class OverlayItem(object):
"""
A Item that holds some scalar or multichannel _data and their drawing related settings.
OverlayItems are held by the OverlayMgr
"""
def __init__(self,
data,
color=0,
alpha=0.4,
colorTable=None,
autoAdd=False,
autoVisible=False,
linkColorTable=False,
autoAlphaChannel=True,
min=None,
max=None):
#whether this overlay can be displayed in 3D using
#extraction of meshes
self.displayable3D = False
#if this overlay can be shown in 3D, the list of labels
#that should be suppressed (not shown)
self.backgroundClasses = set()
self.smooth3D = True
self._data = DataAccessor(data)
self.linkColorTable = linkColorTable
self.colorTable = colorTable
self.defaultColor = color
self.linkColor = False
self.colorGetter = None
self.colorGetterArguments = None
self.alpha = alpha
self.autoAlphaChannel = autoAlphaChannel
self.channel = 0
self.name = "Unnamed Overlay"
self.key = "Unknown Key"
self.autoAdd = autoAdd
self.autoVisible = autoVisible
self.references = []
self.min = min
self.max = max
self.overlayMgr = None
def __getitem__(self, args):
return self._data[args]
def __setitem__(self, args, data):
self._data[args] = data
def __getattr__(self, name):
if name == "color":
return self.getColor()
elif name == "dtype":
return self._data.dtype
elif name == "shape":
return self._data.shape
elif name == "dataItemImage":
return self.overlayMgr.dataItem
else:
raise AttributeError, name
def getColorTab(self):
return self.colorTable
def getSubSlice(self, offsets, sizes, num, axis, time=0, channel=0):
return self._data.getSubSlice(offsets, sizes, num, axis, time, channel)
def setSubSlice(self, offsets, data, num, axis, time=0, channel=0):
self._data.setSubSlice(offsets, data, num, axis, time, channel)
def getColor(self):
if self.linkColor is False:
return self.defaultColor
else:
return self.colorGetter()
def setColorGetter(self, colorGetter, colorGetterArguments):
self.colorGetter = colorGetter
self.colorGetterArguments = colorGetterArguments
self.linkColor = True
def getRef(self):
ref = OverlayItemReference(self)
ref.visible = self.autoVisible
self.references.append(ref)
return ref
def remove(self):
for r in self.references:
r.remove()
self.references = []
self._data = None
def changeKey(self, newKey):
if self.overlayMgr is not None:
self.overlayMgr.changeKey(self.key, newKey)
def setData(self, data):
self.overlayItem._data = data
@classmethod
def normalizeForDisplay(cls, data):
import numpy
dmin = numpy.min(data)
data = data - dmin
dmax = numpy.max(data)
data = 255 * data / dmax
return data
@classmethod
def qrgb(cls, r, g, b):
return long(0xff << 24) | ((r & 0xff) << 16) | (
(g & 0xff) << 8) | (b & 0xff)
@classmethod
def qgray(cls, r, g, b):
return (r * 11 + g * 16 + b * 5) / 32
@classmethod
def createDefaultColorTable(cls,
type,
levels=256,
transparentValues=set()):
typeCap = type.capitalize()
colorTab = []
if (typeCap == "GRAY"):
for i in range(levels):
if i in transparentValues:
colorTab.append(0L)
else:
colorTab.append(OverlayItem.qgray(
i, i, i)) # see qGray function in QtGui
else:
#RGB
import numpy
from ilastik.core.randomSeed import RandomSeed
seed = RandomSeed.getRandomSeed()
if seed is not None:
numpy.random.seed(seed)
for i in range(levels):
if i in transparentValues:
colorTab.append(0L)
else:
colorTab.append(
OverlayItem.qrgb(
numpy.random.randint(255),
numpy.random.randint(255), numpy.random.randint(
255))) # see gRGB function in QtGui
return colorTab
@classmethod
# IMPORTANT: BE AWARE THAT CHANGING THE COLOR TABLE MAY AFFECT TESTS THAT WORK WITH GROUND TRUTH
# DATA FROM EXPORTED OVERLAYS. TYPICALLY, ONLY THE DATA AND NOT THE COLOR TABLE OF AN OVERLAY IS
# COMPARED BUT BETTER MAKE SURE THAT THIS IS INDEED THE CASE.
def createDefault16ColorColorTable(cls):
sublist = []
sublist.append(OverlayItem.qrgb(69, 69, 69)) # dark grey
sublist.append(OverlayItem.qrgb(255, 0, 0))
sublist.append(OverlayItem.qrgb(0, 255, 0))
sublist.append(OverlayItem.qrgb(0, 0, 255))
sublist.append(OverlayItem.qrgb(255, 255, 0))
sublist.append(OverlayItem.qrgb(0, 255, 255))
sublist.append(OverlayItem.qrgb(255, 0, 255))
sublist.append(OverlayItem.qrgb(255, 105, 180)) #hot pink!
sublist.append(OverlayItem.qrgb(102, 205, 170)) #dark aquamarine
sublist.append(OverlayItem.qrgb(165, 42, 42)) #brown
sublist.append(OverlayItem.qrgb(0, 0, 128)) #navy
sublist.append(OverlayItem.qrgb(255, 165, 0)) #orange
sublist.append(OverlayItem.qrgb(173, 255, 47)) #green-yellow
sublist.append(OverlayItem.qrgb(128, 0, 128)) #purple
sublist.append(OverlayItem.qrgb(192, 192, 192)) #silver
sublist.append(OverlayItem.qrgb(240, 230, 140)) #khaki
colorlist = []
colorlist.append(long(0))
colorlist.extend(sublist)
import numpy
from ilastik.core.randomSeed import RandomSeed
seed = RandomSeed.getRandomSeed()
if seed is not None:
numpy.random.seed(seed)
for i in range(17, 256):
color = OverlayItem.qrgb(numpy.random.randint(255),
numpy.random.randint(255),
numpy.random.randint(255))
colorlist.append(color)
return colorlist
class OverlayItem(object):
"""
A Item that holds some scalar or multichannel _data and their drawing related settings.
OverlayItems are held by the OverlayMgr
"""
def __init__(self, data, color = 0, alpha = 0.4, colorTable = None, autoAdd = False, autoVisible = False, linkColorTable = False, autoAlphaChannel = True, min = None, max = None):
#whether this overlay can be displayed in 3D using
#extraction of meshes
self.displayable3D = False
#if this overlay can be shown in 3D, the list of labels
#that should be suppressed (not shown)
self.backgroundClasses = set()
self.smooth3D = True
self._data = DataAccessor(data)
self.linkColorTable = linkColorTable
self.colorTable = colorTable
self.defaultColor = color
self.linkColor = False
self.colorGetter = None
self.colorGetterArguments = None
self.alpha = alpha
self.autoAlphaChannel = autoAlphaChannel
self.channel = 0
self.name = "Unnamed Overlay"
self.key = "Unknown Key"
self.autoAdd = autoAdd
self.autoVisible = autoVisible
self.references = []
self.min = min
self.max = max
self.overlayMgr = None
def __getitem__(self, args):
return self._data[args]
def __setitem__(self, args, data):
self._data[args] = data
def __getattr__(self, name):
if name == "color":
return self.getColor()
elif name == "dtype":
return self._data.dtype
elif name == "shape":
return self._data.shape
elif name == "dataItemImage":
return self.overlayMgr.dataItem
else:
raise AttributeError, name
def getColorTab(self):
return self.colorTable
def getSubSlice(self, offsets, sizes, num, axis, time = 0, channel = 0):
return self._data.getSubSlice(offsets, sizes, num, axis, time, channel)
def setSubSlice(self, offsets, data, num, axis, time = 0, channel = 0):
self._data.setSubSlice(offsets, data, num, axis, time, channel)
def getColor(self):
if self.linkColor is False:
return self.defaultColor
else:
return self.colorGetter()
def setColorGetter(self,colorGetter, colorGetterArguments):
self.colorGetter = colorGetter
self.colorGetterArguments = colorGetterArguments
self.linkColor = True
def getRef(self):
ref = OverlayItemReference(self)
ref.visible = self.autoVisible
self.references.append(ref)
return ref
def remove(self):
for r in self.references:
r.remove()
self.references = []
self._data = None
def changeKey(self, newKey):
if self.overlayMgr is not None:
self.overlayMgr.changeKey(self.key, newKey)
def setData(self, data):
self.overlayItem._data = data
@classmethod
def normalizeForDisplay(cls, data):
import numpy
dmin = numpy.min(data)
data = data - dmin
dmax = numpy.max(data)
data = 255*data/dmax
return data
@classmethod
def qrgb(cls, r, g, b):
return long(0xff << 24) | ((r & 0xff) << 16) | ((g & 0xff) << 8) | (b & 0xff)
@classmethod
def qgray(cls, r, g, b):
return (r*11+g*16+b*5)/32
@classmethod
def createDefaultColorTable(cls, type, levels = 256, transparentValues = set()):
typeCap = type.capitalize()
colorTab = []
if(typeCap == "GRAY"):
for i in range(levels):
if i in transparentValues:
colorTab.append(0L)
else:
colorTab.append(OverlayItem.qgray(i, i, i)) # see qGray function in QtGui
else:
#RGB
import numpy
from ilastik.core.randomSeed import RandomSeed
seed = RandomSeed.getRandomSeed()
if seed is not None:
numpy.random.seed(seed)
for i in range(levels):
if i in transparentValues:
colorTab.append(0L)
else:
colorTab.append(OverlayItem.qrgb(numpy.random.randint(255),numpy.random.randint(255),numpy.random.randint(255))) # see gRGB function in QtGui
return colorTab
@classmethod
# IMPORTANT: BE AWARE THAT CHANGING THE COLOR TABLE MAY AFFECT TESTS THAT WORK WITH GROUND TRUTH
# DATA FROM EXPORTED OVERLAYS. TYPICALLY, ONLY THE DATA AND NOT THE COLOR TABLE OF AN OVERLAY IS
# COMPARED BUT BETTER MAKE SURE THAT THIS IS INDEED THE CASE.
def createDefault16ColorColorTable(cls):
sublist = []
sublist.append(OverlayItem.qrgb(69, 69, 69)) # dark grey
sublist.append(OverlayItem.qrgb(255, 0, 0))
sublist.append(OverlayItem.qrgb(0, 255, 0))
sublist.append(OverlayItem.qrgb(0, 0, 255))
sublist.append(OverlayItem.qrgb(255, 255, 0))
sublist.append(OverlayItem.qrgb(0, 255, 255))
sublist.append(OverlayItem.qrgb(255, 0, 255))
sublist.append(OverlayItem.qrgb(255, 105, 180)) #hot pink!
sublist.append(OverlayItem.qrgb(102, 205, 170)) #dark aquamarine
sublist.append(OverlayItem.qrgb(165, 42, 42)) #brown
sublist.append(OverlayItem.qrgb(0, 0, 128)) #navy
sublist.append(OverlayItem.qrgb(255, 165, 0)) #orange
sublist.append(OverlayItem.qrgb(173, 255, 47)) #green-yellow
sublist.append(OverlayItem.qrgb(128,0, 128)) #purple
sublist.append(OverlayItem.qrgb(192, 192, 192)) #silver
sublist.append(OverlayItem.qrgb(240, 230, 140)) #khaki
colorlist = []
colorlist.append(long(0))
colorlist.extend(sublist)
import numpy
from ilastik.core.randomSeed import RandomSeed
seed = RandomSeed.getRandomSeed()
if seed is not None:
numpy.random.seed(seed)
for i in range(17, 256):
color = OverlayItem.qrgb(numpy.random.randint(255),numpy.random.randint(255),numpy.random.randint(255))
colorlist.append(color)
return colorlist
