簡介
在一些醫學相關的簡單的專案（也許是學生的作業？畢業設計？）中，有時候可能需要整合一些視覺化的功能，本文簡單介紹一下，如何利用PyQt5和VTK來渲染體資料（三維資料），並整合進PyQt的UI框架中。
環境
主要依賴兩個python的包
- PyQt5
- VTK
最好用 Anaconda 來管理你的 python 的環境，可以利用 pip 來安裝上述的包，如何安裝網上有許多教程，這裡不介紹了。
功能展示
- 新增體資料
- 刪除體資料
- 選擇合適的預製的顏色函式
- 縮放、旋轉
程式碼介紹
-
Ui_MainWindow這個類是主要用來定義UI的一些佈局， -
VolumeRendering這個類主要用來處理一些渲染的邏輯，主要是用了VTK的一些現有的渲染方法。 -
readXML函式用來讀取 xml 檔案，因為人體不同的組織、器官在醫學影像中，呈現的強度不同，因此根據這些強度值可以設定一些渲染引數，來繪製不同的人體組織。這些渲染引數如何設定？是有現成的設定好的引數可以參考的，本文采用了 3DSlicer 這個軟體中的設定方式，引數被儲存在preset.xml檔案中，這個檔案是我從 3DSlicer 中拷貝過來的。 -
buildProperty這個函式，根據preset.xml中的引數，構建 VTK 的渲染引數，主要是各種傳輸函式，這裡不過多的對傳輸函式進行解釋了，例如顏色傳輸函式可以理解為，例如強度在0-100的區域用紅色，100-200的用藍色...這個意思。注意：這個函式裡有一個常數值 + 1000，這個和我倉庫裡的test data 的資料分佈有關，因為我的資料是從0開始的，0 代表正常資料的 -1000，所以如果你的資料是正常的範圍的話，可以不加 1000，可以自己試試。 -
渲染：這裡用的是
vtkGPUVolumeRayCastMapper這個函式進行渲染，利用GPU加速，繪製的會比較快。 -
資料：這裡使用的 mha 資料的檔案，其實用格式的檔案都可以，這裡為了方便採用了mha，如果需要讀取別的格式，改一下讀取資料部分就可以了，對格式不太瞭解的同學可以看看我之前寫的一篇關於不同醫學影像格式讀寫的文章。
-
其他：其他的相關部分，可以直接看程式碼，程式碼並不複雜，只有 200+行，可能會一些小 bug，不過不要緊，這裡主要的目的是為了展示：
- 如何在 python 中用 VTK 渲染體資料；
- 如何整合 VTK 渲染進 PyQt5；
- 如何構建合適的渲染引數（和3DSlicer一樣）。
完整程式碼
import os
from PyQt5 import QtCore
from PyQt5 import QtGui
from PyQt5 import QtCore, QtGui, QtWidgets
from functools import partial
from PyQt5.QtWidgets import QFrame,QVBoxLayout,QFileDialog, QMainWindow,QApplication
from vtk.qt.QVTKRenderWindowInteractor import QVTKRenderWindowInteractor
from vtkmodules.vtkCommonColor import vtkNamedColors
from vtkmodules.vtkCommonDataModel import vtkPiecewiseFunction
from vtkmodules.vtkIOImage import vtkMetaImageReader
from vtkmodules.vtkRenderingCore import (
vtkColorTransferFunction,
vtkRenderer,
vtkVolume,
vtkVolumeProperty
)
from vtkmodules.vtkRenderingVolume import vtkGPUVolumeRayCastMapper
from xml.dom.minidom import parse
class Ui_MainWindow(object):
def setupUi(self, MainWindow):
MainWindow.setObjectName("MainWindow")
MainWindow.resize(1140, 887)
self.centralwidget = QtWidgets.QWidget(MainWindow)
self.centralwidget.setObjectName("centralwidget")
self.horizontalLayout = QtWidgets.QHBoxLayout(self.centralwidget)
self.horizontalLayout.setObjectName("horizontalLayout")
self.Tapw = QtWidgets.QTabWidget(self.centralwidget)
font = QtGui.QFont()
font.setPointSize(12)
self.Tapw.setFont(font)
self.Tapw.setObjectName("Tapw")
self.Rendering = QtWidgets.QWidget()
self.Rendering.setObjectName("Rendering")
self.VTK = QtWidgets.QWidget(self.Rendering)
self.VTK.setGeometry(QtCore.QRect(0, 10, 931, 771))
self.VTK.setObjectName("VTK")
self.RenPreset = QtWidgets.QComboBox(self.Rendering)
self.RenPreset.setGeometry(QtCore.QRect(950, 510, 161, 31))
self.RenPreset.setObjectName("RenPreset")
self.RenList = QtWidgets.QListWidget(self.Rendering)
self.RenList.setGeometry(QtCore.QRect(950, 160, 161, 281))
self.RenList.setObjectName("RenList")
self.RenDelVolBtn = QtWidgets.QPushButton(self.Rendering)
self.RenDelVolBtn.setGeometry(QtCore.QRect(940, 80, 171, 51))
self.RenDelVolBtn.setObjectName("RenDelVolBtn")
self.RenLoadVolBtn = QtWidgets.QPushButton(self.Rendering)
self.RenLoadVolBtn.setGeometry(QtCore.QRect(940, 20, 171, 51))
self.RenLoadVolBtn.setObjectName("RenLoadVolBtn")
self.label_4 = QtWidgets.QLabel(self.Rendering)
self.label_4.setGeometry(QtCore.QRect(990, 460, 101, 31))
self.label_4.setObjectName("label_4")
self.RenChange = QtWidgets.QPushButton(self.Rendering)
self.RenChange.setGeometry(QtCore.QRect(940, 570, 171, 51))
self.RenChange.setObjectName("RenChange")
self.Tapw.addTab(self.Rendering, "")
self.horizontalLayout.addWidget(self.Tapw)
MainWindow.setCentralWidget(self.centralwidget)
self.menubar = QtWidgets.QMenuBar(MainWindow)
self.menubar.setGeometry(QtCore.QRect(0, 0, 1140, 23))
self.menubar.setObjectName("menubar")
MainWindow.setMenuBar(self.menubar)
self.statusbar = QtWidgets.QStatusBar(MainWindow)
self.statusbar.setObjectName("statusbar")
MainWindow.setStatusBar(self.statusbar)
self.retranslateUi(MainWindow)
self.Tapw.setCurrentIndex(1)
QtCore.QMetaObject.connectSlotsByName(MainWindow)
def retranslateUi(self, MainWindow):
_translate = QtCore.QCoreApplication.translate
MainWindow.setWindowTitle(_translate("MainWindow", "Volume Rendering"))
self.RenDelVolBtn.setText(_translate("MainWindow", "Remove Volume"))
self.RenLoadVolBtn.setText(_translate("MainWindow", "Add Volume"))
self.label_4.setText(_translate("MainWindow", "Transfer Func"))
self.RenChange.setText(_translate("MainWindow", "Change Transfer Func"))
self.Tapw.setTabText(self.Tapw.indexOf(self.Rendering), _translate("MainWindow", "Volume Rendering"))
class VolumeRendering():
def __init__(self,ui:Ui_MainWindow) -> None:
self.frame = QFrame()
self.ui = ui
self.vl = QVBoxLayout()
self.vtkWidget = QVTKRenderWindowInteractor(self.frame)
self.vl.addWidget(self.vtkWidget)
self.ren = vtkRenderer()
self.vtkWidget.GetRenderWindow().AddRenderer(self.ren)
self.iren = self.vtkWidget.GetRenderWindow().GetInteractor()
self.colors = vtkNamedColors()
self.vtkpros = {}
self.colors.SetColor('BkgColor', [0, 0,0 , 255])
self.ren.SetBackground(self.colors.GetColor3d('BkgColor'))
self.frame.setLayout(self.vl)
self.iren.Initialize()
self.volumes = {}
self.volume_property = vtkVolumeProperty()
self.volume_color = vtkColorTransferFunction()
self.volume_scalar_opacity = vtkPiecewiseFunction()
self.volume_gradient_opacity = vtkPiecewiseFunction()
self.setDefaultProperty()
ui.RenLoadVolBtn.clicked.connect(partial(self.addVolumeBtn))
ui.RenDelVolBtn.clicked.connect(partial(self.delVolumeBtn))
ui.RenChange.clicked.connect(partial(self.changeBtn))
self.readXML()
self.volume_property = self.vtkpros["CT-AAA"]
def readXML(self):
# read preset property from preset.xml
# the preset.xml is copied from 3D-Slicer
cur_dir = os.path.dirname(os.path.abspath(__file__))
domtree = parse(os.path.join(cur_dir,"preset.xml"))
data = domtree.documentElement
propertys = data.getElementsByTagName('VolumeProperty')
for pro in propertys:
name = pro.getAttribute('name')
go = pro.getAttribute('gradientOpacity')
so = pro.getAttribute('scalarOpacity')
ctrans = pro.getAttribute('colorTransfer')
vtkpro = self.buildProperty(go,so,ctrans)
self.vtkpros[name] = vtkpro
self.ui.RenPreset.addItem(name)
def buildProperty(self,go,so,ctrans):
vtkcoltrans = vtkColorTransferFunction()
data = ctrans.split()
data = [float(x) for x in data]
for i in range(int(data[0]/4)):
base = 1 + i * 4
# add 1000 because the intensity of our test data is started from 0
# if you use the normal data, you can delete the const 1000.
vtkcoltrans.AddRGBPoint(data[base] + 1000, data[base+1], data[base+2], data[base+3])
vtkgo = vtkPiecewiseFunction()
data = go.split()
data = [float(x) for x in data]
for i in range(int(data[0]/2)):
base = 1 + i * 2
vtkgo.AddPoint(data[base]+ 1000, data[base+1])
vtkso = vtkPiecewiseFunction()
data = so.split()
data = [float(x) for x in data]
for i in range(int(data[0]/2)):
base = 1 + i * 2
vtkso.AddPoint(data[base]+ 1000, data[base+1])
vtkpro = vtkVolumeProperty()
vtkpro.SetColor(vtkcoltrans)
vtkpro.SetScalarOpacity(vtkso)
#vtkpro.SetGradientOpacity(vtkgo)
vtkpro.SetInterpolationTypeToLinear()
vtkpro.ShadeOn()
vtkpro.SetAmbient(0.4)
vtkpro.SetDiffuse(0.6)
vtkpro.SetSpecular(0.2)
return vtkpro
# add volume to the scene
def addVolumeBtn(self):
file_name,_ =QFileDialog.getOpenFileName(
self.ui.Rendering,"open file dialog",os.getcwd(),"Mha(*.mha)")
if file_name == "":
return
self.addVolume(file_name)
self.ui.RenList.addItem(file_name)
# delete volume from scene
def delVolumeBtn(self):
if not self.ui.RenList.itemAt(0,0):
return
curVol = self.ui.RenList.currentItem()
if not curVol:
curVol = self.ui.RenList.itemAt(0,0)
curVol = curVol.text()
self.delVolume(curVol)
print(curVol)
#change transfer function
def changeBtn(self):
curVol = self.ui.RenList.currentItem()
if not curVol:
curVol = self.ui.RenList.itemAt(0,0)
curVol = curVol.text()
if curVol in self.volumes.keys():
self.volumes[curVol].SetProperty(self.vtkpros[self.ui.RenPreset.currentText()])
def setDefaultProperty(self):
self.volume_color.AddRGBPoint(0, 0.0, 0.0, 0.0)
self.volume_color.AddRGBPoint(500, 240.0 / 255.0, 184.0 / 255.0, 160.0 / 255.0)
self.volume_color.AddRGBPoint(1000, 240.0 / 255.0, 184.0 / 255.0, 160.0 / 255.0)
self.volume_color.AddRGBPoint(1150, 1.0, 1.0, 240.0 / 255.0) # Ivory
self.volume_scalar_opacity = vtkPiecewiseFunction()
self.volume_scalar_opacity.AddPoint(0, 0.00)
self.volume_scalar_opacity.AddPoint(500, 0.15)
self.volume_scalar_opacity.AddPoint(1000, 0.15)
self.volume_scalar_opacity.AddPoint(1150, 0.85)
self.volume_gradient_opacity = vtkPiecewiseFunction()
self.volume_gradient_opacity.AddPoint(0, 0.0)
self.volume_gradient_opacity.AddPoint(90, 0.5)
self.volume_gradient_opacity.AddPoint(100, 1.0)
self.volume_property = vtkVolumeProperty()
self.volume_property.SetColor(self.volume_color)
self.volume_property.SetScalarOpacity(self.volume_scalar_opacity)
self.volume_property.SetGradientOpacity(self.volume_gradient_opacity)
self.volume_property.SetInterpolationTypeToLinear()
self.volume_property.ShadeOn()
self.volume_property.SetAmbient(0.4)
self.volume_property.SetDiffuse(0.6)
self.volume_property.SetSpecular(0.2)
def delVolume(self,path):
self.ren.RemoveViewProp(self.volumes[path])
item = self.ui.RenList.findItems(path,QtCore.Qt.MatchExactly)[0]
row = self.ui.RenList.row(item)
self.ui.RenList.takeItem(row)
self.volumes.pop(path)
self.iren.Initialize()
def addVolume(self,path):
reader = vtkMetaImageReader()
reader.SetFileName(path)
volume_mapper = vtkGPUVolumeRayCastMapper()
volume_mapper.SetInputConnection(reader.GetOutputPort())
volume = vtkVolume()
volume.SetMapper(volume_mapper)
volume.SetProperty(self.volume_property)
self.ren.AddViewProp(volume)
self.volumes[path] = volume
camera = self.ren.GetActiveCamera()
c = volume.GetCenter()
camera.SetViewUp(0, 0, -1)
camera.SetPosition(c[0], c[1] - 800, c[2]-200)
camera.SetFocalPoint(c[0], c[1], c[2])
camera.Azimuth(30.0)
camera.Elevation(30.0)
self.iren.Initialize()
def main():
app = QApplication([])
mainw = QMainWindow()
ui = Ui_MainWindow()
ui.setupUi(mainw)
mvtk = VolumeRendering(ui)
mvtk.frame.setGeometry(0,0,1000,1000)
mvtk.frame.setParent(ui.VTK)
mainw.show()
app.exec_()
if __name__ == "__main__":
main()