def unRotationalAverage(xdata, ydata, shape): """ compute the rotational average of a 2D numpy array """ image = imagefun.fromRadialFunction(funcrad, shape, xdata=xdata, ydata=ydata, dtype=numpy.float64) return image
def unEllipticalAverage(xdata, ydata, ellipratio, ellipangle, shape):
"""
compute the rotational average of a 2D numpy array
ellip angle is positive toward y-axis
"""
radial = getEllipticalDistanceArray(ellipratio, ellipangle, shape)
radial = radial / math.sqrt(ellipratio)
image = imagefun.fromRadialFunction(funcrad,
shape,
xdata=xdata,
ydata=ydata)
def funcrc(r, c, radial, **kwargs):
rr = numpy.array(numpy.floor(r), dtype=numpy.int)
cc = numpy.array(numpy.floor(c), dtype=numpy.int)
rad = radial[rr, cc]
return funcrad(rad, **kwargs)
result = numpy.fromfunction(funcrc,
shape,
radial=radial,
xdata=xdata,
ydata=ydata,
dtype=numpy.float64)
return result
def unRotationalAverage(xdata, ydata, shape):
"""
compute the rotational average of a 2D numpy array
"""
image = imagefun.fromRadialFunction(funcrad, shape,
xdata=xdata, ydata=ydata, dtype=numpy.float64)
return image
def twodHann(size): rsize = int(math.ceil(size*math.sqrt(2))) xdata = numpy.arange(rsize)+0.5 xdata = xdata - xdata.mean() ydata = numpy.hanning(rsize) #ydata = numpy.hstack(([1], ydata)) hanntwod = imagefun.fromRadialFunction(funcrad, (size,size), xdata=xdata, ydata=ydata) return hanntwod
def unEllipticalAverage(xdata, ydata, ellipratio, ellipangle, shape): """ compute the rotational average of a 2D numpy array ellip angle is positive toward y-axis """ radial = getEllipticalDistanceArray(ellipratio, ellipangle, shape) radial = radial/math.sqrt(ellipratio) image = imagefun.fromRadialFunction(funcrad, shape, xdata=xdata, ydata=ydata) def funcrc(r, c, radial, **kwargs): rr = numpy.array(numpy.floor(r), dtype=numpy.int) cc = numpy.array(numpy.floor(c), dtype=numpy.int) rad = radial[rr,cc] return funcrad(rad, **kwargs) result = numpy.fromfunction(funcrc, shape, radial=radial, xdata=xdata, ydata=ydata, dtype=numpy.float64) return result
def prepareEnvelope(self, scaleFactor=1.0):
"""
Original envelop mrc pixel size was 0.98 Angstroms, but may be better to say 1.04 Angstroms
Now converts a 1D array into the 2D spectra
"""
apDisplay.printMsg("Creating 2D envelop from 1D array")
envelope = self.params['envelopefile']
if envelope is None:
return
spi = open(envelope, 'r')
radialdata = []
for line in spi:
sline = line.strip()
if not sline or sline[0] == ";":
continue
spidict = operations.spiderInLine(line)
# second float column
radialvalue = spidict['floatlist'][1]
radialdata.append(radialvalue)
spi.close()
### create envelop in 2D
xdata = numpy.arange(0, len(radialdata), 1.0, dtype=numpy.float32)
rdata = numpy.array(radialdata, dtype=numpy.float32)
def funcrad(r, xdata=None, rdata=None):
return numpy.interp(r, xdata, rdata)
envshape = (4096, 4096)
envcalc = imagefun.fromRadialFunction(funcrad, envshape, xdata=xdata, rdata=rdata)
### scale envelope
if abs(scaleFactor - 1.0) > 0.01:
print "scaling envelope by", scaleFactor
envcalc = ndimage.zoom(envcalc, zoom=scaleFactor, mode='nearest')
### shift center of envelope to the edges
envamp = self.center(envcalc)
### mutliply real envelope function by image fft
self.envamp = (envamp - envamp.min()) / (envamp.max() - envamp.min())
apDisplay.printMsg("Successfully created 2D envelop from 1D array")
def prepareEnvelope(self, scaleFactor=1.0):
"""
Original envelop mrc pixel size was 0.98 Angstroms, but may be better to say 1.04 Angstroms
Now converts a 1D array into the 2D spectra
"""
apDisplay.printMsg("Creating 2D envelop from 1D array")
envelope = self.params['envelopefile']
if envelope is None:
return
spi = open(envelope, 'r')
radialdata = []
for line in spi:
sline = line.strip()
if not sline or sline[0] == ";":
continue
spidict = operations.spiderInLine(line)
# second float column
radialvalue = spidict['floatlist'][1]
radialdata.append(radialvalue)
spi.close()
### create envelop in 2D
xdata = numpy.arange(0, len(radialdata), 1.0, dtype=numpy.float32)
rdata = numpy.array(radialdata, dtype=numpy.float32)
def funcrad(r, xdata=None, rdata=None):
return numpy.interp(r, xdata, rdata)
envshape = (4096, 4096)
envcalc = imagefun.fromRadialFunction(funcrad, envshape, xdata=xdata, rdata=rdata)
### scale envelope
if abs(scaleFactor - 1.0) > 0.01:
print "scaling envelope by", scaleFactor
envcalc = ndimage.zoom(envcalc, zoom=scaleFactor, mode='nearest')
### shift center of envelope to the edges
envamp = self.center(envcalc)
### mutliply real envelope function by image fft
self.envamp = (envamp - envamp.min()) / (envamp.max() - envamp.min())
apDisplay.printMsg("Successfully created 2D envelop from 1D array")
def Array1dintoArray2d(self, array1d, shape): array2d = imagefun.fromRadialFunction(self.funcrad, shape, rdata=rdata, zdata=array1d) return array2d