Script repository 译：脚本存储库

Note 译：注意

Usage: Copy-paste the code lines displayed below or the linked .py file contents into Python console in Slicer. Or save them to a .py file and run them using execfile. 译：**用法：：将下面显示的代码行或链接的.py文件内容复制粘贴到Slicer中的Python控制台中。或者将它们保存到.py文件中，然后使用execfile运行它们。

译者的几点说明:

• 今天开始学习这一章,包括每段代码的结果,我是用JupyterLab操作的,相应的.ipynb我会放到下载区
• 主要感兴趣的内容,重点分析
• 最近在做一个有关医学影像3d重建经皮定位的项目,希望有大神合作.

Markups 译： 标记

Load markups fiducial list from file 译：从文件加载标记Fiducial列表

Markups fiducials can be loaded from file: 译：标记Fiducial可以从文件中加载：

slicer.util.loadMarkupsFiducialList("data/F.fcsv")

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)

In  [3]:
Line 1:     


File /Applications/Slicer.app/Contents/bin/Python/slicer/util.py, in loadMarkupsFiducialList:
Line 746:   node = loadMarkups(filename)


File /Applications/Slicer.app/Contents/bin/Python/slicer/util.py, in loadMarkups:
Line 771:   return loadNodeFromFile(filename, 'MarkupsFile')


File /Applications/Slicer.app/Contents/bin/Python/slicer/util.py, in loadNodeFromFile:
Line 650:   raise RuntimeError(errorMessage)


RuntimeError: Failed to load node from file: data/F.fcsv
---------------------------------------------------------------------------

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新版的文件为下面这个格式mrk.json,用fcsv出错

slicer.util.loadMarkupsFiducialList("data/F.mrk.json")

[True, (vtkSlicerMarkupsModuleMRMLPython.vtkMRMLMarkupsFiducialNode)0x16f2ecd68]

Adding Fiducials Programatically 译： 以编程方式添加Fiducial

Markups fiducials can be added to the currently active list from the python console by using the following module logic command: 译：使用以下模块逻辑命令，可以从python控制台将标记Fiducial点添加到当前活动列表中：

slicer.modules.markups.logic().AddFiducial() # 默认原点加到F

The command with no arguments will place a new fiducial at the origin. You can also pass it an initial location: 译：不带参数的命令将在原点放置一个新Fiducial。您还可以将其传递给初始位置：

slicer.modules.markups.logic().AddFiducial(1.0, -2.0, 3.3)

0

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如何加到指定的列表中

我们将上面那个点加到F-1列表中
加到F里了可是标签却:

[外链图片转存失败,源站可能有防盗链机制,建议将图片保存下来直接上传(img-Qg4zHqMa-1620137485954)(attachment:4e9a83d1-f414-463a-8fcc-bc4aa9aa05a9.png)]

知道为啥吗?

[^1]Python vtkMRMLMarkupsFiducialNode Examples, __main__slicer.vtkMRMLMarkupsFiducialNode Python Examples - HotExamples

# 译者代码
fixedLRS = slicer.util.getNode('F')    
fixedLRS.AddFiducial(-100.0, 0.0, 0.0)
fixedLRS.SetNthFiducialLabel(0, 'FixedL')

How to draw a curve using control points stored in a numpy array 译： 如何使用存储在numpy数组中的控制点绘制曲线

# Create random numpy array to use as input 译：创建随机的numpy数组以用作输入 
import numpy as np
pointPositions = np.random.uniform(-50,50,size=[15,3])

# Create curve from numpy array 译：从numpy数组创建曲线 
curveNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsCurveNode")
slicer.util.updateMarkupsControlPointsFromArray(curveNode, pointPositions)

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Add a button to module GUI to activate fiducial placement 译：向模块GUI添加按钮以激活Fiducial放置

This code snippet creates a toggle button, which activates fiducial placement when pressed (and deactivates when released). 译：此代码段创建一个切换按钮，按下该按钮可激活Fiducial位置（释放时将其禁用）。

The qSlicerMarkupsPlaceWidget widget can automatically activate placement of multiple points and can show buttons for deleting points, changing colors, lock, and hide points. 译：[qSlicerMarkupsPlaceWidget小部件]（http://apidocs.slicer.org/master/classqSlicerMarkupsPlaceWidget.html）可以自动激活多个点的放置，并可以显示用于删除点，更改颜色，锁定和隐藏点的按钮。

w=slicer.qSlicerMarkupsPlaceWidget()
w.setMRMLScene(slicer.mrmlScene)
markupsNodeID = slicer.modules.markups.logic().AddNewFiducialNode()
w.setCurrentNode(slicer.mrmlScene.GetNodeByID(markupsNodeID))
# Hide all buttons and only show place button 译：隐藏所有按钮，仅显示位置按钮 
w.buttonsVisible=False
w.placeButton().show()
w.show()

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如图

Adding Fiducials via mouse clicks 译： 通过鼠标单击添加Fiducial

You can also set the mouse mode into Markups fiducial placement by calling: 译：您还可以通过调用以下命令将鼠标模式设置为标记Fiducial位置：

placeModePersistence = 1
slicer.modules.markups.logic().StartPlaceMode(placeModePersistence)

A lower level way to do this is via the selection and interaction nodes: 译：一种较低级别的方法是通过选择和交互节点：

selectionNode = slicer.mrmlScene.GetNodeByID("vtkMRMLSelectionNodeSingleton")
selectionNode.SetReferenceActivePlaceNodeClassName("vtkMRMLMarkupsFiducialNode")
interactionNode = slicer.mrmlScene.GetNodeByID("vtkMRMLInteractionNodeSingleton")
placeModePersistence = 1
interactionNode.SetPlaceModePersistence(placeModePersistence)
# mode 1 is Place, can also be accessed via slicer.vtkMRMLInteractionNode().Place 译：模式1为Place，也可以通过slicer.vtkMRMLInteractionNode（）访问。 
interactionNode.SetCurrentInteractionMode(1)

To switch back to view transform once you’re done placing fiducials: 译：完成Fiducial放置后，要切换回视图转换：

interactionNode = slicer.mrmlScene.GetNodeByID("vtkMRMLInteractionNodeSingleton")
interactionNode.SwitchToViewTransformMode()
# also turn off place mode persistence if required 译：如果需要，还可以关闭场所模式持久性 
interactionNode.SetPlaceModePersistence(0)

Access to Fiducial Properties 译：访问Fiducial属性

Each vtkMRMLMarkupsFiducialNode has a vector of points in it which can be accessed from python: 译：每个vtkMRMLMarkupsFiducialNode中都有一个点矢量，可以从python访问这些点：

fidNode = getNode("vtkMRMLMarkupsFiducialNode1")
n = fidNode.AddFiducial(4.0, 5.5, -6.0)
fidNode.SetNthFiducialLabel(n, "new label")
# each markup is given a unique id which can be accessed from the superclass level 译：每个标记都有一个唯一的ID，可以从超类级别访问 
id1 = fidNode.GetNthMarkupID(n)
# manually set the position 译：手动设置位置 
fidNode.SetNthFiducialPosition(n, 6.0, 7.0, 8.0)
# set the label 译：设置标签 
fidNode.SetNthFiducialLabel(n, "New label")
# set the selected flag, only selected = 1 fiducials will be passed to CLIs 译：设置选定的标志，只有选定的= 1个Fiducial将被传递到CLI 
fidNode.SetNthFiducialSelected(n, 1)
# set the visibility flag 译：设置可见性标志 
fidNode.SetNthFiducialVisibility(n, 0)

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这组代码比我前面的👍太多…

You can loop over the fiducials in a list and get the coordinates: 译：您可以遍历列表中的Fiducial并获取坐标：

fidList = slicer.util.getNode("F")
numFids = fidList.GetNumberOfFiducials()
for i in range(numFids):
  ras = [0,0,0]
  fidList.GetNthFiducialPosition(i,ras)
  # the world position is the RAS position with any transform matrices applied
  world = [0,0,0,0]
  fidList.GetNthFiducialWorldCoordinates(0,world)
  print(i,": RAS =",ras,", world =",world)

0 : RAS = [-75.94607190857545, -37.56009742901087, -2.1938657726656743] , world = [-75.94607190857545, -37.56009742901087, -2.1938657726656743, 0.0]
1 : RAS = [14.155074704408154, -75.46471772966771, -2.194670949981628] , world = [-75.94607190857545, -37.56009742901087, -2.1938657726656743, 0.0]
2 : RAS = [-95.76510768417384, 85.85852034072332, -2.19344815423176] , world = [-75.94607190857545, -37.56009742901087, -2.1938657726656743, 0.0]
3 : RAS = [-81.11312212763353, -96.62529981603525, -2.1939475814752427] , world = [-75.94607190857545, -37.56009742901087, -2.1938657726656743, 0.0]
4 : RAS = [124.01467571038447, 129.81447702084876, -2.195127093658982] , world = [-75.94607190857545, -37.56009742901087, -2.1938657726656743, 0.0]

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0 : RAS = [-75.94607190857545, -37.56009742901087, -2.1938657726656743] , world = [-75.94607190857545, -37.56009742901087, -2.1938657726656743, 0.0]
1 : RAS = [14.155074704408154, -75.46471772966771, -2.194670949981628] , world = [-75.94607190857545, -37.56009742901087, -2.1938657726656743, 0.0]
2 : RAS = [-95.76510768417384, 85.85852034072332, -2.19344815423176] , world = [-75.94607190857545, -37.56009742901087, -2.1938657726656743, 0.0]
3 : RAS = [-81.11312212763353, -96.62529981603525, -2.1939475814752427] , world = [-75.94607190857545, -37.56009742901087, -2.1938657726656743, 0.0]
4 : RAS = [124.01467571038447, 129.81447702084876, -2.195127093658982] , world = [-75.94607190857545, -37.56009742901087, -2.1938657726656743, 0.0]

比较一下坐标系的差别…

You can also look at the sample code in the Endoscopy module to see how python is used to access fiducials from a scripted module. 译：您还可以查看[内窥镜模块]中的示例代码（https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/Endoscopy/Endoscopy.pyL287）以查看python的运行方式用于从脚本模块访问Fiducial。

Define/edit a circular region of interest in a slice viewer 译：在Slicer查看器中定义/编辑感兴趣的圆形区域

Drop two markup points on a slice view and copy-paste the code below into the Python console. After this, as you move the markups you’ll see a circle following the markups. 译：在Slicer视图上放置两个标记点，然后将以下代码复制粘贴到Python控制台中。此后，当您移动标记时，标记后面会出现一个圆圈。

# Update the sphere from the fiducial points 译：从Fiducial点更新球体 
def UpdateSphere(param1, param2):
  """Update the sphere from the fiducial points
  """
  import math
  centerPointCoord = [0.0, 0.0, 0.0]
  markups.GetNthFiducialPosition(0,centerPointCoord)
  circumferencePointCoord = [0.0, 0.0, 0.0]
  markups.GetNthFiducialPosition(1,circumferencePointCoord)
  sphere.SetCenter(centerPointCoord)
  radius=math.sqrt((centerPointCoord[0]-circumferencePointCoord[0])**2+(centerPointCoord[1]-circumferencePointCoord[1])**2+(centerPointCoord[2]-circumferencePointCoord[2])**2)
  sphere.SetRadius(radius)
  sphere.SetPhiResolution(30)
  sphere.SetThetaResolution(30)
  sphere.Update()

# Get markup node from scene 译：从场景中获取标记节点 
markups=slicer.util.getNode("F")
sphere = vtk.vtkSphereSource()
UpdateSphere(0,0)

# Create model node and add to scene 译：创建模型节点并添加到场景 
modelsLogic = slicer.modules.models.logic()
model = modelsLogic.AddModel(sphere.GetOutput())
model.GetDisplayNode().SetSliceIntersectionVisibility(True)
model.GetDisplayNode().SetSliceIntersectionThickness(3)
model.GetDisplayNode().SetColor(1,1,0)

# Call UpdateSphere whenever the fiducials are changed 译：每当Fiducial点更改时调用UpdateSphere 
markups.AddObserver(slicer.vtkMRMLMarkupsNode.PointModifiedEvent, UpdateSphere, 2)

178

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Specify a sphere by multiple of markups points 译：通过多个标记点指定一个球体

Drop multiple markup points at the boundary of the spherical object and and copy-paste the code below into the Python console to get best-fit sphere. Minimum 4 points are required, it is recommended to place the points far from each other for most accurate fit. 译：在球形对象的边界处放置多个标记点，然后将以下代码复制粘贴到Python控制台中，以获得最合适的球形。至少需要4个点，建议将这些点彼此分开以实现最精确的拟合。

# Get markup node from scene 译：从场景中获取标记节点 
markups = slicer.util.getNode("F")

from scipy.optimize import least_squares
import numpy

def fit_sphere_least_squares(x_values, y_values, z_values, initial_parameters, bounds=((-numpy.inf, -numpy.inf, -numpy.inf, -numpy.inf),(numpy.inf, numpy.inf, numpy.inf, numpy.inf))):
    """
    Source: https://github.com/thompson318/scikit-surgery-sphere-fitting/blob/master/sksurgeryspherefitting/algorithms/sphere_fitting.py
    Uses scipy's least squares optimisor to fit a sphere to a set
    of 3D Points
    :return: x: an array containing the four fitted parameters
    :return: ier: int An integer flag. If it is equal to 1, 2, 3 or 4, the
             solution was found.
    :param: (x,y,z) three arrays of equal length containing the x, y, and z
            coordinates.
    :param: an array containing four initial values (centre, and radius)
    """
    return least_squares(_calculate_residual_sphere, initial_parameters, bounds=bounds, method="trf", jac="3-point", args=(x_values, y_values, z_values))

def _calculate_residual_sphere(parameters, x_values, y_values, z_values):
    """
    Source: https://github.com/thompson318/scikit-surgery-sphere-fitting/blob/master/sksurgeryspherefitting/algorithms/sphere_fitting.py
    Calculates the residual error for an x,y,z coordinates, fitted
    to a sphere with centre and radius defined by the parameters tuple
    :return: The residual error
    :param: A tuple of the parameters to be optimised, should contain [x_centre, y_centre, z_centre, radius]
    :param: arrays containing the x,y, and z coordinates.
    """
    #extract the parameters
    x_centre, y_centre, z_centre, radius = parameters
    #use numpy's sqrt function here, which works by element on arrays
    distance_from_centre = numpy.sqrt((x_values - x_centre)**2 + (y_values - y_centre)**2 + (z_values - z_centre)**2)
    return distance_from_centre - radius

# Fit a sphere to the markups fidicual points 译：使球形适应标记的折点 
markupsPositions = slicer.util.arrayFromMarkupsControlPoints(markups)
import numpy as np
# initial guess 译：初步猜测 
center0 = np.mean(markupsPositions, 0)
radius0 = np.linalg.norm(np.amin(markupsPositions,0)-np.amax(markupsPositions,0))/2.0
fittingResult = fit_sphere_least_squares(markupsPositions[:,0], markupsPositions[:,1], markupsPositions[:,2], [center0[0], center0[1], center0[2], radius0])
[centerX, centerY, centerZ, radius] = fittingResult["x"]

# Create a sphere using the fitted parameters 译：使用拟合的参数创建一个球体 
sphere = vtk.vtkSphereSource()
sphere.SetPhiResolution(30)
sphere.SetThetaResolution(30)
sphere.SetCenter(centerX, centerY, centerZ)
sphere.SetRadius(radius)
sphere.Update()

# Add the sphere to the scene 译：将球体添加到场景 
modelsLogic = slicer.modules.models.logic()
model = modelsLogic.AddModel(sphere.GetOutput())
model.GetDisplayNode().SetSliceIntersectionVisibility(True)
model.GetDisplayNode().SetSliceIntersectionThickness(3)
model.GetDisplayNode().SetColor(1,1,0)

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参阅: 翻译:Slicer脚本存储库
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