def setupUserInterface(self):
""" Initialise the User Interface """
# Left frame
leftFrame = QtGui.QFrame()
leftFrameLayout = QtGui.QHBoxLayout()
leftFrame.setLayout(leftFrameLayout)
leftFrame.setLineWidth(0)
leftFrame.setFrameStyle(QtGui.QFrame.Panel)
leftFrameLayout.setContentsMargins(0,0,5,0)
# Left frame contents
self.viewMain = GraphicsLayoutWidget() # A GraphicsLayout within a GraphicsView
leftFrameLayout.addWidget(self.viewMain)
self.viewMain.setMinimumSize(200,200)
self.vb = MultiRoiViewBox(lockAspect=True,enableMenu=True)
self.viewMain.addItem(self.vb)
self.vb.disableAutoRange()
# Right frame
self.sidePanel = SidePanel(self)
# UI window (containing left and right frames)
UIwindow = QtGui.QWidget(self)
UIwindowLayout = QtGui.QHBoxLayout()
UIwindowSplitter = QtGui.QSplitter(QtCore.Qt.Horizontal)
UIwindowLayout.addWidget(UIwindowSplitter)
UIwindow.setLayout(UIwindowLayout)
self.setCentralWidget(UIwindow)
UIwindowSplitter.addWidget(leftFrame)
UIwindowSplitter.addWidget(self.sidePanel)
# Application window
self.setWindowTitle('BMDanalyse')
self.setWindowIcon(self.icons['BMDanalyseIcon'])
self.setMinimumSize(600,500)
self.resize(self.minimumSize())
# Window menus
self.createMenus()
self.createActions()
def setupUserInterface(self):
""" Initialise the User Interface """
# Left frame
leftFrame = QtGui.QFrame()
leftFrameLayout = QtGui.QHBoxLayout()
leftFrame.setLayout(leftFrameLayout)
leftFrame.setLineWidth(0)
leftFrame.setFrameStyle(QtGui.QFrame.Panel)
leftFrameLayout.setContentsMargins(0, 0, 5, 0)
# Left frame contents
self.viewMain = GraphicsLayoutWidget(
) # A GraphicsLayout within a GraphicsView
leftFrameLayout.addWidget(self.viewMain)
self.viewMain.setMinimumSize(200, 200)
self.vb = MultiRoiViewBox(lockAspect=True, enableMenu=True)
self.viewMain.addItem(self.vb)
self.vb.disableAutoRange()
# Right frame
self.sidePanel = SidePanel(self)
# UI window (containing left and right frames)
UIwindow = QtGui.QWidget(self)
UIwindowLayout = QtGui.QHBoxLayout()
UIwindowSplitter = QtGui.QSplitter(QtCore.Qt.Horizontal)
UIwindowLayout.addWidget(UIwindowSplitter)
UIwindow.setLayout(UIwindowLayout)
self.setCentralWidget(UIwindow)
UIwindowSplitter.addWidget(leftFrame)
UIwindowSplitter.addWidget(self.sidePanel)
# Application window
self.setWindowTitle('BMDanalyse')
self.setWindowIcon(self.icons['BMDanalyseIcon'])
self.setMinimumSize(600, 500)
self.resize(self.minimumSize())
# Window menus
self.createMenus()
self.createActions()
class MainWindow(QtGui.QMainWindow):
def __init__(self, parent=None):
QtGui.QMainWindow.__init__(self, parent)
self.setupUserInterface()
def setupUserInterface(self):
frame = QtGui.QFrame()
frameLayout = QtGui.QHBoxLayout()
frame.setLayout(frameLayout)
frame.setLineWidth(0)
frame.setFrameStyle(QtGui.QFrame.Panel)
frameLayout.setContentsMargins(0,0,5,0)
self.viewMain = GraphicsLayoutWidget()
self.viewMain.setMinimumSize(200,200)
self.vb = MultiRoiViewBox(lockAspect=True,enableMenu=True)
self.viewMain.addItem(self.vb)
self.vb.disableAutoRange()
self.setCentralWidget(self.viewMain)
class MainWindow(QtGui.QMainWindow):
def __init__(self, parent=None):
QtGui.QMainWindow.__init__(self, parent)
self.loadIcons()
self.setupUserInterface()
self.setupSignals()
self.__version__ = __version__
# Initialise variables
self.imageFiles = {}
self.timeData = None
self.plotWin = None
self.imageWin = None
self.BMDchange = None
self.roiNames = None
def loadIcons(self):
""" Load icons """
self.icons = dict([
('BMDanalyseIcon', QtGui.QIcon(os.path.join(absDirPath,"icons","logo.png"))),
('imageAddIcon', QtGui.QIcon(os.path.join(absDirPath,"icons","file_add.png"))),
('imageRemIcon', QtGui.QIcon(os.path.join(absDirPath,"icons","file_delete2.png"))),
('imageDownIcon', QtGui.QIcon(os.path.join(absDirPath,"icons","arrow-up-2.png"))),
('imageUpIcon', QtGui.QIcon(os.path.join(absDirPath,"icons","arrow-down-2.png"))),
('imagePrevIcon', QtGui.QIcon(os.path.join(absDirPath,"icons","arrow-left.png"))),
('imageNextIcon', QtGui.QIcon(os.path.join(absDirPath,"icons","arrow-right.png"))),
('roiAddIcon', QtGui.QIcon(os.path.join(absDirPath,"icons","green-add3.png"))),
('roiRectIcon', QtGui.QIcon(os.path.join(absDirPath,"icons","rectangularIcon.png"))),
('roiPolyIcon', QtGui.QIcon(os.path.join(absDirPath,"icons","polygonIcon.png"))),
('roiRemIcon', QtGui.QIcon(os.path.join(absDirPath,"icons","red_delete.png"))),
('roiSaveIcon', QtGui.QIcon(os.path.join(absDirPath,"icons","filesave.png"))),
('roiCopyIcon', QtGui.QIcon(os.path.join(absDirPath,"icons","file_copy.png"))),
('roiLoadIcon', QtGui.QIcon(os.path.join(absDirPath,"icons","opened-folder.png")))])
def setupUserInterface(self):
""" Initialise the User Interface """
# Left frame
leftFrame = QtGui.QFrame()
leftFrameLayout = QtGui.QHBoxLayout()
leftFrame.setLayout(leftFrameLayout)
leftFrame.setLineWidth(0)
leftFrame.setFrameStyle(QtGui.QFrame.Panel)
leftFrameLayout.setContentsMargins(0,0,5,0)
# Left frame contents
self.viewMain = GraphicsLayoutWidget() # A GraphicsLayout within a GraphicsView
leftFrameLayout.addWidget(self.viewMain)
self.viewMain.setMinimumSize(200,200)
self.vb = MultiRoiViewBox(lockAspect=True,enableMenu=True)
self.viewMain.addItem(self.vb)
self.vb.disableAutoRange()
# Right frame
self.sidePanel = SidePanel(self)
# UI window (containing left and right frames)
UIwindow = QtGui.QWidget(self)
UIwindowLayout = QtGui.QHBoxLayout()
UIwindowSplitter = QtGui.QSplitter(QtCore.Qt.Horizontal)
UIwindowLayout.addWidget(UIwindowSplitter)
UIwindow.setLayout(UIwindowLayout)
self.setCentralWidget(UIwindow)
UIwindowSplitter.addWidget(leftFrame)
UIwindowSplitter.addWidget(self.sidePanel)
# Application window
self.setWindowTitle('BMDanalyse')
self.setWindowIcon(self.icons['BMDanalyseIcon'])
self.setMinimumSize(600,500)
self.resize(self.minimumSize())
# Window menus
self.createMenus()
self.createActions()
def createMenus(self):
# Menus
menubar = self.menuBar()
self.fileMenu = menubar.addMenu('&File')
self.imageMenu = menubar.addMenu('&Images')
self.roiMenu = menubar.addMenu('&ROIs')
self.submenu = self.roiMenu.addMenu(self.icons['roiAddIcon'],"Add ROI")
self.analyseMenu = menubar.addMenu('&Analysis')
self.aboutMenu = menubar.addMenu('A&bout')
def createActions(self):
# Actions for File menu
self.exitAct = QtGui.QAction("&Quit", self, shortcut="Ctrl+Q",statusTip="Exit the application")
self.exitAct.triggered[()].connect(self.close)
self.fileMenu.addAction(self.exitAct)
# Actions for Images menu
self.loadImageAct = QtGui.QAction(self.icons['imageAddIcon'], "&Load image(s)", self, shortcut="Ctrl+L")
self.removeImageAct = QtGui.QAction(self.icons['imageRemIcon'], "&Remove current image", self, shortcut="Ctrl+X")
imageMenuActions = [self.loadImageAct,self.removeImageAct]
imageMenuActFuncs = [self.loadImages,self.removeImage]
for i in xrange(len(imageMenuActions)):
action = imageMenuActions[i]
function = imageMenuActFuncs[i]
action.triggered[()].connect(function)
self.imageMenu.addAction(self.loadImageAct)
self.imageMenu.addAction(self.removeImageAct)
# Actions for ROI menu
self.addROIRectAct = QtGui.QAction("Rectangular",self.submenu)
self.addROIPolyAct = QtGui.QAction("Polygon",self.submenu)
self.addROIRectAct.triggered[()].connect(self.vb.addROI)
self.addROIPolyAct.triggered[()].connect(self.vb.addPolyRoiRequest)
self.submenu.addAction(self.addROIRectAct)
self.submenu.addAction(self.addROIPolyAct)
self.addROIRectAct.setIcon(self.icons['roiRectIcon'])
self.addROIPolyAct.setIcon(self.icons['roiPolyIcon'])
self.addROIRectAct.setShortcut("Ctrl+Shift+R")
self.addROIPolyAct.setShortcut("Ctrl+Shift+P")
self.loadRoiAct = QtGui.QAction(self.icons['roiLoadIcon'], "L&oad ROI", self, shortcut="Ctrl+O")
self.copyRoiAct = QtGui.QAction(self.icons['roiCopyIcon'], "&Copy ROI", self, shortcut="Ctrl+C")
self.saveRoiAct = QtGui.QAction(self.icons['roiSaveIcon'], "&Save ROI", self, shortcut="Ctrl+S")
self.remRoiAct = QtGui.QAction(self.icons['roiRemIcon'] , "&Remove ROI", self, shortcut="Ctrl+D")
roiMenuActions = [self.loadRoiAct,self.copyRoiAct,self.saveRoiAct,self.remRoiAct]
roiMenuActFuncs = [self.vb.loadROI,self.vb.copyROI,self.vb.saveROI,self.vb.removeROI]
for i in xrange(len(roiMenuActions)):
action = roiMenuActions[i]
function = roiMenuActFuncs[i]
action.triggered[()].connect(function)
self.roiMenu.addAction(action)
# Actions for Analyse menu
self.roiAnalysisAct = QtGui.QAction("&ROI analysis", self.viewMain, shortcut="Ctrl+R",triggered=self.getBMD)
self.imgAnalysisAct = QtGui.QAction("&Image analysis", self.viewMain, shortcut="Ctrl+I",triggered=self.imageAnalysis)
self.analyseMenu.addAction(self.roiAnalysisAct)
self.analyseMenu.addAction(self.imgAnalysisAct)
# Actions for
self.aboutAct = QtGui.QAction("&About", self.viewMain, shortcut='F1', triggered=self.onAbout)
self.aboutMenu.addAction(self.aboutAct)
def setupSignals(self):
""" Setup signals """
self.sidePanel.imageFileList.itemSelectionChanged.connect(self.getImageToDisplay)
self.sidePanel.buttImageAdd.clicked.connect(self.loadImages)
self.sidePanel.buttImageRem.clicked.connect(self.removeImage)
self.sidePanel.buttImageUp.clicked.connect(self.sidePanel.moveImageUp)
self.sidePanel.buttImageDown.clicked.connect(self.sidePanel.moveImageDown)
self.sidePanel.roiMenu.button1.clicked[()].connect(self.vb.addROI)
self.sidePanel.roiMenu.button2.clicked[()].connect(self.vb.addPolyRoiRequest)
self.sidePanel.buttRoiCopy.clicked[()].connect(self.vb.copyROI)
self.sidePanel.buttRoiRem.clicked.connect(self.vb.removeROI)
self.sidePanel.buttRoiLoad.clicked.connect(self.vb.loadROI)
self.sidePanel.buttRoiSave.clicked.connect(self.vb.saveROI)
self.sidePanel.buttRoiAnalysis.clicked.connect(self.getBMD)
self.sidePanel.buttImgAnalysis.clicked.connect(self.imageAnalysis)
def onAbout(self):
""" About BMDanalyse message"""
author ='Michael Hogg'
date ='2016'
version = self.__version__
QtGui.QMessageBox.about(self, 'About BMDanalyse',
"""
<b>BMDanalyse</b>
<p>A simple program for the analysis of a time series of Bone Mineral Density (BMD) images.</p>
<p>Used to evaluate the bone gain / loss in a number of regions of interest (ROIs) over time,
typically due to bone remodelling as a result of stress shielding around an orthopaedic implant.</p>
<p><table border="0" width="150">
<tr>
<td>Author:</td>
<td>%s</td>
</tr>
<tr>
<td>Version:</td>
<td>%s</td>
</tr>
<tr>
<td>Date:</td>
<td>%s</td>
</tr>
</table></p>
""" % (author,version,date))
def loadImages(self):
""" Load an image to be analysed """
newImages = {}
fileNames = QtGui.QFileDialog.getOpenFileNames(self, self.tr("Load images"),QtCore.QDir.currentPath())
# Fix for PySide. PySide doesn't support QStringList types. PyQt4 getOpenFileNames returns a QStringList, whereas PySide
# returns a type (the first entry being the list of filenames).
if isinstance(fileNames,types.TupleType): fileNames = fileNames[0]
if hasattr(QtCore,'QStringList') and isinstance(fileNames, QtCore.QStringList): fileNames = [str(i) for i in fileNames]
if len(fileNames)>0:
for fileName in fileNames:
if fileName!='':
img = Image.open(str(fileName))
imgarr = np.array(img.convert('L')) # Convert to 8-bit
imgarr = imgarr.swapaxes(0,1)
imgarr = imgarr[:,::-1]
newImages[fileName] = imgarr
# Add filenames to list widget. Only add new filenames. If filename exists aready, then
# it will not be added, but data will be updated
for fileName in sorted(newImages.keys()):
if not self.imageFiles.has_key(fileName):
self.sidePanel.addImageToList(fileName)
self.imageFiles[fileName] = newImages[fileName]
# Show image in Main window
self.vb.enableAutoRange()
if self.sidePanel.imageFileList.currentRow()==-1:
self.sidePanel.imageFileList.setCurrentRow(0)
self.showImage(str(self.sidePanel.imageFileList.currentItem().text()))
self.vb.disableAutoRange()
def removeImage(self):
""" Remove image from sidePanel imageFileList """
# Return if there is no image to remove
if self.vb.img is None: return
# Get current image in sidePanel imageFileList and remove from list
currentRow = self.sidePanel.imageFileList.currentRow()
image = self.sidePanel.imageFileList.takeItem(currentRow)
imageName = str(image.text())
# Delete key and value from dictionary
if imageName!='': del self.imageFiles[imageName]
# Get image item in imageFileList to replace deleted image
if self.sidePanel.imageFileList.count()==0:
self.vb.enableAutoRange()
self.vb.removeItem(self.vb.img)
self.vb.showImage(None)
self.vb.disableAutoRange()
else:
currentRow = self.sidePanel.imageFileList.currentRow()
imageName = str(self.sidePanel.imageFileList.item(currentRow).text())
self.showImage(imageName)
def showImage(self,imageFilename):
""" Shows image in main view """
self.arr = self.imageFiles[imageFilename]
self.vb.showImage(self.arr)
def getImageToDisplay(self):
""" Get current item in file list and display in main view"""
try: imageFilename = str(self.sidePanel.imageFileList.currentItem().text())
except: pass
else: self.showImage(imageFilename)
def getBMD(self):
""" Get change in BMD over time (e.g. for each image) for all ROIs.
Revised function that converts the list of images into a 3D array
and then uses the relative position of the ROIs to the current
image, self.vb.img, to get the average BMD value e.g. it doesn't use
setImage to change the image in the view. This requires that all
images are the same size and in the same position.
"""
# Return if there is no image or rois in view
if self.vb.img is None or len(self.vb.rois)==0: return
# Collect all images into a 3D array
imageFilenames = self.sidePanel.getListOfImages()
images = [self.imageFiles[str(name.text())] for name in imageFilenames]
imageData = np.dstack(images) # Doesn't work correctly if images are not all the same shape
numImages = len(images)
# Get BMD across image stack for each ROI
numROIs = len(self.vb.rois)
BMD = np.zeros((numImages,numROIs),dtype=float)
self.roiNames = []
for i in xrange(numROIs):
roi = self.vb.rois[i]
self.roiNames.append(roi.name)
arrRegion = roi.getArrayRegion(imageData,self.vb.img, axes=(0,1))
avgROIvalue = arrRegion.mean(axis=0).mean(axis=0)
BMD[:,i] = avgROIvalue
# Calculate the BMD change (percentage of original)
tol = 1.0e-06
for i in xrange(numROIs):
if abs(BMD[0,i])<tol:
BMD[:,i] = 100.
else:
BMD[:,i] = BMD[:,i] / BMD[0,i] * 100.
self.BMDchange = BMD-100.
if self.timeData is None or self.timeData.size!=numImages:
self.timeData = np.arange(numImages,dtype=float)
# Plot results
self.showResults()
def imageAnalysis(self):
# Generate images of BMD change
if self.vb.img is None: return
self.showImageWin()
def sliderValueChanged(self,value):
self.imageWin.sliderLabel.setText('BMD change: >= %d %s' % (value,'%'))
self.setLookupTable(value)
self.imageWin.vb.img2.setLookupTable(self.lut)
self.imageWin.vb.img2.setLevels([0,255])
def setLookupTable(self,val):
lut = []
for i in range(256):
if i > 127+val:
lut.append(matplotlib.cm.jet(255))
elif i < 127-val:
lut.append(matplotlib.cm.jet(0))
else:
lut.append((0.0,0.0,0.0,0.0))
lut = np.array(lut)*255
self.lut = np.array(lut,dtype=np.ubyte)
def createImageWin(self):
self.buttMinimumSize = QtCore.QSize(70,36)
self.iconSize = QtCore.QSize(24,24)
if self.imageWin==None:
self.imageWin = QtGui.QDialog(self, QtCore.Qt.WindowSystemMenuHint | QtCore.Qt.WindowTitleHint | \
QtCore.Qt.WindowMinimizeButtonHint | QtCore.Qt.WindowMaximizeButtonHint)
self.imageWin.setWindowTitle('BMDanalyse')
self.imageWin.setWindowIcon(self.icons['BMDanalyseIcon'])
self.imageWin.setMinimumSize(250,500)
self.imageWin.resize(self.imageWin.minimumSize())
# Create viewBox
self.imageWin.glw = GraphicsLayoutWidget() # A GraphicsLayout within a GraphicsView
self.imageWin.vb = ImageAnalysisViewBox(lockAspect=True,enableMenu=True)
self.imageWin.vb.disableAutoRange()
self.imageWin.glw.addItem(self.imageWin.vb)
arr = self.imageFiles.values()[0]
self.imageWin.vb.img1 = ImageItem(arr,autoRange=False,autoLevels=False)
self.imageWin.vb.addItem(self.imageWin.vb.img1)
self.imageWin.vb.img2 = ImageItem(None,autoRange=False,autoLevels=False)
self.imageWin.vb.addItem(self.imageWin.vb.img2)
self.imageWin.vb.autoRange()
lut = [ [ int(255*val) for val in matplotlib.cm.gray(i)[:3] ] for i in xrange(256) ]
lut = np.array(lut,dtype=np.ubyte)
self.imageWin.vb.img1.setLookupTable(lut)
# Label to show index of current image label
self.imageCurrCont = QtGui.QFrame()
self.imageCurrCont.setLineWidth(2)
self.imageCurrCont.setFrameStyle(QtGui.QFrame.Panel | QtGui.QFrame.Raised)
self.imageCurrCont.setMinimumWidth(70)
self.imageWin.currLabel = QtGui.QLabel("")
self.imageWin.currLabel.setAlignment(QtCore.Qt.AlignHCenter)
imageCurrContLayout = QtGui.QHBoxLayout()
imageCurrContLayout.addWidget(self.imageWin.currLabel)
self.imageCurrCont.setLayout(imageCurrContLayout)
# Create buttons to select images
self.imageWin.buttCont = QtGui.QWidget()
self.imageWin.buttPrev = QtGui.QPushButton(self.icons['imagePrevIcon'],"")
self.imageWin.buttNext = QtGui.QPushButton(self.icons['imageNextIcon'],"")
self.buttLayout = QtGui.QHBoxLayout()
self.buttLayout.addStretch(1)
self.buttLayout.addWidget(self.imageWin.buttPrev)
self.buttLayout.addWidget(self.imageCurrCont)
self.buttLayout.addWidget(self.imageWin.buttNext)
self.buttLayout.addStretch(1)
self.imageWin.buttCont.setLayout(self.buttLayout)
self.imageWin.buttPrev.setMinimumSize(self.buttMinimumSize)
self.imageWin.buttNext.setMinimumSize(self.buttMinimumSize)
self.imageWin.buttPrev.setIconSize(self.iconSize)
self.imageWin.buttNext.setIconSize(self.iconSize)
self.buttLayout.setContentsMargins(0,5,0,5)
self.imageWin.buttPrev.clicked.connect(self.prevImage)
self.imageWin.buttNext.clicked.connect(self.nextImage)
# Create slider
self.imageWin.sliderCon = QtGui.QWidget()
self.imageWin.slider = QtGui.QSlider(self)
self.imageWin.slider.setOrientation(QtCore.Qt.Horizontal)
self.imageWin.slider.setMinimum(1)
self.imageWin.slider.setMaximum(100)
self.imageWin.slider.setMinimumWidth(100)
self.imageWin.slider.valueChanged.connect(self.sliderValueChanged)
self.imageWin.sliderLabel = QtGui.QLabel('1')
self.imageWin.sliderLabel.setMinimumWidth(120)
self.sliderLayout = QtGui.QHBoxLayout()
self.sliderLayout.addStretch(1)
self.sliderLayout.addWidget(self.imageWin.sliderLabel)
self.sliderLayout.addWidget(self.imageWin.slider)
self.sliderLayout.addStretch(1)
self.imageWin.sliderCon.setLayout(self.sliderLayout)
self.sliderLayout.setContentsMargins(0,0,0,5)
# Format image window
self.imageWinLayout = QtGui.QVBoxLayout()
self.imageWinLayout.addWidget(self.imageWin.glw)
self.imageWinLayout.addWidget(self.imageWin.buttCont)
self.imageWinLayout.addWidget(self.imageWin.sliderCon)
self.imageWin.setLayout(self.imageWinLayout)
self.imageWin.imagesRGB = None
# Show
self.imageWin.show()
self.imageWin.slider.setValue(10)
self.sliderValueChanged(10)
self.imageWinIndex = 0
def prevImage(self):
minIndex = 0
currIndex = self.imageWinIndex
prevIndex = currIndex - 1
self.imageWinIndex = max(prevIndex,minIndex)
self.updateImageWin()
def nextImage(self):
numImages = len(self.imageFiles)
maxIndex = numImages - 1
currIndex = self.imageWinIndex
nextIndex = currIndex + 1
self.imageWinIndex = min(nextIndex,maxIndex)
self.updateImageWin()
def updateImageWin(self):
imageFilenames = self.sidePanel.getListOfImages()
imageName = imageFilenames[self.imageWinIndex]
self.imageWin.vb.img1.setImage(self.imageFiles[str(imageName.text())],autoLevels=False)
self.imageWin.vb.img2.setImage(self.imageWin.imagesRGB[self.imageWinIndex],autoLevels=False)
self.imageWin.currLabel.setText("%i / %i" % (self.imageWinIndex+1,len(imageFilenames)))
def showImageWin(self):
self.createImageWin()
self.imagesBMDpercentChange()
self.updateImageWin()
def imagesBMDpercentChange(self):
# Get image arrays and convert to an array of floats
imageFilenames = self.sidePanel.getListOfImages()
images = [ self.imageFiles[str(name.text())] for name in imageFilenames ]
imagesConv = []
for img in images:
image = img.copy()
image[np.where(image==0)] = 1
image = image.astype(np.float)
imagesConv.append(image)
# Calculate percentage change and set with limits -100% to +100%
imagesPercCh = []
imageInitial = imagesConv[0]
for image in imagesConv:
imagePercCh = (image-imageInitial)/imageInitial*100.
imagePercCh[np.where(imagePercCh> 100.)] = 100.
imagePercCh[np.where(imagePercCh<-100.)] = -100.
imagesPercCh.append(imagePercCh)
numImages = len(imagesPercCh)
self.imageWin.imagesRGB = []
for i in xrange(numImages):
image = imagesPercCh[i]
sx,sy = image.shape
imageRGB = image*(255/200.)+(255/2.)
self.imageWin.imagesRGB.append(imageRGB)
def BMDtoCSVfile(self):
""" Write BMD change to csv file """
fileName = QtGui.QFileDialog.getSaveFileName(None,self.tr("Export to CSV"),QtCore.QDir.currentPath(),self.tr("CSV (*.csv)"))
# Fix for PyQt/PySide compatibility. PyQt returns a QString, whereas PySide returns a tuple (first entry is filename as string)
if isinstance(fileName,types.TupleType): fileName = fileName[0]
if hasattr(QtCore,'QString') and isinstance(fileName, QtCore.QString): fileName = str(fileName)
if not fileName=='':
textFile = open(fileName,'w')
numFrames, numROIs = self.BMDchange.shape
roiNames = self.roiNames
header = "%10s," % 'Time'
header += ((numROIs-1)*'%10s,'+'%10s\n') % tuple(roiNames)
textFile.write(header)
for i in xrange(numFrames):
textFile.write('%10.1f,' % self.timeData[i])
for j in xrange(numROIs):
if j<numROIs-1: fmt = '%10.3f,'
else: fmt = '%10.3f\n'
textFile.write(fmt % self.BMDchange[i,j])
textFile.close()
def showResults(self,):
""" Plots BMD change using matplotlib """
# Create plot window
if self.plotWin==None:
self.plotWin = QtGui.QDialog(self, QtCore.Qt.WindowSystemMenuHint | QtCore.Qt.WindowTitleHint | \
QtCore.Qt.WindowMinimizeButtonHint | QtCore.Qt.WindowMaximizeButtonHint)
self.plotWin.setWindowTitle('BMDanalyse')
self.plotWin.setWindowIcon(self.icons['BMDanalyseIcon'])
self.plotWin.setMinimumSize(600,500)
self.plotWin.resize(self.minimumSize())
# Create Matplotlib widget
self.mplw = MatplotlibWidget(size=(5,6))
self.fig = self.mplw.getFigure()
self.editDataButton = QtGui.QPushButton('Edit plot')
self.exportCSVButton = QtGui.QPushButton('Export data')
self.mplw.toolbar.addWidget(self.editDataButton)
self.mplw.toolbar.addWidget(self.exportCSVButton)
self.editDataButton.clicked.connect(self.showEditBox)
self.exportCSVButton.clicked.connect(self.BMDtoCSVfile)
# Format plot window
self.plotWinLayout = QtGui.QVBoxLayout()
self.plotWinLayout.addWidget(self.mplw)
self.plotWin.setLayout(self.plotWinLayout)
self.createFigure()
self.plotWin.show()
self.mplw.draw()
def createFigure(self):
""" Creates plot of results """
self.ax1 = self.fig.add_subplot(111)
self.ax1.clear()
self.fig.subplots_adjust(bottom=0.15,top=0.85,left=0.15,right=0.925)
numFrames, numROIs = self.BMDchange.shape
t = self.timeData
# Plot data
for i in xrange(numROIs):
roiname = self.roiNames[i]
self.ax1.plot(t,self.BMDchange[:,i],'-o',label=roiname,linewidth=2.0)
kwargs = dict(y=1.05) # Or kwargs = {'y':1.05}
self.ax1.set_title('Change in Bone Mineral Density over time',fontsize=14,fontweight='roman',**kwargs)
self.ax1.set_xlabel('Time',fontsize=10)
self.ax1.set_ylabel('Change in BMD (%)',fontsize=10)
self.ax1.legend(loc=0)
matplotlib.pyplot.setp(self.ax1.get_xmajorticklabels(), fontsize=10)
matplotlib.pyplot.setp(self.ax1.get_ymajorticklabels(), fontsize=10)
matplotlib.pyplot.setp(self.ax1.get_legend().get_texts(),fontsize=10)
self.ax1.grid()
def fillEditBox(self):
rows,cols = self.BMDchange.shape
for i in xrange(rows):
itmValue = '%.2f' % self.timeData[i]
itm = QtGui.QTableWidgetItem(itmValue)
self.tableResults.setItem(i,0,itm)
for j in xrange(cols):
itmValue = '%.2f' % self.BMDchange[i,j]
itm = QtGui.QTableWidgetItem(itmValue)
self.tableResults.setItem(i,j+1,itm)
def showEditBox(self):
self.plotWin.editBox = QtGui.QDialog(self.plotWin, QtCore.Qt.WindowSystemMenuHint | QtCore.Qt.WindowTitleHint)
self.plotWin.editBox.setWindowIcon(self.icons['BMDanalyseIcon'])
self.plotWin.editBox.setWindowTitle('BMDanalyse')
self.plotWin.editBox.setModal(True)
# Add table
layout = QtGui.QVBoxLayout()
layout.setContentsMargins(10,10,10,10)
layout.setSpacing(20)
rows,cols = self.BMDchange.shape
self.tableResults = TableWidget(rows,cols+1,self.plotWin.editBox)
self.tableResults.verticalHeader().setVisible(True)
# Set headers
self.tableResults.setHorizontalHeaderItem(0,QtGui.QTableWidgetItem('Time'))
for i in xrange(cols):
header = QtGui.QTableWidgetItem(self.roiNames[i])
self.tableResults.setHorizontalHeaderItem(i+1,header)
# Add values to table
self.fillEditBox()
# Set layout
layout.addWidget(self.tableResults)
self.buttonsFrame = QtGui.QFrame()
self.buttonsLayout = QtGui.QHBoxLayout()
self.buttonReset = QtGui.QPushButton('Reset')
self.buttonSave = QtGui.QPushButton('Save')
self.buttonClose = QtGui.QPushButton('Cancel')
self.buttonReset.setFixedWidth(50)
self.buttonSave.setFixedWidth(50)
self.buttonClose.setFixedWidth(50)
self.buttonClose.clicked.connect(self.plotWin.editBox.close)
self.buttonSave.clicked.connect(self.updateTableValues)
self.buttonReset.clicked.connect(self.fillEditBox)
self.buttonsLayout.addStretch(1)
self.buttonsLayout.addWidget(self.buttonReset)
self.buttonsLayout.addWidget(self.buttonSave)
self.buttonsLayout.addWidget(self.buttonClose)
self.buttonsLayout.setContentsMargins(0,0,0,0)
self.buttonsFrame.setLayout(self.buttonsLayout)
layout.addWidget(self.buttonsFrame)
self.plotWin.editBox.setLayout(layout)
self.plotWin.editBox.setMaximumSize(layout.sizeHint())
self.plotWin.editBox.show()
def updateTableValues(self):
# Create temporary arrays
timeData = self.timeData.copy()
BMDchange = self.BMDchange.copy()
# Put the values from the tables into the temporary arrays
rows = self.tableResults.rowCount()
cols = self.tableResults.columnCount()
for r in xrange(rows):
for c in xrange(cols):
item = self.tableResults.item(r,c)
itemValue = float(item.text())
if c==0:
timeData[r] = itemValue
else:
BMDchange[r,c-1] = itemValue
# Check that time values are in increasing order. If so, then update arrays
if any(np.diff(timeData)<=0):
self.errorMessage = QtGui.QMessageBox()
self.errorMessage.setWindowIcon(self.icons['BMDanalyseIcon'])
self.errorMessage.setWindowTitle('BMDanalyse')
self.errorMessage.setText('Input error: Time values should be in order of increasing value')
self.errorMessage.setIcon(QtGui.QMessageBox.Warning)
self.errorMessage.open()
else:
self.timeData = timeData
self.BMDchange = BMDchange
self.createFigure()
self.mplw.draw()
self.plotWin.editBox.close()
class MainWindow(QtGui.QMainWindow):
def __init__(self, parent=None):
QtGui.QMainWindow.__init__(self, parent)
self.loadIcons()
self.setupUserInterface()
self.setupSignals()
self.__version__ = __version__
# Initialise variables
self.imageFiles = {}
self.timeData = None
self.plotWin = None
self.imageWin = None
self.BMDchange = None
self.roiNames = None
def loadIcons(self):
""" Load icons """
self.icons = dict([
('BMDanalyseIcon',
QtGui.QIcon(os.path.join(absDirPath, "icons", "logo.png"))),
('imageAddIcon',
QtGui.QIcon(os.path.join(absDirPath, "icons", "file_add.png"))),
('imageRemIcon',
QtGui.QIcon(os.path.join(absDirPath, "icons",
"file_delete2.png"))),
('imageDownIcon',
QtGui.QIcon(os.path.join(absDirPath, "icons", "arrow-up-2.png"))),
('imageUpIcon',
QtGui.QIcon(os.path.join(absDirPath, "icons",
"arrow-down-2.png"))),
('imagePrevIcon',
QtGui.QIcon(os.path.join(absDirPath, "icons", "arrow-left.png"))),
('imageNextIcon',
QtGui.QIcon(os.path.join(absDirPath, "icons",
"arrow-right.png"))),
('roiAddIcon',
QtGui.QIcon(os.path.join(absDirPath, "icons", "green-add3.png"))),
('roiRectIcon',
QtGui.QIcon(
os.path.join(absDirPath, "icons", "rectangularIcon.png"))),
('roiPolyIcon',
QtGui.QIcon(os.path.join(absDirPath, "icons",
"polygonIcon.png"))),
('roiRemIcon',
QtGui.QIcon(os.path.join(absDirPath, "icons", "red_delete.png"))),
('roiSaveIcon',
QtGui.QIcon(os.path.join(absDirPath, "icons", "filesave.png"))),
('roiCopyIcon',
QtGui.QIcon(os.path.join(absDirPath, "icons", "file_copy.png"))),
('roiLoadIcon',
QtGui.QIcon(os.path.join(absDirPath, "icons",
"opened-folder.png")))
])
def setupUserInterface(self):
""" Initialise the User Interface """
# Left frame
leftFrame = QtGui.QFrame()
leftFrameLayout = QtGui.QHBoxLayout()
leftFrame.setLayout(leftFrameLayout)
leftFrame.setLineWidth(0)
leftFrame.setFrameStyle(QtGui.QFrame.Panel)
leftFrameLayout.setContentsMargins(0, 0, 5, 0)
# Left frame contents
self.viewMain = GraphicsLayoutWidget(
) # A GraphicsLayout within a GraphicsView
leftFrameLayout.addWidget(self.viewMain)
self.viewMain.setMinimumSize(200, 200)
self.vb = MultiRoiViewBox(lockAspect=True, enableMenu=True)
self.viewMain.addItem(self.vb)
self.vb.disableAutoRange()
# Right frame
self.sidePanel = SidePanel(self)
# UI window (containing left and right frames)
UIwindow = QtGui.QWidget(self)
UIwindowLayout = QtGui.QHBoxLayout()
UIwindowSplitter = QtGui.QSplitter(QtCore.Qt.Horizontal)
UIwindowLayout.addWidget(UIwindowSplitter)
UIwindow.setLayout(UIwindowLayout)
self.setCentralWidget(UIwindow)
UIwindowSplitter.addWidget(leftFrame)
UIwindowSplitter.addWidget(self.sidePanel)
# Application window
self.setWindowTitle('BMDanalyse')
self.setWindowIcon(self.icons['BMDanalyseIcon'])
self.setMinimumSize(600, 500)
self.resize(self.minimumSize())
# Window menus
self.createMenus()
self.createActions()
def createMenus(self):
# Menus
menubar = self.menuBar()
self.fileMenu = menubar.addMenu('&File')
self.roiMenu = menubar.addMenu('&ROIs')
self.submenu = self.roiMenu.addMenu(self.icons['roiAddIcon'],
"Add ROI")
self.analyseMenu = menubar.addMenu('&Analyse')
self.aboutMenu = menubar.addMenu('A&bout')
def createActions(self):
# Actions for File menu
self.loadImageAct = QtGui.QAction(self.icons['imageAddIcon'],
"&Load image(s)",
self,
shortcut="Ctrl+L")
self.removeImageAct = QtGui.QAction(self.icons['imageRemIcon'],
"&Remove current image",
self,
shortcut="Ctrl+X")
self.exitAct = QtGui.QAction("&Quit",
self,
shortcut="Ctrl+Q",
statusTip="Exit the application")
fileMenuActions = [
self.loadImageAct, self.removeImageAct, self.exitAct
]
fileMenuActFuncs = [self.loadImages, self.removeImage, self.close]
for i in xrange(len(fileMenuActions)):
action = fileMenuActions[i]
function = fileMenuActFuncs[i]
action.triggered[()].connect(function)
self.fileMenu.addAction(self.loadImageAct)
self.fileMenu.addAction(self.removeImageAct)
self.fileMenu.addSeparator()
self.fileMenu.addAction(self.exitAct)
# Actions for ROI menu
# Submenu to add ROIs
#self.addROIRectAct = QActionCustom("Rectangular",self.submenu)
#self.addROIPolyAct = QActionCustom("Polygon",self.submenu)
self.addROIRectAct = QtGui.QAction("Rectangular", self.submenu)
self.addROIPolyAct = QtGui.QAction("Polygon", self.submenu)
#self.addROIRectAct.clickEvent.connect(self.vb.addROI)
#self.addROIPolyAct.clickEvent.connect(self.vb.addPolyRoiRequest)
self.addROIRectAct.triggered[()].connect(self.vb.addROI)
self.addROIPolyAct.triggered[()].connect(self.vb.addPolyRoiRequest)
self.submenu.addAction(self.addROIRectAct)
self.submenu.addAction(self.addROIPolyAct)
self.addROIRectAct.setIcon(self.icons['roiRectIcon'])
self.addROIPolyAct.setIcon(self.icons['roiPolyIcon'])
self.addROIRectAct.setShortcut("Ctrl+Shift+R")
self.addROIPolyAct.setShortcut("Ctrl+Shift+P")
self.loadRoiAct = QtGui.QAction(self.icons['roiLoadIcon'],
"L&oad ROI",
self,
shortcut="Ctrl+O")
self.copyRoiAct = QtGui.QAction(self.icons['roiCopyIcon'],
"&Copy ROI",
self,
shortcut="Ctrl+C")
self.saveRoiAct = QtGui.QAction(self.icons['roiSaveIcon'],
"&Save ROI",
self,
shortcut="Ctrl+S")
self.remRoiAct = QtGui.QAction(self.icons['roiRemIcon'],
"&Remove ROI",
self,
shortcut="Ctrl+D")
roiMenuActions = [
self.loadRoiAct, self.copyRoiAct, self.saveRoiAct, self.remRoiAct
]
roiMenuActFuncs = [
self.vb.loadROI, self.vb.copyROI, self.vb.saveROI,
self.vb.removeROI
]
for i in xrange(len(roiMenuActions)):
action = roiMenuActions[i]
function = roiMenuActFuncs[i]
action.triggered[()].connect(function)
self.roiMenu.addAction(action)
# Actions for Analyse menu
self.roiAnalysisAct = QtGui.QAction("&ROI analysis",
self.viewMain,
shortcut="Ctrl+R",
triggered=self.getBMD)
self.imgAnalysisAct = QtGui.QAction("&Image analysis",
self.viewMain,
shortcut="Ctrl+I",
triggered=self.imageAnalysis)
self.analyseMenu.addAction(self.roiAnalysisAct)
self.analyseMenu.addAction(self.imgAnalysisAct)
# Actions for
self.aboutAct = QtGui.QAction("&About",
self.viewMain,
shortcut='F1',
triggered=self.onAbout)
self.aboutMenu.addAction(self.aboutAct)
def setupSignals(self):
""" Setup signals """
self.sidePanel.imageFileList.itemSelectionChanged.connect(
self.getImageToDisplay)
self.sidePanel.buttImageAdd.clicked.connect(self.loadImages)
self.sidePanel.buttImageRem.clicked.connect(self.removeImage)
self.sidePanel.buttImageUp.clicked.connect(self.sidePanel.moveImageUp)
self.sidePanel.buttImageDown.clicked.connect(
self.sidePanel.moveImageDown)
self.sidePanel.roiMenu.button1.clicked[()].connect(self.vb.addROI)
self.sidePanel.roiMenu.button2.clicked[()].connect(
self.vb.addPolyRoiRequest)
self.sidePanel.buttRoiCopy.clicked[()].connect(self.vb.copyROI)
self.sidePanel.buttRoiRem.clicked.connect(self.vb.removeROI)
self.sidePanel.buttRoiLoad.clicked.connect(self.vb.loadROI)
self.sidePanel.buttRoiSave.clicked.connect(self.vb.saveROI)
#self.vb.sigROIchanged.connect(self.updateROItools)
def onAbout(self):
""" About BMDanalyse message"""
author = 'Michael Hogg'
date = '2012 - 2013'
version = self.__version__
QtGui.QMessageBox.about(
self, 'About BMDanalyse', """
<b>BMDanalyse</b>
<p>A simple program for the analysis of a time series of Bone Mineral Density (BMD) images.</p>
<p>Used to evaluate the bone gain / loss in a number of regions of interest (ROIs) over time,
typically due to bone remodelling as a result of stress shielding around an orthopaedic implant.</p>
<p><table border="0" width="150">
<tr>
<td>Author:</td>
<td>%s</td>
</tr>
<tr>
<td>Version:</td>
<td>%s</td>
</tr>
<tr>
<td>Date:</td>
<td>%s</td>
</tr>
</table></p>
""" % (author, version, date))
def updateROItools(self, roi=None):
""" Update ROI info box in side panel """
if roi == None:
self.sidePanel.updateRoiInfoBox()
else:
roiState = roi.getState()
posx, posy = roiState['pos']
sizex, sizey = roiState['size']
angle = roiState['angle']
name = roi.name
pos = '(%.3f, %.3f)' % (posx, posy)
size = '(%.3f, %.3f)' % (sizex, sizey)
angle = '%.3f' % angle
self.sidePanel.updateRoiInfoBox(name, pos, size, angle)
def loadImages(self):
""" Load an image to be analysed """
newImages = {}
fileNames = QtGui.QFileDialog.getOpenFileNames(
self, self.tr("Load images"), QtCore.QDir.currentPath())
# Fix for PySide. PySide doesn't support QStringList types. PyQt4 getOpenFileNames returns a QStringList, whereas PySide
# returns a type (the first entry being the list of filenames).
if isinstance(fileNames, types.TupleType): fileNames = fileNames[0]
if hasattr(QtCore, 'QStringList') and isinstance(
fileNames, QtCore.QStringList):
fileNames = [str(i) for i in fileNames]
if len(fileNames) > 0:
for fileName in fileNames:
if fileName != '':
imgarr = np.array(Image.open(str(fileName)))
imgarr = imgarr.swapaxes(0, 1)
if imgarr.ndim == 2: imgarr = imgarr[:, ::-1]
elif imgarr.ndim == 3: imgarr = imgarr[:, ::-1, :]
newImages[fileName] = imgarr
# Add filenames to list widget. Only add new filenames. If filename exists aready, then
# it will not be added, but data will be updated
for fileName in sorted(newImages.keys()):
if not self.imageFiles.has_key(fileName):
self.sidePanel.addImageToList(fileName)
self.imageFiles[fileName] = newImages[fileName]
# Show image in Main window
self.vb.enableAutoRange()
if self.sidePanel.imageFileList.currentRow() == -1:
self.sidePanel.imageFileList.setCurrentRow(0)
self.showImage(
str(self.sidePanel.imageFileList.currentItem().text()))
self.vb.disableAutoRange()
def removeImage(self):
""" Remove image from sidePanel imageFileList """
# Return if there is no image to remove
if self.vb.img == None: return
# Get current image in sidePanel imageFileList and remove from list
currentRow = self.sidePanel.imageFileList.currentRow()
image = self.sidePanel.imageFileList.takeItem(currentRow)
imageName = str(image.text())
# Delete key and value from dictionary
if imageName != '': del self.imageFiles[imageName]
#self.imageFiles.pop(imageName,None)
# Get image item in imageFileList to replace deleted image
if self.sidePanel.imageFileList.count() == 0:
self.vb.enableAutoRange()
self.vb.removeItem(self.vb.img)
self.vb.showImage(None)
#self.vb.img = None
self.vb.disableAutoRange()
else:
currentRow = self.sidePanel.imageFileList.currentRow()
imageName = str(
self.sidePanel.imageFileList.item(currentRow).text())
self.showImage(imageName)
def showImage(self, imageFilename):
""" Shows image in main view """
self.arr = self.imageFiles[imageFilename]
self.vb.showImage(self.arr)
def getImageToDisplay(self):
""" Get current item in file list and display in main view"""
try:
imageFilename = str(
self.sidePanel.imageFileList.currentItem().text())
except:
pass
else:
self.showImage(imageFilename)
def getBMD(self):
""" Get change in BMD over time (e.g. for each image) for all ROIs.
Revised function that converts the list of images into a 3D array
and then uses the relative position of the ROIs to the current
image, self.vb.img, to get the average BMD value e.g. it doesn't use
setImage to change the image in the view. This requires that all
images are the same size and in the same position.
"""
# Return if there is no image or rois in view
if self.vb.img == None or len(self.vb.rois) == 0: return
# Collect all images into a 3D array
imageFilenames = self.sidePanel.getListOfImages()
images = [self.imageFiles[str(name.text())] for name in imageFilenames]
imageData = np.dstack(images)
numImages = len(images)
# Get BMD across image stack for each ROI
numROIs = len(self.vb.rois)
BMD = np.zeros((numImages, numROIs), dtype=float)
self.roiNames = []
for i in xrange(numROIs):
roi = self.vb.rois[i]
self.roiNames.append(roi.name)
arrRegion = roi.getArrayRegion(imageData, self.vb.img, axes=(0, 1))
avgROIvalue = arrRegion.mean(axis=0).mean(axis=0)
BMD[:, i] = avgROIvalue
# Calculate the BMD change (percentage of original)
tol = 1.0e-06
for i in xrange(numROIs):
if abs(BMD[0, i]) < tol:
BMD[:, i] = 100.
else:
BMD[:, i] = BMD[:, i] / BMD[0, i] * 100.
self.BMDchange = BMD - 100.
if self.timeData == None or self.timeData.size != numImages:
self.timeData = np.arange(numImages, dtype=float)
# Plot results
self.showResults()
def imageAnalysis(self):
# Generate images of BMD change
if self.vb.img == None: return
self.showImageWin()
def sliderValueChanged(self, value):
self.imageWin.sliderLabel.setText('BMD change: >= %d %s' %
(value, '%'))
self.setLookupTable(value)
self.imageWin.vb.img2.setLookupTable(self.lut)
def setLookupTable(self, val):
lut = []
for i in range(256):
if i > 127 + val:
lut.append(matplotlib.cm.jet(255))
elif i < 127 - val:
lut.append(matplotlib.cm.jet(0))
else:
lut.append((0.0, 0.0, 0.0, 0.0))
lut = np.array(lut) * 255
self.lut = np.array(lut, dtype=np.ubyte)
def createImageWin(self):
self.buttMinimumSize = QtCore.QSize(70, 36)
self.iconSize = QtCore.QSize(24, 24)
if self.imageWin == None:
self.imageWin = QtGui.QDialog(self, QtCore.Qt.WindowSystemMenuHint | QtCore.Qt.WindowTitleHint | \
QtCore.Qt.WindowMinimizeButtonHint | QtCore.Qt.WindowMaximizeButtonHint)
self.imageWin.setWindowTitle('BMDanalyse')
self.imageWin.setWindowIcon(self.icons['BMDanalyseIcon'])
self.imageWin.setMinimumSize(250, 500)
self.imageWin.resize(self.imageWin.minimumSize())
# Create viewBox
self.imageWin.glw = GraphicsLayoutWidget(
) # A GraphicsLayout within a GraphicsView
self.imageWin.vb = ImageAnalysisViewBox(lockAspect=True,
enableMenu=True)
self.imageWin.vb.disableAutoRange()
self.imageWin.glw.addItem(self.imageWin.vb)
arr = self.imageFiles.values()[0]
self.imageWin.vb.img1 = pg.ImageItem(arr,
autoRange=False,
autoLevels=False)
self.imageWin.vb.addItem(self.imageWin.vb.img1)
self.imageWin.vb.img2 = pg.ImageItem(None,
autoRange=False,
autoLevels=False)
self.imageWin.vb.addItem(self.imageWin.vb.img2)
self.imageWin.vb.autoRange()
lut = [[int(255 * val) for val in matplotlib.cm.gray(i)[:3]]
for i in xrange(256)]
lut = np.array(lut, dtype=np.ubyte)
self.imageWin.vb.img1.setLookupTable(lut)
# Label to show index of current image label
self.imageCurrCont = QtGui.QFrame()
self.imageCurrCont.setLineWidth(2)
self.imageCurrCont.setFrameStyle(QtGui.QFrame.Panel
| QtGui.QFrame.Raised)
self.imageCurrCont.setMinimumWidth(70)
self.imageWin.currLabel = QtGui.QLabel("")
self.imageWin.currLabel.setAlignment(QtCore.Qt.AlignHCenter)
imageCurrContLayout = QtGui.QHBoxLayout()
imageCurrContLayout.addWidget(self.imageWin.currLabel)
self.imageCurrCont.setLayout(imageCurrContLayout)
# Create buttons to select images
self.imageWin.buttCont = QtGui.QWidget()
self.imageWin.buttPrev = QtGui.QPushButton(
self.icons['imagePrevIcon'], "")
self.imageWin.buttNext = QtGui.QPushButton(
self.icons['imageNextIcon'], "")
self.buttLayout = QtGui.QHBoxLayout()
self.buttLayout.addStretch(1)
self.buttLayout.addWidget(self.imageWin.buttPrev)
self.buttLayout.addWidget(self.imageCurrCont)
self.buttLayout.addWidget(self.imageWin.buttNext)
self.buttLayout.addStretch(1)
self.imageWin.buttCont.setLayout(self.buttLayout)
self.imageWin.buttPrev.setMinimumSize(self.buttMinimumSize)
self.imageWin.buttNext.setMinimumSize(self.buttMinimumSize)
self.imageWin.buttPrev.setIconSize(self.iconSize)
self.imageWin.buttNext.setIconSize(self.iconSize)
self.buttLayout.setContentsMargins(0, 5, 0, 5)
self.imageWin.buttPrev.clicked.connect(self.prevImage)
self.imageWin.buttNext.clicked.connect(self.nextImage)
# Create slider
self.imageWin.sliderCon = QtGui.QWidget()
self.imageWin.slider = QtGui.QSlider(self)
self.imageWin.slider.setOrientation(QtCore.Qt.Horizontal)
self.imageWin.slider.setMinimum(1)
self.imageWin.slider.setMaximum(100)
self.imageWin.slider.setMinimumWidth(100)
self.imageWin.slider.valueChanged.connect(self.sliderValueChanged)
self.imageWin.sliderLabel = QtGui.QLabel('1')
self.imageWin.sliderLabel.setMinimumWidth(120)
self.sliderLayout = QtGui.QHBoxLayout()
self.sliderLayout.addStretch(1)
self.sliderLayout.addWidget(self.imageWin.sliderLabel)
self.sliderLayout.addWidget(self.imageWin.slider)
self.sliderLayout.addStretch(1)
self.imageWin.sliderCon.setLayout(self.sliderLayout)
self.sliderLayout.setContentsMargins(0, 0, 0, 5)
# Format image window
self.imageWinLayout = QtGui.QVBoxLayout()
self.imageWinLayout.addWidget(self.imageWin.glw)
self.imageWinLayout.addWidget(self.imageWin.buttCont)
self.imageWinLayout.addWidget(self.imageWin.sliderCon)
self.imageWin.setLayout(self.imageWinLayout)
self.imageWin.imagesRGB = None
# Show
self.imageWin.show()
self.imageWin.slider.setValue(10)
self.sliderValueChanged(10)
self.imageWinIndex = 0
def prevImage(self):
#numImages = len(self.imageFiles)
minIndex = 0
currIndex = self.imageWinIndex
prevIndex = currIndex - 1
self.imageWinIndex = max(prevIndex, minIndex)
self.updateImageWin()
def nextImage(self):
numImages = len(self.imageFiles)
maxIndex = numImages - 1
currIndex = self.imageWinIndex
nextIndex = currIndex + 1
self.imageWinIndex = min(nextIndex, maxIndex)
self.updateImageWin()
def updateImageWin(self):
imageFilenames = self.sidePanel.getListOfImages()
imageName = imageFilenames[self.imageWinIndex]
self.imageWin.vb.img1.setImage(self.imageFiles[str(imageName.text())],
autoLevels=False)
self.imageWin.vb.img2.setImage(
self.imageWin.imagesRGB[self.imageWinIndex], autoLevels=False)
self.imageWin.currLabel.setText(
"%i / %i" % (self.imageWinIndex + 1, len(imageFilenames)))
def showImageWin(self):
self.createImageWin()
#if self.imageWin.imagesRGB == None: self.imagesBMDpercentChange()
self.imagesBMDpercentChange()
self.updateImageWin()
def imagesBMDpercentChange(self):
# Get image arrays and convert to an array of floats
imageFilenames = self.sidePanel.getListOfImages()
images = [self.imageFiles[str(name.text())] for name in imageFilenames]
imagesConv = []
for img in images:
image = img.copy()
image[np.where(image == 0)] = 1
image = image.astype(np.float)
imagesConv.append(image)
# Calculate percentage change and set with limits -100% to +100%
imagesPercCh = []
imageInitial = imagesConv[0]
for image in imagesConv:
imagePercCh = (image - imageInitial) / imageInitial * 100.
imagePercCh[np.where(imagePercCh > 100.)] = 100.
imagePercCh[np.where(imagePercCh < -100.)] = -100.
imagesPercCh.append(imagePercCh)
numImages = len(imagesPercCh)
self.imageWin.imagesRGB = []
for i in xrange(numImages):
image = imagesPercCh[i]
sx, sy = image.shape
#imageCh = np.zeros((sx,sy),dtype=np.float)
imageRGB = image * (255 / 200.) + (255 / 2.)
self.imageWin.imagesRGB.append(imageRGB)
def BMDtoCSVfile(self):
""" Write BMD change to csv file """
fileName = QtGui.QFileDialog.getSaveFileName(None,
self.tr("Export to CSV"),
QtCore.QDir.currentPath(),
self.tr("CSV (*.csv)"))
# Fix for PyQt/PySide compatibility. PyQt returns a QString, whereas PySide returns a tuple (first entry is filename as string)
if isinstance(fileName, types.TupleType): fileName = fileName[0]
if hasattr(QtCore, 'QString') and isinstance(fileName, QtCore.QString):
fileName = str(fileName)
if not fileName == '':
#if not fileName.isEmpty():
textFile = open(fileName, 'w')
numFrames, numROIs = self.BMDchange.shape
roiNames = self.roiNames
header = "%10s," % 'Time'
header += ((numROIs - 1) * '%10s,' + '%10s\n') % tuple(roiNames)
textFile.write(header)
for i in xrange(numFrames):
textFile.write('%10.1f,' % self.timeData[i])
for j in xrange(numROIs):
if j < numROIs - 1: fmt = '%10.3f,'
else: fmt = '%10.3f\n'
textFile.write(fmt % self.BMDchange[i, j])
textFile.close()
def showResults(self, ):
""" Plots BMD change using matplotlib """
# Create plot window
if self.plotWin == None:
self.plotWin = QtGui.QDialog(self, QtCore.Qt.WindowSystemMenuHint | QtCore.Qt.WindowTitleHint | \
QtCore.Qt.WindowMinimizeButtonHint | QtCore.Qt.WindowMaximizeButtonHint)
self.plotWin.setWindowTitle('BMDanalyse')
self.plotWin.setWindowIcon(self.icons['BMDanalyseIcon'])
self.plotWin.setMinimumSize(600, 500)
self.plotWin.resize(self.minimumSize())
# Create Matplotlib widget
self.mplw = MatplotlibWidget(size=(5, 6))
self.fig = self.mplw.getFigure()
self.editDataButton = QtGui.QPushButton('Edit plot')
self.exportCSVButton = QtGui.QPushButton('Export data')
self.mplw.toolbar.addWidget(self.editDataButton)
self.mplw.toolbar.addWidget(self.exportCSVButton)
self.editDataButton.clicked.connect(self.showEditBox)
self.exportCSVButton.clicked.connect(self.BMDtoCSVfile)
# Format plot window
self.plotWinLayout = QtGui.QVBoxLayout()
self.plotWinLayout.addWidget(self.mplw)
self.plotWin.setLayout(self.plotWinLayout)
self.createFigure()
self.plotWin.show()
self.mplw.draw()
def createFigure(self):
""" Creates plot of results """
self.ax1 = self.fig.add_subplot(111)
self.ax1.clear()
self.fig.subplots_adjust(bottom=0.15, top=0.85, left=0.15, right=0.925)
numFrames, numROIs = self.BMDchange.shape
t = self.timeData
# Plot data
for i in xrange(numROIs):
roiname = self.roiNames[i]
self.ax1.plot(t,
self.BMDchange[:, i],
'-o',
label=roiname,
linewidth=2.0)
kwargs = dict(y=1.05) # Or kwargs = {'y':1.05}
self.ax1.set_title('Change in Bone Mineral Density over time',
fontsize=14,
fontweight='roman',
**kwargs)
self.ax1.set_xlabel('Time', fontsize=10)
self.ax1.set_ylabel('Change in BMD (%)', fontsize=10)
self.ax1.legend(loc=0)
matplotlib.pyplot.setp(self.ax1.get_xmajorticklabels(), fontsize=10)
matplotlib.pyplot.setp(self.ax1.get_ymajorticklabels(), fontsize=10)
matplotlib.pyplot.setp(self.ax1.get_legend().get_texts(), fontsize=10)
self.ax1.grid()
def fillEditBox(self):
rows, cols = self.BMDchange.shape
for i in xrange(rows):
itmValue = '%.2f' % self.timeData[i]
itm = QtGui.QTableWidgetItem(itmValue)
self.tableResults.setItem(i, 0, itm)
for j in xrange(cols):
itmValue = '%.2f' % self.BMDchange[i, j]
itm = QtGui.QTableWidgetItem(itmValue)
self.tableResults.setItem(i, j + 1, itm)
def showEditBox(self):
self.plotWin.editBox = QtGui.QDialog(
self.plotWin,
QtCore.Qt.WindowSystemMenuHint | QtCore.Qt.WindowTitleHint)
self.plotWin.editBox.setWindowIcon(self.icons['BMDanalyseIcon'])
self.plotWin.editBox.setWindowTitle('BMDanalyse')
self.plotWin.editBox.setModal(True)
# Add table
layout = QtGui.QVBoxLayout()
layout.setContentsMargins(10, 10, 10, 10)
layout.setSpacing(20)
rows, cols = self.BMDchange.shape
self.tableResults = MyTableWidget(rows, cols + 1, self.plotWin.editBox)
self.tableResults.verticalHeader().setVisible(True)
# Set headers
self.tableResults.setHorizontalHeaderItem(
0, QtGui.QTableWidgetItem('Time'))
for i in xrange(cols):
header = QtGui.QTableWidgetItem(self.roiNames[i])
self.tableResults.setHorizontalHeaderItem(i + 1, header)
# Add values to table
self.fillEditBox()
# Set layout
layout.addWidget(self.tableResults)
self.buttonsFrame = QtGui.QFrame()
self.buttonsLayout = QtGui.QHBoxLayout()
self.buttonReset = QtGui.QPushButton('Reset')
self.buttonSave = QtGui.QPushButton('Save')
self.buttonClose = QtGui.QPushButton('Cancel')
self.buttonReset.setFixedWidth(50)
self.buttonSave.setFixedWidth(50)
self.buttonClose.setFixedWidth(50)
self.buttonClose.clicked.connect(self.plotWin.editBox.close)
self.buttonSave.clicked.connect(self.updateTableValues)
self.buttonReset.clicked.connect(self.fillEditBox)
self.buttonsLayout.addStretch(1)
self.buttonsLayout.addWidget(self.buttonReset)
self.buttonsLayout.addWidget(self.buttonSave)
self.buttonsLayout.addWidget(self.buttonClose)
self.buttonsLayout.setContentsMargins(0, 0, 0, 0)
self.buttonsFrame.setLayout(self.buttonsLayout)
layout.addWidget(self.buttonsFrame)
self.plotWin.editBox.setLayout(layout)
self.plotWin.editBox.setMaximumSize(layout.sizeHint())
self.plotWin.editBox.show()
def updateTableValues(self):
# Create temporary arrays
timeData = self.timeData.copy()
BMDchange = self.BMDchange.copy()
# Put the values from the tables into the temporary arrays
rows = self.tableResults.rowCount()
cols = self.tableResults.columnCount()
for r in xrange(rows):
for c in xrange(cols):
item = self.tableResults.item(r, c)
itemValue = float(item.text())
if c == 0:
timeData[r] = itemValue
else:
BMDchange[r, c - 1] = itemValue
# Check that time values are in increasing order. If so, then update arrays
if any(np.diff(timeData) <= 0):
self.errorMessage = QtGui.QMessageBox()
self.errorMessage.setWindowIcon(self.icons['BMDanalyseIcon'])
self.errorMessage.setWindowTitle('BMDanalyse')
self.errorMessage.setText(
'Input error: Time values should be in order of increasing value'
)
self.errorMessage.setIcon(QtGui.QMessageBox.Warning)
self.errorMessage.open()
else:
self.timeData = timeData
self.BMDchange = BMDchange
self.createFigure()
self.mplw.draw()
self.plotWin.editBox.close()
