def __init__(self, volfile, **kwargs):
print("on chimera projection client")
ChimeraAngDistClient.__init__(self, volfile, **kwargs)
self.projection = xmipp.Image()
self.projection.setDataType(md.DT_DOUBLE)
#0.5 -> Niquiest frequency
#2 -> bspline interpolation
size = self.kwargs.get('size', None)
defaultSize = self.xdim if self.xdim > 128 else 128
self.size = size if size else defaultSize
paddingFactor = self.kwargs.get('paddingFactor', 1)
maxFreq = self.kwargs.get('maxFreq', 0.5)
splineDegree = self.kwargs.get('splineDegree', 2)
self.fourierprojector = xmipp.FourierProjector(self.image,
paddingFactor, maxFreq,
splineDegree)
self.fourierprojector.projectVolume(self.projection, 0, 0, 0)
self.showjPort = self.kwargs.get('showjPort', None)
self.iw = ImageWindow(filename=os.path.basename(volfile),
image=self.projection,
dim=self.size,
label="Projection")
self.iw.updateData(flipud(self.projection.getData()))
if self.showjPort:
self.showjThread = Thread(target=self.listenShowJ)
self.showjThread.daemon = True
self.showjThread.start()
self.iw.root.protocol("WM_DELETE_WINDOW", self.exitClient)
self.iw.show()
def convertInputStep(self, volName):
# Read volume and convert to DOUBLE
self.vol = xmipp.Image(volName)
self.vol.convert2DataType(xmipp.DT_DOUBLE)
# Mask volume if needed
if self.refMask.get() is not None:
maskName = getImageLocation(self.refMask.get())
self.mask = xmipp.Image(maskName)
self.mask.convert2DataType(xmipp.DT_DOUBLE)
self.vol.inplaceMultiply(self.mask)
padding = 2
maxFreq = 0.5
splineDegree = 3
###
self.fourierProjectVol = xmipp.FourierProjector(
self.vol, padding, maxFreq, splineDegree)
###
partSet = self.inputParticles.get()
nPart = len(partSet)
numberOfTasks = min(nPart, max(self.numberOfThreads.get() - 1, 1))
taskSize = nPart / numberOfTasks
md = xmipp.MetaData()
# Convert angles and shifts from volume system of coordinates to
# projection system of coordinates
mdCount = 0
for index, part in enumerate(partSet):
objId = md.addObject()
imgRow = XmippMdRow()
particleToRow(part, imgRow)
shifts, angles = geometryFromMatrix(
part.getTransform().getMatrix(), True)
imgRow.setValue(xmipp.MDL_SHIFT_X, -shifts[0])
imgRow.setValue(xmipp.MDL_SHIFT_Y, -shifts[1])
imgRow.setValue(xmipp.MDL_SHIFT_Z, 0.)
imgRow.setValue(xmipp.MDL_ANGLE_ROT, angles[0])
imgRow.setValue(xmipp.MDL_ANGLE_TILT, angles[1])
imgRow.setValue(xmipp.MDL_ANGLE_PSI, angles[2])
imgRow.writeToMd(md, objId)
# Write a new metadata every taskSize number of elements
# except in the last chunk where we want to add also the
# remainder and the condition is the last element
if ((index % taskSize == taskSize - 1
and mdCount < numberOfTasks - 1) or index == nPart - 1):
md.write(self._getInputParticlesSubsetFn(mdCount))
md.clear()
mdCount += 1
x, y, _ = partSet.getDim()
xmipp.createEmptyFile(self._getProjGalleryFn(), x, y, 1, nPart)