melage 0.0.65__py3-none-any.whl → 1.0.0__py3-none-any.whl

melage/utils/registration.py

@@ -1,512 +0,0 @@
-import SimpleITK as sitk
-import numpy as np
-pi = np.pi
-__AUTHOR__ = 'Bahram Jafrasteh'
-"""
-Image to image registration using Simple ITK package (it is under development)
-"""
-
-def command_multi_iteration(method):
-    print("--------- Resolution Changing ---------")
-
-
-def command_iteration(method):
-    print(
-        f"{method.GetOptimizerIteration():3} "
-        + f"= {method.GetMetricValue():10.5f} "
-        + f": {method.GetOptimizerPosition()}"
-    )
-
-
-def command_multiresolution_iteration(method):
-    print(f"\tStop Condition: {method.GetOptimizerStopConditionDescription()}")
-    print("============= Resolution Change =============")
-
-def RegistrationSpline(fixed, moving, criterion, *params):
-    criterion = criterion.lower()
-    R = sitk.ImageRegistrationMethod()
-    params = params[0]
-    fixed_mask = params['fixed_mask']
-    fixed_points = params['fixed_points']
-    moving_points = params['moving_points']
-    MultiRes = params['MultiRes']
-    numberOfBins = params['nbins']
-    transformDomainMeshSize = [10] * moving.GetDimension()
-    tx = sitk.BSplineTransformInitializer(fixed, transformDomainMeshSize)
-
-    print("Initial Parameters:")
-    print(tx.GetParameters())
-
-    R = sitk.ImageRegistrationMethod()
-    if criterion not in ['mi', 'correlation', 'jmi']:
-        criterion = 'mi'
-        print('setting criterion as mutual information')
-    if criterion=='mi':
-        R.SetMetricAsMattesMutualInformation(numberOfBins)
-        R.SetOptimizerAsGradientDescentLineSearch(
-        5.0, 100, convergenceMinimumValue=1e-4, convergenceWindowSize=5
-        )
-    elif criterion=='correlation':
-        R.SetMetricAsCorrelation()
-
-        R.SetOptimizerAsLBFGSB(
-            gradientConvergenceTolerance=1e-5,
-            numberOfIterations=100,
-            maximumNumberOfCorrections=5,
-            maximumNumberOfFunctionEvaluations=1000,
-            costFunctionConvergenceFactor=1e7,
-        )
-    elif criterion=='jmi':
-        R.SetMetricAsJointHistogramMutualInformation()
-
-        R.SetOptimizerAsGradientDescentLineSearch(
-            5.0, 100, convergenceMinimumValue=1e-4, convergenceWindowSize=5
-        )
-    R.SetOptimizerScalesFromPhysicalShift()
-    R.SetInitialTransform(tx)
-    R.SetInterpolator(sitk.sitkLinear)
-    if MultiRes:
-        R.SetShrinkFactorsPerLevel([6, 2, 1])
-        R.SetSmoothingSigmasPerLevel([6, 2, 1])
-
-    R.AddCommand(
-        sitk.sitkMultiResolutionIterationEvent, lambda: command_multi_iteration(R)
-    )
-    return run_registration(R, fixed, moving)
-
-
-def RegistrationRigid(fixed, moving, criterion, *params):
-    R = sitk.ImageRegistrationMethod()
-    params = params[0]
-    fixed_mask = params['fixed_mask']
-    fixed_points = params['fixed_points']
-    moving_points = params['moving_points']
-    MultiRes = params['MultiRes']
-    numberOfBins = params['nbins']
-    transform = sitk.CenteredTransformInitializer(
-        fixed,
-        moving,
-        sitk.Euler3DTransform(),
-        sitk.CenteredTransformInitializerFilter.GEOMETRY,
-    )
-    if criterion.lower()=='mse':
-        R.SetMetricAsMeanSquares()
-    elif criterion.lower()=='correlation':
-        R.SetMetricAsCorrelation()
-    elif criterion.lower()=='mi':
-        R.SetMetricAsMattesMutualInformation(numberOfBins)
-    elif criterion.lower()=='jmi':
-        R.SetMetricAsJointHistogramMutualInformation(numberOfBins)
-    R.SetInitialTransform(sitk.TranslationTransform(fixed.GetDimension()))
-    R.SetMetricSamplingStrategy(R.NONE)
-    R.SetInterpolator(sitk.sitkLinear)
-    R.SetOptimizerAsGradientDescent(
-        learningRate=1.0,
-        numberOfIterations=300,
-        convergenceMinimumValue=1e-6,
-        convergenceWindowSize=10,
-    )
-    R.SetOptimizerScalesFromPhysicalShift()
-    R.SetInitialTransform(transform, inPlace=True)
-    R.SetInterpolator(sitk.sitkLinear)
-    if MultiRes:
-        R.SetShrinkFactorsPerLevel([6,2, 1])
-        R.SetSmoothingSigmasPerLevel([6,2, 1])
-    return run_registration(R, fixed, moving)
-
-def registartion1(file_ref, file_target, method='mse', normalized=False, *params):
-    #https://github.com/nvladimus/ITK_sandbox
-    import SimpleITK as sitk
-    import sys
-    import os
-
-
-    fixed = sitk.ReadImage(file_ref, sitk.sitkFloat32)
-
-    moving = sitk.ReadImage(file_target, sitk.sitkFloat32)
-
-    if normalized:
-        fixed = sitk.Normalize(fixed)
-        fixed = sitk.DiscreteGaussian(fixed, 2.0)
-        moving = sitk.Normalize(moving)
-        moving = sitk.DiscreteGaussian(moving, 2.0)
-    R = sitk.ImageRegistrationMethod()
-
-    if method=='rigid':
-        transform = sitk.CenteredTransformInitializer(
-            fixed,
-            moving,
-            sitk.Euler3DTransform(),
-            sitk.CenteredTransformInitializerFilter.GEOMETRY,
-        )
-
-        R.SetMetricAsCorrelation()
-        R.SetMetricSamplingStrategy(R.NONE)
-        R.SetInterpolator(sitk.sitkLinear)
-        R.SetOptimizerAsGradientDescent(
-            learningRate=1.0,
-            numberOfIterations=300,
-            convergenceMinimumValue=1e-6,
-            convergenceWindowSize=10,
-        )
-        R.SetOptimizerScalesFromPhysicalShift()
-        R.SetInitialTransform(transform, inPlace=True)
-        #R.SetOptimizerWeights([0, 0, 1, 1, 1, 1]) # to allow rotate only on z axis
-
-
-    if method=='mse':
-
-        R.SetMetricAsMeanSquares()
-        R.SetOptimizerAsRegularStepGradientDescent(4.0, 0.01, 200)
-        R.SetInitialTransform(sitk.TranslationTransform(fixed.GetDimension()))
-        R.SetInterpolator(sitk.sitkLinear)
-    elif method == 'HMI':
-        R.SetMetricAsJointHistogramMutualInformation()
-
-        R.SetOptimizerAsGradientDescentLineSearch(
-            learningRate=1.0,
-            numberOfIterations=200,
-            convergenceMinimumValue=1e-5,
-            convergenceWindowSize=5,
-        )
-        R.SetInitialTransform(sitk.TranslationTransform(fixed.GetDimension()))
-        R.SetInterpolator(sitk.sitkLinear)
-    elif method=='CC':
-        R.SetMetricAsCorrelation()
-
-        R.SetOptimizerAsRegularStepGradientDescent(
-            learningRate=2.0,
-            minStep=1e-4,
-            numberOfIterations=500,
-            gradientMagnitudeTolerance=1e-8,
-        )
-        R.SetOptimizerScalesFromIndexShift()
-
-        tx = sitk.CenteredTransformInitializer(
-            fixed, moving, sitk.Similarity2DTransform()
-        )
-        R.SetInitialTransform(tx)
-
-        R.SetInterpolator(sitk.sitkLinear)
-    elif method=='MI':
-        numberOfBins = params[0]['nbins']
-        samplingPercentage = params[0]['sp']
-        R.SetMetricAsMattesMutualInformation(numberOfBins)
-        R.SetMetricSamplingPercentage(samplingPercentage, sitk.sitkWallClock)
-        R.SetMetricSamplingStrategy(R.RANDOM)
-        R.SetOptimizerAsRegularStepGradientDescent(1.0, 0.001, 500)
-        R.SetInitialTransform(sitk.TranslationTransform(fixed.GetDimension()))
-        R.SetInterpolator(sitk.sitkLinear)
-    elif method=='BsplineCC':
-        transformDomainMeshSize = [8] * moving.GetDimension()
-        tx = sitk.BSplineTransformInitializer(fixed, transformDomainMeshSize)
-
-        print("Initial Parameters:")
-        print(tx.GetParameters())
-
-        R = sitk.ImageRegistrationMethod()
-        R.SetMetricAsCorrelation()
-
-        R.SetOptimizerAsLBFGSB(
-            gradientConvergenceTolerance=1e-5,
-            numberOfIterations=100,
-            maximumNumberOfCorrections=5,
-            maximumNumberOfFunctionEvaluations=1000,
-            costFunctionConvergenceFactor=1e7,
-        )
-        R.SetInitialTransform(tx, True)
-        R.SetInterpolator(sitk.sitkLinear)
-    elif method=='BsplineMI':
-        transformDomainMeshSize = [10] * moving.GetDimension()
-        tx = sitk.BSplineTransformInitializer(fixed, transformDomainMeshSize)
-
-        print("Initial Parameters:")
-        print(tx.GetParameters())
-
-        R = sitk.ImageRegistrationMethod()
-        R.SetMetricAsMattesMutualInformation(50)
-        R.SetOptimizerAsGradientDescentLineSearch(
-            5.0, 100, convergenceMinimumValue=1e-4, convergenceWindowSize=5
-        )
-        R.SetOptimizerScalesFromPhysicalShift()
-        R.SetInitialTransform(tx)
-        R.SetInterpolator(sitk.sitkLinear)
-
-        R.SetShrinkFactorsPerLevel([6, 2, 1])
-        R.SetSmoothingSigmasPerLevel([6, 2, 1])
-
-        R.AddCommand(
-            sitk.sitkMultiResolutionIterationEvent, lambda: command_multi_iteration(R)
-        )
-    elif method=='BsplineHMI':
-        transformDomainMeshSize = [2] * fixed.GetDimension()
-        tx = sitk.BSplineTransformInitializer(fixed, transformDomainMeshSize)
-
-        print(f"Initial Number of Parameters: {tx.GetNumberOfParameters()}")
-
-        R = sitk.ImageRegistrationMethod()
-        R.SetMetricAsJointHistogramMutualInformation()
-
-        R.SetOptimizerAsGradientDescentLineSearch(
-            5.0, 100, convergenceMinimumValue=1e-4, convergenceWindowSize=5
-        )
-
-        R.SetInterpolator(sitk.sitkLinear)
-
-        R.SetInitialTransformAsBSpline(tx, inPlace=True, scaleFactors=[1, 2, 5])
-        R.SetShrinkFactorsPerLevel([4, 2, 1])
-        R.SetSmoothingSigmasPerLevel([4, 2, 1])
-        R.AddCommand(
-            sitk.sitkMultiResolutionIterationEvent, lambda: command_multi_iteration(R)
-        )
-    elif method=='displacement':
-
-        initialTx = sitk.CenteredTransformInitializer(
-            fixed, moving, sitk.AffineTransform(fixed.GetDimension())
-        )
-
-        R = sitk.ImageRegistrationMethod()
-
-        R.SetShrinkFactorsPerLevel([3, 2, 1])
-        R.SetSmoothingSigmasPerLevel([2, 1, 1])
-
-        R.SetMetricAsJointHistogramMutualInformation(20)
-        R.MetricUseFixedImageGradientFilterOff()
-
-        R.SetOptimizerAsGradientDescent(
-            learningRate=1.0,
-            numberOfIterations=100,
-            estimateLearningRate=R.EachIteration,
-        )
-        R.SetOptimizerScalesFromPhysicalShift()
-
-        R.SetInitialTransform(initialTx)
-
-        R.SetInterpolator(sitk.sitkLinear)
-
-        R.AddCommand(sitk.sitkIterationEvent, lambda: command_iteration(R))
-        R.AddCommand(
-            sitk.sitkMultiResolutionIterationEvent,
-            lambda: command_multiresolution_iteration(R),
-        )
-
-        outTx1 = R.Execute(fixed, moving)
-
-        print("-------")
-        print(outTx1)
-        print(f"Optimizer stop condition: {R.GetOptimizerStopConditionDescription()}")
-        print(f" Iteration: {R.GetOptimizerIteration()}")
-        print(f" Metric value: {R.GetMetricValue()}")
-
-        displacementField = sitk.Image(fixed.GetSize(), sitk.sitkVectorFloat64)
-        displacementField.CopyInformation(fixed)
-        displacementTx = sitk.DisplacementFieldTransform(displacementField)
-        del displacementField
-        displacementTx.SetSmoothingGaussianOnUpdate(
-            varianceForUpdateField=0.0, varianceForTotalField=1.5
-        )
-
-        R.SetMovingInitialTransform(outTx1)
-        R.SetInitialTransform(displacementTx, inPlace=True)
-
-        R.SetMetricAsANTSNeighborhoodCorrelation(4)
-        R.MetricUseFixedImageGradientFilterOff()
-
-        R.SetShrinkFactorsPerLevel([3, 2, 1])
-        R.SetSmoothingSigmasPerLevel([2, 1, 1])
-
-        R.SetOptimizerScalesFromPhysicalShift()
-        R.SetOptimizerAsGradientDescent(
-            learningRate=1,
-            numberOfIterations=300,
-            estimateLearningRate=R.EachIteration,
-        )
-
-        R.Execute(fixed, moving)
-
-        print("-------")
-        print(displacementTx)
-        print(f"Optimizer stop condition: {R.GetOptimizerStopConditionDescription()}")
-        print(f" Iteration: {R.GetOptimizerIteration()}")
-        print(f" Metric value: {R.GetMetricValue()}")
-
-        compositeTx = sitk.CompositeTransform([outTx1, displacementTx])
-
-
-        if "SITK_NOSHOW" not in os.environ:
-            sitk.Show(displacementTx.GetDisplacementField(), "Displacement Field")
-
-            resampler = sitk.ResampleImageFilter()
-            resampler.SetReferenceImage(fixed)
-            resampler.SetInterpolator(sitk.sitkLinear)
-            resampler.SetDefaultPixelValue(100)
-            resampler.SetTransform(compositeTx)
-
-            out = resampler.Execute(moving)
-            return out
-    elif method=='Exhaustive':
-        R = sitk.ImageRegistrationMethod()
-
-        R.SetMetricAsMattesMutualInformation(numberOfHistogramBins=50)
-
-        sample_per_axis = 12
-        if fixed.GetDimension() == 2:
-            tx = sitk.Euler2DTransform()
-            # Set the number of samples (radius) in each dimension, with a
-            # default step size of 1.0
-            R.SetOptimizerAsExhaustive([sample_per_axis // 2, 0, 0])
-            # Utilize the scale to set the step size for each dimension
-            R.SetOptimizerScales([2.0 * pi / sample_per_axis, 1.0, 1.0])
-        elif fixed.GetDimension() == 3:
-            tx = sitk.Euler3DTransform()
-            R.SetOptimizerAsExhaustive(
-                [
-                    sample_per_axis // 2,
-                    sample_per_axis // 2,
-                    sample_per_axis // 4,
-                    0,
-                    0,
-                    0,
-                ]
-            )
-            R.SetOptimizerScales(
-                [
-                    2.0 * pi / sample_per_axis,
-                    2.0 * pi / sample_per_axis,
-                    2.0 * pi / sample_per_axis,
-                    1.0,
-                    1.0,
-                    1.0,
-                ]
-            )
-
-        # Initialize the transform with a translation and the center of
-        # rotation from the moments of intensity.
-        tx = sitk.CenteredTransformInitializer(fixed, moving, tx)
-
-        R.SetInitialTransform(tx)
-
-        R.SetInterpolator(sitk.sitkLinear)
-
-
-    return run_registration(R, fixed, moving)
-
-def run_registration(R, fixed, moving):
-    R.AddCommand(sitk.sitkIterationEvent, lambda: command_iteration(R))
-
-    outTx = R.Execute(fixed, moving)
-
-    print("-------")
-    print(outTx)
-    print(f"Optimizer stop condition: {R.GetOptimizerStopConditionDescription()}")
-    print(f" Iteration: {R.GetOptimizerIteration()}")
-    print(f" Metric value: {R.GetMetricValue()}")
-
-    resampler = sitk.ResampleImageFilter()
-    resampler.SetReferenceImage(fixed)
-    resampler.SetInterpolator(sitk.sitkLinear)
-    resampler.SetDefaultPixelValue(0)
-    resampler.SetTransform(outTx)
-    out = resampler.Execute(moving)
-    return out, outTx
-
-def apply_reg(outTx, fixed, moving):
-    resampler = sitk.ResampleImageFilter()
-    resampler.SetReferenceImage(fixed)
-    resampler.SetInterpolator(sitk.sitkNearestNeighbor)
-    resampler.SetDefaultPixelValue(0)
-    resampler.SetTransform(outTx)
-    out = resampler.Execute(moving)
-    return out
-
-def FFD_registration(fixed, moving, criterion='mse', *params):
-    R = sitk.ImageRegistrationMethod()
-    params = params[0]
-    fixed_mask = params['fixed_mask']
-    fixed_points = params['fixed_points']
-    moving_points = params['moving_points']
-    MultiRes = params['MultiRes']
-    numberOfBins = params['nbins']
-    # Determine the number of BSpline control points using the physical spacing we
-    # want for the finest resolution control grid.
-    grid_physical_spacing = [50.0, 50.0, 50.0]  # A control point every 50mm
-    image_physical_size = [
-        size * spacing
-        for size, spacing in zip(fixed.GetSize(), fixed.GetSpacing())
-    ]
-    mesh_size = [
-        int(image_size / grid_spacing + 0.5)
-        for image_size, grid_spacing in zip(image_physical_size, grid_physical_spacing)
-    ]
-
-    # The starting mesh size will be 1/4 of the original, it will be refined by
-    # the multi-resolution framework.
-    mesh_size = [int(sz / 4 + 0.5) for sz in mesh_size]
-
-    initial_transform = sitk.BSplineTransformInitializer(
-        image1=fixed, transformDomainMeshSize=mesh_size, order=3
-    )
-    # Instead of the standard SetInitialTransform we use the BSpline specific method which also
-    # accepts the scaleFactors parameter to refine the BSpline mesh. In this case we start with
-    # the given mesh_size at the highest pyramid level then we double it in the next lower level and
-    # in the full resolution image we use a mesh that is four times the original size.
-    if MultiRes:
-        R.SetInitialTransformAsBSpline(
-        initial_transform, inPlace=True, scaleFactors=[1, 2, 4]
-        )
-    else:
-        R.SetInitialTransform(initial_transform)
-    if criterion.lower()=='mse':
-        R.SetMetricAsMeanSquares()
-    elif criterion.lower()=='correlation':
-        R.SetMetricAsCorrelation()
-    elif criterion.lower()=='mi':
-        R.SetMetricAsMattesMutualInformation(numberOfBins)
-
-    # Settings for metric sampling, usage of a mask is optional. When given a mask the sample points will be
-    # generated inside that region. Also, this implicitly speeds things up as the mask is smaller than the
-    # whole image.
-    R.SetMetricSamplingStrategy(R.RANDOM)
-    samplingPercentage = params['sp']#0.01
-    R.SetMetricSamplingPercentage(samplingPercentage)
-    if fixed_mask:
-        R.SetMetricFixedMask(fixed_mask)
-
-    # Multi-resolution framework.
-    R.SetShrinkFactorsPerLevel(shrinkFactors=[4, 2, 1])
-    R.SetSmoothingSigmasPerLevel(smoothingSigmas=[2, 1, 0])
-    R.SmoothingSigmasAreSpecifiedInPhysicalUnitsOn()
-
-    R.SetInterpolator(sitk.sitkLinear)
-    if MultiRes:
-        # Use the LBFGS2 instead of LBFGS. The latter cannot adapt to the changing control grid resolution.
-        R.SetOptimizerAsLBFGS2(
-            solutionAccuracy=1e-2, numberOfIterations=100, deltaConvergenceTolerance=0.01
-        )
-    else:
-        R.SetOptimizerAsLBFGSB(
-            gradientConvergenceTolerance=1e-5,
-            numberOfIterations=100,
-            maximumNumberOfCorrections=5,
-            maximumNumberOfFunctionEvaluations=1000,
-            costFunctionConvergenceFactor=1e7,
-        )
-
-    # If corresponding points in the fixed and moving image are given then we display the similarity metric
-    # and the TRE during the registration.
-    if fixed_points and moving_points:
-        import registration_callbacks as rc
-        R.AddCommand(
-            sitk.sitkStartEvent, rc.metric_and_reference_start_plot
-        )
-        R.AddCommand(
-            sitk.sitkEndEvent, rc.metric_and_reference_end_plot
-        )
-        R.AddCommand(
-            sitk.sitkIterationEvent,
-            lambda: rc.metric_and_reference_plot_values(
-                R, fixed_points, moving_points
-            ),
-        )
-
-    return run_registration(R, fixed, moving)

melage/utils/source_folder.py

@@ -1,18 +0,0 @@
-__AUTHOR__ = 'Bahram Jafrasteh'
-# This source code is used to identiy proper environment
-VERSION = '2.1.1'
-VERSION_DATE = 'Aprill 22 2024'
-from sys import platform
-import os
-if platform == "linux" or platform == "linux2":
-    cur_path = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
-    source_folder = os.path.join(cur_path, "resource")
-    desktop = os.path.join(os.path.join(os.path.expanduser('~')), 'Desktop')
-elif platform == "darwin":  # macOS
-    cur_path = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
-    source_folder = os.path.join(cur_path, "resource")
-    desktop = os.path.join(os.path.expanduser('~'), 'Desktop')
-else:
-    cur_path = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
-    source_folder = os.path.join(cur_path, "resource")
-    desktop = os.path.join(os.path.join(os.environ['USERPROFILE']), 'Desktop')

melage/version.txt

@@ -1 +0,0 @@
-2,0,1