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cwmok / LapIRN

Large Deformation Diffeomorphic Image Registration with Laplacian Pyramid Networks
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Jacobian determinant applied on the displacement field (u) or deformation field (\phi) #35

Open VincentYCYao opened 1 month ago

VincentYCYao commented 1 month ago

Hi,

Given the the deformation field is defined as \phi=u+grid, where u is the displacement filed and \phi is the deformation field used as one of the inputs of the grid_sample function in torch, the Jacobian determinant should be computed from the displacement field u.

I was wondering why in the code, the Jacobian determinant of \phi was computed?

More information:

Best, Vincent

cwmok commented 1 month ago

@VincentYCYao

I was wondering why in the code, the Jacobian determinant of \phi was computed?

It is correct. Alternatively, you can use this version of the code to compute the Jacobian determinant. https://github.com/MDL-UzL/L2R/blob/fc713f5baf107932a8f72ab55484bf7ac3210b57/evaluation/utils.py#L10C1-L37C18

As you can see in https://github.com/MDL-UzL/L2R/blob/fc713f5baf107932a8f72ab55484bf7ac3210b57/evaluation/utils.py#L29, it also adds the identity to the field in order to compute the metric.

VincentYCYao commented 1 month ago

Thank you @cwmok !

In the code from L2R, it seems that they add an expended diagonal matrix instead of the grid you are adding in your code.

I wrote my own function and also adopted the ones from L2R and LapIRN. Would you like to run the testing script below for a quick check?

Thank you for your help.

testing script:

import os
import scipy
import nibabel as nib
import SimpleITK as sitk
import numpy as np
import csv
import argparse
import pytest

def cal_jacobian_determinant_V1(deformation_field):
    """
    Calculate the Jacobian determinant of a deformation field.

    :param deformation_field: numpy array of shape [x, y, z, 3]
    :return: Jacobian determinant field of shape [x, y, z]
    """
    # Create identity grid
    grid = np.stack(np.meshgrid(np.arange(deformation_field.shape[0]),
                                    np.arange(deformation_field.shape[1]),
                                    np.arange(deformation_field.shape[2]), 
                                    indexing='ij'), axis=-1).astype(np.float32)

    # Calculate displacement field
    displacement_field = deformation_field - grid

    # Get gradients of displacement field
    grad_x = np.gradient(displacement_field[..., 0], axis=0)
    grad_y = np.gradient(displacement_field[..., 1], axis=1)
    grad_z = np.gradient(displacement_field[..., 2], axis=2)

    # Calculate Jacobian determinant
    jacobian_det = (1 + grad_x) * (1 + grad_y) * (1 + grad_z) + \
                   np.gradient(displacement_field[..., 1], axis=0) * \
                   np.gradient(displacement_field[..., 2], axis=1) * \
                   np.gradient(displacement_field[..., 0], axis=2) + \
                   np.gradient(displacement_field[..., 2], axis=0) * \
                   np.gradient(displacement_field[..., 0], axis=1) * \
                   np.gradient(displacement_field[..., 1], axis=2) - \
                   np.gradient(displacement_field[..., 2], axis=0) * \
                   (1 + grad_y) * np.gradient(displacement_field[..., 0], axis=2) - \
                   np.gradient(displacement_field[..., 1], axis=0) * \
                   np.gradient(displacement_field[..., 0], axis=1) * (1 + grad_z) - \
                   (1 + grad_x) * np.gradient(displacement_field[..., 2], axis=1) * \
                   np.gradient(displacement_field[..., 1], axis=2)

    return jacobian_det

# adapted from LapIRN: 
# https://github.com/cwmok/LapIRN/blob/549a40329d4e8304e35c6f0113c46ad8d7a6da32/Code/miccai2020_model_stage.py#L782C4-L782C29
def cal_jacobian_determinant_V2(deformation_field):
    # the order of xyz does not matter
    # deformation_field: numpy array of shape [x, y, z, 3]
    J = deformation_field[None, ...] # change dimensions to [1, x, y, z, 3] 

    dy = J[:, 1:, :-1, :-1, :] - J[:, :-1, :-1, :-1, :]
    dx = J[:, :-1, 1:, :-1, :] - J[:, :-1, :-1, :-1, :]
    dz = J[:, :-1, :-1, 1:, :] - J[:, :-1, :-1, :-1, :]

    Jdet0 = dx[:,:,:,:,0] * (dy[:,:,:,:,1] * dz[:,:,:,:,2] - dy[:,:,:,:,2] * dz[:,:,:,:,1])
    Jdet1 = dx[:,:,:,:,1] * (dy[:,:,:,:,0] * dz[:,:,:,:,2] - dy[:,:,:,:,2] * dz[:,:,:,:,0])
    Jdet2 = dx[:,:,:,:,2] * (dy[:,:,:,:,0] * dz[:,:,:,:,1] - dy[:,:,:,:,1] * dz[:,:,:,:,0])

    Jdet = Jdet0 - Jdet1 + Jdet2

    return Jdet

# adapted from L2R:
# https://github.com/MDL-UzL/L2R/blob/fc713f5baf107932a8f72ab55484bf7ac3210b57/evaluation/utils.py#L29
def cal_jacobian_determinant_V3(deformation_field):
    # J: deformation_field of shape [x, y, z, 3] 

    # Create identity grid
    grid = np.stack(np.meshgrid(np.arange(deformation_field.shape[0]),
                                    np.arange(deformation_field.shape[1]),
                                    np.arange(deformation_field.shape[2]), 
                                    indexing='ij'), axis=-1).astype(np.float32)

    # Calculate displacement field
    disp = deformation_field - grid

    disp = np.transpose(disp, (3, 0, 1, 2)) # change dimensions to [3, x, y, z] 
    disp = disp[None, ...] # change dimensions to [1, 3, x, y, z] 

    gradx  = np.array([-0.5, 0, 0.5]).reshape(1, 3, 1, 1)
    grady  = np.array([-0.5, 0, 0.5]).reshape(1, 1, 3, 1)
    gradz  = np.array([-0.5, 0, 0.5]).reshape(1, 1, 1, 3)

    gradx_disp = np.stack([scipy.ndimage.correlate(disp[:, 0, :, :, :], gradx, mode='constant', cval=0.0),
                           scipy.ndimage.correlate(disp[:, 1, :, :, :], gradx, mode='constant', cval=0.0),
                           scipy.ndimage.correlate(disp[:, 2, :, :, :], gradx, mode='constant', cval=0.0)], axis=1)

    grady_disp = np.stack([scipy.ndimage.correlate(disp[:, 0, :, :, :], grady, mode='constant', cval=0.0),
                           scipy.ndimage.correlate(disp[:, 1, :, :, :], grady, mode='constant', cval=0.0),
                           scipy.ndimage.correlate(disp[:, 2, :, :, :], grady, mode='constant', cval=0.0)], axis=1)

    gradz_disp = np.stack([scipy.ndimage.correlate(disp[:, 0, :, :, :], gradz, mode='constant', cval=0.0),
                           scipy.ndimage.correlate(disp[:, 1, :, :, :], gradz, mode='constant', cval=0.0),
                           scipy.ndimage.correlate(disp[:, 2, :, :, :], gradz, mode='constant', cval=0.0)], axis=1)

    grad_disp = np.concatenate([gradx_disp, grady_disp, gradz_disp], 0)

    jacobian = grad_disp + np.eye(3, 3).reshape(3, 3, 1, 1, 1)
    jacobian = jacobian[:, :, 2:-2, 2:-2, 2:-2]
    jacdet = jacobian[0, 0, :, :, :] * (jacobian[1, 1, :, :, :] * jacobian[2, 2, :, :, :] - jacobian[1, 2, :, :, :] * jacobian[2, 1, :, :, :]) -\
             jacobian[1, 0, :, :, :] * (jacobian[0, 1, :, :, :] * jacobian[2, 2, :, :, :] - jacobian[0, 2, :, :, :] * jacobian[2, 1, :, :, :]) +\
             jacobian[2, 0, :, :, :] * (jacobian[0, 1, :, :, :] * jacobian[1, 2, :, :, :] - jacobian[0, 2, :, :, :] * jacobian[1, 1, :, :, :])

    return jacdet

def test_jacobian_determinant_V3():
    # testing data: 
    # deformation_field: numpy array of shape [x, y, z, 3] 

    # Test case 1: Identity transformation
    print("Test case 1: Identity transformation should have Jacobian determinant of 1")
    identity = np.stack(np.meshgrid(np.arange(10), np.arange(10), np.arange(10), indexing='ij'), axis=-1).astype(np.float32)
    jac_det = cal_jacobian_determinant_V3(identity)
    assert np.allclose(jac_det, 1.0), "Identity transformation should have Jacobian determinant of 1"

    # Test case 2: Uniform scaling
    scale = 2.0
    print(f"Test case 2: Uniform scaling by {scale} should have Jacobian determinant of {scale**3}")
    scaled = identity * scale
    jac_det = cal_jacobian_determinant_V3(scaled)
    assert np.allclose(jac_det, scale**3), f"Uniform scaling by {scale} should have Jacobian determinant of {scale**3}"

    # Test case 3: Translation
    print("Test case 3: Pure translation should have Jacobian determinant of 1")
    translated = identity + np.array([1.0, 2.0, 3.0])
    jac_det = cal_jacobian_determinant_V3(translated)
    assert np.allclose(jac_det, 1.0), "Pure translation should have Jacobian determinant of 1"

    # Test case 4: Simple shear
    print("Test case 4: Simple shear should have Jacobian determinant of 1")
    shear = identity.copy()
    shear[..., 0] += 0.1 * identity[..., 1]
    jac_det = cal_jacobian_determinant_V3(shear)
    assert np.allclose(jac_det, 1.0), "Simple shear should have Jacobian determinant of 1"

    # Test case 5: Compression in one direction
    print("Test case 5: Compression by 0.5 in one direction should have Jacobian determinant of 0.5")
    compressed = identity.copy()
    compressed[..., 0] *= 0.5
    jac_det = cal_jacobian_determinant_V3(compressed)
    assert np.allclose(jac_det, 0.5), "Compression by 0.5 in one direction should have Jacobian determinant of 0.5"

    print("All tests passed!")

def test_jacobian_determinant_V2():
    # testing data: 
    # deformation_field: numpy array of shape [x, y, z, 3] 

    # Test case 1: Identity transformation
    print("Test case 1: Identity transformation should have Jacobian determinant of 1")
    identity = np.stack(np.meshgrid(np.arange(10), np.arange(10), np.arange(10), indexing='ij'), axis=-1).astype(np.float32)
    jac_det = cal_jacobian_determinant_V2(identity)
    assert np.allclose(jac_det, 1.0), "Identity transformation should have Jacobian determinant of 1"

    # Test case 2: Uniform scaling
    scale = 2.0
    print(f"Test case 2: Uniform scaling by {scale} should have Jacobian determinant of {scale**3}")
    scaled = identity * scale
    jac_det = cal_jacobian_determinant_V2(scaled)
    assert np.allclose(jac_det, scale**3), f"Uniform scaling by {scale} should have Jacobian determinant of {scale**3}"

    # Test case 3: Translation
    print("Test case 3: Pure translation should have Jacobian determinant of 1")
    translated = identity + np.array([1.0, 2.0, 3.0])
    jac_det = cal_jacobian_determinant_V2(translated)
    assert np.allclose(jac_det, 1.0), "Pure translation should have Jacobian determinant of 1"

    # Test case 4: Simple shear
    print("Test case 4: Simple shear should have Jacobian determinant of 1")
    shear = identity.copy()
    shear[..., 0] += 0.1 * identity[..., 1]
    jac_det = cal_jacobian_determinant_V2(shear)
    assert np.allclose(jac_det, 1.0), "Simple shear should have Jacobian determinant of 1"

    # Test case 5: Compression in one direction
    print("Test case 5: Compression by 0.5 in one direction should have Jacobian determinant of 0.5")
    compressed = identity.copy()
    compressed[..., 0] *= 0.5
    jac_det = cal_jacobian_determinant_V2(compressed)
    assert np.allclose(jac_det, 0.5), "Compression by 0.5 in one direction should have Jacobian determinant of 0.5"

    print("All tests passed!")

def test_jacobian_determinant_V1():
    # testing data: 
    # deformation_field: numpy array of shape [x, y, z, 3] 

    # Test case 1: Identity transformation
    print("Test case 1: Identity transformation should have Jacobian determinant of 1")
    identity = np.stack(np.meshgrid(np.arange(10), np.arange(10), np.arange(10), indexing='ij'), axis=-1).astype(np.float32)
    jac_det = cal_jacobian_determinant_V1(identity)
    assert np.allclose(jac_det, 1.0), "Identity transformation should have Jacobian determinant of 1"

    # Test case 2: Uniform scaling
    scale = 2.0
    print(f"Test case 2: Uniform scaling by {scale} should have Jacobian determinant of {scale**3}")
    scaled = identity * scale
    jac_det = cal_jacobian_determinant_V1(scaled)
    assert np.allclose(jac_det, scale**3), f"Uniform scaling by {scale} should have Jacobian determinant of {scale**3}"

    # Test case 3: Translation
    print("Test case 3: Pure translation should have Jacobian determinant of 1")
    translated = identity + np.array([1.0, 2.0, 3.0])
    jac_det = cal_jacobian_determinant_V1(translated)
    assert np.allclose(jac_det, 1.0), "Pure translation should have Jacobian determinant of 1"

    # Test case 4: Simple shear
    print("Test case 4: Simple shear should have Jacobian determinant of 1")
    shear = identity.copy()
    shear[..., 0] += 0.1 * identity[..., 1]
    jac_det = cal_jacobian_determinant_V1(shear)
    assert np.allclose(jac_det, 1.0), "Simple shear should have Jacobian determinant of 1"

    # Test case 5: Compression in one direction
    print("Test case 5: Compression by 0.5 in one direction should have Jacobian determinant of 0.5")
    compressed = identity.copy()
    compressed[..., 0] *= 0.5
    jac_det = cal_jacobian_determinant_V1(compressed)
    assert np.allclose(jac_det, 0.5), "Compression by 0.5 in one direction should have Jacobian determinant of 0.5"

    print("All tests passed!")

def main():
    # Parse command line arguments
    parser = argparse.ArgumentParser(description='Calculate Jacobian determinant of the deformation field of size [d1,d2,d3,3]')
    parser.add_argument('--test', action='store_true', help='testing my mode')
    parser.add_argument('--test_L2R', action='store_true', help='testing code from L2R')
    parser.add_argument('--test_LapIRN', action='store_true', help='testing code from LapIRN')
    parser.add_argument('--deformationField_dir', type=str, help='Path to directory containing deformation fields')
    parser.add_argument('--eval_dir', type=str, help='Path to directory where evaluation results should be saved')
    args = parser.parse_args()

    if args.test:
        print("Testing my code")
        test_jacobian_determinant_V1()
    elif args.test_LapIRN:
        print(f"Testing the code adopted from LapIRN\nhttps://github.com/cwmok/LapIRN/blob/549a40329d4e8304e35c6f0113c46ad8d7a6da32/Code/miccai2020_model_stage.py#L782C4-L782C29")
        test_jacobian_determinant_V2()
    elif args.test_L2R:
        print(f"Testing the code adopted from L2R\nhttps://github.com/MDL-UzL/L2R/blob/fc713f5baf107932a8f72ab55484bf7ac3210b57/evaluation/utils.py#L29")
        test_jacobian_determinant_V3()
    else:
        # Create evaluation directory if it doesn't exist
        if not os.path.exists(args.eval_dir):
            os.makedirs(args.eval_dir)

        # Get list of NIfTI files
        field_files = [f for f in os.listdir(args.deformationField_dir) if f.endswith('.nii.gz')]

        # Initialize results list
        JacoDet_results = []

        # Loop over field_files
        for file in field_files:
            # Read NIfTI file
            field_nii = sitk.ReadImage(os.path.join(args.deformationField_dir, file))
            field_data = sitk.GetArrayFromImage(field_nii).transpose([3,1,2,0])
            # cal std(JacoDet)
            JacoDet = cal_jacobian_determinant_V1(field_data)
            JacoDet_std = np.std(JacoDet)
            JacoDet_nonpositive = np.sum(JacoDet <= 0) / JacoDet.size
            JacoDet_results.append([file, JacoDet_std, JacoDet_nonpositive])

        # Save results to CSV file
        with open(os.path.join(args.eval_dir, 'eval_JacoDet.csv'), 'w', newline='') as csvfile:
            writer = csv.writer(csvfile)
            writer.writerow(['File', 'JacoDet_std', 'JacoDet_nonpositive'])
            for result in JacoDet_results:
                writer.writerow(result)

if __name__ == "__main__":
    main()
cwmok commented 1 month ago

@VincentYCYao

Thanks, Vincent. Your code is very nice. The discrepancy is how you define the identity grid. I change the test code slightly and it passes all the test now.

def test_jacobian_determinant_V2():
    # testing data:
    # deformation_field: numpy array of shape [x, y, z, 3]

    # Test case 1: Identity transformation
    print("Test case 1: Identity transformation should have Jacobian determinant of 1")
    # identity = np.stack(np.meshgrid(np.arange(10), np.arange(10), np.arange(10), indexing='ij'), axis=-1).astype(
    #     np.float32)

    def generate_grid(imgshape):
        x = np.arange(imgshape[0])
        y = np.arange(imgshape[1])
        z = np.arange(imgshape[2])
        grid = np.rollaxis(np.array(np.meshgrid(z, y, x)), 0, 4)
        grid = np.swapaxes(grid, 0, 2)
        grid = np.swapaxes(grid, 1, 2)
        return grid

    identity = generate_grid((10, 10, 10)).astype(np.float32)
    print(identity.shape)

    jac_det = cal_jacobian_determinant_V2(identity)
    print(jac_det)
    assert np.allclose(jac_det, 1.0), "Identity transformation should have Jacobian determinant of 1"

    # Test case 2: Uniform scaling
    scale = 2.0
    print(f"Test case 2: Uniform scaling by {scale} should have Jacobian determinant of {scale ** 3}")
    scaled = identity * scale
    jac_det = cal_jacobian_determinant_V2(scaled)
    assert np.allclose(jac_det,
                       scale ** 3), f"Uniform scaling by {scale} should have Jacobian determinant of {scale ** 3}"

    # Test case 3: Translation
    print("Test case 3: Pure translation should have Jacobian determinant of 1")
    translated = identity + np.array([1.0, 2.0, 3.0])
    jac_det = cal_jacobian_determinant_V2(translated)
    assert np.allclose(jac_det, 1.0), "Pure translation should have Jacobian determinant of 1"

    # Test case 4: Simple shear
    print("Test case 4: Simple shear should have Jacobian determinant of 1")
    shear = identity.copy()
    shear[..., 0] += 0.1 * identity[..., 1]
    jac_det = cal_jacobian_determinant_V2(shear)
    assert np.allclose(jac_det, 1.0), "Simple shear should have Jacobian determinant of 1"

    # Test case 5: Compression in one direction
    print("Test case 5: Compression by 0.5 in one direction should have Jacobian determinant of 0.5")
    compressed = identity.copy()
    compressed[..., 0] *= 0.5
    jac_det = cal_jacobian_determinant_V2(compressed)
    assert np.allclose(jac_det, 0.5), "Compression by 0.5 in one direction should have Jacobian determinant of 0.5"

    print("All tests passed!")
cwmok commented 1 month ago

@VincentYCYao

or simpy change the indexing from 'ij' to 'xy' as below: identity = np.stack(np.meshgrid(np.arange(5), np.arange(5), np.arange(5), indexing='xy'), axis=-1).astype( np.float32)

VincentYCYao commented 1 month ago

Equivalent to using the parameter indexing='xy', we can swap the dx and dy in your code and use identity = np.stack(np.meshgrid(np.arange(5), np.arange(5), np.arange(5), indexing='ij'), axis=-1).astype( np.float32).

Elegant! Thank you @cwmok .

# adapted from LapIRN: 
# https://github.com/cwmok/LapIRN/blob/549a40329d4e8304e35c6f0113c46ad8d7a6da32/Code/miccai2020_model_stage.py#L782C4-L782C29
def cal_jacobian_determinant_V2(deformation_field):
    # deformation_field: numpy array of shape [x, y, z, 3]
    J = deformation_field[None, ...] # change dimensions to [1, x, y, z, 3] 

    dx = J[:, 1:, :-1, :-1, :] - J[:, :-1, :-1, :-1, :]
    dy = J[:, :-1, 1:, :-1, :] - J[:, :-1, :-1, :-1, :]
    dz = J[:, :-1, :-1, 1:, :] - J[:, :-1, :-1, :-1, :]

    Jdet0 = dx[:,:,:,:,0] * (dy[:,:,:,:,1] * dz[:,:,:,:,2] - dy[:,:,:,:,2] * dz[:,:,:,:,1])
    Jdet1 = dx[:,:,:,:,1] * (dy[:,:,:,:,0] * dz[:,:,:,:,2] - dy[:,:,:,:,2] * dz[:,:,:,:,0])
    Jdet2 = dx[:,:,:,:,2] * (dy[:,:,:,:,0] * dz[:,:,:,:,1] - dy[:,:,:,:,1] * dz[:,:,:,:,0])

    Jdet = Jdet0 - Jdet1 + Jdet2

    return Jdet

final testing script:

import os
import scipy
import nibabel as nib
import SimpleITK as sitk
import numpy as np
import csv
import argparse
import pytest

def cal_jacobian_determinant_V1(deformation_field):
    """
    Calculate the Jacobian determinant of a deformation field.

    :param deformation_field: numpy array of shape [x, y, z, 3]
    :return: Jacobian determinant field of shape [x, y, z]
    """
    # Create identity grid
    grid = np.stack(np.meshgrid(np.arange(deformation_field.shape[0]),
                                    np.arange(deformation_field.shape[1]),
                                    np.arange(deformation_field.shape[2]), 
                                    indexing='ij'), axis=-1).astype(np.float32)

    # Calculate displacement field
    displacement_field = deformation_field - grid

    # Get gradients of displacement field
    grad_x = np.gradient(displacement_field[..., 0], axis=0)
    grad_y = np.gradient(displacement_field[..., 1], axis=1)
    grad_z = np.gradient(displacement_field[..., 2], axis=2)

    # Calculate Jacobian determinant
    jacobian_det = (1 + grad_x) * (1 + grad_y) * (1 + grad_z) + \
                   np.gradient(displacement_field[..., 1], axis=0) * \
                   np.gradient(displacement_field[..., 2], axis=1) * \
                   np.gradient(displacement_field[..., 0], axis=2) + \
                   np.gradient(displacement_field[..., 2], axis=0) * \
                   np.gradient(displacement_field[..., 0], axis=1) * \
                   np.gradient(displacement_field[..., 1], axis=2) - \
                   np.gradient(displacement_field[..., 2], axis=0) * \
                   (1 + grad_y) * np.gradient(displacement_field[..., 0], axis=2) - \
                   np.gradient(displacement_field[..., 1], axis=0) * \
                   np.gradient(displacement_field[..., 0], axis=1) * (1 + grad_z) - \
                   (1 + grad_x) * np.gradient(displacement_field[..., 2], axis=1) * \
                   np.gradient(displacement_field[..., 1], axis=2)

    return jacobian_det

# adapted from LapIRN: 
# https://github.com/cwmok/LapIRN/blob/549a40329d4e8304e35c6f0113c46ad8d7a6da32/Code/miccai2020_model_stage.py#L782C4-L782C29
def cal_jacobian_determinant_V2(deformation_field):
    # deformation_field: numpy array of shape [x, y, z, 3]
    J = deformation_field[None, ...] # change dimensions to [1, x, y, z, 3] 

    dx = J[:, 1:, :-1, :-1, :] - J[:, :-1, :-1, :-1, :]
    dy = J[:, :-1, 1:, :-1, :] - J[:, :-1, :-1, :-1, :]
    dz = J[:, :-1, :-1, 1:, :] - J[:, :-1, :-1, :-1, :]

    Jdet0 = dx[:,:,:,:,0] * (dy[:,:,:,:,1] * dz[:,:,:,:,2] - dy[:,:,:,:,2] * dz[:,:,:,:,1])
    Jdet1 = dx[:,:,:,:,1] * (dy[:,:,:,:,0] * dz[:,:,:,:,2] - dy[:,:,:,:,2] * dz[:,:,:,:,0])
    Jdet2 = dx[:,:,:,:,2] * (dy[:,:,:,:,0] * dz[:,:,:,:,1] - dy[:,:,:,:,1] * dz[:,:,:,:,0])

    Jdet = Jdet0 - Jdet1 + Jdet2

    return Jdet

# adapted from L2R:
# https://github.com/MDL-UzL/L2R/blob/fc713f5baf107932a8f72ab55484bf7ac3210b57/evaluation/utils.py#L29
def cal_jacobian_determinant_V3(deformation_field):
    # J: deformation_field of shape [x, y, z, 3] 

    # Create identity grid
    grid = np.stack(np.meshgrid(np.arange(deformation_field.shape[0]),
                                    np.arange(deformation_field.shape[1]),
                                    np.arange(deformation_field.shape[2]), 
                                    indexing='ij'), axis=-1).astype(np.float32)

    # Calculate displacement field
    disp = deformation_field - grid

    disp = np.transpose(disp, (3, 0, 1, 2)) # change dimensions to [3, x, y, z] 
    disp = disp[None, ...] # change dimensions to [1, 3, x, y, z] 

    gradx  = np.array([-0.5, 0, 0.5]).reshape(1, 3, 1, 1)
    grady  = np.array([-0.5, 0, 0.5]).reshape(1, 1, 3, 1)
    gradz  = np.array([-0.5, 0, 0.5]).reshape(1, 1, 1, 3)

    gradx_disp = np.stack([scipy.ndimage.correlate(disp[:, 0, :, :, :], gradx, mode='constant', cval=0.0),
                           scipy.ndimage.correlate(disp[:, 1, :, :, :], gradx, mode='constant', cval=0.0),
                           scipy.ndimage.correlate(disp[:, 2, :, :, :], gradx, mode='constant', cval=0.0)], axis=1)

    grady_disp = np.stack([scipy.ndimage.correlate(disp[:, 0, :, :, :], grady, mode='constant', cval=0.0),
                           scipy.ndimage.correlate(disp[:, 1, :, :, :], grady, mode='constant', cval=0.0),
                           scipy.ndimage.correlate(disp[:, 2, :, :, :], grady, mode='constant', cval=0.0)], axis=1)

    gradz_disp = np.stack([scipy.ndimage.correlate(disp[:, 0, :, :, :], gradz, mode='constant', cval=0.0),
                           scipy.ndimage.correlate(disp[:, 1, :, :, :], gradz, mode='constant', cval=0.0),
                           scipy.ndimage.correlate(disp[:, 2, :, :, :], gradz, mode='constant', cval=0.0)], axis=1)

    grad_disp = np.concatenate([gradx_disp, grady_disp, gradz_disp], 0)

    jacobian = grad_disp + np.eye(3, 3).reshape(3, 3, 1, 1, 1)
    jacobian = jacobian[:, :, 2:-2, 2:-2, 2:-2]
    jacdet = jacobian[0, 0, :, :, :] * (jacobian[1, 1, :, :, :] * jacobian[2, 2, :, :, :] - jacobian[1, 2, :, :, :] * jacobian[2, 1, :, :, :]) -\
             jacobian[1, 0, :, :, :] * (jacobian[0, 1, :, :, :] * jacobian[2, 2, :, :, :] - jacobian[0, 2, :, :, :] * jacobian[2, 1, :, :, :]) +\
             jacobian[2, 0, :, :, :] * (jacobian[0, 1, :, :, :] * jacobian[1, 2, :, :, :] - jacobian[0, 2, :, :, :] * jacobian[1, 1, :, :, :])

    return jacdet

def test_jacobian_determinant_V3():
    # testing data: 
    # deformation_field: numpy array of shape [x, y, z, 3] 

    # Test case 1: Identity transformation
    print("Test case 1: Identity transformation should have Jacobian determinant of 1")
    identity = np.stack(np.meshgrid(np.arange(10), np.arange(10), np.arange(10), indexing='ij'), axis=-1).astype(np.float32)
    jac_det = cal_jacobian_determinant_V3(identity)
    assert np.allclose(jac_det, 1.0), "Identity transformation should have Jacobian determinant of 1"

    # Test case 2: Uniform scaling
    scale = 2.0
    print(f"Test case 2: Uniform scaling by {scale} should have Jacobian determinant of {scale**3}")
    scaled = identity * scale
    jac_det = cal_jacobian_determinant_V3(scaled)
    assert np.allclose(jac_det, scale**3), f"Uniform scaling by {scale} should have Jacobian determinant of {scale**3}"

    # Test case 3: Translation
    print("Test case 3: Pure translation should have Jacobian determinant of 1")
    translated = identity + np.array([1.0, 2.0, 3.0])
    jac_det = cal_jacobian_determinant_V3(translated)
    assert np.allclose(jac_det, 1.0), "Pure translation should have Jacobian determinant of 1"

    # Test case 4: Simple shear
    print("Test case 4: Simple shear should have Jacobian determinant of 1")
    shear = identity.copy()
    shear[..., 0] += 0.1 * identity[..., 1]
    jac_det = cal_jacobian_determinant_V3(shear)
    assert np.allclose(jac_det, 1.0), "Simple shear should have Jacobian determinant of 1"

    # Test case 5: Compression in one direction
    print("Test case 5: Compression by 0.5 in one direction should have Jacobian determinant of 0.5")
    compressed = identity.copy()
    compressed[..., 0] *= 0.5
    jac_det = cal_jacobian_determinant_V3(compressed)
    assert np.allclose(jac_det, 0.5), "Compression by 0.5 in one direction should have Jacobian determinant of 0.5"

    print("All tests passed!")

def test_jacobian_determinant_V2():
    # testing data: 
    # deformation_field: numpy array of shape [x, y, z, 3] 

    # Test case 1: Identity transformation
    print("Test case 1: Identity transformation should have Jacobian determinant of 1")
    identity = np.stack(np.meshgrid(np.arange(10), np.arange(10), np.arange(10), indexing='ij'), axis=-1).astype(np.float32)
    jac_det = cal_jacobian_determinant_V2(identity)
    assert np.allclose(jac_det, 1.0), "Identity transformation should have Jacobian determinant of 1"

    # Test case 2: Uniform scaling
    scale = 2.0
    print(f"Test case 2: Uniform scaling by {scale} should have Jacobian determinant of {scale**3}")
    scaled = identity * scale
    jac_det = cal_jacobian_determinant_V2(scaled)
    assert np.allclose(jac_det, scale**3), f"Uniform scaling by {scale} should have Jacobian determinant of {scale**3}"

    # Test case 3: Translation
    print("Test case 3: Pure translation should have Jacobian determinant of 1")
    translated = identity + np.array([1.0, 2.0, 3.0])
    jac_det = cal_jacobian_determinant_V2(translated)
    assert np.allclose(jac_det, 1.0), "Pure translation should have Jacobian determinant of 1"

    # Test case 4: Simple shear
    print("Test case 4: Simple shear should have Jacobian determinant of 1")
    shear = identity.copy()
    shear[..., 0] += 0.1 * identity[..., 1]
    jac_det = cal_jacobian_determinant_V2(shear)
    assert np.allclose(jac_det, 1.0), "Simple shear should have Jacobian determinant of 1"

    # Test case 5: Compression in one direction
    print("Test case 5: Compression by 0.5 in one direction should have Jacobian determinant of 0.5")
    compressed = identity.copy()
    compressed[..., 0] *= 0.5
    jac_det = cal_jacobian_determinant_V2(compressed)
    assert np.allclose(jac_det, 0.5), "Compression by 0.5 in one direction should have Jacobian determinant of 0.5"

    print("All tests passed!")

def test_jacobian_determinant_V1():
    # testing data: 
    # deformation_field: numpy array of shape [x, y, z, 3] 

    # Test case 1: Identity transformation
    print("Test case 1: Identity transformation should have Jacobian determinant of 1")
    identity = np.stack(np.meshgrid(np.arange(10), np.arange(10), np.arange(10), indexing='ij'), axis=-1).astype(np.float32)
    jac_det = cal_jacobian_determinant_V1(identity)
    assert np.allclose(jac_det, 1.0), "Identity transformation should have Jacobian determinant of 1"

    # Test case 2: Uniform scaling
    scale = 2.0
    print(f"Test case 2: Uniform scaling by {scale} should have Jacobian determinant of {scale**3}")
    scaled = identity * scale
    jac_det = cal_jacobian_determinant_V1(scaled)
    assert np.allclose(jac_det, scale**3), f"Uniform scaling by {scale} should have Jacobian determinant of {scale**3}"

    # Test case 3: Translation
    print("Test case 3: Pure translation should have Jacobian determinant of 1")
    translated = identity + np.array([1.0, 2.0, 3.0])
    jac_det = cal_jacobian_determinant_V1(translated)
    assert np.allclose(jac_det, 1.0), "Pure translation should have Jacobian determinant of 1"

    # Test case 4: Simple shear
    print("Test case 4: Simple shear should have Jacobian determinant of 1")
    shear = identity.copy()
    shear[..., 0] += 0.1 * identity[..., 1]
    jac_det = cal_jacobian_determinant_V1(shear)
    assert np.allclose(jac_det, 1.0), "Simple shear should have Jacobian determinant of 1"

    # Test case 5: Compression in one direction
    print("Test case 5: Compression by 0.5 in one direction should have Jacobian determinant of 0.5")
    compressed = identity.copy()
    compressed[..., 0] *= 0.5
    jac_det = cal_jacobian_determinant_V1(compressed)
    assert np.allclose(jac_det, 0.5), "Compression by 0.5 in one direction should have Jacobian determinant of 0.5"

    print("All tests passed!")

def main():
    # Parse command line arguments
    parser = argparse.ArgumentParser(description='Calculate Jacobian determinant of the deformation field of size [d1,d2,d3,3]')
    parser.add_argument('--test', action='store_true', help='testing my mode')
    parser.add_argument('--test_L2R', action='store_true', help='testing code from L2R')
    parser.add_argument('--test_LapIRN', action='store_true', help='testing code from LapIRN')
    parser.add_argument('--deformationField_dir', type=str, help='Path to directory containing deformation fields')
    parser.add_argument('--eval_dir', type=str, help='Path to directory where evaluation results should be saved')
    args = parser.parse_args()

    if args.test:
        print("Testing my code")
        test_jacobian_determinant_V1()
    elif args.test_LapIRN:
        print(f"Testing the code adapted from LapIRN\nhttps://github.com/cwmok/LapIRN/blob/549a40329d4e8304e35c6f0113c46ad8d7a6da32/Code/miccai2020_model_stage.py#L782C4-L782C29")
        test_jacobian_determinant_V2()
    elif args.test_L2R:
        print(f"Testing the code adapted from L2R\nhttps://github.com/MDL-UzL/L2R/blob/fc713f5baf107932a8f72ab55484bf7ac3210b57/evaluation/utils.py#L29")
        test_jacobian_determinant_V3()
    else:
        # Create evaluation directory if it doesn't exist
        if not os.path.exists(args.eval_dir):
            os.makedirs(args.eval_dir)

        # Get list of NIfTI files
        field_files = [f for f in os.listdir(args.deformationField_dir) if f.endswith('.nii.gz')]

        # Initialize results list
        JacoDet_results = []

        # Loop over field_files
        for file in field_files:
            # Read NIfTI file
            field_nii = sitk.ReadImage(os.path.join(args.deformationField_dir, file))
            field_data = sitk.GetArrayFromImage(field_nii).transpose([3,1,2,0])
            # cal std(JacoDet)
            JacoDet = cal_jacobian_determinant_V1(field_data)
            JacoDet_std = np.std(JacoDet)
            JacoDet_nonpositive = np.sum(JacoDet <= 0) / JacoDet.size
            JacoDet_results.append([file, JacoDet_std, JacoDet_nonpositive])

        # Save results to CSV file
        with open(os.path.join(args.eval_dir, 'eval_JacoDet.csv'), 'w', newline='') as csvfile:
            writer = csv.writer(csvfile)
            writer.writerow(['File', 'JacoDet_std', 'JacoDet_nonpositive'])
            for result in JacoDet_results:
                writer.writerow(result)

if __name__ == "__main__":
    main()
VincentYCYao commented 1 month ago

A summary of the question:

Given the deformation field = displacement filed + grid, the Jacobian matrix of the deformation filed is JacobianMatrix: [dxx, dxy, dxz],[dyx,dyy,dyz],[dzx,dzy,dzz]]. The 2 functions for Jacobian determinant are equivalent.

def cal_jacobian_determinant_V1(deformation_field):
    """
    Calculate the Jacobian determinant of a deformation field.

    :param deformation_field: numpy array of shape [x, y, z, 3]
    :return: Jacobian determinant field of shape [x, y, z]
    """

    # JacobianMatrix: [dxx, dxy, dxz],[dyx,dyy,dyz],[dzx,dzy,dzz]]
    dxx = np.gradient(deformation_field[..., 0], axis=0)
    dyy = np.gradient(deformation_field[..., 1], axis=1)
    dzz = np.gradient(deformation_field[..., 2], axis=2)
    dxy = np.gradient(deformation_field[..., 0], axis=1)
    dyz = np.gradient(deformation_field[..., 1], axis=2)
    dzx = np.gradient(deformation_field[..., 2], axis=0)
    dxz = np.gradient(deformation_field[..., 0], axis=2)
    dyx = np.gradient(deformation_field[..., 1], axis=0)
    dzy = np.gradient(deformation_field[..., 2], axis=1)
    dxz = np.gradient(deformation_field[..., 0], axis=2)
    dzx = np.gradient(deformation_field[..., 2], axis=0)
    dxy = np.gradient(deformation_field[..., 0], axis=1)
    dyx = np.gradient(deformation_field[..., 1], axis=0)
    dyz = np.gradient(deformation_field[..., 1], axis=2)
    dzy = np.gradient(deformation_field[..., 2], axis=1)

    # Calculate Jacobian determinant 
    jacobian_det = (dxx) * (dyy) * (dzz) + dxy * dyz * dzx + dxz * dyx * dzy - dxz * (dyy) * dzx - dxy * dyx * (dzz) - (dxx) * dyz * dzy   

    return jacobian_det

# adapted from LapIRN: 
# https://github.com/cwmok/LapIRN/blob/549a40329d4e8304e35c6f0113c46ad8d7a6da32/Code/miccai2020_model_stage.py#L782C4-L782C29
def cal_jacobian_determinant_V2(deformation_field):
    """
    Calculate the Jacobian determinant of a deformation field.

    :param deformation_field: numpy array of shape [x, y, z, 3]
    :return: Jacobian determinant field of shape [x, y, z]
    """

    dx = deformation_field[1:, :-1, :-1, :] - deformation_field[:-1, :-1, :-1, :]
    dy = deformation_field[:-1, 1:, :-1, :] - deformation_field[:-1, :-1, :-1, :]
    dz = deformation_field[:-1, :-1, 1:, :] - deformation_field[:-1, :-1, :-1, :]

    # JacobianMatrix: [dxx, dxy, dxz],[dyx,dyy,dyz],[dzx,dzy,dzz]]
    Jdet0 = dx[:,:,:,0] * (dy[:,:,:,1] * dz[:,:,:,2] - dy[:,:,:,2] * dz[:,:,:,1]) # this is dxx * (dyy*dzz - dzy*dyz)
    Jdet1 = dx[:, :,:,1] * (dy[:,:,:,0] * dz[:,:,:,2] - dy[:,:,:,2] * dz[:,:,:,0]) # this is dyx * (dxy*dzz - dzy*dxz)
    Jdet2 = dx[:,:,:,2] * (dy[:,:,:,0] * dz[:,:,:,1] - dy[:,:,:,1] * dz[:,:,:,0]) # this is dzx * (dxy*dyz - dyy*dxz)
    Jdet = Jdet0 - Jdet1 + Jdet2

    return Jdet