class ImageAnalysisViewBox(pg.ViewBox):
'''
Custom ViewBox used to over-ride the context menu. I don't want the full context menu,
just a view all and an export. Export does not call a dialog, just prompts user for filename.
'''
def __init__(self,parent=None,border=None,lockAspect=False,enableMouse=True,invertY=False,enableMenu=True,name=None):
pg.ViewBox.__init__(self,parent,border,lockAspect,enableMouse,invertY,enableMenu,name)
self.menu = None # Override pyqtgraph ViewBoxMenu
self.menu = self.getMenu(None)
def raiseContextMenu(self, ev):
if not self.menuEnabled(): return
menu = self.getMenu(ev)
pos = ev.screenPos()
menu.popup(QtCore.QPoint(pos.x(), pos.y()))
def export(self):
self.exp = ImageExporterCustom(self)
self.exp.export()
def getMenu(self,event):
if self.menu is None:
self.menu = QMenuCustom()
self.viewAll = QtGui.QAction("View All", self.menu)
self.exportImage = QtGui.QAction("Export image", self.menu)
self.viewAll.triggered[()].connect(self.autoRange)
self.exportImage.triggered[()].connect(self.export)
self.menu.addAction(self.viewAll)
self.menu.addAction(self.exportImage)
return self.menu
class ImageAnalysisViewBox(pg.ViewBox):
"""
Custom ViewBox used to over-ride the context menu. I don't want the full context menu,
just a view all and an export. Export does not call a dialog, just prompts user for filename.
"""
def __init__(self,
parent=None,
border=None,
lockAspect=False,
enableMouse=True,
invertY=False,
enableMenu=True,
name=None):
pg.ViewBox.__init__(self, parent, border, lockAspect, enableMouse,
invertY, enableMenu, name)
self.menu = None # Override pyqtgraph ViewBoxMenu
self.menu = self.getMenu(None)
def raiseContextMenu(self, ev):
if not self.menuEnabled(): return
menu = self.getMenu(ev)
pos = ev.screenPos()
menu.popup(QtCore.QPoint(pos.x(), pos.y()))
def export(self):
self.exp = ImageExporterCustom(self)
self.exp.export()
def getMenu(self, event):
if self.menu is None:
self.menu = QMenuCustom()
self.viewAll = QtGui.QAction("View All", self.menu)
self.exportImage = QtGui.QAction("Export image", self.menu)
self.viewAll.triggered[()].connect(self.autoRange)
self.exportImage.triggered[()].connect(self.export)
self.menu.addAction(self.viewAll)
self.menu.addAction(self.exportImage)
return self.menu
class MultiRoiViewBox(pg.ViewBox):
sigROIchanged = QtCore.Signal(object)
def __init__(self,
parent=None,
border=None,
lockAspect=False,
enableMouse=True,
invertY=False,
enableMenu=True,
name=None):
pg.ViewBox.__init__(self, parent, border, lockAspect, enableMouse,
invertY, enableMenu, name)
self.rois = []
self.currentROIindex = None
self.img = None
self.menu = None # Override pyqtgraph ViewBoxMenu
self.menu = self.getMenu(None)
self.NORMAL = ViewMode(0, matplotlib.cm.gray)
self.DEXA = ViewMode(1, matplotlib.cm.jet)
self.viewMode = self.NORMAL
self.drawROImode = False
self.drawingROI = None
def getContextMenus(self, ev):
return None
def raiseContextMenu(self, ev):
if not self.menuEnabled(): return
menu = self.getMenu(ev)
pos = ev.screenPos()
menu.popup(QtCore.QPoint(pos.x(), pos.y()))
def export(self):
self.exp = ImageExporterCustom(self)
self.exp.export()
def mouseClickEvent(self, ev):
if self.drawROImode:
ev.accept()
self.drawPolygonRoi(ev)
elif ev.button() == QtCore.Qt.RightButton and self.menuEnabled():
ev.accept()
self.raiseContextMenu(ev)
def addPolyRoiRequest(self):
"""Function to add a Polygon ROI"""
self.drawROImode = True
for roi in self.rois:
roi.setActive(False)
def endPolyRoiRequest(self):
self.drawROImode = False # Deactivate drawing mode
self.drawingROI = None # No roi being drawn, so set to None
for r in self.rois:
r.setActive(True)
def addPolyLineROI(self, handlePositions):
roi = PolyLineROIcustom(handlePositions=handlePositions,
removable=True)
roi.setName('ROI-%i' % self.getROIid())
self.addItem(roi) # Add roi to viewbox
self.rois.append(roi) # Add to list of rois
self.selectROI(roi)
self.sortROIs()
self.setCurrentROIindex(roi)
roi.translatable = True
#roi.setAcceptedMouseButtons(QtCore.Qt.LeftButton or QtCore.Qt.RightButton)
roi.setActive(True)
for seg in roi.segments:
seg.setSelectable(True)
for h in roi.handles:
h['item'].setSelectable(True)
# Setup signals
roi.sigClicked.connect(self.selectROI)
roi.sigRegionChanged.connect(self.roiChanged)
roi.sigRemoveRequested.connect(self.removeROI)
roi.sigCopyRequested.connect(self.copyROI)
roi.sigSaveRequested.connect(self.saveROI)
def drawPolygonRoi(self, ev):
"Function to draw a polygon ROI"
roi = self.drawingROI
pos = self.mapSceneToView(ev.scenePos())
if ev.button() == QtCore.Qt.LeftButton:
if roi is None:
roi = PolyLineROIcustom(removable=False)
roi.setName(
'ROI-%i' %
self.getROIid()) # Do this before self.selectROIs(roi)
self.drawingROI = roi
self.addItem(roi) # Add roi to viewbox
self.rois.append(roi) # Add to list of rois
self.selectROI(roi)
self.sortROIs()
self.setCurrentROIindex(roi)
roi.translatable = False
roi.addFreeHandle(pos)
roi.addFreeHandle(pos)
h = roi.handles[-1]['item']
h.scene().sigMouseMoved.connect(h.movePoint)
else:
h = roi.handles[-1]['item']
h.scene().sigMouseMoved.disconnect()
roi.addFreeHandle(pos)
h = roi.handles[-1]['item']
h.scene().sigMouseMoved.connect(h.movePoint)
# Add a segment between the handles
roi.addSegment(roi.handles[-2]['item'], roi.handles[-1]['item'])
# Set segment and handles to non-selectable
seg = roi.segments[-1]
seg.setSelectable(False)
for h in seg.handles:
h['item'].setSelectable(False)
elif (ev.button() == QtCore.Qt.MiddleButton) or \
(ev.button() == QtCore.Qt.RightButton and (roi==None or len(roi.segments)<3)):
if roi != None:
# Remove handle and disconnect from scene
h = roi.handles[-1]['item']
h.scene().sigMouseMoved.disconnect()
roi.removeHandle(h)
# Removed roi from viewbox
self.removeItem(roi)
self.rois.pop(self.currentROIindex)
self.setCurrentROIindex(None)
# Exit ROI drawing mode
self.endPolyRoiRequest()
elif ev.button() == QtCore.Qt.RightButton:
# Remove last handle
h = roi.handles[-1]['item']
h.scene().sigMouseMoved.disconnect()
roi.removeHandle(h)
# Add segment to close ROI
roi.addSegment(roi.handles[-1]['item'], roi.handles[0]['item'])
# Setup signals
roi.sigClicked.connect(self.selectROI)
roi.sigRegionChanged.connect(self.roiChanged)
roi.sigRemoveRequested.connect(self.removeROI)
roi.sigCopyRequested.connect(self.copyROI)
roi.sigSaveRequested.connect(self.saveROI)
# Re-activate mouse clicks for all roi, segments and handles
roi.removable = True
roi.translatable = True
for seg in roi.segments:
seg.setSelectable(True)
for h in roi.handles:
h['item'].setSelectable(True)
# Exit ROI drawing mode
self.endPolyRoiRequest()
def getMenu(self, event):
if self.menu is None:
self.menu = QtGui.QMenu()
# Submenu to add ROIs
self.submenu = QtGui.QMenu("Add ROI", self.menu)
#self.addROIRectAct = QActionCustom("Rectangular", self.submenu)
self.addROIRectAct = QtGui.QAction("Rectangular", self.submenu)
#self.addROIPolyAct = QActionCustom("Polygon", self.submenu)
self.addROIPolyAct = QtGui.QAction("Polygon", self.submenu)
#self.addROIRectAct.clickEvent.connect(self.addRoiRequest)
self.addROIRectAct.triggered.connect(self.addROI)
#self.addROIPolyAct.clickEvent.connect(self.addPolyRoiRequest)
self.addROIPolyAct.triggered.connect(self.addPolyRoiRequest)
self.submenu.addAction(self.addROIRectAct)
self.submenu.addAction(self.addROIPolyAct)
#self.loadROIAct = QActionCustom("Load ROI", self.menu)
self.loadROIAct = QtGui.QAction("Load ROI", self.menu)
self.dexaMode = QtGui.QAction("DEXA mode", self.menu)
self.viewAll = QtGui.QAction("View All", self.menu)
self.exportImage = QtGui.QAction("Export image", self.menu)
#self.loadROIAct.clickEvent.connect(self.loadROI)
self.loadROIAct.triggered[()].connect(self.loadROI)
self.dexaMode.toggled.connect(self.toggleViewMode)
self.viewAll.triggered[()].connect(self.autoRange)
self.exportImage.triggered[()].connect(self.export)
self.menu.addAction(self.viewAll)
self.menu.addAction(self.dexaMode)
self.menu.addAction(self.exportImage)
self.menu.addSeparator()
self.menu.addMenu(self.submenu)
self.menu.addAction(self.loadROIAct)
self.dexaMode.setCheckable(True)
# Update action event. This enables passing of the event to the fuction connected to the
# action i.e. event will be passed to self.addRoiRequest when a Rectangular ROI is clicked
#self.addROIRectAct.updateEvent(event)
#self.addROIPolyAct.updateEvent(event)
return self.menu
def setCurrentROIindex(self, roi=None):
""" Use this function to change currentROIindex value to ensure a signal is emitted"""
if roi == None: self.currentROIindex = None
else: self.currentROIindex = self.rois.index(roi)
self.sigROIchanged.emit(roi)
def roiChanged(self, roi):
self.sigROIchanged.emit(roi)
def getCurrentROIindex(self):
return self.currentROIindex
def selectROI(self, roi):
""" Selection control of ROIs """
# If no ROI is currently selected (currentROIindex is None), select roi
if self.currentROIindex == None:
roi.setSelected(True)
self.setCurrentROIindex(roi)
# If an ROI is already selected...
else:
roiSelected = self.rois[self.currentROIindex]
roiSelected.setSelected(False)
# If a different roi is already selected, then select roi
if self.currentROIindex != self.rois.index(roi):
self.setCurrentROIindex(roi)
roi.setSelected(True)
# If roi is already selected, then unselect
else:
self.setCurrentROIindex(None)
def addRoiRequest(self, ev):
""" Function to addROI at an event screen position """
# Get position
pos = self.mapSceneToView(ev.scenePos())
xpos = pos.x()
ypos = pos.y()
# Shift down by size
xr, yr = self.viewRange()
xsize = 0.25 * (xr[1] - xr[0])
ysize = 0.25 * (yr[1] - yr[0])
xysize = min(xsize, ysize)
if xysize == 0: xysize = 100
ypos -= xysize
# Create ROI
xypos = (xpos, ypos)
self.addROI(pos=xypos)
def addROI(self, pos=None, size=None, angle=0.0):
""" Add an ROI to the ViewBox """
xr, yr = self.viewRange()
if pos is None:
posx = xr[0] + 0.05 * (xr[1] - xr[0])
posy = yr[0] + 0.05 * (yr[1] - yr[0])
pos = [posx, posy]
if size is None:
xsize = 0.25 * (xr[1] - xr[0])
ysize = 0.25 * (yr[1] - yr[0])
xysize = min(xsize, ysize)
if xysize == 0: xysize = 100
size = [xysize, xysize]
roi = RectROIcustom(pos, size, angle, removable=True, pen=(255, 0, 0))
# Setup signals
roi.setName('ROI-%i' % self.getROIid())
roi.sigClicked.connect(self.selectROI)
roi.sigRegionChanged.connect(self.roiChanged)
roi.sigRemoveRequested.connect(self.removeROI)
roi.sigCopyRequested.connect(self.copyROI)
roi.sigSaveRequested.connect(self.saveROI)
# Keep track of rois
self.addItem(roi)
self.rois.append(roi)
self.selectROI(roi)
self.sortROIs()
self.setCurrentROIindex(roi)
def sortROIs(self):
""" Sort self.rois by roi name and adjust self.currentROIindex as necessary """
if len(self.rois) == 0: return
if self.currentROIindex == None:
self.rois.sort()
else:
roiCurrent = self.rois[self.currentROIindex]
self.rois.sort()
self.currentROIindex = self.rois.index(roiCurrent)
def getROIid(self):
""" Get available and unique number for ROI name """
nums = [
int(roi.name.split('-')[-1]) for roi in self.rois
if roi.name != None
]
nid = 1
if len(nums) > 0:
while (True):
if nid not in nums: break
nid += 1
return nid
def copyROI(self, offset=0.0):
""" Copy current ROI. Offset from original for visibility """
if self.currentROIindex != None:
osFract = 0.05
roi = self.rois[self.currentROIindex]
# For rectangular ROI, offset by a fraction of the rotated size
if type(roi) == RectROIcustom:
roiState = roi.getState()
pos = roiState['pos']
size = roiState['size']
angle = roiState['angle']
dx, dy = np.array(size) * osFract
ang = np.radians(angle)
cosa = np.cos(ang)
sina = np.sin(ang)
dxt = dx * cosa - dy * sina
dyt = dx * sina + dy * cosa
offset = QtCore.QPointF(dxt, dyt)
self.addROI(pos + offset, size, angle)
# For a polyline ROI, offset by a fraction of the bounding rectangle
if type(roi) == PolyLineROIcustom:
br = roi.shape().boundingRect()
size = np.array([br.width(), br.height()])
osx, osy = size * osFract
offset = QtCore.QPointF(osx, osy)
hps = [i[-1] for i in roi.getSceneHandlePositions(index=None)]
hpsOffset = [self.mapSceneToView(hp) + offset for hp in hps]
self.addPolyLineROI(hpsOffset)
def saveROI(self):
""" Save the highlighted ROI to file """
if self.currentROIindex != None:
roi = self.rois[self.currentROIindex]
fileName = QtGui.QFileDialog.getSaveFileName(
None, self.tr("Save ROI"), QtCore.QDir.currentPath(),
self.tr("ROI (*.roi)"))
# 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 type(roi) == RectROIcustom:
roiState = roi.saveState()
roiState['type'] = 'RectROIcustom'
elif type(roi) == PolyLineROIcustom:
roiState = {}
hps = [
self.mapSceneToView(i[-1])
for i in roi.getSceneHandlePositions(index=None)
]
hps = [[hp.x(), hp.y()] for hp in hps]
roiState['type'] = 'PolyLineROIcustom'
roiState['handlePositions'] = hps
pickle.dump(roiState, open(fileName, "wb"))
def loadROI(self):
""" Load a previously saved ROI from file """
fileNames = QtGui.QFileDialog.getOpenFileNames(
None, self.tr("Load ROI"), QtCore.QDir.currentPath(),
self.tr("ROI (*.roi)"))
# Fix for PyQt/PySide compatibility. PyQt returns a QString, whereas PySide returns a tuple (first entry is filename as string)
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 != '':
roiState = pickle.load(open(fileName, "rb"))
if roiState['type'] == 'RectROIcustom':
self.addROI(roiState['pos'], roiState['size'],
roiState['angle'])
elif roiState['type'] == 'PolyLineROIcustom':
self.addPolyLineROI(roiState['handlePositions'])
def removeROI(self):
""" Delete the highlighted ROI """
if self.currentROIindex != None:
roi = self.rois[self.currentROIindex]
self.rois.pop(self.currentROIindex)
self.removeItem(roi)
self.setCurrentROIindex(None)
def toggleViewMode(self, isChecked):
""" Toggles between NORMAL (Black/White) and DEXA mode (colour) """
if isChecked: viewMode = self.DEXA
else: viewMode = self.NORMAL
self.setViewMode(viewMode)
def setViewMode(self, viewMode):
self.viewMode = viewMode
self.updateView()
def updateView(self):
self.background.setBrush(fn.mkBrush(self.viewMode.lut[0]))
self.background.show()
if self.img == None: return
else: self.img.setLookupTable(self.viewMode.lut)
def showImage(self, arr):
if arr == None:
self.img = None
return
if self.img == None:
self.img = pg.ImageItem(arr, autoRange=False, autoLevels=False)
self.addItem(self.img)
self.img.setImage(arr, autoLevels=False)
self.updateView()
def export(self):
self.exp = ImageExporterCustom(self)
self.exp.export()
def export(self):
''' Export viewbox image '''
self.exp = ImageExporterCustom(self)
self.exp.export()
class MultiRoiViewBox(pg.ViewBox):
''' Custom Viewbox for multiple ROIs '''
def __init__(self,parent=None,border=None,lockAspect=False,enableMouse=True,invertY=False,enableMenu=True,name=None):
pg.ViewBox.__init__(self,parent,border,lockAspect,enableMouse,invertY,enableMenu,name)
# Set default values
self.rois = []
self.currentROIindex = None
self.img = None
self.NORMAL = ViewMode(0,matplotlib.cm.gray)
self.DEXA = ViewMode(1,matplotlib.cm.jet)
self.viewMode = self.NORMAL
self.drawROImode = False
self.drawingROI = None
self.menu = None
def getContextMenus(self,ev):
return None
def raiseContextMenu(self, ev):
''' Display context menu at location of right mouse click '''
if not self.menuEnabled(): return
menu = self.getMenu(ev)
pos = ev.screenPos()
menu.popup(QtCore.QPoint(pos.x(), pos.y()))
def export(self):
''' Export viewbox image '''
self.exp = ImageExporterCustom(self)
self.exp.export()
def raiseRoiSelectMenuLeft(self,ev,roiList):
''' Raise roi menu on left mouse click '''
self.roimenu = QtGui.QMenu()
for roi in roiList:
action = QtGui.QAction(roi.name, self.roimenu)
action.triggered[()].connect(lambda arg=roi: self.selectROI(arg))
self.roimenu.addAction(action)
pos = ev.screenPos()
self.roimenu.popup(QtCore.QPoint(pos.x(), pos.y()))
def raiseRoiSelectMenuRight(self,ev,roiList):
''' Raise roi menu on right mouse click
Must use functools.partial (not lamda) here to get signals to work here '''
self.roimenu = QtGui.QMenu()
for roi in roiList:
action = QtGui.QAction(roi.name, self.roimenu)
action.triggered[()].connect(partial(roi.raiseContextMenu, ev))
self.roimenu.addAction(action)
pos = ev.screenPos()
self.roimenu.popup(QtCore.QPoint(pos.x(), pos.y()))
def mouseClickEvent(self, ev):
''' Mouse click event handler '''
# Check if click is over any rois
roisUnderMouse = []
pos = ev.scenePos()
for roi in self.rois:
if roi.isUnderMouse(pos):
roisUnderMouse.append(roi)
numRois = len(roisUnderMouse)
# Drawing mode (all buttons)
if self.drawROImode:
ev.accept()
self.drawPolygonRoi(ev)
# Click not over any rois
elif numRois==0:
# Context menu (right mouse button)
if ev.button() == QtCore.Qt.RightButton and self.menuEnabled():
self.raiseContextMenu(ev)
# Click over any rois
else:
if ev.button() == QtCore.Qt.LeftButton:
if numRois==1:
self.selectROI(roisUnderMouse[0])
elif numRois>1:
self.raiseRoiSelectMenuLeft(ev,roisUnderMouse)
elif ev.button() == QtCore.Qt.RightButton:
if numRois==1:
roisUnderMouse[0].raiseContextMenu(ev)
elif numRois>1:
self.raiseRoiSelectMenuRight(ev,roisUnderMouse)
def addPolyRoiRequest(self):
''' Function to add a Polygon ROI '''
self.drawROImode = True
def endPolyRoiRequest(self):
''' Called at the completion of drawing Polygon ROI '''
self.drawROImode = False # Deactivate drawing mode
self.drawingROI = None # No roi being drawn, so set to None
def addPolyLineROI(self,handlePositions):
''' Add Polygon ROI - Used for copy and load operations '''
roi = PolyLineROIcustom(handlePositions=handlePositions,removable=True)
roi.setName('ROI-%i'% self.getROIid())
self.addItem(roi) # Add roi to viewbox
self.rois.append(roi) # Add to list of rois
self.selectROI(roi)
self.sortROIs()
self.setCurrentROIindex(roi)
roi.translatable = True
for seg in roi.segments:
seg.setSelectable(True)
for h in roi.handles:
h['item'].setSelectable(True)
# Setup signals
roi.sigRemoveRequested.connect(self.removeROI)
roi.sigCopyRequested.connect(self.copyROI)
roi.sigSaveRequested.connect(self.saveROI)
def drawPolygonRoi(self,ev):
''' Function to draw a Polygon ROI - Called directly by MouseClickEvent '''
roi = self.drawingROI
pos = self.mapSceneToView(ev.scenePos())
# TO DRAW ROI
if ev.button() == QtCore.Qt.LeftButton:
if roi is None: # To start drawing a new roi
roi = PolyLineROIcustom(removable = False) # Create new roi
roi.setName('ROI-%i'% self.getROIid()) # Set name. Do this before self.selectROIs(roi)
self.drawingROI = roi
self.addItem(roi) # Add roi to viewbox
self.rois.append(roi) # Add to list of rois
self.selectROI(roi) # Make selected
self.sortROIs() # Sort list of rois
self.setCurrentROIindex(roi) # Make current
roi.translatable = False # Deactivate translation during drawing
roi.addFreeHandle(pos) # Add two handles on first click (1 fixed, 1 draggable)
roi.addFreeHandle(pos)
h = roi.handles[-1]['item'] # Get draggable handle
h.scene().sigMouseMoved.connect(h.movePoint) # Connect signal to move handle with mouse
else: # To continue drawing an existing roi
h = roi.handles[-1]['item'] # Get last handle
h.scene().sigMouseMoved.disconnect() # Make last handle non-draggable
roi.addFreeHandle(pos) # Add new handle
h = roi.handles[-1]['item'] # Get new handle
h.scene().sigMouseMoved.connect(h.movePoint) # Make new handle draggable
# Add a segment between the handles
roi.addSegment(roi.handles[-2]['item'],roi.handles[-1]['item'])
# Set segment and handles to non-selectable
seg = roi.segments[-1]
seg.setSelectable(False)
for h in seg.handles:
h['item'].setSelectable(False)
# TO STOP DRAWING ROI
elif (ev.button() == QtCore.Qt.MiddleButton) or \
(ev.button() == QtCore.Qt.RightButton and (roi==None or len(roi.segments)<3)):
if roi!=None:
# Remove handle and disconnect from scene
h = roi.handles[-1]['item']
h.scene().sigMouseMoved.disconnect()
roi.removeHandle(h)
# Removed roi from viewbox
self.removeItem(roi)
self.rois.pop(self.currentROIindex)
self.setCurrentROIindex(None)
# Exit ROI drawing mode
self.endPolyRoiRequest()
# TO COMPLETE ROI
elif ev.button() == QtCore.Qt.RightButton:
# Remove last handle
h = roi.handles[-1]['item']
h.scene().sigMouseMoved.disconnect()
roi.removeHandle(h)
# Add segment to close ROI
roi.addSegment(roi.handles[-1]['item'],roi.handles[0]['item'])
# Setup signals on completed roi
roi.sigRemoveRequested.connect(self.removeROI)
roi.sigCopyRequested.connect(self.copyROI)
roi.sigSaveRequested.connect(self.saveROI)
# Re-activate mouse clicks for all roi, segments and handles
roi.removable = True
roi.translatable = True
for seg in roi.segments:
seg.setSelectable(True)
for h in roi.handles:
h['item'].setSelectable(True)
# Exit ROI drawing mode
self.endPolyRoiRequest()
def getMenu(self,ev):
'''Create and return context menu '''
# Menu and submenus
self.menu = QtGui.QMenu()
self.submenu = QtGui.QMenu("Add ROI", self.menu)
# Actions
self.addROIRectAct = QtGui.QAction("Rectangular", self.submenu)
self.addROIPolyAct = QtGui.QAction("Polygon", self.submenu)
self.loadROIAct = QtGui.QAction("Load ROI", self.menu)
self.dexaMode = QtGui.QAction("Toggle normal/DEXA view", self.menu)
self.viewAll = QtGui.QAction("View All", self.menu)
self.exportImage = QtGui.QAction("Export image", self.menu)
# Signals
self.loadROIAct.triggered[()].connect(self.loadROI)
self.dexaMode.triggered.connect(self.toggleViewMode)
self.viewAll.triggered[()].connect(self.autoRange)
self.exportImage.triggered[()].connect(self.export)
self.addROIRectAct.triggered[()].connect(lambda arg=ev: self.addRoiRequest(arg))
self.addROIPolyAct.triggered.connect(self.addPolyRoiRequest)
# Add actions to menu and submenus
self.submenu.addAction(self.addROIRectAct)
self.submenu.addAction(self.addROIPolyAct)
self.menu.addAction(self.viewAll)
self.menu.addAction(self.dexaMode)
self.menu.addAction(self.exportImage)
self.menu.addSeparator()
self.menu.addMenu(self.submenu)
self.menu.addAction(self.loadROIAct)
self.dexaMode.setCheckable(True)
# Return menu
return self.menu
def setCurrentROIindex(self,roi=None):
''' Use this function to change currentROIindex value to ensure a signal is emitted '''
if roi==None: self.currentROIindex = None
else: self.currentROIindex = self.rois.index(roi)
def getCurrentROIindex(self):
return self.currentROIindex
def selectROI(self,roi):
'''Selection control of ROIs'''
# If no ROI is currently selected (currentROIindex is None), select roi
if self.currentROIindex==None:
roi.setSelected(True)
self.setCurrentROIindex(roi)
# If an ROI is already selected...
else:
roiSelected = self.rois[self.currentROIindex]
roiSelected.setSelected(False)
# If a different roi is already selected, then select roi
if self.currentROIindex != self.rois.index(roi):
self.setCurrentROIindex(roi)
roi.setSelected(True)
# If roi is already selected, then unselect
else:
self.setCurrentROIindex(None)
def addRoiRequest(self,ev):
''' Function to addROI at an event screen position '''
# Get position
pos = self.mapSceneToView(ev.scenePos())
xpos = pos.x()
ypos = pos.y()
# Shift down by size
xr,yr = self.viewRange()
xsize = 0.25*(xr[1]-xr[0])
ysize = 0.25*(yr[1]-yr[0])
xysize = min(xsize,ysize)
if xysize==0: xysize=100
ypos -= xysize
# Create ROI
xypos = (xpos,ypos)
self.addROI(pos=xypos)
def addROI(self,pos=None,size=None,angle=0.0):
''' Add an ROI to the ViewBox '''
xr,yr = self.viewRange()
if pos is None:
posx = xr[0]+0.05*(xr[1]-xr[0])
posy = yr[0]+0.05*(yr[1]-yr[0])
pos = [posx,posy]
if size is None:
xsize = 0.25*(xr[1]-xr[0])
ysize = 0.25*(yr[1]-yr[0])
xysize = min(xsize,ysize)
if xysize==0: xysize=100
size = [xysize,xysize]
roi = RectROIcustom(pos,size,angle,removable=True,pen=(255,0,0))
# Setup signals
roi.setName('ROI-%i'% self.getROIid())
roi.sigRemoveRequested.connect(self.removeROI)
roi.sigCopyRequested.connect(self.copyROI)
roi.sigSaveRequested.connect(self.saveROI)
# Keep track of rois
self.addItem(roi)
self.rois.append(roi)
self.selectROI(roi)
self.sortROIs()
self.setCurrentROIindex(roi)
def sortROIs(self):
''' Sort self.rois by roi name and adjust self.currentROIindex as necessary '''
if len(self.rois)==0: return
if self.currentROIindex==None:
self.rois.sort()
else:
roiCurrent = self.rois[self.currentROIindex]
self.rois.sort()
self.currentROIindex = self.rois.index(roiCurrent)
def getROIid(self):
''' Get available and unique number for ROI name '''
nums = [ int(roi.name.split('-')[-1]) for roi in self.rois if roi.name!=None ]
nid = 1
if len(nums)>0:
while(True):
if nid not in nums: break
nid+=1
return nid
def copyROI(self):
''' Copy current ROI. Offset from original for visibility '''
osFract = 0.05
if self.currentROIindex!=None:
roi = self.rois[self.currentROIindex]
# For rectangular ROI, offset by a fraction of the rotated size
if type(roi)==RectROIcustom:
roiState = roi.getState()
pos = roiState['pos']
size = roiState['size']
angle = roiState['angle']
dx,dy = np.array(size)*osFract
ang = np.radians(angle)
cosa = np.cos(ang)
sina = np.sin(ang)
dxt = dx*cosa - dy*sina
dyt = dx*sina + dy*cosa
offset = QtCore.QPointF(dxt,dyt)
self.addROI(pos+offset,size,angle)
# For a polyline ROI, offset by a fraction of the bounding rectangle
if type(roi)==PolyLineROIcustom:
br = roi.shape().boundingRect()
size = np.array([br.width(),br.height()])
osx,osy = size * osFract
offset = QtCore.QPointF(osx,osy)
hps = [i[-1] for i in roi.getSceneHandlePositions(index=None)]
hpsOffset = [self.mapSceneToView(hp)+offset for hp in hps]
self.addPolyLineROI(hpsOffset)
def saveROI(self):
''' Save the highlighted ROI to file '''
if self.currentROIindex!=None:
roi = self.rois[self.currentROIindex]
fileName = QtGui.QFileDialog.getSaveFileName(None,self.tr("Save ROI"),QtCore.QDir.currentPath(),self.tr("ROI (*.roi)"))
# 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 type(roi)==RectROIcustom:
roiState = roi.saveState()
roiState['type']='RectROIcustom'
elif type(roi)==PolyLineROIcustom:
roiState = {}
hps = [self.mapSceneToView(i[-1]) for i in roi.getSceneHandlePositions(index=None)]
hps = [[hp.x(),hp.y()] for hp in hps]
roiState['type']='PolyLineROIcustom'
roiState['handlePositions'] = hps
pickle.dump( roiState, open( fileName, "wb" ) )
def loadROI(self):
''' Load a previously saved ROI from file '''
fileNames = QtGui.QFileDialog.getOpenFileNames(None,self.tr("Load ROI"),QtCore.QDir.currentPath(),self.tr("ROI (*.roi)"))
# Fix for PyQt/PySide compatibility. PyQt returns a QString, whereas PySide returns a tuple (first entry is filename as string)
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!='':
roiState = pickle.load( open(fileName, "rb") )
if roiState['type']=='RectROIcustom':
self.addROI(roiState['pos'],roiState['size'],roiState['angle'])
elif roiState['type']=='PolyLineROIcustom':
self.addPolyLineROI(roiState['handlePositions'])
def removeROI(self):
''' Delete the highlighted ROI '''
if self.currentROIindex!=None:
roi = self.rois[self.currentROIindex]
self.rois.pop(self.currentROIindex)
self.removeItem(roi)
self.setCurrentROIindex(None)
def toggleViewMode(self):
''' Toggles between NORMAL (Black/White) and DEXA mode (colour) '''
if self.viewMode == self.NORMAL:
viewMode = self.DEXA
else:
viewMode = self.NORMAL
self.setViewMode(viewMode)
def setViewMode(self,viewMode):
self.viewMode = viewMode
self.updateView()
def updateView(self):
self.background.setBrush(fn.mkBrush(self.viewMode.lut[0]))
self.background.show()
if self.img is None: return
else: self.img.setLookupTable(self.viewMode.lut)
def showImage(self,arr):
if arr is None:
self.img = None
return
if self.img is None:
self.img = pg.ImageItem(arr,autoRange=False,autoLevels=False)
self.addItem(self.img)
self.img.setImage(arr,autoLevels=False)
self.updateView()
def export(self):
self.exp = ImageExporterCustom(self)
self.exp.export()
class MultiRoiViewBox(pg.ViewBox):
sigROIchanged = QtCore.Signal(object)
def __init__(self,parent=None,border=None,lockAspect=False,enableMouse=True,invertY=False,enableMenu=True,name=None):
pg.ViewBox.__init__(self,parent,border,lockAspect,enableMouse,invertY,enableMenu,name)
self.rois = []
self.currentROIindex = None
self.img = None
self.menu = None # Override pyqtgraph ViewBoxMenu
self.menu = self.getMenu(None)
self.NORMAL = ViewMode(0,matplotlib.cm.gray)
self.DEXA = ViewMode(1,matplotlib.cm.jet)
self.viewMode = self.NORMAL
self.drawROImode = False
self.drawingROI = None
def getContextMenus(self,ev):
return None
def raiseContextMenu(self, ev):
if not self.menuEnabled(): return
menu = self.getMenu(ev)
pos = ev.screenPos()
menu.popup(QtCore.QPoint(pos.x(), pos.y()))
def export(self):
self.exp = ImageExporterCustom(self)
self.exp.export()
def mouseClickEvent(self, ev):
if self.drawROImode:
ev.accept()
self.drawPolygonRoi(ev)
elif ev.button() == QtCore.Qt.RightButton and self.menuEnabled():
ev.accept()
self.raiseContextMenu(ev)
def addPolyRoiRequest(self):
"""Function to add a Polygon ROI"""
self.drawROImode = True
for roi in self.rois:
roi.setActive(False)
def endPolyRoiRequest(self):
self.drawROImode = False # Deactivate drawing mode
self.drawingROI = None # No roi being drawn, so set to None
for r in self.rois:
r.setActive(True)
def addPolyLineROI(self,handlePositions):
roi = PolyLineROIcustom(handlePositions=handlePositions,removable=True)
roi.setName('ROI-%i'% self.getROIid())
self.addItem(roi) # Add roi to viewbox
self.rois.append(roi) # Add to list of rois
self.selectROI(roi)
self.sortROIs()
self.setCurrentROIindex(roi)
roi.translatable = True
#roi.setAcceptedMouseButtons(QtCore.Qt.LeftButton or QtCore.Qt.RightButton)
roi.setActive(True)
for seg in roi.segments:
seg.setSelectable(True)
for h in roi.handles:
h['item'].setSelectable(True)
# Setup signals
roi.sigClicked.connect(self.selectROI)
roi.sigRegionChanged.connect(self.roiChanged)
roi.sigRemoveRequested.connect(self.removeROI)
roi.sigCopyRequested.connect(self.copyROI)
roi.sigSaveRequested.connect(self.saveROI)
def drawPolygonRoi(self,ev):
"Function to draw a polygon ROI"
roi = self.drawingROI
pos = self.mapSceneToView(ev.scenePos())
if ev.button() == QtCore.Qt.LeftButton:
if roi is None:
roi = PolyLineROIcustom(removable = False)
roi.setName('ROI-%i'% self.getROIid()) # Do this before self.selectROIs(roi)
self.drawingROI = roi
self.addItem(roi) # Add roi to viewbox
self.rois.append(roi) # Add to list of rois
self.selectROI(roi)
self.sortROIs()
self.setCurrentROIindex(roi)
roi.translatable = False
roi.addFreeHandle(pos)
roi.addFreeHandle(pos)
h = roi.handles[-1]['item']
h.scene().sigMouseMoved.connect(h.movePoint)
else:
h = roi.handles[-1]['item']
h.scene().sigMouseMoved.disconnect()
roi.addFreeHandle(pos)
h = roi.handles[-1]['item']
h.scene().sigMouseMoved.connect(h.movePoint)
# Add a segment between the handles
roi.addSegment(roi.handles[-2]['item'],roi.handles[-1]['item'])
# Set segment and handles to non-selectable
seg = roi.segments[-1]
seg.setSelectable(False)
for h in seg.handles:
h['item'].setSelectable(False)
elif (ev.button() == QtCore.Qt.MiddleButton) or \
(ev.button() == QtCore.Qt.RightButton and (roi==None or len(roi.segments)<3)):
if roi!=None:
# Remove handle and disconnect from scene
h = roi.handles[-1]['item']
h.scene().sigMouseMoved.disconnect()
roi.removeHandle(h)
# Removed roi from viewbox
self.removeItem(roi)
self.rois.pop(self.currentROIindex)
self.setCurrentROIindex(None)
# Exit ROI drawing mode
self.endPolyRoiRequest()
elif ev.button() == QtCore.Qt.RightButton:
# Remove last handle
h = roi.handles[-1]['item']
h.scene().sigMouseMoved.disconnect()
roi.removeHandle(h)
# Add segment to close ROI
roi.addSegment(roi.handles[-1]['item'],roi.handles[0]['item'])
# Setup signals
roi.sigClicked.connect(self.selectROI)
roi.sigRegionChanged.connect(self.roiChanged)
roi.sigRemoveRequested.connect(self.removeROI)
roi.sigCopyRequested.connect(self.copyROI)
roi.sigSaveRequested.connect(self.saveROI)
# Re-activate mouse clicks for all roi, segments and handles
roi.removable = True
roi.translatable = True
for seg in roi.segments:
seg.setSelectable(True)
for h in roi.handles:
h['item'].setSelectable(True)
# Exit ROI drawing mode
self.endPolyRoiRequest()
def getMenu(self,event):
if self.menu is None:
self.menu = QtGui.QMenu()
# Submenu to add ROIs
self.submenu = QtGui.QMenu("Add ROI",self.menu)
#self.addROIRectAct = QActionCustom("Rectangular", self.submenu)
self.addROIRectAct = QtGui.QAction("Rectangular", self.submenu)
#self.addROIPolyAct = QActionCustom("Polygon", self.submenu)
self.addROIPolyAct = QtGui.QAction("Polygon", self.submenu)
#self.addROIRectAct.clickEvent.connect(self.addRoiRequest)
self.addROIRectAct.triggered.connect(self.addROI)
#self.addROIPolyAct.clickEvent.connect(self.addPolyRoiRequest)
self.addROIPolyAct.triggered.connect(self.addPolyRoiRequest)
self.submenu.addAction(self.addROIRectAct)
self.submenu.addAction(self.addROIPolyAct)
#self.loadROIAct = QActionCustom("Load ROI", self.menu)
self.loadROIAct = QtGui.QAction("Load ROI", self.menu)
self.dexaMode = QtGui.QAction("DEXA mode", self.menu)
self.viewAll = QtGui.QAction("View All", self.menu)
self.exportImage = QtGui.QAction("Export image", self.menu)
#self.loadROIAct.clickEvent.connect(self.loadROI)
self.loadROIAct.triggered[()].connect(self.loadROI)
self.dexaMode.toggled.connect(self.toggleViewMode)
self.viewAll.triggered[()].connect(self.autoRange)
self.exportImage.triggered[()].connect(self.export)
self.menu.addAction(self.viewAll)
self.menu.addAction(self.dexaMode)
self.menu.addAction(self.exportImage)
self.menu.addSeparator()
self.menu.addMenu(self.submenu)
self.menu.addAction(self.loadROIAct)
self.dexaMode.setCheckable(True)
# Update action event. This enables passing of the event to the fuction connected to the
# action i.e. event will be passed to self.addRoiRequest when a Rectangular ROI is clicked
#self.addROIRectAct.updateEvent(event)
#self.addROIPolyAct.updateEvent(event)
return self.menu
def setCurrentROIindex(self,roi=None):
""" Use this function to change currentROIindex value to ensure a signal is emitted"""
if roi==None: self.currentROIindex = None
else: self.currentROIindex = self.rois.index(roi)
self.sigROIchanged.emit(roi)
def roiChanged(self,roi):
self.sigROIchanged.emit(roi)
def getCurrentROIindex(self):
return self.currentROIindex
def selectROI(self,roi):
""" Selection control of ROIs """
# If no ROI is currently selected (currentROIindex is None), select roi
if self.currentROIindex==None:
roi.setSelected(True)
self.setCurrentROIindex(roi)
# If an ROI is already selected...
else:
roiSelected = self.rois[self.currentROIindex]
roiSelected.setSelected(False)
# If a different roi is already selected, then select roi
if self.currentROIindex != self.rois.index(roi):
self.setCurrentROIindex(roi)
roi.setSelected(True)
# If roi is already selected, then unselect
else:
self.setCurrentROIindex(None)
def addRoiRequest(self,ev):
""" Function to addROI at an event screen position """
# Get position
pos = self.mapSceneToView(ev.scenePos())
xpos = pos.x()
ypos = pos.y()
# Shift down by size
xr,yr = self.viewRange()
xsize = 0.25*(xr[1]-xr[0])
ysize = 0.25*(yr[1]-yr[0])
xysize = min(xsize,ysize)
if xysize==0: xysize=100
ypos -= xysize
# Create ROI
xypos = (xpos,ypos)
self.addROI(pos=xypos)
def addROI(self,pos=None,size=None,angle=0.0):
""" Add an ROI to the ViewBox """
xr,yr = self.viewRange()
if pos is None:
posx = xr[0]+0.05*(xr[1]-xr[0])
posy = yr[0]+0.05*(yr[1]-yr[0])
pos = [posx,posy]
if size is None:
xsize = 0.25*(xr[1]-xr[0])
ysize = 0.25*(yr[1]-yr[0])
xysize = min(xsize,ysize)
if xysize==0: xysize=100
size = [xysize,xysize]
roi = RectROIcustom(pos,size,angle,removable=True,pen=(255,0,0))
# Setup signals
roi.setName('ROI-%i'% self.getROIid())
roi.sigClicked.connect(self.selectROI)
roi.sigRegionChanged.connect(self.roiChanged)
roi.sigRemoveRequested.connect(self.removeROI)
roi.sigCopyRequested.connect(self.copyROI)
roi.sigSaveRequested.connect(self.saveROI)
# Keep track of rois
self.addItem(roi)
self.rois.append(roi)
self.selectROI(roi)
self.sortROIs()
self.setCurrentROIindex(roi)
def sortROIs(self):
""" Sort self.rois by roi name and adjust self.currentROIindex as necessary """
if len(self.rois)==0: return
if self.currentROIindex==None:
self.rois.sort()
else:
roiCurrent = self.rois[self.currentROIindex]
self.rois.sort()
self.currentROIindex = self.rois.index(roiCurrent)
def getROIid(self):
""" Get available and unique number for ROI name """
nums = [ int(roi.name.split('-')[-1]) for roi in self.rois if roi.name!=None ]
nid = 1
if len(nums)>0:
while(True):
if nid not in nums: break
nid+=1
return nid
def copyROI(self,offset=0.0):
""" Copy current ROI. Offset from original for visibility """
if self.currentROIindex!=None:
osFract = 0.05
roi = self.rois[self.currentROIindex]
# For rectangular ROI, offset by a fraction of the rotated size
if type(roi)==RectROIcustom:
roiState = roi.getState()
pos = roiState['pos']
size = roiState['size']
angle = roiState['angle']
dx,dy = np.array(size)*osFract
ang = np.radians(angle)
cosa = np.cos(ang)
sina = np.sin(ang)
dxt = dx*cosa - dy*sina
dyt = dx*sina + dy*cosa
offset = QtCore.QPointF(dxt,dyt)
self.addROI(pos+offset,size,angle)
# For a polyline ROI, offset by a fraction of the bounding rectangle
if type(roi)==PolyLineROIcustom:
br = roi.shape().boundingRect()
size = np.array([br.width(),br.height()])
osx,osy = size * osFract
offset = QtCore.QPointF(osx,osy)
hps = [i[-1] for i in roi.getSceneHandlePositions(index=None)]
hpsOffset = [self.mapSceneToView(hp)+offset for hp in hps]
self.addPolyLineROI(hpsOffset)
def saveROI(self):
""" Save the highlighted ROI to file """
if self.currentROIindex!=None:
roi = self.rois[self.currentROIindex]
fileName = QtGui.QFileDialog.getSaveFileName(None,self.tr("Save ROI"),QtCore.QDir.currentPath(),self.tr("ROI (*.roi)"))
# 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 type(roi)==RectROIcustom:
roiState = roi.saveState()
roiState['type']='RectROIcustom'
elif type(roi)==PolyLineROIcustom:
roiState = {}
hps = [self.mapSceneToView(i[-1]) for i in roi.getSceneHandlePositions(index=None)]
hps = [[hp.x(),hp.y()] for hp in hps]
roiState['type']='PolyLineROIcustom'
roiState['handlePositions'] = hps
pickle.dump( roiState, open( fileName, "wb" ) )
def loadROI(self):
""" Load a previously saved ROI from file """
fileNames = QtGui.QFileDialog.getOpenFileNames(None,self.tr("Load ROI"),QtCore.QDir.currentPath(),self.tr("ROI (*.roi)"))
# Fix for PyQt/PySide compatibility. PyQt returns a QString, whereas PySide returns a tuple (first entry is filename as string)
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!='':
roiState = pickle.load( open(fileName, "rb") )
if roiState['type']=='RectROIcustom':
self.addROI(roiState['pos'],roiState['size'],roiState['angle'])
elif roiState['type']=='PolyLineROIcustom':
self.addPolyLineROI(roiState['handlePositions'])
def removeROI(self):
""" Delete the highlighted ROI """
if self.currentROIindex!=None:
roi = self.rois[self.currentROIindex]
self.rois.pop(self.currentROIindex)
self.removeItem(roi)
self.setCurrentROIindex(None)
def toggleViewMode(self,isChecked):
""" Toggles between NORMAL (Black/White) and DEXA mode (colour) """
if isChecked: viewMode = self.DEXA
else: viewMode = self.NORMAL
self.setViewMode(viewMode)
def setViewMode(self,viewMode):
self.viewMode = viewMode
self.updateView()
def updateView(self):
self.background.setBrush(fn.mkBrush(self.viewMode.lut[0]))
self.background.show()
if self.img==None: return
else: self.img.setLookupTable(self.viewMode.lut)
def showImage(self,arr):
if arr==None:
self.img = None
return
if self.img==None:
self.img = pg.ImageItem(arr,autoRange=False,autoLevels=False)
self.addItem(self.img)
self.img.setImage(arr,autoLevels=False)
self.updateView()