class CarvingGui(LabelingGui):
def __init__(self, parentApplet, topLevelOperatorView, drawerUiPath=None):
self.topLevelOperatorView = topLevelOperatorView
self.isInitialized = (
False
) # Need this flag in carvingApplet where initialization is terminated with label selection
# members
self._doneSegmentationLayer = None
self._showSegmentationIn3D = False
# self._showUncertaintyLayer = False
# end: members
labelingSlots = LabelingGui.LabelingSlots()
labelingSlots.labelInput = topLevelOperatorView.WriteSeeds
labelingSlots.labelOutput = topLevelOperatorView.opLabelArray.Output
labelingSlots.labelEraserValue = topLevelOperatorView.opLabelArray.EraserLabelValue
labelingSlots.labelNames = topLevelOperatorView.LabelNames
labelingSlots.labelDelete = topLevelOperatorView.opLabelArray.DeleteLabel
labelingSlots.maxLabelValue = topLevelOperatorView.opLabelArray.MaxLabelValue
# We provide our own UI file (which adds an extra control for interactive mode)
directory = os.path.split(__file__)[0]
if drawerUiPath is None:
drawerUiPath = os.path.join(directory, "carvingDrawer.ui")
self.dialogdirCOM = os.path.join(directory,
"carvingObjectManagement.ui")
self.dialogdirSAD = os.path.join(directory, "saveAsDialog.ui")
# Add 3DWidget only if the data is 3D
is_3d = self._is_3d()
super(CarvingGui, self).__init__(parentApplet,
labelingSlots,
topLevelOperatorView,
drawerUiPath,
is_3d_widget_visible=is_3d)
self.parentApplet = parentApplet
self.labelingDrawerUi.currentObjectLabel.setText("<not saved yet>")
# Init special base class members
self.minLabelNumber = 2
self.maxLabelNumber = 2
mgr = ShortcutManager()
ActionInfo = ShortcutManager.ActionInfo
# set up keyboard shortcuts
mgr.register(
"3",
ActionInfo(
"Carving",
"Run interactive segmentation",
"Run interactive segmentation",
self.labelingDrawerUi.segment.click,
self.labelingDrawerUi.segment,
self.labelingDrawerUi.segment,
),
)
# Disable 3D view by default
self.render = False
if is_3d:
try:
self._renderMgr = RenderingManager(self.editor.view3d)
self._shownObjects3D = {}
self.render = True
except:
self.render = False
# Segmentation is toggled on by default in _after_init, below.
# (We can't enable it until the layers are all present.)
self._showSegmentationIn3D = False
self._segmentation_3d_label = None
self.labelingDrawerUi.segment.clicked.connect(self.onSegmentButton)
self.labelingDrawerUi.segment.setEnabled(True)
self.topLevelOperatorView.Segmentation.notifyDirty(
bind(self._segmentation_dirty))
self.topLevelOperatorView.HasSegmentation.notifyValueChanged(
bind(self._updateGui))
## uncertainty
# self.labelingDrawerUi.pushButtonUncertaintyFG.setEnabled(False)
# self.labelingDrawerUi.pushButtonUncertaintyBG.setEnabled(False)
# def onUncertaintyFGButton():
# logger.debug( "uncertFG button clicked" )
# pos = self.topLevelOperatorView.getMaxUncertaintyPos(label=2)
# self.editor.posModel.slicingPos = (pos[0], pos[1], pos[2])
# self.labelingDrawerUi.pushButtonUncertaintyFG.clicked.connect(onUncertaintyFGButton)
# def onUncertaintyBGButton():
# logger.debug( "uncertBG button clicked" )
# pos = self.topLevelOperatorView.getMaxUncertaintyPos(label=1)
# self.editor.posModel.slicingPos = (pos[0], pos[1], pos[2])
# self.labelingDrawerUi.pushButtonUncertaintyBG.clicked.connect(onUncertaintyBGButton)
# def onUncertaintyCombo(value):
# if value == 0:
# value = "none"
# self.labelingDrawerUi.pushButtonUncertaintyFG.setEnabled(False)
# self.labelingDrawerUi.pushButtonUncertaintyBG.setEnabled(False)
# self._showUncertaintyLayer = False
# else:
# if value == 1:
# value = "localMargin"
# elif value == 2:
# value = "exchangeCount"
# elif value == 3:
# value = "gabow"
# else:
# raise RuntimeError("unhandled case '%r'" % value)
# self.labelingDrawerUi.pushButtonUncertaintyFG.setEnabled(True)
# self.labelingDrawerUi.pushButtonUncertaintyBG.setEnabled(True)
# self._showUncertaintyLayer = True
# logger.debug( "uncertainty changed to %r" % value )
# self.topLevelOperatorView.UncertaintyType.setValue(value)
# self.updateAllLayers() #make sure that an added/deleted uncertainty layer is recognized
# self.labelingDrawerUi.uncertaintyCombo.currentIndexChanged.connect(onUncertaintyCombo)
self.labelingDrawerUi.objPrefix.setText(self.objectPrefix)
self.labelingDrawerUi.objPrefix.textChanged.connect(
self.setObjectPrefix)
## save
self.labelingDrawerUi.save.clicked.connect(self.onSaveButton)
## clear
self.labelingDrawerUi.clear.clicked.connect(self._onClearAction)
## object names
self.labelingDrawerUi.namesButton.clicked.connect(
self.onShowObjectNames)
if hasattr(self.labelingDrawerUi, "exportAllMeshesButton"):
self.labelingDrawerUi.exportAllMeshesButton.clicked.connect(
self._exportAllObjectMeshes)
self.labelingDrawerUi.labelListView.allowDelete = False
self._labelControlUi.labelListModel.allowRemove(False)
def layerIndexForName(name):
return self.layerstack.findMatchingIndex(lambda x: x.name == name)
def addLayerToggleShortcut(layername, shortcut):
def toggle():
row = layerIndexForName(layername)
self.layerstack.selectRow(row)
layer = self.layerstack[row]
layer.visible = not layer.visible
self.viewerControlWidget().layerWidget.setFocus()
mgr.register(
shortcut,
ActionInfo(
"Carving",
"Toggle layer %s" % layername,
"Toggle layer %s" % layername,
toggle,
self.viewerControlWidget(),
None,
),
)
# TODO
addLayerToggleShortcut("Completed segments (unicolor)", "d")
addLayerToggleShortcut("Segmentation", "s")
addLayerToggleShortcut("Input Data", "r")
def makeColortable():
self._doneSegmentationColortable = [QColor(0, 0, 0, 0).rgba()]
for i in range(254):
r, g, b = numpy.random.randint(0, 255), numpy.random.randint(
0, 255), numpy.random.randint(0, 255)
# ensure colors have sufficient distance to pure red and pure green
while (255 - r) + g + b < 128 or r + (255 - g) + b < 128:
r, g, b = numpy.random.randint(
0, 255), numpy.random.randint(
0, 255), numpy.random.randint(0, 255)
self._doneSegmentationColortable.append(QColor(r, g, b).rgba())
self._doneSegmentationColortable.append(QColor(0, 255, 0).rgba())
makeColortable()
self._updateGui()
@property
def objectPrefix(self):
return self.topLevelOperatorView.ObjectPrefix.value
def setObjectPrefix(self, value):
self.topLevelOperatorView.ObjectPrefix.setValue(value)
def _is_3d(self):
tagged_shape = defaultdict(lambda: 1)
tagged_shape.update(
self.topLevelOperatorView.InputData.meta.getTaggedShape())
is_3d = tagged_shape["x"] > 1 and tagged_shape[
"y"] > 1 and tagged_shape["z"] > 1
return is_3d
def _after_init(self):
super(CarvingGui, self)._after_init()
if self.render:
self._toggleSegmentation3D()
def _updateGui(self):
self.labelingDrawerUi.save.setEnabled(
self.topLevelOperatorView.dataIsStorable())
def onSegmentButton(self):
logger.debug("segment button clicked")
bkPriorityValue = self.labelingDrawerUi.backgroundPrioritySpin.value()
self.topLevelOperatorView.BackgroundPriority.setValue(bkPriorityValue)
biasValue = self.labelingDrawerUi.noBiasBelowSpin.value()
self.topLevelOperatorView.NoBiasBelow.setValue(biasValue)
self.topLevelOperatorView.Trigger.setDirty(slice(None))
def getObjectNames(self):
return self.topLevelOperatorView.AllObjectNames[:].wait()
def findNextPrefixNumber(self):
names = self.getObjectNames()
last = 0
for n in names:
match = re.match(f"^{self.objectPrefix}(?P<suffix>\d+)", n)
if match:
val = int(match.group("suffix"))
if val > last:
last = val
return last + 1
def saveAsDialog(self, name=""):
"""special functionality: reject names given to other objects"""
namesInUse = self.getObjectNames()
def generateObjectName():
return f"{self.objectPrefix}{self.findNextPrefixNumber()}"
name = name or generateObjectName()
dialog = uic.loadUi(self.dialogdirSAD)
dialog.lineEdit.setText(name)
dialog.lineEdit.selectAll()
dialog.warning.setVisible(False)
dialog.Ok.clicked.connect(dialog.accept)
dialog.Cancel.clicked.connect(dialog.reject)
dialog.isDisabled = False
def validate():
name = dialog.lineEdit.text()
if name in namesInUse:
dialog.Ok.setEnabled(False)
dialog.warning.setVisible(True)
dialog.isDisabled = True
elif dialog.isDisabled:
dialog.Ok.setEnabled(True)
dialog.warning.setVisible(False)
dialog.isDisabled = False
dialog.lineEdit.textChanged.connect(validate)
result = dialog.exec_()
if result:
return str(dialog.lineEdit.text())
def onSaveButton(self):
logger.info("save object as?")
prevName = self.topLevelOperatorView.currentObjectName()
if self.topLevelOperatorView.dataIsStorable():
prevName = ""
if self.topLevelOperatorView.hasCurrentObject():
prevName = self.topLevelOperatorView.currentObjectName()
if prevName == "<not saved yet>":
prevName = ""
name = self.saveAsDialog(name=prevName)
if name is None:
return
namesInUse = self.getObjectNames()
if name in namesInUse and name != prevName:
QMessageBox.critical(
self,
"Save Object As",
"An object with name '%s' already exists.\nPlease choose a different name."
% name,
)
return
self.topLevelOperatorView.saveObjectAs(name)
logger.info("save object as %s" % name)
if prevName != name and prevName != "":
self.topLevelOperatorView.deleteObject(prevName)
elif prevName == name:
self._renderMgr.removeObject(prevName)
self._renderMgr.invalidateObject(prevName)
self._shownObjects3D.pop(prevName, None)
else:
msgBox = QMessageBox(self)
msgBox.setText("The data does not seem fit to be stored.")
msgBox.setWindowTitle("Problem with Data")
msgBox.setIcon(2)
msgBox.exec_()
logger.error("object not saved due to faulty data.")
def onShowObjectNames(self):
"""show object names and allow user to load/delete them"""
dialog = uic.loadUi(self.dialogdirCOM)
names = self.getObjectNames()
dialog.objectNames.addItems(sorted(names, key=_humansort_key))
def loadSelection():
selected = [
str(name.text())
for name in dialog.objectNames.selectedItems()
]
dialog.close()
for objectname in selected:
self.topLevelOperatorView.loadObject(objectname)
def deleteSelection():
items = dialog.objectNames.selectedItems()
if self.confirmAndDelete([str(name.text()) for name in items]):
for name in items:
name.setHidden(True)
dialog.close()
dialog.loadButton.clicked.connect(loadSelection)
dialog.deleteButton.clicked.connect(deleteSelection)
dialog.cancelButton.clicked.connect(dialog.close)
dialog.exec_()
def confirmAndDelete(self, namelist):
logger.info("confirmAndDelete: {}".format(namelist))
objectlist = "".join("\n " + str(i) for i in namelist)
confirmed = QMessageBox.question(
self,
"Delete Object",
"Do you want to delete these objects?" + objectlist,
QMessageBox.Yes | QMessageBox.Cancel,
defaultButton=QMessageBox.Yes,
)
if confirmed == QMessageBox.Yes:
for name in namelist:
self.topLevelOperatorView.deleteObject(name)
return True
return False
def labelingContextMenu(self, names, op, position5d):
menu = QMenu(self)
menu.setObjectName("carving_context_menu")
posItem = menu.addAction("position %d %d %d" %
(position5d[1], position5d[2], position5d[3]))
posItem.setEnabled(False)
menu.addSeparator()
for name in names:
submenu = QMenu(name, menu)
# Load
loadAction = submenu.addAction("Load %s" % name)
loadAction.triggered.connect(partial(op.loadObject, name))
# Delete
def onDelAction(_name):
self.confirmAndDelete([_name])
if self.render and self._renderMgr.ready:
self._update_rendering()
delAction = submenu.addAction("Delete %s" % name)
delAction.triggered.connect(partial(onDelAction, name))
if self.render:
if name in self._shownObjects3D:
# Remove
def onRemove3D(_name):
label = self._shownObjects3D.pop(_name)
self._renderMgr.removeObject(label)
self._update_rendering()
removeAction = submenu.addAction("Remove %s from 3D view" %
name)
removeAction.triggered.connect(partial(onRemove3D, name))
else:
# Show
def onShow3D(_name):
label = self._renderMgr.addObject()
self._shownObjects3D[_name] = label
self._update_rendering()
showAction = submenu.addAction("Show 3D %s" % name)
showAction.triggered.connect(partial(onShow3D, name))
# Export mesh
exportAction = submenu.addAction("Export mesh for %s" % name)
exportAction.triggered.connect(
partial(self._onContextMenuExportMesh, name))
menu.addMenu(submenu)
if names:
menu.addSeparator()
menu.addSeparator()
if self.render:
showSeg3DAction = menu.addAction("Show Editing Segmentation in 3D")
showSeg3DAction.setCheckable(True)
showSeg3DAction.setChecked(self._showSegmentationIn3D)
showSeg3DAction.triggered.connect(self._toggleSegmentation3D)
if op.dataIsStorable():
menu.addAction("Save object").triggered.connect(self.onSaveButton)
menu.addAction("Browse objects").triggered.connect(
self.onShowObjectNames)
menu.addAction("Segment").triggered.connect(self.onSegmentButton)
menu.addAction("Clear").triggered.connect(self._onClearAction)
return menu
def _onClearAction(self):
confirm = QMessageBox.warning(self, "Really Clear?",
"Clear all brushtrokes?",
QMessageBox.Ok | QMessageBox.Cancel)
if confirm == QMessageBox.Ok:
self.topLevelOperatorView.clearCurrentLabeling()
def _clearLabelListGui(self):
# Remove rows until we have the right number
while self._labelControlUi.labelListModel.rowCount() > 2:
self._removeLastLabel()
def _onContextMenuExportMesh(self, _name):
"""
Export a single object mesh to a user-specified filename.
"""
recent_dir = preferences.get("carving", "recent export mesh directory")
if recent_dir is None:
defaultPath = os.path.join(os.path.expanduser("~"),
"{}obj".format(_name))
else:
defaultPath = os.path.join(recent_dir, "{}.obj".format(_name))
filepath, _filter = QFileDialog.getSaveFileName(
self, "Save meshes for object '{}'".format(_name), defaultPath,
"OBJ Files (*.obj)")
if not filepath:
return
obj_filepath = str(filepath)
preferences.set("carving", "recent export mesh directory",
os.path.split(obj_filepath)[0])
self._exportMeshes([_name], [obj_filepath])
def _exportAllObjectMeshes(self):
"""
Export all objects in the project as separate .obj files, stored to a user-specified directory.
"""
mst = self.topLevelOperatorView.MST.value
if not list(mst.object_lut.keys()):
QMessageBox.critical(
self, "Can't Export",
"You have no saved objets, so there are no meshes to export.")
return
recent_dir = preferences.get("carving", "recent export mesh directory")
if recent_dir is None:
defaultPath = os.path.join(os.path.expanduser("~"))
else:
defaultPath = os.path.join(recent_dir)
export_dir = QFileDialog.getExistingDirectory(
self, "Select export directory for mesh files", defaultPath)
if not export_dir:
return
export_dir = str(export_dir)
preferences.set("carving", "recent export mesh directory", export_dir)
# Get the list of all object names
object_names = []
obj_filepaths = []
for object_name in list(mst.object_lut.keys()):
object_names.append(object_name)
obj_filepaths.append(
os.path.join(export_dir, "{}.obj".format(object_name)))
if object_names:
self._exportMeshes(object_names, obj_filepaths)
def _exportMeshes(self, object_names: List[str],
obj_filepaths: List[str]) -> Request:
"""Save objects in the mst to .obj files
Args:
object_names: Names of the objects in the mst
obj_filepaths: One path for each object in object_names
Returns:
Returns the request object, used in testing
"""
def get_label_volume_from_mst(mst, object_name):
object_supervoxels = mst.object_lut[object_name]
object_lut = numpy.zeros(mst.nodeNum + 1, dtype=numpy.int32)
object_lut[object_supervoxels] = 1
supervoxel_volume = mst.supervoxelUint32
object_volume = object_lut[supervoxel_volume]
return object_volume
mst = self.topLevelOperatorView.MST.value
def exportMeshes(object_names, obj_filepaths):
n_objects = len(object_names)
progress_update = 100 / n_objects
try:
for obj, obj_path, obj_n in zip(object_names, obj_filepaths,
range(n_objects)):
object_volume = get_label_volume_from_mst(mst, obj)
unique_ids = len(numpy.unique(object_volume))
if unique_ids <= 1:
logger.info(f"No voxels found for {obj}, skipping")
continue
elif unique_ids > 2:
logger.info(
f"Supervoxel segmentation not unique for {obj}, skipping, got {unique_ids}"
)
continue
logger.info(f"Generating mesh for {obj}")
_, mesh_data = list(labeling_to_mesh(object_volume,
[1]))[0]
self.parentApplet.progressSignal(
(obj_n + 0.5) * progress_update)
logger.info(f"Mesh generation for {obj} complete.")
logger.info(f"Saving mesh for {obj} to {obj_path}")
mesh_to_obj(mesh_data, obj_path, obj)
self.parentApplet.progressSignal(
(obj_n + 1) * progress_update)
finally:
self.parentApplet.busy = False
self.parentApplet.progressSignal(100)
self.parentApplet.appletStateUpdateRequested()
self.parentApplet.busy = True
self.parentApplet.progressSignal(-1)
self.parentApplet.appletStateUpdateRequested()
req = Request(partial(exportMeshes, object_names, obj_filepaths))
req.submit()
return req
def handleEditorRightClick(self, position5d, globalWindowCoordinate):
names = self.topLevelOperatorView.doneObjectNamesForPosition(
position5d[1:4])
op = self.topLevelOperatorView
# (Subclasses may override menu)
menu = self.labelingContextMenu(names, op, position5d)
if menu is not None:
menu.exec_(globalWindowCoordinate)
def _toggleSegmentation3D(self):
self._showSegmentationIn3D = not self._showSegmentationIn3D
if self._showSegmentationIn3D:
self._segmentation_3d_label = self._renderMgr.addObject()
else:
self._renderMgr.removeObject(self._segmentation_3d_label)
self._segmentation_3d_label = None
self._update_rendering()
def _segmentation_dirty(self):
if self.render:
self._renderMgr.invalidateObject(CURRENT_SEGMENTATION_NAME)
self._renderMgr.removeObject(CURRENT_SEGMENTATION_NAME)
self._update_rendering()
def _update_rendering(self):
if not self.render:
return
op = self.topLevelOperatorView
if not self._renderMgr.ready:
shape = op.InputData.meta.shape[1:4]
self._renderMgr.setup(op.InputData.meta.shape[1:4])
# remove nonexistent objects
self._shownObjects3D = dict(
(k, v) for k, v in self._shownObjects3D.items()
if k in list(op.MST.value.object_lut.keys()))
lut = numpy.zeros(op.MST.value.nodeNum + 1, dtype=numpy.int32)
label_name_map = {}
for name, label in self._shownObjects3D.items():
objectSupervoxels = op.MST.value.object_lut[name]
lut[objectSupervoxels] = label
label_name_map[label] = name
label_name_map[name] = label
if self._showSegmentationIn3D:
# Add segmentation as label, which is green
label_name_map[
self._segmentation_3d_label] = CURRENT_SEGMENTATION_NAME
label_name_map[
CURRENT_SEGMENTATION_NAME] = self._segmentation_3d_label
lut[:] = numpy.where(op.MST.value.getSuperVoxelSeg() == 2,
self._segmentation_3d_label, lut)
self._renderMgr.volume = lut[
op.MST.value.
supervoxelUint32], label_name_map # (Advanced indexing)
self._update_colors()
self._renderMgr.update()
def _update_colors(self):
"""Update colors of objects in 3D viewport"""
op = self.topLevelOperatorView
ctable = self._doneSegmentationLayer.colorTable
for name, label in self._shownObjects3D.items():
color = QColor(ctable[op.MST.value.object_names[name]])
color = (color.red() / 255, color.green() / 255,
color.blue() / 255)
self._renderMgr.setColor(label, color)
if self._showSegmentationIn3D and self._segmentation_3d_label is not None:
# color of the foreground label from label list data
labels = self.labelListData
assert len(labels) == 2
fg_label = labels[1]
color = fg_label.pmapColor() # 2 is the foreground index
self._renderMgr.setColor(
self._segmentation_3d_label,
(color.red() / 255, color.green() / 255, color.blue() / 255))
def _getNext(self, slot, parentFun, transform=None):
numLabels = self.labelListData.rowCount()
value = slot.value
if numLabels < len(value):
result = value[numLabels]
if transform is not None:
result = transform(result)
return result
else:
return parentFun()
def getNextLabelName(self):
return self._getNext(self.topLevelOperatorView.LabelNames,
super(CarvingGui, self).getNextLabelName)
def appletDrawers(self):
return [("Carving", self._labelControlUi)]
def setupLayers(self):
logger.debug("setupLayers")
layers = []
def onButtonsEnabled(slot, roi):
currObj = self.topLevelOperatorView.CurrentObjectName.value
hasSeg = self.topLevelOperatorView.HasSegmentation.value
self.labelingDrawerUi.currentObjectLabel.setText(currObj)
self.labelingDrawerUi.save.setEnabled(hasSeg)
self.topLevelOperatorView.CurrentObjectName.notifyDirty(
onButtonsEnabled)
self.topLevelOperatorView.HasSegmentation.notifyDirty(onButtonsEnabled)
self.topLevelOperatorView.opLabelArray.NonzeroBlocks.notifyDirty(
onButtonsEnabled)
# Labels
labellayer, labelsrc = self.createLabelLayer(direct=True)
if labellayer is not None:
labellayer._allowToggleVisible = False
layers.append(labellayer)
# Tell the editor where to draw label data
self.editor.setLabelSink(labelsrc)
# uncertainty
# if self._showUncertaintyLayer:
# uncert = self.topLevelOperatorView.Uncertainty
# if uncert.ready():
# colortable = []
# for i in range(256-len(colortable)):
# r,g,b,a = i,0,0,i
# colortable.append(QColor(r,g,b,a).rgba())
# layer = ColortableLayer(createDataSource(uncert), colortable, direct=True)
# layer.name = "Uncertainty"
# layer.visible = True
# layer.opacity = 0.3
# layers.append(layer)
# segmentation
seg = self.topLevelOperatorView.Segmentation
# seg = self.topLevelOperatorView.MST.value.segmentation
# temp = self._done_lut[self.MST.value.supervoxelUint32[sl[1:4]]]
if seg.ready():
# source = RelabelingArraySource(seg)
# source.setRelabeling(numpy.arange(256, dtype=numpy.uint8))
# assign to the object label color, 0 is transparent, 1 is background
colortable = [
QColor(0, 0, 0, 0).rgba(),
QColor(0, 0, 0, 0).rgba(), labellayer._colorTable[2]
]
for i in range(256 - len(colortable)):
r, g, b = numpy.random.randint(0, 255), numpy.random.randint(
0, 255), numpy.random.randint(0, 255)
colortable.append(QColor(r, g, b).rgba())
layer = ColortableLayer(createDataSource(seg),
colortable,
direct=True)
layer.name = "Segmentation"
layer.setToolTip(
"This layer displays the <i>current</i> segmentation. Simply add foreground and background "
"labels, then press <i>Segment</i>.")
layer.visible = True
layer.opacity = 0.3
layers.append(layer)
# done
doneSeg = self.topLevelOperatorView.DoneSegmentation
if doneSeg.ready():
# FIXME: if the user segments more than 255 objects, those with indices that divide by 255 will be shown as transparent
# both here and in the _doneSegmentationColortable
colortable = 254 * [QColor(230, 25, 75).rgba()]
colortable.insert(0, QColor(0, 0, 0, 0).rgba())
# have to use lazyflow because it provides dirty signals
layer = ColortableLayer(createDataSource(doneSeg),
colortable,
direct=True)
layer.name = "Completed segments (unicolor)"
layer.setToolTip(
"In order to keep track of which objects you have already completed, this layer "
"shows <b>all completed object</b> in one color (<b>blue</b>). "
"The reason for only one color is that for finding out which "
"objects to label next, the identity of already completed objects is unimportant "
"and destracting.")
layer.visible = False
layer.opacity = 0.5
layers.append(layer)
layer = ColortableLayer(createDataSource(doneSeg),
self._doneSegmentationColortable,
direct=True)
layer.name = "Completed segments (one color per object)"
layer.setToolTip(
"<html>In order to keep track of which objects you have already completed, this layer "
"shows <b>all completed object</b>, each with a random color.</html>"
)
layer.visible = False
layer.opacity = 0.5
layer.colortableIsRandom = True
self._doneSegmentationLayer = layer
layers.append(layer)
# supervoxel
sv = self.topLevelOperatorView.Supervoxels
if sv.ready():
colortable = []
for i in range(256):
r, g, b = numpy.random.randint(0, 255), numpy.random.randint(
0, 255), numpy.random.randint(0, 255)
colortable.append(QColor(r, g, b).rgba())
layer = ColortableLayer(createDataSource(sv),
colortable,
direct=True)
layer.name = "Supervoxels"
layer.setToolTip(
"<html>This layer shows the partitioning of the input image into <b>supervoxels</b>. The carving "
"algorithm uses these tiny puzzle-piceces to piece together the segmentation of an "
"object. Sometimes, supervoxels are too large and straddle two distinct objects "
"(undersegmentation). In this case, it will be impossible to achieve the desired "
"segmentation. This layer helps you to understand these cases.</html>"
)
layer.visible = False
layer.colortableIsRandom = True
layer.opacity = 0.5
layers.append(layer)
# Visual overlay (just for easier labeling)
overlaySlot = self.topLevelOperatorView.OverlayData
if overlaySlot.ready():
overlay5D = self.topLevelOperatorView.OverlayData.value
layer = GrayscaleLayer(ArraySource(overlay5D), direct=True)
layer.visible = True
layer.name = "Overlay"
layer.opacity = 1.0
# if the flag window_leveling is set the contrast
# of the layer is adjustable
layer.window_leveling = True
self.labelingDrawerUi.thresToolButton.show()
layers.append(layer)
del layer
inputSlot = self.topLevelOperatorView.InputData
if inputSlot.ready():
layer = GrayscaleLayer(createDataSource(inputSlot), direct=True)
layer.name = "Input Data"
layer.setToolTip(
"<html>The data originally loaded into ilastik (unprocessed).</html>"
)
# layer.visible = not rawSlot.ready()
layer.visible = True
layer.opacity = 1.0
# Window leveling is already active on the Overlay,
# but if no overlay was provided, then activate window_leveling on the raw data instead.
if not overlaySlot.ready():
# if the flag window_leveling is set the contrast
# of the layer is adjustable
layer.window_leveling = True
self.labelingDrawerUi.thresToolButton.show()
layers.append(layer)
del layer
filteredSlot = self.topLevelOperatorView.FilteredInputData
if filteredSlot.ready():
layer = GrayscaleLayer(createDataSource(filteredSlot))
layer.name = "Filtered Input"
layer.visible = False
layer.opacity = 1.0
layers.append(layer)
return layers
class CarvingGui(LabelingGui):
def __init__(self, parentApplet, topLevelOperatorView, drawerUiPath=None ):
self.topLevelOperatorView = topLevelOperatorView
#members
self._doneSegmentationLayer = None
self._showSegmentationIn3D = False
#self._showUncertaintyLayer = False
#end: members
labelingSlots = LabelingGui.LabelingSlots()
labelingSlots.labelInput = topLevelOperatorView.WriteSeeds
labelingSlots.labelOutput = topLevelOperatorView.opLabelArray.Output
labelingSlots.labelEraserValue = topLevelOperatorView.opLabelArray.EraserLabelValue
labelingSlots.labelNames = topLevelOperatorView.LabelNames
labelingSlots.labelDelete = topLevelOperatorView.opLabelArray.DeleteLabel
labelingSlots.maxLabelValue = topLevelOperatorView.opLabelArray.MaxLabelValue
# We provide our own UI file (which adds an extra control for interactive mode)
directory = os.path.split(__file__)[0]
if drawerUiPath is None:
drawerUiPath = os.path.join(directory, 'carvingDrawer.ui')
self.dialogdirCOM = os.path.join(directory, 'carvingObjectManagement.ui')
self.dialogdirSAD = os.path.join(directory, 'saveAsDialog.ui')
# Add 3DWidget only if the data is 3D
is_3d = self._is_3d()
super(CarvingGui, self).__init__(parentApplet, labelingSlots, topLevelOperatorView, drawerUiPath,
is_3d_widget_visible=is_3d)
self.labelingDrawerUi.currentObjectLabel.setText("<not saved yet>")
# Init special base class members
self.minLabelNumber = 2
self.maxLabelNumber = 2
mgr = ShortcutManager()
ActionInfo = ShortcutManager.ActionInfo
#set up keyboard shortcuts
mgr.register( "3", ActionInfo( "Carving",
"Run interactive segmentation",
"Run interactive segmentation",
self.labelingDrawerUi.segment.click,
self.labelingDrawerUi.segment,
self.labelingDrawerUi.segment ) )
# Disable 3D view by default
self.render = False
if is_3d:
try:
self._renderMgr = RenderingManager( self.editor.view3d )
self._shownObjects3D = {}
self.render = True
except:
self.render = False
# Segmentation is toggled on by default in _after_init, below.
# (We can't enable it until the layers are all present.)
self._showSegmentationIn3D = False
self._segmentation_3d_label = None
self.labelingDrawerUi.segment.clicked.connect(self.onSegmentButton)
self.labelingDrawerUi.segment.setEnabled(True)
self.topLevelOperatorView.Segmentation.notifyDirty( bind( self._segmentation_dirty ) )
self.topLevelOperatorView.HasSegmentation.notifyValueChanged( bind( self._updateGui ) )
## uncertainty
#self.labelingDrawerUi.pushButtonUncertaintyFG.setEnabled(False)
#self.labelingDrawerUi.pushButtonUncertaintyBG.setEnabled(False)
#def onUncertaintyFGButton():
# logger.debug( "uncertFG button clicked" )
# pos = self.topLevelOperatorView.getMaxUncertaintyPos(label=2)
# self.editor.posModel.slicingPos = (pos[0], pos[1], pos[2])
#self.labelingDrawerUi.pushButtonUncertaintyFG.clicked.connect(onUncertaintyFGButton)
#def onUncertaintyBGButton():
# logger.debug( "uncertBG button clicked" )
# pos = self.topLevelOperatorView.getMaxUncertaintyPos(label=1)
# self.editor.posModel.slicingPos = (pos[0], pos[1], pos[2])
#self.labelingDrawerUi.pushButtonUncertaintyBG.clicked.connect(onUncertaintyBGButton)
#def onUncertaintyCombo(value):
# if value == 0:
# value = "none"
# self.labelingDrawerUi.pushButtonUncertaintyFG.setEnabled(False)
# self.labelingDrawerUi.pushButtonUncertaintyBG.setEnabled(False)
# self._showUncertaintyLayer = False
# else:
# if value == 1:
# value = "localMargin"
# elif value == 2:
# value = "exchangeCount"
# elif value == 3:
# value = "gabow"
# else:
# raise RuntimeError("unhandled case '%r'" % value)
# self.labelingDrawerUi.pushButtonUncertaintyFG.setEnabled(True)
# self.labelingDrawerUi.pushButtonUncertaintyBG.setEnabled(True)
# self._showUncertaintyLayer = True
# logger.debug( "uncertainty changed to %r" % value )
# self.topLevelOperatorView.UncertaintyType.setValue(value)
# self.updateAllLayers() #make sure that an added/deleted uncertainty layer is recognized
#self.labelingDrawerUi.uncertaintyCombo.currentIndexChanged.connect(onUncertaintyCombo)
## background priority
def onBackgroundPrioritySpin(value):
logger.debug( "background priority changed to %f" % value )
self.topLevelOperatorView.BackgroundPriority.setValue(value)
self.labelingDrawerUi.backgroundPrioritySpin.valueChanged.connect(onBackgroundPrioritySpin)
def onBackgroundPriorityDirty(slot, roi):
oldValue = self.labelingDrawerUi.backgroundPrioritySpin.value()
newValue = self.topLevelOperatorView.BackgroundPriority.value
if newValue != oldValue:
self.labelingDrawerUi.backgroundPrioritySpin.setValue(newValue)
self.topLevelOperatorView.BackgroundPriority.notifyDirty(onBackgroundPriorityDirty)
## bias
def onNoBiasBelowDirty(slot, roi):
oldValue = self.labelingDrawerUi.noBiasBelowSpin.value()
newValue = self.topLevelOperatorView.NoBiasBelow.value
if newValue != oldValue:
self.labelingDrawerUi.noBiasBelowSpin.setValue(newValue)
self.topLevelOperatorView.NoBiasBelow.notifyDirty(onNoBiasBelowDirty)
def onNoBiasBelowSpin(value):
logger.debug( "background priority changed to %f" % value )
self.topLevelOperatorView.NoBiasBelow.setValue(value)
self.labelingDrawerUi.noBiasBelowSpin.valueChanged.connect(onNoBiasBelowSpin)
## save
self.labelingDrawerUi.save.clicked.connect(self.onSaveButton)
## clear
self.labelingDrawerUi.clear.clicked.connect(self._onClearAction)
## object names
self.labelingDrawerUi.namesButton.clicked.connect(self.onShowObjectNames)
if hasattr( self.labelingDrawerUi, 'exportAllMeshesButton' ):
self.labelingDrawerUi.exportAllMeshesButton.clicked.connect(self._exportAllObjectMeshes)
self.labelingDrawerUi.labelListView.allowDelete = False
self._labelControlUi.labelListModel.allowRemove(False)
def layerIndexForName(name):
return self.layerstack.findMatchingIndex(lambda x: x.name == name)
def addLayerToggleShortcut(layername, shortcut):
def toggle():
row = layerIndexForName(layername)
self.layerstack.selectRow(row)
layer = self.layerstack[row]
layer.visible = not layer.visible
self.viewerControlWidget().layerWidget.setFocus()
mgr.register(shortcut, ActionInfo( "Carving",
"Toggle layer %s" % layername,
"Toggle layer %s" % layername,
toggle,
self.viewerControlWidget(),
None ) )
#TODO
addLayerToggleShortcut("Completed segments (unicolor)", "d")
addLayerToggleShortcut("Segmentation", "s")
addLayerToggleShortcut("Input Data", "r")
def makeColortable():
self._doneSegmentationColortable = [QColor(0,0,0,0).rgba()]
for i in range(254):
r,g,b = numpy.random.randint(0,255), numpy.random.randint(0,255), numpy.random.randint(0,255)
# ensure colors have sufficient distance to pure red and pure green
while (255 - r)+g+b<128 or r+(255-g)+b<128:
r,g,b = numpy.random.randint(0,255), numpy.random.randint(0,255), numpy.random.randint(0,255)
self._doneSegmentationColortable.append(QColor(r,g,b).rgba())
self._doneSegmentationColortable.append(QColor(0,255,0).rgba())
makeColortable()
self._updateGui()
def _is_3d(self):
tagged_shape = defaultdict(lambda: 1)
tagged_shape.update(self.topLevelOperatorView.InputData.meta.getTaggedShape())
is_3d = tagged_shape['x'] > 1 and tagged_shape['y'] > 1 and tagged_shape['z'] > 1
return is_3d
def _after_init(self):
super(CarvingGui, self)._after_init()
if self.render:
self._toggleSegmentation3D()
def _updateGui(self):
self.labelingDrawerUi.save.setEnabled( self.topLevelOperatorView.dataIsStorable() )
def onSegmentButton(self):
logger.debug( "segment button clicked" )
self.topLevelOperatorView.Trigger.setDirty(slice(None))
def saveAsDialog(self, name=""):
'''special functionality: reject names given to other objects'''
dialog = uic.loadUi(self.dialogdirSAD)
dialog.lineEdit.setText(name)
dialog.warning.setVisible(False)
dialog.Ok.clicked.connect(dialog.accept)
dialog.Cancel.clicked.connect(dialog.reject)
listOfItems = self.topLevelOperatorView.AllObjectNames[:].wait()
dialog.isDisabled = False
def validate():
name = dialog.lineEdit.text()
if name in listOfItems:
dialog.Ok.setEnabled(False)
dialog.warning.setVisible(True)
dialog.isDisabled = True
elif dialog.isDisabled:
dialog.Ok.setEnabled(True)
dialog.warning.setVisible(False)
dialog.isDisabled = False
dialog.lineEdit.textChanged.connect(validate)
result = dialog.exec_()
if result:
return str(dialog.lineEdit.text())
def onSaveButton(self):
logger.info( "save object as?" )
if self.topLevelOperatorView.dataIsStorable():
prevName = ""
if self.topLevelOperatorView.hasCurrentObject():
prevName = self.topLevelOperatorView.currentObjectName()
if prevName == "<not saved yet>":
prevName = ""
name = self.saveAsDialog(name=prevName)
if name is None:
return
objects = self.topLevelOperatorView.AllObjectNames[:].wait()
if name in objects and name != prevName:
QMessageBox.critical(self, "Save Object As", "An object with name '%s' already exists.\nPlease choose a different name." % name)
return
self.topLevelOperatorView.saveObjectAs(name)
logger.info( "save object as %s" % name )
if prevName != name and prevName != "":
self.topLevelOperatorView.deleteObject(prevName)
elif prevName == name:
self._renderMgr.removeObject(prevName)
self._renderMgr.invalidateObject(prevName)
self._shownObjects3D.pop(prevName, None)
else:
msgBox = QMessageBox(self)
msgBox.setText("The data does not seem fit to be stored.")
msgBox.setWindowTitle("Problem with Data")
msgBox.setIcon(2)
msgBox.exec_()
logger.error( "object not saved due to faulty data." )
def onShowObjectNames(self):
'''show object names and allow user to load/delete them'''
dialog = uic.loadUi(self.dialogdirCOM)
listOfItems = self.topLevelOperatorView.AllObjectNames[:].wait()
dialog.objectNames.addItems(sorted(listOfItems))
def loadSelection():
selected = [str(name.text()) for name in dialog.objectNames.selectedItems()]
dialog.close()
for objectname in selected:
self.topLevelOperatorView.loadObject(objectname)
def deleteSelection():
items = dialog.objectNames.selectedItems()
if self.confirmAndDelete([str(name.text()) for name in items]):
for name in items:
name.setHidden(True)
dialog.close()
dialog.loadButton.clicked.connect(loadSelection)
dialog.deleteButton.clicked.connect(deleteSelection)
dialog.cancelButton.clicked.connect(dialog.close)
dialog.exec_()
def confirmAndDelete(self,namelist):
logger.info( "confirmAndDelete: {}".format( namelist ) )
objectlist = "".join("\n "+str(i) for i in namelist)
confirmed = QMessageBox.question(self, "Delete Object", \
"Do you want to delete these objects?"+objectlist, \
QMessageBox.Yes | QMessageBox.Cancel, \
defaultButton=QMessageBox.Yes)
if confirmed == QMessageBox.Yes:
for name in namelist:
self.topLevelOperatorView.deleteObject(name)
return True
return False
def labelingContextMenu(self,names,op,position5d):
menu = QMenu(self)
menu.setObjectName("carving_context_menu")
posItem = menu.addAction("position %d %d %d" % (position5d[1], position5d[2], position5d[3]))
posItem.setEnabled(False)
menu.addSeparator()
for name in names:
submenu = QMenu(name,menu)
# Load
loadAction = submenu.addAction("Load %s" % name)
loadAction.triggered.connect( partial(op.loadObject, name) )
# Delete
def onDelAction(_name):
self.confirmAndDelete([_name])
if self.render and self._renderMgr.ready:
self._update_rendering()
delAction = submenu.addAction("Delete %s" % name)
delAction.triggered.connect( partial(onDelAction, name) )
if self.render:
if name in self._shownObjects3D:
# Remove
def onRemove3D(_name):
label = self._shownObjects3D.pop(_name)
self._renderMgr.removeObject(label)
self._update_rendering()
removeAction = submenu.addAction("Remove %s from 3D view" % name)
removeAction.triggered.connect( partial(onRemove3D, name) )
else:
# Show
def onShow3D(_name):
label = self._renderMgr.addObject()
self._shownObjects3D[_name] = label
self._update_rendering()
showAction = submenu.addAction("Show 3D %s" % name)
showAction.triggered.connect( partial(onShow3D, name ) )
# Export mesh
exportAction = submenu.addAction("Export mesh for %s" % name)
exportAction.triggered.connect( partial(self._onContextMenuExportMesh, name) )
menu.addMenu(submenu)
if names:
menu.addSeparator()
menu.addSeparator()
if self.render:
showSeg3DAction = menu.addAction( "Show Editing Segmentation in 3D" )
showSeg3DAction.setCheckable(True)
showSeg3DAction.setChecked( self._showSegmentationIn3D )
showSeg3DAction.triggered.connect( self._toggleSegmentation3D )
if op.dataIsStorable():
menu.addAction("Save object").triggered.connect( self.onSaveButton )
menu.addAction("Browse objects").triggered.connect( self.onShowObjectNames )
menu.addAction("Segment").triggered.connect( self.onSegmentButton )
menu.addAction("Clear").triggered.connect( self._onClearAction )
return menu
def _onClearAction(self):
confirm = QMessageBox.warning(self, "Really Clear?", "Clear all brushtrokes?", QMessageBox.Ok | QMessageBox.Cancel)
if confirm == QMessageBox.Ok:
self.topLevelOperatorView.clearCurrentLabeling()
def _onContextMenuExportMesh(self, _name):
"""
Export a single object mesh to a user-specified filename.
"""
recent_dir = PreferencesManager().get( 'carving', 'recent export mesh directory' )
if recent_dir is None:
defaultPath = os.path.join( os.path.expanduser('~'), '{}obj'.format(_name) )
else:
defaultPath = os.path.join( recent_dir, '{}.obj'.format(_name) )
filepath, _filter = QFileDialog.getSaveFileName(self,
"Save meshes for object '{}'".format(_name),
defaultPath,
"OBJ Files (*.obj)")
if not filepath:
return
obj_filepath = str(filepath)
PreferencesManager().set( 'carving', 'recent export mesh directory', os.path.split(obj_filepath)[0] )
self._exportMeshes([_name], [obj_filepath])
def _exportAllObjectMeshes(self):
"""
Export all objects in the project as separate .obj files, stored to a user-specified directory.
"""
mst = self.topLevelOperatorView.MST.value
if not list(mst.object_lut.keys()):
QMessageBox.critical(self, "Can't Export", "You have no saved objets, so there are no meshes to export.")
return
recent_dir = PreferencesManager().get( 'carving', 'recent export mesh directory' )
if recent_dir is None:
defaultPath = os.path.join( os.path.expanduser('~') )
else:
defaultPath = os.path.join( recent_dir )
export_dir = QFileDialog.getExistingDirectory( self,
"Select export directory for mesh files",
defaultPath)
if not export_dir:
return
export_dir = str(export_dir)
PreferencesManager().set( 'carving', 'recent export mesh directory', export_dir )
# Get the list of all object names
object_names = []
obj_filepaths = []
for object_name in list(mst.object_lut.keys()):
object_names.append( object_name )
obj_filepaths.append( os.path.join( export_dir, "{}.obj".format( object_name ) ) )
if object_names:
self._exportMeshes( object_names, obj_filepaths )
def _exportMeshes(self, object_names, obj_filepaths):
"""
Export a mesh .obj file for each object in the object_names list to the corresponding file name from the obj_filepaths list.
This function is pseudo-recursive. It works like this:
1) Pop the first name/file from the args
2) Kick off the export by launching the export mesh dlg
3) return from this function to allow the eventloop to resume while the export is running
4) When the export dlg is finished, create the mesh file
5) If there are still more items in the object_names list to process, repeat this function.
"""
# Pop the first object off the list
object_name = object_names.pop(0)
obj_filepath = obj_filepaths.pop(0)
# Construct a volume with only this object.
# We might be tempted to get the object directly from opCarving.DoneObjects,
# but that won't be correct for overlapping objects.
mst = self.topLevelOperatorView.MST.value
object_supervoxels = mst.object_lut[object_name]
object_lut = numpy.zeros(mst.nodeNum+1, dtype=numpy.int32)
object_lut[object_supervoxels] = 1
supervoxel_volume = mst.supervoxelUint32
object_volume = object_lut[supervoxel_volume]
if len(numpy.unique(object_volume)) <= 1:
if object_names:
self._exportMeshes(object_names, obj_filepaths)
return
# Run the mesh extractor
window = MeshGeneratorDialog(self)
def onMeshesComplete(mesh):
"""
Called when mesh extraction is complete.
Writes the extracted mesh to an .obj file
"""
logger.info( "Mesh generation complete." )
# FIXME: the old comment: Mesh count can sometimes be 0 for the '<not saved yet>' object...
# FIXME: is this still relevant???
'''
mesh_count = len( window.extractor.meshes )
if mesh_count > 0:
assert mesh_count == 1, \
"Found {} meshes processing object '{}',"\
"(only expected 1)".format( mesh_count, object_name )
mesh = list(window.extractor.meshes.values())[0]
logger.info( "Saving meshes to {}".format( obj_filepath ) )
# Use VTK to write to a temporary .vtk file
tmpdir = tempfile.mkdtemp()
vtkpoly_path = os.path.join(tmpdir, 'meshes.vtk')
w = vtkPolyDataWriter()
w.SetFileTypeToASCII()
w.SetInput(mesh)
w.SetFileName(vtkpoly_path)
w.Write()
# Now convert the file to .obj format.
convertVTPtoOBJ(vtkpoly_path, obj_filepath)
'''
logger.info("Saving meshes to {}".format(obj_filepath))
mesh_to_obj(mesh, obj_filepath, object_name)
# Cleanup: We don't need the window anymore.
window.setParent(None)
# If there are still objects left to process,
# start again with the remainder of the list.
if object_names:
self._exportMeshes(object_names, obj_filepaths)
window.finished.connect( onMeshesComplete )
# Kick off the save process and exit to the event loop
window.show()
QTimer.singleShot(0, partial(window.run, object_volume))
def handleEditorRightClick(self, position5d, globalWindowCoordinate):
names = self.topLevelOperatorView.doneObjectNamesForPosition(position5d[1:4])
op = self.topLevelOperatorView
# (Subclasses may override menu)
menu = self.labelingContextMenu(names,op,position5d)
if menu is not None:
menu.exec_(globalWindowCoordinate)
def _toggleSegmentation3D(self):
self._showSegmentationIn3D = not self._showSegmentationIn3D
if self._showSegmentationIn3D:
self._segmentation_3d_label = self._renderMgr.addObject()
else:
self._renderMgr.removeObject(self._segmentation_3d_label)
self._segmentation_3d_label = None
self._update_rendering()
def _segmentation_dirty(self):
if self.render:
self._renderMgr.invalidateObject(CURRENT_SEGMENTATION_NAME)
self._renderMgr.removeObject(CURRENT_SEGMENTATION_NAME)
self._update_rendering()
def _update_rendering(self):
if not self.render:
return
op = self.topLevelOperatorView
if not self._renderMgr.ready:
shape = op.InputData.meta.shape[1:4]
self._renderMgr.setup(op.InputData.meta.shape[1:4])
# remove nonexistent objects
self._shownObjects3D = dict((k, v) for k, v in self._shownObjects3D.items()
if k in list(op.MST.value.object_lut.keys()))
lut = numpy.zeros(op.MST.value.nodeNum+1, dtype=numpy.int32)
label_name_map = {}
for name, label in self._shownObjects3D.items():
objectSupervoxels = op.MST.value.object_lut[name]
lut[objectSupervoxels] = label
label_name_map[label] = name
label_name_map[name] = label
if self._showSegmentationIn3D:
# Add segmentation as label, which is green
label_name_map[self._segmentation_3d_label] = CURRENT_SEGMENTATION_NAME
label_name_map[CURRENT_SEGMENTATION_NAME] = self._segmentation_3d_label
lut[:] = numpy.where( op.MST.value.getSuperVoxelSeg() == 2, self._segmentation_3d_label, lut )
self._renderMgr.volume = lut[op.MST.value.supervoxelUint32], label_name_map # (Advanced indexing)
self._update_colors()
self._renderMgr.update()
def _update_colors(self):
op = self.topLevelOperatorView
ctable = self._doneSegmentationLayer.colorTable
for name, label in self._shownObjects3D.items():
color = QColor(ctable[op.MST.value.object_names[name]])
color = (old_div(color.red(), 255.0), old_div(color.green(), 255.0), old_div(color.blue(), 255.0))
self._renderMgr.setColor(label, color)
if self._showSegmentationIn3D and self._segmentation_3d_label is not None:
self._renderMgr.setColor(self._segmentation_3d_label, (0.0, 1.0, 0.0)) # Green
def _getNext(self, slot, parentFun, transform=None):
numLabels = self.labelListData.rowCount()
value = slot.value
if numLabels < len(value):
result = value[numLabels]
if transform is not None:
result = transform(result)
return result
else:
return parentFun()
def getNextLabelName(self):
return self._getNext(self.topLevelOperatorView.LabelNames,
super(CarvingGui, self).getNextLabelName)
def appletDrawers(self):
return [ ("Carving", self._labelControlUi) ]
def setupLayers( self ):
logger.debug( "setupLayers" )
layers = []
def onButtonsEnabled(slot, roi):
currObj = self.topLevelOperatorView.CurrentObjectName.value
hasSeg = self.topLevelOperatorView.HasSegmentation.value
self.labelingDrawerUi.currentObjectLabel.setText(currObj)
self.labelingDrawerUi.save.setEnabled(hasSeg)
self.topLevelOperatorView.CurrentObjectName.notifyDirty(onButtonsEnabled)
self.topLevelOperatorView.HasSegmentation.notifyDirty(onButtonsEnabled)
self.topLevelOperatorView.opLabelArray.NonzeroBlocks.notifyDirty(onButtonsEnabled)
# Labels
labellayer, labelsrc = self.createLabelLayer(direct=True)
if labellayer is not None:
labellayer._allowToggleVisible = False
layers.append(labellayer)
# Tell the editor where to draw label data
self.editor.setLabelSink(labelsrc)
#uncertainty
#if self._showUncertaintyLayer:
# uncert = self.topLevelOperatorView.Uncertainty
# if uncert.ready():
# colortable = []
# for i in range(256-len(colortable)):
# r,g,b,a = i,0,0,i
# colortable.append(QColor(r,g,b,a).rgba())
# layer = ColortableLayer(LazyflowSource(uncert), colortable, direct=True)
# layer.name = "Uncertainty"
# layer.visible = True
# layer.opacity = 0.3
# layers.append(layer)
#segmentation
seg = self.topLevelOperatorView.Segmentation
#seg = self.topLevelOperatorView.MST.value.segmentation
#temp = self._done_lut[self.MST.value.supervoxelUint32[sl[1:4]]]
if seg.ready():
#source = RelabelingArraySource(seg)
#source.setRelabeling(numpy.arange(256, dtype=numpy.uint8))
colortable = [QColor(0,0,0,0).rgba(), QColor(0,0,0,0).rgba(), QColor(0,255,0).rgba()]
for i in range(256-len(colortable)):
r,g,b = numpy.random.randint(0,255), numpy.random.randint(0,255), numpy.random.randint(0,255)
colortable.append(QColor(r,g,b).rgba())
layer = ColortableLayer(LazyflowSource(seg), colortable, direct=True)
layer.name = "Segmentation"
layer.setToolTip("This layer displays the <i>current</i> segmentation. Simply add foreground and background " \
"labels, then press <i>Segment</i>.")
layer.visible = True
layer.opacity = 0.3
layers.append(layer)
#done
done = self.topLevelOperatorView.DoneObjects
if done.ready():
colortable = [QColor(0,0,0,0).rgba(), QColor(0,0,255).rgba()]
#have to use lazyflow because it provides dirty signals
layer = ColortableLayer(LazyflowSource(done), colortable, direct=True)
layer.name = "Completed segments (unicolor)"
layer.setToolTip("In order to keep track of which objects you have already completed, this layer " \
"shows <b>all completed object</b> in one color (<b>blue</b>). " \
"The reason for only one color is that for finding out which " \
"objects to label next, the identity of already completed objects is unimportant " \
"and destracting.")
layer.visible = False
layer.opacity = 0.5
layers.append(layer)
#done seg
doneSeg = self.topLevelOperatorView.DoneSegmentation
if doneSeg.ready():
layer = ColortableLayer(LazyflowSource(doneSeg), self._doneSegmentationColortable, direct=True)
layer.name = "Completed segments (one color per object)"
layer.setToolTip("<html>In order to keep track of which objects you have already completed, this layer " \
"shows <b>all completed object</b>, each with a random color.</html>")
layer.visible = False
layer.opacity = 0.5
self._doneSegmentationLayer = layer
layers.append(layer)
#supervoxel
sv = self.topLevelOperatorView.Supervoxels
if sv.ready():
colortable = []
for i in range(256):
r,g,b = numpy.random.randint(0,255), numpy.random.randint(0,255), numpy.random.randint(0,255)
colortable.append(QColor(r,g,b).rgba())
layer = ColortableLayer(LazyflowSource(sv), colortable, direct=True)
layer.name = "Supervoxels"
layer.setToolTip("<html>This layer shows the partitioning of the input image into <b>supervoxels</b>. The carving " \
"algorithm uses these tiny puzzle-piceces to piece together the segmentation of an " \
"object. Sometimes, supervoxels are too large and straddle two distinct objects " \
"(undersegmentation). In this case, it will be impossible to achieve the desired " \
"segmentation. This layer helps you to understand these cases.</html>")
layer.visible = False
layer.opacity = 1.0
layers.append(layer)
# Visual overlay (just for easier labeling)
overlaySlot = self.topLevelOperatorView.OverlayData
if overlaySlot.ready():
overlay5D = self.topLevelOperatorView.OverlayData.value
layer = GrayscaleLayer(ArraySource(overlay5D), direct=True)
layer.visible = True
layer.name = 'Overlay'
layer.opacity = 1.0
# if the flag window_leveling is set the contrast
# of the layer is adjustable
layer.window_leveling = True
self.labelingDrawerUi.thresToolButton.show()
layers.append(layer)
del layer
inputSlot = self.topLevelOperatorView.InputData
if inputSlot.ready():
layer = GrayscaleLayer( LazyflowSource(inputSlot), direct=True )
layer.name = "Input Data"
layer.setToolTip("<html>The data originally loaded into ilastik (unprocessed).</html>")
#layer.visible = not rawSlot.ready()
layer.visible = True
layer.opacity = 1.0
# Window leveling is already active on the Overlay,
# but if no overlay was provided, then activate window_leveling on the raw data instead.
if not overlaySlot.ready():
# if the flag window_leveling is set the contrast
# of the layer is adjustable
layer.window_leveling = True
self.labelingDrawerUi.thresToolButton.show()
layers.append(layer)
del layer
filteredSlot = self.topLevelOperatorView.FilteredInputData
if filteredSlot.ready():
layer = GrayscaleLayer( LazyflowSource(filteredSlot) )
layer.name = "Filtered Input"
layer.visible = False
layer.opacity = 1.0
layers.append(layer)
return layers
