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 EMTomoBoxer(QtWidgets.QMainWindow):
"""This class represents the EMTomoBoxer application instance. """
keypress = QtCore.pyqtSignal(QtGui.QKeyEvent)
module_closed = QtCore.pyqtSignal()
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 set_data(self,data):
self.data=data
self.apix=data["apix_x"]
self.datasize=(data["nx"],data["ny"],data["nz"])
self.x_loc, self.y_loc, self.z_loc=data["nx"]//2,data["ny"]//2,data["nz"]//2
self.gbl.setRowMinimumHeight(1,max(250,data["nz"]))
self.gbl.setColumnMinimumWidth(0,max(250,data["nz"]))
print(data["nx"],data["ny"],data["nz"])
self.wdepth.setRange(0,data["nz"]-1)
self.wdepth.setValue(data["nz"]//2)
self.boxes=[]
self.curbox=-1
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"]=r["apix_y"]=r["apix_z"]=self.apix
return r
def get_slice(self,idx,thk=1,axis="z"):
if self.globalxf.is_identity():
data=self.data
else:
data=self.dataxf
t=int(thk-1)
idx=int(idx)
r=data.process("misc.directional_sum",{"axis":axis,"first":idx-t,"last":idx+t})
r.div(t*2+1)
if self.apix!=0 :
r["apix_x"]=r["apix_y"]=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.z_loc!=self.wdepth.value():
self.z_loc=self.wdepth.value()
if self.initialized:
self.update_sliceview()
def event_nlayers(self):
self.update_all()
def event_filter(self):
self.update_all()
def event_localbox(self,tog):
self.update_sliceview(['x','y'])
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 menu_file_read_boxloc(self):
fsp=str(QtWidgets.QFileDialog.getOpenFileName(self, "Select output text file")[0])
if not os.path.isfile(fsp):
print("file does not exist")
return
f=open(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(QtWidgets.QFileDialog.getSaveFileName(self, "Select output text file")[0])
if len(fsp)==0:
return
out=open(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 menu_file_save_boxpdb(self):
fsp=str(QtWidgets.QFileDialog.getSaveFileName(self, "Select output PDB file", filter="PDB (*.pdb)")[0])
if len(fsp)==0:
return
if fsp[-4:].lower()!=".pdb" :
fsp+=".pdb"
clsid=list(self.sets_visible.keys())
if len(clsid)==0:
print("No visible particles to save")
return
bxs=np.array([[b[0], b[1], b[2]] for b in self.boxes if int(b[5]) in clsid])/10
numpy2pdb(bxs, fsp)
print("PDB saved to {}. Use voxel size 0.1".format(fsp))
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=QtWidgets.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 = QtWidgets.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 update_sliceview(self, axis=['x','y','z']):
boxes=self.get_rotated_boxes()
allside=(not self.wlocalbox.isChecked())
pms={'z':[2, self.xyview, self.z_loc],
'y':[1, self.xzview, self.y_loc],
'x':[0, self.zyview, self.x_loc]}
if self.boxshape=="circle": lwi=7
else: lwi=8
for ax in axis:
ia, view, loc=pms[ax]
shp=view.get_shapes()
if len(shp)!=len(boxes):
### something changes the box shapes...
for i,b in enumerate(boxes):
self.update_box_shape(i,b)
for ax in axis:
ia, view, loc=pms[ax]
## update the box shapes
shp=view.get_shapes()
for i,b in enumerate(boxes):
bs=self.get_boxsize(b[5])
dst=abs(b[ia] - loc)
inplane=dst<bs//2
rad=bs//2-dst
if ax!='z' and allside:
## display all side view boxes in this mode
inplane=True
rad=bs//2
if ax=='z' and self.options.mode=="2D":
## boxes are 1 slice thick in 2d mode
inplane=dst<1
if inplane and (b[5] in self.sets_visible):
shp[i][0]=self.boxshape
## selected box is slightly thicker
if self.curbox==i:
shp[i][lwi]=3
else:
shp[i][lwi]=2
if self.options.mode=="3D":
shp[i][6]=rad
else:
shp[i][0]="hidden"
view.shapechange=1
img=self.get_slice(loc, self.nlayers(), ax)
if self.wfilt.getValue()!=0.0:
img.process_inplace("filter.lowpass.gauss",{"cutoff_freq":1.0/self.wfilt.getValue(),"apix":self.apix})
view.set_data(img)
self.update_coords()
def get_rotated_boxes(self):
if len(self.boxes)==0:
return []
if self.globalxf.is_identity():
boxes=self.boxes
else:
cnt=[self.data["nx"]//2,self.data["ny"]//2,self.data["nz"]//2]
pts=np.array([b[:3] for b in self.boxes])-cnt
pts=np.array([self.globalxf.transform(p.tolist()) for p in pts])+cnt
boxes=[]
for i,b in enumerate(self.boxes):
p=pts[i]
boxes.append([p[0],p[1],p[2],b[3],b[4],b[5]])
return boxes
def update_all(self):
"""redisplay of all widgets"""
if self.data==None:
return
self.update_sliceview()
self.update_boximgs()
def update_coords(self):
self.wcoords.setText("X: {:d}\tY: {:d}\tZ: {:d}".format(int(self.x_loc), int(self.y_loc), int(self.z_loc)))
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 del_box(self, delids):
if type(delids)!=list:
delids=[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 update_box_shape(self,n, box):
bs2=self.get_boxsize(box[5])//2
if n==self.curbox:
lw=3
else:
lw=2
color=self.setcolors[box[5]%len(self.setcolors)].color().getRgbF()
if self.options.mode=="3D":
self.xyview.add_shape(n,EMShape(["circle",color[0],color[1],color[2],box[0],box[1],bs2,lw]))
self.xzview.add_shape(n,EMShape(["circle",color[0],color[1],color[2],box[0],box[2],bs2,lw]))
self.zyview.add_shape(n,EMShape(("circle",color[0],color[1],color[2],box[2],box[1],bs2,lw)))
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]))
def update_box(self,n,quiet=False):
"""After adjusting a box, call this"""
# print "upd ",n,quiet
if n<0 or n>=len(self.boxes):
return
box=self.boxes[n]
boxes=self.get_rotated_boxes()
self.update_box_shape(n,boxes[n])
if self.initialized:
self.update_sliceview()
# 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
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:
if event.modifiers()&Qt.ControlModifier:
self.del_box(list(range(lci, len(self.boxes))))
else:
self.del_box(lci)
else:
#self.update_box(lci)
self.curbox=lci
box=self.boxes[lci]
self.x_loc,self.y_loc,self.z_loc=self.rotate_coord([box[0], box[1], box[2]], inv=False)
self.scroll_to(self.x_loc,self.y_loc,self.z_loc)
self.update_sliceview()
def rotate_coord(self, p, inv=True):
if not self.globalxf.is_identity():
cnt=[self.data["nx"]//2,self.data["ny"]//2,self.data["nz"]//2]
p=[p[i]-cnt[i] for i in range(3)]
xf=Transform(self.globalxf)
if inv:
xf.invert()
p=xf.transform(p)+cnt
return p
def del_region_xy(self, x=-1, y=-1, z=-1, rad=-1):
if rad<0:
rad=self.eraser_width()
delids=[]
boxes=self.get_rotated_boxes()
for i,b in enumerate(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.del_box(delids)
def scroll_to(self, x,y,z, axis=""):
if axis!="z": self.xyview.scroll_to(x,y,True)
if axis!="y": self.xzview.scroll_to(x,self.data["nz"]/2,True)
if axis!="x": self.zyview.scroll_to(self.data["nz"]/2,y,True)
#### mouse click
def xy_down(self,event):
x,y=self.xyview.scr_to_img((event.x(),event.y()))
self.mouse_down(event, x,y,self.z_loc, "z")
def xz_down(self,event):
x,z=self.xzview.scr_to_img((event.x(),event.y()))
self.mouse_down(event,x,self.y_loc,z, "y")
def zy_down(self,event):
z,y=self.zyview.scr_to_img((event.x(),event.y()))
self.mouse_down(event,self.x_loc,y,z, "x")
def mouse_down(self,event, x, y, z, axis):
if min(x,y,z)<0: return
xr,yr,zr=self.rotate_coord((x,y,z))
#print(x,y,z,xr,yr,zr)
if self.optionviewer.erasercheckbox.isChecked():
self.del_region_xy(x,y,z)
return
for i in range(len(self.boxes)):
if self.inside_box(i,xr,yr,zr):
if event.modifiers()&Qt.ShiftModifier: ## delete box
self.del_box(i)
else: ## start dragging
self.dragging=i
self.curbox=i
self.scroll_to(x,y,z,axis)
break
else:
if not event.modifiers()&Qt.ShiftModifier: ## add box
self.x_loc, self.y_loc, self.z_loc=x,y,z
self.scroll_to(x,y,z,axis)
self.curbox=len(self.boxes)
self.boxes.append(([xr,yr,zr, 'manual', 0.0, self.currentset]))
self.update_box(len(self.boxes)-1)
self.dragging=len(self.boxes)-1
#### eraser mode
def xy_move(self,event):
self.mouse_move(event, self.xyview)
def xz_move(self,event):
self.mouse_move(event, self.xzview)
def zy_move(self,event):
self.mouse_move(event, self.zyview)
def mouse_move(self,event,view):
if self.optionviewer.erasercheckbox.isChecked():
self.xyview.eraser_shape=self.xzview.eraser_shape=self.zyview.eraser_shape=None
x,y=view.scr_to_img((event.x(),event.y()))
view.eraser_shape=EMShape(["circle",1,1,1,x,y,self.eraser_width(),2])
view.shapechange=1
view.update()
else:
view.eraser_shape=None
#### dragging...
def mouse_drag(self,x, y, z):
if self.dragging<0:
return
if min(x,y,z)<0:
return
self.x_loc, self.y_loc, self.z_loc=x,y,z
x,y,z=self.rotate_coord((x,y,z))
self.boxes[self.dragging][:3]= x,y,z
self.update_box(self.dragging,True)
def xy_drag(self,event):
if self.dragging>=0:
x,y=self.xyview.scr_to_img((event.x(),event.y()))
self.mouse_drag(x,y,self.z_loc)
def xz_drag(self,event):
if self.dragging>=0:
x,z=self.xzview.scr_to_img((event.x(),event.y()))
self.mouse_drag(x,self.y_loc,z)
def zy_drag(self,event):
if self.dragging>=0:
z,y=self.zyview.scr_to_img((event.x(),event.y()))
self.mouse_drag(self.x_loc,y,z)
def mouse_up(self,event):
if self.dragging>=0:
self.update_box(self.dragging)
self.dragging=-1
#### keep the same origin for the 3 views
def xy_origin(self,newor):
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 xz_origin(self,newor):
xyo=self.xyview.get_origin()
self.xyview.set_origin(newor[0],xyo[1],True)
def zy_origin(self,newor):
xyo=self.xyview.get_origin()
self.xyview.set_origin(xyo[0],newor[1],True)
##### go up/down with shift+wheel
def xy_wheel(self, event):
z=int(self.z_loc+ np.sign(event.angleDelta().y()))
if z>0 and z<self.data["nz"]:
self.wdepth.setValue(z)
def xz_wheel(self, event):
y=int(self.y_loc+np.sign(event.angleDelta().y()))
if y>0 and y<self.data["ny"]:
self.y_loc=y
self.update_sliceview(['y'])
def zy_wheel(self, event):
x=int(self.x_loc+np.sign(event.angleDelta().y()))
if x>0 and x<self.data["nx"]:
self.x_loc=x
self.update_sliceview(['x'])
########
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.del_box(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.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: ## "`" to move up a slice since arrow keys are occupied...
self.wdepth.setValue(self.z_loc+1)
elif event.key() == 49: ## "1" to move down a slice
self.wdepth.setValue(self.z_loc-1)
else:
self.keypress.emit(event)
def flatten_tomo(self):
print("Flatten tomogram by particles coordinates")
vis=list(self.sets_visible.keys())
pts=[b[:3] for b in self.boxes if b[5] in vis]
if len(pts)<3:
print("Too few visible particles. Cannot flatten tomogram.")
return
pts=np.array(pts)
pca=PCA(3)
pca.fit(pts);
c=pca.components_
t=Transform()
cc=c[2]
if cc[2]!=0:
cc*=np.sign(cc[2])
t.set_rotation(c[2].tolist())
t.invert()
xyz=t.get_params("xyz")
xyz["ztilt"]=0
print("xtilt {:.02f}, ytilt {:.02f}".format(xyz["xtilt"], xyz["ytilt"]))
t=Transform(xyz)
self.globalxf=t
self.dataxf=self.data.process("xform",{"transform":t})
self.xyview.shapes={}
self.zyview.shapes={}
self.xzview.shapes={}
boxes=self.get_rotated_boxes()
for i,b in enumerate(boxes):
self.update_box_shape(i,b)
self.update_sliceview()
print("Done")
def reset_flatten_tomo(self, event):
self.globalxf=Transform()
self.xyview.shapes={}
self.zyview.shapes={}
self.xzview.shapes={}
boxes=self.get_rotated_boxes()
for i,b in enumerate(boxes):
self.update_box_shape(i,b)
self.update_sliceview()
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]=np.round(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()
E2saveappwin("e2sptboxer","main",self)
E2saveappwin("e2sptboxer","boxes",self.boxesviewer.qt_parent)
E2saveappwin("e2sptboxer","option",self.optionviewer)
#self.boxviewer.close()
self.boxesviewer.close()
self.optionviewer.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 GUIFourierSynth(QtWidgets.QWidget):
"""This class represents an application for interactive Fourier synthesis"""
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)
def closeEvent(self,event):
# QtWidgets.QWidget.closeEvent(self,event)
E2saveappwin("e2fftsynth","main",self)
E2saveappwin("e2fftsynth","synth",self.synthplot.qt_parent)
E2saveappwin("e2fftsynth","fft",self.fftplot.qt_parent)
QtWidgets.qApp.exit(0)
def phaseleft(self,v): # fixed translation in minus direction
ss=self.vshftstep.getValue()
sft=ss*360.0/len(self.xvals)
for i in range(1,len(self.wpha)):
self.wpha[i].setValue(fixang(self.wpha[i].getValue()-sft*i),1)
self.recompute()
def phasecen(self,v): # translation so phase of lowest freqeuncy is zero
sft=self.wpha[1].getValue()
for i in range(1,len(self.wpha)):
self.wpha[i].setValue(fixang(self.wpha[i].getValue()-sft*i),1)
self.recompute()
def phaseright(self,v): # fixed translation in plus direction
ss=self.vshftstep.getValue()
sft=ss*360.0/len(self.xvals)
for i in range(1,len(self.wpha)):
self.wpha[i].setValue(fixang(self.wpha[i].getValue()+sft*i),1)
self.recompute()
def playsound(self,v):
global soundout
f0=int(self.vrootf.getValue())
nsam2=8*44100//(2*f0) # 8x oversampling so high fundamental frequencies come out closer to correct
print(f"play: {f0} ({nsam2})")
svals=np.zeros_like(self.svals,shape=nsam2)
if len(self.svals)>=nsam2//8: svals[::8]=self.svals[:(nsam2-1)//8+1] # interleave zeros for 8 repetitions of the wave. Gives better frequency accuracy at high frequency
else: svals[:len(self.svals)*8:8]=self.svals
# svals=self.svals.copy()
# svals.resize(nsam2)
# if len(self.svals)<nsam2: svals[len(self.svals):]=0.0 # zero fill if we extended the array
total=fft.irfft(svals)*(len(svals)-1)*10000.0
self.assound=np.tile(total.astype("int16"),44100//nsam2)
#print nsam2,len(self.svals),len(svals),len(total)
initsound()
soundout.start()
soundout.write(self.assound)
soundout.stop()
def recsound(self,v):
global soundin
# global kaiser
initsound()
soundin.start()
snd=soundin.read(65536)[0][:,0]
soundin.stop()
np.savetxt("real.txt",snd)
# snd*=kaiser # window didn't really help
ft=fft.rfft(snd)
a=np.absolute(ft)
np.savetxt("fft.txt",a)
p=np.angle(ft)*180./pi
np.savetxt("pha.txt",p)
# If there is only a single strong peak (or maybe 2) the CCF approach won't work very well, but the peak itself should be good
# h=np.argwhere(a>np.max(a)/20.0)
# if len(h)<3: h=np.min(h)
# else:
fta=fft.rfft(a)
fta=fta*np.conj(fta)
fta=fft.irfft(fta)
np.savetxt("fta.txt",fta)
# peak filter, but wasn't useful
# ftap=np.roll(fta,1,0)
# ftam=np.roll(fta,-1,0)
# fta=np.where(fta>ftap,fta,np.zeros(len(fta)))
# fta=np.where(fta>ftam,fta,np.zeros(len(fta)))
# np.savetxt("ftaf.txt",fta)
# ftac=fta.copy()
# # need a clever way to do this in numpy
# for i in range(1,32767):
# if fta[i-1]>fta[i] or fta[i+1]>fta[i] : ftac[i]=0
h=(np.argmax(fta[200:20000])+200)//2
f1=22050.0/32768.0 # lowest frequency pixel, scaling factor for frequency axis
# sum the first 8 harmonics for each fundamental
# hsum=a[:4096]*1.25 # *1.25 helps make sure a solo peak shows up as the first harmonic not a higher one
# for i in range(2,9): hsum+=a[:4096*i:i]
# hsum=np.fmin(hsum,a[:4096]*25.0)
# np.savetxt("fsum.txt",hsum)
# hsum=hsum[100:]
# h=np.min(np.argwhere(hsum>np.std(hsum)*2.0))+100
# h=np.argmax(hsum[100:])+100
maxf=f1*h # should correspond to the strongest single frequency based on harmonic sum
print(f"peak {h} -> {maxf}")
self.vrootf.setValue(floor(maxf))
# pull out the values for up to the first 33 harmonics
sca=0.5/np.max(a[h::h])
for i in range(1,33):
j=h*i # harmonic peak index (rounded)
if j>32767 :
self.wamp[i].setValue(0,True)
continue
amp=float(abs(ft[j]))*sca
pha=float(cmath.phase(ft[j]))*180.0/pi
self.wamp[i].setValue(amp,True)
self.wpha[i].setValue(pha,True)
self.recompute()
def newtargfn(self,index):
"This function has a number of hardcoded 'target' functions"
if index==0 :
self.targfn=None
nsin=int(self.vnsin.getValue())
for i in range(nsin+1):
self.wamp[i].setValue(0,1)
self.wpha[i].setValue(0,1)
elif index==15: # zero phase
nsin=int(self.vnsin.getValue())
for i in range(nsin+1):
self.wpha[i].setValue(0,1)
elif index==16: # random phase
nsin=int(self.vnsin.getValue())
for i in range(nsin+1):
self.wpha[i].setValue(random.uniform(-180.,180.),1)
else :
nx=int(self.vcell.getValue())
x=np.arange(0,1.0,1.0/nx)
y=np.zeros(nx)
if index==1 : # triangle
y[:nx//2]=x[:nx//2]*2.0
y[nx//2:]=(1.0-x[nx//2:])*2.0
elif index==2 : # square
y[:nx//4]=0
y[nx//4:nx*3//4]=1.0
y[nx*3//4:]=0
elif index==3 : # square impulse
y[:nx//2]=0
y[nx//2:nx*3//5]=1.0
y[nx*3//5:]=0
elif index==4 : # delta
y[:]=0
y[nx//2]=10.0
elif index==5 : # noise
y=np.random.random_sample((nx,))-0.5
elif index==6 : # saw
y[:nx//4]=0
y[nx//4:nx//2]=x[:nx//4]
y[nx//2:nx*3//4]=-x[:nx//4]
y[nx*3//4:]=0
elif index==7 : # sin
y=np.sin(x*16.0*pi)
elif index==8 : # modulated sine
y=np.sin(x*4.0*pi)*np.sin(x*32.0*pi)
elif index==9 : # modulated sine 2
y=np.sin(x*2.0*pi)*np.sin(x*32.0*pi)
elif index==10 : # modulated sine 3
y=np.sin(x*8.0*pi)*np.sin(x*32.0*pi)
elif index==11 : # sin low
y=np.sin(x*4.0*pi)
elif index==12 : # double delta
y[:]=0
y[16]=5.0
y[48]=5.0
elif index==13 : # sin bad f
y=np.sin(x*2.3*pi)
elif index==14 : # sin bad f2
y=np.sin(x*17.15*pi)
self.targfn=y
self.target2sliders()
self.recompute()
def target2sliders(self):
f=fft.rfft(self.targfn)*2.0/len(self.targfn)
nsin=int(self.vnsin.getValue())
for i in range(min(len(f),nsin+1)):
# print fft[i]
amp=abs(f[i])
if fabs(amp)<1.0e-6 : amp=0.0
if amp==0 : pha=0
else: pha=cmath.phase(f[i])
self.wamp[i].setValue(amp,quiet=1)
self.wpha[i].setValue(fixang(pha*180.0/pi),quiet=1)
def nsinchange(self,value=None):
if value==None : value=int(self.vnsin.getValue())
for i in range(65):
if i>value:
self.wamp[i].hide()
self.wpha[i].hide()
else :
self.wamp[i].show()
self.wpha[i].show()
if self.targfn!=None :
self.target2sliders()
self.recompute()
def recompute(self,value=None):
nsin=int(self.vnsin.getValue())
cell=int(self.vcell.getValue())
ncells=int(self.vncells.getValue())
oversamp=max(1,int(self.voversamp.getValue()))
samples=int(cell*oversamp)
# arrays since we're using them several ways
self.svals=np.array([cmath.rect(self.wamp[i].getValue(),self.wpha[i].getValue()*pi/180.0) for i in range(nsin+1)])
#self.wamps=np.array([v.getValue() for v in self.wamp[:nsin+1]])
#self.wphas=np.array([v.getValue() for v in self.wpha[:nsin+1]])
self.xvals=np.array([xn/float(oversamp) for xn in range(samples)])
if samples//2>len(self.svals): svals=np.concatenate((self.svals,np.zeros(1+samples//2-len(self.svals))))
else: svals=self.svals
self.total=fft.irfft(svals)*(len(svals)-1)
if ncells>1: self.total=np.tile(self.total,ncells)
self.synthplot.set_data((np.arange(0,len(self.total)/oversamp,1.0/oversamp),self.total),"Sum",replace=True,quiet=True,linewidth=2)
if not self.targfn is None:
self.synthplot.set_data((np.arange(len(self.targfn)),self.targfn),"Target",quiet=True,linewidth=1,linetype=2,symtype=0)
# if self.cbshowall.isChecked() :
# csum=self.total["minimum"]*1.1
# for i in range(nsin):
# if self.wamps[i]==0: continue
# csum-=self.wamps[i]*1.1
# if self.cbshifted.isChecked() : self.curves[i].add(csum)
# self.synthplot.set_data((self.xvals,self.curves[i].get_data_as_vector()),"%d"%i,quiet=True,linewidth=1,color=2)
# csum-=self.wamps[i]*1.1
self.synthplot.updateGL()
self.fftplot.set_data((np.arange(len(self.svals)),np.abs(self.svals)),"Amp",color=0,linetype=0,linewidth=2)
self.fftplot.set_data((np.arange(len(self.svals)),np.angle(self.svals)),"Pha",color=1,linetype=0,linewidth=2)
self.fftplot.updateGL()