def onWIPButtonClicked(self):
import urllib2
reply = urllib2.urlopen('http://www.osa.sunysb.edu/erich.png')
byte_array = reply.read()
image = qt.QImage(qt.QImage.Format_RGB888)
image.loadFromData(byte_array)
imageData = self.QImage2vtkImage(image)
volumeNode = slicer.vtkMRMLVectorVolumeNode()
volumeNode.SetName("WEB")
volumeNode.SetAndObserveImageData(imageData)
displayNode = slicer.vtkMRMLVectorVolumeDisplayNode()
slicer.mrmlScene.AddNode(volumeNode)
slicer.mrmlScene.AddNode(displayNode)
volumeNode.SetAndObserveDisplayNodeID(displayNode.GetID())
displayNode.SetAndObserveColorNodeID('vtkMRMLColorTableNodeGrey')
self.mutate()
def openTargetImage(self):
import string
p = self.v.page()
m = p.mainFrame()
imageBound=m.evaluateJavaScript('viewer.viewport.viewportToImageRectangle(viewer.viewport.getBounds().x, viewer.viewport.getBounds().y, viewer.viewport.getBounds().width, viewer.viewport.getBounds().height)')
x=imageBound[u'x']
y=imageBound[u'y']
width=imageBound[u'width']
height=imageBound[u'height']
self.j['x'] = x
self.j['y'] = y
self.j['width'] = width
self.j['height'] = height
imagedata = m.evaluateJavaScript('imagedata')
tmpfilename= imagedata[u'metaData'][1]
imageFileName=string.rstrip(tmpfilename,'.dzi')
self.tilename = imagedata[u'imageId']
print self.tilename
self.parameterNode.SetParameter("SlicerPathology,tilename", self.tilename)
current_weburl ='http://quip1.uhmc.sunysb.edu/fcgi-bin/iipsrv.fcgi?IIIF=' + imageFileName +'/' + str(x) + ','+ str(y) + ',' + str(width) + ',' + str(height) + '/full/0/default.jpg'
print current_weburl
self.v.setUrl(qt.QUrl(current_weburl))
self.v.show()
reply = urllib2.urlopen(current_weburl)
byte_array = reply.read()
image = qt.QImage(qt.QImage.Format_RGB888)
image.loadFromData(byte_array)
imageData = self.QImage2vtkImage(image)
volumeNode = slicer.vtkMRMLVectorVolumeNode()
volumeNode.SetName("WEB")
volumeNode.SetAndObserveImageData(imageData)
displayNode = slicer.vtkMRMLVectorVolumeDisplayNode()
slicer.mrmlScene.AddNode(volumeNode)
slicer.mrmlScene.AddNode(displayNode)
volumeNode.SetAndObserveDisplayNodeID(displayNode.GetID())
displayNode.SetAndObserveColorNodeID('vtkMRMLColorTableNodeGrey')
self.mutate()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.logic = DataCollectionLogic()
self.moduleDir = os.path.dirname(slicer.modules.datacollection.path)
datasetDirectory = os.path.join(self.moduleDir, os.pardir, "Datasets")
try:
os.listdir(datasetDirectory)
except FileNotFoundError:
os.mkdir(datasetDirectory)
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
#self.imageSaveDirectory = qt.QLineEdit("Select directory to save images")
#parametersFormLayout.addRow(self.imageSaveDirectory)
self.selectRecordingNodeComboBox = qt.QComboBox()
self.selectRecordingNodeComboBox.addItems(["Select Image Node"])
self.recordingNodes = slicer.util.getNodesByClass("vtkMRMLVolumeNode")
recordingNodeNames = []
for recordingNode in self.recordingNodes:
recordingNodeNames.append(recordingNode.GetName())
self.selectRecordingNodeComboBox.addItems(recordingNodeNames)
parametersFormLayout.addRow(self.selectRecordingNodeComboBox)
self.datasetSelector = qt.QComboBox()
self.datasetSelector.addItems(["Select Dataset"])
datasetDirectoryContents = os.listdir(
os.path.join(self.moduleDir, os.pardir, "Datasets"))
datasetNames = [
dir for dir in datasetDirectoryContents if dir.find(".") == -1
]
self.datasetSelector.addItems(["Create New Dataset"])
self.datasetSelector.addItems(datasetNames)
parametersFormLayout.addRow(self.datasetSelector)
self.videoIDComboBox = qt.QComboBox()
self.videoIDComboBox.addItems(
["Select video ID", "Create new video ID"])
parametersFormLayout.addRow(self.videoIDComboBox)
self.fileTypeComboBox = qt.QComboBox()
self.fileTypeComboBox.addItems([".jpg", ".png", ".bmp", ".tiff"])
parametersFormLayout.addRow(self.fileTypeComboBox)
self.fileType = self.fileTypeComboBox.currentText
self.collectFromSequenceCheckBox = qt.QCheckBox(
"Collect from Sequence")
self.collectingFromSequence = False
parametersFormLayout.addRow(self.collectFromSequenceCheckBox)
self.problemTypeComboBox = qt.QComboBox()
self.problemTypeComboBox.addItems([
"Select problem type", "Classification", "Detection",
"Segmentation"
])
parametersFormLayout.addRow(self.problemTypeComboBox)
self.classificationFrame = qt.QFrame()
self.classificationLayout()
parametersFormLayout.addRow(self.classificationFrame)
self.classificationFrame.visible = False
self.detectionFrame = qt.QFrame()
self.detectionLayout()
parametersFormLayout.addRow(self.detectionFrame)
self.detectionFrame.visible = False
self.segmentationFrame = qt.QFrame()
self.segmentationLayout()
parametersFormLayout.addRow(self.segmentationFrame)
self.segmentationFrame.visible = False
#
# Start/Stop Image Collection Button
#
self.startStopCollectingImagesButton = qt.QPushButton(
"Start Image Collection")
self.startStopCollectingImagesButton.toolTip = "Collect images."
self.startStopCollectingImagesButton.enabled = False
parametersFormLayout.addRow(self.startStopCollectingImagesButton)
self.infoLabel = qt.QLabel("")
parametersFormLayout.addRow(self.infoLabel)
# connections
self.fileTypeComboBox.connect('currentIndexChanged(int)',
self.onFileTypeSelected)
self.inputSegmentationSelector.connect(
'currentIndexChanged(int)', self.onSegmentationInputSelected)
self.selectRecordingNodeComboBox.connect("currentIndexChanged(int)",
self.onRecordingNodeSelected)
self.datasetSelector.connect('currentIndexChanged(int)',
self.onDatasetSelected)
self.startStopCollectingImagesButton.connect(
'clicked(bool)', self.onStartStopCollectingImagesButton)
self.videoIDComboBox.connect('currentIndexChanged(int)',
self.onVideoIDSelected)
self.collectFromSequenceCheckBox.connect(
'stateChanged(int)', self.onCollectFromSequenceChecked)
self.problemTypeComboBox.connect('currentIndexChanged(int)',
self.onProblemTypeSelected)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Start/Stop Collecting Images Button state
self.onSelect()
try:
self.webcamReference = slicer.util.getNode('Webcam_Reference')
except slicer.util.MRMLNodeNotFoundException:
#if not self.webcamReference:
imageSpacing = [0.2, 0.2, 0.2]
imageData = vtk.vtkImageData()
imageData.SetDimensions(640, 480, 1)
imageData.AllocateScalars(vtk.VTK_UNSIGNED_CHAR, 1)
thresholder = vtk.vtkImageThreshold()
thresholder.SetInputData(imageData)
thresholder.SetInValue(0)
thresholder.SetOutValue(0)
# Create volume node
self.webcamReference = slicer.vtkMRMLVectorVolumeNode()
self.webcamReference.SetName('Webcam_Reference')
self.webcamReference.SetSpacing(imageSpacing)
self.webcamReference.SetImageDataConnection(
thresholder.GetOutputPort())
# Add volume to scene
slicer.mrmlScene.AddNode(self.webcamReference)
displayNode = slicer.vtkMRMLVectorVolumeDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
self.webcamReference.SetAndObserveDisplayNodeID(
displayNode.GetID())
self.webcamConnectorNode = self.createWebcamPlusConnector()
self.webcamConnectorNode.Start()
self.setupWebcamResliceDriver()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.logic = Collect_Training_ImagesLogic()
self.moduleDir = os.path.dirname(slicer.modules.collect_training_images.path)
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
#self.imageSaveDirectory = qt.QLineEdit("Select directory to save images")
#parametersFormLayout.addRow(self.imageSaveDirectory)
self.modelSelector = qt.QComboBox()
self.modelSelector.addItems(["Select model"])
modelDirectoryContents = os.listdir(os.path.join(self.moduleDir,os.pardir,"Models"))
modelNames = [dir for dir in modelDirectoryContents if dir.find(".") == -1 and dir != "Dockerfile"]
self.modelSelector.addItems(["Create new model"])
self.modelSelector.addItems(modelNames)
parametersFormLayout.addRow(self.modelSelector)
#self.imageSaveDirectoryLabel = qt.QLabel("Training photo directory:")
#parametersFormLayout.addRow(self.imageSaveDirectoryLabel)
self.imageSaveDirectoryLineEdit = ctk.ctkPathLineEdit()
#node = self.logic.getParameterNode()
imageSaveDirectory = os.path.dirname(slicer.modules.collect_training_images.path)
self.imageSaveDirectoryLineEdit.currentPath = imageSaveDirectory
self.imageSaveDirectoryLineEdit.filters = ctk.ctkPathLineEdit.Dirs
self.imageSaveDirectoryLineEdit.options = ctk.ctkPathLineEdit.DontUseSheet
self.imageSaveDirectoryLineEdit.options = ctk.ctkPathLineEdit.ShowDirsOnly
self.imageSaveDirectoryLineEdit.showHistoryButton = False
self.imageSaveDirectoryLineEdit.setMinimumWidth(100)
self.imageSaveDirectoryLineEdit.setMaximumWidth(500)
#parametersFormLayout.addRow(self.imageSaveDirectoryLineEdit)
self.imageClassComboBox = qt.QComboBox()
self.imageClassComboBox.addItems(["Select image class","Create new image class"])
parametersFormLayout.addRow(self.imageClassComboBox)
#
# Start/Stop Image Collection Button
#
self.startStopCollectingImagesButton = qt.QPushButton("Start Image Collection")
self.startStopCollectingImagesButton.toolTip = "Collect training images."
self.startStopCollectingImagesButton.enabled = False
parametersFormLayout.addRow(self.startStopCollectingImagesButton)
self.infoLabel = qt.QLabel("")
parametersFormLayout.addRow(self.infoLabel)
# connections
self.modelSelector.connect('currentIndexChanged(int)',self.onModelSelected)
self.startStopCollectingImagesButton.connect('clicked(bool)', self.onStartStopCollectingImagesButton)
self.imageClassComboBox.connect('currentIndexChanged(int)',self.onImageClassSelected)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Start/Stop Collecting Images Button state
self.onSelect()
try:
self.webcamReference = slicer.util.getNode('Webcam_Reference')
except slicer.util.MRMLNodeNotFoundException:
#if not self.webcamReference:
imageSpacing = [0.2, 0.2, 0.2]
imageData = vtk.vtkImageData()
imageData.SetDimensions(640, 480, 1)
imageData.AllocateScalars(vtk.VTK_UNSIGNED_CHAR, 1)
thresholder = vtk.vtkImageThreshold()
thresholder.SetInputData(imageData)
thresholder.SetInValue(0)
thresholder.SetOutValue(0)
# Create volume node
self.webcamReference = slicer.vtkMRMLVectorVolumeNode()
self.webcamReference.SetName('Webcam_Reference')
self.webcamReference.SetSpacing(imageSpacing)
self.webcamReference.SetImageDataConnection(thresholder.GetOutputPort())
# Add volume to scene
slicer.mrmlScene.AddNode(self.webcamReference)
displayNode = slicer.vtkMRMLVectorVolumeDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
self.webcamReference.SetAndObserveDisplayNodeID(displayNode.GetID())
self.webcamConnectorNode = self.createWebcamPlusConnector()
self.webcamConnectorNode.Start()
self.setupWebcamResliceDriver()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.logic = CNN_Image_ClassifierLogic()
self.moduleDir = os.path.dirname(
slicer.modules.collect_training_images.path)
# Instantiate and connect widgets ...
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
self.modelSelector = qt.QComboBox()
self.modelSelector.addItems(["Select model"])
modelDirectoryContents = os.listdir(
os.path.join(self.moduleDir, os.pardir, "Models/retrainContainer"))
modelNames = [
dir for dir in modelDirectoryContents
if dir.find(".") == -1 and dir != "Dockerfile"
]
self.modelSelector.addItems(["Create new model"])
self.modelSelector.addItems(modelNames)
parametersFormLayout.addRow(self.modelSelector)
#
# Apply Button
#
self.applyButton = qt.QPushButton("Start")
self.applyButton.toolTip = "Run the algorithm."
self.applyButton.enabled = False
parametersFormLayout.addRow(self.applyButton)
#
# Object table
#
self.objectTable = qt.QTableWidget()
self.objectTable.setColumnCount(3)
self.objectTable.setHorizontalHeaderLabels(
["Name", "Found", "Confidence"])
parametersFormLayout.addRow(self.objectTable)
#
# Adjust Confidence Thresholds
#
confidenceThresholdsCollapsibleButton = ctk.ctkCollapsibleButton()
confidenceThresholdsCollapsibleButton.text = "Confidence Thresholds"
self.layout.addWidget(confidenceThresholdsCollapsibleButton)
confidenceFormLayout = qt.QFormLayout(
confidenceThresholdsCollapsibleButton)
self.confidenceSlider = qt.QSlider(0x1) #horizontal slider
self.confidenceSlider.setRange(0, 100)
self.confidenceSlider.setTickInterval(5)
self.confidenceSlider.setTickPosition(2) #Ticks appear below slider
self.confidenceSlider.setSliderPosition(80)
self.confidenceSlider.setToolTip(
"Set the minimum degree of confidence that must be met for an object to be considered found"
)
confidenceFormLayout.addRow("Confidence: ", self.confidenceSlider)
self.confidenceLabel = qt.QLabel("80%")
confidenceFormLayout.addRow(self.confidenceLabel)
# connections
self.applyButton.connect('clicked(bool)', self.onApplyButton)
self.modelSelector.connect('currentIndexChanged(int)',
self.onModelSelected)
self.confidenceSlider.connect('sliderMoved(int)',
self.onConfidenceChanged)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Apply button state
self.onSelect()
self.webcamReference = slicer.util.getNode('Webcam_Reference')
if not self.webcamReference:
imageSpacing = [0.2, 0.2, 0.2]
imageData = vtk.vtkImageData()
imageData.SetDimensions(640, 480, 1)
imageData.AllocateScalars(vtk.VTK_UNSIGNED_CHAR, 1)
thresholder = vtk.vtkImageThreshold()
thresholder.SetInputData(imageData)
thresholder.SetInValue(0)
thresholder.SetOutValue(0)
# Create volume node
self.webcamReference = slicer.vtkMRMLVectorVolumeNode()
self.webcamReference.SetName('Webcam_Reference')
self.webcamReference.SetSpacing(imageSpacing)
self.webcamReference.SetImageDataConnection(
thresholder.GetOutputPort())
# Add volume to scene
slicer.mrmlScene.AddNode(self.webcamReference)
displayNode = slicer.vtkMRMLVectorVolumeDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
self.webcamReference.SetAndObserveDisplayNodeID(
displayNode.GetID())
self.webcamConnectorNode = self.createWebcamPlusConnector()
self.webcamConnectorNode.Start()
self.setupWebcamResliceDriver()
