def OpenOtherFiles(self, group):
# Retreaving matrix from image data
self.matrix, scalar_range, self.filename = image_utils.img2memmap(group)
hdr = group.header
if group.affine.any():
self.affine = group.affine
Publisher.sendMessage('Update affine matrix',
affine=self.affine, status=True)
hdr.set_data_dtype('int16')
dims = hdr.get_zooms()
dimsf = tuple([float(s) for s in dims])
wl = float((scalar_range[0] + scalar_range[1]) * 0.5)
ww = float((scalar_range[1] - scalar_range[0]))
self.Slice = sl.Slice()
self.Slice.matrix = self.matrix
self.Slice.matrix_filename = self.filename
self.Slice.spacing = dimsf
self.Slice.window_level = wl
self.Slice.window_width = ww
scalar_range = int(scalar_range[0]), int(scalar_range[1])
Publisher.sendMessage('Update threshold limits list',
threshold_range=scalar_range)
return self.matrix, self.filename
def OpenOtherFiles(self, group):
# Retreaving matrix from image data
self.matrix, scalar_range, self.filename = image_utils.img2memmap(group)
hdr = group.header
if group.affine.any():
self.affine = group.affine
Publisher.sendMessage('Update affine matrix',
affine=self.affine, status=True)
hdr.set_data_dtype('int16')
dims = hdr.get_zooms()
dimsf = tuple([float(s) for s in dims])
wl = float((scalar_range[0] + scalar_range[1]) * 0.5)
ww = float((scalar_range[1] - scalar_range[0]))
self.Slice = sl.Slice()
self.Slice.matrix = self.matrix
self.Slice.matrix_filename = self.filename
self.Slice.spacing = dimsf
self.Slice.window_level = wl
self.Slice.window_width = ww
scalar_range = int(scalar_range[0]), int(scalar_range[1])
Publisher.sendMessage('Update threshold limits list',
threshold_range=scalar_range)
return self.matrix, self.filename
def OpenOtherFiles(self, group):
# Retreaving matrix from image data
self.matrix, scalar_range, self.filename = image_utils.img2memmap(
group)
hdr = group.header
# if group.affine.any():
# self.affine = group.affine
# Publisher.sendMessage('Update affine matrix',
# affine=self.affine, status=True)
hdr.set_data_dtype('int16')
dims = hdr.get_zooms()
dimsf = tuple([float(s) for s in dims])
wl = float((scalar_range[0] + scalar_range[1]) * 0.5)
ww = float((scalar_range[1] - scalar_range[0]))
self.Slice = sl.Slice()
self.Slice.matrix = self.matrix
self.Slice.matrix_filename = self.filename
self.Slice.spacing = dimsf
self.Slice.window_level = wl
self.Slice.window_width = ww
if group.affine.any():
# TODO: replace the inverse of the affine by the actual affine in the whole code
# remove scaling factor for non-unitary voxel dimensions
# self.affine = image_utils.world2invspace(affine=group.affine)
scale, shear, angs, trans, persp = tr.decompose_matrix(
group.affine)
self.affine = np.linalg.inv(
tr.compose_matrix(scale=None,
shear=shear,
angles=angs,
translate=trans,
perspective=persp))
# print("repos_img: {}".format(repos_img))
self.Slice.affine = self.affine
Publisher.sendMessage('Update affine matrix',
affine=self.affine,
status=True)
scalar_range = int(scalar_range[0]), int(scalar_range[1])
Publisher.sendMessage('Update threshold limits list',
threshold_range=scalar_range)
return self.matrix, self.filename
def OpenOtherFiles(self, group):
# Retreaving matrix from image data
self.matrix, scalar_range, self.filename = image_utils.img2memmap(
group)
hdr = group.header
hdr.set_data_dtype('int16')
wl = float((scalar_range[0] + scalar_range[1]) * 0.5)
ww = float((scalar_range[1] - scalar_range[0]))
self.Slice = sl.Slice()
self.Slice.matrix = self.matrix
self.Slice.matrix_filename = self.filename
# even though the axes 0 and 2 are swapped when creating self.matrix
# the spacing should be kept the original, as it is modified somewhere later
# otherwise generate wrong results
# also need to convert to float because original get_zooms return numpy.float32
# which is unsupported by the plist for saving the project
self.Slice.spacing = tuple([float(s) for s in hdr.get_zooms()])
self.Slice.window_level = wl
self.Slice.window_width = ww
if group.affine.any():
# remove scaling factor for non-unitary voxel dimensions
scale, shear, angs, trans, persp = tr.decompose_matrix(
group.affine)
self.Slice.affine = np.linalg.inv(
tr.compose_matrix(scale=None,
shear=shear,
angles=angs,
translate=trans,
perspective=persp))
else:
self.Slice.affine = None
scalar_range = int(scalar_range[0]), int(scalar_range[1])
Publisher.sendMessage('Update threshold limits list',
threshold_range=scalar_range)
return self.matrix, self.filename