def save(self, baseFn=None):
"""save Mosaic size/pos/scale info in baseFn.txt
save all images into baseFn_xx.mrc
"""
from Priithon.all import Mrc, U
if baseFn is None:
from .usefulX import FN
baseFn = FN(1)
if not baseFn:
return
a = N.concatenate((self.m_imgPosArr,
self.m_imgSizeArr,
N.array(self.m_imgRotArr,)[:,N.newaxis],
self.m_imgScaleMM), 1)
U.writeArray(a, baseFn + '.txt')
n = len(self.m_imgSizeArr)
for i in range( n ):
# Mrc.save(self.m_imgArrL[i], "%s_%02d.mrc" % (baseFn, i))
#20070126 m = Mrc.Mrc("%s_%02d.mrc" % (baseFn, i), "w+", self.m_imgArrL[i] )
#20070126 m.calcMMM()
#20070126 m.hdr('d')[:] = tuple(self.m_imgSizeArr[i] / N.array((self.m_imgArrL[i].shape))[::1]) + (1,)
#20070126 m.hdr('zxy0')[:] = (0,) + tuple(self.m_imgPosArr[i])
#20070126 m.hdr('mmm1')[:] = tuple(self.m_imgScaleMM[i]) + (1,)
#20070126 m.flush()
#20070126 m.close()
d = tuple(self.m_imgSizeArr[i] / N.array((self.m_imgArrL[i].shape), dtype=N.float32)[::1]) + (1,)
zxy0 = (0,) + tuple(self.m_imgPosArr[i])
Mrc.save(self.m_imgArrL[i],
"%s_%02d.mrc" % (baseFn, i),
hdrEval='''hdr.d = d; hdr.zxy0 = zxy0'''
)
def _cutoutForAlign2(fn, py, outFn=''):
"""
if not outFn, default with 'cut' extention
resulting array is imgSequence=0 (t,w,z,y,x)
return outFn
"""
h = imgManager.ImageManager(fn)
slc, shiftZYX, ZYX = makeSlice(h, py)
# input
arr = N.empty((h.nt, h.nw, h.nz, h.ny, h.nx), h.dtype)
for t in range(h.nt):
for w in range(h.nw):
arr[t, w] = h.get3DArr(w=w, t=t)
canvas = N.squeeze(arr[slc].astype(arr.dtype.type))
newNum = (canvas.shape[-1], canvas.shape[-2], N.prod(canvas.shape[:-3]))
if not outFn:
outFn = '_'.join((h.filePath, EXT_CUTOUT)) #arr.Mrc.path, EXT_CUTOUT))
hdr = Mrc.makeHdrArray()
Mrc.initHdrArrayFrom(hdr, h.hdr) #arr.Mrc.hdr)
hdr.ImgSequence = 2
hdr.Num[:] = newNum
mstart = [sl.start for sl in slc[::-1][:3] if isinstance(sl, slice)]
hdr.mst[:len(mstart)] += mstart
Mrc.save(canvas, outFn, ifExists='overwrite', hdr=hdr)
return outFn
def OnSave(self, event=None):
from Priithon.all import Mrc, U, Y
fn = Y.FN(1)#, verbose=0)
if not fn:
return
if fn[-4:] in [ ".mrc", ".dat" ]:
Mrc.save(self.m_imgArr, fn)
elif fn[-5:] in [ ".fits" ]:
U.saveFits(self.m_imgArr, fn)
else:
U.saveImg8(self.m_imgArr, fn)
Y.shellMessage("### section saved to '%s'\n"%fn)
def OnSave(self, event=None):
from Priithon.all import Mrc, U, Y
fn = Y.FN(1) #, verbose=0)
if not fn:
return
if fn[-4:] in [".mrc", ".dat"]:
Mrc.save(self.m_imgArr, fn)
elif fn[-5:] in [".fits"]:
U.saveFits(self.m_imgArr, fn)
else:
U.saveImg8(self.m_imgArr, fn)
Y.shellMessage("### section saved to '%s'\n" % fn)
def __init__(self, fn):
arr = Mrc.bindFile(fn)
self.pxlsiz = arr.Mrc.hdr.d
self.waves = arr.Mrc.hdr.wave[:arr.Mrc.hdr.NumWaves].copy()
self.refwave = self.waves[arr.Mrc.hdr.n1]
self.XYsize = arr.Mrc.hdr.Num[:2]
self.nt = arr.Mrc.hdr.NumTimes
self.nw = len(self.waves)
self.t = 0
self.dtype = arr.dtype.type
if 'SIR' in fn:
self.mid = 512
else:
self.mid = 256
if arr.Mrc.hdr.n2 == 1:
parm = arr
nentry = aligner.NUM_ENTRY
self.map_str = 'None'
else:
parm = arr.Mrc.extFloats[:arr.Mrc.hdr.NumTimes *
arr.Mrc.hdr.NumWaves, :arr.Mrc.hdr.
NumFloats]
nentry = arr.Mrc.hdr.NumFloats
self.nz = arr.Mrc.hdr.Num[-1] / (arr.Mrc.hdr.NumTimes *
arr.Mrc.hdr.NumWaves * 2)
if self.nz == 1:
self.map_str = 'Projection'
else:
self.map_str = 'Section-wise'
parm = parm.reshape(
(arr.Mrc.hdr.NumTimes, arr.Mrc.hdr.NumWaves, nentry))
self.alignParms = parm.copy() # writable
del arr, parm
def OnMenuSaveND(self, ev=None):
if self.data.dtype.type in (N.complex64, N.complex128):
dat = self.dataCplx
datX = abs(self.data) #CHECK
else:
dat = datX = self.data
from Priithon.all import Mrc, U, FN, Y
fn = FN(1,0)
if not fn:
return
if fn[-4:] in [ ".mrc", ".dat" ]:
Mrc.save(dat, fn)
elif fn[-5:] in [ ".fits" ]:
U.saveFits(dat, fn)
else:
# save as sequence of image files
# if fn does contain something like '%0d' auto-insert '_%0NNd'
# with NN to just fit the needed number of digits
datX = datX.view()
datX.shape = (-1,)+datX.shape[-2:]
U.saveImg8_seq(datX, fn)
Y.shellMessage("### Y.vd(%d) saved to '%s'\n"%(self.id, fn))
def OnMenuSaveND(self, ev=None):
if self.data.dtype.type in (N.complex64, N.complex128):
dat = self.dataCplx
datX = abs(self.data) #CHECK
else:
dat = datX = self.data
from Priithon.all import Mrc, U, FN, Y
fn = FN(1, 0)
if not fn:
return
if fn[-4:] in [".mrc", ".dat"]:
Mrc.save(dat, fn)
elif fn[-5:] in [".fits"]:
U.saveFits(dat, fn)
else:
# save as sequence of image files
# if fn does contain something like '%0d' auto-insert '_%0NNd'
# with NN to just fit the needed number of digits
datX = datX.view()
datX.shape = (-1, ) + datX.shape[-2:]
U.saveImg8_seq(datX, fn)
Y.shellMessage("### Y.vd(%d) saved to '%s'\n" % (self.id, fn))
def makeFiles(fns, std=10, div_step=50, div_max=800): #1000):
"""
makes a series of images added Gaussain and Poisson noise
std: standard deviation for Gaussian, and mean=std*10 for Poisson
div_step: the step that the original image is divided while noise is added
div_max: the maximum value that the original image is divided
return output filenames
"""
outs = []
for fn in fns:
a = Mrc.bindFile(fn)
for ns in NOISE_STATS:
hdr = mrcIO.makeHdr_like(a.Mrc.hdr)
if ns == NOISE_STATS[0]:
noise = F.noiseArr(a.shape, stddev=std, mean=0)
else:
noise = F.poissonArr(a.shape, mean=std * 10)
steps = range(div_step, div_max + div_step, div_step)
ag = [a / c + noise for c in steps]
for i, arr in enumerate(ag):
val = steps[i]
if hasattr(arr, "Mrc"):
del arr.Mrc
if arr.dtype == N.float64:
arr = arr.astype(N.float32)
hdr.PixelType = 2
out = a.Mrc.path + ns + '%04d' % val
Mrc.save(arr, out, ifExists='overwrite', hdr=hdr)
outs.append(out)
return outs
def setDimFromMrcHdr(self, hdr):
from Priithon.all import Mrc
self.wave = hdr.wave
self.nw = hdr.NumWaves
self.nt = hdr.NumTimes
self.nx = hdr.Num[0]
self.ny = hdr.Num[1]
self.nz = hdr.Num[2] // (self.nt * self.nw)
self.imgSequence = hdr.ImgSequence
self.dtype = Mrc.MrcMode2dtype(hdr.PixelType)
#if self.multipage:
# self._setSecSize()
#else:
self._setSuffix()
def findOTF(fn, ctfdir=None):
doesnotwork = """
tempfn = tempfile.mktemp(suffix='.txt', prefix='lensNum')
# header does not work on command line! It stops before extended header
com = os.system("header %s |sed -n -e '/Lens ID Number\.\.*/ s/Lens ID Number\.\.*//p' |awk '{print $1}' >> %s" % (fn, tempfn))
if com:
raise RuntimeError, 'problem in reading header %s' % fn
h = open(tempfn)
lensNum = h.readline()
h.close()
print 'lensNum: ', lensNum"""
a = Mrc.Mrc2(fn)
lensNum = str(a.hdr.LensNum)
a.close()
return findOTFfromNum(lensNum, ctfdir)
def load(self, baseFn=None, n=None, n0=0, sparse=1):
"""load Mosaic size/pos/scale from in baseFn.txt
load all images into baseFn_xx.mrc
load only the first n images - n=None means all
skip the first n0 of these
if sparse>1 take only every 'sparse' pixel along x & y
if baseFn end on '.txt' - that suffix gets ignored
"""
from Priithon.all import Mrc, U
if baseFn is None:
from usefulX import FN
baseFn = FN()
if not baseFn:
return
if baseFn[-4:] == '.txt':
baseFn = baseFn[:-4]
a = U.readArray(baseFn + '.txt')
if len(a.shape) == 1:
a.shape = (1, ) + a.shape
nn = len(a)
if n is not None and n < nn:
nn = n
n = nn
apos = a[:, :2]
asiz = a[:, 2:4]
arot = a[:, 4]
ascl = a[:, 5:7]
#n = len( apos )
for i in range(n0, n):
#20070126 aa = Mrc.bindFile("%s_%02d.mrc" % (baseFn, i)).copy()[0]
aa = Mrc.load("%s_%02d.mrc" % (baseFn, i))[0]
# self.appendMosaic( aa,
self.appendNewImg(aa[::sparse, ::sparse],
apos[i],
asiz[i],
ascl[i],
holdBackUpdate=(i + 1 < n),
rot=arot[i])
def load(self, baseFn=None, n=None, n0=0, sparse=1):
"""load Mosaic size/pos/scale from in baseFn.txt
load all images into baseFn_xx.mrc
load only the first n images - n=None means all
skip the first n0 of these
if sparse>1 take only every 'sparse' pixel along x & y
if baseFn end on '.txt' - that suffix gets ignored
"""
from Priithon.all import Mrc, U
if baseFn is None:
from .usefulX import FN
baseFn = FN()
if not baseFn:
return
if baseFn[-4:] == '.txt':
baseFn = baseFn[:-4]
a = U.readArray(baseFn + '.txt')
if len(a.shape) == 1:
a.shape = (1,) + a.shape
nn = len(a)
if n is not None and n<nn:
nn=n
n=nn
apos = a[:, :2]
asiz = a[:, 2:4]
arot = a[:, 4]
ascl = a[:, 5:7]
#n = len( apos )
for i in range(n0, n ):
#20070126 aa = Mrc.bindFile("%s_%02d.mrc" % (baseFn, i)).copy()[0]
aa = Mrc.load("%s_%02d.mrc" % (baseFn, i))[0]
# self.appendMosaic( aa,
self.appendNewImg( aa[::sparse,::sparse],
apos[i], asiz[i], ascl[i],
holdBackUpdate=(i+1<n), rot=arot[i] )