def test_convert_flirt_to_sitk_transform(self):
for dim in [3]:
path_to_flirt_transform = os.path.join(
DIR_TEST, "%dD_flirt_Target_Source.txt" % dim)
path_to_fixed = os.path.join(DIR_DATA,
"%dD_Brain_Target.nii.gz" % dim)
path_to_moving = os.path.join(DIR_DATA,
"%dD_Brain_Source.nii.gz" % dim)
path_to_res = os.path.join(
DIR_TMP, "%dD_flirt2sitk_target_Source_.txt" % dim)
path_to_reference_transform = os.path.join(
DIR_TEST, "%dD_sitk_Target_Source.txt" % dim)
flirt2sitk.convert_flirt_to_sitk_transform(path_to_flirt_transform,
path_to_fixed,
path_to_moving,
path_to_res)
transform_sitk = sitkh.read_transform_sitk(path_to_res)
transform_ref_sitk = sitkh.read_transform_sitk(
path_to_reference_transform)
nda_reference = np.array(transform_ref_sitk.GetParameters())
nda = np.array(transform_sitk.GetParameters())
# Conversion to FLIRT only provides 4 decimal places
self.assertAlmostEqual(np.sum(np.abs(nda - nda_reference)),
0,
places=2)
def test_estimate_motion(self):
filename = "SRR_reference.nii.gz"
output = os.path.join(self.dir_output, filename)
dir_reference = os.path.join(self.dir_data, "estimate_motion")
dir_reference_mc = os.path.join(dir_reference, "motion_correction")
path_to_reference = os.path.join(dir_reference, filename)
path_to_reference_mask = ph.append_to_filename(
os.path.join(dir_reference, filename), self.suffix_mask)
two_step_cycles = 1
iter_max = 5
exe = os.path.abspath(rsfmri_estimate_motion.__file__)
cmd_args = ["python %s" % exe]
cmd_args.append("--filename %s" % self.filename)
cmd_args.append("--filename-mask %s" % ph.append_to_filename(
self.filename, self.suffix_mask))
cmd_args.append("--dir-output %s" % self.dir_output)
cmd_args.append("--two-step-cycles %s" % two_step_cycles)
cmd_args.append("--iter-max %d" % iter_max)
cmd = (" ").join(cmd_args)
self.assertEqual(ph.execute_command(cmd), 0)
# Check SRR volume
res_sitk = sitkh.read_nifti_image_sitk(output)
ref_sitk = sitkh.read_nifti_image_sitk(path_to_reference)
diff_sitk = res_sitk - ref_sitk
error = np.linalg.norm(sitk.GetArrayFromImage(diff_sitk))
self.assertAlmostEqual(error, 0, places=self.precision)
# Check SRR mask volume
res_sitk = sitkh.read_nifti_image_sitk(
ph.append_to_filename(output, self.suffix_mask))
ref_sitk = sitkh.read_nifti_image_sitk(path_to_reference_mask)
diff_sitk = res_sitk - ref_sitk
error = np.linalg.norm(sitk.GetArrayFromImage(diff_sitk))
self.assertAlmostEqual(error, 0, places=self.precision)
# Check transforms
pattern = REGEX_FILENAMES + "[.]tfm"
p = re.compile(pattern)
dir_res_mc = os.path.join(self.dir_output, "motion_correction")
trafos_res = sorted(
[os.path.join(dir_res_mc, t)
for t in os.listdir(dir_res_mc) if p.match(t)])
trafos_ref = sorted(
[os.path.join(dir_reference_mc, t)
for t in os.listdir(dir_reference_mc) if p.match(t)])
self.assertEqual(len(trafos_res), len(trafos_ref))
for i in range(len(trafos_ref)):
nda_res = sitkh.read_transform_sitk(trafos_res[i]).GetParameters()
nda_ref = sitkh.read_transform_sitk(trafos_ref[i]).GetParameters()
nda_diff = np.linalg.norm(np.array(nda_res) - nda_ref)
self.assertAlmostEqual(nda_diff, 0, places=self.precision)
def read_transform(path_to_file, inverse=0, nii_as_nib=0, as_itk=0):
if not ph.file_exists(path_to_file):
raise IOError("Transform file '%s' not found" % path_to_file)
extension = ph.strip_filename_extension(path_to_file)[1]
if extension not in ALLOWED_TRANSFORMS and \
extension not in ALLOWED_TRANSFORMS_DISPLACEMENTS:
raise IOError("Transform file extension must be of type "
"%s (transformation) or %s (displacements)" %
(", ".join(ALLOWED_TRANSFORMS),
", ".join(ALLOWED_TRANSFORMS_DISPLACEMENTS)))
if extension in ALLOWED_TRANSFORMS:
if as_itk:
tranform_sitk = sitk.read_transform_itk(path_to_file,
inverse=inverse)
else:
transform_sitk = sitkh.read_transform_sitk(path_to_file,
inverse=inverse)
else:
# Used for sitk_to_nreg conversion only
if nii_as_nib:
displacement_sitk = nib.load(path_to_file)
return displacement_sitk
else:
displacement_sitk = sitk.ReadImage(path_to_file,
sitk.sitkVectorFloat64)
transform_sitk = sitk.DisplacementFieldTransform(
sitk.Image(displacement_sitk))
if inverse:
# May throw RuntimeError
transform_sitk = transform_sitk.GetInverse()
return transform_sitk
def _run_registrations(self, transformations):
path_to_fixed = os.path.join(DIR_TMP, "fixed.nii.gz")
path_to_moving = os.path.join(DIR_TMP, "moving.nii.gz")
path_to_fixed_mask = os.path.join(DIR_TMP, "fixed_mask.nii.gz")
path_to_moving_mask = os.path.join(DIR_TMP, "moving_mask.nii.gz")
path_to_tmp_output = os.path.join(DIR_TMP, "foo.nii.gz")
path_to_transform_regaladin = os.path.join(DIR_TMP,
"transform_regaladin.txt")
path_to_transform_sitk = os.path.join(DIR_TMP, "transform_sitk.txt")
sitkh.write_nifti_image_sitk(self._fixed.sitk, path_to_fixed)
sitkh.write_nifti_image_sitk(self._moving.sitk, path_to_moving)
sitkh.write_nifti_image_sitk(self._fixed.sitk_mask, path_to_fixed_mask)
# sitkh.write_nifti_image_sitk(
# self._moving.sitk_mask, path_to_moving_mask)
for i in range(len(transformations)):
sitk.WriteTransform(transformations[i], path_to_transform_sitk)
# Convert SimpleITK to RegAladin transform
cmd = "simplereg_transform -sitk2nreg %s %s" % (
path_to_transform_sitk, path_to_transform_regaladin)
ph.execute_command(cmd, verbose=False)
# Run NiftyReg
cmd_args = ["reg_aladin"]
cmd_args.append("-ref %s" % path_to_fixed)
cmd_args.append("-flo %s" % path_to_moving)
cmd_args.append("-res %s" % path_to_tmp_output)
cmd_args.append("-inaff %s" % path_to_transform_regaladin)
cmd_args.append("-aff %s" % path_to_transform_regaladin)
cmd_args.append("-rigOnly")
cmd_args.append("-ln 2")
cmd_args.append("-voff")
cmd_args.append("-rmask %s" % path_to_fixed_mask)
# To avoid error "0 correspondences between blocks were found" that can
# occur for some cases. Also, disable moving mask, as this would be ignored
# anyway
cmd_args.append("-noSym")
ph.print_info(
"Run Registration (RegAladin) based on PCA-init %d ... " %
(i + 1))
ph.execute_command(" ".join(cmd_args), verbose=False)
# Convert RegAladin to SimpleITK transform
cmd = "simplereg_transform -nreg2sitk %s %s" % (
path_to_transform_regaladin, path_to_transform_sitk)
ph.execute_command(cmd, verbose=False)
transformations[i] = sitkh.read_transform_sitk(
path_to_transform_sitk)
return transformations
def main():
time_start = ph.start_timing()
np.set_printoptions(precision=3)
input_parser = InputArgparser(
description="Register an obtained reconstruction (moving) "
"to a template image/space (fixed) using rigid registration. "
"The resulting registration can optionally be applied to previously "
"obtained motion correction slice transforms so that a volumetric "
"reconstruction is possible in the (standard anatomical) space "
"defined by the fixed.", )
input_parser.add_fixed(required=True)
input_parser.add_moving(required=True)
input_parser.add_output(help="Path to registration transform (.txt)",
required=True)
input_parser.add_fixed_mask(required=False)
input_parser.add_moving_mask(required=False)
input_parser.add_option(
option_string="--initial-transform",
type=str,
help="Path to initial transform. "
"If not provided, registration will be initialized based on "
"rigid alignment of eigenbasis of the fixed/moving image masks "
"using principal component analysis",
default=None)
input_parser.add_v2v_method(
option_string="--method",
help="Registration method used for the registration.",
default="RegAladin",
)
input_parser.add_argument(
"--refine-pca",
"-refine-pca",
action='store_true',
help="If given, PCA-based initializations will be refined using "
"RegAladin registrations.")
input_parser.add_dir_input_mc()
input_parser.add_verbose(default=0)
input_parser.add_log_config(default=1)
args = input_parser.parse_args()
input_parser.print_arguments(args)
if args.log_config:
input_parser.log_config(os.path.abspath(__file__))
if not args.output.endswith(".txt"):
raise IOError("output transformation path must end in '.txt'")
dir_output = os.path.dirname(args.output)
ph.create_directory(dir_output)
# --------------------------------Read Data--------------------------------
ph.print_title("Read Data")
fixed = st.Stack.from_filename(file_path=args.fixed,
file_path_mask=args.fixed_mask,
extract_slices=False)
moving = st.Stack.from_filename(file_path=args.moving,
file_path_mask=args.moving_mask,
extract_slices=False)
path_to_tmp_output = os.path.join(
DIR_TMP, ph.append_to_filename(os.path.basename(args.moving),
"_warped"))
# ---------------------------- Initialization ----------------------------
if args.initial_transform is None:
ph.print_title("Estimate initial transform using PCA")
if args.moving_mask is None or args.fixed_mask is None:
ph.print_warning("Fixed and moving masks are strongly recommended")
transform_initializer = tinit.TransformInitializer(
fixed=fixed,
moving=moving,
similarity_measure="NMI",
refine_pca_initializations=args.refine_pca,
)
transform_initializer.run()
transform_init_sitk = transform_initializer.get_transform_sitk()
else:
transform_init_sitk = sitkh.read_transform_sitk(args.initial_transform)
sitk.WriteTransform(transform_init_sitk, args.output)
# -------------------Register Reconstruction to Template-------------------
ph.print_title("Registration")
if args.method == "RegAladin":
path_to_transform_regaladin = os.path.join(DIR_TMP,
"transform_regaladin.txt")
# Convert SimpleITK to RegAladin transform
cmd = "simplereg_transform -sitk2nreg %s %s" % (
args.output, path_to_transform_regaladin)
ph.execute_command(cmd, verbose=False)
# Run NiftyReg
cmd_args = ["reg_aladin"]
cmd_args.append("-ref '%s'" % args.fixed)
cmd_args.append("-flo '%s'" % args.moving)
cmd_args.append("-res '%s'" % path_to_tmp_output)
cmd_args.append("-inaff '%s'" % path_to_transform_regaladin)
cmd_args.append("-aff '%s'" % path_to_transform_regaladin)
cmd_args.append("-rigOnly")
cmd_args.append("-ln 2") # seems to perform better for spina bifida
cmd_args.append("-voff")
if args.fixed_mask is not None:
cmd_args.append("-rmask '%s'" % args.fixed_mask)
# To avoid error "0 correspondences between blocks were found" that can
# occur for some cases. Also, disable moving mask, as this would be ignored
# anyway
cmd_args.append("-noSym")
# if args.moving_mask is not None:
# cmd_args.append("-fmask '%s'" % args.moving_mask)
ph.print_info("Run Registration (RegAladin) ... ", newline=False)
ph.execute_command(" ".join(cmd_args), verbose=False)
print("done")
# Convert RegAladin to SimpleITK transform
cmd = "simplereg_transform -nreg2sitk '%s' '%s'" % (
path_to_transform_regaladin, args.output)
ph.execute_command(cmd, verbose=False)
else:
path_to_transform_flirt = os.path.join(DIR_TMP, "transform_flirt.txt")
# Convert SimpleITK into FLIRT transform
cmd = "simplereg_transform -sitk2flirt '%s' '%s' '%s' '%s'" % (
args.output, args.fixed, args.moving, path_to_transform_flirt)
ph.execute_command(cmd, verbose=False)
# Define search angle ranges for FLIRT in all three dimensions
search_angles = [
"-searchr%s -%d %d" % (x, 180, 180) for x in ["x", "y", "z"]
]
cmd_args = ["flirt"]
cmd_args.append("-in '%s'" % args.moving)
cmd_args.append("-ref '%s'" % args.fixed)
if args.initial_transform is not None:
cmd_args.append("-init '%s'" % path_to_transform_flirt)
cmd_args.append("-omat '%s'" % path_to_transform_flirt)
cmd_args.append("-out '%s'" % path_to_tmp_output)
cmd_args.append("-dof 6")
cmd_args.append((" ").join(search_angles))
if args.moving_mask is not None:
cmd_args.append("-inweight '%s'" % args.moving_mask)
if args.fixed_mask is not None:
cmd_args.append("-refweight '%s'" % args.fixed_mask)
ph.print_info("Run Registration (FLIRT) ... ", newline=False)
ph.execute_command(" ".join(cmd_args), verbose=False)
print("done")
# Convert FLIRT to SimpleITK transform
cmd = "simplereg_transform -flirt2sitk '%s' '%s' '%s' '%s'" % (
path_to_transform_flirt, args.fixed, args.moving, args.output)
ph.execute_command(cmd, verbose=False)
if args.dir_input_mc is not None:
ph.print_title("Update Motion-Correction Transformations")
transform_sitk = sitkh.read_transform_sitk(args.output, inverse=1)
if args.dir_input_mc.endswith("/"):
subdir_mc = args.dir_input_mc.split("/")[-2]
else:
subdir_mc = args.dir_input_mc.split("/")[-1]
dir_output_mc = os.path.join(dir_output, subdir_mc)
ph.create_directory(dir_output_mc, delete_files=True)
pattern = REGEX_FILENAMES + "[.]tfm"
p = re.compile(pattern)
trafos = [t for t in os.listdir(args.dir_input_mc) if p.match(t)]
for t in trafos:
path_to_input_transform = os.path.join(args.dir_input_mc, t)
path_to_output_transform = os.path.join(dir_output_mc, t)
t_sitk = sitkh.read_transform_sitk(path_to_input_transform)
t_sitk = sitkh.get_composite_sitk_affine_transform(
transform_sitk, t_sitk)
sitk.WriteTransform(t_sitk, path_to_output_transform)
ph.print_info("%d transformations written to '%s'" %
(len(trafos), dir_output_mc))
if args.verbose:
ph.show_niftis([args.fixed, path_to_tmp_output])
elapsed_time_total = ph.stop_timing(time_start)
# Summary
ph.print_title("Summary")
print("Computational Time: %s" % (elapsed_time_total))
return 0
def run(self):
if not ph.directory_exists(self._dir_motion_correction):
raise exceptions.DirectoryNotExistent(self._dir_motion_correction)
abs_path_to_directory = os.path.abspath(self._dir_motion_correction)
for i in range(len(self._stacks)):
stack_name = self._stacks[i].get_filename()
# update stack position
path_to_stack_transform = os.path.join(abs_path_to_directory,
"%s.tfm" % stack_name)
if ph.file_exists(path_to_stack_transform):
transform_stack_sitk = sitkh.read_transform_sitk(
path_to_stack_transform)
transform_stack_sitk_inv = sitkh.read_transform_sitk(
path_to_stack_transform, inverse=True)
self._stacks[i].update_motion_correction(transform_stack_sitk)
ph.print_info("Stack '%s': Stack position updated" %
stack_name)
else:
transform_stack_sitk_inv = sitk.Euler3DTransform()
# update slice positions
pattern_trafo_slices = stack_name + self._prefix_slice + \
"([0-9]+)[.]tfm"
p = re.compile(pattern_trafo_slices)
dic_slice_transforms = {
int(p.match(f).group(1)): os.path.join(abs_path_to_directory,
p.match(f).group(0))
for f in os.listdir(abs_path_to_directory) if p.match(f)
}
slices = self._stacks[i].get_slices()
for i_slice in range(self._stacks[i].get_number_of_slices()):
if i_slice in dic_slice_transforms.keys():
transform_slice_sitk = sitkh.read_transform_sitk(
dic_slice_transforms[i_slice])
transform_slice_sitk = \
sitkh.get_composite_sitk_affine_transform(
transform_slice_sitk, transform_stack_sitk_inv)
slices[i_slice].update_motion_correction(
transform_slice_sitk)
# # ------------------------- HACK -------------------------
# # 18 Jan 2019
# # HACK to use results of a previous version where image
# # slices were still exported
# # (Bug was that after stack intensity correction, the
# # previous v2v-reg was not passed on to the final
# # registration transform):
# import niftymic.base.slice as sl
# path_to_slice = re.sub(
# ".tfm", ".nii.gz", dic_slice_transforms[i_slice])
# path_to_slice_mask = re.sub(
# ".tfm", "_mask.nii.gz", dic_slice_transforms[i_slice])
# slice_sitk = sitk.ReadImage(path_to_slice)
# slice_sitk_mask = sitk.ReadImage(path_to_slice_mask)
# hack = sl.Slice.from_sitk_image(
# # slice_sitk=slice_sitk,
# slice_sitk=slice_sitk_mask, # mask for Mask-SRR!
# slice_sitk_mask=slice_sitk_mask,
# slice_number=slices[i_slice].get_slice_number(),
# slice_thickness=slices[i_slice].get_slice_thickness(),
# )
# self._stacks[i]._slices[i_slice] = hack
# # --------------------------------------------------------
else:
self._stacks[i].delete_slice(slices[i_slice])
# print update information
ph.print_info("Stack '%s': Slice positions updated "
"(%d/%d slices deleted)" % (
stack_name,
len(self._stacks[i].get_deleted_slice_numbers()),
self._stacks[i].sitk.GetSize()[-1],
))
# delete entire stack if all slices were rejected
if self._stacks[i].get_number_of_slices() == 0:
ph.print_info("Stack '%s' removed as all slices were deleted" %
stack_name)
self._stacks[i] = None
# only return maintained stacks
self._stacks = [s for s in self._stacks if s is not None]
if len(self._stacks) == 0:
raise RuntimeError(
"All stacks removed. "
"Did you check that the correct motion-correction directory "
"was provided?")
def run(self, older_than_v3=False):
if not ph.directory_exists(self._dir_motion_correction):
raise exceptions.DirectoryNotExistent(
self._dir_motion_correction)
abs_path_to_directory = os.path.abspath(
self._dir_motion_correction)
path_to_rejected_slices = os.path.join(
abs_path_to_directory, "rejected_slices.json")
if ph.file_exists(path_to_rejected_slices):
self._rejected_slices = ph.read_dictionary_from_json(
path_to_rejected_slices)
bool_check = True
else:
self._rejected_slices = None
bool_check = False
for i in range(len(self._stacks)):
stack_name = self._stacks[i].get_filename()
if not older_than_v3:
# update stack position
path_to_stack_transform = os.path.join(
abs_path_to_directory, "%s.tfm" % stack_name)
if ph.file_exists(path_to_stack_transform):
transform_stack_sitk = sitkh.read_transform_sitk(
path_to_stack_transform)
transform_stack_sitk_inv = sitkh.read_transform_sitk(
path_to_stack_transform, inverse=True)
self._stacks[i].update_motion_correction(
transform_stack_sitk)
ph.print_info(
"Stack '%s': Stack position updated" % stack_name)
else:
transform_stack_sitk_inv = sitk.Euler3DTransform()
if self._volume_motion_only:
continue
# update slice positions
pattern_trafo_slices = stack_name + self._prefix_slice + \
"([0-9]+)[.]tfm"
p = re.compile(pattern_trafo_slices)
dic_slice_transforms = {
int(p.match(f).group(1)): os.path.join(
abs_path_to_directory, p.match(f).group(0))
for f in os.listdir(abs_path_to_directory) if p.match(f)
}
slices = self._stacks[i].get_slices()
for i_slice in range(self._stacks[i].get_number_of_slices()):
if i_slice in dic_slice_transforms.keys():
transform_slice_sitk = sitkh.read_transform_sitk(
dic_slice_transforms[i_slice])
transform_slice_sitk = \
sitkh.get_composite_sitk_affine_transform(
transform_slice_sitk, transform_stack_sitk_inv)
slices[i_slice].update_motion_correction(
transform_slice_sitk)
else:
self._stacks[i].delete_slice(slices[i_slice])
# ----------------------------- HACK -----------------------------
# 18 Jan 2019
# HACK to use results of a previous version where image slices were
# still exported.
# (There was a bug after stack intensity correction, which resulted
# in v2v-reg transforms not being part of in the final registration
# transforms; Thus, slice transformations (tfm's) were flawed and
# could not be used):
else:
# Recover suffix for mask
pattern = stack_name + self._prefix_slice + \
"[0-9]+[_]([a-zA-Z]+)[.]nii.gz"
pm = re.compile(pattern)
matches = list(set([pm.match(f).group(1) for f in os.listdir(
abs_path_to_directory) if pm.match(f)]))
if len(matches) > 1:
raise RuntimeError("Suffix mask cannot be determined")
suffix_mask = "_%s" % matches[0]
# Recover stack
path_to_stack = os.path.join(
abs_path_to_directory, "%s.nii.gz" % stack_name)
path_to_stack_mask = os.path.join(
abs_path_to_directory, "%s%s.nii.gz" % (
stack_name, suffix_mask))
stack = st.Stack.from_filename(
path_to_stack, path_to_stack_mask)
# Recover slices
pattern_trafo_slices = stack_name + self._prefix_slice + \
"([0-9]+)[.]tfm"
p = re.compile(pattern_trafo_slices)
dic_slice_transforms = {
int(p.match(f).group(1)): os.path.join(
abs_path_to_directory, p.match(f).group(0))
for f in os.listdir(abs_path_to_directory) if p.match(f)
}
slices = self._stacks[i].get_slices()
for i_slice in range(self._stacks[i].get_number_of_slices()):
if i_slice in dic_slice_transforms.keys():
path_to_slice = re.sub(
".tfm", ".nii.gz", dic_slice_transforms[i_slice])
path_to_slice_mask = re.sub(
".tfm", "%s.nii.gz" % suffix_mask,
dic_slice_transforms[i_slice])
slice_sitk = sitk.ReadImage(path_to_slice)
slice_sitk_mask = sitk.ReadImage(path_to_slice_mask)
hack = sl.Slice.from_sitk_image(
slice_sitk=slice_sitk,
# slice_sitk=slice_sitk_mask, # mask for Mask-SRR!
slice_sitk_mask=slice_sitk_mask,
slice_number=slices[i_slice].get_slice_number(),
slice_thickness=slices[
i_slice].get_slice_thickness(),
)
self._stacks[i]._slices[i_slice] = hack
else:
self._stacks[i].delete_slice(slices[i_slice])
self._stacks[i].sitk = stack.sitk
self._stacks[i].sitk_mask = stack.sitk_mask
self._stacks[i].itk = stack.itk
self._stacks[i].itk_mask = stack.itk_mask
# -----------------------------------------------------------------
# print update information
ph.print_info(
"Stack '%s': Slice positions updated "
"(%d/%d slices deleted)" % (
stack_name,
len(self._stacks[i].get_deleted_slice_numbers()),
self._stacks[i].sitk.GetSize()[-1],
)
)
# delete entire stack if all slices were rejected
if self._stacks[i].get_number_of_slices() == 0:
ph.print_info(
"Stack '%s' removed as all slices were deleted" %
stack_name)
self._stacks[i] = None
# only return maintained stacks
self._stacks = [s for s in self._stacks if s is not None]
if len(self._stacks) == 0:
raise RuntimeError(
"All stacks removed. "
"Did you check that the correct motion-correction directory "
"was provided?")
def test_reconstruct_volume(self):
filename = "SRR_stacks3_TK1_lsmr_alpha0p02_itermax5.nii.gz"
output = os.path.join(self.dir_output, filename)
dir_reference = os.path.join(self.dir_data, "reconstruct_volume")
dir_reference_mc = os.path.join(dir_reference, "motion_correction")
path_to_reference = os.path.join(dir_reference, filename)
path_to_reference_mask = ph.append_to_filename(
os.path.join(dir_reference, filename), self.suffix_mask)
two_step_cycles = 1
iter_max = 5
threshold = 0.75
alpha = 0.02
alpha_first = 0.2
sigma = 1
intensity_correction = 1
isotropic_resolution = 1.02
v2v_method = "RegAladin"
cmd_args = []
cmd_args.append("--filenames %s" % " ".join(self.filenames))
cmd_args.append("--output %s" % output)
cmd_args.append("--suffix-mask %s" % self.suffix_mask)
cmd_args.append("--two-step-cycles %s" % two_step_cycles)
cmd_args.append("--iter-max %d" % iter_max)
cmd_args.append("--threshold-first %f" % threshold)
cmd_args.append("--sigma %f" % sigma)
cmd_args.append("--threshold %f" % threshold)
cmd_args.append("--intensity-correction %d" % intensity_correction)
cmd_args.append("--isotropic-resolution %s" % isotropic_resolution)
cmd_args.append("--alpha %f" % alpha)
cmd_args.append("--alpha-first %f" % alpha_first)
cmd_args.append("--v2v-method %s" % v2v_method)
# cmd_args.append("--verbose 1")
cmd = "niftymic_reconstruct_volume %s" % (" ").join(cmd_args)
self.assertEqual(ph.execute_command(cmd), 0)
# Check SRR volume
res_sitk = sitkh.read_nifti_image_sitk(output)
ref_sitk = sitkh.read_nifti_image_sitk(path_to_reference)
diff_sitk = res_sitk - ref_sitk
error = np.linalg.norm(sitk.GetArrayFromImage(diff_sitk))
self.assertAlmostEqual(error, 0, places=self.precision)
# Check SRR mask volume
res_sitk = sitkh.read_nifti_image_sitk(
ph.append_to_filename(output, "_mask"))
ref_sitk = sitkh.read_nifti_image_sitk(path_to_reference_mask)
diff_sitk = res_sitk - ref_sitk
error = np.linalg.norm(sitk.GetArrayFromImage(diff_sitk))
self.assertAlmostEqual(error, 0, places=self.precision)
# Check transforms
pattern = REGEX_FILENAMES + "[.]tfm"
p = re.compile(pattern)
dir_res_mc = os.path.join(self.dir_output, "motion_correction")
trafos_res = sorted([
os.path.join(dir_res_mc, t) for t in os.listdir(dir_res_mc)
if p.match(t)
])
trafos_ref = sorted([
os.path.join(dir_reference_mc, t)
for t in os.listdir(dir_reference_mc) if p.match(t)
])
self.assertEqual(len(trafos_res), len(trafos_ref))
for i in range(len(trafos_ref)):
nda_res = sitkh.read_transform_sitk(trafos_res[i]).GetParameters()
nda_ref = sitkh.read_transform_sitk(trafos_ref[i]).GetParameters()
nda_diff = np.linalg.norm(np.array(nda_res) - nda_ref)
self.assertAlmostEqual(nda_diff, 0, places=self.precision)
def test_register_image(self):
filename = "registration_transform_sitk.txt"
gestational_age = 28
path_to_recon = os.path.join(
self.dir_data, "register_image",
"SRR_stacks3_TK1_lsmr_alpha0p02_itermax5.nii.gz")
dir_input_mc = os.path.join(self.dir_data, "register_image",
"motion_correction")
path_to_transform_res = os.path.join(self.dir_output, filename)
path_to_transform_ref = os.path.join(self.dir_data, "register_image",
filename)
dir_ref_mc = os.path.join(self.dir_data, "register_image",
"motion_correction_ref")
path_to_rejected_slices_ref = os.path.join(dir_ref_mc,
"rejected_slices.json")
template = os.path.join(DIR_TEMPLATES,
"STA%d.nii.gz" % gestational_age)
template_mask = os.path.join(DIR_TEMPLATES,
"STA%d_mask.nii.gz" % gestational_age)
cmd_args = ["niftymic_register_image"]
cmd_args.append("--fixed %s" % template)
cmd_args.append("--moving %s" % path_to_recon)
cmd_args.append("--fixed-mask %s" % template_mask)
cmd_args.append("--moving-mask %s" %
ph.append_to_filename(path_to_recon, self.suffix_mask))
cmd_args.append("--dir-input-mc %s" % dir_input_mc)
cmd_args.append("--output %s" % path_to_transform_res)
cmd_args.append("--init-pca")
# cmd_args.append("--verbose 1")
self.assertEqual(ph.execute_command(" ".join(cmd_args)), 0)
# Check registration transform
res_sitk = sitkh.read_transform_sitk(path_to_transform_res)
ref_sitk = sitkh.read_transform_sitk(path_to_transform_ref)
res_nda = res_sitk.GetParameters()
ref_nda = ref_sitk.GetParameters()
diff_nda = np.array(res_nda) - ref_nda
self.assertAlmostEqual(np.linalg.norm(diff_nda),
0,
places=self.precision)
# Check individual slice transforms
pattern = REGEX_FILENAMES + "[.]tfm"
p = re.compile(pattern)
dir_res_mc = os.path.join(self.dir_output, "motion_correction")
trafos_res = sorted([
os.path.join(dir_res_mc, t) for t in os.listdir(dir_res_mc)
if p.match(t)
])
trafos_ref = sorted([
os.path.join(dir_ref_mc, t) for t in os.listdir(dir_res_mc)
if p.match(t)
])
self.assertEqual(len(trafos_res), len(trafos_ref))
for i in range(len(trafos_ref)):
nda_res = sitkh.read_transform_sitk(trafos_res[i]).GetParameters()
nda_ref = sitkh.read_transform_sitk(trafos_ref[i]).GetParameters()
nda_diff = np.linalg.norm(np.array(nda_res) - nda_ref)
self.assertAlmostEqual(nda_diff, 0, places=self.precision)
# Check rejected_slices.json
path_to_rejected_slices_res = os.path.join(dir_res_mc,
"rejected_slices.json")
self.assertEqual(ph.file_exists(path_to_rejected_slices_res), True)
rejected_slices_res = ph.read_dictionary_from_json(
path_to_rejected_slices_res)
rejected_slices_ref = ph.read_dictionary_from_json(
path_to_rejected_slices_ref)
self.assertEqual(rejected_slices_res == rejected_slices_ref, True)
def main():
time_start = ph.start_timing()
np.set_printoptions(precision=3)
input_parser = InputArgparser(
description="Register an obtained reconstruction (moving) "
"to a template image/space (fixed) using rigid registration. "
"The resulting registration can optionally be applied to previously "
"obtained motion correction slice transforms so that a volumetric "
"reconstruction is possible in the (standard anatomical) space "
"defined by the fixed.", )
input_parser.add_fixed(required=True)
input_parser.add_moving(required=True)
input_parser.add_output(help="Path to registration transform (.txt)",
required=True)
input_parser.add_fixed_mask()
input_parser.add_moving_mask()
input_parser.add_dir_input_mc()
input_parser.add_search_angle(default=180)
input_parser.add_option(option_string="--initial-transform",
type=str,
help="Path to initial transform.",
default=None)
input_parser.add_option(
option_string="--test-ap-flip",
type=int,
help="Turn on/off functionality to run an additional registration "
"after an AP-flip. Seems to be more robust to find a better "
"registration outcome in general.",
default=1)
input_parser.add_option(
option_string="--use-flirt",
type=int,
help="Turn on/off functionality to use FLIRT for the registration.",
default=1)
input_parser.add_option(
option_string="--use-regaladin",
type=int,
help="Turn on/off functionality to use RegAladin for the "
"registration.",
default=1)
input_parser.add_verbose(default=0)
input_parser.add_log_config(default=1)
args = input_parser.parse_args()
input_parser.print_arguments(args)
debug = 0
if args.log_config:
input_parser.log_config(os.path.abspath(__file__))
if not args.use_regaladin and not args.use_flirt:
raise IOError("Either RegAladin or FLIRT must be activated.")
if not args.output.endswith(".txt"):
raise IOError("output transformation path must end in '.txt'")
dir_output = os.path.dirname(args.output)
# --------------------------------Read Data--------------------------------
ph.print_title("Read Data")
fixed = st.Stack.from_filename(file_path=args.fixed,
file_path_mask=args.fixed_mask,
extract_slices=False)
moving = st.Stack.from_filename(file_path=args.moving,
file_path_mask=args.moving_mask,
extract_slices=False)
if args.initial_transform is not None:
transform_sitk = sitkh.read_transform_sitk(args.initial_transform)
else:
transform_sitk = sitk.AffineTransform(fixed.sitk.GetDimension())
sitk.WriteTransform(transform_sitk, args.output)
path_to_tmp_output = os.path.join(
DIR_TMP, ph.append_to_filename(os.path.basename(args.moving),
"_warped"))
# -------------------Register Reconstruction to Template-------------------
ph.print_title("Register Reconstruction to Template")
if args.use_flirt:
path_to_transform_flirt = os.path.join(DIR_TMP, "transform_flirt.txt")
# Convert SimpleITK into FLIRT transform
cmd = "simplereg_transform -sitk2flirt %s %s %s %s" % (
args.output, args.fixed, args.moving, path_to_transform_flirt)
ph.execute_command(cmd, verbose=False)
# Define search angle ranges for FLIRT in all three dimensions
search_angles = [
"-searchr%s -%d %d" % (x, args.search_angle, args.search_angle)
for x in ["x", "y", "z"]
]
# flt = nipype.interfaces.fsl.FLIRT()
# flt.inputs.in_file = args.moving
# flt.inputs.reference = args.fixed
# if args.initial_transform is not None:
# flt.inputs.in_matrix_file = path_to_transform_flirt
# flt.inputs.out_matrix_file = path_to_transform_flirt
# # flt.inputs.output_type = "NIFTI_GZ"
# flt.inputs.out_file = path_to_tmp_output
# flt.inputs.args = "-dof 6"
# flt.inputs.args += " %s" % " ".join(search_angles)
# if args.moving_mask is not None:
# flt.inputs.in_weight = args.moving_mask
# if args.fixed_mask is not None:
# flt.inputs.ref_weight = args.fixed_mask
# ph.print_info("Run Registration (FLIRT) ... ", newline=False)
# flt.run()
# print("done")
cmd_args = ["flirt"]
cmd_args.append("-in %s" % args.moving)
cmd_args.append("-ref %s" % args.fixed)
if args.initial_transform is not None:
cmd_args.append("-init %s" % path_to_transform_flirt)
cmd_args.append("-omat %s" % path_to_transform_flirt)
cmd_args.append("-out %s" % path_to_tmp_output)
cmd_args.append("-dof 6")
cmd_args.append((" ").join(search_angles))
if args.moving_mask is not None:
cmd_args.append("-inweight %s" % args.moving_mask)
if args.fixed_mask is not None:
cmd_args.append("-refweight %s" % args.fixed_mask)
ph.print_info("Run Registration (FLIRT) ... ", newline=False)
ph.execute_command(" ".join(cmd_args), verbose=False)
print("done")
# Convert FLIRT to SimpleITK transform
cmd = "simplereg_transform -flirt2sitk %s %s %s %s" % (
path_to_transform_flirt, args.fixed, args.moving, args.output)
ph.execute_command(cmd, verbose=False)
if debug:
ph.show_niftis([args.fixed, path_to_tmp_output])
# Additionally, use RegAladin for more accurate alignment
# Rationale: FLIRT has better capture range, but RegAladin seems to
# find better alignment once it is within its capture range.
if args.use_regaladin:
path_to_transform_regaladin = os.path.join(DIR_TMP,
"transform_regaladin.txt")
# Convert SimpleITK to RegAladin transform
cmd = "simplereg_transform -sitk2nreg %s %s" % (
args.output, path_to_transform_regaladin)
ph.execute_command(cmd, verbose=False)
# nreg = nipype.interfaces.niftyreg.RegAladin()
# nreg.inputs.ref_file = args.fixed
# nreg.inputs.flo_file = args.moving
# nreg.inputs.res_file = path_to_tmp_output
# nreg.inputs.in_aff_file = path_to_transform_regaladin
# nreg.inputs.aff_file = path_to_transform_regaladin
# nreg.inputs.args = "-rigOnly -voff"
# if args.moving_mask is not None:
# nreg.inputs.fmask_file = args.moving_mask
# if args.fixed_mask is not None:
# nreg.inputs.rmask_file = args.fixed_mask
# ph.print_info("Run Registration (RegAladin) ... ", newline=False)
# nreg.run()
# print("done")
cmd_args = ["reg_aladin"]
cmd_args.append("-ref %s" % args.fixed)
cmd_args.append("-flo %s" % args.moving)
cmd_args.append("-res %s" % path_to_tmp_output)
if args.initial_transform is not None or args.use_flirt == 1:
cmd_args.append("-inaff %s" % path_to_transform_regaladin)
cmd_args.append("-aff %s" % path_to_transform_regaladin)
# cmd_args.append("-cog")
# cmd_args.append("-ln 2")
cmd_args.append("-rigOnly")
cmd_args.append("-voff")
if args.moving_mask is not None:
cmd_args.append("-fmask %s" % args.moving_mask)
if args.fixed_mask is not None:
cmd_args.append("-rmask %s" % args.fixed_mask)
ph.print_info("Run Registration (RegAladin) ... ", newline=False)
ph.execute_command(" ".join(cmd_args), verbose=False)
print("done")
# Convert RegAladin to SimpleITK transform
cmd = "simplereg_transform -nreg2sitk %s %s" % (
path_to_transform_regaladin, args.output)
ph.execute_command(cmd, verbose=False)
if debug:
ph.show_niftis([args.fixed, path_to_tmp_output])
if args.test_ap_flip:
path_to_transform_flip = os.path.join(DIR_TMP, "transform_flip.txt")
path_to_tmp_output_flip = os.path.join(DIR_TMP, "output_flip.nii.gz")
# Get AP-flip transform
transform_ap_flip_sitk = get_ap_flip_transform(args.fixed)
path_to_transform_flip_regaladin = os.path.join(
DIR_TMP, "transform_flip_regaladin.txt")
sitk.WriteTransform(transform_ap_flip_sitk, path_to_transform_flip)
# Compose current transform with AP flip transform
cmd = "simplereg_transform -c %s %s %s" % (
args.output, path_to_transform_flip, path_to_transform_flip)
ph.execute_command(cmd, verbose=False)
# Convert SimpleITK to RegAladin transform
cmd = "simplereg_transform -sitk2nreg %s %s" % (
path_to_transform_flip, path_to_transform_flip_regaladin)
ph.execute_command(cmd, verbose=False)
# nreg = nipype.interfaces.niftyreg.RegAladin()
# nreg.inputs.ref_file = args.fixed
# nreg.inputs.flo_file = args.moving
# nreg.inputs.res_file = path_to_tmp_output_flip
# nreg.inputs.in_aff_file = path_to_transform_flip_regaladin
# nreg.inputs.aff_file = path_to_transform_flip_regaladin
# nreg.inputs.args = "-rigOnly -voff"
# if args.moving_mask is not None:
# nreg.inputs.fmask_file = args.moving_mask
# if args.fixed_mask is not None:
# nreg.inputs.rmask_file = args.fixed_mask
# ph.print_info("Run Registration AP-flipped (RegAladin) ... ",
# newline=False)
# nreg.run()
# print("done")
cmd_args = ["reg_aladin"]
cmd_args.append("-ref %s" % args.fixed)
cmd_args.append("-flo %s" % args.moving)
cmd_args.append("-res %s" % path_to_tmp_output_flip)
cmd_args.append("-inaff %s" % path_to_transform_flip_regaladin)
cmd_args.append("-aff %s" % path_to_transform_flip_regaladin)
cmd_args.append("-rigOnly")
# cmd_args.append("-ln 2")
cmd_args.append("-voff")
if args.moving_mask is not None:
cmd_args.append("-fmask %s" % args.moving_mask)
if args.fixed_mask is not None:
cmd_args.append("-rmask %s" % args.fixed_mask)
ph.print_info("Run Registration AP-flipped (RegAladin) ... ",
newline=False)
ph.execute_command(" ".join(cmd_args), verbose=False)
print("done")
if debug:
ph.show_niftis(
[args.fixed, path_to_tmp_output, path_to_tmp_output_flip])
warped_moving = st.Stack.from_filename(path_to_tmp_output,
extract_slices=False)
warped_moving_flip = st.Stack.from_filename(path_to_tmp_output_flip,
extract_slices=False)
fixed = st.Stack.from_filename(args.fixed, args.fixed_mask)
stacks = [warped_moving, warped_moving_flip]
image_similarity_evaluator = ise.ImageSimilarityEvaluator(
stacks=stacks, reference=fixed)
image_similarity_evaluator.compute_similarities()
similarities = image_similarity_evaluator.get_similarities()
if similarities["NMI"][1] > similarities["NMI"][0]:
ph.print_info("AP-flipped outcome better")
# Convert RegAladin to SimpleITK transform
cmd = "simplereg_transform -nreg2sitk %s %s" % (
path_to_transform_flip_regaladin, args.output)
ph.execute_command(cmd, verbose=False)
# Copy better outcome
cmd = "cp -p %s %s" % (path_to_tmp_output_flip, path_to_tmp_output)
ph.execute_command(cmd, verbose=False)
else:
ph.print_info("AP-flip does not improve outcome")
if args.dir_input_mc is not None:
transform_sitk = sitkh.read_transform_sitk(args.output, inverse=1)
if args.dir_input_mc.endswith("/"):
subdir_mc = args.dir_input_mc.split("/")[-2]
else:
subdir_mc = args.dir_input_mc.split("/")[-1]
dir_output_mc = os.path.join(dir_output, subdir_mc)
ph.create_directory(dir_output_mc, delete_files=True)
pattern = REGEX_FILENAMES + "[.]tfm"
p = re.compile(pattern)
trafos = [t for t in os.listdir(args.dir_input_mc) if p.match(t)]
for t in trafos:
path_to_input_transform = os.path.join(args.dir_input_mc, t)
path_to_output_transform = os.path.join(dir_output_mc, t)
t_sitk = sitkh.read_transform_sitk(path_to_input_transform)
t_sitk = sitkh.get_composite_sitk_affine_transform(
transform_sitk, t_sitk)
sitk.WriteTransform(t_sitk, path_to_output_transform)
if args.verbose:
ph.show_niftis([args.fixed, path_to_tmp_output])
elapsed_time_total = ph.stop_timing(time_start)
# Summary
ph.print_title("Summary")
print("Computational Time: %s" % (elapsed_time_total))
return 0
