def __init__(self, target):
QtWidgets.QWidget.__init__(self)
#print "aaaaaaaa"
self.setWindowTitle("Options")
self.target = weakref.ref(target)
self.gbl = QtWidgets.QGridLayout(self)
#self.gbl.setContentsMargins(2, 2, 2, 2)
#self.gbl.setSpacing(6)
self.gbl.setObjectName("gbl")
self.erasercheckbox = QtWidgets.QCheckBox("Eraser")
self.gbl.addWidget(self.erasercheckbox, 0, 0)
self.eraser_radius = ValBox(label="Radius:", value=64)
self.gbl.addWidget(self.eraser_radius, 0, 1)
self.tabwidget = QtWidgets.QTabWidget()
self.gbl.addWidget(self.tabwidget, 1, 0, 1, 2)
def __init__(self,application,options,datafile):
QtWidgets.QWidget.__init__(self)
self.initialized=False
self.app=weakref.ref(application)
self.options=options
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"
self.globalxf=Transform()
# 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_boxpdb=self.mfile.addAction("Save Coord as PDB")
self.mfile_save_boxes_stack=self.mfile.addAction("Save Boxes as Stack")
#self.mfile_quit=self.mfile.addAction("Quit")
self.setCentralWidget(QtWidgets.QWidget())
self.gbl = QtWidgets.QGridLayout(self.centralWidget())
# relative stretch factors
self.gbl.setColumnMinimumWidth(0,200)
self.gbl.setRowMinimumHeight(0,200)
self.gbl.setColumnStretch(0,0)
self.gbl.setColumnStretch(1,100)
self.gbl.setColumnStretch(2,0)
self.gbl.setRowStretch(1,0)
self.gbl.setRowStretch(0,100)
# 3 orthogonal restricted projection views
self.xyview = EMImage2DWidget(sizehint=(1024,1024))
self.gbl.addWidget(self.xyview,0,1)
self.xzview = EMImage2DWidget(sizehint=(1024,256))
self.gbl.addWidget(self.xzview,1,1)
self.zyview = EMImage2DWidget(sizehint=(256,1024))
self.gbl.addWidget(self.zyview,0,0)
# Select Z for xy view
self.wdepth = QtWidgets.QSlider()
self.gbl.addWidget(self.wdepth,1,2)
### Control panel area in upper left corner
self.gbl2 = QtWidgets.QGridLayout()
self.gbl.addLayout(self.gbl2,1,0)
#self.wxpos = QtWidgets.QSlider(Qt.Horizontal)
#self.gbl2.addWidget(self.wxpos,0,0)
#self.wypos = QtWidgets.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)
# max or mean
#self.wmaxmean=QtWidgets.QPushButton("MaxProj")
#self.wmaxmean.setCheckable(True)
#self.gbl2.addWidget(self.wmaxmean,3,0)
# number slices
label0=QtWidgets.QLabel("Thickness")
self.gbl2.addWidget(label0,3,0)
self.wnlayers=QtWidgets.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=QtWidgets.QCheckBox("Limit Side Boxes")
self.gbl2.addWidget(self.wlocalbox,4,0)
self.wlocalbox.setChecked(True)
self.button_flat = QtWidgets.QPushButton("Flatten")
self.gbl2.addWidget(self.button_flat,5,0)
self.button_reset = QtWidgets.QPushButton("Reset")
self.gbl2.addWidget(self.button_reset,5,1)
## 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,6,0,1,2)
self.curbox=-1
self.boxes=[] # array of box info, each is (x,y,z,...)
self.boxesimgs=[] # z projection of each box
self.dragging=-1
##coordinate display
self.wcoords=QtWidgets.QLabel("")
self.gbl2.addWidget(self.wcoords, 1, 0, 1, 2)
self.button_flat.clicked[bool].connect(self.flatten_tomo)
self.button_reset.clicked[bool].connect(self.reset_flatten_tomo)
# 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_boxpdb.triggered[bool].connect(self.menu_file_save_boxpdb)
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.mouse_up)
self.xyview.mousewheel.connect(self.xy_wheel)
self.xyview.signal_set_scale.connect(self.event_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.mouse_up)
self.xzview.mousewheel.connect(self.xz_wheel)
self.xzview.signal_set_scale.connect(self.event_scale)
self.xzview.origin_update.connect(self.xz_origin)
self.xzview.mousemove.connect(self.xz_move)
self.zyview.mousedown.connect(self.zy_down)
self.zyview.mousedrag.connect(self.zy_drag)
self.zyview.mouseup.connect(self.mouse_up)
self.zyview.mousewheel.connect(self.zy_wheel)
self.zyview.signal_set_scale.connect(self.event_scale)
self.zyview.origin_update.connect(self.zy_origin)
self.zyview.mousemove.connect(self.zy_move)
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()
self.boxesviewer.mx_image_selected.connect(self.img_selected)
##################
#### deal with metadata in the _info.json file...
self.jsonfile=info_name(datafile)
info=js_open_dict(self.jsonfile)
#### read particle classes
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)]=64
clr=QtGui.QColor
self.setcolors=[QtGui.QBrush(clr("blue")),QtGui.QBrush(clr("green")),QtGui.QBrush(clr("red")),QtGui.QBrush(clr("cyan")),QtGui.QBrush(clr("purple")),QtGui.QBrush(clr("orange")), QtGui.QBrush(clr("yellow")),QtGui.QBrush(clr("hotpink")),QtGui.QBrush(clr("gold"))]
self.sets_visible={}
#### read boxes
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]=64
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]=int(np.round(self.boxsize[k]*self.apix_unbin/apix))
else:
self.apix_unbin=-1
info.close()
E2loadappwin("e2sptboxer","main",self)
E2loadappwin("e2sptboxer","boxes",self.boxesviewer.qt_parent)
E2loadappwin("e2sptboxer","option",self.optionviewer)
#### particle classes
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 __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,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)