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| 17 | </head> |
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| 18 | <body> |
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| 19 | <main> |
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| 20 | <article id="content"> |
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| 21 | <header> |
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| 22 | <h1 class="title">Module <code>pymskt.mesh.meshes</code></h1> |
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| 23 | </header> |
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| 24 | <section id="section-intro"> |
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| 25 | <details class="source"> |
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| 26 | <summary> |
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| 27 | <span>Expand source code</span> |
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| 28 | </summary> |
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| 29 | <pre><code class="python">from logging import error |
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| 30 | from posixpath import supports_unicode_filenames |
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| 31 | import warnings |
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| 32 | import numpy as np |
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| 33 | import vtk |
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| 34 | from pymskt.image.main import apply_transform_retain_array |
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| 35 | from vtk.util.numpy_support import numpy_to_vtk, vtk_to_numpy |
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| 36 | import pyacvd |
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| 37 | import pyvista as pv |
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| 38 | import SimpleITK as sitk |
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| 39 | import os |
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| 40 | import random |
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| 41 | import string |
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| 42 | # import pyfocusr # MAKE THIS AN OPTIONAL IMPORT? |
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| 43 | |||
| 44 | import pymskt |
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| 45 | from pymskt.mesh import createMesh |
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| 46 | from pymskt.utils import safely_delete_tmp_file, copy_image_transform_to_mesh |
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| 47 | from pymskt.image import read_nrrd, crop_bone_based_on_width |
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| 48 | from pymskt.mesh.utils import vtk_deep_copy |
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| 49 | from pymskt.mesh.meshTools import (gaussian_smooth_surface_scalars, |
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| 50 | get_mesh_physical_point_coords, |
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| 51 | get_cartilage_properties_at_points, |
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| 52 | smooth_scalars_from_second_mesh_onto_base, |
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| 53 | transfer_mesh_scalars_get_weighted_average_n_closest, |
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| 54 | resample_surface |
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| 55 | ) |
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| 56 | from pymskt.mesh.createMesh import create_surface_mesh |
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| 57 | from pymskt.mesh.meshTransform import (SitkVtkTransformer, |
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| 58 | get_versor_from_transform, |
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| 59 | break_versor_into_center_rotate_translate_transforms, |
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| 60 | apply_transform) |
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| 61 | from pymskt.mesh.meshRegistration import non_rigidly_register, get_icp_transform |
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| 62 | import pymskt.mesh.io as io |
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| 63 | |||
| 64 | class Mesh: |
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| 65 | """ |
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| 66 | An object to contain surface meshes for musculoskeletal anatomy. Includes helper |
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| 67 | functions to build surface meshes, to process them, and to save them. |
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| 68 | |||
| 69 | Parameters |
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| 70 | ---------- |
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| 71 | mesh : vtk.vtkPolyData, optional |
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| 72 | vtkPolyData object that is basis of surface mesh, by default None |
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| 73 | seg_image : SimpleITK.Image, optional |
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| 74 | Segmentation image that can be used to create surface mesh - used |
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| 75 | instead of mesh, by default None |
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| 76 | path_seg_image : str, optional |
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| 77 | Path to a medical image (.nrrd) to load and create mesh from, |
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| 78 | by default None |
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| 79 | label_idx : int, optional |
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| 80 | Label of anatomy of interest, by default None |
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| 81 | min_n_pixels : int, optional |
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| 82 | All islands smaller than this size are dropped, by default 5000 |
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| 83 | |||
| 84 | |||
| 85 | Attributes |
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| 86 | ---------- |
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| 87 | _mesh : vtk.vtkPolyData |
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| 88 | Item passed from __init__, or created during life of class. |
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| 89 | This is the main surface mesh of this class. |
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| 90 | _seg_image : SimpleITK.Image |
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| 91 | Segmentation image that can be used to create mesh. This is optional. |
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| 92 | path_seg_image : str |
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| 93 | Path to medical image (.nrrd) that can be loaded to create `_seg_image` |
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| 94 | and then creat surface mesh `_mesh` |
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| 95 | label_idx : int |
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| 96 | Integer of anatomy to create surface mesh from `_seg_image` |
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| 97 | min_n_pixels : int |
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| 98 | Minimum number of pixels for an isolated island of a segmentation to be |
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| 99 | retained |
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| 100 | list_applied_transforms : list |
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| 101 | A list of transformations applied to a surface mesh. |
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| 102 | This list allows for undoing of most recent transform, or undoing |
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| 103 | all of them by iterating over the list in reverse. |
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| 104 | |||
| 105 | Methods |
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| 106 | ---------- |
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| 107 | |||
| 108 | """ |
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| 109 | def __init__(self, |
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| 110 | mesh=None, |
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| 111 | seg_image=None, |
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| 112 | path_seg_image=None, |
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| 113 | label_idx=None, |
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| 114 | min_n_pixels=5000 |
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| 115 | ): |
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| 116 | """ |
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| 117 | Initialize Mesh class |
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| 118 | |||
| 119 | Parameters |
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| 120 | ---------- |
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| 121 | mesh : vtk.vtkPolyData, optional |
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| 122 | vtkPolyData object that is basis of surface mesh, by default None |
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| 123 | seg_image : SimpleITK.Image, optional |
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| 124 | Segmentation image that can be used to create surface mesh - used |
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| 125 | instead of mesh, by default None |
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| 126 | path_seg_image : str, optional |
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| 127 | Path to a medical image (.nrrd) to load and create mesh from, |
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| 128 | by default None |
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| 129 | label_idx : int, optional |
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| 130 | Label of anatomy of interest, by default None |
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| 131 | min_n_pixels : int, optional |
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| 132 | All islands smaller than this size are dropped, by default 5000 |
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| 133 | """ |
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| 134 | if type(mesh) in (str,): #accept path like objects? |
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| 135 | print('mesh string passed, loading mesh from disk') |
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| 136 | self._mesh = io.read_vtk(mesh) |
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| 137 | else: |
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| 138 | self._mesh = mesh |
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| 139 | self._seg_image = seg_image |
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| 140 | self._path_seg_image = path_seg_image |
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| 141 | self._label_idx = label_idx |
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| 142 | self._min_n_pixels = min_n_pixels |
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| 143 | |||
| 144 | self._list_applied_transforms = [] |
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| 145 | |||
| 146 | def read_seg_image(self, |
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| 147 | path_seg_image=None): |
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| 148 | """ |
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| 149 | Read segmentation image from disk. Must be a single file (e.g., nrrd, 3D dicom) |
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| 150 | |||
| 151 | Parameters |
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| 152 | ---------- |
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| 153 | path_seg_image : str, optional |
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| 154 | Path to the medical image file to be loaded in, by default None |
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| 155 | |||
| 156 | Raises |
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| 157 | ------ |
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| 158 | Exception |
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| 159 | If path_seg_image does not exist, exception is raised. |
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| 160 | """ |
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| 161 | # If passing new location/seg image name, then update variables. |
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| 162 | if path_seg_image is not None: |
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| 163 | self._path_seg_image = path_seg_image |
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| 164 | |||
| 165 | # If seg image location / name exist, then load image else raise exception |
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| 166 | if (self._path_seg_image is not None): |
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| 167 | self._seg_image = sitk.ReadImage(self._path_seg_image) |
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| 168 | else: |
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| 169 | raise Exception('No file path (self._path_seg_image) provided.') |
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| 170 | |||
| 171 | def create_mesh(self, |
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| 172 | smooth_image=True, |
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| 173 | smooth_image_var=0.3125 / 2, |
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| 174 | marching_cubes_threshold=0.5, |
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| 175 | label_idx=None, |
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| 176 | min_n_pixels=None): |
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| 177 | """ |
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| 178 | Create a surface mesh from the classes `_seg_image`. If `_seg_image` |
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| 179 | does not exist, then read it in using `read_seg_image`. |
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| 180 | |||
| 181 | Parameters |
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| 182 | ---------- |
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| 183 | smooth_image : bool, optional |
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| 184 | Should the `_seg_image` be gaussian filtered, by default True |
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| 185 | smooth_image_var : float, optional |
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| 186 | Variance of gaussian filter to apply to `_seg_image`, by default 0.3125/2 |
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| 187 | marching_cubes_threshold : float, optional |
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| 188 | Threshold contour level to create surface mesh on, by default 0.5 |
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| 189 | label_idx : int, optional |
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| 190 | Label value / index to create mesh from, by default None |
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| 191 | min_n_pixels : int, optional |
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| 192 | Minimum number of continuous pixels to include segmentation island |
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| 193 | in the surface mesh creation, by default None |
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| 194 | |||
| 195 | Raises |
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| 196 | ------ |
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| 197 | Exception |
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| 198 | If the total number of pixels segmentated (`n_pixels_labelled`) is |
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| 199 | < `min_n_pixels` then there is no object in the image. |
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| 200 | Exception |
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| 201 | If no `_seg_image` and no `label_idx` then we don't know what tissue to create the |
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| 202 | surface mesh from. |
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| 203 | Exception |
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| 204 | If no `_seg_image` or `path_seg_image` then we have no image to create mesh from. |
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| 205 | """ |
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| 206 | # allow assigning label idx during mesh creation step. |
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| 207 | if label_idx is not None: |
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| 208 | self._label_idx = label_idx |
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| 209 | |||
| 210 | if self._seg_image is None: |
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| 211 | self.read_seg_image() |
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| 212 | |||
| 213 | # Ensure the image has a certain number of pixels with the label of interest, otherwise there might be an issue. |
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| 214 | if min_n_pixels is None: min_n_pixels = self._min_n_pixels |
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| 215 | seg_view = sitk.GetArrayViewFromImage(self._seg_image) |
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| 216 | n_pixels_labelled = sum(seg_view[seg_view == self._label_idx]) |
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| 217 | |||
| 218 | if n_pixels_labelled < min_n_pixels: |
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| 219 | raise Exception('The mesh does not exist in this segmentation!, only {} pixels detected, threshold # is {}'.format(n_pixels_labelled, |
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| 220 | marching_cubes_threshold)) |
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| 221 | tmp_filename = ''.join(random.choice(string.ascii_lowercase) for i in range(10)) + '.nrrd' |
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| 222 | self._mesh = create_surface_mesh(self._seg_image, |
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| 223 | self._label_idx, |
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| 224 | smooth_image_var, |
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| 225 | loc_tmp_save='/tmp', |
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| 226 | tmp_filename=tmp_filename, |
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| 227 | mc_threshold=marching_cubes_threshold, |
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| 228 | filter_binary_image=smooth_image |
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| 229 | ) |
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| 230 | safely_delete_tmp_file('/tmp', |
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| 231 | tmp_filename) |
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| 232 | |||
| 233 | def save_mesh(self, |
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| 234 | filepath): |
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| 235 | """ |
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| 236 | Save the surface mesh from this class to disk. |
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| 237 | |||
| 238 | Parameters |
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| 239 | ---------- |
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| 240 | filepath : str |
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| 241 | Location & filename to save the surface mesh (vtk.vtkPolyData) to. |
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| 242 | """ |
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| 243 | io.write_vtk(self._mesh, filepath) |
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| 244 | |||
| 245 | def resample_surface(self, |
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| 246 | subdivisions=2, |
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| 247 | clusters=10000 |
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| 248 | ): |
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| 249 | """ |
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| 250 | Resample a surface mesh using the ACVD algorithm: |
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| 251 | Version used: |
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| 252 | - https://github.com/pyvista/pyacvd |
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| 253 | Original version w/ more references: |
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| 254 | - https://github.com/valette/ACVD |
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| 255 | |||
| 256 | Parameters |
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| 257 | ---------- |
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| 258 | subdivisions : int, optional |
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| 259 | Subdivide the mesh to have more points before clustering, by default 2 |
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| 260 | Probably not necessary for very dense meshes. |
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| 261 | clusters : int, optional |
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| 262 | The number of clusters (points/vertices) to create during resampling |
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| 263 | surafce, by default 10000 |
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| 264 | - This is not exact, might have slight differences. |
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| 265 | """ |
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| 266 | self._mesh = resample_surface(self._mesh, subdivisions=subdivisions, clusters=clusters) |
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| 267 | |||
| 268 | def apply_transform_to_mesh(self, |
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| 269 | transform=None, |
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| 270 | transformer=None, |
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| 271 | save_transform=True): |
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| 272 | """ |
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| 273 | Apply a transformation to the surface mesh. |
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| 274 | |||
| 275 | Parameters |
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| 276 | ---------- |
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| 277 | transform : vtk.vtkTransform, optional |
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| 278 | Transformation to apply to mesh, by default None |
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| 279 | transformer : vtk.vtkTransformFilter, optional |
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| 280 | Can supply transformFilter directly, by default None |
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| 281 | save_transform : bool, optional |
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| 282 | Should transform be saved to list of applied transforms, by default True |
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| 283 | |||
| 284 | Raises |
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| 285 | ------ |
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| 286 | Exception |
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| 287 | No `transform` or `transformer` supplied - have not transformation |
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| 288 | to apply. |
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| 289 | """ |
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| 290 | if (transform is not None) & (transformer is None): |
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| 291 | transformer = vtk.vtkTransformPolyDataFilter() |
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| 292 | transformer.SetTransform(transform) |
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| 293 | |||
| 294 | elif (transform is None) & (transformer is not None): |
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| 295 | transform = transformer.GetTransform() |
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| 296 | |||
| 297 | if transformer is not None: |
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| 298 | transformer.SetInputData(self._mesh) |
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| 299 | transformer.Update() |
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| 300 | self._mesh = vtk_deep_copy(transformer.GetOutput()) |
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| 301 | |||
| 302 | if save_transform is True: |
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| 303 | self._list_applied_transforms.append(transform) |
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| 304 | |||
| 305 | else: |
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| 306 | raise Exception('No transform or transformer provided') |
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| 307 | |||
| 308 | def reverse_most_recent_transform(self): |
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| 309 | """ |
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| 310 | Function to undo the most recent transformation stored in self._list_applied_transforms |
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| 311 | """ |
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| 312 | transform = self._list_applied_transforms.pop() |
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| 313 | transform.Inverse() |
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| 314 | self.apply_transform_to_mesh(transform=transform, save_transform=False) |
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| 315 | |||
| 316 | def reverse_all_transforms(self): |
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| 317 | """ |
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| 318 | Function to iterate over all of the self._list_applied_transforms (in reverse order) and undo them. |
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| 319 | """ |
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| 320 | while len(self._list_applied_transforms) > 0: |
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| 321 | self.reverse_most_recent_transform() |
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| 322 | |||
| 323 | def non_rigidly_register( |
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| 324 | self, |
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| 325 | other_mesh, |
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| 326 | as_source=True, |
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| 327 | apply_transform_to_mesh=True, |
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| 328 | return_transformed_mesh=False, |
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| 329 | **kwargs |
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| 330 | ): |
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| 331 | """ |
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| 332 | Function to perform non rigid registration between this mesh and another mesh. |
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| 333 | |||
| 334 | Parameters |
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| 335 | ---------- |
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| 336 | other_mesh : pymskt.mesh.Mesh or vtk.vtkPolyData |
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| 337 | Other mesh to use in registration process |
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| 338 | as_source : bool, optional |
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| 339 | Should the current mesh (in this object) be the source or the target, by default True |
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| 340 | apply_transform_to_mesh : bool, optional |
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| 341 | If as_source is True should we apply transformation to internal mesh, by default True |
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| 342 | return_transformed_mesh : bool, optional |
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| 343 | Should we return the registered mesh, by default False |
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| 344 | |||
| 345 | Returns |
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| 346 | ------- |
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| 347 | _type_ |
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| 348 | _description_ |
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| 349 | """ |
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| 350 | # Setup the source & target meshes based on `as_source`` |
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| 351 | if as_source is True: |
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| 352 | source = self._mesh |
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| 353 | target = other_mesh |
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| 354 | elif as_source is False: |
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| 355 | source = other_mesh |
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| 356 | target = self._mesh |
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| 357 | |||
| 358 | # Get registered mesh (source to target) |
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| 359 | source_transformed_to_target = non_rigidly_register( |
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| 360 | target_mesh=target, |
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| 361 | source_mesh=source, |
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| 362 | **kwargs |
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| 363 | ) |
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| 364 | |||
| 365 | # If current mesh is source & apply_transform_to_mesh is true then replace current mesh. |
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| 366 | if (as_source is True) & (apply_transform_to_mesh is True): |
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| 367 | self._mesh = source_transformed_to_target |
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| 368 | |||
| 369 | # curent mesh is target, or is source & want to return mesh, then return it. |
||
| 370 | if (as_source is False) or ((as_source is True) & (return_transformed_mesh is True)): |
||
| 371 | return source_transformed_to_target |
||
| 372 | |||
| 373 | def rigidly_register( |
||
| 374 | self, |
||
| 375 | other_mesh, |
||
| 376 | as_source=True, |
||
| 377 | apply_transform_to_mesh=True, |
||
| 378 | return_transformed_mesh=False, |
||
| 379 | return_transform=False, |
||
| 380 | max_n_iter=100, |
||
| 381 | n_landmarks=1000, |
||
| 382 | reg_mode='similarity' |
||
| 383 | |||
| 384 | ): |
||
| 385 | """ |
||
| 386 | Function to perform rigid registration between this mesh and another mesh. |
||
| 387 | |||
| 388 | Parameters |
||
| 389 | ---------- |
||
| 390 | other_mesh : pymskt.mesh.Mesh or vtk.vtkPolyData |
||
| 391 | Other mesh to use in registration process |
||
| 392 | as_source : bool, optional |
||
| 393 | Should the current mesh (in this object) be the source or the target, by default True |
||
| 394 | apply_transform_to_mesh : bool, optional |
||
| 395 | If as_source is True should we apply transformation to internal mesh, by default True |
||
| 396 | return_transformed_mesh : bool, optional |
||
| 397 | Should we return the registered mesh, by default False |
||
| 398 | max_n_iter : int, optional |
||
| 399 | Maximum number of iterations to perform, by default 100 |
||
| 400 | n_landmarks : int, optional |
||
| 401 | Number of landmarks to use in registration, by default 1000 |
||
| 402 | reg_mode : str, optional |
||
| 403 | Mode of registration to use, by default 'similarity' (similarity, rigid, or affine) |
||
| 404 | |||
| 405 | Returns |
||
| 406 | ------- |
||
| 407 | _type_ |
||
| 408 | _description_ |
||
| 409 | """ |
||
| 410 | |||
| 411 | if (return_transform is True) & (return_transformed_mesh is True): |
||
| 412 | raise Exception('Cannot return both transformed mesh and transform') |
||
| 413 | |||
| 414 | if type(other_mesh) in (pymskt.mesh.meshes.BoneMesh, pymskt.mesh.meshes.Mesh): |
||
| 415 | other_mesh = other_mesh.mesh |
||
| 416 | |||
| 417 | # Setup the source & target meshes based on `as_source`` |
||
| 418 | if as_source is True: |
||
| 419 | source = self._mesh |
||
| 420 | target = other_mesh |
||
| 421 | elif as_source is False: |
||
| 422 | source = other_mesh |
||
| 423 | target = self._mesh |
||
| 424 | |||
| 425 | icp_transform = get_icp_transform( |
||
| 426 | source=source, |
||
| 427 | target=target, |
||
| 428 | max_n_iter=max_n_iter, |
||
| 429 | n_landmarks=n_landmarks, |
||
| 430 | reg_mode=reg_mode |
||
| 431 | ) |
||
| 432 | |||
| 433 | # If current mesh is source & apply_transform_to_mesh is true then replace current mesh. |
||
| 434 | if (as_source is True) & (apply_transform_to_mesh is True): |
||
| 435 | self.apply_transform_to_mesh(transform=icp_transform) |
||
| 436 | |||
| 437 | if return_transformed_mesh is True: |
||
| 438 | return self._mesh |
||
| 439 | |||
| 440 | elif return_transform is True: |
||
| 441 | return icp_transform |
||
| 442 | |||
| 443 | # curent mesh is target, or is source & want to return mesh, then return it. |
||
| 444 | elif (as_source is False) & (return_transformed_mesh is True): |
||
| 445 | return apply_transform(source=source, transform=icp_transform) |
||
| 446 | |||
| 447 | else: |
||
| 448 | raise Exception('Nothing to return from rigid registration.') |
||
| 449 | |||
| 450 | def copy_scalars_from_other_mesh_to_currect( |
||
| 451 | self, |
||
| 452 | other_mesh, |
||
| 453 | new_scalars_name='scalars_from_other_mesh', |
||
| 454 | weighted_avg=True, # Use weighted average, otherwise guassian smooth transfer |
||
| 455 | n_closest=3, |
||
| 456 | sigma=1., |
||
| 457 | idx_coords_to_smooth_base=None, |
||
| 458 | idx_coords_to_smooth_other=None, |
||
| 459 | set_non_smoothed_scalars_to_zero=True, |
||
| 460 | ): |
||
| 461 | """ |
||
| 462 | Convenience function to enable easy transfer scalars from another mesh to the current. |
||
| 463 | Can use either a gaussian smoothing function, or transfer using nearest neighbours. |
||
| 464 | |||
| 465 | ** This function requires that the `other_mesh` is non-rigidly registered to the surface |
||
| 466 | of the mesh inside of this class. Or rigidly registered but using the same anatomy that |
||
| 467 | VERY closely matches. Otherwise, the transfered scalars will be bad. |
||
| 468 | |||
| 469 | Parameters |
||
| 470 | ---------- |
||
| 471 | other_mesh : pymskt.mesh.Mesh or vtk.vtkPolyData |
||
| 472 | Mesh we want to copy |
||
| 473 | new_scalars_name : str, optional |
||
| 474 | What to name the scalars being transfered to this current mesh, by default 'scalars_from_other_mesh' |
||
| 475 | weighted_avg : bool, optional |
||
| 476 | Should we use `weighted average` or `gaussian smooth` methods for transfer, by default True |
||
| 477 | n_closest : int, optional |
||
| 478 | If `weighted_avg` True, the number of nearest neighbours to use, by default 3 |
||
| 479 | sigma : float, optional |
||
| 480 | If `weighted_avg` False, the standard deviation of gaussian kernel, by default 1. |
||
| 481 | idx_coords_to_smooth_base : list, optional |
||
| 482 | If `weighted_avg` False, list of indices from current mesh to use in transfer, by default None |
||
| 483 | idx_coords_to_smooth_other : list, optional |
||
| 484 | If `weighted_avg` False, list of indices from `other_mesh` to use in transfer, by default None |
||
| 485 | set_non_smoothed_scalars_to_zero : bool, optional |
||
| 486 | Should all other indices (not included in idx_coords_to_smooth_other) be set to 0, by default True |
||
| 487 | """ |
||
| 488 | if type(other_mesh) is Mesh: |
||
| 489 | other_mesh = other_mesh.mesh |
||
| 490 | elif type(other_mesh) is vtk.vtkPolyData: |
||
| 491 | pass |
||
| 492 | else: |
||
| 493 | raise TypeError(f'other_mesh must be type `pymskt.mesh.Mesh` or `vtk.vtkPolyData` and received: {type(other_mesh)}') |
||
| 494 | |||
| 495 | if weighted_avg is True: |
||
| 496 | transferred_scalars = transfer_mesh_scalars_get_weighted_average_n_closest( |
||
| 497 | self._mesh, |
||
| 498 | other_mesh, |
||
| 499 | n=n_closest |
||
| 500 | ) |
||
| 501 | else: |
||
| 502 | transferred_scalars = smooth_scalars_from_second_mesh_onto_base( |
||
| 503 | self._mesh, |
||
| 504 | other_mesh, |
||
| 505 | sigma=sigma, |
||
| 506 | idx_coords_to_smooth_base=idx_coords_to_smooth_base, |
||
| 507 | idx_coords_to_smooth_second=idx_coords_to_smooth_other, |
||
| 508 | set_non_smoothed_scalars_to_zero=set_non_smoothed_scalars_to_zero |
||
| 509 | ) |
||
| 510 | if (new_scalars_name is None) & (weighted_avg is True): |
||
| 511 | if transferred_scalars.shape[1] > 1: |
||
| 512 | n_arrays = other_mesh.GetPointData().GetNumberOfArrays() |
||
| 513 | array_names = [other_mesh.GetPointData().GetArray(array_idx).GetName() for array_idx in range(n_arrays)] |
||
| 514 | for idx, array_name in enumerate(array_names): |
||
| 515 | vtk_transferred_scalars = numpy_to_vtk(transferred_scalars[:,idx]) |
||
| 516 | vtk_transferred_scalars.SetName(array_name) |
||
| 517 | self._mesh.GetPointData().AddArray(vtk_transferred_scalars) |
||
| 518 | return |
||
| 519 | |||
| 520 | vtk_transferred_scalars = numpy_to_vtk(transferred_scalars) |
||
| 521 | vtk_transferred_scalars.SetName(new_scalars_name) |
||
| 522 | self._mesh.GetPointData().AddArray(vtk_transferred_scalars) |
||
| 523 | |||
| 524 | @property |
||
| 525 | def seg_image(self): |
||
| 526 | """ |
||
| 527 | Return the `_seg_image` object |
||
| 528 | |||
| 529 | Returns |
||
| 530 | ------- |
||
| 531 | SimpleITK.Image |
||
| 532 | Segmentation image used to build the surface mesh |
||
| 533 | """ |
||
| 534 | return self._seg_image |
||
| 535 | |||
| 536 | @seg_image.setter |
||
| 537 | def seg_image(self, new_seg_image): |
||
| 538 | """ |
||
| 539 | Set the `_seg_image` of the class to be the inputted `new_seg_image`. |
||
| 540 | |||
| 541 | Parameters |
||
| 542 | ---------- |
||
| 543 | new_seg_image : SimpleITK.Image |
||
| 544 | New image to use for creating surface mesh. This can be used to provide image to |
||
| 545 | class if it was not provided during `__init__` |
||
| 546 | """ |
||
| 547 | self._seg_image = new_seg_image |
||
| 548 | |||
| 549 | @property |
||
| 550 | def mesh(self): |
||
| 551 | """ |
||
| 552 | Return the `_mesh` object |
||
| 553 | |||
| 554 | Returns |
||
| 555 | ------- |
||
| 556 | vtk.vtkPolyData |
||
| 557 | The main mesh of this class. |
||
| 558 | """ |
||
| 559 | return self._mesh |
||
| 560 | |||
| 561 | @mesh.setter |
||
| 562 | def mesh(self, new_mesh): |
||
| 563 | """ |
||
| 564 | Set the `_mesh` of the class to be the inputted `new_mesh` |
||
| 565 | |||
| 566 | Parameters |
||
| 567 | ---------- |
||
| 568 | new_mesh : vtk.vtkPolyData |
||
| 569 | New mesh for this class - or a method to provide a mesh to the class |
||
| 570 | after `__init__` has already been run. |
||
| 571 | """ |
||
| 572 | self._mesh = new_mesh |
||
| 573 | |||
| 574 | @property |
||
| 575 | def point_coords(self): |
||
| 576 | """ |
||
| 577 | Convenience function to return the vertices (point coordinates) for the surface mesh. |
||
| 578 | |||
| 579 | Returns |
||
| 580 | ------- |
||
| 581 | numpy.ndarray |
||
| 582 | Mx3 numpy array containing the x/y/z position of each vertex of the mesh. |
||
| 583 | """ |
||
| 584 | return get_mesh_physical_point_coords(self._mesh) |
||
| 585 | |||
| 586 | @point_coords.setter |
||
| 587 | def point_coords(self, new_point_coords): |
||
| 588 | """ |
||
| 589 | Convenience function to change/update the vertices/points locations |
||
| 590 | |||
| 591 | Parameters |
||
| 592 | ---------- |
||
| 593 | new_point_coords : numpy.ndarray |
||
| 594 | n_points X 3 numpy array to replace exisiting point coordinate locations |
||
| 595 | This can be used to easily/quickly update the x/y/z position of a set of points on a surface mesh. |
||
| 596 | The `new_point_coords` must include the same number of points as the mesh contains. |
||
| 597 | """ |
||
| 598 | orig_point_coords = get_mesh_physical_point_coords(self._mesh) |
||
| 599 | if new_point_coords.shape == orig_point_coords.shape: |
||
| 600 | self._mesh.GetPoints().SetData(numpy_to_vtk(new_point_coords)) |
||
| 601 | |||
| 602 | |||
| 603 | @property |
||
| 604 | def path_seg_image(self): |
||
| 605 | """ |
||
| 606 | Convenience function to get the `path_seg_image` |
||
| 607 | |||
| 608 | Returns |
||
| 609 | ------- |
||
| 610 | str |
||
| 611 | Path to the segmentation image |
||
| 612 | """ |
||
| 613 | return self._path_seg_image |
||
| 614 | |||
| 615 | @path_seg_image.setter |
||
| 616 | def path_seg_image(self, new_path_seg_image): |
||
| 617 | """ |
||
| 618 | Convenience function to set the `path_seg_image` |
||
| 619 | |||
| 620 | Parameters |
||
| 621 | ---------- |
||
| 622 | new_path_seg_image : str |
||
| 623 | String to where segmentation image that should be loaded is. |
||
| 624 | """ |
||
| 625 | self._path_seg_image = new_path_seg_image |
||
| 626 | |||
| 627 | @property |
||
| 628 | def label_idx(self): |
||
| 629 | """ |
||
| 630 | Convenience function to get `label_idx` |
||
| 631 | |||
| 632 | Returns |
||
| 633 | ------- |
||
| 634 | int |
||
| 635 | Integer indeicating the index/value of the tissues in `seg_image` associated with this mesh. |
||
| 636 | """ |
||
| 637 | return self._label_idx |
||
| 638 | |||
| 639 | @label_idx.setter |
||
| 640 | def label_idx(self, new_label_idx): |
||
| 641 | """ |
||
| 642 | Convenience function to set `label_idx` |
||
| 643 | |||
| 644 | Parameters |
||
| 645 | ---------- |
||
| 646 | new_label_idx : int |
||
| 647 | Integer indeicating the index/value of the tissues in `seg_image` associated with this mesh. |
||
| 648 | """ |
||
| 649 | self._label_idx = new_label_idx |
||
| 650 | |||
| 651 | @property |
||
| 652 | def min_n_pixels(self): |
||
| 653 | """ |
||
| 654 | Convenience function to get the minimum number of pixels for a segmentation region to be created as a mesh. |
||
| 655 | |||
| 656 | Returns |
||
| 657 | ------- |
||
| 658 | int |
||
| 659 | Minimum number of pixels needed to create a mesh. Less than this and it will be skipped / error raised. |
||
| 660 | """ |
||
| 661 | return self._min_n_pixels |
||
| 662 | |||
| 663 | @min_n_pixels.setter |
||
| 664 | def min_n_pixels(self, new_min_n_pixels): |
||
| 665 | """ |
||
| 666 | Convenience function to set the minimum number of pixels for a segmentation region to be created as a mesh. |
||
| 667 | |||
| 668 | Parameters |
||
| 669 | ---------- |
||
| 670 | new_min_n_pixels : int |
||
| 671 | Minimum number of pixels needed to create a mesh. Less than this and it will be skipped / error raised. |
||
| 672 | """ |
||
| 673 | self._min_n_pixels = new_min_n_pixels |
||
| 674 | |||
| 675 | @property |
||
| 676 | def list_applied_transforms(self): |
||
| 677 | """ |
||
| 678 | Convenience function to get the list of transformations that have been applied to this mesh. |
||
| 679 | |||
| 680 | Returns |
||
| 681 | ------- |
||
| 682 | list |
||
| 683 | List of vtk.vtkTransform objects that have been applied to the current mesh. |
||
| 684 | """ |
||
| 685 | return self._list_applied_transforms |
||
| 686 | |||
| 687 | |||
| 688 | class CartilageMesh(Mesh): |
||
| 689 | """ |
||
| 690 | Class to create, store, and process cartilage meshes |
||
| 691 | |||
| 692 | Parameters |
||
| 693 | ---------- |
||
| 694 | mesh : vtk.vtkPolyData, optional |
||
| 695 | vtkPolyData object that is basis of surface mesh, by default None |
||
| 696 | seg_image : SimpleITK.Image, optional |
||
| 697 | Segmentation image that can be used to create surface mesh - used |
||
| 698 | instead of mesh, by default None |
||
| 699 | path_seg_image : str, optional |
||
| 700 | Path to a medical image (.nrrd) to load and create mesh from, |
||
| 701 | by default None |
||
| 702 | label_idx : int, optional |
||
| 703 | Label of anatomy of interest, by default None |
||
| 704 | min_n_pixels : int, optional |
||
| 705 | All islands smaller than this size are dropped, by default 5000 |
||
| 706 | |||
| 707 | |||
| 708 | Attributes |
||
| 709 | ---------- |
||
| 710 | _mesh : vtk.vtkPolyData |
||
| 711 | Item passed from __init__, or created during life of class. |
||
| 712 | This is the main surface mesh of this class. |
||
| 713 | _seg_image : SimpleITK.Image |
||
| 714 | Segmentation image that can be used to create mesh. This is optional. |
||
| 715 | path_seg_image : str |
||
| 716 | Path to medical image (.nrrd) that can be loaded to create `_seg_image` |
||
| 717 | and then creat surface mesh `_mesh` |
||
| 718 | label_idx : int |
||
| 719 | Integer of anatomy to create surface mesh from `_seg_image` |
||
| 720 | min_n_pixels : int |
||
| 721 | Minimum number of pixels for an isolated island of a segmentation to be |
||
| 722 | retained |
||
| 723 | list_applied_transforms : list |
||
| 724 | A list of transformations applied to a surface mesh. |
||
| 725 | This list allows for undoing of most recent transform, or undoing |
||
| 726 | all of them by iterating over the list in reverse. |
||
| 727 | |||
| 728 | Methods |
||
| 729 | ---------- |
||
| 730 | |||
| 731 | """ |
||
| 732 | |||
| 733 | def __init__(self, |
||
| 734 | mesh=None, |
||
| 735 | seg_image=None, |
||
| 736 | path_seg_image=None, |
||
| 737 | label_idx=None, |
||
| 738 | min_n_pixels=1000 |
||
| 739 | ): |
||
| 740 | super().__init__(mesh=mesh, |
||
| 741 | seg_image=seg_image, |
||
| 742 | path_seg_image=path_seg_image, |
||
| 743 | label_idx=label_idx, |
||
| 744 | min_n_pixels=min_n_pixels) |
||
| 745 | |||
| 746 | |||
| 747 | class BoneMesh(Mesh): |
||
| 748 | """ |
||
| 749 | Class to create, store, and process bone meshes |
||
| 750 | |||
| 751 | Intention is that this class includes functions to process other data & assign it to the bone surface. |
||
| 752 | It might be possible that instead this class & a cartilage class or, this class and image data etc. are |
||
| 753 | provided to another function or class that does those analyses. |
||
| 754 | |||
| 755 | Parameters |
||
| 756 | ---------- |
||
| 757 | mesh : vtk.vtkPolyData, optional |
||
| 758 | vtkPolyData object that is basis of surface mesh, by default None |
||
| 759 | seg_image : SimpleITK.Image, optional |
||
| 760 | Segmentation image that can be used to create surface mesh - used |
||
| 761 | instead of mesh, by default None |
||
| 762 | path_seg_image : str, optional |
||
| 763 | Path to a medical image (.nrrd) to load and create mesh from, |
||
| 764 | by default None |
||
| 765 | label_idx : int, optional |
||
| 766 | Label of anatomy of interest, by default None |
||
| 767 | min_n_pixels : int, optional |
||
| 768 | All islands smaller than this size are dropped, by default 5000 |
||
| 769 | list_cartilage_meshes : list, optional |
||
| 770 | List object which contains 1+ `CartilageMesh` objects that wrap |
||
| 771 | a vtk.vtkPolyData surface mesh of cartilage, by default None |
||
| 772 | list_cartilage_labels : list, optional |
||
| 773 | List of `int` values that represent the different cartilage |
||
| 774 | regions of interest appropriate for a single bone, by default None |
||
| 775 | crop_percent : float, optional |
||
| 776 | Proportion value to crop long-axis of bone so it is proportional |
||
| 777 | to the width of the bone for standardization purposes, by default 1.0 |
||
| 778 | bone : str, optional |
||
| 779 | String indicating what bone is being analyzed so that cropping |
||
| 780 | can be applied appropriatey. {'femur', 'tibia'}, by default 'femur'. |
||
| 781 | Patella is not an option because we do not need to crop for the patella. |
||
| 782 | |||
| 783 | |||
| 784 | Attributes |
||
| 785 | ---------- |
||
| 786 | _mesh : vtk.vtkPolyData |
||
| 787 | Item passed from __init__, or created during life of class. |
||
| 788 | This is the main surface mesh of this class. |
||
| 789 | _seg_image : SimpleITK.Image |
||
| 790 | Segmentation image that can be used to create mesh. This is optional. |
||
| 791 | path_seg_image : str |
||
| 792 | Path to medical image (.nrrd) that can be loaded to create `_seg_image` |
||
| 793 | and then creat surface mesh `_mesh` |
||
| 794 | label_idx : int |
||
| 795 | Integer of anatomy to create surface mesh from `_seg_image` |
||
| 796 | min_n_pixels : int |
||
| 797 | Minimum number of pixels for an isolated island of a segmentation to be |
||
| 798 | retained |
||
| 799 | list_applied_transforms : list |
||
| 800 | A list of transformations applied to a surface mesh. |
||
| 801 | This list allows for undoing of most recent transform, or undoing |
||
| 802 | all of them by iterating over the list in reverse. |
||
| 803 | crop_percent : float |
||
| 804 | Percent of width to crop along long-axis of bone |
||
| 805 | bone : str |
||
| 806 | A string indicating what bone is being represented by this class. |
||
| 807 | list_cartilage_meshes : list |
||
| 808 | List of cartialge meshes assigned to this bone. |
||
| 809 | list_cartilage_labels : list |
||
| 810 | List of cartilage labels for the `_seg_image` that are associated |
||
| 811 | with this bone. |
||
| 812 | |||
| 813 | Methods |
||
| 814 | ---------- |
||
| 815 | |||
| 816 | """ |
||
| 817 | |||
| 818 | def __init__(self, |
||
| 819 | mesh=None, |
||
| 820 | seg_image=None, |
||
| 821 | path_seg_image=None, |
||
| 822 | label_idx=None, |
||
| 823 | min_n_pixels=5000, |
||
| 824 | list_cartilage_meshes=None, |
||
| 825 | list_cartilage_labels=None, |
||
| 826 | crop_percent=None, |
||
| 827 | bone='femur', |
||
| 828 | ): |
||
| 829 | """ |
||
| 830 | Class initialization |
||
| 831 | |||
| 832 | Parameters |
||
| 833 | ---------- |
||
| 834 | mesh : vtk.vtkPolyData, optional |
||
| 835 | vtkPolyData object that is basis of surface mesh, by default None |
||
| 836 | seg_image : SimpleITK.Image, optional |
||
| 837 | Segmentation image that can be used to create surface mesh - used |
||
| 838 | instead of mesh, by default None |
||
| 839 | path_seg_image : str, optional |
||
| 840 | Path to a medical image (.nrrd) to load and create mesh from, |
||
| 841 | by default None |
||
| 842 | label_idx : int, optional |
||
| 843 | Label of anatomy of interest, by default None |
||
| 844 | min_n_pixels : int, optional |
||
| 845 | All islands smaller than this size are dropped, by default 5000 |
||
| 846 | list_cartilage_meshes : list, optional |
||
| 847 | List object which contains 1+ `CartilageMesh` objects that wrap |
||
| 848 | a vtk.vtkPolyData surface mesh of cartilage, by default None |
||
| 849 | list_cartilage_labels : list, optional |
||
| 850 | List of `int` values that represent the different cartilage |
||
| 851 | regions of interest appropriate for a single bone, by default None |
||
| 852 | crop_percent : float, optional |
||
| 853 | Proportion value to crop long-axis of bone so it is proportional |
||
| 854 | to the width of the bone for standardization purposes, by default 1.0 |
||
| 855 | bone : str, optional |
||
| 856 | String indicating what bone is being analyzed so that cropping |
||
| 857 | can be applied appropriatey. {'femur', 'tibia'}, by default 'femur'. |
||
| 858 | Patella is not an option because we do not need to crop for the patella. |
||
| 859 | """ |
||
| 860 | self._crop_percent = crop_percent |
||
| 861 | self._bone = bone |
||
| 862 | self._list_cartilage_meshes = list_cartilage_meshes |
||
| 863 | self._list_cartilage_labels = list_cartilage_labels |
||
| 864 | |||
| 865 | super().__init__(mesh=mesh, |
||
| 866 | seg_image=seg_image, |
||
| 867 | path_seg_image=path_seg_image, |
||
| 868 | label_idx=label_idx, |
||
| 869 | min_n_pixels=min_n_pixels) |
||
| 870 | |||
| 871 | |||
| 872 | def create_mesh(self, |
||
| 873 | smooth_image=True, |
||
| 874 | smooth_image_var=0.3125 / 2, |
||
| 875 | marching_cubes_threshold=0.5, |
||
| 876 | label_idx=None, |
||
| 877 | min_n_pixels=None, |
||
| 878 | crop_percent=None |
||
| 879 | ): |
||
| 880 | """ |
||
| 881 | This is an extension of `Mesh.create_mesh` that enables cropping of bones. |
||
| 882 | Bones might need to be cropped (this isnt necessary for cartilage) |
||
| 883 | So, adding this functionality to the processing steps before the bone mesh is created. |
||
| 884 | |||
| 885 | All functionality, except for that relevant to `crop_percent` is the same as: |
||
| 886 | `Mesh.create_mesh`. |
||
| 887 | |||
| 888 | Create a surface mesh from the classes `_seg_image`. If `_seg_image` |
||
| 889 | does not exist, then read it in using `read_seg_image`. |
||
| 890 | |||
| 891 | Parameters |
||
| 892 | ---------- |
||
| 893 | smooth_image : bool, optional |
||
| 894 | Should the `_seg_image` be gaussian filtered, by default True |
||
| 895 | smooth_image_var : float, optional |
||
| 896 | Variance of gaussian filter to apply to `_seg_image`, by default 0.3125/2 |
||
| 897 | marching_cubes_threshold : float, optional |
||
| 898 | Threshold contour level to create surface mesh on, by default 0.5 |
||
| 899 | label_idx : int, optional |
||
| 900 | Label value / index to create mesh from, by default None |
||
| 901 | min_n_pixels : int, optional |
||
| 902 | Minimum number of continuous pixels to include segmentation island |
||
| 903 | in the surface mesh creation, by default None |
||
| 904 | crop_percent : [type], optional |
||
| 905 | [description], by default None |
||
| 906 | |||
| 907 | Raises |
||
| 908 | ------ |
||
| 909 | Exception |
||
| 910 | If cropping & bone is not femur or tibia, then raise an error. |
||
| 911 | Exception |
||
| 912 | If the total number of pixels segmentated (`n_pixels_labelled`) is |
||
| 913 | < `min_n_pixels` then there is no object in the image. |
||
| 914 | Exception |
||
| 915 | If no `_seg_image` and no `label_idx` then we don't know what tissue to create the |
||
| 916 | surface mesh from. |
||
| 917 | Exception |
||
| 918 | If no `_seg_image` or `path_seg_image` then we have no image to create mesh from. |
||
| 919 | """ |
||
| 920 | |||
| 921 | if self._seg_image is None: |
||
| 922 | self.read_seg_image() |
||
| 923 | |||
| 924 | # Bones might need to be cropped (this isnt necessary for cartilage) |
||
| 925 | # So, adding this functionality to the processing steps before the bone mesh is created |
||
| 926 | if crop_percent is not None: |
||
| 927 | self._crop_percent = crop_percent |
||
| 928 | if (self._crop_percent is not None) and (('femur' in self._bone) or ('tibia' in self._bone)): |
||
| 929 | if 'femur' in self._bone: |
||
| 930 | bone_crop_distal = True |
||
| 931 | elif 'tibia' in self._bone: |
||
| 932 | bone_crop_distal = False |
||
| 933 | else: |
||
| 934 | raise Exception('var bone should be "femur" or "tiba" got: {} instead'.format(self._bone)) |
||
| 935 | |||
| 936 | self._seg_image = crop_bone_based_on_width(self._seg_image, |
||
| 937 | self._label_idx, |
||
| 938 | percent_width_to_crop_height=self._crop_percent, |
||
| 939 | bone_crop_distal=bone_crop_distal) |
||
| 940 | elif self._crop_percent is not None: |
||
| 941 | warnings.warn(f'Trying to crop bone, but {self._bone} specified and only bones `femur`', |
||
| 942 | 'or `tibia` currently supported for cropping. If using another bone, consider', |
||
| 943 | 'making a pull request. If cropping not desired, set `crop_percent=None`.' |
||
| 944 | ) |
||
| 945 | super().create_mesh(smooth_image=smooth_image, smooth_image_var=smooth_image_var, marching_cubes_threshold=marching_cubes_threshold, label_idx=label_idx, min_n_pixels=min_n_pixels) |
||
| 946 | |||
| 947 | def create_cartilage_meshes(self, |
||
| 948 | image_smooth_var_cart=0.3125 / 2, |
||
| 949 | marching_cubes_threshold=0.5): |
||
| 950 | """ |
||
| 951 | Helper function to create the list of cartilage meshes from the list of cartilage |
||
| 952 | labels. |
||
| 953 | |||
| 954 | Parameters |
||
| 955 | ---------- |
||
| 956 | image_smooth_var_cart : float |
||
| 957 | Variance to smooth cartilage segmentations before finding surface using continuous |
||
| 958 | marching cubes. |
||
| 959 | marching_cubes_threshold : float |
||
| 960 | Threshold value to create cartilage surface at from segmentation images. |
||
| 961 | |||
| 962 | Notes |
||
| 963 | ----- |
||
| 964 | ?? Should this function just be everything inside the for loop and then that |
||
| 965 | function gets called somewhere else? |
||
| 966 | """ |
||
| 967 | |||
| 968 | self._list_cartilage_meshes = [] |
||
| 969 | for cart_label_idx in self._list_cartilage_labels: |
||
| 970 | seg_array_view = sitk.GetArrayViewFromImage(self._seg_image) |
||
| 971 | n_pixels_with_cart = np.sum(seg_array_view == cart_label_idx) |
||
| 972 | if n_pixels_with_cart == 0: |
||
| 973 | warnings.warn( |
||
| 974 | f"Not analyzing cartilage for label {cart_label_idx} because it doesnt have any pixels!", |
||
| 975 | UserWarning |
||
| 976 | ) |
||
| 977 | else: |
||
| 978 | cart_mesh = CartilageMesh(seg_image=self._seg_image, |
||
| 979 | label_idx=cart_label_idx) |
||
| 980 | cart_mesh.create_mesh(smooth_image_var=image_smooth_var_cart, |
||
| 981 | marching_cubes_threshold=marching_cubes_threshold) |
||
| 982 | self._list_cartilage_meshes.append(cart_mesh) |
||
| 983 | |||
| 984 | |||
| 985 | def calc_cartilage_thickness(self, |
||
| 986 | list_cartilage_labels=None, |
||
| 987 | list_cartilage_meshes=None, |
||
| 988 | image_smooth_var_cart=0.3125 / 2, |
||
| 989 | marching_cubes_threshold=0.5, |
||
| 990 | ray_cast_length=10.0, |
||
| 991 | percent_ray_length_opposite_direction=0.25 |
||
| 992 | ): |
||
| 993 | """ |
||
| 994 | Using bone mesh (`_mesh`) and the list of cartilage meshes (`list_cartilage_meshes`) |
||
| 995 | calcualte the cartilage thickness for each node on the bone surface. |
||
| 996 | |||
| 997 | Parameters |
||
| 998 | ---------- |
||
| 999 | list_cartilage_labels : list, optional |
||
| 1000 | Cartilag labels to be used to create cartilage meshes (if they dont |
||
| 1001 | exist), by default None |
||
| 1002 | list_cartilage_meshes : list, optional |
||
| 1003 | Cartilage meshes to be used for calculating cart thickness, by default None |
||
| 1004 | image_smooth_var_cart : float, optional |
||
| 1005 | Variance of gaussian filter to be applied to binary cartilage masks, |
||
| 1006 | by default 0.3125/2 |
||
| 1007 | marching_cubes_threshold : float, optional |
||
| 1008 | Threshold to create bone surface at, by default 0.5 |
||
| 1009 | ray_cast_length : float, optional |
||
| 1010 | Length (mm) of ray to cast from bone surface when trying to find cartilage (inner & |
||
| 1011 | outter shell), by default 10.0 |
||
| 1012 | percent_ray_length_opposite_direction : float, optional |
||
| 1013 | How far to project ray inside of the bone. This is done just in case the cartilage |
||
| 1014 | surface ends up slightly inside of (or coincident with) the bone surface, by default 0.25 |
||
| 1015 | |||
| 1016 | Raises |
||
| 1017 | ------ |
||
| 1018 | Exception |
||
| 1019 | No cartilage available (either `list_cartilage_meshes` or `list_cartilage_labels`) |
||
| 1020 | """ |
||
| 1021 | # If new cartilage infor/labels are provided, then replace existing with these ones. |
||
| 1022 | if list_cartilage_meshes is not None: self._list_cartilage_meshes = list_cartilage_meshes |
||
| 1023 | if list_cartilage_labels is not None: self._list_cartilage_labels = list_cartilage_labels |
||
| 1024 | |||
| 1025 | # If no cartilage stuff provided, then cant do this function - raise exception. |
||
| 1026 | if (self._list_cartilage_meshes is None) & (self._list_cartilage_labels is None): |
||
| 1027 | raise Exception('No cartilage meshes or list of cartilage labels are provided! - These can be provided either to the class function `calc_cartilage_thickness` directly, or can be specified at the time of instantiating the `BoneMesh` class.') |
||
| 1028 | |||
| 1029 | # if cartilage meshes don't exist yet, then make them. |
||
| 1030 | if self._list_cartilage_meshes is None: |
||
| 1031 | self.create_cartilage_meshes(image_smooth_var_cart=image_smooth_var_cart, |
||
| 1032 | marching_cubes_threshold=marching_cubes_threshold) |
||
| 1033 | |||
| 1034 | # pre-allocate empty thicknesses so that as labels are iterated over, they can all be appended to the same bone. |
||
| 1035 | thicknesses = np.zeros(self._mesh.GetNumberOfPoints()) |
||
| 1036 | |||
| 1037 | # iterate over meshes and add their thicknesses to the thicknesses list. |
||
| 1038 | for cart_mesh in self._list_cartilage_meshes: |
||
| 1039 | node_data = get_cartilage_properties_at_points(self._mesh, |
||
| 1040 | cart_mesh._mesh, |
||
| 1041 | t2_vtk_image=None, |
||
| 1042 | # seg_vtk_image=vtk_seg if assign_seg_label_to_bone is True else None, |
||
| 1043 | seg_vtk_image=None, |
||
| 1044 | ray_cast_length=ray_cast_length, |
||
| 1045 | percent_ray_length_opposite_direction=percent_ray_length_opposite_direction |
||
| 1046 | ) |
||
| 1047 | thicknesses += node_data |
||
| 1048 | |||
| 1049 | # Assign the thickness scalars to the bone mesh surface. |
||
| 1050 | thickness_scalars = numpy_to_vtk(thicknesses) |
||
| 1051 | thickness_scalars.SetName('thickness (mm)') |
||
| 1052 | self._mesh.GetPointData().SetScalars(thickness_scalars) |
||
| 1053 | |||
| 1054 | def assign_cartilage_regions(self, |
||
| 1055 | image_smooth_var_cart=0.3125 / 2, |
||
| 1056 | marching_cubes_threshold=0.5, |
||
| 1057 | ray_cast_length=10.0, |
||
| 1058 | percent_ray_length_opposite_direction=0.25): |
||
| 1059 | """ |
||
| 1060 | Assign cartilage regions to the bone surface (e.g. medial/lateral tibial cartilage) |
||
| 1061 | - Can also be used for femur sub-regions (anterior, medial weight-bearing, etc.) |
||
| 1062 | |||
| 1063 | Parameters |
||
| 1064 | ---------- |
||
| 1065 | image_smooth_var_cart : float, optional |
||
| 1066 | Variance of gaussian filter to be applied to binary cartilage masks, |
||
| 1067 | by default 0.3125/2 |
||
| 1068 | marching_cubes_threshold : float, optional |
||
| 1069 | Threshold to create bone surface at, by default 0.5 |
||
| 1070 | ray_cast_length : float, optional |
||
| 1071 | Length (mm) of ray to cast from bone surface when trying to find cartilage (inner & |
||
| 1072 | outter shell), by default 10.0 |
||
| 1073 | percent_ray_length_opposite_direction : float, optional |
||
| 1074 | How far to project ray inside of the bone. This is done just in case the cartilage |
||
| 1075 | surface ends up slightly inside of (or coincident with) the bone surface, by default 0.25 |
||
| 1076 | """ |
||
| 1077 | tmp_filename = ''.join(random.choice(string.ascii_lowercase) for i in range(10)) + '.nrrd' |
||
| 1078 | path_save_tmp_file = os.path.join('/tmp', tmp_filename) |
||
| 1079 | # if self._bone == 'femur': |
||
| 1080 | # new_seg_image = qc.get_knee_segmentation_with_femur_subregions(seg_image, |
||
| 1081 | # fem_cart_label_idx=1) |
||
| 1082 | # sitk.WriteImage(new_seg_image, path_save_tmp_file) |
||
| 1083 | # else: |
||
| 1084 | sitk.WriteImage(self._seg_image, path_save_tmp_file) |
||
| 1085 | vtk_seg_reader = read_nrrd(path_save_tmp_file, |
||
| 1086 | set_origin_zero=True |
||
| 1087 | ) |
||
| 1088 | vtk_seg = vtk_seg_reader.GetOutput() |
||
| 1089 | |||
| 1090 | seg_transformer = SitkVtkTransformer(self._seg_image) |
||
| 1091 | |||
| 1092 | # Delete tmp files |
||
| 1093 | safely_delete_tmp_file('/tmp', |
||
| 1094 | tmp_filename) |
||
| 1095 | |||
| 1096 | self.apply_transform_to_mesh(transform=seg_transformer.get_inverse_transform()) |
||
| 1097 | labels = np.zeros(self._mesh.GetNumberOfPoints(), dtype=np.int) |
||
| 1098 | |||
| 1099 | # if cartilage meshes don't exist yet, then make them. |
||
| 1100 | if self._list_cartilage_meshes is None: |
||
| 1101 | self.create_cartilage_meshes(image_smooth_var_cart=image_smooth_var_cart, |
||
| 1102 | marching_cubes_threshold=marching_cubes_threshold) |
||
| 1103 | |||
| 1104 | # iterate over meshes and add their label (region) |
||
| 1105 | for cart_mesh in self._list_cartilage_meshes: |
||
| 1106 | cart_mesh.apply_transform_to_mesh(transform=seg_transformer.get_inverse_transform()) |
||
| 1107 | node_data = get_cartilage_properties_at_points(self._mesh, |
||
| 1108 | cart_mesh._mesh, |
||
| 1109 | t2_vtk_image=None, |
||
| 1110 | seg_vtk_image=vtk_seg, |
||
| 1111 | ray_cast_length=ray_cast_length, |
||
| 1112 | percent_ray_length_opposite_direction=percent_ray_length_opposite_direction |
||
| 1113 | ) |
||
| 1114 | labels += node_data[1] |
||
| 1115 | cart_mesh.reverse_all_transforms() |
||
| 1116 | |||
| 1117 | # Assign the label (region) scalars to the bone mesh surface. |
||
| 1118 | label_scalars = numpy_to_vtk(labels) |
||
| 1119 | label_scalars.SetName('labels') |
||
| 1120 | self._mesh.GetPointData().AddArray(label_scalars) |
||
| 1121 | |||
| 1122 | self.reverse_all_transforms() |
||
| 1123 | |||
| 1124 | def calc_cartilage_t2(self, |
||
| 1125 | path_t2_nrrd, |
||
| 1126 | path_seg_to_t2_transform=None, |
||
| 1127 | ray_cast_length=10.0, |
||
| 1128 | percent_ray_length_opposite_direction=0.25): |
||
| 1129 | """ |
||
| 1130 | Apply cartilage T2 values to bone surface. |
||
| 1131 | |||
| 1132 | Parameters |
||
| 1133 | ---------- |
||
| 1134 | path_t2_nrrd : str |
||
| 1135 | Path to nrrd image of T2 map to load / use. |
||
| 1136 | path_seg_to_t2_transform : str, optional |
||
| 1137 | Path to a transform file to be used for aligning T2 map with segmentations, |
||
| 1138 | by default None |
||
| 1139 | ray_cast_length : float, optional |
||
| 1140 | Length (mm) of ray to cast from bone surface when trying to find cartilage (inner & |
||
| 1141 | outter shell), by default 10.0 |
||
| 1142 | percent_ray_length_opposite_direction : float, optional |
||
| 1143 | How far to project ray inside of the bone. This is done just in case the cartilage |
||
| 1144 | surface ends up slightly inside of (or coincident with) the bone surface, by default 0.25 |
||
| 1145 | """ |
||
| 1146 | print('Not yet implemented') |
||
| 1147 | # if self._list_cartilage_meshes is None: |
||
| 1148 | # raise('Should calculate cartialge thickness before getting T2') |
||
| 1149 | # # ALTERNATIVELY - COULD ALLOW PASSING OF CARTILAGE REGIONS IN HERE |
||
| 1150 | # # THOUGH, DOES THAT JUST COMPLICATE THINGS? |
||
| 1151 | |||
| 1152 | # if path_seg_transform is not None: |
||
| 1153 | # # this is in case there is a transformation needed to align the segmentation with the |
||
| 1154 | # # underlying T2 image |
||
| 1155 | # seg_transform = sitk.ReadTransform(path_seg_transform) |
||
| 1156 | # seg_image = apply_transform_retain_array(self._seg_image, |
||
| 1157 | # seg_transform, |
||
| 1158 | # interpolator=sitk.sitkNearestNeighbor) |
||
| 1159 | |||
| 1160 | |||
| 1161 | # versor = get_versor_from_transform(seg_transform) |
||
| 1162 | # center_transform, rotate_transform, translate_transform = break_versor_into_center_rotate_translate_transforms(versor) |
||
| 1163 | # # first apply negative of center of rotation to mesh |
||
| 1164 | # self._mesh.apply_transform_to_mesh(transform=center_transform.GetInverse()) |
||
| 1165 | # # now apply the transform (rotation then translation) |
||
| 1166 | # self._mesh.apply_transform_to_mesh(transform=rotate_transform.GetInverse()) |
||
| 1167 | # self._mesh.apply_transform_to_mesh(transform=translate_transform.GetInverse()) |
||
| 1168 | # #then undo the center of rotation |
||
| 1169 | # self._mesh.apply_transform_to_mesh(transform=center_transform) |
||
| 1170 | |||
| 1171 | # # Read t2 map (vtk format) |
||
| 1172 | # vtk_t2map_reader = read_nrrd(path_t2_nrrd, |
||
| 1173 | # set_origin_zero=True) |
||
| 1174 | # vtk_t2map = vtk_t2map_reader.GetOutput() |
||
| 1175 | # sitk_t2map = sitk.ReadImage(path_t2_nrrd) |
||
| 1176 | # t2_transformer = SitkVtkTransformer(sitk_t2map) |
||
| 1177 | |||
| 1178 | # self._mesh.apply_transform_to_mesh(transform=t2_transformer.get_inverse_transform()) |
||
| 1179 | |||
| 1180 | # t2 = np.zeros(self._mesh.GetNumberOfPoints()) |
||
| 1181 | # # iterate over meshes and add their t2 to the t2 list. |
||
| 1182 | # for cart_mesh in self._list_cartilage_meshes: |
||
| 1183 | # if path_seg_to_t2_transform is not None: |
||
| 1184 | # # first apply negative of center of rotation to mesh |
||
| 1185 | # cart_mesh.apply_transform_to_mesh(transform=center_transform.GetInverse()) |
||
| 1186 | # # now apply the transform (rotation then translation) |
||
| 1187 | # cart_mesh.apply_transform_to_mesh(transform=rotate_transform.GetInverse()) |
||
| 1188 | # cart_mesh.apply_transform_to_mesh(transform=translate_transform.GetInverse()) |
||
| 1189 | # #then undo the center of rotation |
||
| 1190 | # cart_mesh.apply_transform_to_mesh(transform=center_transform) |
||
| 1191 | |||
| 1192 | # cart_mesh.apply_transform_to_mesh(transform=t2_transformer.get_inverse_transform()) |
||
| 1193 | # _, t2_data = get_cartilage_properties_at_points(self._mesh, |
||
| 1194 | # cart_mesh._mesh, |
||
| 1195 | # t2_vtk_image=vtk_t2map, |
||
| 1196 | # ray_cast_length=ray_cast_length, |
||
| 1197 | # percent_ray_length_opposite_direction=percent_ray_length_opposite_direction |
||
| 1198 | # ) |
||
| 1199 | # t2 += t2_data |
||
| 1200 | # cart_mesh.reverse_all_transforms() |
||
| 1201 | print('NOT DONE!!!') |
||
| 1202 | |||
| 1203 | |||
| 1204 | |||
| 1205 | def smooth_surface_scalars(self, |
||
| 1206 | smooth_only_cartilage=True, |
||
| 1207 | scalar_sigma=1.6986436005760381, # This is a FWHM = 4 |
||
| 1208 | scalar_array_name='thickness (mm)', |
||
| 1209 | scalar_array_idx=None, |
||
| 1210 | ): |
||
| 1211 | |||
| 1212 | """ |
||
| 1213 | Function to smooth the scalars with name `scalar_array_name` on the bone surface. |
||
| 1214 | |||
| 1215 | Parameters |
||
| 1216 | ---------- |
||
| 1217 | smooth_only_cartilage : bool, optional |
||
| 1218 | Should we only smooth where there is cartialge & ignore everywhere else, by default True |
||
| 1219 | scalar_sigma : float, optional |
||
| 1220 | Smoothing sigma (standard deviation or sqrt(variance)) for gaussian filter, by default 1.6986436005760381 |
||
| 1221 | default is based on a Full Width Half Maximum (FWHM) of 4mm. |
||
| 1222 | scalar_array_name : str |
||
| 1223 | Name of scalar array to smooth, default 'thickness (mm)'. |
||
| 1224 | scalar_array_idx : int, optional |
||
| 1225 | Index of the scalar array to smooth (alternative to using `scalar_array_name`) , by default None |
||
| 1226 | """ |
||
| 1227 | if smooth_only_cartilage is True: |
||
| 1228 | loc_cartilage = np.where(vtk_to_numpy(self._mesh.GetPointData().GetArray('thickness (mm)')) > 0.01)[0] |
||
| 1229 | else: |
||
| 1230 | loc_cartilage = None |
||
| 1231 | self._mesh = gaussian_smooth_surface_scalars(self._mesh, |
||
| 1232 | sigma=scalar_sigma, |
||
| 1233 | idx_coords_to_smooth=loc_cartilage, |
||
| 1234 | array_name=scalar_array_name, |
||
| 1235 | array_idx=scalar_array_idx) |
||
| 1236 | |||
| 1237 | @property |
||
| 1238 | def list_cartilage_meshes(self): |
||
| 1239 | """ |
||
| 1240 | Convenience function to get the list of cartilage meshes |
||
| 1241 | |||
| 1242 | Returns |
||
| 1243 | ------- |
||
| 1244 | list |
||
| 1245 | A list of `CartilageMesh` objects associated with this bone |
||
| 1246 | """ |
||
| 1247 | return self._list_cartilage_meshes |
||
| 1248 | |||
| 1249 | @list_cartilage_meshes.setter |
||
| 1250 | def list_cartilage_meshes(self, new_list_cartilage_meshes): |
||
| 1251 | """ |
||
| 1252 | Convenience function to set the list of cartilage meshes |
||
| 1253 | |||
| 1254 | Parameters |
||
| 1255 | ---------- |
||
| 1256 | new_list_cartilage_meshes : list |
||
| 1257 | A list of `CartilageMesh` objects associated with this bone |
||
| 1258 | """ |
||
| 1259 | if type(new_list_cartilage_meshes) is list: |
||
| 1260 | for mesh in new_list_cartilage_meshes: |
||
| 1261 | if type(mesh) != pymskt.mesh.meshes.CartilageMesh: |
||
| 1262 | raise TypeError('Item in `list_cartilage_meshes` is not a `CartilageMesh`') |
||
| 1263 | elif type(new_list_cartilage_meshes) is pymskt.mesh.meshes.CartilageMesh: |
||
| 1264 | new_list_cartilage_meshes = [new_list_cartilage_meshes,] |
||
| 1265 | self._list_cartilage_meshes = new_list_cartilage_meshes |
||
| 1266 | |||
| 1267 | @property |
||
| 1268 | def list_cartilage_labels(self): |
||
| 1269 | """ |
||
| 1270 | Convenience function to get the list of labels for cartilage tissues associated |
||
| 1271 | with this bone. |
||
| 1272 | |||
| 1273 | Returns |
||
| 1274 | ------- |
||
| 1275 | list |
||
| 1276 | list of `int`s for the cartilage tissues associated with this bone. |
||
| 1277 | """ |
||
| 1278 | return self._list_cartilage_labels |
||
| 1279 | |||
| 1280 | @list_cartilage_labels.setter |
||
| 1281 | def list_cartilage_labels(self, new_list_cartilage_labels): |
||
| 1282 | """ |
||
| 1283 | Convenience function to set the list of labels for cartilage tissues associated |
||
| 1284 | with this bone |
||
| 1285 | |||
| 1286 | Parameters |
||
| 1287 | ---------- |
||
| 1288 | new_list_cartilage_labels : list |
||
| 1289 | list of `int`s for the cartilage tissues associated with this bone. |
||
| 1290 | """ |
||
| 1291 | if type(new_list_cartilage_labels) == list: |
||
| 1292 | for label in new_list_cartilage_labels: |
||
| 1293 | if type(label) != int: |
||
| 1294 | raise TypeError(f'Item in `list_cartilage_labels` is not a `int` - got {type(label)}') |
||
| 1295 | elif type(new_list_cartilage_labels) == int: |
||
| 1296 | new_list_cartilage_labels = [new_list_cartilage_labels,] |
||
| 1297 | self._list_cartilage_labels = new_list_cartilage_labels |
||
| 1298 | |||
| 1299 | @property |
||
| 1300 | def crop_percent(self): |
||
| 1301 | """ |
||
| 1302 | Convenience function to get the value that `crop_percent` is set to. |
||
| 1303 | |||
| 1304 | Returns |
||
| 1305 | ------- |
||
| 1306 | float |
||
| 1307 | Floating point > 0.0 indicating how much of the length of the bone should be included |
||
| 1308 | when cropping - expressed as a proportion of the width. |
||
| 1309 | """ |
||
| 1310 | return self._crop_percent |
||
| 1311 | |||
| 1312 | @crop_percent.setter |
||
| 1313 | def crop_percent(self, new_crop_percent): |
||
| 1314 | """ |
||
| 1315 | Convenience function to set the value that `crop_percent` is set to. |
||
| 1316 | |||
| 1317 | Parameters |
||
| 1318 | ---------- |
||
| 1319 | new_crop_percent : float |
||
| 1320 | Floating point > 0.0 indicating how much of the length of the bone should be included |
||
| 1321 | when cropping - expressed as a proportion of the width. |
||
| 1322 | """ |
||
| 1323 | if type(new_crop_percent) != float: |
||
| 1324 | raise TypeError(f'New `crop_percent` provided is type {type(new_crop_percent)} - expected `float`') |
||
| 1325 | self._crop_percent = new_crop_percent |
||
| 1326 | |||
| 1327 | @property |
||
| 1328 | def bone(self): |
||
| 1329 | """ |
||
| 1330 | Convenience function to get the name of the bone in this object. |
||
| 1331 | |||
| 1332 | Returns |
||
| 1333 | ------- |
||
| 1334 | str |
||
| 1335 | Name of the bone in this object - used to help identify how to crop the bone. |
||
| 1336 | """ |
||
| 1337 | return self._bone |
||
| 1338 | |||
| 1339 | @bone.setter |
||
| 1340 | def bone(self, new_bone): |
||
| 1341 | """ |
||
| 1342 | Convenience function to set the name of the bone in this object. |
||
| 1343 | |||
| 1344 | Parameters |
||
| 1345 | ---------- |
||
| 1346 | new_bone : str |
||
| 1347 | Name of the bone in this object - used to help identify how to crop the bone. |
||
| 1348 | """ |
||
| 1349 | if type(new_bone) != str: |
||
| 1350 | raise TypeError(f'New bone provided is type {type(new_bone)} - expected `str`') |
||
| 1351 | self._bone = new_bone |
||
| 1352 | |||
| 1353 | |||
| 1354 | |||
| 1355 | </code></pre> |
||
| 1356 | </details> |
||
| 1357 | </section> |
||
| 1358 | <section> |
||
| 1359 | </section> |
||
| 1360 | <section> |
||
| 1361 | </section> |
||
| 1362 | <section> |
||
| 1363 | </section> |
||
| 1364 | <section> |
||
| 1365 | <h2 class="section-title" id="header-classes">Classes</h2> |
||
| 1366 | <dl> |
||
| 1367 | <dt id="pymskt.mesh.meshes.BoneMesh"><code class="flex name class"> |
||
| 1368 | <span>class <span class="ident">BoneMesh</span></span> |
||
| 1369 | <span>(</span><span>mesh=None, seg_image=None, path_seg_image=None, label_idx=None, min_n_pixels=5000, list_cartilage_meshes=None, list_cartilage_labels=None, crop_percent=None, bone='femur')</span> |
||
| 1370 | </code></dt> |
||
| 1371 | <dd> |
||
| 1372 | <div class="desc"><p>Class to create, store, and process bone meshes</p> |
||
| 1373 | <p>Intention is that this class includes functions to process other data & assign it to the bone surface. |
||
| 1374 | It might be possible that instead this class & a cartilage class or, this class and image data etc. are |
||
| 1375 | provided to another function or class that does those analyses.</p> |
||
| 1376 | <h2 id="parameters">Parameters</h2> |
||
| 1377 | <dl> |
||
| 1378 | <dt><strong><code>mesh</code></strong> : <code>vtk.vtkPolyData</code>, optional</dt> |
||
| 1379 | <dd>vtkPolyData object that is basis of surface mesh, by default None</dd> |
||
| 1380 | <dt><strong><code>seg_image</code></strong> : <code>SimpleITK.Image</code>, optional</dt> |
||
| 1381 | <dd>Segmentation image that can be used to create surface mesh - used |
||
| 1382 | instead of mesh, by default None</dd> |
||
| 1383 | <dt><strong><code>path_seg_image</code></strong> : <code>str</code>, optional</dt> |
||
| 1384 | <dd>Path to a medical image (.nrrd) to load and create mesh from, |
||
| 1385 | by default None</dd> |
||
| 1386 | <dt><strong><code>label_idx</code></strong> : <code>int</code>, optional</dt> |
||
| 1387 | <dd>Label of anatomy of interest, by default None</dd> |
||
| 1388 | <dt><strong><code>min_n_pixels</code></strong> : <code>int</code>, optional</dt> |
||
| 1389 | <dd>All islands smaller than this size are dropped, by default 5000</dd> |
||
| 1390 | <dt><strong><code>list_cartilage_meshes</code></strong> : <code>list</code>, optional</dt> |
||
| 1391 | <dd>List object which contains 1+ <code><a title="pymskt.mesh.meshes.CartilageMesh" href="#pymskt.mesh.meshes.CartilageMesh">CartilageMesh</a></code> objects that wrap |
||
| 1392 | a vtk.vtkPolyData surface mesh of cartilage, by default None</dd> |
||
| 1393 | <dt><strong><code>list_cartilage_labels</code></strong> : <code>list</code>, optional</dt> |
||
| 1394 | <dd>List of <code>int</code> values that represent the different cartilage |
||
| 1395 | regions of interest appropriate for a single bone, by default None</dd> |
||
| 1396 | <dt><strong><code>crop_percent</code></strong> : <code>float</code>, optional</dt> |
||
| 1397 | <dd>Proportion value to crop long-axis of bone so it is proportional |
||
| 1398 | to the width of the bone for standardization purposes, by default 1.0</dd> |
||
| 1399 | <dt><strong><code>bone</code></strong> : <code>str</code>, optional</dt> |
||
| 1400 | <dd>String indicating what bone is being analyzed so that cropping |
||
| 1401 | can be applied appropriatey. {'femur', 'tibia'}, by default 'femur'. |
||
| 1402 | Patella is not an option because we do not need to crop for the patella.</dd> |
||
| 1403 | </dl> |
||
| 1404 | <h2 id="attributes">Attributes</h2> |
||
| 1405 | <dl> |
||
| 1406 | <dt><strong><code>_mesh</code></strong> : <code>vtk.vtkPolyData</code></dt> |
||
| 1407 | <dd>Item passed from <strong>init</strong>, or created during life of class. |
||
| 1408 | This is the main surface mesh of this class.</dd> |
||
| 1409 | <dt><strong><code>_seg_image</code></strong> : <code>SimpleITK.Image</code></dt> |
||
| 1410 | <dd>Segmentation image that can be used to create mesh. This is optional.</dd> |
||
| 1411 | <dt><strong><code>path_seg_image</code></strong> : <code>str</code></dt> |
||
| 1412 | <dd>Path to medical image (.nrrd) that can be loaded to create <code>_seg_image</code> |
||
| 1413 | and then creat surface mesh <code>_mesh</code></dd> |
||
| 1414 | <dt><strong><code>label_idx</code></strong> : <code>int</code></dt> |
||
| 1415 | <dd>Integer of anatomy to create surface mesh from <code>_seg_image</code></dd> |
||
| 1416 | <dt><strong><code>min_n_pixels</code></strong> : <code>int</code></dt> |
||
| 1417 | <dd>Minimum number of pixels for an isolated island of a segmentation to be |
||
| 1418 | retained</dd> |
||
| 1419 | <dt><strong><code>list_applied_transforms</code></strong> : <code>list</code></dt> |
||
| 1420 | <dd>A list of transformations applied to a surface mesh. |
||
| 1421 | This list allows for undoing of most recent transform, or undoing |
||
| 1422 | all of them by iterating over the list in reverse.</dd> |
||
| 1423 | <dt><strong><code>crop_percent</code></strong> : <code>float</code></dt> |
||
| 1424 | <dd>Percent of width to crop along long-axis of bone</dd> |
||
| 1425 | <dt><strong><code>bone</code></strong> : <code>str</code></dt> |
||
| 1426 | <dd>A string indicating what bone is being represented by this class.</dd> |
||
| 1427 | <dt><strong><code>list_cartilage_meshes</code></strong> : <code>list</code></dt> |
||
| 1428 | <dd>List of cartialge meshes assigned to this bone.</dd> |
||
| 1429 | <dt><strong><code>list_cartilage_labels</code></strong> : <code>list</code></dt> |
||
| 1430 | <dd>List of cartilage labels for the <code>_seg_image</code> that are associated |
||
| 1431 | with this bone.</dd> |
||
| 1432 | </dl> |
||
| 1433 | <h2 id="methods">Methods</h2> |
||
| 1434 | <p>Class initialization</p> |
||
| 1435 | <h2 id="parameters_1">Parameters</h2> |
||
| 1436 | <dl> |
||
| 1437 | <dt><strong><code>mesh</code></strong> : <code>vtk.vtkPolyData</code>, optional</dt> |
||
| 1438 | <dd>vtkPolyData object that is basis of surface mesh, by default None</dd> |
||
| 1439 | <dt><strong><code>seg_image</code></strong> : <code>SimpleITK.Image</code>, optional</dt> |
||
| 1440 | <dd>Segmentation image that can be used to create surface mesh - used |
||
| 1441 | instead of mesh, by default None</dd> |
||
| 1442 | <dt><strong><code>path_seg_image</code></strong> : <code>str</code>, optional</dt> |
||
| 1443 | <dd>Path to a medical image (.nrrd) to load and create mesh from, |
||
| 1444 | by default None</dd> |
||
| 1445 | <dt><strong><code>label_idx</code></strong> : <code>int</code>, optional</dt> |
||
| 1446 | <dd>Label of anatomy of interest, by default None</dd> |
||
| 1447 | <dt><strong><code>min_n_pixels</code></strong> : <code>int</code>, optional</dt> |
||
| 1448 | <dd>All islands smaller than this size are dropped, by default 5000</dd> |
||
| 1449 | <dt><strong><code>list_cartilage_meshes</code></strong> : <code>list</code>, optional</dt> |
||
| 1450 | <dd>List object which contains 1+ <code><a title="pymskt.mesh.meshes.CartilageMesh" href="#pymskt.mesh.meshes.CartilageMesh">CartilageMesh</a></code> objects that wrap |
||
| 1451 | a vtk.vtkPolyData surface mesh of cartilage, by default None</dd> |
||
| 1452 | <dt><strong><code>list_cartilage_labels</code></strong> : <code>list</code>, optional</dt> |
||
| 1453 | <dd>List of <code>int</code> values that represent the different cartilage |
||
| 1454 | regions of interest appropriate for a single bone, by default None</dd> |
||
| 1455 | <dt><strong><code>crop_percent</code></strong> : <code>float</code>, optional</dt> |
||
| 1456 | <dd>Proportion value to crop long-axis of bone so it is proportional |
||
| 1457 | to the width of the bone for standardization purposes, by default 1.0</dd> |
||
| 1458 | <dt><strong><code>bone</code></strong> : <code>str</code>, optional</dt> |
||
| 1459 | <dd>String indicating what bone is being analyzed so that cropping |
||
| 1460 | can be applied appropriatey. {'femur', 'tibia'}, by default 'femur'. |
||
| 1461 | Patella is not an option because we do not need to crop for the patella.</dd> |
||
| 1462 | </dl></div> |
||
| 1463 | <details class="source"> |
||
| 1464 | <summary> |
||
| 1465 | <span>Expand source code</span> |
||
| 1466 | </summary> |
||
| 1467 | <pre><code class="python">class BoneMesh(Mesh): |
||
| 1468 | """ |
||
| 1469 | Class to create, store, and process bone meshes |
||
| 1470 | |||
| 1471 | Intention is that this class includes functions to process other data & assign it to the bone surface. |
||
| 1472 | It might be possible that instead this class & a cartilage class or, this class and image data etc. are |
||
| 1473 | provided to another function or class that does those analyses. |
||
| 1474 | |||
| 1475 | Parameters |
||
| 1476 | ---------- |
||
| 1477 | mesh : vtk.vtkPolyData, optional |
||
| 1478 | vtkPolyData object that is basis of surface mesh, by default None |
||
| 1479 | seg_image : SimpleITK.Image, optional |
||
| 1480 | Segmentation image that can be used to create surface mesh - used |
||
| 1481 | instead of mesh, by default None |
||
| 1482 | path_seg_image : str, optional |
||
| 1483 | Path to a medical image (.nrrd) to load and create mesh from, |
||
| 1484 | by default None |
||
| 1485 | label_idx : int, optional |
||
| 1486 | Label of anatomy of interest, by default None |
||
| 1487 | min_n_pixels : int, optional |
||
| 1488 | All islands smaller than this size are dropped, by default 5000 |
||
| 1489 | list_cartilage_meshes : list, optional |
||
| 1490 | List object which contains 1+ `CartilageMesh` objects that wrap |
||
| 1491 | a vtk.vtkPolyData surface mesh of cartilage, by default None |
||
| 1492 | list_cartilage_labels : list, optional |
||
| 1493 | List of `int` values that represent the different cartilage |
||
| 1494 | regions of interest appropriate for a single bone, by default None |
||
| 1495 | crop_percent : float, optional |
||
| 1496 | Proportion value to crop long-axis of bone so it is proportional |
||
| 1497 | to the width of the bone for standardization purposes, by default 1.0 |
||
| 1498 | bone : str, optional |
||
| 1499 | String indicating what bone is being analyzed so that cropping |
||
| 1500 | can be applied appropriatey. {'femur', 'tibia'}, by default 'femur'. |
||
| 1501 | Patella is not an option because we do not need to crop for the patella. |
||
| 1502 | |||
| 1503 | |||
| 1504 | Attributes |
||
| 1505 | ---------- |
||
| 1506 | _mesh : vtk.vtkPolyData |
||
| 1507 | Item passed from __init__, or created during life of class. |
||
| 1508 | This is the main surface mesh of this class. |
||
| 1509 | _seg_image : SimpleITK.Image |
||
| 1510 | Segmentation image that can be used to create mesh. This is optional. |
||
| 1511 | path_seg_image : str |
||
| 1512 | Path to medical image (.nrrd) that can be loaded to create `_seg_image` |
||
| 1513 | and then creat surface mesh `_mesh` |
||
| 1514 | label_idx : int |
||
| 1515 | Integer of anatomy to create surface mesh from `_seg_image` |
||
| 1516 | min_n_pixels : int |
||
| 1517 | Minimum number of pixels for an isolated island of a segmentation to be |
||
| 1518 | retained |
||
| 1519 | list_applied_transforms : list |
||
| 1520 | A list of transformations applied to a surface mesh. |
||
| 1521 | This list allows for undoing of most recent transform, or undoing |
||
| 1522 | all of them by iterating over the list in reverse. |
||
| 1523 | crop_percent : float |
||
| 1524 | Percent of width to crop along long-axis of bone |
||
| 1525 | bone : str |
||
| 1526 | A string indicating what bone is being represented by this class. |
||
| 1527 | list_cartilage_meshes : list |
||
| 1528 | List of cartialge meshes assigned to this bone. |
||
| 1529 | list_cartilage_labels : list |
||
| 1530 | List of cartilage labels for the `_seg_image` that are associated |
||
| 1531 | with this bone. |
||
| 1532 | |||
| 1533 | Methods |
||
| 1534 | ---------- |
||
| 1535 | |||
| 1536 | """ |
||
| 1537 | |||
| 1538 | def __init__(self, |
||
| 1539 | mesh=None, |
||
| 1540 | seg_image=None, |
||
| 1541 | path_seg_image=None, |
||
| 1542 | label_idx=None, |
||
| 1543 | min_n_pixels=5000, |
||
| 1544 | list_cartilage_meshes=None, |
||
| 1545 | list_cartilage_labels=None, |
||
| 1546 | crop_percent=None, |
||
| 1547 | bone='femur', |
||
| 1548 | ): |
||
| 1549 | """ |
||
| 1550 | Class initialization |
||
| 1551 | |||
| 1552 | Parameters |
||
| 1553 | ---------- |
||
| 1554 | mesh : vtk.vtkPolyData, optional |
||
| 1555 | vtkPolyData object that is basis of surface mesh, by default None |
||
| 1556 | seg_image : SimpleITK.Image, optional |
||
| 1557 | Segmentation image that can be used to create surface mesh - used |
||
| 1558 | instead of mesh, by default None |
||
| 1559 | path_seg_image : str, optional |
||
| 1560 | Path to a medical image (.nrrd) to load and create mesh from, |
||
| 1561 | by default None |
||
| 1562 | label_idx : int, optional |
||
| 1563 | Label of anatomy of interest, by default None |
||
| 1564 | min_n_pixels : int, optional |
||
| 1565 | All islands smaller than this size are dropped, by default 5000 |
||
| 1566 | list_cartilage_meshes : list, optional |
||
| 1567 | List object which contains 1+ `CartilageMesh` objects that wrap |
||
| 1568 | a vtk.vtkPolyData surface mesh of cartilage, by default None |
||
| 1569 | list_cartilage_labels : list, optional |
||
| 1570 | List of `int` values that represent the different cartilage |
||
| 1571 | regions of interest appropriate for a single bone, by default None |
||
| 1572 | crop_percent : float, optional |
||
| 1573 | Proportion value to crop long-axis of bone so it is proportional |
||
| 1574 | to the width of the bone for standardization purposes, by default 1.0 |
||
| 1575 | bone : str, optional |
||
| 1576 | String indicating what bone is being analyzed so that cropping |
||
| 1577 | can be applied appropriatey. {'femur', 'tibia'}, by default 'femur'. |
||
| 1578 | Patella is not an option because we do not need to crop for the patella. |
||
| 1579 | """ |
||
| 1580 | self._crop_percent = crop_percent |
||
| 1581 | self._bone = bone |
||
| 1582 | self._list_cartilage_meshes = list_cartilage_meshes |
||
| 1583 | self._list_cartilage_labels = list_cartilage_labels |
||
| 1584 | |||
| 1585 | super().__init__(mesh=mesh, |
||
| 1586 | seg_image=seg_image, |
||
| 1587 | path_seg_image=path_seg_image, |
||
| 1588 | label_idx=label_idx, |
||
| 1589 | min_n_pixels=min_n_pixels) |
||
| 1590 | |||
| 1591 | |||
| 1592 | def create_mesh(self, |
||
| 1593 | smooth_image=True, |
||
| 1594 | smooth_image_var=0.3125 / 2, |
||
| 1595 | marching_cubes_threshold=0.5, |
||
| 1596 | label_idx=None, |
||
| 1597 | min_n_pixels=None, |
||
| 1598 | crop_percent=None |
||
| 1599 | ): |
||
| 1600 | """ |
||
| 1601 | This is an extension of `Mesh.create_mesh` that enables cropping of bones. |
||
| 1602 | Bones might need to be cropped (this isnt necessary for cartilage) |
||
| 1603 | So, adding this functionality to the processing steps before the bone mesh is created. |
||
| 1604 | |||
| 1605 | All functionality, except for that relevant to `crop_percent` is the same as: |
||
| 1606 | `Mesh.create_mesh`. |
||
| 1607 | |||
| 1608 | Create a surface mesh from the classes `_seg_image`. If `_seg_image` |
||
| 1609 | does not exist, then read it in using `read_seg_image`. |
||
| 1610 | |||
| 1611 | Parameters |
||
| 1612 | ---------- |
||
| 1613 | smooth_image : bool, optional |
||
| 1614 | Should the `_seg_image` be gaussian filtered, by default True |
||
| 1615 | smooth_image_var : float, optional |
||
| 1616 | Variance of gaussian filter to apply to `_seg_image`, by default 0.3125/2 |
||
| 1617 | marching_cubes_threshold : float, optional |
||
| 1618 | Threshold contour level to create surface mesh on, by default 0.5 |
||
| 1619 | label_idx : int, optional |
||
| 1620 | Label value / index to create mesh from, by default None |
||
| 1621 | min_n_pixels : int, optional |
||
| 1622 | Minimum number of continuous pixels to include segmentation island |
||
| 1623 | in the surface mesh creation, by default None |
||
| 1624 | crop_percent : [type], optional |
||
| 1625 | [description], by default None |
||
| 1626 | |||
| 1627 | Raises |
||
| 1628 | ------ |
||
| 1629 | Exception |
||
| 1630 | If cropping & bone is not femur or tibia, then raise an error. |
||
| 1631 | Exception |
||
| 1632 | If the total number of pixels segmentated (`n_pixels_labelled`) is |
||
| 1633 | < `min_n_pixels` then there is no object in the image. |
||
| 1634 | Exception |
||
| 1635 | If no `_seg_image` and no `label_idx` then we don't know what tissue to create the |
||
| 1636 | surface mesh from. |
||
| 1637 | Exception |
||
| 1638 | If no `_seg_image` or `path_seg_image` then we have no image to create mesh from. |
||
| 1639 | """ |
||
| 1640 | |||
| 1641 | if self._seg_image is None: |
||
| 1642 | self.read_seg_image() |
||
| 1643 | |||
| 1644 | # Bones might need to be cropped (this isnt necessary for cartilage) |
||
| 1645 | # So, adding this functionality to the processing steps before the bone mesh is created |
||
| 1646 | if crop_percent is not None: |
||
| 1647 | self._crop_percent = crop_percent |
||
| 1648 | if (self._crop_percent is not None) and (('femur' in self._bone) or ('tibia' in self._bone)): |
||
| 1649 | if 'femur' in self._bone: |
||
| 1650 | bone_crop_distal = True |
||
| 1651 | elif 'tibia' in self._bone: |
||
| 1652 | bone_crop_distal = False |
||
| 1653 | else: |
||
| 1654 | raise Exception('var bone should be "femur" or "tiba" got: {} instead'.format(self._bone)) |
||
| 1655 | |||
| 1656 | self._seg_image = crop_bone_based_on_width(self._seg_image, |
||
| 1657 | self._label_idx, |
||
| 1658 | percent_width_to_crop_height=self._crop_percent, |
||
| 1659 | bone_crop_distal=bone_crop_distal) |
||
| 1660 | elif self._crop_percent is not None: |
||
| 1661 | warnings.warn(f'Trying to crop bone, but {self._bone} specified and only bones `femur`', |
||
| 1662 | 'or `tibia` currently supported for cropping. If using another bone, consider', |
||
| 1663 | 'making a pull request. If cropping not desired, set `crop_percent=None`.' |
||
| 1664 | ) |
||
| 1665 | super().create_mesh(smooth_image=smooth_image, smooth_image_var=smooth_image_var, marching_cubes_threshold=marching_cubes_threshold, label_idx=label_idx, min_n_pixels=min_n_pixels) |
||
| 1666 | |||
| 1667 | def create_cartilage_meshes(self, |
||
| 1668 | image_smooth_var_cart=0.3125 / 2, |
||
| 1669 | marching_cubes_threshold=0.5): |
||
| 1670 | """ |
||
| 1671 | Helper function to create the list of cartilage meshes from the list of cartilage |
||
| 1672 | labels. |
||
| 1673 | |||
| 1674 | Parameters |
||
| 1675 | ---------- |
||
| 1676 | image_smooth_var_cart : float |
||
| 1677 | Variance to smooth cartilage segmentations before finding surface using continuous |
||
| 1678 | marching cubes. |
||
| 1679 | marching_cubes_threshold : float |
||
| 1680 | Threshold value to create cartilage surface at from segmentation images. |
||
| 1681 | |||
| 1682 | Notes |
||
| 1683 | ----- |
||
| 1684 | ?? Should this function just be everything inside the for loop and then that |
||
| 1685 | function gets called somewhere else? |
||
| 1686 | """ |
||
| 1687 | |||
| 1688 | self._list_cartilage_meshes = [] |
||
| 1689 | for cart_label_idx in self._list_cartilage_labels: |
||
| 1690 | seg_array_view = sitk.GetArrayViewFromImage(self._seg_image) |
||
| 1691 | n_pixels_with_cart = np.sum(seg_array_view == cart_label_idx) |
||
| 1692 | if n_pixels_with_cart == 0: |
||
| 1693 | warnings.warn( |
||
| 1694 | f"Not analyzing cartilage for label {cart_label_idx} because it doesnt have any pixels!", |
||
| 1695 | UserWarning |
||
| 1696 | ) |
||
| 1697 | else: |
||
| 1698 | cart_mesh = CartilageMesh(seg_image=self._seg_image, |
||
| 1699 | label_idx=cart_label_idx) |
||
| 1700 | cart_mesh.create_mesh(smooth_image_var=image_smooth_var_cart, |
||
| 1701 | marching_cubes_threshold=marching_cubes_threshold) |
||
| 1702 | self._list_cartilage_meshes.append(cart_mesh) |
||
| 1703 | |||
| 1704 | |||
| 1705 | def calc_cartilage_thickness(self, |
||
| 1706 | list_cartilage_labels=None, |
||
| 1707 | list_cartilage_meshes=None, |
||
| 1708 | image_smooth_var_cart=0.3125 / 2, |
||
| 1709 | marching_cubes_threshold=0.5, |
||
| 1710 | ray_cast_length=10.0, |
||
| 1711 | percent_ray_length_opposite_direction=0.25 |
||
| 1712 | ): |
||
| 1713 | """ |
||
| 1714 | Using bone mesh (`_mesh`) and the list of cartilage meshes (`list_cartilage_meshes`) |
||
| 1715 | calcualte the cartilage thickness for each node on the bone surface. |
||
| 1716 | |||
| 1717 | Parameters |
||
| 1718 | ---------- |
||
| 1719 | list_cartilage_labels : list, optional |
||
| 1720 | Cartilag labels to be used to create cartilage meshes (if they dont |
||
| 1721 | exist), by default None |
||
| 1722 | list_cartilage_meshes : list, optional |
||
| 1723 | Cartilage meshes to be used for calculating cart thickness, by default None |
||
| 1724 | image_smooth_var_cart : float, optional |
||
| 1725 | Variance of gaussian filter to be applied to binary cartilage masks, |
||
| 1726 | by default 0.3125/2 |
||
| 1727 | marching_cubes_threshold : float, optional |
||
| 1728 | Threshold to create bone surface at, by default 0.5 |
||
| 1729 | ray_cast_length : float, optional |
||
| 1730 | Length (mm) of ray to cast from bone surface when trying to find cartilage (inner & |
||
| 1731 | outter shell), by default 10.0 |
||
| 1732 | percent_ray_length_opposite_direction : float, optional |
||
| 1733 | How far to project ray inside of the bone. This is done just in case the cartilage |
||
| 1734 | surface ends up slightly inside of (or coincident with) the bone surface, by default 0.25 |
||
| 1735 | |||
| 1736 | Raises |
||
| 1737 | ------ |
||
| 1738 | Exception |
||
| 1739 | No cartilage available (either `list_cartilage_meshes` or `list_cartilage_labels`) |
||
| 1740 | """ |
||
| 1741 | # If new cartilage infor/labels are provided, then replace existing with these ones. |
||
| 1742 | if list_cartilage_meshes is not None: self._list_cartilage_meshes = list_cartilage_meshes |
||
| 1743 | if list_cartilage_labels is not None: self._list_cartilage_labels = list_cartilage_labels |
||
| 1744 | |||
| 1745 | # If no cartilage stuff provided, then cant do this function - raise exception. |
||
| 1746 | if (self._list_cartilage_meshes is None) & (self._list_cartilage_labels is None): |
||
| 1747 | raise Exception('No cartilage meshes or list of cartilage labels are provided! - These can be provided either to the class function `calc_cartilage_thickness` directly, or can be specified at the time of instantiating the `BoneMesh` class.') |
||
| 1748 | |||
| 1749 | # if cartilage meshes don't exist yet, then make them. |
||
| 1750 | if self._list_cartilage_meshes is None: |
||
| 1751 | self.create_cartilage_meshes(image_smooth_var_cart=image_smooth_var_cart, |
||
| 1752 | marching_cubes_threshold=marching_cubes_threshold) |
||
| 1753 | |||
| 1754 | # pre-allocate empty thicknesses so that as labels are iterated over, they can all be appended to the same bone. |
||
| 1755 | thicknesses = np.zeros(self._mesh.GetNumberOfPoints()) |
||
| 1756 | |||
| 1757 | # iterate over meshes and add their thicknesses to the thicknesses list. |
||
| 1758 | for cart_mesh in self._list_cartilage_meshes: |
||
| 1759 | node_data = get_cartilage_properties_at_points(self._mesh, |
||
| 1760 | cart_mesh._mesh, |
||
| 1761 | t2_vtk_image=None, |
||
| 1762 | # seg_vtk_image=vtk_seg if assign_seg_label_to_bone is True else None, |
||
| 1763 | seg_vtk_image=None, |
||
| 1764 | ray_cast_length=ray_cast_length, |
||
| 1765 | percent_ray_length_opposite_direction=percent_ray_length_opposite_direction |
||
| 1766 | ) |
||
| 1767 | thicknesses += node_data |
||
| 1768 | |||
| 1769 | # Assign the thickness scalars to the bone mesh surface. |
||
| 1770 | thickness_scalars = numpy_to_vtk(thicknesses) |
||
| 1771 | thickness_scalars.SetName('thickness (mm)') |
||
| 1772 | self._mesh.GetPointData().SetScalars(thickness_scalars) |
||
| 1773 | |||
| 1774 | def assign_cartilage_regions(self, |
||
| 1775 | image_smooth_var_cart=0.3125 / 2, |
||
| 1776 | marching_cubes_threshold=0.5, |
||
| 1777 | ray_cast_length=10.0, |
||
| 1778 | percent_ray_length_opposite_direction=0.25): |
||
| 1779 | """ |
||
| 1780 | Assign cartilage regions to the bone surface (e.g. medial/lateral tibial cartilage) |
||
| 1781 | - Can also be used for femur sub-regions (anterior, medial weight-bearing, etc.) |
||
| 1782 | |||
| 1783 | Parameters |
||
| 1784 | ---------- |
||
| 1785 | image_smooth_var_cart : float, optional |
||
| 1786 | Variance of gaussian filter to be applied to binary cartilage masks, |
||
| 1787 | by default 0.3125/2 |
||
| 1788 | marching_cubes_threshold : float, optional |
||
| 1789 | Threshold to create bone surface at, by default 0.5 |
||
| 1790 | ray_cast_length : float, optional |
||
| 1791 | Length (mm) of ray to cast from bone surface when trying to find cartilage (inner & |
||
| 1792 | outter shell), by default 10.0 |
||
| 1793 | percent_ray_length_opposite_direction : float, optional |
||
| 1794 | How far to project ray inside of the bone. This is done just in case the cartilage |
||
| 1795 | surface ends up slightly inside of (or coincident with) the bone surface, by default 0.25 |
||
| 1796 | """ |
||
| 1797 | tmp_filename = ''.join(random.choice(string.ascii_lowercase) for i in range(10)) + '.nrrd' |
||
| 1798 | path_save_tmp_file = os.path.join('/tmp', tmp_filename) |
||
| 1799 | # if self._bone == 'femur': |
||
| 1800 | # new_seg_image = qc.get_knee_segmentation_with_femur_subregions(seg_image, |
||
| 1801 | # fem_cart_label_idx=1) |
||
| 1802 | # sitk.WriteImage(new_seg_image, path_save_tmp_file) |
||
| 1803 | # else: |
||
| 1804 | sitk.WriteImage(self._seg_image, path_save_tmp_file) |
||
| 1805 | vtk_seg_reader = read_nrrd(path_save_tmp_file, |
||
| 1806 | set_origin_zero=True |
||
| 1807 | ) |
||
| 1808 | vtk_seg = vtk_seg_reader.GetOutput() |
||
| 1809 | |||
| 1810 | seg_transformer = SitkVtkTransformer(self._seg_image) |
||
| 1811 | |||
| 1812 | # Delete tmp files |
||
| 1813 | safely_delete_tmp_file('/tmp', |
||
| 1814 | tmp_filename) |
||
| 1815 | |||
| 1816 | self.apply_transform_to_mesh(transform=seg_transformer.get_inverse_transform()) |
||
| 1817 | labels = np.zeros(self._mesh.GetNumberOfPoints(), dtype=np.int) |
||
| 1818 | |||
| 1819 | # if cartilage meshes don't exist yet, then make them. |
||
| 1820 | if self._list_cartilage_meshes is None: |
||
| 1821 | self.create_cartilage_meshes(image_smooth_var_cart=image_smooth_var_cart, |
||
| 1822 | marching_cubes_threshold=marching_cubes_threshold) |
||
| 1823 | |||
| 1824 | # iterate over meshes and add their label (region) |
||
| 1825 | for cart_mesh in self._list_cartilage_meshes: |
||
| 1826 | cart_mesh.apply_transform_to_mesh(transform=seg_transformer.get_inverse_transform()) |
||
| 1827 | node_data = get_cartilage_properties_at_points(self._mesh, |
||
| 1828 | cart_mesh._mesh, |
||
| 1829 | t2_vtk_image=None, |
||
| 1830 | seg_vtk_image=vtk_seg, |
||
| 1831 | ray_cast_length=ray_cast_length, |
||
| 1832 | percent_ray_length_opposite_direction=percent_ray_length_opposite_direction |
||
| 1833 | ) |
||
| 1834 | labels += node_data[1] |
||
| 1835 | cart_mesh.reverse_all_transforms() |
||
| 1836 | |||
| 1837 | # Assign the label (region) scalars to the bone mesh surface. |
||
| 1838 | label_scalars = numpy_to_vtk(labels) |
||
| 1839 | label_scalars.SetName('labels') |
||
| 1840 | self._mesh.GetPointData().AddArray(label_scalars) |
||
| 1841 | |||
| 1842 | self.reverse_all_transforms() |
||
| 1843 | |||
| 1844 | def calc_cartilage_t2(self, |
||
| 1845 | path_t2_nrrd, |
||
| 1846 | path_seg_to_t2_transform=None, |
||
| 1847 | ray_cast_length=10.0, |
||
| 1848 | percent_ray_length_opposite_direction=0.25): |
||
| 1849 | """ |
||
| 1850 | Apply cartilage T2 values to bone surface. |
||
| 1851 | |||
| 1852 | Parameters |
||
| 1853 | ---------- |
||
| 1854 | path_t2_nrrd : str |
||
| 1855 | Path to nrrd image of T2 map to load / use. |
||
| 1856 | path_seg_to_t2_transform : str, optional |
||
| 1857 | Path to a transform file to be used for aligning T2 map with segmentations, |
||
| 1858 | by default None |
||
| 1859 | ray_cast_length : float, optional |
||
| 1860 | Length (mm) of ray to cast from bone surface when trying to find cartilage (inner & |
||
| 1861 | outter shell), by default 10.0 |
||
| 1862 | percent_ray_length_opposite_direction : float, optional |
||
| 1863 | How far to project ray inside of the bone. This is done just in case the cartilage |
||
| 1864 | surface ends up slightly inside of (or coincident with) the bone surface, by default 0.25 |
||
| 1865 | """ |
||
| 1866 | print('Not yet implemented') |
||
| 1867 | # if self._list_cartilage_meshes is None: |
||
| 1868 | # raise('Should calculate cartialge thickness before getting T2') |
||
| 1869 | # # ALTERNATIVELY - COULD ALLOW PASSING OF CARTILAGE REGIONS IN HERE |
||
| 1870 | # # THOUGH, DOES THAT JUST COMPLICATE THINGS? |
||
| 1871 | |||
| 1872 | # if path_seg_transform is not None: |
||
| 1873 | # # this is in case there is a transformation needed to align the segmentation with the |
||
| 1874 | # # underlying T2 image |
||
| 1875 | # seg_transform = sitk.ReadTransform(path_seg_transform) |
||
| 1876 | # seg_image = apply_transform_retain_array(self._seg_image, |
||
| 1877 | # seg_transform, |
||
| 1878 | # interpolator=sitk.sitkNearestNeighbor) |
||
| 1879 | |||
| 1880 | |||
| 1881 | # versor = get_versor_from_transform(seg_transform) |
||
| 1882 | # center_transform, rotate_transform, translate_transform = break_versor_into_center_rotate_translate_transforms(versor) |
||
| 1883 | # # first apply negative of center of rotation to mesh |
||
| 1884 | # self._mesh.apply_transform_to_mesh(transform=center_transform.GetInverse()) |
||
| 1885 | # # now apply the transform (rotation then translation) |
||
| 1886 | # self._mesh.apply_transform_to_mesh(transform=rotate_transform.GetInverse()) |
||
| 1887 | # self._mesh.apply_transform_to_mesh(transform=translate_transform.GetInverse()) |
||
| 1888 | # #then undo the center of rotation |
||
| 1889 | # self._mesh.apply_transform_to_mesh(transform=center_transform) |
||
| 1890 | |||
| 1891 | # # Read t2 map (vtk format) |
||
| 1892 | # vtk_t2map_reader = read_nrrd(path_t2_nrrd, |
||
| 1893 | # set_origin_zero=True) |
||
| 1894 | # vtk_t2map = vtk_t2map_reader.GetOutput() |
||
| 1895 | # sitk_t2map = sitk.ReadImage(path_t2_nrrd) |
||
| 1896 | # t2_transformer = SitkVtkTransformer(sitk_t2map) |
||
| 1897 | |||
| 1898 | # self._mesh.apply_transform_to_mesh(transform=t2_transformer.get_inverse_transform()) |
||
| 1899 | |||
| 1900 | # t2 = np.zeros(self._mesh.GetNumberOfPoints()) |
||
| 1901 | # # iterate over meshes and add their t2 to the t2 list. |
||
| 1902 | # for cart_mesh in self._list_cartilage_meshes: |
||
| 1903 | # if path_seg_to_t2_transform is not None: |
||
| 1904 | # # first apply negative of center of rotation to mesh |
||
| 1905 | # cart_mesh.apply_transform_to_mesh(transform=center_transform.GetInverse()) |
||
| 1906 | # # now apply the transform (rotation then translation) |
||
| 1907 | # cart_mesh.apply_transform_to_mesh(transform=rotate_transform.GetInverse()) |
||
| 1908 | # cart_mesh.apply_transform_to_mesh(transform=translate_transform.GetInverse()) |
||
| 1909 | # #then undo the center of rotation |
||
| 1910 | # cart_mesh.apply_transform_to_mesh(transform=center_transform) |
||
| 1911 | |||
| 1912 | # cart_mesh.apply_transform_to_mesh(transform=t2_transformer.get_inverse_transform()) |
||
| 1913 | # _, t2_data = get_cartilage_properties_at_points(self._mesh, |
||
| 1914 | # cart_mesh._mesh, |
||
| 1915 | # t2_vtk_image=vtk_t2map, |
||
| 1916 | # ray_cast_length=ray_cast_length, |
||
| 1917 | # percent_ray_length_opposite_direction=percent_ray_length_opposite_direction |
||
| 1918 | # ) |
||
| 1919 | # t2 += t2_data |
||
| 1920 | # cart_mesh.reverse_all_transforms() |
||
| 1921 | print('NOT DONE!!!') |
||
| 1922 | |||
| 1923 | |||
| 1924 | |||
| 1925 | def smooth_surface_scalars(self, |
||
| 1926 | smooth_only_cartilage=True, |
||
| 1927 | scalar_sigma=1.6986436005760381, # This is a FWHM = 4 |
||
| 1928 | scalar_array_name='thickness (mm)', |
||
| 1929 | scalar_array_idx=None, |
||
| 1930 | ): |
||
| 1931 | |||
| 1932 | """ |
||
| 1933 | Function to smooth the scalars with name `scalar_array_name` on the bone surface. |
||
| 1934 | |||
| 1935 | Parameters |
||
| 1936 | ---------- |
||
| 1937 | smooth_only_cartilage : bool, optional |
||
| 1938 | Should we only smooth where there is cartialge & ignore everywhere else, by default True |
||
| 1939 | scalar_sigma : float, optional |
||
| 1940 | Smoothing sigma (standard deviation or sqrt(variance)) for gaussian filter, by default 1.6986436005760381 |
||
| 1941 | default is based on a Full Width Half Maximum (FWHM) of 4mm. |
||
| 1942 | scalar_array_name : str |
||
| 1943 | Name of scalar array to smooth, default 'thickness (mm)'. |
||
| 1944 | scalar_array_idx : int, optional |
||
| 1945 | Index of the scalar array to smooth (alternative to using `scalar_array_name`) , by default None |
||
| 1946 | """ |
||
| 1947 | if smooth_only_cartilage is True: |
||
| 1948 | loc_cartilage = np.where(vtk_to_numpy(self._mesh.GetPointData().GetArray('thickness (mm)')) > 0.01)[0] |
||
| 1949 | else: |
||
| 1950 | loc_cartilage = None |
||
| 1951 | self._mesh = gaussian_smooth_surface_scalars(self._mesh, |
||
| 1952 | sigma=scalar_sigma, |
||
| 1953 | idx_coords_to_smooth=loc_cartilage, |
||
| 1954 | array_name=scalar_array_name, |
||
| 1955 | array_idx=scalar_array_idx) |
||
| 1956 | |||
| 1957 | @property |
||
| 1958 | def list_cartilage_meshes(self): |
||
| 1959 | """ |
||
| 1960 | Convenience function to get the list of cartilage meshes |
||
| 1961 | |||
| 1962 | Returns |
||
| 1963 | ------- |
||
| 1964 | list |
||
| 1965 | A list of `CartilageMesh` objects associated with this bone |
||
| 1966 | """ |
||
| 1967 | return self._list_cartilage_meshes |
||
| 1968 | |||
| 1969 | @list_cartilage_meshes.setter |
||
| 1970 | def list_cartilage_meshes(self, new_list_cartilage_meshes): |
||
| 1971 | """ |
||
| 1972 | Convenience function to set the list of cartilage meshes |
||
| 1973 | |||
| 1974 | Parameters |
||
| 1975 | ---------- |
||
| 1976 | new_list_cartilage_meshes : list |
||
| 1977 | A list of `CartilageMesh` objects associated with this bone |
||
| 1978 | """ |
||
| 1979 | if type(new_list_cartilage_meshes) is list: |
||
| 1980 | for mesh in new_list_cartilage_meshes: |
||
| 1981 | if type(mesh) != pymskt.mesh.meshes.CartilageMesh: |
||
| 1982 | raise TypeError('Item in `list_cartilage_meshes` is not a `CartilageMesh`') |
||
| 1983 | elif type(new_list_cartilage_meshes) is pymskt.mesh.meshes.CartilageMesh: |
||
| 1984 | new_list_cartilage_meshes = [new_list_cartilage_meshes,] |
||
| 1985 | self._list_cartilage_meshes = new_list_cartilage_meshes |
||
| 1986 | |||
| 1987 | @property |
||
| 1988 | def list_cartilage_labels(self): |
||
| 1989 | """ |
||
| 1990 | Convenience function to get the list of labels for cartilage tissues associated |
||
| 1991 | with this bone. |
||
| 1992 | |||
| 1993 | Returns |
||
| 1994 | ------- |
||
| 1995 | list |
||
| 1996 | list of `int`s for the cartilage tissues associated with this bone. |
||
| 1997 | """ |
||
| 1998 | return self._list_cartilage_labels |
||
| 1999 | |||
| 2000 | @list_cartilage_labels.setter |
||
| 2001 | def list_cartilage_labels(self, new_list_cartilage_labels): |
||
| 2002 | """ |
||
| 2003 | Convenience function to set the list of labels for cartilage tissues associated |
||
| 2004 | with this bone |
||
| 2005 | |||
| 2006 | Parameters |
||
| 2007 | ---------- |
||
| 2008 | new_list_cartilage_labels : list |
||
| 2009 | list of `int`s for the cartilage tissues associated with this bone. |
||
| 2010 | """ |
||
| 2011 | if type(new_list_cartilage_labels) == list: |
||
| 2012 | for label in new_list_cartilage_labels: |
||
| 2013 | if type(label) != int: |
||
| 2014 | raise TypeError(f'Item in `list_cartilage_labels` is not a `int` - got {type(label)}') |
||
| 2015 | elif type(new_list_cartilage_labels) == int: |
||
| 2016 | new_list_cartilage_labels = [new_list_cartilage_labels,] |
||
| 2017 | self._list_cartilage_labels = new_list_cartilage_labels |
||
| 2018 | |||
| 2019 | @property |
||
| 2020 | def crop_percent(self): |
||
| 2021 | """ |
||
| 2022 | Convenience function to get the value that `crop_percent` is set to. |
||
| 2023 | |||
| 2024 | Returns |
||
| 2025 | ------- |
||
| 2026 | float |
||
| 2027 | Floating point > 0.0 indicating how much of the length of the bone should be included |
||
| 2028 | when cropping - expressed as a proportion of the width. |
||
| 2029 | """ |
||
| 2030 | return self._crop_percent |
||
| 2031 | |||
| 2032 | @crop_percent.setter |
||
| 2033 | def crop_percent(self, new_crop_percent): |
||
| 2034 | """ |
||
| 2035 | Convenience function to set the value that `crop_percent` is set to. |
||
| 2036 | |||
| 2037 | Parameters |
||
| 2038 | ---------- |
||
| 2039 | new_crop_percent : float |
||
| 2040 | Floating point > 0.0 indicating how much of the length of the bone should be included |
||
| 2041 | when cropping - expressed as a proportion of the width. |
||
| 2042 | """ |
||
| 2043 | if type(new_crop_percent) != float: |
||
| 2044 | raise TypeError(f'New `crop_percent` provided is type {type(new_crop_percent)} - expected `float`') |
||
| 2045 | self._crop_percent = new_crop_percent |
||
| 2046 | |||
| 2047 | @property |
||
| 2048 | def bone(self): |
||
| 2049 | """ |
||
| 2050 | Convenience function to get the name of the bone in this object. |
||
| 2051 | |||
| 2052 | Returns |
||
| 2053 | ------- |
||
| 2054 | str |
||
| 2055 | Name of the bone in this object - used to help identify how to crop the bone. |
||
| 2056 | """ |
||
| 2057 | return self._bone |
||
| 2058 | |||
| 2059 | @bone.setter |
||
| 2060 | def bone(self, new_bone): |
||
| 2061 | """ |
||
| 2062 | Convenience function to set the name of the bone in this object. |
||
| 2063 | |||
| 2064 | Parameters |
||
| 2065 | ---------- |
||
| 2066 | new_bone : str |
||
| 2067 | Name of the bone in this object - used to help identify how to crop the bone. |
||
| 2068 | """ |
||
| 2069 | if type(new_bone) != str: |
||
| 2070 | raise TypeError(f'New bone provided is type {type(new_bone)} - expected `str`') |
||
| 2071 | self._bone = new_bone </code></pre> |
||
| 2072 | </details> |
||
| 2073 | <h3>Ancestors</h3> |
||
| 2074 | <ul class="hlist"> |
||
| 2075 | <li><a title="pymskt.mesh.meshes.Mesh" href="#pymskt.mesh.meshes.Mesh">Mesh</a></li> |
||
| 2076 | </ul> |
||
| 2077 | <h3>Instance variables</h3> |
||
| 2078 | <dl> |
||
| 2079 | <dt id="pymskt.mesh.meshes.BoneMesh.bone"><code class="name">var <span class="ident">bone</span></code></dt> |
||
| 2080 | <dd> |
||
| 2081 | <div class="desc"><p>Convenience function to get the name of the bone in this object. </p> |
||
| 2082 | <h2 id="returns">Returns</h2> |
||
| 2083 | <dl> |
||
| 2084 | <dt><code>str</code></dt> |
||
| 2085 | <dd>Name of the bone in this object - used to help identify how to crop the bone.</dd> |
||
| 2086 | </dl></div> |
||
| 2087 | <details class="source"> |
||
| 2088 | <summary> |
||
| 2089 | <span>Expand source code</span> |
||
| 2090 | </summary> |
||
| 2091 | <pre><code class="python">@property |
||
| 2092 | def bone(self): |
||
| 2093 | """ |
||
| 2094 | Convenience function to get the name of the bone in this object. |
||
| 2095 | |||
| 2096 | Returns |
||
| 2097 | ------- |
||
| 2098 | str |
||
| 2099 | Name of the bone in this object - used to help identify how to crop the bone. |
||
| 2100 | """ |
||
| 2101 | return self._bone</code></pre> |
||
| 2102 | </details> |
||
| 2103 | </dd> |
||
| 2104 | <dt id="pymskt.mesh.meshes.BoneMesh.crop_percent"><code class="name">var <span class="ident">crop_percent</span></code></dt> |
||
| 2105 | <dd> |
||
| 2106 | <div class="desc"><p>Convenience function to get the value that <code>crop_percent</code> is set to. </p> |
||
| 2107 | <h2 id="returns">Returns</h2> |
||
| 2108 | <dl> |
||
| 2109 | <dt><code>float</code></dt> |
||
| 2110 | <dd>Floating point > 0.0 indicating how much of the length of the bone should be included |
||
| 2111 | when cropping - expressed as a proportion of the width.</dd> |
||
| 2112 | </dl></div> |
||
| 2113 | <details class="source"> |
||
| 2114 | <summary> |
||
| 2115 | <span>Expand source code</span> |
||
| 2116 | </summary> |
||
| 2117 | <pre><code class="python">@property |
||
| 2118 | def crop_percent(self): |
||
| 2119 | """ |
||
| 2120 | Convenience function to get the value that `crop_percent` is set to. |
||
| 2121 | |||
| 2122 | Returns |
||
| 2123 | ------- |
||
| 2124 | float |
||
| 2125 | Floating point > 0.0 indicating how much of the length of the bone should be included |
||
| 2126 | when cropping - expressed as a proportion of the width. |
||
| 2127 | """ |
||
| 2128 | return self._crop_percent</code></pre> |
||
| 2129 | </details> |
||
| 2130 | </dd> |
||
| 2131 | <dt id="pymskt.mesh.meshes.BoneMesh.list_cartilage_labels"><code class="name">var <span class="ident">list_cartilage_labels</span></code></dt> |
||
| 2132 | <dd> |
||
| 2133 | <div class="desc"><p>Convenience function to get the list of labels for cartilage tissues associated |
||
| 2134 | with this bone. </p> |
||
| 2135 | <h2 id="returns">Returns</h2> |
||
| 2136 | <dl> |
||
| 2137 | <dt><code>list</code></dt> |
||
| 2138 | <dd>list of <code>int</code>s for the cartilage tissues associated with this bone.</dd> |
||
| 2139 | </dl></div> |
||
| 2140 | <details class="source"> |
||
| 2141 | <summary> |
||
| 2142 | <span>Expand source code</span> |
||
| 2143 | </summary> |
||
| 2144 | <pre><code class="python">@property |
||
| 2145 | def list_cartilage_labels(self): |
||
| 2146 | """ |
||
| 2147 | Convenience function to get the list of labels for cartilage tissues associated |
||
| 2148 | with this bone. |
||
| 2149 | |||
| 2150 | Returns |
||
| 2151 | ------- |
||
| 2152 | list |
||
| 2153 | list of `int`s for the cartilage tissues associated with this bone. |
||
| 2154 | """ |
||
| 2155 | return self._list_cartilage_labels</code></pre> |
||
| 2156 | </details> |
||
| 2157 | </dd> |
||
| 2158 | <dt id="pymskt.mesh.meshes.BoneMesh.list_cartilage_meshes"><code class="name">var <span class="ident">list_cartilage_meshes</span></code></dt> |
||
| 2159 | <dd> |
||
| 2160 | <div class="desc"><p>Convenience function to get the list of cartilage meshes</p> |
||
| 2161 | <h2 id="returns">Returns</h2> |
||
| 2162 | <dl> |
||
| 2163 | <dt><code>list</code></dt> |
||
| 2164 | <dd>A list of <code><a title="pymskt.mesh.meshes.CartilageMesh" href="#pymskt.mesh.meshes.CartilageMesh">CartilageMesh</a></code> objects associated with this bone</dd> |
||
| 2165 | </dl></div> |
||
| 2166 | <details class="source"> |
||
| 2167 | <summary> |
||
| 2168 | <span>Expand source code</span> |
||
| 2169 | </summary> |
||
| 2170 | <pre><code class="python">@property |
||
| 2171 | def list_cartilage_meshes(self): |
||
| 2172 | """ |
||
| 2173 | Convenience function to get the list of cartilage meshes |
||
| 2174 | |||
| 2175 | Returns |
||
| 2176 | ------- |
||
| 2177 | list |
||
| 2178 | A list of `CartilageMesh` objects associated with this bone |
||
| 2179 | """ |
||
| 2180 | return self._list_cartilage_meshes</code></pre> |
||
| 2181 | </details> |
||
| 2182 | </dd> |
||
| 2183 | </dl> |
||
| 2184 | <h3>Methods</h3> |
||
| 2185 | <dl> |
||
| 2186 | <dt id="pymskt.mesh.meshes.BoneMesh.assign_cartilage_regions"><code class="name flex"> |
||
| 2187 | <span>def <span class="ident">assign_cartilage_regions</span></span>(<span>self, image_smooth_var_cart=0.15625, marching_cubes_threshold=0.5, ray_cast_length=10.0, percent_ray_length_opposite_direction=0.25)</span> |
||
| 2188 | </code></dt> |
||
| 2189 | <dd> |
||
| 2190 | <div class="desc"><p>Assign cartilage regions to the bone surface (e.g. medial/lateral tibial cartilage) |
||
| 2191 | - Can also be used for femur sub-regions (anterior, medial weight-bearing, etc.)</p> |
||
| 2192 | <h2 id="parameters">Parameters</h2> |
||
| 2193 | <dl> |
||
| 2194 | <dt><strong><code>image_smooth_var_cart</code></strong> : <code>float</code>, optional</dt> |
||
| 2195 | <dd>Variance of gaussian filter to be applied to binary cartilage masks, |
||
| 2196 | by default 0.3125/2</dd> |
||
| 2197 | <dt><strong><code>marching_cubes_threshold</code></strong> : <code>float</code>, optional</dt> |
||
| 2198 | <dd>Threshold to create bone surface at, by default 0.5</dd> |
||
| 2199 | <dt><strong><code>ray_cast_length</code></strong> : <code>float</code>, optional</dt> |
||
| 2200 | <dd>Length (mm) of ray to cast from bone surface when trying to find cartilage (inner & |
||
| 2201 | outter shell), by default 10.0</dd> |
||
| 2202 | <dt><strong><code>percent_ray_length_opposite_direction</code></strong> : <code>float</code>, optional</dt> |
||
| 2203 | <dd>How far to project ray inside of the bone. This is done just in case the cartilage |
||
| 2204 | surface ends up slightly inside of (or coincident with) the bone surface, by default 0.25</dd> |
||
| 2205 | </dl></div> |
||
| 2206 | <details class="source"> |
||
| 2207 | <summary> |
||
| 2208 | <span>Expand source code</span> |
||
| 2209 | </summary> |
||
| 2210 | <pre><code class="python">def assign_cartilage_regions(self, |
||
| 2211 | image_smooth_var_cart=0.3125 / 2, |
||
| 2212 | marching_cubes_threshold=0.5, |
||
| 2213 | ray_cast_length=10.0, |
||
| 2214 | percent_ray_length_opposite_direction=0.25): |
||
| 2215 | """ |
||
| 2216 | Assign cartilage regions to the bone surface (e.g. medial/lateral tibial cartilage) |
||
| 2217 | - Can also be used for femur sub-regions (anterior, medial weight-bearing, etc.) |
||
| 2218 | |||
| 2219 | Parameters |
||
| 2220 | ---------- |
||
| 2221 | image_smooth_var_cart : float, optional |
||
| 2222 | Variance of gaussian filter to be applied to binary cartilage masks, |
||
| 2223 | by default 0.3125/2 |
||
| 2224 | marching_cubes_threshold : float, optional |
||
| 2225 | Threshold to create bone surface at, by default 0.5 |
||
| 2226 | ray_cast_length : float, optional |
||
| 2227 | Length (mm) of ray to cast from bone surface when trying to find cartilage (inner & |
||
| 2228 | outter shell), by default 10.0 |
||
| 2229 | percent_ray_length_opposite_direction : float, optional |
||
| 2230 | How far to project ray inside of the bone. This is done just in case the cartilage |
||
| 2231 | surface ends up slightly inside of (or coincident with) the bone surface, by default 0.25 |
||
| 2232 | """ |
||
| 2233 | tmp_filename = ''.join(random.choice(string.ascii_lowercase) for i in range(10)) + '.nrrd' |
||
| 2234 | path_save_tmp_file = os.path.join('/tmp', tmp_filename) |
||
| 2235 | # if self._bone == 'femur': |
||
| 2236 | # new_seg_image = qc.get_knee_segmentation_with_femur_subregions(seg_image, |
||
| 2237 | # fem_cart_label_idx=1) |
||
| 2238 | # sitk.WriteImage(new_seg_image, path_save_tmp_file) |
||
| 2239 | # else: |
||
| 2240 | sitk.WriteImage(self._seg_image, path_save_tmp_file) |
||
| 2241 | vtk_seg_reader = read_nrrd(path_save_tmp_file, |
||
| 2242 | set_origin_zero=True |
||
| 2243 | ) |
||
| 2244 | vtk_seg = vtk_seg_reader.GetOutput() |
||
| 2245 | |||
| 2246 | seg_transformer = SitkVtkTransformer(self._seg_image) |
||
| 2247 | |||
| 2248 | # Delete tmp files |
||
| 2249 | safely_delete_tmp_file('/tmp', |
||
| 2250 | tmp_filename) |
||
| 2251 | |||
| 2252 | self.apply_transform_to_mesh(transform=seg_transformer.get_inverse_transform()) |
||
| 2253 | labels = np.zeros(self._mesh.GetNumberOfPoints(), dtype=np.int) |
||
| 2254 | |||
| 2255 | # if cartilage meshes don't exist yet, then make them. |
||
| 2256 | if self._list_cartilage_meshes is None: |
||
| 2257 | self.create_cartilage_meshes(image_smooth_var_cart=image_smooth_var_cart, |
||
| 2258 | marching_cubes_threshold=marching_cubes_threshold) |
||
| 2259 | |||
| 2260 | # iterate over meshes and add their label (region) |
||
| 2261 | for cart_mesh in self._list_cartilage_meshes: |
||
| 2262 | cart_mesh.apply_transform_to_mesh(transform=seg_transformer.get_inverse_transform()) |
||
| 2263 | node_data = get_cartilage_properties_at_points(self._mesh, |
||
| 2264 | cart_mesh._mesh, |
||
| 2265 | t2_vtk_image=None, |
||
| 2266 | seg_vtk_image=vtk_seg, |
||
| 2267 | ray_cast_length=ray_cast_length, |
||
| 2268 | percent_ray_length_opposite_direction=percent_ray_length_opposite_direction |
||
| 2269 | ) |
||
| 2270 | labels += node_data[1] |
||
| 2271 | cart_mesh.reverse_all_transforms() |
||
| 2272 | |||
| 2273 | # Assign the label (region) scalars to the bone mesh surface. |
||
| 2274 | label_scalars = numpy_to_vtk(labels) |
||
| 2275 | label_scalars.SetName('labels') |
||
| 2276 | self._mesh.GetPointData().AddArray(label_scalars) |
||
| 2277 | |||
| 2278 | self.reverse_all_transforms()</code></pre> |
||
| 2279 | </details> |
||
| 2280 | </dd> |
||
| 2281 | <dt id="pymskt.mesh.meshes.BoneMesh.calc_cartilage_t2"><code class="name flex"> |
||
| 2282 | <span>def <span class="ident">calc_cartilage_t2</span></span>(<span>self, path_t2_nrrd, path_seg_to_t2_transform=None, ray_cast_length=10.0, percent_ray_length_opposite_direction=0.25)</span> |
||
| 2283 | </code></dt> |
||
| 2284 | <dd> |
||
| 2285 | <div class="desc"><p>Apply cartilage T2 values to bone surface. </p> |
||
| 2286 | <h2 id="parameters">Parameters</h2> |
||
| 2287 | <dl> |
||
| 2288 | <dt><strong><code>path_t2_nrrd</code></strong> : <code>str</code></dt> |
||
| 2289 | <dd>Path to nrrd image of T2 map to load / use.</dd> |
||
| 2290 | <dt><strong><code>path_seg_to_t2_transform</code></strong> : <code>str</code>, optional</dt> |
||
| 2291 | <dd>Path to a transform file to be used for aligning T2 map with segmentations, |
||
| 2292 | by default None</dd> |
||
| 2293 | <dt><strong><code>ray_cast_length</code></strong> : <code>float</code>, optional</dt> |
||
| 2294 | <dd>Length (mm) of ray to cast from bone surface when trying to find cartilage (inner & |
||
| 2295 | outter shell), by default 10.0</dd> |
||
| 2296 | <dt><strong><code>percent_ray_length_opposite_direction</code></strong> : <code>float</code>, optional</dt> |
||
| 2297 | <dd>How far to project ray inside of the bone. This is done just in case the cartilage |
||
| 2298 | surface ends up slightly inside of (or coincident with) the bone surface, by default 0.25</dd> |
||
| 2299 | </dl></div> |
||
| 2300 | <details class="source"> |
||
| 2301 | <summary> |
||
| 2302 | <span>Expand source code</span> |
||
| 2303 | </summary> |
||
| 2304 | <pre><code class="python">def calc_cartilage_t2(self, |
||
| 2305 | path_t2_nrrd, |
||
| 2306 | path_seg_to_t2_transform=None, |
||
| 2307 | ray_cast_length=10.0, |
||
| 2308 | percent_ray_length_opposite_direction=0.25): |
||
| 2309 | """ |
||
| 2310 | Apply cartilage T2 values to bone surface. |
||
| 2311 | |||
| 2312 | Parameters |
||
| 2313 | ---------- |
||
| 2314 | path_t2_nrrd : str |
||
| 2315 | Path to nrrd image of T2 map to load / use. |
||
| 2316 | path_seg_to_t2_transform : str, optional |
||
| 2317 | Path to a transform file to be used for aligning T2 map with segmentations, |
||
| 2318 | by default None |
||
| 2319 | ray_cast_length : float, optional |
||
| 2320 | Length (mm) of ray to cast from bone surface when trying to find cartilage (inner & |
||
| 2321 | outter shell), by default 10.0 |
||
| 2322 | percent_ray_length_opposite_direction : float, optional |
||
| 2323 | How far to project ray inside of the bone. This is done just in case the cartilage |
||
| 2324 | surface ends up slightly inside of (or coincident with) the bone surface, by default 0.25 |
||
| 2325 | """ |
||
| 2326 | print('Not yet implemented') |
||
| 2327 | # if self._list_cartilage_meshes is None: |
||
| 2328 | # raise('Should calculate cartialge thickness before getting T2') |
||
| 2329 | # # ALTERNATIVELY - COULD ALLOW PASSING OF CARTILAGE REGIONS IN HERE |
||
| 2330 | # # THOUGH, DOES THAT JUST COMPLICATE THINGS? |
||
| 2331 | |||
| 2332 | # if path_seg_transform is not None: |
||
| 2333 | # # this is in case there is a transformation needed to align the segmentation with the |
||
| 2334 | # # underlying T2 image |
||
| 2335 | # seg_transform = sitk.ReadTransform(path_seg_transform) |
||
| 2336 | # seg_image = apply_transform_retain_array(self._seg_image, |
||
| 2337 | # seg_transform, |
||
| 2338 | # interpolator=sitk.sitkNearestNeighbor) |
||
| 2339 | |||
| 2340 | |||
| 2341 | # versor = get_versor_from_transform(seg_transform) |
||
| 2342 | # center_transform, rotate_transform, translate_transform = break_versor_into_center_rotate_translate_transforms(versor) |
||
| 2343 | # # first apply negative of center of rotation to mesh |
||
| 2344 | # self._mesh.apply_transform_to_mesh(transform=center_transform.GetInverse()) |
||
| 2345 | # # now apply the transform (rotation then translation) |
||
| 2346 | # self._mesh.apply_transform_to_mesh(transform=rotate_transform.GetInverse()) |
||
| 2347 | # self._mesh.apply_transform_to_mesh(transform=translate_transform.GetInverse()) |
||
| 2348 | # #then undo the center of rotation |
||
| 2349 | # self._mesh.apply_transform_to_mesh(transform=center_transform) |
||
| 2350 | |||
| 2351 | # # Read t2 map (vtk format) |
||
| 2352 | # vtk_t2map_reader = read_nrrd(path_t2_nrrd, |
||
| 2353 | # set_origin_zero=True) |
||
| 2354 | # vtk_t2map = vtk_t2map_reader.GetOutput() |
||
| 2355 | # sitk_t2map = sitk.ReadImage(path_t2_nrrd) |
||
| 2356 | # t2_transformer = SitkVtkTransformer(sitk_t2map) |
||
| 2357 | |||
| 2358 | # self._mesh.apply_transform_to_mesh(transform=t2_transformer.get_inverse_transform()) |
||
| 2359 | |||
| 2360 | # t2 = np.zeros(self._mesh.GetNumberOfPoints()) |
||
| 2361 | # # iterate over meshes and add their t2 to the t2 list. |
||
| 2362 | # for cart_mesh in self._list_cartilage_meshes: |
||
| 2363 | # if path_seg_to_t2_transform is not None: |
||
| 2364 | # # first apply negative of center of rotation to mesh |
||
| 2365 | # cart_mesh.apply_transform_to_mesh(transform=center_transform.GetInverse()) |
||
| 2366 | # # now apply the transform (rotation then translation) |
||
| 2367 | # cart_mesh.apply_transform_to_mesh(transform=rotate_transform.GetInverse()) |
||
| 2368 | # cart_mesh.apply_transform_to_mesh(transform=translate_transform.GetInverse()) |
||
| 2369 | # #then undo the center of rotation |
||
| 2370 | # cart_mesh.apply_transform_to_mesh(transform=center_transform) |
||
| 2371 | |||
| 2372 | # cart_mesh.apply_transform_to_mesh(transform=t2_transformer.get_inverse_transform()) |
||
| 2373 | # _, t2_data = get_cartilage_properties_at_points(self._mesh, |
||
| 2374 | # cart_mesh._mesh, |
||
| 2375 | # t2_vtk_image=vtk_t2map, |
||
| 2376 | # ray_cast_length=ray_cast_length, |
||
| 2377 | # percent_ray_length_opposite_direction=percent_ray_length_opposite_direction |
||
| 2378 | # ) |
||
| 2379 | # t2 += t2_data |
||
| 2380 | # cart_mesh.reverse_all_transforms() |
||
| 2381 | print('NOT DONE!!!')</code></pre> |
||
| 2382 | </details> |
||
| 2383 | </dd> |
||
| 2384 | <dt id="pymskt.mesh.meshes.BoneMesh.calc_cartilage_thickness"><code class="name flex"> |
||
| 2385 | <span>def <span class="ident">calc_cartilage_thickness</span></span>(<span>self, list_cartilage_labels=None, list_cartilage_meshes=None, image_smooth_var_cart=0.15625, marching_cubes_threshold=0.5, ray_cast_length=10.0, percent_ray_length_opposite_direction=0.25)</span> |
||
| 2386 | </code></dt> |
||
| 2387 | <dd> |
||
| 2388 | <div class="desc"><p>Using bone mesh (<code>_mesh</code>) and the list of cartilage meshes (<code>list_cartilage_meshes</code>) |
||
| 2389 | calcualte the cartilage thickness for each node on the bone surface. </p> |
||
| 2390 | <h2 id="parameters">Parameters</h2> |
||
| 2391 | <dl> |
||
| 2392 | <dt><strong><code>list_cartilage_labels</code></strong> : <code>list</code>, optional</dt> |
||
| 2393 | <dd>Cartilag labels to be used to create cartilage meshes (if they dont |
||
| 2394 | exist), by default None</dd> |
||
| 2395 | <dt><strong><code>list_cartilage_meshes</code></strong> : <code>list</code>, optional</dt> |
||
| 2396 | <dd>Cartilage meshes to be used for calculating cart thickness, by default None</dd> |
||
| 2397 | <dt><strong><code>image_smooth_var_cart</code></strong> : <code>float</code>, optional</dt> |
||
| 2398 | <dd>Variance of gaussian filter to be applied to binary cartilage masks, |
||
| 2399 | by default 0.3125/2</dd> |
||
| 2400 | <dt><strong><code>marching_cubes_threshold</code></strong> : <code>float</code>, optional</dt> |
||
| 2401 | <dd>Threshold to create bone surface at, by default 0.5</dd> |
||
| 2402 | <dt><strong><code>ray_cast_length</code></strong> : <code>float</code>, optional</dt> |
||
| 2403 | <dd>Length (mm) of ray to cast from bone surface when trying to find cartilage (inner & |
||
| 2404 | outter shell), by default 10.0</dd> |
||
| 2405 | <dt><strong><code>percent_ray_length_opposite_direction</code></strong> : <code>float</code>, optional</dt> |
||
| 2406 | <dd>How far to project ray inside of the bone. This is done just in case the cartilage |
||
| 2407 | surface ends up slightly inside of (or coincident with) the bone surface, by default 0.25</dd> |
||
| 2408 | </dl> |
||
| 2409 | <h2 id="raises">Raises</h2> |
||
| 2410 | <dl> |
||
| 2411 | <dt><code>Exception</code></dt> |
||
| 2412 | <dd>No cartilage available (either <code>list_cartilage_meshes</code> or <code>list_cartilage_labels</code>)</dd> |
||
| 2413 | </dl></div> |
||
| 2414 | <details class="source"> |
||
| 2415 | <summary> |
||
| 2416 | <span>Expand source code</span> |
||
| 2417 | </summary> |
||
| 2418 | <pre><code class="python">def calc_cartilage_thickness(self, |
||
| 2419 | list_cartilage_labels=None, |
||
| 2420 | list_cartilage_meshes=None, |
||
| 2421 | image_smooth_var_cart=0.3125 / 2, |
||
| 2422 | marching_cubes_threshold=0.5, |
||
| 2423 | ray_cast_length=10.0, |
||
| 2424 | percent_ray_length_opposite_direction=0.25 |
||
| 2425 | ): |
||
| 2426 | """ |
||
| 2427 | Using bone mesh (`_mesh`) and the list of cartilage meshes (`list_cartilage_meshes`) |
||
| 2428 | calcualte the cartilage thickness for each node on the bone surface. |
||
| 2429 | |||
| 2430 | Parameters |
||
| 2431 | ---------- |
||
| 2432 | list_cartilage_labels : list, optional |
||
| 2433 | Cartilag labels to be used to create cartilage meshes (if they dont |
||
| 2434 | exist), by default None |
||
| 2435 | list_cartilage_meshes : list, optional |
||
| 2436 | Cartilage meshes to be used for calculating cart thickness, by default None |
||
| 2437 | image_smooth_var_cart : float, optional |
||
| 2438 | Variance of gaussian filter to be applied to binary cartilage masks, |
||
| 2439 | by default 0.3125/2 |
||
| 2440 | marching_cubes_threshold : float, optional |
||
| 2441 | Threshold to create bone surface at, by default 0.5 |
||
| 2442 | ray_cast_length : float, optional |
||
| 2443 | Length (mm) of ray to cast from bone surface when trying to find cartilage (inner & |
||
| 2444 | outter shell), by default 10.0 |
||
| 2445 | percent_ray_length_opposite_direction : float, optional |
||
| 2446 | How far to project ray inside of the bone. This is done just in case the cartilage |
||
| 2447 | surface ends up slightly inside of (or coincident with) the bone surface, by default 0.25 |
||
| 2448 | |||
| 2449 | Raises |
||
| 2450 | ------ |
||
| 2451 | Exception |
||
| 2452 | No cartilage available (either `list_cartilage_meshes` or `list_cartilage_labels`) |
||
| 2453 | """ |
||
| 2454 | # If new cartilage infor/labels are provided, then replace existing with these ones. |
||
| 2455 | if list_cartilage_meshes is not None: self._list_cartilage_meshes = list_cartilage_meshes |
||
| 2456 | if list_cartilage_labels is not None: self._list_cartilage_labels = list_cartilage_labels |
||
| 2457 | |||
| 2458 | # If no cartilage stuff provided, then cant do this function - raise exception. |
||
| 2459 | if (self._list_cartilage_meshes is None) & (self._list_cartilage_labels is None): |
||
| 2460 | raise Exception('No cartilage meshes or list of cartilage labels are provided! - These can be provided either to the class function `calc_cartilage_thickness` directly, or can be specified at the time of instantiating the `BoneMesh` class.') |
||
| 2461 | |||
| 2462 | # if cartilage meshes don't exist yet, then make them. |
||
| 2463 | if self._list_cartilage_meshes is None: |
||
| 2464 | self.create_cartilage_meshes(image_smooth_var_cart=image_smooth_var_cart, |
||
| 2465 | marching_cubes_threshold=marching_cubes_threshold) |
||
| 2466 | |||
| 2467 | # pre-allocate empty thicknesses so that as labels are iterated over, they can all be appended to the same bone. |
||
| 2468 | thicknesses = np.zeros(self._mesh.GetNumberOfPoints()) |
||
| 2469 | |||
| 2470 | # iterate over meshes and add their thicknesses to the thicknesses list. |
||
| 2471 | for cart_mesh in self._list_cartilage_meshes: |
||
| 2472 | node_data = get_cartilage_properties_at_points(self._mesh, |
||
| 2473 | cart_mesh._mesh, |
||
| 2474 | t2_vtk_image=None, |
||
| 2475 | # seg_vtk_image=vtk_seg if assign_seg_label_to_bone is True else None, |
||
| 2476 | seg_vtk_image=None, |
||
| 2477 | ray_cast_length=ray_cast_length, |
||
| 2478 | percent_ray_length_opposite_direction=percent_ray_length_opposite_direction |
||
| 2479 | ) |
||
| 2480 | thicknesses += node_data |
||
| 2481 | |||
| 2482 | # Assign the thickness scalars to the bone mesh surface. |
||
| 2483 | thickness_scalars = numpy_to_vtk(thicknesses) |
||
| 2484 | thickness_scalars.SetName('thickness (mm)') |
||
| 2485 | self._mesh.GetPointData().SetScalars(thickness_scalars)</code></pre> |
||
| 2486 | </details> |
||
| 2487 | </dd> |
||
| 2488 | <dt id="pymskt.mesh.meshes.BoneMesh.create_cartilage_meshes"><code class="name flex"> |
||
| 2489 | <span>def <span class="ident">create_cartilage_meshes</span></span>(<span>self, image_smooth_var_cart=0.15625, marching_cubes_threshold=0.5)</span> |
||
| 2490 | </code></dt> |
||
| 2491 | <dd> |
||
| 2492 | <div class="desc"><p>Helper function to create the list of cartilage meshes from the list of cartilage |
||
| 2493 | labels. </p> |
||
| 2494 | <h2 id="parameters">Parameters</h2> |
||
| 2495 | <dl> |
||
| 2496 | <dt><strong><code>image_smooth_var_cart</code></strong> : <code>float</code></dt> |
||
| 2497 | <dd>Variance to smooth cartilage segmentations before finding surface using continuous |
||
| 2498 | marching cubes.</dd> |
||
| 2499 | <dt><strong><code>marching_cubes_threshold</code></strong> : <code>float</code></dt> |
||
| 2500 | <dd>Threshold value to create cartilage surface at from segmentation images.</dd> |
||
| 2501 | </dl> |
||
| 2502 | <h2 id="notes">Notes</h2> |
||
| 2503 | <p>?? Should this function just be everything inside the for loop and then that |
||
| 2504 | function gets called somewhere else?</p></div> |
||
| 2505 | <details class="source"> |
||
| 2506 | <summary> |
||
| 2507 | <span>Expand source code</span> |
||
| 2508 | </summary> |
||
| 2509 | <pre><code class="python">def create_cartilage_meshes(self, |
||
| 2510 | image_smooth_var_cart=0.3125 / 2, |
||
| 2511 | marching_cubes_threshold=0.5): |
||
| 2512 | """ |
||
| 2513 | Helper function to create the list of cartilage meshes from the list of cartilage |
||
| 2514 | labels. |
||
| 2515 | |||
| 2516 | Parameters |
||
| 2517 | ---------- |
||
| 2518 | image_smooth_var_cart : float |
||
| 2519 | Variance to smooth cartilage segmentations before finding surface using continuous |
||
| 2520 | marching cubes. |
||
| 2521 | marching_cubes_threshold : float |
||
| 2522 | Threshold value to create cartilage surface at from segmentation images. |
||
| 2523 | |||
| 2524 | Notes |
||
| 2525 | ----- |
||
| 2526 | ?? Should this function just be everything inside the for loop and then that |
||
| 2527 | function gets called somewhere else? |
||
| 2528 | """ |
||
| 2529 | |||
| 2530 | self._list_cartilage_meshes = [] |
||
| 2531 | for cart_label_idx in self._list_cartilage_labels: |
||
| 2532 | seg_array_view = sitk.GetArrayViewFromImage(self._seg_image) |
||
| 2533 | n_pixels_with_cart = np.sum(seg_array_view == cart_label_idx) |
||
| 2534 | if n_pixels_with_cart == 0: |
||
| 2535 | warnings.warn( |
||
| 2536 | f"Not analyzing cartilage for label {cart_label_idx} because it doesnt have any pixels!", |
||
| 2537 | UserWarning |
||
| 2538 | ) |
||
| 2539 | else: |
||
| 2540 | cart_mesh = CartilageMesh(seg_image=self._seg_image, |
||
| 2541 | label_idx=cart_label_idx) |
||
| 2542 | cart_mesh.create_mesh(smooth_image_var=image_smooth_var_cart, |
||
| 2543 | marching_cubes_threshold=marching_cubes_threshold) |
||
| 2544 | self._list_cartilage_meshes.append(cart_mesh)</code></pre> |
||
| 2545 | </details> |
||
| 2546 | </dd> |
||
| 2547 | <dt id="pymskt.mesh.meshes.BoneMesh.create_mesh"><code class="name flex"> |
||
| 2548 | <span>def <span class="ident">create_mesh</span></span>(<span>self, smooth_image=True, smooth_image_var=0.15625, marching_cubes_threshold=0.5, label_idx=None, min_n_pixels=None, crop_percent=None)</span> |
||
| 2549 | </code></dt> |
||
| 2550 | <dd> |
||
| 2551 | <div class="desc"><p>This is an extension of <code><a title="pymskt.mesh.meshes.Mesh.create_mesh" href="#pymskt.mesh.meshes.Mesh.create_mesh">Mesh.create_mesh()</a></code> that enables cropping of bones. |
||
| 2552 | Bones might need to be cropped (this isnt necessary for cartilage) |
||
| 2553 | So, adding this functionality to the processing steps before the bone mesh is created.</p> |
||
| 2554 | <p>All functionality, except for that relevant to <code>crop_percent</code> is the same as: |
||
| 2555 | <code><a title="pymskt.mesh.meshes.Mesh.create_mesh" href="#pymskt.mesh.meshes.Mesh.create_mesh">Mesh.create_mesh()</a></code>. </p> |
||
| 2556 | <p>Create a surface mesh from the classes <code>_seg_image</code>. If <code>_seg_image</code> |
||
| 2557 | does not exist, then read it in using <code>read_seg_image</code>. </p> |
||
| 2558 | <h2 id="parameters">Parameters</h2> |
||
| 2559 | <dl> |
||
| 2560 | <dt><strong><code>smooth_image</code></strong> : <code>bool</code>, optional</dt> |
||
| 2561 | <dd>Should the <code>_seg_image</code> be gaussian filtered, by default True</dd> |
||
| 2562 | <dt><strong><code>smooth_image_var</code></strong> : <code>float</code>, optional</dt> |
||
| 2563 | <dd>Variance of gaussian filter to apply to <code>_seg_image</code>, by default 0.3125/2</dd> |
||
| 2564 | <dt><strong><code>marching_cubes_threshold</code></strong> : <code>float</code>, optional</dt> |
||
| 2565 | <dd>Threshold contour level to create surface mesh on, by default 0.5</dd> |
||
| 2566 | <dt><strong><code>label_idx</code></strong> : <code>int</code>, optional</dt> |
||
| 2567 | <dd>Label value / index to create mesh from, by default None</dd> |
||
| 2568 | <dt><strong><code>min_n_pixels</code></strong> : <code>int</code>, optional</dt> |
||
| 2569 | <dd>Minimum number of continuous pixels to include segmentation island |
||
| 2570 | in the surface mesh creation, by default None</dd> |
||
| 2571 | <dt><strong><code>crop_percent</code></strong> : <code>[type]</code>, optional</dt> |
||
| 2572 | <dd>[description], by default None</dd> |
||
| 2573 | </dl> |
||
| 2574 | <h2 id="raises">Raises</h2> |
||
| 2575 | <dl> |
||
| 2576 | <dt><code>Exception</code></dt> |
||
| 2577 | <dd>If cropping & bone is not femur or tibia, then raise an error.</dd> |
||
| 2578 | <dt><code>Exception</code></dt> |
||
| 2579 | <dd>If the total number of pixels segmentated (<code>n_pixels_labelled</code>) is |
||
| 2580 | < <code>min_n_pixels</code> then there is no object in the image.</dd> |
||
| 2581 | <dt><code>Exception</code></dt> |
||
| 2582 | <dd>If no <code>_seg_image</code> and no <code>label_idx</code> then we don't know what tissue to create the |
||
| 2583 | surface mesh from.</dd> |
||
| 2584 | <dt><code>Exception</code></dt> |
||
| 2585 | <dd>If no <code>_seg_image</code> or <code>path_seg_image</code> then we have no image to create mesh from.</dd> |
||
| 2586 | </dl></div> |
||
| 2587 | <details class="source"> |
||
| 2588 | <summary> |
||
| 2589 | <span>Expand source code</span> |
||
| 2590 | </summary> |
||
| 2591 | <pre><code class="python">def create_mesh(self, |
||
| 2592 | smooth_image=True, |
||
| 2593 | smooth_image_var=0.3125 / 2, |
||
| 2594 | marching_cubes_threshold=0.5, |
||
| 2595 | label_idx=None, |
||
| 2596 | min_n_pixels=None, |
||
| 2597 | crop_percent=None |
||
| 2598 | ): |
||
| 2599 | """ |
||
| 2600 | This is an extension of `Mesh.create_mesh` that enables cropping of bones. |
||
| 2601 | Bones might need to be cropped (this isnt necessary for cartilage) |
||
| 2602 | So, adding this functionality to the processing steps before the bone mesh is created. |
||
| 2603 | |||
| 2604 | All functionality, except for that relevant to `crop_percent` is the same as: |
||
| 2605 | `Mesh.create_mesh`. |
||
| 2606 | |||
| 2607 | Create a surface mesh from the classes `_seg_image`. If `_seg_image` |
||
| 2608 | does not exist, then read it in using `read_seg_image`. |
||
| 2609 | |||
| 2610 | Parameters |
||
| 2611 | ---------- |
||
| 2612 | smooth_image : bool, optional |
||
| 2613 | Should the `_seg_image` be gaussian filtered, by default True |
||
| 2614 | smooth_image_var : float, optional |
||
| 2615 | Variance of gaussian filter to apply to `_seg_image`, by default 0.3125/2 |
||
| 2616 | marching_cubes_threshold : float, optional |
||
| 2617 | Threshold contour level to create surface mesh on, by default 0.5 |
||
| 2618 | label_idx : int, optional |
||
| 2619 | Label value / index to create mesh from, by default None |
||
| 2620 | min_n_pixels : int, optional |
||
| 2621 | Minimum number of continuous pixels to include segmentation island |
||
| 2622 | in the surface mesh creation, by default None |
||
| 2623 | crop_percent : [type], optional |
||
| 2624 | [description], by default None |
||
| 2625 | |||
| 2626 | Raises |
||
| 2627 | ------ |
||
| 2628 | Exception |
||
| 2629 | If cropping & bone is not femur or tibia, then raise an error. |
||
| 2630 | Exception |
||
| 2631 | If the total number of pixels segmentated (`n_pixels_labelled`) is |
||
| 2632 | < `min_n_pixels` then there is no object in the image. |
||
| 2633 | Exception |
||
| 2634 | If no `_seg_image` and no `label_idx` then we don't know what tissue to create the |
||
| 2635 | surface mesh from. |
||
| 2636 | Exception |
||
| 2637 | If no `_seg_image` or `path_seg_image` then we have no image to create mesh from. |
||
| 2638 | """ |
||
| 2639 | |||
| 2640 | if self._seg_image is None: |
||
| 2641 | self.read_seg_image() |
||
| 2642 | |||
| 2643 | # Bones might need to be cropped (this isnt necessary for cartilage) |
||
| 2644 | # So, adding this functionality to the processing steps before the bone mesh is created |
||
| 2645 | if crop_percent is not None: |
||
| 2646 | self._crop_percent = crop_percent |
||
| 2647 | if (self._crop_percent is not None) and (('femur' in self._bone) or ('tibia' in self._bone)): |
||
| 2648 | if 'femur' in self._bone: |
||
| 2649 | bone_crop_distal = True |
||
| 2650 | elif 'tibia' in self._bone: |
||
| 2651 | bone_crop_distal = False |
||
| 2652 | else: |
||
| 2653 | raise Exception('var bone should be "femur" or "tiba" got: {} instead'.format(self._bone)) |
||
| 2654 | |||
| 2655 | self._seg_image = crop_bone_based_on_width(self._seg_image, |
||
| 2656 | self._label_idx, |
||
| 2657 | percent_width_to_crop_height=self._crop_percent, |
||
| 2658 | bone_crop_distal=bone_crop_distal) |
||
| 2659 | elif self._crop_percent is not None: |
||
| 2660 | warnings.warn(f'Trying to crop bone, but {self._bone} specified and only bones `femur`', |
||
| 2661 | 'or `tibia` currently supported for cropping. If using another bone, consider', |
||
| 2662 | 'making a pull request. If cropping not desired, set `crop_percent=None`.' |
||
| 2663 | ) |
||
| 2664 | super().create_mesh(smooth_image=smooth_image, smooth_image_var=smooth_image_var, marching_cubes_threshold=marching_cubes_threshold, label_idx=label_idx, min_n_pixels=min_n_pixels)</code></pre> |
||
| 2665 | </details> |
||
| 2666 | </dd> |
||
| 2667 | <dt id="pymskt.mesh.meshes.BoneMesh.smooth_surface_scalars"><code class="name flex"> |
||
| 2668 | <span>def <span class="ident">smooth_surface_scalars</span></span>(<span>self, smooth_only_cartilage=True, scalar_sigma=1.6986436005760381, scalar_array_name='thickness (mm)', scalar_array_idx=None)</span> |
||
| 2669 | </code></dt> |
||
| 2670 | <dd> |
||
| 2671 | <div class="desc"><p>Function to smooth the scalars with name <code>scalar_array_name</code> on the bone surface. </p> |
||
| 2672 | <h2 id="parameters">Parameters</h2> |
||
| 2673 | <dl> |
||
| 2674 | <dt><strong><code>smooth_only_cartilage</code></strong> : <code>bool</code>, optional</dt> |
||
| 2675 | <dd>Should we only smooth where there is cartialge & ignore everywhere else, by default True</dd> |
||
| 2676 | <dt><strong><code>scalar_sigma</code></strong> : <code>float</code>, optional</dt> |
||
| 2677 | <dd>Smoothing sigma (standard deviation or sqrt(variance)) for gaussian filter, by default 1.6986436005760381 |
||
| 2678 | default is based on a Full Width Half Maximum (FWHM) of 4mm.</dd> |
||
| 2679 | <dt><strong><code>scalar_array_name</code></strong> : <code>str</code></dt> |
||
| 2680 | <dd>Name of scalar array to smooth, default 'thickness (mm)'.</dd> |
||
| 2681 | <dt><strong><code>scalar_array_idx</code></strong> : <code>int</code>, optional</dt> |
||
| 2682 | <dd>Index of the scalar array to smooth (alternative to using <code>scalar_array_name</code>) , by default None</dd> |
||
| 2683 | </dl></div> |
||
| 2684 | <details class="source"> |
||
| 2685 | <summary> |
||
| 2686 | <span>Expand source code</span> |
||
| 2687 | </summary> |
||
| 2688 | <pre><code class="python">def smooth_surface_scalars(self, |
||
| 2689 | smooth_only_cartilage=True, |
||
| 2690 | scalar_sigma=1.6986436005760381, # This is a FWHM = 4 |
||
| 2691 | scalar_array_name='thickness (mm)', |
||
| 2692 | scalar_array_idx=None, |
||
| 2693 | ): |
||
| 2694 | |||
| 2695 | """ |
||
| 2696 | Function to smooth the scalars with name `scalar_array_name` on the bone surface. |
||
| 2697 | |||
| 2698 | Parameters |
||
| 2699 | ---------- |
||
| 2700 | smooth_only_cartilage : bool, optional |
||
| 2701 | Should we only smooth where there is cartialge & ignore everywhere else, by default True |
||
| 2702 | scalar_sigma : float, optional |
||
| 2703 | Smoothing sigma (standard deviation or sqrt(variance)) for gaussian filter, by default 1.6986436005760381 |
||
| 2704 | default is based on a Full Width Half Maximum (FWHM) of 4mm. |
||
| 2705 | scalar_array_name : str |
||
| 2706 | Name of scalar array to smooth, default 'thickness (mm)'. |
||
| 2707 | scalar_array_idx : int, optional |
||
| 2708 | Index of the scalar array to smooth (alternative to using `scalar_array_name`) , by default None |
||
| 2709 | """ |
||
| 2710 | if smooth_only_cartilage is True: |
||
| 2711 | loc_cartilage = np.where(vtk_to_numpy(self._mesh.GetPointData().GetArray('thickness (mm)')) > 0.01)[0] |
||
| 2712 | else: |
||
| 2713 | loc_cartilage = None |
||
| 2714 | self._mesh = gaussian_smooth_surface_scalars(self._mesh, |
||
| 2715 | sigma=scalar_sigma, |
||
| 2716 | idx_coords_to_smooth=loc_cartilage, |
||
| 2717 | array_name=scalar_array_name, |
||
| 2718 | array_idx=scalar_array_idx)</code></pre> |
||
| 2719 | </details> |
||
| 2720 | </dd> |
||
| 2721 | </dl> |
||
| 2722 | <h3>Inherited members</h3> |
||
| 2723 | <ul class="hlist"> |
||
| 2724 | <li><code><b><a title="pymskt.mesh.meshes.Mesh" href="#pymskt.mesh.meshes.Mesh">Mesh</a></b></code>: |
||
| 2725 | <ul class="hlist"> |
||
| 2726 | <li><code><a title="pymskt.mesh.meshes.Mesh.apply_transform_to_mesh" href="#pymskt.mesh.meshes.Mesh.apply_transform_to_mesh">apply_transform_to_mesh</a></code></li> |
||
| 2727 | <li><code><a title="pymskt.mesh.meshes.Mesh.copy_scalars_from_other_mesh_to_currect" href="#pymskt.mesh.meshes.Mesh.copy_scalars_from_other_mesh_to_currect">copy_scalars_from_other_mesh_to_currect</a></code></li> |
||
| 2728 | <li><code><a title="pymskt.mesh.meshes.Mesh.label_idx" href="#pymskt.mesh.meshes.Mesh.label_idx">label_idx</a></code></li> |
||
| 2729 | <li><code><a title="pymskt.mesh.meshes.Mesh.list_applied_transforms" href="#pymskt.mesh.meshes.Mesh.list_applied_transforms">list_applied_transforms</a></code></li> |
||
| 2730 | <li><code><a title="pymskt.mesh.meshes.Mesh.mesh" href="#pymskt.mesh.meshes.Mesh.mesh">mesh</a></code></li> |
||
| 2731 | <li><code><a title="pymskt.mesh.meshes.Mesh.min_n_pixels" href="#pymskt.mesh.meshes.Mesh.min_n_pixels">min_n_pixels</a></code></li> |
||
| 2732 | <li><code><a title="pymskt.mesh.meshes.Mesh.non_rigidly_register" href="#pymskt.mesh.meshes.Mesh.non_rigidly_register">non_rigidly_register</a></code></li> |
||
| 2733 | <li><code><a title="pymskt.mesh.meshes.Mesh.path_seg_image" href="#pymskt.mesh.meshes.Mesh.path_seg_image">path_seg_image</a></code></li> |
||
| 2734 | <li><code><a title="pymskt.mesh.meshes.Mesh.point_coords" href="#pymskt.mesh.meshes.Mesh.point_coords">point_coords</a></code></li> |
||
| 2735 | <li><code><a title="pymskt.mesh.meshes.Mesh.read_seg_image" href="#pymskt.mesh.meshes.Mesh.read_seg_image">read_seg_image</a></code></li> |
||
| 2736 | <li><code><a title="pymskt.mesh.meshes.Mesh.resample_surface" href="#pymskt.mesh.meshes.Mesh.resample_surface">resample_surface</a></code></li> |
||
| 2737 | <li><code><a title="pymskt.mesh.meshes.Mesh.reverse_all_transforms" href="#pymskt.mesh.meshes.Mesh.reverse_all_transforms">reverse_all_transforms</a></code></li> |
||
| 2738 | <li><code><a title="pymskt.mesh.meshes.Mesh.reverse_most_recent_transform" href="#pymskt.mesh.meshes.Mesh.reverse_most_recent_transform">reverse_most_recent_transform</a></code></li> |
||
| 2739 | <li><code><a title="pymskt.mesh.meshes.Mesh.rigidly_register" href="#pymskt.mesh.meshes.Mesh.rigidly_register">rigidly_register</a></code></li> |
||
| 2740 | <li><code><a title="pymskt.mesh.meshes.Mesh.save_mesh" href="#pymskt.mesh.meshes.Mesh.save_mesh">save_mesh</a></code></li> |
||
| 2741 | <li><code><a title="pymskt.mesh.meshes.Mesh.seg_image" href="#pymskt.mesh.meshes.Mesh.seg_image">seg_image</a></code></li> |
||
| 2742 | </ul> |
||
| 2743 | </li> |
||
| 2744 | </ul> |
||
| 2745 | </dd> |
||
| 2746 | <dt id="pymskt.mesh.meshes.CartilageMesh"><code class="flex name class"> |
||
| 2747 | <span>class <span class="ident">CartilageMesh</span></span> |
||
| 2748 | <span>(</span><span>mesh=None, seg_image=None, path_seg_image=None, label_idx=None, min_n_pixels=1000)</span> |
||
| 2749 | </code></dt> |
||
| 2750 | <dd> |
||
| 2751 | <div class="desc"><p>Class to create, store, and process cartilage meshes</p> |
||
| 2752 | <h2 id="parameters">Parameters</h2> |
||
| 2753 | <dl> |
||
| 2754 | <dt><strong><code>mesh</code></strong> : <code>vtk.vtkPolyData</code>, optional</dt> |
||
| 2755 | <dd>vtkPolyData object that is basis of surface mesh, by default None</dd> |
||
| 2756 | <dt><strong><code>seg_image</code></strong> : <code>SimpleITK.Image</code>, optional</dt> |
||
| 2757 | <dd>Segmentation image that can be used to create surface mesh - used |
||
| 2758 | instead of mesh, by default None</dd> |
||
| 2759 | <dt><strong><code>path_seg_image</code></strong> : <code>str</code>, optional</dt> |
||
| 2760 | <dd>Path to a medical image (.nrrd) to load and create mesh from, |
||
| 2761 | by default None</dd> |
||
| 2762 | <dt><strong><code>label_idx</code></strong> : <code>int</code>, optional</dt> |
||
| 2763 | <dd>Label of anatomy of interest, by default None</dd> |
||
| 2764 | <dt><strong><code>min_n_pixels</code></strong> : <code>int</code>, optional</dt> |
||
| 2765 | <dd>All islands smaller than this size are dropped, by default 5000</dd> |
||
| 2766 | </dl> |
||
| 2767 | <h2 id="attributes">Attributes</h2> |
||
| 2768 | <dl> |
||
| 2769 | <dt><strong><code>_mesh</code></strong> : <code>vtk.vtkPolyData</code></dt> |
||
| 2770 | <dd>Item passed from <strong>init</strong>, or created during life of class. |
||
| 2771 | This is the main surface mesh of this class.</dd> |
||
| 2772 | <dt><strong><code>_seg_image</code></strong> : <code>SimpleITK.Image</code></dt> |
||
| 2773 | <dd>Segmentation image that can be used to create mesh. This is optional.</dd> |
||
| 2774 | <dt><strong><code>path_seg_image</code></strong> : <code>str</code></dt> |
||
| 2775 | <dd>Path to medical image (.nrrd) that can be loaded to create <code>_seg_image</code> |
||
| 2776 | and then creat surface mesh <code>_mesh</code></dd> |
||
| 2777 | <dt><strong><code>label_idx</code></strong> : <code>int</code></dt> |
||
| 2778 | <dd>Integer of anatomy to create surface mesh from <code>_seg_image</code></dd> |
||
| 2779 | <dt><strong><code>min_n_pixels</code></strong> : <code>int</code></dt> |
||
| 2780 | <dd>Minimum number of pixels for an isolated island of a segmentation to be |
||
| 2781 | retained</dd> |
||
| 2782 | <dt><strong><code>list_applied_transforms</code></strong> : <code>list</code></dt> |
||
| 2783 | <dd>A list of transformations applied to a surface mesh. |
||
| 2784 | This list allows for undoing of most recent transform, or undoing |
||
| 2785 | all of them by iterating over the list in reverse.</dd> |
||
| 2786 | </dl> |
||
| 2787 | <h2 id="methods">Methods</h2> |
||
| 2788 | <p>Initialize Mesh class</p> |
||
| 2789 | <h2 id="parameters_1">Parameters</h2> |
||
| 2790 | <dl> |
||
| 2791 | <dt><strong><code>mesh</code></strong> : <code>vtk.vtkPolyData</code>, optional</dt> |
||
| 2792 | <dd>vtkPolyData object that is basis of surface mesh, by default None</dd> |
||
| 2793 | <dt><strong><code>seg_image</code></strong> : <code>SimpleITK.Image</code>, optional</dt> |
||
| 2794 | <dd>Segmentation image that can be used to create surface mesh - used |
||
| 2795 | instead of mesh, by default None</dd> |
||
| 2796 | <dt><strong><code>path_seg_image</code></strong> : <code>str</code>, optional</dt> |
||
| 2797 | <dd>Path to a medical image (.nrrd) to load and create mesh from, |
||
| 2798 | by default None</dd> |
||
| 2799 | <dt><strong><code>label_idx</code></strong> : <code>int</code>, optional</dt> |
||
| 2800 | <dd>Label of anatomy of interest, by default None</dd> |
||
| 2801 | <dt><strong><code>min_n_pixels</code></strong> : <code>int</code>, optional</dt> |
||
| 2802 | <dd>All islands smaller than this size are dropped, by default 5000</dd> |
||
| 2803 | </dl></div> |
||
| 2804 | <details class="source"> |
||
| 2805 | <summary> |
||
| 2806 | <span>Expand source code</span> |
||
| 2807 | </summary> |
||
| 2808 | <pre><code class="python">class CartilageMesh(Mesh): |
||
| 2809 | """ |
||
| 2810 | Class to create, store, and process cartilage meshes |
||
| 2811 | |||
| 2812 | Parameters |
||
| 2813 | ---------- |
||
| 2814 | mesh : vtk.vtkPolyData, optional |
||
| 2815 | vtkPolyData object that is basis of surface mesh, by default None |
||
| 2816 | seg_image : SimpleITK.Image, optional |
||
| 2817 | Segmentation image that can be used to create surface mesh - used |
||
| 2818 | instead of mesh, by default None |
||
| 2819 | path_seg_image : str, optional |
||
| 2820 | Path to a medical image (.nrrd) to load and create mesh from, |
||
| 2821 | by default None |
||
| 2822 | label_idx : int, optional |
||
| 2823 | Label of anatomy of interest, by default None |
||
| 2824 | min_n_pixels : int, optional |
||
| 2825 | All islands smaller than this size are dropped, by default 5000 |
||
| 2826 | |||
| 2827 | |||
| 2828 | Attributes |
||
| 2829 | ---------- |
||
| 2830 | _mesh : vtk.vtkPolyData |
||
| 2831 | Item passed from __init__, or created during life of class. |
||
| 2832 | This is the main surface mesh of this class. |
||
| 2833 | _seg_image : SimpleITK.Image |
||
| 2834 | Segmentation image that can be used to create mesh. This is optional. |
||
| 2835 | path_seg_image : str |
||
| 2836 | Path to medical image (.nrrd) that can be loaded to create `_seg_image` |
||
| 2837 | and then creat surface mesh `_mesh` |
||
| 2838 | label_idx : int |
||
| 2839 | Integer of anatomy to create surface mesh from `_seg_image` |
||
| 2840 | min_n_pixels : int |
||
| 2841 | Minimum number of pixels for an isolated island of a segmentation to be |
||
| 2842 | retained |
||
| 2843 | list_applied_transforms : list |
||
| 2844 | A list of transformations applied to a surface mesh. |
||
| 2845 | This list allows for undoing of most recent transform, or undoing |
||
| 2846 | all of them by iterating over the list in reverse. |
||
| 2847 | |||
| 2848 | Methods |
||
| 2849 | ---------- |
||
| 2850 | |||
| 2851 | """ |
||
| 2852 | |||
| 2853 | def __init__(self, |
||
| 2854 | mesh=None, |
||
| 2855 | seg_image=None, |
||
| 2856 | path_seg_image=None, |
||
| 2857 | label_idx=None, |
||
| 2858 | min_n_pixels=1000 |
||
| 2859 | ): |
||
| 2860 | super().__init__(mesh=mesh, |
||
| 2861 | seg_image=seg_image, |
||
| 2862 | path_seg_image=path_seg_image, |
||
| 2863 | label_idx=label_idx, |
||
| 2864 | min_n_pixels=min_n_pixels)</code></pre> |
||
| 2865 | </details> |
||
| 2866 | <h3>Ancestors</h3> |
||
| 2867 | <ul class="hlist"> |
||
| 2868 | <li><a title="pymskt.mesh.meshes.Mesh" href="#pymskt.mesh.meshes.Mesh">Mesh</a></li> |
||
| 2869 | </ul> |
||
| 2870 | <h3>Inherited members</h3> |
||
| 2871 | <ul class="hlist"> |
||
| 2872 | <li><code><b><a title="pymskt.mesh.meshes.Mesh" href="#pymskt.mesh.meshes.Mesh">Mesh</a></b></code>: |
||
| 2873 | <ul class="hlist"> |
||
| 2874 | <li><code><a title="pymskt.mesh.meshes.Mesh.apply_transform_to_mesh" href="#pymskt.mesh.meshes.Mesh.apply_transform_to_mesh">apply_transform_to_mesh</a></code></li> |
||
| 2875 | <li><code><a title="pymskt.mesh.meshes.Mesh.copy_scalars_from_other_mesh_to_currect" href="#pymskt.mesh.meshes.Mesh.copy_scalars_from_other_mesh_to_currect">copy_scalars_from_other_mesh_to_currect</a></code></li> |
||
| 2876 | <li><code><a title="pymskt.mesh.meshes.Mesh.create_mesh" href="#pymskt.mesh.meshes.Mesh.create_mesh">create_mesh</a></code></li> |
||
| 2877 | <li><code><a title="pymskt.mesh.meshes.Mesh.label_idx" href="#pymskt.mesh.meshes.Mesh.label_idx">label_idx</a></code></li> |
||
| 2878 | <li><code><a title="pymskt.mesh.meshes.Mesh.list_applied_transforms" href="#pymskt.mesh.meshes.Mesh.list_applied_transforms">list_applied_transforms</a></code></li> |
||
| 2879 | <li><code><a title="pymskt.mesh.meshes.Mesh.mesh" href="#pymskt.mesh.meshes.Mesh.mesh">mesh</a></code></li> |
||
| 2880 | <li><code><a title="pymskt.mesh.meshes.Mesh.min_n_pixels" href="#pymskt.mesh.meshes.Mesh.min_n_pixels">min_n_pixels</a></code></li> |
||
| 2881 | <li><code><a title="pymskt.mesh.meshes.Mesh.non_rigidly_register" href="#pymskt.mesh.meshes.Mesh.non_rigidly_register">non_rigidly_register</a></code></li> |
||
| 2882 | <li><code><a title="pymskt.mesh.meshes.Mesh.path_seg_image" href="#pymskt.mesh.meshes.Mesh.path_seg_image">path_seg_image</a></code></li> |
||
| 2883 | <li><code><a title="pymskt.mesh.meshes.Mesh.point_coords" href="#pymskt.mesh.meshes.Mesh.point_coords">point_coords</a></code></li> |
||
| 2884 | <li><code><a title="pymskt.mesh.meshes.Mesh.read_seg_image" href="#pymskt.mesh.meshes.Mesh.read_seg_image">read_seg_image</a></code></li> |
||
| 2885 | <li><code><a title="pymskt.mesh.meshes.Mesh.resample_surface" href="#pymskt.mesh.meshes.Mesh.resample_surface">resample_surface</a></code></li> |
||
| 2886 | <li><code><a title="pymskt.mesh.meshes.Mesh.reverse_all_transforms" href="#pymskt.mesh.meshes.Mesh.reverse_all_transforms">reverse_all_transforms</a></code></li> |
||
| 2887 | <li><code><a title="pymskt.mesh.meshes.Mesh.reverse_most_recent_transform" href="#pymskt.mesh.meshes.Mesh.reverse_most_recent_transform">reverse_most_recent_transform</a></code></li> |
||
| 2888 | <li><code><a title="pymskt.mesh.meshes.Mesh.rigidly_register" href="#pymskt.mesh.meshes.Mesh.rigidly_register">rigidly_register</a></code></li> |
||
| 2889 | <li><code><a title="pymskt.mesh.meshes.Mesh.save_mesh" href="#pymskt.mesh.meshes.Mesh.save_mesh">save_mesh</a></code></li> |
||
| 2890 | <li><code><a title="pymskt.mesh.meshes.Mesh.seg_image" href="#pymskt.mesh.meshes.Mesh.seg_image">seg_image</a></code></li> |
||
| 2891 | </ul> |
||
| 2892 | </li> |
||
| 2893 | </ul> |
||
| 2894 | </dd> |
||
| 2895 | <dt id="pymskt.mesh.meshes.Mesh"><code class="flex name class"> |
||
| 2896 | <span>class <span class="ident">Mesh</span></span> |
||
| 2897 | <span>(</span><span>mesh=None, seg_image=None, path_seg_image=None, label_idx=None, min_n_pixels=5000)</span> |
||
| 2898 | </code></dt> |
||
| 2899 | <dd> |
||
| 2900 | <div class="desc"><p>An object to contain surface meshes for musculoskeletal anatomy. Includes helper |
||
| 2901 | functions to build surface meshes, to process them, and to save them. </p> |
||
| 2902 | <h2 id="parameters">Parameters</h2> |
||
| 2903 | <dl> |
||
| 2904 | <dt><strong><code>mesh</code></strong> : <code>vtk.vtkPolyData</code>, optional</dt> |
||
| 2905 | <dd>vtkPolyData object that is basis of surface mesh, by default None</dd> |
||
| 2906 | <dt><strong><code>seg_image</code></strong> : <code>SimpleITK.Image</code>, optional</dt> |
||
| 2907 | <dd>Segmentation image that can be used to create surface mesh - used |
||
| 2908 | instead of mesh, by default None</dd> |
||
| 2909 | <dt><strong><code>path_seg_image</code></strong> : <code>str</code>, optional</dt> |
||
| 2910 | <dd>Path to a medical image (.nrrd) to load and create mesh from, |
||
| 2911 | by default None</dd> |
||
| 2912 | <dt><strong><code>label_idx</code></strong> : <code>int</code>, optional</dt> |
||
| 2913 | <dd>Label of anatomy of interest, by default None</dd> |
||
| 2914 | <dt><strong><code>min_n_pixels</code></strong> : <code>int</code>, optional</dt> |
||
| 2915 | <dd>All islands smaller than this size are dropped, by default 5000</dd> |
||
| 2916 | </dl> |
||
| 2917 | <h2 id="attributes">Attributes</h2> |
||
| 2918 | <dl> |
||
| 2919 | <dt><strong><code>_mesh</code></strong> : <code>vtk.vtkPolyData</code></dt> |
||
| 2920 | <dd>Item passed from <strong>init</strong>, or created during life of class. |
||
| 2921 | This is the main surface mesh of this class.</dd> |
||
| 2922 | <dt><strong><code>_seg_image</code></strong> : <code>SimpleITK.Image</code></dt> |
||
| 2923 | <dd>Segmentation image that can be used to create mesh. This is optional.</dd> |
||
| 2924 | <dt><strong><code>path_seg_image</code></strong> : <code>str</code></dt> |
||
| 2925 | <dd>Path to medical image (.nrrd) that can be loaded to create <code>_seg_image</code> |
||
| 2926 | and then creat surface mesh <code>_mesh</code></dd> |
||
| 2927 | <dt><strong><code>label_idx</code></strong> : <code>int</code></dt> |
||
| 2928 | <dd>Integer of anatomy to create surface mesh from <code>_seg_image</code></dd> |
||
| 2929 | <dt><strong><code>min_n_pixels</code></strong> : <code>int</code></dt> |
||
| 2930 | <dd>Minimum number of pixels for an isolated island of a segmentation to be |
||
| 2931 | retained</dd> |
||
| 2932 | <dt><strong><code>list_applied_transforms</code></strong> : <code>list</code></dt> |
||
| 2933 | <dd>A list of transformations applied to a surface mesh. |
||
| 2934 | This list allows for undoing of most recent transform, or undoing |
||
| 2935 | all of them by iterating over the list in reverse.</dd> |
||
| 2936 | </dl> |
||
| 2937 | <h2 id="methods">Methods</h2> |
||
| 2938 | <p>Initialize Mesh class</p> |
||
| 2939 | <h2 id="parameters_1">Parameters</h2> |
||
| 2940 | <dl> |
||
| 2941 | <dt><strong><code>mesh</code></strong> : <code>vtk.vtkPolyData</code>, optional</dt> |
||
| 2942 | <dd>vtkPolyData object that is basis of surface mesh, by default None</dd> |
||
| 2943 | <dt><strong><code>seg_image</code></strong> : <code>SimpleITK.Image</code>, optional</dt> |
||
| 2944 | <dd>Segmentation image that can be used to create surface mesh - used |
||
| 2945 | instead of mesh, by default None</dd> |
||
| 2946 | <dt><strong><code>path_seg_image</code></strong> : <code>str</code>, optional</dt> |
||
| 2947 | <dd>Path to a medical image (.nrrd) to load and create mesh from, |
||
| 2948 | by default None</dd> |
||
| 2949 | <dt><strong><code>label_idx</code></strong> : <code>int</code>, optional</dt> |
||
| 2950 | <dd>Label of anatomy of interest, by default None</dd> |
||
| 2951 | <dt><strong><code>min_n_pixels</code></strong> : <code>int</code>, optional</dt> |
||
| 2952 | <dd>All islands smaller than this size are dropped, by default 5000</dd> |
||
| 2953 | </dl></div> |
||
| 2954 | <details class="source"> |
||
| 2955 | <summary> |
||
| 2956 | <span>Expand source code</span> |
||
| 2957 | </summary> |
||
| 2958 | <pre><code class="python">class Mesh: |
||
| 2959 | """ |
||
| 2960 | An object to contain surface meshes for musculoskeletal anatomy. Includes helper |
||
| 2961 | functions to build surface meshes, to process them, and to save them. |
||
| 2962 | |||
| 2963 | Parameters |
||
| 2964 | ---------- |
||
| 2965 | mesh : vtk.vtkPolyData, optional |
||
| 2966 | vtkPolyData object that is basis of surface mesh, by default None |
||
| 2967 | seg_image : SimpleITK.Image, optional |
||
| 2968 | Segmentation image that can be used to create surface mesh - used |
||
| 2969 | instead of mesh, by default None |
||
| 2970 | path_seg_image : str, optional |
||
| 2971 | Path to a medical image (.nrrd) to load and create mesh from, |
||
| 2972 | by default None |
||
| 2973 | label_idx : int, optional |
||
| 2974 | Label of anatomy of interest, by default None |
||
| 2975 | min_n_pixels : int, optional |
||
| 2976 | All islands smaller than this size are dropped, by default 5000 |
||
| 2977 | |||
| 2978 | |||
| 2979 | Attributes |
||
| 2980 | ---------- |
||
| 2981 | _mesh : vtk.vtkPolyData |
||
| 2982 | Item passed from __init__, or created during life of class. |
||
| 2983 | This is the main surface mesh of this class. |
||
| 2984 | _seg_image : SimpleITK.Image |
||
| 2985 | Segmentation image that can be used to create mesh. This is optional. |
||
| 2986 | path_seg_image : str |
||
| 2987 | Path to medical image (.nrrd) that can be loaded to create `_seg_image` |
||
| 2988 | and then creat surface mesh `_mesh` |
||
| 2989 | label_idx : int |
||
| 2990 | Integer of anatomy to create surface mesh from `_seg_image` |
||
| 2991 | min_n_pixels : int |
||
| 2992 | Minimum number of pixels for an isolated island of a segmentation to be |
||
| 2993 | retained |
||
| 2994 | list_applied_transforms : list |
||
| 2995 | A list of transformations applied to a surface mesh. |
||
| 2996 | This list allows for undoing of most recent transform, or undoing |
||
| 2997 | all of them by iterating over the list in reverse. |
||
| 2998 | |||
| 2999 | Methods |
||
| 3000 | ---------- |
||
| 3001 | |||
| 3002 | """ |
||
| 3003 | def __init__(self, |
||
| 3004 | mesh=None, |
||
| 3005 | seg_image=None, |
||
| 3006 | path_seg_image=None, |
||
| 3007 | label_idx=None, |
||
| 3008 | min_n_pixels=5000 |
||
| 3009 | ): |
||
| 3010 | """ |
||
| 3011 | Initialize Mesh class |
||
| 3012 | |||
| 3013 | Parameters |
||
| 3014 | ---------- |
||
| 3015 | mesh : vtk.vtkPolyData, optional |
||
| 3016 | vtkPolyData object that is basis of surface mesh, by default None |
||
| 3017 | seg_image : SimpleITK.Image, optional |
||
| 3018 | Segmentation image that can be used to create surface mesh - used |
||
| 3019 | instead of mesh, by default None |
||
| 3020 | path_seg_image : str, optional |
||
| 3021 | Path to a medical image (.nrrd) to load and create mesh from, |
||
| 3022 | by default None |
||
| 3023 | label_idx : int, optional |
||
| 3024 | Label of anatomy of interest, by default None |
||
| 3025 | min_n_pixels : int, optional |
||
| 3026 | All islands smaller than this size are dropped, by default 5000 |
||
| 3027 | """ |
||
| 3028 | if type(mesh) in (str,): #accept path like objects? |
||
| 3029 | print('mesh string passed, loading mesh from disk') |
||
| 3030 | self._mesh = io.read_vtk(mesh) |
||
| 3031 | else: |
||
| 3032 | self._mesh = mesh |
||
| 3033 | self._seg_image = seg_image |
||
| 3034 | self._path_seg_image = path_seg_image |
||
| 3035 | self._label_idx = label_idx |
||
| 3036 | self._min_n_pixels = min_n_pixels |
||
| 3037 | |||
| 3038 | self._list_applied_transforms = [] |
||
| 3039 | |||
| 3040 | def read_seg_image(self, |
||
| 3041 | path_seg_image=None): |
||
| 3042 | """ |
||
| 3043 | Read segmentation image from disk. Must be a single file (e.g., nrrd, 3D dicom) |
||
| 3044 | |||
| 3045 | Parameters |
||
| 3046 | ---------- |
||
| 3047 | path_seg_image : str, optional |
||
| 3048 | Path to the medical image file to be loaded in, by default None |
||
| 3049 | |||
| 3050 | Raises |
||
| 3051 | ------ |
||
| 3052 | Exception |
||
| 3053 | If path_seg_image does not exist, exception is raised. |
||
| 3054 | """ |
||
| 3055 | # If passing new location/seg image name, then update variables. |
||
| 3056 | if path_seg_image is not None: |
||
| 3057 | self._path_seg_image = path_seg_image |
||
| 3058 | |||
| 3059 | # If seg image location / name exist, then load image else raise exception |
||
| 3060 | if (self._path_seg_image is not None): |
||
| 3061 | self._seg_image = sitk.ReadImage(self._path_seg_image) |
||
| 3062 | else: |
||
| 3063 | raise Exception('No file path (self._path_seg_image) provided.') |
||
| 3064 | |||
| 3065 | def create_mesh(self, |
||
| 3066 | smooth_image=True, |
||
| 3067 | smooth_image_var=0.3125 / 2, |
||
| 3068 | marching_cubes_threshold=0.5, |
||
| 3069 | label_idx=None, |
||
| 3070 | min_n_pixels=None): |
||
| 3071 | """ |
||
| 3072 | Create a surface mesh from the classes `_seg_image`. If `_seg_image` |
||
| 3073 | does not exist, then read it in using `read_seg_image`. |
||
| 3074 | |||
| 3075 | Parameters |
||
| 3076 | ---------- |
||
| 3077 | smooth_image : bool, optional |
||
| 3078 | Should the `_seg_image` be gaussian filtered, by default True |
||
| 3079 | smooth_image_var : float, optional |
||
| 3080 | Variance of gaussian filter to apply to `_seg_image`, by default 0.3125/2 |
||
| 3081 | marching_cubes_threshold : float, optional |
||
| 3082 | Threshold contour level to create surface mesh on, by default 0.5 |
||
| 3083 | label_idx : int, optional |
||
| 3084 | Label value / index to create mesh from, by default None |
||
| 3085 | min_n_pixels : int, optional |
||
| 3086 | Minimum number of continuous pixels to include segmentation island |
||
| 3087 | in the surface mesh creation, by default None |
||
| 3088 | |||
| 3089 | Raises |
||
| 3090 | ------ |
||
| 3091 | Exception |
||
| 3092 | If the total number of pixels segmentated (`n_pixels_labelled`) is |
||
| 3093 | < `min_n_pixels` then there is no object in the image. |
||
| 3094 | Exception |
||
| 3095 | If no `_seg_image` and no `label_idx` then we don't know what tissue to create the |
||
| 3096 | surface mesh from. |
||
| 3097 | Exception |
||
| 3098 | If no `_seg_image` or `path_seg_image` then we have no image to create mesh from. |
||
| 3099 | """ |
||
| 3100 | # allow assigning label idx during mesh creation step. |
||
| 3101 | if label_idx is not None: |
||
| 3102 | self._label_idx = label_idx |
||
| 3103 | |||
| 3104 | if self._seg_image is None: |
||
| 3105 | self.read_seg_image() |
||
| 3106 | |||
| 3107 | # Ensure the image has a certain number of pixels with the label of interest, otherwise there might be an issue. |
||
| 3108 | if min_n_pixels is None: min_n_pixels = self._min_n_pixels |
||
| 3109 | seg_view = sitk.GetArrayViewFromImage(self._seg_image) |
||
| 3110 | n_pixels_labelled = sum(seg_view[seg_view == self._label_idx]) |
||
| 3111 | |||
| 3112 | if n_pixels_labelled < min_n_pixels: |
||
| 3113 | raise Exception('The mesh does not exist in this segmentation!, only {} pixels detected, threshold # is {}'.format(n_pixels_labelled, |
||
| 3114 | marching_cubes_threshold)) |
||
| 3115 | tmp_filename = ''.join(random.choice(string.ascii_lowercase) for i in range(10)) + '.nrrd' |
||
| 3116 | self._mesh = create_surface_mesh(self._seg_image, |
||
| 3117 | self._label_idx, |
||
| 3118 | smooth_image_var, |
||
| 3119 | loc_tmp_save='/tmp', |
||
| 3120 | tmp_filename=tmp_filename, |
||
| 3121 | mc_threshold=marching_cubes_threshold, |
||
| 3122 | filter_binary_image=smooth_image |
||
| 3123 | ) |
||
| 3124 | safely_delete_tmp_file('/tmp', |
||
| 3125 | tmp_filename) |
||
| 3126 | |||
| 3127 | def save_mesh(self, |
||
| 3128 | filepath): |
||
| 3129 | """ |
||
| 3130 | Save the surface mesh from this class to disk. |
||
| 3131 | |||
| 3132 | Parameters |
||
| 3133 | ---------- |
||
| 3134 | filepath : str |
||
| 3135 | Location & filename to save the surface mesh (vtk.vtkPolyData) to. |
||
| 3136 | """ |
||
| 3137 | io.write_vtk(self._mesh, filepath) |
||
| 3138 | |||
| 3139 | def resample_surface(self, |
||
| 3140 | subdivisions=2, |
||
| 3141 | clusters=10000 |
||
| 3142 | ): |
||
| 3143 | """ |
||
| 3144 | Resample a surface mesh using the ACVD algorithm: |
||
| 3145 | Version used: |
||
| 3146 | - https://github.com/pyvista/pyacvd |
||
| 3147 | Original version w/ more references: |
||
| 3148 | - https://github.com/valette/ACVD |
||
| 3149 | |||
| 3150 | Parameters |
||
| 3151 | ---------- |
||
| 3152 | subdivisions : int, optional |
||
| 3153 | Subdivide the mesh to have more points before clustering, by default 2 |
||
| 3154 | Probably not necessary for very dense meshes. |
||
| 3155 | clusters : int, optional |
||
| 3156 | The number of clusters (points/vertices) to create during resampling |
||
| 3157 | surafce, by default 10000 |
||
| 3158 | - This is not exact, might have slight differences. |
||
| 3159 | """ |
||
| 3160 | self._mesh = resample_surface(self._mesh, subdivisions=subdivisions, clusters=clusters) |
||
| 3161 | |||
| 3162 | def apply_transform_to_mesh(self, |
||
| 3163 | transform=None, |
||
| 3164 | transformer=None, |
||
| 3165 | save_transform=True): |
||
| 3166 | """ |
||
| 3167 | Apply a transformation to the surface mesh. |
||
| 3168 | |||
| 3169 | Parameters |
||
| 3170 | ---------- |
||
| 3171 | transform : vtk.vtkTransform, optional |
||
| 3172 | Transformation to apply to mesh, by default None |
||
| 3173 | transformer : vtk.vtkTransformFilter, optional |
||
| 3174 | Can supply transformFilter directly, by default None |
||
| 3175 | save_transform : bool, optional |
||
| 3176 | Should transform be saved to list of applied transforms, by default True |
||
| 3177 | |||
| 3178 | Raises |
||
| 3179 | ------ |
||
| 3180 | Exception |
||
| 3181 | No `transform` or `transformer` supplied - have not transformation |
||
| 3182 | to apply. |
||
| 3183 | """ |
||
| 3184 | if (transform is not None) & (transformer is None): |
||
| 3185 | transformer = vtk.vtkTransformPolyDataFilter() |
||
| 3186 | transformer.SetTransform(transform) |
||
| 3187 | |||
| 3188 | elif (transform is None) & (transformer is not None): |
||
| 3189 | transform = transformer.GetTransform() |
||
| 3190 | |||
| 3191 | if transformer is not None: |
||
| 3192 | transformer.SetInputData(self._mesh) |
||
| 3193 | transformer.Update() |
||
| 3194 | self._mesh = vtk_deep_copy(transformer.GetOutput()) |
||
| 3195 | |||
| 3196 | if save_transform is True: |
||
| 3197 | self._list_applied_transforms.append(transform) |
||
| 3198 | |||
| 3199 | else: |
||
| 3200 | raise Exception('No transform or transformer provided') |
||
| 3201 | |||
| 3202 | def reverse_most_recent_transform(self): |
||
| 3203 | """ |
||
| 3204 | Function to undo the most recent transformation stored in self._list_applied_transforms |
||
| 3205 | """ |
||
| 3206 | transform = self._list_applied_transforms.pop() |
||
| 3207 | transform.Inverse() |
||
| 3208 | self.apply_transform_to_mesh(transform=transform, save_transform=False) |
||
| 3209 | |||
| 3210 | def reverse_all_transforms(self): |
||
| 3211 | """ |
||
| 3212 | Function to iterate over all of the self._list_applied_transforms (in reverse order) and undo them. |
||
| 3213 | """ |
||
| 3214 | while len(self._list_applied_transforms) > 0: |
||
| 3215 | self.reverse_most_recent_transform() |
||
| 3216 | |||
| 3217 | def non_rigidly_register( |
||
| 3218 | self, |
||
| 3219 | other_mesh, |
||
| 3220 | as_source=True, |
||
| 3221 | apply_transform_to_mesh=True, |
||
| 3222 | return_transformed_mesh=False, |
||
| 3223 | **kwargs |
||
| 3224 | ): |
||
| 3225 | """ |
||
| 3226 | Function to perform non rigid registration between this mesh and another mesh. |
||
| 3227 | |||
| 3228 | Parameters |
||
| 3229 | ---------- |
||
| 3230 | other_mesh : pymskt.mesh.Mesh or vtk.vtkPolyData |
||
| 3231 | Other mesh to use in registration process |
||
| 3232 | as_source : bool, optional |
||
| 3233 | Should the current mesh (in this object) be the source or the target, by default True |
||
| 3234 | apply_transform_to_mesh : bool, optional |
||
| 3235 | If as_source is True should we apply transformation to internal mesh, by default True |
||
| 3236 | return_transformed_mesh : bool, optional |
||
| 3237 | Should we return the registered mesh, by default False |
||
| 3238 | |||
| 3239 | Returns |
||
| 3240 | ------- |
||
| 3241 | _type_ |
||
| 3242 | _description_ |
||
| 3243 | """ |
||
| 3244 | # Setup the source & target meshes based on `as_source`` |
||
| 3245 | if as_source is True: |
||
| 3246 | source = self._mesh |
||
| 3247 | target = other_mesh |
||
| 3248 | elif as_source is False: |
||
| 3249 | source = other_mesh |
||
| 3250 | target = self._mesh |
||
| 3251 | |||
| 3252 | # Get registered mesh (source to target) |
||
| 3253 | source_transformed_to_target = non_rigidly_register( |
||
| 3254 | target_mesh=target, |
||
| 3255 | source_mesh=source, |
||
| 3256 | **kwargs |
||
| 3257 | ) |
||
| 3258 | |||
| 3259 | # If current mesh is source & apply_transform_to_mesh is true then replace current mesh. |
||
| 3260 | if (as_source is True) & (apply_transform_to_mesh is True): |
||
| 3261 | self._mesh = source_transformed_to_target |
||
| 3262 | |||
| 3263 | # curent mesh is target, or is source & want to return mesh, then return it. |
||
| 3264 | if (as_source is False) or ((as_source is True) & (return_transformed_mesh is True)): |
||
| 3265 | return source_transformed_to_target |
||
| 3266 | |||
| 3267 | def rigidly_register( |
||
| 3268 | self, |
||
| 3269 | other_mesh, |
||
| 3270 | as_source=True, |
||
| 3271 | apply_transform_to_mesh=True, |
||
| 3272 | return_transformed_mesh=False, |
||
| 3273 | return_transform=False, |
||
| 3274 | max_n_iter=100, |
||
| 3275 | n_landmarks=1000, |
||
| 3276 | reg_mode='similarity' |
||
| 3277 | |||
| 3278 | ): |
||
| 3279 | """ |
||
| 3280 | Function to perform rigid registration between this mesh and another mesh. |
||
| 3281 | |||
| 3282 | Parameters |
||
| 3283 | ---------- |
||
| 3284 | other_mesh : pymskt.mesh.Mesh or vtk.vtkPolyData |
||
| 3285 | Other mesh to use in registration process |
||
| 3286 | as_source : bool, optional |
||
| 3287 | Should the current mesh (in this object) be the source or the target, by default True |
||
| 3288 | apply_transform_to_mesh : bool, optional |
||
| 3289 | If as_source is True should we apply transformation to internal mesh, by default True |
||
| 3290 | return_transformed_mesh : bool, optional |
||
| 3291 | Should we return the registered mesh, by default False |
||
| 3292 | max_n_iter : int, optional |
||
| 3293 | Maximum number of iterations to perform, by default 100 |
||
| 3294 | n_landmarks : int, optional |
||
| 3295 | Number of landmarks to use in registration, by default 1000 |
||
| 3296 | reg_mode : str, optional |
||
| 3297 | Mode of registration to use, by default 'similarity' (similarity, rigid, or affine) |
||
| 3298 | |||
| 3299 | Returns |
||
| 3300 | ------- |
||
| 3301 | _type_ |
||
| 3302 | _description_ |
||
| 3303 | """ |
||
| 3304 | |||
| 3305 | if (return_transform is True) & (return_transformed_mesh is True): |
||
| 3306 | raise Exception('Cannot return both transformed mesh and transform') |
||
| 3307 | |||
| 3308 | if type(other_mesh) in (pymskt.mesh.meshes.BoneMesh, pymskt.mesh.meshes.Mesh): |
||
| 3309 | other_mesh = other_mesh.mesh |
||
| 3310 | |||
| 3311 | # Setup the source & target meshes based on `as_source`` |
||
| 3312 | if as_source is True: |
||
| 3313 | source = self._mesh |
||
| 3314 | target = other_mesh |
||
| 3315 | elif as_source is False: |
||
| 3316 | source = other_mesh |
||
| 3317 | target = self._mesh |
||
| 3318 | |||
| 3319 | icp_transform = get_icp_transform( |
||
| 3320 | source=source, |
||
| 3321 | target=target, |
||
| 3322 | max_n_iter=max_n_iter, |
||
| 3323 | n_landmarks=n_landmarks, |
||
| 3324 | reg_mode=reg_mode |
||
| 3325 | ) |
||
| 3326 | |||
| 3327 | # If current mesh is source & apply_transform_to_mesh is true then replace current mesh. |
||
| 3328 | if (as_source is True) & (apply_transform_to_mesh is True): |
||
| 3329 | self.apply_transform_to_mesh(transform=icp_transform) |
||
| 3330 | |||
| 3331 | if return_transformed_mesh is True: |
||
| 3332 | return self._mesh |
||
| 3333 | |||
| 3334 | elif return_transform is True: |
||
| 3335 | return icp_transform |
||
| 3336 | |||
| 3337 | # curent mesh is target, or is source & want to return mesh, then return it. |
||
| 3338 | elif (as_source is False) & (return_transformed_mesh is True): |
||
| 3339 | return apply_transform(source=source, transform=icp_transform) |
||
| 3340 | |||
| 3341 | else: |
||
| 3342 | raise Exception('Nothing to return from rigid registration.') |
||
| 3343 | |||
| 3344 | def copy_scalars_from_other_mesh_to_currect( |
||
| 3345 | self, |
||
| 3346 | other_mesh, |
||
| 3347 | new_scalars_name='scalars_from_other_mesh', |
||
| 3348 | weighted_avg=True, # Use weighted average, otherwise guassian smooth transfer |
||
| 3349 | n_closest=3, |
||
| 3350 | sigma=1., |
||
| 3351 | idx_coords_to_smooth_base=None, |
||
| 3352 | idx_coords_to_smooth_other=None, |
||
| 3353 | set_non_smoothed_scalars_to_zero=True, |
||
| 3354 | ): |
||
| 3355 | """ |
||
| 3356 | Convenience function to enable easy transfer scalars from another mesh to the current. |
||
| 3357 | Can use either a gaussian smoothing function, or transfer using nearest neighbours. |
||
| 3358 | |||
| 3359 | ** This function requires that the `other_mesh` is non-rigidly registered to the surface |
||
| 3360 | of the mesh inside of this class. Or rigidly registered but using the same anatomy that |
||
| 3361 | VERY closely matches. Otherwise, the transfered scalars will be bad. |
||
| 3362 | |||
| 3363 | Parameters |
||
| 3364 | ---------- |
||
| 3365 | other_mesh : pymskt.mesh.Mesh or vtk.vtkPolyData |
||
| 3366 | Mesh we want to copy |
||
| 3367 | new_scalars_name : str, optional |
||
| 3368 | What to name the scalars being transfered to this current mesh, by default 'scalars_from_other_mesh' |
||
| 3369 | weighted_avg : bool, optional |
||
| 3370 | Should we use `weighted average` or `gaussian smooth` methods for transfer, by default True |
||
| 3371 | n_closest : int, optional |
||
| 3372 | If `weighted_avg` True, the number of nearest neighbours to use, by default 3 |
||
| 3373 | sigma : float, optional |
||
| 3374 | If `weighted_avg` False, the standard deviation of gaussian kernel, by default 1. |
||
| 3375 | idx_coords_to_smooth_base : list, optional |
||
| 3376 | If `weighted_avg` False, list of indices from current mesh to use in transfer, by default None |
||
| 3377 | idx_coords_to_smooth_other : list, optional |
||
| 3378 | If `weighted_avg` False, list of indices from `other_mesh` to use in transfer, by default None |
||
| 3379 | set_non_smoothed_scalars_to_zero : bool, optional |
||
| 3380 | Should all other indices (not included in idx_coords_to_smooth_other) be set to 0, by default True |
||
| 3381 | """ |
||
| 3382 | if type(other_mesh) is Mesh: |
||
| 3383 | other_mesh = other_mesh.mesh |
||
| 3384 | elif type(other_mesh) is vtk.vtkPolyData: |
||
| 3385 | pass |
||
| 3386 | else: |
||
| 3387 | raise TypeError(f'other_mesh must be type `pymskt.mesh.Mesh` or `vtk.vtkPolyData` and received: {type(other_mesh)}') |
||
| 3388 | |||
| 3389 | if weighted_avg is True: |
||
| 3390 | transferred_scalars = transfer_mesh_scalars_get_weighted_average_n_closest( |
||
| 3391 | self._mesh, |
||
| 3392 | other_mesh, |
||
| 3393 | n=n_closest |
||
| 3394 | ) |
||
| 3395 | else: |
||
| 3396 | transferred_scalars = smooth_scalars_from_second_mesh_onto_base( |
||
| 3397 | self._mesh, |
||
| 3398 | other_mesh, |
||
| 3399 | sigma=sigma, |
||
| 3400 | idx_coords_to_smooth_base=idx_coords_to_smooth_base, |
||
| 3401 | idx_coords_to_smooth_second=idx_coords_to_smooth_other, |
||
| 3402 | set_non_smoothed_scalars_to_zero=set_non_smoothed_scalars_to_zero |
||
| 3403 | ) |
||
| 3404 | if (new_scalars_name is None) & (weighted_avg is True): |
||
| 3405 | if transferred_scalars.shape[1] > 1: |
||
| 3406 | n_arrays = other_mesh.GetPointData().GetNumberOfArrays() |
||
| 3407 | array_names = [other_mesh.GetPointData().GetArray(array_idx).GetName() for array_idx in range(n_arrays)] |
||
| 3408 | for idx, array_name in enumerate(array_names): |
||
| 3409 | vtk_transferred_scalars = numpy_to_vtk(transferred_scalars[:,idx]) |
||
| 3410 | vtk_transferred_scalars.SetName(array_name) |
||
| 3411 | self._mesh.GetPointData().AddArray(vtk_transferred_scalars) |
||
| 3412 | return |
||
| 3413 | |||
| 3414 | vtk_transferred_scalars = numpy_to_vtk(transferred_scalars) |
||
| 3415 | vtk_transferred_scalars.SetName(new_scalars_name) |
||
| 3416 | self._mesh.GetPointData().AddArray(vtk_transferred_scalars) |
||
| 3417 | |||
| 3418 | @property |
||
| 3419 | def seg_image(self): |
||
| 3420 | """ |
||
| 3421 | Return the `_seg_image` object |
||
| 3422 | |||
| 3423 | Returns |
||
| 3424 | ------- |
||
| 3425 | SimpleITK.Image |
||
| 3426 | Segmentation image used to build the surface mesh |
||
| 3427 | """ |
||
| 3428 | return self._seg_image |
||
| 3429 | |||
| 3430 | @seg_image.setter |
||
| 3431 | def seg_image(self, new_seg_image): |
||
| 3432 | """ |
||
| 3433 | Set the `_seg_image` of the class to be the inputted `new_seg_image`. |
||
| 3434 | |||
| 3435 | Parameters |
||
| 3436 | ---------- |
||
| 3437 | new_seg_image : SimpleITK.Image |
||
| 3438 | New image to use for creating surface mesh. This can be used to provide image to |
||
| 3439 | class if it was not provided during `__init__` |
||
| 3440 | """ |
||
| 3441 | self._seg_image = new_seg_image |
||
| 3442 | |||
| 3443 | @property |
||
| 3444 | def mesh(self): |
||
| 3445 | """ |
||
| 3446 | Return the `_mesh` object |
||
| 3447 | |||
| 3448 | Returns |
||
| 3449 | ------- |
||
| 3450 | vtk.vtkPolyData |
||
| 3451 | The main mesh of this class. |
||
| 3452 | """ |
||
| 3453 | return self._mesh |
||
| 3454 | |||
| 3455 | @mesh.setter |
||
| 3456 | def mesh(self, new_mesh): |
||
| 3457 | """ |
||
| 3458 | Set the `_mesh` of the class to be the inputted `new_mesh` |
||
| 3459 | |||
| 3460 | Parameters |
||
| 3461 | ---------- |
||
| 3462 | new_mesh : vtk.vtkPolyData |
||
| 3463 | New mesh for this class - or a method to provide a mesh to the class |
||
| 3464 | after `__init__` has already been run. |
||
| 3465 | """ |
||
| 3466 | self._mesh = new_mesh |
||
| 3467 | |||
| 3468 | @property |
||
| 3469 | def point_coords(self): |
||
| 3470 | """ |
||
| 3471 | Convenience function to return the vertices (point coordinates) for the surface mesh. |
||
| 3472 | |||
| 3473 | Returns |
||
| 3474 | ------- |
||
| 3475 | numpy.ndarray |
||
| 3476 | Mx3 numpy array containing the x/y/z position of each vertex of the mesh. |
||
| 3477 | """ |
||
| 3478 | return get_mesh_physical_point_coords(self._mesh) |
||
| 3479 | |||
| 3480 | @point_coords.setter |
||
| 3481 | def point_coords(self, new_point_coords): |
||
| 3482 | """ |
||
| 3483 | Convenience function to change/update the vertices/points locations |
||
| 3484 | |||
| 3485 | Parameters |
||
| 3486 | ---------- |
||
| 3487 | new_point_coords : numpy.ndarray |
||
| 3488 | n_points X 3 numpy array to replace exisiting point coordinate locations |
||
| 3489 | This can be used to easily/quickly update the x/y/z position of a set of points on a surface mesh. |
||
| 3490 | The `new_point_coords` must include the same number of points as the mesh contains. |
||
| 3491 | """ |
||
| 3492 | orig_point_coords = get_mesh_physical_point_coords(self._mesh) |
||
| 3493 | if new_point_coords.shape == orig_point_coords.shape: |
||
| 3494 | self._mesh.GetPoints().SetData(numpy_to_vtk(new_point_coords)) |
||
| 3495 | |||
| 3496 | |||
| 3497 | @property |
||
| 3498 | def path_seg_image(self): |
||
| 3499 | """ |
||
| 3500 | Convenience function to get the `path_seg_image` |
||
| 3501 | |||
| 3502 | Returns |
||
| 3503 | ------- |
||
| 3504 | str |
||
| 3505 | Path to the segmentation image |
||
| 3506 | """ |
||
| 3507 | return self._path_seg_image |
||
| 3508 | |||
| 3509 | @path_seg_image.setter |
||
| 3510 | def path_seg_image(self, new_path_seg_image): |
||
| 3511 | """ |
||
| 3512 | Convenience function to set the `path_seg_image` |
||
| 3513 | |||
| 3514 | Parameters |
||
| 3515 | ---------- |
||
| 3516 | new_path_seg_image : str |
||
| 3517 | String to where segmentation image that should be loaded is. |
||
| 3518 | """ |
||
| 3519 | self._path_seg_image = new_path_seg_image |
||
| 3520 | |||
| 3521 | @property |
||
| 3522 | def label_idx(self): |
||
| 3523 | """ |
||
| 3524 | Convenience function to get `label_idx` |
||
| 3525 | |||
| 3526 | Returns |
||
| 3527 | ------- |
||
| 3528 | int |
||
| 3529 | Integer indeicating the index/value of the tissues in `seg_image` associated with this mesh. |
||
| 3530 | """ |
||
| 3531 | return self._label_idx |
||
| 3532 | |||
| 3533 | @label_idx.setter |
||
| 3534 | def label_idx(self, new_label_idx): |
||
| 3535 | """ |
||
| 3536 | Convenience function to set `label_idx` |
||
| 3537 | |||
| 3538 | Parameters |
||
| 3539 | ---------- |
||
| 3540 | new_label_idx : int |
||
| 3541 | Integer indeicating the index/value of the tissues in `seg_image` associated with this mesh. |
||
| 3542 | """ |
||
| 3543 | self._label_idx = new_label_idx |
||
| 3544 | |||
| 3545 | @property |
||
| 3546 | def min_n_pixels(self): |
||
| 3547 | """ |
||
| 3548 | Convenience function to get the minimum number of pixels for a segmentation region to be created as a mesh. |
||
| 3549 | |||
| 3550 | Returns |
||
| 3551 | ------- |
||
| 3552 | int |
||
| 3553 | Minimum number of pixels needed to create a mesh. Less than this and it will be skipped / error raised. |
||
| 3554 | """ |
||
| 3555 | return self._min_n_pixels |
||
| 3556 | |||
| 3557 | @min_n_pixels.setter |
||
| 3558 | def min_n_pixels(self, new_min_n_pixels): |
||
| 3559 | """ |
||
| 3560 | Convenience function to set the minimum number of pixels for a segmentation region to be created as a mesh. |
||
| 3561 | |||
| 3562 | Parameters |
||
| 3563 | ---------- |
||
| 3564 | new_min_n_pixels : int |
||
| 3565 | Minimum number of pixels needed to create a mesh. Less than this and it will be skipped / error raised. |
||
| 3566 | """ |
||
| 3567 | self._min_n_pixels = new_min_n_pixels |
||
| 3568 | |||
| 3569 | @property |
||
| 3570 | def list_applied_transforms(self): |
||
| 3571 | """ |
||
| 3572 | Convenience function to get the list of transformations that have been applied to this mesh. |
||
| 3573 | |||
| 3574 | Returns |
||
| 3575 | ------- |
||
| 3576 | list |
||
| 3577 | List of vtk.vtkTransform objects that have been applied to the current mesh. |
||
| 3578 | """ |
||
| 3579 | return self._list_applied_transforms</code></pre> |
||
| 3580 | </details> |
||
| 3581 | <h3>Subclasses</h3> |
||
| 3582 | <ul class="hlist"> |
||
| 3583 | <li><a title="pymskt.mesh.meshes.BoneMesh" href="#pymskt.mesh.meshes.BoneMesh">BoneMesh</a></li> |
||
| 3584 | <li><a title="pymskt.mesh.meshes.CartilageMesh" href="#pymskt.mesh.meshes.CartilageMesh">CartilageMesh</a></li> |
||
| 3585 | </ul> |
||
| 3586 | <h3>Instance variables</h3> |
||
| 3587 | <dl> |
||
| 3588 | <dt id="pymskt.mesh.meshes.Mesh.label_idx"><code class="name">var <span class="ident">label_idx</span></code></dt> |
||
| 3589 | <dd> |
||
| 3590 | <div class="desc"><p>Convenience function to get <code>label_idx</code></p> |
||
| 3591 | <h2 id="returns">Returns</h2> |
||
| 3592 | <dl> |
||
| 3593 | <dt><code>int</code></dt> |
||
| 3594 | <dd>Integer indeicating the index/value of the tissues in <code>seg_image</code> associated with this mesh.</dd> |
||
| 3595 | </dl></div> |
||
| 3596 | <details class="source"> |
||
| 3597 | <summary> |
||
| 3598 | <span>Expand source code</span> |
||
| 3599 | </summary> |
||
| 3600 | <pre><code class="python">@property |
||
| 3601 | def label_idx(self): |
||
| 3602 | """ |
||
| 3603 | Convenience function to get `label_idx` |
||
| 3604 | |||
| 3605 | Returns |
||
| 3606 | ------- |
||
| 3607 | int |
||
| 3608 | Integer indeicating the index/value of the tissues in `seg_image` associated with this mesh. |
||
| 3609 | """ |
||
| 3610 | return self._label_idx</code></pre> |
||
| 3611 | </details> |
||
| 3612 | </dd> |
||
| 3613 | <dt id="pymskt.mesh.meshes.Mesh.list_applied_transforms"><code class="name">var <span class="ident">list_applied_transforms</span></code></dt> |
||
| 3614 | <dd> |
||
| 3615 | <div class="desc"><p>Convenience function to get the list of transformations that have been applied to this mesh. </p> |
||
| 3616 | <h2 id="returns">Returns</h2> |
||
| 3617 | <dl> |
||
| 3618 | <dt><code>list</code></dt> |
||
| 3619 | <dd>List of vtk.vtkTransform objects that have been applied to the current mesh.</dd> |
||
| 3620 | </dl></div> |
||
| 3621 | <details class="source"> |
||
| 3622 | <summary> |
||
| 3623 | <span>Expand source code</span> |
||
| 3624 | </summary> |
||
| 3625 | <pre><code class="python">@property |
||
| 3626 | def list_applied_transforms(self): |
||
| 3627 | """ |
||
| 3628 | Convenience function to get the list of transformations that have been applied to this mesh. |
||
| 3629 | |||
| 3630 | Returns |
||
| 3631 | ------- |
||
| 3632 | list |
||
| 3633 | List of vtk.vtkTransform objects that have been applied to the current mesh. |
||
| 3634 | """ |
||
| 3635 | return self._list_applied_transforms</code></pre> |
||
| 3636 | </details> |
||
| 3637 | </dd> |
||
| 3638 | <dt id="pymskt.mesh.meshes.Mesh.mesh"><code class="name">var <span class="ident">mesh</span></code></dt> |
||
| 3639 | <dd> |
||
| 3640 | <div class="desc"><p>Return the <code>_mesh</code> object</p> |
||
| 3641 | <h2 id="returns">Returns</h2> |
||
| 3642 | <dl> |
||
| 3643 | <dt><code>vtk.vtkPolyData</code></dt> |
||
| 3644 | <dd>The main mesh of this class.</dd> |
||
| 3645 | </dl></div> |
||
| 3646 | <details class="source"> |
||
| 3647 | <summary> |
||
| 3648 | <span>Expand source code</span> |
||
| 3649 | </summary> |
||
| 3650 | <pre><code class="python">@property |
||
| 3651 | def mesh(self): |
||
| 3652 | """ |
||
| 3653 | Return the `_mesh` object |
||
| 3654 | |||
| 3655 | Returns |
||
| 3656 | ------- |
||
| 3657 | vtk.vtkPolyData |
||
| 3658 | The main mesh of this class. |
||
| 3659 | """ |
||
| 3660 | return self._mesh</code></pre> |
||
| 3661 | </details> |
||
| 3662 | </dd> |
||
| 3663 | <dt id="pymskt.mesh.meshes.Mesh.min_n_pixels"><code class="name">var <span class="ident">min_n_pixels</span></code></dt> |
||
| 3664 | <dd> |
||
| 3665 | <div class="desc"><p>Convenience function to get the minimum number of pixels for a segmentation region to be created as a mesh. </p> |
||
| 3666 | <h2 id="returns">Returns</h2> |
||
| 3667 | <dl> |
||
| 3668 | <dt><code>int</code></dt> |
||
| 3669 | <dd>Minimum number of pixels needed to create a mesh. Less than this and it will be skipped / error raised.</dd> |
||
| 3670 | </dl></div> |
||
| 3671 | <details class="source"> |
||
| 3672 | <summary> |
||
| 3673 | <span>Expand source code</span> |
||
| 3674 | </summary> |
||
| 3675 | <pre><code class="python">@property |
||
| 3676 | def min_n_pixels(self): |
||
| 3677 | """ |
||
| 3678 | Convenience function to get the minimum number of pixels for a segmentation region to be created as a mesh. |
||
| 3679 | |||
| 3680 | Returns |
||
| 3681 | ------- |
||
| 3682 | int |
||
| 3683 | Minimum number of pixels needed to create a mesh. Less than this and it will be skipped / error raised. |
||
| 3684 | """ |
||
| 3685 | return self._min_n_pixels</code></pre> |
||
| 3686 | </details> |
||
| 3687 | </dd> |
||
| 3688 | <dt id="pymskt.mesh.meshes.Mesh.path_seg_image"><code class="name">var <span class="ident">path_seg_image</span></code></dt> |
||
| 3689 | <dd> |
||
| 3690 | <div class="desc"><p>Convenience function to get the <code>path_seg_image</code></p> |
||
| 3691 | <h2 id="returns">Returns</h2> |
||
| 3692 | <dl> |
||
| 3693 | <dt><code>str</code></dt> |
||
| 3694 | <dd>Path to the segmentation image</dd> |
||
| 3695 | </dl></div> |
||
| 3696 | <details class="source"> |
||
| 3697 | <summary> |
||
| 3698 | <span>Expand source code</span> |
||
| 3699 | </summary> |
||
| 3700 | <pre><code class="python">@property |
||
| 3701 | def path_seg_image(self): |
||
| 3702 | """ |
||
| 3703 | Convenience function to get the `path_seg_image` |
||
| 3704 | |||
| 3705 | Returns |
||
| 3706 | ------- |
||
| 3707 | str |
||
| 3708 | Path to the segmentation image |
||
| 3709 | """ |
||
| 3710 | return self._path_seg_image</code></pre> |
||
| 3711 | </details> |
||
| 3712 | </dd> |
||
| 3713 | <dt id="pymskt.mesh.meshes.Mesh.point_coords"><code class="name">var <span class="ident">point_coords</span></code></dt> |
||
| 3714 | <dd> |
||
| 3715 | <div class="desc"><p>Convenience function to return the vertices (point coordinates) for the surface mesh. </p> |
||
| 3716 | <h2 id="returns">Returns</h2> |
||
| 3717 | <dl> |
||
| 3718 | <dt><code>numpy.ndarray</code></dt> |
||
| 3719 | <dd>Mx3 numpy array containing the x/y/z position of each vertex of the mesh.</dd> |
||
| 3720 | </dl></div> |
||
| 3721 | <details class="source"> |
||
| 3722 | <summary> |
||
| 3723 | <span>Expand source code</span> |
||
| 3724 | </summary> |
||
| 3725 | <pre><code class="python">@property |
||
| 3726 | def point_coords(self): |
||
| 3727 | """ |
||
| 3728 | Convenience function to return the vertices (point coordinates) for the surface mesh. |
||
| 3729 | |||
| 3730 | Returns |
||
| 3731 | ------- |
||
| 3732 | numpy.ndarray |
||
| 3733 | Mx3 numpy array containing the x/y/z position of each vertex of the mesh. |
||
| 3734 | """ |
||
| 3735 | return get_mesh_physical_point_coords(self._mesh)</code></pre> |
||
| 3736 | </details> |
||
| 3737 | </dd> |
||
| 3738 | <dt id="pymskt.mesh.meshes.Mesh.seg_image"><code class="name">var <span class="ident">seg_image</span></code></dt> |
||
| 3739 | <dd> |
||
| 3740 | <div class="desc"><p>Return the <code>_seg_image</code> object</p> |
||
| 3741 | <h2 id="returns">Returns</h2> |
||
| 3742 | <dl> |
||
| 3743 | <dt><code>SimpleITK.Image</code></dt> |
||
| 3744 | <dd>Segmentation image used to build the surface mesh</dd> |
||
| 3745 | </dl></div> |
||
| 3746 | <details class="source"> |
||
| 3747 | <summary> |
||
| 3748 | <span>Expand source code</span> |
||
| 3749 | </summary> |
||
| 3750 | <pre><code class="python">@property |
||
| 3751 | def seg_image(self): |
||
| 3752 | """ |
||
| 3753 | Return the `_seg_image` object |
||
| 3754 | |||
| 3755 | Returns |
||
| 3756 | ------- |
||
| 3757 | SimpleITK.Image |
||
| 3758 | Segmentation image used to build the surface mesh |
||
| 3759 | """ |
||
| 3760 | return self._seg_image</code></pre> |
||
| 3761 | </details> |
||
| 3762 | </dd> |
||
| 3763 | </dl> |
||
| 3764 | <h3>Methods</h3> |
||
| 3765 | <dl> |
||
| 3766 | <dt id="pymskt.mesh.meshes.Mesh.apply_transform_to_mesh"><code class="name flex"> |
||
| 3767 | <span>def <span class="ident">apply_transform_to_mesh</span></span>(<span>self, transform=None, transformer=None, save_transform=True)</span> |
||
| 3768 | </code></dt> |
||
| 3769 | <dd> |
||
| 3770 | <div class="desc"><p>Apply a transformation to the surface mesh. </p> |
||
| 3771 | <h2 id="parameters">Parameters</h2> |
||
| 3772 | <dl> |
||
| 3773 | <dt><strong><code>transform</code></strong> : <code>vtk.vtkTransform</code>, optional</dt> |
||
| 3774 | <dd>Transformation to apply to mesh, by default None</dd> |
||
| 3775 | <dt><strong><code>transformer</code></strong> : <code>vtk.vtkTransformFilter</code>, optional</dt> |
||
| 3776 | <dd>Can supply transformFilter directly, by default None</dd> |
||
| 3777 | <dt><strong><code>save_transform</code></strong> : <code>bool</code>, optional</dt> |
||
| 3778 | <dd>Should transform be saved to list of applied transforms, by default True</dd> |
||
| 3779 | </dl> |
||
| 3780 | <h2 id="raises">Raises</h2> |
||
| 3781 | <dl> |
||
| 3782 | <dt><code>Exception</code></dt> |
||
| 3783 | <dd>No <code>transform</code> or <code>transformer</code> supplied - have not transformation |
||
| 3784 | to apply.</dd> |
||
| 3785 | </dl></div> |
||
| 3786 | <details class="source"> |
||
| 3787 | <summary> |
||
| 3788 | <span>Expand source code</span> |
||
| 3789 | </summary> |
||
| 3790 | <pre><code class="python">def apply_transform_to_mesh(self, |
||
| 3791 | transform=None, |
||
| 3792 | transformer=None, |
||
| 3793 | save_transform=True): |
||
| 3794 | """ |
||
| 3795 | Apply a transformation to the surface mesh. |
||
| 3796 | |||
| 3797 | Parameters |
||
| 3798 | ---------- |
||
| 3799 | transform : vtk.vtkTransform, optional |
||
| 3800 | Transformation to apply to mesh, by default None |
||
| 3801 | transformer : vtk.vtkTransformFilter, optional |
||
| 3802 | Can supply transformFilter directly, by default None |
||
| 3803 | save_transform : bool, optional |
||
| 3804 | Should transform be saved to list of applied transforms, by default True |
||
| 3805 | |||
| 3806 | Raises |
||
| 3807 | ------ |
||
| 3808 | Exception |
||
| 3809 | No `transform` or `transformer` supplied - have not transformation |
||
| 3810 | to apply. |
||
| 3811 | """ |
||
| 3812 | if (transform is not None) & (transformer is None): |
||
| 3813 | transformer = vtk.vtkTransformPolyDataFilter() |
||
| 3814 | transformer.SetTransform(transform) |
||
| 3815 | |||
| 3816 | elif (transform is None) & (transformer is not None): |
||
| 3817 | transform = transformer.GetTransform() |
||
| 3818 | |||
| 3819 | if transformer is not None: |
||
| 3820 | transformer.SetInputData(self._mesh) |
||
| 3821 | transformer.Update() |
||
| 3822 | self._mesh = vtk_deep_copy(transformer.GetOutput()) |
||
| 3823 | |||
| 3824 | if save_transform is True: |
||
| 3825 | self._list_applied_transforms.append(transform) |
||
| 3826 | |||
| 3827 | else: |
||
| 3828 | raise Exception('No transform or transformer provided')</code></pre> |
||
| 3829 | </details> |
||
| 3830 | </dd> |
||
| 3831 | <dt id="pymskt.mesh.meshes.Mesh.copy_scalars_from_other_mesh_to_currect"><code class="name flex"> |
||
| 3832 | <span>def <span class="ident">copy_scalars_from_other_mesh_to_currect</span></span>(<span>self, other_mesh, new_scalars_name='scalars_from_other_mesh', weighted_avg=True, n_closest=3, sigma=1.0, idx_coords_to_smooth_base=None, idx_coords_to_smooth_other=None, set_non_smoothed_scalars_to_zero=True)</span> |
||
| 3833 | </code></dt> |
||
| 3834 | <dd> |
||
| 3835 | <div class="desc"><p>Convenience function to enable easy transfer scalars from another mesh to the current. |
||
| 3836 | Can use either a gaussian smoothing function, or transfer using nearest neighbours. </p> |
||
| 3837 | <p>** This function requires that the <code>other_mesh</code> is non-rigidly registered to the surface |
||
| 3838 | of the mesh inside of this class. Or rigidly registered but using the same anatomy that |
||
| 3839 | VERY closely matches. Otherwise, the transfered scalars will be bad. |
||
| 3840 | </p> |
||
| 3841 | <h2 id="parameters">Parameters</h2> |
||
| 3842 | <dl> |
||
| 3843 | <dt><strong><code>other_mesh</code></strong> : <code>pymskt.mesh.Mesh</code> or <code>vtk.vtkPolyData</code></dt> |
||
| 3844 | <dd>Mesh we want to copy</dd> |
||
| 3845 | <dt><strong><code>new_scalars_name</code></strong> : <code>str</code>, optional</dt> |
||
| 3846 | <dd> </dd> |
||
| 3847 | <dt>What to name the scalars being transfered to this current mesh, by default 'scalars_from_other_mesh'</dt> |
||
| 3848 | <dt><strong><code>weighted_avg</code></strong> : <code>bool</code>, optional</dt> |
||
| 3849 | <dd>Should we use <code>weighted average</code> or <code>gaussian smooth</code> methods for transfer, by default True</dd> |
||
| 3850 | <dt><strong><code>n_closest</code></strong> : <code>int</code>, optional</dt> |
||
| 3851 | <dd>If <code>weighted_avg</code> True, the number of nearest neighbours to use, by default 3</dd> |
||
| 3852 | <dt><strong><code>sigma</code></strong> : <code>float</code>, optional</dt> |
||
| 3853 | <dd>If <code>weighted_avg</code> False, the standard deviation of gaussian kernel, by default 1.</dd> |
||
| 3854 | <dt><strong><code>idx_coords_to_smooth_base</code></strong> : <code>list</code>, optional</dt> |
||
| 3855 | <dd>If <code>weighted_avg</code> False, list of indices from current mesh to use in transfer, by default None</dd> |
||
| 3856 | <dt><strong><code>idx_coords_to_smooth_other</code></strong> : <code>list</code>, optional</dt> |
||
| 3857 | <dd>If <code>weighted_avg</code> False, list of indices from <code>other_mesh</code> to use in transfer, by default None</dd> |
||
| 3858 | <dt><strong><code>set_non_smoothed_scalars_to_zero</code></strong> : <code>bool</code>, optional</dt> |
||
| 3859 | <dd>Should all other indices (not included in idx_coords_to_smooth_other) be set to 0, by default True</dd> |
||
| 3860 | </dl></div> |
||
| 3861 | <details class="source"> |
||
| 3862 | <summary> |
||
| 3863 | <span>Expand source code</span> |
||
| 3864 | </summary> |
||
| 3865 | <pre><code class="python">def copy_scalars_from_other_mesh_to_currect( |
||
| 3866 | self, |
||
| 3867 | other_mesh, |
||
| 3868 | new_scalars_name='scalars_from_other_mesh', |
||
| 3869 | weighted_avg=True, # Use weighted average, otherwise guassian smooth transfer |
||
| 3870 | n_closest=3, |
||
| 3871 | sigma=1., |
||
| 3872 | idx_coords_to_smooth_base=None, |
||
| 3873 | idx_coords_to_smooth_other=None, |
||
| 3874 | set_non_smoothed_scalars_to_zero=True, |
||
| 3875 | ): |
||
| 3876 | """ |
||
| 3877 | Convenience function to enable easy transfer scalars from another mesh to the current. |
||
| 3878 | Can use either a gaussian smoothing function, or transfer using nearest neighbours. |
||
| 3879 | |||
| 3880 | ** This function requires that the `other_mesh` is non-rigidly registered to the surface |
||
| 3881 | of the mesh inside of this class. Or rigidly registered but using the same anatomy that |
||
| 3882 | VERY closely matches. Otherwise, the transfered scalars will be bad. |
||
| 3883 | |||
| 3884 | Parameters |
||
| 3885 | ---------- |
||
| 3886 | other_mesh : pymskt.mesh.Mesh or vtk.vtkPolyData |
||
| 3887 | Mesh we want to copy |
||
| 3888 | new_scalars_name : str, optional |
||
| 3889 | What to name the scalars being transfered to this current mesh, by default 'scalars_from_other_mesh' |
||
| 3890 | weighted_avg : bool, optional |
||
| 3891 | Should we use `weighted average` or `gaussian smooth` methods for transfer, by default True |
||
| 3892 | n_closest : int, optional |
||
| 3893 | If `weighted_avg` True, the number of nearest neighbours to use, by default 3 |
||
| 3894 | sigma : float, optional |
||
| 3895 | If `weighted_avg` False, the standard deviation of gaussian kernel, by default 1. |
||
| 3896 | idx_coords_to_smooth_base : list, optional |
||
| 3897 | If `weighted_avg` False, list of indices from current mesh to use in transfer, by default None |
||
| 3898 | idx_coords_to_smooth_other : list, optional |
||
| 3899 | If `weighted_avg` False, list of indices from `other_mesh` to use in transfer, by default None |
||
| 3900 | set_non_smoothed_scalars_to_zero : bool, optional |
||
| 3901 | Should all other indices (not included in idx_coords_to_smooth_other) be set to 0, by default True |
||
| 3902 | """ |
||
| 3903 | if type(other_mesh) is Mesh: |
||
| 3904 | other_mesh = other_mesh.mesh |
||
| 3905 | elif type(other_mesh) is vtk.vtkPolyData: |
||
| 3906 | pass |
||
| 3907 | else: |
||
| 3908 | raise TypeError(f'other_mesh must be type `pymskt.mesh.Mesh` or `vtk.vtkPolyData` and received: {type(other_mesh)}') |
||
| 3909 | |||
| 3910 | if weighted_avg is True: |
||
| 3911 | transferred_scalars = transfer_mesh_scalars_get_weighted_average_n_closest( |
||
| 3912 | self._mesh, |
||
| 3913 | other_mesh, |
||
| 3914 | n=n_closest |
||
| 3915 | ) |
||
| 3916 | else: |
||
| 3917 | transferred_scalars = smooth_scalars_from_second_mesh_onto_base( |
||
| 3918 | self._mesh, |
||
| 3919 | other_mesh, |
||
| 3920 | sigma=sigma, |
||
| 3921 | idx_coords_to_smooth_base=idx_coords_to_smooth_base, |
||
| 3922 | idx_coords_to_smooth_second=idx_coords_to_smooth_other, |
||
| 3923 | set_non_smoothed_scalars_to_zero=set_non_smoothed_scalars_to_zero |
||
| 3924 | ) |
||
| 3925 | if (new_scalars_name is None) & (weighted_avg is True): |
||
| 3926 | if transferred_scalars.shape[1] > 1: |
||
| 3927 | n_arrays = other_mesh.GetPointData().GetNumberOfArrays() |
||
| 3928 | array_names = [other_mesh.GetPointData().GetArray(array_idx).GetName() for array_idx in range(n_arrays)] |
||
| 3929 | for idx, array_name in enumerate(array_names): |
||
| 3930 | vtk_transferred_scalars = numpy_to_vtk(transferred_scalars[:,idx]) |
||
| 3931 | vtk_transferred_scalars.SetName(array_name) |
||
| 3932 | self._mesh.GetPointData().AddArray(vtk_transferred_scalars) |
||
| 3933 | return |
||
| 3934 | |||
| 3935 | vtk_transferred_scalars = numpy_to_vtk(transferred_scalars) |
||
| 3936 | vtk_transferred_scalars.SetName(new_scalars_name) |
||
| 3937 | self._mesh.GetPointData().AddArray(vtk_transferred_scalars)</code></pre> |
||
| 3938 | </details> |
||
| 3939 | </dd> |
||
| 3940 | <dt id="pymskt.mesh.meshes.Mesh.create_mesh"><code class="name flex"> |
||
| 3941 | <span>def <span class="ident">create_mesh</span></span>(<span>self, smooth_image=True, smooth_image_var=0.15625, marching_cubes_threshold=0.5, label_idx=None, min_n_pixels=None)</span> |
||
| 3942 | </code></dt> |
||
| 3943 | <dd> |
||
| 3944 | <div class="desc"><p>Create a surface mesh from the classes <code>_seg_image</code>. If <code>_seg_image</code> |
||
| 3945 | does not exist, then read it in using <code>read_seg_image</code>. </p> |
||
| 3946 | <h2 id="parameters">Parameters</h2> |
||
| 3947 | <dl> |
||
| 3948 | <dt><strong><code>smooth_image</code></strong> : <code>bool</code>, optional</dt> |
||
| 3949 | <dd>Should the <code>_seg_image</code> be gaussian filtered, by default True</dd> |
||
| 3950 | <dt><strong><code>smooth_image_var</code></strong> : <code>float</code>, optional</dt> |
||
| 3951 | <dd>Variance of gaussian filter to apply to <code>_seg_image</code>, by default 0.3125/2</dd> |
||
| 3952 | <dt><strong><code>marching_cubes_threshold</code></strong> : <code>float</code>, optional</dt> |
||
| 3953 | <dd>Threshold contour level to create surface mesh on, by default 0.5</dd> |
||
| 3954 | <dt><strong><code>label_idx</code></strong> : <code>int</code>, optional</dt> |
||
| 3955 | <dd>Label value / index to create mesh from, by default None</dd> |
||
| 3956 | <dt><strong><code>min_n_pixels</code></strong> : <code>int</code>, optional</dt> |
||
| 3957 | <dd>Minimum number of continuous pixels to include segmentation island |
||
| 3958 | in the surface mesh creation, by default None</dd> |
||
| 3959 | </dl> |
||
| 3960 | <h2 id="raises">Raises</h2> |
||
| 3961 | <dl> |
||
| 3962 | <dt><code>Exception</code></dt> |
||
| 3963 | <dd>If the total number of pixels segmentated (<code>n_pixels_labelled</code>) is |
||
| 3964 | < <code>min_n_pixels</code> then there is no object in the image.</dd> |
||
| 3965 | <dt><code>Exception</code></dt> |
||
| 3966 | <dd>If no <code>_seg_image</code> and no <code>label_idx</code> then we don't know what tissue to create the |
||
| 3967 | surface mesh from.</dd> |
||
| 3968 | <dt><code>Exception</code></dt> |
||
| 3969 | <dd>If no <code>_seg_image</code> or <code>path_seg_image</code> then we have no image to create mesh from.</dd> |
||
| 3970 | </dl></div> |
||
| 3971 | <details class="source"> |
||
| 3972 | <summary> |
||
| 3973 | <span>Expand source code</span> |
||
| 3974 | </summary> |
||
| 3975 | <pre><code class="python">def create_mesh(self, |
||
| 3976 | smooth_image=True, |
||
| 3977 | smooth_image_var=0.3125 / 2, |
||
| 3978 | marching_cubes_threshold=0.5, |
||
| 3979 | label_idx=None, |
||
| 3980 | min_n_pixels=None): |
||
| 3981 | """ |
||
| 3982 | Create a surface mesh from the classes `_seg_image`. If `_seg_image` |
||
| 3983 | does not exist, then read it in using `read_seg_image`. |
||
| 3984 | |||
| 3985 | Parameters |
||
| 3986 | ---------- |
||
| 3987 | smooth_image : bool, optional |
||
| 3988 | Should the `_seg_image` be gaussian filtered, by default True |
||
| 3989 | smooth_image_var : float, optional |
||
| 3990 | Variance of gaussian filter to apply to `_seg_image`, by default 0.3125/2 |
||
| 3991 | marching_cubes_threshold : float, optional |
||
| 3992 | Threshold contour level to create surface mesh on, by default 0.5 |
||
| 3993 | label_idx : int, optional |
||
| 3994 | Label value / index to create mesh from, by default None |
||
| 3995 | min_n_pixels : int, optional |
||
| 3996 | Minimum number of continuous pixels to include segmentation island |
||
| 3997 | in the surface mesh creation, by default None |
||
| 3998 | |||
| 3999 | Raises |
||
| 4000 | ------ |
||
| 4001 | Exception |
||
| 4002 | If the total number of pixels segmentated (`n_pixels_labelled`) is |
||
| 4003 | < `min_n_pixels` then there is no object in the image. |
||
| 4004 | Exception |
||
| 4005 | If no `_seg_image` and no `label_idx` then we don't know what tissue to create the |
||
| 4006 | surface mesh from. |
||
| 4007 | Exception |
||
| 4008 | If no `_seg_image` or `path_seg_image` then we have no image to create mesh from. |
||
| 4009 | """ |
||
| 4010 | # allow assigning label idx during mesh creation step. |
||
| 4011 | if label_idx is not None: |
||
| 4012 | self._label_idx = label_idx |
||
| 4013 | |||
| 4014 | if self._seg_image is None: |
||
| 4015 | self.read_seg_image() |
||
| 4016 | |||
| 4017 | # Ensure the image has a certain number of pixels with the label of interest, otherwise there might be an issue. |
||
| 4018 | if min_n_pixels is None: min_n_pixels = self._min_n_pixels |
||
| 4019 | seg_view = sitk.GetArrayViewFromImage(self._seg_image) |
||
| 4020 | n_pixels_labelled = sum(seg_view[seg_view == self._label_idx]) |
||
| 4021 | |||
| 4022 | if n_pixels_labelled < min_n_pixels: |
||
| 4023 | raise Exception('The mesh does not exist in this segmentation!, only {} pixels detected, threshold # is {}'.format(n_pixels_labelled, |
||
| 4024 | marching_cubes_threshold)) |
||
| 4025 | tmp_filename = ''.join(random.choice(string.ascii_lowercase) for i in range(10)) + '.nrrd' |
||
| 4026 | self._mesh = create_surface_mesh(self._seg_image, |
||
| 4027 | self._label_idx, |
||
| 4028 | smooth_image_var, |
||
| 4029 | loc_tmp_save='/tmp', |
||
| 4030 | tmp_filename=tmp_filename, |
||
| 4031 | mc_threshold=marching_cubes_threshold, |
||
| 4032 | filter_binary_image=smooth_image |
||
| 4033 | ) |
||
| 4034 | safely_delete_tmp_file('/tmp', |
||
| 4035 | tmp_filename)</code></pre> |
||
| 4036 | </details> |
||
| 4037 | </dd> |
||
| 4038 | <dt id="pymskt.mesh.meshes.Mesh.non_rigidly_register"><code class="name flex"> |
||
| 4039 | <span>def <span class="ident">non_rigidly_register</span></span>(<span>self, other_mesh, as_source=True, apply_transform_to_mesh=True, return_transformed_mesh=False, **kwargs)</span> |
||
| 4040 | </code></dt> |
||
| 4041 | <dd> |
||
| 4042 | <div class="desc"><p>Function to perform non rigid registration between this mesh and another mesh. </p> |
||
| 4043 | <h2 id="parameters">Parameters</h2> |
||
| 4044 | <dl> |
||
| 4045 | <dt><strong><code>other_mesh</code></strong> : <code>pymskt.mesh.Mesh</code> or <code>vtk.vtkPolyData</code></dt> |
||
| 4046 | <dd>Other mesh to use in registration process</dd> |
||
| 4047 | <dt><strong><code>as_source</code></strong> : <code>bool</code>, optional</dt> |
||
| 4048 | <dd>Should the current mesh (in this object) be the source or the target, by default True</dd> |
||
| 4049 | <dt><strong><code>apply_transform_to_mesh</code></strong> : <code>bool</code>, optional</dt> |
||
| 4050 | <dd>If as_source is True should we apply transformation to internal mesh, by default True</dd> |
||
| 4051 | <dt><strong><code>return_transformed_mesh</code></strong> : <code>bool</code>, optional</dt> |
||
| 4052 | <dd>Should we return the registered mesh, by default False</dd> |
||
| 4053 | </dl> |
||
| 4054 | <h2 id="returns">Returns</h2> |
||
| 4055 | <dl> |
||
| 4056 | <dt><code>_type_</code></dt> |
||
| 4057 | <dd><em>description</em></dd> |
||
| 4058 | </dl></div> |
||
| 4059 | <details class="source"> |
||
| 4060 | <summary> |
||
| 4061 | <span>Expand source code</span> |
||
| 4062 | </summary> |
||
| 4063 | <pre><code class="python">def non_rigidly_register( |
||
| 4064 | self, |
||
| 4065 | other_mesh, |
||
| 4066 | as_source=True, |
||
| 4067 | apply_transform_to_mesh=True, |
||
| 4068 | return_transformed_mesh=False, |
||
| 4069 | **kwargs |
||
| 4070 | ): |
||
| 4071 | """ |
||
| 4072 | Function to perform non rigid registration between this mesh and another mesh. |
||
| 4073 | |||
| 4074 | Parameters |
||
| 4075 | ---------- |
||
| 4076 | other_mesh : pymskt.mesh.Mesh or vtk.vtkPolyData |
||
| 4077 | Other mesh to use in registration process |
||
| 4078 | as_source : bool, optional |
||
| 4079 | Should the current mesh (in this object) be the source or the target, by default True |
||
| 4080 | apply_transform_to_mesh : bool, optional |
||
| 4081 | If as_source is True should we apply transformation to internal mesh, by default True |
||
| 4082 | return_transformed_mesh : bool, optional |
||
| 4083 | Should we return the registered mesh, by default False |
||
| 4084 | |||
| 4085 | Returns |
||
| 4086 | ------- |
||
| 4087 | _type_ |
||
| 4088 | _description_ |
||
| 4089 | """ |
||
| 4090 | # Setup the source & target meshes based on `as_source`` |
||
| 4091 | if as_source is True: |
||
| 4092 | source = self._mesh |
||
| 4093 | target = other_mesh |
||
| 4094 | elif as_source is False: |
||
| 4095 | source = other_mesh |
||
| 4096 | target = self._mesh |
||
| 4097 | |||
| 4098 | # Get registered mesh (source to target) |
||
| 4099 | source_transformed_to_target = non_rigidly_register( |
||
| 4100 | target_mesh=target, |
||
| 4101 | source_mesh=source, |
||
| 4102 | **kwargs |
||
| 4103 | ) |
||
| 4104 | |||
| 4105 | # If current mesh is source & apply_transform_to_mesh is true then replace current mesh. |
||
| 4106 | if (as_source is True) & (apply_transform_to_mesh is True): |
||
| 4107 | self._mesh = source_transformed_to_target |
||
| 4108 | |||
| 4109 | # curent mesh is target, or is source & want to return mesh, then return it. |
||
| 4110 | if (as_source is False) or ((as_source is True) & (return_transformed_mesh is True)): |
||
| 4111 | return source_transformed_to_target</code></pre> |
||
| 4112 | </details> |
||
| 4113 | </dd> |
||
| 4114 | <dt id="pymskt.mesh.meshes.Mesh.read_seg_image"><code class="name flex"> |
||
| 4115 | <span>def <span class="ident">read_seg_image</span></span>(<span>self, path_seg_image=None)</span> |
||
| 4116 | </code></dt> |
||
| 4117 | <dd> |
||
| 4118 | <div class="desc"><p>Read segmentation image from disk. Must be a single file (e.g., nrrd, 3D dicom)</p> |
||
| 4119 | <h2 id="parameters">Parameters</h2> |
||
| 4120 | <dl> |
||
| 4121 | <dt><strong><code>path_seg_image</code></strong> : <code>str</code>, optional</dt> |
||
| 4122 | <dd>Path to the medical image file to be loaded in, by default None</dd> |
||
| 4123 | </dl> |
||
| 4124 | <h2 id="raises">Raises</h2> |
||
| 4125 | <dl> |
||
| 4126 | <dt><code>Exception</code></dt> |
||
| 4127 | <dd>If path_seg_image does not exist, exception is raised.</dd> |
||
| 4128 | </dl></div> |
||
| 4129 | <details class="source"> |
||
| 4130 | <summary> |
||
| 4131 | <span>Expand source code</span> |
||
| 4132 | </summary> |
||
| 4133 | <pre><code class="python">def read_seg_image(self, |
||
| 4134 | path_seg_image=None): |
||
| 4135 | """ |
||
| 4136 | Read segmentation image from disk. Must be a single file (e.g., nrrd, 3D dicom) |
||
| 4137 | |||
| 4138 | Parameters |
||
| 4139 | ---------- |
||
| 4140 | path_seg_image : str, optional |
||
| 4141 | Path to the medical image file to be loaded in, by default None |
||
| 4142 | |||
| 4143 | Raises |
||
| 4144 | ------ |
||
| 4145 | Exception |
||
| 4146 | If path_seg_image does not exist, exception is raised. |
||
| 4147 | """ |
||
| 4148 | # If passing new location/seg image name, then update variables. |
||
| 4149 | if path_seg_image is not None: |
||
| 4150 | self._path_seg_image = path_seg_image |
||
| 4151 | |||
| 4152 | # If seg image location / name exist, then load image else raise exception |
||
| 4153 | if (self._path_seg_image is not None): |
||
| 4154 | self._seg_image = sitk.ReadImage(self._path_seg_image) |
||
| 4155 | else: |
||
| 4156 | raise Exception('No file path (self._path_seg_image) provided.')</code></pre> |
||
| 4157 | </details> |
||
| 4158 | </dd> |
||
| 4159 | <dt id="pymskt.mesh.meshes.Mesh.resample_surface"><code class="name flex"> |
||
| 4160 | <span>def <span class="ident">resample_surface</span></span>(<span>self, subdivisions=2, clusters=10000)</span> |
||
| 4161 | </code></dt> |
||
| 4162 | <dd> |
||
| 4163 | <div class="desc"><p>Resample a surface mesh using the ACVD algorithm: |
||
| 4164 | Version used: |
||
| 4165 | - <a href="https://github.com/pyvista/pyacvd">https://github.com/pyvista/pyacvd</a> |
||
| 4166 | Original version w/ more references: |
||
| 4167 | - <a href="https://github.com/valette/ACVD">https://github.com/valette/ACVD</a></p> |
||
| 4168 | <h2 id="parameters">Parameters</h2> |
||
| 4169 | <dl> |
||
| 4170 | <dt><strong><code>subdivisions</code></strong> : <code>int</code>, optional</dt> |
||
| 4171 | <dd>Subdivide the mesh to have more points before clustering, by default 2 |
||
| 4172 | Probably not necessary for very dense meshes.</dd> |
||
| 4173 | <dt><strong><code>clusters</code></strong> : <code>int</code>, optional</dt> |
||
| 4174 | <dd>The number of clusters (points/vertices) to create during resampling |
||
| 4175 | surafce, by default 10000 |
||
| 4176 | - This is not exact, might have slight differences.</dd> |
||
| 4177 | </dl></div> |
||
| 4178 | <details class="source"> |
||
| 4179 | <summary> |
||
| 4180 | <span>Expand source code</span> |
||
| 4181 | </summary> |
||
| 4182 | <pre><code class="python">def resample_surface(self, |
||
| 4183 | subdivisions=2, |
||
| 4184 | clusters=10000 |
||
| 4185 | ): |
||
| 4186 | """ |
||
| 4187 | Resample a surface mesh using the ACVD algorithm: |
||
| 4188 | Version used: |
||
| 4189 | - https://github.com/pyvista/pyacvd |
||
| 4190 | Original version w/ more references: |
||
| 4191 | - https://github.com/valette/ACVD |
||
| 4192 | |||
| 4193 | Parameters |
||
| 4194 | ---------- |
||
| 4195 | subdivisions : int, optional |
||
| 4196 | Subdivide the mesh to have more points before clustering, by default 2 |
||
| 4197 | Probably not necessary for very dense meshes. |
||
| 4198 | clusters : int, optional |
||
| 4199 | The number of clusters (points/vertices) to create during resampling |
||
| 4200 | surafce, by default 10000 |
||
| 4201 | - This is not exact, might have slight differences. |
||
| 4202 | """ |
||
| 4203 | self._mesh = resample_surface(self._mesh, subdivisions=subdivisions, clusters=clusters)</code></pre> |
||
| 4204 | </details> |
||
| 4205 | </dd> |
||
| 4206 | <dt id="pymskt.mesh.meshes.Mesh.reverse_all_transforms"><code class="name flex"> |
||
| 4207 | <span>def <span class="ident">reverse_all_transforms</span></span>(<span>self)</span> |
||
| 4208 | </code></dt> |
||
| 4209 | <dd> |
||
| 4210 | <div class="desc"><p>Function to iterate over all of the self._list_applied_transforms (in reverse order) and undo them.</p></div> |
||
| 4211 | <details class="source"> |
||
| 4212 | <summary> |
||
| 4213 | <span>Expand source code</span> |
||
| 4214 | </summary> |
||
| 4215 | <pre><code class="python">def reverse_all_transforms(self): |
||
| 4216 | """ |
||
| 4217 | Function to iterate over all of the self._list_applied_transforms (in reverse order) and undo them. |
||
| 4218 | """ |
||
| 4219 | while len(self._list_applied_transforms) > 0: |
||
| 4220 | self.reverse_most_recent_transform()</code></pre> |
||
| 4221 | </details> |
||
| 4222 | </dd> |
||
| 4223 | <dt id="pymskt.mesh.meshes.Mesh.reverse_most_recent_transform"><code class="name flex"> |
||
| 4224 | <span>def <span class="ident">reverse_most_recent_transform</span></span>(<span>self)</span> |
||
| 4225 | </code></dt> |
||
| 4226 | <dd> |
||
| 4227 | <div class="desc"><p>Function to undo the most recent transformation stored in self._list_applied_transforms</p></div> |
||
| 4228 | <details class="source"> |
||
| 4229 | <summary> |
||
| 4230 | <span>Expand source code</span> |
||
| 4231 | </summary> |
||
| 4232 | <pre><code class="python">def reverse_most_recent_transform(self): |
||
| 4233 | """ |
||
| 4234 | Function to undo the most recent transformation stored in self._list_applied_transforms |
||
| 4235 | """ |
||
| 4236 | transform = self._list_applied_transforms.pop() |
||
| 4237 | transform.Inverse() |
||
| 4238 | self.apply_transform_to_mesh(transform=transform, save_transform=False)</code></pre> |
||
| 4239 | </details> |
||
| 4240 | </dd> |
||
| 4241 | <dt id="pymskt.mesh.meshes.Mesh.rigidly_register"><code class="name flex"> |
||
| 4242 | <span>def <span class="ident">rigidly_register</span></span>(<span>self, other_mesh, as_source=True, apply_transform_to_mesh=True, return_transformed_mesh=False, return_transform=False, max_n_iter=100, n_landmarks=1000, reg_mode='similarity')</span> |
||
| 4243 | </code></dt> |
||
| 4244 | <dd> |
||
| 4245 | <div class="desc"><p>Function to perform rigid registration between this mesh and another mesh. </p> |
||
| 4246 | <h2 id="parameters">Parameters</h2> |
||
| 4247 | <dl> |
||
| 4248 | <dt><strong><code>other_mesh</code></strong> : <code>pymskt.mesh.Mesh</code> or <code>vtk.vtkPolyData</code></dt> |
||
| 4249 | <dd>Other mesh to use in registration process</dd> |
||
| 4250 | <dt><strong><code>as_source</code></strong> : <code>bool</code>, optional</dt> |
||
| 4251 | <dd>Should the current mesh (in this object) be the source or the target, by default True</dd> |
||
| 4252 | <dt><strong><code>apply_transform_to_mesh</code></strong> : <code>bool</code>, optional</dt> |
||
| 4253 | <dd>If as_source is True should we apply transformation to internal mesh, by default True</dd> |
||
| 4254 | <dt><strong><code>return_transformed_mesh</code></strong> : <code>bool</code>, optional</dt> |
||
| 4255 | <dd>Should we return the registered mesh, by default False</dd> |
||
| 4256 | <dt><strong><code>max_n_iter</code></strong> : <code>int</code>, optional</dt> |
||
| 4257 | <dd>Maximum number of iterations to perform, by default 100</dd> |
||
| 4258 | <dt><strong><code>n_landmarks</code></strong> : <code>int</code>, optional</dt> |
||
| 4259 | <dd>Number of landmarks to use in registration, by default 1000</dd> |
||
| 4260 | <dt><strong><code>reg_mode</code></strong> : <code>str</code>, optional</dt> |
||
| 4261 | <dd>Mode of registration to use, by default 'similarity' (similarity, rigid, or affine)</dd> |
||
| 4262 | </dl> |
||
| 4263 | <h2 id="returns">Returns</h2> |
||
| 4264 | <dl> |
||
| 4265 | <dt><code>_type_</code></dt> |
||
| 4266 | <dd><em>description</em></dd> |
||
| 4267 | </dl></div> |
||
| 4268 | <details class="source"> |
||
| 4269 | <summary> |
||
| 4270 | <span>Expand source code</span> |
||
| 4271 | </summary> |
||
| 4272 | <pre><code class="python">def rigidly_register( |
||
| 4273 | self, |
||
| 4274 | other_mesh, |
||
| 4275 | as_source=True, |
||
| 4276 | apply_transform_to_mesh=True, |
||
| 4277 | return_transformed_mesh=False, |
||
| 4278 | return_transform=False, |
||
| 4279 | max_n_iter=100, |
||
| 4280 | n_landmarks=1000, |
||
| 4281 | reg_mode='similarity' |
||
| 4282 | |||
| 4283 | ): |
||
| 4284 | """ |
||
| 4285 | Function to perform rigid registration between this mesh and another mesh. |
||
| 4286 | |||
| 4287 | Parameters |
||
| 4288 | ---------- |
||
| 4289 | other_mesh : pymskt.mesh.Mesh or vtk.vtkPolyData |
||
| 4290 | Other mesh to use in registration process |
||
| 4291 | as_source : bool, optional |
||
| 4292 | Should the current mesh (in this object) be the source or the target, by default True |
||
| 4293 | apply_transform_to_mesh : bool, optional |
||
| 4294 | If as_source is True should we apply transformation to internal mesh, by default True |
||
| 4295 | return_transformed_mesh : bool, optional |
||
| 4296 | Should we return the registered mesh, by default False |
||
| 4297 | max_n_iter : int, optional |
||
| 4298 | Maximum number of iterations to perform, by default 100 |
||
| 4299 | n_landmarks : int, optional |
||
| 4300 | Number of landmarks to use in registration, by default 1000 |
||
| 4301 | reg_mode : str, optional |
||
| 4302 | Mode of registration to use, by default 'similarity' (similarity, rigid, or affine) |
||
| 4303 | |||
| 4304 | Returns |
||
| 4305 | ------- |
||
| 4306 | _type_ |
||
| 4307 | _description_ |
||
| 4308 | """ |
||
| 4309 | |||
| 4310 | if (return_transform is True) & (return_transformed_mesh is True): |
||
| 4311 | raise Exception('Cannot return both transformed mesh and transform') |
||
| 4312 | |||
| 4313 | if type(other_mesh) in (pymskt.mesh.meshes.BoneMesh, pymskt.mesh.meshes.Mesh): |
||
| 4314 | other_mesh = other_mesh.mesh |
||
| 4315 | |||
| 4316 | # Setup the source & target meshes based on `as_source`` |
||
| 4317 | if as_source is True: |
||
| 4318 | source = self._mesh |
||
| 4319 | target = other_mesh |
||
| 4320 | elif as_source is False: |
||
| 4321 | source = other_mesh |
||
| 4322 | target = self._mesh |
||
| 4323 | |||
| 4324 | icp_transform = get_icp_transform( |
||
| 4325 | source=source, |
||
| 4326 | target=target, |
||
| 4327 | max_n_iter=max_n_iter, |
||
| 4328 | n_landmarks=n_landmarks, |
||
| 4329 | reg_mode=reg_mode |
||
| 4330 | ) |
||
| 4331 | |||
| 4332 | # If current mesh is source & apply_transform_to_mesh is true then replace current mesh. |
||
| 4333 | if (as_source is True) & (apply_transform_to_mesh is True): |
||
| 4334 | self.apply_transform_to_mesh(transform=icp_transform) |
||
| 4335 | |||
| 4336 | if return_transformed_mesh is True: |
||
| 4337 | return self._mesh |
||
| 4338 | |||
| 4339 | elif return_transform is True: |
||
| 4340 | return icp_transform |
||
| 4341 | |||
| 4342 | # curent mesh is target, or is source & want to return mesh, then return it. |
||
| 4343 | elif (as_source is False) & (return_transformed_mesh is True): |
||
| 4344 | return apply_transform(source=source, transform=icp_transform) |
||
| 4345 | |||
| 4346 | else: |
||
| 4347 | raise Exception('Nothing to return from rigid registration.')</code></pre> |
||
| 4348 | </details> |
||
| 4349 | </dd> |
||
| 4350 | <dt id="pymskt.mesh.meshes.Mesh.save_mesh"><code class="name flex"> |
||
| 4351 | <span>def <span class="ident">save_mesh</span></span>(<span>self, filepath)</span> |
||
| 4352 | </code></dt> |
||
| 4353 | <dd> |
||
| 4354 | <div class="desc"><p>Save the surface mesh from this class to disk. </p> |
||
| 4355 | <h2 id="parameters">Parameters</h2> |
||
| 4356 | <dl> |
||
| 4357 | <dt><strong><code>filepath</code></strong> : <code>str</code></dt> |
||
| 4358 | <dd>Location & filename to save the surface mesh (vtk.vtkPolyData) to.</dd> |
||
| 4359 | </dl></div> |
||
| 4360 | <details class="source"> |
||
| 4361 | <summary> |
||
| 4362 | <span>Expand source code</span> |
||
| 4363 | </summary> |
||
| 4364 | <pre><code class="python">def save_mesh(self, |
||
| 4365 | filepath): |
||
| 4366 | """ |
||
| 4367 | Save the surface mesh from this class to disk. |
||
| 4368 | |||
| 4369 | Parameters |
||
| 4370 | ---------- |
||
| 4371 | filepath : str |
||
| 4372 | Location & filename to save the surface mesh (vtk.vtkPolyData) to. |
||
| 4373 | """ |
||
| 4374 | io.write_vtk(self._mesh, filepath)</code></pre> |
||
| 4375 | </details> |
||
| 4376 | </dd> |
||
| 4377 | </dl> |
||
| 4378 | </dd> |
||
| 4379 | </dl> |
||
| 4380 | </section> |
||
| 4381 | </article> |
||
| 4382 | <nav id="sidebar"> |
||
| 4383 | <h1>Index</h1> |
||
| 4384 | <div class="toc"> |
||
| 4385 | <ul></ul> |
||
| 4386 | </div> |
||
| 4387 | <ul id="index"> |
||
| 4388 | <li><h3>Super-module</h3> |
||
| 4389 | <ul> |
||
| 4390 | <li><code><a title="pymskt.mesh" href="index.html">pymskt.mesh</a></code></li> |
||
| 4391 | </ul> |
||
| 4392 | </li> |
||
| 4393 | <li><h3><a href="#header-classes">Classes</a></h3> |
||
| 4394 | <ul> |
||
| 4395 | <li> |
||
| 4396 | <h4><code><a title="pymskt.mesh.meshes.BoneMesh" href="#pymskt.mesh.meshes.BoneMesh">BoneMesh</a></code></h4> |
||
| 4397 | <ul class=""> |
||
| 4398 | <li><code><a title="pymskt.mesh.meshes.BoneMesh.assign_cartilage_regions" href="#pymskt.mesh.meshes.BoneMesh.assign_cartilage_regions">assign_cartilage_regions</a></code></li> |
||
| 4399 | <li><code><a title="pymskt.mesh.meshes.BoneMesh.bone" href="#pymskt.mesh.meshes.BoneMesh.bone">bone</a></code></li> |
||
| 4400 | <li><code><a title="pymskt.mesh.meshes.BoneMesh.calc_cartilage_t2" href="#pymskt.mesh.meshes.BoneMesh.calc_cartilage_t2">calc_cartilage_t2</a></code></li> |
||
| 4401 | <li><code><a title="pymskt.mesh.meshes.BoneMesh.calc_cartilage_thickness" href="#pymskt.mesh.meshes.BoneMesh.calc_cartilage_thickness">calc_cartilage_thickness</a></code></li> |
||
| 4402 | <li><code><a title="pymskt.mesh.meshes.BoneMesh.create_cartilage_meshes" href="#pymskt.mesh.meshes.BoneMesh.create_cartilage_meshes">create_cartilage_meshes</a></code></li> |
||
| 4403 | <li><code><a title="pymskt.mesh.meshes.BoneMesh.create_mesh" href="#pymskt.mesh.meshes.BoneMesh.create_mesh">create_mesh</a></code></li> |
||
| 4404 | <li><code><a title="pymskt.mesh.meshes.BoneMesh.crop_percent" href="#pymskt.mesh.meshes.BoneMesh.crop_percent">crop_percent</a></code></li> |
||
| 4405 | <li><code><a title="pymskt.mesh.meshes.BoneMesh.list_cartilage_labels" href="#pymskt.mesh.meshes.BoneMesh.list_cartilage_labels">list_cartilage_labels</a></code></li> |
||
| 4406 | <li><code><a title="pymskt.mesh.meshes.BoneMesh.list_cartilage_meshes" href="#pymskt.mesh.meshes.BoneMesh.list_cartilage_meshes">list_cartilage_meshes</a></code></li> |
||
| 4407 | <li><code><a title="pymskt.mesh.meshes.BoneMesh.smooth_surface_scalars" href="#pymskt.mesh.meshes.BoneMesh.smooth_surface_scalars">smooth_surface_scalars</a></code></li> |
||
| 4408 | </ul> |
||
| 4409 | </li> |
||
| 4410 | <li> |
||
| 4411 | <h4><code><a title="pymskt.mesh.meshes.CartilageMesh" href="#pymskt.mesh.meshes.CartilageMesh">CartilageMesh</a></code></h4> |
||
| 4412 | </li> |
||
| 4413 | <li> |
||
| 4414 | <h4><code><a title="pymskt.mesh.meshes.Mesh" href="#pymskt.mesh.meshes.Mesh">Mesh</a></code></h4> |
||
| 4415 | <ul class=""> |
||
| 4416 | <li><code><a title="pymskt.mesh.meshes.Mesh.apply_transform_to_mesh" href="#pymskt.mesh.meshes.Mesh.apply_transform_to_mesh">apply_transform_to_mesh</a></code></li> |
||
| 4417 | <li><code><a title="pymskt.mesh.meshes.Mesh.copy_scalars_from_other_mesh_to_currect" href="#pymskt.mesh.meshes.Mesh.copy_scalars_from_other_mesh_to_currect">copy_scalars_from_other_mesh_to_currect</a></code></li> |
||
| 4418 | <li><code><a title="pymskt.mesh.meshes.Mesh.create_mesh" href="#pymskt.mesh.meshes.Mesh.create_mesh">create_mesh</a></code></li> |
||
| 4419 | <li><code><a title="pymskt.mesh.meshes.Mesh.label_idx" href="#pymskt.mesh.meshes.Mesh.label_idx">label_idx</a></code></li> |
||
| 4420 | <li><code><a title="pymskt.mesh.meshes.Mesh.list_applied_transforms" href="#pymskt.mesh.meshes.Mesh.list_applied_transforms">list_applied_transforms</a></code></li> |
||
| 4421 | <li><code><a title="pymskt.mesh.meshes.Mesh.mesh" href="#pymskt.mesh.meshes.Mesh.mesh">mesh</a></code></li> |
||
| 4422 | <li><code><a title="pymskt.mesh.meshes.Mesh.min_n_pixels" href="#pymskt.mesh.meshes.Mesh.min_n_pixels">min_n_pixels</a></code></li> |
||
| 4423 | <li><code><a title="pymskt.mesh.meshes.Mesh.non_rigidly_register" href="#pymskt.mesh.meshes.Mesh.non_rigidly_register">non_rigidly_register</a></code></li> |
||
| 4424 | <li><code><a title="pymskt.mesh.meshes.Mesh.path_seg_image" href="#pymskt.mesh.meshes.Mesh.path_seg_image">path_seg_image</a></code></li> |
||
| 4425 | <li><code><a title="pymskt.mesh.meshes.Mesh.point_coords" href="#pymskt.mesh.meshes.Mesh.point_coords">point_coords</a></code></li> |
||
| 4426 | <li><code><a title="pymskt.mesh.meshes.Mesh.read_seg_image" href="#pymskt.mesh.meshes.Mesh.read_seg_image">read_seg_image</a></code></li> |
||
| 4427 | <li><code><a title="pymskt.mesh.meshes.Mesh.resample_surface" href="#pymskt.mesh.meshes.Mesh.resample_surface">resample_surface</a></code></li> |
||
| 4428 | <li><code><a title="pymskt.mesh.meshes.Mesh.reverse_all_transforms" href="#pymskt.mesh.meshes.Mesh.reverse_all_transforms">reverse_all_transforms</a></code></li> |
||
| 4429 | <li><code><a title="pymskt.mesh.meshes.Mesh.reverse_most_recent_transform" href="#pymskt.mesh.meshes.Mesh.reverse_most_recent_transform">reverse_most_recent_transform</a></code></li> |
||
| 4430 | <li><code><a title="pymskt.mesh.meshes.Mesh.rigidly_register" href="#pymskt.mesh.meshes.Mesh.rigidly_register">rigidly_register</a></code></li> |
||
| 4431 | <li><code><a title="pymskt.mesh.meshes.Mesh.save_mesh" href="#pymskt.mesh.meshes.Mesh.save_mesh">save_mesh</a></code></li> |
||
| 4432 | <li><code><a title="pymskt.mesh.meshes.Mesh.seg_image" href="#pymskt.mesh.meshes.Mesh.seg_image">seg_image</a></code></li> |
||
| 4433 | </ul> |
||
| 4434 | </li> |
||
| 4435 | </ul> |
||
| 4436 | </li> |
||
| 4437 | </ul> |
||
| 4438 | </nav> |
||
| 4439 | </main> |
||
| 4440 | <footer id="footer"> |
||
| 4441 | <p>Generated by <a href="https://pdoc3.github.io/pdoc" title="pdoc: Python API documentation generator"><cite>pdoc</cite> 0.10.0</a>.</p> |
||
| 4442 | </footer> |
||
| 4443 | </body> |
||
| 4444 | </html> |