def _make_random_transforms_cmd(self,
in_path,
out_path,
count,
param=None):
if param is None:
param = self.get_random_transforms_param_defaults()
st.check_exists(in_path, "Input")
dim_str = " -dim %d" % (self.dim)
count_str = " -count %d" % (count)
cmd = self.bin_path + "ACRandomTransforms" + exe_extension
cmd = cmd + " -in " + in_path + " -out " + out_path + dim_str + count_str + st.param_dict_to_string(
param)
return cmd
def make_transform(index, atlas_id, params):
# atlas image
#label_atlas_str = atlas_path + "MI" + atlas_id + "labels.nii.gz"#ind_str("S", index, ".labels.nii.gz")
mask_atlas_str = atlas_path + "MI" + atlas_id + "mask.nii.gz"
#mri_atlas_str = atlas_path + "MI" + atlas_id + "template.nii.gz"
# ref image
#label_ref_str = labels_path + ind_str("S", index, ".labels.nii.gz")
mask_ref_str = masks_path + ind_str("S", index, ".brainmask.nii.gz")
#mri_ref_str = mri_path + ind_str("S", index, ".nii.gz")
out = out_path + ind_str("S", index, "/")
out_image = out + "mask.nii.gz"
transform_path = out + "transform_complete.txt"
overlap_out = out_path + ind_str("S", index,
"/") + "brain_mask_overlap.csv"
#" -mask1 " + mask_ref_str + " -mask2 " + mask_atlas_str +
return exe_path + " -ref " + mask_ref_str + " -in " + mask_atlas_str + " -out " + out_image + " -label_overlap_out " + overlap_out + " -transform " + transform_path + st.param_dict_to_string(
params)
def _make_register_cmd(self,
ref_im_path,
flo_im_path,
out_path,
is_rigid,
param=None):
if param is None:
print("Using default param.")
param = self.get_register_param_defaults()
st.check_exists(ref_im_path, "Reference")
st.check_exists(ref_im_path, "Floating")
if self.dim == 2:
three_d_str = " -3d 0"
else:
three_d_str = " -3d 1"
if is_rigid:
rigid_str = " -rigid 1"
else:
rigid_str = " -rigid 0"
cmd = self.bin_path + "ACRegister" + exe_extension
st.check_exists(cmd, "Executable")
cmd = cmd + " -in1 " + ref_im_path + " -in2 " + flo_im_path + " -out " + out_path + rigid_str + three_d_str + st.param_dict_to_string(
param)
return cmd
def _make_label_overlap_cmd(self,
ref_im_path,
transformed_im_path,
out_path,
param=None):
if param is None:
param = self.get_label_overlap_param_defaults()
st.check_exists(ref_im_path, "Reference")
st.check_exists(transformed_im_path, "Transformed")
dim_str = " -dim %d" % (self.dim)
cmd = self.bin_path + "ACLabelOverlap" + exe_extension
st.check_exists(cmd, "Executable")
cmd = cmd + " -in1 " + ref_im_path + " -in2 " + transformed_im_path + " -out " + out_path + dim_str + st.param_dict_to_string(
param)
return cmd
def _make_transform_cmd(self,
ref_im_path,
flo_im_path,
out_path,
transform_path,
param=None):
if param is None:
param = self.get_transform_param_defaults()
st.check_exists(ref_im_path, "Reference")
st.check_exists(flo_im_path, "Floating")
dim_str = " -dim %d" % (self.dim)
cmd = self.bin_path + "ACTransform" + exe_extension
st.check_exists(cmd, "Executable")
cmd = cmd + " -ref " + ref_im_path + " -in " + flo_im_path + " -out " + out_path + " -transform " + transform_path + dim_str + st.param_dict_to_string(
param)
return cmd