def select_folder(self, row, col):
idx=int(self.imglst.item(row, 0).text())
sfx=self.dp_folder.currentText()
self.path="{}_{:02d}".format(sfx, idx)
#if self.browser.isup == False:
# self.show_browser()
# print("Showing {} in browser.".format(path))
self.browser.setPath(self.path)
vols = []
for f in os.listdir(self.path):
if "threed" in f:
if "even" not in f and "odd" not in f:
vols.append(f)#"{}".format(self.path,f))
lastvol = sorted(vols)[-1]
print("Displaying {} from {}".format(lastvol,self.path))
volpath = "{}/{}".format(self.path,lastvol)
name = os.path.basename(str(volpath))
if self.wg_thumbnail.newnode:
self.wg_thumbnail.newnode.setData(volpath)
else:
self.wg_thumbnail.newnode = EMDataItem3D(volpath)
self.cur_3d_node=self.wg_thumbnail.newnode
self.wg_thumbnail.insertNewNode(name, self.wg_thumbnail.newnode)
self.wg_thumbnail.newnode.setTransform(self.wg_thumbnail.newnode.getParentMatrixProduct().inverse()*self.wg_thumbnail.newnode.getTransform())
self.wg_thumbnail.isonode = EMIsosurface(self.wg_thumbnail.newnode, transform=Transform())
self.wg_thumbnail.insertNewNode("Isosurface", self.wg_thumbnail.isonode, parentnode=self.wg_thumbnail.newnode)
self.wg_thumbnail.updateSG()
def menu_add_3dwin(self):
if self.viewer == None: return
self.viewer.append(EMScene3D())
self.sgdata = EMDataItem3D(test_image_3d(3), transform=Transform())
self.viewer[-1].insertNewNode('Data',
self.sgdata,
parentnode=self.viewer[-1])
isosurface = EMIsosurface(self.sgdata, transform=Transform())
self.viewer[-1].insertNewNode("Iso",
isosurface,
parentnode=self.sgdata)
volslice = EMSliceItem3D(self.sgdata, transform=Transform())
self.viewer[-1].insertNewNode("Slice",
volslice,
parentnode=self.sgdata)
self.viewer[-1].show()
self.needupdate = 1
def setData(self, data):
if data == None:
self.data = None
return
elif isinstance(data, str):
self.datafile = data
self.nimg = EMUtil.get_image_count(data)
if self.dataidx >= 0 and self.dataidx < self.nimg:
ii = self.dataidx
self.nimg = 1
else:
ii = 0
hdr = EMData(data, 0, 1)
self.origdata = EMData(data, ii)
if self.origdata["nz"] == 1:
if self.nimg > 20 and hdr["ny"] > 512:
self.origdata = EMData.read_images(
data, list(range(0, self.nimg, self.nimg // 20))
) # read regularly separated images from the file totalling ~20
elif self.nimg > 100:
self.origdata = EMData.read_images(
data,
list(range(0, 72)) +
list(range(72, self.nimg, self.nimg // 100))
) # read the first 36 then regularly separated images from the file
elif self.nimg > 1:
self.origdata = EMData.read_images(data,
list(range(self.nimg)))
else:
self.origdata = [self.origdata]
else:
self.origdata = [self.origdata]
else:
self.datafile = None
if isinstance(data, EMData): self.origdata = [data]
else: self.origdata = data
self.nx = self.origdata[0]["nx"]
self.ny = self.origdata[0]["ny"]
self.nz = self.origdata[0]["nz"]
if self.apix <= 0.0: self.apix = self.origdata[0]["apix_x"]
EMProcessorWidget.parmdefault["apix"] = (0, (0.2, 10.0), self.apix,
None)
origfft = self.origdata[0].do_fft()
self.pspecorig = origfft.calc_radial_dist(old_div(self.ny, 2), 0.0,
1.0, 1)
ds = old_div(1.0, (self.apix * self.ny))
self.pspecs = [ds * i for i in range(len(self.pspecorig))]
if self.viewer != None:
for v in self.viewer:
v.close()
if self.nz == 1 or self.force2d or (self.nx > 320
and self.safemode == False):
if len(self.origdata) > 1:
self.viewer = [EMImageMXWidget()]
self.mfile_save_stack.setEnabled(True)
else:
self.viewer = [EMImage2DWidget()]
self.mfile_save_stack.setEnabled(False)
else:
self.mfile_save_stack.setEnabled(False)
self.viewer = [EMScene3D()]
self.sgdata = EMDataItem3D(test_image_3d(3), transform=Transform())
self.viewer[0].insertNewNode('Data',
self.sgdata,
parentnode=self.viewer[0])
isosurface = EMIsosurface(self.sgdata, transform=Transform())
self.viewer[0].insertNewNode("Iso",
isosurface,
parentnode=self.sgdata)
volslice = EMSliceItem3D(self.sgdata, transform=Transform())
self.viewer[0].insertNewNode("Slice",
volslice,
parentnode=self.sgdata)
if self.nz > 1: self.mfile_save_map.setEnabled(True)
else: self.mfile_save_map.setEnabled(False)
E2loadappwin("e2filtertool", "image", self.viewer[0].qt_parent)
if self.origdata[0].has_attr("source_path"):
winname = str(self.origdata[0]["source_path"])
else:
winname = "FilterTool"
self.viewer[0].setWindowTitle(winname)
self.procChange(-1)
def main():
usage = """prog --path <spt_xx> --iter <X> --tomo <tomogram>
map aligned particles back to tomograms """
parser = EMArgumentParser(usage=usage, version=EMANVERSION)
parser.add_argument("--path",
type=str,
help="spt_xx path",
default="",
guitype='strbox',
row=0,
col=0,
rowspan=1,
colspan=1)
parser.add_argument("--iter",
type=int,
help="iteration number",
default=1,
guitype='intbox',
row=0,
col=1,
rowspan=1,
colspan=1)
parser.add_argument(
"--tomo",
type=str,
help="tomogram file name",
default="",
guitype='filebox',
browser="EMBrowserWidget(withmodal=True, startpath='tomograms')",
row=2,
col=0,
rowspan=1,
colspan=2,
)
parser.add_argument(
"--avg",
type=str,
help="3D volume to insert. spt_xx/threed_xx if unspecified",
default="",
guitype='filebox',
browser="EMBrowserWidget(withmodal=True, startpath='.')",
row=3,
col=0,
rowspan=1,
colspan=2)
parser.add_argument("--postxf",
type=str,
help="extra shift after alignment",
default="")
parser.add_argument(
"--keep",
type=float,
help=
"propotion to keep. will exclude bad particles if this is smaller than 1.0",
default=1.0)
parser.add_argument(
"--gui",
action="store_true",
help="open the resulting map and tomogram in a GUI display",
default=False,
guitype="boolbox",
row=4,
col=0,
rowspan=1,
colspan=1)
parser.add_argument("--ppid", type=int, help="ppid...", default=-1)
(options, args) = parser.parse_args()
logid = E2init(sys.argv)
path = options.path
itr = options.iter
try:
postxf = options.postxf.split(',')
postxf = [float(i) for i in postxf]
print("post shift : ", postxf)
except:
postxf = [0, 0, 0]
js = js_open_dict("{}/particle_parms_{:02d}.json".format(path, itr))
tomo = EMData(options.tomo)
if options.gui: tomo_orig = tomo.copy()
if len(options.avg) == 0:
options.avg = "{}/threed_{:02d}.hdf".format(path, itr)
avg = EMData(options.avg, 0)
print("Using averaged map {}".format(options.avg))
apix_tomo = tomo["apix_x"]
apix_ptcl = avg["apix_x"]
shrink = apix_tomo / apix_ptcl
print(
"Apix from tomogram {:.2f}, apix from average {:.2f}. Shrinking factor {:.1f}"
.format(apix_tomo, apix_ptcl, shrink))
avg.process_inplace("math.fft.resample", {"n": shrink})
avg.process_inplace("normalize.edgemean")
tomo.to_zero()
ptcl = []
scr = []
llfile = ""
bname = base_name(options.tomo)
for k in js.keys():
fsp, i = eval(k)
if fsp[-4:] == ".lst":
if llfile != fsp:
llfile = fsp
lsx = LSXFile(fsp, True)
i, fsp, x = lsx.read(i)
if base_name(fsp) == bname:
ptcl.append((js[k]["score"], fsp, i, js[k]["xform.align3d"]))
ptcl.sort()
print(ptcl)
nptcl = int(len(ptcl) * options.keep)
if options.keep < 1.0:
sthr = ptcl[nptcl][0]
else:
sthr = 100
pts = []
print("{:d} particles total.".format(int(nptcl)))
if nptcl == 0:
print("No particles. Exiting")
sys.exit(0)
for s, fsp, i, xf in ptcl:
if s > sthr:
continue
a = EMData(fsp, i, True)
if tomo.has_attr("zshift"):
zs = tomo["zshift"]
else:
zs = 0
crd = np.array(a["ptcl_source_coord"]) / shrink + [
tomo["nx"] // 2, tomo["ny"] // 2, tomo["nz"] // 2 + zs / shrink
]
ts = np.array(xf.get_trans())
ts += postxf
xf.set_trans((ts / shrink).tolist())
xf = xf.inverse()
t = avg.process("xform", {"transform": xf})
pts.append(crd - ts / 4)
tomo.insert_scaled_sum(t, crd.tolist())
print("\t{}/{} finished.".format(len(pts), nptcl), end='\r')
sys.stdout.flush()
pts = np.array(pts)
pfile = "{}/ptcls_pos_{:02d}.pdb".format(path, itr)
tfile = "{}/ptcls_in_tomo_{}_{:02d}.hdf".format(path, bname, itr)
tomo.write_compressed(tfile, 0, 8)
numpy2pdb(fname=pfile, data=pts)
print("Map {} particles to the tomogram".format(len(pts)))
print("Particle coordinates written to {}".format(pfile))
print("Map with particles written to {}".format(tfile))
js = None
E2end(logid)
if options.gui:
print("opening GUI")
from eman2_gui.emapplication import get_application, EMApp
from eman2_gui.emscene3d import EMScene3D
from eman2_gui.emdataitem3d import EMDataItem3D, EMIsosurface, EMSliceItem3D
from eman2_gui.emshape import EMShape
app = EMApp()
view = EMScene3D()
# slice through the original tomogram
tomo_orig_di = EMDataItem3D(tomo_orig, transform=Transform())
view.insertNewNode('Data', tomo_orig_di, parentnode=view)
volslice = EMSliceItem3D(tomo_orig_di, transform=Transform())
view.insertNewNode("Slice", volslice, parentnode=tomo_orig_di)
# isosurface of reconstituted particles
tomo_di = EMDataItem3D(tomo, transform=Transform())
view.insertNewNode('Data', tomo_di, parentnode=view)
isosurface = EMIsosurface(tomo_di, transform=Transform())
view.insertNewNode("Iso", isosurface, parentnode=tomo_di)
view.show()
try:
view.raise_()
except:
pass
app.execute()
print("Done.")
def setData(self, data):
if data == None:
self.data = None
return
elif isinstance(data, str):
self.datafile = data
self.nimg = EMUtil.get_image_count(data)
self.origdata = EMData(data, 0)
if self.origdata["nz"] == 1:
if self.nimg > 20:
self.origdata = EMData.read_images(
data, list(range(0, self.nimg, old_div(self.nimg, 20)))
) # read regularly separated images from the file totalling ~20
elif self.nimg > 1:
self.origdata = EMData.read_images(data,
list(range(self.nimg)))
else:
self.origdata = [self.origdata]
else:
self.origdata = [self.origdata]
else:
self.datafile = None
if isinstance(data, EMData): self.origdata = [data]
else: self.origdata = data
self.nx = self.origdata[0]["nx"]
self.ny = self.origdata[0]["ny"]
self.nz = self.origdata[0]["nz"]
if self.apix <= 0.0: self.apix = self.origdata[0]["apix_x"]
EMProcessorWidget.parmdefault["apix"] = (0, (0.2, 10.0), self.apix,
None)
origfft = self.origdata[0].do_fft()
self.pspecorig = origfft.calc_radial_dist(old_div(self.ny, 2), 0.0,
1.0, 1)
ds = old_div(1.0, (self.apix * self.ny))
self.pspecs = [ds * i for i in range(len(self.pspecorig))]
if self.viewer != None:
for v in self.viewer:
v.close()
if self.nz == 1 or self.force2d:
if len(self.origdata) > 1:
self.viewer = [EMImageMXWidget()]
self.mfile_save_stack.setEnabled(True)
self.mfile_save_map.setEnabled(False)
else:
self.viewer = [EMImage2DWidget()]
self.mfile_save_stack.setEnabled(False)
self.mfile_save_map.setEnabled(True)
else:
self.mfile_save_stack.setEnabled(False)
self.mfile_save_map.setEnabled(True)
self.viewer = [EMScene3D()]
self.sgdata = EMDataItem3D(test_image_3d(3), transform=Transform())
self.viewer[0].insertNewNode('Data',
self.sgdata,
parentnode=self.viewer[0])
isosurface = EMIsosurface(self.sgdata, transform=Transform())
self.viewer[0].insertNewNode("Iso",
isosurface,
parentnode=self.sgdata)
volslice = EMSliceItem3D(self.sgdata, transform=Transform())
self.viewer[0].insertNewNode("Slice",
volslice,
parentnode=self.sgdata)
E2loadappwin("e2filtertool", "image", self.viewer[0].qt_parent)
self.procChange(-1)
def __init__(self, application, opt):
self.options = opt
"""application is an QApplication instance. path is the path for ouput files"""
QtWidgets.QWidget.__init__(self)
self.particles = None
self.app = weakref.ref(application)
self.setWindowTitle("Main Window (e2gmm.py)")
# Menu Bar
#self.mfile=self.menuBar().addMenu("File")
#self.mfileopen=self.mfile.addAction("Select Particles")
#self.mfileopencls=self.mfile.addAction("Particles from Classes")
#self.mfileopencls.setEnabled(False)
#self.mfilequit=self.mfile.addAction("Quit")
self.setCentralWidget(QtWidgets.QWidget())
self.gbl = QtWidgets.QGridLayout(self.centralWidget())
cen = self.centralWidget()
self.gbl.setColumnStretch(0, 0)
self.gbl.setColumnStretch(2, 4)
self.gbl.setColumnStretch(4, 5)
# Plot
self.wplot2d = EMPlot2DWidget()
self.gbl.addWidget(self.wplot2d, 0, 2, 3, 1)
self.wplot2d.set_mouse_emit(True)
# 3-D View
self.wview3d = EMScene3D()
self.gbl.addWidget(self.wview3d, 0, 4, 3, 1)
# Left pane for GMM folder and parameters
self.gbll = QtWidgets.QGridLayout()
self.gbl.addLayout(self.gbll, 0, 0, 4, 1) # 4 rows tall, 1 column wide
# gmm_XX folder selection
self.gblfld = QtWidgets.QGridLayout()
self.gbll.addLayout(self.gblfld, 0, 0)
self.wlistgmm = QtWidgets.QListWidget()
self.wlistgmm.setSizePolicy(QtWidgets.QSizePolicy.Preferred,
QtWidgets.QSizePolicy.Expanding)
self.update_gmms()
self.gblfld.addWidget(self.wlistgmm, 0, 0, 1, 2)
self.wbutnewgmm = QtWidgets.QPushButton("New GMM")
self.gblfld.addWidget(self.wbutnewgmm, 1, 0)
self.wbutrefine = QtWidgets.QPushButton("refine_XX")
self.gblfld.addWidget(self.wbutrefine, 1, 1)
# run selection
self.gblrun = QtWidgets.QGridLayout()
self.gbll.addLayout(self.gblrun, 1, 0)
self.wlistrun = QtWidgets.QListWidget()
self.wlistrun.setSizePolicy(QtWidgets.QSizePolicy.Preferred,
QtWidgets.QSizePolicy.Expanding)
# self.update_runs()
self.gblrun.addWidget(self.wlistrun, 0, 0, 1, 2)
self.wbutrerun = QtWidgets.QPushButton("Rerun")
self.gblrun.addWidget(self.wbutrerun, 1, 1)
self.wbutnewrun = QtWidgets.QPushButton("New Run")
self.gblrun.addWidget(self.wbutnewrun, 1, 0)
# The form with details about the selected gmm_XX folder
self.gflparm = QtWidgets.QFormLayout()
self.gbll.addLayout(self.gflparm, 2, 0)
self.wlpath = QtWidgets.QLabel("-")
self.wlpath.setToolTip("Path this GMM is based on")
self.gflparm.addRow("Path:", self.wlpath)
self.wedbox = QtWidgets.QLineEdit("256")
self.wedbox.setToolTip("Box size of input particles in pixels")
self.gflparm.addRow("Box Size:", self.wedbox)
self.wedres = QtWidgets.QLineEdit("25")
self.wedres.setToolTip(
"Maximum resolution to use for gaussian fitting")
self.gflparm.addRow("Target Res:", self.wedres)
self.wedsym = QtWidgets.QLineEdit("c1")
self.wedsym.setToolTip("Symmetry used during refinement")
self.gflparm.addRow("Symmetry:", self.wedsym)
self.wedapix = QtWidgets.QLineEdit("1.0")
self.wedapix.setToolTip("A/pix of input particles")
self.gflparm.addRow("A/pix:", self.wedapix)
self.wedmask = QtWidgets.QLineEdit("")
self.wedmask.setToolTip("3-D volume mask")
self.gflparm.addRow("Mask:", self.wedmask)
self.wedngauss = QtWidgets.QLineEdit("64")
self.wedngauss.setToolTip("Number of Gaussians")
self.gflparm.addRow("N Gauss:", self.wedngauss)
self.weddim = QtWidgets.QLineEdit("4")
self.weddim.setToolTip(
"Number of dimensions in the latent space (middle network layer)")
self.gflparm.addRow("Latent Dim:", self.weddim)
self.wedtrainiter = QtWidgets.QLineEdit("10")
self.wedtrainiter.setToolTip("Training iterations per stage")
self.gflparm.addRow("Train iter:", self.wedtrainiter)
self.wbutpos = QtWidgets.QPushButton("Position")
self.wbutpos.setCheckable(True)
self.wbutpos.setChecked(True)
self.wbutpos.setToolTip(
"Include changes of position in the GMM (motion)")
self.gflparm.addRow("Parameters", self.wbutpos)
self.wbutamp = QtWidgets.QPushButton("Amplitude")
self.wbutamp.setCheckable(True)
self.wbutamp.setChecked(False)
self.wbutamp.setToolTip(
"Include changes of amplitude in the GMM (ligand binding)")
self.gflparm.addRow(" ", self.wbutamp)
self.wbutsig = QtWidgets.QPushButton("Sigma")
self.wbutsig.setCheckable(True)
self.wbutsig.setChecked(False)
self.wbutsig.setToolTip(
"Include changes of Gaussian Width in the GMM (rarely useful)")
self.gflparm.addRow(" ", self.wbutsig)
self.wlabruntime = QtWidgets.QLabel("-")
self.gflparm.addRow("Run:", self.wlabruntime)
# Widgets below plot
self.gblpltctl = QtWidgets.QGridLayout()
self.gbl.addLayout(self.gblpltctl, 3, 2)
self.gblpltctl.addWidget(QtWidgets.QLabel("X Col:", self), 0, 0,
Qt.AlignRight)
self.wsbxcol = QtWidgets.QSpinBox(self)
self.wsbxcol.setRange(0, 10)
self.gblpltctl.addWidget(self.wsbxcol, 0, 1, Qt.AlignLeft)
self.wsbxcol.setValue(0)
self.gblpltctl.addWidget(QtWidgets.QLabel("Y Col:", self), 1, 0,
Qt.AlignRight)
self.wsbycol = QtWidgets.QSpinBox(self)
self.wsbycol.setRange(0, 10)
self.gblpltctl.addWidget(self.wsbycol, 1, 1, Qt.AlignLeft)
self.wsbycol.setValue(1)
self.wbutdrgrp = QtWidgets.QButtonGroup()
self.wbutdrmid = QtWidgets.QPushButton("Net Mid")
self.wbutdrmid.setCheckable(True)
self.wbutdrmid.setChecked(True)
self.gblpltctl.addWidget(self.wbutdrmid, 0, 2)
self.wbutdrgrp.addButton(self.wbutdrmid, 0)
self.wbutdrpca = QtWidgets.QPushButton("PCA")
self.wbutdrpca.setCheckable(True)
self.gblpltctl.addWidget(self.wbutdrpca, 0, 3)
self.wbutdrgrp.addButton(self.wbutdrpca, 1)
self.wbutdrpca = QtWidgets.QPushButton("ICA")
self.wbutdrpca.setCheckable(True)
self.gblpltctl.addWidget(self.wbutdrpca, 0, 4)
self.wbutdrgrp.addButton(self.wbutdrpca, 2)
self.gblpltctl.addWidget(QtWidgets.QLabel("New Dim:", self), 1, 3,
Qt.AlignRight)
self.wsbnewdim = QtWidgets.QSpinBox(self)
self.wsbnewdim.setRange(2, 10)
self.gblpltctl.addWidget(self.wsbnewdim, 1, 4, Qt.AlignLeft)
self.wcbpntpln = QtWidgets.QComboBox()
self.wcbpntpln.addItem("Plane")
self.wcbpntpln.addItem("Point")
self.wcbpntpln.addItem("Region")
self.gblpltctl.addWidget(self.wcbpntpln, 1, 2)
# Widgets below 3D
self.gbl3dctl = QtWidgets.QGridLayout()
self.gbl.addLayout(self.gbl3dctl, 3, 4)
#self.wbutmap=QtWidgets.QPushButton("Map")
#self.wbutmap.setCheckable(True)
#self.wbutmap.setChecked(True)
#self.gbl3dctl.addWidget(self.wbutmap,0,0)
#self.wbutspheres=QtWidgets.QPushButton("Sphere Mdl")
#self.wbutspheres.setCheckable(True)
#self.wbutspheres.setChecked(True)
#self.gbl3dctl.addWidget(self.wbutspheres,0,1)
self.wvssphsz = ValSlider(self, (1, 50), "Size:", 3.0, 90)
self.gbl3dctl.addWidget(self.wvssphsz, 0, 2)
# Connections
self.wlistgmm.currentRowChanged[int].connect(self.sel_gmm)
#self.wbutspheres.clicked[bool].connect(self.new_3d_opt)
#self.wbutmap.clicked[bool].connect(self.new_3d_opt)
self.wvssphsz.valueChanged.connect(self.new_sph_size)
self.wbutnewgmm.clicked[bool].connect(self.add_gmm)
self.wbutrefine.clicked[bool].connect(self.setgmm_refine)
self.wlistrun.currentRowChanged[int].connect(self.sel_run)
self.wbutnewrun.clicked[bool].connect(self.new_run)
self.wbutrerun.clicked[bool].connect(self.do_run)
self.wbutdrgrp.buttonClicked[QtWidgets.QAbstractButton].connect(
self.plot_mode_sel)
self.wsbxcol.valueChanged[int].connect(self.wplot2d.setXAxisAll)
self.wsbycol.valueChanged[int].connect(self.wplot2d.setYAxisAll)
self.wplot2d.mousedown[QtGui.QMouseEvent,
tuple].connect(self.plot_mouse)
self.wplot2d.mouseup[QtGui.QMouseEvent, tuple].connect(self.plot_mouse)
self.wplot2d.mousedrag[QtGui.QMouseEvent,
tuple].connect(self.plot_mouse)
E2loadappwin("e2gmm", "main", self)
self.gaussplot = EMScatterPlot3D()
self.mapdataitem = EMDataItem3D(None)
self.mapiso = EMIsosurface(self.mapdataitem)
self.wview3d.insertNewNode("Neutral Map", self.mapdataitem)
self.wview3d.insertNewNode("Isosurface",
self.mapiso,
parentnode=self.mapdataitem)
self.wview3d.insertNewNode("Gauss Model", self.gaussplot)