def testEverythingDirtyPropagation( self ):
self.lsm.append(self.layer2)
tiling = Tiling((900,400), blockSize=100)
tp = TileProvider(tiling, self.pump.stackedImageSources)
try:
tp.requestRefresh(QRectF(100,100,200,200))
tp.join()
tiles = tp.getTiles(QRectF(100,100,200,200))
for tile in tiles:
aimg = byte_view(tile.qimg)
self.assertTrue(np.all(aimg[:,:,0:3] == self.CONSTANT))
self.assertTrue(np.all(aimg[:,:,3] == 255))
NEW_CONSTANT = self.CONSTANT+1
self.ds2.constant = NEW_CONSTANT
tp.requestRefresh(QRectF(100,100,200,200))
tp.join()
tiles = tp.getTiles(QRectF(100,100,200,200))
for tile in tiles:
aimg = byte_view(tile.qimg)
self.assertTrue(np.all(aimg[:,:,0:3] == NEW_CONSTANT))
self.assertTrue(np.all(aimg[:,:,3] == 255))
finally:
tp.notifyThreadsToStop()
tp.joinThreads()
def testEverythingDirtyPropagation(self):
self.lsm.append(self.layer2)
tiling = Tiling((900, 400), blockSize=100)
tp = TileProvider(tiling, self.pump.stackedImageSources)
try:
tp.requestRefresh(QRectF(100, 100, 200, 200))
tp.join()
tiles = tp.getTiles(QRectF(100, 100, 200, 200))
for tile in tiles:
aimg = byte_view(tile.qimg)
self.assertTrue(np.all(aimg[:, :, 0:3] == self.CONSTANT))
self.assertTrue(np.all(aimg[:, :, 3] == 255))
NEW_CONSTANT = self.CONSTANT + 1
self.ds2.constant = NEW_CONSTANT
tp.requestRefresh(QRectF(100, 100, 200, 200))
tp.join()
tiles = tp.getTiles(QRectF(100, 100, 200, 200))
for tile in tiles:
aimg = byte_view(tile.qimg)
self.assertTrue(np.all(aimg[:, :, 0:3] == NEW_CONSTANT))
self.assertTrue(np.all(aimg[:, :, 3] == 255))
finally:
tp.notifyThreadsToStop()
tp.joinThreads()
def testSetAllLayersInvisible( self ):
tiling = Tiling((900,400), blockSize=100)
tp = TileProvider(tiling, self.sims)
try:
tp.requestRefresh(QRectF(100,100,200,200))
tp.join()
tiles = tp.getTiles(QRectF(100,100,200,200))
for tile in tiles:
aimg = byte_view(tile.qimg)
self.assertTrue(np.all(aimg[:,:,0:3] == self.GRAY3))
self.assertTrue(np.all(aimg[:,:,3] == 255))
self.layer1.visible = False
self.layer2.visible = False
self.layer3.visible = False
tp.requestRefresh(QRectF(100,100,200,200))
tp.join()
tiles = tp.getTiles(QRectF(100,100,200,200))
for tile in tiles:
aimg = byte_view(tile.qimg)
self.assertTrue(np.all(aimg[:,:,0:3] == 255)) # all white
self.assertTrue(np.all(aimg[:,:,3] == 255))
self.layer1.visible = False
self.layer2.visible = True
self.layer2.opacity = 1.0
self.layer3.visible = False
tp.requestRefresh(QRectF(100,100,200,200))
tp.join()
tiles = tp.getTiles(QRectF(100,100,200,200))
for tile in tiles:
aimg = byte_view(tile.qimg)
self.assertTrue(np.all(aimg[:,:,0:3] == self.GRAY2))
self.assertTrue(np.all(aimg[:,:,3] == 255))
finally:
tp.notifyThreadsToStop()
tp.joinThreads()
def testSetAllLayersInvisible(self):
tiling = Tiling((900, 400), blockSize=100)
tp = TileProvider(tiling, self.sims)
try:
tp.requestRefresh(QRectF(100, 100, 200, 200))
tp.join()
tiles = tp.getTiles(QRectF(100, 100, 200, 200))
for tile in tiles:
aimg = byte_view(tile.qimg)
self.assertTrue(np.all(aimg[:, :, 0:3] == self.GRAY3))
self.assertTrue(np.all(aimg[:, :, 3] == 255))
self.layer1.visible = False
self.layer2.visible = False
self.layer3.visible = False
tp.requestRefresh(QRectF(100, 100, 200, 200))
tp.join()
tiles = tp.getTiles(QRectF(100, 100, 200, 200))
for tile in tiles:
# If all tiles are invisible, then no tile is even rendered at all.
assert tile.qimg is None
self.layer1.visible = False
self.layer2.visible = True
self.layer2.opacity = 1.0
self.layer3.visible = False
tp.requestRefresh(QRectF(100, 100, 200, 200))
tp.join()
tiles = tp.getTiles(QRectF(100, 100, 200, 200))
for tile in tiles:
aimg = byte_view(tile.qimg)
self.assertTrue(np.all(aimg[:, :, 0:3] == self.GRAY2))
self.assertTrue(np.all(aimg[:, :, 3] == 255))
finally:
tp.notifyThreadsToStop()
tp.joinThreads()
def testOutOfViewDirtyPropagation( self ):
self.lsm.append(self.layer1)
tiling = Tiling((900,400), blockSize=100)
tp = TileProvider(tiling, self.pump.stackedImageSources)
try:
# Navigate down to the second z-slice
self.pump.syncedSliceSources.through = [0,1,0]
tp.requestRefresh(QRectF(100,100,200,200))
tp.join()
# Sanity check: Do we see the right data on the second slice? (should be all 1s)
tiles = tp.getTiles(QRectF(100,100,200,200))
for tile in tiles:
aimg = byte_view(tile.qimg)
self.assertTrue(np.all(aimg[:,:,0:3] == 1))
self.assertTrue(np.all(aimg[:,:,3] == 255))
# Navigate down to the third z-slice
self.pump.syncedSliceSources.through = [0,2,0]
tp.requestRefresh(QRectF(100,100,200,200))
tp.join()
# Sanity check: Do we see the right data on the third slice?(should be all 2s)
tiles = tp.getTiles(QRectF(100,100,200,200))
for tile in tiles:
aimg = byte_view(tile.qimg)
self.assertTrue(np.all(aimg[:,:,0:3] == 2))
self.assertTrue(np.all(aimg[:,:,3] == 255))
# Navigate back up to the second z-slice
self.pump.syncedSliceSources.through = [0,1,0]
tp.requestRefresh(QRectF(100,100,200,200))
tp.join()
for tile in tiles:
aimg = byte_view(tile.qimg)
self.assertTrue(np.all(aimg[:,:,0:3] == 1))
self.assertTrue(np.all(aimg[:,:,3] == 255))
# Change some of the data in the (out-of-view) third z-slice
slicing = (slice(None), slice(100,300), slice(100,300), slice(2,3), slice(None))
slicing = tuple(slicing)
self.ds1._array[slicing] = 99
self.ds1.setDirty( slicing )
# Navigate back down to the third z-slice
self.pump.syncedSliceSources.through = [0,2,0]
tp.requestRefresh(QRectF(100,100,200,200))
tp.join()
# Even though the data was out-of-view when it was changed, it should still have new values.
# If dirtiness wasn't propagated correctly, the cache's old values will be used.
# (For example, this fails if you comment out the call to setDirty, above.)
tiles = tp.getTiles(QRectF(100,100,200,200))
for tile in tiles:
aimg = byte_view(tile.qimg)
# Use any() because the tile borders may not be perfectly aligned with the data we changed.
self.assertTrue(np.any(aimg[:,:,0:3] == 99))
finally:
tp.notifyThreadsToStop()
tp.joinThreads()
def testOutOfViewDirtyPropagation(self):
self.lsm.append(self.layer1)
tiling = Tiling((900, 400), blockSize=100)
tp = TileProvider(tiling, self.pump.stackedImageSources)
try:
# Navigate down to the second z-slice
self.pump.syncedSliceSources.through = [0, 1, 0]
tp.requestRefresh(QRectF(100, 100, 200, 200))
tp.join()
# Sanity check: Do we see the right data on the second
# slice? (should be all 1s)
tiles = tp.getTiles(QRectF(100, 100, 200, 200))
for tile in tiles:
aimg = byte_view(tile.qimg)
self.assertTrue(np.all(aimg[:, :, 0:3] == 1))
self.assertTrue(np.all(aimg[:, :, 3] == 255))
# Navigate down to the third z-slice
self.pump.syncedSliceSources.through = [0, 2, 0]
tp.requestRefresh(QRectF(100, 100, 200, 200))
tp.join()
# Sanity check: Do we see the right data on the third
# slice?(should be all 2s)
tiles = tp.getTiles(QRectF(100, 100, 200, 200))
for tile in tiles:
aimg = byte_view(tile.qimg)
self.assertTrue(np.all(aimg[:, :, 0:3] == 2))
self.assertTrue(np.all(aimg[:, :, 3] == 255))
# Navigate back up to the second z-slice
self.pump.syncedSliceSources.through = [0, 1, 0]
tp.requestRefresh(QRectF(100, 100, 200, 200))
tp.join()
for tile in tiles:
aimg = byte_view(tile.qimg)
self.assertTrue(np.all(aimg[:, :, 0:3] == 1))
self.assertTrue(np.all(aimg[:, :, 3] == 255))
# Change some of the data in the (out-of-view) third z-slice
slicing = (slice(None), slice(100, 300), slice(100, 300),
slice(2, 3), slice(None))
slicing = tuple(slicing)
self.ds1._array[slicing] = 99
self.ds1.setDirty(slicing)
# Navigate back down to the third z-slice
self.pump.syncedSliceSources.through = [0, 2, 0]
tp.requestRefresh(QRectF(100, 100, 200, 200))
tp.join()
# Even though the data was out-of-view when it was
# changed, it should still have new values. If dirtiness
# wasn't propagated correctly, the cache's old values will
# be used. (For example, this fails if you comment out the
# call to setDirty, above.)
# Shrink accessed rect by 1 pixel on each side (Otherwise,
# tiling overlap_draw causes getTiles() to return
# surrounding tiles that we haven't actually touched in
# this test)
tiles = tp.getTiles(QRectF(101, 101, 198, 198))
for tile in tiles:
aimg = byte_view(tile.qimg)
# Use any() because the tile borders may not be
# perfectly aligned with the data we changed.
self.assertTrue(np.any(aimg[:, :, 0:3] == 99))
finally:
tp.notifyThreadsToStop()
tp.joinThreads()
class ImageScene2D(QGraphicsScene):
"""
The 2D scene description of a tiled image generated by evaluating
an overlay stack, together with a 2D cursor.
"""
axesChanged = pyqtSignal(int, bool)
@property
def stackedImageSources(self):
return self._stackedImageSources
@stackedImageSources.setter
def stackedImageSources(self, s):
self._stackedImageSources = s
s.sizeChanged.connect(self._onSizeChanged)
@property
def showTileOutlines(self):
return self._showTileOutlines
@showTileOutlines.setter
def showTileOutlines(self, show):
self._showTileOutlines = show
self.invalidate()
@property
def showTileProgress(self):
return self._showTileProgress
@showTileProgress.setter
def showTileProgress(self, show):
self._showTileProgress = show
self._dirtyIndicator.setVisible(show)
def resetAxes(self, finish=True):
# rotation is in range(4) and indicates in which corner of the
# view the origin lies. 0 = top left, 1 = top right, etc.
self._rotation = 0
self._swapped = self._swappedDefault # whether axes are swapped
self._newAxes()
self._setSceneRect()
self.scene2data, isInvertible = self.data2scene.inverted()
assert isInvertible
if finish:
self._finishViewMatrixChange()
def _newAxes(self):
"""Given self._rotation and self._swapped, calculates and sets
the appropriate data2scene transformation.
"""
# TODO: this function works, but it is not elegant. There must
# be a simpler way to calculate the appropriate tranformation.
w, h = self.dataShape
assert self._rotation in range(0, 4)
# unlike self._rotation, the local variable 'rotation'
# indicates how many times to rotate clockwise after swapping
# axes.
# t1 : do axis swap
t1 = QTransform()
if self._swapped:
t1 = QTransform(0, 1, 0, 1, 0, 0, 0, 0, 1)
h, w = w, h
# t2 : do rotation
t2 = QTransform()
t2.rotate(self._rotation * 90)
# t3: shift to re-center
rot2trans = {0 : (0, 0),
1 : (h, 0),
2 : (w, h),
3 : (0, w)}
trans = rot2trans[self._rotation]
t3 = QTransform.fromTranslate(*trans)
self.data2scene = t1 * t2 * t3
if self._tileProvider:
self._tileProvider.axesSwapped = self._swapped
self.axesChanged.emit(self._rotation, self._swapped)
def rot90(self, transform, rect, direction):
""" direction: left ==> -1, right ==> +1"""
assert direction in [-1, 1]
self._rotation = (self._rotation + direction) % 4
self._newAxes()
def swapAxes(self, transform):
self._swapped = not self._swapped
self._newAxes()
def _onRotateLeft(self):
self.rot90(self.data2scene, self.sceneRect(), -1)
self._finishViewMatrixChange()
def _onRotateRight(self):
self.rot90(self.data2scene, self.sceneRect(), 1)
self._finishViewMatrixChange()
def _onSwapAxes(self):
self.swapAxes(self.data2scene)
self._finishViewMatrixChange()
def _finishViewMatrixChange(self):
self.scene2data, isInvertible = self.data2scene.inverted()
self._setSceneRect()
self._tiling.data2scene = self.data2scene
self._tileProvider._onSizeChanged()
QGraphicsScene.invalidate(self, self.sceneRect())
@property
def sceneShape(self):
return (self.sceneRect().width(), self.sceneRect().height())
def _setSceneRect(self):
w, h = self.dataShape
rect = self.data2scene.mapRect(QRect(0, 0, w, h))
sw, sh = rect.width(), rect.height()
self.setSceneRect(0, 0, sw, sh)
@property
def dataShape(self):
"""
The shape of the scene in QGraphicsView's coordinate system.
"""
return self._dataShape
@dataShape.setter
def dataShape(self, value):
"""
Set the size of the scene in QGraphicsView's coordinate system.
dataShape -- (widthX, widthY),
where the origin of the coordinate system is in the upper left corner
of the screen and 'x' points right and 'y' points down
"""
assert len(value) == 2
self._dataShape = value
self.reset()
self._finishViewMatrixChange()
def setCacheSize(self, cache_size):
if cache_size != self._tileProvider._cache_size:
self._tileProvider = TileProvider(self._tiling, self._stackedImageSources, cache_size=cache_size)
self._tileProvider.sceneRectChanged.connect(self.invalidateViewports)
def cacheSize(self):
return self._tileProvider._cache_size
def setPrefetchingEnabled(self, enable):
self._prefetching_enabled = enable
def setPreemptiveFetchNumber(self, n):
if n > self.cacheSize() - 1:
self._n_preemptive = self.cacheSize() - 1
else:
self._n_preemptive = n
def preemptiveFetchNumber(self):
return self._n_preemptive
def invalidateViewports(self, sceneRectF):
'''Call invalidate on the intersection of all observing viewport-rects and rectF.'''
sceneRectF = sceneRectF if sceneRectF.isValid() else self.sceneRect()
for view in self.views():
QGraphicsScene.invalidate(self, sceneRectF.intersected(view.viewportRect()))
def reset(self):
"""Reset rotations, tiling, etc. Called when first initialized
and when the underlying data changes.
"""
self.resetAxes(finish=False)
self._tiling = Tiling(self._dataShape, self.data2scene, name=self.name)
self._brushingLayer = TiledImageLayer(self._tiling)
if self._tileProvider:
self._tileProvider.notifyThreadsToStop() # prevent ref cycle
self._tileProvider = TileProvider(self._tiling, self._stackedImageSources)
self._tileProvider.sceneRectChanged.connect(self.invalidateViewports)
if self._dirtyIndicator:
self.removeItem(self._dirtyIndicator)
del self._dirtyIndicator
self._dirtyIndicator = DirtyIndicator(self._tiling)
self.addItem(self._dirtyIndicator)
def __init__(self, posModel, along, preemptive_fetch_number=5,
parent=None, name="Unnamed Scene",
swapped_default=False):
"""
* preemptive_fetch_number -- number of prefetched slices; 0 turns the feature off
* swapped_default -- whether axes should be swapped by default.
"""
QGraphicsScene.__init__(self, parent=parent)
self._along = along
self._posModel = posModel
self._dataShape = (0, 0)
self._offsetX = 0
self._offsetY = 0
self.name = name
self._stackedImageSources = StackedImageSources(LayerStackModel())
self._showTileOutlines = False
self._showTileProgress = True
self._tileProvider = None
self._dirtyIndicator = None
self._prefetching_enabled = False
self._swappedDefault = swapped_default
self.reset()
# BowWave preemptive caching
self.setPreemptiveFetchNumber(preemptive_fetch_number)
self._course = (1,1) # (along, pos or neg direction)
self._time = self._posModel.time
self._channel = self._posModel.channel
self._posModel.timeChanged.connect(self._onTimeChanged)
self._posModel.channelChanged.connect(self._onChannelChanged)
self._posModel.slicingPositionChanged.connect(self._onSlicingPositionChanged)
self._allTilesCompleteEvent = threading.Event()
def __del__(self):
if self._tileProvider:
self._tileProvider.notifyThreadsToStop()
self.joinRendering()
def _onSizeChanged(self):
self._brushingLayer = TiledImageLayer(self._tiling)
def drawForeground(self, painter, rect):
if self._tiling is None:
return
tile_nos = self._tiling.intersected(rect)
for tileId in tile_nos:
p = self._brushingLayer[tileId]
if p.dataVer == p.imgVer:
continue
p.paint(painter) #access to the underlying image patch is serialized
## draw tile outlines
if self._showTileOutlines:
# Dashed black line
pen = QPen()
pen.setDashPattern([5,5])
painter.setPen(pen)
painter.drawRect(self._tiling.imageRects[tileId])
# Dashed white line
# (offset to occupy the spaces in the dashed black line)
pen = QPen()
pen.setDashPattern([5,5])
pen.setDashOffset(5)
pen.setColor(QColor(Qt.white))
painter.setPen(pen)
painter.drawRect(self._tiling.imageRects[tileId])
def indicateSlicingPositionSettled(self, settled):
if self._showTileProgress:
self._dirtyIndicator.setVisible(settled)
def drawBackground(self, painter, sceneRectF):
if self._tileProvider is None:
return
tiles = self._tileProvider.getTiles(sceneRectF)
allComplete = True
for tile in tiles:
#We always draw the tile, even though it might not be up-to-date
#In ilastik's live mode, the user sees the old result while adding
#new brush strokes on top
#See also ilastik issue #132 and tests/lazy_test.py
if tile.qimg is not None:
painter.drawImage(tile.rectF, tile.qimg)
if tile.progress < 1.0:
allComplete = False
if self._showTileProgress:
self._dirtyIndicator.setTileProgress(tile.id, tile.progress)
if allComplete:
self._allTilesCompleteEvent.set()
else:
self._allTilesCompleteEvent.clear()
# preemptive fetching
if self._prefetching_enabled:
for through in self._bowWave(self._n_preemptive):
self._tileProvider.prefetch(sceneRectF, through)
def joinRendering(self):
return self._tileProvider.join()
def joinRenderingAllTiles(self):
"""
Wait until all tiles in the scene have been 100% rendered.
Note: This is useful for testing only. If called from the GUI thread, the GUI thread will block until all tiles are rendered!
"""
# If this is the main thread, keep repainting (otherwise we'll deadlock).
if threading.current_thread().name == "MainThread":
finished = False
sceneRectF = self.views()[0].viewportRect()
while not finished:
finished = True
tiles = self._tileProvider.getTiles(sceneRectF)
for tile in tiles:
finished &= tile.progress >= 1.0
else:
self._allTilesCompleteEvent.wait()
def _bowWave(self, n):
shape5d = self._posModel.shape5D
sl5d = self._posModel.slicingPos5D
through = [sl5d[self._along[i]] for i in xrange(3)]
t_max = [shape5d[self._along[i]] for i in xrange(3)]
BowWave = []
a = self._course[0]
for d in xrange(1,n+1):
m = through[a] + d * self._course[1]
if m < t_max[a] and m >= 0:
t = list(through)
t[a] = m
BowWave.append(tuple(t))
return BowWave
def _onSlicingPositionChanged(self, new, old):
if (new[self._along[1] - 1] - old[self._along[1] - 1]) < 0:
self._course = (1, -1)
else:
self._course = (1, 1)
def _onChannelChanged(self, new):
if (new - self._channel) < 0:
self._course = (2, -1)
else:
self._course = (2, 1)
self._channel = new
def _onTimeChanged(self, new):
if (new - self._time) < 0:
self._course = (0, -1)
else:
self._course = (0, 1)
self._time = new