def localization_fv(data3dr, voxelsize_mm, seeds=None, unique_cls=None): # scale
import scipy
import numpy as np
import os.path as op
try:
from lisa import organ_localizator
except:
import organ_localizator
import organ_localizator
fvall = organ_localizator.localization_fv(data3dr, voxelsize_mm)
return combine_fv_and_seeds([fvall], seeds, unique_cls)
def localization_fv(data3dr, voxelsize_mm, seeds=None, unique_cls=None): # scale
import scipy
import numpy as np
import os.path as op
try:
from lisa import organ_localizator
except:
import organ_localizator
import organ_localizator
fvall = organ_localizator.localization_fv(data3dr, voxelsize_mm)
return combine_fv_and_seeds([fvall], seeds, unique_cls)
def intensity_localization_fv(data3dr,
voxelsize_mm,
seeds=None,
unique_cls=None): # scale
"""
Use organ_localizator features plus intensity features
:param data3dr:
:param voxelsize_mm:
:param seeds:
:param unique_cls:
:return:
"""
import scipy
import numpy as np
import os.path as op
try:
from lisa import organ_localizator
except:
import organ_localizator
f0 = scipy.ndimage.filters.gaussian_filter(data3dr,
sigma=0.5).reshape(-1, 1)
f1 = scipy.ndimage.filters.gaussian_filter(data3dr, sigma=3).reshape(-1, 1)
import organ_localizator
fvall = organ_localizator.localization_fv(data3dr, voxelsize_mm)
# fvall = organ_localizator.localization_intensity_fv(data3dr, voxelsize_mm)
fv = np.concatenate(
[
f0,
f1,
# f2, f3, # f4,
# fd1, fd2, fd3, fd4, fd5, fd6,
fvall,
# f6, f7, f8,
],
1)
if seeds is not None:
# logger.debug("seeds " + str(seeds))
# print "seeds ", seeds
sd = seeds.reshape(-1, 1)
selection = np.in1d(sd, unique_cls)
fv = fv[selection]
sd = sd[selection]
# sd = sd[]
return fv, sd
return fv
def intensity_localization_fv(data3dr, voxelsize_mm, seeds=None, unique_cls=None): # scale
"""
Use organ_localizator features plus intensity features
:param data3dr:
:param voxelsize_mm:
:param seeds:
:param unique_cls:
:return:
"""
import scipy
import numpy as np
import os.path as op
try:
from lisa import organ_localizator
except:
import organ_localizator
f0 = scipy.ndimage.filters.gaussian_filter(data3dr, sigma=0.5).reshape(-1, 1)
f1 = scipy.ndimage.filters.gaussian_filter(data3dr, sigma=3).reshape(-1, 1)
import organ_localizator
fvall = organ_localizator.localization_fv(data3dr, voxelsize_mm)
# fvall = organ_localizator.localization_intensity_fv(data3dr, voxelsize_mm)
fv = np.concatenate([
f0,
f1,
# f2, f3, # f4,
# fd1, fd2, fd3, fd4, fd5, fd6,
fvall,
# f6, f7, f8,
], 1)
if seeds is not None:
# logger.debug("seeds " + str(seeds))
# print "seeds ", seeds
sd = seeds.reshape(-1,1)
selection = np.in1d(sd, unique_cls)
fv = fv[selection]
sd = sd[selection]
# sd = sd[]
return fv, sd
return fv