Fix PolyLineROI.getArrayRegion and a few other bugs
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Luke Campagnola
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@ -991,8 +991,9 @@ class ROI(GraphicsObject):
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# p.restore()
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def getArraySlice(self, data, img, axes=(0,1), returnSlice=True):
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"""Return a tuple of slice objects that can be used to slice the region from data covered by this ROI.
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Also returns the transform which maps the ROI into data coordinates.
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"""Return a tuple of slice objects that can be used to slice the region
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from *data* that is covered by the bounding rectangle of this ROI.
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Also returns the transform that maps the ROI into data coordinates.
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If returnSlice is set to False, the function returns a pair of tuples with the values that would have
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been used to generate the slice objects. ((ax0Start, ax0Stop), (ax1Start, ax1Stop))
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@ -1075,8 +1076,10 @@ class ROI(GraphicsObject):
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All extra keyword arguments are passed to :func:`affineSlice <pyqtgraph.affineSlice>`.
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"""
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# this is a hidden argument for internal use
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fromBR = kwds.pop('fromBoundingRect', False)
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shape, vectors, origin = self.getAffineSliceParams(data, img, axes)
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shape, vectors, origin = self.getAffineSliceParams(data, img, axes, fromBoundingRect=fromBR)
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if not returnMappedCoords:
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return fn.affineSlice(data, shape=shape, vectors=vectors, origin=origin, axes=axes, **kwds)
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else:
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@ -1087,7 +1090,7 @@ class ROI(GraphicsObject):
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mapped = fn.transformCoordinates(img.transform(), coords)
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return result, mapped
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def getAffineSliceParams(self, data, img, axes=(0,1)):
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def getAffineSliceParams(self, data, img, axes=(0,1), fromBoundingRect=False):
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"""
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Returns the parameters needed to use :func:`affineSlice <pyqtgraph.affineSlice>`
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(shape, vectors, origin) to extract a subset of *data* using this ROI
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@ -1098,8 +1101,6 @@ class ROI(GraphicsObject):
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if self.scene() is not img.scene():
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raise Exception("ROI and target item must be members of the same scene.")
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shape = self.state['size']
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origin = self.mapToItem(img, QtCore.QPointF(0, 0))
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## vx and vy point in the directions of the slice axes, but must be scaled properly
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@ -1109,17 +1110,43 @@ class ROI(GraphicsObject):
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lvx = np.sqrt(vx.x()**2 + vx.y()**2)
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lvy = np.sqrt(vy.x()**2 + vy.y()**2)
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pxLen = img.width() / float(data.shape[axes[0]])
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#img.width is number of pixels or width of item?
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#img.width is number of pixels, not width of item.
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#need pxWidth and pxHeight instead of pxLen ?
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sx = pxLen / lvx
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sy = pxLen / lvy
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vectors = ((vx.x()*sx, vx.y()*sx), (vy.x()*sy, vy.y()*sy))
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shape = self.state['size']
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if fromBoundingRect is True:
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shape = self.boundingRect().width(), self.boundingRect().height()
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origin = self.mapToItem(img, self.boundingRect().topLeft())
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origin = (origin.x(), origin.y())
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else:
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shape = self.state['size']
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origin = (origin.x(), origin.y())
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shape = [abs(shape[0]/sx), abs(shape[1]/sy)]
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origin = (origin.x(), origin.y())
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return shape, vectors, origin
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def renderShapeMask(self, width, height):
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"""Return an array of 0.0-1.0 into which the shape of the item has been drawn.
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This can be used to mask array selections.
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"""
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# QImage(width, height, format)
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im = QtGui.QImage(width, height, QtGui.QImage.Format_ARGB32)
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im.fill(0x0)
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p = QtGui.QPainter(im)
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p.setPen(fn.mkPen(None))
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p.setBrush(fn.mkBrush('w'))
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shape = self.shape()
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bounds = shape.boundingRect()
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p.scale(im.width() / bounds.width(), im.height() / bounds.height())
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p.translate(-bounds.topLeft())
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p.drawPath(shape)
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p.end()
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mask = fn.imageToArray(im)[:,:,0].astype(float) / 255.
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return mask
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def getGlobalTransform(self, relativeTo=None):
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"""Return global transformation (rotation angle+translation) required to move
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@ -1579,10 +1606,10 @@ class MultiRectROI(QtGui.QGraphicsObject):
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pos.append(self.mapFromScene(l.getHandles()[1].scenePos()))
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return pos
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def getArrayRegion(self, arr, img=None, axes=(0,1)):
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def getArrayRegion(self, arr, img=None, axes=(0,1), **kwds):
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rgns = []
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for l in self.lines:
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rgn = l.getArrayRegion(arr, img, axes=axes)
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rgn = l.getArrayRegion(arr, img, axes=axes, **kwds)
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if rgn is None:
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continue
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#return None
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@ -1652,6 +1679,7 @@ class MultiLineROI(MultiRectROI):
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def __init__(self, *args, **kwds):
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MultiRectROI.__init__(self, *args, **kwds)
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print("Warning: MultiLineROI has been renamed to MultiRectROI. (and MultiLineROI may be redefined in the future)")
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class EllipseROI(ROI):
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"""
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@ -1682,19 +1710,27 @@ class EllipseROI(ROI):
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p.drawEllipse(r)
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def getArrayRegion(self, arr, img=None):
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def getArrayRegion(self, arr, img=None, axes=(0, 1), **kwds):
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"""
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Return the result of ROI.getArrayRegion() masked by the elliptical shape
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of the ROI. Regions outside the ellipse are set to 0.
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"""
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arr = ROI.getArrayRegion(self, arr, img)
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if arr is None or arr.shape[0] == 0 or arr.shape[1] == 0:
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return None
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w = arr.shape[0]
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h = arr.shape[1]
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# Note: we could use the same method as used by PolyLineROI, but this
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# implementation produces a nicer mask.
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arr = ROI.getArrayRegion(self, arr, img, axes, **kwds)
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if arr is None or arr.shape[axes[0]] == 0 or arr.shape[axes[1]] == 0:
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return arr
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w = arr.shape[axes[0]]
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h = arr.shape[axes[1]]
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## generate an ellipsoidal mask
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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))
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# reshape to match array axes
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if axes[0] > axes[1]:
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mask = mask.T
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shape = [(n if i in axes else 1) for i,n in enumerate(arr.shape)]
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mask = mask.reshape(shape)
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return arr * mask
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def shape(self):
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@ -1775,6 +1811,7 @@ class PolygonROI(ROI):
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#sc['handles'] = self.handles
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return sc
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class PolyLineROI(ROI):
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"""
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Container class for multiple connected LineSegmentROIs.
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@ -1923,20 +1960,10 @@ class PolyLineROI(ROI):
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return len(self.handles) > 2
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def paint(self, p, *args):
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#for s in self.segments:
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#s.update()
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#p.setPen(self.currentPen)
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#p.setPen(fn.mkPen('w'))
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#p.drawRect(self.boundingRect())
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#p.drawPath(self.shape())
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pass
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def boundingRect(self):
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return self.shape().boundingRect()
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#r = QtCore.QRectF()
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#for h in self.handles:
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#r |= self.mapFromItem(h['item'], h['item'].boundingRect()).boundingRect() ## |= gives the union of the two QRectFs
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#return r
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def shape(self):
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p = QtGui.QPainterPath()
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@ -1948,30 +1975,18 @@ class PolyLineROI(ROI):
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p.lineTo(self.handles[0]['item'].pos())
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return p
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def getArrayRegion(self, data, img, axes=(0,1), returnMappedCoords=False, **kwds):
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def getArrayRegion(self, data, img, axes=(0,1)):
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"""
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Return the result of ROI.getArrayRegion(), masked by the shape of the
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ROI. Values outside the ROI shape are set to 0.
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"""
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sl = self.getArraySlice(data, img, axes=(0,1))
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if sl is None:
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return None
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sliced = data[sl[0]]
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im = QtGui.QImage(sliced.shape[axes[0]], sliced.shape[axes[1]], QtGui.QImage.Format_ARGB32)
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im.fill(0x0)
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p = QtGui.QPainter(im)
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p.setPen(fn.mkPen(None))
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p.setBrush(fn.mkBrush('w'))
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p.setTransform(self.itemTransform(img)[0])
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bounds = self.mapRectToItem(img, self.boundingRect())
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p.translate(-bounds.left(), -bounds.top())
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p.drawPath(self.shape())
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p.end()
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mask = fn.imageToArray(im)[:,:,0].astype(float) / 255.
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sliced = ROI.getArrayRegion(self, data, img, axes=axes, fromBoundingRect=True)
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mask = self.renderShapeMask(sliced.shape[axes[0]], sliced.shape[axes[1]])
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shape = [1] * data.ndim
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shape[axes[0]] = sliced.shape[axes[0]]
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shape[axes[1]] = sliced.shape[axes[1]]
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return sliced * mask.reshape(shape)
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mask = mask.reshape(shape)
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return sliced * mask
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def setPen(self, *args, **kwds):
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ROI.setPen(self, *args, **kwds)
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@ -1042,7 +1042,6 @@ class ViewBox(GraphicsWidget):
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finally:
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view.blockLink(False)
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def screenGeometry(self):
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"""return the screen geometry of the viewbox"""
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v = self.getViewWidget()
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@ -1053,8 +1052,6 @@ class ViewBox(GraphicsWidget):
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pos = v.mapToGlobal(v.pos())
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wr.adjust(pos.x(), pos.y(), pos.x(), pos.y())
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return wr
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def itemsChanged(self):
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## called when items are added/removed from self.childGroup
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@ -1067,18 +1064,23 @@ class ViewBox(GraphicsWidget):
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self.update()
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#self.updateAutoRange()
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def _invertAxis(self, ax, inv):
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key = 'xy'[ax] + 'Inverted'
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if self.state[key] == inv:
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return
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self.state[key] = inv
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self._matrixNeedsUpdate = True # updateViewRange won't detect this for us
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self.updateViewRange()
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self.update()
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self.sigStateChanged.emit(self)
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self.sigYRangeChanged.emit(self, tuple(self.state['viewRange'][ax]))
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def invertY(self, b=True):
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"""
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By default, the positive y-axis points upward on the screen. Use invertY(True) to reverse the y-axis.
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"""
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if self.state['yInverted'] == b:
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return
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self.state['yInverted'] = b
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self._matrixNeedsUpdate = True # updateViewRange won't detect this for us
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self.updateViewRange()
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self.sigStateChanged.emit(self)
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self.sigYRangeChanged.emit(self, tuple(self.state['viewRange'][1]))
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self._invertAxis(1, b)
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def yInverted(self):
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return self.state['yInverted']
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@ -1087,14 +1089,7 @@ class ViewBox(GraphicsWidget):
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"""
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By default, the positive x-axis points rightward on the screen. Use invertX(True) to reverse the x-axis.
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"""
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if self.state['xInverted'] == b:
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return
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self.state['xInverted'] = b
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#self.updateMatrix(changed=(False, True))
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self.updateViewRange()
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self.sigStateChanged.emit(self)
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self.sigXRangeChanged.emit(self, tuple(self.state['viewRange'][0]))
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self._invertAxis(0, b)
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def xInverted(self):
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return self.state['xInverted']
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@ -12,6 +12,7 @@ def test_getArrayRegion():
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(pg.ROI([1, 1], [27, 28], pen='y'), 'baseroi'),
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(pg.RectROI([1, 1], [27, 28], pen='y'), 'rectroi'),
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(pg.EllipseROI([1, 1], [27, 28], pen='y'), 'ellipseroi'),
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(pg.PolyLineROI([[0, 0], [27, 0], [0, 28]], closed=True), 'polylineroi'),
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]
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for roi, name in rois:
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check_getArrayRegion(roi, name)
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@ -45,7 +46,7 @@ def check_getArrayRegion(roi, name):
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vb1.addItem(roi)
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rgn = roi.getArrayRegion(data, img1, axes=(1, 2))
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assert np.all(rgn == data[:, 1:-2, 1:-2, :])
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#assert np.all((rgn == data[:, 1:-2, 1:-2, :]) | (rgn == 0))
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img2.setImage(rgn[0, ..., 0])
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vb2.setAspectLocked()
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vb2.enableAutoRange(True, True)
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@ -111,6 +112,9 @@ def check_getArrayRegion(roi, name):
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# restore state
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# getarrayregion
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# getarrayslice
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# returnMappedCoords
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# getAffineSliceParams
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# getGlobalTransform
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#
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# test conditions:
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# y inverted
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