def execute(self, slot, subindex, roi, result):
assert slot == self.Output, "Unknown slot: {}".format( slot.name )
radius = self.CrosshairRadius.value
points = map(TinyVector, self.PointList.value)
result[:] = 0
result_view = result.view(vigra.VigraArray)
result_view.axistags = self.Output.meta.axistags
result_3d = result_view.withAxes(*'xyz')
axiskeys = self.Output.meta.getAxisKeys()
roi_start_3d = TinyVector(roi.start)
roi_stop_3d = TinyVector(roi.stop)
try:
roi_start_3d.pop( axiskeys.index('c') )
roi_stop_3d.pop( axiskeys.index('c') )
except ValueError:
pass
try:
roi_start_3d.pop( axiskeys.index('t') )
roi_stop_3d.pop( axiskeys.index('t') )
except ValueError:
pass
for point3d in points:
point3d -= roi_start_3d
cross_min = point3d - radius
cross_max = point3d + radius+1
# If the cross would be entirely out-of-view, skip it.
if (cross_max < [0,0,0]).any() or \
(cross_min >= result_3d.shape).any():
continue
cross_min = numpy.maximum(cross_min, (0,0,0))
cross_max = numpy.minimum(cross_max, result_3d.shape)
x,y,z = point3d
x1,y1,z1 = cross_min
x2,y2,z2 = cross_max
if 0 <= y < result_3d.shape[1] and 0 <= z < result_3d.shape[2]:
result_3d[x1:x2, y, z ] = 1
if 0 <= x < result_3d.shape[0] and 0 <= z < result_3d.shape[2]:
result_3d[x, y1:y2, z ] = 1
if 0 <= x < result_3d.shape[0] and 0 <= y < result_3d.shape[1]:
result_3d[x, y, z1:z2] = 1
return result
def execute(self, slot, subindex, roi, result):
assert slot == self.Output, "Unknown slot: {}".format(slot.name)
radius = self.CrosshairRadius.value
points = map(TinyVector, self.PointList.value)
result[:] = 0
result_view = result.view(vigra.VigraArray)
result_view.axistags = self.Output.meta.axistags
result_3d = result_view.withAxes(*'xyz')
axiskeys = self.Output.meta.getAxisKeys()
roi_start_3d = TinyVector(roi.start)
roi_stop_3d = TinyVector(roi.stop)
try:
roi_start_3d.pop(axiskeys.index('c'))
roi_stop_3d.pop(axiskeys.index('c'))
except ValueError:
pass
try:
roi_start_3d.pop(axiskeys.index('t'))
roi_stop_3d.pop(axiskeys.index('t'))
except ValueError:
pass
for point3d in points:
point3d -= roi_start_3d
cross_min = point3d - radius
cross_max = point3d + radius + 1
# If the cross would be entirely out-of-view, skip it.
if (cross_max < [0,0,0]).any() or \
(cross_min >= result_3d.shape).any():
continue
cross_min = numpy.maximum(cross_min, (0, 0, 0))
cross_max = numpy.minimum(cross_max, result_3d.shape)
x, y, z = point3d
x1, y1, z1 = cross_min
x2, y2, z2 = cross_max
if 0 <= y < result_3d.shape[1] and 0 <= z < result_3d.shape[2]:
result_3d[x1:x2, y, z] = 1
if 0 <= x < result_3d.shape[0] and 0 <= z < result_3d.shape[2]:
result_3d[x, y1:y2, z] = 1
if 0 <= x < result_3d.shape[0] and 0 <= y < result_3d.shape[1]:
result_3d[x, y, z1:z2] = 1
return result
class SubRegion(Roi):
def __init__(self, slot, start = None, stop = None, pslice = None):
super(SubRegion,self).__init__(slot)
shape = None
if slot is not None:
shape = slot.meta.shape
if pslice != None or start is not None and stop is None and pslice is None:
if pslice is None:
pslice = start
if shape is None:
# Okay to use a shapeless slot if the key is bounded
# AND if the key has the correct length
assert slicingtools.is_bounded(pslice)
# Supply a dummy shape
shape = [0] * len(pslice)
self.start, self.stop = sliceToRoi(pslice,shape)
elif start is None and pslice is None:
assert shape is not None, "Can't create a default subregion without a slot and a shape."
self.start, self.stop = roiFromShape(shape)
else:
self.start = TinyVector(start)
self.stop = TinyVector(stop)
self.dim = len(self.start)
for start, stop in zip(self.start, self.stop):
assert isinstance(start, (int, long, numpy.integer)), "Roi contains non-integers: {}".format( self )
assert isinstance(start, (int, long, numpy.integer)), "Roi contains non-integers: {}".format( self )
# FIXME: This assertion is good at finding bugs, but it is currently triggered by
# the DataExport applet when the output axis order is changed.
#
# if self.slot is not None self.slot.meta.shape is not None:
# assert all(self.stop <= self.slot.meta.shape), \
# "Roi is out of bounds. roi={}, {}.{}.meta.shape={}"\
# .format((self.start, self.stop), slot.getRealOperator().name, slot.name, self.slot.meta.shape)
def __setstate__(self, state):
"""
Support copy.copy()
"""
self.slot = state['slot']
self.start = TinyVector( state['start'] )
self.stop = TinyVector( state['stop'] )
self.dim = len( state['start'] )
def __str__( self ):
return "".join(("Subregion: start '", str(self.start), "' stop '", str(self.stop), "'"))
def pprint(self):
"""pretty-print this object"""
ret = ""
for a,b in zip(self.start, self.stop):
ret += "%d-%d " % (a,b)
return ret
@staticmethod
def _toString(roi):
assert isinstance(roi, SubRegion)
assert roi.slot is None, "Can't stringify SubRegions with no slot"
return "SubRegion(None, {}, {})".format(roi.start, roi.stop)
@staticmethod
def _fromString(s):
return eval(s)
def setInputShape(self,inputShape):
assert type(inputShape) == tuple
self.inputShape = inputShape
def copy(self):
return copy.copy(self)
def popDim(self, dim):
"""
remove the i'th dimension from the SubRegion
works inplace !
"""
if dim is not None:
self.start.pop(dim)
self.stop.pop(dim)
return self
def setDim(self, dim , start, stop):
"""
change the subarray at dim, to begin at start
and to end at stop
"""
self.start[dim] = start
self.stop[dim] = stop
return self
def insertDim(self, dim, start, stop):
"""
insert a new dimension before dim.
set start to start, stop to stop
and the axistags to at
"""
self.start = self.start.insert(dim,start)
self.stop = self.stop.insert(dim,stop)
return self
def expandByShape(self,shape,cIndex,tIndex):
"""
extend a roi by a given in shape
"""
#TODO: Warn if bounds are exceeded
cStart = self.start[cIndex]
cStop = self.stop[cIndex]
if tIndex is not None:
tStart = self.start[tIndex]
tStop = self.stop[tIndex]
if isinstance(shape, collections.Iterable):
#add a dummy number for the channel dimension
shape = shape+(1,)
else:
tmp = shape
shape = numpy.zeros(self.dim).astype(int)
shape[:] = tmp
tmpStart = [int(x-s) for x,s in zip(self.start,shape)]
tmpStop = [int(x+s) for x,s in zip(self.stop,shape)]
start = [int(max(t,i)) for t,i in zip(tmpStart,numpy.zeros_like(self.inputShape))]
stop = [int(min(t,i)) for t,i in zip(tmpStop,self.inputShape)]
start[cIndex] = cStart
stop[cIndex] = cStop
if tIndex is not None:
start[tIndex] = tStart
stop[tIndex] = tStop
self.start = TinyVector(start)
self.stop = TinyVector(stop)
return self
def adjustRoi(self,halo,cIndex=None):
if type(halo) != list:
halo = [halo]*len(self.start)
notAtStartEgde = map(lambda x,y: True if x<y else False,halo,self.start)
for i in range(len(notAtStartEgde)):
if notAtStartEgde[i]:
self.stop[i] = int(self.stop[i]-self.start[i]+halo[i])
self.start[i] = int(halo[i])
return self
def adjustChannel(self,cPerC,cIndex,channelRes):
if cPerC != 1 and channelRes == 1:
start = [self.start[i]/cPerC if i == cIndex else self.start[i] for i in range(len(self.start))]
stop = [self.stop[i]/cPerC+1 if i==cIndex else self.stop[i] for i in range(len(self.stop))]
self.start = TinyVector(start)
self.stop = TinyVector(stop)
elif channelRes > 1:
start = [0 if i == cIndex else self.start[i] for i in range(len(self.start))]
stop = [channelRes if i==cIndex else self.stop[i] for i in range(len(self.stop))]
self.start = TinyVector(start)
self.stop = TinyVector(stop)
return self
def toSlice(self, hardBind = False):
return roiToSlice(self.start,self.stop, hardBind)
class SubRegion(Roi):
def __init__(self, slot, start=None, stop=None, pslice=None):
super(SubRegion, self).__init__(slot)
if pslice != None or start is not None and stop is None and pslice is None:
if pslice is None:
pslice = start
shape = self.slot.meta.shape
if shape is None:
# Okay to use a shapeless slot if the key is bounded
# AND if the key has the correct length
assert slicingtools.is_bounded(pslice)
# Supply a dummy shape
shape = [0] * len(pslice)
self.start, self.stop = sliceToRoi(pslice, shape)
elif start is None and pslice is None:
self.start, self.stop = sliceToRoi(slice(None, None, None), self.slot.meta.shape)
else:
self.start = TinyVector(start)
self.stop = TinyVector(stop)
self.dim = len(self.start)
def __str__(self):
return "".join(("Subregion: start '", str(self.start), "' stop '", str(self.stop), "'"))
@staticmethod
def _toString(roi):
assert isinstance(roi, SubRegion)
assert roi.slot is None, "Can't stringify SubRegions with no slot"
return "SubRegion(None, {}, {})".format(roi.start, roi.stop)
@staticmethod
def _fromString(s):
return eval(s)
def setInputShape(self, inputShape):
assert type(inputShape) == tuple
self.inputShape = inputShape
def copy(self):
return copy.copy(self)
def popDim(self, dim):
"""
remove the i'th dimension from the SubRegion
works inplace !
"""
if dim is not None:
self.start.pop(dim)
self.stop.pop(dim)
return self
def setDim(self, dim, start, stop):
"""
change the subarray at dim, to begin at start
and to end at stop
"""
self.start[dim] = start
self.stop[dim] = stop
return self
def insertDim(self, dim, start, stop, at):
"""
insert a new dimension before dim.
set start to start, stop to stop
and the axistags to at
"""
self.start.insert(0, start)
self.stop.insert(0, stop)
return self
def expandByShape(self, shape, cIndex, tIndex):
"""
extend a roi by a given in shape
"""
# TODO: Warn if bounds are exceeded
cStart = self.start[cIndex]
cStop = self.stop[cIndex]
if tIndex is not None:
tStart = self.start[tIndex]
tStop = self.stop[tIndex]
if isinstance(shape, collections.Iterable):
# add a dummy number for the channel dimension
shape = shape + (1,)
else:
tmp = shape
shape = numpy.zeros(self.dim).astype(int)
shape[:] = tmp
tmpStart = [int(x - s) for x, s in zip(self.start, shape)]
tmpStop = [int(x + s) for x, s in zip(self.stop, shape)]
start = [int(max(t, i)) for t, i in zip(tmpStart, numpy.zeros_like(self.inputShape))]
stop = [int(min(t, i)) for t, i in zip(tmpStop, self.inputShape)]
start[cIndex] = cStart
stop[cIndex] = cStop
if tIndex is not None:
start[tIndex] = tStart
stop[tIndex] = tStop
self.start = TinyVector(start)
self.stop = TinyVector(stop)
return self
def adjustRoi(self, halo, cIndex=None):
if type(halo) != list:
halo = [halo] * len(self.start)
notAtStartEgde = map(lambda x, y: True if x < y else False, halo, self.start)
for i in range(len(notAtStartEgde)):
if notAtStartEgde[i]:
self.stop[i] = int(self.stop[i] - self.start[i] + halo[i])
self.start[i] = int(halo[i])
return self
def adjustChannel(self, cPerC, cIndex, channelRes):
if cPerC != 1 and channelRes == 1:
start = [self.start[i] / cPerC if i == cIndex else self.start[i] for i in range(len(self.start))]
stop = [self.stop[i] / cPerC + 1 if i == cIndex else self.stop[i] for i in range(len(self.stop))]
self.start = TinyVector(start)
self.stop = TinyVector(stop)
elif channelRes > 1:
start = [0 if i == cIndex else self.start[i] for i in range(len(self.start))]
stop = [channelRes if i == cIndex else self.stop[i] for i in range(len(self.stop))]
self.start = TinyVector(start)
self.stop = TinyVector(stop)
return self
def toSlice(self, hardBind=False):
return roiToSlice(self.start, self.stop, hardBind)
