diff --git a/examples/ITK_Example01_SimpleRegistration.ipynb b/examples/ITK_Example01_SimpleRegistration.ipynb index 9003741..03ab083 100644 --- a/examples/ITK_Example01_SimpleRegistration.ipynb +++ b/examples/ITK_Example01_SimpleRegistration.ipynb @@ -66,7 +66,7 @@ "outputs": [], "source": [ "parameter_object = itk.ParameterObject.New()\n", - "default_rigid_parameter_map = parameter_object.GetDefaultParameterMap('rigid')\n", + "default_rigid_parameter_map = itk.ParameterObject.GetDefaultParameterMap('rigid')\n", "parameter_object.AddParameterMap(default_rigid_parameter_map)" ] }, diff --git a/examples/ITK_Example02_CustomOrMultipleParameterMaps.ipynb b/examples/ITK_Example02_CustomOrMultipleParameterMaps.ipynb index 2ce29e2..bab4c73 100644 --- a/examples/ITK_Example02_CustomOrMultipleParameterMaps.ipynb +++ b/examples/ITK_Example02_CustomOrMultipleParameterMaps.ipynb @@ -182,11 +182,11 @@ "# Import Default Parameter Map\n", "parameter_object = itk.ParameterObject.New()\n", "resolutions = 3\n", - "parameter_map_rigid = parameter_object.GetDefaultParameterMap('rigid',3)\n", + "parameter_map_rigid = itk.ParameterObject.GetDefaultParameterMap('rigid',3)\n", "parameter_object.AddParameterMap(parameter_map_rigid)\n", "\n", "# For the bspline default parameter map, an extra argument can be specified that define the final bspline grid spacing in physical space. \n", - "parameter_map_bspline = parameter_object.GetDefaultParameterMap(\"bspline\", resolutions, 20.0)\n", + "parameter_map_bspline = itk.ParameterObject.GetDefaultParameterMap(\"bspline\", resolutions, 20.0)\n", "parameter_object.AddParameterMap(parameter_map_bspline)\n", "\n", "\n", @@ -194,7 +194,7 @@ "parameter_object.AddParameterFile('data/parameters_BSpline.txt')\n", "\n", "# ... and/or load and customize more\n", - "parameter_map_custom = parameter_object.GetDefaultParameterMap('rigid')\n", + "parameter_map_custom = itk.ParameterObject.GetDefaultParameterMap('rigid')\n", "parameter_map_custom['Transform'] = ['BSplineTransform']\n", "parameter_map_custom['Metric'] = ['AdvancedMattesMutualInformation']\n", "parameter_object.AddParameterMap(parameter_map_custom)\n", diff --git a/examples/ITK_Example04_InitialTransformAndMultiThreading.ipynb b/examples/ITK_Example04_InitialTransformAndMultiThreading.ipynb index e6976b8..d2ca6ed 100644 --- a/examples/ITK_Example04_InitialTransformAndMultiThreading.ipynb +++ b/examples/ITK_Example04_InitialTransformAndMultiThreading.ipynb @@ -50,7 +50,7 @@ "\n", "# Import Default Parameter Map\n", "parameter_object = itk.ParameterObject.New()\n", - "parameter_map_rigid = parameter_object.GetDefaultParameterMap('rigid')\n", + "parameter_map_rigid = itk.ParameterObject.GetDefaultParameterMap('rigid')\n", "parameter_object.AddParameterMap(parameter_map_rigid)" ] }, diff --git a/examples/ITK_Example05_PointRegistration.ipynb b/examples/ITK_Example05_PointRegistration.ipynb index b532c6f..04b552a 100644 --- a/examples/ITK_Example05_PointRegistration.ipynb +++ b/examples/ITK_Example05_PointRegistration.ipynb @@ -55,7 +55,7 @@ "\n", "# Import and adjust Parameter Map\n", "parameter_object = itk.ParameterObject.New()\n", - "parameter_map_rigid = parameter_object.GetDefaultParameterMap('rigid')\n", + "parameter_map_rigid = itk.ParameterObject.GetDefaultParameterMap('rigid')\n", "parameter_map_rigid['Registration'] = [\n", " 'MultiMetricMultiResolutionRegistration']\n", "original_metric = parameter_map_rigid['Metric']\n", diff --git a/examples/ITK_Example06_GroupwiseRegistration.ipynb b/examples/ITK_Example06_GroupwiseRegistration.ipynb index 0053a0d..e7bbfda 100644 --- a/examples/ITK_Example06_GroupwiseRegistration.ipynb +++ b/examples/ITK_Example06_GroupwiseRegistration.ipynb @@ -50,7 +50,7 @@ "source": [ "# Create Groupwise Parameter Object\n", "parameter_object = itk.ParameterObject.New()\n", - "groupwise_parameter_map = parameter_object.GetDefaultParameterMap('groupwise')\n", + "groupwise_parameter_map = itk.ParameterObject.GetDefaultParameterMap('groupwise')\n", "parameter_object.AddParameterMap(groupwise_parameter_map)" ] }, diff --git a/examples/ITK_Example08_SimpleTransformix.ipynb b/examples/ITK_Example08_SimpleTransformix.ipynb index f42e5bd..825d879 100644 --- a/examples/ITK_Example08_SimpleTransformix.ipynb +++ b/examples/ITK_Example08_SimpleTransformix.ipynb @@ -47,7 +47,7 @@ "\n", "# Import Default Parameter Map\n", "parameter_object = itk.ParameterObject.New()\n", - "parameter_map_rigid = parameter_object.GetDefaultParameterMap('rigid')\n", + "parameter_map_rigid = itk.ParameterObject.GetDefaultParameterMap('rigid')\n", "parameter_object.AddParameterMap(parameter_map_rigid)" ] }, diff --git a/examples/ITK_Example09_PointSetAndMaskTransformation.ipynb b/examples/ITK_Example09_PointSetAndMaskTransformation.ipynb index 6fb1058..613e6e1 100644 --- a/examples/ITK_Example09_PointSetAndMaskTransformation.ipynb +++ b/examples/ITK_Example09_PointSetAndMaskTransformation.ipynb @@ -51,11 +51,11 @@ "\n", "# Import Default Parameter Map\n", "parameter_object = itk.ParameterObject.New()\n", - "parameter_map_rigid = parameter_object.GetDefaultParameterMap('rigid')\n", + "parameter_map_rigid = itk.ParameterObject.GetDefaultParameterMap('rigid')\n", "parameter_object.AddParameterMap(parameter_map_rigid)\n", - "parameter_map_affine= parameter_object.GetDefaultParameterMap('affine')\n", + "parameter_map_affine= itk.ParameterObject.GetDefaultParameterMap('affine')\n", "parameter_object.AddParameterMap(parameter_map_affine)\n", - "parameter_map_bspline = parameter_object.GetDefaultParameterMap('bspline')\n", + "parameter_map_bspline = itk.ParameterObject.GetDefaultParameterMap('bspline')\n", "parameter_object.AddParameterMap(parameter_map_bspline)" ] }, diff --git a/examples/ITK_Example10_Transformix_Jacobian.ipynb b/examples/ITK_Example10_Transformix_Jacobian.ipynb index 0209721..3f9a804 100644 --- a/examples/ITK_Example10_Transformix_Jacobian.ipynb +++ b/examples/ITK_Example10_Transformix_Jacobian.ipynb @@ -45,7 +45,7 @@ "\n", "# Import Default Parameter Map\n", "parameter_object = itk.ParameterObject.New()\n", - "parameter_map_rigid = parameter_object.GetDefaultParameterMap('rigid')\n", + "parameter_map_rigid = itk.ParameterObject.GetDefaultParameterMap('rigid')\n", "parameter_object.AddParameterMap(parameter_map_rigid)" ] }, diff --git a/examples/ITK_Example11_Transformix_DeformationField.ipynb b/examples/ITK_Example11_Transformix_DeformationField.ipynb index 4d8597e..3ebddfe 100644 --- a/examples/ITK_Example11_Transformix_DeformationField.ipynb +++ b/examples/ITK_Example11_Transformix_DeformationField.ipynb @@ -43,8 +43,8 @@ "\n", "# Import Default Parameter Map\n", "parameter_object = itk.ParameterObject.New()\n", - "parameter_map_rigid = parameter_object.GetDefaultParameterMap('rigid')\n", - "parameter_map_bspline = parameter_object.GetDefaultParameterMap('bspline')\n", + "parameter_map_rigid = itk.ParameterObject.GetDefaultParameterMap('rigid')\n", + "parameter_map_bspline = itk.ParameterObject.GetDefaultParameterMap('bspline')\n", "\n", "parameter_object.AddParameterMap(parameter_map_rigid)\n", "parameter_object.AddParameterMap(parameter_map_bspline)" @@ -170,8 +170,8 @@ "source": [ "# Import Default Parameter Map and adjust parameters\n", "parameter_object = itk.ParameterObject.New()\n", - "# parameter_map_rigid = parameter_object.GetDefaultParameterMap('rigid')\n", - "# parameter_map_bspline = parameter_object.GetDefaultParameterMap('rigid')\n", + "# parameter_map_rigid = itk.ParameterObject.GetDefaultParameterMap('rigid')\n", + "# parameter_map_bspline = itk.ParameterObject.GetDefaultParameterMap('rigid')\n", "parameter_map_bspline['HowToCombineTransforms'] = ['Compose']\n", "parameter_map_rigid['HowToCombineTransforms'] = ['Compose']\n", "parameter_object.AddParameterMap(parameter_map_rigid)\n", diff --git a/examples/ITK_Example12_DifferentSizeTransformation.ipynb b/examples/ITK_Example12_DifferentSizeTransformation.ipynb index d3d3c9d..32da692 100644 --- a/examples/ITK_Example12_DifferentSizeTransformation.ipynb +++ b/examples/ITK_Example12_DifferentSizeTransformation.ipynb @@ -70,7 +70,7 @@ "\n", "# Import Default Parameter Map\n", "parameter_object = itk.ParameterObject.New()\n", - "parameter_map_rigid = parameter_object.GetDefaultParameterMap('affine')\n", + "parameter_map_rigid = itk.ParameterObject.GetDefaultParameterMap('affine')\n", "parameter_object.AddParameterMap(parameter_map_rigid)" ] }, diff --git a/examples/ITK_Example13_ITKResampling.ipynb b/examples/ITK_Example13_ITKResampling.ipynb index 65fd180..75e81ea 100644 --- a/examples/ITK_Example13_ITKResampling.ipynb +++ b/examples/ITK_Example13_ITKResampling.ipynb @@ -47,9 +47,9 @@ "\n", "# Import Default Parameter Maps\n", "parameter_object = itk.ParameterObject.New()\n", - "parameter_map_rigid = parameter_object.GetDefaultParameterMap('rigid')\n", + "parameter_map_rigid = itk.ParameterObject.GetDefaultParameterMap('rigid')\n", "parameter_object.AddParameterMap(parameter_map_rigid)\n", - "parameter_map_affine = parameter_object.GetDefaultParameterMap('affine')\n", + "parameter_map_affine = itk.ParameterObject.GetDefaultParameterMap('affine')\n", "parameter_object.AddParameterMap(parameter_map_affine)" ] }, diff --git a/examples/ITK_Example17_MONAIWithPreregistration.ipynb b/examples/ITK_Example17_MONAIWithPreregistration.ipynb index 91c8524..926fcb4 100644 --- a/examples/ITK_Example17_MONAIWithPreregistration.ipynb +++ b/examples/ITK_Example17_MONAIWithPreregistration.ipynb @@ -169,7 +169,7 @@ "source": [ "# Elastix affine parameter map\n", "parameter_object = itk.ParameterObject()\n", - "affine_parameter_map = parameter_object.GetDefaultParameterMap('affine')\n", + "affine_parameter_map = itk.ParameterObject.GetDefaultParameterMap('affine')\n", "affine_parameter_map['NumberOfResolutions'] = \"2\"\n", "affine_parameter_map['MaximumNumberOfIterations'] = (\"64\", )\n", "parameter_object.AddParameterMap(affine_parameter_map)\n", diff --git a/examples/ITK_Example18_MONAI_affine_Elastix_nonlinear.ipynb b/examples/ITK_Example18_MONAI_affine_Elastix_nonlinear.ipynb index ab2caed..e50640b 100644 --- a/examples/ITK_Example18_MONAI_affine_Elastix_nonlinear.ipynb +++ b/examples/ITK_Example18_MONAI_affine_Elastix_nonlinear.ipynb @@ -442,7 +442,7 @@ "source": [ "# B-spline parameter object\n", "parameter_object = itk.ParameterObject()\n", - "parameter_map = parameter_object.GetDefaultParameterMap('bspline')\n", + "parameter_map = itk.ParameterObject.GetDefaultParameterMap('bspline')\n", "parameter_object.AddParameterMap(parameter_map)\n", "\n", "result_image, _ = itk.elastix_registration_method(fixed_image, \n", diff --git a/examples/ITK_Example20_PixelTypes.ipynb b/examples/ITK_Example20_PixelTypes.ipynb index f1346fa..6d8e8a0 100644 --- a/examples/ITK_Example20_PixelTypes.ipynb +++ b/examples/ITK_Example20_PixelTypes.ipynb @@ -69,7 +69,7 @@ "source": [ "# Define a rigid parameter object\n", "parameter_object = itk.ParameterObject.New()\n", - "default_rigid_parameter_map = parameter_object.GetDefaultParameterMap('rigid')\n", + "default_rigid_parameter_map = itk.ParameterObject.GetDefaultParameterMap('rigid')\n", "parameter_object.AddParameterMap(default_rigid_parameter_map)\n", "\n", "# Non-exhaustive list of image types supported by itk-elastix\n", diff --git a/examples/ITK_Example21_ConstrainedRegistration.ipynb b/examples/ITK_Example21_ConstrainedRegistration.ipynb index b1f32a7..393ef3c 100644 --- a/examples/ITK_Example21_ConstrainedRegistration.ipynb +++ b/examples/ITK_Example21_ConstrainedRegistration.ipynb @@ -177,7 +177,7 @@ ], "source": [ "rigid_parameter_object = itk.ParameterObject.New()\n", - "rigid_parameter_map = rigid_parameter_object.GetDefaultParameterMap('rigid')\n", + "rigid_parameter_map = itk.ParameterObject.GetDefaultParameterMap('rigid')\n", "rigid_parameter_map['FinalBSplineInterpolationOrder'] = ('0')\n", "rigid_parameter_object.AddParameterMap(rigid_parameter_map)\n", "\n", @@ -288,7 +288,7 @@ ], "source": [ "constrained_rigid_parameter_object = itk.ParameterObject.New()\n", - "constrained_rigid_parameter_map = constrained_rigid_parameter_object.GetDefaultParameterMap('rigid')\n", + "constrained_rigid_parameter_map = itk.ParameterObject.GetDefaultParameterMap('rigid')\n", "constrained_rigid_parameter_map['FinalBSplineInterpolationOrder'] = ('0')\n", "constrained_rigid_parameter_map['AutomaticScalesEstimation'] = ('false',)\n", "constrained_rigid_parameter_map['Scales'] = ('1666.5', '1', str(np.finfo(fixed_image.dtype).max))\n", diff --git a/examples/ITK_Example22_ConvertToITKTransform.ipynb b/examples/ITK_Example22_ConvertToITKTransform.ipynb index 001dde4..e809661 100644 --- a/examples/ITK_Example22_ConvertToITKTransform.ipynb +++ b/examples/ITK_Example22_ConvertToITKTransform.ipynb @@ -269,7 +269,7 @@ "\n", "for transform_info in transform_schedule:\n", " parameter_object.AddParameterMap(\n", - " parameter_object.GetDefaultParameterMap(transform_info.elastix_name)\n", + " itk.ParameterObject.GetDefaultParameterMap(transform_info.elastix_name)\n", " )\n", "\n", "print(parameter_object)" diff --git a/examples/ITK_Registration_App.ipynb b/examples/ITK_Registration_App.ipynb index 5caaed3..b556054 100644 --- a/examples/ITK_Registration_App.ipynb +++ b/examples/ITK_Registration_App.ipynb @@ -204,17 +204,17 @@ " parameters = itk.ParameterObject.New()\n", "\n", " resolutions = 3\n", - " default_rigid = parameters.GetDefaultParameterMap(\"rigid\", resolutions)\n", + " default_rigid = itk.ParameterObject.GetDefaultParameterMap(\"rigid\", resolutions)\n", " parameters.AddParameterMap(default_rigid)\n", "\n", " if (regType.value!='rigid'):\n", " resolutions = 2\n", - " default_affine = parameters.GetDefaultParameterMap(\"affine\", resolutions)\n", + " default_affine = itk.ParameterObject.GetDefaultParameterMap(\"affine\", resolutions)\n", " parameters.AddParameterMap(default_affine)\n", "\n", " if (regType.value=='bspline'):\n", " resolutions = 1\n", - " default_bspline = parameters.GetDefaultParameterMap(\"bspline\", resolutions)\n", + " default_bspline = itk.ParameterObject.GetDefaultParameterMap(\"bspline\", resolutions)\n", " parameters.AddParameterMap(default_bspline)\n", "\n", " parameters.RemoveParameter(\"ResultImageFormat\")\n", diff --git a/examples/ITK_UnitTestExample1_RigidRegistration.ipynb b/examples/ITK_UnitTestExample1_RigidRegistration.ipynb index b2ff0fe..b51b7b4 100644 --- a/examples/ITK_UnitTestExample1_RigidRegistration.ipynb +++ b/examples/ITK_UnitTestExample1_RigidRegistration.ipynb @@ -59,7 +59,7 @@ "\n", "# Import Default Parameter Map\n", "parameter_object = itk.ParameterObject.New()\n", - "default_rigid_parameter_map = parameter_object.GetDefaultParameterMap('rigid')\n", + "default_rigid_parameter_map = itk.ParameterObject.GetDefaultParameterMap('rigid')\n", "parameter_object.AddParameterMap(default_rigid_parameter_map)" ] }, diff --git a/examples/ITK_UnitTestExample2_AffineRegistration.ipynb b/examples/ITK_UnitTestExample2_AffineRegistration.ipynb index 33a96f1..c4ef8c5 100644 --- a/examples/ITK_UnitTestExample2_AffineRegistration.ipynb +++ b/examples/ITK_UnitTestExample2_AffineRegistration.ipynb @@ -59,7 +59,7 @@ "\n", "# Import Default Parameter Map\n", "parameter_object = itk.ParameterObject.New()\n", - "default_affine_parameter_map = parameter_object.GetDefaultParameterMap('affine',4)\n", + "default_affine_parameter_map = itk.ParameterObject.GetDefaultParameterMap('affine',4)\n", "default_affine_parameter_map['FinalBSplineInterpolationOrder'] = ['0']\n", "parameter_object.AddParameterMap(default_affine_parameter_map)" ] diff --git a/examples/ITK_UnitTestExample3_BsplineRegistration.ipynb b/examples/ITK_UnitTestExample3_BsplineRegistration.ipynb index 83829cb..406b020 100644 --- a/examples/ITK_UnitTestExample3_BsplineRegistration.ipynb +++ b/examples/ITK_UnitTestExample3_BsplineRegistration.ipynb @@ -68,10 +68,10 @@ "\n", "# Import Default Parameter Map\n", "parameter_object = itk.ParameterObject.New()\n", - "default_affine_parameter_map = parameter_object.GetDefaultParameterMap('affine',4)\n", + "default_affine_parameter_map = itk.ParameterObject.GetDefaultParameterMap('affine',4)\n", "default_affine_parameter_map['FinalBSplineInterpolationOrder'] = ['1']\n", "parameter_object.AddParameterMap(default_affine_parameter_map)\n", - "default_bspline_parameter_map = parameter_object.GetDefaultParameterMap('bspline',4)\n", + "default_bspline_parameter_map = itk.ParameterObject.GetDefaultParameterMap('bspline',4)\n", "default_bspline_parameter_map['FinalBSplineInterpolationOrder'] = ['1']\n", "parameter_object.AddParameterMap(default_bspline_parameter_map)" ] diff --git a/examples/ITK_UnitTestExample4_MaskedRegistration.ipynb b/examples/ITK_UnitTestExample4_MaskedRegistration.ipynb index 4941638..592bceb 100644 --- a/examples/ITK_UnitTestExample4_MaskedRegistration.ipynb +++ b/examples/ITK_UnitTestExample4_MaskedRegistration.ipynb @@ -68,7 +68,7 @@ "\n", "# Import Default Parameter Map\n", "parameter_object = itk.ParameterObject.New()\n", - "default_rigid_parameter_map = parameter_object.GetDefaultParameterMap('rigid')\n", + "default_rigid_parameter_map = itk.ParameterObject.GetDefaultParameterMap('rigid')\n", "parameter_object.AddParameterMap(default_rigid_parameter_map)\n", "\n", "# Call registration function\n", diff --git a/examples/ITK_UnitTestExample5_GroupwiseRegistration.ipynb b/examples/ITK_UnitTestExample5_GroupwiseRegistration.ipynb index ad9b29e..1d93a16 100644 --- a/examples/ITK_UnitTestExample5_GroupwiseRegistration.ipynb +++ b/examples/ITK_UnitTestExample5_GroupwiseRegistration.ipynb @@ -81,7 +81,7 @@ "\n", "# Create Groupwise Parameter Object\n", "parameter_object = itk.ParameterObject.New()\n", - "groupwise_parameter_map = parameter_object.GetDefaultParameterMap('groupwise',4)\n", + "groupwise_parameter_map = itk.ParameterObject.GetDefaultParameterMap('groupwise',4)\n", "groupwise_parameter_map['FinalBSplineInterpolationOrder'] = ['0']\n", "groupwise_parameter_map['Transform'] = ['EulerStackTransform']\n", "groupwise_parameter_map['AutomaticScalesEstimation'] = ['true']\n", @@ -157,7 +157,7 @@ "\n", "# Create Groupwise Parameter Object\n", "parameter_object = itk.ParameterObject.New()\n", - "groupwise_parameter_map = parameter_object.GetDefaultParameterMap('groupwise',2)\n", + "groupwise_parameter_map = itk.ParameterObject.GetDefaultParameterMap('groupwise',2)\n", "groupwise_parameter_map['FinalBSplineInterpolationOrder'] = ['0']\n", "groupwise_parameter_map['Transform'] = ['EulerStackTransform']\n", "groupwise_parameter_map['AutomaticScalesEstimation'] = ['true']\n", diff --git a/examples/ITK_UnitTestExample6_PointSetTransformation.ipynb b/examples/ITK_UnitTestExample6_PointSetTransformation.ipynb index e095a2b..70f018f 100644 --- a/examples/ITK_UnitTestExample6_PointSetTransformation.ipynb +++ b/examples/ITK_UnitTestExample6_PointSetTransformation.ipynb @@ -96,7 +96,7 @@ "\n", "# Import Default Parameter Map\n", "parameter_object = itk.ParameterObject.New()\n", - "default_rigid_parameter_map = parameter_object.GetDefaultParameterMap('rigid')\n", + "default_rigid_parameter_map = itk.ParameterObject.GetDefaultParameterMap('rigid')\n", "parameter_object.AddParameterMap(default_rigid_parameter_map)\n", "\n", "# # Call registration function\n", diff --git a/examples/ITK_UnitTestExample7_SizeTransformation.ipynb b/examples/ITK_UnitTestExample7_SizeTransformation.ipynb index 2c8372a..ea54c10 100644 --- a/examples/ITK_UnitTestExample7_SizeTransformation.ipynb +++ b/examples/ITK_UnitTestExample7_SizeTransformation.ipynb @@ -68,7 +68,7 @@ "\n", "# Import Default Parameter Map\n", "parameter_object = itk.ParameterObject.New()\n", - "default_rigid_parameter_map = parameter_object.GetDefaultParameterMap('rigid',4)\n", + "default_rigid_parameter_map = itk.ParameterObject.GetDefaultParameterMap('rigid',4)\n", "default_rigid_parameter_map['FinalBSplineInterpolationOrder'] = ['0']\n", "parameter_object.AddParameterMap(default_rigid_parameter_map)\n", "\n",