class TrackerControl(QtGui.QWidget):
def __init__(self,
app,
maxshift,
invert=False,
seqali=False,
tiltstep=2.0):
self.app = app
self.maxshift = maxshift
self.seqali = seqali
self.invert = invert
self.tiltstep = tiltstep
# the control panel
QtGui.QWidget.__init__(self, None)
self.gbl = QtGui.QGridLayout(self)
self.gbl.setMargin(0)
self.gbl.setSpacing(6)
self.gbl.setObjectName("hbl")
# action buttons
self.bcenalign = QtGui.QPushButton("Center Align")
self.bprojalign = QtGui.QPushButton("Proj. Realign")
self.btiltaxis = QtGui.QPushButton("Tilt Axis")
self.btiltaxisval = QtGui.QLineEdit("90.0")
self.bsavedata = QtGui.QPushButton("Save Data")
self.breconst = QtGui.QPushButton("3D Normal")
self.sbmode = QtGui.QSpinBox(self)
self.sbmode.setRange(0, 2)
self.sbmode.setValue(0)
self.bmagict = QtGui.QPushButton("3D Tomofill")
self.bmagics = QtGui.QPushButton("3D Sph")
self.bmagicc = QtGui.QPushButton("3D Cyl")
self.vslpfilt = ValSlider(self, (0, .5), "Filter", 0.5, 50)
self.gbl.addWidget(self.bcenalign, 0, 0)
self.gbl.addWidget(self.bprojalign, 0, 1)
self.gbl.addWidget(self.btiltaxis, 0, 2)
self.gbl.addWidget(self.btiltaxisval, 0, 3)
# self.gbl.addWidget(self.bsavedata,0,3)
self.gbl.addWidget(self.breconst, 1, 0)
self.gbl.addWidget(self.sbmode, 2, 0, 1, 1)
self.gbl.addWidget(self.vslpfilt, 3, 0, 1, 4)
self.gbl.addWidget(self.bmagict, 1, 1)
self.gbl.addWidget(self.bmagics, 1, 2)
self.gbl.addWidget(self.bmagicc, 1, 3)
QtCore.QObject.connect(self.bcenalign, QtCore.SIGNAL("clicked(bool)"),
self.do_cenalign)
QtCore.QObject.connect(self.bprojalign, QtCore.SIGNAL("clicked(bool)"),
self.do_projalign)
QtCore.QObject.connect(self.btiltaxis, QtCore.SIGNAL("clicked(bool)"),
self.do_tiltaxis)
QtCore.QObject.connect(self.bsavedata, QtCore.SIGNAL("clicked(bool)"),
self.do_savedata)
QtCore.QObject.connect(self.breconst, QtCore.SIGNAL("clicked(bool)"),
self.do_reconst)
QtCore.QObject.connect(self.bmagict, QtCore.SIGNAL("clicked(bool)"),
self.do_magict)
QtCore.QObject.connect(self.bmagics, QtCore.SIGNAL("clicked(bool)"),
self.do_magics)
QtCore.QObject.connect(self.bmagicc, QtCore.SIGNAL("clicked(bool)"),
self.do_magicc)
QtCore.QObject.connect(self.vslpfilt, QtCore.SIGNAL("valueChanged"),
self.do_filter)
# the single image display widget
self.im2d = EMImage2DWidget(application=app, winid="tomotrackbox.big")
self.imboxed = EMImage2DWidget(application=app,
winid="tomotrackbox.small")
self.improj = EMImage2DWidget(application=app,
winid="tomotrackbox.proj")
self.imslice = EMImage2DWidget(application=app,
winid="tomotrackbox.3dslice")
self.imvol = EMImage3DModule(application=app, winid="tomotrackbox.3d")
# get some signals from the window.
QtCore.QObject.connect(self.im2d, QtCore.SIGNAL("mousedown"),
self.down)
QtCore.QObject.connect(self.im2d, QtCore.SIGNAL("mousedrag"),
self.drag)
QtCore.QObject.connect(self.im2d, QtCore.SIGNAL("mouseup"), self.up)
QtCore.QObject.connect(self.im2d, QtCore.SIGNAL("increment_list_data"),
self.change_tilt)
self.imagefile = None
self.imageparm = None
self.tiltshapes = None
self.curtilt = 0
self.oldtilt = self.curtilt
self.map3d = None
self.downloc = None
self.downadjloc = None
self.show()
self.im2d.show()
def closeEvent(self, event):
self.im2d.closeEvent(QtGui.QCloseEvent())
self.imboxed.closeEvent(QtGui.QCloseEvent())
self.improj.closeEvent(QtGui.QCloseEvent())
self.imslice.closeEvent(QtGui.QCloseEvent())
self.imvol.closeEvent(QtGui.QCloseEvent())
event.accept()
def do_cenalign(self, x=0):
"""In response to the center align button. Just a wrapper"""
self.cenalign_stack()
self.update_stack()
def do_projalign(self, x=0):
"""In response to the projection align button. Just a wrapper"""
self.projection_align(self.tiltstep)
self.update_stack()
# self.do_reconst()
def do_tiltaxis(self):
"""In response to the tilt axis button. Just a wrapper"""
self.tilt_axis()
def do_reconst(self, x=0):
"""In response to the normal reconstruction button. Just a wrapper"""
stack = self.get_boxed_stack()
mode = self.sbmode.value()
self.map3d = self.reconstruct(stack, self.tiltstep, mode)
self.update_3d()
def do_magict(self, x):
"""In response to tomographic filling reconstruction button. Just a wrapper"""
stack = self.get_boxed_stack()
# self.map3d=self.reconstruct_ca(stack[5:-4],0.5)
# init=self.reconstruct_ca(stack[5:-4],0.5)
mode = self.sbmode.value()
self.map3d = self.reconstruct_wedgefill(stack, self.tiltstep, mode)
self.update_3d()
def do_magics(self, x):
"""In response to the 3D Sph button. Just a wrapper"""
return
def do_magicc(self, x):
"""In response to the 3D cyl button. Just a wrapper"""
return
def do_filter(self, v):
"""In response to the filter ValSlider"""
if self.map3d == None: return
self.lpfilt = v
self.update_3d()
def do_savedata(self):
""
def update_3d(self):
if self.map3d == None: return
self.filt3d = self.map3d.process(
"filter.lowpass.gauss", {"cutoff_abs": self.vslpfilt.getValue()})
self.imvol.set_data(self.filt3d)
self.imvol.show()
self.imvol.updateGL()
sz = self.map3d["nx"]
xsum = self.filt3d.process("misc.directional_sum", {"axis": "x"})
xsum.set_size(sz, sz, 1)
ysum = self.filt3d.process("misc.directional_sum", {"axis": "y"})
ysum.set_size(sz, sz, 1)
zsum = self.filt3d.process("misc.directional_sum", {"axis": "z"})
zsum.set_size(sz, sz, 1)
self.improj.set_data([zsum, ysum, xsum])
self.improj.show()
self.improj.updateGL()
self.imslice.set_data(self.filt3d)
self.imslice.show()
self.imslice.updateGL()
def update_stack(self):
stack = self.get_boxed_stack()
self.imboxed.set_data(stack)
self.imboxed.show()
self.imboxed.updateGL()
def set_image(self, fsp):
"""Takes an ali file to process"""
self.imageparm = EMData(fsp, 0, True).get_attr_dict()
print "%d slices at %d x %d" % (
self.imageparm["nz"], self.imageparm["nx"], self.imageparm["ny"])
self.imagefile = fsp
self.curtilt = self.imageparm["nz"] / 2
self.tiltshapes = [None for i in range(self.imageparm["nz"])]
self.update_tilt()
def update_tilt(self):
if self.imagefile == None: return
self.curimg = EMData(
self.imagefile, 0, False,
Region(0, 0, self.curtilt, self.imageparm["nx"],
self.imageparm["ny"], 1))
if self.invert: self.curimg.mult(-1.0)
self.im2d.set_data(self.curimg)
s = EMShape(
["scrlabel", .7, .3, 0, 20.0, 20.0,
"%d" % self.curtilt, 200.0, 1])
self.im2d.add_shape("tilt", s)
if self.tiltshapes[self.curtilt] != None:
self.im2d.add_shape("finalbox", self.tiltshapes[self.curtilt])
s0 = self.tiltshapes[self.oldtilt].getShape()
s1 = self.tiltshapes[self.curtilt].getShape()
dx = s0[4] - s1[4]
dy = s0[5] - s1[5]
self.im2d.set_origin(self.im2d.origin[0] - dx,
self.im2d.origin[1] - dy)
self.oldtilt = self.curtilt
self.im2d.updateGL()
def change_tilt(self, direc):
"""When the user presses the up or down arrow"""
self.oldtilt = self.curtilt
self.curtilt += direc
if self.curtilt < 0: self.curtilt = 0
if self.curtilt >= self.imageparm["nz"]:
self.curtilt = self.imageparm["nz"] - 1
self.update_tilt()
def down(self, event, lc):
"""The event contains the x,y coordinates in window space, lc are the coordinates in image space"""
if event.buttons() & Qt.LeftButton:
if event.modifiers() & Qt.ShiftModifier:
self.downadjloc = (
lc, self.tiltshapes[self.curtilt].getShape()[4:8])
else:
self.downloc = lc
def drag(self, event, lc):
if self.downloc != None:
dx = abs(lc[0] - self.downloc[0])
dy = abs(lc[1] - self.downloc[1])
dx = max(dx, dy) # Make box square
dx = good_size(dx * 2) / 2 # use only good sizes
dy = dx
s = EMShape([
"rectpoint", 0, .7, 0, self.downloc[0] - dx,
self.downloc[1] - dy, self.downloc[0] + dx,
self.downloc[1] + dy, 1
])
self.im2d.add_shape("box", s)
s = EMShape([
"scrlabel", .7, .7, 0, 20.0, 20.0,
"%d (%d x %d)" % (self.curtilt, dx * 2, dy * 2), 200.0, 1
])
self.im2d.add_shape("tilt", s)
elif self.downadjloc != None:
dx = (lc[0] - self.downadjloc[0][0])
dy = (lc[1] - self.downadjloc[0][1])
s = self.tiltshapes[self.curtilt].getShape()[:]
s[4] = self.downadjloc[1][0] + dx
s[5] = self.downadjloc[1][1] + dy
s[6] = self.downadjloc[1][2] + dx
s[7] = self.downadjloc[1][3] + dy
self.im2d.add_shape("box", EMShape(s))
self.im2d.updateGL()
def up(self, event, lc):
if self.downloc != None:
dx = abs(lc[0] - self.downloc[0])
dy = abs(lc[1] - self.downloc[1])
dx = max(dx, dy) # Make box square
dx = good_size(dx * 2) / 2 # use only good sizes
dy = dx
s = EMShape([
"rectpoint", .7, .2, 0, self.downloc[0] - dx,
self.downloc[1] - dy, self.downloc[0] + dx,
self.downloc[1] + dy, 1
])
self.im2d.del_shape("box")
if hypot(lc[0] - self.downloc[0], lc[1] - self.downloc[1]) > 5:
self.tiltshapes = [None for i in range(self.imageparm["nz"])]
self.find_boxes(s)
self.update_tilt()
self.downloc = None
elif self.downadjloc != None:
dx = (lc[0] - self.downadjloc[0][0])
dy = (lc[1] - self.downadjloc[0][1])
s = self.tiltshapes[self.curtilt].getShape()[:]
s[4] = self.downadjloc[1][0] + dx
s[5] = self.downadjloc[1][1] + dy
s[6] = self.downadjloc[1][2] + dx
s[7] = self.downadjloc[1][3] + dy
self.tiltshapes[self.curtilt] = EMShape(s)
self.im2d.add_shape("finalbox", self.tiltshapes[self.curtilt])
self.im2d.del_shape("box")
self.update_tilt()
self.update_stack()
self.downadjloc = None
def get_boxed_stack(self):
stack = []
for i in range(self.imageparm["nz"]):
refshape = self.tiltshapes[i].getShape()
img = EMData(
self.imagefile, 0, False,
Region(refshape[4], refshape[5], i, refshape[6] - refshape[4],
refshape[7] - refshape[5], 1))
img["ptcl_source_coord"] = (int((refshape[6] + refshape[4]) / 2.0),
int((refshape[7] + refshape[5]) / 2.0),
i)
img["ptcl_source_image"] = str(self.imagefile)
if self.invert: img.mult(-1.0)
img.process_inplace("normalize.edgemean")
stack.append(img)
return stack
def cenalign_stack(self):
"""This will perform an iterative centering process on a stack of particle images, centering each on the average.
It will modify the current stack of boxing parameters in-place"""
for it in range(5):
stack = self.get_boxed_stack()
# Average the stack, and center it
av = stack[0].copy()
for im in stack[1:]:
av.add(im)
av.process_inplace("filter.lowpass.gauss", {"cutoff_abs": .1})
av.process_inplace("filter.highpass.gauss", {"cutoff_abs": .02})
av.process_inplace("xform.centeracf")
#display((av,av2))
# align to the average
for i, im in enumerate(stack):
im.process_inplace("filter.lowpass.gauss", {"cutoff_abs": .1})
im.process_inplace("filter.highpass.gauss",
{"cutoff_abs": .02})
ali = im.align("translational", av)
trans = ali["xform.align2d"].get_trans()
shape = self.tiltshapes[i]
shape.translate(-trans[0], -trans[1])
# Update the stack display
stack = self.get_boxed_stack()
self.imboxed.set_data(stack)
def reconstruct_wedgefill(self, stack, angstep, mode=2):
"""Fills the missing wedge with the average of the slices"""
print "Making 3D tomofill"
taxis = float(self.btiltaxisval.text())
boxsize = stack[0]["nx"]
pad = Util.calc_best_fft_size(int(boxsize * 1.5))
# average all of the slices together
av = stack[0].copy()
for p in stack[1:]:
av += p
av.del_attr("xform.projection")
av.mult(1.0 / (len(stack)))
av = av.get_clip(
Region(-(pad - boxsize) / 2, -(pad - boxsize) / 2, pad, pad))
for i, p in enumerate(stack):
p["alt"] = (i - len(stack) / 2) * angstep
# Determine a good angular step for filling Fourier space
fullsamp = 360.0 / (boxsize * pi)
if angstep / fullsamp > 2.0:
samp = 1.0 / (floor(angstep / fullsamp))
else:
samp = angstep
print "Subsampling = %1.2f" % samp
# Now the reconstruction
recon = Reconstructors.get(
"fourier", {
"sym": "c1",
"size": (pad, pad, pad),
"mode": reconmodes[mode],
"verbose": True
})
recon.setup()
for ri in range(5):
print "Iteration ", ri
for a in [
i * samp for i in range(-int(90.0 / samp),
int(90.0 / samp) + 1)
]:
for ii in range(len(stack) - 1):
if stack[ii]["alt"] <= a and stack[ii + 1]["alt"] > a:
break
else:
ii = -1
if a < stack[0]["alt"]:
p = av
#frac=0.5*(a-stack[0]["alt"])/(-90.0-stack[0]["alt"])
## a bit wierd. At the ends (missing wedge) we use the average over all tilts. This could be improved
#p=stack[0].get_clip(Region(-(pad-boxsize)/2,-(pad-boxsize)/2,pad,pad))*(1.0-frac)+stack[-1].get_clip(Region(-(pad-boxsize)/2,-(pad-boxsize)/2,pad,pad))*frac
# print a," avg ",frac,stack[0]["alt"]
elif ii == -1:
p = av
#frac=0.5*(a-stack[-1]["alt"])/(90.0-stack[-1]["alt"])+.5
## a bit wierd. At the ends (missing wedge) we use the average over all tilts. This could be improved
#p=stack[-1].get_clip(Region(-(pad-boxsize)/2,-(pad-boxsize)/2,pad,pad))*(1.0-frac)+stack[0].get_clip(Region(-(pad-boxsize)/2,-(pad-boxsize)/2,pad,pad))*frac
# print a," avg ",frac
else:
# We average slices in real space, producing a rotational 'smearing' effect
frac = (a - stack[ii]["alt"]) / angstep
p = stack[ii].get_clip(
Region(-(pad - boxsize) / 2, -(pad - boxsize) / 2, pad,
pad)) * (1.0 - frac) + stack[ii + 1].get_clip(
Region(-(pad - boxsize) / 2,
-(pad - boxsize) / 2, pad,
pad)) * frac
# print a,ii,ii+1,stack[ii]["alt"],frac
xf = Transform({
"type": "eman",
"alt": a,
"az": -taxis,
"phi": taxis
})
p["xform.projection"] = xf
if ri % 2 == 1:
recon.determine_slice_agreement(p, xf, 1)
else:
recon.insert_slice(p, xf)
ret = recon.finish()
print "Done"
ret = ret.get_clip(
Region((pad - boxsize) / 2, (pad - boxsize) / 2,
(pad - boxsize) / 2, boxsize, boxsize, boxsize))
ret.process_inplace("normalize.edgemean")
# ret=ret.get_clip(Region((pad-boxsize)/2,(pad-boxsize)/2,(pad-boxsize)/2,boxsize,boxsize,boxsize))
return ret
def reconstruct_ca(self, stack, angstep, mode=2):
"""Cylindrically averaged tomographic model, generally used for filling empty spaces. Returned volume is padded."""
print "Making CA"
taxis = float(self.btiltaxisval.text())
boxsize = stack[0]["nx"]
pad = Util.calc_best_fft_size(int(boxsize * 1.5))
# average all of the slices together
av = stack[0].copy()
for p in stack[1:]:
av += p
av.del_attr("xform.projection")
p.mult(1.0 / len(stack))
av = av.get_clip(
Region(-(pad - boxsize) / 2, -(pad - boxsize) / 2, pad, pad))
recon = Reconstructors.get("fourier", {
"quiet": True,
"sym": "c1",
"x_in": pad,
"y_in": pad
})
recon.setup()
for ri in range(3):
if ri > 0:
alt = -180.0
while (alt < 180.0):
recon.determine_slice_agreement(
av,
Transform({
"type": "eman",
"alt": alt,
"az": -taxis,
"phi": taxis
}), 1)
alt += angstep
alt = -180.0
while (alt < 180.0):
recon.insert_slice(
av,
Transform({
"type": "eman",
"alt": alt,
"az": -taxis,
"phi": taxis
}))
alt += angstep
ret = recon.finish()
ret.process_inplace("normalize.edgemean")
# ret=ret.get_clip(Region((pad-boxsize)/2,(pad-boxsize)/2,(pad-boxsize)/2,boxsize,boxsize,boxsize))
return ret
def reconstruct(self, stack, angstep, mode=0, initmodel=None):
""" Tomographic reconstruction of the current stack """
if initmodel != None: print "Using initial model"
taxis = float(self.btiltaxisval.text())
boxsize = stack[0]["nx"]
pad = good_size(int(boxsize * 1.5))
for i, p in enumerate(stack):
p["xform.projection"] = Transform({
"type": "eman",
"alt": (i - len(stack) / 2) * angstep,
"az": -taxis,
"phi": taxis
})
recon = Reconstructors.get(
"fourier", {
"sym": "c1",
"size": (pad, pad, pad),
"mode": reconmodes[mode],
"verbose": True
})
if initmodel != None: recon.setup(initmodel, .01)
else: recon.setup()
scores = []
# First pass to assess qualities and normalizations
for i, p in enumerate(stack):
p2 = p.get_clip(
Region(-(pad - boxsize) / 2, -(pad - boxsize) / 2, pad, pad))
p2 = recon.preprocess_slice(p2, p["xform.projection"])
recon.insert_slice(p2, p["xform.projection"], 1.0)
print " %d \r" % i
print ""
# after building the model once we can assess how well everything agrees
for p in stack:
p2 = p.get_clip(
Region(-(pad - boxsize) / 2, -(pad - boxsize) / 2, pad, pad))
p2 = recon.preprocess_slice(p2, p["xform.projection"])
recon.determine_slice_agreement(p2, p["xform.projection"], 1.0,
True)
scores.append((p2["reconstruct_absqual"], p2["reconstruct_norm"]))
print " %d\t%1.3f \r" % (i, scores[-1][0])
print ""
# clear out the first reconstruction (probably no longer necessary)
# ret=recon.finish(True)
# ret=None
# setup for the second run
if initmodel != None: recon.setup(initmodel, .01)
else: recon.setup()
thr = 0.7 * (scores[len(scores) / 2][0] +
scores[len(scores) / 2 - 1][0] +
scores[len(scores) / 2 + 1][0]) / 3
# this is rather arbitrary
# First pass to assess qualities and normalizations
for i, p in enumerate(stack):
if scores[i][0] < thr:
print "%d. %1.3f *" % (i, scores[i][0])
continue
print "%d. %1.2f \t%1.3f\t%1.3f" % (
i, p["xform.projection"].get_rotation("eman")["alt"],
scores[i][0], scores[i][1])
p2 = p.get_clip(
Region(-(pad - boxsize) / 2, -(pad - boxsize) / 2, pad, pad))
p2 = recon.preprocess_slice(p2, p["xform.projection"])
p2.mult(scores[i][1])
recon.insert_slice(p2, p["xform.projection"], 1.0)
# plot(scores)
recon.set_param("savenorm", "norm.mrc")
ret = recon.finish(True)
ret = ret.get_clip(
Region((pad - boxsize) / 2, (pad - boxsize) / 2,
(pad - boxsize) / 2, boxsize, boxsize, boxsize))
# print "Quality: ",qual
return ret
def tilt_axis(self):
ntilt = self.imageparm["nz"]
sz = good_size(self.imageparm["nx"] / 2)
while 1:
av = None
n = 0
for i in range(ntilt):
refshape = self.tiltshapes[i].getShape()
if refshape[4] <= sz / 2 or refshape[
5] <= sz / 2 or self.imageparm["nx"] - refshape[
4] <= sz / 2 or self.imageparm["ny"] - refshape[
5] <= sz / 2:
break
img = EMData(
self.imagefile, 0, False,
Region(refshape[4] - sz / 2, refshape[5] - sz / 2, i, sz,
sz, 1))
if self.invert: img.mult(-1.0)
img.process_inplace("normalize.edgemean")
if av == None: av = img
else: av.add(img)
n += 1
if n == ntilt: break
sz /= 2
if sz < 32: return
print "You may wish to center on a feature closer to the center of the image next time -> ", sz
sz2 = good_size(sz + 128)
av2 = av.get_clip(Region((sz - sz2) / 2, (sz - sz2) / 2, sz2, sz2))
av2.process_inplace("mask.zeroedgefill")
av2.process_inplace("filter.flattenbackground", {"radius": 64})
av = av2.get_clip(Region((sz2 - sz) / 2, (sz2 - sz) / 2, sz, sz))
av.process_inplace("normalize.edgemean")
av.process_inplace("mask.sharp", {"outer_radius": sz / 2 - 1})
# display(av)
f = av.do_fft()
d = f.calc_az_dist(360, -90.25, 0.5, 10.0, sz / 2 - 1)
d = [(i, j * 0.5 - 90) for j, i in enumerate(d)]
self.btiltaxisval.setText(str(max(d)[1]))
# print max(d)
# print min(d)
# plot(d)
def projection_align(self, angstep=2.0):
"""realign the current set of boxes using iterative projection matching"""
taxis = float(self.btiltaxisval.text())
stack = self.get_boxed_stack()
for i, p in enumerate(stack):
ort = Transform({
"type": "eman",
"alt": (i - len(stack) / 2) * angstep,
"az": -taxis,
"phi": taxis
}) # is this right ?
curshape = self.tiltshapes[i].getShape()
# Read the reference at the user specified size, then pad it a bit
ref = self.map3d.project("standard", ort)
ref.process_inplace("filter.lowpass.gauss", {"cutoff_abs": .1})
ref.process_inplace("normalize.edgemean")
ref = ref.get_clip(
Region(-self.maxshift, -self.maxshift,
ref["nx"] + self.maxshift * 2,
ref["ny"] + self.maxshift * 2))
# when we read the alignment target, we pad with actual image data since the object will have moved
trg = EMData(
self.imagefile, 0, False,
Region(curshape[4] - self.maxshift,
curshape[5] - self.maxshift, i,
curshape[6] - curshape[4] + self.maxshift * 2,
curshape[7] - curshape[5] + self.maxshift * 2, 1))
trg.process_inplace("filter.lowpass.gauss", {"cutoff_abs": .1})
trg.process_inplace("normalize.edgemean")
if self.invert: trg.mult(-1.0)
aln = ref.align("translational", trg, {
"intonly": 1,
"maxshift": self.maxshift * 4 / 5
})
trans = aln["xform.align2d"].get_trans()
print i, trans[0], trans[1]
if i > len(stack) - 4: display([ref, trg, aln])
# if i==self.curtilt+3 : display((ref,trg,aln,ref.calc_ccf(trg)))
self.tiltshapes[i].translate(trans[0], trans[1])
def find_boxes(self, mainshape):
"""Starting with a user selected box at the current tilt, search for the same shape in the entire
tilt series"""
if self.imagefile == None: return
self.tiltshapes[self.curtilt] = mainshape
lref = None
for i in range(self.curtilt + 1, self.imageparm["nz"]):
refshape = self.tiltshapes[i - 1].getShape()
# Read the reference at the user specified size, then pad it a bit
ref = EMData(
self.imagefile, 0, False,
Region(refshape[4], refshape[5], i - 1,
refshape[6] - refshape[4], refshape[7] - refshape[5],
1))
ref.process_inplace("threshold.clampminmax.nsigma",
{"nsigma": 4.0})
ref.process_inplace("filter.lowpass.gauss", {"cutoff_abs": .1})
ref.process_inplace("normalize.edgemean")
ref = ref.get_clip(
Region(-self.maxshift, -self.maxshift,
ref["nx"] + self.maxshift * 2,
ref["ny"] + self.maxshift * 2))
if lref != None and self.seqali: ref.add(lref)
ref.process_inplace(
"normalize.edgemean") # older images contribute less
lref = ref
# when we read the alignment target, we pad with actual image data since the object will have moved
trg = EMData(
self.imagefile, 0, False,
Region(refshape[4] - self.maxshift,
refshape[5] - self.maxshift, i,
refshape[6] - refshape[4] + self.maxshift * 2,
refshape[7] - refshape[5] + self.maxshift * 2, 1))
trg.process_inplace("threshold.clampminmax.nsigma",
{"nsigma": 4.0})
trg.process_inplace("filter.lowpass.gauss", {"cutoff_abs": .1})
trg.process_inplace("normalize.edgemean")
aln = ref.align("translational", trg, {
"intonly": 1,
"maxshift": self.maxshift * 4 / 5,
"masked": 1
})
ref.write_image("dbug.hdf", -1)
trg.write_image("dbug.hdf", -1)
aln.write_image("dbug.hdf", -1)
trans = aln["xform.align2d"].get_trans()
# if i==self.curtilt+3 : display((ref,trg,aln,ref.calc_ccf(trg)))
self.tiltshapes[i] = EMShape([
"rectpoint", .7, .2, 0, refshape[4] + trans[0],
refshape[5] + trans[1], refshape[6] + trans[0],
refshape[7] + trans[1], 1
])
print i, trans[0], trans[1]
lref = None
for i in range(self.curtilt - 1, -1, -1):
refshape = self.tiltshapes[i + 1].getShape()
# Read the reference at the user specified size, then pad it a bit
ref = EMData(
self.imagefile, 0, False,
Region(refshape[4], refshape[5], i + 1,
refshape[6] - refshape[4], refshape[7] - refshape[5],
1))
ref.process_inplace("filter.lowpass.gauss", {"cutoff_abs": .1})
ref.process_inplace("normalize.edgemean")
ref = ref.get_clip(
Region(-self.maxshift, -self.maxshift,
ref["nx"] + self.maxshift * 2,
ref["ny"] + self.maxshift * 2))
if lref != None and self.seqali: ref.add(lref)
ref.process_inplace("normalize.edgemean")
lref = ref
# when we read the alignment target, we pad with actual image data since the object will have moved
trg = EMData(
self.imagefile, 0, False,
Region(refshape[4] - self.maxshift,
refshape[5] - self.maxshift, i,
refshape[6] - refshape[4] + self.maxshift * 2,
refshape[7] - refshape[5] + self.maxshift * 2, 1))
trg.process_inplace("filter.lowpass.gauss", {"cutoff_abs": .1})
trg.process_inplace("normalize.edgemean")
aln = ref.align("translational", trg, {
"intonly": 1,
"maxshift": self.maxshift * 4 / 5,
"masked": 1
})
trans = aln["xform.align2d"].get_trans()
if i == self.curtilt + 3:
display((ref, trg, aln, ref.calc_ccf(trg)))
self.tiltshapes[i] = EMShape([
"rectpoint", .7, .2, 0, refshape[4] + trans[0],
refshape[5] + trans[1], refshape[6] + trans[0],
refshape[7] + trans[1], 1
])
print i, trans[0], trans[1]
self.update_stack()
class EMItem3DInspector(QtGui.QTabWidget):
"""
Class to make the EMItem GUI controls
"""
def __init__(self, name, item3d):
QtGui.QTabWidget.__init__(self)
self.item3d = weakref.ref(item3d)
self.name = name
self.inspector = None
self.transfromboxmaxheight = 400 # This might be problematic
self.addTabs()
def setInspector(self, inspector):
""" This is a reference back to the main inspector, which holds all the item inspectors"""
self.inspector = weakref.ref(inspector)
def addTabs(self):
""" Add a tab for each 'column' """
tabwidget = QtGui.QWidget()
gridbox = QtGui.QGridLayout()
EMItem3DInspector.addControls(self, gridbox)
tabwidget.setLayout(gridbox)
self.addTab(tabwidget, "basic")
def addControls(self, gridbox):
""" Construct all the widgets in this Item Inspector """
# selection box and label
font = QtGui.QFont()
font.setBold(True)
label = QtGui.QLabel(self.name, self)
label.setFont(font)
label.setAlignment(QtCore.Qt.AlignCenter)
gridbox.addWidget(label, 0, 0, 1, 1)
databox = QtGui.QHBoxLayout()
self.boundingbox = None
if self.item3d().boundingboxsize:
self.boundingbox = QtGui.QLabel(
"Size: " + self.item3d().boundingboxsize, self)
databox.addWidget(self.boundingbox)
gridbox.addLayout(databox, 1, 0, 1, 1)
# angluar controls
xformframe = QtGui.QFrame()
xformframe.setFrameShape(QtGui.QFrame.StyledPanel)
xformbox = QtGui.QGridLayout()
xformlabel = QtGui.QLabel("Transformation", xformframe)
xformlabel.setFont(font)
xformlabel.setAlignment(QtCore.Qt.AlignCenter)
xformbox.addWidget(xformlabel, 0, 0, 1, 2)
# Rotations
self.rotcombobox = QtGui.QComboBox()
xformbox.addWidget(self.rotcombobox, 1, 0, 1, 2)
self.rotstackedwidget = QtGui.QStackedWidget()
self.addRotationWidgets()
xformbox.addWidget(self.rotstackedwidget, 2, 0, 1, 2)
#translations
txlabel = QtGui.QLabel("TX", xformframe)
txlabel.setAlignment(QtCore.Qt.AlignCenter)
xformbox.addWidget(txlabel, 3, 0, 1, 1)
tylabel = QtGui.QLabel("TY", xformframe)
tylabel.setAlignment(QtCore.Qt.AlignCenter)
xformbox.addWidget(tylabel, 3, 1, 1, 1)
self.tx = EMSpinWidget(0.0, 1.0)
self.ty = EMSpinWidget(0.0, 1.0)
xformbox.addWidget(self.tx, 4, 0, 1, 1)
xformbox.addWidget(self.ty, 4, 1, 1, 1)
tzlabel = QtGui.QLabel("TZ", xformframe)
tzlabel.setAlignment(QtCore.Qt.AlignCenter)
xformbox.addWidget(tzlabel, 5, 0, 1, 1)
zoomlabel = QtGui.QLabel("Zoom", xformframe)
zoomlabel.setAlignment(QtCore.Qt.AlignCenter)
xformbox.addWidget(zoomlabel, 5, 1, 1, 1)
self.tz = EMSpinWidget(0.0, 1.0)
self.zoom = EMSpinWidget(1.0, 0.1, postivemode=True, wheelstep=0.1)
xformbox.addWidget(self.tz, 6, 0, 1, 1)
xformbox.addWidget(self.zoom, 6, 1, 1, 1)
self.resetbuttontx = QtGui.QPushButton("Reset Tx")
self.resetbuttonrot = QtGui.QPushButton("Reset Rot")
xformbox.addWidget(self.resetbuttontx, 7, 0, 1, 1)
xformbox.addWidget(self.resetbuttonrot, 7, 1, 1, 1)
xformframe.setLayout(xformbox)
xformframe.setMaximumWidth(350)
xformframe.setMaximumHeight(self.transfromboxmaxheight)
xformframe.setLayout(xformbox)
gridbox.addWidget(xformframe, 2, 0, 1, 1)
# set to default, but run only as a base class
if type(self) == EMItem3DInspector: self.updateItemControls()
QtCore.QObject.connect(self.tx, QtCore.SIGNAL("valueChanged(int)"),
self._on_translation)
QtCore.QObject.connect(self.ty, QtCore.SIGNAL("valueChanged(int)"),
self._on_translation)
QtCore.QObject.connect(self.tz, QtCore.SIGNAL("valueChanged(int)"),
self._on_translation)
QtCore.QObject.connect(self.zoom, QtCore.SIGNAL("valueChanged(int)"),
self._on_scale)
QtCore.QObject.connect(self.resetbuttontx, QtCore.SIGNAL("clicked()"),
self._on_resettx)
QtCore.QObject.connect(self.resetbuttonrot, QtCore.SIGNAL("clicked()"),
self._on_resetrot)
def _on_translation(self, value):
"""
Need to contain the right coords. And do translation in the correct corrd system
"""
tt = t = Transform({
"tx": self.tx.getValue(),
"ty": self.ty.getValue(),
"tz": self.tz.getValue()
})
tp = self.item3d().getParentMatrixProduct()
if tp: tt = tp.inverse() * t
self.item3d().getTransform().set_trans(tt.get_trans())
self.inspector().updateSceneGraph()
def _on_scale(self, value):
self.item3d().getTransform().set_scale(self.zoom.getValue())
self.inspector().updateSceneGraph()
def _on_resettx(self):
self.item3d().getTransform().set_trans(0.0, 0.0, 0.0)
self.updateItemControls()
self.inspector().updateSceneGraph()
def _on_resetrot(self):
self.item3d().getTransform().set_rotation({
"type": "eman",
"az": 0.0,
"alt": 0.0,
"phi": 0.0
})
self.updateItemControls()
self.inspector().updateSceneGraph()
def _isRotNaN(self, rot1, rot2, rot3):
""" Better check to make sure get_rotation did not return Nan, so to prevent a crash """
if rot1 != rot1: return True
if rot2 != rot2: return True
if rot3 != rot3: return True
return False
def updateItemControls(self):
""" Updates this item inspector. Function is called by the item it observes"""
# Translation update
stdtransfrom = self.item3d().getTransformStdCoord()
translation = stdtransfrom.get_trans()
self.tx.setValue(translation[0])
self.ty.setValue(translation[1])
self.tz.setValue(translation[2])
# Rotation update
rotation = stdtransfrom.get_rotation(
str(self.rotcombobox.currentText()))
is_identity = stdtransfrom.is_rot_identity()
comboboxidx = self.rotcombobox.currentIndex()
if comboboxidx == 0:
if self._isRotNaN(rotation["az"], rotation["alt"],
rotation["phi"]):
return
self.emanazslider.setValue(rotation["az"], quiet=1)
self.emanaltslider.setValue(rotation["alt"], quiet=1)
self.emanphislider.setValue(rotation["phi"], quiet=1)
if comboboxidx == 1:
if self._isRotNaN(rotation["gamma"], rotation["beta"],
rotation["alpha"]):
return
self.imagicgammaslider.setValue(rotation["gamma"], quiet=1)
self.imagicbetaslider.setValue(rotation["beta"], quiet=1)
self.imagicalphaslider.setValue(rotation["alpha"], quiet=1)
if comboboxidx == 2:
if self._isRotNaN(rotation["psi"], rotation["theta"],
rotation["phi"]):
return
self.spiderpsislider.setValue(rotation["psi"], quiet=1)
self.spiderthetaslider.setValue(rotation["theta"], quiet=1)
self.spiderphislider.setValue(rotation["phi"], quiet=1)
if comboboxidx == 3:
if self._isRotNaN(rotation["phi"], rotation["theta"],
rotation["omega"]):
return
self.mrcpsislider.setValue(rotation["phi"], quiet=1)
self.mrcthetaslider.setValue(rotation["theta"], quiet=1)
self.mrcomegaslider.setValue(rotation["omega"], quiet=1)
if comboboxidx == 4:
if self._isRotNaN(rotation["ztilt"], rotation["ytilt"],
rotation["xtilt"]):
return
self.xyzzslider.setValue(rotation["ztilt"], quiet=1)
self.xyzyslider.setValue(rotation["ytilt"], quiet=1)
self.xyzxslider.setValue(rotation["xtilt"], quiet=1)
if comboboxidx == 5:
if self._isRotNaN(rotation["n1"], rotation["n2"], rotation["n3"]):
return
if is_identity and self.spinn1slider.getValue(
) == 0.0 and self.spinn2slider.getValue(
) == 0.0 and self.spinn3slider.getValue() == 0.0:
self.spinomegaslider.setValue(0.0, quiet=1)
self.spinn1slider.setValue(0.0, quiet=1)
self.spinn2slider.setValue(0.0, quiet=1)
self.spinn3slider.setValue(1.0, quiet=1)
else:
self.spinomegaslider.setValue(rotation["omega"], quiet=1)
# Don't change slider if reult is Nan
if rotation["n1"] == rotation["n1"]:
self.spinn1slider.setValue(rotation["n1"], quiet=1)
if rotation["n2"] == rotation["n2"]:
self.spinn2slider.setValue(rotation["n2"], quiet=1)
if rotation["n3"] == rotation["n3"]:
self.spinn3slider.setValue(rotation["n3"], quiet=1)
if comboboxidx == 6:
if self._isRotNaN(rotation["n1"], rotation["n2"], rotation["n3"]):
return
if is_identity and self.spinn1slider.getValue(
) == 0.0 and self.spinn2slider.getValue(
) == 0.0 and self.spinn3slider.getValue() == 0.0:
self.spinomegaslider.setValue(0.0, quiet=1)
self.sgirotn1slider.setValue(0.0, quiet=1)
self.sgirotn2slider.setValue(0.0, quiet=1)
self.sgirotn3slider.setValue(1.0, quiet=1)
else:
self.spinomegaslider.setValue(rotation["q"], quiet=1)
# Don't change slider if reult is Nan
if rotation["n1"] == rotation["n1"]:
self.sgirotn1slider.setValue(rotation["n1"], quiet=1)
if rotation["n2"] == rotation["n2"]:
self.sgirotn2slider.setValue(rotation["n2"], quiet=1)
if rotation["n3"] == rotation["n3"]:
self.sgirotn3slider.setValue(rotation["n3"], quiet=1)
if comboboxidx == 7:
if self._isRotNaN(rotation["e1"], rotation["e2"], rotation["e3"]):
return
if is_identity:
self.quaternione0slider.setValue(1.0, quiet=1)
self.quaternione1slider.setValue(0.0, quiet=1)
self.quaternione2slider.setValue(0.0, quiet=1)
self.quaternione3slider.setValue(0.0, quiet=1)
else:
self.quaternione0slider.setValue(rotation["e0"], quiet=1)
self.quaternione1slider.setValue(rotation["e1"], quiet=1)
self.quaternione2slider.setValue(rotation["e2"], quiet=1)
self.quaternione3slider.setValue(rotation["e3"], quiet=1)
# Scaling update
self.zoom.setValue(self.item3d().getTransform().get_scale())
def updateMetaData(self):
"""
I didn't want to put this in update b/c this data doesn't change very often, and I don't want to waste CPU
Its a judgement call really, less coupling vs. more efficiency
"""
if self.boundingbox:
self.boundingbox.setText("Size: " + self.item3d().boundingboxsize)
def addRotationWidgets(self):
""" Add alll the widgets for the various EMAN2 rotation conventions """
EMANwidget = QtGui.QWidget()
Imagicwidget = QtGui.QWidget()
Spiderwidget = QtGui.QWidget()
MRCwidget = QtGui.QWidget()
XYZwidget = QtGui.QWidget()
spinwidget = QtGui.QWidget()
sgirotwidget = QtGui.QWidget()
quaternionwidget = QtGui.QWidget()
# EMAN
emanbox = QtGui.QVBoxLayout()
self.emanazslider = ValSlider(EMANwidget, (0.0, 360.0),
" Az",
rounding=1)
self.emanaltslider = ValSlider(EMANwidget, (0.0, 180.0),
"Alt",
rounding=1)
self.emanphislider = ValSlider(EMANwidget, (0.0, 360.0),
"Phi",
rounding=1)
emanbox.addWidget(self.emanazslider)
emanbox.addWidget(self.emanaltslider)
emanbox.addWidget(self.emanphislider)
EMANwidget.setLayout(emanbox)
# Imagic
imagicbox = QtGui.QVBoxLayout()
self.imagicgammaslider = ValSlider(Imagicwidget, (0.0, 360.0),
"Gamma",
rounding=1)
self.imagicbetaslider = ValSlider(Imagicwidget, (0.0, 180.0),
" Beta",
rounding=1)
self.imagicalphaslider = ValSlider(Imagicwidget, (0.0, 360.0),
" Alpha",
rounding=1)
imagicbox.addWidget(self.imagicgammaslider)
imagicbox.addWidget(self.imagicbetaslider)
imagicbox.addWidget(self.imagicalphaslider)
Imagicwidget.setLayout(imagicbox)
# Spider
spiderbox = QtGui.QVBoxLayout()
self.spiderpsislider = ValSlider(Spiderwidget, (0.0, 360.0),
" Psi",
rounding=1)
self.spiderthetaslider = ValSlider(Spiderwidget, (0.0, 180.0),
"Theta",
rounding=1)
self.spiderphislider = ValSlider(Spiderwidget, (0.0, 360.0),
" Phi",
rounding=1)
spiderbox.addWidget(self.spiderpsislider)
spiderbox.addWidget(self.spiderthetaslider)
spiderbox.addWidget(self.spiderphislider)
Spiderwidget.setLayout(spiderbox)
# MRC
mrcbox = QtGui.QVBoxLayout()
self.mrcpsislider = ValSlider(MRCwidget, (0.0, 360.0),
" Psi",
rounding=1)
self.mrcthetaslider = ValSlider(MRCwidget, (0.0, 180.0),
" Theta",
rounding=1)
self.mrcomegaslider = ValSlider(MRCwidget, (0.0, 360.0),
"Omega",
rounding=1)
mrcbox.addWidget(self.mrcpsislider)
mrcbox.addWidget(self.mrcthetaslider)
mrcbox.addWidget(self.mrcomegaslider)
MRCwidget.setLayout(mrcbox)
# XYZ
xyzbox = QtGui.QVBoxLayout()
self.xyzzslider = ValSlider(XYZwidget, (0.0, 360.0), "Z", rounding=1)
self.xyzyslider = ValSlider(XYZwidget, (0.0, 180.0), "Y", rounding=1)
self.xyzxslider = ValSlider(XYZwidget, (0.0, 360.0), "X", rounding=1)
xyzbox.addWidget(self.xyzzslider)
xyzbox.addWidget(self.xyzyslider)
xyzbox.addWidget(self.xyzxslider)
XYZwidget.setLayout(xyzbox)
# spin
spinbox = QtGui.QVBoxLayout()
self.spinomegaslider = ValSlider(spinwidget, (0.0, 180.0),
"Omega",
rounding=1)
self.spinn1slider = ValSlider(spinwidget, (0.0, 1.0),
" N1",
rounding=4)
self.spinn2slider = ValSlider(spinwidget, (0.0, 1.0),
" N2",
rounding=4)
self.spinn3slider = ValSlider(spinwidget, (0.0, 1.0),
" N3",
rounding=4)
spinbox.addWidget(self.spinomegaslider)
spinbox.addWidget(self.spinn1slider)
spinbox.addWidget(self.spinn2slider)
spinbox.addWidget(self.spinn3slider)
spinwidget.setLayout(spinbox)
# sgirot
sgirotbox = QtGui.QVBoxLayout()
self.sgirotqslider = ValSlider(sgirotwidget, (0.0, 180.0),
" Q",
rounding=1)
self.sgirotn1slider = ValSlider(sgirotwidget, (0.0, 1.0),
"N1",
rounding=4)
self.sgirotn2slider = ValSlider(sgirotwidget, (0.0, 1.0),
"N2",
rounding=4)
self.sgirotn3slider = ValSlider(sgirotwidget, (0.0, 1.0),
"N3",
rounding=4)
sgirotbox.addWidget(self.sgirotqslider)
sgirotbox.addWidget(self.sgirotn1slider)
sgirotbox.addWidget(self.sgirotn2slider)
sgirotbox.addWidget(self.sgirotn3slider)
sgirotwidget.setLayout(sgirotbox)
# quaternion
quaternionbox = QtGui.QVBoxLayout()
self.quaternione0slider = ValSlider(quaternionwidget, (0.0, 1.0),
"E0",
rounding=4)
self.quaternione1slider = ValSlider(quaternionwidget, (0.0, 1.0),
"E1",
rounding=4)
self.quaternione2slider = ValSlider(quaternionwidget, (0.0, 1.0),
"E2",
rounding=4)
self.quaternione3slider = ValSlider(quaternionwidget, (0.0, 1.0),
"E3",
rounding=4)
quaternionbox.addWidget(self.quaternione0slider)
quaternionbox.addWidget(self.quaternione1slider)
quaternionbox.addWidget(self.quaternione2slider)
quaternionbox.addWidget(self.quaternione3slider)
quaternionwidget.setLayout(quaternionbox)
# Add widgets to the stack
self.rotstackedwidget.addWidget(EMANwidget)
self.rotstackedwidget.addWidget(Imagicwidget)
self.rotstackedwidget.addWidget(Spiderwidget)
self.rotstackedwidget.addWidget(MRCwidget)
self.rotstackedwidget.addWidget(XYZwidget)
self.rotstackedwidget.addWidget(spinwidget)
self.rotstackedwidget.addWidget(sgirotwidget)
self.rotstackedwidget.addWidget(quaternionwidget)
# add choices to combobox
self.rotcombobox.addItem("EMAN")
self.rotcombobox.addItem("Imagic")
self.rotcombobox.addItem("Spider")
self.rotcombobox.addItem("MRC")
self.rotcombobox.addItem("XYZ")
self.rotcombobox.addItem("spin")
self.rotcombobox.addItem("sgirot")
self.rotcombobox.addItem("quaternion")
# Signal for all sliders
QtCore.QObject.connect(self.rotcombobox,
QtCore.SIGNAL("activated(int)"),
self._rotcombobox_changed)
QtCore.QObject.connect(self.emanazslider,
QtCore.SIGNAL("valueChanged"),
self._on_EMAN_rotation)
QtCore.QObject.connect(self.emanaltslider,
QtCore.SIGNAL("valueChanged"),
self._on_EMAN_rotation)
QtCore.QObject.connect(self.emanphislider,
QtCore.SIGNAL("valueChanged"),
self._on_EMAN_rotation)
QtCore.QObject.connect(self.imagicgammaslider,
QtCore.SIGNAL("valueChanged"),
self._on_Imagic_rotation)
QtCore.QObject.connect(self.imagicbetaslider,
QtCore.SIGNAL("valueChanged"),
self._on_Imagic_rotation)
QtCore.QObject.connect(self.imagicalphaslider,
QtCore.SIGNAL("valueChanged"),
self._on_Imagic_rotation)
QtCore.QObject.connect(self.spiderpsislider,
QtCore.SIGNAL("valueChanged"),
self._on_Spider_rotation)
QtCore.QObject.connect(self.spiderthetaslider,
QtCore.SIGNAL("valueChanged"),
self._on_Spider_rotation)
QtCore.QObject.connect(self.spiderphislider,
QtCore.SIGNAL("valueChanged"),
self._on_Spider_rotation)
QtCore.QObject.connect(self.mrcpsislider,
QtCore.SIGNAL("valueChanged"),
self._on_MRC_rotation)
QtCore.QObject.connect(self.mrcthetaslider,
QtCore.SIGNAL("valueChanged"),
self._on_MRC_rotation)
QtCore.QObject.connect(self.mrcomegaslider,
QtCore.SIGNAL("valueChanged"),
self._on_MRC_rotation)
QtCore.QObject.connect(self.xyzzslider, QtCore.SIGNAL("valueChanged"),
self._on_XYZ_rotation)
QtCore.QObject.connect(self.xyzyslider, QtCore.SIGNAL("valueChanged"),
self._on_XYZ_rotation)
QtCore.QObject.connect(self.xyzxslider, QtCore.SIGNAL("valueChanged"),
self._on_XYZ_rotation)
QtCore.QObject.connect(self.spinomegaslider,
QtCore.SIGNAL("valueChanged"),
self._on_spin_rotation)
QtCore.QObject.connect(self.spinn1slider,
QtCore.SIGNAL("valueChanged"),
self._on_spin_rotation)
QtCore.QObject.connect(self.spinn2slider,
QtCore.SIGNAL("valueChanged"),
self._on_spin_rotation)
QtCore.QObject.connect(self.spinn3slider,
QtCore.SIGNAL("valueChanged"),
self._on_spin_rotation)
QtCore.QObject.connect(self.sgirotqslider,
QtCore.SIGNAL("valueChanged"),
self._on_sgirot_rotation)
QtCore.QObject.connect(self.sgirotn1slider,
QtCore.SIGNAL("valueChanged"),
self._on_sgirot_rotation)
QtCore.QObject.connect(self.sgirotn2slider,
QtCore.SIGNAL("valueChanged"),
self._on_sgirot_rotation)
QtCore.QObject.connect(self.sgirotn3slider,
QtCore.SIGNAL("valueChanged"),
self._on_sgirot_rotation)
QtCore.QObject.connect(self.quaternione0slider,
QtCore.SIGNAL("valueChanged"),
self._on_quaternion_rotation)
QtCore.QObject.connect(self.quaternione1slider,
QtCore.SIGNAL("valueChanged"),
self._on_quaternion_rotation)
QtCore.QObject.connect(self.quaternione2slider,
QtCore.SIGNAL("valueChanged"),
self._on_quaternion_rotation)
QtCore.QObject.connect(self.quaternione3slider,
QtCore.SIGNAL("valueChanged"),
self._on_quaternion_rotation)
def _rotcombobox_changed(self, idx):
self.rotstackedwidget.setCurrentIndex(idx)
self.updateItemControls()
def _on_EMAN_rotation(self, value):
self._set_rotation_std_coords(
Transform({
"type": "eman",
"az": self.emanazslider.getValue(),
"alt": self.emanaltslider.getValue(),
"phi": self.emanphislider.getValue()
}))
self.inspector().updateSceneGraph()
def _on_Imagic_rotation(self, value):
self._set_rotation_std_coords(
Transform({
"type": "imagic",
"gamma": self.imagicgammaslider.getValue(),
"beta": self.imagicbetaslider.getValue(),
"alpha": self.imagicalphaslider.getValue()
}))
self.inspector().updateSceneGraph()
def _on_Spider_rotation(self, value):
self._set_rotation_std_coords(
Transform({
"type": "spider",
"psi": self.spiderpsislider.getValue(),
"theta": self.spiderthetaslider.getValue(),
"phi": self.spiderphislider.getValue()
}))
self.inspector().updateSceneGraph()
def _on_MRC_rotation(self, value):
self._set_rotation_std_coords(
Transform({
"type": "mrc",
"phi": self.mrcpsislider.getValue(),
"theta": self.mrcthetaslider.getValue(),
"omega": self.mrcomegaslider.getValue()
}))
self.inspector().updateSceneGraph()
def _on_XYZ_rotation(self, value):
self._set_rotation_std_coords(
Transform({
"type": "xyz",
"ztilt": self.xyzzslider.getValue(),
"ytilt": self.xyzyslider.getValue(),
"xtilt": self.xyzxslider.getValue()
}))
self.inspector().updateSceneGraph()
def _on_spin_rotation(self, value):
v = Vec3f(self.spinn1slider.getValue(), self.spinn2slider.getValue(),
self.spinn3slider.getValue())
v.normalize()
self._set_rotation_std_coords(
Transform({
"type": "spin",
"omega": self.spinomegaslider.getValue(),
"n1": v[0],
"n2": v[1],
"n3": v[2]
}))
self.inspector().updateSceneGraph()
def _on_sgirot_rotation(self, value):
v = Vec3f(self.sgirotn1slider.getValue(),
self.sgirotn2slider.getValue(),
self.sgirotn3slider.getValue())
v.normalize()
self._set_rotation_std_coords(
Transform({
"type": "sgirot",
"q": self.sgirotqslider.getValue(),
"n1": v[0],
"n2": v[1],
"n3": v[2]
}))
self.inspector().updateSceneGraph()
def _on_quaternion_rotation(self, value):
v = Vec4f(self.quaternione0slider.getValue(),
self.quaternione1slider.getValue(),
self.quaternione2slider.getValue(),
self.quaternione3slider.getValue())
v.normalize()
self._set_rotation_std_coords(
Transform({
"type": "quaternion",
"e0": v[0],
"e1": v[1],
"e2": v[2],
"e3": v[3]
}))
self.inspector().updateSceneGraph()
def _set_rotation_std_coords(self, rotation):
""" This function sets the rotation as if there were no preceeding ones, otherwise a rot around Z could be arounf y,x, etc.
Works by transforming local coords into global corrds"""
tt = rotation
tp = self.item3d().getParentMatrixProduct()
if tp: tt = tp.inverse() * rotation
self.item3d().getTransform().set_rotation(tt.get_rotation())
class TrackerControl(QtGui.QWidget):
def __init__(self,app,maxshift,invert=False,seqali=False,tiltstep=2.0):
self.app=app
self.maxshift=maxshift
self.seqali=seqali
self.invert=invert
self.tiltstep=tiltstep
# the control panel
QtGui.QWidget.__init__(self,None)
self.gbl = QtGui.QGridLayout(self)
self.gbl.setMargin(0)
self.gbl.setSpacing(6)
self.gbl.setObjectName("hbl")
# action buttons
self.bcenalign=QtGui.QPushButton("Center Align")
self.bprojalign=QtGui.QPushButton("Proj. Realign")
self.btiltaxis=QtGui.QPushButton("Tilt Axis")
self.btiltaxisval=QtGui.QLineEdit("90.0")
self.bsavedata=QtGui.QPushButton("Save Data")
self.breconst=QtGui.QPushButton("3D Normal")
self.sbmode=QtGui.QSpinBox(self)
self.sbmode.setRange(0,2)
self.sbmode.setValue(0)
self.bmagict=QtGui.QPushButton("3D Tomofill")
self.bmagics=QtGui.QPushButton("3D Sph")
self.bmagicc=QtGui.QPushButton("3D Cyl")
self.vslpfilt=ValSlider(self,(0,.5),"Filter",0.5,50)
self.gbl.addWidget(self.bcenalign,0,0)
self.gbl.addWidget(self.bprojalign,0,1)
self.gbl.addWidget(self.btiltaxis,0,2)
self.gbl.addWidget(self.btiltaxisval,0,3)
# self.gbl.addWidget(self.bsavedata,0,3)
self.gbl.addWidget(self.breconst,1,0)
self.gbl.addWidget(self.sbmode,2,0,1,1)
self.gbl.addWidget(self.vslpfilt,3,0,1,4)
self.gbl.addWidget(self.bmagict,1,1)
self.gbl.addWidget(self.bmagics,1,2)
self.gbl.addWidget(self.bmagicc,1,3)
QtCore.QObject.connect(self.bcenalign,QtCore.SIGNAL("clicked(bool)"),self.do_cenalign)
QtCore.QObject.connect(self.bprojalign,QtCore.SIGNAL("clicked(bool)"),self.do_projalign)
QtCore.QObject.connect(self.btiltaxis,QtCore.SIGNAL("clicked(bool)"),self.do_tiltaxis)
QtCore.QObject.connect(self.bsavedata,QtCore.SIGNAL("clicked(bool)"),self.do_savedata)
QtCore.QObject.connect(self.breconst,QtCore.SIGNAL("clicked(bool)"),self.do_reconst)
QtCore.QObject.connect(self.bmagict,QtCore.SIGNAL("clicked(bool)"),self.do_magict)
QtCore.QObject.connect(self.bmagics,QtCore.SIGNAL("clicked(bool)"),self.do_magics)
QtCore.QObject.connect(self.bmagicc,QtCore.SIGNAL("clicked(bool)"),self.do_magicc)
QtCore.QObject.connect(self.vslpfilt,QtCore.SIGNAL("valueChanged"),self.do_filter)
# the single image display widget
self.im2d = EMImage2DWidget(application=app,winid="tomotrackbox.big")
self.imboxed = EMImage2DWidget(application=app,winid="tomotrackbox.small")
self.improj = EMImage2DWidget(application=app,winid="tomotrackbox.proj")
self.imslice = EMImage2DWidget(application=app,winid="tomotrackbox.3dslice")
self.imvol = EMImage3DModule(application=app,winid="tomotrackbox.3d")
# get some signals from the window.
QtCore.QObject.connect(self.im2d,QtCore.SIGNAL("mousedown"),self.down)
QtCore.QObject.connect(self.im2d,QtCore.SIGNAL("mousedrag"),self.drag)
QtCore.QObject.connect(self.im2d,QtCore.SIGNAL("mouseup"),self.up)
QtCore.QObject.connect(self.im2d,QtCore.SIGNAL("increment_list_data"),self.change_tilt)
self.imagefile=None
self.imageparm=None
self.tiltshapes=None
self.curtilt=0
self.oldtilt=self.curtilt
self.map3d=None
self.downloc=None
self.downadjloc=None
self.show()
self.im2d.show()
def closeEvent(self,event):
self.im2d.closeEvent(QtGui.QCloseEvent())
self.imboxed.closeEvent(QtGui.QCloseEvent())
self.improj.closeEvent(QtGui.QCloseEvent())
self.imslice.closeEvent(QtGui.QCloseEvent())
self.imvol.closeEvent(QtGui.QCloseEvent())
event.accept()
def do_cenalign(self,x=0):
"""In response to the center align button. Just a wrapper"""
self.cenalign_stack()
self.update_stack()
def do_projalign(self,x=0):
"""In response to the projection align button. Just a wrapper"""
self.projection_align(self.tiltstep)
self.update_stack()
# self.do_reconst()
def do_tiltaxis(self):
"""In response to the tilt axis button. Just a wrapper"""
self.tilt_axis()
def do_reconst(self,x=0):
"""In response to the normal reconstruction button. Just a wrapper"""
stack=self.get_boxed_stack()
mode=self.sbmode.value()
self.map3d=self.reconstruct(stack,self.tiltstep,mode)
self.update_3d()
def do_magict(self,x):
"""In response to tomographic filling reconstruction button. Just a wrapper"""
stack=self.get_boxed_stack()
# self.map3d=self.reconstruct_ca(stack[5:-4],0.5)
# init=self.reconstruct_ca(stack[5:-4],0.5)
mode=self.sbmode.value()
self.map3d=self.reconstruct_wedgefill(stack,self.tiltstep,mode)
self.update_3d()
def do_magics(self,x):
"""In response to the 3D Sph button. Just a wrapper"""
return
def do_magicc(self,x):
"""In response to the 3D cyl button. Just a wrapper"""
return
def do_filter(self,v):
"""In response to the filter ValSlider"""
if self.map3d==None : return
self.lpfilt=v
self.update_3d()
def do_savedata(self):
""
def update_3d(self):
if self.map3d==None : return
self.filt3d=self.map3d.process("filter.lowpass.gauss",{"cutoff_abs":self.vslpfilt.getValue()})
self.imvol.set_data(self.filt3d)
self.imvol.show()
self.imvol.updateGL()
sz=self.map3d["nx"]
xsum=self.filt3d.process("misc.directional_sum",{"axis":"x"})
xsum.set_size(sz,sz,1)
ysum=self.filt3d.process("misc.directional_sum",{"axis":"y"})
ysum.set_size(sz,sz,1)
zsum=self.filt3d.process("misc.directional_sum",{"axis":"z"})
zsum.set_size(sz,sz,1)
self.improj.set_data([zsum,ysum,xsum])
self.improj.show()
self.improj.updateGL()
self.imslice.set_data(self.filt3d)
self.imslice.show()
self.imslice.updateGL()
def update_stack(self):
stack=self.get_boxed_stack()
self.imboxed.set_data(stack)
self.imboxed.show()
self.imboxed.updateGL()
def set_image(self,fsp):
"""Takes an ali file to process"""
self.imageparm=EMData(fsp,0,True).get_attr_dict()
print "%d slices at %d x %d"%(self.imageparm["nz"],self.imageparm["nx"],self.imageparm["ny"])
self.imagefile=fsp
self.curtilt=self.imageparm["nz"]/2
self.tiltshapes=[None for i in range(self.imageparm["nz"])]
self.update_tilt()
def update_tilt(self):
if self.imagefile==None : return
self.curimg=EMData(self.imagefile,0,False,Region(0,0,self.curtilt,self.imageparm["nx"],self.imageparm["ny"],1))
if self.invert : self.curimg.mult(-1.0)
self.im2d.set_data(self.curimg)
s=EMShape(["scrlabel",.7,.3,0,20.0,20.0,"%d"%self.curtilt,200.0,1])
self.im2d.add_shape("tilt",s)
if self.tiltshapes[self.curtilt]!=None :
self.im2d.add_shape("finalbox",self.tiltshapes[self.curtilt])
s0=self.tiltshapes[self.oldtilt].getShape()
s1=self.tiltshapes[self.curtilt].getShape()
dx=s0[4]-s1[4]
dy=s0[5]-s1[5]
self.im2d.set_origin(self.im2d.origin[0]-dx,self.im2d.origin[1]-dy)
self.oldtilt=self.curtilt
self.im2d.updateGL()
def change_tilt(self,direc):
"""When the user presses the up or down arrow"""
self.oldtilt=self.curtilt
self.curtilt+=direc
if self.curtilt<0 : self.curtilt=0
if self.curtilt>=self.imageparm["nz"] : self.curtilt=self.imageparm["nz"]-1
self.update_tilt()
def down(self,event,lc):
"""The event contains the x,y coordinates in window space, lc are the coordinates in image space"""
if event.buttons()&Qt.LeftButton:
if event.modifiers()&Qt.ShiftModifier :
self.downadjloc=(lc,self.tiltshapes[self.curtilt].getShape()[4:8])
else :
self.downloc=lc
def drag(self,event,lc):
if self.downloc!=None:
dx=abs(lc[0]-self.downloc[0])
dy=abs(lc[1]-self.downloc[1])
dx=max(dx,dy) # Make box square
dx=good_size(dx*2)/2 # use only good sizes
dy=dx
s=EMShape(["rectpoint",0,.7,0,self.downloc[0]-dx,self.downloc[1]-dy,self.downloc[0]+dx,self.downloc[1]+dy,1])
self.im2d.add_shape("box",s)
s=EMShape(["scrlabel",.7,.7,0,20.0,20.0,"%d (%d x %d)"%(self.curtilt,dx*2,dy*2),200.0,1])
self.im2d.add_shape("tilt",s)
elif self.downadjloc!=None:
dx=(lc[0]-self.downadjloc[0][0])
dy=(lc[1]-self.downadjloc[0][1])
s=self.tiltshapes[self.curtilt].getShape()[:]
s[4]=self.downadjloc[1][0]+dx
s[5]=self.downadjloc[1][1]+dy
s[6]=self.downadjloc[1][2]+dx
s[7]=self.downadjloc[1][3]+dy
self.im2d.add_shape("box",EMShape(s))
self.im2d.updateGL()
def up(self,event,lc):
if self.downloc!=None :
dx=abs(lc[0]-self.downloc[0])
dy=abs(lc[1]-self.downloc[1])
dx=max(dx,dy) # Make box square
dx=good_size(dx*2)/2 # use only good sizes
dy=dx
s=EMShape(["rectpoint",.7,.2,0,self.downloc[0]-dx,self.downloc[1]-dy,self.downloc[0]+dx,self.downloc[1]+dy,1])
self.im2d.del_shape("box")
if hypot(lc[0]-self.downloc[0],lc[1]-self.downloc[1])>5 :
self.tiltshapes=[None for i in range(self.imageparm["nz"])]
self.find_boxes(s)
self.update_tilt()
self.downloc=None
elif self.downadjloc!=None :
dx=(lc[0]-self.downadjloc[0][0])
dy=(lc[1]-self.downadjloc[0][1])
s=self.tiltshapes[self.curtilt].getShape()[:]
s[4]=self.downadjloc[1][0]+dx
s[5]=self.downadjloc[1][1]+dy
s[6]=self.downadjloc[1][2]+dx
s[7]=self.downadjloc[1][3]+dy
self.tiltshapes[self.curtilt]=EMShape(s)
self.im2d.add_shape("finalbox",self.tiltshapes[self.curtilt])
self.im2d.del_shape("box")
self.update_tilt()
self.update_stack()
self.downadjloc=None
def get_boxed_stack(self):
stack=[]
for i in range(self.imageparm["nz"]):
refshape=self.tiltshapes[i].getShape()
img=EMData(self.imagefile,0,False,Region(refshape[4],refshape[5],i,refshape[6]-refshape[4],refshape[7]-refshape[5],1))
img["ptcl_source_coord"]=(int((refshape[6]+refshape[4])/2.0),int((refshape[7]+refshape[5])/2.0),i)
img["ptcl_source_image"]=str(self.imagefile)
if self.invert : img.mult(-1.0)
img.process_inplace("normalize.edgemean")
stack.append(img)
return stack
def cenalign_stack(self):
"""This will perform an iterative centering process on a stack of particle images, centering each on the average.
It will modify the current stack of boxing parameters in-place"""
for it in range(5):
stack=self.get_boxed_stack()
# Average the stack, and center it
av=stack[0].copy()
for im in stack[1:]:
av.add(im)
av.process_inplace("filter.lowpass.gauss",{"cutoff_abs":.1})
av.process_inplace("filter.highpass.gauss",{"cutoff_abs":.02})
av.process_inplace("xform.centeracf")
#display((av,av2))
# align to the average
for i,im in enumerate(stack):
im.process_inplace("filter.lowpass.gauss",{"cutoff_abs":.1})
im.process_inplace("filter.highpass.gauss",{"cutoff_abs":.02})
ali=im.align("translational",av)
trans=ali["xform.align2d"].get_trans()
shape=self.tiltshapes[i]
shape.translate(-trans[0],-trans[1])
# Update the stack display
stack=self.get_boxed_stack()
self.imboxed.set_data(stack)
def reconstruct_wedgefill(self,stack,angstep,mode=2):
"""Fills the missing wedge with the average of the slices"""
print "Making 3D tomofill"
taxis=float(self.btiltaxisval.text())
boxsize=stack[0]["nx"]
pad=Util.calc_best_fft_size(int(boxsize*1.5))
# average all of the slices together
av=stack[0].copy()
for p in stack[1:]: av+=p
av.del_attr("xform.projection")
av.mult(1.0/(len(stack)))
av=av.get_clip(Region(-(pad-boxsize)/2,-(pad-boxsize)/2,pad,pad))
for i,p in enumerate(stack) :
p["alt"]=(i-len(stack)/2)*angstep
# Determine a good angular step for filling Fourier space
fullsamp=360.0/(boxsize*pi)
if angstep/fullsamp>2.0 :
samp=1.0/(floor(angstep/fullsamp))
else :
samp=angstep
print "Subsampling = %1.2f"%samp
# Now the reconstruction
recon=Reconstructors.get("fourier", {"sym":"c1","size":(pad,pad,pad),"mode":reconmodes[mode],"verbose":True})
recon.setup()
for ri in range(5):
print "Iteration ",ri
for a in [i*samp for i in range(-int(90.0/samp),int(90.0/samp)+1)]:
for ii in range(len(stack)-1):
if stack[ii]["alt"]<=a and stack[ii+1]["alt"]>a : break
else: ii=-1
if a<stack[0]["alt"] :
p=av
#frac=0.5*(a-stack[0]["alt"])/(-90.0-stack[0]["alt"])
## a bit wierd. At the ends (missing wedge) we use the average over all tilts. This could be improved
#p=stack[0].get_clip(Region(-(pad-boxsize)/2,-(pad-boxsize)/2,pad,pad))*(1.0-frac)+stack[-1].get_clip(Region(-(pad-boxsize)/2,-(pad-boxsize)/2,pad,pad))*frac
# print a," avg ",frac,stack[0]["alt"]
elif ii==-1 :
p=av
#frac=0.5*(a-stack[-1]["alt"])/(90.0-stack[-1]["alt"])+.5
## a bit wierd. At the ends (missing wedge) we use the average over all tilts. This could be improved
#p=stack[-1].get_clip(Region(-(pad-boxsize)/2,-(pad-boxsize)/2,pad,pad))*(1.0-frac)+stack[0].get_clip(Region(-(pad-boxsize)/2,-(pad-boxsize)/2,pad,pad))*frac
# print a," avg ",frac
else:
# We average slices in real space, producing a rotational 'smearing' effect
frac=(a-stack[ii]["alt"])/angstep
p=stack[ii].get_clip(Region(-(pad-boxsize)/2,-(pad-boxsize)/2,pad,pad))*(1.0-frac)+stack[ii+1].get_clip(Region(-(pad-boxsize)/2,-(pad-boxsize)/2,pad,pad))*frac
# print a,ii,ii+1,stack[ii]["alt"],frac
xf=Transform({"type":"eman","alt":a,"az":-taxis,"phi":taxis})
p["xform.projection"]=xf
if ri%2==1:
recon.determine_slice_agreement(p,xf,1)
else :
recon.insert_slice(p,xf)
ret=recon.finish()
print "Done"
ret=ret.get_clip(Region((pad-boxsize)/2,(pad-boxsize)/2,(pad-boxsize)/2,boxsize,boxsize,boxsize))
ret.process_inplace("normalize.edgemean")
# ret=ret.get_clip(Region((pad-boxsize)/2,(pad-boxsize)/2,(pad-boxsize)/2,boxsize,boxsize,boxsize))
return ret
def reconstruct_ca(self,stack,angstep,mode=2):
"""Cylindrically averaged tomographic model, generally used for filling empty spaces. Returned volume is padded."""
print "Making CA"
taxis=float(self.btiltaxisval.text())
boxsize=stack[0]["nx"]
pad=Util.calc_best_fft_size(int(boxsize*1.5))
# average all of the slices together
av=stack[0].copy()
for p in stack[1:]: av+=p
av.del_attr("xform.projection")
p.mult(1.0/len(stack))
av=av.get_clip(Region(-(pad-boxsize)/2,-(pad-boxsize)/2,pad,pad))
recon=Reconstructors.get("fourier", {"quiet":True,"sym":"c1","x_in":pad,"y_in":pad})
recon.setup()
for ri in range(3):
if ri>0 :
alt=-180.0
while (alt<180.0):
recon.determine_slice_agreement(av,Transform({"type":"eman","alt":alt,"az":-taxis,"phi":taxis}),1)
alt+=angstep
alt=-180.0
while (alt<180.0) :
recon.insert_slice(av,Transform({"type":"eman","alt":alt,"az":-taxis,"phi":taxis}))
alt+=angstep
ret=recon.finish()
ret.process_inplace("normalize.edgemean")
# ret=ret.get_clip(Region((pad-boxsize)/2,(pad-boxsize)/2,(pad-boxsize)/2,boxsize,boxsize,boxsize))
return ret
def reconstruct(self,stack,angstep,mode=0,initmodel=None):
""" Tomographic reconstruction of the current stack """
if initmodel!=None : print "Using initial model"
taxis=float(self.btiltaxisval.text())
boxsize=stack[0]["nx"]
pad=good_size(int(boxsize*1.5))
for i,p in enumerate(stack) : p["xform.projection"]=Transform({"type":"eman","alt":(i-len(stack)/2)*angstep,"az":-taxis,"phi":taxis})
recon=Reconstructors.get("fourier", {"sym":"c1","size":(pad,pad,pad),"mode":reconmodes[mode],"verbose":True})
if initmodel!=None : recon.setup(initmodel,.01)
else : recon.setup()
scores=[]
# First pass to assess qualities and normalizations
for i,p in enumerate(stack):
p2=p.get_clip(Region(-(pad-boxsize)/2,-(pad-boxsize)/2,pad,pad))
p2=recon.preprocess_slice(p2,p["xform.projection"])
recon.insert_slice(p2,p["xform.projection"],1.0)
print " %d \r"%i
print ""
# after building the model once we can assess how well everything agrees
for p in stack:
p2=p.get_clip(Region(-(pad-boxsize)/2,-(pad-boxsize)/2,pad,pad))
p2=recon.preprocess_slice(p2,p["xform.projection"])
recon.determine_slice_agreement(p2,p["xform.projection"],1.0,True)
scores.append((p2["reconstruct_absqual"],p2["reconstruct_norm"]))
print " %d\t%1.3f \r"%(i,scores[-1][0])
print ""
# clear out the first reconstruction (probably no longer necessary)
# ret=recon.finish(True)
# ret=None
# setup for the second run
if initmodel!=None : recon.setup(initmodel,.01)
else : recon.setup()
thr=0.7*(scores[len(scores)/2][0]+scores[len(scores)/2-1][0]+scores[len(scores)/2+1][0])/3; # this is rather arbitrary
# First pass to assess qualities and normalizations
for i,p in enumerate(stack):
if scores[i][0]<thr :
print "%d. %1.3f *"%(i,scores[i][0])
continue
print "%d. %1.2f \t%1.3f\t%1.3f"%(i,p["xform.projection"].get_rotation("eman")["alt"],scores[i][0],scores[i][1])
p2=p.get_clip(Region(-(pad-boxsize)/2,-(pad-boxsize)/2,pad,pad))
p2=recon.preprocess_slice(p2,p["xform.projection"])
p2.mult(scores[i][1])
recon.insert_slice(p2,p["xform.projection"],1.0)
# plot(scores)
recon.set_param("savenorm","norm.mrc")
ret=recon.finish(True)
ret=ret.get_clip(Region((pad-boxsize)/2,(pad-boxsize)/2,(pad-boxsize)/2,boxsize,boxsize,boxsize))
# print "Quality: ",qual
return ret
def tilt_axis(self):
ntilt=self.imageparm["nz"]
sz=good_size(self.imageparm["nx"]/2)
while 1:
av=None
n=0
for i in range(ntilt):
refshape=self.tiltshapes[i].getShape()
if refshape[4]<=sz/2 or refshape[5]<=sz/2 or self.imageparm["nx"]-refshape[4]<=sz/2 or self.imageparm["ny"]-refshape[5]<=sz/2 : break
img=EMData(self.imagefile,0,False,Region(refshape[4]-sz/2,refshape[5]-sz/2,i,sz,sz,1))
if self.invert : img.mult(-1.0)
img.process_inplace("normalize.edgemean")
if av==None: av=img
else : av.add(img)
n+=1
if n==ntilt : break
sz/=2
if sz<32: return
print "You may wish to center on a feature closer to the center of the image next time -> ",sz
sz2=good_size(sz+128)
av2=av.get_clip(Region((sz-sz2)/2,(sz-sz2)/2,sz2,sz2))
av2.process_inplace("mask.zeroedgefill")
av2.process_inplace("filter.flattenbackground",{"radius":64})
av=av2.get_clip(Region((sz2-sz)/2,(sz2-sz)/2,sz,sz))
av.process_inplace("normalize.edgemean")
av.process_inplace("mask.sharp",{"outer_radius":sz/2-1})
# display(av)
f=av.do_fft()
d=f.calc_az_dist(360,-90.25,0.5,10.0,sz/2-1)
d=[(i,j*0.5-90) for j,i in enumerate(d)]
self.btiltaxisval.setText(str(max(d)[1]))
# print max(d)
# print min(d)
# plot(d)
def projection_align(self,angstep=2.0):
"""realign the current set of boxes using iterative projection matching"""
taxis=float(self.btiltaxisval.text())
stack=self.get_boxed_stack()
for i,p in enumerate(stack) :
ort=Transform({"type":"eman","alt":(i-len(stack)/2)*angstep,"az":-taxis,"phi":taxis}) # is this right ?
curshape=self.tiltshapes[i].getShape()
# Read the reference at the user specified size, then pad it a bit
ref=self.map3d.project("standard",ort)
ref.process_inplace("filter.lowpass.gauss",{"cutoff_abs":.1})
ref.process_inplace("normalize.edgemean")
ref=ref.get_clip(Region(-self.maxshift,-self.maxshift,ref["nx"]+self.maxshift*2,ref["ny"]+self.maxshift*2))
# when we read the alignment target, we pad with actual image data since the object will have moved
trg=EMData(self.imagefile,0,False,Region(curshape[4]-self.maxshift,curshape[5]-self.maxshift,i,curshape[6]-curshape[4]+self.maxshift*2,curshape[7]-curshape[5]+self.maxshift*2,1))
trg.process_inplace("filter.lowpass.gauss",{"cutoff_abs":.1})
trg.process_inplace("normalize.edgemean")
if self.invert : trg.mult(-1.0)
aln=ref.align("translational",trg,{"intonly":1,"maxshift":self.maxshift*4/5})
trans=aln["xform.align2d"].get_trans()
print i,trans[0],trans[1]
if i>len(stack)-4 : display([ref,trg,aln])
# if i==self.curtilt+3 : display((ref,trg,aln,ref.calc_ccf(trg)))
self.tiltshapes[i].translate(trans[0],trans[1])
def find_boxes(self,mainshape):
"""Starting with a user selected box at the current tilt, search for the same shape in the entire
tilt series"""
if self.imagefile==None: return
self.tiltshapes[self.curtilt]=mainshape
lref=None
for i in range(self.curtilt+1,self.imageparm["nz"]):
refshape=self.tiltshapes[i-1].getShape()
# Read the reference at the user specified size, then pad it a bit
ref=EMData(self.imagefile,0,False,Region(refshape[4],refshape[5],i-1,refshape[6]-refshape[4],refshape[7]-refshape[5],1))
ref.process_inplace("threshold.clampminmax.nsigma",{"nsigma":4.0})
ref.process_inplace("filter.lowpass.gauss",{"cutoff_abs":.1})
ref.process_inplace("normalize.edgemean")
ref=ref.get_clip(Region(-self.maxshift,-self.maxshift,ref["nx"]+self.maxshift*2,ref["ny"]+self.maxshift*2))
if lref!=None and self.seqali : ref.add(lref)
ref.process_inplace("normalize.edgemean") # older images contribute less
lref=ref
# when we read the alignment target, we pad with actual image data since the object will have moved
trg=EMData(self.imagefile,0,False,Region(refshape[4]-self.maxshift,refshape[5]-self.maxshift,i,refshape[6]-refshape[4]+self.maxshift*2,refshape[7]-refshape[5]+self.maxshift*2,1))
trg.process_inplace("threshold.clampminmax.nsigma",{"nsigma":4.0})
trg.process_inplace("filter.lowpass.gauss",{"cutoff_abs":.1})
trg.process_inplace("normalize.edgemean")
aln=ref.align("translational",trg,{"intonly":1,"maxshift":self.maxshift*4/5,"masked":1})
ref.write_image("dbug.hdf",-1)
trg.write_image("dbug.hdf",-1)
aln.write_image("dbug.hdf",-1)
trans=aln["xform.align2d"].get_trans()
# if i==self.curtilt+3 : display((ref,trg,aln,ref.calc_ccf(trg)))
self.tiltshapes[i]=EMShape(["rectpoint",.7,.2,0,refshape[4]+trans[0],refshape[5]+trans[1],refshape[6]+trans[0],refshape[7]+trans[1],1])
print i,trans[0],trans[1]
lref=None
for i in range(self.curtilt-1,-1,-1):
refshape=self.tiltshapes[i+1].getShape()
# Read the reference at the user specified size, then pad it a bit
ref=EMData(self.imagefile,0,False,Region(refshape[4],refshape[5],i+1,refshape[6]-refshape[4],refshape[7]-refshape[5],1))
ref.process_inplace("filter.lowpass.gauss",{"cutoff_abs":.1})
ref.process_inplace("normalize.edgemean")
ref=ref.get_clip(Region(-self.maxshift,-self.maxshift,ref["nx"]+self.maxshift*2,ref["ny"]+self.maxshift*2))
if lref!=None and self.seqali : ref.add(lref)
ref.process_inplace("normalize.edgemean")
lref=ref
# when we read the alignment target, we pad with actual image data since the object will have moved
trg=EMData(self.imagefile,0,False,Region(refshape[4]-self.maxshift,refshape[5]-self.maxshift,i,refshape[6]-refshape[4]+self.maxshift*2,refshape[7]-refshape[5]+self.maxshift*2,1))
trg.process_inplace("filter.lowpass.gauss",{"cutoff_abs":.1})
trg.process_inplace("normalize.edgemean")
aln=ref.align("translational",trg,{"intonly":1,"maxshift":self.maxshift*4/5,"masked":1})
trans=aln["xform.align2d"].get_trans()
if i==self.curtilt+3 : display((ref,trg,aln,ref.calc_ccf(trg)))
self.tiltshapes[i]=EMShape(["rectpoint",.7,.2,0,refshape[4]+trans[0],refshape[5]+trans[1],refshape[6]+trans[0],refshape[7]+trans[1],1])
print i,trans[0],trans[1]
self.update_stack()
class EMTransformPanel:
def __init__(self,target,parent):
self.target = weakref.ref(target)
self.parent = weakref.ref(parent)
self.label_src = QtGui.QLabel(parent)
self.label_src.setText('Rotation Convention')
self.src = QtGui.QComboBox(parent)
self.load_src_options(self.src)
self.x_label = QtGui.QLabel()
self.x_label.setText('x')
self.x_trans = QtGui.QDoubleSpinBox(parent)
self.x_trans.setMinimum(-10000)
self.x_trans.setMaximum(10000)
self.x_trans.setValue(0.0)
self.y_label = QtGui.QLabel()
self.y_label.setText('y')
self.y_trans = QtGui.QDoubleSpinBox(parent)
self.y_trans.setMinimum(-10000)
self.y_trans.setMaximum(10000)
self.y_trans.setValue(0.0)
self.z_label = QtGui.QLabel()
self.z_label.setText('z')
self.z_trans = QtGui.QDoubleSpinBox(parent)
self.z_trans.setMinimum(-10000)
self.z_trans.setMaximum(10000)
self.z_trans.setValue(0.0)
self.az = ValSlider(parent,(-360.0,360.0),"az",-1)
self.az.setObjectName("az")
self.az.setValue(0.0)
self.alt = ValSlider(parent,(-180.0,180.0),"alt",-1)
self.alt.setObjectName("alt")
self.alt.setValue(0.0)
self.phi = ValSlider(parent,(-360.0,360.0),"phi",-1)
self.phi.setObjectName("phi")
self.phi.setValue(0.0)
self.scale = ValSlider(parent,(0.01,30.0),"Zoom:")
self.scale.setObjectName("scale")
self.scale.setValue(1.0)
self.n3_showing = False
self.current_src = "eman"
QtCore.QObject.connect(self.az, QtCore.SIGNAL("valueChanged"), self.slider_rotate)
QtCore.QObject.connect(self.alt, QtCore.SIGNAL("valueChanged"), self.slider_rotate)
QtCore.QObject.connect(self.phi, QtCore.SIGNAL("valueChanged"), self.slider_rotate)
QtCore.QObject.connect(self.src, QtCore.SIGNAL("currentIndexChanged(QString)"), self.set_src)
QtCore.QObject.connect(self.scale, QtCore.SIGNAL("valueChanged"), self.target().set_scale)
QtCore.QObject.connect(self.x_trans, QtCore.SIGNAL("valueChanged(double)"), self.target().set_cam_x)
QtCore.QObject.connect(self.y_trans, QtCore.SIGNAL("valueChanged(double)"), self.target().set_cam_y)
QtCore.QObject.connect(self.z_trans, QtCore.SIGNAL("valueChanged(double)"), self.target().set_cam_z)
def set_defaults(self):
self.x_trans.setValue(0.0)
self.y_trans.setValue(0.0)
self.z_trans.setValue(0.0)
self.scale.setValue(1.0)
self.az.setValue(0.0)
self.alt.setValue(0.0)
self.phi.setValue(0.0)
def slider_rotate(self):
self.target().load_rotation(self.get_current_rotation())
def get_current_rotation(self):
convention = self.src.currentText()
rot = {}
if ( self.current_src == "spin" ):
rot[self.az.getLabel()] = self.az.getValue()
n1 = self.alt.getValue()
n2 = self.phi.getValue()
n3 = self.n3.getValue()
norm = sqrt(n1*n1 + n2*n2 + n3*n3)
n1 /= norm
n2 /= norm
n3 /= norm
rot[self.alt.getLabel()] = n1
rot[self.phi.getLabel()] = n2
rot[self.n3.getLabel()] = n3
else:
rot[self.az.getLabel()] = self.az.getValue()
rot[self.alt.getLabel()] = self.alt.getValue()
rot[self.phi.getLabel()] = self.phi.getValue()
rot["type"] = self.current_src
return Transform(rot)
def addWidgets(self,target):
target.addWidget(self.scale)
self.hbl_trans = QtGui.QHBoxLayout()
self.hbl_trans.setMargin(0)
self.hbl_trans.setSpacing(6)
self.hbl_trans.setObjectName("Trans")
self.hbl_trans.addWidget(self.x_label)
self.hbl_trans.addWidget(self.x_trans)
self.hbl_trans.addWidget(self.y_label)
self.hbl_trans.addWidget(self.y_trans)
self.hbl_trans.addWidget(self.z_label)
self.hbl_trans.addWidget(self.z_trans)
target.addLayout(self.hbl_trans)
self.hbl_src = QtGui.QHBoxLayout()
self.hbl_src.setMargin(0)
self.hbl_src.setSpacing(6)
self.hbl_src.setObjectName("hbl")
self.hbl_src.addWidget(self.label_src)
self.hbl_src.addWidget(self.src)
target.addLayout(self.hbl_src)
target.addWidget(self.az)
target.addWidget(self.alt)
target.addWidget(self.phi)
def set_src(self, val):
t3d = self.get_current_rotation()
if (self.n3_showing) :
self.parent().get_transform_layout().removeWidget(self.n3)
self.n3.deleteLater()
self.n3_showing = False
self.az.setRange(-360,360)
self.alt.setRange(-180,180)
self.phi.setRange(-360,660)
if ( self.src_map[str(val)] == "spider" ):
self.az.setLabel('phi')
self.alt.setLabel('theta')
self.phi.setLabel('psi')
elif ( self.src_map[str(val)] == "eman" ):
self.az.setLabel('az')
self.alt.setLabel('alt')
self.phi.setLabel('phi')
elif ( self.src_map[str(val)] == "imagic"):
self.az.setLabel('alpha')
self.alt.setLabel('beta')
self.phi.setLabel('gamma')
elif ( self.src_map[str(val)] == "xyz"):
self.az.setLabel('xtilt')
self.alt.setLabel('ytilt')
self.phi.setLabel('ztilt')
elif ( self.src_map[str(val)] == "mrc" ):
self.az.setLabel('phi')
self.alt.setLabel('theta')
self.phi.setLabel('omega')
elif ( self.src_map[str(val)] == "spin" ):
self.az.setLabel('Omega')
self.alt.setRange(-1,1)
self.phi.setRange(-1,1)
self.alt.setLabel('n1')
self.phi.setLabel('n2')
self.n3 = ValSlider(self.parent(),(-360.0,360.0),"n3",-1)
self.n3.setRange(-1,1)
self.n3.setObjectName("n3")
self.parent().get_transform_layout().addWidget(self.n3)
QtCore.QObject.connect(self.n3, QtCore.SIGNAL("valueChanged"), self.slider_rotate)
self.n3_showing = True
self.current_src = self.src_map[str(val)]
self.update_rotations(t3d)
def load_src_options(self,widgit):
self.load_src()
for i in self.src_strings:
widgit.addItem(i)
def load_src(self):
# supported_rot_conventions
src_flags = []
src_flags.append("eman")
src_flags.append("spider")
src_flags.append("imagic")
src_flags.append("mrc")
src_flags.append("spin")
src_flags.append("xyz")
self.src_strings = []
self.src_map = {}
for i in src_flags:
self.src_strings.append(str(i))
self.src_map[str(i)] = i
def update_rotations(self,t3d):
rot = t3d.get_rotation(self.src_map[str(self.src.itemText(self.src.currentIndex()))])
convention = self.src.currentText()
if ( self.src_map[str(convention)] == "spin" ):
self.n3.setValue(rot[self.n3.getLabel()],True)
self.az.setValue(rot[self.az.getLabel()],True)
self.alt.setValue(rot[self.alt.getLabel()],True)
self.phi.setValue(rot[self.phi.getLabel()],True)
def set_scale(self,newscale):
self.scale.setValue(newscale)
def set_xy_trans(self, x, y):
self.x_trans.setValue(x)
self.y_trans.setValue(y)
def set_xyz_trans(self, x, y,z):
self.x_trans.setValue(x)
self.y_trans.setValue(y)
self.z_trans.setValue(z)
class EMItem3DInspector(QtGui.QTabWidget):
"""
Class to make the EMItem GUI controls
"""
def __init__(self, name, item3d):
QtGui.QTabWidget.__init__(self)
self.item3d = weakref.ref(item3d)
self.name = name
self.inspector = None
self.transfromboxmaxheight = 400 # This might be problematic
self.addTabs()
def setInspector(self, inspector):
""" This is a reference back to the main inspector, which holds all the item inspectors"""
self.inspector = weakref.ref(inspector)
def addTabs(self):
""" Add a tab for each 'column' """
tabwidget = QtGui.QWidget()
gridbox = QtGui.QGridLayout()
EMItem3DInspector.addControls(self, gridbox)
tabwidget.setLayout(gridbox)
self.addTab(tabwidget, "basic")
def addControls(self, gridbox):
""" Construct all the widgets in this Item Inspector """
# selection box and label
font = QtGui.QFont()
font.setBold(True)
label = QtGui.QLabel(self.name,self)
label.setFont(font)
label.setAlignment(QtCore.Qt.AlignCenter)
gridbox.addWidget(label, 0, 0, 1, 1)
databox = QtGui.QHBoxLayout()
self.boundingbox = None
if self.item3d().boundingboxsize:
self.boundingbox = QtGui.QLabel("Size: "+self.item3d().boundingboxsize,self)
databox.addWidget(self.boundingbox)
gridbox.addLayout(databox, 1, 0, 1, 1)
# angluar controls
xformframe = QtGui.QFrame()
xformframe.setFrameShape(QtGui.QFrame.StyledPanel)
xformbox = QtGui.QGridLayout()
xformlabel = QtGui.QLabel("Transformation", xformframe)
xformlabel.setFont(font)
xformlabel.setAlignment(QtCore.Qt.AlignCenter)
xformbox.addWidget(xformlabel, 0, 0, 1, 2)
# Rotations
self.rotcombobox = QtGui.QComboBox()
xformbox.addWidget(self.rotcombobox, 1, 0, 1, 2)
self.rotstackedwidget = QtGui.QStackedWidget()
self.addRotationWidgets()
xformbox.addWidget(self.rotstackedwidget, 2, 0, 1, 2)
#translations
txlabel = QtGui.QLabel("TX",xformframe)
txlabel.setAlignment(QtCore.Qt.AlignCenter)
xformbox.addWidget(txlabel, 3, 0, 1, 1)
tylabel = QtGui.QLabel("TY",xformframe)
tylabel.setAlignment(QtCore.Qt.AlignCenter)
xformbox.addWidget(tylabel, 3, 1, 1, 1)
self.tx = EMSpinWidget(0.0, 1.0)
self.ty = EMSpinWidget(0.0, 1.0)
xformbox.addWidget(self.tx, 4, 0, 1, 1)
xformbox.addWidget(self.ty, 4, 1, 1, 1)
tzlabel = QtGui.QLabel("TZ",xformframe)
tzlabel.setAlignment(QtCore.Qt.AlignCenter)
xformbox.addWidget(tzlabel, 5, 0, 1, 1)
zoomlabel = QtGui.QLabel("Zoom",xformframe)
zoomlabel.setAlignment(QtCore.Qt.AlignCenter)
xformbox.addWidget(zoomlabel, 5, 1, 1, 1)
self.tz = EMSpinWidget(0.0, 1.0)
self.zoom = EMSpinWidget(1.0, 0.1, postivemode=True, wheelstep=0.1)
xformbox.addWidget(self.tz, 6, 0, 1, 1)
xformbox.addWidget(self.zoom, 6, 1, 1, 1)
self.resetbuttontx = QtGui.QPushButton("Reset Tx")
self.resetbuttonrot = QtGui.QPushButton("Reset Rot")
xformbox.addWidget(self.resetbuttontx, 7, 0, 1, 1)
xformbox.addWidget(self.resetbuttonrot, 7, 1, 1, 1)
xformframe.setLayout(xformbox)
xformframe.setMaximumWidth(350)
xformframe.setMaximumHeight(self.transfromboxmaxheight)
xformframe.setLayout(xformbox)
gridbox.addWidget(xformframe, 2, 0, 1, 1)
# set to default, but run only as a base class
if type(self) == EMItem3DInspector: self.updateItemControls()
QtCore.QObject.connect(self.tx,QtCore.SIGNAL("valueChanged(int)"),self._on_translation)
QtCore.QObject.connect(self.ty,QtCore.SIGNAL("valueChanged(int)"),self._on_translation)
QtCore.QObject.connect(self.tz,QtCore.SIGNAL("valueChanged(int)"),self._on_translation)
QtCore.QObject.connect(self.zoom,QtCore.SIGNAL("valueChanged(int)"),self._on_scale)
QtCore.QObject.connect(self.resetbuttontx,QtCore.SIGNAL("clicked()"),self._on_resettx)
QtCore.QObject.connect(self.resetbuttonrot,QtCore.SIGNAL("clicked()"),self._on_resetrot)
def _on_translation(self, value):
"""
Need to contain the right coords. And do translation in the correct corrd system
"""
tt = t = Transform({"tx":self.tx.getValue(),"ty":self.ty.getValue(),"tz":self.tz.getValue()})
tp = self.item3d().getParentMatrixProduct()
if tp: tt = tp.inverse()*t
self.item3d().getTransform().set_trans(tt.get_trans())
self.inspector().updateSceneGraph()
def _on_scale(self, value):
self.item3d().getTransform().set_scale(self.zoom.getValue())
self.inspector().updateSceneGraph()
def _on_resettx(self):
self.item3d().getTransform().set_trans(0.0, 0.0, 0.0)
self.updateItemControls()
self.inspector().updateSceneGraph()
def _on_resetrot(self):
self.item3d().getTransform().set_rotation({"type":"eman","az":0.0,"alt":0.0,"phi":0.0})
self.updateItemControls()
self.inspector().updateSceneGraph()
def _isRotNaN(self, rot1, rot2, rot3):
""" Better check to make sure get_rotation did not return Nan, so to prevent a crash """
if rot1 != rot1: return True
if rot2 != rot2: return True
if rot3 != rot3: return True
return False
def updateItemControls(self):
""" Updates this item inspector. Function is called by the item it observes"""
# Translation update
stdtransfrom = self.item3d().getTransformStdCoord()
translation = stdtransfrom.get_trans()
self.tx.setValue(translation[0])
self.ty.setValue(translation[1])
self.tz.setValue(translation[2])
# Rotation update
rotation = stdtransfrom.get_rotation(str(self.rotcombobox.currentText()))
is_identity = stdtransfrom.is_rot_identity()
comboboxidx = self.rotcombobox.currentIndex()
if comboboxidx == 0:
if self._isRotNaN(rotation["az"],rotation["alt"],rotation["phi"]): return
self.emanazslider.setValue(rotation["az"], quiet=1)
self.emanaltslider.setValue(rotation["alt"], quiet=1)
self.emanphislider.setValue(rotation["phi"], quiet=1)
if comboboxidx == 1:
if self._isRotNaN(rotation["gamma"],rotation["beta"],rotation["alpha"]): return
self.imagicgammaslider.setValue(rotation["gamma"], quiet=1)
self.imagicbetaslider.setValue(rotation["beta"], quiet=1)
self.imagicalphaslider.setValue(rotation["alpha"], quiet=1)
if comboboxidx == 2:
if self._isRotNaN(rotation["psi"],rotation["theta"],rotation["phi"]): return
self.spiderpsislider.setValue(rotation["psi"], quiet=1)
self.spiderthetaslider.setValue(rotation["theta"], quiet=1)
self.spiderphislider.setValue(rotation["phi"], quiet=1)
if comboboxidx == 3:
if self._isRotNaN(rotation["phi"],rotation["theta"],rotation["omega"]): return
self.mrcpsislider.setValue(rotation["phi"], quiet=1)
self.mrcthetaslider.setValue(rotation["theta"], quiet=1)
self.mrcomegaslider.setValue(rotation["omega"], quiet=1)
if comboboxidx == 4:
if self._isRotNaN(rotation["ztilt"],rotation["ytilt"],rotation["xtilt"]): return
self.xyzzslider.setValue(rotation["ztilt"], quiet=1)
self.xyzyslider.setValue(rotation["ytilt"], quiet=1)
self.xyzxslider.setValue(rotation["xtilt"], quiet=1)
if comboboxidx == 5:
if self._isRotNaN(rotation["n1"],rotation["n2"],rotation["n3"]): return
if is_identity and self.spinn1slider.getValue() == 0.0 and self.spinn2slider.getValue() == 0.0 and self.spinn3slider.getValue() == 0.0:
self.spinomegaslider .setValue(0.0, quiet=1)
self.spinn1slider.setValue(0.0, quiet=1)
self.spinn2slider.setValue(0.0, quiet=1)
self.spinn3slider.setValue(1.0, quiet=1)
else:
self.spinomegaslider .setValue(rotation["omega"], quiet=1)
# Don't change slider if reult is Nan
if rotation["n1"] == rotation["n1"]: self.spinn1slider.setValue(rotation["n1"], quiet=1)
if rotation["n2"] == rotation["n2"]: self.spinn2slider.setValue(rotation["n2"], quiet=1)
if rotation["n3"] == rotation["n3"]: self.spinn3slider.setValue(rotation["n3"], quiet=1)
if comboboxidx == 6:
if self._isRotNaN(rotation["n1"],rotation["n2"],rotation["n3"]): return
if is_identity and self.spinn1slider.getValue() == 0.0 and self.spinn2slider.getValue() == 0.0 and self.spinn3slider.getValue() == 0.0:
self.spinomegaslider.setValue(0.0, quiet=1)
self.sgirotn1slider.setValue(0.0, quiet=1)
self.sgirotn2slider.setValue(0.0, quiet=1)
self.sgirotn3slider.setValue(1.0, quiet=1)
else:
self.spinomegaslider.setValue(rotation["q"], quiet=1)
# Don't change slider if reult is Nan
if rotation["n1"] == rotation["n1"]: self.sgirotn1slider.setValue(rotation["n1"], quiet=1)
if rotation["n2"] == rotation["n2"]: self.sgirotn2slider.setValue(rotation["n2"], quiet=1)
if rotation["n3"] == rotation["n3"]: self.sgirotn3slider.setValue(rotation["n3"], quiet=1)
if comboboxidx == 7:
if self._isRotNaN(rotation["e1"],rotation["e2"],rotation["e3"]): return
if is_identity:
self.quaternione0slider.setValue(1.0, quiet=1)
self.quaternione1slider.setValue(0.0, quiet=1)
self.quaternione2slider.setValue(0.0, quiet=1)
self.quaternione3slider.setValue(0.0, quiet=1)
else:
self.quaternione0slider.setValue(rotation["e0"], quiet=1)
self.quaternione1slider.setValue(rotation["e1"], quiet=1)
self.quaternione2slider.setValue(rotation["e2"], quiet=1)
self.quaternione3slider.setValue(rotation["e3"], quiet=1)
# Scaling update
self.zoom.setValue(self.item3d().getTransform().get_scale())
def updateMetaData(self):
"""
I didn't want to put this in update b/c this data doesn't change very often, and I don't want to waste CPU
Its a judgement call really, less coupling vs. more efficiency
"""
if self.boundingbox: self.boundingbox.setText("Size: "+self.item3d().boundingboxsize)
def addRotationWidgets(self):
""" Add alll the widgets for the various EMAN2 rotation conventions """
EMANwidget = QtGui.QWidget()
Imagicwidget = QtGui.QWidget()
Spiderwidget = QtGui.QWidget()
MRCwidget = QtGui.QWidget()
XYZwidget = QtGui.QWidget()
spinwidget = QtGui.QWidget()
sgirotwidget = QtGui.QWidget()
quaternionwidget = QtGui.QWidget()
# EMAN
emanbox = QtGui.QVBoxLayout()
self.emanazslider = ValSlider(EMANwidget, (0.0, 360.0), " Az", rounding = 1)
self.emanaltslider = ValSlider(EMANwidget, (0.0, 180.0), "Alt", rounding = 1)
self.emanphislider = ValSlider(EMANwidget, (0.0, 360.0), "Phi", rounding = 1)
emanbox.addWidget(self.emanazslider)
emanbox.addWidget(self.emanaltslider)
emanbox.addWidget(self.emanphislider)
EMANwidget.setLayout(emanbox)
# Imagic
imagicbox = QtGui.QVBoxLayout()
self.imagicgammaslider = ValSlider(Imagicwidget, (0.0, 360.0), "Gamma", rounding = 1)
self.imagicbetaslider = ValSlider(Imagicwidget, (0.0, 180.0), " Beta", rounding = 1)
self.imagicalphaslider = ValSlider(Imagicwidget, (0.0, 360.0), " Alpha", rounding = 1)
imagicbox.addWidget(self.imagicgammaslider)
imagicbox.addWidget(self.imagicbetaslider)
imagicbox.addWidget(self.imagicalphaslider)
Imagicwidget.setLayout(imagicbox)
# Spider
spiderbox = QtGui.QVBoxLayout()
self.spiderpsislider = ValSlider(Spiderwidget, (0.0, 360.0), " Psi", rounding = 1)
self.spiderthetaslider = ValSlider(Spiderwidget, (0.0, 180.0), "Theta", rounding = 1)
self.spiderphislider = ValSlider(Spiderwidget, (0.0, 360.0), " Phi", rounding = 1)
spiderbox.addWidget(self.spiderpsislider)
spiderbox.addWidget(self.spiderthetaslider)
spiderbox.addWidget(self.spiderphislider)
Spiderwidget.setLayout(spiderbox)
# MRC
mrcbox = QtGui.QVBoxLayout()
self.mrcpsislider = ValSlider(MRCwidget, (0.0, 360.0), " Psi", rounding = 1)
self.mrcthetaslider = ValSlider(MRCwidget, (0.0, 180.0), " Theta", rounding = 1)
self.mrcomegaslider = ValSlider(MRCwidget, (0.0, 360.0), "Omega", rounding = 1)
mrcbox.addWidget(self.mrcpsislider)
mrcbox.addWidget(self.mrcthetaslider)
mrcbox.addWidget(self.mrcomegaslider)
MRCwidget.setLayout(mrcbox)
# XYZ
xyzbox = QtGui.QVBoxLayout()
self.xyzzslider = ValSlider(XYZwidget, (0.0, 360.0), "Z", rounding = 1)
self.xyzyslider = ValSlider(XYZwidget, (0.0, 180.0), "Y", rounding = 1)
self.xyzxslider = ValSlider(XYZwidget, (0.0, 360.0), "X", rounding = 1)
xyzbox.addWidget(self.xyzzslider)
xyzbox.addWidget(self.xyzyslider)
xyzbox.addWidget(self.xyzxslider)
XYZwidget.setLayout(xyzbox)
# spin
spinbox = QtGui.QVBoxLayout()
self.spinomegaslider = ValSlider(spinwidget, (0.0, 180.0), "Omega", rounding = 1)
self.spinn1slider = ValSlider(spinwidget, (0.0, 1.0), " N1", rounding = 4)
self.spinn2slider = ValSlider(spinwidget, (0.0, 1.0), " N2", rounding = 4)
self.spinn3slider = ValSlider(spinwidget, (0.0, 1.0), " N3", rounding = 4)
spinbox.addWidget(self.spinomegaslider)
spinbox.addWidget(self.spinn1slider)
spinbox.addWidget(self.spinn2slider)
spinbox.addWidget(self.spinn3slider)
spinwidget.setLayout(spinbox)
# sgirot
sgirotbox = QtGui.QVBoxLayout()
self.sgirotqslider = ValSlider(sgirotwidget, (0.0, 180.0), " Q", rounding = 1)
self.sgirotn1slider = ValSlider(sgirotwidget, (0.0, 1.0), "N1", rounding = 4)
self.sgirotn2slider = ValSlider(sgirotwidget, (0.0, 1.0), "N2", rounding = 4)
self.sgirotn3slider = ValSlider(sgirotwidget, (0.0, 1.0), "N3", rounding = 4)
sgirotbox.addWidget(self.sgirotqslider)
sgirotbox.addWidget(self.sgirotn1slider)
sgirotbox.addWidget(self.sgirotn2slider)
sgirotbox.addWidget(self.sgirotn3slider)
sgirotwidget.setLayout(sgirotbox)
# quaternion
quaternionbox = QtGui.QVBoxLayout()
self.quaternione0slider = ValSlider(quaternionwidget, (0.0, 1.0), "E0", rounding = 4)
self.quaternione1slider = ValSlider(quaternionwidget, (0.0, 1.0), "E1", rounding = 4)
self.quaternione2slider = ValSlider(quaternionwidget, (0.0, 1.0), "E2", rounding = 4)
self.quaternione3slider = ValSlider(quaternionwidget, (0.0, 1.0), "E3", rounding = 4)
quaternionbox.addWidget(self.quaternione0slider)
quaternionbox.addWidget(self.quaternione1slider)
quaternionbox.addWidget(self.quaternione2slider)
quaternionbox.addWidget(self.quaternione3slider)
quaternionwidget.setLayout(quaternionbox)
# Add widgets to the stack
self.rotstackedwidget.addWidget(EMANwidget)
self.rotstackedwidget.addWidget(Imagicwidget)
self.rotstackedwidget.addWidget(Spiderwidget)
self.rotstackedwidget.addWidget(MRCwidget)
self.rotstackedwidget.addWidget(XYZwidget)
self.rotstackedwidget.addWidget(spinwidget)
self.rotstackedwidget.addWidget(sgirotwidget)
self.rotstackedwidget.addWidget(quaternionwidget)
# add choices to combobox
self.rotcombobox.addItem("EMAN")
self.rotcombobox.addItem("Imagic")
self.rotcombobox.addItem("Spider")
self.rotcombobox.addItem("MRC")
self.rotcombobox.addItem("XYZ")
self.rotcombobox.addItem("spin")
self.rotcombobox.addItem("sgirot")
self.rotcombobox.addItem("quaternion")
# Signal for all sliders
QtCore.QObject.connect(self.rotcombobox, QtCore.SIGNAL("activated(int)"), self._rotcombobox_changed)
QtCore.QObject.connect(self.emanazslider,QtCore.SIGNAL("valueChanged"),self._on_EMAN_rotation)
QtCore.QObject.connect(self.emanaltslider,QtCore.SIGNAL("valueChanged"),self._on_EMAN_rotation)
QtCore.QObject.connect(self.emanphislider,QtCore.SIGNAL("valueChanged"),self._on_EMAN_rotation)
QtCore.QObject.connect(self.imagicgammaslider,QtCore.SIGNAL("valueChanged"),self._on_Imagic_rotation)
QtCore.QObject.connect(self.imagicbetaslider,QtCore.SIGNAL("valueChanged"),self._on_Imagic_rotation)
QtCore.QObject.connect(self.imagicalphaslider,QtCore.SIGNAL("valueChanged"),self._on_Imagic_rotation)
QtCore.QObject.connect(self.spiderpsislider,QtCore.SIGNAL("valueChanged"),self._on_Spider_rotation)
QtCore.QObject.connect(self.spiderthetaslider,QtCore.SIGNAL("valueChanged"),self._on_Spider_rotation)
QtCore.QObject.connect(self.spiderphislider,QtCore.SIGNAL("valueChanged"),self._on_Spider_rotation)
QtCore.QObject.connect(self.mrcpsislider,QtCore.SIGNAL("valueChanged"),self._on_MRC_rotation)
QtCore.QObject.connect(self.mrcthetaslider,QtCore.SIGNAL("valueChanged"),self._on_MRC_rotation)
QtCore.QObject.connect(self.mrcomegaslider,QtCore.SIGNAL("valueChanged"),self._on_MRC_rotation)
QtCore.QObject.connect(self.xyzzslider,QtCore.SIGNAL("valueChanged"),self._on_XYZ_rotation)
QtCore.QObject.connect(self.xyzyslider,QtCore.SIGNAL("valueChanged"),self._on_XYZ_rotation)
QtCore.QObject.connect(self.xyzxslider,QtCore.SIGNAL("valueChanged"),self._on_XYZ_rotation)
QtCore.QObject.connect(self.spinomegaslider,QtCore.SIGNAL("valueChanged"),self._on_spin_rotation)
QtCore.QObject.connect(self.spinn1slider,QtCore.SIGNAL("valueChanged"),self._on_spin_rotation)
QtCore.QObject.connect(self.spinn2slider,QtCore.SIGNAL("valueChanged"),self._on_spin_rotation)
QtCore.QObject.connect(self.spinn3slider,QtCore.SIGNAL("valueChanged"),self._on_spin_rotation)
QtCore.QObject.connect(self.sgirotqslider,QtCore.SIGNAL("valueChanged"),self._on_sgirot_rotation)
QtCore.QObject.connect(self.sgirotn1slider,QtCore.SIGNAL("valueChanged"),self._on_sgirot_rotation)
QtCore.QObject.connect(self.sgirotn2slider,QtCore.SIGNAL("valueChanged"),self._on_sgirot_rotation)
QtCore.QObject.connect(self.sgirotn3slider,QtCore.SIGNAL("valueChanged"),self._on_sgirot_rotation)
QtCore.QObject.connect(self.quaternione0slider,QtCore.SIGNAL("valueChanged"),self._on_quaternion_rotation)
QtCore.QObject.connect(self.quaternione1slider,QtCore.SIGNAL("valueChanged"),self._on_quaternion_rotation)
QtCore.QObject.connect(self.quaternione2slider,QtCore.SIGNAL("valueChanged"),self._on_quaternion_rotation)
QtCore.QObject.connect(self.quaternione3slider,QtCore.SIGNAL("valueChanged"),self._on_quaternion_rotation)
def _rotcombobox_changed(self, idx):
self.rotstackedwidget.setCurrentIndex(idx)
self.updateItemControls()
def _on_EMAN_rotation(self, value):
self._set_rotation_std_coords(Transform({"type":"eman","az":self.emanazslider.getValue(),"alt":self.emanaltslider.getValue(),"phi":self.emanphislider.getValue()}))
self.inspector().updateSceneGraph()
def _on_Imagic_rotation(self, value):
self._set_rotation_std_coords(Transform({"type":"imagic","gamma":self.imagicgammaslider.getValue(),"beta":self.imagicbetaslider.getValue(),"alpha":self.imagicalphaslider.getValue()}))
self.inspector().updateSceneGraph()
def _on_Spider_rotation(self, value):
self._set_rotation_std_coords(Transform({"type":"spider","psi":self.spiderpsislider.getValue(),"theta":self.spiderthetaslider.getValue(),"phi":self.spiderphislider.getValue()}))
self.inspector().updateSceneGraph()
def _on_MRC_rotation(self, value):
self._set_rotation_std_coords(Transform({"type":"mrc","phi":self.mrcpsislider.getValue(),"theta":self.mrcthetaslider.getValue(),"omega":self.mrcomegaslider.getValue()}))
self.inspector().updateSceneGraph()
def _on_XYZ_rotation(self, value):
self._set_rotation_std_coords(Transform({"type":"xyz","ztilt":self.xyzzslider.getValue(),"ytilt":self.xyzyslider.getValue(),"xtilt":self.xyzxslider.getValue()}))
self.inspector().updateSceneGraph()
def _on_spin_rotation(self, value):
v = Vec3f(self.spinn1slider.getValue(), self.spinn2slider.getValue(), self.spinn3slider.getValue())
v.normalize()
self._set_rotation_std_coords(Transform({"type":"spin","omega":self.spinomegaslider.getValue(),"n1":v[0],"n2":v[1],"n3":v[2]}))
self.inspector().updateSceneGraph()
def _on_sgirot_rotation(self, value):
v = Vec3f(self.sgirotn1slider.getValue(), self.sgirotn2slider.getValue(), self.sgirotn3slider.getValue())
v.normalize()
self._set_rotation_std_coords(Transform({"type":"sgirot","q":self.sgirotqslider.getValue(),"n1":v[0],"n2":v[1],"n3":v[2]}))
self.inspector().updateSceneGraph()
def _on_quaternion_rotation(self, value):
v = Vec4f(self.quaternione0slider.getValue(), self.quaternione1slider.getValue(), self.quaternione2slider.getValue(), self.quaternione3slider.getValue())
v.normalize()
self._set_rotation_std_coords(Transform({"type":"quaternion","e0":v[0],"e1":v[1],"e2":v[2],"e3":v[3]}))
self.inspector().updateSceneGraph()
def _set_rotation_std_coords(self, rotation):
""" This function sets the rotation as if there were no preceeding ones, otherwise a rot around Z could be arounf y,x, etc.
Works by transforming local coords into global corrds"""
tt = rotation
tp = self.item3d().getParentMatrixProduct()
if tp: tt = tp.inverse()*rotation
self.item3d().getTransform().set_rotation(tt.get_rotation())
class GUIctfsim(QtGui.QWidget):
def __init__(self,
application,
apix=1.0,
voltage=300.0,
cs=4.1,
ac=10.0,
samples=256):
"""CTF simulation dialog
"""
try:
from emimage2d import EMImage2DWidget
except:
print "Cannot import EMAN image GUI objects (EMImage2DWidget)"
sys.exit(1)
try:
from 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
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.guirealim.connect(self.guirealim,QtCore.SIGNAL("keypress"),self.realimgkey)
self.guiim.connect(self.guiim, QtCore.SIGNAL("mousedown"),
self.imgmousedown)
self.guiim.connect(self.guiim, QtCore.SIGNAL("mousedrag"),
self.imgmousedrag)
self.guiim.connect(self.guiim, QtCore.SIGNAL("mouseup"),
self.imgmouseup)
self.guiplot.connect(self.guiplot, QtCore.SIGNAL("mousedown"),
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:", 0, 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.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()
QtCore.QObject.connect(self.sdefocus, QtCore.SIGNAL("valueChanged"),
self.newCTF)
QtCore.QObject.connect(self.sbfactor, QtCore.SIGNAL("valueChanged"),
self.newCTF)
QtCore.QObject.connect(self.sdfdiff, QtCore.SIGNAL("valueChanged"),
self.newCTF)
QtCore.QObject.connect(self.sdfang, QtCore.SIGNAL("valueChanged"),
self.newCTF)
QtCore.QObject.connect(self.sapix, QtCore.SIGNAL("valueChanged"),
self.newCTF)
QtCore.QObject.connect(self.sampcont, QtCore.SIGNAL("valueChanged"),
self.newCTF)
QtCore.QObject.connect(self.svoltage, QtCore.SIGNAL("valueChanged"),
self.newCTF)
QtCore.QObject.connect(self.scs, QtCore.SIGNAL("valueChanged"),
self.newCTF)
QtCore.QObject.connect(self.ssamples, QtCore.SIGNAL("valueChanged"),
self.newCTF)
QtCore.QObject.connect(self.setlist,
QtCore.SIGNAL("currentRowChanged(int)"),
self.newSet)
QtCore.QObject.connect(self.setlist, QtCore.SIGNAL("keypress"),
self.listkey)
QtCore.QObject.connect(self.splotmode,
QtCore.SIGNAL("currentIndexChanged(int)"),
self.newPlotMode)
QtCore.QObject.connect(self.newbut, QtCore.SIGNAL("clicked(bool)"),
self.on_new_but)
self.resize(
720, 380
) # figured these values out by printing the width and height in resize event
E2loadappwin("e2ctfsim", "main", self)
E2loadappwin("e2ctfsim", "image", self.guiim.qt_parent)
# E2loadappwin("e2ctf","realimage",self.guirealim.qt_parent)
E2loadappwin("e2ctfsim", "plot", self.guiplot.qt_parent)
self.setWindowTitle("CTF")
def listkey(self, event):
if event.key() >= Qt.Key_0 and event.key() <= Qt.Key_9:
q = int(event.key()) - Qt.Key_0
self.squality.setValue(q)
elif event.key() == Qt.Key_Left:
self.sdefocus.setValue(self.sdefocus.getValue() - 0.01)
elif event.key() == Qt.Key_Right:
self.sdefocus.setValue(self.sdefocus.getValue() + 0.01)
elif event.key() == Qt.Key_R:
self.on_recall_params()
def on_new_but(self):
ctf = EMAN2Ctf()
ctf.defocus = 1.0
ctf.voltage = self.df_voltage
ctf.apix = self.df_apix
ctf.cs = self.df_cs
ctf.ac = self.df_ac
ctf.samples = self.df_samples
self.data.append((str(len(self.setlist) + 1), ctf))
self.curset = len(self.data)
self.update_data()
def show_guis(self):
if self.guiim != None:
self.app().show_specific(self.guiim)
if self.guiplot != None:
self.app().show_specific(self.guiplot)
#if self.guirealim != None:
#self.app().show_specific(self.guirealim)
self.show()
def closeEvent(self, event):
# QtGui.QWidget.closeEvent(self,event)
# self.app.app.closeAllWindows()
E2saveappwin("e2ctf", "main", self)
if self.guiim != None:
E2saveappwin("e2ctf", "image", self.guiim.qt_parent)
self.app().close_specific(self.guiim)
self.guiim = None
if self.guiplot != None:
E2saveappwin("e2ctf", "plot", self.guiplot.qt_parent)
self.app().close_specific(self.guiplot)
#if self.guirealim != None:
#E2saveappwin("e2ctf","realimage",self.guirealim.qt_parent)
#self.app().close_specific(self.guirealim)
event.accept()
self.app().close_specific(self)
self.emit(
QtCore.SIGNAL("module_closed")
) # this signal is important when e2ctf is being used by a program running its own event loop
def update_data(self):
"""This will make sure the various widgets properly show the current data sets"""
self.setlist.clear()
for i, j in enumerate(self.data):
self.setlist.addItem(j[0])
self.setlist.setCurrentRow(self.curset)
def update_plot(self):
if self.guiplot == None: return # it's closed/not visible
for d in xrange(len(self.data)):
ctf = self.data[d][1]
ds = 1.0 / (ctf.apix * 2.0 * ctf.samples)
s = arange(0, ds * ctf.samples, ds)
curve = array(ctf.compute_1d(len(s) * 2, ds, Ctf.CtfType.CTF_AMP))
if self.plotmode == 1 or self.plotmode == 2:
curve = curve**2
if self.plotmode == 2 or self.plotmode == 3:
if d == 0: avg = curve[:]
else:
if len(curve) != len(avg):
print "Number of samples must be fixed to compute an average ({})".format(
d + 1)
else:
avg += curve
self.guiplot.set_data((s, curve),
self.data[d][0],
d == 0,
True,
color=d + 1)
if self.plotmode in (2, 3):
self.guiplot.set_data((s, avg), "Sum", False, True, color=0)
self.guiplot.setAxisParms("s (1/$\AA$)", "CTF")
ctf.compute_2d_complex(self.img, Ctf.CtfType.CTF_AMP, None)
self.guiim.set_data(self.img)
def newSet(self, val=0):
"called when a new data set is selected from the list"
self.curset = val
self.sdefocus.setValue(self.data[val][1].defocus, True)
self.sbfactor.setValue(self.data[val][1].bfactor, True)
self.sapix.setValue(self.data[val][1].apix, True)
self.sampcont.setValue(self.data[val][1].ampcont, True)
self.svoltage.setValue(self.data[val][1].voltage, True)
self.scs.setValue(self.data[val][1].cs, True)
self.sdfdiff.setValue(self.data[val][1].dfdiff, True)
self.sdfang.setValue(self.data[val][1].dfang, True)
self.ssamples.setValue(self.data[val][1].samples, True)
# make new image if necessary
if self.img == None or self.img["ny"] != self.data[val][1].samples:
self.img = EMData(self.data[val][1].samples + 2,
self.data[val][1].samples)
self.img.to_zero()
self.img.set_complex(1)
self.guiim.set_data(self.img)
# self.imginfo.setText("%s particles SNR = %s"%(ptcl,ssnr))
#if self.guiim != None:
## print self.data
#self.guiim.set_data(self.data[val][4])
#if self.guiiminit:
#self.guiim.optimally_resize()
#self.guiiminit = False
#self.guiim.updateGL()
#self.update_plot()
# print "self.data[val]=",self.data[val][0].split('#')[-1]
self.guiim.qt_parent.setWindowTitle("e2ctfsim - 2D FFT - " +
self.data[val][0])
# self.guirealim.qt_parent.setWindowTitle("e2ctf - "+self.data[val][0].split('#')[-1])
self.guiplot.qt_parent.setWindowTitle("e2ctfsim - Plot ")
#n=EMUtil.get_image_count(self.data[val][0])
#if n>1:
#self.ptcldata=EMData.read_images(self.data[val][0],range(0,min(20,n)))
#im=sum(self.ptcldata)
#im.mult(1.0/len(self.ptcldata))
#self.ptcldata.insert(0,im)
#self.guirealim.set_data(self.ptcldata)
#else : self.guirealim.set_data([EMData()])
self.update_plot()
def newPlotMode(self, mode):
self.plotmode = mode
self.update_plot()
def newCTF(self):
# print traceback.print_stack()
self.data[self.curset][1].defocus = self.sdefocus.value
self.data[self.curset][1].bfactor = self.sbfactor.value
self.data[self.curset][1].dfdiff = self.sdfdiff.value
self.data[self.curset][1].dfang = self.sdfang.value
self.data[self.curset][1].apix = self.sapix.value
self.data[self.curset][1].ampcont = self.sampcont.value
self.data[self.curset][1].voltage = self.svoltage.value
self.data[self.curset][1].cs = self.scs.value
self.data[self.curset][1].samples = self.ssamples.value
if self.img == None or self.img["ny"] != self.ssamples.value:
self.img = EMData(self.ssamples.value + 2, self.ssamples.value)
self.img.to_zero()
self.img.set_complex(1)
self.guiim.set_data(self.img)
self.update_plot()
def realimgkey(self, event):
"""Keypress in the image display window"""
if event.key(
) == Qt.Key_I: # if user presses I in this window we invert the stack on disk
fsp = self.data[self.curset][0]
n = EMUtil.get_image_count(fsp)
print "Inverting images in %s" % fsp
for i in xrange(n):
img = EMData(fsp, i)
img.mult(-1.0)
img.write_image(fsp, i)
#self.ptcldata=EMData.read_images(fsp,range(0,20))
#self.guirealim.set_data(self.ptcldata)
def imgmousedown(self, event):
m = self.guiim.scr_to_img((event.x(), event.y()))
#self.guiim.add_shape("cen",["rect",.9,.9,.4,x0,y0,x0+2,y0+2,1.0])
def imgmousedrag(self, event):
m = self.guiim.scr_to_img((event.x(), event.y()))
# box deletion when shift held down
#if event.modifiers()&Qt.ShiftModifier:
#for i,j in enumerate(self.boxes):
def imgmouseup(self, event):
m = self.guiim.scr_to_img((event.x(), event.y()))
def plotmousedown(self, event):
m = self.guiim.scr_to_img((event.x(), event.y()))
def run(self):
"""If you make your own application outside of this object, you are free to use
your own local app.exec_(). This is a convenience for ctf-only programs."""
self.app.exec_()
# E2saveappwin("boxer","imagegeom",self.guiim)
# try:
# E2setappval("boxer","imcontrol",self.guiim.inspector.isVisible())
# if self.guiim.inspector.isVisible() : E2saveappwin("boxer","imcontrolgeom",self.guiim.inspector)
# except : E2setappval("boxer","imcontrol",False)
return
class EMGLPlotInspector(QtGui.QWidget):
def __init__(self,target) :
QtGui.QWidget.__init__(self,None)
self.target=target
self.vbl = QtGui.QVBoxLayout(self)
self.vbl.setMargin(0)
self.vbl.setSpacing(6)
self.vbl.setObjectName("vbl")
self.hbl = QtGui.QHBoxLayout()
self.hbl.setMargin(0)
self.hbl.setSpacing(6)
self.hbl.setObjectName("hbl")
self.vbl.addLayout(self.hbl)
self.hist = ImgHistogram(self)
self.hist.setObjectName("hist")
self.hbl.addWidget(self.hist)
self.vbl2 = QtGui.QVBoxLayout()
self.vbl2.setMargin(0)
self.vbl2.setSpacing(6)
self.vbl2.setObjectName("vbl2")
self.hbl.addLayout(self.vbl2)
self.wiretog = QtGui.QPushButton("Wire")
self.wiretog.setCheckable(1)
self.vbl2.addWidget(self.wiretog)
self.lighttog = QtGui.QPushButton("Light")
self.lighttog.setCheckable(1)
self.vbl2.addWidget(self.lighttog)
self.tabwidget = QtGui.QTabWidget()
self.maintab = None
self.tabwidget.addTab(self.get_main_tab(), "Main")
self.tabwidget.addTab(self.get_GL_tab(),"GL")
self.vbl.addWidget(self.tabwidget)
self.n3_showing = False
QtCore.QObject.connect(self.scale, QtCore.SIGNAL("valueChanged"), target.set_scale)
QtCore.QObject.connect(self.az, QtCore.SIGNAL("valueChanged"), self.slider_rotate)
QtCore.QObject.connect(self.alt, QtCore.SIGNAL("valueChanged"), self.slider_rotate)
QtCore.QObject.connect(self.phi, QtCore.SIGNAL("valueChanged"), self.slider_rotate)
QtCore.QObject.connect(self.cbb, QtCore.SIGNAL("currentIndexChanged(QString)"), target.setColor)
QtCore.QObject.connect(self.src, QtCore.SIGNAL("currentIndexChanged(QString)"), self.set_src)
QtCore.QObject.connect(self.x_trans, QtCore.SIGNAL("valueChanged(double)"), target.set_cam_x)
QtCore.QObject.connect(self.y_trans, QtCore.SIGNAL("valueChanged(double)"), target.set_cam_y)
QtCore.QObject.connect(self.z_trans, QtCore.SIGNAL("valueChanged(double)"), target.set_cam_z)
QtCore.QObject.connect(self.wiretog, QtCore.SIGNAL("toggled(bool)"), target.toggle_wire)
QtCore.QObject.connect(self.lighttog, QtCore.SIGNAL("toggled(bool)"), target.toggle_light)
QtCore.QObject.connect(self.glcontrast, QtCore.SIGNAL("valueChanged"), target.set_GL_contrast)
QtCore.QObject.connect(self.glbrightness, QtCore.SIGNAL("valueChanged"), target.set_GL_brightness)
def get_GL_tab(self):
self.gltab = QtGui.QWidget()
gltab = self.gltab
gltab.vbl = QtGui.QVBoxLayout(self.gltab )
gltab.vbl.setMargin(0)
gltab.vbl.setSpacing(6)
gltab.vbl.setObjectName("Main")
self.glcontrast = ValSlider(gltab,(1.0,5.0),"GLShd:")
self.glcontrast.setObjectName("GLShade")
self.glcontrast.setValue(1.0)
gltab.vbl.addWidget(self.glcontrast)
self.glbrightness = ValSlider(gltab,(-1.0,0.0),"GLBst:")
self.glbrightness.setObjectName("GLBoost")
self.glbrightness.setValue(0.1)
self.glbrightness.setValue(0.0)
gltab.vbl.addWidget(self.glbrightness)
return gltab
def get_main_tab(self):
if ( self.maintab == None ):
self.maintab = QtGui.QWidget()
maintab = self.maintab
maintab.vbl = QtGui.QVBoxLayout(self.maintab)
maintab.vbl.setMargin(0)
maintab.vbl.setSpacing(6)
maintab.vbl.setObjectName("Main")
self.scale = ValSlider(maintab,(0.01,30.0),"Zoom:")
self.scale.setObjectName("scale")
self.scale.setValue(1.0)
maintab.vbl.addWidget(self.scale)
self.hbl_color = QtGui.QHBoxLayout()
self.hbl_color.setMargin(0)
self.hbl_color.setSpacing(6)
self.hbl_color.setObjectName("Material")
maintab.vbl.addLayout(self.hbl_color)
self.color_label = QtGui.QLabel()
self.color_label.setText('Material')
self.hbl_color.addWidget(self.color_label)
self.cbb = QtGui.QComboBox(maintab)
self.hbl_color.addWidget(self.cbb)
self.hbl_trans = QtGui.QHBoxLayout()
self.hbl_trans.setMargin(0)
self.hbl_trans.setSpacing(6)
self.hbl_trans.setObjectName("Trans")
maintab.vbl.addLayout(self.hbl_trans)
self.x_label = QtGui.QLabel()
self.x_label.setText('x')
self.hbl_trans.addWidget(self.x_label)
self.x_trans = QtGui.QDoubleSpinBox(self)
self.x_trans.setMinimum(-10000)
self.x_trans.setMaximum(10000)
self.x_trans.setValue(0.0)
self.hbl_trans.addWidget(self.x_trans)
self.y_label = QtGui.QLabel()
self.y_label.setText('y')
self.hbl_trans.addWidget(self.y_label)
self.y_trans = QtGui.QDoubleSpinBox(maintab)
self.y_trans.setMinimum(-10000)
self.y_trans.setMaximum(10000)
self.y_trans.setValue(0.0)
self.hbl_trans.addWidget(self.y_trans)
self.z_label = QtGui.QLabel()
self.z_label.setText('z')
self.hbl_trans.addWidget(self.z_label)
self.z_trans = QtGui.QDoubleSpinBox(maintab)
self.z_trans.setMinimum(-10000)
self.z_trans.setMaximum(10000)
self.z_trans.setValue(0.0)
self.hbl_trans.addWidget(self.z_trans)
self.hbl_src = QtGui.QHBoxLayout()
self.hbl_src.setMargin(0)
self.hbl_src.setSpacing(6)
self.hbl_src.setObjectName("hbl")
maintab.vbl.addLayout(self.hbl_src)
self.label_src = QtGui.QLabel()
self.label_src.setText('Rotation Convention')
self.hbl_src.addWidget(self.label_src)
self.src = QtGui.QComboBox(maintab)
self.load_src_options(self.src)
self.hbl_src.addWidget(self.src)
# set default value -1 ensures that the val slider is updated the first time it is created
self.az = ValSlider(self,(-360.0,360.0),"az",-1)
self.az.setObjectName("az")
maintab.vbl.addWidget(self.az)
self.alt = ValSlider(self,(-180.0,180.0),"alt",-1)
self.alt.setObjectName("alt")
maintab.vbl.addWidget(self.alt)
self.phi = ValSlider(self,(-360.0,360.0),"phi",-1)
self.phi.setObjectName("phi")
maintab.vbl.addWidget(self.phi)
self.current_src = EULER_EMAN
return self.maintab
def set_xy_trans(self, x, y):
self.x_trans.setValue(x)
self.y_trans.setValue(y)
def set_translate_scale(self, xscale,yscale,zscale):
self.x_trans.setSingleStep(xscale)
self.y_trans.setSingleStep(yscale)
self.z_trans.setSingleStep(zscale)
def update_rotations(self,t3d):
rot = t3d.get_rotation(self.src_map[str(self.src.itemText(self.src.currentIndex()))])
convention = self.src.currentText()
if ( self.src_map[str(convention)] == EULER_SPIN ):
self.n3.setValue(rot[self.n3.getLabel()],True)
self.az.setValue(rot[self.az.getLabel()],True)
self.alt.setValue(rot[self.alt.getLabel()],True)
self.phi.setValue(rot[self.phi.getLabel()],True)
def slider_rotate(self):
self.target.load_rotation(self.get_current_rotation())
def get_current_rotation(self):
convention = self.src.currentText()
rot = {}
if ( self.current_src == EULER_SPIN ):
rot[self.az.getLabel()] = self.az.getValue()
n1 = self.alt.getValue()
n2 = self.phi.getValue()
n3 = self.n3.getValue()
norm = sqrt(n1*n1 + n2*n2 + n3*n3)
n1 /= norm
n2 /= norm
n3 /= norm
rot[self.alt.getLabel()] = n1
rot[self.phi.getLabel()] = n2
rot[self.n3.getLabel()] = n3
else:
rot[self.az.getLabel()] = self.az.getValue()
rot[self.alt.getLabel()] = self.alt.getValue()
rot[self.phi.getLabel()] = self.phi.getValue()
return Transform3D(self.current_src, rot)
def set_src(self, val):
t3d = self.get_current_rotation()
if (self.n3_showing) :
self.vbl.removeWidget(self.n3)
self.n3.deleteLater()
self.n3_showing = False
self.az.setRange(-360,360)
self.alt.setRange(-180,180)
self.phi.setRange(-360,660)
if ( self.src_map[str(val)] == EULER_SPIDER ):
self.az.setLabel('phi')
self.alt.setLabel('theta')
self.phi.setLabel('psi')
elif ( self.src_map[str(val)] == EULER_EMAN ):
self.az.setLabel('az')
self.alt.setLabel('alt')
self.phi.setLabel('phi')
elif ( self.src_map[str(val)] == EULER_IMAGIC ):
self.az.setLabel('alpha')
self.alt.setLabel('beta')
self.phi.setLabel('gamma')
elif ( self.src_map[str(val)] == EULER_XYZ ):
self.az.setLabel('xtilt')
self.alt.setLabel('ytilt')
self.phi.setLabel('ztilt')
elif ( self.src_map[str(val)] == EULER_MRC ):
self.az.setLabel('phi')
self.alt.setLabel('theta')
self.phi.setLabel('omega')
elif ( self.src_map[str(val)] == EULER_SPIN ):
self.az.setLabel('Omega')
self.alt.setRange(-1,1)
self.phi.setRange(-1,1)
self.alt.setLabel('n1')
self.phi.setLabel('n2')
self.n3 = ValSlider(self,(-360.0,360.0),"n3",-1)
self.n3.setRange(-1,1)
self.n3.setObjectName("n3")
self.vbl.addWidget(self.n3)
QtCore.QObject.connect(self.n3, QtCore.SIGNAL("valueChanged"), self.slider_rotate)
self.n3_showing = True
self.current_src = self.src_map[str(val)]
self.update_rotations(t3d)
def load_src_options(self,widgit):
self.load_src()
for i in self.src_strings:
widgit.addItem(i)
# read src as 'supported rotation conventions'
def load_src(self):
# supported_rot_conventions
src_flags = []
src_flags.append(EULER_EMAN)
src_flags.append(EULER_SPIDER)
src_flags.append(EULER_IMAGIC)
src_flags.append(EULER_MRC)
src_flags.append(EULER_SPIN)
src_flags.append(EULER_XYZ)
self.src_strings = []
self.src_map = {}
for i in src_flags:
self.src_strings.append(str(i))
self.src_map[str(i)] = i
def setColors(self,colors,current_color):
a = 0
for i in colors:
self.cbb.addItem(i)
if ( i == current_color):
self.cbb.setCurrentIndex(a)
a += 1
def set_scale(self,newscale):
self.scale.setValue(newscale)
class GUIctfsim(QtGui.QWidget):
def __init__(self,application,apix=1.0,voltage=300.0,cs=4.1,ac=10.0,samples=256):
"""CTF simulation dialog
"""
try:
from emimage2d import EMImage2DWidget
except:
print "Cannot import EMAN image GUI objects (EMImage2DWidget)"
sys.exit(1)
try:
from 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
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.guirealim.connect(self.guirealim,QtCore.SIGNAL("keypress"),self.realimgkey)
self.guiim.connect(self.guiim,QtCore.SIGNAL("mousedown"),self.imgmousedown)
self.guiim.connect(self.guiim,QtCore.SIGNAL("mousedrag"),self.imgmousedrag)
self.guiim.connect(self.guiim,QtCore.SIGNAL("mouseup") ,self.imgmouseup)
self.guiplot.connect(self.guiplot,QtCore.SIGNAL("mousedown"),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:",0,90)
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.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()
QtCore.QObject.connect(self.sdefocus, QtCore.SIGNAL("valueChanged"), self.newCTF)
QtCore.QObject.connect(self.sbfactor, QtCore.SIGNAL("valueChanged"), self.newCTF)
QtCore.QObject.connect(self.sdfdiff, QtCore.SIGNAL("valueChanged"), self.newCTF)
QtCore.QObject.connect(self.sdfang, QtCore.SIGNAL("valueChanged"), self.newCTF)
QtCore.QObject.connect(self.sapix, QtCore.SIGNAL("valueChanged"), self.newCTF)
QtCore.QObject.connect(self.sampcont, QtCore.SIGNAL("valueChanged"), self.newCTF)
QtCore.QObject.connect(self.svoltage, QtCore.SIGNAL("valueChanged"), self.newCTF)
QtCore.QObject.connect(self.scs, QtCore.SIGNAL("valueChanged"), self.newCTF)
QtCore.QObject.connect(self.ssamples, QtCore.SIGNAL("valueChanged"), self.newCTF)
QtCore.QObject.connect(self.setlist,QtCore.SIGNAL("currentRowChanged(int)"),self.newSet)
QtCore.QObject.connect(self.setlist,QtCore.SIGNAL("keypress"),self.listkey)
QtCore.QObject.connect(self.splotmode,QtCore.SIGNAL("currentIndexChanged(int)"),self.newPlotMode)
QtCore.QObject.connect(self.newbut,QtCore.SIGNAL("clicked(bool)"),self.on_new_but)
self.resize(720,380) # figured these values out by printing the width and height in resize event
E2loadappwin("e2ctfsim","main",self)
E2loadappwin("e2ctfsim","image",self.guiim.qt_parent)
# E2loadappwin("e2ctf","realimage",self.guirealim.qt_parent)
E2loadappwin("e2ctfsim","plot",self.guiplot.qt_parent)
self.setWindowTitle("CTF")
def listkey(self,event):
if event.key()>=Qt.Key_0 and event.key()<=Qt.Key_9 :
q=int(event.key())-Qt.Key_0
self.squality.setValue(q)
elif event.key() == Qt.Key_Left:
self.sdefocus.setValue(self.sdefocus.getValue()-0.01)
elif event.key() == Qt.Key_Right:
self.sdefocus.setValue(self.sdefocus.getValue()+0.01)
elif event.key()==Qt.Key_R :
self.on_recall_params()
def on_new_but(self):
ctf=EMAN2Ctf()
ctf.defocus=1.0
ctf.voltage=self.df_voltage
ctf.apix=self.df_apix
ctf.cs=self.df_cs
ctf.ac=self.df_ac
ctf.samples=self.df_samples
self.data.append((str(len(self.setlist)+1),ctf))
self.curset=len(self.data)
self.update_data()
def show_guis(self):
if self.guiim != None:
self.app().show_specific(self.guiim)
if self.guiplot != None:
self.app().show_specific(self.guiplot)
#if self.guirealim != None:
#self.app().show_specific(self.guirealim)
self.show()
def closeEvent(self,event):
# QtGui.QWidget.closeEvent(self,event)
# self.app.app.closeAllWindows()
E2saveappwin("e2ctf","main",self)
if self.guiim != None:
E2saveappwin("e2ctf","image",self.guiim.qt_parent)
self.app().close_specific(self.guiim)
self.guiim = None
if self.guiplot != None:
E2saveappwin("e2ctf","plot",self.guiplot.qt_parent)
self.app().close_specific(self.guiplot)
#if self.guirealim != None:
#E2saveappwin("e2ctf","realimage",self.guirealim.qt_parent)
#self.app().close_specific(self.guirealim)
event.accept()
self.app().close_specific(self)
self.emit(QtCore.SIGNAL("module_closed")) # this signal is important when e2ctf is being used by a program running its own event loop
def update_data(self):
"""This will make sure the various widgets properly show the current data sets"""
self.setlist.clear()
for i,j in enumerate(self.data):
self.setlist.addItem(j[0])
self.setlist.setCurrentRow(self.curset)
def update_plot(self):
if self.guiplot == None: return # it's closed/not visible
for d in xrange(len(self.data)):
ctf=self.data[d][1]
ds=1.0/(ctf.apix*2.0*ctf.samples)
s=arange(0,ds*ctf.samples,ds)
curve=array(ctf.compute_1d(len(s)*2,ds,Ctf.CtfType.CTF_AMP))
if self.plotmode==1 or self.plotmode==2:
curve=curve**2
if self.plotmode==2 or self.plotmode==3:
if d==0 : avg=curve[:]
else:
if len(curve)!=len(avg) :
print "Number of samples must be fixed to compute an average ({})".format(d+1)
else:
avg+=curve
self.guiplot.set_data((s,curve),self.data[d][0],d==0,True,color=d+1)
if self.plotmode in (2,3) :
self.guiplot.set_data((s,avg),"Sum",False,True,color=0)
self.guiplot.setAxisParms("s (1/$\AA$)","CTF")
ctf.compute_2d_complex(self.img,Ctf.CtfType.CTF_AMP,None)
self.guiim.set_data(self.img)
def newSet(self,val=0):
"called when a new data set is selected from the list"
self.curset=val
self.sdefocus.setValue(self.data[val][1].defocus,True)
self.sbfactor.setValue(self.data[val][1].bfactor,True)
self.sapix.setValue(self.data[val][1].apix,True)
self.sampcont.setValue(self.data[val][1].ampcont,True)
self.svoltage.setValue(self.data[val][1].voltage,True)
self.scs.setValue(self.data[val][1].cs,True)
self.sdfdiff.setValue(self.data[val][1].dfdiff,True)
self.sdfang.setValue(self.data[val][1].dfang,True)
self.ssamples.setValue(self.data[val][1].samples,True)
# make new image if necessary
if self.img==None or self.img["ny"]!=self.data[val][1].samples :
self.img=EMData(self.data[val][1].samples+2,self.data[val][1].samples)
self.img.to_zero()
self.img.set_complex(1)
self.guiim.set_data(self.img)
# self.imginfo.setText("%s particles SNR = %s"%(ptcl,ssnr))
#if self.guiim != None:
## print self.data
#self.guiim.set_data(self.data[val][4])
#if self.guiiminit:
#self.guiim.optimally_resize()
#self.guiiminit = False
#self.guiim.updateGL()
#self.update_plot()
# print "self.data[val]=",self.data[val][0].split('#')[-1]
self.guiim.qt_parent.setWindowTitle("e2ctfsim - 2D FFT - "+self.data[val][0])
# self.guirealim.qt_parent.setWindowTitle("e2ctf - "+self.data[val][0].split('#')[-1])
self.guiplot.qt_parent.setWindowTitle("e2ctfsim - Plot ")
#n=EMUtil.get_image_count(self.data[val][0])
#if n>1:
#self.ptcldata=EMData.read_images(self.data[val][0],range(0,min(20,n)))
#im=sum(self.ptcldata)
#im.mult(1.0/len(self.ptcldata))
#self.ptcldata.insert(0,im)
#self.guirealim.set_data(self.ptcldata)
#else : self.guirealim.set_data([EMData()])
self.update_plot()
def newPlotMode(self,mode):
self.plotmode=mode
self.update_plot()
def newCTF(self) :
# print traceback.print_stack()
self.data[self.curset][1].defocus=self.sdefocus.value
self.data[self.curset][1].bfactor=self.sbfactor.value
self.data[self.curset][1].dfdiff=self.sdfdiff.value
self.data[self.curset][1].dfang=self.sdfang.value
self.data[self.curset][1].apix=self.sapix.value
self.data[self.curset][1].ampcont=self.sampcont.value
self.data[self.curset][1].voltage=self.svoltage.value
self.data[self.curset][1].cs=self.scs.value
self.data[self.curset][1].samples=self.ssamples.value
if self.img==None or self.img["ny"]!=self.ssamples.value :
self.img=EMData(self.ssamples.value+2,self.ssamples.value)
self.img.to_zero()
self.img.set_complex(1)
self.guiim.set_data(self.img)
self.update_plot()
def realimgkey(self,event):
"""Keypress in the image display window"""
if event.key()==Qt.Key_I: # if user presses I in this window we invert the stack on disk
fsp=self.data[self.curset][0]
n=EMUtil.get_image_count(fsp)
print "Inverting images in %s"%fsp
for i in xrange(n):
img=EMData(fsp,i)
img.mult(-1.0)
img.write_image(fsp,i)
#self.ptcldata=EMData.read_images(fsp,range(0,20))
#self.guirealim.set_data(self.ptcldata)
def imgmousedown(self,event) :
m=self.guiim.scr_to_img((event.x(),event.y()))
#self.guiim.add_shape("cen",["rect",.9,.9,.4,x0,y0,x0+2,y0+2,1.0])
def imgmousedrag(self,event) :
m=self.guiim.scr_to_img((event.x(),event.y()))
# box deletion when shift held down
#if event.modifiers()&Qt.ShiftModifier:
#for i,j in enumerate(self.boxes):
def imgmouseup(self,event) :
m=self.guiim.scr_to_img((event.x(),event.y()))
def plotmousedown(self,event) :
m=self.guiim.scr_to_img((event.x(),event.y()))
def run(self):
"""If you make your own application outside of this object, you are free to use
your own local app.exec_(). This is a convenience for ctf-only programs."""
self.app.exec_()
# E2saveappwin("boxer","imagegeom",self.guiim)
# try:
# E2setappval("boxer","imcontrol",self.guiim.inspector.isVisible())
# if self.guiim.inspector.isVisible() : E2saveappwin("boxer","imcontrolgeom",self.guiim.inspector)
# except : E2setappval("boxer","imcontrol",False)
return
class EMTransformPanel:
def __init__(self, target, parent):
self.target = weakref.ref(target)
self.parent = weakref.ref(parent)
self.label_src = QtGui.QLabel(parent)
self.label_src.setText('Rotation Convention')
self.src = QtGui.QComboBox(parent)
self.load_src_options(self.src)
self.x_label = QtGui.QLabel()
self.x_label.setText('x')
self.x_trans = QtGui.QDoubleSpinBox(parent)
self.x_trans.setMinimum(-10000)
self.x_trans.setMaximum(10000)
self.x_trans.setValue(0.0)
self.y_label = QtGui.QLabel()
self.y_label.setText('y')
self.y_trans = QtGui.QDoubleSpinBox(parent)
self.y_trans.setMinimum(-10000)
self.y_trans.setMaximum(10000)
self.y_trans.setValue(0.0)
self.z_label = QtGui.QLabel()
self.z_label.setText('z')
self.z_trans = QtGui.QDoubleSpinBox(parent)
self.z_trans.setMinimum(-10000)
self.z_trans.setMaximum(10000)
self.z_trans.setValue(0.0)
self.az = ValSlider(parent, (-360.0, 360.0), "az", -1)
self.az.setObjectName("az")
self.az.setValue(0.0)
self.alt = ValSlider(parent, (-180.0, 180.0), "alt", -1)
self.alt.setObjectName("alt")
self.alt.setValue(0.0)
self.phi = ValSlider(parent, (-360.0, 360.0), "phi", -1)
self.phi.setObjectName("phi")
self.phi.setValue(0.0)
self.scale = ValSlider(parent, (0.01, 30.0), "Zoom:")
self.scale.setObjectName("scale")
self.scale.setValue(1.0)
self.n3_showing = False
self.current_src = "eman"
QtCore.QObject.connect(self.az, QtCore.SIGNAL("valueChanged"),
self.slider_rotate)
QtCore.QObject.connect(self.alt, QtCore.SIGNAL("valueChanged"),
self.slider_rotate)
QtCore.QObject.connect(self.phi, QtCore.SIGNAL("valueChanged"),
self.slider_rotate)
QtCore.QObject.connect(self.src,
QtCore.SIGNAL("currentIndexChanged(QString)"),
self.set_src)
QtCore.QObject.connect(self.scale, QtCore.SIGNAL("valueChanged"),
self.target().set_scale)
QtCore.QObject.connect(self.x_trans,
QtCore.SIGNAL("valueChanged(double)"),
self.target().set_cam_x)
QtCore.QObject.connect(self.y_trans,
QtCore.SIGNAL("valueChanged(double)"),
self.target().set_cam_y)
QtCore.QObject.connect(self.z_trans,
QtCore.SIGNAL("valueChanged(double)"),
self.target().set_cam_z)
def set_defaults(self):
self.x_trans.setValue(0.0)
self.y_trans.setValue(0.0)
self.z_trans.setValue(0.0)
self.scale.setValue(1.0)
self.az.setValue(0.0)
self.alt.setValue(0.0)
self.phi.setValue(0.0)
def slider_rotate(self):
self.target().load_rotation(self.get_current_rotation())
def get_current_rotation(self):
convention = self.src.currentText()
rot = {}
if (self.current_src == "spin"):
rot[self.az.getLabel()] = self.az.getValue()
n1 = self.alt.getValue()
n2 = self.phi.getValue()
n3 = self.n3.getValue()
norm = sqrt(n1 * n1 + n2 * n2 + n3 * n3)
n1 /= norm
n2 /= norm
n3 /= norm
rot[self.alt.getLabel()] = n1
rot[self.phi.getLabel()] = n2
rot[self.n3.getLabel()] = n3
else:
rot[self.az.getLabel()] = self.az.getValue()
rot[self.alt.getLabel()] = self.alt.getValue()
rot[self.phi.getLabel()] = self.phi.getValue()
rot["type"] = self.current_src
return Transform(rot)
def addWidgets(self, target):
target.addWidget(self.scale)
self.hbl_trans = QtGui.QHBoxLayout()
self.hbl_trans.setMargin(0)
self.hbl_trans.setSpacing(6)
self.hbl_trans.setObjectName("Trans")
self.hbl_trans.addWidget(self.x_label)
self.hbl_trans.addWidget(self.x_trans)
self.hbl_trans.addWidget(self.y_label)
self.hbl_trans.addWidget(self.y_trans)
self.hbl_trans.addWidget(self.z_label)
self.hbl_trans.addWidget(self.z_trans)
target.addLayout(self.hbl_trans)
self.hbl_src = QtGui.QHBoxLayout()
self.hbl_src.setMargin(0)
self.hbl_src.setSpacing(6)
self.hbl_src.setObjectName("hbl")
self.hbl_src.addWidget(self.label_src)
self.hbl_src.addWidget(self.src)
target.addLayout(self.hbl_src)
target.addWidget(self.az)
target.addWidget(self.alt)
target.addWidget(self.phi)
def set_src(self, val):
t3d = self.get_current_rotation()
if (self.n3_showing):
self.parent().get_transform_layout().removeWidget(self.n3)
self.n3.deleteLater()
self.n3_showing = False
self.az.setRange(-360, 360)
self.alt.setRange(-180, 180)
self.phi.setRange(-360, 660)
if (self.src_map[str(val)] == "spider"):
self.az.setLabel('phi')
self.alt.setLabel('theta')
self.phi.setLabel('psi')
elif (self.src_map[str(val)] == "eman"):
self.az.setLabel('az')
self.alt.setLabel('alt')
self.phi.setLabel('phi')
elif (self.src_map[str(val)] == "imagic"):
self.az.setLabel('alpha')
self.alt.setLabel('beta')
self.phi.setLabel('gamma')
elif (self.src_map[str(val)] == "xyz"):
self.az.setLabel('xtilt')
self.alt.setLabel('ytilt')
self.phi.setLabel('ztilt')
elif (self.src_map[str(val)] == "mrc"):
self.az.setLabel('phi')
self.alt.setLabel('theta')
self.phi.setLabel('omega')
elif (self.src_map[str(val)] == "spin"):
self.az.setLabel('omega')
self.alt.setRange(-1, 1)
self.phi.setRange(-1, 1)
self.alt.setLabel('n1')
self.phi.setLabel('n2')
self.n3 = ValSlider(self.parent(), (-360.0, 360.0), "n3", -1)
self.n3.setRange(-1, 1)
self.n3.setObjectName("n3")
self.parent().get_transform_layout().addWidget(self.n3)
QtCore.QObject.connect(self.n3, QtCore.SIGNAL("valueChanged"),
self.slider_rotate)
self.n3_showing = True
self.current_src = self.src_map[str(val)]
self.update_rotations(t3d)
def load_src_options(self, widgit):
self.load_src()
for i in self.src_strings:
widgit.addItem(i)
def load_src(self):
# supported_rot_conventions
src_flags = []
src_flags.append("eman")
src_flags.append("spider")
src_flags.append("imagic")
src_flags.append("mrc")
src_flags.append("spin")
src_flags.append("xyz")
self.src_strings = []
self.src_map = {}
for i in src_flags:
self.src_strings.append(str(i))
self.src_map[str(i)] = i
def update_rotations(self, t3d):
rot = t3d.get_rotation(self.src_map[str(
self.src.itemText(self.src.currentIndex()))])
convention = self.src.currentText()
if (self.src_map[str(convention)] == "spin"):
self.n3.setValue(rot[self.n3.getLabel()], True)
self.az.setValue(rot[self.az.getLabel()], True)
self.alt.setValue(rot[self.alt.getLabel()], True)
self.phi.setValue(rot[self.phi.getLabel()], True)
def set_scale(self, newscale):
self.scale.setValue(newscale)
def set_xy_trans(self, x, y):
self.x_trans.setValue(x)
self.y_trans.setValue(y)
def set_xyz_trans(self, x, y, z):
self.x_trans.setValue(x)
self.y_trans.setValue(y)
self.z_trans.setValue(z)
class EMInspectorControlLine(EMInspectorControlShape):
"""
Class to make EMItem GUI SHAPE Line Inspector
"""
def __init__(self, name, item3d):
EMInspectorControlShape.__init__(self, name, item3d)
def updateItemControls(self):
""" Updates this item inspector. Function is called by the item it observes"""
super(EMInspectorControlLine, self).updateItemControls()
def updateMetaData(self):
""" Updates the items metadata, such as line length, width. Function is called by the item it observes when the items meta data changes """
super(EMInspectorControlLine, self).updateMetaData()
self.leftArrowSize.setValue(self.item3d().leftArrowSize, quiet=1)
self.leftArrowLength.setValue(self.item3d().leftArrowLength, quiet=1)
self.rightArrowSize.setValue(self.item3d().rightArrowSize, quiet=1)
self.rightArrowLength.setValue(self.item3d().rightArrowLength, quiet=1)
self.slice.setValue(self.item3d().slices, quiet=1)
self.stack.setValue(self.item3d().stacks, quiet=1)
self.linelength.setValue(int(self.item3d().length), quiet=1)
def addTabs(self):
""" Add a tab for each 'column' """
super(EMInspectorControlLine, self).addTabs()
tabwidget = QtGui.QWidget()
gridbox = QtGui.QGridLayout()
EMInspectorControlLine.addControls(self, gridbox)
tabwidget.setLayout(gridbox)
self.addTab(tabwidget, "line")
def addControls(self, gridbox):
""" Construct all the widgets in this Item Inspector """
#frame to control properties of left/right arrows
lineframe = QtGui.QFrame()
lineframe.setFrameShape(QtGui.QFrame.StyledPanel)
lfont = QtGui.QFont()
lfont.setBold(True)
linegridbox = QtGui.QGridLayout()
leftlabel = QtGui.QLabel("Left arrow")
leftlabel.setFont(lfont)
leftlabel.setAlignment(QtCore.Qt.AlignCenter)
linegridbox.addWidget(leftlabel, 0, 1, 1, 1)
sidelabel1 = QtGui.QLabel("Size")
sidelabel1.setFont(lfont)
sidelabel1.setAlignment(QtCore.Qt.AlignVCenter)
linegridbox.addWidget(sidelabel1, 2, 0, 1, 1)
sidelabel2 = QtGui.QLabel("Length")
sidelabel2.setFont(lfont)
sidelabel2.setAlignment(QtCore.Qt.AlignVCenter)
linegridbox.addWidget(sidelabel2, 3, 0, 1, 1)
self.leftShowArrow = QtGui.QCheckBox("Show")
self.leftShowArrow.setChecked(self.item3d().showLeftArrow)
linegridbox.addWidget(self.leftShowArrow, 1, 1, 1, 1)
self.leftArrowSize = EMSpinWidget(int(self.item3d().leftArrowSize), 1.0, rounding=0)
self.leftArrowSize.setMinimumWidth(120)
linegridbox.addWidget(self.leftArrowSize, 2, 1, 1, 1)
self.leftArrowLength = EMSpinWidget(int(self.item3d().leftArrowLength), 1.0, rounding=0)
self.leftArrowLength.setMinimumWidth(120)
linegridbox.addWidget(self.leftArrowLength, 3, 1, 1, 1)
rightlabel = QtGui.QLabel("Right arrow")
rightlabel.setFont(lfont)
rightlabel.setAlignment(QtCore.Qt.AlignCenter)
linegridbox.addWidget(rightlabel, 0, 2, 1, 1)
self.rightShowArrow = QtGui.QCheckBox("Show")
self.rightShowArrow.setChecked(self.item3d().showRightArrow)
linegridbox.addWidget(self.rightShowArrow, 1, 2, 1, 1)
self.rightArrowSize = EMSpinWidget(int(self.item3d().rightArrowSize), 1.0, rounding=0)
self.rightArrowSize.setMinimumWidth(120)
linegridbox.addWidget(self.rightArrowSize, 2, 2, 1, 1)
self.rightArrowLength = EMSpinWidget(int(self.item3d().rightArrowLength), 1.0, rounding=0)
self.rightArrowLength.setMinimumWidth(120)
linegridbox.addWidget(self.rightArrowLength, 3, 2, 1, 1)
linelengthlabel = QtGui.QLabel("Line Length")
linelengthlabel.setFont(lfont)
linelengthlabel.setAlignment(QtCore.Qt.AlignCenter)
linegridbox.addWidget(linelengthlabel, 4, 0, 2, 2)
self.linelength = EMSpinWidget(int(self.item3d().length), 1.0, rounding=0)
linegridbox.addWidget(self.linelength, 4, 2, 2, 2)
linewidthlabel = QtGui.QLabel("Line Width")
linewidthlabel.setFont(lfont)
linewidthlabel.setAlignment(QtCore.Qt.AlignCenter)
linegridbox.addWidget(linewidthlabel, 5, 0, 1, 2)
self.linewidth = EMSpinWidget(int(self.item3d().width), 1.0, rounding=0)
linegridbox.addWidget(self.linewidth, 5, 2, 1, 2)
lineframe.setLayout(linegridbox)
gridbox.addWidget(lineframe, 2, 0)
#frame to control slice/stack of the line
lineframe2 = QtGui.QFrame()
lineframe2.setFrameShape(QtGui.QFrame.StyledPanel)
linehbox = QtGui.QVBoxLayout()
self.slice = ValSlider(lineframe2, (1, 100), "Slice", rounding=0)
self.slice.setValue(self.item3d().slices)
self.stack = ValSlider(lineframe2, (1, 100), "Stack", rounding=0)
self.slice.setValue(self.item3d().stacks)
linehbox.addWidget(self.slice)
linehbox.addWidget(self.stack)
lineframe2.setLayout(linehbox)
gridbox.addWidget(lineframe2, 3, 0)
# set to default, but run only as a base class
if type(self) == EMInspectorControl3DText:
self.updateItemControls()
self.updateMetaData()
QtCore.QObject.connect(self.leftShowArrow, QtCore.SIGNAL("stateChanged(int)"), self.redraw)
QtCore.QObject.connect(self.rightShowArrow, QtCore.SIGNAL("stateChanged(int)"), self.redraw)
QtCore.QObject.connect(self.leftArrowSize,QtCore.SIGNAL("valueChanged(int)"),self.redraw)
QtCore.QObject.connect(self.leftArrowLength,QtCore.SIGNAL("valueChanged(int)"),self.redraw)
QtCore.QObject.connect(self.rightArrowSize,QtCore.SIGNAL("valueChanged(int)"),self.redraw)
QtCore.QObject.connect(self.rightArrowLength,QtCore.SIGNAL("valueChanged(int)"),self.redraw)
QtCore.QObject.connect(self.linelength,QtCore.SIGNAL("valueChanged(int)"),self.redraw)
QtCore.QObject.connect(self.linewidth,QtCore.SIGNAL("valueChanged(int)"),self.redraw)
QtCore.QObject.connect(self.slice,QtCore.SIGNAL("valueChanged"),self.redraw)
QtCore.QObject.connect(self.stack,QtCore.SIGNAL("valueChanged"),self.redraw)
def redraw(self):
self.item3d().setShowLeftArrow(self.leftShowArrow.isChecked())
self.item3d().setShowRightArrow(self.rightShowArrow.isChecked())
self.item3d().leftArrowSize = self.leftArrowSize.getValue()
self.item3d().leftArrowLength = self.leftArrowLength.getValue()
self.item3d().rightArrowSize = self.rightArrowSize.getValue()
self.item3d().rightArrowLength = self.rightArrowLength.getValue()
self.item3d().setLength(self.linelength.getValue())
self.item3d().setWidth(self.linewidth.getValue())
self.item3d().setSlices(self.slice.getValue())
self.item3d().setStacks(self.stack.getValue())
if self.inspector:
self.inspector().updateSceneGraph()
class EMHelloWorldInspector(QtGui.QWidget):
def __init__(self,target) :
QtGui.QWidget.__init__(self,None)
self.target=target
self.vbl = QtGui.QVBoxLayout(self)
self.vbl.setMargin(0)
self.vbl.setSpacing(6)
self.vbl.setObjectName("vbl")
self.hbl = QtGui.QHBoxLayout()
self.hbl.setMargin(0)
self.hbl.setSpacing(6)
self.hbl.setObjectName("hbl")
self.vbl.addLayout(self.hbl)
self.vbl2 = QtGui.QVBoxLayout()
self.vbl2.setMargin(0)
self.vbl2.setSpacing(6)
self.vbl2.setObjectName("vbl2")
self.hbl.addLayout(self.vbl2)
self.wiretog = QtGui.QPushButton("Wire")
self.wiretog.setCheckable(1)
self.vbl2.addWidget(self.wiretog)
self.lighttog = QtGui.QPushButton("Light")
self.lighttog.setCheckable(1)
self.vbl2.addWidget(self.lighttog)
self.tabwidget = QtGui.QTabWidget()
self.maintab = None
self.tabwidget.addTab(self.get_main_tab(), "Main")
self.tabwidget.addTab(self.get_GL_tab(),"GL")
self.vbl.addWidget(self.tabwidget)
self.n3_showing = False
QtCore.QObject.connect(self.scale, QtCore.SIGNAL("valueChanged"), target.set_scale)
QtCore.QObject.connect(self.az, QtCore.SIGNAL("valueChanged"), self.slider_rotate)
QtCore.QObject.connect(self.alt, QtCore.SIGNAL("valueChanged"), self.slider_rotate)
QtCore.QObject.connect(self.phi, QtCore.SIGNAL("valueChanged"), self.slider_rotate)
QtCore.QObject.connect(self.cbb, QtCore.SIGNAL("currentIndexChanged(QString)"), target.setColor)
QtCore.QObject.connect(self.src, QtCore.SIGNAL("currentIndexChanged(QString)"), self.set_src)
QtCore.QObject.connect(self.x_trans, QtCore.SIGNAL("valueChanged(double)"), target.set_cam_x)
QtCore.QObject.connect(self.y_trans, QtCore.SIGNAL("valueChanged(double)"), target.set_cam_y)
QtCore.QObject.connect(self.z_trans, QtCore.SIGNAL("valueChanged(double)"), target.set_cam_z)
QtCore.QObject.connect(self.wiretog, QtCore.SIGNAL("toggled(bool)"), target.toggle_wire)
QtCore.QObject.connect(self.lighttog, QtCore.SIGNAL("toggled(bool)"), target.toggle_light)
QtCore.QObject.connect(self.glcontrast, QtCore.SIGNAL("valueChanged"), target.set_GL_contrast)
QtCore.QObject.connect(self.glbrightness, QtCore.SIGNAL("valueChanged"), target.set_GL_brightness)
def get_GL_tab(self):
self.gltab = QtGui.QWidget()
gltab = self.gltab
gltab.vbl = QtGui.QVBoxLayout(self.gltab )
gltab.vbl.setMargin(0)
gltab.vbl.setSpacing(6)
gltab.vbl.setObjectName("Main")
self.glcontrast = ValSlider(gltab,(1.0,5.0),"GLShd:")
self.glcontrast.setObjectName("GLShade")
self.glcontrast.setValue(1.0)
gltab.vbl.addWidget(self.glcontrast)
self.glbrightness = ValSlider(gltab,(-1.0,0.0),"GLBst:")
self.glbrightness.setObjectName("GLBoost")
self.glbrightness.setValue(0.1)
self.glbrightness.setValue(0.0)
gltab.vbl.addWidget(self.glbrightness)
return gltab
def get_main_tab(self):
if ( self.maintab == None ):
self.maintab = QtGui.QWidget()
maintab = self.maintab
maintab.vbl = QtGui.QVBoxLayout(self.maintab)
maintab.vbl.setMargin(0)
maintab.vbl.setSpacing(6)
maintab.vbl.setObjectName("Main")
self.scale = ValSlider(maintab,(0.01,30.0),"Zoom:")
self.scale.setObjectName("scale")
self.scale.setValue(1.0)
maintab.vbl.addWidget(self.scale)
self.hbl_color = QtGui.QHBoxLayout()
self.hbl_color.setMargin(0)
self.hbl_color.setSpacing(6)
self.hbl_color.setObjectName("Material")
maintab.vbl.addLayout(self.hbl_color)
self.color_label = QtGui.QLabel()
self.color_label.setText('Material')
self.hbl_color.addWidget(self.color_label)
self.cbb = QtGui.QComboBox(maintab)
self.hbl_color.addWidget(self.cbb)
self.hbl_trans = QtGui.QHBoxLayout()
self.hbl_trans.setMargin(0)
self.hbl_trans.setSpacing(6)
self.hbl_trans.setObjectName("Trans")
maintab.vbl.addLayout(self.hbl_trans)
self.x_label = QtGui.QLabel()
self.x_label.setText('x')
self.hbl_trans.addWidget(self.x_label)
self.x_trans = QtGui.QDoubleSpinBox(self)
self.x_trans.setMinimum(-10000)
self.x_trans.setMaximum(10000)
self.x_trans.setValue(0.0)
self.hbl_trans.addWidget(self.x_trans)
self.y_label = QtGui.QLabel()
self.y_label.setText('y')
self.hbl_trans.addWidget(self.y_label)
self.y_trans = QtGui.QDoubleSpinBox(maintab)
self.y_trans.setMinimum(-10000)
self.y_trans.setMaximum(10000)
self.y_trans.setValue(0.0)
self.hbl_trans.addWidget(self.y_trans)
self.z_label = QtGui.QLabel()
self.z_label.setText('z')
self.hbl_trans.addWidget(self.z_label)
self.z_trans = QtGui.QDoubleSpinBox(maintab)
self.z_trans.setMinimum(-10000)
self.z_trans.setMaximum(10000)
self.z_trans.setValue(0.0)
self.hbl_trans.addWidget(self.z_trans)
self.hbl_src = QtGui.QHBoxLayout()
self.hbl_src.setMargin(0)
self.hbl_src.setSpacing(6)
self.hbl_src.setObjectName("hbl")
maintab.vbl.addLayout(self.hbl_src)
self.label_src = QtGui.QLabel()
self.label_src.setText('Rotation Convention')
self.hbl_src.addWidget(self.label_src)
self.src = QtGui.QComboBox(maintab)
self.load_src_options(self.src)
self.hbl_src.addWidget(self.src)
# set default value -1 ensures that the val slider is updated the first time it is created
self.az = ValSlider(self,(-360.0,360.0),"az",-1)
self.az.setObjectName("az")
maintab.vbl.addWidget(self.az)
self.alt = ValSlider(self,(-180.0,180.0),"alt",-1)
self.alt.setObjectName("alt")
maintab.vbl.addWidget(self.alt)
self.phi = ValSlider(self,(-360.0,360.0),"phi",-1)
self.phi.setObjectName("phi")
maintab.vbl.addWidget(self.phi)
self.current_src = EULER_EMAN
return self.maintab
def set_xy_trans(self, x, y):
self.x_trans.setValue(x)
self.y_trans.setValue(y)
def set_xyz_trans(self,x,y,z):
self.x_trans.setValue(x)
self.y_trans.setValue(y)
self.z_trans.setValue(z)
def set_translate_scale(self, xscale,yscale,zscale):
self.x_trans.setSingleStep(xscale)
self.y_trans.setSingleStep(yscale)
self.z_trans.setSingleStep(zscale)
def update_rotations(self,t3d):
convention = str( self.src.currentText() )
#FIXME: Transform.get_rotation() wants a string sometimes and a EulerType other times
try:
rot = t3d.get_rotation(str(self.src_map[convention]))
except Exception as e: #doing a quick fix
print(e)
print("Developers: This catches a large range of exceptions... a better way surely exists")
rot = t3d.get_rotation(self.src_map[convention])
if ( self.src_map[convention] == EULER_SPIN ):
self.n3.setValue(rot[self.n3.getLabel()],True)
self.az.setValue(rot[self.az.getLabel()],True)
self.alt.setValue(rot[self.alt.getLabel()],True)
self.phi.setValue(rot[self.phi.getLabel()],True)
def slider_rotate(self):
self.target.load_rotation(self.get_current_rotation())
def get_current_rotation(self):
convention = self.src.currentText()
rot = {}
if ( self.current_src == EULER_SPIN ):
rot[self.az.getLabel()] = self.az.getValue()
n1 = self.alt.getValue()
n2 = self.phi.getValue()
n3 = self.n3.getValue()
norm = sqrt(n1*n1 + n2*n2 + n3*n3)
n1 /= norm
n2 /= norm
n3 /= norm
rot[self.alt.getLabel()] = n1
rot[self.phi.getLabel()] = n2
rot[self.n3.getLabel()] = n3
else:
rot[self.az.getLabel()] = self.az.getValue()
rot[self.alt.getLabel()] = self.alt.getValue()
rot[self.phi.getLabel()] = self.phi.getValue()
return Transform(self.current_src, rot)
def set_src(self, val):
t3d = self.get_current_rotation()
if (self.n3_showing) :
self.vbl.removeWidget(self.n3)
self.n3.deleteLater()
self.n3_showing = False
self.az.setRange(-360,360)
self.alt.setRange(-180,180)
self.phi.setRange(-360,660)
if ( self.src_map[str(val)] == EULER_SPIDER ):
self.az.setLabel('phi')
self.alt.setLabel('theta')
self.phi.setLabel('psi')
elif ( self.src_map[str(val)] == EULER_EMAN ):
self.az.setLabel('az')
self.alt.setLabel('alt')
self.phi.setLabel('phi')
elif ( self.src_map[str(val)] == EULER_IMAGIC ):
self.az.setLabel('alpha')
self.alt.setLabel('beta')
self.phi.setLabel('gamma')
elif ( self.src_map[str(val)] == EULER_XYZ ):
self.az.setLabel('xtilt')
self.alt.setLabel('ytilt')
self.phi.setLabel('ztilt')
elif ( self.src_map[str(val)] == EULER_MRC ):
self.az.setLabel('phi')
self.alt.setLabel('theta')
self.phi.setLabel('omega')
elif ( self.src_map[str(val)] == EULER_SPIN ):
self.az.setLabel('omega')
self.alt.setRange(-1,1)
self.phi.setRange(-1,1)
self.alt.setLabel('n1')
self.phi.setLabel('n2')
self.n3 = ValSlider(self,(-360.0,360.0),"n3",-1)
self.n3.setRange(-1,1)
self.n3.setObjectName("n3")
self.vbl.addWidget(self.n3)
QtCore.QObject.connect(self.n3, QtCore.SIGNAL("valueChanged"), self.slider_rotate)
self.n3_showing = True
self.current_src = self.src_map[str(val)]
self.update_rotations(t3d)
def load_src_options(self,widgit):
self.load_src()
for i in self.src_strings:
widgit.addItem(i)
# read src as 'supported rotation conventions'
def load_src(self):
# supported_rot_conventions
src_flags = []
src_flags.append(EULER_EMAN)
src_flags.append(EULER_SPIDER)
src_flags.append(EULER_IMAGIC)
src_flags.append(EULER_MRC)
src_flags.append(EULER_SPIN)
src_flags.append(EULER_XYZ)
self.src_strings = []
self.src_map = {}
for i in src_flags:
self.src_strings.append(str(i))
self.src_map[str(i)] = i
def setColors(self,colors,current_color):
a = 0
for i in colors:
self.cbb.addItem(i)
if ( i == current_color):
self.cbb.setCurrentIndex(a)
a += 1
def set_scale(self,newscale):
self.scale.setValue(newscale)
