# -*- coding: utf-8 -*- """ ROI.py - Interactive graphics items for GraphicsView (ROI widgets) Copyright 2010 Luke Campagnola Distributed under MIT/X11 license. See license.txt for more infomation. Implements a series of graphics items which display movable/scalable/rotatable shapes for use as region-of-interest markers. ROI class automatically handles extraction of array data from ImageItems. The ROI class is meant to serve as the base for more specific types; see several examples of how to build an ROI at the bottom of the file. """ from pyqtgraph.Qt import QtCore, QtGui #if not hasattr(QtCore, 'Signal'): #QtCore.Signal = QtCore.pyqtSignal import numpy as np from numpy.linalg import norm import scipy.ndimage as ndimage from pyqtgraph.Point import * from pyqtgraph.Transform import Transform from math import cos, sin import pyqtgraph.functions as fn from GraphicsObject import GraphicsObject from UIGraphicsItem import UIGraphicsItem __all__ = [ 'ROI', 'TestROI', 'RectROI', 'EllipseROI', 'CircleROI', 'PolygonROI', 'LineROI', 'MultiLineROI', 'LineSegmentROI', 'SpiralROI', ] def rectStr(r): return "[%f, %f] + [%f, %f]" % (r.x(), r.y(), r.width(), r.height()) class ROI(GraphicsObject): """Generic region-of-interest widget. Can be used for implementing many types of selection box with rotate/translate/scale handles. """ sigRegionChangeFinished = QtCore.Signal(object) sigRegionChangeStarted = QtCore.Signal(object) sigRegionChanged = QtCore.Signal(object) sigHoverEvent = QtCore.Signal(object) def __init__(self, pos, size=Point(1, 1), angle=0.0, invertible=False, maxBounds=None, snapSize=1.0, scaleSnap=False, translateSnap=False, rotateSnap=False, parent=None, pen=None, movable=True): #QObjectWorkaround.__init__(self) GraphicsObject.__init__(self, parent) pos = Point(pos) size = Point(size) self.aspectLocked = False self.translatable = movable self.rotateAllowed = True self.freeHandleMoved = False ## keep track of whether free handles have moved since last change signal was emitted. self.mouseHovering = False if pen is None: pen = (255, 255, 255) self.setPen(pen) self.handlePen = QtGui.QPen(QtGui.QColor(150, 255, 255)) self.handles = [] self.state = {'pos': Point(0,0), 'size': Point(1,1), 'angle': 0} ## angle is in degrees for ease of Qt integration self.lastState = None self.setPos(pos) self.setAngle(angle) self.setSize(size) self.setZValue(10) self.isMoving = False self.handleSize = 5 self.invertible = invertible self.maxBounds = maxBounds self.snapSize = snapSize self.translateSnap = translateSnap self.rotateSnap = rotateSnap self.scaleSnap = scaleSnap #self.setFlag(self.ItemIsSelectable, True) def getState(self): return self.stateCopy() def stateCopy(self): sc = {} sc['pos'] = Point(self.state['pos']) sc['size'] = Point(self.state['size']) sc['angle'] = self.state['angle'] return sc def saveState(self): """Return the state of the widget in a format suitable for storing to disk. (Points are converted to tuple)""" state = {} state['pos'] = tuple(self.state['pos']) state['size'] = tuple(self.state['size']) state['angle'] = self.state['angle'] return state def setState(self, state, update=True): self.setPos(state['pos'], update=False) self.setSize(state['size'], update=False) self.setAngle(state['angle'], update=update) def setZValue(self, z): QtGui.QGraphicsItem.setZValue(self, z) for h in self.handles: h['item'].setZValue(z+1) def parentBounds(self): return self.mapToParent(self.boundingRect()).boundingRect() def setPen(self, pen): self.pen = fn.mkPen(pen) self.currentPen = self.pen self.update() def size(self): return self.getState()['size'] def pos(self): return self.getState()['pos'] def angle(self): return self.getState()['angle'] def setPos(self, pos, update=True, finish=True): """Set the position of the ROI (in the parent's coordinate system). By default, this will cause both sigStateChanged and sigStateChangeFinished to be emitted. If finish is False, then sigStateChangeFinished will not be emitted. You can then use stateChangeFinished() to cause the signal to be emitted after a series of state changes. If update is False, the state change will be remembered but not processed and no signals will be emitted. You can then use stateChanged() to complete the state change. This allows multiple change functions to be called sequentially while minimizing processing overhead and repeated signals. Setting update=False also forces finish=False. """ pos = Point(pos) self.state['pos'] = pos QtGui.QGraphicsItem.setPos(self, pos) if update: self.stateChanged(finish=finish) def setSize(self, size, update=True, finish=True): """Set the size of the ROI. May be specified as a QPoint, Point, or list of two values. See setPos() for an explanation of the update and finish arguments. """ size = Point(size) self.prepareGeometryChange() self.state['size'] = size if update: self.stateChanged(finish=finish) def setAngle(self, angle, update=True, finish=True): """Set the angle of rotation (in degrees) for this ROI. See setPos() for an explanation of the update and finish arguments. """ self.state['angle'] = angle tr = QtGui.QTransform() #tr.rotate(-angle * 180 / np.pi) tr.rotate(angle) self.setTransform(tr) if update: self.stateChanged(finish=finish) def scale(self, s, center=[0,0], update=True, finish=True): """ Resize the ROI by scaling relative to *center*. See setPos() for an explanation of the *update* and *finish* arguments. """ c = self.mapToScene(Point(center) * self.state['size']) self.prepareGeometryChange() newSize = self.state['size'] * s c1 = self.mapToScene(Point(center) * newSize) newPos = self.state['pos'] + c - c1 self.setSize(newSize, update=False) self.setPos(self.state['pos'], update=update, finish=finish) def translate(self, *args, **kargs): """ Move the ROI to a new position. Accepts either (x, y, snap) or ([x,y], snap) as arguments If the ROI is bounded and the move would exceed boundaries, then the ROI is moved to the nearest acceptable position instead. snap can be: None (default): use self.translateSnap and self.snapSize to determine whether/how to snap False: do not snap Point(w,h) snap to rectangular grid with spacing (w,h) True: snap using self.snapSize (and ignoring self.translateSnap) Also accepts *update* and *finish* arguments (see setPos() for a description of these). """ if len(args) == 1: pt = args[0] else: pt = args newState = self.stateCopy() newState['pos'] = newState['pos'] + pt ## snap position #snap = kargs.get('snap', None) #if (snap is not False) and not (snap is None and self.translateSnap is False): snap = kargs.get('snap', None) if snap is None: snap = self.translateSnap if snap is not False: newState['pos'] = self.getSnapPosition(newState['pos'], snap=snap) #d = ev.scenePos() - self.mapToScene(self.pressPos) if self.maxBounds is not None: r = self.stateRect(newState) #r0 = self.sceneTransform().mapRect(self.boundingRect()) d = Point(0,0) if self.maxBounds.left() > r.left(): d[0] = self.maxBounds.left() - r.left() elif self.maxBounds.right() < r.right(): d[0] = self.maxBounds.right() - r.right() if self.maxBounds.top() > r.top(): d[1] = self.maxBounds.top() - r.top() elif self.maxBounds.bottom() < r.bottom(): d[1] = self.maxBounds.bottom() - r.bottom() newState['pos'] += d #self.state['pos'] = newState['pos'] update = kargs.get('update', True) finish = kargs.get('finish', True) self.setPos(newState['pos'], update=update, finish=finish) #if 'update' not in kargs or kargs['update'] is True: #self.stateChanged() def rotate(self, angle, update=True, finish=True): self.setAngle(self.angle()+angle, update=update, finish=finish) def addTranslateHandle(self, pos, axes=None, item=None, name=None): pos = Point(pos) return self.addHandle({'name': name, 'type': 't', 'pos': pos, 'item': item}) def addFreeHandle(self, pos, axes=None, item=None, name=None): pos = Point(pos) return self.addHandle({'name': name, 'type': 'f', 'pos': pos, 'item': item}) def addScaleHandle(self, pos, center, axes=None, item=None, name=None, lockAspect=False): pos = Point(pos) center = Point(center) info = {'name': name, 'type': 's', 'center': center, 'pos': pos, 'item': item, 'lockAspect': lockAspect} if pos.x() == center.x(): info['xoff'] = True if pos.y() == center.y(): info['yoff'] = True return self.addHandle(info) def addRotateHandle(self, pos, center, item=None, name=None): pos = Point(pos) center = Point(center) return self.addHandle({'name': name, 'type': 'r', 'center': center, 'pos': pos, 'item': item}) def addScaleRotateHandle(self, pos, center, item=None, name=None): pos = Point(pos) center = Point(center) if pos[0] != center[0] and pos[1] != center[1]: raise Exception("Scale/rotate handles must have either the same x or y coordinate as their center point.") return self.addHandle({'name': name, 'type': 'sr', 'center': center, 'pos': pos, 'item': item}) def addRotateFreeHandle(self, pos, center, axes=None, item=None, name=None): pos = Point(pos) center = Point(center) return self.addHandle({'name': name, 'type': 'rf', 'center': center, 'pos': pos, 'item': item}) def addHandle(self, info): if not info.has_key('item') or info['item'] is None: #print "BEFORE ADD CHILD:", self.childItems() h = Handle(self.handleSize, typ=info['type'], pen=self.handlePen, parent=self) #print "AFTER ADD CHILD:", self.childItems() h.setPos(info['pos'] * self.state['size']) info['item'] = h else: h = info['item'] iid = len(self.handles) h.connectROI(self, iid) #h.mouseMoveEvent = lambda ev: self.pointMoveEvent(iid, ev) #h.mousePressEvent = lambda ev: self.pointPressEvent(iid, ev) #h.mouseReleaseEvent = lambda ev: self.pointReleaseEvent(iid, ev) self.handles.append(info) h.setZValue(self.zValue()+1) #if self.isSelected(): #h.show() #else: #h.hide() return h def getLocalHandlePositions(self, index=None): """Returns the position of a handle in ROI coordinates""" if index == None: positions = [] for h in self.handles: positions.append((h['name'], h['pos'])) return positions else: return (self.handles[index]['name'], self.handles[index]['pos']) def getSceneHandlePositions(self, index = None): if index == None: positions = [] for h in self.handles: positions.append((h['name'], h['item'].scenePos())) return positions else: return (self.handles[index]['name'], self.handles[index]['item'].scenePos()) def mapSceneToParent(self, pt): return self.mapToParent(self.mapFromScene(pt)) def setSelected(self, s): QtGui.QGraphicsItem.setSelected(self, s) #print "select", self, s if s: for h in self.handles: h['item'].show() else: for h in self.handles: h['item'].hide() def hoverEvent(self, ev): if self.translatable and (not ev.isExit()) and ev.acceptDrags(QtCore.Qt.LeftButton): self.setMouseHover(True) self.sigHoverEvent.emit(self) else: self.setMouseHover(False) def setMouseHover(self, hover): ## Inform the ROI that the mouse is(not) hovering over it if self.mouseHovering == hover: return self.mouseHovering = hover if hover: self.currentPen = fn.mkPen(255, 255, 0) else: self.currentPen = self.pen self.update() def mouseDragEvent(self, ev): if ev.isStart(): #p = ev.pos() #if not self.isMoving and not self.shape().contains(p): #ev.ignore() #return if ev.button() == QtCore.Qt.LeftButton: self.setSelected(True) if self.translatable: self.isMoving = True self.preMoveState = self.getState() self.cursorOffset = self.pos() - self.mapToParent(ev.buttonDownPos()) self.sigRegionChangeStarted.emit(self) ev.accept() else: ev.ignore() elif ev.isFinish(): if self.translatable: if self.isMoving: self.stateChangeFinished() self.isMoving = False return if self.translatable and self.isMoving and ev.buttons() == QtCore.Qt.LeftButton: snap = True if (ev.modifiers() & QtCore.Qt.ControlModifier) else None newPos = self.mapToParent(ev.pos()) + self.cursorOffset self.translate(newPos - self.pos(), snap=snap, finish=False) def mouseClickEvent(self, ev): if ev.button() == QtCore.Qt.RightButton: if self.isMoving: ev.accept() self.cancelMove() else: ev.ignore() def cancelMove(self): self.isMoving = False self.setState(self.preMoveState) #def pointDragEvent(self, pt, ev): ### just for handling drag start/stop. ### drag moves are handled through movePoint() #if ev.isStart(): #self.isMoving = True #self.preMoveState = self.getState() #self.sigRegionChangeStarted.emit(self) #elif ev.isFinish(): #self.isMoving = False #self.sigRegionChangeFinished.emit(self) #return #def pointPressEvent(self, pt, ev): ##print "press" #self.isMoving = True #self.preMoveState = self.getState() ##self.emit(QtCore.SIGNAL('regionChangeStarted'), self) #self.sigRegionChangeStarted.emit(self) ##self.pressPos = self.mapFromScene(ev.scenePos()) ##self.pressHandlePos = self.handles[pt]['item'].pos() #def pointReleaseEvent(self, pt, ev): ##print "release" #self.isMoving = False ##self.emit(QtCore.SIGNAL('regionChangeFinished'), self) #self.sigRegionChangeFinished.emit(self) #def pointMoveEvent(self, pt, ev): #self.movePoint(pt, ev.scenePos(), ev.modifiers()) def checkPointMove(self, pt, pos, modifiers): """When handles move, they must ask the ROI if the move is acceptable. By default, this always returns True. Subclasses may wish override. """ return True def movePoint(self, pt, pos, modifiers=QtCore.Qt.KeyboardModifier(), finish=True): ## called by Handles when they are moved. ## pos is the new position of the handle in scene coords, as requested by the handle. newState = self.stateCopy() h = self.handles[pt] p0 = self.mapToScene(h['pos'] * self.state['size']) p1 = Point(pos) ## transform p0 and p1 into parent's coordinates (same as scene coords if there is no parent). I forget why. p0 = self.mapSceneToParent(p0) p1 = self.mapSceneToParent(p1) ## Handles with a 'center' need to know their local position relative to the center point (lp0, lp1) if h.has_key('center'): c = h['center'] cs = c * self.state['size'] lp0 = self.mapFromParent(p0) - cs lp1 = self.mapFromParent(p1) - cs if h['type'] == 't': snap = True if (modifiers & QtCore.Qt.ControlModifier) else None #if self.translateSnap or (): #snap = Point(self.snapSize, self.snapSize) self.translate(p1-p0, snap=snap, update=False) elif h['type'] == 'f': h['item'].setPos(self.mapFromScene(pos)) self.freeHandleMoved = True #self.sigRegionChanged.emit(self) ## should be taken care of by call to stateChanged() elif h['type'] == 's': ## If a handle and its center have the same x or y value, we can't scale across that axis. if h['center'][0] == h['pos'][0]: lp1[0] = 0 if h['center'][1] == h['pos'][1]: lp1[1] = 0 ## snap if self.scaleSnap or (modifiers & QtCore.Qt.ControlModifier): lp1[0] = round(lp1[0] / self.snapSize) * self.snapSize lp1[1] = round(lp1[1] / self.snapSize) * self.snapSize ## preserve aspect ratio (this can override snapping) if h['lockAspect'] or (modifiers & QtCore.Qt.AltModifier): #arv = Point(self.preMoveState['size']) - lp1 = lp1.proj(lp0) ## determine scale factors and new size of ROI hs = h['pos'] - c if hs[0] == 0: hs[0] = 1 if hs[1] == 0: hs[1] = 1 newSize = lp1 / hs ## Perform some corrections and limit checks if newSize[0] == 0: newSize[0] = newState['size'][0] if newSize[1] == 0: newSize[1] = newState['size'][1] if not self.invertible: if newSize[0] < 0: newSize[0] = newState['size'][0] if newSize[1] < 0: newSize[1] = newState['size'][1] if self.aspectLocked: newSize[0] = newSize[1] ## Move ROI so the center point occupies the same scene location after the scale s0 = c * self.state['size'] s1 = c * newSize cc = self.mapToParent(s0 - s1) - self.mapToParent(Point(0, 0)) ## update state, do more boundary checks newState['size'] = newSize newState['pos'] = newState['pos'] + cc if self.maxBounds is not None: r = self.stateRect(newState) if not self.maxBounds.contains(r): return self.setPos(newState['pos'], update=False) self.setSize(newState['size'], update=False) elif h['type'] in ['r', 'rf']: if h['type'] == 'rf': self.freeHandleMoved = True if not self.rotateAllowed: return ## If the handle is directly over its center point, we can't compute an angle. if lp1.length() == 0 or lp0.length() == 0: return ## determine new rotation angle, constrained if necessary ang = newState['angle'] - lp0.angle(lp1) if ang is None: ## this should never happen.. return if self.rotateSnap or (modifiers & QtCore.Qt.ControlModifier): ang = round(ang / 15.) * 15. ## 180/12 = 15 ## create rotation transform tr = QtGui.QTransform() tr.rotate(ang) ## move ROI so that center point remains stationary after rotate cc = self.mapToParent(cs) - (tr.map(cs) + self.state['pos']) newState['angle'] = ang newState['pos'] = newState['pos'] + cc ## check boundaries, update if self.maxBounds is not None: r = self.stateRect(newState) if not self.maxBounds.contains(r): return #self.setTransform(tr) self.setPos(newState['pos'], update=False) self.setAngle(ang, update=False) #self.state = newState ## If this is a free-rotate handle, its distance from the center may change. if h['type'] == 'rf': h['item'].setPos(self.mapFromScene(p1)) ## changes ROI coordinates of handle elif h['type'] == 'sr': if h['center'][0] == h['pos'][0]: scaleAxis = 1 else: scaleAxis = 0 if lp1.length() == 0 or lp0.length() == 0: return ang = newState['angle'] - lp0.angle(lp1) if ang is None: return if self.rotateSnap or (modifiers & QtCore.Qt.ControlModifier): #ang = round(ang / (np.pi/12.)) * (np.pi/12.) ang = round(ang / 15.) * 15. hs = abs(h['pos'][scaleAxis] - c[scaleAxis]) newState['size'][scaleAxis] = lp1.length() / hs #if self.scaleSnap or (modifiers & QtCore.Qt.ControlModifier): if self.scaleSnap: ## use CTRL only for angular snap here. newState['size'][scaleAxis] = round(newState['size'][scaleAxis] / self.snapSize) * self.snapSize if newState['size'][scaleAxis] == 0: newState['size'][scaleAxis] = 1 c1 = c * newState['size'] tr = QtGui.QTransform() tr.rotate(ang) cc = self.mapToParent(cs) - (tr.map(c1) + self.state['pos']) newState['angle'] = ang newState['pos'] = newState['pos'] + cc if self.maxBounds is not None: r = self.stateRect(newState) if not self.maxBounds.contains(r): return #self.setTransform(tr) #self.setPos(newState['pos'], update=False) #self.prepareGeometryChange() #self.state = newState self.setState(newState, update=False) self.stateChanged(finish=finish) def stateChanged(self, finish=True): """Process changes to the state of the ROI. If there are any changes, then the positions of handles are updated accordingly and sigRegionChanged is emitted. If finish is True, then sigRegionChangeFinished will also be emitted.""" changed = False if self.lastState is None: changed = True else: for k in self.state.keys(): if self.state[k] != self.lastState[k]: changed = True self.lastState = self.stateCopy() if changed: ## Move all handles to match the current configuration of the ROI for h in self.handles: if h['item'] in self.childItems(): p = h['pos'] h['item'].setPos(h['pos'] * self.state['size']) self.update() self.sigRegionChanged.emit(self) elif self.freeHandleMoved: self.sigRegionChanged.emit(self) self.freeHandleMoved = False if finish: self.stateChangeFinished() def stateChangeFinished(self): self.sigRegionChangeFinished.emit(self) def stateRect(self, state): r = QtCore.QRectF(0, 0, state['size'][0], state['size'][1]) tr = QtGui.QTransform() #tr.rotate(-state['angle'] * 180 / np.pi) tr.rotate(-state['angle']) r = tr.mapRect(r) return r.adjusted(state['pos'][0], state['pos'][1], state['pos'][0], state['pos'][1]) def getSnapPosition(self, pos, snap=None): ## Given that pos has been requested, return the nearest snap-to position ## optionally, snap may be passed in to specify a rectangular snap grid. ## override this function for more interesting snap functionality.. if snap is None or snap is True: if self.snapSize is None: return pos snap = Point(self.snapSize, self.snapSize) return Point( round(pos[0] / snap[0]) * snap[0], round(pos[1] / snap[1]) * snap[1] ) def boundingRect(self): return QtCore.QRectF(0, 0, self.state['size'][0], self.state['size'][1]).normalized() def paint(self, p, opt, widget): p.save() r = self.boundingRect() p.setRenderHint(QtGui.QPainter.Antialiasing) p.setPen(self.currentPen) p.translate(r.left(), r.top()) p.scale(r.width(), r.height()) p.drawRect(0, 0, 1, 1) p.restore() def getArraySlice(self, data, img, axes=(0,1), returnSlice=True): """Return a tuple of slice objects that can be used to slice the region from data covered by this ROI. Also returns the transform which maps the ROI into data coordinates. If returnSlice is set to False, the function returns a pair of tuples with the values that would have been used to generate the slice objects. ((ax0Start, ax0Stop), (ax1Start, ax1Stop))""" #print "getArraySlice" ## Determine shape of array along ROI axes dShape = (data.shape[axes[0]], data.shape[axes[1]]) #print " dshape", dShape ## Determine transform that maps ROI bounding box to image coordinates tr = self.sceneTransform() * img.sceneTransform().inverted()[0] ## Modify transform to scale from image coords to data coords #m = QtGui.QTransform() tr.scale(float(dShape[0]) / img.width(), float(dShape[1]) / img.height()) #tr = tr * m ## Transform ROI bounds into data bounds dataBounds = tr.mapRect(self.boundingRect()) #print " boundingRect:", self.boundingRect() #print " dataBounds:", dataBounds ## Intersect transformed ROI bounds with data bounds intBounds = dataBounds.intersect(QtCore.QRectF(0, 0, dShape[0], dShape[1])) #print " intBounds:", intBounds ## Determine index values to use when referencing the array. bounds = ( (int(min(intBounds.left(), intBounds.right())), int(1+max(intBounds.left(), intBounds.right()))), (int(min(intBounds.bottom(), intBounds.top())), int(1+max(intBounds.bottom(), intBounds.top()))) ) #print " bounds:", bounds if returnSlice: ## Create slice objects sl = [slice(None)] * data.ndim sl[axes[0]] = slice(*bounds[0]) sl[axes[1]] = slice(*bounds[1]) return tuple(sl), tr else: return bounds, tr def getArrayRegion(self, data, img, axes=(0,1)): """Use the position of this ROI relative to an imageItem to pull a slice from an array.""" shape = self.state['size'] origin = self.mapToItem(img, QtCore.QPointF(0, 0)) ## vx and vy point in the directions of the slice axes, but must be scaled properly vx = self.mapToItem(img, QtCore.QPointF(1, 0)) - origin vy = self.mapToItem(img, QtCore.QPointF(0, 1)) - origin lvx = np.sqrt(vx.x()**2 + vx.y()**2) lvy = np.sqrt(vy.x()**2 + vy.y()**2) pxLen = img.width() / float(data.shape[axes[0]]) sx = pxLen / lvx sy = pxLen / lvy vectors = ((vx.x()*sx, vx.y()*sx), (vy.x()*sy, vy.y()*sy)) shape = self.state['size'] shape = [abs(shape[0]/sx), abs(shape[1]/sy)] origin = (origin.x(), origin.y()) #print "shape", shape, "vectors", vectors, "origin", origin return fn.affineSlice(data, shape=shape, vectors=vectors, origin=origin, axes=axes, order=1) ### transpose data so x and y are the first 2 axes #trAx = range(0, data.ndim) #trAx.remove(axes[0]) #trAx.remove(axes[1]) #tr1 = tuple(axes) + tuple(trAx) #arr = data.transpose(tr1) ### Determine the minimal area of the data we will need #(dataBounds, roiDataTransform) = self.getArraySlice(data, img, returnSlice=False, axes=axes) ### Pad data boundaries by 1px if possible #dataBounds = ( #(max(dataBounds[0][0]-1, 0), min(dataBounds[0][1]+1, arr.shape[0])), #(max(dataBounds[1][0]-1, 0), min(dataBounds[1][1]+1, arr.shape[1])) #) ### Extract minimal data from array #arr1 = arr[dataBounds[0][0]:dataBounds[0][1], dataBounds[1][0]:dataBounds[1][1]] ### Update roiDataTransform to reflect this extraction #roiDataTransform *= QtGui.QTransform().translate(-dataBounds[0][0], -dataBounds[1][0]) #### (roiDataTransform now maps from ROI coords to extracted data coords) ### Rotate array #if abs(self.state['angle']) > 1e-5: #arr2 = ndimage.rotate(arr1, self.state['angle'] * 180 / np.pi, order=1) ### update data transforms to reflect this rotation #rot = QtGui.QTransform().rotate(self.state['angle'] * 180 / np.pi) #roiDataTransform *= rot ### The rotation also causes a shift which must be accounted for: #dataBound = QtCore.QRectF(0, 0, arr1.shape[0], arr1.shape[1]) #rotBound = rot.mapRect(dataBound) #roiDataTransform *= QtGui.QTransform().translate(-rotBound.left(), -rotBound.top()) #else: #arr2 = arr1 #### Shift off partial pixels ## 1. map ROI into current data space #roiBounds = roiDataTransform.mapRect(self.boundingRect()) ## 2. Determine amount to shift data #shift = (int(roiBounds.left()) - roiBounds.left(), int(roiBounds.bottom()) - roiBounds.bottom()) #if abs(shift[0]) > 1e-6 or abs(shift[1]) > 1e-6: ## 3. pad array with 0s before shifting #arr2a = np.zeros((arr2.shape[0]+2, arr2.shape[1]+2) + arr2.shape[2:], dtype=arr2.dtype) #arr2a[1:-1, 1:-1] = arr2 ## 4. shift array and udpate transforms #arr3 = ndimage.shift(arr2a, shift + (0,)*(arr2.ndim-2), order=1) #roiDataTransform *= QtGui.QTransform().translate(1+shift[0], 1+shift[1]) #else: #arr3 = arr2 #### Extract needed region from rotated/shifted array ## 1. map ROI into current data space (round these values off--they should be exact integer values at this point) #roiBounds = roiDataTransform.mapRect(self.boundingRect()) ##print self, roiBounds.height() ##import traceback ##traceback.print_stack() #roiBounds = QtCore.QRect(round(roiBounds.left()), round(roiBounds.top()), round(roiBounds.width()), round(roiBounds.height())) ##2. intersect ROI with data bounds #dataBounds = roiBounds.intersect(QtCore.QRect(0, 0, arr3.shape[0], arr3.shape[1])) ##3. Extract data from array #db = dataBounds #bounds = ( #(db.left(), db.right()+1), #(db.top(), db.bottom()+1) #) #arr4 = arr3[bounds[0][0]:bounds[0][1], bounds[1][0]:bounds[1][1]] #### Create zero array in size of ROI #arr5 = np.zeros((roiBounds.width(), roiBounds.height()) + arr4.shape[2:], dtype=arr4.dtype) ### Fill array with ROI data #orig = Point(dataBounds.topLeft() - roiBounds.topLeft()) #subArr = arr5[orig[0]:orig[0]+arr4.shape[0], orig[1]:orig[1]+arr4.shape[1]] #subArr[:] = arr4[:subArr.shape[0], :subArr.shape[1]] ### figure out the reverse transpose order #tr2 = np.array(tr1) #for i in range(0, len(tr2)): #tr2[tr1[i]] = i #tr2 = tuple(tr2) ### Untranspose array before returning #return arr5.transpose(tr2) def getGlobalTransform(self, relativeTo=None): """Return global transformation (rotation angle+translation) required to move from relative state to current state. If relative state isn't specified, then we use the state of the ROI when mouse is pressed.""" if relativeTo == None: relativeTo = self.preMoveState st = self.getState() ## this is only allowed because we will be comparing the two relativeTo['scale'] = relativeTo['size'] st['scale'] = st['size'] t1 = Transform(relativeTo) t2 = Transform(st) return t2/t1 #st = self.getState() ### rotation #ang = (st['angle']-relativeTo['angle']) * 180. / 3.14159265358 #rot = QtGui.QTransform() #rot.rotate(-ang) ### We need to come up with a universal transformation--one that can be applied to other objects ### such that all maintain alignment. ### More specifically, we need to turn the ROI's position and angle into ### a rotation _around the origin_ and a translation. #p0 = Point(relativeTo['pos']) ### base position, rotated #p1 = rot.map(p0) #trans = Point(st['pos']) - p1 #return trans, ang def applyGlobalTransform(self, tr): st = self.getState() st['scale'] = st['size'] st = Transform(st) st = (st * tr).saveState() st['size'] = st['scale'] self.setState(st) class Handle(UIGraphicsItem): types = { ## defines number of sides, start angle for each handle type 't': (4, np.pi/4), 'f': (4, np.pi/4), 's': (4, 0), 'r': (12, 0), 'sr': (12, 0), 'rf': (12, 0), } def __init__(self, radius, typ=None, pen=(200, 200, 220), parent=None): #print " create item with parent", parent #self.bounds = QtCore.QRectF(-1e-10, -1e-10, 2e-10, 2e-10) #self.setFlags(self.ItemIgnoresTransformations | self.ItemSendsScenePositionChanges) self.roi = [] self.radius = radius self.typ = typ self.pen = fn.mkPen(pen) self.currentPen = self.pen self.pen.setWidth(0) self.pen.setCosmetic(True) self.isMoving = False self.sides, self.startAng = self.types[typ] self.buildPath() self._shape = None UIGraphicsItem.__init__(self, parent=parent) #self.updateShape() self.setZValue(11) def connectROI(self, roi, i): self.roi.append((roi, i)) #def boundingRect(self): #return self.bounds def hoverEvent(self, ev): if (not ev.isExit()) and ev.acceptDrags(QtCore.Qt.LeftButton): self.currentPen = fn.mkPen(255, 255,0) else: self.currentPen = self.pen self.update() def mouseClickEvent(self, ev): ## right-click cancels drag if ev.button() == QtCore.Qt.RightButton and self.isMoving: self.isMoving = False ## prevents any further motion self.movePoint(self.startPos, finish=True) #for r in self.roi: #r[0].cancelMove() ev.accept() def mouseDragEvent(self, ev): if ev.button() != QtCore.Qt.LeftButton: return ev.accept() ## Inform ROIs that a drag is happening ## note: the ROI is informed that the handle has moved using ROI.movePoint ## this is for other (more nefarious) purposes. #for r in self.roi: #r[0].pointDragEvent(r[1], ev) if ev.isFinish(): if self.isMoving: for r in self.roi: r[0].stateChangeFinished() self.isMoving = False elif ev.isStart(): self.isMoving = True self.startPos = self.scenePos() self.cursorOffset = self.scenePos() - ev.buttonDownScenePos() if self.isMoving: ## note: isMoving may become False in mid-drag due to right-click. pos = ev.scenePos() + self.cursorOffset self.movePoint(pos, ev.modifiers(), finish=False) def movePoint(self, pos, modifiers=QtCore.Qt.KeyboardModifier(), finish=True): for r in self.roi: if not r[0].checkPointMove(r[1], pos, modifiers): return #print "point moved; inform %d ROIs" % len(self.roi) # A handle can be used by multiple ROIs; tell each to update its handle position for r in self.roi: r[0].movePoint(r[1], pos, modifiers, finish=finish) def buildPath(self): size = self.radius self.path = QtGui.QPainterPath() ang = self.startAng dt = 2*np.pi / self.sides for i in range(0, self.sides+1): x = size * cos(ang) y = size * sin(ang) ang += dt if i == 0: self.path.moveTo(x, y) else: self.path.lineTo(x, y) def paint(self, p, opt, widget): ### determine rotation of transform #m = self.sceneTransform() ##mi = m.inverted()[0] #v = m.map(QtCore.QPointF(1, 0)) - m.map(QtCore.QPointF(0, 0)) #va = np.arctan2(v.y(), v.x()) ### Determine length of unit vector in painter's coords ##size = mi.map(Point(self.radius, self.radius)) - mi.map(Point(0, 0)) ##size = (size.x()*size.x() + size.y() * size.y()) ** 0.5 #size = self.radius #bounds = QtCore.QRectF(-size, -size, size*2, size*2) #if bounds != self.bounds: #self.bounds = bounds #self.prepareGeometryChange() p.setRenderHints(p.Antialiasing, True) p.setPen(self.currentPen) #p.rotate(va * 180. / 3.1415926) #p.drawPath(self.path) p.drawPath(self.shape()) #ang = self.startAng + va #dt = 2*np.pi / self.sides #for i in range(0, self.sides): #x1 = size * cos(ang) #y1 = size * sin(ang) #x2 = size * cos(ang+dt) #y2 = size * sin(ang+dt) #ang += dt #p.drawLine(Point(x1, y1), Point(x2, y2)) def shape(self): if self._shape is None: s = self.generateShape() if s is None: return self.shape self._shape = s self.prepareGeometryChange() return self._shape def boundingRect(self): return self.shape().boundingRect() def generateShape(self): ## determine rotation of transform #m = self.sceneTransform() ## Qt bug: do not access sceneTransform() until we know this object has a scene. #mi = m.inverted()[0] dt = self.deviceTransform() if dt is None: self._shape = self.path return None v = dt.map(QtCore.QPointF(1, 0)) - dt.map(QtCore.QPointF(0, 0)) va = np.arctan2(v.y(), v.x()) dti = dt.inverted()[0] devPos = dt.map(QtCore.QPointF(0,0)) tr = QtGui.QTransform() tr.translate(devPos.x(), devPos.y()) tr.rotate(va * 180. / 3.1415926) return dti.map(tr.map(self.path)) def viewChangedEvent(self): self._shape = None ## invalidate shape, recompute later if requested. #self.updateShape() #def itemChange(self, change, value): #if change == self.ItemScenePositionHasChanged: #self.updateShape() class TestROI(ROI): def __init__(self, pos, size, **args): #QtGui.QGraphicsRectItem.__init__(self, pos[0], pos[1], size[0], size[1]) ROI.__init__(self, pos, size, **args) #self.addTranslateHandle([0, 0]) self.addTranslateHandle([0.5, 0.5]) self.addScaleHandle([1, 1], [0, 0]) self.addScaleHandle([0, 0], [1, 1]) self.addScaleRotateHandle([1, 0.5], [0.5, 0.5]) self.addScaleHandle([0.5, 1], [0.5, 0.5]) self.addRotateHandle([1, 0], [0, 0]) self.addRotateHandle([0, 1], [1, 1]) class RectROI(ROI): def __init__(self, pos, size, centered=False, sideScalers=False, **args): #QtGui.QGraphicsRectItem.__init__(self, 0, 0, size[0], size[1]) ROI.__init__(self, pos, size, **args) if centered: center = [0.5, 0.5] else: center = [0, 0] #self.addTranslateHandle(center) self.addScaleHandle([1, 1], center) if sideScalers: self.addScaleHandle([1, 0.5], [center[0], 0.5]) self.addScaleHandle([0.5, 1], [0.5, center[1]]) class LineROI(ROI): def __init__(self, pos1, pos2, width, **args): pos1 = Point(pos1) pos2 = Point(pos2) d = pos2-pos1 l = d.length() ang = Point(1, 0).angle(d) ra = ang * np.pi / 180. c = Point(-width/2. * sin(ra), -width/2. * cos(ra)) pos1 = pos1 + c ROI.__init__(self, pos1, size=Point(l, width), angle=ang, **args) self.addScaleRotateHandle([0, 0.5], [1, 0.5]) self.addScaleRotateHandle([1, 0.5], [0, 0.5]) self.addScaleHandle([0.5, 1], [0.5, 0.5]) class MultiLineROI(QtGui.QGraphicsObject): sigRegionChangeFinished = QtCore.Signal(object) sigRegionChangeStarted = QtCore.Signal(object) sigRegionChanged = QtCore.Signal(object) def __init__(self, points, width, pen=None, **args): QtGui.QGraphicsObject.__init__(self) self.pen = pen self.roiArgs = args if len(points) < 2: raise Exception("Must start with at least 2 points") self.lines = [] self.lines.append(ROI([0, 0], [1, 5], parent=self, pen=pen, **args)) self.lines[-1].addScaleHandle([0.5, 1], [0.5, 0.5]) h = self.lines[-1].addScaleRotateHandle([0, 0.5], [1, 0.5]) h.movePoint(points[0]) h.movePoint(points[0]) for i in range(1, len(points)): h = self.lines[-1].addScaleRotateHandle([1, 0.5], [0, 0.5]) if i < len(points)-1: self.lines.append(ROI([0, 0], [1, 5], parent=self, pen=pen, **args)) self.lines[-1].addScaleRotateHandle([0, 0.5], [1, 0.5], item=h) h.movePoint(points[i]) h.movePoint(points[i]) for l in self.lines: l.translatable = False #self.addToGroup(l) #l.connect(l, QtCore.SIGNAL('regionChanged'), self.roiChangedEvent) l.sigRegionChanged.connect(self.roiChangedEvent) #l.connect(l, QtCore.SIGNAL('regionChangeStarted'), self.roiChangeStartedEvent) l.sigRegionChangeStarted.connect(self.roiChangeStartedEvent) #l.connect(l, QtCore.SIGNAL('regionChangeFinished'), self.roiChangeFinishedEvent) l.sigRegionChangeFinished.connect(self.roiChangeFinishedEvent) def paint(self, *args): pass def boundingRect(self): return QtCore.QRectF() def roiChangedEvent(self): w = self.lines[0].state['size'][1] for l in self.lines[1:]: w0 = l.state['size'][1] l.scale([1.0, w/w0], center=[0.5,0.5]) #self.emit(QtCore.SIGNAL('regionChanged'), self) self.sigRegionChanged.emit(self) def roiChangeStartedEvent(self): #self.emit(QtCore.SIGNAL('regionChangeStarted'), self) self.sigRegionChangeStarted.emit(self) def roiChangeFinishedEvent(self): #self.emit(QtCore.SIGNAL('regionChangeFinished'), self) self.sigRegionChangeFinished.emit(self) def getArrayRegion(self, arr, img=None, axes=(0,1)): rgns = [] for l in self.lines: rgn = l.getArrayRegion(arr, img, axes=axes) if rgn is None: continue #return None rgns.append(rgn) #print l.state['size'] ## make sure orthogonal axis is the same size ## (sometimes fp errors cause differences) ms = min([r.shape[axes[1]] for r in rgns]) sl = [slice(None)] * rgns[0].ndim sl[axes[1]] = slice(0,ms) rgns = [r[sl] for r in rgns] #print [r.shape for r in rgns], axes return np.concatenate(rgns, axis=axes[0]) class EllipseROI(ROI): def __init__(self, pos, size, **args): #QtGui.QGraphicsRectItem.__init__(self, 0, 0, size[0], size[1]) ROI.__init__(self, pos, size, **args) self.addRotateHandle([1.0, 0.5], [0.5, 0.5]) self.addScaleHandle([0.5*2.**-0.5 + 0.5, 0.5*2.**-0.5 + 0.5], [0.5, 0.5]) def paint(self, p, opt, widget): r = self.boundingRect() p.setRenderHint(QtGui.QPainter.Antialiasing) p.setPen(self.currentPen) p.scale(r.width(), r.height())## workaround for GL bug r = QtCore.QRectF(r.x()/r.width(), r.y()/r.height(), 1,1) p.drawEllipse(r) def getArrayRegion(self, arr, img=None): arr = ROI.getArrayRegion(self, arr, img) if arr is None or arr.shape[0] == 0 or arr.shape[1] == 0: return None w = arr.shape[0] h = arr.shape[1] ## generate an ellipsoidal mask mask = np.fromfunction(lambda x,y: (((x+0.5)/(w/2.)-1)**2+ ((y+0.5)/(h/2.)-1)**2)**0.5 < 1, (w, h)) return arr * mask def shape(self): self.path = QtGui.QPainterPath() self.path.addEllipse(self.boundingRect()) return self.path class CircleROI(EllipseROI): def __init__(self, pos, size, **args): ROI.__init__(self, pos, size, **args) self.aspectLocked = True #self.addTranslateHandle([0.5, 0.5]) self.addScaleHandle([0.5*2.**-0.5 + 0.5, 0.5*2.**-0.5 + 0.5], [0.5, 0.5]) class PolygonROI(ROI): def __init__(self, positions, pos=None, **args): if pos is None: pos = [0,0] ROI.__init__(self, pos, [1,1], **args) #ROI.__init__(self, positions[0]) for p in positions: self.addFreeHandle(p) self.setZValue(1000) def listPoints(self): return [p['item'].pos() for p in self.handles] def movePoint(self, *args, **kargs): ROI.movePoint(self, *args, **kargs) self.prepareGeometryChange() for h in self.handles: h['pos'] = h['item'].pos() def paint(self, p, *args): p.setRenderHint(QtGui.QPainter.Antialiasing) p.setPen(self.currentPen) for i in range(len(self.handles)): h1 = self.handles[i]['item'].pos() h2 = self.handles[i-1]['item'].pos() p.drawLine(h1, h2) def boundingRect(self): r = QtCore.QRectF() for h in self.handles: r |= self.mapFromItem(h['item'], h['item'].boundingRect()).boundingRect() ## |= gives the union of the two QRectFs return r def shape(self): p = QtGui.QPainterPath() p.moveTo(self.handles[0]['item'].pos()) for i in range(len(self.handles)): p.lineTo(self.handles[i]['item'].pos()) return p def stateCopy(self): sc = {} sc['pos'] = Point(self.state['pos']) sc['size'] = Point(self.state['size']) sc['angle'] = self.state['angle'] #sc['handles'] = self.handles return sc class LineSegmentROI(ROI): """ ROI subclass with two or more freely-moving handles connecting lines. """ def __init__(self, positions, pos=None, **args): if pos is None: pos = [0,0] ROI.__init__(self, pos, [1,1], **args) #ROI.__init__(self, positions[0]) for p in positions: self.addFreeHandle(p) self.setZValue(1000) def listPoints(self): return [p['item'].pos() for p in self.handles] def movePoint(self, *args, **kargs): ROI.movePoint(self, *args, **kargs) self.prepareGeometryChange() for h in self.handles: h['pos'] = h['item'].pos() def paint(self, p, *args): p.setRenderHint(QtGui.QPainter.Antialiasing) p.setPen(self.currentPen) for i in range(len(self.handles)-1): h1 = self.handles[i]['item'].pos() h2 = self.handles[i+1]['item'].pos() p.drawLine(h1, h2) def boundingRect(self): r = QtCore.QRectF() for h in self.handles: r |= self.mapFromItem(h['item'], h['item'].boundingRect()).boundingRect() ## |= gives the union of the two QRectFs return r def shape(self): p = QtGui.QPainterPath() p.moveTo(self.handles[0]['item'].pos()) for i in range(len(self.handles)): p.lineTo(self.handles[i]['item'].pos()) return p def stateCopy(self): sc = {} sc['pos'] = Point(self.state['pos']) sc['size'] = Point(self.state['size']) sc['angle'] = self.state['angle'] #sc['handles'] = self.handles return sc def getArrayRegion(self, data, img, axes=(0,1)): """ Use the position of this ROI relative to an imageItem to pull a slice from an array. Since this pulls 1D data from a 2D coordinate system, the return value will have ndim = data.ndim-1 """ #shape = self.state['size'] #origin = self.mapToItem(img, QtCore.QPointF(0, 0)) ## vx and vy point in the directions of the slice axes, but must be scaled properly #vx = self.mapToItem(img, QtCore.QPointF(1, 0)) - origin #vy = self.mapToItem(img, QtCore.QPointF(0, 1)) - origin imgPts = [self.mapToItem(img, h['item'].pos()) for h in self.handles] rgns = [] for i in range(len(imgPts)-1): d = Point(imgPts[i+1] - imgPts[i]) o = Point(imgPts[i]) r = fn.affineSlice(data, shape=(int(d.length()),), vectors=[d.norm()], origin=o, axes=axes, order=1) rgns.append(r) return np.concatenate(rgns, axis=axes[0]) #lvx = np.sqrt(vx.x()**2 + vx.y()**2) #lvy = np.sqrt(vy.x()**2 + vy.y()**2) #pxLen = img.width() / float(data.shape[axes[0]]) #sx = pxLen / lvx #sy = pxLen / lvy #vectors = ((vx.x()*sx, vx.y()*sx), (vy.x()*sy, vy.y()*sy)) #shape = self.state['size'] #shape = [abs(shape[0]/sx), abs(shape[1]/sy)] #origin = (origin.x(), origin.y()) ##print "shape", shape, "vectors", vectors, "origin", origin #return fn.affineSlice(data, shape=shape, vectors=vectors, origin=origin, axes=axes, order=1) class SpiralROI(ROI): def __init__(self, pos=None, size=None, **args): if size == None: size = [100e-6,100e-6] if pos == None: pos = [0,0] ROI.__init__(self, pos, size, **args) self.translateSnap = False self.addFreeHandle([0.25,0], name='a') self.addRotateFreeHandle([1,0], [0,0], name='r') #self.getRadius() #QtCore.connect(self, QtCore.SIGNAL('regionChanged'), self. def getRadius(self): radius = Point(self.handles[1]['item'].pos()).length() #r2 = radius[1] #r3 = r2[0] return radius def boundingRect(self): r = self.getRadius() return QtCore.QRectF(-r*1.1, -r*1.1, 2.2*r, 2.2*r) #return self.bounds def movePoint(self, *args, **kargs): ROI.movePoint(self, *args, **kargs) self.prepareGeometryChange() for h in self.handles: h['pos'] = h['item'].pos()/self.state['size'][0] def stateChanged(self): ROI.stateChanged(self) if len(self.handles) > 1: self.path = QtGui.QPainterPath() h0 = Point(self.handles[0]['item'].pos()).length() a = h0/(2.0*np.pi) theta = 30.0*(2.0*np.pi)/360.0 self.path.moveTo(QtCore.QPointF(a*theta*cos(theta), a*theta*sin(theta))) x0 = a*theta*cos(theta) y0 = a*theta*sin(theta) radius = self.getRadius() theta += 20.0*(2.0*np.pi)/360.0 i = 0 while Point(x0, y0).length() < radius and i < 1000: x1 = a*theta*cos(theta) y1 = a*theta*sin(theta) self.path.lineTo(QtCore.QPointF(x1,y1)) theta += 20.0*(2.0*np.pi)/360.0 x0 = x1 y0 = y1 i += 1 return self.path def shape(self): p = QtGui.QPainterPath() p.addEllipse(self.boundingRect()) return p def paint(self, p, *args): p.setRenderHint(QtGui.QPainter.Antialiasing) #path = self.shape() p.setPen(self.currentPen) p.drawPath(self.path) p.setPen(QtGui.QPen(QtGui.QColor(255,0,0))) p.drawPath(self.shape()) p.setPen(QtGui.QPen(QtGui.QColor(0,0,255))) p.drawRect(self.boundingRect())