def _smoothBorder(arr, start, stop, smooth, value): """ start, stop: [z,y,x] """ # prepare coordinates shape = N.array(arr.shape) start = N.ceil(start).astype(N.int16) stop = N.ceil(stop).astype(N.int16) smooth_start = start - smooth smooth_stop = stop + smooth smooth_start = N.where(smooth_start < 0, 0, smooth_start) smooth_stop = N.where(smooth_stop > shape, shape, smooth_stop) #print smooth_start, smooth_stop import copy sliceTemplate = [slice(None, None, None)] * arr.ndim shapeTemplate = list(shape) for d in range(arr.ndim): smooth_shape = shapeTemplate[:d] + shapeTemplate[d + 1:] # make an array containing the edge value edges = N.empty([2] + smooth_shape, N.float32) # start side slc = copy.copy(sliceTemplate) slc[d] = slice(start[d], start[d] + 1, None) edges[0] = arr[slc].reshape(smooth_shape) # stop side slc = copy.copy(sliceTemplate) slc[d] = slice(stop[d] - 1, stop[d], None) edges[1] = arr[slc].reshape(smooth_shape) edges = (edges - value) / float( smooth + 1) # this value can be array?? # both side for s, side in enumerate([start, stop]): if s == 0: rs = range(smooth_start[d], start[d]) rs.sort(reverse=True) elif s == 1: rs = range(stop[d], smooth_stop[d]) # smoothing for f, i in enumerate(rs): slc = copy.copy(sliceTemplate) slc[d] = slice(i, i + 1, None) edgeArr = edges[s].reshape(arr[slc].shape) #arr[slc] += edgeArr * (smooth - f) arr[slc] = arr[slc] + edgeArr * (smooth - f) # casting rule arr = N.ascontiguousarray(arr) return arr
def paddingValue(img, shape, value=0, shift=None, smooth=0, interpolate=True): """ shape: in the same dimension as img value: value in padded region, can be scaler or array with the shape shift: scaler or in the same dimension as img and shape (default 0) smooth: scaler value to smoothen border (here value must be scaler) interpolate: shift array by subpixel interpolation to adjust center return: padded array with shape """ # create buffer dtype = img.dtype.type canvas = N.empty(shape, dtype) canvas[:] = value # calculate position shape = N.array(shape) shapeS = img.shape center = N.divide(shape, 2) if shift is None: shift = 0 #[0] * len(shapeS) shapeL = shape #N.add(shapeS, center+shift) start, stop = (shapeL - shapeS) / 2., (shapeL + shapeS) / 2. slc = [slice(start[d], stop[d], None) for d in range(img.ndim)] #print slc, shapeS, shapeL # shift if necessary if interpolate: subpx_shift = start % 1 # should be 0.5 or 0 if N.sometrue(subpx_shift): img = U.nd.shift(img, subpx_shift) # padding canvas[slc] = img if smooth: canvas = _smoothBorder(canvas, start, stop, smooth, value) canvas = N.ascontiguousarray(canvas) #print shapeS, shapeL, slc return canvas
def pointsCutOutND(arr, posList, windowSize=100, sectWise=None, interpolate=True): """ array: nd array posList: ([(z,)y,x]...) windowSize: scalar (in pixel or as percent < 1.) or ((z,)y,x) if arr.ndim > 2, and len(windowSize) == 2, then cut out section-wise (higher dimensions stay the same) sectWise: conern only XY of windowSize (higher dimensions stay the same) interpolate: shift array by subpixel interpolation to adjust center return: list of array centered at each pos in posList """ shape = N.array(arr.shape) center = shape / 2. # prepare N-dimensional window size try: len(windowSize) # seq if sectWise: windowSize = windowSize[-2:] if len(windowSize) != arr.ndim: dim = len(windowSize) windowSize = tuple(shape[:-dim]) + tuple(windowSize) except TypeError: # scaler if windowSize < 1 and windowSize > 0: # percentage w = shape * windowSize if sectWise: w[:-2] = shape[:-2] windowSize = w.astype(N.uint16) else: windowSize = N.where(shape >= windowSize, windowSize, shape) if sectWise: windowSize = arr.shape[:-2] + windowSize[-2:] windowSize = N.asarray(windowSize) # cutout individual position arrList = [] for pos in posList: # prepare N-dimensional coordinate n = len(pos) if n != len(windowSize): temp = center.copy() center[-n:] = pos pos = center # calculate idx ori = pos - (windowSize / 2.) # float value oidx = N.ceil(ori) # idx subpxl = oidx - ori # subpixel mod if interpolate and N.sometrue(subpxl): # comit to make shift SHIFT = 1 else: SHIFT = 0 # prepare slice # when comitted to make shift, first cut out window+1, # then make subpixle shift, and then cutout 1 edge slc = [Ellipsis] # Ellipsis is unnecessary, just in case... slc_edge = [slice(1, -1, None)] * arr.ndim for d in range(arr.ndim): start = oidx[d] - SHIFT if start < 0: start = 0 slc_edge[d] = slice(0, slc_edge[d].stop, None) stop = oidx[d] + windowSize[d] + SHIFT if stop > shape[d]: stop = shape[d] slc_edge[d] = slice(slc_edge[d].start, shape[d], None) slc += [slice(int(start), int(stop), None)] # cutout, shift and cutout try: canvas = arr[slc] if SHIFT: canvas = U.nd.shift(canvas, subpxl) canvas = canvas[slc_edge] check = 1 except IndexError: print 'position ', pos, ' was skipped' check = 0 raise if check: arrList += [N.ascontiguousarray(canvas)] return arrList