def onReload(self):
EditUtil.EditUtil().setCurrentEffect("DefaultTool")
import Isobrush
# TODO: this causes a flash of the new widget, but not a big deal since it's only devel mode
w = Isobrush.IsobrushWidget()
w.onReload()
del (w.parent)
EditUtil.EditUtil().setCurrentEffect("Isobrush")
def updateParam(self, p, v):
r = self.structuresView.currentIndex().row()
if (r > -1):
ei = slicer.modules.SlicerPathologyWidget.editorWidget.helper.structures.item(
r, 3).text()
else:
ei = EditUtil.EditUtil().getParameterNode().GetParameter(
'SlicerPathology,tilename') + '-label'
if ei not in params:
params[ei] = cparams.copy()
if (r < 0):
params[ei][
'label'] = slicer.modules.SlicerPathologyWidget.editorWidget.helper.editUtil.getLabelName(
)
else:
params[ei][
'label'] = slicer.modules.SlicerPathologyWidget.editorWidget.helper.structures.item(
r, 2).text()
params[ei][p] = v
cparams[p] = v
jstr = json.dumps(params,
sort_keys=True,
indent=4,
separators=(',', ': '))
self.parameterNode.SetParameter("QuickTCGAEffect,erich", jstr)
def updateParameterNode(self, caller, event):
node = EditUtil.EditUtil().getParameterNode()
if node != self.parameterNode:
if self.parameterNode:
node.RemoveObserver(self.parameterNodeTag)
self.parameterNode = node
self.parameterNodeTag = node.AddObserver("ModifiedEvent", self.updateGUIFromMRML)
def updateSliders(self):
r = self.structuresView.currentIndex().row()
if (r > -1):
ei = slicer.modules.SlicerPathologyWidget.editorWidget.helper.structures.item(
r, 3).text()
else:
ei = EditUtil.EditUtil().getParameterNode().GetParameter(
'SlicerPathology,tilename') + '-label'
if ei not in params:
params[ei] = cparams.copy()
if (r < 0):
params[ei][
'label'] = slicer.modules.SlicerPathologyWidget.editorWidget.helper.editUtil.getLabelName(
)
else:
params[ei][
'label'] = slicer.modules.SlicerPathologyWidget.editorWidget.helper.structures.item(
r, 2).text()
jstr = json.dumps(params,
sort_keys=True,
indent=4,
separators=(',', ': '))
self.parameterNode.SetParameter("QuickTCGAEffect,erich", jstr)
self.frameOtsuSlider.value = params[ei]["otsuRatio"]
self.frameCurvatureWeightSlider.value = params[ei]["curvatureWeight"]
self.frameSizeThldSlider.value = params[ei]["sizeThld"]
self.frameSizeUpperThldSlider.value = params[ei]["sizeUpperThld"]
self.frameMPPSlider.value = params[ei]["mpp"]
def setDefaultParams(self):
"""Configure here all the required params for any LabelEffect (Paint, Draw, ect.)"""
self.editUtil = EditUtil.EditUtil()
self.parameterNode = self.editUtil.getParameterNode()
self.parameterNode.SetParameter("LabelEffect,paintOver", "1") # Enable paintOver
self.parameterNode.SetParameter("LabelEffect,paintThreshold", "0") # Enable Threshold checkbox
def step(self, iterations=1):
if self.pendingEvent:
if self.pendingEvent.command_execution_status == 0:
# TODO: is there an attribute for CL_COMPLETE?
# TODO: also catch error codes here
#
# put data back in node
#
self.steeredArray[:] = self.labelNext_dev.get()
self.steeredNode.GetImageData().Modified()
self.steeredNode.Modified()
else:
return
#
# get the parameters from MRML
#
# TODO: handl any real growcut parameters
node = EditUtil.EditUtil().getParameterNode()
#
# initialize candidates if needed
#
if not self.candidatesInitialized:
self.clProgram.clearShort(
self.clQueue, self.shape, None, self.candidatesNext_dev.data).wait()
print("self.candidatesNext_dev mean ", self.candidatesNext_dev.get().mean())
self.clProgram.initialCandidates(
self.clQueue, self.shape, None, self.labelArray_dev.data,
self.candidates_dev.data).wait()
print("self.labelArray_dev mean ", self.labelArray_dev.get().mean())
print("self.candidates_dev mean ", self.candidates_dev.get().mean())
self.candidatesInitialized = True
#
# run iterations
# - save the pending event from the last call so that we can
# know when the execution is finished (so the main event loop
# is not blocked on this execution)
#
for iteration in xrange(iterations):
self.clProgram.growCut(self.clQueue, self.work_size, None,
self.backgroundArray_dev.data, self.labelArray_dev.data,
self.theta_dev.data,
self.thetaNext_dev.data, self.labelNext_dev.data,
self.candidates_dev.data, self.candidatesNext_dev.data,
self.backgroundArrayMax, global_offset=self.work_offset)
self.clProgram.copyShort(self.clQueue, self.work_size, None,
self.labelNext_dev.data, self.labelArray_dev.data, global_offset=self.work_offset)
self.clProgram.copyShort(self.clQueue, self.work_size, None,
self.candidatesNext_dev.data, self.candidates_dev.data, global_offset=self.work_offset)
self.clProgram.clearShort(self.clQueue, self.work_size, None,
self.candidatesNext_dev.data, global_offset=self.work_offset)
self.pendingEvent = self.clProgram.copyFloat(self.clQueue, self.work_size, None,
self.thetaNext_dev.data, self.theta_dev.data, global_offset=self.work_offset)
def __init__(self,options,preferredDeviceType='GPU'):
self.preferredDeviceType = preferredDeviceType
self.editUtil = EditUtil.EditUtil()
self.sliceWidget = options.tools[0].sliceWidget
if hasattr(slicer.modules, 'editorBot'):
slicer.modules.editorBot.active = False
del(slicer.modules.editorBot)
slicer.modules.editorBot = self
self.interval = 100
self.active = False
self.start()
def apply(self, xy, mode=0, forced_path=None, forced_point=None):
#
# get the parameters from MRML
#
# For sanity purposes, tool can always "paint" over existing labels. If we find some foreseeable reason why we might
# not want this in all cases, we can re-add to the GUI.
#
# get the label and background volume nodes
#
labelLogic = self.sliceLogic.GetLabelLayer()
labelNode = labelLogic.GetVolumeNode()
backgroundLogic = self.sliceLogic.GetBackgroundLayer()
backgroundNode = backgroundLogic.GetVolumeNode()
##### self.errorMessageFrame.textCursor().insertHtml('Error Detected!')
##### self.errorMessageFrame.setStyleSheet("QTextEdit {color:red}")
#
# get the ijk location of the clicked point
# by projecting through patient space back into index
# space of the volume. Result is sub-pixel, so round it
# (note: bg and lb will be the same for volumes created
# by the editor, but can be different if the use selected
# different bg nodes, but that is not handled here).
#
xyToIJK = labelLogic.GetXYToIJKTransform()
ijkFloat = xyToIJK.TransformDoublePoint(xy + (0, ))
ijk = []
for element in ijkFloat:
try:
intElement = int(round(element))
except ValueError:
intElement = 0
ijk.append(intElement)
ijk.reverse()
ijk = tuple(ijk)
### IJK ACTIVE HERE
#
# Get the numpy array for the bg and label
#
node = EditUtil.EditUtil().getParameterNode()
offset = float(node.GetParameter("TraceAndSelect,offsetvalue"))
if offset != 0 and mode == 0:
self.progress = qt.QProgressDialog()
self.progress.setLabelText("Processing Slices...")
self.progress.setCancelButtonText("Abort Fill")
self.progress.setMinimum(0)
self.progress.setMaximum(abs(offset))
self.progress.setAutoClose(1)
self.progress.open()
return self.fill(ijk, [], mode, forced_path, forced_point)
def __init__(self, options):
self.editUtil = EditUtil.EditUtil()
#self.sliceWidget = options.tools[0].sliceWidget
self.sliceWidget = slicer.app.layoutManager().sliceWidget('Red')
if hasattr(slicer.modules, 'TCGAEditorBot'):
slicer.modules.TCGAEditorBot.active = False
del (slicer.modules.TCGAEditorBot)
slicer.modules.TCGAEditorBot = self
self.redSliceWidget = options.redSliceWidget
self.greenSliceWidget = options.greenSliceWidget
self.yellowSliceWidget = options.yellowSliceWidget
self.start()
def onloadCTButtonClicked(self):
# widge to load file
w = qt.QWidget()
w.resize(320, 240)
w.setWindowTitle("Select CT Image")
image_path = qt.QFileDialog.getOpenFileName(w, 'Open File', '/')
path = str('/'.join(image_path.split('/')[0:-1])) + '/'
print(path)
print(image_path)
if image_path is not None:
self.image_loaded = True
print(image_path)
filetype = ".nrrd"
self.filetype = filetype
lm = slicer.app.layoutManager()
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpView)
view = lm.threeDWidget(0).threeDView()
viewNode = view.mrmlViewNode()
viewNode.SetBackgroundColor((0, 0, 0))
viewNode.SetBackgroundColor2((0, 0, 0))
viewNode.SetAxisLabelsVisible(0)
viewNode.SetBoxVisible(0)
# load image (master volume)
load, image = slicer.util.loadVolume(image_path, returnNode=True)
volumesLogic = slicer.modules.volumes.logic()
label_name = image.GetName() + "-rough-label"
label = volumesLogic.CreateLabelVolume(slicer.mrmlScene, image,
label_name)
label_path = str(path + label_name + filetype)
print(label_path)
self.view = view
self.path = path
self.image_path = image_path
self.label_path = label_path
self.image_name = image.GetName()
self.label_name = label_name
self.labelpostfix1 = '_tumor_label'
self.labelpostfix2 = '_lung_label'
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetReferenceActiveLabelVolumeID(label.GetID())
EditUtil.EditUtil().propagateVolumeSelection()
# switch to Edit module
slicer.util.selectModule('Editor')
slicer.modules.EditorWidget.toolsBox.selectEffect('PaintEffect')
def __init__(self, sliceLogic):
print("Preparing Growcut interaction")
self.attributes = ('MouseTool')
self.displayName = 'FastGrowCut Effect'
#disconnect all shortcuts that may exist, to allow Fast GrowCut's to work, reconnect once bot is turned off
slicer.modules.EditorWidget.removeShortcutKeys()
self.sliceLogic = sliceLogic
self.editUtil = EditUtil.EditUtil()
#initialize Fast GrowCut
self.init_fGrowCut()
self.fastCrowCutCreated = False
def __init__(self, sliceLogic):
print("Preparing CleverSeg interaction")
self.attributes = ('MouseTool')
self.displayName = 'CleverSeg Effect'
# disconnect all shortcuts that may exist, to allow CleverSeg's to work, reconnect once bot is turned off
slicer.modules.EditorWidget.removeShortcutKeys()
self.sliceLogic = sliceLogic
self.editUtil = EditUtil.EditUtil()
# initialize CleverSeg
self.init_fCleverSeg()
self.CleverSegCreated = False
def onloadMRIFLAIRButtonClicked(self):
# widge to load file
w = qt.QWidget()
w.resize(320, 240)
w.setWindowTitle("Select MRI FLAIR Image")
self.FLAIR_image_path = qt.QFileDialog.getOpenFileName(
w, 'Open File', '/')
self.FLAIR_path = str('/'.join(
self.FLAIR_image_path.split('/')[0:-1])) + '/'
lm = slicer.app.layoutManager()
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpView)
view = lm.threeDWidget(0).threeDView()
viewNode = view.mrmlViewNode()
viewNode.SetBackgroundColor((0, 0, 0))
viewNode.SetBackgroundColor2((0, 0, 0))
viewNode.SetAxisLabelsVisible(0)
viewNode.SetBoxVisible(0)
self.view = view
load, image = slicer.util.loadVolume(self.FLAIR_image_path,
returnNode=True)
# adding a automated seed point
volumesLogic = slicer.modules.volumes.logic()
label_name = image.GetName() + "-rough-label"
label = volumesLogic.CreateLabelVolume(slicer.mrmlScene, image,
label_name)
# label_path = str(path+label_name+filetype)
# print(label_path)
#
# self.view = view
# self.path = path
# self.image_path = image_path
# self.label_path = label_path
# self.image_name = image.GetName()
self.label_name = label_name
# self.labelpostfix1 = '_tumor_confidenceconnected'
# self.labelpostfix2 = '_lung_confidenceconnected'
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetReferenceActiveLabelVolumeID(label.GetID())
EditUtil.EditUtil().propagateVolumeSelection()
# switch to Edit module
slicer.util.selectModule('Editor')
slicer.modules.EditorWidget.toolsBox.selectEffect('PaintEffect')
def run_qtcga_segmentation_1(self):
"""
Original recipe
:return:
"""
if self.bEditTCGA:
self.currentMessage = "Quick TCGA: running nucleus segmentation ..."
slicer.util.showStatusMessage(self.currentMessage)
seedArray = slicer.util.array(self.labelNode.GetName())
self.qTCGASeedArray[:] = seedArray[:]
node = EditUtil.EditUtil().getParameterNode() # get the parameters from MRML
otsuRatio = float(node.GetParameter("ShortCut,otsuRatio"))
print(otsuRatio)
curvatureWeight = float(node.GetParameter("ShortCut,curvatureWeight")) / 10
print(curvatureWeight)
sizeThld = float(node.GetParameter("ShortCut,sizeThld"))
print(sizeThld)
sizeUpperThld = float(node.GetParameter("ShortCut,sizeUpperThld"))
print(sizeUpperThld)
mpp = float(node.GetParameter("ShortCut,mpp")) / 100
print(mpp)
self.qTCGAMod.SetotsuRatio(otsuRatio)
self.qTCGAMod.SetcurvatureWeight(curvatureWeight)
self.qTCGAMod.SetsizeThld(sizeThld)
self.qTCGAMod.SetsizeUpperThld(sizeUpperThld)
self.qTCGAMod.Setmpp(mpp)
self.qTCGAMod.SetSourceVol(self.foregroundNode.GetImageData())
self.qTCGAMod.SetSeedVol(self.labelNode.GetImageData())
self.qTCGASegArray[:] = seedArray[:]
self.labelNode.GetImageData().Modified()
self.labelNode.Modified()
self.bEditTCGA = False
self.currentMessage = "Quick TCGA done: nuclei segmentation is done; press 'F' to enable ROI selection for refinement"
slicer.util.showStatusMessage(self.currentMessage)
else:
self.currentMessage = "Quick TCGA: go to seed labels first by pressing 'E'"
slicer.util.showStatusMessage(self.currentMessage)
def setErrorMessage(self, errorText, errorColor=0):
"""Call this to seet the message in the error box.
Parameters:
errorText: string to be displayed in the box
errorColor: int 1 or 0 (DEFAULT IS 0) that sets the color of the text as either green (1) or red (0)
Returns: none"""
if (errorColor == 1):
errorColor = "QTextEdit {color:Green}"
elif (errorColor == 0):
errorColor = "QTextEdit {color:red}"
else:
# Why did you do this? Read the function? I'm going to make the text white to punish you
errorColor = "QTextEdit {color:white}"
node = EditUtil.EditUtil().getParameterNode()
node.SetParameter("TraceAndSelect,errorMessage", str(errorText))
node.SetParameter("TraceAndSelect,errorMessageColor", str(errorColor))
return
def runQTCGA_NucleiSegYi(self):
self.currentMessage = "Quick TCGA: running nucleus segmentation ..."
slicer.util.showStatusMessage(self.currentMessage)
seedArray = slicer.util.array(self.labelNode.GetName())
self.qTCGASeedArray[:] = seedArray[:]
node = EditUtil.EditUtil().getParameterNode(
) # get the parameters from MRML
otsuRatio = float(node.GetParameter("QuickTCGAEffect,otsuRatio"))
curvatureWeight = float(
node.GetParameter("QuickTCGAEffect,curvatureWeight")) / 10
sizeThld = float(node.GetParameter("QuickTCGAEffect,sizeThld"))
sizeUpperThld = float(
node.GetParameter("QuickTCGAEffect,sizeUpperThld"))
mpp = float(node.GetParameter("QuickTCGAEffect,mpp")) / 100
self.qTCGAMod.SetotsuRatio(otsuRatio)
self.qTCGAMod.SetcurvatureWeight(curvatureWeight)
self.qTCGAMod.SetsizeThld(sizeThld)
self.qTCGAMod.SetsizeUpperThld(sizeUpperThld)
self.qTCGAMod.Setmpp(mpp)
AA = self.foregroundNode.GetImageData()
a1 = 0
b1 = 0
ddd = AA.GetDimensions()
a2 = ddd[0] - 1
b2 = ddd[1] - 1
LL = self.labelNode.GetImageData()
BB = self.GetTile(AA, a1, b1, a2, b2)
LL = self.GetTile(LL, a1, b1, a2, b2)
self.qTCGAMod.SetSourceVol(BB)
self.qTCGAMod.SetSeedVol(LL)
self.qTCGAMod.Run_NucleiSegYi()
self.qTCGASegArray[:] = seedArray[:]
self.MergeImages(LL, self.labelNode.GetImageData(), a1, b1)
self.foregroundNode.GetImageData().Modified()
self.foregroundNode.Modified()
self.labelNode.GetImageData().Modified()
self.labelNode.Modified()
self.currentMessage = "Quick TCGA done: nuclei segmetnation is done; press 'F' to enable ROI selection for refinement"
slicer.util.showStatusMessage(self.currentMessage)
def __init__(self, sliceLogic):
print("Preparing Quick TCGA Interaction")
self.attributes = 'MouseTool'
self.displayName = 'ShortCut Effect'
# disconnect all shortcuts that may exist, to allow ShortCut's to work, reconnect once bot is turned off
if hasattr(slicer.modules, 'EditorWidget'):
slicer.modules.EditorWidget.removeShortcutKeys()
self.sliceLogic = sliceLogic
self.editUtil = EditUtil.EditUtil()
self.swRed = slicer.app.layoutManager().sliceWidget('Red').sliceLogic()
self.sw = slicer.app.layoutManager().sliceWidget('Red')
self.interactor = self.sw.sliceView().interactor() # initialize to red slice interactor
# self.computeCurrSliceSmarter() # initialize the current slice to something meaningful
self.mouse_obs_growcut, self.swLUT_growcut = bind_view_observers(self.updateShortCutROI)
# initialize Fast GrowCut
self.init_ShortCut()
self.ShortCutCreated = False
def onSaveButtonClicked(self):
bundle = EditUtil.EditUtil().getParameterNode().GetParameter(
'QuickTCGAEffect,erich')
tran = json.loads(bundle)
layers = []
for key in tran:
nn = tran[key]
nn["file"] = key + '.tif'
layers.append(tran[key])
j = {}
j['layers'] = layers
j['username'] = self.setupUserName.text
j['sourcetile'] = self.tilename
j['generator'] = "3DSlicer-4.5.0 with SlicerPathology v1.0a"
j['timestamp'] = datetime.datetime.now().strftime("%Y%m%d%H%M%S")
labelNodes = slicer.util.getNodes('vtkMRMLLabelMapVolumeNode*')
savedMessage = 'Segmentations for the following series were saved:\n\n'
for label in labelNodes.values():
labelName = label.GetName()
labelFileName = os.path.join(self.dataDirButton.directory,
labelName + '.tif')
print "labelFileName : " + labelFileName
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.SetFileName(labelFileName)
sNode.SetWriteFileFormat('tif')
sNode.SetURI(None)
success = sNode.WriteData(label)
if success:
print "successful writing " + labelFileName
else:
print "failed writing " + labelFileName
jstr = json.dumps(j, sort_keys=True, indent=4, separators=(',', ': '))
f = open(
os.path.join(self.dataDirButton.directory,
self.tilename + '.json'), 'w')
f.write(jstr)
f.close()
def fill(self,
ijk,
optional_seeds=[],
mode=0,
forced_path=None,
forced_point=None):
print("Mode: %d" % mode)
paintOver = 1
mean = (0, 0)
count = 0
node = EditUtil.EditUtil().getParameterNode()
# Max number of pixels to fill in (does not include path)
print("@@@MaxPixels:%s" %
node.GetParameter("TraceAndSelect,maxPixels"))
maxPixels = float(node.GetParameter("TraceAndSelect,maxPixels"))
# Minimum intensity value to be detected
print("@@@Theshold Min:%s" %
node.GetParameter("TraceAndSelect,paintThresholdMin"))
thresholdMin = float(
node.GetParameter("TraceAndSelect,paintThresholdMin"))
# Maximum intensity value to be detected
print("@@@Theshold Max:%s" %
node.GetParameter("TraceAndSelect,paintThresholdMax"))
thresholdMax = float(
node.GetParameter("TraceAndSelect,paintThresholdMax"))
labelLogic = self.sliceLogic.GetLabelLayer()
labelNode = labelLogic.GetVolumeNode()
backgroundLogic = self.sliceLogic.GetBackgroundLayer()
backgroundNode = backgroundLogic.GetVolumeNode()
import vtk.util.numpy_support, numpy
backgroundImage = backgroundNode.GetImageData()
labelImage = labelNode.GetImageData()
shape = list(backgroundImage.GetDimensions())
shape.reverse()
backgroundArray = vtk.util.numpy_support.vtk_to_numpy(
backgroundImage.GetPointData().GetScalars()).reshape(shape)
labelArray = vtk.util.numpy_support.vtk_to_numpy(
labelImage.GetPointData().GetScalars()).reshape(shape)
ijk_reconstruction_indexes = []
# THIS SHOULD ALWAYS BE TRUE
# VOLUME MODE IS DISABLED BECAUSE I HAVE NO CLUE WHAT IT IS
original_ijk = list(ijk)
if self.fillMode == 'Plane':
# select the plane corresponding to current slice orientation
# for the input volume
ijkPlane = self.sliceIJKPlane()
i, j, k = ijk
if ijkPlane == 'JK':
backgroundDrawArray = backgroundArray[:, :, k]
labelDrawArray = labelArray[:, :, k]
ijk = (i, j)
ijk_reconstruction_indexes = (0, 1)
if ijkPlane == 'IK':
backgroundDrawArray = backgroundArray[:, j, :]
labelDrawArray = labelArray[:, j, :]
ijk = (i, k)
ijk_reconstruction_indexes = (0, 2)
if ijkPlane == 'IJ':
backgroundDrawArray = backgroundArray[i, :, :]
labelDrawArray = labelArray[i, :, :]
ijk = (j, k)
ijk_reconstruction_indexes = (1, 2)
else:
print(
"HOW DID YOU DO THAT??? WHAT DID YOU DO TO ACTIVATE VOLUME MODE???"
)
self.setErrorMessage("Error: volume mode not supported.")
return
# Log info about where the user clicked for debugging purposes
value = backgroundDrawArray[ijk]
print("@@@location=", ijk)
print("@@@value=", value)
# Get the current label that the user wishes to assign using the tool
label = EditUtil.EditUtil().getLabel()
# Use lo and hi for threshold checks
# Easiest way to do things is check if a pixel is outside the threshold, ie.
lo = thresholdMin
hi = thresholdMax
best_path = []
fill_point = ijk
if mode == 0 and forced_path is not None and forced_point is not None:
best_path = forced_path
fill_point = forced_point
else:
# Build path
best_path, visited, dead_ends = gimme_a_path(
ijk, 200, hi, lo, backgroundDrawArray, optional_seeds)
print("@@@Dead ends:", dead_ends)
attempts = 0
max_attempts = 2
while dead_ends > 150 or dead_ends < 0 and attempts < max_attempts:
attempts += 1
lo -= 25
print("Lowering min tolerance to:", lo)
node.SetParameter("LabelEffect,paintThresholdMin", str(lo))
best_path, visited, dead_ends = gimme_a_path(
ijk, 200, hi, lo, backgroundDrawArray, optional_seeds)
print("@@@Dead ends:", dead_ends)
if dead_ends < 0:
print("@@@No path found? Weird.")
self.setErrorMessage(
"Error: could not find any suitable path.")
return
# Save state before doing anything
self.undoRedo.saveState()
for pixel in visited:
labelDrawArray[pixel] = label
EditUtil.EditUtil().markVolumeNodeAsModified(labelNode)
if mode == 1: # Outline only mode
print("Outline made, returning.")
self.setErrorMessage(
"Preview complete. No errrors detected.\nLeft click to confirm.\nRight click to try a new outline.\nUndo to remove.",
1)
return (best_path, ijk)
#
# Fill path
#
# Fill the path using a recursive search
toVisit = [
fill_point,
]
extrema = get_extrema(best_path)
# Create a map that contains the location of the pixels
# that have been already visited (added or considered to be added).
# This is required if paintOver is enabled because then we reconsider
# all pixels (not just the ones that have not labelled yet).
if paintOver:
labelDrawVisitedArray = numpy.zeros(labelDrawArray.shape,
dtype='bool')
pixelsSet = 0
print("@@@FILLING PATH")
while toVisit != []:
location = toVisit.pop(0)
try:
l = fetch_val(labelDrawArray, location)
b = fetch_val(backgroundDrawArray, location)
except IndexError:
continue
if (not paintOver and l != 0):
# label filled already and not painting over, leave it alone
continue
try:
if (paintOver and l == label):
temp1 = mean[0] + location[0]
temp2 = mean[1] + location[1]
mean = (temp1, temp2)
count += 1
# label is the current one, but maybe it was filled with another high/low value,
# so we have to visit it once (and only once) in this session, too
if labelDrawVisitedArray[location]:
# visited already, so don't try to fill it again
continue
else:
# we'll visit this pixel now, so mark it as visited
labelDrawVisitedArray[location] = True
except ValueError:
print("@@@VALUE ERROR!", l)
print("@@@Location: ", location)
print("@@@fill_point:", fill_point)
print("@@@toVisit:", toVisit)
continue
if location in best_path:
continue
if not (extrema[0] < location[0] < extrema[1]
and extrema[2] < location[1] < extrema[3]):
# Went out of bounds for path
print("@@@WENT OUT OF BOUNDS FOR PATH!")
self.setErrorMessage("Error: Went out of bounds for path.")
self.undoRedo.undo()
return
labelDrawArray[location] = label
if l != label:
# only count those pixels that were changed (to allow step-by-step growing by multiple mouse clicks)
pixelsSet += 1
if pixelsSet > maxPixels:
toVisit = []
else:
# add the 4 neighbors to the stack
toVisit.append((location[0] - 1, location[1]))
toVisit.append((location[0] + 1, location[1]))
toVisit.append((location[0], location[1] - 1))
toVisit.append((location[0], location[1] + 1))
# signal to slicer that the label needs to be updated
## CHANGE OFFSET
print("@@@Offset:|%s|" %
node.GetParameter("TraceAndSelect,offsetvalue"))
self.offset = float(node.GetParameter("TraceAndSelect,offsetvalue"))
print("OFFSET SIGN: %s" % math.copysign(1, self.offset))
if self.offset != 0:
slices_seen = self.progress.maximum - abs(self.offset)
if self.progress.wasCanceled:
self.offset = 0
layoutManager = slicer.app.layoutManager()
widget = layoutManager.sliceWidget('Red')
rednode = widget.sliceLogic().GetSliceNode()
rednode.SetSliceOffset(rednode.GetSliceOffset() +
math.copysign(1, self.offset))
node.SetParameter("TraceAndSelect,offsetvalue", str(0))
self.setErrorMessage(
"Fill abandoned after {} slice(s)".format(
int(slices_seen)), 1)
return
self.progress.setValue(slices_seen)
layoutManager = slicer.app.layoutManager()
widget = layoutManager.sliceWidget('Red')
rednode = widget.sliceLogic().GetSliceNode()
rednode.SetSliceOffset(rednode.GetSliceOffset() +
math.copysign(1, self.offset))
node.SetParameter("TraceAndSelect,offsetvalue",
str(self.offset - math.copysign(1, self.offset)))
print(self.offset)
### Calc centoid mean stuff here
recs_mean = (mean[0] / count, mean[1] / count)
rec_mean = get_optional_seeds(best_path, recs_mean)[0]
print("MEAN:", rec_mean, recs_mean)
rec_ijk = list(original_ijk)
for i in range(0, 3):
rec_ijk[i] = int(rec_ijk[i] +
int(math.copysign(1, self.offset)))
rec_ijk[ijk_reconstruction_indexes[0]] = rec_mean[0]
rec_ijk[ijk_reconstruction_indexes[1]] = rec_mean[1]
print("RECURSIVE IJK:", rec_ijk)
print("#########RECURSE#########")
return self.fill(rec_ijk,
optional_seeds=get_optional_seeds(
best_path, recs_mean))
###
print("@@@FILL DONE")
EditUtil.EditUtil().markVolumeNodeAsModified(labelNode)
self.setErrorMessage("Fill complete. No errors detected.", 1)
return
def apply(self,xy):
#
# get the parameters from MRML
#
node = EditUtil.EditUtil().getParameterNode()
tolerance = float(node.GetParameter("WandEffect,tolerance"))
maxPixels = float(node.GetParameter("WandEffect,maxPixels"))
paintOver = int(node.GetParameter("LabelEffect,paintOver"))
#
# get the label and background volume nodes
#
labelLogic = self.sliceLogic.GetLabelLayer()
labelNode = labelLogic.GetVolumeNode()
backgroundLogic = self.sliceLogic.GetBackgroundLayer()
backgroundNode = backgroundLogic.GetVolumeNode()
#
# get the ijk location of the clicked point
# by projecting through patient space back into index
# space of the volume. Result is sub-pixel, so round it
# (note: bg and lb will be the same for volumes created
# by the editor, but can be different if the use selected
# different bg nodes, but that is not handled here).
#
xyToIJK = labelLogic.GetXYToIJKTransform().GetMatrix()
ijkFloat = xyToIJK.MultiplyPoint(xy+(0,1))[:3]
ijk = []
for element in ijkFloat:
try:
intElement = int(round(element))
except ValueError:
intElement = 0
ijk.append(intElement)
ijk.reverse()
ijk = tuple(ijk)
#
# Get the numpy array for the bg and label
#
import vtk.util.numpy_support
backgroundImage = backgroundNode.GetImageData()
labelImage = labelNode.GetImageData()
shape = list(backgroundImage.GetDimensions())
shape.reverse()
backgroundArray = vtk.util.numpy_support.vtk_to_numpy(backgroundImage.GetPointData().GetScalars()).reshape(shape)
labelArray = vtk.util.numpy_support.vtk_to_numpy(labelImage.GetPointData().GetScalars()).reshape(shape)
if self.fillMode == 'Plane':
# select the plane corresponding to current slice orientation
# for the input volume
ijkPlane = self.sliceIJKPlane()
i,j,k = ijk
if ijkPlane == 'JK':
backgroundDrawArray = backgroundArray[:,:,k]
labelDrawArray = labelArray[:,:,k]
ijk = (i, j)
if ijkPlane == 'IK':
backgroundDrawArray = backgroundArray[:,j,:]
labelDrawArray = labelArray[:,j,:]
ijk = (i, k)
if ijkPlane == 'IJ':
backgroundDrawArray = backgroundArray[i,:,:]
labelDrawArray = labelArray[i,:,:]
ijk = (j, k)
elif self.fillMode == 'Volume':
backgroundDrawArray = backgroundArray
labelDrawArray = labelArray
#
# do a recursive search for pixels to change
#
self.undoRedo.saveState()
value = backgroundDrawArray[ijk]
label = EditUtil.EditUtil().getLabel()
lo = value - tolerance
hi = value + tolerance
pixelsSet = 0
toVisit = [ijk,]
visited = []
while toVisit != []:
location = toVisit.pop(0)
try:
l = labelDrawArray[location]
b = backgroundDrawArray[location]
except IndexError:
continue
if (not paintOver and l != 0):
# label filled already and not painting over, leave it alone
continue
if (paintOver and l == label):
# label is the current one, but maybe it was filled with another high/low value,
# so we have to visit it once (and only once) in this session, too
visitedCurrentLocation = True
try:
visited.index(location)
except ValueError:
# not found, so not visited yet
visitedCurrentLocation = False
if visitedCurrentLocation:
continue
else:
visited.append(location)
if b < lo or b > hi:
continue
labelDrawArray[location] = label
if l != label:
# only count those pixels that were changed (to allow step-by-step growing by multiple mouse clicks)
pixelsSet += 1
if pixelsSet > maxPixels:
toVisit = []
else:
if self.fillMode == 'Plane':
# add the 4 neighbors to the stack
toVisit.append((location[0] - 1, location[1] ))
toVisit.append((location[0] + 1, location[1] ))
toVisit.append((location[0] , location[1] - 1 ))
toVisit.append((location[0] , location[1] + 1 ))
elif self.fillMode == 'Volume':
# add the 6 neighbors to the stack
toVisit.append((location[0] - 1, location[1] , location[2] ))
toVisit.append((location[0] + 1, location[1] , location[2] ))
toVisit.append((location[0] , location[1] - 1, location[2] ))
toVisit.append((location[0] , location[1] + 1, location[2] ))
toVisit.append((location[0] , location[1] , location[2] - 1))
toVisit.append((location[0] , location[1] , location[2] + 1))
# signal to slicer that the label needs to be updated
labelImage.Modified()
labelNode.Modified()
def init_QuickTCGA(self):
self.emergencyStopFunc = None
self.dialogBox = qt.QMessageBox(
) #will display messages to draw users attention if he does anything wrong
self.dialogBox.setWindowTitle("QuickTCGA Error")
self.dialogBox.setWindowModality(
qt.Qt.NonModal
) #will allow user to continue interacting with Slicer
# TODO: check this claim- might be causing leaks
# set the image, label nodes (this will not change although the user can
# alter what is bgrnd/frgrnd in editor)
# Confused about how info propagates UIarray to UIVol, not the other way, NEEDS AUTO TESTS
self.labelNode = self.editUtil.getLabelVolume(
) #labelLogic.GetVolumeNode()
self.backgroundNode = self.editUtil.getBackgroundVolume(
) #backgroundLogic.GetVolumeNode()
self.foregroundNode = self.swRed.GetForegroundLayer().GetVolumeNode()
#perform safety check on right images/labels being selected, #set up images
#if red slice doesnt have a label or image, go no further
if type(self.backgroundNode) == type(None) or type(
self.labelNode) == type(None):
self.dialogBox.setText(
"Either Image (must be Background Image) or Label not set in slice views."
)
self.dialogBox.show()
if self.emergencyStopFunc:
self.emergencyStopFunc()
return
volumesLogic = slicer.modules.volumes.logic()
self.labelName = self.labelNode.GetName(
) # record name of label so user, cant trick us
self.imgBgrdName = self.backgroundNode.GetName()
self.imgFgrdName = self.foregroundNode.GetName()
if self.sliceViewMatchEditor(
self.sliceLogic
) == False: # do nothing, exit function if user has played with images
if self.emergencyStopFunc:
self.emergencyStopFunc()
return
# QuickTCGA shortcuts
##resetQTCGAKey = qt.QKeySequence(qt.Qt.Key_R) # reset initialization flag
##runQTCGAClusterKey = qt.QKeySequence(qt.Qt.Key_S) # run fast growcut
runNucleiSegKey = qt.QKeySequence(qt.Qt.Key_Y)
##editTCGAKey = qt.QKeySequence(qt.Qt.Key_E) # edit seed labels
##runQTCGATemplateKey = qt.QKeySequence(qt.Qt.Key_T)
##runQTCGARefineCurvatureKey = qt.QKeySequence(qt.Qt.Key_U)
##runQTCGAShortCutKey = qt.QKeySequence(qt.Qt.Key_C)
##runQTCGAShortEditCutKey = qt.QKeySequence(qt.Qt.Key_F)
print " key to run QuickTCGA segmentation is Y"
self.qtkeyconnections = []
self.qtkeydefsQTCGA = [[runNucleiSegKey, self.runQTCGA_NucleiSegYi]]
for keydef in self.qtkeydefsQTCGA:
s = qt.QShortcut(keydef[0], slicer.util.mainWindow()
) # connect this qt event to mainWindow focus
s.connect('activated()', keydef[1])
self.qtkeyconnections.append(s)
self.qTCGALabMod_tag = self.sliceLogic.AddObserver(
"ModifiedEvent", self.QTCGAChangeLabelInput
) # put test listener on the whole window
# Quick TCGA parameters
self.bEditTCGA = True
self.bEditShortCut = False
self.currentMessage = ""
seedArray = slicer.util.array(self.labelName)
self.qTCGASeedArray = seedArray.copy()
self.qTCGASegArray = seedArray.copy()
self.qTCGASeedArray[:] = 0
self.qTCGASegArray[:] = 0
self.SCutROIRad = 50
self.volSize = self.labelNode.GetImageData().GetDimensions()
self.qSCutROIArray = seedArray.copy(
) #np.zeros([self.volSize[0],self.volSize[1],1])
self.qSCutROIArray[:] = 0
roiVTK = vtk.vtkImageData()
roiVTK.DeepCopy(self.labelNode.GetImageData())
self.roiVTK = roiVTK
import vtkSlicerQuickTCGAModuleLogicPython
node = EditUtil.EditUtil().getParameterNode(
) # get the parameters from MRML
otsuRatio = float(node.GetParameter("QuickTCGAEffect,otsuRatio"))
curvatureWeight = float(
node.GetParameter("QuickTCGAEffect,curvatureWeight")) / 10
sizeThld = float(node.GetParameter("QuickTCGAEffect,sizeThld"))
sizeUpperThld = float(
node.GetParameter("QuickTCGAEffect,sizeUpperThld"))
mpp = float(node.GetParameter("QuickTCGAEffect,mpp")) / 100
cparams["otsuRatio"] = otsuRatio
cparams["curvatureWeight"] = curvatureWeight
cparams["sizeThld"] = sizeThld
cparams["sizeUpperThld"] = sizeUpperThld
cparams["mpp"] = mpp
qTCGAMod = vtkSlicerQuickTCGAModuleLogicPython.vtkQuickTCGA()
qTCGAMod.SetSourceVol(self.foregroundNode.GetImageData())
qTCGAMod.SetotsuRatio(otsuRatio)
qTCGAMod.SetcurvatureWeight(curvatureWeight)
qTCGAMod.SetsizeThld(sizeThld)
qTCGAMod.SetsizeUpperThld(sizeUpperThld)
qTCGAMod.Setmpp(mpp)
qTCGAMod.Initialization()
self.qTCGAMod = qTCGAMod
self.QuickTCGACreated = True #tracks if completed the initializtion (so can do stop correctly) of KSlice
def apply(self,xy):
# TODO: save the undo state - not yet available for extensions
# EditorStoreCheckPoint $_layers(label,node)
#
# get the parameters from MRML
#
node = EditUtil.EditUtil().getParameterNode()
tolerance = float(node.GetParameter("GooCut,tolerance"))
maxPixels = float(node.GetParameter("GooCut,maxPixels"))
#
# get the label and background volume nodes
#
labelLogic = self.sliceLogic.GetLabelLayer()
labelNode = labelLogic.GetVolumeNode()
labelNode.SetModifiedSinceRead(1)
backgroundLogic = self.sliceLogic.GetBackgroundLayer()
backgroundNode = backgroundLogic.GetVolumeNode()
#
# get the ijk location of the clicked point
# by projecting through patient space back into index
# space of the volume. Result is sub-pixel, so round it
# (note: bg and lb will be the same for volumes created
# by the editor, but can be different if the use selected
# different bg nodes, but that is not handled here).
#
xyToIJK = labelLogic.GetXYToIJKTransform().GetMatrix()
ijkFloat = xyToIJK.MultiplyPoint(xy+(0,1))[:3]
ijk = []
for element in ijkFloat:
try:
intElement = int(element)
except ValueError:
intElement = 0
ijk.append(intElement)
ijk.reverse()
ijk = tuple(ijk)
#
# Get the numpy array for the bg and label
#
import vtk.util.numpy_support
backgroundImage = backgroundNode.GetImageData()
labelImage = labelNode.GetImageData()
shape = list(backgroundImage.GetDimensions())
shape.reverse()
backgroundArray = vtk.util.numpy_support.vtk_to_numpy(backgroundImage.GetPointData().GetScalars()).reshape(shape)
labelArray = vtk.util.numpy_support.vtk_to_numpy(labelImage.GetPointData().GetScalars()).reshape(shape)
#
# do a region growing
#
try:
value = backgroundArray[ijk]
except IndexError:
# outside of volume
return
label = EditUtil.EditUtil().getLabel()
lo = value - tolerance
hi = value + tolerance
pixelsSet = 0
toVisit = [ijk,]
while toVisit != []:
location = toVisit.pop()
try:
l = labelArray[location]
b = backgroundArray[location]
except IndexError:
continue
if l != 0 or b < lo or b > hi:
continue
labelArray[location] = label
pixelsSet += 1
if pixelsSet > maxPixels:
toVisit = []
else:
# add the 6 neighbors to the stack
toVisit.append((location[0] - 1, location[1] , location[2] ))
toVisit.append((location[0] + 1, location[1] , location[2] ))
toVisit.append((location[0] , location[1] - 1, location[2] ))
toVisit.append((location[0] , location[1] + 1, location[2] ))
toVisit.append((location[0] , location[1] , location[2] - 1))
toVisit.append((location[0] , location[1] , location[2] + 1))
labelImage.Modified()
labelNode.Modified()
def processEvent(self, caller=None, event=None):
"""
handle events from the render window interactor
"""
node = EditUtil.EditUtil().getParameterNode()
preview = int(node.GetParameter("TraceAndSelect,preview"))
# Clear any saved outlines if preview has been just disabled
if not preview:
if self.prevPath != []:
self.prevPath = []
self.prevFillPoint = None
self.undoRedo.undo()
# let the superclass deal with the event if it wants to
super(TraceAndSelectTool, self).processEvent(caller, event)
# LEFT CLICK
if event == "LeftButtonPressEvent":
xy = self.interactor.GetEventPosition()
sliceLogic = self.sliceWidget.sliceLogic()
logic = TraceAndSelectLogic(sliceLogic)
logic.undoRedo = self.undoRedo
if self.prevPath != []:
logic.apply(xy,
forced_path=self.prevPath,
forced_point=self.prevFillPoint)
self.prevPath = []
self.prevFillPoint = None
else:
logic.apply(xy)
print("Got a %s at %s in %s" %
(event, str(xy),
self.sliceWidget.sliceLogic().GetSliceNode().GetName()))
self.abortEvent(event)
# RIGHT CLICK
elif event == "RightButtonPressEvent" and preview:
xy = self.interactor.GetEventPosition()
sliceLogic = self.sliceWidget.sliceLogic()
logic = TraceAndSelectLogic(sliceLogic)
logic.undoRedo = self.undoRedo
# Erase stored path and remove from view
if self.prevPath != []:
self.prevPath = []
self.prevFillPoint = None
logic.undoRedo.undo()
# Store prevPath and prevFillPoint
self.prevPath, self.prevFillPoint = logic.apply(xy, 1)
print("Got a %s at %s in %s" %
(event, str(xy),
self.sliceWidget.sliceLogic().GetSliceNode().GetName()))
self.abortEvent(event)
# SLICE VIEW HAS CHANGED
elif event == "ModifiedEvent": # Offset was changed on one of the viewing panels
# Erase stored path and remove from view
if self.prevPath != []:
self.prevPath = []
self.prevFillPoint = None
self.undoRedo.undo()
sliceLogic = self.sliceWidget.sliceLogic()
logic = TraceAndSelectLogic(sliceLogic)
logic.setErrorMessage("Previewed path was discarded.", 1)
else:
pass
# events from the slice node
if caller and caller.IsA('vtkMRMLSliceNode'):
# here you can respond to pan/zoom or other changes
# to the view
pass