def test2(mrc1, mrc2):
import Mrc
import correlator
cor = correlator.Correlator()
im1 = Mrc.mrc_to_numeric(mrc1)
im2 = Mrc.mrc_to_numeric(mrc2)
'''
im1 = im1[:512,:512]
im2 = im2[200:712,200:712]
'''
cor.insertImage(im1)
cor.insertImage(im2)
pc = cor.phaseCorrelate()
Mrc.numeric_to_mrc(pc, 'pc.mrc')
print findSubpixelPeak(pc, npix=7, lpf=1.0)
def test2(mrc1, mrc2): import Mrc import correlator cor = correlator.Correlator() im1 = Mrc.mrc_to_numeric(mrc1) im2 = Mrc.mrc_to_numeric(mrc2) ''' im1 = im1[:512,:512] im2 = im2[200:712,200:712] ''' cor.insertImage(im1) cor.insertImage(im2) pc = cor.phaseCorrelate() Mrc.numeric_to_mrc(pc, 'pc.mrc') print findSubpixelPeak(pc, npix=7, lpf=1.0)
if fromrange is None:
fromrange = image.getextrema()
# ?
image = scaleImage(image, fromrange, (0, 255))
return image.convert('RGB')
def numpy2wxImage(*args, **kwargs):
rgbimage = numpy2RGBImage(*args, **kwargs)
wximage = wx.EmptyImage(*rgbimage.size)
wximage.SetData(rgbimage.tostring())
return wximage
def numpy2wxBitmap(*args, **kwargs):
return wx.BitmapFromImage(numpy2wxImage(*args, **kwargs))
if __name__ == '__main__':
import Mrc
import sys
array = Mrc.mrc_to_numeric(sys.argv[1])
#app = wx.App(0)
#print numpy2wxBitmap(array)
numpy2RGBImage(array).show()
sobel_row_kernel = numpy.array((1, 2, 1, 0, 0, 0, -1, -2, -1), numpy.float32)
sobel_row_kernel.shape = (3, 3)
#### Sobel Column Derivative
sobel_col_kernel = numpy.array((1, 0, -1, 2, 0, -2, 1, 0, -1), numpy.float32)
sobel_col_kernel.shape = (3, 3)
if __name__ == '__main__':
import Mrc
import sys
import imagefun
filename = sys.argv[1]
sobel_row = numpy.array((1, 2, 1, 0, 0, 0, -1, -2, -1), numpy.float32)
sobel_row.shape = (3, 3)
sobel_col = numpy.array((1, 0, -1, 2, 0, -2, 1, 0, -1), numpy.float32)
sobel_col.shape = (3, 3)
gauss = imagefun.gaussian_kernel(1.6)
c = Convolver()
im = Mrc.mrc_to_numeric(filename)
c.setImage(image=im)
s = c.convolve(kernel=gauss)
r = c.convolve(kernel=sobel_row, image=s)
c = c.convolve(kernel=sobel_col, image=s)
edge = numpy.sqrt(r**2 + c**2)
Mrc.numeric_to_mrc(edge, 'edge.mrc')
def threeD_MM(a, res, o, nAngles=2, verboseLvl=1, tmp='/tmp/'):
import Mrc
if o < 1:
raise ValueError, "order need to >= 1"
if nAngles < 1:
raise ValueError, "nAngles need to >= 1"
if verboseLvl >=1:
import time
startTime = time.clock()
res[:] = 0
# aWV = Mrc.bindNew(tmp+"wvl_aWV", N.float32, a.shape)
# aRot= Mrc.bindNew(tmp+"wvl_aRot", N.float32, a.shape)
# c = Mrc.bindNew(tmp+"wvl_c", N.float32, a.shape)
aWV = F.zeroArrF(a.shape)
angles = N.arange(90./nAngles, 90., 90./nAngles)
nOffAngles = len(angles) # = nAngles -1
# do first fastwv6 on original data
if verboseLvl >=1:
print "begin angle 0"
if verboseLvl >=2:
print
print " perm "
Y.refresh()
for i in range(len(_perm)):
if verboseLvl >=2:
print " ", i
Y.refresh()
tmpTrans = N.transpose(a, _perm[i]).copy() # force contiguous!
aWV.shape = tmpTrans.shape
W.fastwv6(tmpTrans,aWV, o,o,o, verboseLvl>=3)
tmpTrans = N.transpose(aWV,_invperm[i])
tmpTrans /= len(_perm) * (1 + (nOffAngles * 3))
res += tmpTrans
# now do it for a bunch of angles
if len(angles):
c = Mrc.bindNew(tmp+"wvl_c", N.float32, a.shape)
for angle in angles:
for axis in (0,1,2):
if verboseLvl >=1:
print "begin angle ",angle
print " axis:", axis
Y.refresh()
aRot = aWV
U.rot3d(a,aRot, angle, axis)
if verboseLvl >=2:
print " perm "
c[:] = 0
for i in range(len(_perm)):
#dbg print " perm:", i
if verboseLvl >=2:
print " ", i
Y.refresh()
tmpTrans = N.transpose(aRot, _perm[i]).copy() # force contiguous!
aWV.shape = tmpTrans.shape
W.fastwv6(tmpTrans,aWV, o,o,o, verboseLvl>=3)
tmpTrans = N.transpose(aWV,_invperm[i])
tmpTrans /= len(_perm) * (1 + (nOffAngles * 3))
c += tmpTrans
U.rot3d(c,aRot,-angle,axis)
res += aRot
if verboseLvl >=1:
print
if verboseLvl >=1:
import time
d = time.clock()-startTime
print "time: %.2lf secs - %.2lf min - %.2lf h " % (d, d/60., d/60./60.)
sobel_row_kernel.shape = (3,3) #### Sobel Column Derivative sobel_col_kernel = numpy.array((1,0,-1,2,0,-2,1,0,-1), numpy.float32) sobel_col_kernel.shape = (3,3) if __name__ == '__main__': import Mrc import sys import imagefun filename = sys.argv[1] sobel_row = numpy.array((1,2,1,0,0,0,-1,-2,-1), numpy.float32) sobel_row.shape = (3,3) sobel_col = numpy.array((1,0,-1,2,0,-2,1,0,-1), numpy.float32) sobel_col.shape = (3,3) gauss = imagefun.gaussian_kernel(1.6) c = Convolver() im = Mrc.mrc_to_numeric(filename) c.setImage(image=im) s = c.convolve(kernel=gauss) r = c.convolve(kernel=sobel_row, image=s) c = c.convolve(kernel=sobel_col, image=s) edge = numpy.sqrt(r**2 + c**2) Mrc.numeric_to_mrc(edge, 'edge.mrc')
image = image.transform((width, height), Image.EXTENT,
(left, upper, right, bottom), filter)
if fromrange is None:
fromrange = image.getextrema()
# ?
image = scaleImage(image, fromrange, (0, 255))
return image.convert('RGB')
def numarray2wxImage(*args, **kwargs):
rgbimage = numarray2RGBImage(*args, **kwargs)
wximage = wx.EmptyImage(*rgbimage.size)
wximage.SetData(rgbimage.tostring())
return wximage
def numarray2wxBitmap(*args, **kwargs):
return wx.BitmapFromImage(numarray2wxImage(*args, **kwargs))
if __name__ == '__main__':
import Mrc
import sys
array = Mrc.mrc_to_numeric(sys.argv[1])
#app = wx.App(0)
#print numarray2wxBitmap(array)
numarray2RGBImage(array).show()
def load_mrc( mrcfn):
stack = Mrc.load(mrcfn)
return stack
def write_mrc(stack, mrcfn):
#stackf32 = stack.astype(np.float32)
Mrc.save(stack, mrcfn,ifExists='overwrite',calcMMM=False)