def exec_(self):
if not QtGui.QDialog.exec_(self):
return
activeItem = self.ilastik.project.dataMgr[
self.ilastik._activeImageNumber]
ovm = self.ilastik.project.dataMgr[
self.ilastik._activeImageNumber].overlayMgr
try:
file_name = str(self.ui.filenameEdit.text())
if self.ui.randomColorsButton.isChecked():
transparentValues = set()
if self.ui.valueZeroTransparentCheck.isChecked():
transparentValues.add(0)
self.attrs.colorTable = OverlayItem.createDefaultColorTable(
"RGB", transparentValues=transparentValues)
elif self.ui.grayScaleButton.isChecked():
self.attrs.colorTable = OverlayItem.createDefaultColorTable(
"GRAY")
self.attrs.key = str(self.ui.nameEdit.text())
ov = dataImpex.DataImpex.importOverlay(activeItem,
file_name,
attrs=self.attrs)
if ov is None:
print "No _data item loaded"
except Exception, e:
traceback.print_exc()
print e
QtGui.QErrorMessage.qtHandler().showMessage(str(e))
def finalizeResults(self):
activeItem = self.dataMgr[self.dataMgr._activeImageNumber]
activeItem._dataVol.unsupervised = self.decompThread.result
#create overlays for unsupervised decomposition:
if self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr["Unsupervised/" + self.dataMgr.module["Unsupervised_Decomposition"].unsupervisedMethod.shortname] is None:
data = self.decompThread.result[:,:,:,:,:]
myColor = OverlayItem.qrgb(0, 0, 0)
for o in range(0, data.shape[4]):
data2 = OverlayItem.normalizeForDisplay(data[:,:,:,:,o:(o+1)])
# for some strange reason we have to invert the data before displaying it
ov = OverlayItem(255 - data2, color = myColor, alpha = 1.0, colorTable = None, autoAdd = True, autoVisible = True)
self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr["Unsupervised/" + self.dataMgr.module["Unsupervised_Decomposition"].unsupervisedMethod.shortname + " component %d" % (o+1)] = ov
# remove outdated overlays (like PCA components 5-10 if a decomposition with 4 components is done)
numOverlaysBefore = len(self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr.keys())
finished = False
while finished != True:
o = o + 1
# assumes consecutive numbering
key = "Unsupervised/" + self.dataMgr.module["Unsupervised_Decomposition"].unsupervisedMethod.shortname + " component %d" % (o+1)
self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr.remove(key)
numOverlaysAfter = len(self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr.keys())
if(numOverlaysBefore == numOverlaysAfter):
finished = True
else:
numOverlaysBefore = numOverlaysAfter
else:
self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr["Unsupervised/" + self.dataMgr.module["Unsupervised_Decomposition"].unsupervisedMethod.shortname]._data = DataAccessor(self.decompThread.result)
def importOverlay(dataItem, filename, prefix="File Overlays/", attrs=None):
theDataItem = DataImpex.importDataItem(filename, None)
if theDataItem is None:
print "could not load", filename
return None
data = theDataItem[:, :, :, :, :]
if attrs == None:
attrs = OverlayAttributes(filename)
if attrs.min is None:
attrs.min = numpy.min(data)
if attrs.max is None:
attrs.max = numpy.max(data)
if data.shape[0:-1] == dataItem.shape[0:-1]:
ov = OverlayItem(data,
color=attrs.color,
alpha=attrs.alpha,
colorTable=attrs.colorTable,
autoAdd=attrs.autoAdd,
autoVisible=attrs.autoVisible,
min=attrs.min,
max=attrs.max)
ov.key = attrs.key
if len(prefix) > 0:
if prefix[-1] != "/":
prefix = prefix + "/"
dataItem.overlayMgr[prefix + ov.key] = ov
return ov
def exec_(self):
if not QtGui.QDialog.exec_(self):
return
activeItem = self.ilastik.project.dataMgr[self.ilastik._activeImageNumber]
ovm = self.ilastik.project.dataMgr[self.ilastik._activeImageNumber].overlayMgr
try:
file_name = str(self.ui.filenameEdit.text())
if self.ui.randomColorsButton.isChecked():
transparentValues = set()
if self.ui.valueZeroTransparentCheck.isChecked():
transparentValues.add(0)
self.attrs.colorTable = OverlayItem.createDefaultColorTable("RGB", transparentValues=transparentValues)
elif self.ui.grayScaleButton.isChecked():
self.attrs.colorTable = OverlayItem.createDefaultColorTable("GRAY")
self.attrs.key = str(self.ui.nameEdit.text())
ov = dataImpex.DataImpex.importOverlay(activeItem, file_name, attrs=self.attrs)
if ov is None:
print "No _data item loaded"
except Exception, e:
traceback.print_exc()
print e
QtGui.QErrorMessage.qtHandler().showMessage(str(e))
def importOverlay(dataItem, filename, prefix="File Overlays/", attrs=None):
theDataItem = DataImpex.importDataItem(filename, None)
if theDataItem is None:
print "could not load", filename
return None
data = theDataItem[:, :, :, :, :]
if attrs == None:
attrs = OverlayAttributes(filename)
if attrs.min is None:
attrs.min = numpy.min(data)
if attrs.max is None:
attrs.max = numpy.max(data)
if data.shape[0:-1] == dataItem.shape[0:-1]:
ov = OverlayItem(
data,
color=attrs.color,
alpha=attrs.alpha,
colorTable=attrs.colorTable,
autoAdd=attrs.autoAdd,
autoVisible=attrs.autoVisible,
min=attrs.min,
max=attrs.max,
)
ov.key = attrs.key
if len(prefix) > 0:
if prefix[-1] != "/":
prefix = prefix + "/"
dataItem.overlayMgr[prefix + ov.key] = ov
return ov
def finalizeResults(self):
#create Overlay for connected components:
if self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr["Connected Components/CC Results"] is None:
colortab = OverlayItem.createDefault16ColorColorTable()
myColor = OverlayItem.qrgb(255, 0, 0)
ov = OverlayItem(self.ccThread.result, color = myColor, alpha = 1.0, colorTable = colortab, autoAdd = True, autoVisible = True)
self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr["Connected Components/CC Results"] = ov
else:
self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr["Connected Components/CC Results"]._data = DataAccessor(self.ccThread.result)
def filterSynapses(self, inputOverlay, label, minsize, maxsize):
#This is a special function to filter synapses. It assumes that the input overlay
#is a threhsold overlay and computes it for equal probabilities, and then dilates the
#the current connected components to the size of their counterparts in the equal
#probability connected components. The resulting objects are filtered to be between minsize
#and maxsize pixels in volume.
#FIXME: This function is very specific and is only put here until ilastik 0.6 allows
#to make it into a special workflow. Remove as soon as possible!
parts = label.split(" ")
labelnum = int(parts[0])
#labelname = parts[1]
thres = self.dataMgr[self.dataMgr._activeImageNumber].Connected_Components.inputData
cc = self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr["Connected Components/CC Results"]
if thres is None:
print "no threshold overlay"
return
if not isinstance(thres._data, MultivariateThresholdAccessor):
print "no threshold overlay used for connected components"
return
if cc is None:
print "No connected components overlay"
return
sfad = SynapseFilterAndSegmentor(self.dataMgr, labelnum, minsize, maxsize, cc, inputOverlay)
objs_user = sfad.computeUserThreshObjects()
objs_ref = sfad.computeReferenceObjects()
#goodsizes = [s for s in goodsizes if s>100]
#mingoodsize = min(goodsizes)
#maxgoodsize = max(goodsizes)
objs_final = sfad.filterObjects(objs_user, objs_ref)
#create a new, filtered overlay:
result = numpy.zeros(cc.shape, dtype = 'int32')
objcounter = 1
for iobj in objs_final:
for i in range(len(iobj[0])):
result[0, iobj[0][i], iobj[1][i], iobj[2][i], 0] = int(objcounter)
objcounter = objcounter +1
if self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr["Connected Components/CC Filtered"] is None:
#colortab = [QtGui.qRgb(i, i, i) for i in range(256)]
colortab = OverlayItem.createDefault16ColorColorTable()
myColor = OverlayItem.qrgb(255, 0, 0) #QtGui.QColor(255, 0, 0)
ov = OverlayItem(result, color = myColor, alpha = 1.0, colorTable = colortab, autoAdd = True, autoVisible = True)
self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr["Connected Components/CC Filtered"] = ov
else:
self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr["Connected Components/CC Filtered"]._data = DataAccessor(result)
def on_doneOverlaysAvailable(self):
s = self.ilastik._activeImage.Interactive_Segmentation
bluetable = [QtGui.qRgb(0, 0, 255) for i in range(256)]
bluetable[0] = long(0) #transparency
randomColorTable = [QtGui.qRgb(random.randint(0,255),random.randint(0,255),random.randint(0,255)) for i in range(256)]
randomColorTable[0] = long(0) #transparency
self.doneBinaryOverlay = OverlayItem(s.done, color = 0, colorTable=bluetable, alpha = 0.5, autoAdd = True, autoVisible = True, min = 0, max = 255)
self.ilastik._activeImage.overlayMgr["Segmentation/Done"] = self.doneBinaryOverlay
self.doneObjectsOverlay = OverlayItem(s.done, color=0, colorTable=randomColorTable, alpha=0.7, autoAdd=False, autoVisible=False, min = 0, max = 255)
self.ilastik._activeImage.overlayMgr["Segmentation/Objects"] = self.doneObjectsOverlay
self.overlayWidget.addOverlayRef(self.doneBinaryOverlay.getRef())
def __init__(self,
objectListWidget,
data,
color=0,
alpha=0.4,
colorTable=None,
autoAdd=False,
autoVisible=False,
linkColorTable=False,
autoAlphaChannel=True,
min=None,
max=None):
self.objectListWidget = objectListWidget
OverlayItem.__init__(self, data, color, alpha, autoAdd, autoVisible,
linkColorTable, autoAlphaChannel, min, max)
def on_overlaysChanged(self):
if type(self.parent.labelWidget.labelWidget) is DummyLabelWidget: return
s = self.ilastik._activeImage.Interactive_Segmentation
if s.segmentation is None:
#the segmentation has been cleared, remove overlay
self.activeImage.overlayMgr.remove("Segmentation/Segmentation")
self.segmentationOverlay = None
elif self.activeImage.overlayMgr["Segmentation/Segmentation"] is None:
#ensure that we have a 'Segmentation' overlay which will display the result of the segmentation algorithm
origColorTable = copy.deepcopy(self.parent.labelWidget.labelWidget.colorTab)
origColorTable[1] = 255
self.segmentationOverlay = OverlayItem(self.localMgr.segmentation, color = 0, alpha = 1.0, colorTable = origColorTable, autoAdd = True, autoVisible = True, linkColorTable = True)
#this overlay can be shown in 3D
#the label 0 never occurs, label 1 is assigned to the background class
self.segmentationOverlay.displayable3D = True
self.segmentationOverlay.backgroundClasses = set([1])
self.activeImage.overlayMgr["Segmentation/Segmentation"] = self.segmentationOverlay
if s.segmentation is not None:
#create Overlay for segmentation:
res = self.localMgr.segmentation
self.segmentationOverlay._data = DataAccessor(res)
origColorTable = copy.deepcopy(self.parent.labelWidget.labelWidget.colorTab)
origColorTable[1] = 255
self.segmentationOverlay.colorTable = origColorTable
if self.localMgr.potentials is not None:
origColorTable = copy.deepcopy(self.parent.labelWidget.labelWidget.colorTab)
ov = OverlayItem(self.localMgr.potentials,color = origColorTable[1], alpha = 1.0, autoAdd = True, autoVisible = True, min = 0.0, max = 1.0)
self.activeImage.overlayMgr["Segmentation/Potentials"] = ov
else:
self.activeImage.overlayMgr.remove("Segmentation/Potentials")
if self.localMgr.borders is not None:
#colorTab = []
#for i in range(256):
# color = QtGui.QColor(random.randint(0,255),random.randint(0,255),random.randint(0,255)).rgba()
# colorTab.append(color)
ov = OverlayItem(self.localMgr.borders, color = QtGui.QColor(), alpha = 1.0, autoAdd = True, autoVisible = False, min = 0, max = 1.0)
self.activeImage.overlayMgr["Segmentation/Supervoxels"] = ov
else:
self.activeImage.overlayMgr.remove("Segmentation/Supervoxels")
self.parent.labelWidget.repaint()
def finalizeResults(self):
colortable = OverlayItem.createDefaultColorTable('RGB', 256)
#create Overlay for segmentation:
if self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr[
"Auto Segmentation/Segmentation"] is None:
ov = OverlayItem(self.res,
color=0,
alpha=1.0,
colorTable=colortable,
autoAdd=True,
autoVisible=True)
self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr[
"Auto Segmentation/Segmentation"] = ov
else:
self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr[
"Auto Segmentation/Segmentation"]._data = DataAccessor(
self.res)
def finalizeResults(self):
#create Overlay for connected components:
if self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr[
"Connected Components/CC Results"] is None:
colortab = OverlayItem.createDefault16ColorColorTable()
myColor = OverlayItem.qrgb(255, 0, 0)
ov = OverlayItem(self.ccThread.result,
color=myColor,
alpha=1.0,
colorTable=colortab,
autoAdd=True,
autoVisible=True)
self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr[
"Connected Components/CC Results"] = ov
else:
self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr[
"Connected Components/CC Results"]._data = DataAccessor(
self.ccThread.result)
def finalizeResults(self):
colortable = OverlayItem.createDefaultColorTable('RGB', 256)
#create Overlay for segmentation:
if self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr["Auto Segmentation/Segmentation"] is None:
ov = OverlayItem(self.res, color = 0, alpha = 1.0, colorTable = colortable, autoAdd = True, autoVisible = True)
self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr["Auto Segmentation/Segmentation"] = ov
else:
self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr["Auto Segmentation/Segmentation"]._data = DataAccessor(self.res)
def on_activation(self):
if self.ilastik.project is None: return
self._initContent()
self._initConnects()
self.interactionLog = []
self.defaultSegmentor = False
#initially add 'Raw Data' overlay
ovs = self.ilastik._activeImage.module[self.__class__.moduleName].getOverlayRefs()
if "Raw Data" in self.ilastik._activeImage.overlayMgr.keys():
raw = self.ilastik._activeImage.overlayMgr["Raw Data"]
if raw is not None: ovs.append(raw.getRef())
self.ilastik.labelWidget.interactionLog = self.interactionLog
self.ilastik.labelWidget._history.volumeEditor = self.ilastik.labelWidget
self.overlayWidget = OverlayWidget(self.ilastik.labelWidget, self.ilastik.project.dataMgr)
self.ilastik.labelWidget.setOverlayWidget(self.overlayWidget)
if self.parent.project.dataMgr.Interactive_Segmentation.segmentor is None:
segmentors = self.parent.project.dataMgr.Interactive_Segmentation.segmentorClasses
for i, seg in enumerate(segmentors):
if seg.name == "Supervoxel Segmentation":
self.parent.project.dataMgr.Interactive_Segmentation.segmentor = seg()
ui = self.parent.project.dataMgr.Interactive_Segmentation.segmentor.getInlineSettingsWidget(self.inlineSettings.childWidget, view='default')
self.inlineSettings.changeWidget(ui)
self.defaultSegmentor = True
break
#Finally, initialize the core module
s = self.ilastik._activeImage.Interactive_Segmentation
self.connect(s, QtCore.SIGNAL('overlaysChanged()'), self.on_overlaysChanged)
self.connect(s, QtCore.SIGNAL('doneOverlaysAvailable()'), self.on_doneOverlaysAvailable)
self.connect(s, QtCore.SIGNAL('weightsSetup()'), self.on_setupWeights)
self.connect(s, QtCore.SIGNAL('newSegmentation()'), self.on_newSegmentation)
self.connect(s, QtCore.SIGNAL('numColorsNeeded(int)'), self.on_numColorsNeeded)
self.connect(s, QtCore.SIGNAL('saveAsPossible(bool)'), lambda b: self.btnSaveAs.setEnabled(b))
self.connect(s, QtCore.SIGNAL('savePossible(bool)'), lambda b: self.btnSave.setEnabled(b))
self.connect(s, QtCore.SIGNAL('seedsAvailable(bool)'), lambda b: self.btnSegment.setEnabled(b))
s.init()
#add 'Seeds' overlay
self.seedOverlay = OverlayItem(s.seedLabelsVolume._data, color = 0, alpha = 1.0, colorTable = s.seedLabelsVolume.getColorTab(), autoAdd = True, autoVisible = True, linkColorTable = True)
self.ilastik._activeImage.overlayMgr["Segmentation/Seeds"] = self.seedOverlay
self.seedWidget = SeedListWidget(self.ilastik.project.dataMgr.Interactive_Segmentation.seedMgr, s.seedLabelsVolume, self.ilastik.labelWidget, self.seedOverlay)
self.ilastik.labelWidget.setLabelWidget(self.seedWidget)
self.seedOverlay.displayable3D = True
self.seedOverlay.backgroundClasses = set([0])
self.seedOverlay.smooth3D = False
def on_activation(self):
if self.ilastik.project is None:
return
ovs = self.ilastik._activeImage._dataVol.backgroundOverlays
if len(ovs) == 0:
raw = self.ilastik._activeImage.overlayMgr["Raw Data"]
if raw is not None:
ovs.append(raw.getRef())
overlayWidget = OverlayWidget(self.ilastik.labelWidget, self.ilastik.project.dataMgr)
self.ilastik.labelWidget.setOverlayWidget(overlayWidget)
#create background overlay
ov = OverlayItem(self.ilastik._activeImage._dataVol.background._data, color=0, alpha=1.0, colorTable = self.ilastik._activeImage._dataVol.background.getColorTab(), autoAdd = True, autoVisible = True, linkColorTable = True)
self.ilastik._activeImage.overlayMgr["Connected Components/Background"] = ov
ov = self.ilastik._activeImage.overlayMgr["Connected Components/Background"]
self.ilastik.labelWidget.setLabelWidget(BackgroundWidget(self.ilastik.project.backgroundMgr, self.ilastik._activeImage._dataVol.background, self.ilastik.labelWidget, ov))
def __init__(self, labelMgr, volumeLabels, volumeEditor):
QtGui.QGroupBox.__init__(self, "Object Picker")
BaseLabelWidget.__init__(self, None)
self.setLayout(QtGui.QVBoxLayout())
self.layout().setMargin(5)
self.listWidget = QtGui.QListWidget(self)
self.layout().addWidget(self.listWidget)
self.volumeEditor = volumeEditor
self.labelMgr = labelMgr
self.listWidget.setContextMenuPolicy(QtCore.Qt.CustomContextMenu)
self.listWidget.connect(
self.listWidget,
QtCore.SIGNAL("customContextMenuRequested(QPoint)"),
self.onContext)
self.volumeLabels = volumeLabels
self.colorTab = []
self.items = []
self.volumeEditor = volumeEditor
self.labelColorTable = [
QtGui.QColor(QtCore.Qt.red),
QtGui.QColor(QtCore.Qt.green),
QtGui.QColor(QtCore.Qt.yellow),
QtGui.QColor(QtCore.Qt.blue),
QtGui.QColor(QtCore.Qt.magenta),
QtGui.QColor(QtCore.Qt.darkYellow),
QtGui.QColor(QtCore.Qt.lightGray)
]
#self.connect(self, QtCore.SIGNAL("currentTextChanged(QString)"), self.changeText)
self.labelPropertiesChanged_callback = None
self.listWidget.setSelectionMode(
QtGui.QAbstractItemView.SingleSelection)
self.initFromVolumeLabels(volumeLabels)
if self.listWidget.model().rowCount() == 0:
self.addLabel("Picker", 1, QtGui.QColor(0, 0, 255))
self.overlayItem = OverlayItem(self.labelMgr.objects._data)
def __init__(self, backgroundListWidget, data, color = 0, alpha = 0.4, colorTable = None, autoAdd = False, autoVisible = False, linkColorTable = False, autoAlphaChannel = True, min = None, max = None):
self.backgroundListWidget = backgroundListWidget
OverlayItem.__init__(self, data, color, alpha, autoAdd, autoVisible, linkColorTable, autoAlphaChannel, min, max)
class InteractiveSegmentationTab(IlastikTabBase, QtGui.QWidget):
name = 'Interactive Segmentation'
position = 3
moduleName = "Interactive_Segmentation"
def __init__(self, parent=None):
IlastikTabBase.__init__(self, parent)
QtGui.QWidget.__init__(self, parent)
self.outputPath = os.path.expanduser("~/test-segmentation/")
self.mapping = dict()
self.doneBinaryOverlay = None
self.doneObjectsOverlay = None
def on_doneOverlaysAvailable(self):
s = self.ilastik._activeImage.Interactive_Segmentation
bluetable = [QtGui.qRgb(0, 0, 255) for i in range(256)]
bluetable[0] = long(0) #transparency
randomColorTable = [QtGui.qRgb(random.randint(0,255),random.randint(0,255),random.randint(0,255)) for i in range(256)]
randomColorTable[0] = long(0) #transparency
self.doneBinaryOverlay = OverlayItem(s.done, color = 0, colorTable=bluetable, alpha = 0.5, autoAdd = True, autoVisible = True, min = 0, max = 255)
self.ilastik._activeImage.overlayMgr["Segmentation/Done"] = self.doneBinaryOverlay
self.doneObjectsOverlay = OverlayItem(s.done, color=0, colorTable=randomColorTable, alpha=0.7, autoAdd=False, autoVisible=False, min = 0, max = 255)
self.ilastik._activeImage.overlayMgr["Segmentation/Objects"] = self.doneObjectsOverlay
self.overlayWidget.addOverlayRef(self.doneBinaryOverlay.getRef())
def on_activation(self):
if self.ilastik.project is None: return
self._initContent()
self._initConnects()
self.interactionLog = []
self.defaultSegmentor = False
#initially add 'Raw Data' overlay
ovs = self.ilastik._activeImage.module[self.__class__.moduleName].getOverlayRefs()
if "Raw Data" in self.ilastik._activeImage.overlayMgr.keys():
raw = self.ilastik._activeImage.overlayMgr["Raw Data"]
if raw is not None: ovs.append(raw.getRef())
self.ilastik.labelWidget.interactionLog = self.interactionLog
self.ilastik.labelWidget._history.volumeEditor = self.ilastik.labelWidget
self.overlayWidget = OverlayWidget(self.ilastik.labelWidget, self.ilastik.project.dataMgr)
self.ilastik.labelWidget.setOverlayWidget(self.overlayWidget)
if self.parent.project.dataMgr.Interactive_Segmentation.segmentor is None:
segmentors = self.parent.project.dataMgr.Interactive_Segmentation.segmentorClasses
for i, seg in enumerate(segmentors):
if seg.name == "Supervoxel Segmentation":
self.parent.project.dataMgr.Interactive_Segmentation.segmentor = seg()
ui = self.parent.project.dataMgr.Interactive_Segmentation.segmentor.getInlineSettingsWidget(self.inlineSettings.childWidget, view='default')
self.inlineSettings.changeWidget(ui)
self.defaultSegmentor = True
break
#Finally, initialize the core module
s = self.ilastik._activeImage.Interactive_Segmentation
self.connect(s, QtCore.SIGNAL('overlaysChanged()'), self.on_overlaysChanged)
self.connect(s, QtCore.SIGNAL('doneOverlaysAvailable()'), self.on_doneOverlaysAvailable)
self.connect(s, QtCore.SIGNAL('weightsSetup()'), self.on_setupWeights)
self.connect(s, QtCore.SIGNAL('newSegmentation()'), self.on_newSegmentation)
self.connect(s, QtCore.SIGNAL('numColorsNeeded(int)'), self.on_numColorsNeeded)
self.connect(s, QtCore.SIGNAL('saveAsPossible(bool)'), lambda b: self.btnSaveAs.setEnabled(b))
self.connect(s, QtCore.SIGNAL('savePossible(bool)'), lambda b: self.btnSave.setEnabled(b))
self.connect(s, QtCore.SIGNAL('seedsAvailable(bool)'), lambda b: self.btnSegment.setEnabled(b))
s.init()
#add 'Seeds' overlay
self.seedOverlay = OverlayItem(s.seedLabelsVolume._data, color = 0, alpha = 1.0, colorTable = s.seedLabelsVolume.getColorTab(), autoAdd = True, autoVisible = True, linkColorTable = True)
self.ilastik._activeImage.overlayMgr["Segmentation/Seeds"] = self.seedOverlay
self.seedWidget = SeedListWidget(self.ilastik.project.dataMgr.Interactive_Segmentation.seedMgr, s.seedLabelsVolume, self.ilastik.labelWidget, self.seedOverlay)
self.ilastik.labelWidget.setLabelWidget(self.seedWidget)
self.seedOverlay.displayable3D = True
self.seedOverlay.backgroundClasses = set([0])
self.seedOverlay.smooth3D = False
def on_numColorsNeeded(self, numColors):
"""make sure that there are enough label colors.
numColors refers to the _total_ number of colors,
including the background. Note that the background label color
is always present."""
if self.seedWidget.count() >= numColors: return
for i in range(numColors-self.seedWidget.count()):
self.seedWidget.createLabel()
def on_deActivation(self):
if self.ilastik.project is None:
return
self.interactionLog = self.ilastik.labelWidget.interactionLog
self.ilastik.labelWidget.interactionLog = None
if self.ilastik.labelWidget._history != self.ilastik._activeImage.Interactive_Segmentation.seedLabelsVolume._history:
self.ilastik._activeImage.Interactive_Segmentation.seedLabelsVolume._history = self.ilastik.labelWidget._history
if self.ilastik._activeImage.Interactive_Segmentation.seedLabelsVolume._history is not None:
self.ilastik.labelWidget._history = self.ilastik._activeImage.Interactive_Segmentation.seedLabelsVolume._history
def _initContent(self):
tl = QtGui.QHBoxLayout()
tl.setMargin(0)
self.btnChooseWeights = TabButton('Choose Weights', ilastikIcons.Select)
self.btnChooseDimensions = TabButton('Using 3D', ilastikIcons.Select)
self.btnSegment = TabButton('Segment', ilastikIcons.Play)
self.btnSaveAs = TabButton('Save As', ilastikIcons.SaveAs)
self.btnSave = TabButton('Save', ilastikIcons.Save)
self.btnSegmentorsOptions = TabButton('Change Segmentor', ilastikIcons.System)
self.inlineSettings = InlineSettingsWidget(self)
self.only2D = False
self.btnChooseWeights.setToolTip('Choose the edge weights for the segmentation task')
self.btnSegment.setToolTip('Segment the image into foreground/background')
self.btnChooseDimensions.setToolTip('Switch between slice based 2D segmentation and full 3D segmentation\n This is mainly useful for 3D Date with very weak border indicators, where seeds placed in one slice can bleed out badly to other regions')
self.btnSegmentorsOptions.setToolTip('Select a segmentation plugin and change settings')
tl.addWidget(self.btnChooseWeights)
#tl.addWidget(self.btnChooseDimensions)
tl.addWidget(self.btnSegment)
tl.addWidget(self.inlineSettings)
tl.addWidget(self.btnSave)
tl.addWidget(self.btnSaveAs)
tl.addStretch()
tl.addWidget(self.btnSegmentorsOptions)
self.btnSegment.setEnabled(False)
self.btnSaveAs.setEnabled(False)
self.btnSave.setEnabled(False)
self.btnChooseDimensions.setEnabled(False)
self.btnSegmentorsOptions.setEnabled(False)
self.setLayout(tl)
def _initConnects(self):
s = self.ilastik._activeImage.Interactive_Segmentation
self.connect(self.btnChooseWeights, QtCore.SIGNAL('clicked()'), self.on_btnChooseWeights_clicked)
self.connect(self.btnSegment, QtCore.SIGNAL('clicked()'), s.segment)
self.connect(self.btnSaveAs, QtCore.SIGNAL('clicked()'), self.on_btnSaveAs_clicked)
self.connect(self.btnSave, QtCore.SIGNAL('clicked()'), self.on_btnSave_clicked)
self.connect(self.btnChooseDimensions, QtCore.SIGNAL('clicked()'), self.on_btnDimensions)
self.connect(self.btnSegmentorsOptions, QtCore.SIGNAL('clicked()'), self.on_btnSegmentorsOptions_clicked)
self.shortcutSegment = QtGui.QShortcut(QtGui.QKeySequence("s"), self, s.segment, s.segment)
#shortcutManager.register(self.shortcutNextLabel, "Labeling", "Go to next label (cyclic, forward)")
def on_btnDimensions(self):
self.only2D = not self.only2D
if self.only2D:
ov = self.parent.project.dataMgr[self.parent._activeImageNumber].overlayMgr["Segmentation/Segmentation"]
if ov is not None:
zerod = numpy.zeros(ov._data.shape, numpy.uint8)
ov._data = DataAccessor(zerod)
self.btnChooseDimensions.setText('Using 2D')
else:
self.btnChooseDimensions.setText('Using 3D')
self.setupWeights()
def on_btnChooseWeights_clicked(self):
#First question: Which overlay?
dlg = OverlaySelectionDialog(self.ilastik, singleSelection = True)
answer = dlg.exec_()
if len(answer) == 0: return #dialog was dismissed
s = self.ilastik._activeImage.Interactive_Segmentation
overlay = answer[0]
self.parent.labelWidget.overlayWidget.addOverlayRef(overlay.getRef())
volume = overlay._data[0,:,:,:,0]
#Second question: Which border indicator?
borderIndicator = QtGui.QInputDialog.getItem(self.ilastik, \
"Select Border Indicator", "Indicator", \
["Brightness", "Darkness", "Gradient Magnitude"], \
editable = False)
if not borderIndicator[1]: return #Dialog was dismissed
borderIndicator = str(borderIndicator[0])
#Write the choice of weights to a file so that they can be reproduced
if s.outputPath:
f = open(s.outputPath+'/'+'config.txt', 'w')
f.write("overlay=%s\n" % (dlg.selectedOverlayPaths[0]))
f.write("borderIndicator=%s" % (borderIndicator))
f.close()
#calculate the weights
#this will call on_setupWeights via a signal/slot connection
s.calculateWeights(volume, borderIndicator)
def on_setupWeights(self, weights = None):
self.ilastik.labelWidget.interactionLog = []
self.btnSegmentorsOptions.setEnabled(True)
def clearSeeds(self):
self._seedL = None
self._seedIndices = None
def mouseReleaseEvent(self, event):
"""
mouse button release event
"""
button = event.button()
# select an item on which we clicked
def on_btnSave_clicked(self):
s = self.ilastik._activeImage.Interactive_Segmentation
s.saveCurrentSegment()
def on_btnSaveAs_clicked(self):
(segmentKey, accepted) = QtGui.QInputDialog.getText(self, "Finish object", "Enter object name:")
segmentKey = str(segmentKey) #convert to native python string
if not accepted: return #dialog was canceled
s = self.ilastik._activeImage.Interactive_Segmentation
#make sure the name is unique
if s.hasSegmentsKey(segmentKey):
msg = QtGui.QMessageBox.critical(self, "Finish object", \
"An object with name '%s' already exists. Please choose a different name" % (segmentKey))
return
s.saveCurrentSegmentsAs(segmentKey)
path = s.outputPath+'/'+str(segmentKey)
f = open(path + "/interactions.log", "w")
for l in self.ilastik.labelWidget.interactionLog:
f.write(l + "\n")
f.close()
self.ilastik.labelWidget.interactionLog = []
f = h5py.File(path + "/history.h5", 'w')
self.ilastik.labelWidget._history.serialize(f)
f.close()
self.ilastik.labelWidget.repaint()
def on_overlaysChanged(self):
if type(self.parent.labelWidget.labelWidget) is DummyLabelWidget: return
s = self.ilastik._activeImage.Interactive_Segmentation
if s.segmentation is None:
#the segmentation has been cleared, remove overlay
self.activeImage.overlayMgr.remove("Segmentation/Segmentation")
self.segmentationOverlay = None
elif self.activeImage.overlayMgr["Segmentation/Segmentation"] is None:
#ensure that we have a 'Segmentation' overlay which will display the result of the segmentation algorithm
origColorTable = copy.deepcopy(self.parent.labelWidget.labelWidget.colorTab)
origColorTable[1] = 255
self.segmentationOverlay = OverlayItem(self.localMgr.segmentation, color = 0, alpha = 1.0, colorTable = origColorTable, autoAdd = True, autoVisible = True, linkColorTable = True)
#this overlay can be shown in 3D
#the label 0 never occurs, label 1 is assigned to the background class
self.segmentationOverlay.displayable3D = True
self.segmentationOverlay.backgroundClasses = set([1])
self.activeImage.overlayMgr["Segmentation/Segmentation"] = self.segmentationOverlay
if s.segmentation is not None:
#create Overlay for segmentation:
res = self.localMgr.segmentation
self.segmentationOverlay._data = DataAccessor(res)
origColorTable = copy.deepcopy(self.parent.labelWidget.labelWidget.colorTab)
origColorTable[1] = 255
self.segmentationOverlay.colorTable = origColorTable
if self.localMgr.potentials is not None:
origColorTable = copy.deepcopy(self.parent.labelWidget.labelWidget.colorTab)
ov = OverlayItem(self.localMgr.potentials,color = origColorTable[1], alpha = 1.0, autoAdd = True, autoVisible = True, min = 0.0, max = 1.0)
self.activeImage.overlayMgr["Segmentation/Potentials"] = ov
else:
self.activeImage.overlayMgr.remove("Segmentation/Potentials")
if self.localMgr.borders is not None:
#colorTab = []
#for i in range(256):
# color = QtGui.QColor(random.randint(0,255),random.randint(0,255),random.randint(0,255)).rgba()
# colorTab.append(color)
ov = OverlayItem(self.localMgr.borders, color = QtGui.QColor(), alpha = 1.0, autoAdd = True, autoVisible = False, min = 0, max = 1.0)
self.activeImage.overlayMgr["Segmentation/Supervoxels"] = ov
else:
self.activeImage.overlayMgr.remove("Segmentation/Supervoxels")
self.parent.labelWidget.repaint()
def on_newSegmentation(self):
if hasattr(self.ilastik.project.dataMgr.Interactive_Segmentation.segmentor, "bias"):
bias = self.ilastik.project.dataMgr.Interactive_Segmentation.segmentor.bias
s = "%f: segment(bias) %f" % (time.clock(),bias)
self.ilastik.labelWidget.interactionLog.append(s)
self.on_overlaysChanged()
def on_btnSegmentorsOptions_clicked(self):
dialog = SegmentorSelectionDlg(self.parent)
answer = dialog.exec_()
if answer != None:
self.parent.project.dataMgr.Interactive_Segmentation.segmentor = answer
self.setupWeights(self.parent.project.dataMgr[self.parent._activeImageNumber].Interactive_Segmentation._segmentationWeights)
ui = self.parent.project.dataMgr.Interactive_Segmentation.segmentor.getInlineSettingsWidget(self.inlineSettings.childWidget)
self.inlineSettings.changeWidget(ui)
self.defaultSegmentor = False
elif self.defaultSegmentor is True:
ui = self.parent.project.dataMgr.Interactive_Segmentation.segmentor.getInlineSettingsWidget(self.inlineSettings.childWidget)
self.inlineSettings.changeWidget(ui)
self.defaultSegmentor = False
def filterSynapses(self, inputOverlay, label, minsize, maxsize):
#This is a special function to filter synapses. It assumes that the input overlay
#is a threhsold overlay and computes it for equal probabilities, and then dilates the
#the current connected components to the size of their counterparts in the equal
#probability connected components. The resulting objects are filtered to be between minsize
#and maxsize pixels in volume.
#FIXME: This function is very specific and is only put here until ilastik 0.6 allows
#to make it into a special workflow. Remove as soon as possible!
parts = label.split(" ")
labelnum = int(parts[0])
#labelname = parts[1]
thres = self.dataMgr[
self.dataMgr._activeImageNumber].Connected_Components.inputData
cc = self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr[
"Connected Components/CC Results"]
if thres is None:
print "no threshold overlay"
return
if not isinstance(thres._data, MultivariateThresholdAccessor):
print "no threshold overlay used for connected components"
return
if cc is None:
print "No connected components overlay"
return
sfad = SynapseFilterAndSegmentor(self.dataMgr, labelnum, minsize,
maxsize, cc, inputOverlay)
objs_user = sfad.computeUserThreshObjects()
objs_ref = sfad.computeReferenceObjects()
#goodsizes = [s for s in goodsizes if s>100]
#mingoodsize = min(goodsizes)
#maxgoodsize = max(goodsizes)
objs_final = sfad.filterObjects(objs_user, objs_ref)
#create a new, filtered overlay:
result = numpy.zeros(cc.shape, dtype='int32')
objcounter = 1
for iobj in objs_final:
for i in range(len(iobj[0])):
result[0, iobj[0][i], iobj[1][i], iobj[2][i],
0] = int(objcounter)
objcounter = objcounter + 1
if self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr[
"Connected Components/CC Filtered"] is None:
#colortab = [QtGui.qRgb(i, i, i) for i in range(256)]
colortab = OverlayItem.createDefault16ColorColorTable()
myColor = OverlayItem.qrgb(255, 0, 0) #QtGui.QColor(255, 0, 0)
ov = OverlayItem(result,
color=myColor,
alpha=1.0,
colorTable=colortab,
autoAdd=True,
autoVisible=True)
self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr[
"Connected Components/CC Filtered"] = ov
else:
self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr[
"Connected Components/CC Filtered"]._data = DataAccessor(
result)
