def recalcHist(self, i, postponeToIdle):
if postponeToIdle:
self.recalcHist_todo_Set.add(i)
return
img = self.data[ tuple(self.zsec) ][i]
from . import useful as U
mmms = U.mmms( img )
self.mmms[i] = mmms
#time import time
#time x = time.clock()
# print mmms
from . import useful as U
if self.hist_arr[i] is not None:
#glSeb import time
#glSeb x = time.clock()
# print U.mmms(self.hist_arr[i]),
U.histogram(img, amin=self.hist_min[i], amax=self.hist_max[i], histArr=self.hist_arr[i])
# print U.mmms(self.hist_arr[i])
self.hist[i].setHist(self.hist_arr[i], self.hist_min[i], self.hist_max[i])
#glSeb print "ms: %.2f"% ((time.clock()-x)*1000.0)
## FIXME setHist needs to NOT alloc xArray every time !!!
else:
resolution = 10000
a_h = U.histogram(img, resolution, mmms[0], mmms[1])
self.hist[i].setHist(a_h, mmms[0], mmms[1])
def recalcHist(self, i, postponeToIdle):
if postponeToIdle:
self.recalcHist_todo_Set.add(i)
return
img = self.data[tuple(self.zsec)][i]
from . import useful as U
mmms = U.mmms(img)
self.mmms[i] = mmms
#time import time
#time x = time.clock()
# print mmms
from . import useful as U
if self.hist_arr[i] is not None:
#glSeb import time
#glSeb x = time.clock()
# print U.mmms(self.hist_arr[i]),
U.histogram(img,
amin=self.hist_min[i],
amax=self.hist_max[i],
histArr=self.hist_arr[i])
# print U.mmms(self.hist_arr[i])
self.hist[i].setHist(self.hist_arr[i], self.hist_min[i],
self.hist_max[i])
#glSeb print "ms: %.2f"% ((time.clock()-x)*1000.0)
## FIXME setHist needs to NOT alloc xArray every time !!!
else:
resolution = 10000
a_h = U.histogram(img, resolution, mmms[0], mmms[1])
self.hist[i].setHist(a_h, mmms[0], mmms[1])
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 findBestRefZs(ref, sigma=1):
"""
PSF spread along the Z axis is often tilted in the Y or X axis.
Thus simple maximum intensity projection may lead to the wrong answer to estimate rotation and magnification.
On the other hands, taking a single section may also contain out of focus flare from neighboring sections that are tilted.
Therefore, here sections with high complexity are selected and projected.
ref: 3D array
return z idx at the focus
"""
nz = ref.shape[0]
if ref.ndim == 2:
return [0]
elif nz <= 3:
return range(nz)
# Due to the roll up after FFT, the edge sections in Z may contain different information among the channels. Thus these sections are left unused.
ms = N.zeros((nz - 2, ), N.float32)
for z in range(1, nz - 1):
arr = ref[z]
ms[z - 1] = N.prod(U.mmms(arr)[-2:]) # mean * std
mi, ma, me, st = U.mmms(ms)
thr = me + st * sigma
ids = [idx for idx in range(1, nz - 1) if ms[idx - 1] > thr]
if not ids:
ids = range(1, nz - 1)
return ids
def rotateIndices2DNew(shape, rot, orig=None, dtype=N.float64):
"""
shape: 2D
rot: anti-clockwise
orig: (y, x)
return: yi, xi
"""
# FIX ME Rot is something wrong!! 081027
shape = N.asarray(shape, N.int)
if orig is None:
y, x = shape / 2.
else:
y, x = orig
print(y, x)
if not rot:
yi, xi = N.indices(shape, dtype=N.float64)
yi -= y - 0.5 # remove pix center
xi -= x - 0.5
return yi, xi
# twice as large window
# mo = N.abs(N.mod(shape, 2) + [-1,-1])
s2 = shape * 2 #+ mo # always odd for even shape, even for odd shape
yi, xi = N.indices(s2, dtype=N.float32)
mm = N.ceil(shape / 2.) #(s2 -1 - shape)//2 # offset always int
yi -= mm[0]
xi -= mm[1]
pxc = imgGeo.RotateXY((0.5, 0.5), rot) # remove pix center
yi += pxc[0]
xi += pxc[1]
y0, x0 = shape / 2. #N.ceil(shape / 2) # img center
yc = y0 - y # delta rotation center
xc = x0 - x
yi = U.trans2d(yi, None, (xc, yc, rot, 1, 0, 1))
xi = U.trans2d(xi, None, (xc, yc, rot, 1, 0, 1))
yi = U.trans2d(yi, None, (-xc, -yc, 0, 1, 0, 1))
xi = U.trans2d(xi, None, (-xc, -yc, 0, 1, 0, 1))
yi = yi.astype(dtype)
xi = xi.astype(dtype)
yi -= y
xi -= x
yi = imgFilters.cutOutCenter(yi, shape)
xi = imgFilters.cutOutCenter(xi, shape)
return yi, xi
def rotateIndices2DNew(shape, rot, orig=None, dtype=N.float64):
"""
shape: 2D
rot: anti-clockwise
orig: (y, x)
return: yi, xi
"""
# FIX ME Rot is something wrong!! 081027
shape = N.asarray(shape, N.int)
if orig is None:
y, x = shape / 2.
else:
y, x = orig
print(y,x)
if not rot:
yi,xi = N.indices(shape, dtype=N.float64)
yi -= y - 0.5 # remove pix center
xi -= x - 0.5
return yi,xi
# twice as large window
# mo = N.abs(N.mod(shape, 2) + [-1,-1])
s2 = shape * 2 #+ mo # always odd for even shape, even for odd shape
yi, xi = N.indices(s2, dtype=N.float32)
mm = N.ceil(shape / 2.)#(s2 -1 - shape)//2 # offset always int
yi -= mm[0]
xi -= mm[1]
pxc = imgGeo.RotateXY((0.5,0.5), rot) # remove pix center
yi += pxc[0]
xi += pxc[1]
y0, x0 = shape / 2. #N.ceil(shape / 2) # img center
yc = y0 - y # delta rotation center
xc = x0 - x
yi = U.trans2d(yi, None, (xc,yc,rot,1,0,1))
xi = U.trans2d(xi, None, (xc,yc,rot,1,0,1))
yi = U.trans2d(yi, None, (-xc,-yc,0,1,0,1))
xi = U.trans2d(xi, None, (-xc,-yc,0,1,0,1))
yi = yi.astype(dtype)
xi = xi.astype(dtype)
yi -= y
xi -= x
yi = imgFilters.cutOutCenter(yi, shape)
xi = imgFilters.cutOutCenter(xi, shape)
return yi, xi
def yCos(parm, r=0):
"""
parm: (amp,freq,phase,mean)
amp * N.sin(freq*r + phase(deg)) + mean
r: degree (not radian!!)
"""
a, b, c, d = parm
r = U.deg2rad(r)
c = U.deg2rad(c)
return a * N.cos(b * r + c) + d
def yCos(parm, r=0):
"""
parm: (amp,freq,phase,mean)
amp * N.sin(freq*r + phase(deg)) + mean
r: degree (not radian!!)
"""
a, b, c, d = parm
r = U.deg2rad(r)
c = U.deg2rad(c)
return a * N.cos(b*r + c) + d
def fitSkew1D(img, ts=None, sigma=0.5, exp=0):
"""
img: 1D array containg one skewd gaussian peak
"""
mi, ma, me, sd = U.mmms(img)
ma, _1, _2, t = U.findMax(img)
if ts is not None:
t = ts[t]
img = list(zip(ts, img))
return U.fitAny(ySkew, (mi, ma - mi, t, sigma, exp), img, warning=None)
def fitSkew1D(img, ts=None, sigma=0.5, exp=0):
"""
img: 1D array containg one skewd gaussian peak
"""
mi, ma, me, sd = U.mmms(img)
ma, _1, _2, t = U.findMax(img)
if ts is not None:
t = ts[t]
img = list(zip(ts, img))
return U.fitAny(ySkew, (mi, ma-mi, t, sigma, exp), img, warning=None)
def onMove(self, xEff, yEff, ev):
#self.oldOnMouse(xEff, yEff, xyEffVal) # show label info
self.yx1 = y1,x1 = int(round(yEff)), int(round(xEff))
y0,x0 = self.yx0
dy = y1-y0
dx = x1-x0
from Priithon.all import U
# even size
if ev.AltDown():
dy2 = int(dy / 2) * 2
dx2 = int(dx / 2) * 2
y1 = y0 + dy2
x1 = x0 + dx2
self.yx1 = (y1,x1)
dy = y1-y0
dx = x1-x0
#power of two
if ev.ShiftDown() and ev.ControlDown():
ddy = N.log(abs(dy)) / log2
dy2 = 2 ** int(ddy+.5)
ddx = N.log(abs(dx)) / log2
dx2 = 2 ** int(ddx+.5)
y1 = y0 + dy2 * U.sgn(dy)
x1 = x0 + dx2 * U.sgn(dx)
self.yx1 = (y1,x1)
dy = y1-y0
dx = x1-x0
#square
elif ev.ShiftDown() or ev.ControlDown():
if abs(dx) < abs(dy):
x1 = x0 + abs(dy) * U.sgn(dx)
self.yx1 = (y1,x1)
elif abs(dy) < abs(dx):
y1 = y0 + abs(dx) * U.sgn(dy)
self.yx1 = (y1,x1)
dx = x1-x0
dy = y1-y0
if self.splitND is not None:
self.splitND.label.SetLabel("h,w: %3d %3d" % (abs(dy),abs(dx)))
self.gfxUpdate()
#self.viewer.updateGlList( self.my_defGlList )
self.doThisAlsoOnMove()
def OnSaveScreenShort(self, event=None):
'''always flipY'''
from Priithon.all import U, FN
fn = FN(1, verbose=0)
if not fn:
return
flipY=1
if flipY:
U.saveImg(self.readGLviewport(copy=1)[:, ::-1], fn)
else:
U.saveImg(self.readGLviewport(copy=1), fn)
def OnSaveScreenShort(self, event=None):
'''always flipY'''
from Priithon.all import U, FN
fn = FN(1, verbose=0)
if not fn:
return
flipY = 1
if flipY:
U.saveImg(self.readGLviewport(copy=1)[:, ::-1], fn)
else:
U.saveImg(self.readGLviewport(copy=1), fn)
def onMove(self, xEff, yEff, ev):
#self.oldOnMouse(xEff, yEff, xyEffVal) # show label info
self.yx1 = y1, x1 = int(round(yEff)), int(round(xEff))
y0, x0 = self.yx0
dy = y1 - y0
dx = x1 - x0
from Priithon.all import U
# even size
if ev.AltDown():
dy2 = int(dy / 2) * 2
dx2 = int(dx / 2) * 2
y1 = y0 + dy2
x1 = x0 + dx2
self.yx1 = (y1, x1)
dy = y1 - y0
dx = x1 - x0
#power of two
if ev.ShiftDown() and ev.ControlDown():
ddy = N.log(abs(dy)) / log2
dy2 = 2**int(ddy + .5)
ddx = N.log(abs(dx)) / log2
dx2 = 2**int(ddx + .5)
y1 = y0 + dy2 * U.sgn(dy)
x1 = x0 + dx2 * U.sgn(dx)
self.yx1 = (y1, x1)
dy = y1 - y0
dx = x1 - x0
#square
elif ev.ShiftDown() or ev.ControlDown():
if abs(dx) < abs(dy):
x1 = x0 + abs(dy) * U.sgn(dx)
self.yx1 = (y1, x1)
elif abs(dy) < abs(dx):
y1 = y0 + abs(dx) * U.sgn(dy)
self.yx1 = (y1, x1)
dx = x1 - x0
dy = y1 - y0
if self.splitND is not None:
self.splitND.label.SetLabel("h,w: %3d %3d" % (abs(dy), abs(dx)))
self.gfxUpdate()
#self.viewer.updateGlList( self.my_defGlList )
self.doThisAlsoOnMove()
def recalcHist(self, triggeredFromIdle):
if not triggeredFromIdle:
self.recalcHist_todo_Set.add(0)
return
#CHECK img = self.viewer.m_imgArr
img = self.img
from . import useful as U
mmms = U.mmms( img )
self.mmms = mmms
#time import time
#time x = time.clock()
# print mmms
if self.hist_arr is not None:
#glSeb import time
#glSeb x = time.clock()
if sys.platform.startswith('linux'): # 20180712 win SIM error
wx.Yield() # 20180406 dileptus linux
U.histogram(img, amin=self.hist_min, amax=self.hist_max, histArr=self.hist_arr)
self.hist.setHist(self.hist_arr, self.hist_min, self.hist_max)
#glSeb print "ms: %.2f"% ((time.clock()-x)*1000.0)
## FIXME setHist needs to NOT alloc xArray every time !!!
else:
# self.viewer.m_imgChanged = True
# self.viewer.Refresh(False)
#20040915(OverflowError: float too large to convert) resolution = int(mmms[1]-mmms[0]+2)
#20040915if resolution > 10000:
#20040915 resolution = 10000
#20040915elif resolution < 1000: #CHECK
#20040915 resolution = 10000 # CHECK
resolution = 10000
a_h = U.histogram(img, resolution, mmms[0], mmms[1])
# self.hist.setHist(a_h, mmms[0], mmms[1])
self.recalcHist__a_h = a_h
self.recalcHist__Done = 1
#time print "recalcHist ms: %.2f"% ((time.clock()-x)*1000.0)
#20171225 py2to3
if wx.VERSION[0] <= 3:
mainthread = wx.Thread_IsMain()
elif wx.VERSION[0] >= 4:
mainthread = wx.IsMainThread()
if mainthread:#wx.IsMainThread():#Thread_IsMain():
self.hist.setHist(self.recalcHist__a_h,
self.mmms[0],
self.mmms[1])
else:
wx.PostEvent(self.frame, self.__class__.ResultEvent(None))
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 OnSaveScreenShort(self, event=None):
"""always flipY"""
from Priithon.all import U, FN, Y
fn = FN(1)#, verbose=0)
if not fn:
return
flipY=1
if flipY:
U.saveImg(self.readGLviewport(copy=1)[:, ::-1], fn)
else:
U.saveImg(self.readGLviewport(copy=1), fn)
Y.shellMessage("### screenshot saved to '%s'\n"%fn)
def OnSaveScreenShort(self, event=None):
"""always flipY"""
from Priithon.all import U, FN, Y
fn = FN(1) #, verbose=0)
if not fn:
return
flipY = 1
if flipY:
U.saveImg(self.readGLviewport(copy=1)[:, ::-1], fn)
else:
U.saveImg(self.readGLviewport(copy=1), fn)
Y.shellMessage("### screenshot saved to '%s'\n" % fn)
def recalcHist(self, triggeredFromIdle):
if not triggeredFromIdle:
self.recalcHist_todo_Set.add(0)
return
#CHECK img = self.viewer.m_imgArr
img = self.img
from . import useful as U
mmms = U.mmms(img)
self.mmms = mmms
#time import time
#time x = time.clock()
# print mmms
if self.hist_arr is not None:
#glSeb import time
#glSeb x = time.clock()
wx.Yield() # 20180406 dileptus
U.histogram(img,
amin=self.hist_min,
amax=self.hist_max,
histArr=self.hist_arr)
self.hist.setHist(self.hist_arr, self.hist_min, self.hist_max)
#glSeb print "ms: %.2f"% ((time.clock()-x)*1000.0)
## FIXME setHist needs to NOT alloc xArray every time !!!
else:
# self.viewer.m_imgChanged = True
# self.viewer.Refresh(False)
#20040915(OverflowError: float too large to convert) resolution = int(mmms[1]-mmms[0]+2)
#20040915if resolution > 10000:
#20040915 resolution = 10000
#20040915elif resolution < 1000: #CHECK
#20040915 resolution = 10000 # CHECK
resolution = 10000
a_h = U.histogram(img, resolution, mmms[0], mmms[1])
# self.hist.setHist(a_h, mmms[0], mmms[1])
self.recalcHist__a_h = a_h
self.recalcHist__Done = 1
#time print "recalcHist ms: %.2f"% ((time.clock()-x)*1000.0)
#20171225 py2to3
if wx.IsMainThread(): #Thread_IsMain():
self.hist.setHist(self.recalcHist__a_h, self.mmms[0],
self.mmms[1])
else:
wx.PostEvent(self.frame, self.__class__.ResultEvent(None))
def findBestChannel(self, t=0):
"""
the reference wavelength is determined from the wavelength and intensity
set self.refwave (in index)
"""
if self.refwave is not None:
self.refwave = self.img.getWaveIdx(self.refwave)
else:
# if time laplse
if self.img.nt > 1:
# how large the object is...
arrs = [self.img.get3DArr(w=w, t=t).ravel() for w in range(self.img.nw)]
modes = [imgFilters.mode(a[::50]) for a in arrs]
fpxls = [N.where(a > modes[i])[0].size/float(a.size) for i, a in enumerate(arrs)]
# bleach half time
halfs = []
for w in range(self.nw):
mes = [self.img.get3DArr(w=w, t=t).mean() for t in range(self.nt)]
parm, check = U.fitDecay(mes)
halfs.append(parm[-1] / float(self.nt))
channels = N.add(fpxls, halfs)
refwave = N.argmax(channels)
print('The channel to align is %i' % refwave)
# if wavelengths are only 2, then use the channel 0
elif self.img.nw <= 2:
refwave = 0
# take into account for the PSF distortion due to chromatic aberration
elif self.img.nw > 2:
pwrs = N.array([self.img.get3DArr(w=w, t=t).mean() for w in range(self.img.nw)])
# the middle channel should have the intermediate PSF shape
waves = [self.img.getWaveFromIdx(w) for w in range(self.img.nw)]
waves.sort()
candidates = [self.img.getWaveIdx(wave) for wave in waves[1:-1]]
# remove channels with lots of saturation
candidates = [w for w in candidates if not self.getSaturation(w=w,t=t)]
# find out channels with enough signal
thr = N.mean(pwrs) / 1.25
bol = N.where(pwrs[candidates] > thr, 1, 0)
if N.any(bol):
ids = N.nonzero(bol)[0]
if len(ids) == 1:
idx = ids[0]
else:
candidates = N.array(candidates)[ids]
idx = N.argmax(pwrs[candidates])
refwave = candidates[idx]
else:
refwave = N.argmax(pwrs)
self.refwave = refwave
self.fixAlignParmWithCurrRefWave()
self.progress()
def _fitGaussian2DR(img, LD, y, x, sigma=[2.,2.], mean_max=None, window=5, rot=0, searchRot=None):
"""
img: already cut out with indy, indx
"""
if mean_max is None:
mi, ma, me, sd = U.mmms(img)
#ma = img[y,x]
else:
me, ma = mean_max
if searchRot:
param0 = (me, float(ma-me), y, x, float(sigma[0]), float(sigma[1]), rot)
else:
param0 = (me, float(ma-me), y, x, float(sigma[0]), float(sigma[1]))
img = img.flatten()
def func(p, shape, LD, rot):
return yGaussian2DR(p, shape, LD, rot).flatten() - img
from scipy import optimize
ret, check = optimize.leastsq(func, param0,
args=((window,window), LD, rot), warning=None)
if searchRot and ret[-1] < 0:
ret[-1] += 90
ret[4:] = N.abs(ret[4:])
return ret, check
def findMaxWithGFit(img, sigma=0.5, win=11):
'''
find sub-pixel peaks from input img using n-dimensional Guassian fitting
sigma: scaler or [simgaZ,sigmaY..]
window: a window where the Guassian fit is performed on
return [v, zyx, sigma]
'''
vzyx = N.array(U.findMax(img))
ndim = img.ndim
try:
ret, check = imgFit.fitGaussianND(img, vzyx[-ndim:], sigma, win)
except IndexError: # too close to the edge
imgFit.fitFailedAppend("at %s" % str(vzyx[-ndim:]))
sigma = imgFit._scalerToSeq(sigma, ndim)
return vzyx[0:1], vzyx[-ndim:], list(sigma)
if check == 5 or N.any(ret[2:2 + ndim] > (vzyx[-ndim:] + win)) or N.any(
ret[2:2 + ndim] < (vzyx[-ndim:] - win)):
imgFit.fitFailedAppend("at %s, %s, check=%i" %
(str(vzyx[-ndim:]), str(ret), check))
sigma = imgFit._scalerToSeq(sigma, ndim)
return [vzyx[0:1], vzyx[-ndim:], sigma]
#x= (vzyx[0:1] + [vzyx[-ndim:]] + [sigma])
# print x
# return x
else:
v = ret[1]
zyx = ret[2:2 + ndim]
sigma = ret[2 + ndim:2 + ndim * 2]
return [v, zyx, sigma]
def findMaxWithGFit(img, sigma=0.5, win=11):
'''
find sub-pixel peaks from input img using n-dimensional Guassian fitting
sigma: scaler or [simgaZ,sigmaY..]
window: a window where the Guassian fit is performed on
return [v, zyx, sigma]
'''
imgFit.fitFailedClear()
vzyx = U.findMax(img)
ndim = img.ndim
try:
ret, check = imgFit.fitGaussianND(img, vzyx[-ndim:], sigma, win)
except IndexError: # too close to the edge
imgFit.fitFailedAppend("at %s" % str(vzyx[-ndim:]))
sigma = imgFit._scalerToSeq(sigma, ndim)
return list(vzyx)[0:1] + [vzyx[-ndim:]] + [list(sigma)]
if check == 5:
imgFit.fitFailedAppend("at %s, %s, check=%i" % (str(vzyx[-ndim:]), str(ret), check))
sigma = imgFit._scalerToSeq(sigma, ndim)
return list(vzyx)[0:1] + [vzyx[-ndim:]] + [sigma]
else:
v = ret[1]
zyx = ret[2:2+ndim]
sigma = ret[2+ndim:2+ndim*2]
return [v,zyx,sigma]
def findMaxWithGFit(img, sigma=0.5, win=11):
'''
find sub-pixel peaks from input img using n-dimensional Guassian fitting
sigma: scaler or [simgaZ,sigmaY..]
window: a window where the Guassian fit is performed on
return [v, zyx, sigma]
'''
imgFit.fitFailedClear()
vzyx = U.findMax(img)
ndim = img.ndim
try:
ret, check = imgFit.fitGaussianND(img, vzyx[-ndim:], sigma, win)
except IndexError: # too close to the edge
imgFit.fitFailedAppend("at %s" % str(vzyx[-ndim:]))
sigma = imgFit._scalerToSeq(sigma, ndim)
return list(vzyx)[0:1] + [vzyx[-ndim:]] + [list(sigma)]
if check == 5:
imgFit.fitFailedAppend("at %s, %s, check=%i" %
(str(vzyx[-ndim:]), str(ret), check))
sigma = imgFit._scalerToSeq(sigma, ndim)
return list(vzyx)[0:1] + [vzyx[-ndim:]] + [sigma]
else:
v = ret[1]
zyx = ret[2:2 + ndim]
sigma = ret[2 + ndim:2 + ndim * 2]
return [v, zyx, sigma]
def zoomToAll(self):
if self.m_nImgs < 1:
return
posA=N.array(self.m_imgPosArr)
sizA=N.array(self.m_imgSizeArr)
a=N.array([N.minimum.reduce(posA),
N.maximum.reduce(posA+sizA),
])
from Priithon.all import U
MC = N.array([0.5, 0.5]) # mosaic viewer's center (0.5, 0.5)
a -= MC
hypot = N.array((N.hypot(a[0][0], a[0][1]),
N.hypot(a[1][0], a[1][1])))
theta = N.array((N.arctan2(a[0][1], a[0][0]),
N.arctan2(a[1][1], a[1][0]))) # radians
phi = theta + U.deg2rad(self.m_rot)
mimXY = N.array((hypot[0]*N.cos(phi[0]), hypot[0]*N.sin(phi[0])))
maxXY = N.array((hypot[1]*N.cos(phi[1]), hypot[1]*N.sin(phi[1])))
a = N.array((mimXY, maxXY))
a.sort(0)
if self.m_aspectRatio == -1:
a = N.array(([a[0][0],-a[1][1]],[a[1][0],-a[0][1]]))
self.zoomToRect(x0=a[0][0], y0=a[0][1],
x1=a[-1][0],y1=a[-1][1])
def _fitGaussian2D(img, indy, indx, y, x, sigma=[2.,2.], mean_max=None):
"""
img: already cut out with indy, indx
"""
if mean_max is None:
mi, ma, me, sd = U.mmms(img)
#ma = img[y,x]
else:
me, ma = mean_max
try:
sigma, sigma2 = sigma
param0 = (me, float(ma-me), y, x, float(sigma), float(sigma2))
# func = _gaussian2D_ellipse
except (ValueError, TypeError):
try:
len(sigma)
sigma = [0]
except TypeError:
pass
param0 = (me, float(ma-me), y, x, float(sigma))
#func = _gaussian2D
img = img.flatten()
def func(p, indy, indx):
return yGaussian2D(p, indy, indx) - img
from scipy import optimize
ret, check = optimize.leastsq(func, param0,
args=(indy.flatten(), indx.flatten()), warning=None)
ret[2:4] += 0.5 # use pixel center
ret[4:] = N.abs(ret[4:])
return ret, check
def findMaxWithGFit(img, sigma=0.5, win=11):
'''
find sub-pixel peaks from input img using n-dimensional Guassian fitting
sigma: scaler or [simgaZ,sigmaY..]
window: a window where the Guassian fit is performed on
return [v, zyx, sigma]
'''
vzyx = N.array(U.findMax(img))
ndim = img.ndim
try:
ret, check = imgFit.fitGaussianND(img, vzyx[-ndim:], sigma, win)
except IndexError: # too close to the edge
imgFit.fitFailedAppend("at %s" % str(vzyx[-ndim:]))
sigma = imgFit._scalerToSeq(sigma, ndim)
return vzyx[0:1], vzyx[-ndim:], list(sigma)
if check == 5 or N.any(ret[2:2+ndim] > (vzyx[-ndim:] + win)) or N.any(ret[2:2+ndim] < (vzyx[-ndim:] - win)):
imgFit.fitFailedAppend("at %s, %s, check=%i" % (str(vzyx[-ndim:]), str(ret), check))
sigma = imgFit._scalerToSeq(sigma, ndim)
return [vzyx[0:1], vzyx[-ndim:], sigma]
#x= (vzyx[0:1] + [vzyx[-ndim:]] + [sigma])
# print x
# return x
else:
v = ret[1]
zyx = ret[2:2+ndim]
sigma = ret[2+ndim:2+ndim*2]
return [v,zyx,sigma]
def findMaxWithGFitAll(img, thre=0, sigma_peak=0.5, win=11, mask_npxls=3):
"""
find peaks until either
1. any pxls becomes below thre
2. the same peak was found as the maximum
mask_npxls: number of pixels to mask when Gaussian fitting failed
return poslist
"""
img = img.copy()
imgFit.fitFailedClear()
ndim = img.ndim
sigma_peak = imgFit._scalerToSeq(sigma_peak, ndim)
poses = []
vzyx = U.findMax(img)
while vzyx[0] > thre:
prev = vzyx
try:
ret, check = imgFit.fitGaussianND(img, vzyx[-ndim:], sigma_peak, win)
except IndexError: # too close to the edge
imgFit.fitFailedAppend("at %s" % str(vzyx[-ndim:]))
mask_value(img, vzyx[-ndim:], r=mask_npxls, value=img.min())
poses.append(list(vzyx)[0:1] + [vzyx[-ndim:]] + [list(sigma_peak)])
if check == 5:
imgFit.fitFailedAppend("at %s, %s, check=%i" % (str(vzyx[-ndim:]), str(ret), check))
mask_value(img, vzyx[-ndim:], r=mask_npxls, value=img.min())
poses.append(list(vzyx)[0:1] + [vzyx[-ndim:]] + [sigma_peak])
else:
v = ret[1]
zyx = ret[2:2+ndim]
if N.any(N.abs(zyx - vzyx[1:]) > win/2.):#zyx < 0 or zyx > img.shape or ):
mask_value(img, vzyx[-ndim:], r=mask_npxls, value=img.min())
poses.append(list(vzyx)[0:1] + [vzyx[-ndim:]] + [sigma_peak])
else:
sigma = ret[2+ndim:2+ndim*2]
mask_gaussianND(img, zyx, v, sigma)
poses.append([v,zyx,sigma])
vzyx = U.findMax(img)
if N.all(vzyx == prev):
break
return poses#, img
def findBestChannel(self, t=0):
"""
the reference wavelength is determined from the wavelength and intensity
set self.refwave (in index)
"""
# if time laplse
if self.img.nt > 1:
# how large the object is...
arrs = [self.img.get3DArr(w=w, t=t).ravel() for w in range(self.img.nw)]
modes = [imgFilters.mode(a[::50]) for a in arrs]
fpxls = [N.where(a > modes[i])[0].size/float(a.size) for i, a in enumerate(arrs)]
# bleach half time
halfs = []
for w in range(self.nw):
mes = [self.img.get3DArr(w=w, t=t).mean() for t in range(self.nt)]
parm, check = U.fitDecay(mes)
halfs.append(parm[-1] / float(self.nt))
channels = N.add(fpxls, halfs)
refwave = N.argmax(channels)
print('The channel to align is %i' % refwave)
# if wavelengths are only 2, then use the channel 0
elif self.img.nw <= 2:
refwave = 0
# take into account for the PSF distortion due to chromatic aberration
elif self.img.nw > 2:
pwrs = N.array([self.img.get3DArr(w=w, t=t).mean() for w in range(self.img.nw)])
# the middle channel should have the intermediate PSF shape
waves = [self.img.getWaveFromIdx(w) for w in range(self.img.nw)]
waves.sort()
candidates = [self.img.getWaveIdx(wave) for wave in waves[1:-1]]
# remove channels with lots of saturation
candidates = [w for w in candidates if not self.getSaturation(w=w,t=t)]
# find out channels with enough signal
thr = N.mean(pwrs) / 1.25
bol = N.where(pwrs[candidates] > thr, 1, 0)
if N.any(bol):
ids = N.nonzero(bol)[0]
if len(ids) == 1:
idx = ids[0]
else:
candidates = N.array(candidates)[ids]
idx = N.argmax(pwrs[candidates])
refwave = candidates[idx]
else:
refwave = N.argmax(pwrs)
self.refwave = refwave
self.fixAlignParmWithCurrRefWave()
self.progress()
def findMaxWithGFitAll(img, thre=0, sigma_peak=0.5, win=11, mask_npxls=3):
"""
find peaks until either
1. any pxls becomes below thre
2. the same peak was found as the maximum
mask_npxls: number of pixels to mask when Gaussian fitting failed
return poslist
"""
img = img.copy()
imgFit.fitFailedClear()
ndim = img.ndim
sigma_peak = imgFit._scalerToSeq(sigma_peak, ndim)
poses = []
vzyx = U.findMax(img)
while vzyx[0] > thre:
prev = vzyx
try:
ret, check = imgFit.fitGaussianND(img, vzyx[-ndim:], sigma_peak,
win)
except IndexError: # too close to the edge
imgFit.fitFailedAppend("at %s" % str(vzyx[-ndim:]))
mask_value(img, vzyx[-ndim:], r=mask_npxls, value=img.min())
poses.append(list(vzyx)[0:1] + [vzyx[-ndim:]] + [list(sigma_peak)])
if check == 5:
imgFit.fitFailedAppend("at %s, %s, check=%i" %
(str(vzyx[-ndim:]), str(ret), check))
mask_value(img, vzyx[-ndim:], r=mask_npxls, value=img.min())
poses.append(list(vzyx)[0:1] + [vzyx[-ndim:]] + [sigma_peak])
else:
v = ret[1]
zyx = ret[2:2 + ndim]
sigma = ret[2 + ndim:2 + ndim * 2]
mask_gaussianND(img, zyx, v, sigma)
poses.append([v, zyx, sigma])
vzyx = U.findMax(img)
if N.all(vzyx == prev):
break
return poses #, img
def paddingMed(img, shape, shift=None, smooth=10):
"""
pad with median
see doc for paddingValue
"""
try:
med = N.median(img, axis=None)
except TypeError: # numpy version < 1.1
med = U.median(img)
return paddingValue(img, shape, med, shift, smooth)
def paddingMed(img, shape, shift=None, smooth=10):
"""
pad with median
see doc for paddingValue
"""
try:
med = N.median(img, axis=None)
except TypeError: # numpy version < 1.1
med = U.median(img)
return paddingValue(img, shape, med, shift, smooth)
def maskEdgeWithValue2D(arr, val=None):
"""
overwrite 2D image edge (s[:-2,2:]) with value **in place**
if val is None, use median
"""
if not val:
val = U.median(arr[:-2, 2:])
arr[-2:] = val
arr[:, :2] = val
return arr
def maskEdgeWithValue2D(arr, val=None):
"""
overwrite 2D image edge (s[:-2,2:]) with value **in place**
if val is None, use median
"""
if not val:
val = U.median(arr[:-2,2:])
arr[-2:] = val
arr[:,:2] = val
return arr
def _findMaxXcor(c, win, gFit=True, niter=2):
if gFit:
for i in range(niter):
v, zyx, s = findMaxWithGFit(c, win=win + (i * 2))
if v:
if N.any(zyx > N.array(c.shape)) or N.any(zyx < 0):
vzyx = N.array(U.findMax(c)) #continue
v = vzyx[0]
zyx = vzyx[-c.ndim:] + 0.5 # pixel center
s = 2.5
else:
break
if not v:
v = U.findMax(c)[0]
else:
vzyx = U.findMax(c)
v = vzyx[0]
zyx = N.array(vzyx[-c.ndim:]) + 0.5 # pixel center
s = 2.5
return v, zyx, s
def _findMaxXcor(c, win, gFit=True, niter=2):
if gFit:
for i in range(niter):
v, zyx, s = findMaxWithGFit(c, win=win+(i*2))
if v:
if N.any(zyx > N.array(c.shape)) or N.any(zyx < 0):
vzyx = N.array(U.findMax(c))#continue
v = vzyx[0]
zyx = vzyx[-c.ndim:] + 0.5 # pixel center
s = 2.5
else:
break
if not v:
v = U.findMax(c)[0]
else:
vzyx = U.findMax(c)
v = vzyx[0]
zyx = N.array(vzyx[-c.ndim:]) + 0.5 # pixel center
s = 2.5
return v, zyx, s
def _doBilinear2D(a2d, tyx=(0,0), r=0, mag=1, anismag=1, dyx=(0,0), mr=0, b2d=None):
if b2d is None:
b2d = N.empty_like(a2d)
else:
b2d = N.ascontiguousarray(b2d)
a2d = a2d.copy() # otherwise, the following code will mess up the input
if N.any(dyx[-2:]) or mr:
temp = b2d
target = a2d
U.trans2d(target, temp, (dyx[-1], dyx[-2], mr, 1, 0, 1))
else:
temp = a2d
target = b2d
# rot mag first to make consistent with affine
magaxis = 1 # only this axis works
if r or mag != 1 or anismag != 1:
U.trans2d(temp, target, (0, 0, r, mag, magaxis, anismag))
else:
target[:] = temp[:]
# then translate
tyx2 = N.array(tyx) # copy
tyx2[-2:] -= dyx[-2:]
if N.any(tyx2[-2:]) or mr:
U.trans2d(target, temp, (tyx2[-1], tyx2[-2], -mr, 1, 0, 1))
else:
temp[:] = target[:]
#a[z] = temp[:]
return temp
def _doBilinear2D(a2d, tyx=(0,0), r=0, mag=1, anismag=1, dyx=(0,0), mr=0, b2d=None):
if b2d is None:
b2d = N.empty_like(a2d)
else:
b2d = N.ascontiguousarray(b2d)
a2d = a2d.copy() # otherwise, the following code will mess up the input
if N.any(dyx[-2:]) or mr:
temp = b2d
target = a2d
U.trans2d(target, temp, (dyx[-1], dyx[-2], mr, 1, 0, 1))
else:
temp = a2d
target = b2d
# rot mag first to make consistent with affine
magaxis = 1 # only this axis works
if r or mag != 1 or anismag != 1:
U.trans2d(temp, target, (0, 0, r, mag, magaxis, anismag))
else:
target[:] = temp[:]
# then translate
tyx2 = N.array(tyx) # copy
tyx2[-2:] -= dyx[-2:]
if N.any(tyx2[-2:]) or mr:
U.trans2d(target, temp, (tyx2[-1], tyx2[-2], -mr, 1, 0, 1))
else:
temp[:] = target[:]
#a[z] = temp[:]
return temp
def roughRotMag(a, b, yxrm, idx, step=0.02, nstep=20):
guess = yxrm[idx]
Range = (guess - (step * nstep), guess + (step * nstep), step)
xs = N.arange(*Range)
yxrms = N.empty((len(xs), ) + yxrm.shape, yxrm.dtype.type)
yxrms[:] = yxrm
yxrms[:, idx] = xs
#for r in Range:
# yxrm2 = N.copy(yxrm)
# yxrm2[idx] = r
# yxrms.append(yxrm2)
pp = ppro.pmap(_compCost, yxrms, ppro.NCPU, a, b)
#pp = [_compCost(yx, a, b) for yx in yxrms]
xi = N.argmin(pp)
pmin = pp[xi]
base = max(pp)
if pmin == base: # failed to get the curve for some reason
# usually this happens if one used ndimage.zoom() in scipy
# ndimage.zoom only interpolate pixel-wise.
# no subpixel interpolation is done...
x = int(idx >= 3)
check = 5
else: # go ahead and fit poly
x = xs[xi]
data = zip(xs, pp)
fit, check = U.fitPoly(data, p=(1, 1, 1, 1, 1, 1, 1))
if check == 5:
answer = x
else:
xx = U.nd.zoom(xs, 100)
yy = U.yPoly(fit, xx)
ii = N.argmin(yy)
answer = xx[ii]
return answer
def prepImg4AffineZ(fn, w=None, phaseContrast=True):
an = aligner.Chromagnon(fn)
an.findBestChannel()
an.setRefImg()
ref = an.img.get3DArr(w=an.refwave, t=0)
prefyx = U.project(ref)
#prefyz = U.project(ref, -1)
if w is None:
waves = range(an.img.nw)
waves.remove(an.refwave)
w = waves[0]
img = an.img.get3DArr(w=w, t=0)
pimgyx = U.project(img)
#pimgyz = U.project(img, -1)
#yz, c = xcorr.Xcorr(prefyz, pimgyz, phaseContrast=phaseContrast)
yx, c = xcorr.Xcorr(prefyx, pimgyx, phaseContrast=phaseContrast)
xs = N.round_(an.refxs - yx[1]).astype(N.int)
if xs.max() >= an.img.nx:
xsbool = (xs < an.img.nx)
xsinds = N.nonzero(xsbool)[0]
xs = xs[xsinds]
imgyz = alignfuncs.prep2D(img.T, zs=xs)
a1234 = alignfuncs.chopImg(an.refyz)
b1234 = alignfuncs.chopImg(imgyz)
ab = zip(a1234, b1234)
yxcs = [xcorr.Xcorr(a, b, phaseContrast=phaseContrast) for a, b in ab]
yxs = [yx for yx, c in yxcs]
cqs = [c.max() - c[c.shape[0] // 4].std() for yx, c in yxcs]
return ab, cqs, [c for yx, c in yxcs], yxs, an
def arr_normalize(a, normalize_with='intens'):
"""
normalize_with: intens or std
"""
choices = ('intens', 'std')
mi, ma, me, sd = U.mmms(a)
if normalize_with == choices[0]:
a = (a - mi) / (ma - mi)
elif normalize_with == choices[1]:
a = (a - me) / sd
else:
raise ValueError('normalize only with %s' % choices)
return a
def chopYX(shapeYX, ncpu=8):
"""
return axis, YXmmlist
"""
n, _1, _2, axis = U.findMax(shapeYX)
n0 = n // ncpu
mms = []
pixel = 0
for cpu in range(ncpu):
mms += [[pixel, pixel + n0]]
pixel += n0
mms[-1][-1] = n
return axis, mms
def arr_normalize(a, normalize_with='intens'):
"""
normalize_with: intens or std
"""
choices = ('intens', 'std')
mi, ma, me, sd = U.mmms(a)
if normalize_with == choices[0]:
a = (a-mi) / (ma-mi)
elif normalize_with == choices[1]:
a = (a - me) / sd
else:
raise ValueError('normalize only with %s' % choices)
return a
def chopYX(shapeYX, ncpu=8):
"""
return axis, YXmmlist
"""
n, _1, _2, axis = U.findMax(shapeYX)
n0 = n // ncpu
mms = []
pixel = 0
for cpu in range(ncpu):
mms += [[pixel, pixel + n0]]
pixel += n0
mms[-1][-1] = n
return axis, mms
def writeSec(self, arr, i=0, singleOutFn=None):
if self._rescaleTo8bit:
if self._rescaleTo8bit is True:
self.rescaleTo8bit(arr)
arr = (arr-self._rescaleTo8bit[0])*255./self._rescaleTo8bit[1]
# astype changes byteorder as well
arr = arr.astype(self.dtype)
img = U.array2image(arr, rgbOrder=self.rgbOrder)
if not singleOutFn:
singleOutFn = self.outfn
img.save(singleOutFn, **self.saveOptions)
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 rot2D(img2D, yx, sigma, rlist, mean_max=None, win=11):
y, x = yx
yi, xi, LD = _indLD(win, y, x)
imgP = img2D[yi, xi]
if mean_max is None:
mi, ma, me, sd = U.mmms(imgP)
else:
me, ma = mean_max
yy = []
for r in rlist:
ret, check = _fitGaussian2DR(imgP, LD, y, x, sigma, [me, ma], win, r)
syx = ret[4] / ret[5] # width y / x
yy.append(syx)
return yy
def writeSec(self, arr, i=0, singleOutFn=None):
if self._rescaleTo8bit:
if self._rescaleTo8bit is True:
self.rescaleTo8bit(arr)
arr = (arr -
self._rescaleTo8bit[0]) * 255. / self._rescaleTo8bit[1]
# astype changes byteorder as well
arr = arr.astype(self.dtype)
img = U.array2image(arr, rgbOrder=self.rgbOrder)
if not singleOutFn:
singleOutFn = self.outfn
img.save(singleOutFn, **self.saveOptions)
def rot2D(img2D, yx, sigma, rlist, mean_max=None, win=11):
y, x = yx
yi, xi, LD = _indLD(win, y, x)
imgP = img2D[yi,xi]
if mean_max is None:
mi, ma, me, sd = U.mmms(imgP)
else:
me, ma = mean_max
yy = []
for r in rlist:
ret, check = _fitGaussian2DR(imgP, LD, y, x, sigma, [me,ma], win, r)
syx = ret[4] / ret[5] # width y / x
yy.append(syx)
return yy
def testCorrelation(arr, win=64):
from Priithon.all import U
half = win / 2.
arr = arr.copy()
for i in range(10):
v, z, y, x = U.findMax(arr)
if y - half >= 0 and y + half < arr.shape[
0] and x - half >= 0 and x + half < arr.shape[1]:
a = arr[y - half:y + half, x - half:x + half]
break
else:
arr[y, x] = 0
b = a.copy()
yx, c = xcorr.Xcorr(a, b, phaseContrast=True)
cme = c[:c.shape[0] // 4].mean()
return c.max() - cme
def setupHistArr(self, i):
self.hist_arr[i] = None
img = self.data[tuple(self.zsec)][i]
if img.dtype.type == N.uint8:
self.hist_min[i], self.hist_max[i] = 0, (1 << 8) - 1
elif img.dtype.type == N.uint16:
self.hist_min[i], self.hist_max[i] = 0, (1 << 16) - 1
elif img.dtype.type == N.int16:
self.hist_min[i], self.hist_max[i] = 0 - (1 << 15), (1 << 15) - 1
from Priithon.all import U
self.hist[i].hist_min, self.hist[i].hist_max = U.mm(img) #self.img)
if img.dtype.type in (N.uint8, N.int16, N.uint16):
self.hist_range[i] = self.hist_max[i] - self.hist_min[i] + 1
self.hist_arr[i] = N.zeros(shape=self.hist_range[i], dtype=N.int32)
def onViewSeq(self, ev):
from Priithon.all import Y,U
try:
Y.view( U.loadImg_seq( self.fn_or_fns ) )
except:
if NO_SPECIAL_GUI_EXCEPT:
raise
import sys
e = sys.exc_info()
wx.MessageBox("Error when loading image sequence: %s - %s" %\
(str(e[0]), str(e[1]) ),
"Non consistent image shapes !?",
style=wx.ICON_ERROR)
else:
s = "Y.view( U.loadImg_seq(<fileslist>) )"
Y.shellMessage("### %s\n"% s)
def rotND(img, zyx, sigma, rlist, mean_max=None, win=10):
# y, x = yx
# yi, xi, LD = _indLD(win, y, x)
slices = imgGeo.nearbyRegion(img.shape, zyx, win)
imgP = img[slices]
if mean_max is None:
mi, ma, me, sd = U.mmms(imgP)
else:
me, ma = mean_max
yy = []
for r in rlist:
ret, check = fitGaussianND(img, zyx, sigma, win, [me, ma], r)#_fitGaussian2DR(imgP, LD, y, x, sigma, [me,ma], win, r)
syx = ret[4] / ret[5] # width y / x
yy.append(syx)
return yy
def onViewSeq(self, ev):
from Priithon.all import Y,U
try:
Y.view( U.loadImg_seq( self.fn_or_fns ) )
except:
if NO_SPECIAL_GUI_EXCEPT:
raise
import sys
e = sys.exc_info()
wx.MessageBox("Error when loading image sequence: %s - %s" %\
(str(e[0]), str(e[1]) ),
"Non consistent image shapes !?",
style=wx.ICON_ERROR)
else:
s = "Y.view( U.loadImg_seq(<fileslist>) )"
Y.shellMessage("### %s\n"% s)
def setupHistArr(self,i):
self.hist_arr[i] = None
img = self.data[ tuple(self.zsec) ][i]
if img.dtype.type == N.uint8:
self.hist_min[i], self.hist_max[i] = 0, (1<<8)-1
elif img.dtype.type == N.uint16:
self.hist_min[i], self.hist_max[i] = 0, (1<<16)-1
elif img.dtype.type == N.int16:
self.hist_min[i], self.hist_max[i] = 0-(1<<15), (1<<15)-1
from Priithon.all import U
self.hist[i].hist_min,self.hist[i].hist_max = U.mm(img)#self.img)
if img.dtype.type in (N.uint8, N.int16, N.uint16):
self.hist_range[i] = self.hist_max[i] - self.hist_min[i] + 1
self.hist_arr[i] = N.zeros(shape=self.hist_range[i], dtype=N.int32)
def setupHistArr(self):
self.hist_arr = None
if self.img.dtype.type == N.uint8:
self.hist_min, self.hist_max = 0, (1<<8)-1
elif self.img.dtype.type == N.uint16:
self.hist_min, self.hist_max = 0, (1<<16)-1
elif self.img.dtype.type == N.int16:
self.hist_min, self.hist_max = 0-(1<<15), (1<<15)-1
from Priithon.all import U
self.hist.hist_min,self.hist.hist_max = U.mm(self.img)#self.hist_min
#if self.hist.m_histPlotArray is not None:
# self.hist.m_histPlotArray[0,0],self.hist.m_histPlotArray[-1,0] = U.mm(self.img)
# print self.hist.m_histPlotArray[0,0],self.hist.m_histPlotArray[-1,0]
if self.img.dtype.type in (N.uint8, N.int16, N.uint16):
self.hist_range = self.hist_max - self.hist_min + 1
self.hist_arr = N.zeros(shape=self.hist_range, dtype=N.int32)