def __init__(self, location_path=UTILITIES_DIR, save_img=(None, True)):
A_Filter.__init__(self,
'choose_lungsV2',
FILTER_TYPE.PRE_FILTER,
location_path,
built_in=False,
save_img=save_img)
def __init__(self, mask_image, save_img=(None, True)):
A_Filter.__init__(self,
'Mask',
FILTER_TYPE.OTHERS,
built_in=True,
save_img=save_img)
self.mask_image = mask_image
def __init__(self, location_path=UTILITIES_DIR, save_img=(None, True)):
A_Filter.__init__(self,
'hu_threshold',
FILTER_TYPE.PRE_FILTER,
location_path,
built_in=False,
save_img=save_img)
def __init__(self,
location_path=UTILITIES_DIR,
save_img=(None, True),
radius=1):
A_Filter.__init__(self,
"apply_median",
FILTER_TYPE.PRE_FILTER,
location_path,
built_in=False,
save_img=save_img)
self.radius = radius
def __init__(self,
location_path=UTILITIES_DIR,
save_img=(None, True),
start_slice=trachea_start_slice):
A_Filter.__init__(self,
'find_trachea',
FILTER_TYPE.OTHERS,
location_path,
built_in=False,
save_img=save_img)
self.start_slice = start_slice
def __init__(self,
n_objects=3,
feature=SIZE,
order=0,
bck_val=0,
save_img=(None, True)):
A_Filter.__init__(self,
'Keep-Objects',
FILTER_TYPE.OTHERS,
built_in=True,
save_img=save_img)
self.n_objects = n_objects
self.feature = feature
self.order = order
self.bck_val = bck_val
def __init__(self,
lower_th=1,
upper_th=255,
inside_val=255,
outside_val=0,
save_img=(None, True)):
A_Filter.__init__(self,
'Binarize',
FILTER_TYPE.OTHERS,
built_in=True,
save_img=save_img)
self.lower_th = lower_th
self.upper_th = upper_th
self.inside_val = inside_val
self.outside_val = outside_val
def __init__(
self,
location_path='/home/pmacias/Projects/MRI-PET_Tuberculosis/Fiji.app/',
save_img=(None, True),
q=25,
three_dim=True,
averages=False):
A_Filter.__init__(self,
'ImageJ-linux64',
FILTER_TYPE.OTHERS,
location_path,
built_in=False,
save_img=save_img)
self.q = q
self.three_dim = three_dim
self.averages = averages
def __init__(self,
radius=1,
kernel=SimpleITK.sitkBall,
backgorund=0.0,
foregorund=255.0,
boundary_foreground=False,
save_img=(None, True)):
A_Filter.__init__(self,
'Erode',
FILTER_TYPE.OTHERS,
built_in=True,
save_img=save_img)
self.radius = radius
self.kernel = kernel
self.backgorund = backgorund
self.foregorund = foregorund
self.boundary_foreground = boundary_foreground
def __init__(self,
iniTh=0.0,
thrPlusOne=-600,
huDiff=0.01,
ct_HUnits_error=290,
outside_val=0.0,
inside_val=255.0,
save_img=(None, True)):
A_Filter.__init__(self,
'Hu_trheshold',
FILTER_TYPE.PRE_FILTER,
built_in=True,
save_img=save_img)
self.iniTh = iniTh
self.huDiff = huDiff
self.errFac = ct_HUnits_error
self.inside_val = inside_val
self.outside_val = outside_val
self.thrPlusOne = thrPlusOne
def __init__(self,
radius=1,
iterations=20,
foregorund=255,
background=0,
threads=4,
majority_thr=1,
save_img=(None, True)):
A_Filter.__init__(self,
'Filling',
FILTER_TYPE.POST_FILTER,
built_in=True,
save_img=save_img)
self.radius = radius
self.background = background
self.foregorund = foregorund
self.iterations = iterations
self.threads = threads
self.majority_thr = majority_thr
def __init__(self,
location_path=UTILITIES_DIR,
save_img=(None, True),
intial_postion=None,
trachea_expected_perimeter=MACAQUE_EXPECTED_PERIMETER,
time_Step=0.8,
variable_thr=(-625, -300),
fixed_thr=1.4):
A_Filter.__init__(self,
'air_ext_fm',
FILTER_TYPE.TRAQUEA_EXTRACTION,
location_path,
built_in=False,
save_img=save_img)
self.time_step = time_Step
self.variable_thr = variable_thr
self.fixed_threshold = fixed_thr
self.trachea_expected_perimeter = trachea_expected_perimeter
self.initial_postion = intial_postion