def compute_length(fname_segmentation, remove_temp_files, verbose=0):
from math import sqrt
# Extract path, file and extension
fname_segmentation = os.path.abspath(fname_segmentation)
path_data, file_data, ext_data = sct.extract_fname(fname_segmentation)
# create temporary folder
path_tmp = 'tmp.' + time.strftime("%y%m%d%H%M%S")
sct.run('mkdir ' + path_tmp)
# copy files into tmp folder
sct.run('cp ' + fname_segmentation + ' ' + path_tmp)
# go to tmp folder
os.chdir(path_tmp)
# Change orientation of the input centerline into RPI
sct.printv('\nOrient centerline to RPI orientation...', param.verbose)
fname_segmentation_orient = 'segmentation_rpi' + ext_data
set_orientation(file_data + ext_data, 'RPI', fname_segmentation_orient)
# Get dimension
sct.printv('\nGet dimensions...', param.verbose)
nx, ny, nz, nt, px, py, pz, pt = Iamge(fname_segmentation_orient).dim
sct.printv(
'.. matrix size: ' + str(nx) + ' x ' + str(ny) + ' x ' + str(nz),
param.verbose)
sct.printv(
'.. voxel size: ' + str(px) + 'mm x ' + str(py) + 'mm x ' + str(pz) +
'mm', param.verbose)
# smooth segmentation/centerline
#x_centerline_fit, y_centerline_fit, z_centerline, x_centerline_deriv,y_centerline_deriv,z_centerline_deriv = smooth_centerline(fname_segmentation_orient, param, 'hanning', 1)
x_centerline_fit, y_centerline_fit, z_centerline, x_centerline_deriv, y_centerline_deriv, z_centerline_deriv = smooth_centerline(
fname_segmentation_orient,
type_window='hanning',
window_length=80,
algo_fitting='hanning',
verbose=verbose)
# compute length of centerline
result_length = 0.0
for i in range(len(x_centerline_fit) - 1):
result_length += sqrt(
((x_centerline_fit[i + 1] - x_centerline_fit[i]) * px)**2 +
((y_centerline_fit[i + 1] - y_centerline_fit[i]) * py)**2 +
((z_centerline[i + 1] - z_centerline[i]) * pz)**2)
return result_length
def compute_length(fname_segmentation, remove_temp_files, verbose=0):
from math import sqrt
# Extract path, file and extension
fname_segmentation = os.path.abspath(fname_segmentation)
path_data, file_data, ext_data = sct.extract_fname(fname_segmentation)
# create temporary folder
path_tmp = "tmp." + time.strftime("%y%m%d%H%M%S")
sct.run("mkdir " + path_tmp)
# copy files into tmp folder
sct.run("cp " + fname_segmentation + " " + path_tmp)
# go to tmp folder
os.chdir(path_tmp)
# Change orientation of the input centerline into RPI
sct.printv("\nOrient centerline to RPI orientation...", param.verbose)
fname_segmentation_orient = "segmentation_rpi" + ext_data
set_orientation(file_data + ext_data, "RPI", fname_segmentation_orient)
# Get dimension
sct.printv("\nGet dimensions...", param.verbose)
nx, ny, nz, nt, px, py, pz, pt = sct.get_dimension(fname_segmentation_orient)
sct.printv(".. matrix size: " + str(nx) + " x " + str(ny) + " x " + str(nz), param.verbose)
sct.printv(".. voxel size: " + str(px) + "mm x " + str(py) + "mm x " + str(pz) + "mm", param.verbose)
# smooth segmentation/centerline
# x_centerline_fit, y_centerline_fit, z_centerline, x_centerline_deriv,y_centerline_deriv,z_centerline_deriv = smooth_centerline(fname_segmentation_orient, param, 'hanning', 1)
x_centerline_fit, y_centerline_fit, z_centerline, x_centerline_deriv, y_centerline_deriv, z_centerline_deriv = smooth_centerline(
fname_segmentation_orient, type_window="hanning", window_length=80, algo_fitting="hanning", verbose=verbose
)
# compute length of centerline
result_length = 0.0
for i in range(len(x_centerline_fit) - 1):
result_length += sqrt(
((x_centerline_fit[i + 1] - x_centerline_fit[i]) * px) ** 2
+ ((y_centerline_fit[i + 1] - y_centerline_fit[i]) * py) ** 2
+ ((z_centerline[i + 1] - z_centerline[i]) * pz) ** 2
)
return result_length
def extract_centerline(
fname_segmentation, remove_temp_files, verbose=0, algo_fitting="hanning", type_window="hanning", window_length=80
):
# Extract path, file and extension
fname_segmentation = os.path.abspath(fname_segmentation)
path_data, file_data, ext_data = sct.extract_fname(fname_segmentation)
# create temporary folder
path_tmp = "tmp." + time.strftime("%y%m%d%H%M%S")
sct.run("mkdir " + path_tmp)
# copy files into tmp folder
sct.run("cp " + fname_segmentation + " " + path_tmp)
# go to tmp folder
os.chdir(path_tmp)
# Change orientation of the input centerline into RPI
sct.printv("\nOrient centerline to RPI orientation...", verbose)
fname_segmentation_orient = "segmentation_rpi" + ext_data
set_orientation(file_data + ext_data, "RPI", fname_segmentation_orient)
# Get dimension
sct.printv("\nGet dimensions...", verbose)
nx, ny, nz, nt, px, py, pz, pt = sct.get_dimension(fname_segmentation_orient)
sct.printv(".. matrix size: " + str(nx) + " x " + str(ny) + " x " + str(nz), verbose)
sct.printv(".. voxel size: " + str(px) + "mm x " + str(py) + "mm x " + str(pz) + "mm", verbose)
# Extract orientation of the input segmentation
orientation = get_orientation(file_data + ext_data)
sct.printv("\nOrientation of segmentation image: " + orientation, verbose)
sct.printv("\nOpen segmentation volume...", verbose)
file = nibabel.load(fname_segmentation_orient)
data = file.get_data()
hdr = file.get_header()
# Extract min and max index in Z direction
X, Y, Z = (data > 0).nonzero()
min_z_index, max_z_index = min(Z), max(Z)
x_centerline = [0 for i in range(0, max_z_index - min_z_index + 1)]
y_centerline = [0 for i in range(0, max_z_index - min_z_index + 1)]
z_centerline = [iz for iz in range(min_z_index, max_z_index + 1)]
# Extract segmentation points and average per slice
for iz in range(min_z_index, max_z_index + 1):
x_seg, y_seg = (data[:, :, iz] > 0).nonzero()
x_centerline[iz - min_z_index] = np.mean(x_seg)
y_centerline[iz - min_z_index] = np.mean(y_seg)
for k in range(len(X)):
data[X[k], Y[k], Z[k]] = 0
# extract centerline and smooth it
x_centerline_fit, y_centerline_fit, z_centerline_fit, x_centerline_deriv, y_centerline_deriv, z_centerline_deriv = smooth_centerline(
fname_segmentation_orient,
type_window=type_window,
window_length=window_length,
algo_fitting=algo_fitting,
verbose=verbose,
)
if verbose == 2:
import matplotlib.pyplot as plt
# Creation of a vector x that takes into account the distance between the labels
nz_nonz = len(z_centerline)
x_display = [0 for i in range(x_centerline_fit.shape[0])]
y_display = [0 for i in range(y_centerline_fit.shape[0])]
for i in range(0, nz_nonz, 1):
x_display[int(z_centerline[i] - z_centerline[0])] = x_centerline[i]
y_display[int(z_centerline[i] - z_centerline[0])] = y_centerline[i]
plt.figure(1)
plt.subplot(2, 1, 1)
plt.plot(z_centerline_fit, x_display, "ro")
plt.plot(z_centerline_fit, x_centerline_fit)
plt.xlabel("Z")
plt.ylabel("X")
plt.title("x and x_fit coordinates")
plt.subplot(2, 1, 2)
plt.plot(z_centerline_fit, y_display, "ro")
plt.plot(z_centerline_fit, y_centerline_fit)
plt.xlabel("Z")
plt.ylabel("Y")
plt.title("y and y_fit coordinates")
plt.show()
# Create an image with the centerline
for iz in range(min_z_index, max_z_index + 1):
data[
round(x_centerline_fit[iz - min_z_index]), round(y_centerline_fit[iz - min_z_index]), iz
] = (
1
) # if index is out of bounds here for hanning: either the segmentation has holes or labels have been added to the file
# Write the centerline image in RPI orientation
hdr.set_data_dtype("uint8") # set imagetype to uint8
sct.printv("\nWrite NIFTI volumes...", verbose)
img = nibabel.Nifti1Image(data, None, hdr)
nibabel.save(img, "centerline.nii.gz")
sct.generate_output_file("centerline.nii.gz", file_data + "_centerline" + ext_data, verbose)
# create a txt file with the centerline
file_name = file_data + "_centerline" + ".txt"
sct.printv("\nWrite text file...", verbose)
file_results = open(file_name, "w")
for i in range(min_z_index, max_z_index + 1):
file_results.write(
str(int(i))
+ " "
+ str(x_centerline_fit[i - min_z_index])
+ " "
+ str(y_centerline_fit[i - min_z_index])
+ "\n"
)
file_results.close()
# Copy result into parent folder
sct.run("cp " + file_name + " ../")
del data
# come back to parent folder
os.chdir("..")
# Change orientation of the output centerline into input orientation
sct.printv("\nOrient centerline image to input orientation: " + orientation, verbose)
fname_segmentation_orient = "tmp.segmentation_rpi" + ext_data
set_orientation(
path_tmp + "/" + file_data + "_centerline" + ext_data, orientation, file_data + "_centerline" + ext_data
)
# Remove temporary files
if remove_temp_files:
sct.printv("\nRemove temporary files...", verbose)
sct.run("rm -rf " + path_tmp, verbose)
return file_data + "_centerline" + ext_data
def main():
# get default parameters
step1 = Paramreg(step='1',
type='seg',
algo='slicereg',
metric='MeanSquares',
iter='10')
step2 = Paramreg(step='2', type='im', algo='syn', metric='MI', iter='3')
# step1 = Paramreg()
paramreg = ParamregMultiStep([step1, step2])
# step1 = Paramreg_step(step='1', type='seg', algo='bsplinesyn', metric='MeanSquares', iter='10', shrink='1', smooth='0', gradStep='0.5')
# step2 = Paramreg_step(step='2', type='im', algo='syn', metric='MI', iter='10', shrink='1', smooth='0', gradStep='0.5')
# paramreg = ParamregMultiStep([step1, step2])
# Initialize the parser
parser = Parser(__file__)
parser.usage.set_description('Register anatomical image to the template.')
parser.add_option(name="-i",
type_value="file",
description="Anatomical image.",
mandatory=True,
example="anat.nii.gz")
parser.add_option(name="-s",
type_value="file",
description="Spinal cord segmentation.",
mandatory=True,
example="anat_seg.nii.gz")
parser.add_option(
name="-l",
type_value="file",
description=
"Labels. See: http://sourceforge.net/p/spinalcordtoolbox/wiki/create_labels/",
mandatory=True,
default_value='',
example="anat_labels.nii.gz")
parser.add_option(name="-t",
type_value="folder",
description="Path to MNI-Poly-AMU template.",
mandatory=False,
default_value=param.path_template)
parser.add_option(
name="-p",
type_value=[[':'], 'str'],
description=
"""Parameters for registration (see sct_register_multimodal). Default:\n--\nstep=1\ntype="""
+ paramreg.steps['1'].type + """\nalgo=""" + paramreg.steps['1'].algo +
"""\nmetric=""" + paramreg.steps['1'].metric + """\npoly=""" +
paramreg.steps['1'].poly + """\n--\nstep=2\ntype=""" +
paramreg.steps['2'].type + """\nalgo=""" + paramreg.steps['2'].algo +
"""\nmetric=""" + paramreg.steps['2'].metric + """\niter=""" +
paramreg.steps['2'].iter + """\nshrink=""" +
paramreg.steps['2'].shrink + """\nsmooth=""" +
paramreg.steps['2'].smooth + """\ngradStep=""" +
paramreg.steps['2'].gradStep + """\n--""",
mandatory=False,
example=
"step=2,type=seg,algo=bsplinesyn,metric=MeanSquares,iter=5,shrink=2:step=3,type=im,algo=syn,metric=MI,iter=5,shrink=1,gradStep=0.3"
)
parser.add_option(name="-r",
type_value="multiple_choice",
description="""Remove temporary files.""",
mandatory=False,
default_value='1',
example=['0', '1'])
parser.add_option(
name="-v",
type_value="multiple_choice",
description="""Verbose. 0: nothing. 1: basic. 2: extended.""",
mandatory=False,
default_value=param.verbose,
example=['0', '1', '2'])
if param.debug:
print '\n*** WARNING: DEBUG MODE ON ***\n'
fname_data = '/Users/julien/data/temp/sct_example_data/t2/t2.nii.gz'
fname_landmarks = '/Users/julien/data/temp/sct_example_data/t2/labels.nii.gz'
fname_seg = '/Users/julien/data/temp/sct_example_data/t2/t2_seg.nii.gz'
path_template = param.path_template
remove_temp_files = 0
verbose = 2
# speed = 'superfast'
#param_reg = '2,BSplineSyN,0.6,MeanSquares'
else:
arguments = parser.parse(sys.argv[1:])
# get arguments
fname_data = arguments['-i']
fname_seg = arguments['-s']
fname_landmarks = arguments['-l']
path_template = arguments['-t']
remove_temp_files = int(arguments['-r'])
verbose = int(arguments['-v'])
if '-p' in arguments:
paramreg_user = arguments['-p']
# update registration parameters
for paramStep in paramreg_user:
paramreg.addStep(paramStep)
# initialize other parameters
file_template = param.file_template
file_template_label = param.file_template_label
file_template_seg = param.file_template_seg
output_type = param.output_type
zsubsample = param.zsubsample
# smoothing_sigma = param.smoothing_sigma
# start timer
start_time = time.time()
# get absolute path - TO DO: remove! NEVER USE ABSOLUTE PATH...
path_template = os.path.abspath(path_template)
# get fname of the template + template objects
fname_template = sct.slash_at_the_end(path_template, 1) + file_template
fname_template_label = sct.slash_at_the_end(path_template,
1) + file_template_label
fname_template_seg = sct.slash_at_the_end(path_template,
1) + file_template_seg
# check file existence
sct.printv('\nCheck template files...')
sct.check_file_exist(fname_template, verbose)
sct.check_file_exist(fname_template_label, verbose)
sct.check_file_exist(fname_template_seg, verbose)
# print arguments
sct.printv('\nCheck parameters:', verbose)
sct.printv('.. Data: ' + fname_data, verbose)
sct.printv('.. Landmarks: ' + fname_landmarks, verbose)
sct.printv('.. Segmentation: ' + fname_seg, verbose)
sct.printv('.. Path template: ' + path_template, verbose)
sct.printv('.. Output type: ' + str(output_type), verbose)
sct.printv('.. Remove temp files: ' + str(remove_temp_files), verbose)
sct.printv('\nParameters for registration:')
for pStep in range(1, len(paramreg.steps) + 1):
sct.printv('Step #' + paramreg.steps[str(pStep)].step, verbose)
sct.printv('.. Type #' + paramreg.steps[str(pStep)].type, verbose)
sct.printv(
'.. Algorithm................ ' + paramreg.steps[str(pStep)].algo,
verbose)
sct.printv(
'.. Metric................... ' +
paramreg.steps[str(pStep)].metric, verbose)
sct.printv(
'.. Number of iterations..... ' + paramreg.steps[str(pStep)].iter,
verbose)
sct.printv(
'.. Shrink factor............ ' +
paramreg.steps[str(pStep)].shrink, verbose)
sct.printv(
'.. Smoothing factor......... ' +
paramreg.steps[str(pStep)].smooth, verbose)
sct.printv(
'.. Gradient step............ ' +
paramreg.steps[str(pStep)].gradStep, verbose)
sct.printv(
'.. Degree of polynomial..... ' + paramreg.steps[str(pStep)].poly,
verbose)
path_data, file_data, ext_data = sct.extract_fname(fname_data)
sct.printv('\nCheck input labels...')
# check if label image contains coherent labels
image_label = Image(fname_landmarks)
# -> all labels must be different
labels = image_label.getNonZeroCoordinates(sorting='value')
hasDifferentLabels = True
for lab in labels:
for otherlabel in labels:
if lab != otherlabel and lab.hasEqualValue(otherlabel):
hasDifferentLabels = False
break
if not hasDifferentLabels:
sct.printv(
'ERROR: Wrong landmarks input. All labels must be different.',
verbose, 'error')
# all labels must be available in tempalte
image_label_template = Image(fname_template_label)
labels_template = image_label_template.getNonZeroCoordinates(
sorting='value')
if labels[-1].value > labels_template[-1].value:
sct.printv(
'ERROR: Wrong landmarks input. Labels must have correspondance in tempalte space. \nLabel max '
'provided: ' + str(labels[-1].value) +
'\nLabel max from template: ' + str(labels_template[-1].value),
verbose, 'error')
# create temporary folder
sct.printv('\nCreate temporary folder...', verbose)
path_tmp = 'tmp.' + time.strftime("%y%m%d%H%M%S")
status, output = sct.run('mkdir ' + path_tmp)
# copy files to temporary folder
sct.printv('\nCopy files...', verbose)
sct.run('isct_c3d ' + fname_data + ' -o ' + path_tmp + '/data.nii')
sct.run('isct_c3d ' + fname_landmarks + ' -o ' + path_tmp +
'/landmarks.nii.gz')
sct.run('isct_c3d ' + fname_seg + ' -o ' + path_tmp +
'/segmentation.nii.gz')
sct.run('isct_c3d ' + fname_template + ' -o ' + path_tmp + '/template.nii')
sct.run('isct_c3d ' + fname_template_label + ' -o ' + path_tmp +
'/template_labels.nii.gz')
sct.run('isct_c3d ' + fname_template_seg + ' -o ' + path_tmp +
'/template_seg.nii.gz')
# go to tmp folder
os.chdir(path_tmp)
# resample data to 1mm isotropic
sct.printv('\nResample data to 1mm isotropic...', verbose)
sct.run(
'isct_c3d data.nii -resample-mm 1.0x1.0x1.0mm -interpolation Linear -o datar.nii'
)
sct.run(
'isct_c3d segmentation.nii.gz -resample-mm 1.0x1.0x1.0mm -interpolation NearestNeighbor -o segmentationr.nii.gz'
)
# N.B. resampling of labels is more complicated, because they are single-point labels, therefore resampling with neighrest neighbour can make them disappear. Therefore a more clever approach is required.
resample_labels('landmarks.nii.gz', 'datar.nii', 'landmarksr.nii.gz')
# # TODO
# sct.run('sct_label_utils -i datar.nii -t create -x 124,186,19,2:129,98,23,8 -o landmarksr.nii.gz')
# Change orientation of input images to RPI
sct.printv('\nChange orientation of input images to RPI...', verbose)
set_orientation('datar.nii', 'RPI', 'data_rpi.nii')
set_orientation('landmarksr.nii.gz', 'RPI', 'landmarks_rpi.nii.gz')
set_orientation('segmentationr.nii.gz', 'RPI', 'segmentation_rpi.nii.gz')
# # Change orientation of input images to RPI
# sct.printv('\nChange orientation of input images to RPI...', verbose)
# set_orientation('data.nii', 'RPI', 'data_rpi.nii')
# set_orientation('landmarks.nii.gz', 'RPI', 'landmarks_rpi.nii.gz')
# set_orientation('segmentation.nii.gz', 'RPI', 'segmentation_rpi.nii.gz')
# get landmarks in native space
# crop segmentation
# output: segmentation_rpi_crop.nii.gz
sct.run(
'sct_crop_image -i segmentation_rpi.nii.gz -o segmentation_rpi_crop.nii.gz -dim 2 -bzmax'
)
# straighten segmentation
sct.printv('\nStraighten the spinal cord using centerline/segmentation...',
verbose)
sct.run(
'sct_straighten_spinalcord -i segmentation_rpi_crop.nii.gz -c segmentation_rpi_crop.nii.gz -r 0 -v '
+ str(verbose), verbose)
# re-define warping field using non-cropped space (to avoid issue #367)
sct.run(
'sct_concat_transfo -w warp_straight2curve.nii.gz -d data_rpi.nii -o warp_straight2curve.nii.gz'
)
# Label preparation:
# --------------------------------------------------------------------------------
# Remove unused label on template. Keep only label present in the input label image
sct.printv(
'\nRemove unused label on template. Keep only label present in the input label image...',
verbose)
sct.run(
'sct_label_utils -t remove -i template_labels.nii.gz -o template_label.nii.gz -r landmarks_rpi.nii.gz'
)
# Make sure landmarks are INT
sct.printv('\nConvert landmarks to INT...', verbose)
sct.run(
'isct_c3d template_label.nii.gz -type int -o template_label.nii.gz',
verbose)
# Create a cross for the template labels - 5 mm
sct.printv('\nCreate a 5 mm cross for the template labels...', verbose)
sct.run(
'sct_label_utils -t cross -i template_label.nii.gz -o template_label_cross.nii.gz -c 5'
)
# Create a cross for the input labels and dilate for straightening preparation - 5 mm
sct.printv(
'\nCreate a 5mm cross for the input labels and dilate for straightening preparation...',
verbose)
sct.run(
'sct_label_utils -t cross -i landmarks_rpi.nii.gz -o landmarks_rpi_cross3x3.nii.gz -c 5 -d'
)
# Apply straightening to labels
sct.printv('\nApply straightening to labels...', verbose)
sct.run(
'sct_apply_transfo -i landmarks_rpi_cross3x3.nii.gz -o landmarks_rpi_cross3x3_straight.nii.gz -d segmentation_rpi_crop_straight.nii.gz -w warp_curve2straight.nii.gz -x nn'
)
# Convert landmarks from FLOAT32 to INT
sct.printv('\nConvert landmarks from FLOAT32 to INT...', verbose)
sct.run(
'isct_c3d landmarks_rpi_cross3x3_straight.nii.gz -type int -o landmarks_rpi_cross3x3_straight.nii.gz'
)
# Remove labels that do not correspond with each others.
sct.printv('\nRemove labels that do not correspond with each others.',
verbose)
sct.run(
'sct_label_utils -t remove-symm -i landmarks_rpi_cross3x3_straight.nii.gz -o landmarks_rpi_cross3x3_straight.nii.gz,template_label_cross.nii.gz -r template_label_cross.nii.gz'
)
# Estimate affine transfo: straight --> template (landmark-based)'
sct.printv(
'\nEstimate affine transfo: straight anat --> template (landmark-based)...',
verbose)
# converting landmarks straight and curved to physical coordinates
image_straight = Image('landmarks_rpi_cross3x3_straight.nii.gz')
landmark_straight = image_straight.getNonZeroCoordinates(sorting='value')
image_template = Image('template_label_cross.nii.gz')
landmark_template = image_template.getNonZeroCoordinates(sorting='value')
# Reorganize landmarks
points_fixed, points_moving = [], []
landmark_straight_mean = []
for coord in landmark_straight:
if coord.value not in [c.value for c in landmark_straight_mean]:
temp_landmark = coord
temp_number = 1
for other_coord in landmark_straight:
if coord.hasEqualValue(other_coord) and coord != other_coord:
temp_landmark += other_coord
temp_number += 1
landmark_straight_mean.append(temp_landmark / temp_number)
for coord in landmark_straight_mean:
point_straight = image_straight.transfo_pix2phys(
[[coord.x, coord.y, coord.z]])
points_moving.append(
[point_straight[0][0], point_straight[0][1], point_straight[0][2]])
for coord in landmark_template:
point_template = image_template.transfo_pix2phys(
[[coord.x, coord.y, coord.z]])
points_fixed.append(
[point_template[0][0], point_template[0][1], point_template[0][2]])
# Register curved landmarks on straight landmarks based on python implementation
sct.printv(
'\nComputing rigid transformation (algo=translation-scaling-z) ...',
verbose)
import msct_register_landmarks
(rotation_matrix, translation_array, points_moving_reg, points_moving_barycenter) = \
msct_register_landmarks.getRigidTransformFromLandmarks(
points_fixed, points_moving, constraints='translation-scaling-z', show=False)
# writing rigid transformation file
text_file = open("straight2templateAffine.txt", "w")
text_file.write("#Insight Transform File V1.0\n")
text_file.write("#Transform 0\n")
text_file.write(
"Transform: FixedCenterOfRotationAffineTransform_double_3_3\n")
text_file.write(
"Parameters: %.9f %.9f %.9f %.9f %.9f %.9f %.9f %.9f %.9f %.9f %.9f %.9f\n"
% (1.0 / rotation_matrix[0, 0], rotation_matrix[0, 1],
rotation_matrix[0, 2], rotation_matrix[1, 0],
1.0 / rotation_matrix[1, 1], rotation_matrix[1, 2],
rotation_matrix[2, 0], rotation_matrix[2, 1],
1.0 / rotation_matrix[2, 2], translation_array[0, 0],
translation_array[0, 1], -translation_array[0, 2]))
text_file.write("FixedParameters: %.9f %.9f %.9f\n" %
(points_moving_barycenter[0], points_moving_barycenter[1],
points_moving_barycenter[2]))
text_file.close()
# Apply affine transformation: straight --> template
sct.printv('\nApply affine transformation: straight --> template...',
verbose)
sct.run(
'sct_concat_transfo -w warp_curve2straight.nii.gz,straight2templateAffine.txt -d template.nii -o warp_curve2straightAffine.nii.gz'
)
sct.run(
'sct_apply_transfo -i data_rpi.nii -o data_rpi_straight2templateAffine.nii -d template.nii -w warp_curve2straightAffine.nii.gz'
)
sct.run(
'sct_apply_transfo -i segmentation_rpi.nii.gz -o segmentation_rpi_straight2templateAffine.nii.gz -d template.nii -w warp_curve2straightAffine.nii.gz -x linear'
)
# threshold to 0.5
nii = Image('segmentation_rpi_straight2templateAffine.nii.gz')
data = nii.data
data[data < 0.5] = 0
nii.data = data
nii.setFileName('segmentation_rpi_straight2templateAffine_th.nii.gz')
nii.save()
# find min-max of anat2template (for subsequent cropping)
zmin_template, zmax_template = find_zmin_zmax(
'segmentation_rpi_straight2templateAffine_th.nii.gz')
# crop template in z-direction (for faster processing)
sct.printv('\nCrop data in template space (for faster processing)...',
verbose)
sct.run(
'sct_crop_image -i template.nii -o template_crop.nii -dim 2 -start ' +
str(zmin_template) + ' -end ' + str(zmax_template))
sct.run(
'sct_crop_image -i template_seg.nii.gz -o template_seg_crop.nii.gz -dim 2 -start '
+ str(zmin_template) + ' -end ' + str(zmax_template))
sct.run(
'sct_crop_image -i data_rpi_straight2templateAffine.nii -o data_rpi_straight2templateAffine_crop.nii -dim 2 -start '
+ str(zmin_template) + ' -end ' + str(zmax_template))
sct.run(
'sct_crop_image -i segmentation_rpi_straight2templateAffine.nii.gz -o segmentation_rpi_straight2templateAffine_crop.nii.gz -dim 2 -start '
+ str(zmin_template) + ' -end ' + str(zmax_template))
# sub-sample in z-direction
sct.printv('\nSub-sample in z-direction (for faster processing)...',
verbose)
sct.run(
'sct_resample -i template_crop.nii -o template_crop_r.nii -f 1x1x' +
zsubsample, verbose)
sct.run(
'sct_resample -i template_seg_crop.nii.gz -o template_seg_crop_r.nii.gz -f 1x1x'
+ zsubsample, verbose)
sct.run(
'sct_resample -i data_rpi_straight2templateAffine_crop.nii -o data_rpi_straight2templateAffine_crop_r.nii -f 1x1x'
+ zsubsample, verbose)
sct.run(
'sct_resample -i segmentation_rpi_straight2templateAffine_crop.nii.gz -o segmentation_rpi_straight2templateAffine_crop_r.nii.gz -f 1x1x'
+ zsubsample, verbose)
# Registration straight spinal cord to template
sct.printv('\nRegister straight spinal cord to template...', verbose)
# loop across registration steps
warp_forward = []
warp_inverse = []
for i_step in range(1, len(paramreg.steps) + 1):
sct.printv(
'\nEstimate transformation for step #' + str(i_step) + '...',
verbose)
# identify which is the src and dest
if paramreg.steps[str(i_step)].type == 'im':
src = 'data_rpi_straight2templateAffine_crop_r.nii'
dest = 'template_crop_r.nii'
interp_step = 'linear'
elif paramreg.steps[str(i_step)].type == 'seg':
src = 'segmentation_rpi_straight2templateAffine_crop_r.nii.gz'
dest = 'template_seg_crop_r.nii.gz'
interp_step = 'nn'
else:
sct.printv('ERROR: Wrong image type.', 1, 'error')
# if step>1, apply warp_forward_concat to the src image to be used
if i_step > 1:
# sct.run('sct_apply_transfo -i '+src+' -d '+dest+' -w '+','.join(warp_forward)+' -o '+sct.add_suffix(src, '_reg')+' -x '+interp_step, verbose)
sct.run(
'sct_apply_transfo -i ' + src + ' -d ' + dest + ' -w ' +
','.join(warp_forward) + ' -o ' + sct.add_suffix(src, '_reg') +
' -x ' + interp_step, verbose)
src = sct.add_suffix(src, '_reg')
# register src --> dest
warp_forward_out, warp_inverse_out = register(src, dest, paramreg,
param, str(i_step))
warp_forward.append(warp_forward_out)
warp_inverse.append(warp_inverse_out)
# Concatenate transformations:
sct.printv('\nConcatenate transformations: anat --> template...', verbose)
sct.run(
'sct_concat_transfo -w warp_curve2straightAffine.nii.gz,' +
','.join(warp_forward) +
' -d template.nii -o warp_anat2template.nii.gz', verbose)
# sct.run('sct_concat_transfo -w warp_curve2straight.nii.gz,straight2templateAffine.txt,'+','.join(warp_forward)+' -d template.nii -o warp_anat2template.nii.gz', verbose)
warp_inverse.reverse()
sct.run(
'sct_concat_transfo -w ' + ','.join(warp_inverse) +
',-straight2templateAffine.txt,warp_straight2curve.nii.gz -d data.nii -o warp_template2anat.nii.gz',
verbose)
# Apply warping fields to anat and template
if output_type == 1:
sct.run(
'sct_apply_transfo -i template.nii -o template2anat.nii.gz -d data.nii -w warp_template2anat.nii.gz -c 1',
verbose)
sct.run(
'sct_apply_transfo -i data.nii -o anat2template.nii.gz -d template.nii -w warp_anat2template.nii.gz -c 1',
verbose)
# come back to parent folder
os.chdir('..')
# Generate output files
sct.printv('\nGenerate output files...', verbose)
sct.generate_output_file(path_tmp + '/warp_template2anat.nii.gz',
'warp_template2anat.nii.gz', verbose)
sct.generate_output_file(path_tmp + '/warp_anat2template.nii.gz',
'warp_anat2template.nii.gz', verbose)
if output_type == 1:
sct.generate_output_file(path_tmp + '/template2anat.nii.gz',
'template2anat' + ext_data, verbose)
sct.generate_output_file(path_tmp + '/anat2template.nii.gz',
'anat2template' + ext_data, verbose)
# Delete temporary files
if remove_temp_files:
sct.printv('\nDelete temporary files...', verbose)
sct.run('rm -rf ' + path_tmp)
# display elapsed time
elapsed_time = time.time() - start_time
sct.printv(
'\nFinished! Elapsed time: ' + str(int(round(elapsed_time))) + 's',
verbose)
# to view results
sct.printv('\nTo view results, type:', verbose)
sct.printv('fslview ' + fname_data + ' template2anat -b 0,4000 &', verbose,
'info')
sct.printv('fslview ' + fname_template + ' -b 0,5000 anat2template &\n',
verbose, 'info')
def main():
# Initialization
fname_data = ''
suffix_out = '_crop'
remove_temp_files = param.remove_temp_files
verbose = param.verbose
fsloutput = 'export FSLOUTPUTTYPE=NIFTI; ' # for faster processing, all outputs are in NIFTI
remove_temp_files = param.remove_temp_files
# Parameters for debug mode
if param.debug:
print '\n*** WARNING: DEBUG MODE ON ***\n'
fname_data = path_sct + '/testing/data/errsm_23/t2/t2.nii.gz'
remove_temp_files = 0
else:
# Check input parameters
try:
opts, args = getopt.getopt(sys.argv[1:], 'hi:r:v:')
except getopt.GetoptError:
usage()
if not opts:
usage()
for opt, arg in opts:
if opt == '-h':
usage()
elif opt in ('-i'):
fname_data = arg
elif opt in ('-r'):
remove_temp_files = int(arg)
elif opt in ('-v'):
verbose = int(arg)
# display usage if a mandatory argument is not provided
if fname_data == '':
usage()
# Check file existence
sct.printv('\nCheck file existence...', verbose)
sct.check_file_exist(fname_data, verbose)
# Get dimensions of data
sct.printv('\nGet dimensions of data...', verbose)
nx, ny, nz, nt, px, py, pz, pt = Image(fname_data).dim
sct.printv('.. ' + str(nx) + ' x ' + str(ny) + ' x ' + str(nz), verbose)
# check if 4D data
if not nt == 1:
sct.printv(
'\nERROR in ' + os.path.basename(__file__) +
': Data should be 3D.\n', 1, 'error')
sys.exit(2)
# print arguments
print '\nCheck parameters:'
print ' data ................... ' + fname_data
print
# Extract path/file/extension
path_data, file_data, ext_data = sct.extract_fname(fname_data)
path_out, file_out, ext_out = '', file_data + suffix_out, ext_data
# create temporary folder
path_tmp = 'tmp.' + time.strftime("%y%m%d%H%M%S") + '/'
sct.run('mkdir ' + path_tmp)
# copy files into tmp folder
sct.run('isct_c3d ' + fname_data + ' -o ' + path_tmp + 'data.nii')
# go to tmp folder
os.chdir(path_tmp)
# change orientation
sct.printv('\nChange orientation to RPI...', verbose)
set_orientation('data.nii', 'RPI', 'data_rpi.nii')
# get image of medial slab
sct.printv('\nGet image of medial slab...', verbose)
image_array = nibabel.load('data_rpi.nii').get_data()
nx, ny, nz = image_array.shape
scipy.misc.imsave('image.jpg', image_array[math.floor(nx / 2), :, :])
# Display the image
sct.printv('\nDisplay image and get cropping region...', verbose)
fig = plt.figure()
# fig = plt.gcf()
# ax = plt.gca()
ax = fig.add_subplot(111)
img = mpimg.imread("image.jpg")
implot = ax.imshow(img.T)
implot.set_cmap('gray')
plt.gca().invert_yaxis()
# mouse callback
ax.set_title(
'Left click on the top and bottom of your cropping field.\n Right click to remove last point.\n Close window when your done.'
)
line, = ax.plot([], [], 'ro') # empty line
cropping_coordinates = LineBuilder(line)
plt.show()
# disconnect callback
# fig.canvas.mpl_disconnect(line)
# check if user clicked two times
if len(cropping_coordinates.xs) != 2:
sct.printv('\nERROR: You have to select two points. Exit program.\n',
1, 'error')
sys.exit(2)
# convert coordinates to integer
zcrop = [int(i) for i in cropping_coordinates.ys]
# sort coordinates
zcrop.sort()
# crop image
sct.printv('\nCrop image...', verbose)
nii = Image('data_rpi.nii')
data_crop = nii.data[:, :, zcrop[0]:zcrop[1]]
nii.data = data_crop
nii.setFileName('data_rpi_crop.nii')
nii.save()
# come back to parent folder
os.chdir('..')
sct.printv('\nGenerate output files...', verbose)
sct.generate_output_file(path_tmp + 'data_rpi_crop.nii',
path_out + file_out + ext_out)
# Remove temporary files
if remove_temp_files == 1:
print('\nRemove temporary files...')
sct.run('rm -rf ' + path_tmp)
# to view results
print '\nDone! To view results, type:'
print 'fslview ' + path_out + file_out + ext_out + ' &'
print
def main():
# get default parameters
step1 = Paramreg(step='1', type='seg', algo='slicereg', metric='MeanSquares', iter='10')
step2 = Paramreg(step='2', type='im', algo='syn', metric='MI', iter='3')
# step1 = Paramreg()
paramreg = ParamregMultiStep([step1, step2])
# step1 = Paramreg_step(step='1', type='seg', algo='bsplinesyn', metric='MeanSquares', iter='10', shrink='1', smooth='0', gradStep='0.5')
# step2 = Paramreg_step(step='2', type='im', algo='syn', metric='MI', iter='10', shrink='1', smooth='0', gradStep='0.5')
# paramreg = ParamregMultiStep([step1, step2])
# Initialize the parser
parser = Parser(__file__)
parser.usage.set_description('Register anatomical image to the template.')
parser.add_option(name="-i",
type_value="file",
description="Anatomical image.",
mandatory=True,
example="anat.nii.gz")
parser.add_option(name="-s",
type_value="file",
description="Spinal cord segmentation.",
mandatory=True,
example="anat_seg.nii.gz")
parser.add_option(name="-l",
type_value="file",
description="Labels. See: http://sourceforge.net/p/spinalcordtoolbox/wiki/create_labels/",
mandatory=True,
default_value='',
example="anat_labels.nii.gz")
parser.add_option(name="-t",
type_value="folder",
description="Path to MNI-Poly-AMU template.",
mandatory=False,
default_value=param.path_template)
parser.add_option(name="-p",
type_value=[[':'], 'str'],
description="""Parameters for registration (see sct_register_multimodal). Default:\n--\nstep=1\ntype="""+paramreg.steps['1'].type+"""\nalgo="""+paramreg.steps['1'].algo+"""\nmetric="""+paramreg.steps['1'].metric+"""\npoly="""+paramreg.steps['1'].poly+"""\n--\nstep=2\ntype="""+paramreg.steps['2'].type+"""\nalgo="""+paramreg.steps['2'].algo+"""\nmetric="""+paramreg.steps['2'].metric+"""\niter="""+paramreg.steps['2'].iter+"""\nshrink="""+paramreg.steps['2'].shrink+"""\nsmooth="""+paramreg.steps['2'].smooth+"""\ngradStep="""+paramreg.steps['2'].gradStep+"""\n--""",
mandatory=False,
example="step=2,type=seg,algo=bsplinesyn,metric=MeanSquares,iter=5,shrink=2:step=3,type=im,algo=syn,metric=MI,iter=5,shrink=1,gradStep=0.3")
parser.add_option(name="-r",
type_value="multiple_choice",
description="""Remove temporary files.""",
mandatory=False,
default_value='1',
example=['0', '1'])
parser.add_option(name="-v",
type_value="multiple_choice",
description="""Verbose. 0: nothing. 1: basic. 2: extended.""",
mandatory=False,
default_value=param.verbose,
example=['0', '1', '2'])
if param.debug:
print '\n*** WARNING: DEBUG MODE ON ***\n'
fname_data = '/Users/julien/data/temp/sct_example_data/t2/t2.nii.gz'
fname_landmarks = '/Users/julien/data/temp/sct_example_data/t2/labels.nii.gz'
fname_seg = '/Users/julien/data/temp/sct_example_data/t2/t2_seg.nii.gz'
path_template = param.path_template
remove_temp_files = 0
verbose = 2
# speed = 'superfast'
#param_reg = '2,BSplineSyN,0.6,MeanSquares'
else:
arguments = parser.parse(sys.argv[1:])
# get arguments
fname_data = arguments['-i']
fname_seg = arguments['-s']
fname_landmarks = arguments['-l']
path_template = arguments['-t']
remove_temp_files = int(arguments['-r'])
verbose = int(arguments['-v'])
if '-p' in arguments:
paramreg_user = arguments['-p']
# update registration parameters
for paramStep in paramreg_user:
paramreg.addStep(paramStep)
# initialize other parameters
file_template = param.file_template
file_template_label = param.file_template_label
file_template_seg = param.file_template_seg
output_type = param.output_type
zsubsample = param.zsubsample
# smoothing_sigma = param.smoothing_sigma
# start timer
start_time = time.time()
# get absolute path - TO DO: remove! NEVER USE ABSOLUTE PATH...
path_template = os.path.abspath(path_template)
# get fname of the template + template objects
fname_template = sct.slash_at_the_end(path_template, 1)+file_template
fname_template_label = sct.slash_at_the_end(path_template, 1)+file_template_label
fname_template_seg = sct.slash_at_the_end(path_template, 1)+file_template_seg
# check file existence
sct.printv('\nCheck template files...')
sct.check_file_exist(fname_template, verbose)
sct.check_file_exist(fname_template_label, verbose)
sct.check_file_exist(fname_template_seg, verbose)
# print arguments
sct.printv('\nCheck parameters:', verbose)
sct.printv('.. Data: '+fname_data, verbose)
sct.printv('.. Landmarks: '+fname_landmarks, verbose)
sct.printv('.. Segmentation: '+fname_seg, verbose)
sct.printv('.. Path template: '+path_template, verbose)
sct.printv('.. Output type: '+str(output_type), verbose)
sct.printv('.. Remove temp files: '+str(remove_temp_files), verbose)
sct.printv('\nParameters for registration:')
for pStep in range(1, len(paramreg.steps)+1):
sct.printv('Step #'+paramreg.steps[str(pStep)].step, verbose)
sct.printv('.. Type #'+paramreg.steps[str(pStep)].type, verbose)
sct.printv('.. Algorithm................ '+paramreg.steps[str(pStep)].algo, verbose)
sct.printv('.. Metric................... '+paramreg.steps[str(pStep)].metric, verbose)
sct.printv('.. Number of iterations..... '+paramreg.steps[str(pStep)].iter, verbose)
sct.printv('.. Shrink factor............ '+paramreg.steps[str(pStep)].shrink, verbose)
sct.printv('.. Smoothing factor......... '+paramreg.steps[str(pStep)].smooth, verbose)
sct.printv('.. Gradient step............ '+paramreg.steps[str(pStep)].gradStep, verbose)
sct.printv('.. Degree of polynomial..... '+paramreg.steps[str(pStep)].poly, verbose)
path_data, file_data, ext_data = sct.extract_fname(fname_data)
sct.printv('\nCheck input labels...')
# check if label image contains coherent labels
image_label = Image(fname_landmarks)
# -> all labels must be different
labels = image_label.getNonZeroCoordinates(sorting='value')
hasDifferentLabels = True
for lab in labels:
for otherlabel in labels:
if lab != otherlabel and lab.hasEqualValue(otherlabel):
hasDifferentLabels = False
break
if not hasDifferentLabels:
sct.printv('ERROR: Wrong landmarks input. All labels must be different.', verbose, 'error')
# all labels must be available in tempalte
image_label_template = Image(fname_template_label)
labels_template = image_label_template.getNonZeroCoordinates(sorting='value')
if labels[-1].value > labels_template[-1].value:
sct.printv('ERROR: Wrong landmarks input. Labels must have correspondance in tempalte space. \nLabel max '
'provided: ' + str(labels[-1].value) + '\nLabel max from template: ' +
str(labels_template[-1].value), verbose, 'error')
# create temporary folder
sct.printv('\nCreate temporary folder...', verbose)
path_tmp = 'tmp.'+time.strftime("%y%m%d%H%M%S")
status, output = sct.run('mkdir '+path_tmp)
# copy files to temporary folder
sct.printv('\nCopy files...', verbose)
sct.run('isct_c3d '+fname_data+' -o '+path_tmp+'/data.nii')
sct.run('isct_c3d '+fname_landmarks+' -o '+path_tmp+'/landmarks.nii.gz')
sct.run('isct_c3d '+fname_seg+' -o '+path_tmp+'/segmentation.nii.gz')
sct.run('isct_c3d '+fname_template+' -o '+path_tmp+'/template.nii')
sct.run('isct_c3d '+fname_template_label+' -o '+path_tmp+'/template_labels.nii.gz')
sct.run('isct_c3d '+fname_template_seg+' -o '+path_tmp+'/template_seg.nii.gz')
# go to tmp folder
os.chdir(path_tmp)
# resample data to 1mm isotropic
sct.printv('\nResample data to 1mm isotropic...', verbose)
sct.run('isct_c3d data.nii -resample-mm 1.0x1.0x1.0mm -interpolation Linear -o datar.nii')
sct.run('isct_c3d segmentation.nii.gz -resample-mm 1.0x1.0x1.0mm -interpolation NearestNeighbor -o segmentationr.nii.gz')
# N.B. resampling of labels is more complicated, because they are single-point labels, therefore resampling with neighrest neighbour can make them disappear. Therefore a more clever approach is required.
resample_labels('landmarks.nii.gz', 'datar.nii', 'landmarksr.nii.gz')
# # TODO
# sct.run('sct_label_utils -i datar.nii -t create -x 124,186,19,2:129,98,23,8 -o landmarksr.nii.gz')
# Change orientation of input images to RPI
sct.printv('\nChange orientation of input images to RPI...', verbose)
set_orientation('datar.nii', 'RPI', 'data_rpi.nii')
set_orientation('landmarksr.nii.gz', 'RPI', 'landmarks_rpi.nii.gz')
set_orientation('segmentationr.nii.gz', 'RPI', 'segmentation_rpi.nii.gz')
# # Change orientation of input images to RPI
# sct.printv('\nChange orientation of input images to RPI...', verbose)
# set_orientation('data.nii', 'RPI', 'data_rpi.nii')
# set_orientation('landmarks.nii.gz', 'RPI', 'landmarks_rpi.nii.gz')
# set_orientation('segmentation.nii.gz', 'RPI', 'segmentation_rpi.nii.gz')
# get landmarks in native space
# crop segmentation
# output: segmentation_rpi_crop.nii.gz
sct.run('sct_crop_image -i segmentation_rpi.nii.gz -o segmentation_rpi_crop.nii.gz -dim 2 -bzmax')
# straighten segmentation
sct.printv('\nStraighten the spinal cord using centerline/segmentation...', verbose)
sct.run('sct_straighten_spinalcord -i segmentation_rpi_crop.nii.gz -c segmentation_rpi_crop.nii.gz -r 0 -v '+str(verbose), verbose)
# re-define warping field using non-cropped space (to avoid issue #367)
sct.run('sct_concat_transfo -w warp_straight2curve.nii.gz -d data_rpi.nii -o warp_straight2curve.nii.gz')
# Label preparation:
# --------------------------------------------------------------------------------
# Remove unused label on template. Keep only label present in the input label image
sct.printv('\nRemove unused label on template. Keep only label present in the input label image...', verbose)
sct.run('sct_label_utils -t remove -i template_labels.nii.gz -o template_label.nii.gz -r landmarks_rpi.nii.gz')
# Make sure landmarks are INT
sct.printv('\nConvert landmarks to INT...', verbose)
sct.run('isct_c3d template_label.nii.gz -type int -o template_label.nii.gz', verbose)
# Create a cross for the template labels - 5 mm
sct.printv('\nCreate a 5 mm cross for the template labels...', verbose)
sct.run('sct_label_utils -t cross -i template_label.nii.gz -o template_label_cross.nii.gz -c 5')
# Create a cross for the input labels and dilate for straightening preparation - 5 mm
sct.printv('\nCreate a 5mm cross for the input labels and dilate for straightening preparation...', verbose)
sct.run('sct_label_utils -t cross -i landmarks_rpi.nii.gz -o landmarks_rpi_cross3x3.nii.gz -c 5 -d')
# Apply straightening to labels
sct.printv('\nApply straightening to labels...', verbose)
sct.run('sct_apply_transfo -i landmarks_rpi_cross3x3.nii.gz -o landmarks_rpi_cross3x3_straight.nii.gz -d segmentation_rpi_crop_straight.nii.gz -w warp_curve2straight.nii.gz -x nn')
# Convert landmarks from FLOAT32 to INT
sct.printv('\nConvert landmarks from FLOAT32 to INT...', verbose)
sct.run('isct_c3d landmarks_rpi_cross3x3_straight.nii.gz -type int -o landmarks_rpi_cross3x3_straight.nii.gz')
# Remove labels that do not correspond with each others.
sct.printv('\nRemove labels that do not correspond with each others.', verbose)
sct.run('sct_label_utils -t remove-symm -i landmarks_rpi_cross3x3_straight.nii.gz -o landmarks_rpi_cross3x3_straight.nii.gz,template_label_cross.nii.gz -r template_label_cross.nii.gz')
# Estimate affine transfo: straight --> template (landmark-based)'
sct.printv('\nEstimate affine transfo: straight anat --> template (landmark-based)...', verbose)
# converting landmarks straight and curved to physical coordinates
image_straight = Image('landmarks_rpi_cross3x3_straight.nii.gz')
landmark_straight = image_straight.getNonZeroCoordinates(sorting='value')
image_template = Image('template_label_cross.nii.gz')
landmark_template = image_template.getNonZeroCoordinates(sorting='value')
# Reorganize landmarks
points_fixed, points_moving = [], []
landmark_straight_mean = []
for coord in landmark_straight:
if coord.value not in [c.value for c in landmark_straight_mean]:
temp_landmark = coord
temp_number = 1
for other_coord in landmark_straight:
if coord.hasEqualValue(other_coord) and coord != other_coord:
temp_landmark += other_coord
temp_number += 1
landmark_straight_mean.append(temp_landmark / temp_number)
for coord in landmark_straight_mean:
point_straight = image_straight.transfo_pix2phys([[coord.x, coord.y, coord.z]])
points_moving.append([point_straight[0][0], point_straight[0][1], point_straight[0][2]])
for coord in landmark_template:
point_template = image_template.transfo_pix2phys([[coord.x, coord.y, coord.z]])
points_fixed.append([point_template[0][0], point_template[0][1], point_template[0][2]])
# Register curved landmarks on straight landmarks based on python implementation
sct.printv('\nComputing rigid transformation (algo=translation-scaling-z) ...', verbose)
import msct_register_landmarks
(rotation_matrix, translation_array, points_moving_reg, points_moving_barycenter) = \
msct_register_landmarks.getRigidTransformFromLandmarks(
points_fixed, points_moving, constraints='translation-scaling-z', show=False)
# writing rigid transformation file
text_file = open("straight2templateAffine.txt", "w")
text_file.write("#Insight Transform File V1.0\n")
text_file.write("#Transform 0\n")
text_file.write("Transform: FixedCenterOfRotationAffineTransform_double_3_3\n")
text_file.write("Parameters: %.9f %.9f %.9f %.9f %.9f %.9f %.9f %.9f %.9f %.9f %.9f %.9f\n" % (
1.0/rotation_matrix[0, 0], rotation_matrix[0, 1], rotation_matrix[0, 2],
rotation_matrix[1, 0], 1.0/rotation_matrix[1, 1], rotation_matrix[1, 2],
rotation_matrix[2, 0], rotation_matrix[2, 1], 1.0/rotation_matrix[2, 2],
translation_array[0, 0], translation_array[0, 1], -translation_array[0, 2]))
text_file.write("FixedParameters: %.9f %.9f %.9f\n" % (points_moving_barycenter[0],
points_moving_barycenter[1],
points_moving_barycenter[2]))
text_file.close()
# Apply affine transformation: straight --> template
sct.printv('\nApply affine transformation: straight --> template...', verbose)
sct.run('sct_concat_transfo -w warp_curve2straight.nii.gz,straight2templateAffine.txt -d template.nii -o warp_curve2straightAffine.nii.gz')
sct.run('sct_apply_transfo -i data_rpi.nii -o data_rpi_straight2templateAffine.nii -d template.nii -w warp_curve2straightAffine.nii.gz')
sct.run('sct_apply_transfo -i segmentation_rpi.nii.gz -o segmentation_rpi_straight2templateAffine.nii.gz -d template.nii -w warp_curve2straightAffine.nii.gz -x linear')
# threshold to 0.5
nii = Image('segmentation_rpi_straight2templateAffine.nii.gz')
data = nii.data
data[data < 0.5] = 0
nii.data = data
nii.setFileName('segmentation_rpi_straight2templateAffine_th.nii.gz')
nii.save()
# find min-max of anat2template (for subsequent cropping)
zmin_template, zmax_template = find_zmin_zmax('segmentation_rpi_straight2templateAffine_th.nii.gz')
# crop template in z-direction (for faster processing)
sct.printv('\nCrop data in template space (for faster processing)...', verbose)
sct.run('sct_crop_image -i template.nii -o template_crop.nii -dim 2 -start '+str(zmin_template)+' -end '+str(zmax_template))
sct.run('sct_crop_image -i template_seg.nii.gz -o template_seg_crop.nii.gz -dim 2 -start '+str(zmin_template)+' -end '+str(zmax_template))
sct.run('sct_crop_image -i data_rpi_straight2templateAffine.nii -o data_rpi_straight2templateAffine_crop.nii -dim 2 -start '+str(zmin_template)+' -end '+str(zmax_template))
sct.run('sct_crop_image -i segmentation_rpi_straight2templateAffine.nii.gz -o segmentation_rpi_straight2templateAffine_crop.nii.gz -dim 2 -start '+str(zmin_template)+' -end '+str(zmax_template))
# sub-sample in z-direction
sct.printv('\nSub-sample in z-direction (for faster processing)...', verbose)
sct.run('sct_resample -i template_crop.nii -o template_crop_r.nii -f 1x1x'+zsubsample, verbose)
sct.run('sct_resample -i template_seg_crop.nii.gz -o template_seg_crop_r.nii.gz -f 1x1x'+zsubsample, verbose)
sct.run('sct_resample -i data_rpi_straight2templateAffine_crop.nii -o data_rpi_straight2templateAffine_crop_r.nii -f 1x1x'+zsubsample, verbose)
sct.run('sct_resample -i segmentation_rpi_straight2templateAffine_crop.nii.gz -o segmentation_rpi_straight2templateAffine_crop_r.nii.gz -f 1x1x'+zsubsample, verbose)
# Registration straight spinal cord to template
sct.printv('\nRegister straight spinal cord to template...', verbose)
# loop across registration steps
warp_forward = []
warp_inverse = []
for i_step in range(1, len(paramreg.steps)+1):
sct.printv('\nEstimate transformation for step #'+str(i_step)+'...', verbose)
# identify which is the src and dest
if paramreg.steps[str(i_step)].type == 'im':
src = 'data_rpi_straight2templateAffine_crop_r.nii'
dest = 'template_crop_r.nii'
interp_step = 'linear'
elif paramreg.steps[str(i_step)].type == 'seg':
src = 'segmentation_rpi_straight2templateAffine_crop_r.nii.gz'
dest = 'template_seg_crop_r.nii.gz'
interp_step = 'nn'
else:
sct.printv('ERROR: Wrong image type.', 1, 'error')
# if step>1, apply warp_forward_concat to the src image to be used
if i_step > 1:
# sct.run('sct_apply_transfo -i '+src+' -d '+dest+' -w '+','.join(warp_forward)+' -o '+sct.add_suffix(src, '_reg')+' -x '+interp_step, verbose)
sct.run('sct_apply_transfo -i '+src+' -d '+dest+' -w '+','.join(warp_forward)+' -o '+sct.add_suffix(src, '_reg')+' -x '+interp_step, verbose)
src = sct.add_suffix(src, '_reg')
# register src --> dest
warp_forward_out, warp_inverse_out = register(src, dest, paramreg, param, str(i_step))
warp_forward.append(warp_forward_out)
warp_inverse.append(warp_inverse_out)
# Concatenate transformations:
sct.printv('\nConcatenate transformations: anat --> template...', verbose)
sct.run('sct_concat_transfo -w warp_curve2straightAffine.nii.gz,'+','.join(warp_forward)+' -d template.nii -o warp_anat2template.nii.gz', verbose)
# sct.run('sct_concat_transfo -w warp_curve2straight.nii.gz,straight2templateAffine.txt,'+','.join(warp_forward)+' -d template.nii -o warp_anat2template.nii.gz', verbose)
warp_inverse.reverse()
sct.run('sct_concat_transfo -w '+','.join(warp_inverse)+',-straight2templateAffine.txt,warp_straight2curve.nii.gz -d data.nii -o warp_template2anat.nii.gz', verbose)
# Apply warping fields to anat and template
if output_type == 1:
sct.run('sct_apply_transfo -i template.nii -o template2anat.nii.gz -d data.nii -w warp_template2anat.nii.gz -c 1', verbose)
sct.run('sct_apply_transfo -i data.nii -o anat2template.nii.gz -d template.nii -w warp_anat2template.nii.gz -c 1', verbose)
# come back to parent folder
os.chdir('..')
# Generate output files
sct.printv('\nGenerate output files...', verbose)
sct.generate_output_file(path_tmp+'/warp_template2anat.nii.gz', 'warp_template2anat.nii.gz', verbose)
sct.generate_output_file(path_tmp+'/warp_anat2template.nii.gz', 'warp_anat2template.nii.gz', verbose)
if output_type == 1:
sct.generate_output_file(path_tmp+'/template2anat.nii.gz', 'template2anat'+ext_data, verbose)
sct.generate_output_file(path_tmp+'/anat2template.nii.gz', 'anat2template'+ext_data, verbose)
# Delete temporary files
if remove_temp_files:
sct.printv('\nDelete temporary files...', verbose)
sct.run('rm -rf '+path_tmp)
# display elapsed time
elapsed_time = time.time() - start_time
sct.printv('\nFinished! Elapsed time: '+str(int(round(elapsed_time)))+'s', verbose)
# to view results
sct.printv('\nTo view results, type:', verbose)
sct.printv('fslview '+fname_data+' template2anat -b 0,4000 &', verbose, 'info')
sct.printv('fslview '+fname_template+' -b 0,5000 anat2template &\n', verbose, 'info')
def compute_csa(fname_segmentation, name_method, volume_output, verbose, remove_temp_files, step, smoothing_param, figure_fit, name_output, slices, vert_levels, path_to_template, algo_fitting = 'hanning', type_window = 'hanning', window_length = 80):
# Extract path, file and extension
fname_segmentation = os.path.abspath(fname_segmentation)
path_data, file_data, ext_data = sct.extract_fname(fname_segmentation)
# create temporary folder
sct.printv('\nCreate temporary folder...', verbose)
path_tmp = sct.slash_at_the_end('tmp.'+time.strftime("%y%m%d%H%M%S"), 1)
sct.run('mkdir '+path_tmp, verbose)
# Copying input data to tmp folder and convert to nii
sct.printv('\nCopying input data to tmp folder and convert to nii...', verbose)
sct.run('isct_c3d '+fname_segmentation+' -o '+path_tmp+'segmentation.nii')
# go to tmp folder
os.chdir(path_tmp)
# Change orientation of the input segmentation into RPI
sct.printv('\nChange orientation of the input segmentation into RPI...', verbose)
fname_segmentation_orient = set_orientation('segmentation.nii', 'RPI', 'segmentation_orient.nii')
# Get size of data
sct.printv('\nGet data dimensions...', verbose)
nx, ny, nz, nt, px, py, pz, pt = Image(fname_segmentation_orient).dim
sct.printv(' ' + str(nx) + ' x ' + str(ny) + ' x ' + str(nz), verbose)
# Open segmentation volume
sct.printv('\nOpen segmentation volume...', verbose)
file_seg = nibabel.load(fname_segmentation_orient)
data_seg = file_seg.get_data()
hdr_seg = file_seg.get_header()
# # Extract min and max index in Z direction
X, Y, Z = (data_seg > 0).nonzero()
min_z_index, max_z_index = min(Z), max(Z)
# Xp, Yp = (data_seg[:, :, 0] >= 0).nonzero() # X and Y range
# extract centerline and smooth it
x_centerline_fit, y_centerline_fit, z_centerline, x_centerline_deriv, y_centerline_deriv, z_centerline_deriv = smooth_centerline(fname_segmentation_orient, algo_fitting=algo_fitting, type_window=type_window, window_length=window_length, verbose=verbose)
z_centerline_scaled = [x*pz for x in z_centerline]
# Compute CSA
sct.printv('\nCompute CSA...', verbose)
# Empty arrays in which CSA for each z slice will be stored
csa = np.zeros(max_z_index-min_z_index+1)
# csa = [0.0 for i in xrange(0, max_z_index-min_z_index+1)]
for iz in xrange(0, len(z_centerline)):
# compute the vector normal to the plane
normal = normalize(np.array([x_centerline_deriv[iz], y_centerline_deriv[iz], z_centerline_deriv[iz]]))
# compute the angle between the normal vector of the plane and the vector z
angle = np.arccos(np.dot(normal, [0, 0, 1]))
# compute the number of voxels, assuming the segmentation is coded for partial volume effect between 0 and 1.
number_voxels = sum(sum(data_seg[:, :, iz+min_z_index]))
# compute CSA, by scaling with voxel size (in mm) and adjusting for oblique plane
csa[iz] = number_voxels * px * py * np.cos(angle)
if smoothing_param:
from msct_smooth import smoothing_window
sct.printv('\nSmooth CSA across slices...', verbose)
sct.printv('.. Hanning window: '+str(smoothing_param)+' mm', verbose)
csa_smooth = smoothing_window(csa, window_len=smoothing_param/pz, window='hanning', verbose=0)
# display figure
if verbose == 2:
import matplotlib.pyplot as plt
plt.figure()
pltx, = plt.plot(z_centerline_scaled, csa, 'bo')
pltx_fit, = plt.plot(z_centerline_scaled, csa_smooth, 'r', linewidth=2)
plt.title("Cross-sectional area (CSA)")
plt.xlabel('z (mm)')
plt.ylabel('CSA (mm^2)')
plt.legend([pltx, pltx_fit], ['Raw', 'Smoothed'])
plt.show()
# update variable
csa = csa_smooth
# Create output text file
sct.printv('\nWrite text file...', verbose)
file_results = open('csa.txt', 'w')
for i in range(min_z_index, max_z_index+1):
file_results.write(str(int(i)) + ',' + str(csa[i-min_z_index])+'\n')
# Display results
sct.printv('z='+str(i-min_z_index)+': '+str(csa[i-min_z_index])+' mm^2', verbose, 'bold')
file_results.close()
# output volume of csa values
if volume_output:
sct.printv('\nCreate volume of CSA values...', verbose)
# get orientation of the input data
orientation = get_orientation('segmentation.nii')
data_seg = data_seg.astype(np.float32, copy=False)
# loop across slices
for iz in range(min_z_index, max_z_index+1):
# retrieve seg pixels
x_seg, y_seg = (data_seg[:, :, iz] > 0).nonzero()
seg = [[x_seg[i],y_seg[i]] for i in range(0, len(x_seg))]
# loop across pixels in segmentation
for i in seg:
# replace value with csa value
data_seg[i[0], i[1], iz] = csa[iz-min_z_index]
# create header
hdr_seg.set_data_dtype('float32') # set imagetype to uint8
# save volume
img = nibabel.Nifti1Image(data_seg, None, hdr_seg)
nibabel.save(img, 'csa_RPI.nii')
# Change orientation of the output centerline into input orientation
fname_csa_volume = set_orientation('csa_RPI.nii', orientation, 'csa_RPI_orient.nii')
# come back to parent folder
os.chdir('..')
# Generate output files
sct.printv('\nGenerate output files...', verbose)
from shutil import copyfile
copyfile(path_tmp+'csa.txt', path_data+param.fname_csa)
# sct.generate_output_file(path_tmp+'csa.txt', path_data+param.fname_csa) # extension already included in param.fname_csa
if volume_output:
sct.generate_output_file(fname_csa_volume, path_data+name_output) # extension already included in name_output
# average csa across vertebral levels or slices if asked (flag -z or -l)
if slices or vert_levels:
if vert_levels and not path_to_template:
sct.printv('\nERROR: Path to template is missing. See usage.\n', 1, 'error')
sys.exit(2)
elif vert_levels and path_to_template:
abs_path_to_template = os.path.abspath(path_to_template)
# go to tmp folder
os.chdir(path_tmp)
# create temporary folder
sct.printv('\nCreate temporary folder to average csa...', verbose)
path_tmp_extract_metric = sct.slash_at_the_end('label_temp', 1)
sct.run('mkdir '+path_tmp_extract_metric, verbose)
# Copying output CSA volume in the temporary folder
sct.printv('\nCopy data to tmp folder...', verbose)
sct.run('cp '+fname_segmentation+' '+path_tmp_extract_metric)
# create file info_label
path_fname_seg, file_fname_seg, ext_fname_seg = sct.extract_fname(fname_segmentation)
create_info_label('info_label.txt', path_tmp_extract_metric, file_fname_seg+ext_fname_seg)
# average CSA
if slices:
os.system("sct_extract_metric -i "+path_data+name_output+" -f "+path_tmp_extract_metric+" -m wa -o ../csa_mean.txt -z "+slices)
if vert_levels:
sct.run('cp -R '+abs_path_to_template+' .')
os.system("sct_extract_metric -i "+path_data+name_output+" -f "+path_tmp_extract_metric+" -m wa -o ../csa_mean.txt -v "+vert_levels)
os.chdir('..')
# Remove temporary files
print('\nRemove temporary folder used to average CSA...')
sct.run('rm -rf '+path_tmp_extract_metric)
# Remove temporary files
if remove_temp_files:
print('\nRemove temporary files...')
sct.run('rm -rf '+path_tmp)
def compute_csa(fname_segmentation,
name_method,
volume_output,
verbose,
remove_temp_files,
step,
smoothing_param,
figure_fit,
name_output,
slices,
vert_levels,
path_to_template,
algo_fitting='hanning',
type_window='hanning',
window_length=80):
# Extract path, file and extension
fname_segmentation = os.path.abspath(fname_segmentation)
path_data, file_data, ext_data = sct.extract_fname(fname_segmentation)
# create temporary folder
sct.printv('\nCreate temporary folder...', verbose)
path_tmp = sct.slash_at_the_end('tmp.' + time.strftime("%y%m%d%H%M%S"), 1)
sct.run('mkdir ' + path_tmp, verbose)
# Copying input data to tmp folder and convert to nii
sct.printv('\nCopying input data to tmp folder and convert to nii...',
verbose)
sct.run('isct_c3d ' + fname_segmentation + ' -o ' + path_tmp +
'segmentation.nii')
# go to tmp folder
os.chdir(path_tmp)
# Change orientation of the input segmentation into RPI
sct.printv('\nChange orientation of the input segmentation into RPI...',
verbose)
fname_segmentation_orient = set_orientation('segmentation.nii', 'RPI',
'segmentation_orient.nii')
# Get size of data
sct.printv('\nGet data dimensions...', verbose)
nx, ny, nz, nt, px, py, pz, pt = Image(fname_segmentation_orient).dim
sct.printv(' ' + str(nx) + ' x ' + str(ny) + ' x ' + str(nz), verbose)
# Open segmentation volume
sct.printv('\nOpen segmentation volume...', verbose)
file_seg = nibabel.load(fname_segmentation_orient)
data_seg = file_seg.get_data()
hdr_seg = file_seg.get_header()
# # Extract min and max index in Z direction
X, Y, Z = (data_seg > 0).nonzero()
min_z_index, max_z_index = min(Z), max(Z)
# Xp, Yp = (data_seg[:, :, 0] >= 0).nonzero() # X and Y range
# extract centerline and smooth it
x_centerline_fit, y_centerline_fit, z_centerline, x_centerline_deriv, y_centerline_deriv, z_centerline_deriv = smooth_centerline(
fname_segmentation_orient,
algo_fitting=algo_fitting,
type_window=type_window,
window_length=window_length,
verbose=verbose)
z_centerline_scaled = [x * pz for x in z_centerline]
# Compute CSA
sct.printv('\nCompute CSA...', verbose)
# Empty arrays in which CSA for each z slice will be stored
csa = np.zeros(max_z_index - min_z_index + 1)
# csa = [0.0 for i in xrange(0, max_z_index-min_z_index+1)]
for iz in xrange(0, len(z_centerline)):
# compute the vector normal to the plane
normal = normalize(
np.array([
x_centerline_deriv[iz], y_centerline_deriv[iz],
z_centerline_deriv[iz]
]))
# compute the angle between the normal vector of the plane and the vector z
angle = np.arccos(np.dot(normal, [0, 0, 1]))
# compute the number of voxels, assuming the segmentation is coded for partial volume effect between 0 and 1.
number_voxels = sum(sum(data_seg[:, :, iz + min_z_index]))
# compute CSA, by scaling with voxel size (in mm) and adjusting for oblique plane
csa[iz] = number_voxels * px * py * np.cos(angle)
if smoothing_param:
from msct_smooth import smoothing_window
sct.printv('\nSmooth CSA across slices...', verbose)
sct.printv('.. Hanning window: ' + str(smoothing_param) + ' mm',
verbose)
csa_smooth = smoothing_window(csa,
window_len=smoothing_param / pz,
window='hanning',
verbose=0)
# display figure
if verbose == 2:
import matplotlib.pyplot as plt
plt.figure()
pltx, = plt.plot(z_centerline_scaled, csa, 'bo')
pltx_fit, = plt.plot(z_centerline_scaled,
csa_smooth,
'r',
linewidth=2)
plt.title("Cross-sectional area (CSA)")
plt.xlabel('z (mm)')
plt.ylabel('CSA (mm^2)')
plt.legend([pltx, pltx_fit], ['Raw', 'Smoothed'])
plt.show()
# update variable
csa = csa_smooth
# Create output text file
sct.printv('\nWrite text file...', verbose)
file_results = open('csa.txt', 'w')
for i in range(min_z_index, max_z_index + 1):
file_results.write(
str(int(i)) + ',' + str(csa[i - min_z_index]) + '\n')
# Display results
sct.printv(
'z=' + str(i - min_z_index) + ': ' + str(csa[i - min_z_index]) +
' mm^2', verbose, 'bold')
file_results.close()
# output volume of csa values
if volume_output:
sct.printv('\nCreate volume of CSA values...', verbose)
# get orientation of the input data
orientation = get_orientation('segmentation.nii')
data_seg = data_seg.astype(np.float32, copy=False)
# loop across slices
for iz in range(min_z_index, max_z_index + 1):
# retrieve seg pixels
x_seg, y_seg = (data_seg[:, :, iz] > 0).nonzero()
seg = [[x_seg[i], y_seg[i]] for i in range(0, len(x_seg))]
# loop across pixels in segmentation
for i in seg:
# replace value with csa value
data_seg[i[0], i[1], iz] = csa[iz - min_z_index]
# create header
hdr_seg.set_data_dtype('float32') # set imagetype to uint8
# save volume
img = nibabel.Nifti1Image(data_seg, None, hdr_seg)
nibabel.save(img, 'csa_RPI.nii')
# Change orientation of the output centerline into input orientation
fname_csa_volume = set_orientation('csa_RPI.nii', orientation,
'csa_RPI_orient.nii')
# come back to parent folder
os.chdir('..')
# Generate output files
sct.printv('\nGenerate output files...', verbose)
from shutil import copyfile
copyfile(path_tmp + 'csa.txt', path_data + param.fname_csa)
# sct.generate_output_file(path_tmp+'csa.txt', path_data+param.fname_csa) # extension already included in param.fname_csa
if volume_output:
sct.generate_output_file(
fname_csa_volume, path_data +
name_output) # extension already included in name_output
# average csa across vertebral levels or slices if asked (flag -z or -l)
if slices or vert_levels:
if vert_levels and not path_to_template:
sct.printv('\nERROR: Path to template is missing. See usage.\n', 1,
'error')
sys.exit(2)
elif vert_levels and path_to_template:
abs_path_to_template = os.path.abspath(path_to_template)
# go to tmp folder
os.chdir(path_tmp)
# create temporary folder
sct.printv('\nCreate temporary folder to average csa...', verbose)
path_tmp_extract_metric = sct.slash_at_the_end('label_temp', 1)
sct.run('mkdir ' + path_tmp_extract_metric, verbose)
# Copying output CSA volume in the temporary folder
sct.printv('\nCopy data to tmp folder...', verbose)
sct.run('cp ' + fname_segmentation + ' ' + path_tmp_extract_metric)
# create file info_label
path_fname_seg, file_fname_seg, ext_fname_seg = sct.extract_fname(
fname_segmentation)
create_info_label('info_label.txt', path_tmp_extract_metric,
file_fname_seg + ext_fname_seg)
# average CSA
if slices:
os.system("sct_extract_metric -i " + path_data + name_output +
" -f " + path_tmp_extract_metric +
" -m wa -o ../csa_mean.txt -z " + slices)
if vert_levels:
sct.run('cp -R ' + abs_path_to_template + ' .')
os.system("sct_extract_metric -i " + path_data + name_output +
" -f " + path_tmp_extract_metric +
" -m wa -o ../csa_mean.txt -v " + vert_levels)
os.chdir('..')
# Remove temporary files
print('\nRemove temporary folder used to average CSA...')
sct.run('rm -rf ' + path_tmp_extract_metric)
# Remove temporary files
if remove_temp_files:
print('\nRemove temporary files...')
sct.run('rm -rf ' + path_tmp)
def crop_with_gui(self):
# Initialization
fname_data = self.input_filename
suffix_out = '_crop'
remove_temp_files = self.rm_tmp_files
verbose = self.verbose
# for faster processing, all outputs are in NIFTI
fsloutput = 'export FSLOUTPUTTYPE=NIFTI; '
# Check file existence
sct.printv('\nCheck file existence...', verbose)
sct.check_file_exist(fname_data, verbose)
# Get dimensions of data
sct.printv('\nGet dimensions of data...', verbose)
nx, ny, nz, nt, px, py, pz, pt = sct.get_dimension(fname_data)
sct.printv('.. '+str(nx)+' x '+str(ny)+' x '+str(nz), verbose)
# check if 4D data
if not nt == 1:
sct.printv('\nERROR in '+os.path.basename(__file__)+': Data should be 3D.\n', 1, 'error')
sys.exit(2)
# print arguments
print '\nCheck parameters:'
print ' data ................... '+fname_data
print
# Extract path/file/extension
path_data, file_data, ext_data = sct.extract_fname(fname_data)
path_out, file_out, ext_out = '', file_data+suffix_out, ext_data
# create temporary folder
path_tmp = 'tmp.'+time.strftime("%y%m%d%H%M%S")+'/'
sct.run('mkdir '+path_tmp)
# copy files into tmp folder
sct.run('isct_c3d '+fname_data+' -o '+path_tmp+'data.nii')
# go to tmp folder
os.chdir(path_tmp)
# change orientation
sct.printv('\nChange orientation to RPI...', verbose)
set_orientation('data.nii', 'RPI', 'data_rpi.nii')
# get image of medial slab
sct.printv('\nGet image of medial slab...', verbose)
image_array = nibabel.load('data_rpi.nii').get_data()
nx, ny, nz = image_array.shape
scipy.misc.imsave('image.jpg', image_array[math.floor(nx/2), :, :])
# Display the image
sct.printv('\nDisplay image and get cropping region...', verbose)
fig = plt.figure()
# fig = plt.gcf()
# ax = plt.gca()
ax = fig.add_subplot(111)
img = mpimg.imread("image.jpg")
implot = ax.imshow(img.T)
implot.set_cmap('gray')
plt.gca().invert_yaxis()
# mouse callback
ax.set_title('Left click on the top and bottom of your cropping field.\n Right click to remove last point.\n Close window when your done.')
line, = ax.plot([], [], 'ro') # empty line
cropping_coordinates = LineBuilder(line)
plt.show()
# disconnect callback
# fig.canvas.mpl_disconnect(line)
# check if user clicked two times
if len(cropping_coordinates.xs) != 2:
sct.printv('\nERROR: You have to select two points. Exit program.\n', 1, 'error')
sys.exit(2)
# convert coordinates to integer
zcrop = [int(i) for i in cropping_coordinates.ys]
# sort coordinates
zcrop.sort()
# crop image
sct.printv('\nCrop image...', verbose)
sct.run(fsloutput+'fslroi data_rpi.nii data_rpi_crop.nii 0 -1 0 -1 '+str(zcrop[0])+' '+str(zcrop[1]-zcrop[0]+1))
# come back to parent folder
os.chdir('..')
sct.printv('\nGenerate output files...', verbose)
sct.generate_output_file(path_tmp+'data_rpi_crop.nii', path_out+file_out+ext_out)
# Remove temporary files
if remove_temp_files == 1:
print('\nRemove temporary files...')
sct.run('rm -rf '+path_tmp)
# to view results
print '\nDone! To view results, type:'
print 'fslview '+path_out+file_out+ext_out+' &'
print
def compute_csa(fname_segmentation, name_method, volume_output, verbose, remove_temp_files, spline_smoothing, step, smoothing_param, figure_fit, name_output, slices, vert_levels, path_to_template, algo_fitting = 'hanning', type_window = 'hanning', window_length = 80):
#param.algo_fitting = 'hanning'
# Extract path, file and extension
fname_segmentation = os.path.abspath(fname_segmentation)
path_data, file_data, ext_data = sct.extract_fname(fname_segmentation)
# create temporary folder
sct.printv('\nCreate temporary folder...', verbose)
path_tmp = sct.slash_at_the_end('tmp.'+time.strftime("%y%m%d%H%M%S"), 1)
sct.run('mkdir '+path_tmp, verbose)
# Copying input data to tmp folder and convert to nii
sct.printv('\nCopying input data to tmp folder and convert to nii...', verbose)
sct.run('isct_c3d '+fname_segmentation+' -o '+path_tmp+'segmentation.nii')
# go to tmp folder
os.chdir(path_tmp)
# Change orientation of the input segmentation into RPI
sct.printv('\nChange orientation of the input segmentation into RPI...', verbose)
fname_segmentation_orient = set_orientation('segmentation.nii', 'RPI', 'segmentation_orient.nii')
# Get size of data
sct.printv('\nGet data dimensions...', verbose)
nx, ny, nz, nt, px, py, pz, pt = sct.get_dimension(fname_segmentation_orient)
sct.printv(' ' + str(nx) + ' x ' + str(ny) + ' x ' + str(nz), verbose)
# Open segmentation volume
sct.printv('\nOpen segmentation volume...', verbose)
file_seg = nibabel.load(fname_segmentation_orient)
data_seg = file_seg.get_data()
hdr_seg = file_seg.get_header()
#
# # Extract min and max index in Z direction
X, Y, Z = (data_seg > 0).nonzero()
# coords_seg = np.array([str([X[i], Y[i], Z[i]]) for i in xrange(0,len(Z))]) # don't know why but finding strings in array of array of strings is WAY faster than doing the same with integers
min_z_index, max_z_index = min(Z), max(Z)
Xp,Yp = (data_seg[:,:,0]>=0).nonzero() # X and Y range
#
# x_centerline = [0 for i in xrange(0,max_z_index-min_z_index+1)]
# y_centerline = [0 for i in xrange(0,max_z_index-min_z_index+1)]
# z_centerline = np.array([iz for iz in xrange(min_z_index, max_z_index+1)])
#
# # Extract segmentation points and average per slice
# for iz in xrange(min_z_index, max_z_index+1):
# x_seg, y_seg = (data_seg[:,:,iz]>0).nonzero()
# x_centerline[iz-min_z_index] = np.mean(x_seg)
# y_centerline[iz-min_z_index] = np.mean(y_seg)
#
# # Fit the centerline points with spline and return the new fitted coordinates
# x_centerline_fit, y_centerline_fit,x_centerline_deriv,y_centerline_deriv,z_centerline_deriv = b_spline_centerline(x_centerline,y_centerline,z_centerline)
# extract centerline and smooth it
x_centerline_fit, y_centerline_fit, z_centerline, x_centerline_deriv,y_centerline_deriv,z_centerline_deriv = smooth_centerline(fname_segmentation_orient, algo_fitting=algo_fitting, type_window=type_window, window_length=window_length, verbose = verbose)
z_centerline_scaled = [x*pz for x in z_centerline]
# # 3D plot of the fit
# fig=plt.figure()
# ax=Axes3D(fig)
# ax.plot(x_centerline,y_centerline,z_centerline,zdir='z')
# ax.plot(x_centerline_fit,y_centerline_fit,z_centerline,zdir='z')
# plt.show()
# Defining cartesian basis vectors
x = np.array([1, 0, 0])
y = np.array([0, 1, 0])
z = np.array([0, 0, 1])
# Creating folder in which JPG files will be stored
sct.printv('\nCreating folder in which JPG files will be stored...', verbose)
sct.create_folder('JPG_Results')
# Compute CSA
sct.printv('\nCompute CSA...', verbose)
# Empty arrays in which CSA for each z slice will be stored
csa = [0.0 for i in xrange(0,max_z_index-min_z_index+1)]
# sections_ortho_counting = [0 for i in xrange(0,max_z_index-min_z_index+1)]
# sections_ortho_ellipse = [0 for i in xrange(0,max_z_index-min_z_index+1)]
# sections_z_ellipse = [0 for i in xrange(0,max_z_index-min_z_index+1)]
# sections_z_counting = [0 for i in xrange(0,max_z_index-min_z_index+1)]
sct.printv('\nCross-Section Area:', verbose, 'bold')
for iz in xrange(0, len(z_centerline)):
# Equation of the the plane which is orthogonal to the spline at z=iz
a = x_centerline_deriv[iz]
b = y_centerline_deriv[iz]
c = z_centerline_deriv[iz]
#vector normal to the plane
normal = normalize(np.array([a, b, c]))
# angle between normal vector and z
angle = np.arccos(np.dot(normal, z))
if name_method == 'counting_ortho_plane' or name_method == 'ellipse_ortho_plane':
x_center = x_centerline_fit[iz]
y_center = y_centerline_fit[iz]
z_center = z_centerline[iz]
# use of x in order to get orientation of each plane, basis_1 is in the plane ax+by+cz+d=0
basis_1 = normalize(np.cross(normal,x))
basis_2 = normalize(np.cross(normal,basis_1))
# maximum dimension of the tilted plane. Try multiply numerator by sqrt(2) ?
max_diameter = (max([(max(X)-min(X))*px,(max(Y)-min(Y))*py]))/(np.cos(angle))
# Forcing the step to be the min of x and y scale (default value is 1 mm)
step = min([px,py])
# discretized plane which will be filled with 0/1
plane_seg = np.zeros((int(max_diameter/step),int(max_diameter/step)))
# how the plane will be skimmed through
plane_grid = np.linspace(-int(max_diameter/2),int(max_diameter/2),int(max_diameter/step))
# we go through the plane
for i_b1 in plane_grid :
for i_b2 in plane_grid :
point = np.array([x_center*px,y_center*py,z_center*pz]) + i_b1*basis_1 +i_b2*basis_2
# to which voxel belongs each point of the plane
coord_voxel = str([ int(point[0]/px), int(point[1]/py), int(point[2]/pz)])
if (coord_voxel in coords_seg) is True : # if this voxel is 1
plane_seg[int((plane_grid==i_b1).nonzero()[0])][int((plane_grid==i_b2).nonzero()[0])] = 1
# number of voxels that are in the intersection of each plane and the nonzeros values of segmentation, times the area of one cell of the discretized plane
if name_method == 'counting_ortho_plane':
csa[iz] = len((plane_seg>0).nonzero()[0])*step*step
# if verbose ==1 and name_method == 'counting_ortho_plane' :
# print('Cross-Section Area : ' + str(csa[iz]) + ' mm^2')
if name_method == 'ellipse_ortho_plane':
# import scipy stuff
from scipy.misc import imsave
os.chdir('JPG_Results')
imsave('plane_ortho_' + str(iz) + '.jpg', plane_seg)
# Tresholded gradient image
mag = edge_detection('plane_ortho_' + str(iz) + '.jpg')
#Coordinates of the contour
x_contour,y_contour = (mag>0).nonzero()
x_contour = x_contour*step
y_contour = y_contour*step
#Fitting an ellipse
fit = Ellipse_fit(x_contour,y_contour)
# Semi-minor axis, semi-major axis
a_ellipse, b_ellipse = ellipse_dim(fit)
#Section = pi*a*b
csa[iz] = a_ellipse*b_ellipse*np.pi
# if verbose == 1 and name_method == 'ellipse_ortho_plane':
# print('Cross-Section Area : ' + str(csa[iz]) + ' mm^2')
# os.chdir('..')
if name_method == 'counting_z_plane' or name_method == 'ellipse_z_plane':
# getting the segmentation for each z plane
x_seg, y_seg = (data_seg[:, :, iz+min_z_index] > 0).nonzero()
seg = [[x_seg[i], y_seg[i]] for i in range(0, len(x_seg))]
plane = np.zeros((max(Xp), max(Yp)))
for i in seg:
# filling the plane with 0 and 1 regarding to the segmentation
plane[i[0] - 1][i[1] - 1] = data_seg[i[0] - 1, i[1] - 1, iz+min_z_index]
if name_method == 'counting_z_plane':
x, y = (plane > 0.0).nonzero()
len_x = len(x)
for i in range(0, len_x):
csa[iz] += plane[x[i], y[i]]*px*py
csa[iz] *= np.cos(angle)
# if verbose == 1 and name_method == 'counting_z_plane':
# print('Cross-Section Area : ' + str(csa[iz]) + ' mm^2')
if name_method == 'ellipse_z_plane':
# import scipy stuff
from scipy.misc import imsave
os.chdir('JPG_Results')
imsave('plane_z_' + str(iz) + '.jpg', plane)
# Tresholded gradient image
mag = edge_detection('plane_z_' + str(iz) + '.jpg')
x_contour,y_contour = (mag>0).nonzero()
x_contour = x_contour*px
y_contour = y_contour*py
# Fitting an ellipse
fit = Ellipse_fit(x_contour,y_contour)
a_ellipse, b_ellipse = ellipse_dim(fit)
csa[iz] = a_ellipse*b_ellipse*np.pi*np.cos(angle)
# if verbose == 1 and name_method == 'ellipse_z_plane':
# print('Cross-Section Area : ' + str(csa[iz]) + ' mm^2')
if spline_smoothing == 1:
sct.printv('\nSmoothing results with spline...', verbose)
tck = scipy.interpolate.splrep(z_centerline_scaled, csa, s=smoothing_param)
csa_smooth = scipy.interpolate.splev(z_centerline_scaled, tck)
if figure_fit == 1:
import matplotlib.pyplot as plt
plt.figure()
plt.plot(z_centerline_scaled, csa)
plt.plot(z_centerline_scaled, csa_smooth)
plt.legend(['CSA values', 'Smoothed values'], 2)
plt.savefig('Spline_fit.png')
csa = csa_smooth # update variable
# Create output text file
sct.printv('\nWrite text file...', verbose)
file_results = open('csa.txt', 'w')
for i in range(min_z_index, max_z_index+1):
file_results.write(str(int(i)) + ',' + str(csa[i-min_z_index])+'\n')
# Display results
sct.printv('z='+str(i-min_z_index)+': '+str(csa[i-min_z_index])+' mm^2', verbose, 'bold')
file_results.close()
# output volume of csa values
if volume_output:
sct.printv('\nCreate volume of CSA values...', verbose)
# get orientation of the input data
orientation = get_orientation('segmentation.nii')
data_seg = data_seg.astype(np.float32, copy=False)
# loop across slices
for iz in range(min_z_index, max_z_index+1):
# retrieve seg pixels
x_seg, y_seg = (data_seg[:, :, iz] > 0).nonzero()
seg = [[x_seg[i],y_seg[i]] for i in range(0, len(x_seg))]
# loop across pixels in segmentation
for i in seg:
# replace value with csa value
data_seg[i[0], i[1], iz] = csa[iz-min_z_index]
# create header
hdr_seg.set_data_dtype('float32') # set imagetype to uint8
# save volume
img = nibabel.Nifti1Image(data_seg, None, hdr_seg)
nibabel.save(img, 'csa_RPI.nii')
# Change orientation of the output centerline into input orientation
fname_csa_volume = set_orientation('csa_RPI.nii', orientation, 'csa_RPI_orient.nii')
# come back to parent folder
os.chdir('..')
# Generate output files
sct.printv('\nGenerate output files...', verbose)
sct.generate_output_file(path_tmp+'csa.txt', path_data+param.fname_csa) # extension already included in param.fname_csa
if volume_output:
sct.generate_output_file(fname_csa_volume, path_data+name_output) # extension already included in name_output
# average csa across vertebral levels or slices if asked (flag -z or -l)
if slices or vert_levels:
if vert_levels and not path_to_template:
sct.printv('\nERROR: Path to template is missing. See usage.\n', 1, 'error')
sys.exit(2)
elif vert_levels and path_to_template:
abs_path_to_template = os.path.abspath(path_to_template)
# go to tmp folder
os.chdir(path_tmp)
# create temporary folder
sct.printv('\nCreate temporary folder to average csa...', verbose)
path_tmp_extract_metric = sct.slash_at_the_end('label_temp', 1)
sct.run('mkdir '+path_tmp_extract_metric, verbose)
# Copying output CSA volume in the temporary folder
sct.printv('\nCopy data to tmp folder...', verbose)
sct.run('cp '+fname_segmentation+' '+path_tmp_extract_metric)
# create file info_label
path_fname_seg, file_fname_seg, ext_fname_seg = sct.extract_fname(fname_segmentation)
create_info_label('info_label.txt', path_tmp_extract_metric, file_fname_seg+ext_fname_seg)
if slices:
# average CSA
os.system("sct_extract_metric -i "+path_data+name_output+" -f "+path_tmp_extract_metric+" -m wa -o "+sct.slash_at_the_end(path_data)+"mean_csa -z "+slices)
if vert_levels:
sct.run('cp -R '+abs_path_to_template+' .')
# average CSA
os.system("sct_extract_metric -i "+path_data+name_output+" -f "+path_tmp_extract_metric+" -m wa -o "+sct.slash_at_the_end(path_data)+"mean_csa -v "+vert_levels)
os.chdir('..')
# Remove temporary files
print('\nRemove temporary folder used to average CSA...')
sct.run('rm -rf '+path_tmp_extract_metric)
# Remove temporary files
if remove_temp_files:
print('\nRemove temporary files...')
sct.run('rm -rf '+path_tmp)
def main(segmentation_file=None,
label_file=None,
output_file_name=None,
parameter="binary_centerline",
remove_temp_files=1,
verbose=0):
#Process for a binary file as output:
if parameter == "binary_centerline":
# Binary_centerline: Process for only a segmentation file:
if "-i" in arguments and "-l" not in arguments:
# Extract path, file and extension
segmentation_file = os.path.abspath(segmentation_file)
path_data, file_data, ext_data = sct.extract_fname(
segmentation_file)
# create temporary folder
path_tmp = 'tmp.' + time.strftime("%y%m%d%H%M%S")
sct.run('mkdir ' + path_tmp)
# copy files into tmp folder
sct.run('cp ' + segmentation_file + ' ' + path_tmp)
# go to tmp folder
os.chdir(path_tmp)
# Change orientation of the input segmentation into RPI
print '\nOrient segmentation image to RPI orientation...'
fname_segmentation_orient = 'tmp.segmentation_rpi' + ext_data
set_orientation(file_data + ext_data, 'RPI',
fname_segmentation_orient)
# Extract orientation of the input segmentation
orientation = get_orientation(file_data + ext_data)
print '\nOrientation of segmentation image: ' + orientation
# Get size of data
print '\nGet dimensions data...'
nx, ny, nz, nt, px, py, pz, pt = sct.get_dimension(
fname_segmentation_orient)
print '.. ' + str(nx) + ' x ' + str(ny) + ' y ' + str(
nz) + ' z ' + str(nt)
print '\nOpen segmentation volume...'
file = nibabel.load(fname_segmentation_orient)
data = file.get_data()
hdr = file.get_header()
# Extract min and max index in Z direction
X, Y, Z = (data > 0).nonzero()
min_z_index, max_z_index = min(Z), max(Z)
x_centerline = [0 for i in range(0, max_z_index - min_z_index + 1)]
y_centerline = [0 for i in range(0, max_z_index - min_z_index + 1)]
z_centerline = [iz for iz in range(min_z_index, max_z_index + 1)]
# Extract segmentation points and average per slice
for iz in range(min_z_index, max_z_index + 1):
x_seg, y_seg = (data[:, :, iz] > 0).nonzero()
x_centerline[iz - min_z_index] = np.mean(x_seg)
y_centerline[iz - min_z_index] = np.mean(y_seg)
#ne sert a rien
for k in range(len(X)):
data[X[k], Y[k], Z[k]] = 0
print len(x_centerline)
# Fit the centerline points with splines and return the new fitted coordinates
#done with nurbs for now
x_centerline_fit, y_centerline_fit, x_centerline_deriv, y_centerline_deriv, z_centerline_deriv = b_spline_centerline(
x_centerline, y_centerline, z_centerline)
# Create an image with the centerline
for iz in range(min_z_index, max_z_index + 1):
data[round(x_centerline_fit[iz - min_z_index]),
round(y_centerline_fit[iz - min_z_index]),
iz] = 1 #with nurbs fitting
#data[round(x_centerline[iz-min_z_index]), round(y_centerline[iz-min_z_index]), iz] = 1 #without nurbs fitting
# Write the centerline image in RPI orientation
hdr.set_data_dtype('uint8') # set imagetype to uint8
print '\nWrite NIFTI volumes...'
img = nibabel.Nifti1Image(data, None, hdr)
if output_file_name != None:
file_name = output_file_name
else:
file_name = file_data + '_centerline' + ext_data
nibabel.save(img, 'tmp.centerline.nii')
sct.generate_output_file('tmp.centerline.nii', file_name)
del data
# come back to parent folder
os.chdir('..')
# Change orientation of the output centerline into input orientation
print '\nOrient centerline image to input orientation: ' + orientation
set_orientation(path_tmp + '/' + file_name, orientation, file_name)
# Remove temporary files
if remove_temp_files:
print('\nRemove temporary files...')
sct.run('rm -rf ' + path_tmp)
return file_name
# Binary_centerline: Process for only a label file:
if "-l" in arguments and "-i" not in arguments:
file = os.path.abspath(label_file)
path_data, file_data, ext_data = sct.extract_fname(file)
file = nibabel.load(label_file)
data = file.get_data()
hdr = file.get_header()
X, Y, Z = (data > 0).nonzero()
Z_new = np.linspace(min(Z), max(Z), (max(Z) - min(Z) + 1))
# sort X and Y arrays using Z
X = [X[i] for i in Z[:].argsort()]
Y = [Y[i] for i in Z[:].argsort()]
Z = [Z[i] for i in Z[:].argsort()]
#print X, Y, Z
f1 = interpolate.UnivariateSpline(Z, X)
f2 = interpolate.UnivariateSpline(Z, Y)
X_fit = f1(Z_new)
Y_fit = f2(Z_new)
#print X_fit
#print Y_fit
if verbose == 1:
import matplotlib.pyplot as plt
plt.figure()
plt.plot(Z_new, X_fit)
plt.plot(Z, X, 'o', linestyle='None')
plt.show()
plt.figure()
plt.plot(Z_new, Y_fit)
plt.plot(Z, Y, 'o', linestyle='None')
plt.show()
data = data * 0
for i in xrange(len(X_fit)):
data[X_fit[i], Y_fit[i], Z_new[i]] = 1
# Create NIFTI image
print '\nSave volume ...'
hdr.set_data_dtype('float32') # set image type to uint8
img = nibabel.Nifti1Image(data, None, hdr)
if output_file_name != None:
file_name = output_file_name
else:
file_name = file_data + '_centerline' + ext_data
# save volume
nibabel.save(img, file_name)
print '\nFile created : ' + file_name
del data
#### Binary_centerline: Process for a segmentation file and a label file:
if "-l" and "-i" in arguments:
## Creation of a temporary file that will contain each centerline file of the process
path_tmp = 'tmp.' + time.strftime("%y%m%d%H%M%S")
sct.run('mkdir ' + path_tmp)
##From label file create centerline image
print '\nPROCESS PART 1: From label file create centerline image.'
file_label = os.path.abspath(label_file)
path_data_label, file_data_label, ext_data_label = sct.extract_fname(
file_label)
file_label = nibabel.load(label_file)
#Copy label_file into temporary folder
sct.run('cp ' + label_file + ' ' + path_tmp)
data_label = file_label.get_data()
hdr_label = file_label.get_header()
if verbose == 1:
from copy import copy
data_label_to_show = copy(data_label)
X, Y, Z = (data_label > 0).nonzero()
Z_new = np.linspace(min(Z), max(Z), (max(Z) - min(Z) + 1))
# sort X and Y arrays using Z
X = [X[i] for i in Z[:].argsort()]
Y = [Y[i] for i in Z[:].argsort()]
Z = [Z[i] for i in Z[:].argsort()]
#print X, Y, Z
f1 = interpolate.UnivariateSpline(Z, X)
f2 = interpolate.UnivariateSpline(Z, Y)
X_fit = f1(Z_new)
Y_fit = f2(Z_new)
#print X_fit
#print Y_fit
if verbose == 1:
import matplotlib.pyplot as plt
plt.figure()
plt.plot(Z_new, X_fit)
plt.plot(Z, X, 'o', linestyle='None')
plt.show()
plt.figure()
plt.plot(Z_new, Y_fit)
plt.plot(Z, Y, 'o', linestyle='None')
plt.show()
data_label = data_label * 0
for i in xrange(len(X_fit)):
data_label[X_fit[i], Y_fit[i], Z_new[i]] = 1
# Create NIFTI image
print '\nSave volume ...'
hdr_label.set_data_dtype('float32') # set image type to uint8
img = nibabel.Nifti1Image(data_label, None, hdr_label)
# save volume
file_name_label = file_data_label + '_centerline' + ext_data_label
nibabel.save(img, file_name_label)
print '\nFile created : ' + file_name_label
# copy files into tmp folder
sct.run('cp ' + file_name_label + ' ' + path_tmp)
#effacer fichier dans folder parent
os.remove(file_name_label)
del data_label
##From segmentation file create centerline image
print '\nPROCESS PART 2: From segmentation file create centerline image.'
# Extract path, file and extension
segmentation_file = os.path.abspath(segmentation_file)
path_data_seg, file_data_seg, ext_data_seg = sct.extract_fname(
segmentation_file)
# copy files into tmp folder
sct.run('cp ' + segmentation_file + ' ' + path_tmp)
# go to tmp folder
os.chdir(path_tmp)
# Change orientation of the input segmentation into RPI
print '\nOrient segmentation image to RPI orientation...'
fname_segmentation_orient = 'tmp.segmentation_rpi' + ext_data_seg
set_orientation(file_data_seg + ext_data_seg, 'RPI',
fname_segmentation_orient)
# Extract orientation of the input segmentation
orientation = get_orientation(file_data_seg + ext_data_seg)
print '\nOrientation of segmentation image: ' + orientation
# Get size of data
print '\nGet dimensions data...'
nx, ny, nz, nt, px, py, pz, pt = sct.get_dimension(
fname_segmentation_orient)
print '.. ' + str(nx) + ' x ' + str(ny) + ' y ' + str(
nz) + ' z ' + str(nt)
print '\nOpen segmentation volume...'
file_seg = nibabel.load(fname_segmentation_orient)
data_seg = file_seg.get_data()
hdr_seg = file_seg.get_header()
if verbose == 1:
data_seg_to_show = copy(data_seg)
# Extract min and max index in Z direction
X, Y, Z = (data_seg > 0).nonzero()
min_z_index, max_z_index = min(Z), max(Z)
x_centerline = [0 for i in range(0, max_z_index - min_z_index + 1)]
y_centerline = [0 for i in range(0, max_z_index - min_z_index + 1)]
z_centerline = [iz for iz in range(min_z_index, max_z_index + 1)]
# Extract segmentation points and average per slice
for iz in range(min_z_index, max_z_index + 1):
x_seg, y_seg = (data_seg[:, :, iz] > 0).nonzero()
x_centerline[iz - min_z_index] = np.mean(x_seg)
y_centerline[iz - min_z_index] = np.mean(y_seg)
for k in range(len(X)):
data_seg[X[k], Y[k], Z[k]] = 0
# Fit the centerline points with splines and return the new fitted coordinates
#done with nurbs for now
x_centerline_fit, y_centerline_fit, x_centerline_deriv, y_centerline_deriv, z_centerline_deriv = b_spline_centerline(
x_centerline, y_centerline, z_centerline)
# Create an image with the centerline
for iz in range(min_z_index, max_z_index + 1):
data_seg[round(x_centerline_fit[iz - min_z_index]),
round(y_centerline_fit[iz - min_z_index]), iz] = 1
# Write the centerline image in RPI orientation
hdr_seg.set_data_dtype('uint8') # set imagetype to uint8
print '\nWrite NIFTI volumes...'
img = nibabel.Nifti1Image(data_seg, None, hdr_seg)
nibabel.save(img, 'tmp.centerline.nii')
file_name_seg = file_data_seg + '_centerline' + ext_data_seg
sct.generate_output_file('tmp.centerline.nii',
file_name_seg) #pb ici
# copy files into parent folder
#sct.run('cp '+file_name_seg+' ../')
del data_seg
# come back to parent folder
# os.chdir('..')
# Change orientation of the output centerline into input orientation
print '\nOrient centerline image to input orientation: ' + orientation
set_orientation(file_name_seg, orientation, file_name_seg)
print '\nRemoving overlap of the centerline obtain with label file if there are any:'
## Remove overlap from centerline file obtain with label file
remove_overlap(file_name_label, file_name_seg,
"generated_centerline_without_overlap.nii.gz")
## Concatenation of the two centerline files
print '\nConcatenation of the two centerline files:'
if output_file_name != None:
file_name = output_file_name
else:
file_name = 'centerline_total_from_label_and_seg'
sct.run(
'fslmaths generated_centerline_without_overlap.nii.gz -add ' +
file_name_seg + ' ' + file_name)
if verbose == 1:
import matplotlib.pyplot as plt
from scipy import ndimage
#Get back concatenation of segmentation and labels before any processing
data_concatenate = data_seg_to_show + data_label_to_show
z_centerline = [
iz for iz in range(0, nz, 1)
if data_concatenate[:, :, iz].any()
]
nz_nonz = len(z_centerline)
x_centerline = [0 for iz in range(0, nz_nonz, 1)]
y_centerline = [0 for iz in range(0, nz_nonz, 1)]
# Calculate centerline coordinates and create image of the centerline
for iz in range(0, nz_nonz, 1):
x_centerline[iz], y_centerline[
iz] = ndimage.measurements.center_of_mass(
data_concatenate[:, :, z_centerline[iz]])
#Load file with resulting centerline
file_centerline_fit = nibabel.load(file_name)
data_centerline_fit = file_centerline_fit.get_data()
z_centerline_fit = [
iz for iz in range(0, nz, 1)
if data_centerline_fit[:, :, iz].any()
]
nz_nonz_fit = len(z_centerline_fit)
x_centerline_fit_total = [0 for iz in range(0, nz_nonz_fit, 1)]
y_centerline_fit_total = [0 for iz in range(0, nz_nonz_fit, 1)]
#Convert to array
x_centerline_fit_total = np.asarray(x_centerline_fit_total)
y_centerline_fit_total = np.asarray(y_centerline_fit_total)
#Calculate overlap between seg and label
length_overlap = X_fit.shape[0] + x_centerline_fit.shape[
0] - x_centerline_fit_total.shape[0]
# The total fitting is the concatenation of the two fitting (
for i in range(x_centerline_fit.shape[0]):
x_centerline_fit_total[i] = x_centerline_fit[i]
y_centerline_fit_total[i] = y_centerline_fit[i]
for i in range(X_fit.shape[0] - length_overlap):
x_centerline_fit_total[x_centerline_fit.shape[0] +
i] = X_fit[i + length_overlap]
y_centerline_fit_total[x_centerline_fit.shape[0] +
i] = Y_fit[i + length_overlap]
print x_centerline_fit.shape[0] + i
#for iz in range(0, nz_nonz_fit, 1):
# x_centerline_fit[iz], y_centerline_fit[iz] = ndimage.measurements.center_of_mass(data_centerline_fit[:, :, z_centerline_fit[iz]])
#Creation of a vector x that takes into account the distance between the labels
#x_centerline_fit = np.asarray(x_centerline_fit)
#y_centerline_fit = np.asarray(y_centerline_fit)
x_display = [0 for i in range(x_centerline_fit_total.shape[0])]
y_display = [0 for i in range(y_centerline_fit_total.shape[0])]
for i in range(0, nz_nonz, 1):
x_display[z_centerline[i] -
z_centerline[0]] = x_centerline[i]
y_display[z_centerline[i] -
z_centerline[0]] = y_centerline[i]
plt.figure(1)
plt.subplot(2, 1, 1)
plt.plot(z_centerline_fit, x_display, 'ro')
plt.plot(z_centerline_fit, x_centerline_fit_total)
plt.xlabel("Z")
plt.ylabel("X")
plt.title("x and x_fit coordinates")
plt.subplot(2, 1, 2)
plt.plot(z_centerline_fit, y_display, 'ro')
plt.plot(z_centerline_fit, y_centerline_fit_total)
plt.xlabel("Z")
plt.ylabel("Y")
plt.title("y and y_fit coordinates")
plt.show()
del data_concatenate, data_label_to_show, data_seg_to_show, data_centerline_fit
sct.run('cp ' + file_name + ' ../')
# Copy result into parent folder
sct.run('cp ' + file_name + ' ../')
# Come back to parent folder
os.chdir('..')
# Remove temporary centerline files
if remove_temp_files:
print('\nRemove temporary files...')
sct.run('rm -rf ' + path_tmp)
#Process for a text file as output:
if parameter == "text_file":
print "\nText file process"
#Process for only a segmentation file:
if "-i" in arguments and "-l" not in arguments:
# Extract path, file and extension
segmentation_file = os.path.abspath(segmentation_file)
path_data, file_data, ext_data = sct.extract_fname(
segmentation_file)
# create temporary folder
path_tmp = 'tmp.' + time.strftime("%y%m%d%H%M%S")
sct.run('mkdir ' + path_tmp)
# copy files into tmp folder
sct.run('cp ' + segmentation_file + ' ' + path_tmp)
# go to tmp folder
os.chdir(path_tmp)
# Change orientation of the input segmentation into RPI
print '\nOrient segmentation image to RPI orientation...'
fname_segmentation_orient = 'tmp.segmentation_rpi' + ext_data
set_orientation(file_data + ext_data, 'RPI',
fname_segmentation_orient)
# Extract orientation of the input segmentation
orientation = get_orientation(file_data + ext_data)
print '\nOrientation of segmentation image: ' + orientation
# Get size of data
print '\nGet dimensions data...'
nx, ny, nz, nt, px, py, pz, pt = sct.get_dimension(
fname_segmentation_orient)
print '.. ' + str(nx) + ' x ' + str(ny) + ' y ' + str(
nz) + ' z ' + str(nt)
print '\nOpen segmentation volume...'
file = nibabel.load(fname_segmentation_orient)
data = file.get_data()
hdr = file.get_header()
# Extract min and max index in Z direction
X, Y, Z = (data > 0).nonzero()
min_z_index, max_z_index = min(Z), max(Z)
x_centerline = [0 for i in range(0, max_z_index - min_z_index + 1)]
y_centerline = [0 for i in range(0, max_z_index - min_z_index + 1)]
z_centerline = [iz for iz in range(min_z_index, max_z_index + 1)]
# Extract segmentation points and average per slice
for iz in range(min_z_index, max_z_index + 1):
x_seg, y_seg = (data[:, :, iz] > 0).nonzero()
x_centerline[iz - min_z_index] = np.mean(x_seg)
y_centerline[iz - min_z_index] = np.mean(y_seg)
for k in range(len(X)):
data[X[k], Y[k], Z[k]] = 0
# Fit the centerline points with splines and return the new fitted coordinates
x_centerline_fit, y_centerline_fit, x_centerline_deriv, y_centerline_deriv, z_centerline_deriv = b_spline_centerline(
x_centerline, y_centerline, z_centerline)
# Create output text file
if output_file_name != None:
file_name = output_file_name
else:
file_name = file_data + '_centerline' + '.txt'
sct.printv('\nWrite text file...', verbose)
#file_results = open("../"+file_name, 'w')
file_results = open(file_name, 'w')
for i in range(min_z_index, max_z_index + 1):
file_results.write(
str(int(i)) + ' ' +
str(x_centerline_fit[i - min_z_index]) + ' ' +
str(y_centerline_fit[i - min_z_index]) + '\n')
file_results.close()
# Copy result into parent folder
sct.run('cp ' + file_name + ' ../')
del data
# come back to parent folder
os.chdir('..')
# Remove temporary files
if remove_temp_files:
print('\nRemove temporary files...')
sct.run('rm -rf ' + path_tmp)
return file_name
#Process for only a label file:
if "-l" in arguments and "-i" not in arguments:
file = os.path.abspath(label_file)
path_data, file_data, ext_data = sct.extract_fname(file)
file = nibabel.load(label_file)
data = file.get_data()
hdr = file.get_header()
X, Y, Z = (data > 0).nonzero()
Z_new = np.linspace(min(Z), max(Z), (max(Z) - min(Z) + 1))
# sort X and Y arrays using Z
X = [X[i] for i in Z[:].argsort()]
Y = [Y[i] for i in Z[:].argsort()]
Z = [Z[i] for i in Z[:].argsort()]
#print X, Y, Z
f1 = interpolate.UnivariateSpline(Z, X)
f2 = interpolate.UnivariateSpline(Z, Y)
X_fit = f1(Z_new)
Y_fit = f2(Z_new)
#print X_fit
#print Y_fit
if verbose == 1:
import matplotlib.pyplot as plt
plt.figure()
plt.plot(Z_new, X_fit)
plt.plot(Z, X, 'o', linestyle='None')
plt.show()
plt.figure()
plt.plot(Z_new, Y_fit)
plt.plot(Z, Y, 'o', linestyle='None')
plt.show()
data = data * 0
for iz in xrange(len(X_fit)):
data[X_fit[iz], Y_fit[iz], Z_new[iz]] = 1
# Create output text file
sct.printv('\nWrite text file...', verbose)
if output_file_name != None:
file_name = output_file_name
else:
file_name = file_data + '_centerline' + ext_data
file_results = open(file_name, 'w')
min_z_index, max_z_index = min(Z), max(Z)
for i in range(min_z_index, max_z_index + 1):
file_results.write(
str(int(i)) + ' ' + str(X_fit[i - min_z_index]) + ' ' +
str(Y_fit[i - min_z_index]) + '\n')
file_results.close()
del data
#Process for a segmentation file and a label file:
if "-l" and "-i" in arguments:
## Creation of a temporary file that will contain each centerline file of the process
path_tmp = 'tmp.' + time.strftime("%y%m%d%H%M%S")
sct.run('mkdir ' + path_tmp)
##From label file create centerline text file
print '\nPROCESS PART 1: From label file create centerline text file.'
file_label = os.path.abspath(label_file)
path_data_label, file_data_label, ext_data_label = sct.extract_fname(
file_label)
file_label = nibabel.load(label_file)
#Copy label_file into temporary folder
sct.run('cp ' + label_file + ' ' + path_tmp)
data_label = file_label.get_data()
hdr_label = file_label.get_header()
X, Y, Z = (data_label > 0).nonzero()
Z_new = np.linspace(min(Z), max(Z), (max(Z) - min(Z) + 1))
# sort X and Y arrays using Z
X = [X[i] for i in Z[:].argsort()]
Y = [Y[i] for i in Z[:].argsort()]
Z = [Z[i] for i in Z[:].argsort()]
#print X, Y, Z
f1 = interpolate.UnivariateSpline(Z, X)
f2 = interpolate.UnivariateSpline(Z, Y)
X_fit = f1(Z_new)
Y_fit = f2(Z_new)
#print X_fit
#print Y_fit
if verbose == 1:
import matplotlib.pyplot as plt
plt.figure()
plt.plot(Z_new, X_fit)
plt.plot(Z, X, 'o', linestyle='None')
plt.show()
plt.figure()
plt.plot(Z_new, Y_fit)
plt.plot(Z, Y, 'o', linestyle='None')
plt.show()
data_label = data_label * 0
for i in xrange(len(X_fit)):
data_label[X_fit[i], Y_fit[i], Z_new[i]] = 1
# Create output text file
sct.printv('\nWrite text file...', verbose)
file_name_label = file_data_label + '_centerline' + '.txt'
file_results = open(path_tmp + '/' + file_name_label, 'w')
min_z_index, max_z_index = min(Z), max(Z)
for i in range(min_z_index, max_z_index + 1):
file_results.write(
str(int(i)) + ' ' + str(X_fit[i - min_z_index]) + ' ' +
str(Y_fit[i - min_z_index]) + '\n')
file_results.close()
# copy files into tmp folder
#sct.run('cp '+file_name_label+' '+path_tmp)
del data_label
##From segmentation file create centerline text file
print '\nPROCESS PART 2: From segmentation file create centerline image.'
# Extract path, file and extension
segmentation_file = os.path.abspath(segmentation_file)
path_data_seg, file_data_seg, ext_data_seg = sct.extract_fname(
segmentation_file)
# copy files into tmp folder
sct.run('cp ' + segmentation_file + ' ' + path_tmp)
# go to tmp folder
os.chdir(path_tmp)
# Change orientation of the input segmentation into RPI
print '\nOrient segmentation image to RPI orientation...'
fname_segmentation_orient = 'tmp.segmentation_rpi' + ext_data_seg
set_orientation(file_data_seg + ext_data_seg, 'RPI',
fname_segmentation_orient)
# Extract orientation of the input segmentation
orientation = get_orientation(file_data_seg + ext_data_seg)
print '\nOrientation of segmentation image: ' + orientation
# Get size of data
print '\nGet dimensions data...'
nx, ny, nz, nt, px, py, pz, pt = sct.get_dimension(
fname_segmentation_orient)
print '.. ' + str(nx) + ' x ' + str(ny) + ' y ' + str(
nz) + ' z ' + str(nt)
print '\nOpen segmentation volume...'
file_seg = nibabel.load(fname_segmentation_orient)
data_seg = file_seg.get_data()
hdr_seg = file_seg.get_header()
# Extract min and max index in Z direction
X, Y, Z = (data_seg > 0).nonzero()
min_z_index, max_z_index = min(Z), max(Z)
x_centerline = [0 for i in range(0, max_z_index - min_z_index + 1)]
y_centerline = [0 for i in range(0, max_z_index - min_z_index + 1)]
z_centerline = [iz for iz in range(min_z_index, max_z_index + 1)]
# Extract segmentation points and average per slice
for iz in range(min_z_index, max_z_index + 1):
x_seg, y_seg = (data_seg[:, :, iz] > 0).nonzero()
x_centerline[iz - min_z_index] = np.mean(x_seg)
y_centerline[iz - min_z_index] = np.mean(y_seg)
for k in range(len(X)):
data_seg[X[k], Y[k], Z[k]] = 0
# Fit the centerline points with splines and return the new fitted coordinates
#done with nurbs for now
x_centerline_fit, y_centerline_fit, x_centerline_deriv, y_centerline_deriv, z_centerline_deriv = b_spline_centerline(
x_centerline, y_centerline, z_centerline)
# Create output text file
file_name_seg = file_data_seg + '_centerline' + '.txt'
sct.printv('\nWrite text file...', verbose)
file_results = open(file_name_seg, 'w')
for i in range(min_z_index, max_z_index + 1):
file_results.write(
str(int(i)) + ' ' +
str(x_centerline_fit[i - min_z_index]) + ' ' +
str(y_centerline_fit[i - min_z_index]) + '\n')
file_results.close()
del data_seg
print '\nRemoving overlap of the centerline obtain with label file if there are any:'
## Remove overlap from centerline file obtain with label file
remove_overlap(file_name_label,
file_name_seg,
"generated_centerline_without_overlap1.txt",
parameter=1)
## Concatenation of the two centerline files
print '\nConcatenation of the two centerline files:'
if output_file_name != None:
file_name = output_file_name
else:
file_name = 'centerline_total_from_label_and_seg.txt'
f_output = open(file_name, "w")
f_output.close()
with open(file_name_seg, "r") as f_seg:
with open("generated_centerline_without_overlap1.txt",
"r") as f:
with open(file_name, "w") as f_output:
data_line_seg = f_seg.readlines()
data_line = f.readlines()
for line in data_line_seg:
f_output.write(line)
for line in data_line:
f_output.write(line)
# Copy result into parent folder
sct.run('cp ' + file_name + ' ../')
# Come back to parent folder
os.chdir('..')
# Remove temporary centerline files
if remove_temp_files:
print('\nRemove temporary files...')
sct.run('rm -rf ' + path_tmp)
def main():
# Initialization
fname_anat = ''
fname_centerline = ''
gapxy = param.gapxy
gapz = param.gapz
padding = param.padding
remove_temp_files = param.remove_temp_files
verbose = param.verbose
interpolation_warp = param.interpolation_warp
algo_fitting = param.algo_fitting
window_length = param.window_length
type_window = param.type_window
crop = param.crop
# start timer
start_time = time.time()
# get path of the toolbox
status, path_sct = commands.getstatusoutput('echo $SCT_DIR')
print path_sct
# Parameters for debug mode
if param.debug == 1:
print '\n*** WARNING: DEBUG MODE ON ***\n'
fname_anat = '/Users/julien/data/temp/sct_example_data/t2/tmp.150401221259/anat_rpi.nii' #path_sct+'/testing/sct_testing_data/data/t2/t2.nii.gz'
fname_centerline = '/Users/julien/data/temp/sct_example_data/t2/tmp.150401221259/centerline_rpi.nii' # path_sct+'/testing/sct_testing_data/data/t2/t2_seg.nii.gz'
remove_temp_files = 0
type_window = 'hanning'
verbose = 2
else:
# Check input param
try:
opts, args = getopt.getopt(sys.argv[1:],'hi:c:p:r:v:x:a:f:')
except getopt.GetoptError as err:
print str(err)
usage()
if not opts:
usage()
for opt, arg in opts:
if opt == '-h':
usage()
elif opt in ('-i'):
fname_anat = arg
elif opt in ('-c'):
fname_centerline = arg
elif opt in ('-r'):
remove_temp_files = int(arg)
elif opt in ('-p'):
padding = int(arg)
elif opt in ('-x'):
interpolation_warp = str(arg)
elif opt in ('-a'):
algo_fitting = str(arg)
elif opt in ('-f'):
crop = int(arg)
# elif opt in ('-f'):
# centerline_fitting = str(arg)
elif opt in ('-v'):
verbose = int(arg)
# display usage if a mandatory argument is not provided
if fname_anat == '' or fname_centerline == '':
usage()
# check if algorithm for fitting is correct
if algo_fitting not in ['hanning','nurbs']:
sct.printv('ERROR: wrong fitting algorithm',1,'warning')
usage()
# update field
param.verbose = verbose
# check existence of input files
sct.check_file_exist(fname_anat)
sct.check_file_exist(fname_centerline)
# Display arguments
print '\nCheck input arguments...'
print ' Input volume ...................... '+fname_anat
print ' Centerline ........................ '+fname_centerline
print ' Final interpolation ............... '+interpolation_warp
print ' Verbose ........................... '+str(verbose)
print ''
# Extract path/file/extension
path_anat, file_anat, ext_anat = sct.extract_fname(fname_anat)
path_centerline, file_centerline, ext_centerline = sct.extract_fname(fname_centerline)
# create temporary folder
path_tmp = 'tmp.'+time.strftime("%y%m%d%H%M%S")
sct.run('mkdir '+path_tmp, verbose)
# copy files into tmp folder
sct.run('cp '+fname_anat+' '+path_tmp)
sct.run('cp '+fname_centerline+' '+path_tmp)
# go to tmp folder
os.chdir(path_tmp)
# Change orientation of the input centerline into RPI
sct.printv('\nOrient centerline to RPI orientation...', verbose)
fname_centerline_orient = file_centerline+'_rpi.nii.gz'
set_orientation(fname_centerline, 'RPI', fname_centerline_orient)
# Get dimension
sct.printv('\nGet dimensions...', verbose)
nx, ny, nz, nt, px, py, pz, pt = sct.get_dimension(fname_centerline_orient)
sct.printv('.. matrix size: '+str(nx)+' x '+str(ny)+' x '+str(nz), verbose)
sct.printv('.. voxel size: '+str(px)+'mm x '+str(py)+'mm x '+str(pz)+'mm', verbose)
# smooth centerline
x_centerline_fit, y_centerline_fit, z_centerline, x_centerline_deriv, y_centerline_deriv, z_centerline_deriv = smooth_centerline(fname_centerline_orient, algo_fitting=algo_fitting, type_window=type_window, window_length=window_length,verbose=verbose)
# Get coordinates of landmarks along curved centerline
#==========================================================================================
sct.printv('\nGet coordinates of landmarks along curved centerline...', verbose)
# landmarks are created along the curved centerline every z=gapz. They consist of a "cross" of size gapx and gapy. In voxel space!!!
# find z indices along centerline given a specific gap: iz_curved
nz_nonz = len(z_centerline)
nb_landmark = int(round(float(nz_nonz)/gapz))
if nb_landmark == 0:
nb_landmark = 1
if nb_landmark == 1:
iz_curved = [0]
else:
iz_curved = [i*gapz for i in range(0, nb_landmark-1)]
iz_curved.append(nz_nonz-1)
#print iz_curved, len(iz_curved)
n_iz_curved = len(iz_curved)
#print n_iz_curved
# landmark_curved initialisation
landmark_curved = [ [ [ 0 for i in range(0, 3)] for i in range(0, 5) ] for i in iz_curved ]
### TODO: THIS PART IS SLOW AND CAN BE MADE FASTER
### >>==============================================================================================================
for index in range(0, n_iz_curved, 1):
# calculate d (ax+by+cz+d=0)
# print iz_curved[index]
a=x_centerline_deriv[iz_curved[index]]
b=y_centerline_deriv[iz_curved[index]]
c=z_centerline_deriv[iz_curved[index]]
x=x_centerline_fit[iz_curved[index]]
y=y_centerline_fit[iz_curved[index]]
z=z_centerline[iz_curved[index]]
d=-(a*x+b*y+c*z)
#print a,b,c,d,x,y,z
# set coordinates for landmark at the center of the cross
landmark_curved[index][0][0], landmark_curved[index][0][1], landmark_curved[index][0][2] = x_centerline_fit[iz_curved[index]], y_centerline_fit[iz_curved[index]], z_centerline[iz_curved[index]]
# set y coordinate to y_centerline_fit[iz] for elements 1 and 2 of the cross
for i in range(1, 3):
landmark_curved[index][i][1] = y_centerline_fit[iz_curved[index]]
# set x and z coordinates for landmarks +x and -x, forcing de landmark to be in the orthogonal plan and the distance landmark/curve to be gapxy
x_n = Symbol('x_n')
landmark_curved[index][2][0], landmark_curved[index][1][0]=solve((x_n-x)**2+((-1/c)*(a*x_n+b*y+d)-z)**2-gapxy**2,x_n) #x for -x and +x
landmark_curved[index][1][2] = (-1/c)*(a*landmark_curved[index][1][0]+b*y+d) # z for +x
landmark_curved[index][2][2] = (-1/c)*(a*landmark_curved[index][2][0]+b*y+d) # z for -x
# set x coordinate to x_centerline_fit[iz] for elements 3 and 4 of the cross
for i in range(3, 5):
landmark_curved[index][i][0] = x_centerline_fit[iz_curved[index]]
# set coordinates for landmarks +y and -y. Here, x coordinate is 0 (already initialized).
y_n = Symbol('y_n')
landmark_curved[index][4][1],landmark_curved[index][3][1] = solve((y_n-y)**2+((-1/c)*(a*x+b*y_n+d)-z)**2-gapxy**2,y_n) #y for -y and +y
landmark_curved[index][3][2] = (-1/c)*(a*x+b*landmark_curved[index][3][1]+d) # z for +y
landmark_curved[index][4][2] = (-1/c)*(a*x+b*landmark_curved[index][4][1]+d) # z for -y
### <<==============================================================================================================
if verbose == 2:
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
fig = plt.figure()
ax = Axes3D(fig)
ax.plot(x_centerline_fit, y_centerline_fit,z_centerline,zdir='z')
ax.plot([landmark_curved[i][j][0] for i in range(0, n_iz_curved) for j in range(0, 5)], \
[landmark_curved[i][j][1] for i in range(0, n_iz_curved) for j in range(0, 5)], \
[landmark_curved[i][j][2] for i in range(0, n_iz_curved) for j in range(0, 5)], '.')
ax.set_xlabel('x')
ax.set_ylabel('y')
ax.set_zlabel('z')
plt.show()
# Get coordinates of landmarks along straight centerline
#==========================================================================================
sct.printv('\nGet coordinates of landmarks along straight centerline...', verbose)
landmark_straight = [ [ [ 0 for i in range(0,3)] for i in range (0,5) ] for i in iz_curved ] # same structure as landmark_curved
# calculate the z indices corresponding to the Euclidean distance between two consecutive points on the curved centerline (approximation curve --> line)
# TODO: DO NOT APPROXIMATE CURVE --> LINE
if nb_landmark == 1:
iz_straight = [0 for i in range(0, nb_landmark+1)]
else:
iz_straight = [0 for i in range(0, nb_landmark)]
# print iz_straight,len(iz_straight)
iz_straight[0] = iz_curved[0]
for index in range(1, n_iz_curved, 1):
# compute vector between two consecutive points on the curved centerline
vector_centerline = [x_centerline_fit[iz_curved[index]] - x_centerline_fit[iz_curved[index-1]], \
y_centerline_fit[iz_curved[index]] - y_centerline_fit[iz_curved[index-1]], \
z_centerline[iz_curved[index]] - z_centerline[iz_curved[index-1]] ]
# compute norm of this vector
norm_vector_centerline = linalg.norm(vector_centerline, ord=2)
# round to closest integer value
norm_vector_centerline_rounded = int(round(norm_vector_centerline, 0))
# assign this value to the current z-coordinate on the straight centerline
iz_straight[index] = iz_straight[index-1] + norm_vector_centerline_rounded
# initialize x0 and y0 to be at the center of the FOV
x0 = int(round(nx/2))
y0 = int(round(ny/2))
for index in range(0, n_iz_curved, 1):
# set coordinates for landmark at the center of the cross
landmark_straight[index][0][0], landmark_straight[index][0][1], landmark_straight[index][0][2] = x0, y0, iz_straight[index]
# set x, y and z coordinates for landmarks +x
landmark_straight[index][1][0], landmark_straight[index][1][1], landmark_straight[index][1][2] = x0 + gapxy, y0, iz_straight[index]
# set x, y and z coordinates for landmarks -x
landmark_straight[index][2][0], landmark_straight[index][2][1], landmark_straight[index][2][2] = x0-gapxy, y0, iz_straight[index]
# set x, y and z coordinates for landmarks +y
landmark_straight[index][3][0], landmark_straight[index][3][1], landmark_straight[index][3][2] = x0, y0+gapxy, iz_straight[index]
# set x, y and z coordinates for landmarks -y
landmark_straight[index][4][0], landmark_straight[index][4][1], landmark_straight[index][4][2] = x0, y0-gapxy, iz_straight[index]
# # display
# fig = plt.figure()
# ax = fig.add_subplot(111, projection='3d')
# #ax.plot(x_centerline_fit, y_centerline_fit,z_centerline, 'r')
# ax.plot([landmark_straight[i][j][0] for i in range(0, n_iz_curved) for j in range(0, 5)], \
# [landmark_straight[i][j][1] for i in range(0, n_iz_curved) for j in range(0, 5)], \
# [landmark_straight[i][j][2] for i in range(0, n_iz_curved) for j in range(0, 5)], '.')
# ax.set_xlabel('x')
# ax.set_ylabel('y')
# ax.set_zlabel('z')
# plt.show()
#
# Create NIFTI volumes with landmarks
#==========================================================================================
# Pad input volume to deal with the fact that some landmarks on the curved centerline might be outside the FOV
# N.B. IT IS VERY IMPORTANT TO PAD ALSO ALONG X and Y, OTHERWISE SOME LANDMARKS MIGHT GET OUT OF THE FOV!!!
#sct.run('fslview ' + fname_centerline_orient)
sct.printv('\nPad input volume to account for landmarks that fall outside the FOV...', verbose)
sct.run('isct_c3d '+fname_centerline_orient+' -pad '+str(padding)+'x'+str(padding)+'x'+str(padding)+'vox '+str(padding)+'x'+str(padding)+'x'+str(padding)+'vox 0 -o tmp.centerline_pad.nii.gz')
# Open padded centerline for reading
sct.printv('\nOpen padded centerline for reading...', verbose)
file = load('tmp.centerline_pad.nii.gz')
data = file.get_data()
hdr = file.get_header()
# Create volumes containing curved and straight landmarks
data_curved_landmarks = data * 0
data_straight_landmarks = data * 0
# initialize landmark value
landmark_value = 1
# Loop across cross index
for index in range(0, n_iz_curved, 1):
# loop across cross element index
for i_element in range(0, 5, 1):
# get x, y and z coordinates of curved landmark (rounded to closest integer)
x, y, z = int(round(landmark_curved[index][i_element][0])), int(round(landmark_curved[index][i_element][1])), int(round(landmark_curved[index][i_element][2]))
# attribute landmark_value to the voxel and its neighbours
data_curved_landmarks[x+padding-1:x+padding+2, y+padding-1:y+padding+2, z+padding-1:z+padding+2] = landmark_value
# get x, y and z coordinates of straight landmark (rounded to closest integer)
x, y, z = int(round(landmark_straight[index][i_element][0])), int(round(landmark_straight[index][i_element][1])), int(round(landmark_straight[index][i_element][2]))
# attribute landmark_value to the voxel and its neighbours
data_straight_landmarks[x+padding-1:x+padding+2, y+padding-1:y+padding+2, z+padding-1:z+padding+2] = landmark_value
# increment landmark value
landmark_value = landmark_value + 1
# Write NIFTI volumes
sct.printv('\nWrite NIFTI volumes...', verbose)
hdr.set_data_dtype('uint32') # set imagetype to uint8 #TODO: maybe use int32
img = Nifti1Image(data_curved_landmarks, None, hdr)
save(img, 'tmp.landmarks_curved.nii.gz')
sct.printv('.. File created: tmp.landmarks_curved.nii.gz', verbose)
img = Nifti1Image(data_straight_landmarks, None, hdr)
save(img, 'tmp.landmarks_straight.nii.gz')
sct.printv('.. File created: tmp.landmarks_straight.nii.gz', verbose)
# Estimate deformation field by pairing landmarks
#==========================================================================================
# This stands to avoid overlapping between landmarks
sct.printv('\nMake sure all labels between landmark_curved and landmark_curved match...', verbose)
sct.run('sct_label_utils -t remove -i tmp.landmarks_straight.nii.gz -o tmp.landmarks_straight.nii.gz -r tmp.landmarks_curved.nii.gz', verbose)
# convert landmarks to INT
sct.printv('\nConvert landmarks to INT...', verbose)
sct.run('isct_c3d tmp.landmarks_straight.nii.gz -type int -o tmp.landmarks_straight.nii.gz', verbose)
sct.run('isct_c3d tmp.landmarks_curved.nii.gz -type int -o tmp.landmarks_curved.nii.gz', verbose)
# Estimate rigid transformation
sct.printv('\nEstimate rigid transformation between paired landmarks...', verbose)
sct.run('isct_ANTSUseLandmarkImagesToGetAffineTransform tmp.landmarks_straight.nii.gz tmp.landmarks_curved.nii.gz rigid tmp.curve2straight_rigid.txt', verbose)
# Apply rigid transformation
sct.printv('\nApply rigid transformation to curved landmarks...', verbose)
sct.run('sct_apply_transfo -i tmp.landmarks_curved.nii.gz -o tmp.landmarks_curved_rigid.nii.gz -d tmp.landmarks_straight.nii.gz -w tmp.curve2straight_rigid.txt -x nn', verbose)
# Estimate b-spline transformation curve --> straight
sct.printv('\nEstimate b-spline transformation: curve --> straight...', verbose)
sct.run('isct_ANTSUseLandmarkImagesToGetBSplineDisplacementField tmp.landmarks_straight.nii.gz tmp.landmarks_curved_rigid.nii.gz tmp.warp_curve2straight.nii.gz 5x5x10 3 2 0', verbose)
# remove padding for straight labels
if crop == 1:
sct.run('sct_crop_image -i tmp.landmarks_straight.nii.gz -o tmp.landmarks_straight_crop.nii.gz -dim 0 -bzmax', verbose)
sct.run('sct_crop_image -i tmp.landmarks_straight_crop.nii.gz -o tmp.landmarks_straight_crop.nii.gz -dim 1 -bzmax', verbose)
sct.run('sct_crop_image -i tmp.landmarks_straight_crop.nii.gz -o tmp.landmarks_straight_crop.nii.gz -dim 2 -bzmax', verbose)
else:
sct.run('cp tmp.landmarks_straight.nii.gz tmp.landmarks_straight_crop.nii.gz', verbose)
# Concatenate rigid and non-linear transformations...
sct.printv('\nConcatenate rigid and non-linear transformations...', verbose)
#sct.run('isct_ComposeMultiTransform 3 tmp.warp_rigid.nii -R tmp.landmarks_straight.nii tmp.warp.nii tmp.curve2straight_rigid.txt')
# !!! DO NOT USE sct.run HERE BECAUSE isct_ComposeMultiTransform OUTPUTS A NON-NULL STATUS !!!
cmd = 'isct_ComposeMultiTransform 3 tmp.curve2straight.nii.gz -R tmp.landmarks_straight_crop.nii.gz tmp.warp_curve2straight.nii.gz tmp.curve2straight_rigid.txt'
sct.printv(cmd, verbose, 'code')
commands.getstatusoutput(cmd)
# Estimate b-spline transformation straight --> curve
# TODO: invert warping field instead of estimating a new one
sct.printv('\nEstimate b-spline transformation: straight --> curve...', verbose)
sct.run('isct_ANTSUseLandmarkImagesToGetBSplineDisplacementField tmp.landmarks_curved_rigid.nii.gz tmp.landmarks_straight.nii.gz tmp.warp_straight2curve.nii.gz 5x5x10 3 2 0', verbose)
# Concatenate rigid and non-linear transformations...
sct.printv('\nConcatenate rigid and non-linear transformations...', verbose)
# cmd = 'isct_ComposeMultiTransform 3 tmp.straight2curve.nii.gz -R tmp.landmarks_straight.nii.gz -i tmp.curve2straight_rigid.txt tmp.warp_straight2curve.nii.gz'
cmd = 'isct_ComposeMultiTransform 3 tmp.straight2curve.nii.gz -R '+file_anat+ext_anat+' -i tmp.curve2straight_rigid.txt tmp.warp_straight2curve.nii.gz'
sct.printv(cmd, verbose, 'code')
commands.getstatusoutput(cmd)
# Apply transformation to input image
sct.printv('\nApply transformation to input image...', verbose)
sct.run('sct_apply_transfo -i '+file_anat+ext_anat+' -o tmp.anat_rigid_warp.nii.gz -d tmp.landmarks_straight_crop.nii.gz -x '+interpolation_warp+' -w tmp.curve2straight.nii.gz', verbose)
# compute the error between the straightened centerline/segmentation and the central vertical line.
# Ideally, the error should be zero.
# Apply deformation to input image
print '\nApply transformation to input image...'
c = sct.run('sct_apply_transfo -i '+fname_centerline_orient+' -o tmp.centerline_straight.nii.gz -d tmp.landmarks_straight_crop.nii.gz -x nn -w tmp.curve2straight.nii.gz')
#c = sct.run('sct_crop_image -i tmp.centerline_straight.nii.gz -o tmp.centerline_straight_crop.nii.gz -dim 2 -bzmax')
from msct_image import Image
file_centerline_straight = Image('tmp.centerline_straight.nii.gz')
coordinates_centerline = file_centerline_straight.getNonZeroCoordinates(sorting='z')
mean_coord = []
for z in range(coordinates_centerline[0].z, coordinates_centerline[-1].z):
mean_coord.append(mean([[coord.x*coord.value, coord.y*coord.value] for coord in coordinates_centerline if coord.z == z], axis=0))
# compute error between the input data and the nurbs
from math import sqrt
mse_curve = 0.0
max_dist = 0.0
x0 = int(round(file_centerline_straight.data.shape[0]/2.0))
y0 = int(round(file_centerline_straight.data.shape[1]/2.0))
count_mean = 0
for coord_z in mean_coord:
if not isnan(sum(coord_z)):
dist = ((x0-coord_z[0])*px)**2 + ((y0-coord_z[1])*py)**2
mse_curve += dist
dist = sqrt(dist)
if dist > max_dist:
max_dist = dist
count_mean += 1
mse_curve = mse_curve/float(count_mean)
# come back to parent folder
os.chdir('..')
# Generate output file (in current folder)
# TODO: do not uncompress the warping field, it is too time consuming!
sct.printv('\nGenerate output file (in current folder)...', verbose)
sct.generate_output_file(path_tmp+'/tmp.curve2straight.nii.gz', 'warp_curve2straight.nii.gz', verbose) # warping field
sct.generate_output_file(path_tmp+'/tmp.straight2curve.nii.gz', 'warp_straight2curve.nii.gz', verbose) # warping field
fname_straight = sct.generate_output_file(path_tmp+'/tmp.anat_rigid_warp.nii.gz', file_anat+'_straight'+ext_anat, verbose) # straightened anatomic
# Remove temporary files
if remove_temp_files:
sct.printv('\nRemove temporary files...', verbose)
sct.run('rm -rf '+path_tmp, verbose)
print '\nDone!\n'
sct.printv('Maximum x-y error = '+str(round(max_dist,2))+' mm', verbose, 'bold')
sct.printv('Accuracy of straightening (MSE) = '+str(round(mse_curve,2))+' mm', verbose, 'bold')
# display elapsed time
elapsed_time = time.time() - start_time
sct.printv('\nFinished! Elapsed time: '+str(int(round(elapsed_time)))+'s', verbose)
sct.printv('\nTo view results, type:', verbose)
sct.printv('fslview '+fname_straight+' &\n', verbose, 'info')
def main():
# Initialization to defaults parameters
fname_data = '' # data is empty by default
path_label = '' # empty by default
method = param.method # extraction mode by default
labels_of_interest = param.labels_of_interest
slices_of_interest = param.slices_of_interest
vertebral_levels = param.vertebral_levels
average_all_labels = param.average_all_labels
fname_output = param.fname_output
fname_vertebral_labeling = param.fname_vertebral_labeling
fname_normalizing_label = '' # optional then default is empty
normalization_method = '' # optional then default is empty
actual_vert_levels = None # variable used in case the vertebral levels asked by the user don't correspond exactly to the vertebral levels available in the metric data
warning_vert_levels = None # variable used to warn the user in case the vertebral levels he asked don't correspond exactly to the vertebral levels available in the metric data
verbose = param.verbose
flag_h = 0
ml_clusters = param.ml_clusters
adv_param = param.adv_param
adv_param_user = ''
# Parameters for debug mode
if param.debug:
print '\n*** WARNING: DEBUG MODE ON ***\n'
status, path_sct_data = commands.getstatusoutput('echo $SCT_TESTING_DATA_DIR')
fname_data = '/Users/julien/data/temp/sct_example_data/mt/mtr.nii.gz'
path_label = '/Users/julien/data/temp/sct_example_data/mt/label/atlas/'
method = 'map'
ml_clusters = '0:29,30,31'
labels_of_interest = '0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29'
slices_of_interest = ''
vertebral_levels = ''
average_all_labels = 1
fname_normalizing_label = '' #path_sct+'/testing/data/errsm_23/mt/label/template/MNI-Poly-AMU_CSF.nii.gz'
normalization_method = '' #'whole'
else:
# Check input parameters
try:
opts, args = getopt.getopt(sys.argv[1:], 'haf:i:l:m:n:o:p:v:w:z:') # define flags
except getopt.GetoptError as err: # check if the arguments are defined
print str(err) # error
usage() # display usage
if not opts:
usage()
for opt, arg in opts: # explore flags
if opt in '-a':
average_all_labels = 1
elif opt in '-f':
path_label = os.path.abspath(arg) # save path of labels folder
elif opt == '-h': # help option
flag_h = 1
elif opt in '-i':
fname_data = arg
elif opt in '-l':
labels_of_interest = arg
elif opt in '-m': # method for metric extraction
method = arg
elif opt in '-n': # filename of the label by which the user wants to normalize
fname_normalizing_label = arg
elif opt in '-o': # output option
fname_output = arg # fname of output file
elif opt in '-p':
adv_param_user = arg
elif opt in '-v':
# vertebral levels option, if the user wants to average the metric across specific vertebral levels
vertebral_levels = arg
elif opt in '-w':
# method used for the normalization by the metric estimation into the normalizing label (see flag -n): 'sbs' for slice-by-slice or 'whole' for normalization after estimation in the whole labels
normalization_method = arg
elif opt in '-z': # slices numbers option
slices_of_interest = arg # save labels numbers
# Display usage with tract parameters by default in case files aren't chosen in arguments inputs
if fname_data == '' or path_label == '' or flag_h:
param.path_label = path_label
usage()
# Check existence of data file
sct.printv('\ncheck existence of input files...', verbose)
sct.check_file_exist(fname_data)
sct.check_folder_exist(path_label)
if fname_normalizing_label:
sct.check_folder_exist(fname_normalizing_label)
# add slash at the end
path_label = sct.slash_at_the_end(path_label, 1)
# Find path to the vertebral labeling file if vertebral levels were specified by the user
if vertebral_levels:
if slices_of_interest: # impossible to select BOTH specific slices and specific vertebral levels
print '\nERROR: You cannot select BOTH vertebral levels AND slice numbers.'
usage()
else:
fname_vertebral_labeling_list = sct.find_file_within_folder(fname_vertebral_labeling, path_label + '..')
if len(fname_vertebral_labeling_list) > 1:
print color.red + 'ERROR: More than one file named \'' + fname_vertebral_labeling + ' were found in ' + path_label + '. Exit program.' + color.end
sys.exit(2)
elif len(fname_vertebral_labeling_list) == 0:
print color.red + 'ERROR: No file named \'' + fname_vertebral_labeling + ' were found in ' + path_label + '. Exit program.' + color.end
sys.exit(2)
else:
fname_vertebral_labeling = os.path.abspath(fname_vertebral_labeling_list[0])
# Check input parameters
check_method(method, fname_normalizing_label, normalization_method)
# parse argument for param
if not adv_param_user == '':
adv_param = adv_param_user.replace(' ', '').split(',') # remove spaces and parse with comma
del adv_param_user # clean variable
# TODO: check integrity of input
# Extract label info
label_id, label_name, label_file = read_label_file(path_label, param.file_info_label)
nb_labels_total = len(label_id)
# check consistency of label input parameter.
label_id_user, average_all_labels = check_labels(labels_of_interest, nb_labels_total, average_all_labels, method) # If 'labels_of_interest' is empty, then
# 'label_id_user' contains the index of all labels in the file info_label.txt
# print parameters
print '\nChecked parameters:'
print ' data ...................... '+fname_data
print ' folder label .............. '+path_label
print ' selected labels ........... '+str(label_id_user)
print ' estimation method ......... '+method
print ' slices of interest ........ '+slices_of_interest
print ' vertebral levels .......... '+vertebral_levels
print ' vertebral labeling file.... '+fname_vertebral_labeling
print ' advanced parameters ....... '+str(adv_param)
# Check if the orientation of the data is RPI
orientation_data = get_orientation(fname_data)
# If orientation is not RPI, change to RPI
if orientation_data != 'RPI':
sct.printv('\nCreate temporary folder to change the orientation of the NIFTI files into RPI...', verbose)
path_tmp = sct.slash_at_the_end('tmp.'+time.strftime("%y%m%d%H%M%S"), 1)
sct.create_folder(path_tmp)
# change orientation and load data
sct.printv('\nChange image orientation and load it...', verbose)
data = nib.load(set_orientation(fname_data, 'RPI', path_tmp+'orient_data.nii')).get_data()
# Do the same for labels
sct.printv('\nChange labels orientation and load them...', verbose)
labels = np.empty([nb_labels_total], dtype=object) # labels(nb_labels_total, x, y, z)
for i_label in range(0, nb_labels_total):
labels[i_label] = nib.load(set_orientation(path_label+label_file[i_label], 'RPI', path_tmp+'orient_'+label_file[i_label])).get_data()
if fname_normalizing_label: # if the "normalization" option is wanted,
normalizing_label = np.empty([1], dtype=object) # choose this kind of structure so as to keep easily the
# compatibility with the rest of the code (dimensions: (1, x, y, z))
normalizing_label[0] = nib.load(set_orientation(fname_normalizing_label, 'RPI', path_tmp+'orient_normalizing_volume.nii')).get_data()
if vertebral_levels: # if vertebral levels were selected,
data_vertebral_labeling = nib.load(set_orientation(fname_vertebral_labeling, 'RPI', path_tmp+'orient_vertebral_labeling.nii.gz')).get_data()
# Remove the temporary folder used to change the NIFTI files orientation into RPI
sct.printv('\nRemove the temporary folder...', verbose)
status, output = commands.getstatusoutput('rm -rf ' + path_tmp)
else:
# Load image
sct.printv('\nLoad image...', verbose)
data = nib.load(fname_data).get_data()
# Load labels
sct.printv('\nLoad labels...', verbose)
labels = np.empty([nb_labels_total], dtype=object) # labels(nb_labels_total, x, y, z)
for i_label in range(0, nb_labels_total):
labels[i_label] = nib.load(path_label+label_file[i_label]).get_data()
if fname_normalizing_label: # if the "normalization" option is wanted,
normalizing_label = np.empty([1], dtype=object) # choose this kind of structure so as to keep easily the
# compatibility with the rest of the code (dimensions: (1, x, y, z))
normalizing_label[0] = nib.load(fname_normalizing_label).get_data() # load the data of the normalizing label
if vertebral_levels: # if vertebral levels were selected,
data_vertebral_labeling = nib.load(fname_vertebral_labeling).get_data()
# Change metric data type into floats for future manipulations (normalization)
data = np.float64(data)
# Get dimensions of data
sct.printv('\nGet dimensions of data...', verbose)
nx, ny, nz = data.shape
sct.printv(' ' + str(nx) + ' x ' + str(ny) + ' x ' + str(nz), verbose)
# Get dimensions of labels
sct.printv('\nGet dimensions of label...', verbose)
nx_atlas, ny_atlas, nz_atlas = labels[0].shape
sct.printv('.. '+str(nx_atlas)+' x '+str(ny_atlas)+' x '+str(nz_atlas)+' x '+str(nb_labels_total), verbose)
# Check dimensions consistency between atlas and data
if (nx, ny, nz) != (nx_atlas, ny_atlas, nz_atlas):
print '\nERROR: Metric data and labels DO NOT HAVE SAME DIMENSIONS.'
sys.exit(2)
# Update the flag "slices_of_interest" according to the vertebral levels selected by user (if it's the case)
if vertebral_levels:
slices_of_interest, actual_vert_levels, warning_vert_levels = \
get_slices_matching_with_vertebral_levels(data, vertebral_levels, data_vertebral_labeling)
# select slice of interest by cropping data and labels
if slices_of_interest:
data = remove_slices(data, slices_of_interest)
for i_label in range(0, nb_labels_total):
labels[i_label] = remove_slices(labels[i_label], slices_of_interest)
if fname_normalizing_label: # if the "normalization" option was selected,
normalizing_label[0] = remove_slices(normalizing_label[0], slices_of_interest)
# if user wants to get unique value across labels, then combine all labels together
if average_all_labels == 1:
sum_labels_user = np.sum(labels[label_id_user]) # sum the labels selected by user
if method == 'ml' or method == 'map': # in case the maximum likelihood and the average across different labels are wanted
labels_tmp = np.empty([nb_labels_total - len(label_id_user) + 1], dtype=object)
labels = np.delete(labels, label_id_user) # remove the labels selected by user
labels_tmp[0] = sum_labels_user # put the sum of the labels selected by user in first position of the tmp
# variable
for i_label in range(1, len(labels_tmp)):
labels_tmp[i_label] = labels[i_label-1] # fill the temporary array with the values of the non-selected labels
labels = labels_tmp # replace the initial labels value by the updated ones (with the summed labels)
del labels_tmp # delete the temporary labels
else: # in other cases than the maximum likelihood, we can remove other labels (not needed for estimation)
labels = np.empty(1, dtype=object)
labels[0] = sum_labels_user # we create a new label array that includes only the summed labels
if fname_normalizing_label: # if the "normalization" option is wanted
sct.printv('\nExtract normalization values...', verbose)
if normalization_method == 'sbs': # case: the user wants to normalize slice-by-slice
for z in range(0, data.shape[-1]):
normalizing_label_slice = np.empty([1], dtype=object) # in order to keep compatibility with the function
# 'extract_metric_within_tract', define a new array for the slice z of the normalizing labels
normalizing_label_slice[0] = normalizing_label[0][..., z]
metric_normalizing_label = extract_metric_within_tract(data[..., z], normalizing_label_slice, method, 0)
# estimate the metric mean in the normalizing label for the slice z
if metric_normalizing_label[0][0] != 0:
data[..., z] = data[..., z]/metric_normalizing_label[0][0] # divide all the slice z by this value
elif normalization_method == 'whole': # case: the user wants to normalize after estimations in the whole labels
metric_mean_norm_label, metric_std_norm_label = extract_metric_within_tract(data, normalizing_label, method, param.verbose) # mean and std are lists
# identify cluster for each tract (for use with robust ML)
ml_clusters_array = get_clusters(ml_clusters, labels)
# extract metrics within labels
sct.printv('\nExtract metric within labels...', verbose)
metric_mean, metric_std = extract_metric_within_tract(data, labels, method, verbose, ml_clusters_array, adv_param) # mean and std are lists
if fname_normalizing_label and normalization_method == 'whole': # case: user wants to normalize after estimations in the whole labels
metric_mean, metric_std = np.divide(metric_mean, metric_mean_norm_label), np.divide(metric_std, metric_std_norm_label)
# update label name if average
if average_all_labels == 1:
label_name[0] = 'AVERAGED'+' -'.join(label_name[i] for i in label_id_user) # concatenate the names of the
# labels selected by the user if the average tag was asked
label_id_user = [0] # update "label_id_user" to select the "averaged" label (which is in first position)
metric_mean = metric_mean[label_id_user]
metric_std = metric_std[label_id_user]
# display metrics
sct.printv('\nEstimation results:', 1)
for i in range(0, metric_mean.size):
sct.printv(str(label_id_user[i])+', '+str(label_name[label_id_user[i]])+': '+str(metric_mean[i])+' +/- '+str(metric_std[i]), 1, 'info')
# save and display metrics
save_metrics(label_id_user, label_name, slices_of_interest, metric_mean, metric_std, fname_output, fname_data,
method, fname_normalizing_label, actual_vert_levels, warning_vert_levels)
def main(segmentation_file=None, label_file=None, output_file_name=None, parameter = "binary_centerline", remove_temp_files = 1, verbose = 0 ):
#Process for a binary file as output:
if parameter == "binary_centerline":
# Binary_centerline: Process for only a segmentation file:
if "-i" in arguments and "-l" not in arguments:
# Extract path, file and extension
segmentation_file = os.path.abspath(segmentation_file)
path_data, file_data, ext_data = sct.extract_fname(segmentation_file)
# create temporary folder
path_tmp = 'tmp.'+time.strftime("%y%m%d%H%M%S")
sct.run('mkdir '+path_tmp)
# copy files into tmp folder
sct.run('cp '+segmentation_file+' '+path_tmp)
# go to tmp folder
os.chdir(path_tmp)
# Change orientation of the input segmentation into RPI
print '\nOrient segmentation image to RPI orientation...'
fname_segmentation_orient = 'tmp.segmentation_rpi' + ext_data
set_orientation(file_data+ext_data, 'RPI', fname_segmentation_orient)
# Extract orientation of the input segmentation
orientation = get_orientation(file_data+ext_data)
print '\nOrientation of segmentation image: ' + orientation
# Get size of data
print '\nGet dimensions data...'
nx, ny, nz, nt, px, py, pz, pt = sct.get_dimension(fname_segmentation_orient)
print '.. '+str(nx)+' x '+str(ny)+' y '+str(nz)+' z '+str(nt)
print '\nOpen segmentation volume...'
file = nibabel.load(fname_segmentation_orient)
data = file.get_data()
hdr = file.get_header()
# Extract min and max index in Z direction
X, Y, Z = (data>0).nonzero()
min_z_index, max_z_index = min(Z), max(Z)
x_centerline = [0 for i in range(0,max_z_index-min_z_index+1)]
y_centerline = [0 for i in range(0,max_z_index-min_z_index+1)]
z_centerline = [iz for iz in range(min_z_index, max_z_index+1)]
# Extract segmentation points and average per slice
for iz in range(min_z_index, max_z_index+1):
x_seg, y_seg = (data[:,:,iz]>0).nonzero()
x_centerline[iz-min_z_index] = np.mean(x_seg)
y_centerline[iz-min_z_index] = np.mean(y_seg)
#ne sert a rien
for k in range(len(X)):
data[X[k],Y[k],Z[k]] = 0
print len(x_centerline)
# Fit the centerline points with splines and return the new fitted coordinates
#done with nurbs for now
x_centerline_fit, y_centerline_fit,x_centerline_deriv,y_centerline_deriv,z_centerline_deriv = b_spline_centerline(x_centerline,y_centerline,z_centerline)
# Create an image with the centerline
for iz in range(min_z_index, max_z_index+1):
data[round(x_centerline_fit[iz-min_z_index]), round(y_centerline_fit[iz-min_z_index]), iz] = 1 #with nurbs fitting
#data[round(x_centerline[iz-min_z_index]), round(y_centerline[iz-min_z_index]), iz] = 1 #without nurbs fitting
# Write the centerline image in RPI orientation
hdr.set_data_dtype('uint8') # set imagetype to uint8
print '\nWrite NIFTI volumes...'
img = nibabel.Nifti1Image(data, None, hdr)
if output_file_name != None :
file_name = output_file_name
else: file_name = file_data+'_centerline'+ext_data
nibabel.save(img,'tmp.centerline.nii')
sct.generate_output_file('tmp.centerline.nii',file_name)
del data
# come back to parent folder
os.chdir('..')
# Change orientation of the output centerline into input orientation
print '\nOrient centerline image to input orientation: ' + orientation
set_orientation(path_tmp+'/'+file_name, orientation, file_name)
# Remove temporary files
if remove_temp_files:
print('\nRemove temporary files...')
sct.run('rm -rf '+path_tmp)
return file_name
# Binary_centerline: Process for only a label file:
if "-l" in arguments and "-i" not in arguments:
file = os.path.abspath(label_file)
path_data, file_data, ext_data = sct.extract_fname(file)
file = nibabel.load(label_file)
data = file.get_data()
hdr = file.get_header()
X,Y,Z = (data>0).nonzero()
Z_new = np.linspace(min(Z),max(Z),(max(Z)-min(Z)+1))
# sort X and Y arrays using Z
X = [X[i] for i in Z[:].argsort()]
Y = [Y[i] for i in Z[:].argsort()]
Z = [Z[i] for i in Z[:].argsort()]
#print X, Y, Z
f1 = interpolate.UnivariateSpline(Z, X)
f2 = interpolate.UnivariateSpline(Z, Y)
X_fit = f1(Z_new)
Y_fit = f2(Z_new)
#print X_fit
#print Y_fit
if verbose==1 :
import matplotlib.pyplot as plt
plt.figure()
plt.plot(Z_new,X_fit)
plt.plot(Z,X,'o',linestyle = 'None')
plt.show()
plt.figure()
plt.plot(Z_new,Y_fit)
plt.plot(Z,Y,'o',linestyle = 'None')
plt.show()
data =data*0
for i in xrange(len(X_fit)):
data[X_fit[i],Y_fit[i],Z_new[i]] = 1
# Create NIFTI image
print '\nSave volume ...'
hdr.set_data_dtype('float32') # set image type to uint8
img = nibabel.Nifti1Image(data, None, hdr)
if output_file_name != None :
file_name = output_file_name
else: file_name = file_data+'_centerline'+ext_data
# save volume
nibabel.save(img,file_name)
print '\nFile created : ' + file_name
del data
#### Binary_centerline: Process for a segmentation file and a label file:
if "-l" and "-i" in arguments:
## Creation of a temporary file that will contain each centerline file of the process
path_tmp = 'tmp.'+time.strftime("%y%m%d%H%M%S")
sct.run('mkdir '+path_tmp)
##From label file create centerline image
print '\nPROCESS PART 1: From label file create centerline image.'
file_label = os.path.abspath(label_file)
path_data_label, file_data_label, ext_data_label = sct.extract_fname(file_label)
file_label = nibabel.load(label_file)
#Copy label_file into temporary folder
sct.run('cp '+label_file+' '+path_tmp)
data_label = file_label.get_data()
hdr_label = file_label.get_header()
if verbose == 1:
from copy import copy
data_label_to_show = copy(data_label)
X,Y,Z = (data_label>0).nonzero()
Z_new = np.linspace(min(Z),max(Z),(max(Z)-min(Z)+1))
# sort X and Y arrays using Z
X = [X[i] for i in Z[:].argsort()]
Y = [Y[i] for i in Z[:].argsort()]
Z = [Z[i] for i in Z[:].argsort()]
#print X, Y, Z
f1 = interpolate.UnivariateSpline(Z, X)
f2 = interpolate.UnivariateSpline(Z, Y)
X_fit = f1(Z_new)
Y_fit = f2(Z_new)
#print X_fit
#print Y_fit
if verbose==1 :
import matplotlib.pyplot as plt
plt.figure()
plt.plot(Z_new,X_fit)
plt.plot(Z,X,'o',linestyle = 'None')
plt.show()
plt.figure()
plt.plot(Z_new,Y_fit)
plt.plot(Z,Y,'o',linestyle = 'None')
plt.show()
data_label =data_label*0
for i in xrange(len(X_fit)):
data_label[X_fit[i],Y_fit[i],Z_new[i]] = 1
# Create NIFTI image
print '\nSave volume ...'
hdr_label.set_data_dtype('float32') # set image type to uint8
img = nibabel.Nifti1Image(data_label, None, hdr_label)
# save volume
file_name_label = file_data_label + '_centerline' + ext_data_label
nibabel.save(img, file_name_label)
print '\nFile created : ' + file_name_label
# copy files into tmp folder
sct.run('cp '+file_name_label+' '+path_tmp)
#effacer fichier dans folder parent
os.remove(file_name_label)
del data_label
##From segmentation file create centerline image
print '\nPROCESS PART 2: From segmentation file create centerline image.'
# Extract path, file and extension
segmentation_file = os.path.abspath(segmentation_file)
path_data_seg, file_data_seg, ext_data_seg = sct.extract_fname(segmentation_file)
# copy files into tmp folder
sct.run('cp '+segmentation_file+' '+path_tmp)
# go to tmp folder
os.chdir(path_tmp)
# Change orientation of the input segmentation into RPI
print '\nOrient segmentation image to RPI orientation...'
fname_segmentation_orient = 'tmp.segmentation_rpi' + ext_data_seg
set_orientation(file_data_seg+ext_data_seg, 'RPI', fname_segmentation_orient)
# Extract orientation of the input segmentation
orientation = get_orientation(file_data_seg+ext_data_seg)
print '\nOrientation of segmentation image: ' + orientation
# Get size of data
print '\nGet dimensions data...'
nx, ny, nz, nt, px, py, pz, pt = sct.get_dimension(fname_segmentation_orient)
print '.. '+str(nx)+' x '+str(ny)+' y '+str(nz)+' z '+str(nt)
print '\nOpen segmentation volume...'
file_seg = nibabel.load(fname_segmentation_orient)
data_seg = file_seg.get_data()
hdr_seg = file_seg.get_header()
if verbose == 1:
data_seg_to_show = copy(data_seg)
# Extract min and max index in Z direction
X, Y, Z = (data_seg>0).nonzero()
min_z_index, max_z_index = min(Z), max(Z)
x_centerline = [0 for i in range(0,max_z_index-min_z_index+1)]
y_centerline = [0 for i in range(0,max_z_index-min_z_index+1)]
z_centerline = [iz for iz in range(min_z_index, max_z_index+1)]
# Extract segmentation points and average per slice
for iz in range(min_z_index, max_z_index+1):
x_seg, y_seg = (data_seg[:,:,iz]>0).nonzero()
x_centerline[iz-min_z_index] = np.mean(x_seg)
y_centerline[iz-min_z_index] = np.mean(y_seg)
for k in range(len(X)):
data_seg[X[k],Y[k],Z[k]] = 0
# Fit the centerline points with splines and return the new fitted coordinates
#done with nurbs for now
x_centerline_fit, y_centerline_fit,x_centerline_deriv,y_centerline_deriv,z_centerline_deriv = b_spline_centerline(x_centerline,y_centerline,z_centerline)
# Create an image with the centerline
for iz in range(min_z_index, max_z_index+1):
data_seg[round(x_centerline_fit[iz-min_z_index]), round(y_centerline_fit[iz-min_z_index]), iz] = 1
# Write the centerline image in RPI orientation
hdr_seg.set_data_dtype('uint8') # set imagetype to uint8
print '\nWrite NIFTI volumes...'
img = nibabel.Nifti1Image(data_seg, None, hdr_seg)
nibabel.save(img,'tmp.centerline.nii')
file_name_seg = file_data_seg+'_centerline'+ext_data_seg
sct.generate_output_file('tmp.centerline.nii',file_name_seg) #pb ici
# copy files into parent folder
#sct.run('cp '+file_name_seg+' ../')
del data_seg
# come back to parent folder
# os.chdir('..')
# Change orientation of the output centerline into input orientation
print '\nOrient centerline image to input orientation: ' + orientation
set_orientation(file_name_seg, orientation, file_name_seg)
print '\nRemoving overlap of the centerline obtain with label file if there are any:'
## Remove overlap from centerline file obtain with label file
remove_overlap(file_name_label, file_name_seg, "generated_centerline_without_overlap.nii.gz")
## Concatenation of the two centerline files
print '\nConcatenation of the two centerline files:'
if output_file_name != None :
file_name = output_file_name
else: file_name = 'centerline_total_from_label_and_seg'
sct.run('fslmaths generated_centerline_without_overlap.nii.gz -add ' + file_name_seg + ' ' + file_name)
if verbose == 1 :
import matplotlib.pyplot as plt
from scipy import ndimage
#Get back concatenation of segmentation and labels before any processing
data_concatenate = data_seg_to_show + data_label_to_show
z_centerline = [iz for iz in range(0, nz, 1) if data_concatenate[:, :, iz].any()]
nz_nonz = len(z_centerline)
x_centerline = [0 for iz in range(0, nz_nonz, 1)]
y_centerline = [0 for iz in range(0, nz_nonz, 1)]
# Calculate centerline coordinates and create image of the centerline
for iz in range(0, nz_nonz, 1):
x_centerline[iz], y_centerline[iz] = ndimage.measurements.center_of_mass(data_concatenate[:, :, z_centerline[iz]])
#Load file with resulting centerline
file_centerline_fit = nibabel.load(file_name)
data_centerline_fit = file_centerline_fit.get_data()
z_centerline_fit = [iz for iz in range(0, nz, 1) if data_centerline_fit[:, :, iz].any()]
nz_nonz_fit = len(z_centerline_fit)
x_centerline_fit_total = [0 for iz in range(0, nz_nonz_fit, 1)]
y_centerline_fit_total = [0 for iz in range(0, nz_nonz_fit, 1)]
#Convert to array
x_centerline_fit_total = np.asarray(x_centerline_fit_total)
y_centerline_fit_total = np.asarray(y_centerline_fit_total)
#Calculate overlap between seg and label
length_overlap = X_fit.shape[0] + x_centerline_fit.shape[0] - x_centerline_fit_total.shape[0]
# The total fitting is the concatenation of the two fitting (
for i in range(x_centerline_fit.shape[0]):
x_centerline_fit_total[i] = x_centerline_fit[i]
y_centerline_fit_total[i] = y_centerline_fit[i]
for i in range(X_fit.shape[0]-length_overlap):
x_centerline_fit_total[x_centerline_fit.shape[0] + i] = X_fit[i+length_overlap]
y_centerline_fit_total[x_centerline_fit.shape[0] + i] = Y_fit[i+length_overlap]
print x_centerline_fit.shape[0] + i
#for iz in range(0, nz_nonz_fit, 1):
# x_centerline_fit[iz], y_centerline_fit[iz] = ndimage.measurements.center_of_mass(data_centerline_fit[:, :, z_centerline_fit[iz]])
#Creation of a vector x that takes into account the distance between the labels
#x_centerline_fit = np.asarray(x_centerline_fit)
#y_centerline_fit = np.asarray(y_centerline_fit)
x_display = [0 for i in range(x_centerline_fit_total.shape[0])]
y_display = [0 for i in range(y_centerline_fit_total.shape[0])]
for i in range(0, nz_nonz, 1):
x_display[z_centerline[i]-z_centerline[0]] = x_centerline[i]
y_display[z_centerline[i]-z_centerline[0]] = y_centerline[i]
plt.figure(1)
plt.subplot(2,1,1)
plt.plot(z_centerline_fit, x_display, 'ro')
plt.plot(z_centerline_fit, x_centerline_fit_total)
plt.xlabel("Z")
plt.ylabel("X")
plt.title("x and x_fit coordinates")
plt.subplot(2,1,2)
plt.plot(z_centerline_fit, y_display, 'ro')
plt.plot(z_centerline_fit, y_centerline_fit_total)
plt.xlabel("Z")
plt.ylabel("Y")
plt.title("y and y_fit coordinates")
plt.show()
del data_concatenate, data_label_to_show, data_seg_to_show, data_centerline_fit
sct.run('cp '+file_name+' ../')
# Copy result into parent folder
sct.run('cp '+file_name+' ../')
# Come back to parent folder
os.chdir('..')
# Remove temporary centerline files
if remove_temp_files:
print('\nRemove temporary files...')
sct.run('rm -rf '+path_tmp)
#Process for a text file as output:
if parameter == "text_file" :
print "\nText file process"
#Process for only a segmentation file:
if "-i" in arguments and "-l" not in arguments:
# Extract path, file and extension
segmentation_file = os.path.abspath(segmentation_file)
path_data, file_data, ext_data = sct.extract_fname(segmentation_file)
# create temporary folder
path_tmp = 'tmp.'+time.strftime("%y%m%d%H%M%S")
sct.run('mkdir '+path_tmp)
# copy files into tmp folder
sct.run('cp '+segmentation_file+' '+path_tmp)
# go to tmp folder
os.chdir(path_tmp)
# Change orientation of the input segmentation into RPI
print '\nOrient segmentation image to RPI orientation...'
fname_segmentation_orient = 'tmp.segmentation_rpi' + ext_data
set_orientation(file_data+ext_data, 'RPI', fname_segmentation_orient)
# Extract orientation of the input segmentation
orientation = get_orientation(file_data+ext_data)
print '\nOrientation of segmentation image: ' + orientation
# Get size of data
print '\nGet dimensions data...'
nx, ny, nz, nt, px, py, pz, pt = sct.get_dimension(fname_segmentation_orient)
print '.. '+str(nx)+' x '+str(ny)+' y '+str(nz)+' z '+str(nt)
print '\nOpen segmentation volume...'
file = nibabel.load(fname_segmentation_orient)
data = file.get_data()
hdr = file.get_header()
# Extract min and max index in Z direction
X, Y, Z = (data>0).nonzero()
min_z_index, max_z_index = min(Z), max(Z)
x_centerline = [0 for i in range(0,max_z_index-min_z_index+1)]
y_centerline = [0 for i in range(0,max_z_index-min_z_index+1)]
z_centerline = [iz for iz in range(min_z_index, max_z_index+1)]
# Extract segmentation points and average per slice
for iz in range(min_z_index, max_z_index+1):
x_seg, y_seg = (data[:,:,iz]>0).nonzero()
x_centerline[iz-min_z_index] = np.mean(x_seg)
y_centerline[iz-min_z_index] = np.mean(y_seg)
for k in range(len(X)):
data[X[k],Y[k],Z[k]] = 0
# Fit the centerline points with splines and return the new fitted coordinates
x_centerline_fit, y_centerline_fit,x_centerline_deriv,y_centerline_deriv,z_centerline_deriv = b_spline_centerline(x_centerline,y_centerline,z_centerline)
# Create output text file
if output_file_name != None :
file_name = output_file_name
else: file_name = file_data+'_centerline'+'.txt'
sct.printv('\nWrite text file...', verbose)
#file_results = open("../"+file_name, 'w')
file_results = open(file_name, 'w')
for i in range(min_z_index, max_z_index+1):
file_results.write(str(int(i)) + ' ' + str(x_centerline_fit[i-min_z_index]) + ' ' + str(y_centerline_fit[i-min_z_index]) + '\n')
file_results.close()
# Copy result into parent folder
sct.run('cp '+file_name+' ../')
del data
# come back to parent folder
os.chdir('..')
# Remove temporary files
if remove_temp_files:
print('\nRemove temporary files...')
sct.run('rm -rf '+path_tmp)
return file_name
#Process for only a label file:
if "-l" in arguments and "-i" not in arguments:
file = os.path.abspath(label_file)
path_data, file_data, ext_data = sct.extract_fname(file)
file = nibabel.load(label_file)
data = file.get_data()
hdr = file.get_header()
X,Y,Z = (data>0).nonzero()
Z_new = np.linspace(min(Z),max(Z),(max(Z)-min(Z)+1))
# sort X and Y arrays using Z
X = [X[i] for i in Z[:].argsort()]
Y = [Y[i] for i in Z[:].argsort()]
Z = [Z[i] for i in Z[:].argsort()]
#print X, Y, Z
f1 = interpolate.UnivariateSpline(Z, X)
f2 = interpolate.UnivariateSpline(Z, Y)
X_fit = f1(Z_new)
Y_fit = f2(Z_new)
#print X_fit
#print Y_fit
if verbose==1 :
import matplotlib.pyplot as plt
plt.figure()
plt.plot(Z_new,X_fit)
plt.plot(Z,X,'o',linestyle = 'None')
plt.show()
plt.figure()
plt.plot(Z_new,Y_fit)
plt.plot(Z,Y,'o',linestyle = 'None')
plt.show()
data =data*0
for iz in xrange(len(X_fit)):
data[X_fit[iz],Y_fit[iz],Z_new[iz]] = 1
# Create output text file
sct.printv('\nWrite text file...', verbose)
if output_file_name != None :
file_name = output_file_name
else: file_name = file_data+'_centerline'+ext_data
file_results = open(file_name, 'w')
min_z_index, max_z_index = min(Z), max(Z)
for i in range(min_z_index, max_z_index+1):
file_results.write(str(int(i)) + ' ' + str(X_fit[i-min_z_index]) + ' ' + str(Y_fit[i-min_z_index]) + '\n')
file_results.close()
del data
#Process for a segmentation file and a label file:
if "-l" and "-i" in arguments:
## Creation of a temporary file that will contain each centerline file of the process
path_tmp = 'tmp.'+time.strftime("%y%m%d%H%M%S")
sct.run('mkdir '+path_tmp)
##From label file create centerline text file
print '\nPROCESS PART 1: From label file create centerline text file.'
file_label = os.path.abspath(label_file)
path_data_label, file_data_label, ext_data_label = sct.extract_fname(file_label)
file_label = nibabel.load(label_file)
#Copy label_file into temporary folder
sct.run('cp '+label_file+' '+path_tmp)
data_label = file_label.get_data()
hdr_label = file_label.get_header()
X,Y,Z = (data_label>0).nonzero()
Z_new = np.linspace(min(Z),max(Z),(max(Z)-min(Z)+1))
# sort X and Y arrays using Z
X = [X[i] for i in Z[:].argsort()]
Y = [Y[i] for i in Z[:].argsort()]
Z = [Z[i] for i in Z[:].argsort()]
#print X, Y, Z
f1 = interpolate.UnivariateSpline(Z, X)
f2 = interpolate.UnivariateSpline(Z, Y)
X_fit = f1(Z_new)
Y_fit = f2(Z_new)
#print X_fit
#print Y_fit
if verbose==1 :
import matplotlib.pyplot as plt
plt.figure()
plt.plot(Z_new,X_fit)
plt.plot(Z,X,'o',linestyle = 'None')
plt.show()
plt.figure()
plt.plot(Z_new,Y_fit)
plt.plot(Z,Y,'o',linestyle = 'None')
plt.show()
data_label =data_label*0
for i in xrange(len(X_fit)):
data_label[X_fit[i],Y_fit[i],Z_new[i]] = 1
# Create output text file
sct.printv('\nWrite text file...', verbose)
file_name_label = file_data_label+'_centerline'+'.txt'
file_results = open(path_tmp + '/' + file_name_label, 'w')
min_z_index, max_z_index = min(Z), max(Z)
for i in range(min_z_index, max_z_index+1):
file_results.write(str(int(i)) + ' ' + str(X_fit[i-min_z_index]) + ' ' + str(Y_fit[i-min_z_index]) + '\n')
file_results.close()
# copy files into tmp folder
#sct.run('cp '+file_name_label+' '+path_tmp)
del data_label
##From segmentation file create centerline text file
print '\nPROCESS PART 2: From segmentation file create centerline image.'
# Extract path, file and extension
segmentation_file = os.path.abspath(segmentation_file)
path_data_seg, file_data_seg, ext_data_seg = sct.extract_fname(segmentation_file)
# copy files into tmp folder
sct.run('cp '+segmentation_file+' '+path_tmp)
# go to tmp folder
os.chdir(path_tmp)
# Change orientation of the input segmentation into RPI
print '\nOrient segmentation image to RPI orientation...'
fname_segmentation_orient = 'tmp.segmentation_rpi' + ext_data_seg
set_orientation(file_data_seg+ext_data_seg, 'RPI', fname_segmentation_orient)
# Extract orientation of the input segmentation
orientation = get_orientation(file_data_seg+ext_data_seg)
print '\nOrientation of segmentation image: ' + orientation
# Get size of data
print '\nGet dimensions data...'
nx, ny, nz, nt, px, py, pz, pt = sct.get_dimension(fname_segmentation_orient)
print '.. '+str(nx)+' x '+str(ny)+' y '+str(nz)+' z '+str(nt)
print '\nOpen segmentation volume...'
file_seg = nibabel.load(fname_segmentation_orient)
data_seg = file_seg.get_data()
hdr_seg = file_seg.get_header()
# Extract min and max index in Z direction
X, Y, Z = (data_seg>0).nonzero()
min_z_index, max_z_index = min(Z), max(Z)
x_centerline = [0 for i in range(0,max_z_index-min_z_index+1)]
y_centerline = [0 for i in range(0,max_z_index-min_z_index+1)]
z_centerline = [iz for iz in range(min_z_index, max_z_index+1)]
# Extract segmentation points and average per slice
for iz in range(min_z_index, max_z_index+1):
x_seg, y_seg = (data_seg[:,:,iz]>0).nonzero()
x_centerline[iz-min_z_index] = np.mean(x_seg)
y_centerline[iz-min_z_index] = np.mean(y_seg)
for k in range(len(X)):
data_seg[X[k],Y[k],Z[k]] = 0
# Fit the centerline points with splines and return the new fitted coordinates
#done with nurbs for now
x_centerline_fit, y_centerline_fit,x_centerline_deriv,y_centerline_deriv,z_centerline_deriv = b_spline_centerline(x_centerline,y_centerline,z_centerline)
# Create output text file
file_name_seg = file_data_seg+'_centerline'+'.txt'
sct.printv('\nWrite text file...', verbose)
file_results = open(file_name_seg, 'w')
for i in range(min_z_index, max_z_index+1):
file_results.write(str(int(i)) + ' ' + str(x_centerline_fit[i-min_z_index]) + ' ' + str(y_centerline_fit[i-min_z_index]) + '\n')
file_results.close()
del data_seg
print '\nRemoving overlap of the centerline obtain with label file if there are any:'
## Remove overlap from centerline file obtain with label file
remove_overlap(file_name_label, file_name_seg, "generated_centerline_without_overlap1.txt", parameter=1)
## Concatenation of the two centerline files
print '\nConcatenation of the two centerline files:'
if output_file_name != None :
file_name = output_file_name
else: file_name = 'centerline_total_from_label_and_seg.txt'
f_output = open(file_name, "w")
f_output.close()
with open(file_name_seg, "r") as f_seg:
with open("generated_centerline_without_overlap1.txt", "r") as f:
with open(file_name, "w") as f_output:
data_line_seg = f_seg.readlines()
data_line = f.readlines()
for line in data_line_seg :
f_output.write(line)
for line in data_line :
f_output.write(line)
# Copy result into parent folder
sct.run('cp '+file_name+' ../')
# Come back to parent folder
os.chdir('..')
# Remove temporary centerline files
if remove_temp_files:
print('\nRemove temporary files...')
sct.run('rm -rf '+path_tmp)
def main():
# Initialization to defaults parameters
fname_data = '' # data is empty by default
path_label = '' # empty by default
method = param.method # extraction mode by default
labels_of_interest = param.labels_of_interest
slices_of_interest = param.slices_of_interest
vertebral_levels = param.vertebral_levels
average_all_labels = param.average_all_labels
fname_output = param.fname_output
fname_vertebral_labeling = param.fname_vertebral_labeling
fname_normalizing_label = '' # optional then default is empty
normalization_method = '' # optional then default is empty
actual_vert_levels = None # variable used in case the vertebral levels asked by the user don't correspond exactly to the vertebral levels available in the metric data
warning_vert_levels = None # variable used to warn the user in case the vertebral levels he asked don't correspond exactly to the vertebral levels available in the metric data
verbose = param.verbose
flag_h = 0
ml_clusters = param.ml_clusters
adv_param = param.adv_param
adv_param_user = ''
# Parameters for debug mode
if param.debug:
print '\n*** WARNING: DEBUG MODE ON ***\n'
status, path_sct_data = commands.getstatusoutput(
'echo $SCT_TESTING_DATA_DIR')
fname_data = '/Users/julien/data/temp/sct_example_data/mt/mtr.nii.gz'
path_label = '/Users/julien/data/temp/sct_example_data/mt/label/atlas/'
method = 'map'
ml_clusters = '0:29,30,31'
labels_of_interest = '0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29'
slices_of_interest = ''
vertebral_levels = ''
average_all_labels = 1
fname_normalizing_label = '' #path_sct+'/testing/data/errsm_23/mt/label/template/MNI-Poly-AMU_CSF.nii.gz'
normalization_method = '' #'whole'
else:
# Check input parameters
try:
opts, args = getopt.getopt(
sys.argv[1:], 'haf:i:l:m:n:o:p:v:w:z:') # define flags
except getopt.GetoptError as err: # check if the arguments are defined
print str(err) # error
usage() # display usage
if not opts:
usage()
for opt, arg in opts: # explore flags
if opt in '-a':
average_all_labels = 1
elif opt in '-f':
path_label = os.path.abspath(arg) # save path of labels folder
elif opt == '-h': # help option
flag_h = 1
elif opt in '-i':
fname_data = arg
elif opt in '-l':
labels_of_interest = arg
elif opt in '-m': # method for metric extraction
method = arg
elif opt in '-n': # filename of the label by which the user wants to normalize
fname_normalizing_label = arg
elif opt in '-o': # output option
fname_output = arg # fname of output file
elif opt in '-p':
adv_param_user = arg
elif opt in '-v':
# vertebral levels option, if the user wants to average the metric across specific vertebral levels
vertebral_levels = arg
elif opt in '-w':
# method used for the normalization by the metric estimation into the normalizing label (see flag -n): 'sbs' for slice-by-slice or 'whole' for normalization after estimation in the whole labels
normalization_method = arg
elif opt in '-z': # slices numbers option
slices_of_interest = arg # save labels numbers
# Display usage with tract parameters by default in case files aren't chosen in arguments inputs
if fname_data == '' or path_label == '' or flag_h:
param.path_label = path_label
usage()
# Check existence of data file
sct.printv('\ncheck existence of input files...', verbose)
sct.check_file_exist(fname_data)
sct.check_folder_exist(path_label)
if fname_normalizing_label:
sct.check_folder_exist(fname_normalizing_label)
# add slash at the end
path_label = sct.slash_at_the_end(path_label, 1)
# Find path to the vertebral labeling file if vertebral levels were specified by the user
if vertebral_levels:
if slices_of_interest: # impossible to select BOTH specific slices and specific vertebral levels
print '\nERROR: You cannot select BOTH vertebral levels AND slice numbers.'
usage()
else:
fname_vertebral_labeling_list = sct.find_file_within_folder(
fname_vertebral_labeling, path_label + '..')
if len(fname_vertebral_labeling_list) > 1:
print color.red + 'ERROR: More than one file named \'' + fname_vertebral_labeling + ' were found in ' + path_label + '. Exit program.' + color.end
sys.exit(2)
elif len(fname_vertebral_labeling_list) == 0:
print color.red + 'ERROR: No file named \'' + fname_vertebral_labeling + ' were found in ' + path_label + '. Exit program.' + color.end
sys.exit(2)
else:
fname_vertebral_labeling = os.path.abspath(
fname_vertebral_labeling_list[0])
# Check input parameters
check_method(method, fname_normalizing_label, normalization_method)
# parse argument for param
if not adv_param_user == '':
adv_param = adv_param_user.replace(' ', '').split(
',') # remove spaces and parse with comma
del adv_param_user # clean variable
# TODO: check integrity of input
# Extract label info
label_id, label_name, label_file = read_label_file(path_label,
param.file_info_label)
nb_labels_total = len(label_id)
# check consistency of label input parameter.
label_id_user, average_all_labels = check_labels(
labels_of_interest, nb_labels_total, average_all_labels,
method) # If 'labels_of_interest' is empty, then
# 'label_id_user' contains the index of all labels in the file info_label.txt
# print parameters
print '\nChecked parameters:'
print ' data ...................... ' + fname_data
print ' folder label .............. ' + path_label
print ' selected labels ........... ' + str(label_id_user)
print ' estimation method ......... ' + method
print ' slices of interest ........ ' + slices_of_interest
print ' vertebral levels .......... ' + vertebral_levels
print ' vertebral labeling file.... ' + fname_vertebral_labeling
print ' advanced parameters ....... ' + str(adv_param)
# Check if the orientation of the data is RPI
orientation_data = get_orientation(fname_data)
# If orientation is not RPI, change to RPI
if orientation_data != 'RPI':
sct.printv(
'\nCreate temporary folder to change the orientation of the NIFTI files into RPI...',
verbose)
path_tmp = sct.slash_at_the_end('tmp.' + time.strftime("%y%m%d%H%M%S"),
1)
sct.create_folder(path_tmp)
# change orientation and load data
sct.printv('\nChange image orientation and load it...', verbose)
data = nib.load(
set_orientation(fname_data, 'RPI',
path_tmp + 'orient_data.nii')).get_data()
# Do the same for labels
sct.printv('\nChange labels orientation and load them...', verbose)
labels = np.empty([nb_labels_total],
dtype=object) # labels(nb_labels_total, x, y, z)
for i_label in range(0, nb_labels_total):
labels[i_label] = nib.load(
set_orientation(path_label + label_file[i_label], 'RPI',
path_tmp + 'orient_' +
label_file[i_label])).get_data()
if fname_normalizing_label: # if the "normalization" option is wanted,
normalizing_label = np.empty(
[1], dtype=object
) # choose this kind of structure so as to keep easily the
# compatibility with the rest of the code (dimensions: (1, x, y, z))
normalizing_label[0] = nib.load(
set_orientation(fname_normalizing_label, 'RPI', path_tmp +
'orient_normalizing_volume.nii')).get_data()
if vertebral_levels: # if vertebral levels were selected,
data_vertebral_labeling = nib.load(
set_orientation(
fname_vertebral_labeling, 'RPI',
path_tmp + 'orient_vertebral_labeling.nii.gz')).get_data()
# Remove the temporary folder used to change the NIFTI files orientation into RPI
sct.printv('\nRemove the temporary folder...', verbose)
status, output = commands.getstatusoutput('rm -rf ' + path_tmp)
else:
# Load image
sct.printv('\nLoad image...', verbose)
data = nib.load(fname_data).get_data()
# Load labels
sct.printv('\nLoad labels...', verbose)
labels = np.empty([nb_labels_total],
dtype=object) # labels(nb_labels_total, x, y, z)
for i_label in range(0, nb_labels_total):
labels[i_label] = nib.load(path_label +
label_file[i_label]).get_data()
if fname_normalizing_label: # if the "normalization" option is wanted,
normalizing_label = np.empty(
[1], dtype=object
) # choose this kind of structure so as to keep easily the
# compatibility with the rest of the code (dimensions: (1, x, y, z))
normalizing_label[0] = nib.load(fname_normalizing_label).get_data(
) # load the data of the normalizing label
if vertebral_levels: # if vertebral levels were selected,
data_vertebral_labeling = nib.load(
fname_vertebral_labeling).get_data()
# Change metric data type into floats for future manipulations (normalization)
data = np.float64(data)
# Get dimensions of data
sct.printv('\nGet dimensions of data...', verbose)
nx, ny, nz = data.shape
sct.printv(' ' + str(nx) + ' x ' + str(ny) + ' x ' + str(nz), verbose)
# Get dimensions of labels
sct.printv('\nGet dimensions of label...', verbose)
nx_atlas, ny_atlas, nz_atlas = labels[0].shape
sct.printv(
'.. ' + str(nx_atlas) + ' x ' + str(ny_atlas) + ' x ' + str(nz_atlas) +
' x ' + str(nb_labels_total), verbose)
# Check dimensions consistency between atlas and data
if (nx, ny, nz) != (nx_atlas, ny_atlas, nz_atlas):
print '\nERROR: Metric data and labels DO NOT HAVE SAME DIMENSIONS.'
sys.exit(2)
# Update the flag "slices_of_interest" according to the vertebral levels selected by user (if it's the case)
if vertebral_levels:
slices_of_interest, actual_vert_levels, warning_vert_levels = \
get_slices_matching_with_vertebral_levels(data, vertebral_levels, data_vertebral_labeling)
# select slice of interest by cropping data and labels
if slices_of_interest:
data = remove_slices(data, slices_of_interest)
for i_label in range(0, nb_labels_total):
labels[i_label] = remove_slices(labels[i_label],
slices_of_interest)
if fname_normalizing_label: # if the "normalization" option was selected,
normalizing_label[0] = remove_slices(normalizing_label[0],
slices_of_interest)
# if user wants to get unique value across labels, then combine all labels together
if average_all_labels == 1:
sum_labels_user = np.sum(
labels[label_id_user]) # sum the labels selected by user
if method == 'ml' or method == 'map': # in case the maximum likelihood and the average across different labels are wanted
labels_tmp = np.empty([nb_labels_total - len(label_id_user) + 1],
dtype=object)
labels = np.delete(
labels, label_id_user) # remove the labels selected by user
labels_tmp[
0] = sum_labels_user # put the sum of the labels selected by user in first position of the tmp
# variable
for i_label in range(1, len(labels_tmp)):
labels_tmp[i_label] = labels[
i_label -
1] # fill the temporary array with the values of the non-selected labels
labels = labels_tmp # replace the initial labels value by the updated ones (with the summed labels)
del labels_tmp # delete the temporary labels
else: # in other cases than the maximum likelihood, we can remove other labels (not needed for estimation)
labels = np.empty(1, dtype=object)
labels[
0] = sum_labels_user # we create a new label array that includes only the summed labels
if fname_normalizing_label: # if the "normalization" option is wanted
sct.printv('\nExtract normalization values...', verbose)
if normalization_method == 'sbs': # case: the user wants to normalize slice-by-slice
for z in range(0, data.shape[-1]):
normalizing_label_slice = np.empty(
[1], dtype=object
) # in order to keep compatibility with the function
# 'extract_metric_within_tract', define a new array for the slice z of the normalizing labels
normalizing_label_slice[0] = normalizing_label[0][..., z]
metric_normalizing_label = extract_metric_within_tract(
data[..., z], normalizing_label_slice, method, 0)
# estimate the metric mean in the normalizing label for the slice z
if metric_normalizing_label[0][0] != 0:
data[..., z] = data[..., z] / metric_normalizing_label[0][
0] # divide all the slice z by this value
elif normalization_method == 'whole': # case: the user wants to normalize after estimations in the whole labels
metric_mean_norm_label, metric_std_norm_label = extract_metric_within_tract(
data, normalizing_label, method,
param.verbose) # mean and std are lists
# identify cluster for each tract (for use with robust ML)
ml_clusters_array = get_clusters(ml_clusters, labels)
# extract metrics within labels
sct.printv('\nExtract metric within labels...', verbose)
metric_mean, metric_std = extract_metric_within_tract(
data, labels, method, verbose, ml_clusters_array,
adv_param) # mean and std are lists
if fname_normalizing_label and normalization_method == 'whole': # case: user wants to normalize after estimations in the whole labels
metric_mean, metric_std = np.divide(metric_mean,
metric_mean_norm_label), np.divide(
metric_std,
metric_std_norm_label)
# update label name if average
if average_all_labels == 1:
label_name[0] = 'AVERAGED' + ' -'.join(
label_name[i]
for i in label_id_user) # concatenate the names of the
# labels selected by the user if the average tag was asked
label_id_user = [
0
] # update "label_id_user" to select the "averaged" label (which is in first position)
metric_mean = metric_mean[label_id_user]
metric_std = metric_std[label_id_user]
# display metrics
sct.printv('\nEstimation results:', 1)
for i in range(0, metric_mean.size):
sct.printv(
str(label_id_user[i]) + ', ' + str(label_name[label_id_user[i]]) +
': ' + str(metric_mean[i]) + ' +/- ' + str(metric_std[i]), 1,
'info')
# save and display metrics
save_metrics(label_id_user, label_name, slices_of_interest, metric_mean,
metric_std, fname_output, fname_data, method,
fname_normalizing_label, actual_vert_levels,
warning_vert_levels)
def straighten(self):
# Initialization
fname_anat = self.input_filename
fname_centerline = self.centerline_filename
fname_output = self.output_filename
gapxy = self.gapxy
gapz = self.gapz
padding = self.padding
remove_temp_files = self.remove_temp_files
verbose = self.verbose
interpolation_warp = self.interpolation_warp
algo_fitting = self.algo_fitting
window_length = self.window_length
type_window = self.type_window
crop = self.crop
# start timer
start_time = time.time()
# get path of the toolbox
status, path_sct = commands.getstatusoutput("echo $SCT_DIR")
sct.printv(path_sct, verbose)
if self.debug == 1:
print "\n*** WARNING: DEBUG MODE ON ***\n"
fname_anat = (
"/Users/julien/data/temp/sct_example_data/t2/tmp.150401221259/anat_rpi.nii"
) # path_sct+'/testing/sct_testing_data/data/t2/t2.nii.gz'
fname_centerline = (
"/Users/julien/data/temp/sct_example_data/t2/tmp.150401221259/centerline_rpi.nii"
) # path_sct+'/testing/sct_testing_data/data/t2/t2_seg.nii.gz'
remove_temp_files = 0
type_window = "hanning"
verbose = 2
# check existence of input files
sct.check_file_exist(fname_anat, verbose)
sct.check_file_exist(fname_centerline, verbose)
# Display arguments
sct.printv("\nCheck input arguments...", verbose)
sct.printv(" Input volume ...................... " + fname_anat, verbose)
sct.printv(" Centerline ........................ " + fname_centerline, verbose)
sct.printv(" Final interpolation ............... " + interpolation_warp, verbose)
sct.printv(" Verbose ........................... " + str(verbose), verbose)
sct.printv("", verbose)
# Extract path/file/extension
path_anat, file_anat, ext_anat = sct.extract_fname(fname_anat)
path_centerline, file_centerline, ext_centerline = sct.extract_fname(fname_centerline)
# create temporary folder
path_tmp = "tmp." + time.strftime("%y%m%d%H%M%S")
sct.run("mkdir " + path_tmp, verbose)
# copy files into tmp folder
sct.run("cp " + fname_anat + " " + path_tmp, verbose)
sct.run("cp " + fname_centerline + " " + path_tmp, verbose)
# go to tmp folder
os.chdir(path_tmp)
try:
# Change orientation of the input centerline into RPI
sct.printv("\nOrient centerline to RPI orientation...", verbose)
fname_centerline_orient = file_centerline + "_rpi.nii.gz"
set_orientation(file_centerline + ext_centerline, "RPI", fname_centerline_orient)
# Get dimension
sct.printv("\nGet dimensions...", verbose)
nx, ny, nz, nt, px, py, pz, pt = sct.get_dimension(fname_centerline_orient)
sct.printv(".. matrix size: " + str(nx) + " x " + str(ny) + " x " + str(nz), verbose)
sct.printv(".. voxel size: " + str(px) + "mm x " + str(py) + "mm x " + str(pz) + "mm", verbose)
# smooth centerline
x_centerline_fit, y_centerline_fit, z_centerline, x_centerline_deriv, y_centerline_deriv, z_centerline_deriv = smooth_centerline(
fname_centerline_orient,
algo_fitting=algo_fitting,
type_window=type_window,
window_length=window_length,
verbose=verbose,
)
# Get coordinates of landmarks along curved centerline
# ==========================================================================================
sct.printv("\nGet coordinates of landmarks along curved centerline...", verbose)
# landmarks are created along the curved centerline every z=gapz. They consist of a "cross" of size gapx and gapy. In voxel space!!!
# find z indices along centerline given a specific gap: iz_curved
nz_nonz = len(z_centerline)
nb_landmark = int(round(float(nz_nonz) / gapz))
if nb_landmark == 0:
nb_landmark = 1
if nb_landmark == 1:
iz_curved = [0]
else:
iz_curved = [i * gapz for i in range(0, nb_landmark - 1)]
iz_curved.append(nz_nonz - 1)
# print iz_curved, len(iz_curved)
n_iz_curved = len(iz_curved)
# print n_iz_curved
# landmark_curved initialisation
# landmark_curved = [ [ [ 0 for i in range(0, 3)] for i in range(0, 5) ] for i in iz_curved ]
from msct_types import Coordinate
landmark_curved = []
landmark_curved_value = 1
### TODO: THIS PART IS SLOW AND CAN BE MADE FASTER
### >>==============================================================================================================
for iz in range(min(iz_curved), max(iz_curved) + 1, 1):
if iz in iz_curved:
index = iz_curved.index(iz)
# calculate d (ax+by+cz+d=0)
# print iz_curved[index]
a = x_centerline_deriv[iz]
b = y_centerline_deriv[iz]
c = z_centerline_deriv[iz]
x = x_centerline_fit[iz]
y = y_centerline_fit[iz]
z = z_centerline[iz]
d = -(a * x + b * y + c * z)
# print a,b,c,d,x,y,z
# set coordinates for landmark at the center of the cross
coord = Coordinate([0, 0, 0, landmark_curved_value])
coord.x, coord.y, coord.z = x_centerline_fit[iz], y_centerline_fit[iz], z_centerline[iz]
landmark_curved.append(coord)
# set y coordinate to y_centerline_fit[iz] for elements 1 and 2 of the cross
cross_coordinates = [
Coordinate([0, 0, 0, landmark_curved_value + 1]),
Coordinate([0, 0, 0, landmark_curved_value + 2]),
Coordinate([0, 0, 0, landmark_curved_value + 3]),
Coordinate([0, 0, 0, landmark_curved_value + 4]),
]
cross_coordinates[0].y = y_centerline_fit[iz]
cross_coordinates[1].y = y_centerline_fit[iz]
# set x and z coordinates for landmarks +x and -x, forcing de landmark to be in the orthogonal plan and the distance landmark/curve to be gapxy
x_n = Symbol("x_n")
cross_coordinates[1].x, cross_coordinates[0].x = solve(
(x_n - x) ** 2 + ((-1 / c) * (a * x_n + b * y + d) - z) ** 2 - gapxy ** 2, x_n
) # x for -x and +x
cross_coordinates[0].z = (-1 / c) * (a * cross_coordinates[0].x + b * y + d) # z for +x
cross_coordinates[1].z = (-1 / c) * (a * cross_coordinates[1].x + b * y + d) # z for -x
# set x coordinate to x_centerline_fit[iz] for elements 3 and 4 of the cross
cross_coordinates[2].x = x_centerline_fit[iz]
cross_coordinates[3].x = x_centerline_fit[iz]
# set coordinates for landmarks +y and -y. Here, x coordinate is 0 (already initialized).
y_n = Symbol("y_n")
cross_coordinates[3].y, cross_coordinates[2].y = solve(
(y_n - y) ** 2 + ((-1 / c) * (a * x + b * y_n + d) - z) ** 2 - gapxy ** 2, y_n
) # y for -y and +y
cross_coordinates[2].z = (-1 / c) * (a * x + b * cross_coordinates[2].y + d) # z for +y
cross_coordinates[3].z = (-1 / c) * (a * x + b * cross_coordinates[3].y + d) # z for -y
for coord in cross_coordinates:
landmark_curved.append(coord)
landmark_curved_value += 5
else:
if self.all_labels == 1:
landmark_curved.append(
Coordinate(
[x_centerline_fit[iz], y_centerline_fit[iz], z_centerline[iz], landmark_curved_value],
mode="continuous",
)
)
landmark_curved_value += 1
### <<==============================================================================================================
# Get coordinates of landmarks along straight centerline
# ==========================================================================================
sct.printv("\nGet coordinates of landmarks along straight centerline...", verbose)
# landmark_straight = [ [ [ 0 for i in range(0,3)] for i in range (0,5) ] for i in iz_curved ] # same structure as landmark_curved
landmark_straight = []
# calculate the z indices corresponding to the Euclidean distance between two consecutive points on the curved centerline (approximation curve --> line)
# TODO: DO NOT APPROXIMATE CURVE --> LINE
if nb_landmark == 1:
iz_straight = [0 for i in range(0, nb_landmark + 1)]
else:
iz_straight = [0 for i in range(0, nb_landmark)]
# print iz_straight,len(iz_straight)
iz_straight[0] = iz_curved[0]
for index in range(1, n_iz_curved, 1):
# compute vector between two consecutive points on the curved centerline
vector_centerline = [
x_centerline_fit[iz_curved[index]] - x_centerline_fit[iz_curved[index - 1]],
y_centerline_fit[iz_curved[index]] - y_centerline_fit[iz_curved[index - 1]],
z_centerline[iz_curved[index]] - z_centerline[iz_curved[index - 1]],
]
# compute norm of this vector
norm_vector_centerline = linalg.norm(vector_centerline, ord=2)
# round to closest integer value
norm_vector_centerline_rounded = int(round(norm_vector_centerline, 0))
# assign this value to the current z-coordinate on the straight centerline
iz_straight[index] = iz_straight[index - 1] + norm_vector_centerline_rounded
# initialize x0 and y0 to be at the center of the FOV
x0 = int(round(nx / 2))
y0 = int(round(ny / 2))
landmark_curved_value = 1
for iz in range(min(iz_curved), max(iz_curved) + 1, 1):
if iz in iz_curved:
index = iz_curved.index(iz)
# set coordinates for landmark at the center of the cross
landmark_straight.append(Coordinate([x0, y0, iz_straight[index], landmark_curved_value]))
# set x, y and z coordinates for landmarks +x
landmark_straight.append(
Coordinate([x0 + gapxy, y0, iz_straight[index], landmark_curved_value + 1])
)
# set x, y and z coordinates for landmarks -x
landmark_straight.append(
Coordinate([x0 - gapxy, y0, iz_straight[index], landmark_curved_value + 2])
)
# set x, y and z coordinates for landmarks +y
landmark_straight.append(
Coordinate([x0, y0 + gapxy, iz_straight[index], landmark_curved_value + 3])
)
# set x, y and z coordinates for landmarks -y
landmark_straight.append(
Coordinate([x0, y0 - gapxy, iz_straight[index], landmark_curved_value + 4])
)
landmark_curved_value += 5
else:
if self.all_labels == 1:
landmark_straight.append(Coordinate([x0, y0, iz, landmark_curved_value]))
landmark_curved_value += 1
# Create NIFTI volumes with landmarks
# ==========================================================================================
# Pad input volume to deal with the fact that some landmarks on the curved centerline might be outside the FOV
# N.B. IT IS VERY IMPORTANT TO PAD ALSO ALONG X and Y, OTHERWISE SOME LANDMARKS MIGHT GET OUT OF THE FOV!!!
# sct.run('fslview ' + fname_centerline_orient)
sct.printv("\nPad input volume to account for landmarks that fall outside the FOV...", verbose)
sct.run(
"isct_c3d "
+ fname_centerline_orient
+ " -pad "
+ str(padding)
+ "x"
+ str(padding)
+ "x"
+ str(padding)
+ "vox "
+ str(padding)
+ "x"
+ str(padding)
+ "x"
+ str(padding)
+ "vox 0 -o tmp.centerline_pad.nii.gz",
verbose,
)
# Open padded centerline for reading
sct.printv("\nOpen padded centerline for reading...", verbose)
file = load("tmp.centerline_pad.nii.gz")
data = file.get_data()
hdr = file.get_header()
if self.algo_landmark_rigid is not None and self.algo_landmark_rigid != "None":
# Reorganize landmarks
points_fixed, points_moving = [], []
for coord in landmark_straight:
points_fixed.append([coord.x, coord.y, coord.z])
for coord in landmark_curved:
points_moving.append([coord.x, coord.y, coord.z])
# Register curved landmarks on straight landmarks based on python implementation
sct.printv("\nComputing rigid transformation (algo=" + self.algo_landmark_rigid + ") ...", verbose)
import msct_register_landmarks
(
rotation_matrix,
translation_array,
points_moving_reg,
) = msct_register_landmarks.getRigidTransformFromLandmarks(
points_fixed, points_moving, constraints=self.algo_landmark_rigid, show=False
)
# reorganize registered points
landmark_curved_rigid = []
for index_curved, ind in enumerate(range(0, len(points_moving_reg), 1)):
coord = Coordinate()
coord.x, coord.y, coord.z, coord.value = (
points_moving_reg[ind][0],
points_moving_reg[ind][1],
points_moving_reg[ind][2],
index_curved + 1,
)
landmark_curved_rigid.append(coord)
# Create volumes containing curved and straight landmarks
data_curved_landmarks = data * 0
data_curved_rigid_landmarks = data * 0
data_straight_landmarks = data * 0
# Loop across cross index
for index in range(0, len(landmark_curved_rigid)):
x, y, z = (
int(round(landmark_curved[index].x)),
int(round(landmark_curved[index].y)),
int(round(landmark_curved[index].z)),
)
# attribute landmark_value to the voxel and its neighbours
data_curved_landmarks[
x + padding - 1 : x + padding + 2,
y + padding - 1 : y + padding + 2,
z + padding - 1 : z + padding + 2,
] = landmark_curved[index].value
# get x, y and z coordinates of curved landmark (rounded to closest integer)
x, y, z = (
int(round(landmark_curved_rigid[index].x)),
int(round(landmark_curved_rigid[index].y)),
int(round(landmark_curved_rigid[index].z)),
)
# attribute landmark_value to the voxel and its neighbours
data_curved_rigid_landmarks[
x + padding - 1 : x + padding + 2,
y + padding - 1 : y + padding + 2,
z + padding - 1 : z + padding + 2,
] = landmark_curved_rigid[index].value
# get x, y and z coordinates of straight landmark (rounded to closest integer)
x, y, z = (
int(round(landmark_straight[index].x)),
int(round(landmark_straight[index].y)),
int(round(landmark_straight[index].z)),
)
# attribute landmark_value to the voxel and its neighbours
data_straight_landmarks[
x + padding - 1 : x + padding + 2,
y + padding - 1 : y + padding + 2,
z + padding - 1 : z + padding + 2,
] = landmark_straight[index].value
# Write NIFTI volumes
sct.printv("\nWrite NIFTI volumes...", verbose)
hdr.set_data_dtype("uint32") # set imagetype to uint8 #TODO: maybe use int32
img = Nifti1Image(data_curved_landmarks, None, hdr)
save(img, "tmp.landmarks_curved.nii.gz")
sct.printv(".. File created: tmp.landmarks_curved.nii.gz", verbose)
hdr.set_data_dtype("uint32") # set imagetype to uint8 #TODO: maybe use int32
img = Nifti1Image(data_curved_rigid_landmarks, None, hdr)
save(img, "tmp.landmarks_curved_rigid.nii.gz")
sct.printv(".. File created: tmp.landmarks_curved_rigid.nii.gz", verbose)
img = Nifti1Image(data_straight_landmarks, None, hdr)
save(img, "tmp.landmarks_straight.nii.gz")
sct.printv(".. File created: tmp.landmarks_straight.nii.gz", verbose)
# writing rigid transformation file
text_file = open("tmp.curve2straight_rigid.txt", "w")
text_file.write("#Insight Transform File V1.0\n")
text_file.write("#Transform 0\n")
text_file.write("Transform: AffineTransform_double_3_3\n")
text_file.write(
"Parameters: %.9f %.9f %.9f %.9f %.9f %.9f %.9f %.9f %.9f %.9f %.9f %.9f\n"
% (
rotation_matrix[0, 0],
rotation_matrix[0, 1],
rotation_matrix[0, 2],
rotation_matrix[1, 0],
rotation_matrix[1, 1],
rotation_matrix[1, 2],
rotation_matrix[2, 0],
rotation_matrix[2, 1],
rotation_matrix[2, 2],
-translation_array[0, 0],
translation_array[0, 1],
-translation_array[0, 2],
)
)
text_file.write("FixedParameters: 0 0 0\n")
text_file.close()
else:
# Create volumes containing curved and straight landmarks
data_curved_landmarks = data * 0
data_straight_landmarks = data * 0
# Loop across cross index
for index in range(0, len(landmark_curved)):
x, y, z = (
int(round(landmark_curved[index].x)),
int(round(landmark_curved[index].y)),
int(round(landmark_curved[index].z)),
)
# attribute landmark_value to the voxel and its neighbours
data_curved_landmarks[
x + padding - 1 : x + padding + 2,
y + padding - 1 : y + padding + 2,
z + padding - 1 : z + padding + 2,
] = landmark_curved[index].value
# get x, y and z coordinates of straight landmark (rounded to closest integer)
x, y, z = (
int(round(landmark_straight[index].x)),
int(round(landmark_straight[index].y)),
int(round(landmark_straight[index].z)),
)
# attribute landmark_value to the voxel and its neighbours
data_straight_landmarks[
x + padding - 1 : x + padding + 2,
y + padding - 1 : y + padding + 2,
z + padding - 1 : z + padding + 2,
] = landmark_straight[index].value
# Write NIFTI volumes
sct.printv("\nWrite NIFTI volumes...", verbose)
hdr.set_data_dtype("uint32") # set imagetype to uint8 #TODO: maybe use int32
img = Nifti1Image(data_curved_landmarks, None, hdr)
save(img, "tmp.landmarks_curved.nii.gz")
sct.printv(".. File created: tmp.landmarks_curved.nii.gz", verbose)
img = Nifti1Image(data_straight_landmarks, None, hdr)
save(img, "tmp.landmarks_straight.nii.gz")
sct.printv(".. File created: tmp.landmarks_straight.nii.gz", verbose)
# Estimate deformation field by pairing landmarks
# ==========================================================================================
# convert landmarks to INT
sct.printv("\nConvert landmarks to INT...", verbose)
sct.run("isct_c3d tmp.landmarks_straight.nii.gz -type int -o tmp.landmarks_straight.nii.gz", verbose)
sct.run("isct_c3d tmp.landmarks_curved.nii.gz -type int -o tmp.landmarks_curved.nii.gz", verbose)
# This stands to avoid overlapping between landmarks
sct.printv("\nMake sure all labels between landmark_curved and landmark_curved match...", verbose)
label_process_straight = ProcessLabels(
fname_label="tmp.landmarks_straight.nii.gz",
fname_output="tmp.landmarks_straight.nii.gz",
fname_ref="tmp.landmarks_curved.nii.gz",
verbose=verbose,
)
label_process_straight.process("remove")
label_process_curved = ProcessLabels(
fname_label="tmp.landmarks_curved.nii.gz",
fname_output="tmp.landmarks_curved.nii.gz",
fname_ref="tmp.landmarks_straight.nii.gz",
verbose=verbose,
)
label_process_curved.process("remove")
# Estimate rigid transformation
sct.printv("\nEstimate rigid transformation between paired landmarks...", verbose)
sct.run(
"isct_ANTSUseLandmarkImagesToGetAffineTransform tmp.landmarks_straight.nii.gz tmp.landmarks_curved.nii.gz rigid tmp.curve2straight_rigid.txt",
verbose,
)
# Apply rigid transformation
sct.printv("\nApply rigid transformation to curved landmarks...", verbose)
# sct.run('sct_apply_transfo -i tmp.landmarks_curved.nii.gz -o tmp.landmarks_curved_rigid.nii.gz -d tmp.landmarks_straight.nii.gz -w tmp.curve2straight_rigid.txt -x nn', verbose)
Transform(
input_filename="tmp.landmarks_curved.nii.gz",
source_reg="tmp.landmarks_curved_rigid.nii.gz",
output_filename="tmp.landmarks_straight.nii.gz",
warp="tmp.curve2straight_rigid.txt",
interp="nn",
verbose=verbose,
).apply()
if verbose == 2:
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
fig = plt.figure()
ax = Axes3D(fig)
ax.plot(x_centerline_fit, y_centerline_fit, z_centerline, zdir="z")
ax.plot(
[coord.x for coord in landmark_curved],
[coord.y for coord in landmark_curved],
[coord.z for coord in landmark_curved],
".",
)
ax.plot(
[coord.x for coord in landmark_straight],
[coord.y for coord in landmark_straight],
[coord.z for coord in landmark_straight],
"r.",
)
if self.algo_landmark_rigid is not None and self.algo_landmark_rigid != "None":
ax.plot(
[coord.x for coord in landmark_curved_rigid],
[coord.y for coord in landmark_curved_rigid],
[coord.z for coord in landmark_curved_rigid],
"b.",
)
ax.set_xlabel("x")
ax.set_ylabel("y")
ax.set_zlabel("z")
plt.show()
# This stands to avoid overlapping between landmarks
sct.printv("\nMake sure all labels between landmark_curved and landmark_curved match...", verbose)
label_process = ProcessLabels(
fname_label="tmp.landmarks_straight.nii.gz",
fname_output="tmp.landmarks_straight.nii.gz",
fname_ref="tmp.landmarks_curved_rigid.nii.gz",
verbose=verbose,
)
label_process.process("remove")
label_process = ProcessLabels(
fname_label="tmp.landmarks_curved_rigid.nii.gz",
fname_output="tmp.landmarks_curved_rigid.nii.gz",
fname_ref="tmp.landmarks_straight.nii.gz",
verbose=verbose,
)
label_process.process("remove")
# Estimate b-spline transformation curve --> straight
sct.printv("\nEstimate b-spline transformation: curve --> straight...", verbose)
sct.run(
"isct_ANTSUseLandmarkImagesToGetBSplineDisplacementField tmp.landmarks_straight.nii.gz tmp.landmarks_curved_rigid.nii.gz tmp.warp_curve2straight.nii.gz "
+ self.bspline_meshsize
+ " "
+ self.bspline_numberOfLevels
+ " "
+ self.bspline_order
+ " 0",
verbose,
)
# remove padding for straight labels
if crop == 1:
ImageCropper(
input_file="tmp.landmarks_straight.nii.gz",
output_file="tmp.landmarks_straight_crop.nii.gz",
dim="0,1,2",
bmax=True,
verbose=verbose,
).crop()
pass
else:
sct.run("cp tmp.landmarks_straight.nii.gz tmp.landmarks_straight_crop.nii.gz", verbose)
# Concatenate rigid and non-linear transformations...
sct.printv("\nConcatenate rigid and non-linear transformations...", verbose)
# sct.run('isct_ComposeMultiTransform 3 tmp.warp_rigid.nii -R tmp.landmarks_straight.nii tmp.warp.nii tmp.curve2straight_rigid.txt')
# !!! DO NOT USE sct.run HERE BECAUSE isct_ComposeMultiTransform OUTPUTS A NON-NULL STATUS !!!
cmd = "isct_ComposeMultiTransform 3 tmp.curve2straight.nii.gz -R tmp.landmarks_straight_crop.nii.gz tmp.warp_curve2straight.nii.gz tmp.curve2straight_rigid.txt"
sct.printv(cmd, verbose, "code")
sct.run(cmd, self.verbose)
# commands.getstatusoutput(cmd)
# Estimate b-spline transformation straight --> curve
# TODO: invert warping field instead of estimating a new one
sct.printv("\nEstimate b-spline transformation: straight --> curve...", verbose)
sct.run(
"isct_ANTSUseLandmarkImagesToGetBSplineDisplacementField tmp.landmarks_curved_rigid.nii.gz tmp.landmarks_straight.nii.gz tmp.warp_straight2curve.nii.gz "
+ self.bspline_meshsize
+ " "
+ self.bspline_numberOfLevels
+ " "
+ self.bspline_order
+ " 0",
verbose,
)
# Concatenate rigid and non-linear transformations...
sct.printv("\nConcatenate rigid and non-linear transformations...", verbose)
cmd = (
"isct_ComposeMultiTransform 3 tmp.straight2curve.nii.gz -R "
+ file_anat
+ ext_anat
+ " -i tmp.curve2straight_rigid.txt tmp.warp_straight2curve.nii.gz"
)
sct.printv(cmd, verbose, "code")
# commands.getstatusoutput(cmd)
sct.run(cmd, self.verbose)
# Apply transformation to input image
sct.printv("\nApply transformation to input image...", verbose)
Transform(
input_filename=str(file_anat + ext_anat),
source_reg="tmp.anat_rigid_warp.nii.gz",
output_filename="tmp.landmarks_straight_crop.nii.gz",
interp=interpolation_warp,
warp="tmp.curve2straight.nii.gz",
verbose=verbose,
).apply()
# compute the error between the straightened centerline/segmentation and the central vertical line.
# Ideally, the error should be zero.
# Apply deformation to input image
sct.printv("\nApply transformation to centerline image...", verbose)
# sct.run('sct_apply_transfo -i '+fname_centerline_orient+' -o tmp.centerline_straight.nii.gz -d tmp.landmarks_straight_crop.nii.gz -x nn -w tmp.curve2straight.nii.gz')
Transform(
input_filename=fname_centerline_orient,
source_reg="tmp.centerline_straight.nii.gz",
output_filename="tmp.landmarks_straight_crop.nii.gz",
interp="nn",
warp="tmp.curve2straight.nii.gz",
verbose=verbose,
).apply()
# c = sct.run('sct_crop_image -i tmp.centerline_straight.nii.gz -o tmp.centerline_straight_crop.nii.gz -dim 2 -bzmax')
from msct_image import Image
file_centerline_straight = Image("tmp.centerline_straight.nii.gz", verbose=verbose)
coordinates_centerline = file_centerline_straight.getNonZeroCoordinates(sorting="z")
mean_coord = []
for z in range(coordinates_centerline[0].z, coordinates_centerline[-1].z):
mean_coord.append(
mean(
[
[coord.x * coord.value, coord.y * coord.value]
for coord in coordinates_centerline
if coord.z == z
],
axis=0,
)
)
# compute error between the input data and the nurbs
from math import sqrt
x0 = file_centerline_straight.data.shape[0] / 2.0
y0 = file_centerline_straight.data.shape[1] / 2.0
count_mean = 0
for coord_z in mean_coord:
if not isnan(sum(coord_z)):
dist = ((x0 - coord_z[0]) * px) ** 2 + ((y0 - coord_z[1]) * py) ** 2
self.mse_straightening += dist
dist = sqrt(dist)
if dist > self.max_distance_straightening:
self.max_distance_straightening = dist
count_mean += 1
self.mse_straightening = sqrt(self.mse_straightening / float(count_mean))
except Exception as e:
sct.printv("WARNING: Exception during Straightening:", 1, "warning")
print e
os.chdir("..")
# Generate output file (in current folder)
# TODO: do not uncompress the warping field, it is too time consuming!
sct.printv("\nGenerate output file (in current folder)...", verbose)
sct.generate_output_file(
path_tmp + "/tmp.curve2straight.nii.gz", "warp_curve2straight.nii.gz", verbose
) # warping field
sct.generate_output_file(
path_tmp + "/tmp.straight2curve.nii.gz", "warp_straight2curve.nii.gz", verbose
) # warping field
if fname_output == "":
fname_straight = sct.generate_output_file(
path_tmp + "/tmp.anat_rigid_warp.nii.gz", file_anat + "_straight" + ext_anat, verbose
) # straightened anatomic
else:
fname_straight = sct.generate_output_file(
path_tmp + "/tmp.anat_rigid_warp.nii.gz", fname_output, verbose
) # straightened anatomic
# Remove temporary files
if remove_temp_files:
sct.printv("\nRemove temporary files...", verbose)
sct.run("rm -rf " + path_tmp, verbose)
sct.printv("\nDone!\n", verbose)
sct.printv("Maximum x-y error = " + str(round(self.max_distance_straightening, 2)) + " mm", verbose, "bold")
sct.printv(
"Accuracy of straightening (MSE) = " + str(round(self.mse_straightening, 2)) + " mm", verbose, "bold"
)
# display elapsed time
elapsed_time = time.time() - start_time
sct.printv("\nFinished! Elapsed time: " + str(int(round(elapsed_time))) + "s", verbose)
sct.printv("\nTo view results, type:", verbose)
sct.printv("fslview " + fname_straight + " &\n", verbose, "info")
def extract_centerline(fname_segmentation,
remove_temp_files,
name_output='',
verbose=0,
algo_fitting='hanning',
type_window='hanning',
window_length=80):
# Extract path, file and extension
fname_segmentation = os.path.abspath(fname_segmentation)
path_data, file_data, ext_data = sct.extract_fname(fname_segmentation)
# create temporary folder
path_tmp = 'tmp.' + time.strftime("%y%m%d%H%M%S")
sct.run('mkdir ' + path_tmp)
# copy files into tmp folder
sct.run('cp ' + fname_segmentation + ' ' + path_tmp)
# go to tmp folder
os.chdir(path_tmp)
# Change orientation of the input centerline into RPI
sct.printv('\nOrient centerline to RPI orientation...', verbose)
fname_segmentation_orient = 'segmentation_rpi' + ext_data
set_orientation(file_data + ext_data, 'RPI', fname_segmentation_orient)
# Get dimension
sct.printv('\nGet dimensions...', verbose)
nx, ny, nz, nt, px, py, pz, pt = Image(fname_segmentation_orient).dim
sct.printv(
'.. matrix size: ' + str(nx) + ' x ' + str(ny) + ' x ' + str(nz),
verbose)
sct.printv(
'.. voxel size: ' + str(px) + 'mm x ' + str(py) + 'mm x ' + str(pz) +
'mm', verbose)
# Extract orientation of the input segmentation
orientation = get_orientation(file_data + ext_data)
sct.printv('\nOrientation of segmentation image: ' + orientation, verbose)
sct.printv('\nOpen segmentation volume...', verbose)
file = nibabel.load(fname_segmentation_orient)
data = file.get_data()
hdr = file.get_header()
# Extract min and max index in Z direction
X, Y, Z = (data > 0).nonzero()
min_z_index, max_z_index = min(Z), max(Z)
x_centerline = [0 for i in range(0, max_z_index - min_z_index + 1)]
y_centerline = [0 for i in range(0, max_z_index - min_z_index + 1)]
z_centerline = [iz for iz in range(min_z_index, max_z_index + 1)]
# Extract segmentation points and average per slice
for iz in range(min_z_index, max_z_index + 1):
x_seg, y_seg = (data[:, :, iz] > 0).nonzero()
x_centerline[iz - min_z_index] = np.mean(x_seg)
y_centerline[iz - min_z_index] = np.mean(y_seg)
for k in range(len(X)):
data[X[k], Y[k], Z[k]] = 0
# extract centerline and smooth it
x_centerline_fit, y_centerline_fit, z_centerline_fit, x_centerline_deriv, y_centerline_deriv, z_centerline_deriv = smooth_centerline(
fname_segmentation_orient,
type_window=type_window,
window_length=window_length,
algo_fitting=algo_fitting,
verbose=verbose)
if verbose == 2:
import matplotlib.pyplot as plt
#Creation of a vector x that takes into account the distance between the labels
nz_nonz = len(z_centerline)
x_display = [0 for i in range(x_centerline_fit.shape[0])]
y_display = [0 for i in range(y_centerline_fit.shape[0])]
for i in range(0, nz_nonz, 1):
x_display[int(z_centerline[i] - z_centerline[0])] = x_centerline[i]
y_display[int(z_centerline[i] - z_centerline[0])] = y_centerline[i]
plt.figure(1)
plt.subplot(2, 1, 1)
plt.plot(z_centerline_fit, x_display, 'ro')
plt.plot(z_centerline_fit, x_centerline_fit)
plt.xlabel("Z")
plt.ylabel("X")
plt.title("x and x_fit coordinates")
plt.subplot(2, 1, 2)
plt.plot(z_centerline_fit, y_display, 'ro')
plt.plot(z_centerline_fit, y_centerline_fit)
plt.xlabel("Z")
plt.ylabel("Y")
plt.title("y and y_fit coordinates")
plt.show()
# Create an image with the centerline
for iz in range(min_z_index, max_z_index + 1):
data[
round(x_centerline_fit[iz - min_z_index]),
round(y_centerline_fit[iz - min_z_index]),
iz] = 1 # if index is out of bounds here for hanning: either the segmentation has holes or labels have been added to the file
# Write the centerline image in RPI orientation
hdr.set_data_dtype('uint8') # set imagetype to uint8
sct.printv('\nWrite NIFTI volumes...', verbose)
img = nibabel.Nifti1Image(data, None, hdr)
nibabel.save(img, 'centerline.nii.gz')
# Define name if output name is not specified
if name_output == 'csa_volume.nii.gz' or name_output == '':
# sct.generate_output_file('centerline.nii.gz', file_data+'_centerline'+ext_data, verbose)
name_output = file_data + '_centerline' + ext_data
sct.generate_output_file('centerline.nii.gz', name_output, verbose)
# create a txt file with the centerline
path, rad_output, ext = sct.extract_fname(name_output)
name_output_txt = rad_output + '.txt'
sct.printv('\nWrite text file...', verbose)
file_results = open(name_output_txt, 'w')
for i in range(min_z_index, max_z_index + 1):
file_results.write(
str(int(i)) + ' ' + str(x_centerline_fit[i - min_z_index]) + ' ' +
str(y_centerline_fit[i - min_z_index]) + '\n')
file_results.close()
# Copy result into parent folder
sct.run('cp ' + name_output_txt + ' ../')
del data
# come back to parent folder
os.chdir('..')
# Change orientation of the output centerline into input orientation
sct.printv(
'\nOrient centerline image to input orientation: ' + orientation,
verbose)
fname_segmentation_orient = 'tmp.segmentation_rpi' + ext_data
set_orientation(path_tmp + '/' + name_output, orientation, name_output)
# Remove temporary files
if remove_temp_files:
sct.printv('\nRemove temporary files...', verbose)
sct.run('rm -rf ' + path_tmp, verbose)
return name_output
def main():
# get default parameters
step1 = Paramreg(step='1', type='seg', algo='slicereg', metric='MeanSquares', iter='10')
step2 = Paramreg(step='2', type='im', algo='syn', metric='MI', iter='3')
# step1 = Paramreg()
paramreg = ParamregMultiStep([step1, step2])
# step1 = Paramreg_step(step='1', type='seg', algo='bsplinesyn', metric='MeanSquares', iter='10', shrink='1', smooth='0', gradStep='0.5')
# step2 = Paramreg_step(step='2', type='im', algo='syn', metric='MI', iter='10', shrink='1', smooth='0', gradStep='0.5')
# paramreg = ParamregMultiStep([step1, step2])
# Initialize the parser
parser = Parser(__file__)
parser.usage.set_description('Register anatomical image to the template.')
parser.add_option(name="-i",
type_value="file",
description="Anatomical image.",
mandatory=True,
example="anat.nii.gz")
parser.add_option(name="-s",
type_value="file",
description="Spinal cord segmentation.",
mandatory=True,
example="anat_seg.nii.gz")
parser.add_option(name="-l",
type_value="file",
description="Labels. See: http://sourceforge.net/p/spinalcordtoolbox/wiki/create_labels/",
mandatory=True,
default_value='',
example="anat_labels.nii.gz")
parser.add_option(name="-t",
type_value="folder",
description="Path to MNI-Poly-AMU template.",
mandatory=False,
default_value=param.path_template)
parser.add_option(name="-p",
type_value=[[':'], 'str'],
description="""Parameters for registration (see sct_register_multimodal). Default:\n--\nstep=1\ntype="""+paramreg.steps['1'].type+"""\nalgo="""+paramreg.steps['1'].algo+"""\nmetric="""+paramreg.steps['1'].metric+"""\npoly="""+paramreg.steps['1'].poly+"""\n--\nstep=2\ntype="""+paramreg.steps['2'].type+"""\nalgo="""+paramreg.steps['2'].algo+"""\nmetric="""+paramreg.steps['2'].metric+"""\niter="""+paramreg.steps['2'].iter+"""\nshrink="""+paramreg.steps['2'].shrink+"""\nsmooth="""+paramreg.steps['2'].smooth+"""\ngradStep="""+paramreg.steps['2'].gradStep+"""\n--""",
mandatory=False,
example="step=2,type=seg,algo=bsplinesyn,metric=MeanSquares,iter=5,shrink=2:step=3,type=im,algo=syn,metric=MI,iter=5,shrink=1,gradStep=0.3")
parser.add_option(name="-r",
type_value="multiple_choice",
description="""Remove temporary files.""",
mandatory=False,
default_value='1',
example=['0', '1'])
parser.add_option(name="-v",
type_value="multiple_choice",
description="""Verbose. 0: nothing. 1: basic. 2: extended.""",
mandatory=False,
default_value=param.verbose,
example=['0', '1', '2'])
if param.debug:
print '\n*** WARNING: DEBUG MODE ON ***\n'
fname_data = '/Users/julien/data/temp/sct_example_data/t2/t2.nii.gz'
fname_landmarks = '/Users/julien/data/temp/sct_example_data/t2/labels.nii.gz'
fname_seg = '/Users/julien/data/temp/sct_example_data/t2/t2_seg.nii.gz'
path_template = param.path_template
remove_temp_files = 0
verbose = 2
# speed = 'superfast'
#param_reg = '2,BSplineSyN,0.6,MeanSquares'
else:
arguments = parser.parse(sys.argv[1:])
# get arguments
fname_data = arguments['-i']
fname_seg = arguments['-s']
fname_landmarks = arguments['-l']
path_template = arguments['-t']
remove_temp_files = int(arguments['-r'])
verbose = int(arguments['-v'])
if '-p' in arguments:
paramreg_user = arguments['-p']
# update registration parameters
for paramStep in paramreg_user:
paramreg.addStep(paramStep)
# initialize other parameters
file_template = param.file_template
file_template_label = param.file_template_label
file_template_seg = param.file_template_seg
output_type = param.output_type
zsubsample = param.zsubsample
# smoothing_sigma = param.smoothing_sigma
# start timer
start_time = time.time()
# get absolute path - TO DO: remove! NEVER USE ABSOLUTE PATH...
path_template = os.path.abspath(path_template)
# get fname of the template + template objects
fname_template = sct.slash_at_the_end(path_template, 1)+file_template
fname_template_label = sct.slash_at_the_end(path_template, 1)+file_template_label
fname_template_seg = sct.slash_at_the_end(path_template, 1)+file_template_seg
# check file existence
sct.printv('\nCheck template files...')
sct.check_file_exist(fname_template, verbose)
sct.check_file_exist(fname_template_label, verbose)
sct.check_file_exist(fname_template_seg, verbose)
# print arguments
sct.printv('\nCheck parameters:', verbose)
sct.printv('.. Data: '+fname_data, verbose)
sct.printv('.. Landmarks: '+fname_landmarks, verbose)
sct.printv('.. Segmentation: '+fname_seg, verbose)
sct.printv('.. Path template: '+path_template, verbose)
sct.printv('.. Output type: '+str(output_type), verbose)
sct.printv('.. Remove temp files: '+str(remove_temp_files), verbose)
sct.printv('\nParameters for registration:')
for pStep in range(1, len(paramreg.steps)+1):
sct.printv('Step #'+paramreg.steps[str(pStep)].step, verbose)
sct.printv('.. Type #'+paramreg.steps[str(pStep)].type, verbose)
sct.printv('.. Algorithm................ '+paramreg.steps[str(pStep)].algo, verbose)
sct.printv('.. Metric................... '+paramreg.steps[str(pStep)].metric, verbose)
sct.printv('.. Number of iterations..... '+paramreg.steps[str(pStep)].iter, verbose)
sct.printv('.. Shrink factor............ '+paramreg.steps[str(pStep)].shrink, verbose)
sct.printv('.. Smoothing factor......... '+paramreg.steps[str(pStep)].smooth, verbose)
sct.printv('.. Gradient step............ '+paramreg.steps[str(pStep)].gradStep, verbose)
sct.printv('.. Degree of polynomial..... '+paramreg.steps[str(pStep)].poly, verbose)
path_data, file_data, ext_data = sct.extract_fname(fname_data)
sct.printv('\nCheck input labels...')
# check if label image contains coherent labels
image_label = Image(fname_landmarks)
# -> all labels must be different
labels = image_label.getNonZeroCoordinates()
hasDifferentLabels = True
for lab in labels:
for otherlabel in labels:
if lab != otherlabel and lab.hasEqualValue(otherlabel):
hasDifferentLabels = False
break
if not hasDifferentLabels:
sct.printv('ERROR: Wrong landmarks input. All labels must be different.', verbose, 'error')
# create temporary folder
sct.printv('\nCreate temporary folder...', verbose)
path_tmp = 'tmp.'+time.strftime("%y%m%d%H%M%S")
status, output = sct.run('mkdir '+path_tmp)
# copy files to temporary folder
sct.printv('\nCopy files...', verbose)
sct.run('isct_c3d '+fname_data+' -o '+path_tmp+'/data.nii')
sct.run('isct_c3d '+fname_landmarks+' -o '+path_tmp+'/landmarks.nii.gz')
sct.run('isct_c3d '+fname_seg+' -o '+path_tmp+'/segmentation.nii.gz')
sct.run('isct_c3d '+fname_template+' -o '+path_tmp+'/template.nii')
sct.run('isct_c3d '+fname_template_label+' -o '+path_tmp+'/template_labels.nii.gz')
sct.run('isct_c3d '+fname_template_seg+' -o '+path_tmp+'/template_seg.nii.gz')
# go to tmp folder
os.chdir(path_tmp)
# Change orientation of input images to RPI
sct.printv('\nChange orientation of input images to RPI...', verbose)
set_orientation('data.nii', 'RPI', 'data_rpi.nii')
set_orientation('landmarks.nii.gz', 'RPI', 'landmarks_rpi.nii.gz')
set_orientation('segmentation.nii.gz', 'RPI', 'segmentation_rpi.nii.gz')
# crop segmentation
# output: segmentation_rpi_crop.nii.gz
sct.run('sct_crop_image -i segmentation_rpi.nii.gz -o segmentation_rpi_crop.nii.gz -dim 2 -bzmax')
# straighten segmentation
sct.printv('\nStraighten the spinal cord using centerline/segmentation...', verbose)
sct.run('sct_straighten_spinalcord -i segmentation_rpi_crop.nii.gz -c segmentation_rpi_crop.nii.gz -r 0')
# Label preparation:
# --------------------------------------------------------------------------------
# Remove unused label on template. Keep only label present in the input label image
sct.printv('\nRemove unused label on template. Keep only label present in the input label image...', verbose)
sct.run('sct_label_utils -t remove -i template_labels.nii.gz -o template_label.nii.gz -r landmarks_rpi.nii.gz')
# Make sure landmarks are INT
sct.printv('\nConvert landmarks to INT...', verbose)
sct.run('isct_c3d template_label.nii.gz -type int -o template_label.nii.gz', verbose)
# Create a cross for the template labels - 5 mm
sct.printv('\nCreate a 5 mm cross for the template labels...', verbose)
sct.run('sct_label_utils -t cross -i template_label.nii.gz -o template_label_cross.nii.gz -c 5')
# Create a cross for the input labels and dilate for straightening preparation - 5 mm
sct.printv('\nCreate a 5mm cross for the input labels and dilate for straightening preparation...', verbose)
sct.run('sct_label_utils -t cross -i landmarks_rpi.nii.gz -o landmarks_rpi_cross3x3.nii.gz -c 5 -d')
# Apply straightening to labels
sct.printv('\nApply straightening to labels...', verbose)
sct.run('sct_apply_transfo -i landmarks_rpi_cross3x3.nii.gz -o landmarks_rpi_cross3x3_straight.nii.gz -d segmentation_rpi_crop_straight.nii.gz -w warp_curve2straight.nii.gz -x nn')
# Convert landmarks from FLOAT32 to INT
sct.printv('\nConvert landmarks from FLOAT32 to INT...', verbose)
sct.run('isct_c3d landmarks_rpi_cross3x3_straight.nii.gz -type int -o landmarks_rpi_cross3x3_straight.nii.gz')
# Estimate affine transfo: straight --> template (landmark-based)'
sct.printv('\nEstimate affine transfo: straight anat --> template (landmark-based)...', verbose)
sct.run('isct_ANTSUseLandmarkImagesToGetAffineTransform template_label_cross.nii.gz landmarks_rpi_cross3x3_straight.nii.gz affine straight2templateAffine.txt')
# Apply affine transformation: straight --> template
sct.printv('\nApply affine transformation: straight --> template...', verbose)
sct.run('sct_concat_transfo -w warp_curve2straight.nii.gz,straight2templateAffine.txt -d template.nii -o warp_curve2straightAffine.nii.gz')
sct.run('sct_apply_transfo -i data_rpi.nii -o data_rpi_straight2templateAffine.nii -d template.nii -w warp_curve2straightAffine.nii.gz')
sct.run('sct_apply_transfo -i segmentation_rpi.nii.gz -o segmentation_rpi_straight2templateAffine.nii.gz -d template.nii -w warp_curve2straightAffine.nii.gz -x linear')
# find min-max of anat2template (for subsequent cropping)
sct.run('export FSLOUTPUTTYPE=NIFTI; fslmaths segmentation_rpi_straight2templateAffine.nii.gz -thr 0.5 segmentation_rpi_straight2templateAffine_th.nii.gz', param.verbose)
zmin_template, zmax_template = find_zmin_zmax('segmentation_rpi_straight2templateAffine_th.nii.gz')
# crop template in z-direction (for faster processing)
sct.printv('\nCrop data in template space (for faster processing)...', verbose)
sct.run('sct_crop_image -i template.nii -o template_crop.nii -dim 2 -start '+str(zmin_template)+' -end '+str(zmax_template))
sct.run('sct_crop_image -i template_seg.nii.gz -o template_seg_crop.nii.gz -dim 2 -start '+str(zmin_template)+' -end '+str(zmax_template))
sct.run('sct_crop_image -i data_rpi_straight2templateAffine.nii -o data_rpi_straight2templateAffine_crop.nii -dim 2 -start '+str(zmin_template)+' -end '+str(zmax_template))
sct.run('sct_crop_image -i segmentation_rpi_straight2templateAffine.nii.gz -o segmentation_rpi_straight2templateAffine_crop.nii.gz -dim 2 -start '+str(zmin_template)+' -end '+str(zmax_template))
# sub-sample in z-direction
sct.printv('\nSub-sample in z-direction (for faster processing)...', verbose)
sct.run('sct_resample -i template_crop.nii -o template_crop_r.nii -f 1x1x'+zsubsample, verbose)
sct.run('sct_resample -i template_seg_crop.nii.gz -o template_seg_crop_r.nii.gz -f 1x1x'+zsubsample, verbose)
sct.run('sct_resample -i data_rpi_straight2templateAffine_crop.nii -o data_rpi_straight2templateAffine_crop_r.nii -f 1x1x'+zsubsample, verbose)
sct.run('sct_resample -i segmentation_rpi_straight2templateAffine_crop.nii.gz -o segmentation_rpi_straight2templateAffine_crop_r.nii.gz -f 1x1x'+zsubsample, verbose)
# Registration straight spinal cord to template
sct.printv('\nRegister straight spinal cord to template...', verbose)
# loop across registration steps
warp_forward = []
warp_inverse = []
for i_step in range(1, len(paramreg.steps)+1):
sct.printv('\nEstimate transformation for step #'+str(i_step)+'...', verbose)
# identify which is the src and dest
if paramreg.steps[str(i_step)].type == 'im':
src = 'data_rpi_straight2templateAffine_crop_r.nii'
dest = 'template_crop_r.nii'
interp_step = 'linear'
elif paramreg.steps[str(i_step)].type == 'seg':
src = 'segmentation_rpi_straight2templateAffine_crop_r.nii.gz'
dest = 'template_seg_crop_r.nii.gz'
interp_step = 'nn'
else:
sct.run('ERROR: Wrong image type.', 1, 'error')
# if step>1, apply warp_forward_concat to the src image to be used
if i_step > 1:
# sct.run('sct_apply_transfo -i '+src+' -d '+dest+' -w '+','.join(warp_forward)+' -o '+sct.add_suffix(src, '_reg')+' -x '+interp_step, verbose)
sct.run('sct_apply_transfo -i '+src+' -d '+dest+' -w '+','.join(warp_forward)+' -o '+sct.add_suffix(src, '_reg')+' -x '+interp_step, verbose)
src = sct.add_suffix(src, '_reg')
# register src --> dest
warp_forward_out, warp_inverse_out = register(src, dest, paramreg, param, str(i_step))
warp_forward.append(warp_forward_out)
warp_inverse.append(warp_inverse_out)
# Concatenate transformations:
sct.printv('\nConcatenate transformations: anat --> template...', verbose)
sct.run('sct_concat_transfo -w warp_curve2straightAffine.nii.gz,'+','.join(warp_forward)+' -d template.nii -o warp_anat2template.nii.gz', verbose)
# sct.run('sct_concat_transfo -w warp_curve2straight.nii.gz,straight2templateAffine.txt,'+','.join(warp_forward)+' -d template.nii -o warp_anat2template.nii.gz', verbose)
warp_inverse.reverse()
sct.run('sct_concat_transfo -w '+','.join(warp_inverse)+',-straight2templateAffine.txt,warp_straight2curve.nii.gz -d data.nii -o warp_template2anat.nii.gz', verbose)
# Apply warping fields to anat and template
if output_type == 1:
sct.run('sct_apply_transfo -i template.nii -o template2anat.nii.gz -d data.nii -w warp_template2anat.nii.gz -c 1', verbose)
sct.run('sct_apply_transfo -i data.nii -o anat2template.nii.gz -d template.nii -w warp_anat2template.nii.gz -c 1', verbose)
# come back to parent folder
os.chdir('..')
# Generate output files
sct.printv('\nGenerate output files...', verbose)
sct.generate_output_file(path_tmp+'/warp_template2anat.nii.gz', 'warp_template2anat.nii.gz', verbose)
sct.generate_output_file(path_tmp+'/warp_anat2template.nii.gz', 'warp_anat2template.nii.gz', verbose)
if output_type == 1:
sct.generate_output_file(path_tmp+'/template2anat.nii.gz', 'template2anat'+ext_data, verbose)
sct.generate_output_file(path_tmp+'/anat2template.nii.gz', 'anat2template'+ext_data, verbose)
# Delete temporary files
if remove_temp_files:
sct.printv('\nDelete temporary files...', verbose)
sct.run('rm -rf '+path_tmp)
# display elapsed time
elapsed_time = time.time() - start_time
sct.printv('\nFinished! Elapsed time: '+str(int(round(elapsed_time)))+'s', verbose)
# to view results
sct.printv('\nTo view results, type:', verbose)
sct.printv('fslview '+fname_data+' template2anat -b 0,4000 &', verbose, 'info')
sct.printv('fslview '+fname_template+' -b 0,5000 anat2template &\n', verbose, 'info')
def extract_centerline(fname_segmentation, remove_temp_files, name_output='', verbose = 0, algo_fitting = 'hanning', type_window = 'hanning', window_length = 80):
# Extract path, file and extension
fname_segmentation = os.path.abspath(fname_segmentation)
path_data, file_data, ext_data = sct.extract_fname(fname_segmentation)
# create temporary folder
path_tmp = 'tmp.'+time.strftime("%y%m%d%H%M%S")
sct.run('mkdir '+path_tmp)
# copy files into tmp folder
sct.run('cp '+fname_segmentation+' '+path_tmp)
# go to tmp folder
os.chdir(path_tmp)
# Change orientation of the input centerline into RPI
sct.printv('\nOrient centerline to RPI orientation...', verbose)
fname_segmentation_orient = 'segmentation_rpi' + ext_data
set_orientation(file_data+ext_data, 'RPI', fname_segmentation_orient)
# Get dimension
sct.printv('\nGet dimensions...', verbose)
nx, ny, nz, nt, px, py, pz, pt = Image(fname_segmentation_orient).dim
sct.printv('.. matrix size: '+str(nx)+' x '+str(ny)+' x '+str(nz), verbose)
sct.printv('.. voxel size: '+str(px)+'mm x '+str(py)+'mm x '+str(pz)+'mm', verbose)
# Extract orientation of the input segmentation
orientation = get_orientation(file_data+ext_data)
sct.printv('\nOrientation of segmentation image: ' + orientation, verbose)
sct.printv('\nOpen segmentation volume...', verbose)
file = nibabel.load(fname_segmentation_orient)
data = file.get_data()
hdr = file.get_header()
# Extract min and max index in Z direction
X, Y, Z = (data>0).nonzero()
min_z_index, max_z_index = min(Z), max(Z)
x_centerline = [0 for i in range(0,max_z_index-min_z_index+1)]
y_centerline = [0 for i in range(0,max_z_index-min_z_index+1)]
z_centerline = [iz for iz in range(min_z_index, max_z_index+1)]
# Extract segmentation points and average per slice
for iz in range(min_z_index, max_z_index+1):
x_seg, y_seg = (data[:,:,iz]>0).nonzero()
x_centerline[iz-min_z_index] = np.mean(x_seg)
y_centerline[iz-min_z_index] = np.mean(y_seg)
for k in range(len(X)):
data[X[k], Y[k], Z[k]] = 0
# extract centerline and smooth it
x_centerline_fit, y_centerline_fit, z_centerline_fit, x_centerline_deriv,y_centerline_deriv,z_centerline_deriv = smooth_centerline(fname_segmentation_orient, type_window = type_window, window_length = window_length, algo_fitting = algo_fitting, verbose = verbose)
if verbose == 2:
import matplotlib.pyplot as plt
#Creation of a vector x that takes into account the distance between the labels
nz_nonz = len(z_centerline)
x_display = [0 for i in range(x_centerline_fit.shape[0])]
y_display = [0 for i in range(y_centerline_fit.shape[0])]
for i in range(0, nz_nonz, 1):
x_display[int(z_centerline[i]-z_centerline[0])] = x_centerline[i]
y_display[int(z_centerline[i]-z_centerline[0])] = y_centerline[i]
plt.figure(1)
plt.subplot(2,1,1)
plt.plot(z_centerline_fit, x_display, 'ro')
plt.plot(z_centerline_fit, x_centerline_fit)
plt.xlabel("Z")
plt.ylabel("X")
plt.title("x and x_fit coordinates")
plt.subplot(2,1,2)
plt.plot(z_centerline_fit, y_display, 'ro')
plt.plot(z_centerline_fit, y_centerline_fit)
plt.xlabel("Z")
plt.ylabel("Y")
plt.title("y and y_fit coordinates")
plt.show()
# Create an image with the centerline
for iz in range(min_z_index, max_z_index+1):
data[round(x_centerline_fit[iz-min_z_index]), round(y_centerline_fit[iz-min_z_index]), iz] = 1 # if index is out of bounds here for hanning: either the segmentation has holes or labels have been added to the file
# Write the centerline image in RPI orientation
hdr.set_data_dtype('uint8') # set imagetype to uint8
sct.printv('\nWrite NIFTI volumes...', verbose)
img = nibabel.Nifti1Image(data, None, hdr)
nibabel.save(img, 'centerline.nii.gz')
# Define name if output name is not specified
if name_output=='csa_volume.nii.gz' or name_output=='':
# sct.generate_output_file('centerline.nii.gz', file_data+'_centerline'+ext_data, verbose)
name_output = file_data+'_centerline'+ext_data
sct.generate_output_file('centerline.nii.gz', name_output, verbose)
# create a txt file with the centerline
path, rad_output, ext = sct.extract_fname(name_output)
name_output_txt = rad_output + '.txt'
sct.printv('\nWrite text file...', verbose)
file_results = open(name_output_txt, 'w')
for i in range(min_z_index, max_z_index+1):
file_results.write(str(int(i)) + ' ' + str(x_centerline_fit[i-min_z_index]) + ' ' + str(y_centerline_fit[i-min_z_index]) + '\n')
file_results.close()
# Copy result into parent folder
sct.run('cp '+name_output_txt+' ../')
del data
# come back to parent folder
os.chdir('..')
# Change orientation of the output centerline into input orientation
sct.printv('\nOrient centerline image to input orientation: ' + orientation, verbose)
fname_segmentation_orient = 'tmp.segmentation_rpi' + ext_data
set_orientation(path_tmp+'/'+name_output, orientation, name_output)
# Remove temporary files
if remove_temp_files:
sct.printv('\nRemove temporary files...', verbose)
sct.run('rm -rf '+path_tmp, verbose)
return name_output
def main():
# Initialization
fname_anat = ''
fname_centerline = ''
sigma = 3 # default value of the standard deviation for the Gaussian smoothing (in terms of number of voxels)
remove_temp_files = param.remove_temp_files
verbose = param.verbose
start_time = time.time()
# Check input param
try:
opts, args = getopt.getopt(sys.argv[1:], 'hi:c:r:s:v:')
except getopt.GetoptError as err:
print str(err)
usage()
if not opts:
usage()
for opt, arg in opts:
if opt == '-h':
usage()
elif opt in ('-c'):
fname_centerline = arg
elif opt in ('-i'):
fname_anat = arg
elif opt in ('-r'):
remove_temp_files = arg
elif opt in ('-s'):
sigma = arg
elif opt in ('-v'):
verbose = int(arg)
# Display usage if a mandatory argument is not provided
if fname_anat == '' or fname_centerline == '':
usage()
# Display arguments
print '\nCheck input arguments...'
print ' Volume to smooth .................. ' + fname_anat
print ' Centerline ........................ ' + fname_centerline
print ' FWHM .............................. '+str(sigma)
print ' Verbose ........................... '+str(verbose)
# Check existence of input files
print('\nCheck existence of input files...')
sct.check_file_exist(fname_anat)
sct.check_file_exist(fname_centerline)
# Extract path/file/extension
path_anat, file_anat, ext_anat = sct.extract_fname(fname_anat)
path_centerline, file_centerline, ext_centerline = sct.extract_fname(fname_centerline)
# create temporary folder
print('\nCreate temporary folder...')
path_tmp = 'tmp.'+time.strftime("%y%m%d%H%M%S")
sct.run('mkdir '+path_tmp)
# copy files to temporary folder
print('\nCopy files...')
sct.run('isct_c3d '+fname_anat+' -o '+path_tmp+'/anat.nii')
sct.run('isct_c3d '+fname_centerline+' -o '+path_tmp+'/centerline.nii')
# go to tmp folder
os.chdir(path_tmp)
# Change orientation of the input image into RPI
print '\nOrient input volume to RPI orientation...'
set_orientation('anat.nii', 'RPI', 'anat_rpi.nii')
# Change orientation of the input image into RPI
print '\nOrient centerline to RPI orientation...'
set_orientation('centerline.nii', 'RPI', 'centerline_rpi.nii')
# Straighten the spinal cord
print '\nStraighten the spinal cord...'
sct.run('sct_straighten_spinalcord -i anat_rpi.nii -c centerline_rpi.nii -x spline -v '+str(verbose))
# Smooth the straightened image along z
print '\nSmooth the straightened image along z...'
sct.run('isct_c3d anat_rpi_straight.nii -smooth 0x0x'+str(sigma)+'vox -o anat_rpi_straight_smooth.nii', verbose)
# Apply the reversed warping field to get back the curved spinal cord
print '\nApply the reversed warping field to get back the curved spinal cord...'
sct.run('sct_apply_transfo -i anat_rpi_straight_smooth.nii -o anat_rpi_straight_smooth_curved.nii -d anat.nii -w warp_straight2curve.nii.gz -x spline', verbose)
# come back to parent folder
os.chdir('..')
# Generate output file
print '\nGenerate output file...'
sct.generate_output_file(path_tmp+'/anat_rpi_straight_smooth_curved.nii', file_anat+'_smooth'+ext_anat)
# Remove temporary files
if remove_temp_files == 1:
print('\nRemove temporary files...')
sct.run('rm -rf '+path_tmp)
# Display elapsed time
elapsed_time = time.time() - start_time
print '\nFinished! Elapsed time: '+str(int(round(elapsed_time)))+'s\n'
# to view results
sct.printv('Done! To view results, type:', verbose)
sct.printv('fslview '+file_anat+' '+file_anat+'_smooth &\n', verbose, 'info')
def main():
# Initialization
fname_anat = ''
fname_point = ''
slice_gap = param.gap
remove_tmp_files = param.remove_tmp_files
gaussian_kernel = param.gaussian_kernel
start_time = time.time()
# get path of the toolbox
status, path_sct = commands.getstatusoutput('echo $SCT_DIR')
path_sct = sct.slash_at_the_end(path_sct, 1)
# Parameters for debug mode
if param.debug == 1:
sct.printv('\n*** WARNING: DEBUG MODE ON ***\n\t\t\tCurrent working directory: '+os.getcwd(), 'warning')
status, path_sct_testing_data = commands.getstatusoutput('echo $SCT_TESTING_DATA_DIR')
fname_anat = path_sct_testing_data+'/t2/t2.nii.gz'
fname_point = path_sct_testing_data+'/t2/t2_centerline_init.nii.gz'
slice_gap = 5
else:
# Check input param
try:
opts, args = getopt.getopt(sys.argv[1:],'hi:p:g:r:k:')
except getopt.GetoptError as err:
print str(err)
usage()
if not opts:
usage()
for opt, arg in opts:
if opt == '-h':
usage()
elif opt in ('-i'):
fname_anat = arg
elif opt in ('-p'):
fname_point = arg
elif opt in ('-g'):
slice_gap = int(arg)
elif opt in ('-r'):
remove_tmp_files = int(arg)
elif opt in ('-k'):
gaussian_kernel = int(arg)
# display usage if a mandatory argument is not provided
if fname_anat == '' or fname_point == '':
usage()
# check existence of input files
sct.check_file_exist(fname_anat)
sct.check_file_exist(fname_point)
# extract path/file/extension
path_anat, file_anat, ext_anat = sct.extract_fname(fname_anat)
path_point, file_point, ext_point = sct.extract_fname(fname_point)
# extract path of schedule file
# TODO: include schedule file in sct
# TODO: check existence of schedule file
file_schedule = path_sct + param.schedule_file
# Get input image orientation
input_image_orientation = get_orientation(fname_anat)
# Display arguments
print '\nCheck input arguments...'
print ' Anatomical image: '+fname_anat
print ' Orientation: '+input_image_orientation
print ' Point in spinal cord: '+fname_point
print ' Slice gap: '+str(slice_gap)
print ' Gaussian kernel: '+str(gaussian_kernel)
print ' Degree of polynomial: '+str(param.deg_poly)
# create temporary folder
print('\nCreate temporary folder...')
path_tmp = 'tmp.'+time.strftime("%y%m%d%H%M%S")
sct.create_folder(path_tmp)
print '\nCopy input data...'
sct.run('cp '+fname_anat+ ' '+path_tmp+'/tmp.anat'+ext_anat)
sct.run('cp '+fname_point+ ' '+path_tmp+'/tmp.point'+ext_point)
# go to temporary folder
os.chdir(path_tmp)
# convert to nii
sct.run('fslchfiletype NIFTI tmp.anat')
sct.run('fslchfiletype NIFTI tmp.point')
# Reorient input anatomical volume into RL PA IS orientation
print '\nReorient input volume to RL PA IS orientation...'
#sct.run(sct.fsloutput + 'fslswapdim tmp.anat RL PA IS tmp.anat_orient')
set_orientation('tmp.anat.nii', 'RPI', 'tmp.anat_orient.nii')
# Reorient binary point into RL PA IS orientation
print '\nReorient binary point into RL PA IS orientation...'
sct.run(sct.fsloutput + 'fslswapdim tmp.point RL PA IS tmp.point_orient')
set_orientation('tmp.point.nii', 'RPI', 'tmp.point_orient')
# Get image dimensions
print '\nGet image dimensions...'
nx, ny, nz, nt, px, py, pz, pt = sct.get_dimension('tmp.anat_orient')
print '.. matrix size: '+str(nx)+' x '+str(ny)+' x '+str(nz)
print '.. voxel size: '+str(px)+'mm x '+str(py)+'mm x '+str(pz)+'mm'
# Split input volume
print '\nSplit input volume...'
sct.run(sct.fsloutput + 'fslsplit tmp.anat_orient tmp.anat_orient_z -z')
file_anat_split = ['tmp.anat_orient_z'+str(z).zfill(4) for z in range(0,nz,1)]
# Get the coordinates of the input point
print '\nGet the coordinates of the input point...'
file = nibabel.load('tmp.point_orient.nii')
data = file.get_data()
x_init, y_init, z_init = (data > 0).nonzero()
x_init = x_init[0]
y_init = y_init[0]
z_init = z_init[0]
print '('+str(x_init)+', '+str(y_init)+', '+str(z_init)+')'
# Extract the slice corresponding to z=z_init
print '\nExtract the slice corresponding to z='+str(z_init)+'...'
file_point_split = ['tmp.point_orient_z'+str(z).zfill(4) for z in range(0,nz,1)]
sct.run(sct.fsloutput+'fslroi tmp.point_orient '+file_point_split[z_init]+' 0 -1 0 -1 '+str(z_init)+' 1')
# Create gaussian mask from point
print '\nCreate gaussian mask from point...'
file_mask_split = ['tmp.mask_orient_z'+str(z).zfill(4) for z in range(0,nz,1)]
sct.run(sct.fsloutput+'fslmaths '+file_point_split[z_init]+' -s '+str(gaussian_kernel)+' '+file_mask_split[z_init])
# Obtain max value from mask
print '\nFind maximum value from mask...'
file = nibabel.load(file_mask_split[z_init]+'.nii')
data = file.get_data()
max_value_mask = numpy.max(data)
print '..'+str(max_value_mask)
# Normalize mask beween 0 and 1
print '\nNormalize mask beween 0 and 1...'
sct.run(sct.fsloutput+'fslmaths '+file_mask_split[z_init]+' -div '+str(max_value_mask)+' '+file_mask_split[z_init])
## Take the square of the mask
#print '\nCalculate the square of the mask...'
#sct.run(sct.fsloutput+'fslmaths '+file_mask_split[z_init]+' -mul '+file_mask_split[z_init]+' '+file_mask_split[z_init])
# initialize variables
file_mat = ['tmp.mat_z'+str(z).zfill(4) for z in range(0,nz,1)]
file_mat_inv = ['tmp.mat_inv_z'+str(z).zfill(4) for z in range(0,nz,1)]
file_mat_inv_cumul = ['tmp.mat_inv_cumul_z'+str(z).zfill(4) for z in range(0,nz,1)]
# create identity matrix for initial transformation matrix
fid = open(file_mat_inv_cumul[z_init], 'w')
fid.write('%i %i %i %i\n' %(1, 0, 0, 0) )
fid.write('%i %i %i %i\n' %(0, 1, 0, 0) )
fid.write('%i %i %i %i\n' %(0, 0, 1, 0) )
fid.write('%i %i %i %i\n' %(0, 0, 0, 1) )
fid.close()
# initialize centerline: give value corresponding to initial point
x_centerline = [x_init]
y_centerline = [y_init]
z_centerline = [z_init]
warning_count = 0
# go up (1), then down (2) in reference to the binary point
for iUpDown in range(1, 3):
if iUpDown == 1:
# z increases
slice_gap_signed = slice_gap
elif iUpDown == 2:
# z decreases
slice_gap_signed = -slice_gap
# reverse centerline (because values will be appended at the end)
x_centerline.reverse()
y_centerline.reverse()
z_centerline.reverse()
# initialization before looping
z_dest = z_init # point given by user
z_src = z_dest + slice_gap_signed
# continue looping if 0 < z < nz
while 0 <= z_src and z_src <= nz-1:
# print current z:
print 'z='+str(z_src)+':'
# estimate transformation
sct.run(fsloutput+'flirt -in '+file_anat_split[z_src]+' -ref '+file_anat_split[z_dest]+' -schedule '+file_schedule+ ' -verbose 0 -omat '+file_mat[z_src]+' -cost normcorr -forcescaling -inweight '+file_mask_split[z_dest]+' -refweight '+file_mask_split[z_dest])
# display transfo
status, output = sct.run('cat '+file_mat[z_src])
print output
# check if transformation is bigger than 1.5x slice_gap
tx = float(output.split()[3])
ty = float(output.split()[7])
norm_txy = numpy.linalg.norm([tx, ty],ord=2)
if norm_txy > 1.5*slice_gap:
print 'WARNING: Transformation is too large --> using previous one.'
warning_count = warning_count + 1
# if previous transformation exists, replace current one with previous one
if os.path.isfile(file_mat[z_dest]):
sct.run('cp '+file_mat[z_dest]+' '+file_mat[z_src])
# estimate inverse transformation matrix
sct.run('convert_xfm -omat '+file_mat_inv[z_src]+' -inverse '+file_mat[z_src])
# compute cumulative transformation
sct.run('convert_xfm -omat '+file_mat_inv_cumul[z_src]+' -concat '+file_mat_inv[z_src]+' '+file_mat_inv_cumul[z_dest])
# apply inverse cumulative transformation to initial gaussian mask (to put it in src space)
sct.run(fsloutput+'flirt -in '+file_mask_split[z_init]+' -ref '+file_mask_split[z_init]+' -applyxfm -init '+file_mat_inv_cumul[z_src]+' -out '+file_mask_split[z_src])
# open inverse cumulative transformation file and generate centerline
fid = open(file_mat_inv_cumul[z_src])
mat = fid.read().split()
x_centerline.append(x_init + float(mat[3]))
y_centerline.append(y_init + float(mat[7]))
z_centerline.append(z_src)
#z_index = z_index+1
# define new z_dest (target slice) and new z_src (moving slice)
z_dest = z_dest + slice_gap_signed
z_src = z_src + slice_gap_signed
# Reconstruct centerline
# ====================================================================================================
# reverse back centerline (because it's been reversed once, so now all values are in the right order)
x_centerline.reverse()
y_centerline.reverse()
z_centerline.reverse()
# fit centerline in the Z-X plane using polynomial function
print '\nFit centerline in the Z-X plane using polynomial function...'
coeffsx = numpy.polyfit(z_centerline, x_centerline, deg=param.deg_poly)
polyx = numpy.poly1d(coeffsx)
x_centerline_fit = numpy.polyval(polyx, z_centerline)
# calculate RMSE
rmse = numpy.linalg.norm(x_centerline_fit-x_centerline)/numpy.sqrt( len(x_centerline) )
# calculate max absolute error
max_abs = numpy.max( numpy.abs(x_centerline_fit-x_centerline) )
print '.. RMSE (in mm): '+str(rmse*px)
print '.. Maximum absolute error (in mm): '+str(max_abs*px)
# fit centerline in the Z-Y plane using polynomial function
print '\nFit centerline in the Z-Y plane using polynomial function...'
coeffsy = numpy.polyfit(z_centerline, y_centerline, deg=param.deg_poly)
polyy = numpy.poly1d(coeffsy)
y_centerline_fit = numpy.polyval(polyy, z_centerline)
# calculate RMSE
rmse = numpy.linalg.norm(y_centerline_fit-y_centerline)/numpy.sqrt( len(y_centerline) )
# calculate max absolute error
max_abs = numpy.max( numpy.abs(y_centerline_fit-y_centerline) )
print '.. RMSE (in mm): '+str(rmse*py)
print '.. Maximum absolute error (in mm): '+str(max_abs*py)
# display
if param.debug == 1:
import matplotlib.pyplot as plt
plt.figure()
plt.plot(z_centerline,x_centerline,'.',z_centerline,x_centerline_fit,'r')
plt.legend(['Data','Polynomial Fit'])
plt.title('Z-X plane polynomial interpolation')
plt.show()
plt.figure()
plt.plot(z_centerline,y_centerline,'.',z_centerline,y_centerline_fit,'r')
plt.legend(['Data','Polynomial Fit'])
plt.title('Z-Y plane polynomial interpolation')
plt.show()
# generate full range z-values for centerline
z_centerline_full = [iz for iz in range(0, nz, 1)]
# calculate X and Y values for the full centerline
x_centerline_fit_full = numpy.polyval(polyx, z_centerline_full)
y_centerline_fit_full = numpy.polyval(polyy, z_centerline_full)
# Generate fitted transformation matrices and write centerline coordinates in text file
print '\nGenerate fitted transformation matrices and write centerline coordinates in text file...'
file_mat_inv_cumul_fit = ['tmp.mat_inv_cumul_fit_z'+str(z).zfill(4) for z in range(0,nz,1)]
file_mat_cumul_fit = ['tmp.mat_cumul_fit_z'+str(z).zfill(4) for z in range(0,nz,1)]
fid_centerline = open('tmp.centerline_coordinates.txt', 'w')
for iz in range(0, nz, 1):
# compute inverse cumulative fitted transformation matrix
fid = open(file_mat_inv_cumul_fit[iz], 'w')
fid.write('%i %i %i %f\n' %(1, 0, 0, x_centerline_fit_full[iz]-x_init) )
fid.write('%i %i %i %f\n' %(0, 1, 0, y_centerline_fit_full[iz]-y_init) )
fid.write('%i %i %i %i\n' %(0, 0, 1, 0) )
fid.write('%i %i %i %i\n' %(0, 0, 0, 1) )
fid.close()
# compute forward cumulative fitted transformation matrix
sct.run('convert_xfm -omat '+file_mat_cumul_fit[iz]+' -inverse '+file_mat_inv_cumul_fit[iz])
# write centerline coordinates in x, y, z format
fid_centerline.write('%f %f %f\n' %(x_centerline_fit_full[iz], y_centerline_fit_full[iz], z_centerline_full[iz]) )
fid_centerline.close()
# Prepare output data
# ====================================================================================================
# write centerline as text file
for iz in range(0, nz, 1):
# compute inverse cumulative fitted transformation matrix
fid = open(file_mat_inv_cumul_fit[iz], 'w')
fid.write('%i %i %i %f\n' %(1, 0, 0, x_centerline_fit_full[iz]-x_init) )
fid.write('%i %i %i %f\n' %(0, 1, 0, y_centerline_fit_full[iz]-y_init) )
fid.write('%i %i %i %i\n' %(0, 0, 1, 0) )
fid.write('%i %i %i %i\n' %(0, 0, 0, 1) )
fid.close()
# write polynomial coefficients
numpy.savetxt('tmp.centerline_polycoeffs_x.txt',coeffsx)
numpy.savetxt('tmp.centerline_polycoeffs_y.txt',coeffsy)
# apply transformations to data
print '\nApply fitted transformation matrices...'
file_anat_split_fit = ['tmp.anat_orient_fit_z'+str(z).zfill(4) for z in range(0,nz,1)]
file_mask_split_fit = ['tmp.mask_orient_fit_z'+str(z).zfill(4) for z in range(0,nz,1)]
file_point_split_fit = ['tmp.point_orient_fit_z'+str(z).zfill(4) for z in range(0,nz,1)]
for iz in range(0, nz, 1):
# forward cumulative transformation to data
sct.run(fsloutput+'flirt -in '+file_anat_split[iz]+' -ref '+file_anat_split[iz]+' -applyxfm -init '+file_mat_cumul_fit[iz]+' -out '+file_anat_split_fit[iz])
# inverse cumulative transformation to mask
sct.run(fsloutput+'flirt -in '+file_mask_split[z_init]+' -ref '+file_mask_split[z_init]+' -applyxfm -init '+file_mat_inv_cumul_fit[iz]+' -out '+file_mask_split_fit[iz])
# inverse cumulative transformation to point
sct.run(fsloutput+'flirt -in '+file_point_split[z_init]+' -ref '+file_point_split[z_init]+' -applyxfm -init '+file_mat_inv_cumul_fit[iz]+' -out '+file_point_split_fit[iz]+' -interp nearestneighbour')
# Merge into 4D volume
print '\nMerge into 4D volume...'
sct.run(fsloutput+'fslmerge -z tmp.anat_orient_fit tmp.anat_orient_fit_z*')
sct.run(fsloutput+'fslmerge -z tmp.mask_orient_fit tmp.mask_orient_fit_z*')
sct.run(fsloutput+'fslmerge -z tmp.point_orient_fit tmp.point_orient_fit_z*')
# Copy header geometry from input data
print '\nCopy header geometry from input data...'
sct.run(fsloutput+'fslcpgeom tmp.anat_orient.nii tmp.anat_orient_fit.nii ')
sct.run(fsloutput+'fslcpgeom tmp.anat_orient.nii tmp.mask_orient_fit.nii ')
sct.run(fsloutput+'fslcpgeom tmp.anat_orient.nii tmp.point_orient_fit.nii ')
# Reorient outputs into the initial orientation of the input image
print '\nReorient the centerline into the initial orientation of the input image...'
set_orientation('tmp.point_orient_fit.nii', input_image_orientation, 'tmp.point_orient_fit.nii')
set_orientation('tmp.mask_orient_fit.nii', input_image_orientation, 'tmp.mask_orient_fit.nii')
# Generate output file (in current folder)
print '\nGenerate output file (in current folder)...'
os.chdir('..') # come back to parent folder
#sct.generate_output_file('tmp.centerline_polycoeffs_x.txt','./','centerline_polycoeffs_x','.txt')
#sct.generate_output_file('tmp.centerline_polycoeffs_y.txt','./','centerline_polycoeffs_y','.txt')
#sct.generate_output_file('tmp.centerline_coordinates.txt','./','centerline_coordinates','.txt')
#sct.generate_output_file('tmp.anat_orient.nii','./',file_anat+'_rpi',ext_anat)
#sct.generate_output_file('tmp.anat_orient_fit.nii', file_anat+'_rpi_align'+ext_anat)
#sct.generate_output_file('tmp.mask_orient_fit.nii', file_anat+'_mask'+ext_anat)
fname_output_centerline = sct.generate_output_file(path_tmp+'/tmp.point_orient_fit.nii', file_anat+'_centerline'+ext_anat)
# Delete temporary files
if remove_tmp_files == 1:
print '\nRemove temporary files...'
sct.run('rm -rf '+path_tmp)
# print number of warnings
print '\nNumber of warnings: '+str(warning_count)+' (if >10, you should probably reduce the gap and/or increase the kernel size'
# display elapsed time
elapsed_time = time.time() - start_time
print '\nFinished! \n\tGenerated file: '+fname_output_centerline+'\n\tElapsed time: '+str(int(round(elapsed_time)))+'s\n'
def main():
# Initialization
fname_anat = ''
fname_centerline = ''
sigma = 3 # default value of the standard deviation for the Gaussian smoothing (in terms of number of voxels)
remove_temp_files = param.remove_temp_files
verbose = param.verbose
start_time = time.time()
# Check input param
try:
opts, args = getopt.getopt(sys.argv[1:], 'hi:c:r:s:v:')
except getopt.GetoptError as err:
print str(err)
usage()
if not opts:
usage()
for opt, arg in opts:
if opt == '-h':
usage()
elif opt in ('-c'):
fname_centerline = arg
elif opt in ('-i'):
fname_anat = arg
elif opt in ('-r'):
remove_temp_files = arg
elif opt in ('-s'):
sigma = arg
elif opt in ('-v'):
verbose = int(arg)
# Display usage if a mandatory argument is not provided
if fname_anat == '' or fname_centerline == '':
usage()
# Display arguments
print '\nCheck input arguments...'
print ' Volume to smooth .................. ' + fname_anat
print ' Centerline ........................ ' + fname_centerline
print ' FWHM .............................. '+str(sigma)
print ' Verbose ........................... '+str(verbose)
# Check existence of input files
print('\nCheck existence of input files...')
sct.check_file_exist(fname_anat, verbose)
sct.check_file_exist(fname_centerline, verbose)
# Extract path/file/extension
path_anat, file_anat, ext_anat = sct.extract_fname(fname_anat)
path_centerline, file_centerline, ext_centerline = sct.extract_fname(fname_centerline)
# create temporary folder
print('\nCreate temporary folder...')
path_tmp = 'tmp.'+time.strftime("%y%m%d%H%M%S")
sct.run('mkdir '+path_tmp)
# copy files to temporary folder
print('\nCopy files...')
sct.run('isct_c3d '+fname_anat+' -o '+path_tmp+'/anat.nii')
sct.run('isct_c3d '+fname_centerline+' -o '+path_tmp+'/centerline.nii')
# go to tmp folder
os.chdir(path_tmp)
# Change orientation of the input image into RPI
print '\nOrient input volume to RPI orientation...'
set_orientation('anat.nii', 'RPI', 'anat_rpi.nii')
# Change orientation of the input image into RPI
print '\nOrient centerline to RPI orientation...'
set_orientation('centerline.nii', 'RPI', 'centerline_rpi.nii')
## new
### Make sure that centerline file does not have halls
file_c = load('centerline_rpi.nii')
data_c = file_c.get_data()
hdr_c = file_c.get_header()
data_temp = copy(data_c)
data_temp *= 0
data_output = copy(data_c)
data_output *= 0
nx, ny, nz, nt, px, py, pz, pt = sct.get_dimension('centerline_rpi.nii')
## Change seg to centerline if it is a segmentation
sct.printv('\nChange segmentation to centerline if it is a centerline...\n')
z_centerline = [iz for iz in range(0, nz, 1) if data_c[:,:,iz].any() ]
nz_nonz = len(z_centerline)
if nz_nonz==0 :
print '\nERROR: Centerline is empty'
sys.exit()
x_centerline = [0 for iz in range(0, nz_nonz, 1)]
y_centerline = [0 for iz in range(0, nz_nonz, 1)]
#print("z_centerline", z_centerline,nz_nonz,len(x_centerline))
print '\nGet center of mass of the centerline ...'
for iz in xrange(len(z_centerline)):
x_centerline[iz], y_centerline[iz] = ndimage.measurements.center_of_mass(array(data_c[:,:,z_centerline[iz]]))
data_temp[x_centerline[iz], y_centerline[iz], z_centerline[iz]] = 1
## Complete centerline
sct.printv('\nComplete the halls of the centerline if there are any...\n')
X,Y,Z = data_temp.nonzero()
x_centerline_extended = [0 for i in range(0, nz, 1)]
y_centerline_extended = [0 for i in range(0, nz, 1)]
for iz in range(len(Z)):
x_centerline_extended[Z[iz]] = X[iz]
y_centerline_extended[Z[iz]] = Y[iz]
X_centerline_extended = nonzero(x_centerline_extended)
X_centerline_extended = transpose(X_centerline_extended)
Y_centerline_extended = nonzero(y_centerline_extended)
Y_centerline_extended = transpose(Y_centerline_extended)
# initialization: we set the extrem values to avoid edge effects
x_centerline_extended[0] = x_centerline_extended[X_centerline_extended[0]]
x_centerline_extended[-1] = x_centerline_extended[X_centerline_extended[-1]]
y_centerline_extended[0] = y_centerline_extended[Y_centerline_extended[0]]
y_centerline_extended[-1] = y_centerline_extended[Y_centerline_extended[-1]]
# Add two rows to the vector X_means_smooth_extended:
# one before as means_smooth_extended[0] is now diff from 0
# one after as means_smooth_extended[-1] is now diff from 0
X_centerline_extended = append(X_centerline_extended, len(x_centerline_extended)-1)
X_centerline_extended = insert(X_centerline_extended, 0, 0)
Y_centerline_extended = append(Y_centerline_extended, len(y_centerline_extended)-1)
Y_centerline_extended = insert(Y_centerline_extended, 0, 0)
#recurrence
count_zeros_x=0
count_zeros_y=0
for i in range(1,nz-1):
if x_centerline_extended[i]==0:
x_centerline_extended[i] = 0.5*(x_centerline_extended[X_centerline_extended[i-1-count_zeros_x]] + x_centerline_extended[X_centerline_extended[i-count_zeros_x]])
count_zeros_x += 1
if y_centerline_extended[i]==0:
y_centerline_extended[i] = 0.5*(y_centerline_extended[Y_centerline_extended[i-1-count_zeros_y]] + y_centerline_extended[Y_centerline_extended[i-count_zeros_y]])
count_zeros_y += 1
# Save image centerline completed to be used after
sct.printv('\nSave image completed: centerline_rpi_completed.nii...\n')
for i in range(nz):
data_output[x_centerline_extended[i],y_centerline_extended[i],i] = 1
img = Nifti1Image(data_output, None, hdr_c)
save(img, 'centerline_rpi_completed.nii')
#end new
# Straighten the spinal cord
print '\nStraighten the spinal cord...'
sct.run('sct_straighten_spinalcord -i anat_rpi.nii -c centerline_rpi_completed.nii -x spline -v '+str(verbose))
# Smooth the straightened image along z
print '\nSmooth the straightened image along z...'
sct.run('isct_c3d anat_rpi_straight.nii -smooth 0x0x'+str(sigma)+'vox -o anat_rpi_straight_smooth.nii', verbose)
# Apply the reversed warping field to get back the curved spinal cord
print '\nApply the reversed warping field to get back the curved spinal cord...'
sct.run('sct_apply_transfo -i anat_rpi_straight_smooth.nii -o anat_rpi_straight_smooth_curved.nii -d anat.nii -w warp_straight2curve.nii.gz -x spline', verbose)
# come back to parent folder
os.chdir('..')
# Generate output file
print '\nGenerate output file...'
sct.generate_output_file(path_tmp+'/anat_rpi_straight_smooth_curved.nii', file_anat+'_smooth'+ext_anat)
# Remove temporary files
if remove_temp_files == 1:
print('\nRemove temporary files...')
sct.run('rm -rf '+path_tmp)
# Display elapsed time
elapsed_time = time.time() - start_time
print '\nFinished! Elapsed time: '+str(int(round(elapsed_time)))+'s\n'
# to view results
sct.printv('Done! To view results, type:', verbose)
sct.printv('fslview '+file_anat+' '+file_anat+'_smooth &\n', verbose, 'info')
def main():
# Initialization
fname_data = ''
suffix_out = '_crop'
remove_temp_files = param.remove_temp_files
verbose = param.verbose
fsloutput = 'export FSLOUTPUTTYPE=NIFTI; ' # for faster processing, all outputs are in NIFTI
remove_temp_files = param.remove_temp_files
# Parameters for debug mode
if param.debug:
print '\n*** WARNING: DEBUG MODE ON ***\n'
fname_data = path_sct+'/testing/data/errsm_23/t2/t2.nii.gz'
remove_temp_files = 0
else:
# Check input parameters
try:
opts, args = getopt.getopt(sys.argv[1:],'hi:r:v:')
except getopt.GetoptError:
usage()
if not opts:
usage()
for opt, arg in opts:
if opt == '-h':
usage()
elif opt in ('-i'):
fname_data = arg
elif opt in ('-r'):
remove_temp_files = int(arg)
elif opt in ('-v'):
verbose = int(arg)
# display usage if a mandatory argument is not provided
if fname_data == '':
usage()
# Check file existence
sct.printv('\nCheck file existence...', verbose)
sct.check_file_exist(fname_data, verbose)
# Get dimensions of data
sct.printv('\nGet dimensions of data...', verbose)
nx, ny, nz, nt, px, py, pz, pt = Image(fname_data).dim
sct.printv('.. '+str(nx)+' x '+str(ny)+' x '+str(nz), verbose)
# check if 4D data
if not nt == 1:
sct.printv('\nERROR in '+os.path.basename(__file__)+': Data should be 3D.\n', 1, 'error')
sys.exit(2)
# print arguments
print '\nCheck parameters:'
print ' data ................... '+fname_data
print
# Extract path/file/extension
path_data, file_data, ext_data = sct.extract_fname(fname_data)
path_out, file_out, ext_out = '', file_data+suffix_out, ext_data
# create temporary folder
path_tmp = 'tmp.'+time.strftime("%y%m%d%H%M%S")+'/'
sct.run('mkdir '+path_tmp)
# copy files into tmp folder
sct.run('isct_c3d '+fname_data+' -o '+path_tmp+'data.nii')
# go to tmp folder
os.chdir(path_tmp)
# change orientation
sct.printv('\nChange orientation to RPI...', verbose)
set_orientation('data.nii', 'RPI', 'data_rpi.nii')
# get image of medial slab
sct.printv('\nGet image of medial slab...', verbose)
image_array = nibabel.load('data_rpi.nii').get_data()
nx, ny, nz = image_array.shape
scipy.misc.imsave('image.jpg', image_array[math.floor(nx/2), :, :])
# Display the image
sct.printv('\nDisplay image and get cropping region...', verbose)
fig = plt.figure()
# fig = plt.gcf()
# ax = plt.gca()
ax = fig.add_subplot(111)
img = mpimg.imread("image.jpg")
implot = ax.imshow(img.T)
implot.set_cmap('gray')
plt.gca().invert_yaxis()
# mouse callback
ax.set_title('Left click on the top and bottom of your cropping field.\n Right click to remove last point.\n Close window when your done.')
line, = ax.plot([], [], 'ro') # empty line
cropping_coordinates = LineBuilder(line)
plt.show()
# disconnect callback
# fig.canvas.mpl_disconnect(line)
# check if user clicked two times
if len(cropping_coordinates.xs) != 2:
sct.printv('\nERROR: You have to select two points. Exit program.\n', 1, 'error')
sys.exit(2)
# convert coordinates to integer
zcrop = [int(i) for i in cropping_coordinates.ys]
# sort coordinates
zcrop.sort()
# crop image
sct.printv('\nCrop image...', verbose)
nii = Image('data_rpi.nii')
data_crop = nii.data[:, :, zcrop[0]:zcrop[1]]
nii.data = data_crop
nii.setFileName('data_rpi_crop.nii')
nii.save()
# come back to parent folder
os.chdir('..')
sct.printv('\nGenerate output files...', verbose)
sct.generate_output_file(path_tmp+'data_rpi_crop.nii', path_out+file_out+ext_out)
# Remove temporary files
if remove_temp_files == 1:
print('\nRemove temporary files...')
sct.run('rm -rf '+path_tmp)
# to view results
print '\nDone! To view results, type:'
print 'fslview '+path_out+file_out+ext_out+' &'
print
def main():
# Initialization
fname_anat = ''
fname_centerline = ''
centerline_fitting = 'polynome'
remove_temp_files = param.remove_temp_files
interp = param.interp
degree_poly = param.deg_poly
# extract path of the script
path_script = os.path.dirname(__file__) + '/'
# Parameters for debug mode
if param.debug == 1:
print '\n*** WARNING: DEBUG MODE ON ***\n'
status, path_sct_data = commands.getstatusoutput(
'echo $SCT_TESTING_DATA_DIR')
fname_anat = path_sct_data + '/t2/t2.nii.gz'
fname_centerline = path_sct_data + '/t2/t2_seg.nii.gz'
else:
# Check input param
try:
opts, args = getopt.getopt(sys.argv[1:], 'hi:c:r:d:f:s:')
except getopt.GetoptError as err:
print str(err)
usage()
if not opts:
usage()
for opt, arg in opts:
if opt == '-h':
usage()
elif opt in ('-i'):
fname_anat = arg
elif opt in ('-c'):
fname_centerline = arg
elif opt in ('-r'):
remove_temp_files = int(arg)
elif opt in ('-d'):
degree_poly = int(arg)
elif opt in ('-f'):
centerline_fitting = str(arg)
elif opt in ('-s'):
interp = str(arg)
# display usage if a mandatory argument is not provided
if fname_anat == '' or fname_centerline == '':
usage()
# check existence of input files
sct.check_file_exist(fname_anat)
sct.check_file_exist(fname_centerline)
# extract path/file/extension
path_anat, file_anat, ext_anat = sct.extract_fname(fname_anat)
# Display arguments
print '\nCheck input arguments...'
print ' Input volume ...................... ' + fname_anat
print ' Centerline ........................ ' + fname_centerline
print ''
# Get input image orientation
input_image_orientation = get_orientation(fname_anat)
# Reorient input data into RL PA IS orientation
set_orientation(fname_anat, 'RPI', 'tmp.anat_orient.nii')
set_orientation(fname_centerline, 'RPI', 'tmp.centerline_orient.nii')
# Open centerline
#==========================================================================================
print '\nGet dimensions of input centerline...'
nx, ny, nz, nt, px, py, pz, pt = Image('tmp.centerline_orient.nii').dim
print '.. matrix size: ' + str(nx) + ' x ' + str(ny) + ' x ' + str(nz)
print '.. voxel size: ' + str(px) + 'mm x ' + str(py) + 'mm x ' + str(
pz) + 'mm'
print '\nOpen centerline volume...'
file = nibabel.load('tmp.centerline_orient.nii')
data = file.get_data()
X, Y, Z = (data > 0).nonzero()
min_z_index, max_z_index = min(Z), max(Z)
# loop across z and associate x,y coordinate with the point having maximum intensity
x_centerline = [0 for iz in range(min_z_index, max_z_index + 1, 1)]
y_centerline = [0 for iz in range(min_z_index, max_z_index + 1, 1)]
z_centerline = [iz for iz in range(min_z_index, max_z_index + 1, 1)]
# Two possible scenario:
# 1. the centerline is probabilistic: each slices contains voxels with the probability of containing the centerline [0:...:1]
# We only take the maximum value of the image to aproximate the centerline.
# 2. The centerline/segmentation image contains many pixels per slice with values {0,1}.
# We take all the points and approximate the centerline on all these points.
X, Y, Z = ((data < 1) * (data > 0)).nonzero() # X is empty if binary image
if (len(X) > 0): # Scenario 1
for iz in range(min_z_index, max_z_index + 1, 1):
x_centerline[iz - min_z_index], y_centerline[
iz - min_z_index] = numpy.unravel_index(
data[:, :, iz].argmax(), data[:, :, iz].shape)
else: # Scenario 2
for iz in range(min_z_index, max_z_index + 1, 1):
x_seg, y_seg = (data[:, :, iz] > 0).nonzero()
if len(x_seg) > 0:
x_centerline[iz - min_z_index] = numpy.mean(x_seg)
y_centerline[iz - min_z_index] = numpy.mean(y_seg)
# TODO: find a way to do the previous loop with this, which is more neat:
# [numpy.unravel_index(data[:,:,iz].argmax(), data[:,:,iz].shape) for iz in range(0,nz,1)]
# clear variable
del data
# Fit the centerline points with the kind of curve given as argument of the script and return the new smoothed coordinates
if centerline_fitting == 'splines':
try:
x_centerline_fit, y_centerline_fit = b_spline_centerline(
x_centerline, y_centerline, z_centerline)
except ValueError:
print "splines fitting doesn't work, trying with polynomial fitting...\n"
x_centerline_fit, y_centerline_fit = polynome_centerline(
x_centerline, y_centerline, z_centerline)
elif centerline_fitting == 'polynome':
x_centerline_fit, y_centerline_fit = polynome_centerline(
x_centerline, y_centerline, z_centerline)
#==========================================================================================
# Split input volume
print '\nSplit input volume...'
from sct_split_data import split_data
if not split_data('tmp.anat_orient.nii', 2, '_z'):
sct.printv('ERROR in split_data.', 1, 'error')
file_anat_split = [
'tmp.anat_orient_z' + str(z).zfill(4) for z in range(0, nz, 1)
]
# initialize variables
file_mat_inv_cumul = [
'tmp.mat_inv_cumul_z' + str(z).zfill(4) for z in range(0, nz, 1)
]
z_init = min_z_index
displacement_max_z_index = x_centerline_fit[
z_init - min_z_index] - x_centerline_fit[max_z_index - min_z_index]
# write centerline as text file
print '\nGenerate fitted transformation matrices...'
file_mat_inv_cumul_fit = [
'tmp.mat_inv_cumul_fit_z' + str(z).zfill(4) for z in range(0, nz, 1)
]
for iz in range(min_z_index, max_z_index + 1, 1):
# compute inverse cumulative fitted transformation matrix
fid = open(file_mat_inv_cumul_fit[iz], 'w')
if (x_centerline[iz - min_z_index] == 0
and y_centerline[iz - min_z_index] == 0):
displacement = 0
else:
displacement = x_centerline_fit[
z_init - min_z_index] - x_centerline_fit[iz - min_z_index]
fid.write('%i %i %i %f\n' % (1, 0, 0, displacement))
fid.write('%i %i %i %f\n' % (0, 1, 0, 0))
fid.write('%i %i %i %i\n' % (0, 0, 1, 0))
fid.write('%i %i %i %i\n' % (0, 0, 0, 1))
fid.close()
# we complete the displacement matrix in z direction
for iz in range(0, min_z_index, 1):
fid = open(file_mat_inv_cumul_fit[iz], 'w')
fid.write('%i %i %i %f\n' % (1, 0, 0, 0))
fid.write('%i %i %i %f\n' % (0, 1, 0, 0))
fid.write('%i %i %i %i\n' % (0, 0, 1, 0))
fid.write('%i %i %i %i\n' % (0, 0, 0, 1))
fid.close()
for iz in range(max_z_index + 1, nz, 1):
fid = open(file_mat_inv_cumul_fit[iz], 'w')
fid.write('%i %i %i %f\n' % (1, 0, 0, displacement_max_z_index))
fid.write('%i %i %i %f\n' % (0, 1, 0, 0))
fid.write('%i %i %i %i\n' % (0, 0, 1, 0))
fid.write('%i %i %i %i\n' % (0, 0, 0, 1))
fid.close()
# apply transformations to data
print '\nApply fitted transformation matrices...'
file_anat_split_fit = [
'tmp.anat_orient_fit_z' + str(z).zfill(4) for z in range(0, nz, 1)
]
for iz in range(0, nz, 1):
# forward cumulative transformation to data
sct.run(fsloutput + 'flirt -in ' + file_anat_split[iz] + ' -ref ' +
file_anat_split[iz] + ' -applyxfm -init ' +
file_mat_inv_cumul_fit[iz] + ' -out ' +
file_anat_split_fit[iz] + ' -interp ' + interp)
# Merge into 4D volume
print '\nMerge into 4D volume...'
from sct_concat_data import concat_data
from glob import glob
concat_data(glob('tmp.anat_orient_fit_z*.nii'),
'tmp.anat_orient_fit.nii',
dim=2)
# sct.run(fsloutput+'fslmerge -z tmp.anat_orient_fit tmp.anat_orient_fit_z*')
# Reorient data as it was before
print '\nReorient data back into native orientation...'
set_orientation('tmp.anat_orient_fit.nii', input_image_orientation,
'tmp.anat_orient_fit_reorient.nii')
# Generate output file (in current folder)
print '\nGenerate output file (in current folder)...'
sct.generate_output_file('tmp.anat_orient_fit_reorient.nii',
file_anat + '_flatten' + ext_anat)
# Delete temporary files
if remove_temp_files == 1:
print '\nDelete temporary files...'
sct.run('rm -rf tmp.*')
# to view results
print '\nDone! To view results, type:'
print 'fslview ' + file_anat + ext_anat + ' ' + file_anat + '_flatten' + ext_anat + ' &\n'
def main():
# Initialization
fname_anat = ''
fname_centerline = ''
centerline_fitting = 'polynome'
remove_temp_files = param.remove_temp_files
interp = param.interp
degree_poly = param.deg_poly
# extract path of the script
path_script = os.path.dirname(__file__)+'/'
# Parameters for debug mode
if param.debug == 1:
print '\n*** WARNING: DEBUG MODE ON ***\n'
status, path_sct_data = commands.getstatusoutput('echo $SCT_TESTING_DATA_DIR')
fname_anat = path_sct_data+'/t2/t2.nii.gz'
fname_centerline = path_sct_data+'/t2/t2_seg.nii.gz'
else:
# Check input param
try:
opts, args = getopt.getopt(sys.argv[1:],'hi:c:r:d:f:s:')
except getopt.GetoptError as err:
print str(err)
usage()
if not opts:
usage()
for opt, arg in opts:
if opt == '-h':
usage()
elif opt in ('-i'):
fname_anat = arg
elif opt in ('-c'):
fname_centerline = arg
elif opt in ('-r'):
remove_temp_files = int(arg)
elif opt in ('-d'):
degree_poly = int(arg)
elif opt in ('-f'):
centerline_fitting = str(arg)
elif opt in ('-s'):
interp = str(arg)
# display usage if a mandatory argument is not provided
if fname_anat == '' or fname_centerline == '':
usage()
# check existence of input files
sct.check_file_exist(fname_anat)
sct.check_file_exist(fname_centerline)
# extract path/file/extension
path_anat, file_anat, ext_anat = sct.extract_fname(fname_anat)
# Display arguments
print '\nCheck input arguments...'
print ' Input volume ...................... '+fname_anat
print ' Centerline ........................ '+fname_centerline
print ''
# Get input image orientation
input_image_orientation = get_orientation(fname_anat)
# Reorient input data into RL PA IS orientation
set_orientation(fname_anat, 'RPI', 'tmp.anat_orient.nii')
set_orientation(fname_centerline, 'RPI', 'tmp.centerline_orient.nii')
# Open centerline
#==========================================================================================
print '\nGet dimensions of input centerline...'
nx, ny, nz, nt, px, py, pz, pt = sct.get_dimension('tmp.centerline_orient.nii')
print '.. matrix size: '+str(nx)+' x '+str(ny)+' x '+str(nz)
print '.. voxel size: '+str(px)+'mm x '+str(py)+'mm x '+str(pz)+'mm'
print '\nOpen centerline volume...'
file = nibabel.load('tmp.centerline_orient.nii')
data = file.get_data()
X, Y, Z = (data>0).nonzero()
min_z_index, max_z_index = min(Z), max(Z)
# loop across z and associate x,y coordinate with the point having maximum intensity
x_centerline = [0 for iz in range(min_z_index, max_z_index+1, 1)]
y_centerline = [0 for iz in range(min_z_index, max_z_index+1, 1)]
z_centerline = [iz for iz in range(min_z_index, max_z_index+1, 1)]
# Two possible scenario:
# 1. the centerline is probabilistic: each slices contains voxels with the probability of containing the centerline [0:...:1]
# We only take the maximum value of the image to aproximate the centerline.
# 2. The centerline/segmentation image contains many pixels per slice with values {0,1}.
# We take all the points and approximate the centerline on all these points.
X, Y, Z = ((data<1)*(data>0)).nonzero() # X is empty if binary image
if (len(X) > 0): # Scenario 1
for iz in range(min_z_index, max_z_index+1, 1):
x_centerline[iz-min_z_index], y_centerline[iz-min_z_index] = numpy.unravel_index(data[:,:,iz].argmax(), data[:,:,iz].shape)
else: # Scenario 2
for iz in range(min_z_index, max_z_index+1, 1):
x_seg, y_seg = (data[:,:,iz]>0).nonzero()
if len(x_seg) > 0:
x_centerline[iz-min_z_index] = numpy.mean(x_seg)
y_centerline[iz-min_z_index] = numpy.mean(y_seg)
# TODO: find a way to do the previous loop with this, which is more neat:
# [numpy.unravel_index(data[:,:,iz].argmax(), data[:,:,iz].shape) for iz in range(0,nz,1)]
# clear variable
del data
# Fit the centerline points with the kind of curve given as argument of the script and return the new smoothed coordinates
if centerline_fitting == 'splines':
try:
x_centerline_fit, y_centerline_fit = b_spline_centerline(x_centerline,y_centerline,z_centerline)
except ValueError:
print "splines fitting doesn't work, trying with polynomial fitting...\n"
x_centerline_fit, y_centerline_fit = polynome_centerline(x_centerline,y_centerline,z_centerline)
elif centerline_fitting == 'polynome':
x_centerline_fit, y_centerline_fit = polynome_centerline(x_centerline,y_centerline,z_centerline)
#==========================================================================================
# Split input volume
print '\nSplit input volume...'
sct.run(sct.fsloutput + 'fslsplit tmp.anat_orient.nii tmp.anat_z -z')
file_anat_split = ['tmp.anat_z'+str(z).zfill(4) for z in range(0,nz,1)]
# initialize variables
file_mat_inv_cumul = ['tmp.mat_inv_cumul_z'+str(z).zfill(4) for z in range(0,nz,1)]
z_init = min_z_index
displacement_max_z_index = x_centerline_fit[z_init-min_z_index]-x_centerline_fit[max_z_index-min_z_index]
# write centerline as text file
print '\nGenerate fitted transformation matrices...'
file_mat_inv_cumul_fit = ['tmp.mat_inv_cumul_fit_z'+str(z).zfill(4) for z in range(0,nz,1)]
for iz in range(min_z_index, max_z_index+1, 1):
# compute inverse cumulative fitted transformation matrix
fid = open(file_mat_inv_cumul_fit[iz], 'w')
if (x_centerline[iz-min_z_index] == 0 and y_centerline[iz-min_z_index] == 0):
displacement = 0
else:
displacement = x_centerline_fit[z_init-min_z_index]-x_centerline_fit[iz-min_z_index]
fid.write('%i %i %i %f\n' %(1, 0, 0, displacement) )
fid.write('%i %i %i %f\n' %(0, 1, 0, 0) )
fid.write('%i %i %i %i\n' %(0, 0, 1, 0) )
fid.write('%i %i %i %i\n' %(0, 0, 0, 1) )
fid.close()
# we complete the displacement matrix in z direction
for iz in range(0, min_z_index, 1):
fid = open(file_mat_inv_cumul_fit[iz], 'w')
fid.write('%i %i %i %f\n' %(1, 0, 0, 0) )
fid.write('%i %i %i %f\n' %(0, 1, 0, 0) )
fid.write('%i %i %i %i\n' %(0, 0, 1, 0) )
fid.write('%i %i %i %i\n' %(0, 0, 0, 1) )
fid.close()
for iz in range(max_z_index+1, nz, 1):
fid = open(file_mat_inv_cumul_fit[iz], 'w')
fid.write('%i %i %i %f\n' %(1, 0, 0, displacement_max_z_index) )
fid.write('%i %i %i %f\n' %(0, 1, 0, 0) )
fid.write('%i %i %i %i\n' %(0, 0, 1, 0) )
fid.write('%i %i %i %i\n' %(0, 0, 0, 1) )
fid.close()
# apply transformations to data
print '\nApply fitted transformation matrices...'
file_anat_split_fit = ['tmp.anat_orient_fit_z'+str(z).zfill(4) for z in range(0,nz,1)]
for iz in range(0, nz, 1):
# forward cumulative transformation to data
sct.run(fsloutput+'flirt -in '+file_anat_split[iz]+' -ref '+file_anat_split[iz]+' -applyxfm -init '+file_mat_inv_cumul_fit[iz]+' -out '+file_anat_split_fit[iz]+' -interp '+interp)
# Merge into 4D volume
print '\nMerge into 4D volume...'
sct.run(fsloutput+'fslmerge -z tmp.anat_orient_fit tmp.anat_orient_fit_z*')
# Reorient data as it was before
print '\nReorient data back into native orientation...'
set_orientation('tmp.anat_orient_fit.nii', input_image_orientation, 'tmp.anat_orient_fit_reorient.nii')
# Generate output file (in current folder)
print '\nGenerate output file (in current folder)...'
sct.generate_output_file('tmp.anat_orient_fit_reorient.nii', file_anat+'_flatten'+ext_anat)
# Delete temporary files
if remove_temp_files == 1:
print '\nDelete temporary files...'
sct.run('rm -rf tmp.*')
# to view results
print '\nDone! To view results, type:'
print 'fslview '+file_anat+ext_anat+' '+file_anat+'_flatten'+ext_anat+' &\n'
def main():
# Initialization
fname_anat = ''
fname_centerline = ''
sigma = 3 # default value of the standard deviation for the Gaussian smoothing (in terms of number of voxels)
remove_temp_files = param.remove_temp_files
verbose = param.verbose
start_time = time.time()
# Check input param
try:
opts, args = getopt.getopt(sys.argv[1:], 'hi:c:r:s:v:')
except getopt.GetoptError as err:
print str(err)
usage()
if not opts:
usage()
for opt, arg in opts:
if opt == '-h':
usage()
elif opt in ('-c'):
fname_centerline = arg
elif opt in ('-i'):
fname_anat = arg
elif opt in ('-r'):
remove_temp_files = arg
elif opt in ('-s'):
sigma = arg
elif opt in ('-v'):
verbose = int(arg)
# Display usage if a mandatory argument is not provided
if fname_anat == '' or fname_centerline == '':
usage()
# Display arguments
print '\nCheck input arguments...'
print ' Volume to smooth .................. ' + fname_anat
print ' Centerline ........................ ' + fname_centerline
print ' FWHM .............................. '+str(sigma)
print ' Verbose ........................... '+str(verbose)
# Check existence of input files
print('\nCheck existence of input files...')
sct.check_file_exist(fname_anat, verbose)
sct.check_file_exist(fname_centerline, verbose)
# Extract path/file/extension
path_anat, file_anat, ext_anat = sct.extract_fname(fname_anat)
path_centerline, file_centerline, ext_centerline = sct.extract_fname(fname_centerline)
# create temporary folder
sct.printv('\nCreate temporary folder...', verbose)
path_tmp = sct.slash_at_the_end('tmp.'+time.strftime("%y%m%d%H%M%S"), 1)
sct.run('mkdir '+path_tmp, verbose)
# Copying input data to tmp folder
sct.printv('\nCopying input data to tmp folder and convert to nii...', verbose)
sct.run('cp '+fname_anat+' '+path_tmp+'anat'+ext_anat, verbose)
sct.run('cp '+fname_centerline+' '+path_tmp+'centerline'+ext_centerline, verbose)
# go to tmp folder
os.chdir(path_tmp)
# convert to nii format
convert('anat'+ext_anat, 'anat.nii')
convert('centerline'+ext_centerline, 'centerline.nii')
# Change orientation of the input image into RPI
print '\nOrient input volume to RPI orientation...'
set_orientation('anat.nii', 'RPI', 'anat_rpi.nii')
# Change orientation of the input image into RPI
print '\nOrient centerline to RPI orientation...'
set_orientation('centerline.nii', 'RPI', 'centerline_rpi.nii')
# ## new
#
# ### Make sure that centerline file does not have halls
# file_c = load('centerline_rpi.nii')
# data_c = file_c.get_data()
# hdr_c = file_c.get_header()
#
# data_temp = copy(data_c)
# data_temp *= 0
# data_output = copy(data_c)
# data_output *= 0
# nx, ny, nz, nt, px, py, pz, pt = sct.get_dimension('centerline_rpi.nii')
#
# ## Change seg to centerline if it is a segmentation
# sct.printv('\nChange segmentation to centerline if it is a centerline...\n')
# z_centerline = [iz for iz in range(0, nz, 1) if data_c[:,:,iz].any() ]
# nz_nonz = len(z_centerline)
# if nz_nonz==0 :
# print '\nERROR: Centerline is empty'
# sys.exit()
# x_centerline = [0 for iz in range(0, nz_nonz, 1)]
# y_centerline = [0 for iz in range(0, nz_nonz, 1)]
# #print("z_centerline", z_centerline,nz_nonz,len(x_centerline))
# print '\nGet center of mass of the centerline ...'
# for iz in xrange(len(z_centerline)):
# x_centerline[iz], y_centerline[iz] = ndimage.measurements.center_of_mass(array(data_c[:,:,z_centerline[iz]]))
# data_temp[x_centerline[iz], y_centerline[iz], z_centerline[iz]] = 1
#
# ## Complete centerline
# sct.printv('\nComplete the halls of the centerline if there are any...\n')
# X,Y,Z = data_temp.nonzero()
#
# x_centerline_extended = [0 for i in range(0, nz, 1)]
# y_centerline_extended = [0 for i in range(0, nz, 1)]
# for iz in range(len(Z)):
# x_centerline_extended[Z[iz]] = X[iz]
# y_centerline_extended[Z[iz]] = Y[iz]
#
# X_centerline_extended = nonzero(x_centerline_extended)
# X_centerline_extended = transpose(X_centerline_extended)
# Y_centerline_extended = nonzero(y_centerline_extended)
# Y_centerline_extended = transpose(Y_centerline_extended)
#
# # initialization: we set the extrem values to avoid edge effects
# x_centerline_extended[0] = x_centerline_extended[X_centerline_extended[0]]
# x_centerline_extended[-1] = x_centerline_extended[X_centerline_extended[-1]]
# y_centerline_extended[0] = y_centerline_extended[Y_centerline_extended[0]]
# y_centerline_extended[-1] = y_centerline_extended[Y_centerline_extended[-1]]
#
# # Add two rows to the vector X_means_smooth_extended:
# # one before as means_smooth_extended[0] is now diff from 0
# # one after as means_smooth_extended[-1] is now diff from 0
# X_centerline_extended = append(X_centerline_extended, len(x_centerline_extended)-1)
# X_centerline_extended = insert(X_centerline_extended, 0, 0)
# Y_centerline_extended = append(Y_centerline_extended, len(y_centerline_extended)-1)
# Y_centerline_extended = insert(Y_centerline_extended, 0, 0)
#
# #recurrence
# count_zeros_x=0
# count_zeros_y=0
# for i in range(1,nz-1):
# if x_centerline_extended[i]==0:
# x_centerline_extended[i] = 0.5*(x_centerline_extended[X_centerline_extended[i-1-count_zeros_x]] + x_centerline_extended[X_centerline_extended[i-count_zeros_x]])
# count_zeros_x += 1
# if y_centerline_extended[i]==0:
# y_centerline_extended[i] = 0.5*(y_centerline_extended[Y_centerline_extended[i-1-count_zeros_y]] + y_centerline_extended[Y_centerline_extended[i-count_zeros_y]])
# count_zeros_y += 1
#
# # Save image centerline completed to be used after
# sct.printv('\nSave image completed: centerline_rpi_completed.nii...\n')
# for i in range(nz):
# data_output[x_centerline_extended[i],y_centerline_extended[i],i] = 1
# img = Nifti1Image(data_output, None, hdr_c)
# save(img, 'centerline_rpi_completed.nii')
#
# #end new
# Straighten the spinal cord
print '\nStraighten the spinal cord...'
sct.run('sct_straighten_spinalcord -i anat_rpi.nii -c centerline_rpi.nii -x spline -v '+str(verbose))
# Smooth the straightened image along z
print '\nSmooth the straightened image along z...'
sct.run('isct_c3d anat_rpi_straight.nii -smooth 0x0x'+str(sigma)+'vox -o anat_rpi_straight_smooth.nii', verbose)
# Apply the reversed warping field to get back the curved spinal cord
print '\nApply the reversed warping field to get back the curved spinal cord...'
sct.run('sct_apply_transfo -i anat_rpi_straight_smooth.nii -o anat_rpi_straight_smooth_curved.nii -d anat.nii -w warp_straight2curve.nii.gz -x spline', verbose)
# come back to parent folder
os.chdir('..')
# Generate output file
print '\nGenerate output file...'
sct.generate_output_file(path_tmp+'/anat_rpi_straight_smooth_curved.nii', file_anat+'_smooth'+ext_anat)
# Remove temporary files
if remove_temp_files == 1:
print('\nRemove temporary files...')
sct.run('rm -rf '+path_tmp)
# Display elapsed time
elapsed_time = time.time() - start_time
print '\nFinished! Elapsed time: '+str(int(round(elapsed_time)))+'s\n'
# to view results
sct.printv('Done! To view results, type:', verbose)
sct.printv('fslview '+file_anat+' '+file_anat+'_smooth &\n', verbose, 'info')
