Python SimpleITK.sitkBSpline() Examples

The following are 8 code examples of SimpleITK.sitkBSpline(). You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may also want to check out all available functions/classes of the module SimpleITK , or try the search function .
Example #1
Source File: download_IXI_Guys.py    From DLTK with Apache License 2.0 8 votes vote down vote up 
def resample_image(itk_image, out_spacing=[1.0, 1.0, 1.0], is_label=False):
    original_spacing = itk_image.GetSpacing()
    original_size = itk_image.GetSize()

    out_size = [
        int(np.round(original_size[0] * (original_spacing[0] / out_spacing[0]))),
        int(np.round(original_size[1] * (original_spacing[1] / out_spacing[1]))),
        int(np.round(original_size[2] * (original_spacing[2] / out_spacing[2])))
    ]

    resample = sitk.ResampleImageFilter()
    resample.SetOutputSpacing(out_spacing)
    resample.SetSize(out_size)
    resample.SetOutputDirection(itk_image.GetDirection())
    resample.SetOutputOrigin(itk_image.GetOrigin())
    resample.SetTransform(sitk.Transform())
    resample.SetDefaultPixelValue(itk_image.GetPixelIDValue())

    if is_label:
        resample.SetInterpolator(sitk.sitkNearestNeighbor)
    else:
        resample.SetInterpolator(sitk.sitkBSpline)

    return resample.Execute(itk_image)
Example #2
Source File: download_IXI_HH.py    From DLTK with Apache License 2.0 6 votes vote down vote up 
def resample_image(itk_image, out_spacing=(1.0, 1.0, 1.0), is_label=False):
    original_spacing = itk_image.GetSpacing()
    original_size = itk_image.GetSize()

    out_size = [int(np.round(original_size[0] * (original_spacing[0] / out_spacing[0]))),
                int(np.round(original_size[1] * (original_spacing[1] / out_spacing[1]))),
                int(np.round(original_size[2] * (original_spacing[2] / out_spacing[2])))]

    resample = sitk.ResampleImageFilter()
    resample.SetOutputSpacing(out_spacing)
    resample.SetSize(out_size)
    resample.SetOutputDirection(itk_image.GetDirection())
    resample.SetOutputOrigin(itk_image.GetOrigin())
    resample.SetTransform(sitk.Transform())
    resample.SetDefaultPixelValue(itk_image.GetPixelIDValue())

    if is_label:
        resample.SetInterpolator(sitk.sitkNearestNeighbor)
    else:
        resample.SetInterpolator(sitk.sitkBSpline)

    return resample.Execute(itk_image)
Example #3
Source File: download_IXI_Guys.py    From DLTK with Apache License 2.0 5 votes vote down vote up 
def reslice_image(itk_image, itk_ref, is_label=False):
    resample = sitk.ResampleImageFilter()
    resample.SetReferenceImage(itk_ref)

    if is_label:
        resample.SetInterpolator(sitk.sitkNearestNeighbor)
    else:
        resample.SetInterpolator(sitk.sitkBSpline)

    return resample.Execute(itk_image)
Example #4
Source File: processing.py    From istn with Apache License 2.0 5 votes vote down vote up 
def resample_image_to_ref(image, ref, is_label=False, pad_value=0):
    """Resamples an image to match the resolution and size of a given reference image."""

    resample = sitk.ResampleImageFilter()
    resample.SetReferenceImage(ref)
    resample.SetDefaultPixelValue(pad_value)

    if is_label:
        resample.SetInterpolator(sitk.sitkNearestNeighbor)
    else:
        #resample.SetInterpolator(sitk.sitkBSpline)
        resample.SetInterpolator(sitk.sitkLinear)

    return resample.Execute(image)
Example #5
Source File: processing.py    From istn with Apache License 2.0 5 votes vote down vote up 
def resample_image(image, out_spacing=(1.0, 1.0, 1.0), out_size=None, is_label=False, pad_value=0):
    """Resamples an image to given element spacing and output size."""

    original_spacing = np.array(image.GetSpacing())
    original_size = np.array(image.GetSize())

    if out_size is None:
        out_size = np.round(np.array(original_size * original_spacing / np.array(out_spacing))).astype(int)
    else:
        out_size = np.array(out_size)

    original_direction = np.array(image.GetDirection()).reshape(len(original_spacing),-1)
    original_center = (np.array(original_size, dtype=float) - 1.0) / 2.0 * original_spacing
    out_center = (np.array(out_size, dtype=float) - 1.0) / 2.0 * np.array(out_spacing)

    original_center = np.matmul(original_direction, original_center)
    out_center = np.matmul(original_direction, out_center)
    out_origin = np.array(image.GetOrigin()) + (original_center - out_center)

    resample = sitk.ResampleImageFilter()
    resample.SetOutputSpacing(out_spacing)
    resample.SetSize(out_size.tolist())
    resample.SetOutputDirection(image.GetDirection())
    resample.SetOutputOrigin(out_origin.tolist())
    resample.SetTransform(sitk.Transform())
    resample.SetDefaultPixelValue(pad_value)

    if is_label:
        resample.SetInterpolator(sitk.sitkNearestNeighbor)
    else:
        #resample.SetInterpolator(sitk.sitkBSpline)
        resample.SetInterpolator(sitk.sitkLinear)

    return resample.Execute(sitk.Cast(image, sitk.sitkFloat32))
Example #6
Source File: sitk_image.py    From MedicalDataAugmentationTool with GNU General Public License v3.0 5 votes vote down vote up 
def get_sitk_interpolator(interpolator):
    if interpolator == 'nearest':
        return sitk.sitkNearestNeighbor
    elif interpolator == 'linear':
        return sitk.sitkLinear
    elif interpolator == 'cubic':
        return sitk.sitkBSpline
    elif interpolator == 'label_gaussian':
        return sitk.sitkLabelGaussian
    elif interpolator == 'gaussian':
        return sitk.sitkGaussian
    elif interpolator == 'lanczos':
        return sitk.sitkLanczosWindowedSinc
    else:
        raise Exception('invalid interpolator type')
Example #7
Source File: download_IXI_HH.py    From DLTK with Apache License 2.0 4 votes vote down vote up 
def reslice_image(itk_image, itk_ref, is_label=False):
    resample = sitk.ResampleImageFilter()
    resample.SetReferenceImage(itk_ref)

    if is_label:
        resample.SetInterpolator(sitk.sitkNearestNeighbor)
    else:
        resample.SetInterpolator(sitk.sitkBSpline)

    return resample.Execute(itk_image)
Example #8
Source File: niftyreg_test.py    From NiftyMIC with BSD 3-Clause "New" or "Revised" License 4 votes vote down vote up 
def test_affine_transform_reg_aladin(self):

        # Read data
        filename_fixed = "stack1_rotated_angle_z_is_pi_over_10.nii.gz"
        filename_moving = "FetalBrain_reconstruction_3stacks_myAlg.nii.gz"

        diff_ref = os.path.join(
            DIR_TEST,  "stack1_rotated_angle_z_is_pi_over_10_nreg_diff.nii.gz")
        moving = st.Stack.from_filename(
            os.path.join(self.dir_test_data, filename_moving),
        )
        fixed = st.Stack.from_filename(
            os.path.join(self.dir_test_data, filename_fixed)
        )

        # Set up NiftyReg
        nifty_reg = nreg.RegAladin()
        nifty_reg.set_fixed(fixed)
        nifty_reg.set_moving(moving)
        nifty_reg.set_registration_type("Rigid")
        nifty_reg.use_verbose(False)

        # Register via NiftyReg
        nifty_reg.run()

        # Get associated results
        affine_transform_sitk = nifty_reg.get_registration_transform_sitk()
        moving_warped = nifty_reg.get_warped_moving()

        # Get SimpleITK result with "similar" interpolator (NiftyReg does not
        # state what interpolator is used but it seems to be BSpline)
        moving_warped_sitk = sitk.Resample(
            moving.sitk, fixed.sitk, affine_transform_sitk, sitk.sitkBSpline, 0.0, moving.sitk.GetPixelIDValue())

        diff_res_sitk = moving_warped.sitk - moving_warped_sitk
        sitkh.write_nifti_image_sitk(diff_res_sitk, diff_ref)
        diff_ref_sitk = sitk.ReadImage(diff_ref)

        res_diff_nda = sitk.GetArrayFromImage(diff_res_sitk - diff_ref_sitk)

        self.assertAlmostEqual(
            np.linalg.norm(res_diff_nda), 0, places=self.accuracy)