def launch_sagittal_viewer(img: Image,
labels: Sequence[int],
msg: str,
previous_points: Sequence[Coordinate] = None,
output_img: Image = None) -> Image:
from spinalcordtoolbox.gui import base
from spinalcordtoolbox.gui.sagittal import launch_sagittal_dialog
params = base.AnatomicalParams()
params.vertebraes = labels
params.input_file_name = img.absolutepath
if output_img is not None:
params.output_file_name = output_img.absolutepath
else:
params.output_file_name = img.absolutepath
params.subtitle = msg
if previous_points is not None:
params.message_warn = 'Please select the label you want to add \nor correct in the list below before clicking \non the image'
out = zeros_like(img, dtype='uint8')
out.absolutepath = params.output_file_name
launch_sagittal_dialog(img, out, params, previous_points)
return out
def launch_sagittal_viewer(self, labels):
from spinalcordtoolbox.gui import base
from spinalcordtoolbox.gui.sagittal import launch_sagittal_dialog
params = base.AnatomicalParams()
params.vertebraes = labels
params.input_file_name = self.image_input.absolutepath
params.output_file_name = self.fname_output
params.subtitle = self.msg
output = msct_image.zeros_like(self.image_input)
output.absolutepath = self.fname_output
launch_sagittal_dialog(self.image_input, output, params)
return output
def launch_sagittal_viewer(self, labels):
from spinalcordtoolbox.gui import base
from spinalcordtoolbox.gui.sagittal import launch_sagittal_dialog
params = base.AnatomicalParams()
params.vertebraes = labels
params.input_file_name = self.image_input.file_name
params.output_file_name = self.fname_output
output = self.image_input.copy()
output.data *= 0
output.setFileName(self.fname_output)
launch_sagittal_dialog(self.image_input, output, params)
return output
def launch_sagittal_viewer(self, labels, previous_points=None):
from spinalcordtoolbox.gui import base
from spinalcordtoolbox.gui.sagittal import launch_sagittal_dialog
params = base.AnatomicalParams()
params.vertebraes = labels
params.input_file_name = self.image_input.absolutepath
params.output_file_name = self.fname_output
params.subtitle = self.msg
if previous_points is not None:
params.message_warn = 'Please select the label you want to add \nor correct in the list below before clicking \non the image'
output = msct_image.zeros_like(self.image_input)
output.absolutepath = self.fname_output
launch_sagittal_dialog(self.image_input, output, params,
previous_points)
return output
def get_bbox_from_gui(self):
"""
Launch a GUI. The medial sagittal plane of the image is shown. User selects two points: top-left and bottom-
right of the cropping window.
Note: There is no cropping along the right-left direction.
:return:
"""
from spinalcordtoolbox.gui import base
from spinalcordtoolbox.gui.sagittal import launch_sagittal_dialog
# Change orientation to SAL (for displaying sagittal view in the GUI)
native_orientation = self.img_in.orientation
self.img_in.change_orientation('SAL')
# Launch GUI
params = base.AnatomicalParams()
params.vertebraes = [
1, 2
] # TODO: Have user draw a sliding rectangle instead (more intuitive)
params.subtitle = "Click on the top-left (Label 1) and bottom-right (Label 2) of the image to select your " \
"cropping window."
img_labels = zeros_like(self.img_in)
launch_sagittal_dialog(self.img_in, img_labels, params)
# Extract coordinates
img_labels.change_orientation(native_orientation)
cropping_coord = img_labels.getNonZeroCoordinates(sorting='value')
# Since there is no cropping along the R-L direction, xmin/xmax are based on image dimension
self.bbox.xmin, self.bbox.ymin, self.bbox.zmin = (
0,
min(cropping_coord[0].y, cropping_coord[1].y),
min(cropping_coord[0].z, cropping_coord[1].z),
)
self.bbox.xmax, self.bbox.ymax, self.bbox.zmax = (
img_labels.dim[0],
max(cropping_coord[0].y, cropping_coord[1].y),
max(cropping_coord[0].z, cropping_coord[1].z),
)
# Put back input image in native orientation
self.img_in.change_orientation(native_orientation)
def segment_image_cli():
parser = get_parser()
args = sys.argv[1:]
try:
arguments = parser.parse(args)
except SyntaxError as err:
printv(str(err), type='error')
launch_modes = {
'centerline': launch_centerline_dialog,
'sagittal': launch_sagittal_dialog
}
mode = arguments['-mode']
input_file_name = arguments['-i']
output_file_name = arguments['-o']
params = base.AnatomicalParams()
params.input_file_name = input_file_name
params.num_points = arguments.get('-n', params.num_points)
params.vertebraes = arguments.get('-labels', params.vertebraes)
input_file = Image(input_file_name)
if os.path.exists:
printv('The output file exists, the contents will be overwritten',
type='warning')
output_file = input_file.copy()
output_file.data *= 0
output_file.absolutepath = output_file_name
controller = launch_modes[mode](input_file, output_file, params)
if controller.saved:
controller.as_niftii()
printv('Output file %s' % output_file_name, type='info')
else:
printv('Aborted Manual labeling', type='warning')
def setUp(self):
self.image = msct_image.Image(sct_test_path('t2', 't2.nii.gz'))
self.overlay = msct_image.Image(self.image)
self.params = base.AnatomicalParams()
def setUp(self):
self.image = msct_image.Image(
os.path.expanduser('~/sct_example_data/t2/t2.nii.gz'))
self.overlay = msct_image.Image(self.image)
self.params = base.AnatomicalParams()
