def addNoiseToMapSolvent(map, varNoise):
#*********************************
#****** add Noise To Map *********
#*********************************
mapData = np.copy(map)
mapSize = mapData.shape
noiseMap = np.random.randn(mapSize[0], mapSize[1],
mapSize[2]) * math.sqrt(varNoise)
mask = EMData()
mask.set_size(mapSize[0], mapSize[1], mapSize[2])
mask.to_zero()
sphere_radius = (np.min(mapSize) / 2.0 - 60)
mask.process_inplace("testimage.circlesphere", {"radius": sphere_radius})
maskData = np.copy(EMNumPy.em2numpy(mask))
maskData[maskData > 0] = 10
maskData[maskData <= 0] = 0
maskData[maskData == 0] = 1
maskData[maskData == 10] = 0
noiseMap = noiseMap * maskData
mapData = mapData + noiseMap
return mapData
def setup_test_data(voldim=30, size=10):
from sparx import model_gauss
emmap = model_gauss(size, voldim, voldim, voldim)
modmap = EMData()
modmap.set_size(voldim, voldim, voldim)
modmap.process_inplace("testimage.noise.gauss", {"sigma": 1, "seed": 99})
mask = model_square(size, voldim, voldim, voldim)
return emmap, modmap, mask
def internal_test_image2(self, nx, ny=1, nz=1):
from EMAN2 import EMData, display
from fundamentals import cyclic_shift, mirror
e = EMData()
e.set_size(nx, ny, nz)
e.process_inplace("testimage.tomo.objects")
e = cyclic_shift(e, nx/2, ny/3, nz/5)
e = mirror(e)
return e
def prepare_mask_and_maps_for_scaling(args):
emmap = get_image(args.em_map)
modmap = get_image(args.model_map)
if args.mask is None:
mask = EMData()
xsize, ysize, zsize = emmap.get_xsize(), emmap.get_ysize(
), emmap.get_zsize()
mask.set_size(xsize, ysize, zsize)
mask.to_zero()
if xsize == ysize and xsize == zsize and ysize == zsize:
sphere_radius = xsize // 2
mask.process_inplace("testimage.circlesphere",
{"radius": sphere_radius})
else:
mask += 1
mask = Util.window(mask, xsize - 1, ysize - 1, zsize - 1)
mask = Util.pad(mask, xsize, ysize, zsize, 0, 0, 0, '0')
elif args.mask is not None:
mask = binarize(get_image(args.mask), 0.5)
if args.window_size is None:
wn = int(math.ceil(round((7 * 3 * args.apix)) / 2.) * 2)
elif args.window_size is not None:
wn = int(math.ceil(args.window_size / 2.) * 2)
window_bleed_and_pad = check_for_window_bleeding(mask, wn)
if window_bleed_and_pad:
pad_int_emmap = compute_padding_average(emmap, mask)
pad_int_modmap = compute_padding_average(modmap, mask)
map_shape = [(emmap.get_xsize() + wn), (emmap.get_ysize() + wn),
(emmap.get_zsize() + wn)]
emmap = Util.pad(emmap, map_shape[0], map_shape[1], map_shape[2], 0, 0,
0, 'pad_int_emmap')
modmap = Util.pad(modmap, map_shape[0], map_shape[1], map_shape[2], 0,
0, 0, 'pad_int_modmap')
mask = Util.pad(mask, map_shape[0], map_shape[1], map_shape[2], 0, 0,
0, '0')
return emmap, modmap, mask, wn, window_bleed_and_pad
def internal_test_image(self, nx, ny=1, nz=1):
from EMAN2 import EMData
e = EMData()
e.set_size(nx, ny, nz)
e.process_inplace("testimage.tomo.objects")
return e
