0)
# The form with details about the selected gmm_XX folder
self.gflparm = QtWidgets.QFormLayout()
self.gbll.addLayout(self.gflparm, 2, 0)
self.wlpath = QtWidgets.QLabel("-")
self.wlpath.setToolTip("Path this GMM is based on")
self.gflparm.addRow("Path:", self.wlpath)
self.wedbox = QtWidgets.QLineEdit("256")
self.wedbox.setToolTip("Box size of input particles in pixels")
self.gflparm.addRow("Box Size:", self.wedbox)
self.wedres = QtWidgets.QLineEdit("25")
self.wedres.setToolTip(
"Maximum resolution to use for gaussian fitting")
self.gflparm.addRow("Target Res:", self.wedres)
self.wedsym = QtWidgets.QLineEdit("c1")
self.wedsym.setToolTip("Symmetry used during refinement")
self.gflparm.addRow("Symmetry:", self.wedsym)
self.wedapix = QtWidgets.QLineEdit("1.0")
self.wedapix.setToolTip("A/pix of input particles")
self.gflparm.addRow("A/pix:", self.wedapix)
self.wedmask = QtWidgets.QLineEdit("")
self.wedmask.setToolTip("3-D volume mask")
self.gflparm.addRow("Mask:", self.wedmask)
self.wedngauss = QtWidgets.QLineEdit("64")
self.wedngauss.setToolTip("Number of Gaussians")
self.gflparm.addRow("N Gauss:", self.wedngauss)
self.weddim = QtWidgets.QLineEdit("4")
self.weddim.setToolTip(
"Number of dimensions in the latent space (middle network layer)")
self.gflparm.addRow("Latent Dim:", self.weddim)
self.wedtrainiter = QtWidgets.QLineEdit("10")
self.wedtrainiter.setToolTip("Training iterations per stage")
self.gflparm.addRow("Train iter:", self.wedtrainiter)
self.wbutpos = QtWidgets.QPushButton("Position")
self.wbutpos.setCheckable(True)
self.wbutpos.setChecked(True)
self.wbutpos.setToolTip(
"Include changes of position in the GMM (motion)")
self.gflparm.addRow("Parameters", self.wbutpos)
self.wbutamp = QtWidgets.QPushButton("Amplitude")
self.wbutamp.setCheckable(True)
self.wbutamp.setChecked(False)
self.wbutamp.setToolTip(
"Include changes of amplitude in the GMM (ligand binding)")
self.gflparm.addRow(" ", self.wbutamp)
self.wbutsig = QtWidgets.QPushButton("Sigma")
self.wbutsig.setCheckable(True)
self.wbutsig.setChecked(False)
self.wbutsig.setToolTip(
"Include changes of Gaussian Width in the GMM (rarely useful)")
self.gflparm.addRow(" ", self.wbutsig)
self.wlabruntime = QtWidgets.QLabel("-")
self.gflparm.addRow("Run:", self.wlabruntime)
# Widgets below plot
self.gblpltctl = QtWidgets.QGridLayout()
self.gbl.addLayout(self.gblpltctl, 3, 2)
self.gblpltctl.addWidget(QtWidgets.QLabel("X Col:", self), 0, 0,
Qt.AlignRight)
self.wsbxcol = QtWidgets.QSpinBox(self)
self.wsbxcol.setRange(0, 10)
self.gblpltctl.addWidget(self.wsbxcol, 0, 1, Qt.AlignLeft)
self.wsbxcol.setValue(0)
self.gblpltctl.addWidget(QtWidgets.QLabel("Y Col:", self), 1, 0,
Qt.AlignRight)
self.wsbycol = QtWidgets.QSpinBox(self)
self.wsbycol.setRange(0, 10)
self.gblpltctl.addWidget(self.wsbycol, 1, 1, Qt.AlignLeft)
self.wsbycol.setValue(1)
self.wbutdrgrp = QtWidgets.QButtonGroup()
self.wbutdrmid = QtWidgets.QPushButton("Net Mid")
self.wbutdrmid.setCheckable(True)
self.wbutdrmid.setChecked(True)
self.gblpltctl.addWidget(self.wbutdrmid, 0, 2)
self.wbutdrgrp.addButton(self.wbutdrmid, 0)
self.wbutdrpca = QtWidgets.QPushButton("PCA")
self.wbutdrpca.setCheckable(True)
self.gblpltctl.addWidget(self.wbutdrpca, 0, 3)
self.wbutdrgrp.addButton(self.wbutdrpca, 1)
self.wbutdrpca = QtWidgets.QPushButton("ICA")
self.wbutdrpca.setCheckable(True)
self.gblpltctl.addWidget(self.wbutdrpca, 0, 4)
self.wbutdrgrp.addButton(self.wbutdrpca, 2)
self.gblpltctl.addWidget(QtWidgets.QLabel("New Dim:", self), 1, 3,
Qt.AlignRight)
self.wsbnewdim = QtWidgets.QSpinBox(self)
self.wsbnewdim.setRange(2, 10)
self.gblpltctl.addWidget(self.wsbnewdim, 1, 4, Qt.AlignLeft)
self.wcbpntpln = QtWidgets.QComboBox()
self.wcbpntpln.addItem("Plane")
self.wcbpntpln.addItem("Point")
self.wcbpntpln.addItem("Region")
self.gblpltctl.addWidget(self.wcbpntpln, 1, 2)
# Widgets below 3D
self.gbl3dctl = QtWidgets.QGridLayout()
self.gbl.addLayout(self.gbl3dctl, 3, 4)
#self.wbutmap=QtWidgets.QPushButton("Map")
#self.wbutmap.setCheckable(True)
#self.wbutmap.setChecked(True)
#self.gbl3dctl.addWidget(self.wbutmap,0,0)
#self.wbutspheres=QtWidgets.QPushButton("Sphere Mdl")
#self.wbutspheres.setCheckable(True)
#self.wbutspheres.setChecked(True)
#self.gbl3dctl.addWidget(self.wbutspheres,0,1)
self.wvssphsz = ValSlider(self, (1, 50), "Size:", 3.0, 90)
self.gbl3dctl.addWidget(self.wvssphsz, 0, 2)
# Connections
self.wlistgmm.currentRowChanged[int].connect(self.sel_gmm)
#self.wbutspheres.clicked[bool].connect(self.new_3d_opt)
#self.wbutmap.clicked[bool].connect(self.new_3d_opt)
self.wvssphsz.valueChanged.connect(self.new_sph_size)
self.wbutnewgmm.clicked[bool].connect(self.add_gmm)
self.wbutrefine.clicked[bool].connect(self.setgmm_refine)
self.wlistrun.currentRowChanged[int].connect(self.sel_run)
self.wbutnewrun.clicked[bool].connect(self.new_run)
self.wbutrerun.clicked[bool].connect(self.do_run)
self.wbutdrgrp.buttonClicked[QtWidgets.QAbstractButton].connect(
self.plot_mode_sel)
self.wsbxcol.valueChanged[int].connect(self.wplot2d.setXAxisAll)
self.wsbycol.valueChanged[int].connect(self.wplot2d.setYAxisAll)
self.wplot2d.mousedown[QtGui.QMouseEvent,
tuple].connect(self.plot_mouse)
self.wplot2d.mouseup[QtGui.QMouseEvent, tuple].connect(self.plot_mouse)
self.wplot2d.mousedrag[QtGui.QMouseEvent,
tuple].connect(self.plot_mouse)
E2loadappwin("e2gmm", "main", self)
self.gaussplot = EMScatterPlot3D()
self.mapdataitem = EMDataItem3D(None)
self.mapiso = EMIsosurface(self.mapdataitem)
self.wview3d.insertNewNode("Neutral Map", self.mapdataitem)
self.wview3d.insertNewNode("Isosurface",
self.mapiso,
parentnode=self.mapdataitem)
self.wview3d.insertNewNode("Gauss Model", self.gaussplot)
def __init__(self, options):
self.path = "tomograms/"
QtWidgets.QWidget.__init__(self, None)
self.win_size = [1000, 680]
self.setMinimumSize(self.win_size[0], self.win_size[1])
# This object is itself a widget we need to set up
self.gbl = QtWidgets.QGridLayout(self)
self.gbl.setContentsMargins(8, 8, 8, 8)
self.gbl.setSpacing(6)
self.gbl.setColumnStretch(0, 4)
self.gbl.setColumnStretch(1, 1)
self.gbl.setColumnStretch(2, 1)
self.gbl.setRowStretch(0, 1)
# Micrograph list
self.imglst = QtWidgets.QTableWidget(1, 3, self)
self.imglst.verticalHeader().hide()
self.gbl.addWidget(self.imglst, 0, 0, 11, 1)
self.imglst.setColumnWidth(0, 50)
self.imglst.setColumnWidth(1, 200)
self.imglst_srtby = 0
hdr = self.imglst.horizontalHeader()
self.imglst.cellClicked[int, int].connect(self.selimg)
hdr.sectionPressed[int].connect(self.sortlst)
self.wg_thumbnail = EMImage2DWidget(parent=self)
self.wg_thumbnail.set_scale(1)
self.wg_thumbnail_width = old_div(self.size().width(), 3) * .9
self.wg_thumbnail.resize(self.wg_thumbnail_width,
self.wg_thumbnail_width)
#print self.wg_thumbnail_width
self.wg_thumbnail.setMinimumHeight(330)
self.gbl.addWidget(self.wg_thumbnail, 0, 1, 3, 2)
self.bt_show2d = QtWidgets.QPushButton("Show2D")
self.bt_show2d.setToolTip("Show 2D images")
self.gbl.addWidget(self.bt_show2d, 4, 1, 1, 2)
self.bt_runboxer = QtWidgets.QPushButton("Boxer")
self.bt_runboxer.setToolTip("Run spt_boxer")
self.gbl.addWidget(self.bt_runboxer, 5, 1)
self.bt_refresh = QtWidgets.QPushButton("Refresh")
self.bt_refresh.setToolTip("Refresh")
self.gbl.addWidget(self.bt_refresh, 5, 2)
self.bt_showtlts = QtWidgets.QPushButton("ShowTilts")
self.bt_showtlts.setToolTip("Show raw tilt series")
self.gbl.addWidget(self.bt_showtlts, 6, 1)
self.bt_plottpm = QtWidgets.QPushButton("TiltParams")
self.bt_plottpm.setToolTip("Plot tilt parameters")
self.gbl.addWidget(self.bt_plottpm, 6, 2)
self.bt_plotloss = QtWidgets.QPushButton("PlotLoss")
self.bt_plotloss.setToolTip("Plot alignment loss")
self.gbl.addWidget(self.bt_plotloss, 7, 1)
self.bt_plotctf = QtWidgets.QPushButton("PlotCtf")
self.bt_plotctf.setToolTip("Plot CTF estimation")
self.gbl.addWidget(self.bt_plotctf, 7, 2)
self.bt_show2d.clicked[bool].connect(self.show2d)
self.bt_runboxer.clicked[bool].connect(self.runboxer)
self.bt_plotloss.clicked[bool].connect(self.plot_loss)
self.bt_plottpm.clicked[bool].connect(self.plot_tltparams)
self.bt_showtlts.clicked[bool].connect(self.show_tlts)
self.bt_refresh.clicked[bool].connect(self.update_files)
self.bt_plotctf.clicked[bool].connect(self.plot_ctf)
self.wg_2dimage = EMImage2DWidget()
self.wg_2dimage.setWindowTitle("Tomo2D")
self.cur_data = None
self.wg_tltimage = EMImage2DWidget()
self.wg_tltimage.setWindowTitle("Tiltseries")
self.wg_tltimage.set_scale(.2)
self.cur_tlt = None
self.setspanel = TomoListWidget(self)
self.gbl.addWidget(self.setspanel, 8, 1, 2, 2)
self.wg_notes = QtWidgets.QLineEdit(self)
self.wg_notes.setText("Comments:")
#self.wg_notes.setStyleSheet("color: rgb(150, 150, 150);")
self.gbl.addWidget(self.wg_notes, 10, 1, 1, 2)
#self.setspanel.itemClicked[QtWidgets.QListWidgetItem].connect(self.clickset)
self.wg_notes.textChanged.connect(self.noteupdate)
self.wg_plot2d = EMPlot2DWidget()
self.update_files()
def menu_add_plotwin(self):
if self.viewer == None: return
self.viewer.append(EMPlot2DWidget())
self.viewer[-1].show()
self.needupdate = 1
def __init__(self,app):
self.app=app
QtWidgets.QWidget.__init__(self,None)
self.synthplot=EMPlot2DWidget(self.app)
self.synthplot.show()
self.fftplot=EMPlot2DWidget(self.app) # not shown initially
self.fftplot.show()
# self.bispecimg=EMImage2DWidget(self.app) # not shown initially
# overall layout
self.vbl1=QtWidgets.QVBoxLayout()
self.setLayout(self.vbl1)
# First row contains general purpose controls
self.hbl1=QtWidgets.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:",32)
self.vnsin.intonly=1
self.hbl1.addWidget(self.vnsin)
self.cbshowall=QtWidgets.QCheckBox("Show All")
self.hbl1.addWidget(self.cbshowall)
self.cbshifted=QtWidgets.QCheckBox("Shifted")
self.hbl1.addWidget(self.cbshifted)
self.vshftstep=ValBox(self,(1,64),"Shft:",1)
self.hbl1.addWidget(self.vshftstep)
self.bphaseleft=QtWidgets.QPushButton("\u2190") # phase left
self.hbl1.addWidget(self.bphaseleft)
self.bphasecen=QtWidgets.QPushButton("O")
self.hbl1.addWidget(self.bphasecen)
self.bphaseright=QtWidgets.QPushButton("\u2192") # phase right
self.hbl1.addWidget(self.bphaseright)
self.cbtargfn=QtWidgets.QComboBox(self)
self.cbtargfn.addItem("None") # 0
self.cbtargfn.addItem("triangle") # 1
self.cbtargfn.addItem("square") # 2
self.cbtargfn.addItem("square imp") # 3
self.cbtargfn.addItem("delta") # 4
self.cbtargfn.addItem("noise")
self.cbtargfn.addItem("saw")
self.cbtargfn.addItem("sin")
self.cbtargfn.addItem("modsin")
self.cbtargfn.addItem("modsin2")
self.cbtargfn.addItem("modsin3") #10
self.cbtargfn.addItem("sin low")
self.cbtargfn.addItem("doubledelta")
self.cbtargfn.addItem("sin bad f")
self.cbtargfn.addItem("sin bad f2")
self.cbtargfn.addItem("0 phase") #15
self.cbtargfn.addItem("rand phase")
self.hbl1.addWidget(self.cbtargfn)
self.bsound=QtWidgets.QPushButton("Play")
self.hbl1.addWidget(self.bsound)
self.bsoundr=QtWidgets.QPushButton("Rec")
self.hbl1.addWidget(self.bsoundr)
self.vrootf=ValBox(self,(1,64),"Root F:",264) # 264 is middle C
#self.vrootf.intonly=1
self.hbl1.addWidget(self.vrootf)
# Widget containing valsliders
self.wapsliders=QtWidgets.QWidget(self)
# self.wapsliders.setMinimumSize(800,640)
self.gblap=QtWidgets.QGridLayout()
self.gblap.setSizeConstraint(QtWidgets.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=QtWidgets.QScrollArea(self)
self.wapsarea.setWidgetResizable(True)
self.wapsarea.setWidget(self.wapsliders)
self.vbl1.addWidget(self.wapsarea)
self.vcell.valueChanged.connect(self.recompute)
self.vncells.valueChanged.connect(self.recompute)
self.voversamp.valueChanged.connect(self.recompute)
self.vnsin.valueChanged.connect(self.nsinchange)
self.cbshowall.stateChanged[int].connect(self.recompute)
self.cbshifted.stateChanged[int].connect(self.recompute)
self.cbtargfn.activated[int].connect(self.newtargfn)
self.bphaseleft.clicked.connect(self.phaseleft)
self.bphasecen.clicked.connect(self.phasecen)
self.bphaseright.clicked.connect(self.phaseright)
self.bsound.clicked.connect(self.playsound)
self.bsoundr.clicked.connect(self.recsound)
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)
self.wamp[-1].valueChanged.connect(self.recompute)
self.wpha.append(ValSlider(self,(-180.0,180.0),"%2d:"%i,0.0))
self.gblap.addWidget(self.wpha[-1],i,1)
self.wpha[-1].valueChanged.connect(self.recompute)
self.curves.append(EMData(64,1))
# if self.cbshowall.isChecked() :
# self.synthplot
self.total=EMData(64,1)
self.nsinchange()
E2loadappwin("e2fftsynth","main",self)
E2loadappwin("e2fftsynth","synth",self.synthplot.qt_parent)
E2loadappwin("e2fftsynth","fft",self.fftplot.qt_parent)